COMPOUNDS FOR THE TREATMENT OF BACTERIAL INFECTIONS AND POTENTIATION OF ANTIBIOTICS

CROSS REFERENCE TO PRIORITY APPLICATION

This application claims priority to U.S. Provisional Application No. 62/950,852, filed December 19, 2019, which is incorporated by reference herein in its entirety.

FIELD OF THE INVENTION

The invention provides compounds for use in the treatment of medical disorders caused by bacteria or for use as a potentiator of an antibiotic in the treatment of medical disorders caused by bacteria.

BACKGROUND OF THE INVENTION

Despite the overall success of antibiotics in diminishing the effects of infectious disease in the modem world, their ease of access has led to overuse, resulting in the development of bacterial resistance. Antibiotic resistance is on the rise globally, leading the World Health Organization to classify antibiotic resistance as a “serious threat [that] is no longer a prediction for the future” (“Antimicrobial resistance: global report on surveillance 2014” The World Health Organization, April 2014). Antibiotic resistance is linked to inappropriate prescribing of antibiotics, incorrect dosing, and missing doses. In the United States, approximately 2.8 million people become infected with antibiotic resistant bacteria each year and roughly 35,000 die as a result (“Antibiotic/ Antimicrobial Resistance (AR/AMR)” Centers for Disease Control and Prevention, https://www.cdc.gov/drugresistance/). Some bacteria harbor a natural resistance to certain types of antibiotics, while others may gain resistance by genetic mutation or horizontal gene transfer from already-resistant species. Bacteria diminish the effectiveness of antibiotics by modifying or inactivating the drug, altering the target or binding site, altering the metabolic pathways that propagate the drug’s effects, or reducing accumulation of the drug within the cell by decreasing drug permeability or increasing efflux. Certain bacteria, colloquially known as “superbugs”, may eventually develop resistance to multiple types of antibiotics, requiring alternative medications at higher doses, often with higher cost and greater toxicity.

Several preventative measures have been proposed to slow bacterial resistance to currently available antibiotics. Proper antibiotic stewardship along with increased hygiene provides significant strides in preventing future resistance. Despite this, new therapeutics are necessary to treat infections caused by currently resistant bacterial strains. The period from the 1950s until the 1970s represented the peak of antibiotic discovery, but since that time no new classes of antibiotics have been discovered, and development of new antibiotics within existing classes has been low. Alternative strategies, such as the development of bacterial vaccines and phage therapy, have not seen the success necessary to become widely used.

Investigators in the 1920s discovered that an anti-diabetic drug, Synthalin, had therapeutic activity against Trypanosoma brucei infections in mice. Out of a series of subsequently developed analogs, pentamidine was found to be curative of murine T. rhodesiense infections (Yorke W. “Recent work on the chemotherapy of protozoal infections”, Trans. R., Soc. Trop. Med. Hyg. 1940, 33:463). It was not until the 1960s that pentamidine became available on a restricted basis for use in the treatment of protozoal infections, and only in the 1980s did it see more extensive use as a treatment of pnuemocystis pneumonia in immunocompromised individuals such as HIV patients (Sands et al. “Pentamidine: A Review”, Reviews of Infectious Diseases 1985, 7(5):625-634). In recentyears, pentamidine has received renewed interest as a possible therapeutic in the treatment of infections by antibiotic resistant bacteria. For example, pentamidine has been demonstrated to sensitize resistant bacteria to colistin, one of the antibiotics of last resort (Stokes et al. “Pentamidine sensitizes Gram negative pathogens to antibiotics and overcomes acquired colistin resistance”, Nat. Microbiol. 2017, 2:17028; Bean et al. “Pentamidine: a drug to consider re-purposing in the targeted treatment of multi-drug resistant bacterial infections?” J. Lab. Precis. Med. 2017, 2:49).

The use of amidine compounds for biological applications is described in Geratz et al. “Novel Bis(benzamidino) Compounds with an Aromatic Central Link. Inhibitors of Thrombin, Pancreatic Kallikrein, Trypsin, and Complement” J. Med. Chem. 1976, 19(5):634; Parrish et al. “Structure-Activity Relationships for the Inhibition of Acrosin by Benzamidine Derivatives” J. Med. Chem. 1978, 21(11)1132; Patrick et al. “Synthesis and antiprotozoal activities of dicationic bis(phenoxymethyl)benzenes, bis(phenoxymethyl)naphthalenes, and bis(benzyoxy)naphthalenes” Eur. J. Med. Chem. 2009, 44:3543; Giordani et al. “Green Fluorescent Diamidine as Diagnostic Probes for Trypanosomes” Antimicrobial Agents and Chemotherapy 2014, 58: 1793; Munde et al. “The Unusual Monomer Recognition of Guanine- Containing Mixed Sequence DNA by a Dithiophene Heterocyclic Diamidine” Biochemistry 2014, 53:1218; Arafa et al. “Novel linear triaryl guanidines, N-substituted guanidines and potential prodrugs as antiprotozoal agents” European Journal of Medicinal Chemistry, 2008, 43:2901; Stephens et al. “Diguanidino and “Reversed” Diamidino 2,5 -Diary lfurans as Antimicrobial Agents” J. Med. Chem, 2001, 44:1741; Munde et al. “Structure-dependent inhibition of the ETS-family transcription factor PU.l by novel heterocyclic diamidines” Nucleic Acids Research, 2014, 42: 1379; Gonzalez, et al. “Synthesis and antiparasitic evaluation of bis-2,5-[4-guanidinophenyl]thiophenes” Eur J Med Chem, 2007, 42: 552; and Wang et al. “Evaluation of the Influence of Compound Structure on Stacked-Dimer Formation in the DNA Minor Groove” Biochemistry, 2001, 40, 2511.

University of North Carolina describes the use of ami dine compounds to inhibit RSV- induced cell fusion in U.S. Patent No. 4,619,942 titled “Inhibition of Respiratory Syncytial Virus-Induced Cell Fusion by Amidino Compounds”.

Eisai Co., Ltd. describes the use of amidine compounds as antifungal, antibacterial, and anti-trichomonal therapeutics in “U.S. Patent No. 4,034,010 titled “Bis-(Meta- Amidinophenoxy)-Compounds and Pharmacologically Acceptable Acid Addition Salts Thereof’.

Berlex Laboratories describes the use of amidine compounds as anticoagulants in International Patent Application Publication Nos. W096/28427 titled “Benzamidine Derivatives Their Preparation and Their Use as Anti-Coagulants”; WO97/29067 titled “Benzamidine Derivatives Substituted by Amino Acid and Hydroxy Acid Derivatives and Their Use as Anti-Coagulants”; and WO00/31068 titled “Polyhydroxylated Heterocyclic Derivatives as Anticoagulants”.

Georgia State University Research Foundation, Inc. and the University of North Carolina jointly disclosed the use of amidine compounds in amyloidosis and the treatment of microbial infections in International Patent Application Publication Nos. W02003/103598 titled “Amidine Derivatives for Treating Amyloidosis” and W02005/033065 titled “Novel Amidine Compounds for Treating Microbial Infections”. The use of compounds for the treatment of microbial infections, including protozoa are disclosed in WO 2005/086808 and WO 2005/040132. Bichalcophenes as antiprotozoal agents are also described in US 2006/0293540 assigned to the University of North Carolina and the Georgia State University Research Foundation, Inc. Georgia State University Research Foundation and the Albert Einstein College of Medicine, Inc. disclosed the use of amidine and diamidine compounds for the inhibition of PU.l and for the treatment of disorders associated with abnormal PU.l levels in WO 2017/223260.

Georgia State University Research Foundation and the Ohio State Innovation Foundation disclosed the use of amidine compounds for the treatment of fungal infections in WO 2018/045106 and compounds for the treatment of parasites in WO 2018/045104.

Georgia State University Research Foundation, Inc. has also disclosed the use of amidine compounds as DNA-targeting agents in US 2010/0249175 and compounds for the use of protozoa in WO 2009/051796 and WO 2005/086754.

Neurochem, Inc. describes the use of amidine compounds in the treatment of amyloidosis in International Patent Application Publication No. W003/017994 titled “Amidine Derivatives for Treating Amyloidosis”.

Altana Pharma AG describes compounds including amidine derivatives for use as tryptase inhibitors in U.S. Patent No. 9,960,588 titled “Tryptase Inhibitors”.

Mpex Pharmaceuticals describes the use of amidine compounds as bacterial efflux inhibitors in International Patent Application Publication No. W02005/089738 title “Use and Administration of Bacterial Efflux Inhibitors”. Bostian et al. also describe a similar use of amidine compounds as bacterial efflux inhibitors in the treatment of ophthalmic and otic infections in U.S. Patent Application Publication No. US2008/0132457 titled “Bacterial Efflux Inhibitors for the Treatment of Ophthalmic and Otic Infections”.

The University of Cincinnati describes the use of amidine compounds for the treatment of pneumonia in International Patent Application Publication No. W02006/021833 titled “Bisbenzami dines for the Treatment of Pneumonia”. Xavier University of Louisiana describes the use of amidine compounds for the treatment of trypanosomiasis in International Patent Application Publication No. W02008/090831 titled “Bisbenzamidines and Bisbenzami doximes for the Treatment of Human African Trypanosomiasis”.

The University of Oregon describes the use of pentamidine and related compounds in the treatment of myotonic dystrophy in International Patent Application Publication No. W02009/105691 titled “Use of Pentamidine and Related Compounds”.

Orion Corporation describes the use of amidine compounds as protease inhibitors in Intemationla Patent Application Publication No. WO2010/133748 titled “Protease Inhibitors”.

There remains a need for the development of novel therapeutics and pharmaceutical compositions and their use for the treatment of bacterial infections, including therapeutics that potentiate the effect of antibiotics on bacterial strains, including bacterial strains resistant to certain antibiotics.

SUMMARY OF THE INVENTION

The present invention provides compounds and methods for the treatment of bacterial infections as well as for the potentiation of the therapeutic effect of antibiotics in the treatment of bacterial infections that comprise administering an effective amount of a compound described herein or its pharmaceutically acceptable salt, optionally in a pharmaceutically acceptable carrier. The bacterial infection may be caused by gram-positive bacteria, gram negative bacteria, and/or antibiotic resistant bacteria. In one embodiment, the bacterial infection is caused by mycobacteria.

In one aspect, the invention is a compound of Formula I or a pharmaceutically acceptable salt thereof: wherein: m and o are independently selected from 0, 1, 2, or 3; n is 0, 1, 2, 3, or 4;

X ¹ is O, S, or NR ⁴ ;

X ³ is independently at each occurrence selected from the group consisting of C(R ³ )2, O, S, and NR ⁴ ;

X ⁴ is independently at each occurrence selected from the group consisting of CR ³ and N;

X ⁵ is C(R ³ ) ₂ , O, or S;

R is independently at each occurrence selected from the group consisting of hydrogen, hydroxyl, Ci-C6alkyl, Ci-C6alkoxy, Ci-C6haloalkoxy, Ci-C6alkanoyl, aliphatic, carbocyclic, Ci-C6hydroxyalkyl, Ci-C6haloalkyl, N(R ³ ) ₂ , -NHSC alkyl, -N(alkyl)S0 ₂ alkyl, -NHSC aryl, -N(alkyl)S0 ₂ aryl, -NHSC alkenyl, -N(alkyl)S0 ₂ alkenyl, -NHSC alkynyl, N(alkyl)S S0 ₂ N(R ³ )

-N(R ³ )S02R ³ , azide, aryl, heteroaryl, heterocyclyl, fluorine, chlorine, bromine, iodine, thiol and cyano;

R ¹ and R ² are independently at each occurrence selected from the group consisting of:

R ³ is independently at each occurrence selected from the group consisting of hydrogen, hydroxyl, Ci-C6alkyl, Ci-C6alkoxy, Ci-C6haloalkoxy, Ci-C6alkanoyl, carbocyclic, C2- Cealkenyl, C2-C6alkynyl, heteroaryl, aryl, heterocyclyl, -COOR, -C(0)R, fluorine, chlorine, bromine, and iodine; and

R ⁴ and R ⁵ are independently at each occurrence selected from the group consisting of hydrogen and Ci-C6alkyl.

In one aspect a method is provided for treating a bacterial infection in a host, typically a human, comprising administering an effective amount of a compound of Formula I or a pharmaceutically acceptable salt thereof, optionally in a pharmaceutically acceptable carrier.

In one aspect a method is provided for potentiating the effect of a bacterial infection in a host, typically a human, comprising administering an effective amount of a compound of Formula I or a pharmaceutically acceptable salt thereof, optionally in a pharmaceutically acceptable carrier, in combination with an antibiotic.

A pharmaceutical composition is also provided comprising an effective amount of a compound of Formula I or a pharmaceutically acceptable salt thereof in a pharmaceutically acceptable carrier either alone or in combination with an effective amount of an additional antibiotic.

In another aspect, a method is provided for treating a bacterial infection comprising administering an effective amount of a compound of Formula II, Formula III, Formula IV, or Formula V or a pharmaceutically acceptable salt thereof to a host in need thereof: wherein

L ¹ is selected from

L ² is selected from v and w are independently selected from 0, 1, 2, 3, and 4;

R is independently at each occurrence selected from the group consisting of hydrogen, hydroxyl, Ci-C6alkyl, Ci-C6alkoxy, Ci-C6haloalkoxy, Ci-C6alkanoyl, aliphatic, carbocyclic, Ci-C6hydroxyalkyl, Ci-C6haloalkyl, N(R ³ )2, -NHSC alkyl, -N(alkyl)S02alkyl, -NHS02aryl, -N(alkyl)S02aryl, -NHS02alkenyl, -N(alkyl)S02alkenyl, -NHSC alkynyl, N(alkyl)S0 ₂ alkynyl, N0 ₂ , -COOH, -CONH2, -P(0)(0H) ₂ , -S(0)R ³ , -SO2R ³ , -SO3R ³ , - S0 ₂ N(R ³ )2, -OSO2R ³ ,

-N(R ³ )S02R ³ , azide, aryl, heteroaryl, heterocyclyl, fluorine, chlorine, bromine, iodine, thiol, and cyano;

X ⁶ , X ⁷ , X ⁸ , and X ⁹ are independently selected from O, S, NH, and Se;

X ¹⁰ is selected from Se, S, or NH;

R ⁶ and R ⁷ are independently at each occurrence selected from the group consisting of:

X ³ , X ⁴ , R ⁴ , and R ⁵ are as defined herein.

In some embodiments of Formula II, Formula III, Formula IV, and/or Formula V, X ¹⁰ is not S.

In some embodiments of Formula II, Formula III, Formula IV, and/or Formula V, X ¹⁰ is not NH.

In some embodiments of Formula II, Formula III, Formula IV and/or Formula V, L ² is not

In some embodiments of Formula II, Formula III, Formula IV and/or Formula V, one or more of X ⁶ , X ⁷ , X ⁸ , and X ⁹ is not NH.

In another aspect, a method is provided for treating a bacterial infection comprising administering an effective amount of Compound A, Compound B, or Compound C

Compound C or a pharmaceutically acceptable salt thereof to a host in need thereof. In certain embodiments a compound of Formula I, Formula II, Formula III, Formula

IV, or Formula V or a pharmaceutically acceptable salt thereof can be used to potentiate the effect of an antibiotic in the treatment of a bacterial infection.

In certain embodiments Compound A, Compound B, or Compound C or a pharmaceutically acceptable salt thereof can be used to potentiate the effect of an antibiotic in the treatment of a bacterial infection.

In certain embodiment, the bacterial infection is caused by a gram-positive bacterium. In certain embodiment, the bacterial infection is caused by a gram-negative bacterium. In certain embodiment, the bacterial infection is caused by a mycobacterium.

In another aspect, a method is provided for treating a gram-positive or a gram-negative bacterial infection comprising administering an effective amount of a compound of Formula

VI: or a pharmaceutically acceptable salt thereof wherein

R ⁹ and R ¹² are independently at each occurrence selected from the group consisting of hydrogen, hydroxyl, Ci-C6alkyl, Ci-C6alkoxy, Ci-C6haloalkoxy, Ci-C6alkanoyl, aliphatic, carbocyclic, Ci-C6hydroxyalkyl, Ci-C6haloalkyl, N(R ³ )2, -NHS02alkyl, -N(alkyl)S02alkyl, -NHS02aryl, -N(alkyl)S02aryl, -NHSC alkenyl, -N(alkyl)S02alkenyl, -NHS02alkynyl, -N(alkyl)S0 ₂ alkynyl, NO2, -COOH, -CONH2, -P(0)(0H) ₂ , -S(0)R ³ , -SO2R ³ , -SO3R ³ , -S0 ₂ N(R ³ ) ₂ , -OSO2R ³ , -N(R ³ )S02R ³ , azide, aryl, heteroaryl, heterocyclyl, fluorine, chlorine, bromine, iodine, thiol, and cyano; and

R ¹⁰ and R ¹¹ are independently at each occurrence selected from the group consisting of hydroxyl, Ci-C6alkanoyl, carbocyclic, Ci-C6hydroxy alkyl, Ci-C6haloalkyl, N(R ³ )2, -NHSC alkyl, -N(alkyl)S02alkyl, -NHS02aryl, -N(alkyl)S02aryl, -NHS02alkenyl, -N(alkyl)S02alkenyl, -NHS02alkynyl, -N(alkyl)S02alkynyl, NO2, -COOH, -CONH2, - C(0)R, -P(0)(0H) ₂ , -S(0)R ³ , -SO2R ³ , -SO3R ³ , -S0 ₂ N(R ³ ) ₂ , -OSO2R ³ , -N(R ³ )S0 ₂ R ³ , azide, aryl, heteroaryl, heterocyclyl, fluorine, bromine, iodine, thiol, and cyano.

In another aspect, a method is provided for treating a gram-positive or a gram-negative bacterial infection comprising administering an effective amount of Compound D or Compound E:

Compound D or a pharmaceutically acceptable salt thereof to a host in need thereof.

In some cases, the compound for use in treating a bacterial infection is not Compound D or Compound E.

In one aspect, the invention is a compound selected from Compound F - Compound L or a pharmaceutically acceptable salt thereof:

A pharmaceutical composition is also provided comprising an effective amount of a compound of Formula I, Formula II, Formula III, Formula IV, Formula V, or Formula VI or a compound selected from Compound A - Compound L or a pharmaceutically acceptable salt thereof in a pharmaceutically acceptable carrier in combination with an effective amount of an additional antibiotic. In one embodiment, the pharmaceutical composition is suitable for topical administration, for example a cream or an ointment. The topical composition can include any carrier or carriers that do not adversely interact with the active agent and achieve the desired effect.

In another aspect, provided herein is a compound of Formula VII or a pharmaceutically acceptable salt thereof: wherein: m and n are independently selected from 1, 2, 3, or 4; p is 0, 1, 2, or 3; q and t are independently at each occurrence 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10;

L ³ and L ⁴ are each independently C(R ³ )2, O, or S;

R is independently at each occurrence selected from the group consisting of hydrogen, hydroxyl, Ci-C6alkyl, Ci-C6alkoxy, Ci-C6haloalkoxy, Ci-C6alkanoyl, aliphatic, carbocyclic, Ci-C6hydroxyalkyl, Ci-C6haloalkyl, N(R ³ )2, -NHS02alkyl, -N(alkyl)S02alkyl, -NHS02aryl, -N(alkyl)S02aryl, -NHS02alkenyl, -N(alkyl)S02alkenyl, -NHS02alkynyl, N(alkyl)S0 ₂ alkynyl, NO2, -COOH, -CONH2, -P(0)(OH) ₂ , -S(0)R ³ , -SO2R ³ , -SO3R ³ , - S0 ₂ N(R ³ ) ₂ , -OSO2R ³ ,

-N(R ³ )S02R ³ , azide, aryl, heteroaryl, heterocyclyl, fluorine, chlorine, bromine, iodine, thiol, and cyano;

R ³ is independently at each occurrence selected from the group consisting of hydrogen, hydroxyl, Ci-C6alkyl, Ci-C6alkoxy, Ci-C6haloalkoxy, Ci-C6alkanoyl, carbocyclic, C2- Cealkenyl, C2-C6alkynyl, heteroaryl, aryl, heterocyclyl, -COOR, -C(0)R, fluorine, chlorine, bromine, and iodine;

R ¹³ and R ¹⁴ are independently at each occurrence selected from the group consisting of wherein R ⁴ and R ⁵ are independently at each occurrence selected from the group consisting of hydrogen and Ci-C6alkyl and o is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10;

X ¹¹ and X ¹² are each independently selected from the group consisting of C(R ³ )2, O, NH, or S;

Y ¹ and Y ² are each independently selected from the group consisting of C(R ³ )2, O,

NH, or S; and

Z is CR ³ or N.

Optionally, R ⁴ and R ⁵ are hydrogen.

Optionally, X ¹¹ and X ¹² are the same. In some cases, X ¹¹ and X ¹² are selected from the group consisting of O, CH2, and S.

Optionally, Y ¹ and Y ² are the same. In some cases, Y ¹ and Y ² are selected from the group consisting of O and CH2.

Optionally, each R is independently selected from the group consisting of hydrogen, Ci-C6alkyl, Ci-C6alkoxy, Ci-C6haloalkyl, and fluorine. Optionally, the compound has the following structure:

In another aspect, a method is provided for treatment of a bacterial infection comprising administering a compound of Formula VII or a pharmaceutically acceptable salt thereof. Also provided is a method of potentiating the therapeutic effect of an antibiotic during the treatment of a bacterial infection comprising administering a compound of Formula VII or a pharmaceutically acceptable salt thereof. In some cases, the bacterial infection is caused by gram-positive bacteria. In other cases, the bacterial infection is caused by gram-negative bacteria. Optionally, the bacterial infection is caused by a mycobacterium.

In another aspect, provided herein is a compound of Formula VIII or a pharmaceutically acceptable salt thereof: wherein: m and n are independently selected from 1, 2, 3, or 4; p is 0, 1, 2, or 3; q and t are independently at each occurrence 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10;

L ³ and L ⁴ are each independently C(R ³ )2, O, or S; R is independently at each occurrence selected from the group consisting of hydrogen, hydroxyl, Ci-C6alkyl, Ci-C6alkoxy, Ci-C6haloalkoxy, Ci-C6alkanoyl, aliphatic, carbocyclic, Ci-C6hydroxyalkyl, Ci-C6haloalkyl, N(R ³ )2, -NHS02alkyl, -N(alkyl)S02alkyl, -NHS02aryl, -N(alkyl)S02aryl, -NHS02alkenyl, -N(alkyl)S02alkenyl, -NHS02alkynyl, N(alkyl)S0 ₂ alkynyl, N0 ₂ , -COOH, -CONH2, -P(0)(0H) ₂ , -S(0)R ³ , -SO2R ³ , -SO3R ³ , - S0 ₂ N(R ³ ) ₂ , -OSO2R ³ ,

-N(R ³ )S02R ³ , azide, aryl, heteroaryl, heterocyclyl, fluorine, chlorine, bromine, iodine, thiol, and cyano;

R ³ is independently at each occurrence selected from the group consisting of hydrogen, hydroxyl, Ci-C6alkyl, Ci-C6alkoxy, Ci-C6haloalkoxy, Ci-C6alkanoyl, carbocyclic, C2- Cealkenyl, C2-C6alkynyl, heteroaryl, aryl, heterocyclyl, -COOR, -C(0)R, fluorine, chlorine, bromine, and iodine;

R ¹³ and R ¹⁴ are independently at each occurrence selected from the group consisting of wherein R ⁴ and R ⁵ are independently at each occurrence selected from the group consisting of hydrogen and Ci-C6alkyl and 0 is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10;

X ¹¹ and X ¹² are each independently selected from the group consisting of C(R ³ )2, O, NH, or S;

Y ¹ and Y ² are each independently selected from the group consisting of C(R ³ )2, O, NH, or S; and

Z is CR ³ or N.

Optionally, R ⁴ and R ⁵ are hydrogen.

Optionally, X ¹¹ and X ¹² are the same. In some cases, X ¹¹ and X ¹² are selected from the group consisting of O, CH2, and S.

Optionally, Y ¹ and Y ² are the same. In some cases, Y ¹ and Y ² are selected from the group consisting of O and CH2.

Optionally, each R is independently selected from the group consisting of hydrogen, Ci-C6alkyl, Ci-C6alkoxy, Ci-C6haloalkyl, and fluorine.

Optionally, the compound has the following structure:

In another aspect, a method is provided for treatment of a bacterial infection comprising administering a compound of Formula VIII or a pharmaceutically acceptable salt thereof. Also provided is a method of potentiating the therapeutic effect of an antibiotic during the treatment of a bacterial infection comprising administering a compound of Formula VIII or a pharmaceutically acceptable salt thereof. In some cases, the bacterial infection is caused by gram-positive bacteria. In other cases, the bacterial infection is caused by gram-negative bacteria. Optionally, the bacterial infection is caused by a mycobacterium. In another aspect, provided herein is a pharmaceutical composition comprising a compound of Formula VII or Formula VIII or a pharmaceutically acceptable salt thereof, optionally in a pharmaceutically acceptable carrier.

The present invention also provides a topical composition containing, either alone or in combination with an effective amount of an antibiotic, an effective amount of a compound selected from Formula I, Formula II, Formula III, Formula IV, Formula V, Formula VI, Formula VII, or Formula VIII or a compound selected from Compound A - Compound L or a pharmaceutically acceptable salt thereof for the treatment of acne vulgaris. The compounds used in the topical compositions and methods provided herein have an anti-microbial effect that helps alleviate the symptoms of acne vulgaris and treat the underlying overgrowth of bacterial that cause acne, for example, the bacterium Propionibacterium acnes or Staphylococcus epidermidis.

The present invention also provides treatment options that may complement or replace those currently available in the treatment of this highly common dermatological condition.

For example, the topical carrier can be water-based or anhydrous. Water-based topical compositions are well known and described further below. Anhydrous pharmaceutically acceptable topical materials are also well known, and include silicon-based oils, aliphatic-based compositions, oleaginous materials, jellies, mineral oil, dimethicone, and other substantially anhydrous lipophilic carriers.

The active compound of Formula I, Formula II, Formula III, Formula IV, Formula V, Formula VI, Formula VII, or Formula VIII or a compound selected from Compound A - Compound L can be provided in the topical formulation in any amount that achieves the desired effect. In certain non-limiting examples, the weight percentage of the active compound in the topical formulation is from about 0.1% to about 50%, or from about 0.1% to about 40%, or about 1% to about 30%, or from about 2, 3, 4 or 5 % to about 20%, or between about 5% to about 10%.

Examples include at least about 0.5, 1, 2, 3, 4, 5, 10 or 15% by weight. In one embodiment, the topical formulation contains a compound of Formula I, Formula II, Formula III, Formula IV, Formula V, Formula VI, Formula VII, or Formula VIII or a compound selected from Compound A - Compound L or a pharmaceutically acceptable salt thereof in combination with an additional active agent, for example benzoyl peroxide, a retinoid, azelaic acid, an antibiotic, or salicylic acid, as long as it does not adversely affect the active agent.

In one embodiment, at least one hydrogen within a compound of Formula I, Formula II, Formula III, Formula IV, Formula V, Formula VI, Formula VII, or Formula VIII is replaced with a deuterium. In one aspect, the deuterium is at a location of metabolism. In one embodiment, at least one hydrogen within Compound A - Compound L is replaced with a deuterium. In one aspect, the deuterium is at a location of metabolism.

Thus, the present invention includes at least the following features:

(a) a compound of Formula I or a pharmaceutically salt thereof;

(b) a pharmaceutical composition comprising a compound of Formula I or a pharmaceutically acceptable salt thereof optionally in a pharmaceutically acceptable carrier;

(c) a method for the treatment of a bacterial infection comprising administering a compound of Formula I, Formula II, Formula III, Formula IV, or Formula V or a pharmaceutically acceptable salt to a host in need thereof;

(d) a method for the treatment of a bacterial infection comprising administering a compound of Formula I, Formula II, Formula III, Formula IV, or Formula V or a pharmaceutically acceptable salt in combination with an effective amount of an antibiotic to a host in need thereof;

(e) a method for potentiating the effect of an antibiotic in the treatment of a bacterial infection comprising administering the antibiotic in combination with a compound of Formula I, Formula II, Formula III, Formula IV, or Formula V or a pharmaceutically acceptable salt thereof to a host in need thereof;

(1) the method of (c), (d), or (e) wherein the bacterial infection is caused by a gram-positive bacterial infection;

(g) the method of (c), (d), or (e) wherein the bacterial infection is caused by a gram negative bacterial infection;

(h) the method of (c), (d), or (e) wherein the bacterial infection is caused by a mycobacterium;

(i) a method for the treatment of acne vulgaris comprising administering a compound of Formula I, Formula II, Formula III, Formula IV, Formula V, or Formula VI or a pharmaceutically acceptable salt thereof, either alone or in combination with an antibiotic, to a host in need thereof;

(j) the method of (i) wherein the acne vulgaris is caused by the bacterium Propionibacterium acnes or Staphylococcus epidermidis

(k) a compound of Formula I, Formula II, Formula III, Formula IV, or Formula V or a pharmaceutically acceptable salt thereof for use to treat a bacterial infection in a host in need thereof; (l) a compound of Formula I, Formula II, Formula III, Formula IV, or Formula V or a pharmaceutically acceptable salt thereof in combination with an effective amount of an antibiotic for use to treat a bacterial infection in a host in need thereof;

(m)a compound of Formula I, Formula II, Formula III, Formula IV, or Formula V or a pharmaceutically acceptable salt thereof for use in the potentiation of the effect of an antibiotic in the treatment of a bacterial infection;

(n) the compound of (k), (1) or (m) wherein the bacterial infection is caused by a gram positive bacterial infection;

(o) the compound of (k), (1) or (m) wherein the bacterial infection is caused by a gram negative bacterial infection;

(p) the compound of (k), (1) or (m) wherein the bacterial infection is caused by a mycobacterium;

(q) acompound of Formula I, Formula II, Formulalll, Formula IV, Formula V, or Formula VI or a pharmaceutically acceptable salt thereof for use to treat acne vulgaris in a host in need thereof;

(r) the compound of (q) wherein the acne vulgaris is caused by the bacterium Propionibacterium acnes or Staphylococcus epidermidis

(s) the use of a compound of Formula I, Formula II, Formula III, Formula IV, or Formula

V or a pharmaceutically acceptable salt thereof in the manufacture of a medicament for the treatment of a bacterial infection in a host in need thereof;

(t) the use of a compound of Formula I, Formula II, Formula III, Formula IV, or Formula

V or a pharmaceutically acceptable salt thereof in combination with an effective amount of an antibiotic in the manufacture of a medicament for the treatment of a bacterial infection in a host in need thereof;

(u) the use of a compound of Formula I, Formula II, Formula III, Formula IV, or Formula

V or a pharmaceutically acceptable salt thereof in the manufacture of a medicament for the potentiation of the effect of an antibiotic in the treatment of a bacterial infection in a host in need thereof;

(v) the use of (s), (t), or (u) wherein the bacterial infection is caused by a gram-positive bacterial infection;

(w)the use of (s), (t), or (u) wherein the bacterial infection is caused by a gram-negative bacterial infection;

(x) the use of (s), (t), or (u) wherein the bacterial infection is caused by a mycobacterium; (y) the use of a compound of Formula I, Formula II, Formula III, Formula IV, Formula V, or Formula VI or a pharmaceutically acceptable salt thereof in the manufacture of a medicament for the treatment of acne vulgaris in a host in need thereof;

(z) the use of (y) wherein the acne vulgaris is caused by the bacterium Propionibacterium acnes or Staphylococcus epidermidis

(aa) a method for the treatment of a bacterial infection comprising administering a compound selected from Compound A, Compound B, Compound C, or Compound F

- Compound L or a pharmaceutically acceptable salt to a host in need thereof;

(bb) a method for the treatment of a bacterial infection comprising administering a compound selected from Compound A, Compound B, Compound C, or Compound F

- Compound L or a pharmaceutically acceptable salt in combination with an effective amount of an antibiotic to a host in need thereof;

(cc) a method for potentiating the effect of an antibiotic in the treatment of a bacterial infection comprising administering the antibiotic in combination with a compound selected from Compound A, Compound B, Compound C, or Compound F - Compound L or a pharmaceutically acceptable salt thereof to a host in need thereof;

(dd) the method of (aa), (bb), or (cc) wherein the bacterial infection is caused by a gram-positive bacterial infection;

(ee) the method of (aa), (bb), or (cc) wherein the bacterial infection is caused by a gram-negative bacterial infection; the method of (aa), (bb), or (cc) wherein the bacterial infection is caused by a mycobacterium;

(ff) a method for the treatment of acne vulgaris comprising administering a compound selected from Compound A, Compound B, Compound C, or Compound F - Compound L or a pharmaceutically acceptable salt thereof, either alone or in combination with an antibiotic, to a host in need thereof;

(gg) the method of (ff) wherein the acne vulgaris is caused by the bacterium Propionibacterium acnes or Staphylococcus epidermidis,

(hh) a method for the treatment of a gram-positive or a gram-negative bacterial infection comprising administering a compound of Formula VI or a pharmaceutically acceptable salt to a host in need thereof;

(ii) a method for the treatment of a gram-positive or a gram-negative bacterial infection comprising administering a compound of Formula VI or a pharmaceutically acceptable salt in combination with an effective amount of an antibiotic to a host in need thereof; (jj) a method for potentiating the effect of an antibiotic in the treatment of a gram-positive or a gram-negative bacterial infection comprising administering the antibiotic in combination with a compound of Formula VI or a pharmaceutically acceptable salt thereof to a host in need thereof;

(kk) a method for the treatment of a gram-positive or a gram-negative bacterial infection comprising administering Compound D or Compound E or a pharmaceutically acceptable salt to a host in need thereof;

(11) a method for the treatment of a gram-positive or a gram-negative bacterial infection comprising administering a compound selected from Compound D or Compound E or a pharmaceutically acceptable salt in combination with an effective amount of an antibiotic to a host in need thereof;

(mm)a method for potentiating the effect of an antibiotic in the treatment of a gram-positive or a gram-negative bacterial infection comprising administering the antibiotic in combination with a compound selected from Compound D or Compound E or a pharmaceutically acceptable salt thereof to a host in need thereof;

(nn) a pharmaceutical composition comprising an effective amount of a compound of Formula I, Formula II, Formula III, Formula IV, Formula V, or Formula VI or a pharmaceutically acceptable salt thereof, optionally in a pharmaceutically acceptable carrier in combination with an effective amount of an antibiotic;

(oo) a topical formulation comprising an effective amount of a compound Formula I, Formula II, Formula III, Formula IV, Formula V, or Formula VI or a pharmaceutically acceptable salt thereof in a topically acceptable carrier for the treatment of acne;

(pp) a pharmaceutical composition comprising an effective amount of a compound selected from Compound A, Compound B, Compound C, or Compound F - Compound L or a pharmaceutically acceptable salt thereof, optionally in a pharmaceutically acceptable carrier in combination with an effective amount of an antibiotic;

(qq) a topical formulation comprising an effective amount of a compound selected from Compound A, Compound B, Compound C, or Compound F - Compound L or a pharmaceutically acceptable salt thereof in a topically acceptable carrier for the treatment of acne;

(rr) a compound of Formula VII or Formula VIII or a pharmaceutically salt thereof;

(ss) a pharmaceutical composition comprising a compound of Formula VII or Formula VIII or a pharmaceutically acceptable salt thereof optionally in a pharmaceutically acceptable carrier; (tt) a method for the treatment of a bacterial infection comprising administering a compound of Formula VII or Formula VIII or a pharmaceutically acceptable salt to a host in need thereof;

(uu) a method for the treatment of a bacterial infection comprising administering a compound of Formula VII or Formula VIII or a pharmaceutically acceptable salt in combination with an effective amount of an antibiotic to a host in need thereof;

(vv) a method for potentiating the effect of an antibiotic in the treatment of a bacterial infection comprising administering the antibiotic in combination with a compound of Formula VII or Formula VIII or a pharmaceutically acceptable salt thereof to a host in need thereof;

(ww) the method of (tt), (uu), or (vv) wherein the bacterial infection is caused by a gram-positive bacterial infection;

(xx) the method of (tt), (uu), or (vv) wherein the bacterial infection is caused by a gram-negative bacterial infection;

(yy) the method of (tt), (uu), or (vv) wherein the bacterial infection is caused by a mycobacterium;

(zz) a process for the preparation of a therapeutic product that contains an effective amount of a compound of Formula I, Formula II, Formula III, Formula IV, Formula V, Formula VI, Formula VII, or Formula VIII or a pharmaceutically acceptable salt thereof, either alone or in combination with an effective amount of an antibiotic.

The details of one or more embodiments are set forth in the drawings and the description below. Other features, objects, and advantages will be apparent from the description and drawings, and from the claims.

DESCRIPTION OF DRAWINGS

Figure 1 demonstrates that MD-124 sensitizes Gram-negative bacteria towards various existing antibiotics. Panel (A) is the structure of MD-124. Panel (B) shows that 5 pg/ml MD- 124 sensitizes E. coli towards rifampicin (Rii). Values are means ± SD. n = 3. Panel (C) demonstrates that 5 pg/ml MD-124 itself showed no bacterial the growth inhibition effect. Values are means ± SD. n = 3. Panel (D) shows the results of a checkerboard assay of MD-124 (0 to 100 pg/ml) and rifampicin on E. coli. Panel (E) shows the results of a checkerboard assay of MD-124 (0 to 10 pg/ml) and rifampicin on E. coli. Panel (F) is a graph showing that MD- 124 sensitizes various Gram-negative bacterial strains towards rifampicin (Rii). Sensitization fold = MIC of rifampicin only /MIC of rifampicin with MD-124. Panel (G) is a graph showing the bacterial sensitizations of E. coli towards rifampicin activity comparison between MD-124, pentamidine and PMBN. Panel (H) shows that 5 pg/ml MD-124 sensitizes E. coli toward a broad range of existing antibiotics. All results represent 3 replications.

Figure 2 shows the results of a resistance frequency study of MD-124. Panel (A) shows the resistance frequency of E. coli towards clindamycin (4, 6 and 7 times of the MIC) and clindamycin/MD-124 combination. Panel (B) shows the resistance frequency of A ^’ coli towards trovafloxacin (2, 3 and 4 times of the MIC) and trovafloxacin/MD-124 combination. Panel (C) shows the resistance frequency of E. coli towards novobiocin (4, 5 and 6 times of the MIC) and novobiocin/MD-124 combination. The blue stars in Panels (A), (B), and (C) means no resistant colony was observed from 3 ^c 10 ⁹ CFUs. Values are means ± SD. n = 3. ***: P < 0.001.

Figure 3 depicts results from a mechanistic study that revealed that MD-100 and MD- 124 sensitize E.coli by disrupting the outer membrane and increasing antibiotics uptake. Panel (A) shows the proposed sensitization mechanism of MD-124 and MD-100. Panel (B) is a graph depicting that MD-124 showed compromised ability to sensitize a mutated, outer membrane “leaky” E. coli strain NR698 towards clarithromycin. Values are means ± SD. n = 3. Panel (C) shows that bacterial sensitizers can facilitate the E.coli lysis process by lysozyme. E.coli stock was incubated with 50 pg/ml lysozyme in the presence and absence of various bacterial sensitizers for 10 minutes at r.t and then the OD6oo was recorded. Poly B and penta are short for polymyxin B and pentamidine, respectively. E.coli stock was also incubated with the same concentration of various bacterial sensitizers in the absence of lysozyme as control. Values are means ± SD. n = 3. ***: P < 0.001 compared with vehicle group. Panel (D) shows the correlation between outer membrane disruption ability and bacterial sensitization activity of the various bacterial sensitizer. Panel (E) shows the HPLC results of the O-methyl novobiocin concentration inside E.coli in the presence (a) and absence (b) of 25 pg/ml MD-100.

Figure 4 shows molecular mechanistic studies of bacterial sensitizers. Panel (A) shows that LPS can decrease the sensitization ability of MD-124 in a concentration dependent manner. E. coli was treated with 10 pM MD-124 (about 5 pg/ml) and rifampicin combination with varying concentration of LPS (from 0 to 40 pM) for 20 h at 37 °C, then the OD6oo was measured and the sensitization fold were calculated as mentioned above. Panel (B) shows that Mg ²⁺ can decrease the sensitization ability of MD-124 in a concentration dependent manner. E. coli was treated with 10 pM MD-124 (about 5 pg/ml) with vary concentration of Mg ²⁺ (from 0 to 15 mM) for 20 hours at 37 °C, then the OD6oo was measured and the sensitization fold under different conditions were calculated. Panel (C) depicts a Dansyl-PMBN displacement assay. To E.coli stock (OD6oo = 0.3) in HEPES buffer (pH = 7.4) was added 10 pM Dansyl-PMBN and the fluorescent intensity was recorded as FI (Ex = 340 nm; Em = 520 nm), then different concentration of bacterial sensitizers was added, and the fluorescent intensity was recorded as Fx. The fluorescent intensity of 10 mM Dansyl-PMBN in HEPES buffer was recorded as baseline F0. Fluorescent intensity/% = (Fl-Fx)/(F1-F0). Values are means ± SD. n = 3; D) MD- 124 sensitize mcr-1 over-expressing E. coli strains towards rifampicin. All results are triplicates.

Figure 5 shows that MD-124 sensitizes wild type A. baumannii, K. pneumoniae and drug-resistant Gram-negative strains towards existing antibiotics. Panels (A) and (B) are the results from checkerboard assays that showed MD-124 sensitized A. baumannii towards rifampicin and novobiocin. Panels (C) and (D) are the results from checkerboard assays that showed MD-124 sensitized K. pneumoniae towards rifampicin and clarithromycin. Panel (E) shows that MD-124 sensitized NDM-1 overexpression E. coli towards rifampicin. Panel (F) shows that MD-124 sensitized MCR-1 overexpression E. coli towards rifampicin. All experiments are at least duplicate results.

Figure 6 shows that MD-124 and antibiotic combinations achieved A. coli (wild-type and drug-resistant strain) growth inhibition in an ex vivo skin bum infection model. Panel (A) shows that MD-124 and novobiocin combination inhibited wild-type E. coli growth. Concentration (w/w) for polymyxin B (poly B), novobiocin (Novo) and MD-124 were l%o, 4% and 1.5%o. The same novobiocin and MD-124 concentration was used in the combination group (Novo + MD-124). Panel (B) shows that MD-124 and clindamycin combination inhibited NDM-1 expressing E. coli growth. The concentrations (w/w) for polymyxin B (poly B), clindamycin (Clind) and MD-124 were l%o, 3%o and 1.5%o, respectively. The same clindamycin and MD-124 concentration was used in the combination group (Clind + MD-124). Values are means ± SEM. n = 5, ***P < 0.001 vs vehicle or antibiotic alone group. Panel (C) shows that the combination of MD-124 with various polymyxin B led to growth inhibition of mcr-1 positive E. coli in an ex vivo skin bum infection model. Concentration (w/w) for polymyxin B (poly B) and MD-124 were 3 o and 1.5 o. The same concentration was used for polymyxin B and MD-124 in the combination groups (Poly B + MD-124). Values are means ± SEM. n = 5, ***P < 0.001 vs antibiotics or the MD-124 alone group.

Figure 7 shows the results of a molecular mechanism study of bacterial sensitizers. Panel (A) shows that MD-100 failed to sensitize a mutated, outer membrane “leaky” E. coli strain NR698. Ery is short for erythromycin. 10 pg/ml MD-100 sensitized wild-type E. coli towards erythromycin for 32-fold (the comparison between the “Ery+10 pg/ml MD-100 line” and the “Ery only” line in Figure B, MIC of erythromycin is 50 pg/ml, and the MIC of erythromycin in the presence of 10 pg/ml MD-100 is 1.6 pg/ml ). E. coli NR698 was cultured with the antibiotic at various concentrations in the presence or absence of bacterial sensitizer for 24 h at 37 °C. Then bacterial growth density was determined by measuring Oϋboo. Panel (B) shows the LPS and high concentration of Mg ²⁺ decreased the sensitization ability of MD- 100. E. coli was treated with 10 pg/ml MD-100 and erythromycin combination in the presence and absence of 40 mM LPS for 20 h at 37 °C. Then the growth density/% was calculated based on OD6OO. E. coli was treated with 10 pg/ml MD-100 and erythromycin combination in the presence and absence of 20 mM Mg ²⁺ for 20 h at 37 °C, then the growth density/% was calculated based on Oϋboo.

Figure 8 demonstrates that 5 pg/ml MD-124 sensitizes E. coli towards polymyxin B. E. coli was cultured with the polymyxin B at various concentrations in the presence or absence of 5 pg/ml MD-124 for 20 h at 37 °C. Then bacterial growth density was determined by measuring OD6oo.

Figure 9 shows the effect of phosphatidylcholine on MD-124 sensitization activity.

Figure 10 contains graphs showing that Membrane disruptor sensitize B. subtilis (Panel A) and MRS A (Panel B) towards Rifampicin. Bacteria was cultured with antibiotics at various concentrations in the presence or absence of bacteria sensitizer for 24 hours at 37 °C. Then bacterial growth density was determined by measuring Oϋboo. ***: p <0.01.

Figure 11 contains graphs showing that MD-108 can change the composition between MRSA and E. coli (Panel A) or MRSA and B. subtilis (Panel B) when the bacteria strains are under the same antibiotic pressure.

DETAILED DESCRIPTION OF THE INVENTION

Described herein are compounds and methods for the treatment of bacterial infections as well as for the potentiation of the therapeutic effect of antibiotics in the treatment of bacterial infections. The methods include administering an effective amount of a compound described herein or its pharmaceutically acceptable salt, optionally in a pharmaceutically acceptable carrier. The bacterial infection may be caused by gram-positive bacteria, gram-negative bacteria, and/or antibiotic resistant bacteria. In one embodiment, the bacterial infection is caused by mycobacteria.

I. DEFINITIONS

Compounds are described using standard nomenclature. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as is commonly understood by one of skill in the art to which the invention belongs. The terms “a” and “an” do not denote a limitation of quantity, but rather denote the presence of at least one of the referenced item. The term “or” means “and/or”. Recitation of ranges of values merely intended to serve as a shorthand method of referring individually to each separate value falling within the range, unless otherwise indicated herein, and each separate value is incorporated into the specification as if it were individually recited herein. The endpoints of all ranges are included within the range and independently combinable. All methods described herein can be performed in a suitable order unless otherwise indicated herein or otherwise clearly contradicted by context. The use of example, or exemplary language (e.g. “such as”), is intended merely to better illustrate the invention and does not pose a limitation on the scope of the invention unless otherwise claimed.

A dash (“-”) that is not between two letters or symbols is used to indicate a point of attachment for a substituent. For example, -(C=0)NH2 is attached through the carbon of the keto (C=0) group.

“Alkyl” is a branched or straight chain saturated aliphatic hydrocarbon group. In one non-limiting, preferred embodiment, the alkyl group generally contains from 1 to about 12 carbon atoms, from 1 to about 8 carbon atoms, from 1 to about 6 carbon atoms, or from 1 to about 4 carbon atoms. In certain embodiments, the alkyl is C1-C2, C1-C3, C1-C4, C1-C5, C1-C6, C1-C7, Ci-Ce, C1-C9, or C1-C10. In one embodiment, the alkyl group contains from about 1 to about 50 carbon atoms or from about 1 to about 36 carbon atoms. For example, the term Ci- Cealkyl as used herein indicates a straight chain or branched alkyl group having from 1, 2, 3, 4, 5, or 6 carbon atoms and is intended to mean that each of these are described as an independent species. For example, the term C1-C4 alkyl as used herein indicates a straight or branched alkyl group having from 1, 2, 3, or 4 carbon atoms and is intended to mean that each of these is described as an independent species. Examples of alkyl include, but are not limited to, methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, sec-butyl, t-butyl, n-pentyl, isopentyl, tert-pentyl, ve -pentyl. 3 -pentyl, active pentyl, neopentyl, n-hexyl, sec-hexyl, tert- hexyl, isohexyl, 2-methylpentance, 3-methylpentane, 2,2-dimethylbutane, and 2,3-dimethylbutane. In some embodiments, the alkyl group is optionally substituted as defined herein.

In one embodiment “alkyl” is a Ci-Cioalkyl, Ci-C9alkyl, Ci-Csalkyl, Ci-C7alkyl, Ci-Cealkyl, Ci-Csalkyl, Ci-C ₄ alkyl, Ci-Csalkyl, or Ci-C ₂ alkyl.

When a term is used that includes “alk” it should be understood that “cycloalkyl” or “carbocyclic” can be considered part of the definition, unless unambiguously excluded by the context. For example and without limitation, the terms alkyl, alkenyl, alkynyl, alkoxy, alkanoyl, alkenloxy, haloalkyl, etc. can all be considered to include the cyclic forms of alkyl, unless unambiguously excluded by context.

For example, “cycloalkyl” is an alkyl group that forms or includes a ring. When composed of two or more rings, the rings may be joined together in a fused fashion. Non limiting examples of typical cycloalkyl groups include cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, and cyclooctyl.

As used herein, “aryl” refers to a radical of a monocyclic or polycyclic (e.g., bicyclic or tricyclic) 4n+2 aromatic ring system (e.g., having 6, 10, or 14 p electrons shared in a cyclic array) having 6-14 ring carbon atoms and zero heteroatoms provided in the aromatic system (“C6-Ci4aryl”). In some embodiments, an aryl group has 6 ring carbon atoms ( G.aryl ; e.g., phenyl). In some embodiments, an aryl group has 10 ring carbon atoms (“Cioaryl”; e.g., naphthyl such as 1 -naphthyl and 2-naphthyl). In some embodiments, an aryl group has 14 ring carbon atoms ( Cuaryl ; e.g., anthracyl). “Aryl” also includes ring systems wherein the aryl ring, as defined above, is fused with one or more cycloalkyl or heterocycloalkyl groups wherein the point of attachment is on the aryl ring, and in such instances, the number of carbon atoms continue to designate the number of carbon atoms in the aryl ring system. The one or more fused cycloalkyl or heterocycloalkyl groups can be 4 to 7 or 5 to 7-membered cycloalkyl or heterocycloalkyl groups that optionally contain 1, 2, or 3 heteroatoms independently selected from nitrogen, oxygen, phosphorous, sulfur, silicon, and boron. In one non-limiting embodiment, aryl groups are pendant. An example of a pendant ring is a phenyl group substituted with a phenyl group. In some embodiments, the aryl group is optionally substituted as defined herein.

In one embodiment “aryl” is a 6-carbon aromatic group (phenyl).

In one embodiment “aryl” is a 10-carbon aromatic group (naphthyl).

In one embodiment “aryl” is a 6-carbon aromatic group fused to a heterocycle wherein the point of attachment is the aryl ring. Non-limiting examples of “aryl” include indoline, tetrahydroquinoline, tetrahydroisoquinoline, and dihydrobenzofuran wherein the point of attachment for each group is on the aromatic ring. In one embodiment “aryl” is a 6-carbon aromatic group fused to a cycloalkyl wherein the point of attachment is the aryl ring. Non-limiting examples of “aryl” include dihydro-indene and tetrahydronaphthalene wherein the point of attachment for each group is on the aromatic ring.

In one embodiment “aryl” is “substituted aryl”.

In one embodiment “heteroaryl” is a 5-membered aromatic group containing 1, 2, 3, or 4 nitrogen atoms.

Non-limiting examples of 5 membered “heteroaryl” groups include pyrrole, furan, thiophene, pyrazole, imidazole, triazole, tetrazole, isoxazole, oxazole, oxadiazole, oxatriazole, isothiazole, thiazole, thiadiazole, and thiatriazole.

In one embodiment “heteroaryl” is a 6-membered aromatic group containing 1, 2, or 3 nitrogen atoms (i.e. pyridinyl, pyridazinyl, triazinyl, pyrimidinyl, and pyrazinyl).

In one embodiment “heteroaryl” is a 9-membered bicyclic aromatic group containing 1 or 2 atoms selected from nitrogen, oxygen, and sulfur.

Non-limiting examples of “heteroaryl” groups that are bicyclic include indole, benzofuran, isoindole, indazole, benzimidazole, azaindole, azaindazole, purine, isobenzofuran, benzothiophene, benzoisoxazole, benzoisothiazole, benzooxazole, and benzothiazole.

In one embodiment “heteroaryl” is a 10-membered bicyclic aromatic group containing 1 or 2 atoms selected from nitrogen, oxygen, and sulfur.

Non-limiting examples of “heteroaryl” groups that are bicyclic include quinoline, isoquinoline, quinoxaline, phthalazine, quinazoline, cinnoline, and naphthyridine.

In one embodiment “heteroaryl” is “substituted heteroaryl”.

“Haloalkyl” is a branched or straight-chain alkyl groups substituted with 1 or more halo atoms described above, up to the maximum allowable number of halogen atoms. Examples of haloalkyl groups include, but are not limited to, fluoromethyl, difluoromethyl, trifluoromethyl, chloromethyl, dichloromethyl, trichloromethyl, pentafluoroethyl, heptafluoropropyl, difluorochloromethyl, dichlorofluoromethyl, difluoroethyl, difluoropropyl, dichloroethyl and dichloropropyl. “Perhaloalkyl” means an alkyl group having all hydrogen atoms replaced with halogen atoms. Examples include but are not limited to, trifluoromethyl and pentafluoroethyl. In one embodiment “haloalkyl” is a Ci-Ciohaloalkyl, Ci-C9haloalkyl, Ci-Cshaloalkyl, Ci-C7haloalkyl, Ci-C6haloalkyl, Ci-Cshaloalkyl, Ci-Cdialoalkyl, Ci-C3haloalkyl, and Ci- C2haloalkyl. “Alkoxy” is alkyl group as defined above covalently bounds through an oxygen bridge

(-0-). Examples of alkoxy include, but are not limited to, methoxy, ethoxy, «-propoxy. isopropoxy, «-butoxy, 2-butoxy, t-butoxy, «-pentoxy. 2-pentoxy, 3-pentoxy, isopentoxy, neopentoxy,

«-hexyoxy, 2-hexoxy, 3-hexoxy, and 3-methylpentoxy. “Haloalkoxy” indicates a haloalkyl group as defined herein attached through an oxygen bridge (-0-).

As used herein, the term "active agent" refers to any type of drug, medicine, pharmaceutical, hormone, antibiotic, protein, gene, growth factor, bioactive material, etc., used for treating, controlling, or preventing diseases or medical conditions as described herein. The term “active agent” also includes the active compounds as described in the present application.

A “dosage form” means a unit of administration of an active agent. Examples of dosage forms include tablets, capsules, injections, suspensions, liquids, emulsions, implants, particles, spheres, creams, ointments, suppositories, inhalable forms, transdermal forms, buccal, sublingual, topical, gel, mucosal, and the like. A “dosage form” can also include an implant, for example an optical implant.

An “effective amount” as used herein means an amount which provides a therapeutic or prophylactic benefit.

“Parenteral” administration of a pharmaceutical composition includes, e.g., subcutaneous (s.c.), intravenous (i.v.), intramuscular (i.m), intrastemal injection, or infusion techniques.

To “treat” a disease as the term is used herein means to reduce the frequency or severity of at least one sign or symptom of a disease or disorder experienced by a subject (i.e., palliative treatment) or to decrease a cause or effect of the disease or disorder (i.e. disease-modifying treatment).

As used herein, “pharmaceutical compositions” are compositions comprising at least one active agent and at least one other substance, such as a carrier. “Pharmaceutical combinations” are combinations of at least two active agents which may be combined in a single dosage form or provided together in separate dosage forms with instructions that the active agents are to be used together to treat any disorder described herein.

The term “carrier” applied to pharmaceutical compositions/combinations of the invention refers to a diluent, excipient, or vehicle with which an active compound is provided. A “pharmaceutically acceptable excipient” means an excipient that is useful in preparing a pharmaceutical composition/combination that is generally safe, non-toxic and neither biologically nor otherwise inappropriate for administration to a host, typically a human. In one embodiment, an excipient is used that is acceptable for veterinary use.

A “patient” or “host” or “subj ect” is a human or non-human animal in need of treatment or prevention of any of the disorders specifically described herein. Typically, the host is a human. A “host” may alternatively refer to for example, a mammal, primate (e.g. human), cow, sheep, goat, horse, dog, cat, rabbit, rat, mice, fish, bird, and the like.

A “therapeutically effective amount” of a pharmaceutical composition/combination of this invention means an amount effective, when administered to a host, to provide a therapeutic benefit such as an amelioration of symptoms or reduction or diminution of the disease itself.

The compounds in any of the Formulas described herein or Compound A - Compound L may be in the form of a racemate, enantiomer, mixture of enantiomers, diastereomer, mixture of diastereomers, tautomer, N- oxide, or other isomers, such as a rotamer, as if each is specifically described unless specifically excluded by context.

The present invention includes compounds of Formula I, Formula II, Formula III, Formula IV, or Formula V with at least one desired isotopic substitution of an atom, at an amount above the natural abundance of the isotope, i.e., enriched. The present invention also includes compounds selected from Compound A - Compound L with at least one desired isotopic substitution of an atom, at an amount above the natural abundance of the isotope, i.e., enriched. Isotopes are atoms having the same atomic number but different mass numbers, i.e., the same number of protons but a different number of neutrons.

Examples of isotopes that can be incorporated into compounds of the invention include isotopes of hydrogen, carbon, nitrogen, oxygen, phosphorous, fluorine, chlorine and iodine such as ² H, ³ H, ⁿ C, ¹³ C, ¹⁴ C, ¹⁵ N, ¹⁷ 0, ¹⁸ 0, ¹⁸ F ³¹ P, ³² P, ³⁵ S, ³⁶ CI, and ¹²⁵ I respectively. In one non-limiting embodiment, isotopically labelled compounds can be used in metabolic studies (with ¹⁴ C), reaction kinetic studies (with, for example ² H or ¾), detection or imaging techniques, such as positron emission tomography (PET) or single-photon emission computed tomography (SPECT) including drug or substrate tissue distribution assays, or in radioactive treatment of patients. In particular, an ¹⁸ F labeled compound may be particularly desirable for PET or SPECT studies. Isotopically labeled compounds of this invention and prodrugs thereof can generally be prepared by carrying out the procedures disclosed in the schemes or in the examples and preparations described below by substituting a readily available isotopically labeled reagent for a non-isotopically labeled reagent. By way of general example and without limitation, isotopes of hydrogen, for example, deuterium ( ² H) and tritium ( ³ H) may be used anywhere in described structures that achieves the desired result. Alternatively or in addition, isotopes of carbon, e.g., ¹³ C and ¹⁴ C, may be used.

Isotopic substitutions, for example deuterium substitutions, can be partial or complete. Partial deuterium substitution means that at least one hydrogen is substituted with deuterium. In certain embodiments, the isotope is 90, 95 or 99% or more enriched in an isotope at any location of interest. In one non-limiting embodiment, deuterium is 90, 95 or 99% enriched at a desired location.

In one non-limiting embodiment, the substitution of one or more hydrogen atoms for a deuterium atoms can be provided in any of Formula I, Formula II, Formula III, Formula IV, Formula V, or Formula VI. In one non-limiting embodiment, the substitution of one or more hydrogen atoms for a deuterium atoms can be provided in a compound selected from Compound A - Compound L. In one non-limiting embodiment, the substitution of a hydrogen atom for a deuterium atom occurs within a group selected from any of R, R ¹ , R ² , R ³ , R ⁴ , and R ⁵ . For example, when any of the groups are, or contain for example through substitution, methyl, ethyl, or methoxy, the alkyl residue may be deuterated (in non-limiting embodiments,

CDH ₂ , CD ₂ H, CD _3, CH ₂ CD ₃ , CD ₂ CD ₃ , CHDCH ₂ D, CH ₂ CD ₃ , CHDCHD ₂ , OCDH ₂ , OCD ₂ H, or OCD ₃ etc.). In certain other embodiments, when two substituents are combined to form a cycle the unsubstituted carbons may be deuterated.

The compounds of the present invention may form a solvate with solvents. Therefore, in one non-limiting embodiment, the invention includes a solvated form of the compound. The term “solvate” refers to a molecular complex of a compound of the present invention (including a salt thereol) with one or more solvent molecules. Non-limiting examples of solvents are water, ethanol, dimethyl sulfoxide, acetone and other common organic solvents. Additional non-limiting examples of solvents are dimethyl acetamide and N-methyl-2-pyrrolidine. The term “hydrate” refers to a molecular complex comprising a compound of the invention and water. Pharmaceutically acceptable solvates in accordance with the invention include those wherein the solvent may be isotopically substituted, e.g. D ₂ 0, d6-acetone, d6-DMSO. A solvate can be in a liquid or solid form.

As used herein, “pharmaceutically acceptable salt” is a derivative of the disclosed compound in which the parent compound is modified by making inorganic or organic, non toxic, acid or base addition salts thereof. The salts of the present compounds can be synthesized from a parent compound that contains a basic or acidic moiety by conventional chemical methods.

Generally, such salts can be prepared by reacting free acid forms of these compounds with a stoichiometric amount of the appropriate base (such as Na, Ca, Mg, or K hydroxide, carbonate, bicarbonate, or the like), or by reactive free base forms of these compounds with a stoichiometric amount of the appropriate acid. Such reactions are typically carried out in a variety of solvents or solvent mixtures which are compatible with the compound. Generally, non-aqueous media like ether, ethyl acetate, ethanol, isopropanol, or acetonitrile are typical, where practical. Salts of the present compounds further include solvates of the compound and the compound salts.

Examples of pharmaceutically acceptable salts include, but are not limited to, mineral or organic acid salts of basic residues such as amines; alkali or organic salts of acidic residues such as carboxylic acids; and the like. The pharmaceutically acceptable salts include the conventional non-toxic salts and the quaternary ammonium salts of the parent compound formed, for example, from non-toxic organic acids. For example, conventional non-toxic acid salts include the salts prepared from organic acids such as acetic, propionic, succinic, glycolic, stearic, lactic, malic, tartaric, citric, ascorbic, pamoic, maleic, hydroxymaleic, phenylacetic, glutamic, benzoic, salicylic, mesylic, esylic, besylic, sulfanilic, 2-acetoxybenzoic, fumaric, toluenesulfonic, methanesulfonic, ethane disulfonic, oxalic, isethionic, HOOC-(CH2)n-COOH where n is 0-4, and the like, or using a different acid that produces the same counterion. Lists of additional suitable salts may be found, e.g., in Remington's Pharmaceutical Sciences , 17 ^th ed., Mack Publishing Company, Easton, Pa., p. 1418 (1985).

II. COMPOUNDS OF THE PRESENT INVENTION wherein: m and 0 are independently selected from 0, 1, 2, or 3; n is 0, 1, 2, 3, or 4;

X ¹ is O, S, or NR ⁴ ;

X ³ is independently at each occurrence selected from the group consisting of C(R ³ )2, O, S, and NR ⁴ ;

X ⁴ is independently at each occurrence selected from the group consisting of CR ³ and N;

X ⁵ is C(R ³ ) ₂ , O, or S;

R is independently at each occurrence selected from the group consisting of hydrogen, hydroxyl, Ci-C6alkyl, Ci-C6alkoxy, Ci-C6haloalkoxy, Ci-C6alkanoyl, aliphatic, carbocyclic, Ci-C6hydroxyalkyl, Ci-C6haloalkyl, N(R ³ )2, -NHSC alkyl, -N(alkyl)S02alkyl, -NHS02aryl, -N(alkyl)S02aryl, -NHS02alkenyl, -N(alkyl)S02alkenyl, -NHS02alkynyl, N(alkyl)S0 ₂ alkynyl, NO2, -COOH, -CONH2, -P(0)(0H) ₂ , -S(0)R ³ , -SO2R ³ , -SO3R ³ , - S0 ₂ N(R ³ ) ₂ , -OSO2R ³ ,

-N(R ³ )S02R ³ , azide, aryl, heteroaryl, heterocyclyl, fluorine, chlorine, bromine, iodine, thiol, and cyano;

R ¹ and R ² are independently at each occurrence selected from the group consisting of:

R ³ is independently at each occurrence selected from the group consisting of hydrogen, hydroxyl, Ci-C6alkyl, Ci-C6alkoxy, Ci-C6haloalkoxy, Ci-C6alkanoyl, carbocyclic, C2- Cealkenyl, C2-C6alkynyl, heteroaryl, aryl, heterocyclyl, -COOR, -C(0)R, fluorine, chlorine, bromine, and iodine; and

R ⁴ and R ⁵ are independently at each occurrence selected from the group consisting of hydrogen, Ci-C6alkyl, Ci-C6alkoxy, Ci-C6haloalkoxy, Ci-C6alkanoyl, carbocyclic, C2- Cealkenyl, C2-C6alkynyl, aryl, heteroaryl, heterocyclyl, -COOR, and -C(0)R.

In one embodiment, a compound is provided of Formula I or a pharmaceutically acceptable salt thereof, optionally in a pharmaceutically acceptable carrier, to form a pharmaceutical composition. In one embodiment of Formula I, m is 0. In one embodiment of Formula I, m is 1. In one embodiment of Formula I, m is 2. In one embodiment of Formula I, m is 3.

In one embodiment of Formula I, n is 0. In one embodiment of Formula I, n is 1. In one embodiment of Formula I, n is 2. In one embodiment of Formula I, n is 3. In one embodiment of Formula I, n is 4.

In one embodiment ofFormulal, o is 0. In one embodiment of Formula I, o is 1. In one embodiment of Formula I, o is 2. In one embodiment of Formula I, o is 3.

In one embodiment of Formula I, p is 0. In one embodiment of Formula I, p is 1. In one embodiment of Formula I, p is 2.

In one embodiment of Formula I, X ¹ is O. In one embodiment of Formula I, X ¹ is NR ⁴ and R ⁴ is hydrogen. In one embodiment of Formula I, X ¹ is NR ⁴ and R ⁴ is Ci-C6alkyl.

In one embodiment of Formula I, X ² is O. In one embodiment of Formula I, X ² is S. In one embodiment of Formula I, X ² is NR ⁴ and R ⁴ is hydrogen. In one embodiment of Formula I, X ² is NR ⁴ and R ⁴ is Ci-C6alkyl.

In one embodiment of Formula I, X ³ is C(R ³ )2 and R ³ is hydrogen. In one embodiment of Formula I, X ³ is S. In one embodiment of Formula I, X ³ is C(R ³ )2 and R ³ is Ci-C6alkyl. In one embodiment of Formula I, X ³ is C(R ³ )2 and one R ³ is hydrogen and the other is Ci-C6alkyl. In one embodiment of Formula I, X ³ is C(R ³ )2 and one R ³ is fluorine, chlorine, bromine iodine or Ci-C6haloalkyl. In one embodiment of Formula I, X ³ is O. In one embodiment of Formula I, X ³ is NR ⁴ and R ⁴ is hydrogen. In one embodiment of Formula I, X ³ is NR ⁴ and R ⁴ is alkyl. In one embodiment of Formula I, X ⁴ is N. In one embodiment of Formula I, X ⁴ is CR ³ and R ³ is hydrogen. In one embodiment of Formula I, X ⁴ is CR ³ and R ³ is Ci-C6alkyl. In one embodiment of Formula I, X ⁴ is C(R ³ )2 and R ³ is fluorine, chlorine, bromine, iodine or Ci- Cehaloalkyl.

In one embodiment of Formula I, X ⁵ is C(R ³ )2 and R ³ is hydrogen. In one embodiment of Formula I, X ⁵ is C(R ³ )2 and R ³ is Ci-C6alkyl. In one embodiment of Formula I, X ⁵ is C(R ³ )2 and one R ³ is hydrogen and the other is alkyl, hydroxyl, fluorine, chlorine, bromine iodine or Ci-C6haloalkyl. In one embodiment of Formula I, X ⁵ is O.

In one embodiment of Formula I, R is hydrogen, fluorine, chlorine, bromine, or iodine. NR 4

In one embodiment of Formula I, R ¹ is , wherein R ⁴ and R ⁵ are

NR ⁴ D independently hydrogen or Ci-C6alkyl. In certain embodiments R ¹ is ^/ ^NR ^'4 ^NR ⁴ R ⁵ , wherein R ⁴ and R ⁵ are independently hydrogen or Ci-C6alkyl.

NR ⁴

In one embodiment of Formula I, R ² is wherein R ⁴ and R ⁵ are NR ⁴ independently hydrogen or alkyl. In certain embodiments R ² is wherein R ⁴ and R ⁵ are independently hydrogen or Ci-C6alkyl.

NR 4

In one embodiment of Formula I, R ¹ and R ² are each , wherein R ⁴ and R ⁵ are independently hydrogen or Ci-C6alkyl. In one embodiment of Formula I, R ¹ and R ² are NR ⁴ each ^/ i ^NR ^'4 ^NR ⁴ R ⁵ wherein R ⁴ and R ⁵ are independently hydrogen or Ci-C6alkyl.

In one embodiment of Formula selected from the group consisting of: In one embodiment of Formula selected from the group consisting of:

In certain embodiments, the compound of Formula I is a compound of the formula:

5

In certain embodiments, the compound of Formula I is a compound of the formula:

In certain embodiments, the compound of Formula I is a compound of the formula: Non-l ⁱ m ⁱ t ⁱ ng examples of compounds of Formula I _i nclude:

In another aspect, a method is provided for treating a bacterial infection comprising administering an effective amount of a compound of Formula II, Formula III, Formula IV, or Formula V or a pharmaceutically acceptable salt thereof to a host in need thereof: wherein

L ¹ is selected from

L ² is selected from v and w are independently selected from 0, 1, 2, 3, and 4;

R is independently at each occurrence selected from the group consisting of hydrogen, hydroxyl, Ci-C6alkyl, Ci-C6alkoxy, Ci-C6haloalkoxy, Ci-C6alkanoyl, aliphatic, carbocyclic, Ci-C6hydroxyalkyl, Ci-C6haloalkyl, N(R ³ )2, -NHSC alkyl, -N(alkyl)S02alkyl, -NHSC aryl, -N(alkyl)S02aryl, -NHSC alkenyl, -N(alkyl)S02alkenyl, -NHSC alkynyl, N(alkyl)S S0 ₂ N(R ³ )

-N(R ³ )S02R ³ , azide, aryl, heteroaryl, heterocyclyl, fluorine, chlorine, bromine, iodine, thiol, and cyano;

X ⁶ , X ⁷ , X ⁸ , and X ⁹ are independently selected from O, S, NH, or Se;

X ¹⁰ is selected from Se, S, or NH;

R ⁶ and R ⁷ are independently at each occurrence selected from the group consisting of: R, R ¹ , R ² , R ⁴ , and R ⁵ are as defined herein.

In some embodiments of Formula II, Formula III, Formula IV, and/or Formula V, X ¹⁰ is not S.

In some embodiments of Formula II, Formula III, Formula IV, and/or Formula V, X ¹⁰ is not NH.

In some embodiments of Formula II, Formula III, Formula IV and/or Formula V, L ² is not

In some embodiments of Formula II, Formula III, Formula IV and/or Formula V, one or more of X ⁶ , X ⁷ , X ⁸ , and X ⁹ is not NH.

In some embodiments of Formula II, the compound has a chemical structure selected from:

Non-limiting examples of compounds of Formula II include:

In some embodiments of Formula III, the compound has a chemical structure selected from:

Non-limiting examples of compounds of Formula III include: In some embodiments of Formula IV, the compound has a chemical structure selected from:

Non-limiting examples of compounds of Formula IV include:

In some embodiments of Formula V, the compound has a chemical structure selected from:

Non-limiting examples of compounds of Formula V include:

In another aspect, a method is provided for treating a gram-positive or a gram-negative bacterial infection comprising administering an effective amount of a compound of Formula

VI: or a pharmaceutically acceptable salt thereof wherein

R ⁹ and R ¹² are independently at each occurrence selected from the group consisting of hydrogen, hydroxyl, Ci-C6alkyl, Ci-C6alkoxy, Ci-C6haloalkoxy, Ci-C6alkanoyl, aliphatic, carbocyclic, Ci-C6hydroxyalkyl, Ci-C6haloalkyl, N(R ³ )2, -NHS02alkyl, -N(alkyl)S02alkyl, -NHS02aryl, -N(alkyl)S02aryl, -NHSC alkenyl, -N(alkyl)S02alkenyl, -NHS02alkynyl, -N(alkyl)S0 ₂ alkynyl, NC , -COOH, -CONH2, -P(0)(0H) ₂ , -S(0)R ³ , -SO2R ³ , -SO3R ³ , -S0 ₂ N(R ³ ) ₂ , -OSO2R ³ , -N(R ³ )S02R ³ , azide, aryl, heteroaryl, heterocyclyl, fluorine, chlorine, bromine, iodine, thiol, and cyano; and

R ¹⁰ and R ¹¹ are independently at each occurrence selected from the group consisting of hydroxyl, Ci-C6alkanoyl, carbocyclic, Ci-C6hydroxy alkyl, Ci-C6haloalkyl, N(R ³ ) ₂ , -NHSC alkyl, -N(alkyl)S02alkyl, -NHS02aryl, -N(alkyl)S02aryl, -NHSC alkenyl, -N(alkyl)S02alkenyl, -NHS02alkynyl, -N(alkyl)S02alkynyl, NO2, -COOH, -CONH2-, - C(0)R, -P(0)(0H) ₂ , -S(0)R ³ , -SO2R ³ , -SO3R ³ , -S0 ₂ N(R ³ ) ₂ , -OSO2R ³ , -N(R ³ )S0 ₂ R ³ , azide, aryl, heteroaryl, heterocyclyl, fluorine, bromine, iodine, thiol, and cyano.

In one embodiment, the compound of Formula VI is a compound of the Formula:

In one aspect, a compound of Formula VII or Formula VIII or a pharmaceutically acceptable salt is provided: wherein: m and n are independently selected from 1, 2, 3, or 4; p is 0, 1, 2, or 3; q and t are independently at each occurrence 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10;

L ³ and L ⁴ are each independently C(R ³ )2, O, or S;

R is independently at each occurrence selected from the group consisting of hydrogen, hydroxyl, Ci-C6alkyl, Ci-C6alkoxy, Ci-C6haloalkoxy, Ci-C6alkanoyl, aliphatic, carbocyclic, Ci-C6hydroxyalkyl, Ci-C6haloalkyl, N(R ³ )2, -NHSC alkyl, -N(alkyl)S02alkyl, -NHSC aryl, -N(alkyl)S02aryl, -NHSC alkenyl, -N(alkyl)S02alkenyl, -NHS02alkynyl,

N(alkyl)S0 ₂ alkynyl, N0 ₂ , -COOH, -CONH2, -P(0)(OH) ₂ , -S(0)R ³ , -SO2R ³ , -SO3R ³ , - S0 ₂ N(R ³ ) ₂ , -OSO2R ³ ,

-N(R ³ )S02R ³ , azide, aryl, heteroaryl, heterocyclyl, fluorine, chlorine, bromine, iodine, thiol, and cyano;

R ³ is independently at each occurrence selected from the group consisting of hydrogen, hydroxyl, Ci-C6alkyl, Ci-C6alkoxy, Ci-C6haloalkoxy, Ci-C6alkanoyl, carbocyclic, C2- Cealkenyl, C2-C6alkynyl, heteroaryl, aryl, heterocyclyl, -COOR, -C(0)R, fluorine, chlorine, bromine, and iodine;

R ¹³ and R ¹⁴ are independently selected from the group consisting of wherein R ⁴ and R ⁵ are independently at each occurrence selected from the group consisting of hydrogen and Ci-C6alkyl and 0 is 0 to 10 (i.e., 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10);

X ¹¹ and X ¹² are each independently selected from the group consisting of C(R ³ )2, O, NH, or S, wherein R ³ is independently at each occurrence selected from a group as defined above;

Y ¹ and Y ² are each independently selected from the group consisting of C(R ³ )2, O,

NH, or S, wherein R ³ is independently at each occurrence selected from a group as defined above; and

Z is CR ³ or N, wherein R ³ is as defined above.

In some cases, a compound is provided of Formula VII or Formula VIII or a pharmaceutically acceptable salt thereof, optionally in a pharmaceutically acceptable carrier, to form a pharmaceutical composition. NR 4

In some cases of Formula VII or Formula VIII, R ¹³ is wherein R ⁴ and R ⁵ are independently hydrogen or Ci-C6alkyl. In some cases of Formula VII or Formula VIII, R ¹³

NR ⁴ is , wherein R ⁴ and R ⁵ are independently hydrogen or Ci-C6alkyl.

NR ⁴

In some examples of Formula VII or Formula VIII, R ¹⁴ is , wherein R ⁴ and R ⁵ are independently hydrogen or alkyl. In some examples of Formula VII or Formula VIII,

NR ,4'

R ¹⁴ is wherein R ⁴ and R ⁵ are independently hydrogen or Ci-C6alkyl.

NR ⁴

In some examples of Formula VII or Formula VIII, R ¹³ and R ¹⁴ are each wherein R ⁴ and R ⁵ are independently hydrogen or Ci-C6alkyl. In some examples of Formula

NR ⁴

/ U

VII or Formula VIII, R ¹³ and R ¹⁴ are each ^/ ^ ^'' NR ⁴⁴ ^ 'NR ⁴⁴ R ⁵⁵ . wherein R ⁴ and R ⁵ are independently hydrogen or Ci-C6alkyl. In some cases, R ⁴ and R ⁵ are hydrogen.

Optionally, X ¹¹ and X ¹² are selected from the group consisting of O, CFh, and S. In some cases, X ¹¹ and X ¹² are the same (e.g., X ¹¹ and X ¹² are each O, X ¹¹ and X ¹² are each CFh, or X ¹¹ and X ¹² are each S).

Optionally, Y ¹ and Y ² are selected from the group consisting of O and CFk. In some cases, Y ¹ and Y ² are the same (e.g., Y ¹ and Y ² are each O or Y ¹ and Y ² are each CFh).

In some cases, each R is independently selected from the group consisting of hydrogen, Ci-C6alkyl, Ci-C6alkoxy, Ci-C6haloalkyl, and fluorine is Ci-C6alkyl, Ci-C6alkoxy, or Ci- Cehaloalkyl.

In Formula VII, when t is 0, L ³ is absent and a direct bond is present between X ¹¹ and the ring to which L ³ is connected in the structure. Similarly, in Formula VII, when q is 0, L ⁴ is absent and a direct bond is present between X ¹² and the ring to which L ⁴ is connected in the structure. In some embodiments of Formula VII, both t and q are absent, resulting in a compound that has a chemical structure as shown below: wherein m, n, p, R, R ¹³ , R ¹⁴ , X ¹¹ , X ¹² , Y ¹ , Y ² , and Z are as defined herein for Formula VII.

In Formula VIII, when t is 0, L ³ is absent and a direct bond is present between X ¹¹ and the ring to which L ³ is connected in the structure. Similarly, in Formula VIII, when q is 0, L ⁴ is absent and a direct bond is present between X ¹² and the ring to which L ⁴ is connected in the structure. In some embodiments of Formula VIII, both t and q are absent, resulting in a compound that has a chemical structure as shown below: wherein m, n, p, R, R ¹³ , R ¹⁴ , X ¹¹ , X ¹² , Y ¹ , Y ² , and Z are as defined herein for Formula VIII.

In certain aspects, the compound of Formula VII is a compound of the following formula:

In certain aspects, the compound of Formula VIII is a compound of the following formula:

Additional compounds described herein include the following compounds. In some cases, the compounds are useful in the methods of treating bacterial infections as described herein.

The compounds in any of the Formulas described herein may be in the form of a racemate, enantiomer, mixture of enantiomers, diastereomer, mixture of diastereomers, tautomer, N-oxide, or other isomer, such as a rotamer, as if each is specifically described unless specifically excluded by context. Compound A - Compound L may be in the form of a racemate, enantiomer, mixture of enantiomers, diastereomer, mixture of diastereomers, tautomer, N- oxide, or other isomer, such as a rotamer, as if each is specifically described unless specifically excluded by context.

The present invention includes compounds of Formula I, Formula II, Formula III, Formula IV, Formula V, Formula VI, Formula VII, or Formula VIII with at least one desired isotopic substitution of an atom, at an amount above the natural abundance of the isotope, i.e. enriched. The present invention also includes a compound selected from Compound A - Compound L with at least one desired isotopic substitution of an atom, at an amount above the natural abundance of the isotope, i.e. enriched.

III. PHARMACEUTICAL COMPOSITIONS

An active compound as described herein can be administered to a host, for example, a human in need thereof in an effective amount as the neat chemical, but is more typically administered as a pharmaceutical composition that includes a pharmaceutically acceptable carrier suitable for the selected means of delivery. In one embodiment, the disclosure provides pharmaceutical compositions comprising an effective amount of compound or pharmaceutically acceptable salt thereof together with at least one pharmaceutically acceptable carrier for any of the uses described herein. The pharmaceutical composition may contain the compound or salt as the only active agent, or, in an alternative embodiment, the compound and at least one additional active agent.

Effective amount, when used to describe an amount of compound in a method, refers to the amount of a compound that achieves the desired pharmacological effect or other biological effect. For example, an effective amount can be a 10% reduction in a symptom or sign of a disease or condition as compared to a control. As used herein, control refers to the untreated condition (e.g., a subject or cell not treated with the compounds and compositions described herein). Thus, the reduction can be a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, or any percent reduction in between 10% and 100% as compared to native or control levels. It is understood that treatment does not necessarily refer to a cure or complete ablation of the disease, condition, or symptoms of the disease or condition.

An effective amount of the active compound as described herein, or the active compound described herein in combination or alternation with, or preceded by, concomitant with or followed by another active agent, can be used in an amount sufficient to (a) inhibit the progression of a bacterial infection; (b) cause a regression of a bacterial infection; (c) cause a cure of a bacterial infection; or (d) inhibit or prevent the development of a bacterial infection. The effective amount can be, for example, the concentrations of compounds at which a reduction in bacterial load is observed (e.g., a 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, or any percent reduction in between 10% and 100% as compared to native or control levels).

A selected compound disclosed herein or used as described herein may be administered, for example, orally, topically, parenterally, by inhalation or spray, sublingually, via implant, including ocular implant, transdermally, via buccal administration, rectally, as an ophthalmic solution, injection, including ocular injection, intravenous, intra-aortal, intracranial, subdermal, intraperitoneal, subcutaneous, transnasal, sublingual, intrathecal, or rectal or by other means, in dosage unit formulations containing conventional pharmaceutically acceptable carriers.

For ocular delivery, the compound can be administered, as desired, for example, as a solution, suspension, or other formulation via intravitreal, intrastromal, intracameral, sub-tenon, sub-retinal, retro-bulbar, peribulbar, suprachorodial, subchorodial, chorodial, conjunctival, subconjunctival, episcleral, periocular, transscleral, retrobulbar, posterior juxtascleral, circumcomeal, or tear duct injections, or through a mucus, mucin, or a mucosal barrier, in an immediate or controlled release fashion or via an ocular device, injection, or topically administered formulation, for example a solution or suspension provided as an eye drop. The exact amount of the active compound or pharmaceutical composition described herein to be delivered to the host, typically a human, in need thereof, may be determined at the discretion of the health care provider to achieve the desired clinical benefit.

In certain embodiments the pharmaceutical composition is in a dosage form that contains from about 0.1 mg to about 1000 mg, from about 10 mg to about 750 mg, from about 100 mg to about 800 mg, or from about 200 mg to about 600 mg of the active compound and optionally from about 0.1 mg to about 2000 mg, from about 10 mg to about 750 mg, from about 100 mg to about 800 mg, or from about 200 mg to about 600 mg of an additional active agent in a unit dosage form.

Examples are dosage forms with at least about 0.5, 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 10, 15, 20, 25, 50, 75, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 900, 1000, 1100, 1200, 1250, 1300, 1400, 1500, or 1600 mg of active compound, or pharmaceutically acceptable salt thereof or prodrug. In one embodiment, the dosage form has at least about 1 mg, 5 mg, 10 mg, 25 mg, 50 mg, 75 mg, 100 mg, 200 mg, 400 mg, 500 mg, 600 mg, 1000 mg, 1200 mg, or 1600 mg of active compound, or pharmaceutically acceptable salt thereof. The amount of active compound in the dosage form is calculated without reference to the salt. The dosage form can be administered, for example, once a day (q.d.), twice a day (b.i.d.), three times a day (t.i.d.), four times a day (q.i.d.), once every other day (Q2d), once every third day (Q3d), as needed, or any dosage schedule that provides treatment of a disorder described herein.

The pharmaceutical composition may for example include a molar ratio of the active compound and an additional active agent that achieves the desired result. For example, the pharmaceutical composition may contain a molar ratio of about 0.5:1, about 1:1, about 2:1, about 3:1 or from about 1.5:1 to about 4:1 of an additional active agent in combination with the active compound (additional active agent: active compound), or pharmaceutically acceptable salt thereof, described herein. In one embodiment, the additional active agent is an antibiotic.

The pharmaceutical composition may be formulated as any pharmaceutically useful form, e.g., as a cream, a gel, a gel cap, a pill, a capsule, a microparticle, a nanoparticle, an injection or infusion solution, a capsule, a tablet, a syrup, as an aerosol, a transdermal patch, a subcutaneous patch, a dry powder, an inhalation formulation, in a medical device, suppository, buccal, or sublingual formulation, parenteral formulation, or an ophthalmic solution or suspension. Some dosage forms, such as tablets and capsules, are subdivided into suitably sized unit doses containing appropriate quantities of the active components, e.g., an effective amount to achieve the desired purpose.

Pharmaceutical compositions, and methods of manufacturing such compositions, suitable for administration as contemplated herein are known in the art. Examples of known techniques include, for example, US Patent Nos. 4,983,593, 5,013,557, 5,456,923, 5,576,025,

5,723,269, 5,858,411, 6,254,889, 6,303,148, 6,395,302, 6,497,903, 7,060,296, 7,078,057 7,404,828, 8,202,912, 8,257,741, 8,263,128, 8,337,899, 8,431,159, 9,028,870, 9,060,938

9,211,261, 9,265,731, 9,358,478, and 9,387,252, incorporated by reference herein.

The pharmaceutical compositions contemplated here can optionally include a carrier. Carriers must be of sufficiently high purity and sufficiently low toxicity to render them suitable for administration to the patient being treated. The carrier can be inert, or it can possess pharmaceutical benefits of its own. The amount of carrier employed in conjunction with the compound is sufficient to provide a practical quantity of material for administration per unit dose of the compound.

Classes of carriers include, but are not limited to binders, buffering agents, coloring agents, diluents, disintegrants, emulsifiers, fillers, flavorants, glidents, lubricants, pH modifiers, preservatives, stabilizers, surfactants, solubilizers, tableting agents, and wetting agents. Some carriers may be listed in more than one class, for example vegetable oil may be used as a lubricant in some formulations and a diluent in others. Exemplary pharmaceutically acceptable carriers include sugars, starches, celluloses, powdered tragacanth, malt, gelatin; talc, and vegetable oils.

Examples of other matrix materials, fillers, or diluents include lactose, mannitol, xylitol, microcrystalline cellulose, calcium diphosphate, and starch.

Examples of surface-active agents include sodium lauryl sulfate and polysorbate 80. Examples of drug complexing agents or solubilizers include the polyethylene glycols, caffeine, xanthene, gentisic acid and cylodextrins.

Examples of disintegrants include sodium starch gycolate, sodium alginate, carboxymethyl cellulose sodium, methyl cellulose, colloidal silicon dioxide, and croscarmellose sodium. Examples of binders include methyl cellulose, microcrystalline cellulose, starch, and gums such as guar gum, and tragacanth.

Examples of lubricants include magnesium stearate and calcium stearate. Examples of pH modifiers include acids such as citric acid, acetic acid, ascorbic acid, lactic acid, aspartic acid, succinic acid, phosphoric acid, and the like; bases such as sodium acetate, potassium acetate, calcium oxide, magnesium oxide, trisodium phosphate, sodium hydroxide, calcium hydroxide, aluminum hydroxide, and the like, and buffers generally comprising mixtures of acids and the salts of said acids. Optional other active agents may be included in a pharmaceutical composition, which do not substantially interfere with the activity of the compound of the present invention.

In certain embodiments, the pharmaceutical composition for administration further includes a compound or salt described herein and optionally comprises one or more of a phosphoglyceride; phosphatidylcholine; dipalmitoyl phosphatidylcholine (DPPC); dioleylphosphatidyl ethanolamine (DOPE); dioleyloxypropyltriethylammonium (DOTMA); dioleoylphosphatidylcholine; cholesterol; cholesterol ester; diacylglycerol; diacylglycerolsuccinate; diphosphatidyl glycerol (DPPG); hexanedecanol; fatty alcohol such as polyethylene glycol (PEG); polyoxyethylene-9-lauryl ether; a surface active fatty acid, such as palmitic acid or oleic acid; fatty acid; fatty acid monoglyceride; fatty acid diglyceride; fatty acid amide; sorbitan trioleate (Span®85) glycocholate; sorbitan monolaurate (Span®20); polysorbate 20 (Tween®20); polysorbate 60 (Tween®60); polysorbate 65 (Tween®65); polysorbate 80 (Tween®80); polysorbate 85 (Tween®85); polyoxyethylene monostearate; surfactin; a poloxomer; a sorbitan fatty acid ester such as sorbitan trioleate; lecithin; lysolecithin; phosphatidylserine; phosphatidylinositol; sphingomyelin; phosphatidylethanolamine (cephalin); cardiolipin; phosphatidic acid; cerebroside; dicetylphosphate; dipalmitoylphosphatidylglycerol; stearylamine; dodecylamine; hexadecyl- amine; acetyl palmitate; glycerol ricinoleate; hexadecyl sterate; isopropyl myristate; tyloxapol; poly(ethylene glycol)5000-phosphatidylethanolamine; poly(ethylene glycol)400- monostearate; phospholipid; synthetic and/or natural detergent having high surfactant properties; deoxycholate; cyclodextrin; chaotropic salt; ion pairing agent; glucose, fructose, galactose, ribose, lactose, sucrose, maltose, trehalose, cellbiose, mannose, xylose, arabinose, glucoronic acid, galactoronic acid, mannuronic acid, glucosamine, galatosamine, and neuramic acid; pullulan, cellulose, microcrystalline cellulose, hydroxypropyl methylcellulose (HPMC), hydroxycellulose (HC), methylcellulose (MC), dextran, cyclodextran, glycogen, hydroxyethylstarch, carageenan, glycon, amylose, chitosan, N,O-carboxylmethylchitosan, algin and alginic acid, starch, chitin, inulin, konjac, glucommannan, pustulan, heparin, hyaluronic acid, curdlan, and xanthan, mannitol, sorbitol, xylitol, erythritol, maltitol, and lactitol, a pluronic polymer, polyethylene, polycarbonate (e.g. poly(l,3-dioxan-2one)), polyanhydride (e.g. poly(sebacic anhydride)), polypropylfumerate, polyamide (e.g. polycaprolactam), polyacetal, polyether, polyester (e.g., polylactide, polyglycolide, polylactide-co-glycolide, polycaprolactone, polyhydroxyacid (e.g. ro1n((b- hydroxyalkanoate))), poly(orthoester), polycyanoacrylate, polyvinyl alcohol, polyurethane, polyphosphazene, polyacrylate, polymethacrylate, polyurea, polystyrene, and polyamine, polylysine, polylysine-PEG copolymer, and poly(ethyleneimine), poly(ethylene imine)-PEG copolymer, glycerol monocaprylocaprate, propylene glycol, Vitamin E TPGS (also known as d-a-Tocopheryl polyethylene glycol 1000 succinate), gelatin, titanium dioxide, polyvinylpyrrolidone (PVP), hydroxypropyl methyl cellulose (HPMC), hydroxypropyl cellulose (HPC), methyl cellulose (MC), block copolymers of ethylene oxide and propylene oxide (PEO/PPO), polyethyleneglycol (PEG), sodium carboxymethylcellulose (NaCMC), hydroxypropylmethyl cellulose acetate succinate (HPMCAS).

In some embodiments, the pharmaceutical preparation may include polymers for controlled delivery of the described compounds, including, but not limited to pluronic polymers, polyesters (e.g., polylactic acid, poly(lactic-co-glycolic acid), polycaprolactone, polyvalerolactone, poly(l,3-dioxan-2one)); polyanhydrides (e.g., poly(sebacic anhydride)); polyethers (e.g., polyethylene glycol); polyurethanes; polymethacrylates; polyacrylates; and polycyanoacrylates. In some embodiments, polymers may be modified with polyethylene glycol (PEG), with a carbohydrate, and/or with acyclic polyacetals derived from polysaccharides. See, e.g., Papisov, 2001, ACS Symposium Series, 786:301, incorporated by reference herein.

The compounds of the present invention can be formulated as particles. In one embodiment the particles are or include microparticles. In an alternative embodiment the particles are or include nanoparticles.

Common techniques for preparing particles include, but are not limited to, solvent evaporation, solvent removal, spray drying, phase inversion, coacervation, and low temperature casting. Suitable methods of particle formulation are briefly described below. Pharmaceutically acceptable excipients, including pH modifying agents, disintegrants, preservatives, and antioxidants, can optionally be incorporated into the particles during particle formation.

In one embodiment, the particles are derived through a solvent evaporation method. In this method, a compound described herein (or polymer matrix and one or more compounds described herein) is dissolved in a volatile organic solvent, such as methylene chloride. The organic solution containing a compound described herein is then suspended in an aqueous solution that contains a surface active agent such as poly(vinyl alcohol). The resulting emulsion is stirred until most of the organic solvent evaporated, leaving solid nanoparticles or microparticles. The resulting nanoparticles or microparticles are washed with water and dried overnight in a lyophilizer. Nanoparticles with different sizes and morphologies can be obtained by this method.

Pharmaceutical compositions which contain labile polymers, such as certain polyanhydrides, may degrade during the fabrication process due to the presence of water. For these polymers, methods which are performed in completely or substantially anhydrous organic solvents can be used to make the particles.

Solvent removal can also be used to prepare particles from a compound that is hydrolytically unstable. In this method, the compound (or polymer matrix and one or more

In one embodiment an active compound as described herein is administered to a patient in need thereof as a spray dried dispersion (SDD). In another embodiment the present invention provides a spray dried dispersion (SDD) comprising a compound of the present invention and one or more pharmaceutically acceptable excipients as defined herein. In another embodiment the SDD comprises a compound of the present invention and an additional active agent. In a further embodiment the SDD comprises a compound of the present invention, an additional active agent, and one or more pharmaceutically acceptable excipients.

In another embodiment any of the described spray dried dispersions can be coated to form a coated tablet. In an alternative embodiment the spray dried dispersion is formulated into a tablet but is uncoated. Particles can be formed from the active compound as described herein using a phase inversion method. In this method, the compound (or polymer matrix and one or more active compounds) is dissolved in a suitable solvent, and the solution is poured into a strong non-solvent for the compound to spontaneously produce, under favorable conditions, microparticles or nanoparticles. The method can be used to produce nanoparticles in a wide range of sizes, including, for example, from nanoparticles to microparticles, typically possessing a narrow particle size distribution.

In one embodiment, the polymeric particle is between about 0.1 nmto about 10000 nm, between about 1 nm to about 1000 nm, between about 10 nm and 1000 nm, between about 1 and 100 nm, between about 1 and 10 nm, between about 1 and 50 nm, between about 100 nm and 800 nm, between about 400 nm and 600 nm, or about 500 nm. In one embodiment, the micro-particles are no more than about 0.1 nm, 0.5 nm, 1.0 nm, 5.0 nm, 10 nm, 25 nm, 50 nm, 75 nm, 100 nm, 150 nm, 200 nm, 250 nm, 300 nm, 400 nm, 450 nm, 500 nm, 550 nm, 600 nm, 650 nm, 700 nm, 750 nm, 800 nm, 850 nm, 900 nm, 950 nm, 1000 nm, 1250 nm, 1500 nm, 1750 nm, or 2000 nm. In some embodiments, a compound described herein may be covalently coupled to a polymer used in the nanoparticle, for example a polystyrene particle, PLGA particle, PLA particle, or other nanoparticle. The pharmaceutical compositions can be formulated for oral administration. These compositions can contain any amount of active compound that achieves the desired result, for example between 0.1 and 99 weight % (wt.%) of the compound and usually at least about 5 wt.% of the compound. Some embodiments contain at least about 10%, 15%, 20%, 25 wt.% to about 50 wt. % or from about 5 wt.% to about 75 wt.% of the compound.

Pharmaceutical compositions suitable for rectal administration are typically presented as unit dose suppositories. These may be prepared by admixing the active compound with one or more conventional solid carriers, for example, cocoa butter, and then shaping the resulting mixture.

Pharmaceutical compositions suitable for topical application to the skin preferably take the form of an ointment, cream, lotion, paste, gel, spray, aerosol, or oil. Carriers which may be used include petroleum jelly, lanoline, polyethylene glycols, alcohols, transdermal enhancers, and combinations of two or more thereof.

Pharmaceutical compositions suitable for transdermal administration may be presented as discrete patches adapted to remain in intimate contact with the epidermis of the recipient for a prolonged period of time. Pharmaceutical compositions suitable for transdermal administration may also be delivered by iontophoresis (see, for example, Pharmaceutical Research 3 (6) : 318 (1986)) and typically take the form of an optionally buffered aqueous solution of the active compound. In one embodiment, microneedle patches or devices are provided for delivery of drugs across or into biological tissue, particularly the skin. The microneedle patches or devices permit drug delivery at clinically relevant rates across or into skin or other tissue barriers, with minimal or no damage, pain, or irritation to the tissue.

Pharmaceutical compositions suitable for administration to the lungs can be delivered by a wide range of passive breath driven and active power driven single/-multiple dose dry powder inhalers (DPI). The devices most commonly used for respiratory delivery include nebulizers, metered-dose inhalers, and dry powder inhalers. Several types of nebulizers are available, including jet nebulizers, ultrasonic nebulizers, and vibrating mesh nebulizers. Selection of a suitable lung delivery device depends on parameters, such as nature of the drug and its formulation, the site of action, and pathophysiology of the lung.

Additional non-limiting examples of inhalation drug delivery devices and methods include, for example, US 7,383,837 titled “Inhalation device” (SmithKline Beecham Corporation); WO/2006/033584 titled “Powder inhaler” (Glaxo SmithKline Pharmaceuticals SA); WO/2005/044186 titled “Inhalable pharmaceutical formulations employing desiccating agents and methods of administering the same” (Glaxo Group Ltd and SmithKline Beecham Corporation); US9,095,670 titled “Inhalation device and method of dispensing medicament”, US 8,205,611 titled “Dry powder inhaler” (Astrazeneca AB); WO/2013/038170 titled “Inhaler” (Astrazeneca AB and Astrazeneca UK Ltd.); US/2014/0352690 titled “Inhalation Device with Feedback System”, US 8,910,625 and US/2015/0165137 titled “Inhalation Device for Use in Aerosol Therapy” (Vectura GmbH); US 6,948,496 titled “Inhalers”, US/2005/0152849 titled “Powders comprising anti-adherent materials for use in dry powder inhalers”, US 6,582,678, US 8,137,657, US/2003/0202944, and US/2010/0330188 titled “Carrier particles for use in dry powder inhalers”, US 6,221,338 titled “Method of producing particles for use in dry powder inhalers”, US 6,989,155 titled “Powders”, US/2007/0043030 titled “Pharmaceutical compositions for treating premature ejaculation by pulmonary inhalation”, US 7,845,349 titled “Inhaler”, US/2012/0114709 and US 8,101,160 titled “Formulations for Use in Inhaler Devices”, US/2013/0287854 titled “Compositions and Uses”, US/2014/0037737 and US 8,580,306 titled “Particles for Use in a Pharmaceutical Composition”, US/2015/0174343 titled “Mixing Channel for an Inhalation Device”, US 7,744,855 and US/2010/0285142 titled “Method of making particles for use in a pharmaceutical composition”, US 7,541,022, US/2009/0269412, and US/2015/0050350 titled “Pharmaceutical formulations for dry powder inhalers” (Vectura Limited).

IV. METHODS OF TREATMENT

In one embodiment, an effective amount of a compound of Formula I through Formula V or a pharmaceutically acceptable salt or composition thereof or a compound of Formula VII or Formula VIII or a pharmaceutically acceptable salt or composition thereof is used to treat or to prevent a medical disorder which is caused by the presence of a bacterium, for example a bacterial infection. Optionally, the compound is MD-124 as described herein. In one embodiment, an effective amount of a compound selected from Compound A, Compound B, or Compound F - Compound L or a pharmaceutically acceptable salt or composition thereof is used to treat or to prevent a medical disorder which is mediated by the presence of a bacterium, for example a bacterial infection. In one embodiment, the compounds of the present invention may be used to treat a disorder, typically an infection, caused by a pathogenic bacterium. In one embodiment, a method is provided comprising administering an effective amount of a compound of Formula I through Formula V or a pharmaceutically acceptable salt or composition thereof or a compound of Formula VIII or a pharmaceutically acceptable salt or composition thereof to a subject, typically a human, to treat an infection caused by a pathogenic bacterium. The compounds described herein are particularly effective in combination with antibiotics due to their potentiation of the antimicrobial effect of the antibiotic. In one embodiment, an active compound or its salt or composition as described herein may be used in combination or alternation with an antibiotic to potentiate the antibacterial effect of the antibiotic. Commonly used antibiotics include clindamycin, erythromycin, metronidazole, sulfacetamide, and tetracyclines such as doxycycbne and minocycline. Other representative topical antibiotics include bacitracin, polymycin b, neomycin, retapamulin, mupirocin, pramoxine, gentamicin, mafenide, and ozenoxacin. In one embodiment, an active compound or its salt is formulated in combination with an antibiotic in a topical formulation as described herein.

In one embodiment, the compounds of the present invention may be used to treat a disorder, typically an infection, caused by a gram-positive bacterium. In one embodiment, a method is provided comprising administering an effective amount of a compound of Formula I through Formula VIII or a pharmaceutically acceptable salt or composition thereof to treat an infection caused by a gram-positive bacterium. In one embodiment, a method is provided comprising administering an effective amount of a compound selected from Compound A - Compound L or a pharmaceutically acceptable salt or composition thereof to treat an infection caused by a gram-positive bacterium.

Non-limiting examples of gram-positive bacteria which may be treated using the compounds of the present invention either alone or in combination with another therapeutic include: Actinomyces species including Actinomyces israelii, Actinomyces naeslundii, Actinomyces viscosus, Actinomyces odontolyticus , and Actinomyces pyogenes, Bacillus species including Bacillus anthracis, Bacillus cereus, and Bacillus subtilis; Clostridium species including Clostridium botulinum, Clostridium difficile, Clostridium perfringens, Clostridium sordellii, and Clostridium tetani; Corynebacterium species including Corynebacterium diphtheriae, Corynebacterium jeikeium, Corynebacterium minutissimum, Corynebacterium mucifaciens, Corynebacterium pseudotuberculosis, Corynebacterium striatum, Corynebacterium tenuis, and Corynebacterium ulcerans; Enterococcus species including Enterococcus casseliflavus, Enterococcus faecalis, Enterococcus faecium, Enterococcus rafflnosus, and Enterococcus hirae, Leuconostoc species including Leuconostoc pseudomesenteroides; Micrococcus species such as Microccocus luteus; Nocardia species including Nocardia asteroides; Propionibacterium species including Propionibacterium acnes; Staphylococcus species including Staphylococcus aureus, Staphylococcus capitis, Staphylococcus epidermidis, Staphylococcus haemolyticus , Staphylococcus hominis, Staphylococcus lugdunensis, Staphyloccocus pasteuri, and Staphyloccocus saprophyticus; and Streptococcus species including Streptococcus agalactiae, Streptococcus anginosus, Streptococcus bovis, Streptococcus dysgalactiae, Streptococcus mitis, Streptococcus mutans, Streptococcus pneumoniae, Streptococcus pyogenes, Streptococcus sanguinis, Streptococcus suis, and Streptococcus viridans.

In one embodiment, the compounds of the present invention may be used to treat a disorder, typically an infection, caused by a gram-negative bacterium. In one embodiment, a method is provided comprising administering an effective amount of a compound of Formula I through Formula VIII or a pharmaceutically acceptable salt or composition thereof to treat an infection caused by a gram-negative bacterium. In one embodiment, a method is provided comprising administering an effective amount of a compound selected from Compound A - Compound L or a pharmaceutically acceptable salt or composition thereof to treat an infection caused by a gram-negative bacterium.

Non-limiting examples of gram-negative bacteria which may be treated using the compounds of the present invention either alone or in combination with another therapeutic include: Acinetobacter species including Acinetobacter baumannii and Acinetobacter iwoffii; Aeromonas species including Aeromonas veronii biovar sobria (previously Aeromonas sobrid), Aeromonas caviae, and Aeromonas hydrophila;AlcaligeneslAchromobacter species including Alcaligenes faecalis mdAlcaligenes xylosoxidans; Bacteroides species including Bacteroides fragilis; Bartonella species including Bartonella bacilliformis , Bartonella clarridgeiae, Bartonella elizabethae, Bartonella henselae, Bartonella koehlerae, Bartonalla naantalienis , Bartonella quintana, Bartonella rochalimae, Bartonella vinsonii, and Bartonella washoensis; Bordetella species including Bordetella bronchispetica, Bordetella pertussis, and Bordetella parapertussis, Borrelia species including Borrelia afzelii, Borrelia burgdorferi, Borrelia crocidurae, Borrelia duttoni, Borrelia garinii, Borrelia hermsii, Borrelia hispanica, Borellia miyamotoi, Borrelia parkeri, Borrelia persica, Borrelia recurrentis, Borrelia turicatae, and Borrelia venezuelensis; Brevundimonas species including Brevundimonas diminuta and Brevundimonas vesicularis; Brucella species including Brucella abortus, Brucella canis, Brucella melitensis, and Brucella suis; Burkholderia species including Burkholderia cepacia, Burkholderia mallei, and Burkholderia pseudomallei; Campylobacter species including Campylobacter jejuni, Campylobacter coli, Campylobacter upsaliensis, Campylobacter lari, and Campylobacter coli; Chlamydial Chlamidophila species including Chlamydophila pneumoniae, Chlamydophila psittaci, Chlamidophila pecorum, and Chlamydia trachomatis; Citrobacter species including Citrobacter amalonaticus , Citrobacter freundii, Citrobacter koseri, and Citrobacter diver sus; Coxiella burnetti; Ehrlichia species including Ehrlichia canis and Ehrlichia chaffeensis Enterohacter species including Enterohacter aerogenes and Enterobacter cloacae, Escherichia species including Escherichia coir, Francisella species including Francisella novicida, Francisella philomiragia, and Francisella tularensis; Haemophilus species including Haemophilus influenzae and Haemophilus ducreyi, Helicobacter species including Helicobacter pylori, Klebsiella species including Klebsiella granulomatis , Klebsiella oxytoca, and Klebsiella pneumoniae, Leclercia adecarboxylata; Legionella species including Legionella pneumophila , Leptospira species including Leptospira interrogans, Leptospira noguchii, Leptospira santarosai, and Leptospira weilii; Listeria species including Listeria monocytogenes; Moraxella species including Moraxella catarrhalis, Moraxella lacunata, and Moraxella bovis; Morganella species including Morganella morganii; Mycoplasma species including Mycoplasma amphoriforme, Mycoplasma buccale, Mycoplasma faucium, Mycoplasma fermentans, Mycoplasma genitalium, Mycoplasma hominis, Mycoplasma lipophilum, Mycoplasma orale, Mycoplasma penetrans, Mycoplasma pirum, Mycoplasma pneumoniae, Mycoplasma primatum, Mycoplasma salivarium, and Mycoplasma spermatophilum; Neisseria species including Neisseria meningitidis and Neisseria gonorrhoeae; Orientia species including Orientia tsutsugamushi and Orientia chuto; Pantoea species including Pantoea agglomerans; Paracoccus species including Paracoccus yeei; Prevotella species including Prevotella intermedia and Prevotella melaninogenica; Proteus species including Proteus mirabilis, Proteus penneri, and Proteus vulgaris; Providencia species including Providencia rettgeri and Providencia stuartii; Pseudomonas species including Pseudomonas aeruginoas, Pseudomonas oryzihabitans, Pseudomonas plecoglossidica, and Pseudomonas stutzeri; Ralstonia species including Ralstonia pickettii and Ralstonia insidiosa; Rickettsia species including Rickettsia africae, Rickettsia akari, Rickettsia australis, Rickettsia conorii, Rickettsia felis, Rickettsia japonica, Rickettsia prowazekii, Rickettsia rickettsia, Rickettsia sibirica, and Rickettsia typhi; Roseomonas species including Roseomonas gilardii; Salmonella species including Salmonella bongori, Salmonella enterica, Salmonella paratyphi, Salmonella typhi, and Salmonella typhimurium; Serratia species including Serratia marcescens, Serratia liquefaciens , Serratia rubidaea, and Serratia odoriferae; Shigella species including Shigella dysenteriae and Shigella sonnei; Sphingomonas species including Sphingomonas mucosissima and Sphingomonas paucimobilus; Stenotrophomas species including Stenotrophomas maltophilia; Treponema species including Treponema carateum, Treponema paraluiscuniculi, and Treponema pallidum; Ureaplasma species including Ureaplasma urealyticum; Vibrio species including Vibrio cholera, Vibrio parahaemolyticus , and Vibrio vulnificus ; and Yersinia species including Yersinia enterocolitica, Yersinia pestis, and Yersinia pseudotuberculosis .

In one embodiment, the compounds of the present invention may be used to treat a disorder, typically an infection, caused by a mycobacterium. In one embodiment, a method is provided comprising administering an effective amount of a compound of Formula I through Formula V or a pharmaceutically acceptable salt or composition thereof to treat an infection caused by a mycobacterium. In one embodiment, a method is provided comprising administering an effective amount of a compound of Formula VII or Formula VIII or a pharmaceutically acceptable salt or composition thereof to treat an infection caused by a mycobacterium. In one embodiment, a method is provided comprising administering an effective amount of a compound selected from Compound A, Compound B, or Compound F - Compound L or a pharmaceutically acceptable salt or composition thereof to treat an infection caused by a mycobacterium.

Non-limiting examples of mycobacteria which may be treated using the compounds of the present invention either alone or in combination with another therapeutic include

Mycobacterium abcessus, Mycobacterium africanum, Mycobacterium agri, Mycobacterium aichiense, Mycobacterium alvei, Mycobacterium arabiense, Mycobacterium aromaticivorans, Mycobacterium arosiense, Mycobacterium arupense, Mycobacterium aquaticum, Mycobacterium asiaticum, Mycobacterium aubagnese, Mycobacterium aurum, Mycobacterium austroafricanum, Mycobacterium avium, Mycobacterium avium paratuberculosis, Mycobacterium avium silvaticum, Mycobacterium avium hominussuis , Mycobacterium bacteremicum, Mycobacterium barrassiae, Mycobacterium boenickei, Mycobacterium bohemicum, Mycobacterium bolletii, Mycobacterium botniense, Mycobacterium bovis , Mycobacterium branderi, Mycobacterium brisbanense, Mycobacterium brumae, Mycobacterium canariasense, Mycobacterium canettii, Mycobacterium caprae, Mycobacterium chimaera, Mycobacterium chelonae, Mycobacterium chitae, Mycobacterium chubuense, Mycobacterium colombiense, Mycobacterium conceptionense, Mycobacterium confluentis, Mycobacterium conspicuum, Mycobacterium cookii, Mycobacterium cosmeticum, Mycobacterium diernhoferi, Mycobacterium doricum, Mycobacterium duvalii, Mycobacterium elephantis, Mycobacterium fallax, Mycobacterium farcinogenes , Mycobacterium flavescens, Mycobacterium florentinum, Mycobacterium fortuitum, Mycobacterium frederikbergense, Mycobacterium gadium, Mycobacterium gastri, Mycobacterium genavense, Mycobacterium gilvum, Mycobacterium gordonae, Mycobacterium haemophilum, Mycobacterium hassiacum, Mycobacterium heidelbergense, Mycobacterium heckshornense, Mycobacterium hiberniae, Mycobacterium hodleri, Mycobacterium holsaticum, Mycobacterium houstonense, Mycobacterium icosiumassilensis, Mycobacterium immunogenum, Mycobacterium indicus pranii, Mycobacterium intacellulare, Mycobacterium intracellulare, Mycobacterium interjectum, Mycobacterium intermedium, Mycobacterium iranicum, Mycobacterium kansasii, Mycobacterium komossense, Mycobacterium kubicae, Mycobacterium lentiflavum,

Mycobacterium leprae, Mycobacterium lepraemurium, Mycobacterium lepromatosis , Mycobacterium liflandii, Mycobacterium llatzerense, Mycobacterium madagascariense, Mycobacterium mageritense, Mycobacterium malmoense, Mycobacterium marinum, Mycobacterium massiliense, Mycobacterium massilipolynesiensis , Mycobacterium microti, Mycobacterium monacense, Mycobacterium montfiorense, Mycobacterium morokaense, Mycobacterium mucogenicum, Mycobacterium mungi, Mycobacterium murale, Mycobacterium nebraskense, Mycobacterium neoaurum, Mycobacterium neworleansense, Mycobacterium nonchromogenicum, Mycobacterium obuense, Mycobacterium orygis, Mycobacterium palustre, Mycobacterium parascofulaceum, Mycobacterium parafortuitum, Mycobacterium perigrinum, Mycobacterium phlei, Mycobacterium phocaicum,

Mycobacterium pinnipedii, Mycobacterium porcinum, Mycobacterium pseudoshottsii, Mycobacterium psychotolerans, Mycobacterium pulveris, Mycobacterium pyrenivorans , Mycobacterium saskatchewanense, Mycobacterium sediminis, Mycobacterium senegalense, Mycobacterium septicum, Mycobacterium shimoidei, Mycobacterium shottsii, Mycobacterium simiae, Mycobacterium smegmatis, Mycobacterium sphagni, Mycobacterium stephanolepidis , Mycobacterium suricattae, Mycobacterium szulgai, Mycobacterium talmoniae,

Mycobacterium terrae, Mycobacterium thermoresistibile, Mycobacterium triplex,

Mycobacterium triviale, Mycobacterium tuberculosis , Mycobacterium tusciae, Mycobacterium ulcerans, Mycobacterium vaccae, Mycobacterium vanbaalenii, Mycobacterium xenopi, and Mycobacterium yongonense.

In one embodiment, an effective amount of an active compound or pharmaceutically acceptable salt thereof or composition as described herein is used to treat or to prevent a medical disorder which is mediated by the presence of an antibiotic-resistant bacterium. In one embodiment, the compounds of the present invention may be used to treat a disorder, typically an infection, caused by a pathogenic antibiotic-resistant bacterium.

In one embodiment, a method is provided comprising administering an effective amount of a compound or a pharmaceutically acceptable salt thereof or composition thereof described herein to a subject, typically a human, to treat an infection caused by a pathogenic antibiotic-resistant bacterium. Non-limiting examples of gram-positive antibiotic-resistant bacteria include: antibiotic-resistant Clostridium difficile, drug-resistant Streptococcus pneumoniae, clindamycin-resistant Group B Streptococcus, erythromycin-resistant Group A Streptococcus, methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Staphylococcus aureus (VRS A), and vancomycin-resistant Enterococcus (VRE).

Non-limiting examples of gram-negative antibiotic-resistant bacteria include: antibiotic-resistant Burkholderia cepacia, carbapenem-resistant Enterobacteriaceae (CRE) gut bacteria, drug-resistant Campylobacter, drug-resistant non-typhoidal Salmonella, drug- resistant Shigella, multi-drug-resistant Acinetobacter , multi-drug-resistant Escherichia coli, multi-drug-resistant Klebsiella pneumoniae, multi-drug-resistant Neisseria Gonorrhoeae, and multi drug-resistant Pseudomonas aeruginosa.

In one embodiment, an effective amount of a compound of Formula I through Formula V or a pharmaceutically acceptable salt or composition thereof is used to treat or to prevent a medical disorder which is mediated by the presence of an antibiotic-resistant mycobacterium. Optionally, an effective amount of a compound of Formula VII or Formula VIII or a pharmaceutically acceptable salt or composition thereof is used to treat or to prevent a medical disorder which is mediated by the presence of an antibiotic-resistant mycobacterium. In one embodiment, an effective amount of a compound selected from Compound A - Compound L or a pharmaceutically acceptable salt or composition thereof is used to treat or to prevent a medical disorder which is mediated by the presence of an antibiotic-resistant mycobacterium. In one embodiment, the compounds of the present invention may be used to treat a disorder, typically an infection, caused by a pathogenic antibiotic-resistant mycobacterium. In one embodiment, a method is provided comprising administering an effective amount of a compound as described herein or a pharmaceutically acceptable salt thereof or composition thereof described herein to a subject, typically a human, to treat an infection caused by a pathogenic antibiotic-resistant mycobacterium. In one embodiment, the antibiotic-resistant mycobacterium is multi-drug-resistant Mycobacterium tuberculosis (MDR-TB).

Non-limiting examples of disorders mediated by a bacterium that may be treated by the compounds of the present invention, either alone or in combination with another therapeutic, include actinomycosis, anaplasmosis, anthrax, bacillary angiomatosis, actinomycetoma, bacterial pneumonia, bacterial vaginosis, bacterial endocarditis, bartonellosis, botulism, boutenneuse fever, brucellosis, bejel, brucellosis spondylitis, bubonic plague, Buruli ulcer, Baimsdale ulcer, bacillary dysentery, campylobacteriosis, Carrion’s disease, cat-scratch disease, cellulitis, chancroid, chlamydia, chlamydia conjunctivitis, clostridial myonecrosis, cholera, Clostridium difficile colitis, diphtheria, Daintree ulcer, donavanosis, dysentery, erhlichiosis, epidemic typhus, fried rice syndrome, five-day fever, floppy baby syndrome, Far East scarlet-like fever, gas gangrene, glanders, gonorrhea, granuloma inguinale, human necrobacillosis, hemolytic-uremic syndrome, human ewingii ehrlichiosis, human monocytic ehrlichiosis, human granulocytic anaplasmosis, infant botulism, Izumi fever, Kawasaki disease, Kumusi ulder, lymphogranuloma venereum, Lemierre’s syndrome, Legionellosis, leprosy, leptospirosis, listeriosis, Lyme disease, lymphogranuloma venereum, Malta fever, Mediterranean fever, myonecrosis, mycoburuli ulcer, mucocutaneous lymph node syndrome, meliodosis, meningococcal disease, murine typhus, Mycoplasma pneumonia, mycetoma, neonatal conjunctivitis, nocardiosis, Oroya fever, ophthalmia neonatorum, ornithosis, Pontiac fever, peliosis hepatis, pneumonic plague, postanginal shock including sepsis, pasteurellosis, pelvic inflammatory disease, pertussis, plague, pneumococcal infection, pneumonia, psittacosis, parrot fever, pseudotuberculosis, Q fever, quintan fever, rabbit fever, relapsing fever, rickettsialpox, Rocky Mountain spotted fever, rat-bite fever, Reiter syndrome, rheumatic fever, salmonellosis, scarlet fever, sepsis, septicemic plague, Searls ulcer, shigellosis, soft chancre, syphilis, streptobacillary fever, scrub typhus, Taiwan acute respiratory agent, Trench fever, trachoma, tuberculosis, tularemia, typhoid fever, typhus, tetanus, toxic shock syndrome, undulant fever, ulcus molle, Vibrio parahaemolyticus enteritis, Whitmore’s disease, walking pneumonia, Waterhouse-Friderichsen syndrome, yaws, and yersiniosis.

In one embodiment, the compounds of the present invention may be used to treat an inflammatory disorder caused by the presence of a bacterial infection. Non-limiting examples of such inflammatory disorders include adenoiditis, appendicitis, arteritis, ascending cholangitis, balanitis, blepharitis, bronchitis, bursitis, cellulitis, cerebral vasculitis, cervicitis, chemosis, cholecystitis, chondritis, choroioamnionitis, colitis, conjunctivitis, constrictive pericarditis, cryptitis, dacryoadenitis, dermatitis, duodenal lymphocytosis, encephalitis, endocarditis, endometritis, endotheliitis, enteritis, enterocolitis, eosinophilis fasciitis, epididymitis, esophagitis, folliculitis, gastritis, gingivitis, glomerulonephritis, glossitis, hepatitis, infectious arthritis, ileitis, intertrigo, keratitis, keratoconjunctivitis, labyrithitis, lymphadenitis, mastitis, mastoiditis, myocarditis, myopericarditis, myositis, necrotizing fasciitis, nephritis, omaphalitis, oophoritis, ophthalmitis, orchitis, osteitis, osteomyelitis, pancreatitis, paraproctitis, parotitis, pericarditis, perichondritis, perifolliculitis, periodontitis, peritonitis, pharyngitis, phlebitis, pleurisy, pneumonitis, pulmonitis, proctitis, prostatitis, pulpitis, pyelonephritis, pyomyositis, retinal vasculitis, rheumatic fever, rhinitis, scleritis, salpingitis, sialadenitis, sinusitis, stomatitis, synovitis, septicemia, tenosynovitis, thyroiditis, tonsillitis, tularemia, urethritis, uveitis, vaginitis, vasculitis, and vulvitus.

V. COMBINATION THERAPY

In one embodiment, an active compound of Formula I through Formula VIII or a pharmaceutically acceptable salt or composition thereof may be provided in combination or alternation with or preceded by, concomitant with or followed by, an effective amount of at least one additional active agent, for example, for treatment of a disorder listed herein. Non- limiting examples of additional active agents for such combination therapy are provided below.

In the described below and herein generally, whenever any of the terms referring to an active compound or pharmaceutically acceptable salt thereof or composition as described herein are used, it should be understood that pharmaceutically acceptable salt, prodrugs, or compositions are considered included, unless otherwise stated or inconsistent with the text.

In one embodiment, an active compound of Formula I through Formula VIII or a pharmaceutically acceptable salt or composition thereof as described herein may be used in combination or alternation with an antibiotic.

In one embodiment, a compound selected from Compound A - Compound L or a pharmaceutically acceptable salt or composition thereof as described herein may be used in combination or alternation with an antibiotic.

In one embodiment, the antibiotic is an aminoglycoside. In one embodiment, the antibiotic is selected from amikacin, gentamicin, kanamycin, neomycin, netilmicin, tobramycin, paromomycin, streptomycin, and spectinomycin.

In one embodiment, the antibiotic is an ansamycin. In one embodiment, the antibiotic is selected from geldanamycin, herbimycin, and rifaximin.

In one embodiment, the antibiotic is a carbapenem. In one embodiment, the antibiotic is selected from ertapenem, doripenem, imipenem, panipenem, biapenem, tebipenem, and meropenem.

In one embodiment, the antibiotic is a cephalosporin. In one embodiment, the antibiotic is selected from cefacetrile, cefadroxil, cephalexin, cefaloglycin, cefalonium, cefaloridine, cefalotin, cefapirin, cefatrizine, cefazaflur, cefazedone, cefazobn, cefradrine, cefroxadine, and ceftezole. In one embodiment, the antibiotic is selected from cefaclor, cefonicid, cefprozil, cefuroxime, cefuzonam, cefmetazole, cefotetan, cefoxitin, loracarbef, cefbuperazone, cefminox, cefoxitin, and cefotiam. In one embodiment, the antibiotic is selected from cefcapene, cefdaloxime, cefdinir, cefditoren, cefetamet, cefixime, cefmenoxime, cefodizime, cefotaxime, cefovecin, cefpimizole, cefpodoxime, cefteram, ceftamere, ceftibuten, ceftiofur, ceftiolene, ceftizoxime, ceftriaxone, cefoperazone, ceftazidime, and latamoxef. In one embodiment, the antibiotic is selected from cefclidine, cefepime, cefluprenam, cefoselis, cefozopran, cefpirome, cefquinome, and flomoxef. In one embodiment, the antibiotic is selected from ceftobiprole, ceftaroline, and ceftolozane.

In one embodiment, the antibiotic is a gly copeptide. In one embodiment, the antibiotic is selected from teicoplanin, vancomycin, telavancin, dalbavancin, ramoplanin, decaplanin, and oritavancin.

In one embodiment, the antibiotic is a lincosamide. In one embodiment, the antibiotic is selected from lincomycin, clindamycin, and pirlimycin. In one embodiment, the antibiotic is daptomycin.

In one embodiment, the antibiotic is a macrolide. In one embodiment, the antibiotic is selected from azithromycin, clarithromycin, erythromycin, fidaxomicin, telithromycin, carbomycin A, josamycin, kitasamycin, midecamycin, oleandomycin, solithromycin, spiramycin, troleandomycin, tylosin, and roxithromycin.

In one embodiment, the antibiotic is a ketolide. In one embodiment, the antibiotic is selected from telithromycin, cethromycin, and solithromycin.

In one embodiment, the antibiotic is a monobactam.

In one embodiment, the antibiotic is selected from aztreonam. In one embodiment, the antibiotic is a nitrofuran. In one embodiment, the antibiotic is selected from diruazone, furazolidone, nifurfoline, nifuroxazide, nifurquinazol, nifurtoinol, nifurzide, nitrofural, and nitrofurantoin.

In one embodiment, the antibiotic is an oxazolidinone. In one embodiment, the antibiotic is selected from linezolid, posizolid, tedizolid, radezolid, torezolid, and cycloserine.

In one embodiment, the antibiotic is a penicillin. In one embodiment, the antibiotic is selected from penicillin G, penicillin K, penicillin N, penicillin O, and penicillin V. In one embodiment, the antibiotic is selected from meticillin, nafcillin, oxacillin, cloxacillin, dicloxacillin, and flucoxacillin. In one embodiment, the antibiotic is selected from ampicillin, amoxicillin, pivampicillin, hetacillin, bacampicillin, metampicillin, talampicillin, and epicillin. In one embodiment, the antibiotic is selected from carbenicilin, ticarcillin, and temocillin. In one embodiment, the antibiotic is selected from mezlocillin and piperacillin. In one embodiment, the antibiotic is selected from clavulanic acid, sulbactam, and tazobactam.

In one embodiment, the antibiotic is a polypeptide antibiotic. In one embodiment, the antibiotic is selected from bacitracin, colistin, and polymyxin B. In one embodiment, the antibiotic is a quinolone or fluoroquinolone antibiotic. In one embodiment, the antibiotic is selected from flumequine, oxolinic acid, rosoxacin, cinoxacin, nalidixic acid, and piromidic acid. In one embodiment, the antibiotic is selected from ciprofloxacin, fleroxacin, lomefloxacin, nadifloxacin, norfloxacin, ofloxacin, pefloxacin, rufloxacin, and enoxacin. In one embodiment, the antibiotic is selected from balofloxacin, grepafloxacin, lev ofloxacin, pazufloxacin, sparfloxacin, temafloxacin, and tosufloxacin. In one embodiment, the antibiotic is selected from clinafloxacin, gatifloxacin, moxifloxacin, sitafloxacin, prulifloxacin, besifloxacin, gemifloxacin, trovafloxacin, delafloxacin, and ozenoxacin.

In one embodiment, the antibiotic is a sulfonamide. In one embodiment, the antibiotic is selected from sulfacetamide, sulfadiazine, sulfadimidine, sulfafurazole, sulfisomidine, sulfadoxine, sulfamethoxazole, sulfamoxole, sulfanitran, sulfadimethoxine, sulfamethoxypyridazine, sulfametoxydiazine, sulfadoxine, sulfametopyrazine, terephtyl, mafenide, sulfanilamide, sulfasalazine, sulfisoxazole, and sulfonamicochrysoidine.

In one embodiment, the antibiotic is a tetracycline. In one embodiment, the antibiotic is selected from tetracycline, chlortetracy cline, oxy tetracycline, demeclocy cline, lymecy cline, meclocycline, metacycline, minocycline, and rolitetracycline. In one embodiment, the antibiotic is selected from clofazimine, dapsone, capreomycin, cycloserine, ethambutol, ethionamide, isoniazid, pyrazinamide, rifampicin, rifabutin, rifapentine, and streptomycin. In another embodiment, the antibiotic is selected from arsphenamide, chloramphenicol, fosfomycin, fusidic acid, metronidazole, mupirocin, platensimycin, quinupristin, dalfopristin, thiamphenicol, tigecy cline, and trimethoprim.

VI. TOPICAL FORMULATIONS FOR THE TREATMENT OF ACNE VULGARIS

Acne vulgaris is a skin disease caused in part by excessive outgrowth of Propionibacterium acnes bacteria and inflammation induced in response to the P. acnes bacteria. Acne, a common skin disease, occurs when hair follicles become clogged with dead skin cells and oil from the skin. Acne develops due to blockages that occur through increased sebum production influenced by androgens, excessive deposition of keratin in the hair follicle leading to comedo formation. The earliest pathological change involves the formation of a microcomedone due to the accumulation of skin cells in the hair follicle, which mix with oily sebum to block the follicle, a process further exacerbated by the presence of the P. acnes biofilm. If the microcomedone is superficial, melanin within the plug oxidizes upon exposure to air, forming a blackhead or open comedo. If the microcomedone is deeper within the hair follicle, a whitehead or closed comedo forms.

Propionibacterium acnes (reclassified as Cutibacterium acnes in 2016) is a Gram positive bacterium (rod) linked to acne that belongs to the Cutibacterium Genus and the Propionibacteriaceae Family. Typically, slow growing, it is aerotolerant anaerobe, meaning that it can tolerate the presence of oxygen, but does not utilize oxygen for its growth. While the bacteria is involved in the maintenance of healthy skin, it can also cause many common skin disorders such as acne vulgaris. The bacteria predominately live deep within follicles and pores, where it uses sebum, cellular debris, and metabolic byproducts from surrounding skin tissue as a source of energy and nutrients. Elevated production of sebum or blockage of follicles can cause the bacteria to grow and this rapid growth can trigger inflammation that can led to the symptoms of common skin disorders, such as folliculitis and acne vulgaris.

While less common, Staphylococcus epidermidis can also cause acne. It is a Gram-positive bacterium belonging to the Staphylococcus Genus and the Staphylococcaceae Family that is part of the normal human flora and typically skin flora or mucosal flora. It is a facultative anaerobic bacterium and can therefore grow with or without oxygen. It is usually not pathogenic, but in patients with comprised immune systems, the bacteria can cause an infection. Staphylococcus epidermidis has ability to form biofilms on plastic and its infections are generally related to catheters or surgical implants.

The presence ofP. acnes induces skin inflammation due to the bacteria’s ability to bind to toll like receptors (TLRs), especially TLR2 and TLR4 and by altering the fatty composition of the oily sebum by oxidizing squalene. The subsequent inflammatory cascades lead to the formation of inflammatory acne lesions such as papules, pustules, or nodules. If the inflammatory reaction is very severe, the follicle will break into the dermis and subcutaneous tissue as a deep nodule, leading to local tissue destruction and scarring.

Traditionally, acne is classified as either non-inflammatory (open/closed comedones) or inflammatory (papules, pustules, or nodules). Mounting evidence indicates that inflammation exists throughout the entire duration of the acne lesion lifecycle, establishing the critical role of inflammation in the pathology of acne. In the earliest stages of acne lesion development, CD3+ T cell, CD4+ T cell, and macrophage populations are elevated, while the levels of the pro-inflammatory cytokine interleukin- 1 are also upregulated. Initiation of inflammatory events have been documented even before clinical detection of acne lesions.

An active compound described herein can be administered to a human in need thereof as a neat chemical or as a topical formulation that includes an effective amount of a compound described herein, or its pharmaceutically acceptable salt, for a human in need of treatment of acne vulgaris. Thus, in one embodiment, the disclosure provides topical formulations comprising an effective amount of a compound described herein, or its pharmaceutically acceptable salt, together with at least one topically acceptable carrier for any of the uses described herein. The topical formulation may contain a compound or salt as the only active ingredient, or, in an alternative embodiment, the compound and at least one additional active agent.

An effective amount of a compound as described herein, or a compound described herein in combination or alternation with, or preceded by, concomitant with or followed by another active agent, can be used in an amount sufficient to (a) inhibit the progression of acne vulgaris; (b) cause a regression of acne vulgaris; (c) cause a cure of acne vulgaris; or inhibit or prevent the development of acne vulgaris. Accordingly, an effective amount of a compound or pharmaceutically acceptable salt thereof or composition described herein will provide a sufficient amount of the agent when administered to human to provide a desired benefit.

Topical formulations are classified into three major categories: solid forms (such as dusting powders); liquid forms (such as lotions and liniments); and semi-liquid forms (such as ointments, pastes, creams, and gels). Additives or excipients are used as inactive ingredients in topical formulations for structuring. The main use of topical formulation additives is to control the extent of absorption of the active compound, maintaining the viscosity, improving the stability and organoleptic properties, and increasing the bulk of the formulation. The main goal of topical formulations is to confine the desired effect to the skin or within the skin. Such formulations are preferred because they are protective, emollient, and deliver the active agent to exert local activity when applied to the skin or mucous membranes.

In one embodiment, the topical formulation is a solid formulation such as a dusting powder. A dusting powder is a finely divided insoluble powder containing ingredients used on skin especially for allaying irritation or absorbing moisture, discouraging bacterial growth and providing lubricant properties. Easy powder flow ability and spreadability are important parameters that are considered in the manufacture and evaluation of a dusting powder formulation. The dusting powder should adhere to the skin, provide good coverage and skin adsorption, should be free of irritant properties, and should protect the skin from drying and irritation. Representative examples of excipients that can be used in dusting powder formulations include, but are not limited to, talc, starch (such as com starch, wheat starch, or potato starch), kaolin, zinc stearate, zinc oxide, aluminum chlorohydrate, aluminum zirconium chlorhydrex, micronized wax, and chlorhexidine (as the acetate, gluconate, or hydrochloride salt).

In one embodiment, the topical formulation is a cream formulation. Creams are semisolid emulsion formulation for application to the skin or mucous membranes. Creams may be formulated as water in oil (w/o) emulsions or as oil in water (o/w) emulsions. Water in oil emulsion creams are less greasy and provide good spreadability compared to ointments. Oil in water emulsion creams, often called vanishing creams, readily rub into the skin and are easily removed by water.

Water in oil emulsion formulations typically consist of a hydrophilic component, e.g. water or other hydrophilic diluent, and a hydrophobic component, e.g. a lipid, oil, or oily material. The hydrophilic component is typically dispersed, i.e. exists as small particles and droplets, within the hydrophobic component. Water in oil emulsions typically comprise from about 1% to about 98% of the dispersed hydrophilic phase and from about 1% to about 50% of the hydrophobic phase. Additives commonly used in water in oil emulsion formulations include wool fat (containing sterols, cholesterol, oxycholesterol, triterpene, or aliphatic alcohols), waxes, bivalent soaps, sorbitan esters, borax, and oleic acid. In some embodiments, the water in oil emulsion refers to a water in silicone emulsion.

Oil in water emulsion formulations typically consist of a hydrophilic component, e.g. water or other hydrophilic diluent, and a hydrophobic component, e.g. a lipid, oil, or oily material. The hydrophobic component is typically dispersed, i.e. exists as small particles and droplets, within the hydrophilic component. Water in oil emulsions typically comprise from about 1% to about 98% of the hydrophilic phase and from about 1% to about 50% of the dispersed hydrophobic phase. Additives commonly used in oil in water emulsion formulations include polysorbates (such as Tween 80, Tween 21, and Tween 40), methylcellulose, acacia, tragacanth, triethanolamine oleate, arachis oil, and cetostearyl alcohol.

In one embodiment, the topical formulation is an ointment formulation. Ointments are greasy semisolid preparations of a dissolved or dispersed active compound. Ointment bases often influence topical drug bioavailability due to their occlusive properties of the stratum comeum, which enhances the flux of drug across the skin and affects drug dissolution or partitioning within and from the ointment to the skin. Ointments usually are moisturizing and are good for dry skin, as well as having a low risk of sensitization or irritation due to having few ingredients beyond the base oil or fat. The vehicle for an ointment formulation, known as an ointment base, may be an oleaginous base, an absorption base, or a water-soluble base. Oleaginous bases are composed entirely of lipophilic materials. They are anhydrous, insoluble in water, and not easily removable with water. Oleaginous bases are inexpensive, non-reactive, nonirritating, are good emollients, have protective and occlusive properties, and are not water washable. Representative examples of oleaginous bases include hydrocarbons (such as petrolatum, paraffin wax, liquid paraffin, microcrystalline wax, plastibase, or Ceresi), vegetable oils and animal fat (such as coconut oil, bees wax, olive oil, lanolin, peanut oil, spermacetic wax, sesame oil, or almond oil), hydrogenated and sulfated oils (such as hydrogenated castor oil, hydrogenated cotton seed oil, hydrogenated soya bean oil, hydrogenated com oil, or hydrogenated sulfated castor oils), alcohols/acids/esters (such as cetyl alcohol, stearic acid, stearyl alcohol, oleic acid, olelyl alcohol, palmitic acid, lauryl alcohol, lauraic acid, myristyl alcohol, ethyl oleate, isopropyl myristicate, or ethylene glycol), and silicones (such as dimethylpropylsiloxanes, methyl phenyl polysiloxanes, and steryl esters of dimethyl polysiloxanes).

Absorption bases are known to take up several times their own weights in water but not permit absorption of medicament form the base. The advantages of absorption bases are their protective, occlusive, and emollient properties, their ability to absorb liquids, and that they do not wash off easily, so they hold the incorporated compound with sufficient contact with the skin. Representative examples of absorption bases include hydrophilic petrolatum and anhydrous lanolin.

Water-soluble bases, also known as greaseless ointment bases, consists of water-soluble ingredients such as polyethylene glycol polymer (carbowax). Polyethylene glycol is water soluble, nonvolatile, and inert. Other water-soluble bases include glyceryl monostearate, cellulose derivatives, sodium alginate, bentonite, and carbopol 934.

In one embodiment, the topical formulation is a gel formulation. Gels are transparent or translucent semisolid preparations of one or more active ingredients in suitable hydrophilic or hydrophobic bases. Gels may be clear or opaque, and polar hydroalcoholic or nonpolar. Gels are prepared by either a fusion process or a special procedure necessitated by the gelling agents, humectants, and preservatives. Gelling agents exhibit pseudoplastic properties that give the formulation a thixotropic consistency. Gelling agents are typically used in concentrations of 0.5-10% to allow for easy addition of the active drug before the gel is formed. Representative examples of agents used in gel formulations include tragacanth, fenugreek mucilage, methyl cellulose, hydroxy ethyl cellulose, hydroxy propyl cellulose, hydroxy propyl methyl cellulose, carboxy methylcellulose, carbopol, pectin, poloxamers, alginates (such as sodium, potassium, or ammonium alginates), gelatin, starch, polyvinyl alcohol, povidone, propylene glycol, and ethyldiamine tetraacetic acid.

In one embodiment, the topical formulation is a paste formulation. Pastes are stiff preparations containing a high proportion of a finely powdered solid such as starch, zinc oxide, calcium carbonate, or talc. Pastes are often less greasy than ointment formulations.

In one embodiment, the topical formulation is a lotion formulation. Lotions are low- to medium-viscosity preparations intended for application to unbroken skin. Lotions are applied to external skin with bare hands, a clean cloth, cotton wool or gauze. Lotions provide cooling effects to the skin by the evaporation of solvents formulated therein. Typical additives in lotion formulations include bentonite, sodium carboxymethylcellulose, alcohols, and glycerin.

In one embodiment, the topical formulation is a liniment formulation. Liniments are liquid or semiliquid preparations meant for application to the skin with friction or rubbing. They act as a rubefacient, soother, or stimulant. Typical vehicles for liniment formulations are alcohol, oil, or soap based. Typical additives in a liniment formulation include castor oil, cotton seed oil, peanut oil, sesame oil, and oleic acid.

A wide variety of optional components/ingredients may be included in the topical formulations including, but not limited to, absorbents, abrasives, anticaking agents, antifoaming agents, antimicrobial agents, binders, biological actives, buffering agents, bulking agents, chemical additives, cosmetic biocides, denaturants, cosmetic astringents, drug astringents, external analgesics, film formers, humectants, opacifying agents, fragrances, pigments, colorings, essential oils, skin sensates, emollients, skin soothing agents, skin healing agents, pH adjusters, plasticizers, preservatives, preservative enhancers, propellants, reducing agents, additional skin-conditioning agents, skin penetration enhancing agents, skin protectants, solvents, suspending agents, emulsifiers, thickening agents, solubilizing agents, sunscreens, sunblocks, ultraviolet light absorbers or scattering agents, sunless tanning agents, antioxidants and/or radical scavengers, chelating agents, oil/sebum control agents, sweat control agents, sequestrants, anti-inflammatory agents, anti-androgens, depilation agents, desquamation agents/exfoliants, organic hydroxy acids, vitamins and derivatives thereof, and natural extracts.

An effective amount of a compound of Formula I through Formula VIII or a pharmaceutically acceptable salt or composition thereof can also be used to treat or prevent acne vulgaris in a human, due to any bacteria that causes such acne, including P. acnes and S. epidermis. An effective amount of a compound selected from Compound A - Compound L or a pharmaceutically acceptable salt or composition thereof can also be used to treat or prevent acne vulgaris in a human, due to any bacteria that causes such acne, including P. acnes and S. epidermis. In one embodiment, a method is provided comprising administering to a human an effective amount of a compound described herein or its pharmaceutically acceptable salt thereof or composition either alone or in combination with an effective amount of an additional active agent, for example an antibiotic or anti-inflammatory agent, to treat acne vulgaris.

Acne vulgaris severity may be classified as mild, moderate, or severe. Mild acne is classically defined by the presence of clogged skin follicle (known as comedones) limited to the face with occasional inflammatory lesions. Moderate acne occurs when a higher number of inflammatory papules and pustules occur on the face, with some being found on the trunk of the body. Severe acne occurs when nodules are the characteristic facial lesions and involvement of the trunk is extensive.

The present method includes identifying a target portion of skin affected with acne vulgaris and in need of treatment and applying a compound of Formula I through Formula VIII or a pharmaceutically acceptable salt or composition thereof to the target portion of skin. In some instances, the target portion of skin may not appear to be suffering from acne vulgaris, i.e. the compound Formula I through Formula VIII or a pharmaceutically acceptable salt or composition as described herein may be used as a preventative therapy for acne vulgaris. The compound of Formula I through Formula VIII or a pharmaceutically acceptable salt or composition as described herein, may be applied to the target skin portion and, if desired, to the surrounding skin at least once a day, twice a day, or on a more frequent daily basis during the treatment period. Typically, the compound described herein or pharmaceutically acceptable salt thereof or composition is applied in the morning and/or in the evening before bed.

The treatment period is ideally sufficient time for the active compound to reduce or eliminate the appearance of acne vulgaris on the target portion of skin. The treatment period may last for at least 1 week, about two weeks, about 4 weeks, about 8 weeks, or about 12 weeks. The treatment period may extend over multiple months (about 3-12 months) or multiple years. The step of applying a compound described herein or a pharmaceutically acceptable salt or composition may be accomplished by localized application, i.e. by applying to the targeted area while minimizing delivery to skin surfaces where treatment is not desired, or by applying more generally or broadly to one or more skin surfaces. Propionibacterium acnes (reclassified as Cutibacterium acnes in 2016) is a Gram-positive bacterium (rod) linked to acne that belongs to the Cutibacterium Genus and the Propionibacteriaceae Family. Typically, slow growing, it is aerotolerant anaerobe, meaning that it can tolerate the presence of oxygen, but does not utilize oxygen for its growth. While the bacteria is involved in the maintenance of healthy skin, it can also cause many common skin disorders such as acne vulgaris. The bacteria predominately live deep within follicles and pores, where it uses sebum, cellular debris, and metabolic byproducts from surrounding skin tissue as a source of energy and nutrients. Elevated production of sebum or blockage of follicles can cause the bacteria to grow and this rapid growth can trigger inflammation that can led to the symptoms of common skin disorders, such as folliculitis and acne vulgaris.

Staphylococcus epidermidis is a Gram-positive bacterium belonging to the Staphylococcus Genus and the Staphylococcaceae Family that is part of the normal human flora and typically skin flora or mucosal flora. It is a facultative anaerobic bacterium and can therefore grow with or without oxygen. It is usually not pathogenic, but in patients with comprised immune systems, the bacteria can cause an infection. Staphylococcus epidermidis has ability to form biofilms on plastic and its infections are generally related to catheters or surgical implants.

In one embodiment, a compound of Formula I through Formula VIII or a pharmaceutically acceptable salt or composition thereof may be used in combination or alternation with benzoyl peroxide. In the skin follicle, benzoyl peroxide kills P. acnes by oxidizing its proteins through the formation of oxygen free radicals and benzoic acid. These radicals are believed to interfere with the bacterium’s metabolism and ability to make proteins. Additionally, benzoyl peroxide is mildly effective at breaking down comedones and inhibiting inflammation. In one embodiment, a compound of Formula I through Formula VIII or a pharmaceutically acceptable salt is formulated in combination with benzoyl peroxide in a topical formulation as described herein.

In one embodiment, a compound of Formula I through Formula VIII or a pharmaceutically acceptable salt or composition as described herein may be used in combination or alternation with a retinoid. Retinoids are medications which reduce inflammation, normalize the follicle cell life cycle, and reduce sebum production. They are structurally related to vitamin A. The retinoids appear to influence the cell life cycle in the follicle lining; this helps prevent the accumulation of skin cells within the hair follicle that can create a blockage. Frequently used topical retinoids include adapalene, isotretinoin, retinol, tazarotene, and tretinoin. In one embodiment, a compound of Formula I through Formula VIII or a pharmaceutically acceptable salt thereof is formulated in combination with a retinoid in a topical formulation as described herein.

In one embodiment, a compound of Formula I through Formula VIII or a pharmaceutically acceptable salt or composition as described herein may be used in combination or alternation with an antibiotic. Antibiotics are frequently applied to the skin or taken orally to treat acne and are thought to work due to their antimicrobial activity against P. acnes and their ability to reduce inflammation. Commonly used antibiotics include clindamycin, erythromycin, metronidazole, sulfacetamide, and tetracyclines such as doxycycline and minocycline. Other representative topical antibiotics include bacitracin, polymycin b, neomycin, retapamulin, mupirocin, pramoxine, gentamicin, mafenide, and ozenoxacin. The antibiotics described herein can be applied to the skin, taken orally, or administered in any other suitable way as determined by one of skill in the art. The compounds described herein are particularly effective in combination with antibiotics due to their potentiation of the antimicrobial effect of the antibiotic. In one embodiment, a compound of Formula I through Formula VIII or a pharmaceutically acceptable salt thereof, is formulated in combination with an antibiotic in a topical formulation as described herein.

In one embodiment, a compound of Formula I through Formula VIII or a pharmaceutically acceptable salt or composition as described herein may be used in combination or alternation with azelaic acid. Azelaic acid is thought to be an effective acne treatment due to its ability to reduce skin cell accumulation in the follicle, along with its antibacterial and anti-inflammatory properties. In one embodiment, a compound of Formula I through Formula VIII or a pharmaceutically acceptable salt thereof is formulated in combination with an antibiotic in a topical formulation as described herein.

In one embodiment, a compound of Formula I through Formula VIII or a pharmaceutically acceptable salt thereof or composition as described herein may be used in combination or alternation with salicyclic acid. Salicyclic acid is a topically applied beta- hydroxy acid that has keratolytic properties in addition to stopping bacterial reproduction. In one embodiment, a compound of Formula I through Formula VIII or a pharmaceutically acceptable salt thereof is formulated in combination with salicyclic acid in a topical formulation as described herein.

In one embodiment, a compound of Formula I through Formula VIII or a pharmaceutically acceptable salt thereof or composition as described herein may be used in combination or alternation with niacinamide. Niacinamide can improve acne by decreasing inflammation, suppressing sebum production, and promoting wound healing. In one embodiment, a compound of Formula I through Formula VIII or a pharmaceutically acceptable salt thereof is formulated in combination with salicyclic acid in a topical formulation as described herein.

VII. GENERAL SYNTHESIS

The compounds described herein can be prepared by methods known to those skilled in the art. In one non-limiting example, the disclosed compounds can be made using the routes provided below.

Compounds of the present invention with stereocenters may be drawn without stereochemistry for convenience. One skilled in the art will recognize that pure enantiomers and diastereomers can be prepared by methods known in the art. Example of methods to obtain optically active materials include at least the following. i. physical separation of crystals -a technique whereby macroscopic crystals of the individual enantiomers are manually separated. This technique can be used if crystals of the separate enantiomers exist, i.e., the material is a conglomerate, and the crystals are visually distinct; ii. simultaneous crystallization - a technique whereby the individual enantiomers are separately crystallized from a solution of the racemate, possible only if the enantiomer is a conglomerate in the solid state; iii. enzymatic resolutions - a technique whereby partial or complete separation of a racemate by virtue of differing rates of reaction for the enantiomers with an enzyme; iv. enzymatic asymmetric synthesis - a synthetic technique whereby at least one step in the synthesis uses an enzymatic reaction to obtain an enantiomerically pure or enriched synthetic precursor of the desired enantiomer; v. chemical asymmetric synthesis - a synthetic technique whereby the desired enantiomer is synthesized from an achiral precursor under conditions that produce asymmetry (i.e. chirality) in the product, which may be achieved by chiral catalysts or chiral auxiliaries; vi. diastereomer separations - a technique whereby a racemic compound is reaction with an enantiomerically pure reagent (the chiral auxiliary) that converts the individual enantiomers to diastereomers. The resulting diastereomers are then separated by chromatography or crystallization by virtue of their now more distinct structural differences the chiral auxiliary later removed to obtain the desired enantiomer; vii. first- and second-order asymmetric transformations - a technique whereby diastereomers from the racemate quickly equilibrate to yield a preponderance in solution of the diastereomer from the desired enantiomer of where preferential crystallization of the diastereomer from the desired enantiomer perturbs the equilibrium such that eventually in principle all the material is converted to the crystalline diastereomer from the desired enantiomers. The desired enantiomer is then released from the diastereomer; viii. kinetic resolutions - this technique refers to the achievement of partial or complete resolution of a racemate (or of a further resolution of a partially resolved compound) by virtue of unequal reaction rates of the enantiomers with a chiral, non-racemic reagent or catalyst under kinetic conditions; ix. enantiospecific synthesis from non-racemic precursors - a synthetic technique whereby the desired enantiomer is obtained from non-chiral starting materials and where the stereochemical integrity is not or is only minimally compromised over the course of the synthesis; x. chiral liquid chromatography - a technique whereby the enantiomers of a racemate are separated in a liquid mobile phase by virtue of their differing interactions with a stationary phase (including vial chiral HPLC). The stationary phase can be made of chiral material or the mobile phase can contain an additional chiral material to provoke the differing interactions; xi. chiral gas chromatography - a technique whereby the racemate is volatilized and enantiomers are separated by virtue of their differing interactions in the gaseous mobile phase with a column containing a fixed non-racemic chiral adsorbent phase; xii. extraction with chiral solvents - a technique whereby the enantiomers are separated by virtue of preferential dissolution of one enantiomer into a particular chiral solvent; xiii. transport across chiral membranes - a technique whereby a racemate is place in contact with a thin 5 membrane barrier. The barrier typically separates two miscible fluids, one containing the racemate, and a driving force such as concentration or pressure differential causes preferential transport across the membrane barrier. Separation occurs as a result of the non-racemic chiral nature of the membrane that allows only one enantiomer of the racemate to pass through; and xiv. simulated moving bed chromatography is used in one embodiment. A wide variety of chiral stationary phases are commercially available. VIII. EXAMPLES

Example 1. Synthesis of Representative Examples of the Present Invention

The synthesis of representative compounds of the present invention are described in Arafa et. Al., “Novel linear triaryl guanidines, N-substituted guanidines and potential prodrugs as antiprotozal agents”, European Journal of Medicinal Chemistry, 2008, 43, 2901-2908 (Compound A); Wang et al. “Evaluation of the Influence of Compound Structure on Stacked- Dimer Formation in the DNA Minor Groove” Biochemistry, 2001, 40, 2511 (Compound B); W02002/055025, Scheme 1 and page 22, paragraph 120 (Compound D); Giordani et al. “Green Fluorescent Diamidine as Diagnostic Probes for Trypanosomes” Antimicrobial Agents and Chemotherapy 2014, 58: 1793 (Compound M, Compound N, Compound P, Compound Q); Ismail MA, Boykin DW, and Stephens CE, “An efficient synthesis of 2,5’- diarylbichalcophenes”, Tetrahedron Letters, 2006, 47, pg. 795-797 (Compound O); W02009/051796, Example 1, Scheme 1 on page 40 and 41 (Compound R); Gonzalez et. al., “Synthesis and antiparasitic evaluation of bis-2,5-[4-guanidinophenyl]thiophenes”, European Journal of Medicinal Chemistry, 2007, 42, 552-557 (Compound C); EP1726589, Example 3, Scheme 4 on page 27, and paragraph 142 (Compound T).

Synthesis of Compound U 5-(4-Cyanophenyl)indole-3-carbaldehyde (U-l)

To a solution of 5-bromoindole-3-carbaldehyde (1.12 g, 5.0 mmol) and Pd(PPh3)4 (0.30 g, 0.26 mmol) in 20 mL of toluene under a nitrogen atmosphere was added 10 mL of 2M aqueous NaHCCb and 0.74 g (5.0 mmol) of 4-cyanobenzeneboronic acid in 5 mL of methanol. The mixture was vigorously stirred and heated under reflux overnight. The mixture was cooled and extracted with dichloromethane. The organic layer was dried and concentrated to dryness under reduced pressure to afford 1.0 g (81%) of product, mp 248-250 °C. lH-NMR(DMSO-de)5 10.98 (d, 1H, J = 2), 8.40 (d, 1H, J = 2), 7.87 (dd, 4H, J = 8 and J = 2), 7.62 (s, 1H); 13C-NMR (DMSO-d6) 5185.2, 145.7, 139.4, 137.2, 132.8, 132.7, 127.6, 124.9, 122.9, 119.4, 119.0, 118.4, 113.2, 109.3. Anal calcd. C16H10N2O: C, 78.03; H, 4.09. Found: C, 77.73; H, 4.17. 3-(5-Cyanobenzimidazol-2-yl)-5-(4-cyanophenyl)indole (U-2)

A solution of 5-(4-cyanophenyl)indole-3-carbaldehyde (0.80 g, 3.25 mmol), 3,4- diaminobenzonitrile (0.44 g, 3.3 mmol) and sodium bisulfite (0.40 g, 3.9 mmol) in 5 mL DMF was heated under reflux overnight. After cooling, the mixture was poured onto chipped ice. The solid was collected by filtration and washed with aqueous sodium bicarbonate (2.5%) and water to yield 1.0 g (85%) of an off white solid, mp 311-313 °C. ¹ H-NMR(DMSO-d6) d 8.82 (s, 1H), 8.28(s, 1H), 7.93(s, 4H), 7.61 (m, 4H); ¹³ C-NMR(DMSO-de) d 152.3, 146.3, 136.8, 132.9, 131.4, 128.7, 125.7, 125.2, 122.0, 120.4, 119.1, 113.0, 109.1, 106.3, 103.0; FIRMS (FAB) calcd. mass for C23H13N5 (M + H): 360.383; observed mass, 360.125. 3-(5-Hydroxyamidinobenzimidazol-2-yl)-5-(4-hydroxyamidinophe nyl)indole (U-3)

To a solution of hydroxylamine hydrochloride (0.72 g, 10. 3 mmol) in 5 mL of DMSO, potassium t-butoxide (1.16 g, 10.3 mmol) was added in portions under nitrogen. After stirring the mixture for 30 minutes, 0.37 g (1.01 mmol) of 3-(5-cyanobenzimidazol-2-yl)-5-(4- cyanophenyl)indole was added and the mixture was stirred at room temperature overnight. The mixture was poured into ice water and filtered to yield the expected 3-(5- hydroxyamidinobenzimidazol-2-yl)-5-(4-hydroxyamidinophenyl)i ndole as a white solid, 0.43 g (98%); mp 370 °C (decomp.); ¾-NMR (DMSO-de) d 9.71(s, 1H), 9.60 (s, 1H), 8.79 (s, 1H), 8.23 (d, 1H, J = 2.7), 7.84 (d, 2H, J = 8.4), 7.76 (d, 2H, J = 8.4), 7.60 (m, 5H), 5.98 (s, 2H), 5.91 (s, 4H); ¹³ C-NMR (DMSO-de) d 172.1, 152.3, 150.8, 150.4, 142.3, 136.3, 132.5, 131.5, 127.4 , 126.6, 126.4, 126.0, 125.7, 121.7, 119.5, 119.4, 112.6, 106.9. Anal calcd. for C23H19N7O22.3H2O: C, 59.17; H, 5.09. Found: C, 59.11; H, 4.99. 3-(5-Acetoxyamidinobenzimidazol-2-yl)-5-(4-acetoxyamidinophe nyl)indole

The above amidoxime (0.35 g, 2.0 mmol) was dissolved in glacial acetic acid (5 mL) and acetic anhydride (0.5 mL, 6.5 mmol) was added. The mixture was allowed to stir for 2 hours and the solvent was evaporated. The product was used in the next step without further characterization. 3-(5-Amidinobenzimidazol-2-yl)-5-(4-amidinophenyl)indole acetate salt (Compound U) Crude 3-(5-acetoxyamidinobenzimidazol-2-yl)-5-(4-acetoxyamidinophe nyl)indole was submitted to catalytic hydrogenation in the presence of Pd/C to afford 0.25 g (43% yield) of Compound L, mp >228 °C. Tf-NMR (DMSO-de) d 8.86(s, 1H), 8.37(s, 1H), 8.12(s, 1H), 7.93(m, 4H), 7.62(m, 4H), 5.99(br, 1H), 1.82(s, 1 lH);13C-NMR(DMSO-de) 5175.5, 166.7, 165.9, 152.5, 146.5, 136.9, 131.5, 128.8, 128.4, 127.1, 127.0, 125.9, 121.9, 121.4, 120.9, 119.9,

112.9, 106.6, 24.0; HRMS (FAB) calcd. mass for C23H19N6 (M + H): 394.450; observed mass, 394.178. Anal calcd. for C23H19N6.3 5CH3COOH 3.OH2O: C, 54.78, H, 5.97; N, 14.90. Found: C, 54.83, H, 5.79; N, 14.81.

General Methods for the Synthesis of Diamidine Compounds Diamidine compounds were synthesized from dinitrile compounds, either through method B or method C. Substituted amidine or cyclized amidine compounds (MD-102, MD- 112, MD-113 and MD-129) were synthesized from dinitrile compounds through method D.

Substituted orcyclized Diamidine General procedures for the preparation of dinitriles (Method A)

A mixture of 1,3-bis (bromomethyl)-benzene/substituted benzene (5 mmol), 4- hydroxybenzonitrile or 4-hydroxy substituted benzonitrile (10 mmol) and anhydrous K2CO3 (2.07 g, 15 mmol) in 10 mL DMF was heated at 45 °C for 4 hours. Then the reaction mixture was diluted with ice water (70 mL) and stirred for 30 minutes. The white precipitate was filtered, washed with water, and dried in air. Then the white solid was dissolved in organic solvent (75 mL) (DCM, methanol or THF). The organic phase was dried over anhydrous MgSCri. MgSCri was then filtered and the supernatant was concentrated with rotavapor to afford crude product. The crude product was then triturated with hexane, filtered and dried in vacuum to yield white solid in 80-90% yield.

General procedures for diamidines as dihydrochloride salt (Method B)

To a cold and stirred suspension of dinitrile (1 mmol) in 15 mL dry THF was added 6.0 mL (6 mmol) of LiN(TMS)2 (1M in THF). The reaction was stirred for 24 hours at room temperature. Then the mixture was cooled and acidified with saturated ethanolic-HCl to form a white solid. The mixture was stirred for 2 hours, after which all solvents were removed under vacuum to afford a crude product. The crude product was then diluted with ether and the mixture was filtered to obtain a white solid. The white solid was then diluted with 10 mL ice water and basified with 2M NaOH to afford a white precipitate. The white precipitate was then filtered, washed with water and dried in air. The solid was suspended in anhydrous ethanol (15 mL) and 5 mL saturated ethanolic HC1 for 6 hours. Then ethanol was distilled off and the product was triturated with dry ether and filtered. The solid was dried in vacuum at 80 °C for 12 hours to yield (65-75%) diamidine dihydrochloride as white solid.

General procedures for diamidines as dihydrochloride salt (Method C)

Dinitrile (1 mmol) was added to anhydrous ethanol (EtOH) saturated with hydrogen chloride (20 mL) at 0 °C in a dry flask. The reaction mixture was then sealed, slowly warmed to ambient temperature, and stirred for 7 days. Ethanol was removed using rotary evaporator. Anhydrous diethyl ether (20 mL) was added to the reaction mixture and the precipitated imidate ester dihydrochloride was filtered off and dried under high vacuum. Ammonia gas (using a cylinder) was passed through imidate ester in EtOH (10 mL) and stirred for a day. The reaction mixture was concentrated in vacuum. Then anhydrous ether was added, and the product was filtered and dried under vacuum. The diamidine was converted to its dihydrochloride salt by stirring the diamidine with saturated ethanolic HC1 (2 mL) for 2-3hours. The solvent was removed, and the solid was dried in vacuum at 80 °C for 12 hours to yield final product (65- 75%). General procedure for the preparation of substituted diamidine or cyclized diamidine as dihydrochloride salts (Method D)

The nitrile compound was added to anhydrous EtOH saturated with hydrogen chloride at 0 °C in a dry flask. The reaction mixture was then sealed, slowly warmed to ambient temperature, and stirred until the nitrile compound was no longer detectable by TLC. The reaction mixture was diluted with anhydrous ether. The precipitated imidate ester dihydrochloride was filtered off under nitrogen and dried under high vacuum. The imidate was then reacted immediately with 2.5 equivalents of the appropriate amine in EtOH for 24hours. The reaction mixture was concentrated in vacuum. Then ether was added, and the product was filtered. The solid was suspended in 10 mL ice-water and basified with 2M NaOH. The resulting white precipitate was filtered, washed with water, and air dried. The free base was converted to its dihydrochloride salt using saturated ethanolic HC1 as white solid, which was dried in vacuum at 80 °C for 12 hours to yield final product (65-75%).

Synthesis of MD-100

Synthesis of 4,4'-(((5-methyl-l,3-phenylene)his(methylene))his(oxy))dihen zonitrile (10). Reaction of 1,3-bis (bromomethyl)-5-methylbenzene (8, 1.38 g, 5 mmol) and 4- hydroxybenzonitrile (9, 1.19 g, 10 mmol) in the presence of anhydrous K2CO3 (2.07 g, 15 mmol) in 10 mL DMF yielded 1, 3-bis (4-cyano-phenoxy methyl)-5-methyl-benzene as white solid (10, 1.58 g, 90%) using method A. ¾ NMR (CDCb): d 7.59 (d, J= 8.8 Hz, 4H), 7.26 (s, 1H), 7.22 (s, 2H), 7.02 (d, J = 8.8 Hz, 4H), 5.09 (s, 4H), 2.40 (s, 3H). ¹³ C NMR (CDCb): d

161.9, 139.3, 136.4, 134.1, 128.3, 123.7, 119.2, 115.6, 104.3, 70.1, 21.4. HRMS calcd for C23Hi8N ₂ 0 ₂ Na [M+Na] ⁺ : 377.1266, found: 377.1269.

Synthesis of 4,4'-(((5-methyl-l,3-phenylene)bis(methylene))bis(oxy))diben zimidamide dihydrochloride (MD-100). 10 (0.354 g, 1 mmol) was converted to MD-100 as brown solid following method B (MD-100, 0.33 g, 71%). ¾ NMR (DMSO-de): d 9.24 (s, 4H), 8.90 (s, 4H), 7.82 (d, J= 8.8 Hz, 4H), 7.34 (s, 1H), 7.25 (s, 2H), 7.20 (d, J= 8.8 Hz, 4H), 5.18 (s, 4H), 2.32 (s, 3H). ¹³ C NMR (DMSO-de): d 165.0, 162.9, 138.6, 136.9, 130.5, 128.5, 124.6, 120.0, 115.5,

69.9, 21.2. HRMS calcd for C23H25N4O2 [M+H] ⁺ : 389.1972, found: 389.1976. 1, 4-Bis [(4-amidino)-phenoxy methyl] benzene dihydrochloride (MD-101)

Reaction of 1,4-bis (bromomethyl)lbenzene (1.32 g, 5 mmol) and 4-hydroxybenzonitrile (1.19 g, 10 mmol) yielded 1, 4-bis (4-cyano-phenoxy methyl) benzene as white solid (1.74 g, 78%), using method A; ¾ NMR (CDCb): 7.59 (d, 4H, J= 8.9 Hz), 7.45 (s, 4H), 7.02 (d, J= 8.9 Hz, 4H), 5.13 (s, 4H); ¹³ C NMR (CDCb): 161.82, 136.01, 134.07, 127.86, 119.10, 115.57, 104.45, 69.88; MS: HRMS-ESI-POS.: calc for C22H17N2O2 m/z 341.1285 (M ⁺ +l), found m/z 341.1283. Dinitrile (0.340 g, 1 mmol) was converted to 1, 4-bis (4-amidino (phenoxy methyl))benzene dihydrochloride as pale yellow solid following Method B (0.33 g, 76%). 'H NMR (DMSO-de): 9.25 (s, 4H), 9.02 (s, 4H), 7.85 (d, J= 8.9 Hz, 4H), 7.51 (s, 4H), 7.23 (d, J= 9.0 Hz, 4H), 5.26 (s, 4H); ¹³ C NMR (DMSO-de): 165.16, 163.12, 136.67, 130.67, 128.49, 120.12, 115.64, 69.79; MS: HRMS-ESI-POS.: calc for C22H24N4O2 m/z 188.0944(M/2 ⁺ +2), found m/z 188.0936. Synthesis of MD-102

Synthesis of 4,4'-( ( (5-methyl- 1 , 3-phenylene)bis(methylene))bis(oxy))bis(N- isopropylbenzimidamide) dihydrochloride (MD-102). Dinitrile (10, 0.35 g, 1 mmol) was converted to MD-102 by the reaction with isopropyl amine (0.15 g, 2.5 mmol) in ethanol (10 mL) at room temperature for 24 hours as a pale yellow solid using general method D (MD-102, 0.27 g, 50%). ¾ NMR (DMSO-de): d 9.43 (d, J= 8.0 Hz, 2H), 9.33 (s, 2H), 8.99 (s, 2H), 7.73 (d, J= 8.8 Hz, 4H), 7.36 (s, 1H), 7.27 (s, 2H) , 7.21 (d, J= 8.8 Hz, 4H), 5.20 (s, 4H), 4.09-4.04 (m, 2H), 2.34 (s, 3H), 1.26 (d, = 6.4 Hz, 12H). ¹³ C NMR (DMSO-de): d 162.1, 161.2, 138.1, 136.7, 130.3, 128.1, 124.3, 121.2, 114.9, 69.5, 54.9, 44.9, 21.3, 21.0. HRMS calcd for C29H38N4O2 [M+2H] ²⁺ /2: 237.1492, found 237.1482.

Synthesis of MD-103

Synthesis of 4,4'-((( 5-methyl- 1, 3-phenylene)bis(methylene))bis(oxy))bis (3- methoxybenzonitrile) (12). Reaction of 1,3-bis (bromomethyl)-5-methylbenzene (8, 1.4 g, 5 mmol) and 4-hydroxy- 2-methoxybenzonitrile (11, 1.37 g, 10 mmol) in the presence of anhydrous K2CO3 (2.07 g, 15 mmol) in 10 mL DMF yielded 4,4'-(((5-methyl-l,3- phenylene)bis(methylene))bis(oxy))bis(3-methoxybenzonitrile) as white solid (12, 1.57 g, 76%) following method A. ¾ NMR (DMSO-de): d 7.41-7.39 (m, 4H), 7.30 (s, 1H), 7.24 (s, 2H), 7.18 (d, J= 8.8 Hz, 2H), 5.15 (s, 4H), 3.80 (s, 6H), 2.33 (s, 3H). ¹³ C NMR (DMSO-de): d 151.8, 149.2, 138.0, 136.5, 128.5, 126.3, 124.6, 119.2, 114.7, 113.4, 102.9, 69.9, 56.0, 21.0. HRMS calcd for C ₂₅ H ₂₃ N ₂ 04[M+H] ⁺ : 415.1652, found 415.1643.

Synthesis of 4,4'-((( 5-methyl-l, 3-phenylene)bis(methylene))bis(oxy))bis (3- methoxybenzimidamide) dihydrochloride (MD-103). Dinitrile (12, 0.41 g, 1 mmol) was converted to yield 4,4'-(((5-methyl-l,3-phenylene)bis(methylene))bis(oxy))bis(3 - methoxybenzimidamide) dihydrochloride as brown solid following method B (MD-103, 0.39 g, 76%). ¾ NMR (DMSO-de): d 9.27 (s, 4H), 8.97 (s, 4H), 7.49 - 7.48 (m, 4H), 7.33 (s, 1H), 7.26 - 7.24 (m, 4H), 5.18 (s, 4H), 3.86 (s, 6H), 2.34 (s, 3H). ¹³ C NMR (DMSO-de): d 164.7, 152.3, 148.81, 138.1, 136.7, 128.5, 124.7, 121.9, 119.5, 112.8, 111.6, 70.0, 56.1, 21.0. HRMS calcd for CrsHsoNrOr [M+2H] ²⁺ /2: 225.1128, found 225.1119.

1, 4-Bis [((4-amidino)-2-methoxy)-phenoxy methyl] 2-fluorobenzene dihydrochloride (MD-104)

Dinitrile (0.41 g, 1 mmol) was converted to 1, 4-Bis [((4-ami dino)-2-methoxy)-phenoxy methyl] 2-fluorobenzene dihydrochloride as a brown solid following Method B (0.37 g, 72%). ¾_NMR (DMSO-de): 9.32 (s, 4H), 9.04 (s, 4H), 7.61(t, 2H, J = 7.2Hz),7.53 (m, 4H), 7.39- 7.28 (m,4H ), 5.27 (s, 4H), 3.863 (s, 6H); ¹³ C NMR (DMSO-de): 165.30, 159.29 (d, C-F = 250 Hz), 152.58, 149.19, 131.86 (d, C-F = 2.9 Hz), 125.03 (d, JC-F = 3.6 Hz), 123.88 (d, JC-F = 14.7 Hz), 122.23, 120.32, 113.18, 111.99, 64.79 (d, JC-F = 3.2 Hz), 56.40; MS: HRMS-ESI-POS.: calc for CrrH^FNrOr in z 237.1003 (M/2 ⁺ +2), found in z 237.0995.

Synthesis of MD-105

(i) LiAIH ₄ ,THF, 0°C - rt, overnight (ii) PBr ₃ , CH ₂ CI ₂ , 0°C - r.t, 4h. Synthesis ofdiol (5-(tert-butyl)-l,3-phenylene)dimethanol (14). 5-tert-butylisophthalic acid (13, 4 g, 18 mmol) in THF (100 mL) was added dropwise under ice-bath condition to a solution of lithium aluminium hydride (1.5 g, 38mmol) in THF (100 mL). The reaction was stirred for 1 hour at 0 °C, after which the reaction was heated at 60 °C for 24 hours. The reaction was monitored by TLC. Upon completion, the reaction mixture was cooled to 0 °C and quenched with methanol and water. The quenched reaction was filtered through celite and washed with EtOAc (100 mL). The combined organic solvent was removed under reduced pressure and was extracted with EtOAc (3 x 100 mL), dried over MgS04 and concentrated to give the required diol (5-(tert-butyl)-l,3-phenylene)dimethanol (14, 3.2 g, 94%). Ή NMR (CDCb): d 7.32 (s, 2H), 7.19 (s, 1H), 4.69 (s, 4H), 1.33 (s, 6H). ¹³ C NMR (CDCb): d 152.2, 141.1, 123.6, 123.1, 65.7, 34.9, 31.5. HRMS calcd for Ci2HnO[M- H ₂ 0] ⁺ : 177.1274, found 177.1274. Synthesis of 1, 3-bis (4-cyano-phenoxy methyl)- 5-(tert-butyl)benzene (16). PBr ₃ (2.5 mL, 26 mmol) was added dropwise to a solution of diol (5-(tert-butyl)-l,3-phenylene)dimethanol (14, 2.3 g, 11.8mmol) in DCM at 0°C. The reaction mixture was stirred at room temperature for 4 hours and then quenched with ice water. The solution was extracted with CH2CI2 (3 x 100 mL), dried over MgS04 and concentrated to give the required dibromo compound (1,3- bis(bromomethyl)-5-(tert-butyl)benzene) as a white solid (15, 3.4 g, 90%). Reaction of 1,3- bis(bromomethyl)-5-(tert-butyl)benzene (15, 1.6 g, 5 mmol) and 4-hydroxybenzonitrile (9,

1.19 g, 10 mmol) yielded dinitrile compound as white solid (16, 1.54 g, 78%) using method A. ¾ NMR (DMSO-de): d 7.79 -7.78 (m, 4H), 7.48 (s, 2H), 7.36 (s, 1H), 7.20 - 7.18 (m, 4H),

5.20 (s, 4H), 1.29 (s, 9H). ¹³ C NMR (CDCb): d 161.8, 151.3, 136.1, 134.2, 124.8, 119.1, 115.9,

103.0, 69.9, 34.5, 31.1. HRMS calcd for C ₂₆ H25N ₂ 02[M+H] ⁺ : 397.1911, found 397.1912. Synthesis of 4,4'-(((5-(tert-butyl)-l,3-phenylene)bis(methylene))bis(oxy) )dibenzimidamide dihydrochloride (MD-105). 1, 3-bis (4-cyano-phenoxy methyl)- 5-(tert-butyl)benzene (16, 0.370 g, 1 mmol) was converted to yielded 4,4'-(((5-(tert-butyl)-l,3- phenylene)bis(methylene))bis(oxy))dibenzimidamide dihydrochloride as brown solid following method B (MD-105, 0.35 g, 70%). ¾ NMR (DMSO-de): d 9.42 (s, 4H), 9.21 (s, 4H), 7.94 (d, J= 8.4 Hz, 4H), 7.49 (s, 2H), 7.39 (s, 1H), 7.23 (d, J= 8.4 Hz, 4H), 5.23 (s, 4H), 1.28 (s, 9H). ¹³ C NMR (DMSO-de): d 165.7, 163.5, 152.5, 137.0, 131.0, 125.6, 120.3, 116.1, 70.7, 35.2, 31.8. HRMS calcd for C2eH _3i N40 ₂ [M+H] ⁺ : 431.2442, found 431.2425. Synthesis of MD-106

(i) LiAIH ₄ ,THF, 0°C - rt, 16 h.

Synthesis of ((((5-methyl-l,3-phenylene)bis(methylene))bis(oxy))bis(4,l- phenylene))dimethanamine dihydrochloride (MD-106). A solution of 1, 3-bis (4-cyano- phenoxy methyl)-5 -methyl-benzene (10, 1.0 g, 2.8 mmol) in THF (20 mL) was added dropwise to a suspension of LiAlFU (0.32 g, 7.4 mmol) in THF under argon gas at 0 ^° C and the mixture was stirred at room temperature for 16 hours. The reaction was quenched with the addition of H2O (5 mL) at 0 ^° C followed by addition of 16% NaOH solution (2 mL). The mixture was stirred at room temperature for around 2 hours after which it was filtered through celite. The solution was then concentrated in vacuo to obtain the free diamine. The product residue was then dissolved in ethanol followed by addition of HC1 in ethanol (2 mL) for salt formation. The reaction mixture was evaporated in vacuo followed by ether precipitation to obtain the product as a green solid. (MD-106, 1.0 g, 87%). ¾ NMR (DMSO-de): d 8.45 (s, 6H), 7.43 (d, J= 8.4 Hz, 4H), 7.32 (s, 1H), 7.22 (s, 2H), 7.03 (d, J= 8.4 Hz, 4H), 5.09 (s, 4H), 2.32 (s, 3H). ¹³ C NMR (DMSO-de): d 158.4, 137.9, 137.2, 130.5, 127.8, 126.2, 124.3, 114.8, 69.2, 41.6, 21.0. HRMS calcd for C23H27N2O2 [M+H] ⁺ : 363.2079, found 363.2067.

Synthesis of MD-107

Synthesis of 4,4',4”-((benzene-l,3,5-triyltris(methylene))tris(oxy))tri benzonitrile (18). Reaction of 1,3,5-tris (bromomethyl)benzene (17, 1.54 g, 4.3 mmol) and 4-hydroxybenzonitrile (9, 1.64 g, 14 mmol) the presence of anhydrous K2CO3 (2.35 g, 17 mmol) in 10 mL DMF yielded 4,4',4"-((benzene-l,3,5-triyltris(methylene))tris(oxy))tribe nzonitrile as a white solid (18, 1.69 g, 84%), using method A. ¾ NMR (DMSO-de): d 7.77 (d, J= 9.2 Hz, 6H), 7.53 (s, 3H), 7.18 (d, J= 9.2 Hz, 6H), 5.24 (s, 6H). ¹³ C NMR (DMSO-de): d 161.7, 137.0, 134.2, 126.9, 119.1, 115.9, 103.2, 69.3. HRMS calcd for CsoftiNsCbNa [M+Na] ⁺ : 494.1481, found 494.1481.

Synthesis of 4,4',4"-( (benzene-1, 3, 5-triyltris(methylene))tris(oxy))tribenzimidamide trihydrochloride (MD-107). Trinitrile (18, 0.56 g, 1.2 mmol) was converted to 4, 4', 4"- ((benzene-l,3,5-triyltris(methylene))tris(oxy))tribenzimidam ide trihydrochloride (MD-107) as brown solid using method B (MD-107, 0.58 g, 78%). ¾ NMR (DMSO-de): d 9.45 (s, 6H), 9.25 (s, 6H), 7.95 (d, J= 8.4 Hz), 7.56 (s, 3H), 7.22 (d, J= 8.4 Hz, 6H), 5.27 (s, 6H). ¹³ C NMR (DMSO-de): d 164.7, 162.6, 137.1, 130.3, 126.9, 119.6, 115.1, 69.4. HRMS calcd for C30H32N6O3 [M+2H] ²⁺ /2: 262.1262, found 262.1258.

Synthesis of MD-108

(i) 3 mol% Pd(PPh3) ₄ , 6 mol% sodium ascorbate, 1 mol% CuS0 ₄ , 1:1 Et ₃ N; DMSO (ii) H ₂ ,

Pd/C, MeOH, overnight.

Synthesis of 4,4'-((5-methyl-l,3-phenylene)bis(ethyne-2,l-diyl))dibenzoni trile (21). 3,5- dibromotoluene (19, 0.98 g, 3.9 mmol) was dissolved with 1:1 DMF-Et3N (6 mL). To this solution, 3 mole% Pd(PPh3)4 and 4-ethynylbenzonitrile (1 g, 7.8 mmol) were added and the mixture was stirred for 5 minutes. Further, 6 mol% sodium ascorbate solution, 1 mol% CuS04 solution in DMF were added to the reaction mixture and stirred for 4 h at 80 °C. The reaction mixture was extracted with ethyl acetate followed by ammonium chloride and brine wash. The combined organic layer was dried over anhydrous Na2S04 and then concentrated in vacuo. The product was purified using column chromatography and obtained using 5:1 hexane: ethyl acetate system as a white solid (21, 0.67 g, 50%). ¹ ¾ NMR (CDCb): d 7.66 - 7.59 (m, 8H), 7.55 (s, 1H), 7.38 (s, 2H), 2.38 (s, 3H). ¹³ C NMR (CDCb): d 38.9, 133.1, 132.3, 132.2, 128.1, 122.8, 118.6, 111.9, 92.9, 88.3, 21.2. HRMS-calcd for C25Hi ₄ N ₂ Na[M+Na] ⁺ : 365.1055 found 365.1068.

Synthesis of 4,4'-((5-methyl-l,3-phenylene)bis(ethane-2,l-diyl))dibenzoni trile (22). To 10% Pd/C in THF (30 mL) under argon gas was added 4,4'-((5-methyl-l,3-phenylene)bis(ethyne- 2,l-diyl))dibenzonitrile (21, 0.5 g, 1.46 mmol). The argon gas was exchanged for H2 gas and the reaction mixture was stirred overnight. The reaction mixture was quenched with CH2CI2 and filtered through celite. Extraction was carried out with CH2CI2 followed by washing with H2O. The combined organic layer was dried over anhydrous Na2S04 and then concentrated under vacuum to give the product as a pale-yellow solid (22, 0.45 g, 87.6%). ¾ NMR (CDCh): d 7.56 (d, J= 8.4 Hz, 4H), 7.24 (d, J= 8.4 Hz, 4H,), 6.81 (s, 2H), 6.67 (s, 1H), 2.95 - 2.90 (m, 4H), 2.85 - 2.81 (m, 4H), 2.29 (s, 3H). ¹³ C NMR (CDCh): d 147.5, 141.0, 138.4, 132.3, 129.4, 127.3, 125.8, 119.2, 110.0, 38.1, 37.3, 21.5. HRMS calcd for C25H23N2 [M+H] ⁺ : 351.1856 found 351.1846.

Synthesis of 4,4'-((5-methyl-l , 3-phenylene)bis (ethane-2, l-diyl))dihenzimidamide dihydrochloride (MD-108). Dinitrile compound (21, 0.35 g, 1 mmol) was converted to 4,4'- ((5-methyl-l,3-phenylene)bis(ethane-2,l-diyl))dibenzimidamid e dihydrochloride (MD-108) as a white solid following method B (MD-108, 0.32 g, 70%). ¾ NMR (DMSO-de): d 9.34 (s, 4H), 9.12 (s, 4H), 7.78 (d, J= 8.4 Hz, 4H), 7.49 (d, J= 8.4 Hz, , 4H), 6.94 (s, 1H), 6.90 (s, 2H), 2.98 - 2.94 (m, 4H), 2.85 - 2.81 (m, 4H), 2.24 (s, 3H). ¹³ C NMR (DMSO-de): d 165.5, 148.4, 141.0, 137.3, 129.1, 128.2, 126.9, 125.6, 125.5, 36.9, 36.6, 21.1. HRMS calcd for C25H30N4 [M+2H] ²⁺ /2: 193.1230, found 193.1222.

Synthesis of MD-109 i) K ₂ CO ₃ , DMF, rt, overnight.

Synthesis of 4,4'-(((5-methyl-l,3-phenylene)his(oxy))his(methylene))dihen zonitrile (25). A mixture of orcinol (23, 0.5 g, 4.1 mmol), 4-cyanobenzyl bromide (24, 1.65 g, 8.4 mmol) and anhydrous K2CO3 (1.66 g, 12 mmol) in 10 mL DMF was stirred at room temperature overnight. Then the reaction mixture was diluted with ice water (70 mL) and stirred for 30 minutes. The yellow precipitate was filtered, washed with water, and dried in air. Then the yellow solid was dissolved in a dichloromethane (100 mL), dried over anhydrous MgSCri, filtered and concentrated with rotavapor. The crude product was triturated with hexane and the precipitate was filtered, which was then dried in vacuo to yield 4,4'-(((5-methyl-l,3- phenylene)bis(oxy))bis(methylene))dibenzonitrile as a yellow solid (25, 0.97 g, 66.5%). 'H NMR (CDCh): d 7.68 (d, J= 8.4 Hz, 4H), 7.53 (d, J= 8.4 Hz, 4H), 6.43 (d, J= 2.0 Hz, 2H), 6.39 (t, J= 2.0 Hz, 1H), 5.08 (s, 4H), 2.30 (s, 3H). ¹³ C NMR (CDCh): d 159.5, 142.5, 140.9, 132.5, 127.7, 118.8, 111.9, 108.7, 99.5, 69.0, 22.0. HRMS calcd for C23Hi8N ₂ 0 ₂ Na [M+Na] ⁺ : 377.1266, found 377.1283.

Synthesis of 4,4'-(((5-methyl-l,3-phenylene)bis(oxy))bis(methylene))diben zimidamide dihydrochloride (MD-109). Dinitrile (25, 0.33 g, 0.93 mmol) was converted to 4,4'-(((5- methyl-l,3-phenylene)bis(oxy))bis(methylene))dibenzimidamide dihydrochloride as white solid following method C (MD-109, 0.3 g, 75%). ¾ NMR (DMSO-de): d 9.45 (s, 4H), 9.25 (s, 4H), 7.86 (d, J= 7.6 Hz, 4H), 7.64 (d, J= 8.0 Hz, 4H), 6.50 (s, 1H), 6.48 (s, 2H), 5.20 (s, 4H), 2.23 (s, 3H). ¹³ C NMR (DMSO-de): d 165.5, 159.1, 143.4, 140.0, 128.4, 127.6, 127.3, 108.3, 99.3, 68.3, 21.5. HRMS calcd for C ₂₃ H ₂₅ N40 ₂ [M+H] ⁺ : 389.1978, found 389.1960.

1, 3-Bis{(4-isopropylamidino)-phenoxy methyl}-2-fluorobenzene dihydrochloride (MD- 110)

Reaction of 1,3-bis (bromomethyl)-2-fluorobenzene (1.4 g, 5 mmol) and 4- hydroxybenzonitrile (1.19 g, 10 mmol) yielded 1, 3-bis (4-cyano-phenoxy methyl)-2- fluorobenzene as white solid (2.53 g, 70%), following method A; mp 173-5 °C; Ή NMR (DMSO-de): 7.78 (d, 4H, J= 8.4Hz), 7.59 (t, 2H, J= 7.2Hz), 7.29 (t, 1H, J= 7.2Hz), 7.23 (d, 4H, J= 8.4Hz), 5.3 (s, 4H); ¹³ C NMR (DMSO-de): 161.4, 158.4 (d, JC-F = 248Hz), 134.0, 130.7 (d, Jc-F = 4.1Hz), 124.2 (d, JC-F = 4.1Hz), 123.1 (d, JC-F = 13.5Hz), 118.7, 115.6, 103.3,63.8 (d, JC-F = 3.3Hz); MS: HRMS-ESI-POS.: calc for C ₂₂ Hi ₅ FN ₂ 0 ₂ Nam/z 381.1015 (M ⁺ +Na), found m/z 381.1005.

Dinitrile (0.35 g, 0.97 mmol) was converted to 1, 3-bis {4-isopropylamidino (phenoxy methyl)- 2-fluorobenzene dihydrochloride as white solid following Method D (0.38 g, 73%) with isopropylamine (0.17g, 2.92mmol); mp. 269-70 °C; ¾ NMR (DMSO-de): 9.48 (d, 2H, J= 8.0 Hz,), 9.37 (s, 2H), 9.06 (s, 2H), 7.76 (d, 4H, J= 8.7 Hz), 7.62 (t, 2H, J= 7.2 Hz), 7.30 (t, 1H, J= 7.6 Hz), 7.25 (d, 4H, J= 8.7 Hz), 5.30 (s, 4H), 4.10 (dd, 2H, J= 13.6, 6.6 Hz), 1.27 (d, 12H, J = 6.3 Hz) ; ¹³ C NMR (DMSO-de): 162.31, 161.55, 159.23(d, JC-F = 249.7 Hz), 131.66 (d, Jc-F = 3.4 Hz), 130.85, 125.01 (d, JC-F = 3.6 Hz), 123.93 (d, JC-F = 14.6 Hz), 121.86, 115.28, 64.45 (d, JC-F = 3.5 Hz), 45.42, 21.76; MS: HRMS-ESI-POS.: calc for C28H34FN4O2 m/z 477.2660 (M ⁺ +1), found m/z 477.2643; analysis calc for C28H34FN4O2.2HCI.I.I9H2O): C, 58.79; H, 6.76; N, 9.79; Found: C, 58.49; H, 6.05; N, 9.85.

1, 3-Bis {(4-isopropylamidino-2-fluoro)-phenoxy methyl}-2-fluorobenzene dihydrochloride (

Reaction of l,3-bis(bromomethyl)-2-fluorobenzene (1.4 g, 5 mmol) and 2-fluoro-4- hydroxybenzonitrile (1.37 g, 10 mmol) following Method A yielded 1, 3-bis (2-fluoro-4-cyano- phenoxymethyl)-2-fluorobenzene as white solid (2.8g, 71%); mp 185-7 °C; 'H NMR (DMSO- de): 7.88 (d, 2H, J = 8.4 Hz), 7.72 (d, 8.4 Hz), 7.64 (t, 2H, J = 7.6 Hz), 7.54 (t, 2H, J= 7.6 Hz), 7.33 (t, 1H, J = 7.6 Hz), 7.23 (d, 4H, J = 8.4 Hz), 5.37 (s, 4H); ¹³ C NMR (DMSO-de): 158.50 (d, JC-F =250 Hz), 151.0 (d, JC-F =248 Hz), 150.1 (d, JC-F =1 1.0HZ), 131.1 (d, JC-F = 4.4 Hz), 130.1 (d, JC-F =3.75Hz), 124.4 (d, JC-F = 4.28Hz), 122.7 (d, JC-F =15.4Hz), 119.6 (d, JC-F = 21.4 Hz), 117.6 (d, JC-F = 3.4 Hz), 115.91 (d, JC-F = 2.25 Hz), 103.3 (d, JC-F = 8.73 Hz), 64.84 (d, Jc- F = 4.21 Hz); MS: HRMS-ESI-POS.: calc for C22Hi3F3N ₂ 0 ₂ Na»J/z 417.0827 (M ⁺ +Na), found m/z 417.0832.

Dinitrile (0.32g, 0.81 mmol) was converted to 1, 3-bis (4-isopropylamidino-2-fluoro-phenoxy methyl)-2-fluorobenzene dihydrochloride as white solid following (Method D) (0.28 g, 70%) using isopropylamine (0.14g, 2.43mmol); mp. 193-5°C; ¾ NMR (DMSO-de): 9.50 (s, 2H), 9.21 (s, 2H), 7.77 (dd, 2H, J= 11.9, 2.2 Hz), 7.69 - 7.62 (m, 4H), 7.57 (t, 2H, J= 8.6 Hz), 7.33 (t, 1H, J = 7.6 Hz), 5.39 (s, 4H), 4.10 (dt, 2H, J = 13.0, 6.5 Hz), 1.27 (d, 12H, J = 6.4 Hz); ¹³ C NMR (DMSO-de): 160.01, 158.90 (d, JC-F = 250.6 Hz), 151.95, 149.85, 149.63 (d, Jc- F = 24.1 Hz), 131.56 (d, JC-F = 2.5 Hz), 125.91 (d, JC-F = 2.9 Hz), 124.68 (d, JC-F = 3.8 Hz), 123.08 (d, JC-F = 14.5 Hz), 121.60 (d, JC-F = 7.2 Hz), 116.63 (d, JC-F = 20.9 Hz), 114.91, 64.89 (d, JC-F = 3.7 Hz), 45.13, 21.25, MS: HRMS-ESI-POS.: calc for C28H32F3N4O2 m/z 513.2472 (M ⁺ +1), found m/z 513.2450; analysis calc for C22H19F3N4O2.2HCI.I.25H2O; C, 55.31; H, 5.88; N, 9.21; Found: C, 55.39; H, 5.85; N, 8.95. Synthesis of MD-112

Synthesis Of 4,4'-(((5-methyl-l,3-phenylene)bis(oxy))bis(methylene))bis(N - propylbenzimidamide) dihydrochloride (MD-112). Dinitrile (10, 0.35 g, 0.98 mmol) was converted to 4,4'-(((5-methyl-l,3-phenylene)bis(oxy))bis(methylene))bis(N - propylbenzimidamide) dihydrochloride (MD-112) by the reaction with n-propylamine (0.14 g, 2.45 mmol) in ethanol (10 mL) at 49 °C for 24 h as white solid following method D (0.37 g, 70%). ¾ NMR (DMSO-de): d 9.90 (s, 2H), 9.53 (s, 2H), 9.18 (s, 2H), 7.79 (d, J= 8.4 Hz, 4H), 7.63 (d, J= 8.4 Hz, 4H), 6.50 - 6.48 (m, 3H), 5.19 (s, 4H), 3.41 - 3.36 (m, 2H), 2.23 (s, 3H), 1.68-1.63 (m, 4H), 0.95 (t, .7= 7.2 Hz, 6H). ¹³ C NMR (DMSO-de): d 162.5, 159.1, 142.7,

140.2, 128.5, 128.3, 127.6, 108.3, 99.7, 68.3, 44.2, 21.5, 20.9, 11.2. HRMS- calcd for C29H37N4O2 [M+H] ⁺ : 473.2917, found 473.2940.

Synthesis of MD-113 Synthesis of 2,2'-((((5-methyl-l,3-phenylene)bis(methylene))bis(oxy))bis( 4,l- phenylene))bis(l,4,5,6-tetrahydropyrimidine) dihydrochloride (MD-113). Dinitrile (10, 0.4 g, 1.12 mmol) was converted to 2,2'-((((5-methyl-l,3- phenylene)bis(methylene))bis(oxy))bis(4,l-phenylene))bis(l,4 ,5,6-tetrahydropyrimidine) dihydrochloride (MD-113) by the reaction with 1,3-diaminopropane (0.25 g, 3.4 mmol) in ethanol (10 mL) at 140 °C as white solid following method D (MD-113, 0.48 g, 75%). ¹ HNMR (DMSO-de): d 10.23 (s, 4H), 7.82 (d, J= 8.0 Hz, 4H), 7.63 (d, .7=8.0 Hz, 4H), 6.51 (s, 1H), 6.48 (s, 2H), 5.19 (s, 4H), 3.48 - 3.37 (m, 8H), 2.23 (s, 3H), 1.98-1.95 (m, 4H). ¹³ C NMR (DMSO-de): d 159.1, 158.5, 142.6, 139.9, 128.0, 127.6, 127.6, 108.3, 99.2, 68.3, 38.7, 21.4, 17.7. HRMS calcd for C29H33N4O2 [M+H] ⁺ : 469.2604, found 469.2617. 1, 3-Bis {[4-amidino-2-methoxy)-phenoxy methyl]} - 5-(tert-butyl)benzene dihydrochloride (

Reaction of l,3-bis(bromomethyl)-5-(tert-butyl)benzene (1.2g, 3.75mmol) and 2-methoxy-4- hydroxybenzonitrile (1.2g, 7.5mmol) yielded yielded 1, 3-bis (2-methoxy-4-cyano-phenoxy methyl)- 5-(tert-butyl)benzene as white solid (1.35g, 79%) following Method A. 'H NMR (CDCb): 7.41 (s, 2H), 7.31 (s, 1H), 7.23 (dd, J=8.3, 1.5 Hz, 2H), 7.11 (d, J= 1.4 Hz, 2H), 6.93 (d, J=8.4 Hz, 2H), 5.19 (s, 4H), 3.90 (s, 6H), 1.32 (s, 9H); ¹³ C NMR (CDCb) : 152.36, 152.05, 149.70, 136.07, 126.26, 124.48, 123.58, 119.18, 114.46, 113.45, 104.31, 71.17, 56.21, 34.81, 31.29; MS: HRMS-ESI-POS.: calc for C ₂₈ H ₂₈ N ₂ 04Na m/z 479.1947 (M ⁺ +Na), found m/z

479.1942.

Dinitrile (0.35g, 0.76mmol) was converted to yielded 1, 3-bis (2-methoxy-4-cyano-phenoxy methyl)- 5-(tert-butyl)benzene dihydrochloride as white solid following Method B (0.30g, 72%);¾ NMR (DMSO-de): 9.33 (s,4H), 9.04 (s, 4H), 7.55-7.46 (m, 6H), 7.35 (s, 1H), 7.28 (d,

J=9.2 Hz, 2H), 5.21 (s, 4H), 3.86 (s, 6H), 1.29 (s, 9H); ¹³ C NMR (DMSO-de): 165.11, 152.79. 151.78, 149.26, 136.74, 125.39, 122.29, 119.97, 113.35, 111.94, 70.80, 56.45, 34.91, 31.55; MS: HRMS-ESI-POS.: calc for C ₂₈ H ₃₅ N ₄ 04 m/z 479.1947 (M ⁺ +l) 491.2658, found m/z 491.2645. Synthesis of BW-MD-115 Synthesis of 4,4'-(((5-(tert-butyl)-l,3-phenylene)bis(methylene))bis(oxy) )bis(3- fluorobenzonitrile) (27). Reaction of l,3-bis(bromomethyl)-5-(tert-butyl)benzene (15, 1.5g, 4.7mmol) and 2-fluoro-4-hydroxybenzonitrile (26, 1.3 g, 9.4 mmol) yielded 4,4'-(((5-(tert- butyl)-l,3-phenylene)bis(methylene))bis(oxy))bis(3-fluoroben zonitrile) as white solid (27, 1.52 g, 75%) using method A. ¾ NMR (DMSO-de): d 7.85 (dd, J= 11.2, 1.6 Hz, 2H), 7.68- 7.66 (m, 2H), 7.50 (s, 2H), 7.44 (t, J= 8.8 Hz, 2H), 7.36 (s, 1H), 5.29 (s, 4H), 1.29 (s, 9H). ¹³ C NMR (DMSO-de): d 153.4, 151.8 (d, C-F = 186 Hz), 151.0, 135.6, 129.7 (d, C-F = 4 Hz), 125.0, 123.9, 120.0 (d, JC-F = 21 Hz), 118.0 (d, JC-F = 3 Hz), 115.4 (d, JC-F = 3 Hz), 104.6 (d, JC-F = 9 Hz), 71.5, 35.0, 31.4. HRMS calcd for C26H22F ₂ N ₂ 02Na [M+Na] ⁺ : 455.1547, found 455.1541.

Synthesis of 4,4'-(((5-(tert-butyl)-l,3-phenylene)bis(methylene))bis(oxy) )bis(3- fluorobenzimidamide) dihydrochloride (MD-115). Dinitrile (27, 0.35 g, 0.8 mmol) was converted to 4,4'-(((5-(tert-butyl)-l,3-phenylene)bis(methylene))bis(oxy) )bis(3- fluorobenzimidamide) dihydrochloride (MD-115) as brown solid following method B (0.30 g, 70.1%). ¾ NMR (DMSO-de): d 9.49 (s, 4H), 9.26 (s, 4H), 7.90 (dd, J = 12.4, 2.4 Hz, 2H), 7.81-7.79 (m, 2H), 7.52-7.50 (m, 4H), 7.39 (s, 1H), 5.31 (s, 4H), 1.28 (s, 9H). ¹³ C NMR (DMSO-de): d 164.0, 152.3, 151.0 (d, JC-F = 11 Hz), 150.8 (d, JC-F = 177 Hz), 136.0, 126.0 (d, JC-F = 3 Hz), 125.2, 124.9, 120.0 (d, JC-F = 7 Hz), 116.3 (d, JC-F = 20 Hz), 115.3, 70.9, 34.6, 31.2. HRMS calcd for C26H29F2N4O2 [M+H] ⁺ : 467.2272, found 467.2271.

Synthesis of MD-116

Synthesis of 3,3'-(((5-methyl-l,3-phenylene)bis(methylene))bis(oxy))diben zonitrile (29). Reaction of 1,3-bis (bromomethyl)-5-methylbenzene (8, 2.13 g, 7.7 mmol) and 3-cyanophenol (28, 2.05 g, 17 mmol) yielded 3,3'-(((5-methyl-l,3- phenylene)bis(methylene))bis(oxy))dibenzonitrile as white solid (29, 2.6 g, 91%) using method A. ¾ NMR (CDCh): d 7.38-7.36 (m, 2H), 7.27-7.25 (m, 3H), 7.22-7.19 (m, 6H), 5.06 (s, 4H), 2.41 (s, 3H). ¹³ C NMR (CDCh): d 158.8, 139.3, 136.6, 130.6, 128.3, 125.0, 123.6, 120.2, 118.8, 117.9, 113.4, 70.2, 21.5. HRMS calcd for C ₂₃ Hi8N ₂ 0 ₂ Na[M+Na] ⁺ : 377.1266, found 377.1250. Synthesis of 3,3'-(((5-methyl-l,3-phenylene)bis(methylene))bis(oxy))diben zimidamide dihydrochloride (MD-116). Dinitrile (29, 0.32 g, 0.9 mmol) was converted to 3,3'-(((5-methyl- l,3-phenylene)bis(methylene))bis(oxy))dibenzimidamide dihydrochloride (MD-116) as white solid using method B (0.32 g, 76%). ¾ NMR (DMSO-de): d 9.40 (s, 4H), 9.07 (s, 4H), 7.53 (t, J= 8.0 Hz, 2H), 7.47 (s, 2H), 7.41-7.34 (m, 5H), 7.26 (s, 2H), 5.16 (s, 4H), 2.33 (s, 3H). ¹³ C NMR (DMSO-de): d 165.6, 158.7, 138.5, 137.0, 130.8, 129.5, 128.5, 124.6, 120.7, 120.5, 114.5, 69.9, 21.2. HRMS calcd for C23H25N4O2 [M+H] ⁺ : 389.1978, found 389.1980.

Synthesis of MD-117

Synthesis of 4,4'-(((5-methyl-l,3-phenylene)his(methylene))his(sulfanediy l))dihenzonitrile (31). Reaction of 1,3-bis (bromomethyl)-5-methylbenzene (8, 0.93 g, 3.3 mmol) and 4- mercaptobenzonitrile (30, 1.0 g, 7.3 mmol) yielded 4,4'-(((5-methyl-l,3- phenylene)bis(methylene))bis(sulfanediyl))dibenzonitrile as white solid (1.12 g, 85%), using method A. ¾ NMR (CDCb): d 7.50 (d, J= 8.4 Hz, 4H), 7.28 (d, J= 8.4 Hz, 4H), 7.14 (s, 1H), 7.08 (s, 2H), 4.13 (s, 4H), 2.32 (s, 3H). ¹³ C NMR (DMSO-de): d 144.3, 139.0, 136.2, 132.1, 128.9, 127.1, 126.1, 118.7, 108.4, 36.7, 21.2. HRMS calcd for C23H19N2S2 [M+H] ⁺ : 387.0984, found 387.1003. Synthesis of 4,4'-(((5-methyl-l,3-phenylene)bis(methylene))bis(sulfanediy l)) dibenzimidamide dihydrochloride (MD-117). Dinitrile (31, 0.30 g, 0.74 mmol) was converted to 4,4'-(((5- methyl-l,3-phenylene)bis(methylene))bis(sulfanediyl))dibenzi midamide dihydrochloride (MD-117) as green solid following method C (MD-117, 0.19 g, 50%). ¾ NMR (DMSO-de): d 9.30 (s, 4H), 9.03 (s, 4H), 7.74 (d, J = 8.4 Hz, 4H), 7.51 (d, J = 8.4 Hz, 4H), 7.31 (s, 1H), 7.16 (s, 2H) , 4.33 (s, 4H), 2.26 (s, 3H). ¹³ C NMR (DMSO-de): d 164.9, 144.8, 138.1, 136.8,

128.6, 128.5, 126.5, 126.3, 124.1, 35.0, 20.9. HRMS calcd for C23H25N4S2 [M+H] ⁺ : 421.1521, found 421.1532.

1, 3-Bis {(4-(2-imidazolino))-thiophenoxy methyl }-5-methylbenzene dihydrochloride (MD-118)

Dinitrile (0.386 g, 1 mmol) was converted to 1, 3-Bis {(4-(2-imidazolino))-thiophenoxy methyl} -5-methylbenzene dihydrochloride as a brown solid following Method D (0.39 g, 72%) by refluxing imidate ester with 1,2 diaminoethane. 'H NMR (DMSO-de): 10.73(s, 4H), 7.96 (d, 4H, J = 8.6 Hz), 7.54 (d, 4H, J= 8.6Hz), 7.32 (s, 1H), 7.16 (s, 2H), 4.36 (s, 4H), 3.98 (s, 8H), 2.26 (s, 3H); ¹³ C NMR (DMSO-de): 164.00, 145.86, 138.05, 136.70, 129.01, 128.61, 126.32, 118.23, 44.19, 34.77, 20.88; MS:HRMS-ESI-POS.: calc for C27H29N4S2 m/z 473.1834(M ⁺ +1), found m/z 473.1842.

1, 3-Bis {(4-amidino)-phenoxy methyl }-6-methylbenzene dihydrochloride (BW-MD-119)

3-bromo-4 methylbenzoic acid (5g, 23.25mmol) was added to 50 ml dry THF in a three neck round bottom flask under Ar gas atmosphere. The temperature of this reaction mixture was cooled to 0 ^° C and a solution of 3.0 M methyl magnesium bromide (8.5ml, 25.57mmol) was added to it and stirred for 2hrs. The temperature was further lowered to -65 ^° C and 1 6M n-butyl lithium solution (29 mL, 46.5mmol) in hexane was added to it with constant stirring. After 4 h of reaction time, dry ice was added to the reaction mixture, sealed and stirred overnight. On completion of reaction, mixture was acidified and then filtered. This residue was taken with catalytic amounts of cone. H2SO4 in methanol and refluxed overnight to form the methyl ester. The reaction mixture was cooled to room temperature on completion, 10 ml water was added to it and extracted with ethyl acetate (3 X 50 mL). The organic layer was dried with anhydrous Na2S04 and concentrated in vacuo to yield Dimethyl 4-methylisophthalate as white solid (3.92g, 81%). ¾ NMR (CDCb): 8.57 (d, J= 1.7 Hz, 1H), 8.04 (dd, .7= 8.0, 1.8 Hz, 1H), 7.33 (d, , J= 8.0 Hz 1H), 3.92 (d, J= 3.2 Hz, 6H), 2.66 (s, 3H); ¹³ C NMR (CDCb): 167.34, 166.50, 145.73, 132.79, 132.12, 132.04, 129.90, 128.11, 52.36, 52.20, 22.03; MS: HRMS-ESI-POS.: calc for C11H12O4 m/z 231.0633 (M ⁺ +Na), found in z 231.0642.

Dimethyl 4-methylisophthalate (lg, 4.8mmol) in THF (20 ml) was added dropwise under ice- bath condition in a solution of lithium aluminium hydride (0.73g, 19.2mmol) in THF (30ml). The reaction was stirred for 1 h at 0 °C following which the reaction was stirred overnight at room temperature. The reaction was monitored by TLC. On completion, the reaction mixture was cooled to 0 °C and quenched with methanol and water. The quenched reaction was filtered through Celite and washed with EtOAc (50 mL). The solvent was removed under reduced pressure and was extracted with EtOAc (3 x 50 mL), dried over MgSCri and concentrated to give the required diol (4-methyl-l,3-phenylene)dimethanol (0.62g, 85%) as a white solid. %). ¾ NMR (CDCb): 7.32 (s, 1H), 7.14 (d, J= 1.8 Hz, 2H), 4.60 (d, J= 14.4 Hz, 4H), 2.29 (s, 3H); ¹³ C NMR (CDCb): 139.13, 138.71, 135.34, 130.50, 126.45, 126.24, 65.14, 63.21, 18.45; MS: HRMS-ESI-POS. : calc for C9H12O2 m/z 175.0735 (M ⁺ +Na), found in z 175.0730.

PBr ₃ (0.7mL, 7.38 mmol) was added dropwise to a solution of diol (0.51 lg, 3.35 mmol)inDCM maintained at 0°C. The reaction mixture was stirred at room temperature for 4 h and then quenched with ice water. The solution was extracted with CH2CI2 (3 x 25 mL), dried over MgS04 and concentrated to give the required dibromo compound as a white solid (0.93g, 90%). ¾ NMR (CDCb): 7.34(d, J= 1.6 Hz, 1H), 7.28-7.24 (m, 1H), 7.17(d, J= 7.8 Hz, 1H), 4.48(d, J = 12.6 Hz, 4H), 2.41 (s, 3H); ¹³ C NMR (CDCb): 137.81, 136.37, 136.10, 131.47, 130.64, 129.66, 33.10, 31.82, 18.70;

Reaction of 2,4-bis(bromomethyl)-l-methylbenzene (0.9 g, 3.2 mmol) and 4- hydroxybenzonitrile (0.84 g, 7 mmol) yielded 1, 3-bis (4-cyano-phenoxy methyl)-6-methyl- benzene as white solid (0.81 g, 72%), using method A; ¾ NMR (CDCb): 7.59(dd, J = 11.2, 8.9 Hz, 4H), 7.44 (s, 1H), 7.36-7.27 (m, 2H), 7.08-6.96 (m, 4H), 5.09(d, J= 1.6 Hz, 4H), 2.38 (s, 3H); ¹³ C NMR (CDCb): 162.05, 162.01, 137.10, 134.28, 134.21, 134.15, 133.81, 131.18, 128.02, 127.87, 119.24, 115.68, 115.59, 104.59, 104.44, 70.08, 68.74, 18.83; MS: HRMS-ESI- POS.: calc for C23H18N2O2 m/z 377.1266 (M ⁺ +Na), found m/z 377.1256.

Dinitrile (0.35 g, 1 mmol) was converted to 1, 3-bis {4-amidino (phenoxy methyl)-6-methyl- benzene dihydrochloride as brown solid following Method B (0.32 g, 70%); 'H NMR (DMSO- de):9.33 (d, J= 9.8 Hz, 4H), 9.14 (d, J= 6.6 Hz, 4H), 7.90 (dd, J= 12.8, 8.9 Hz, 4H), 7.55 (s, 1H), 7.41-7.35 (m, 1H), 7.31-7.18 (m, 5H), ), 5.23 (d, J= 7.0 Hz, 4H), 2.34 (s, 3H); ¹³ C NMR (DMSO-de): 164.73, 162.73, 162.61, 136.74, 134.52, 133.87, 130.45, 130.24, 130.20, 128.21, 127.95, 119.70, 119.59, 115.15, 115.08, 69.45, 68.36, 18.29; MS: HRMS-ESI-POS.: calc for C23H24N4O2 m/z 389.1978 (M ⁺ +1), found in z 389.1971.

Synthesis of MD-120

Synthesis of 4,4'-(((5-methyl-l,3-phenylene)bis(methylene))bis(oxy))bis(3 -fluorobenzonitrile) (32). Reaction of 1,3-bis (bromomethyl)-5-methylbenzene (8, 0.99 g, 3.6 mmol) and 3-fluoro- 4-hydroxybenzonitrile (26, 1.1 g, 7.9 mmol) yielded 4,4'-(((5-methyl-l,3- phenylene)bis(methylene))bis(oxy))bis(3-fluorobenzonitrile) as white solid (32, 1.12 g, 80%), using method A. ¾ NMR (CDCb): d 7.40 - 7.37 (m, 4H), 7.28 (s, 1H), 7.23 (s, 2H), 7.04 (t, J = 8.4 Hz, 2H), 5.17 (s, 4H), 2.40 (s, 3H). ¹³ C NMR (CDCb): d 152.2 (d, C-F = 242 Hz), 150.9 (d, c-F = 4 Hz), 139.5, 135.9, 129.7 (d, C-F = 4 Hz), 128.5, 123.6, 120.0 (d, C-F = 21 Hz), 118.0 (d, c-F = 2 Hz), 115.3 (d, C-F = 2 Hz), 104.6 (d, JC-F = 8 Hz), 71.1, 21.5. HRMS calcd for C23Hi6F2N ₂ 02Na [M+Na] ⁺ : 413.1078, found 413.1087.

Synthesis of 4,4'-((( 5-methyl-l, 3-phenylene)bis(methylene))bis(oxy))bis (3- fluorobenzimidamide) dihydrochloride (MD-120). Dinitrile (32, 0.35 g, 0.9 mmol) was converted to 4,4'-(((5-methyl-l,3-phenylene)bis(methylene))bis(oxy))bis(3 - fluorobenzimidamide) dihydrochloride as white solid following method B (MD-120, 0.32 g, 72%). ¾ NMR (DMSO-de): d 9.42 (s, 4H), 9.24 (s, 4H), 7.90 (dd, J= 12.0, 2.0 Hz, 2H), 7.78- 7.76 (m, 2H), 7.49 (t, J= 8.8 Hz, 2H), 7.38 (s, 1H), 7.29 (s, 2H), 5.30 (s, 4H), 2.35 (s, 3H). ¹³ C NMR (DMSO-de): d 163.8, 150.9 (d, JC-F = 244 Hz), 150.6 (d, JC-F = 10 Hz), 138.3, 136.2, 128.5, 125.8 (d, JC-F = 3 Hz), 124.5, 119.8 (d, JC-F = 7 Hz), 116.1 (d, JC-F = 21 Hz), 151.0, 70.3, 20.9. HRMS calcd for C23H23F2N4O2 [M+H] ⁺ : 425.1789, found 425.1777.

Synthesis of MD-123 i) K C , DMF, rt, overnight. Synthesis of 4,4'-(((5-butyl-l,3-phenylene)bis(oxy))bis(methylene))dibenz onitrile (34). A mixture of olivetol (33, 1.4 g, 8.2 mmol), 4-cyanobenzyl bromide (24, 3.53 g, 18 mmol) and anhydrous K2CO3 (3.4 g, 24.6 mmol) in 100 mL DMF was stirred at room temperature overnight. Then the reaction mixture was diluted with ice water (50 mL) and extracted with ethyl acetate (3 x 100 mL) followed by water and brine wash. The combined organic layer is dried over anhydrous Na ₂ S04, filtered, concentrated in vacuum to yield 4,4'-(((5-butyl-l,3- phenylene)bis(oxy))bis(methylene))dibenzonitrile (34) as an orange solid (34, 3.2 g, 95.0%). ¾ NMR (CDCh): d 7.67 (d, J= 8.4 Hz, 4H), 7.53 (d, J= 8.4 Hz, 4H), 6.44 (d, J= 2.0 Hz, 2H), 6.40 (t, J= 2.0 Hz, 1H), 5.09 (s, 4H), 2.56 - 2.52 (m, 2H), 1.60 - 1.57 (m, 2H), 1.33 - 1.27 (m, 4H), 0.89 (t, J= 7.2 Hz, 3H). ¹³ C NMR (CDCh): d 59.4, 146.0, 142.5, 132.5, 127.7, 118.8, 111.8, 108.0, 99.5, 69.0, 36.3, 31.5, 31.0, 22.6, 14.1. HRMS calcd for C27H ₂₆ N ₂ 02Na [M+Na] ⁺ : 433.1892, found 433.1873.

Synthesis of 4,4'-( f5-pentyl- 1 , 3-phenylene)bis (ethane-2, l-diyl))dibenzimidamide dihydrochloride (MD-123). Dinitrile (34, 0.32 g, 0.78 mmol) was converted to 4, 4'-((5 -pentyl- 1, 3-phenylene)bis(ethane-2,l-diyl))dibenzimidamide dihydrochloride (MD-123) as white solid following method C (MD-123, 0.32 g, 80%). ¾ NMR (DMSO-de): d 9.47 (s, 4H), 9.28 (s, 4H), 7.87 (d, J = 8.4 Hz, 4H), 7.65 (d, J = 8.4 Hz, 4H), 6.51 (t, J = 2.0 Hz, 1H), 6.48 (d, J = 2.0 Hz, 2H), 5.20 (s, 4H) , 2.50 - 2.46 (m, 2H), 1.55 - 1.52 (m. 2H), 1.29 - 1.20 (m, 4H), 0.84 (t, J = 6.8 Hz, 3H). ¹³ C NMR (DMSO-de): d 165.4, 159.1, 145.0, 143.4, 128.3, 127.7, 127.3, 107.6, 99.6, 68.3, 35.4, 30.9, 30.4, 22.0, 14.0. HRMS calcd for C ₂₇ H ₃₃ N ₄ 0 ₂ [M+H] ⁺ : 445.2604, found 445.2624.

Synthesis of MD-124

Synthesis of 4,4'-(((5-(trifluoromethyl)-l,3-phenylene)bis(oxy))bis(methy lene)) dibenzonitrile (36). A mixture of 5-(Trifluoromethyl)-l,3-diol (35, 0.7 g, 4.2 mmol), 4-cyanobenzyl bromide (24, 1.80 g, 9.21 mmol) and anhydrous K2CO3 (1.73 g, 12.6 mmol) in 20 mL DMF was stirred at room temperature overnight. Then the reaction mixture was diluted with ice water (50 mL) and stirred for 30 min. The grey precipitate was filtered, washed with water, and dried in air. Then the yellow solid was dissolved in a dichloromethane (100 mL), dried over anhydrous Na ₂ S04, filtered, concentrated in vacuum to afford crude product. The crude product was triturated with hexane, filtered and dried in vacuum to yield 4,4'-(((5-(trifluoromethyl)-l,3- phenylene)bis(oxy))bis(meihy\ _Q n _Q ))dib _Q nzonitFi\ _Q (36) as a grey solid (36, 1.48 g, 87.0%). Ή NMR (CDCb): d 7.70 (d, J= 8.4 Hz, 4H), 7.54 (d, J= 8.4 Hz, 4H), 6.85 (d, J= 2.0 Hz, 2H), 6.71 (t, J= 2.0 Hz, 1H), 5.13 (s, 4H). ¹³ C NMR (CDCb): 159.8, 141.5, 132.7, 127.8, 118.7, 112.3, 105.4, 104.9, 104.8, 69.4. HRMS- calcd for C23Hi ₅ N ₂ 02F3Na [M+Na] ⁺ : 431.0961, found 431.0983.

Synthesis of 4,4'-(((5-( trifluoromethyl)-!, 3-phenylene)bis(oxy))bis (methylene)) dibenzimidamide dihydrochloride (MD-124). Dinitrile (36, 0.35 g, 0.85 mmol) was converted to 4,4'-(((5-(trifluoromethyl)-l,3-phenylene)bis(oxy))bis(methy lene))dibenzimidamide dihydrochloride as pale-yellow solid following method C (MD-124, 0.3 g, 70%). Ή NMR (DMSO-de): 9.43 (s, 4H), 9.20 (s, 4H), 7.87 (d, J = 8.4 Hz, 4H), 7.68 (d, J = 8.4 Hz, 4H), 7.03

(s, 1H), 6.99 (s, 2H) , 5.32 (s, 4H). ¹³ C NMR (DMSO-de): d 165.4, 159.7, 142.5, 131.1 (q, C-F = 32 Hz), 128.4, 127.8, 127.6 (q, JC-F = 240 Hz), 122.4, 105.9, 104.2, 68.9. HRMS calcd for C23H22F3N4O2 [M+H] ⁺ : 443.1695, found 443.1687.

Synthesis of MD-125

MD-125 i) 0 °C , 10 min, HgCI ₂ , 20 h ii) TFA, DCM, rt, 2h.

Synthesis ofp-[N N”-Di(Boc)guanidino] phenol (39). / -aminophenol (37, 1.64 g, 15.0 mmol) and/V,/V'-Di(Boc)-5'-methybsothiourea (38, 2.90 g, 10.0 mmol) were stirred in THF (100 mL) for 10 minutes after which the reaction was cooled to 0°C. HgCh (2.99 g, 11.0 mmol) was added slowly to this solution and stirred for 20 h. The reaction mixture was concentrated and purified with column chromatography using 5:1 Hexane: EA as eluant to give p-[N’, N”- Di(Boc)guanidino]phenol (39) as a white solid (3.16 g, 60%). ² ¾ NMR (CDCb): d 11.61 (s, 1H), 9.96 (s, 1H), 7.01 (d, J= 8.8 Hz, 2 H), 6.58 (d, J= 8.8 Hz, 2 H),1.53 (s, 9 H), 1.44 (s, 9 H). ¹³ C NMR (CDCb): d 156.1, 155.7, 153.3, 126.7, 116.4, 84.0, 80.4, 28.3, 28.2. HRMS calcd for C17H26N3O5 [M+H] ⁺ : 352.1872, found 352.1863. Synthesis of 1 , l'-((((5-methyl-l ,3-phenylene)bis(methylene))bis(oxy))bis(4, 1 -phenylene)) diguanidine diftrifluoroacetate). Reaction of 1,3-bis (bromomethyl)-5-methylbenzene (0.36 g, 1.3 mmol),/?-[/V',/V"-Di(Boc)guanidino]phenol (39, 1.0 g, 2.84 mmol) and K2CO3 (0.54 g, 3.9 mmol) yielded 1, 3 -Bis ² -5-methylbenzene (40) as white solid (40, 0.74 g, 70%) using method A. Compound 40 (32 mg, 0.039 mmol) in DCM (2 mL) was treated with TFA (1 mL) for 2 h The solvent was removed in vacuo to yield 1, 3-Bis ² -5-methylbenzene di(trifluoroacetate) (MD-125) salt as a white solid (MD-125, 20 mg, 80%). ¾ NMR (MeOD): d 7.33 (s, 1H), 7.23 (s, 2H), 7.22- 7.20 (m, 4H), 7.09- 7.07 (m, 4H), 5.09 (s, 4H), 2.36 (s, 3H). ¹³ C NMR (MeOD): d 159.8, 158.5, 139.8, 138.7, 128.8, 128.8, 128.6, 124.8, 117.2, 71.1, 21.4. HRMS calcd for C23H27N6O2 [M+H] ⁺ : 419.2195, found 419.2212.

Synthesis of MD-126

Synthesis of 4,4'-(((5-methoxy-l,3-phenylene)bis(oxy))bis(methylene))dibe nzonitrile (42). A mixture of 5-methoxyresorcinol (41, 1.22 g, 8.7 mmol), 4-cyanobenzyl bromide (24, 3.74 g, 18 mmol) and anhydrous K2CO3 (3.6 g, 26.02 mmol) in 100 mL DMF was stirred at room temperature overnight. Then the reaction mixture was diluted with ice water (50 mL) and extracted with ethyl acetate (3 x 100 mL) followed by water and brine wash. The combined organic layer is dried over anhydrous Na2SC>4, filtered, concentrated with rotavapor and purified with column chromatography using 5:1 hexane: EA as elution buffer to yield of 4,4'- (((5-methoxy-l,3-phenylene)bis(oxy))bis(methylene))dibenzoni trile (42) as a white solid (42, 2.94 g, 71.0%). ¾ NMR (CDCb): d 7.64 (d, J= 8.4 Hz, 4H), 7.51 (d, J= 8.4 Hz, 4H), 6.18 (t, J= 2.0 Hz, 1H), 6.16 (d J= 2.0 Hz, 2H), 5.06 (s, 4H), 3.75 (s, 3H). ¹³ C NMR (CDCb): d 161.8, 160.3, 142.3, 132.6, 127.7, 118.8, 111.9, 94.7, 94.5, 69.11, 55.6. HRMS calcd for C23Hi8N ₂ 0 ₃ Na [M+Na] ⁺ : 393.1215, found 393.1201.

Synthesis of 4,4'-(((5-methoxy-l,3-phenylene)bis(oxy))bis(methylene))dibe nzimidamide dihydrochloride (MD-126). Dinitrile (42, 0.37 g, 0.99 mmol) was converted to 4,4'-(((5- methoxy-l,3-phenylene)bis(oxy))bis(methylene))dibenzimidamid e dihydrochloride as yellow solid following method C (MD-126, 0.35 g, 75%) using ammonia gas. Ή NMR (DMSO-de): d 9.44 (s, 4H), 9.23 (s, 4H), 7.86 (d, J= 8.0 Hz, 4H), 7.65 (d, J= 8.0 Hz, 4H), 6.31 (s, 1H), 6.22 (s, 2H), 5.21 (s, 4H), 3.70 (s, 3 H). ¹³ C NMR (DMSO-de): d 165.4, 161.2, 159.8, 143.2, 128.3, 127.6, 94.7, 94.1, 68.4, 55.3. HRMS calcd for C23H25N4O3 [M+H] ⁺ : 405.1927, found 405.1923.

1, 3-Bis {(4-amidino-2-fluoro)-benzyloxy}-5-(methoxy)benzene dihydrochloride (MD- 127)

A mixture of 5-(Trifluoromethyl)-l,3-diol (0.42 g, 2.4 mmol), 4-cyano2-fluorobenzyl bromide (1.07 g, 5.04 mmol) and anhydrous K2CO3 (0.99 g, 7.2 mmol) in 20 ml DMF was stirred at 45°C for 4h [TLC (Hex: EtOAc 4:1) monitored]. Then the reaction mixture was diluted with ice water (30 ml) and stirred for 30 min. The white precipitate was filtered, washed with water, and dried in air. Then the grey white was dissolved in a dichloromethane (50 ml), dried over anhydrous Na2SC>4, filtered, concentrated with rotavapor and dried in vacuum to yield 1, 3-Bis {(4-cyano 2-fluoro)-benzyloxy}-5-trifluoromethylbenzene as a white solid (0.73 g, 70 %); ¾ NMR (CDCh) : 7.67 (t, J = 7.5 Hz, 2H), 7.51 (s, 2H), 7.42 (d, J = 9.3 Hz, 2H), 6.89 (s, 2H), 6.75 (s, 1H), 5.19 (s, 4H); ¹³ C NMR (DMSO-de): 159.53(d, JC-F =251.1 Hz), 159.45, 130.13 (d, JC-F =4.4 Hz), 129.29(d, JC-F =14.0 Hz), 128.54 (d, JC-F = 4.1 Hz), 119.16 (d, JC-F =24.4 Hz), 117.30 (d, JC-F = 2.8 Hz), 113.58 (d, JC-F =9.4Hz), 105.06, 104.97(d, JC-F ₍ CF3) = 4.0 Hz), 63.42 (d, JC-F = 4.4 Hz); MS: HRMS-ESI-POS.: calc for C23Hi3N ₂ 02F5Na m/z 467.077 (M ⁺ +Na), found m/z 467.0468 .

Dinitrile (0.30 g, 0.68 mmol) was added to anhydrous EtOH saturated with hydrogen chloride (20 mL) at 0 °C in a dry flask. The reaction mixture was then sealed, slowly warmed to ambient temperature, and stirred for 7 days. Ethanol was removed using rotary evaporator. Anhydrous diethyl ether (20 mL) was added to the reaction mixture and the precipitated imidate ester dihydrochloride was filtered off and dried under high vacuum. Ammonia gas (using a cylinder) was passed through imidate ester in EtOH (10 mL) and stirred for a day. The reaction mixture was concentrated in vacuum. Then anhydrous ether was added, and the product was filtered and dried in the oil pump. The free base was converted to its dihydrochloride salt by stirring the diamidine with saturated ethanolic HC1 (2 mL) for 2-3h. The solvent was removed thoroughly and the obtained product was dried in vacuum at 80 °C for 12 h to yield 1, 3-Bis {(4-amidino2-fluoro)-benzyloxy}-5-trifluoromethylbenzene dihydrochloride as a white solid (0.3 g, 60%). ¾ NMR (DMSO-d6); Ή NMR (DMSO-dr,): 9.42 (s, 4H), 9.23 (s, 4H), 7 83 (f J= 7.2 Hz, 4 H), 7.76 (d, J= 10.5 Hz, 2 H), 7 70 (d, J= 7.9 Hz, 2 H), 7.08 (s, 1H), 7.04 (s, 211). 5.35 (s, 4H); MS: HRMS-ESI-POS.: calc for C23H20N4O2F5 m/z 479.1506 (M ⁺ +1), found m/z 479.1512.

1, 3-Bis {(4-amidino)-phenethyl}-5-trifluoromethylbenzene dihydrochloride(MD-128)

To 3,5-dibromobenzotrifluoride (1.57 g, 5.2 mmol) was added 1:1 DMF-Et3N (10 ml). To this solution, 3 mole% Pd(PPh3)4 and 4-Ethynylbenzonitrile (1.32 g, 10.4 mmol) were added and stirred for 5 minutes. Further, 6 mol% Na ascorbate solution, 1 mol% CuSCri solution in DMF were added to the reaction mixture and stirred for 4h at 80 ^° C. The reaction mixture was extracted with ethyl acetate followed by ammonium chloride and brine wash. The combined organic layer was dried over anhydrous Na2SC>4 and then concentrated invacuo. The product was purified using column chromatography and obtained using 5:1 Hexane: Ethyl acetate system as a white solid (1.23 g, 60%). ¾ NMR (CDCb) 7.88 (s, 1H), 7.79 (s, 2H), 7.70 - 7.61 (m, 8H); ¹³ C NMR (CDCb): d 137.70, 132.39, 132.36, 128.79, 127.19, 124.06, 118.40, 112.55, 90.90, 90.03; MS: HRMS-ESI-POS.: calc for C25HiiN ₂ F3Na m/z 419.0772 (M ⁺ +Na), found m/z 419.0771 .

To 10% Pd//0C in THF (30ml) under argon gas was added 4,4'-((5-trifluoromethyl-l,3- phenylene)bis(ethyne-2,l-diyl))dibenzonitrile (1.23 g, 3.1 mmol). The argon gas was exchanged for ¾ gas and the reaction mixture was stirred overnight. The reaction mixture was quenched with CH2CI2 and filtered through celite. Extraction was carried out with CH2CI2 followed by water wash. The combined organic layer was dried over anhydrous Na2S04 and then concentrated invacuo to give the product as a white solid (1.22 g, 97.3%). 'H NMR (CDCb) d 7.58 (d, J = 8.2 Hz, 4H), 7.22 (d, J = 8.3 Hz, 6H), 7.00 (s, 1H), 2.94 (s, 8H); ); ¹³ C NMR (DMSO-de): 146.56, 141.85, 132.40, 132.18, 129.40, 123.38 (dd, C-F ₍ CF3) = 7.7, 3.5 Hz) , 123.19, 123.15, 123.12, 119.04, 110.30, 37.78, 37.03); MS: HRMS-ESI-POS.: calc for C ₂₅ Hi9N ₂ F3Na m/z 427.1377 (M ⁺ +Na), found m/z 427.1398 .

Dinitrile (0.31 g, 0.76 mmol) was added to anhydrous EtOH saturated with hydrogen chloride (20 mL) at 0 °C in a dry flask. The reaction mixture was then sealed, slowly warmed to ambient temperature, and stirred for 7 days. Ethanol was removed using rotary evaporator. Anhydrous diethyl ether (20 mL) was added to the reaction mixture and the precipitated imidate ester dihydrochloride was filtered off and dried under high vacuum. Ammonia gas (using a cylinder) was passed through imidate ester in EtOH (10 mL) and stirred for a day. The reaction mixture was concentrated in vacuum. Then anhydrous ether was added, and the product was filtered and dried in the oil pump. The free base was converted to its dihydrochloride salt by stirring the diamidine with saturated ethanolic HC1 (2 mL) for 2-3h. The solvent was removed thoroughly and the obtained product was dried in vacuum at 80 °C for 12 h to yield 1, 3-Bis {(4-amidino)-benzyloxy}-5-trifluoromethylbenzene dihydrochloride as a white solid (0.31 g, 62%). ¾ NMR (DMSO-de): ¾ NMR (DMSO-de) d 9.24 (s, 4H), 9.12 (s, 4H), 7.76 (d, J = 8.2 Hz, 4H), 7.51 (m, 5H), 7.46 (s, 2H), 2.99 (s, 8H); NMR (CDCb) d 7.58 (d, J = 8.2 Hz, 4H), 7.22 (d, J = 8.3 Hz, 6H), 7.00 (s, 1H), 2.94 (s, 8H); ); ¹³ C NMR (DMSO-de): 165.40, 147.92, 142.59, 132.70, 129.05, 128.13, 125.75, 122.75, 36.46, 56.13; MS: HRMS-ESI-POS.: calc for C25H26N4F3 m/z 439.2110 (M ⁺ +1), found m/z 439.2111 .

1, 3-Bis {(4-amidino)-phenoxy methyl}-benzene dihydrochloride (DB 2559)

A mixture of 1,3-bis (bromomethyl)-benzene (1.30 g, 5 mmol) and 4-hydroxybenzonitrile (1.19, 10 mmol) used reacted using Method A, yielding 1, 3-bis {(4-cyano)-phenoxy methyl}- benzene as white solid (2.6 g, 76%); ¾ NMR (DMSO-de): 7.78 (d, 4H, J= 8.8 Hz), 7.55 (s, 1H), 7.45 (s, 3H), 7.19 (d, 4H, J= 8.8 Hz), 5.23 (s, 4H); ¹³ C NMR (DMSO-de): 161.7, 136.5, 134.2, 128.8, 127.6, 127.2, 119.1, 115.9, 103.1, 69.5; MS: HRMS-ESI-POS.: calc for C ₂₂ H ₂₂ N ₄ 0 ₂ Na m/z 363.1109(M ⁺ +Na), found m/z 363.1105. Dinitrile (0.34 g, 1 mmol) was converted to 1, 3-bis {(4-amidino) phenoxy methyl} -benzene dihydrochloride as white solid (0.35 g, 74%) following Method B; mp 168-70 °C; Ή NMR (DMSO-de): 9.35 (s, 4H), 9.18 (s, 4H), 7.91 (d, 4H, J= 8.8 Hz), 7.59 (s, 1H), 7.46 (s, 3H), 7.23 (d, 4H, J = 8.8 Hz), 5.27 (s, 4H); ¹³ C NMR (DMSO-de): 164.7, 162.5, 136.7, 130.2, 128.8, 127.6, 127.1, 119.7, 115.1, 69.5; MS: HRMS-ESI-POS.: calc for C22H23N4O2 m/z 375.1816 (M ⁺ +1), found m/z 375.1816; analysis calc for C22H22N4O2.2HCI.I.25H2O: C, 56.23; H, 5.68; N, 11.92; Found: C, 56.48; H, 5.66; N, 11.85.

1, 3-Bis {(4-(2-imidazolino))-phenoxy methyl}-benzene dihydrochloride (DB 2538)

Dinitrile (0.34 g, 10 mmol) was converted to imidate dihydrochloride, which was reacted with 1,2- diamino ethane to yield diimidazoline dihydrochloride as white solid (0.36 g, 72%) following Method D; mp 245-7 °C; ¾ NMR (DMSO-de): 10.73 (s, 4H), 8.12 (d, 4H, J =8.4Hz), 7.58 (s, 1H), 7.46 (s, 3H), 7.26 (d, 4H, J= 8.4Hz), 5.28 (s, 4H), 3.96 (s, 8H); ¹³ C NMR (DMSO- de): 163.9, 162.9, 136.6, 131.0, 128.8, 127.7, 127.2, 115.4, 114.3, 69.5, 44.0; MS: HRMS-ESI- POS.: calc for C26H27N4O2 m/z 427.2148 (M ⁺ +l), found m/z 427.2134; analysis calc for C26H26N4O2.2HCI.O.75H2O: C, 60.97; H, 5.81; N, 10.97; Found: C, 60.88; H, 5.89; N, 10.90.

1, 3-Bis {(4-(2-imidazolino))-phenoxy methyl}-5-methylbenzene dihydrochloride (MD- 129)

Dinitrile (0.354 g, 1 mmol) was converted to 1, 3-bis {4-(2-imidazolino)-phenoxy methyl-5- methylbenzene dihydrochloride as white solid following Method C (0.38 g, 72%), mp 274- 6 °C; ¾ NMR (DMSO-de): 10.9(s, 4H), 8.09 (d, 4H, J= 8.0 Hz), 7.68 (d, 4H, J= 8.0Hz), 6.52 (s, 1H), 6.49 (s, 2H), 5.22 (s, 4H), 4.0 (s, 8H), 2.42 (s, 3H); ¹³ C NMR (DMSO-de): 164.4, 159.0, 144.1, 128.9, 127.7, 121.4, 108.3, 99.3, 68.2, 44.2, 21.4; MS: HRMS-ESI-POS.: calc for C27H29N4O2 m/z 441.2291(M ⁺ +1), found m/z 441.2292; analysis calc. for C27H24N4O2.2HCI.I.55H2O: C, 60.09; H, 6.17; N, 10.39; Found: C, 60.38; H,5.99; N, 10.33.

1, 3-Bis{ (4-amidino)-phenoxy methyl}-2-fluorobenzene dihydrochloride (DB 2573) Reaction of 1, 3-bis (bromomethyl)-2-fluorobenzene (1.4 g, 5 mmol) and 4- hydroxybenzonitrile (1.19 g, 10 mmol) yielded 1, 3-bis (4-cyano-phenoxy methyl)-2- fluorobenzene as white solid (2.53 g, 70%), following method A; mp 173-5 °C; 'H NMR (DMSO-de): 7.78 (d, 4H, J= 8.4Hz), 7.59 (t, 2H, J= 7.2Hz), 7.29 (t, 1H, J= 7.2Hz), 7.23 (d, 4H, J= 8.4Hz), 5.3 (s, 4H); ¹³ C NMR (DMSO-de): 161.4, 158.4 (d, C-F = 248Hz), 134.0, 130.7 (d, c-F = 4.1Hz), 124.2 (d, C-F = 4.1Hz), 123.1 (d, C-F = 13.5Hz), 118.7, 115.6, 103.3,63.8 (d, Jc-F = 3.3Hz); MS: HRMS-ESI-POS.: calc for C22Hi5FN ₂ 02Nam/z 381.1015 (M ⁺ +Na), found m/z 381.1005. Dinitrile (0.358 g, 1 mmol) was converted to 1, 3-bis {4-amidino (phenoxy methyl)-2- fluorobenzene dihydrochloride as white solid following Method B (0.36 g, 71%); mp. 175- 7 °C; ¾ NMR (DMSO-de): 9.22 (s, 4H), 8.95 (s, 4H), 7.87 (d, 4H, J= 9.2Hz), 7.64 (t, 2H , J = 7.6 Hz), 7.31 (t, 1H, J = 7.6 Hz), 7.29 (d, 4H, J = 9.2 Hz), 5.31 (s, 4H); ¹³ C NMR (DMSO-de): 164.7, 162.4, 158.8 (d, JC-F = 248 Hz), 131.2 (d, JC-F = 3.7 Hz), 130.3, 124.6 (d, JC-F = 3.7 Hz),

123.4 (d, Jc-F = 14.5 Hz), 119.9, 115.0, 64.1 (d, JC-F = 2.98 Hz), MS: HRMS-ESI-POS.: calc for C22H22FN4O2 m/z 393.1721 (M ⁺ +Na), found m/z 393.1707; analysis calc for C22H21FN4O2.2HCLl.5H2O. O.2C4H10O 9ether): C, 54.07; H, 5.57; N, 11.07; Found: C, 54.38;

H, 5.27; N, 10.89.

I, 3-Bis {(4-(2-imidazolino))-phenoxy methyl}-2-fluorobenzene dihydrochloride (DB 2510)

Dinitrile (0.358 g, 1 mmol) was converted to di-imidazoline dihydrochloride as white solid following Method D (0.38 g, 70%); mp. 250-2 °C; ¾ NMR (DMSO-de): 10.81 (s, 4H), 8.15 (d, 4H, J = 7.6 Hz), 7.64 (t, 2H, J = 7.2 Hz), 7.33-7.30 (m, 5H, J = 7.6 Hz), 5.23 (s, 4H), 3.39 (s. 8H); ¹³ C NMR (DMSO-de): 163.8, 162.7, 154.6 (d, JC-F = 248 Hz), 130.0 (d, JC-F = 4.2 Hz),

124.4 (d, JC-F = 2.25Hz), 123.2 (d, JC-F = 15.2 Hz), 115.2, 114.4, 64.5 (d, JC-F = 3.5Hz), 43.9; MS: HRMS-ESI-POS.: calc for C26H26FN4O2 m/z 445.2034 (M ⁺ +Na), found m/z 440.2047; analysis calc for C26H25FN4O2.2HCI.I.75H2O: C, 56.88; H, 5.60; N, 10.20; Found: C, 58.99;

H, 5.63; N, 10.41.

I, 3-Bis {(4-amidino-2-fluoro)-phenoxy methyl}-2-fluorobenzene dihydrochloride (DB 2558)

Reaction of l,3-bis(bromomethyl)-2-fluorobenzene (1.4 g, 5 mmol) and 2-fluoro-4- hydroxybenzonitrile (1.37 g, 10 mmol) following Method A yielded 1, 3-bis (2-fluoro-4-cyano- phenoxymethyl)-2-fluorobenzene as white solid (2.8g, 71%); mp 185-7 °C; Ή NMR (DMSO- de): 7.88 (d, 2H, J = 8.4 Hz), 7.72 (d, 8.4 Hz), 7.64 (t, 2H, J = 7.6 Hz), 7.54 (t, 2H, J= 7.6 Hz), 7.33 (t, 1H, J = 7.6 Hz), 7.23 (d, 4H, J = 8.4 Hz), 5.37 (s, 4H); ¹³ C NMR (DMSO-de): 158.50 (d, JC-F =250 Hz), 151.0 (d, JC-F =248 Hz), 150.1 (d, JC-F =11.0HZ), 131.1 (d, JC-F = 4.4 Hz), 130.1 (d, JC-F =3.75Hz), 124.4 (d, JC-F = 4.28Hz), 122.7 (d, JC-F =15.4Hz), 119.6 (d, JC-F = 21.4 Hz), 117.6 (d, JC-F = 3.4 Hz), 115.91 (d, JC-F = 2.25 Hz), 103.3 (d, JC-F = 8.73 Hz), 64.84 (d, Jc- F = 4.21 Hz); MS: HRMS-ESI-POS.: calc for C22Hi3F3N ₂ 0 ₂ Na»J/z 417.0827 (M ⁺ +Na), found m/z 417.0832

Dinitrile (0.394g, 1 mmol) was converted to 1, 3-bis (4-amidino-2-fluoro-phenoxy methyl)-2- fluorobenzene dihydrochloride as white solid following (Method B) (0.303 g, 71%); mp. 2255- 7°C; ¾ NMR (DMSO-de): 9.27 (br, 8H), 7.88 (dd, 2H, J = 2.4 Hz, J = 12.0 Hz), 7.78 (dd, 2H, 2H, J = 1.6Hz, J = 8.4 Hz), 7.66 (t, 2H, 2H, J = 7.6 Hz), 7.61 (d, 2H, J = 8.8 Hz), 7.34 (d, 1H, J = 7.6 Hz), 5.40 (s, 4H); ¹³ C NMR (DMSO-de): 164.3, 159.35 (d, JC-F = 249 Hz), 151.31 (d, JC-F = 245 Hz), 150.88 (d, JC-F = 11.0 Hz), 152.1 (d, JC-F = 4.5 Hz), 126.33 (d, JC-F = 3.0 Hz), 125.14 (d, JC-F = 3.0Hz), 123.44 (d, JC-F = 14.0 Hz), 120.65 (d, JC-F = 7 Hz), 116.71 (d, JC-F = 21.0 Hz), 115.5, 65.42 (d, JC-F = 2.98 Hz), MS: HRMS-ESI-POS.: calc for C22H20F3N4O2 m/z 429.1533 (M ⁺ +1), found m/z 429.1536; analysis calc for C22H19F3N4O2.2HCI.O.75H2O; C, 51.32; H, 4.40; N, 10.88; Found: C, 51.47; H, 4.39; N, 10.69.

1, 3-Bis {4-(2-imidazolino)-2-fluoro)-phenoxy methyl}-2-fluorobenzene dihydrochloride (DB 2554)

Dinitrile (0.394 g, 1 mmol) was converted to di-imidazoline dihydrochloride as white solid following Method D (0.4g, 70%); mp. 218-20 °C; ¾ NMR (DMSO-de): 10.78 (br, 4H), 8.12 (d, 2H, J=12.0Hz), 8.02 (d, 2H, J=9.2Hz), 7.63 (t, 2H, J=7.6Hz), 7.58 (t, 2H, J=8.4Hz), 7.32 (t, 1H,J = 7.6Hz), 5.43 (s, 4H), 3.99 (s, 8H); ¹³ C NMR (DMSO-de): 164.2, 159.12 (d, JC-F = 250 Hz), 151.68 (d, JC-F = 247 Hz), 151.3 (d, JC-F = 10.5 Hz), 131.74 (d, JC-F = 4.5 Hz), 126.6 (d, JC-F = 3.3 Hz), 124.91 (d, JC-F = 4.5 Hz), 123.18 (d, JC-F =14.5 Hz), 116.61 (d, JC-F = 21.0 Hz), 116.3, 115.18 (d, JC-F = 7.5 Hz), 65.73 (d, JC-F = 4.0 Hz), MS: HRMS-ESI-POS.: calc for C26H24F3N4O2 m/z 481.1846 (M ⁺ +l), found m/z 481.1857; analysis calc for C2eH23F3N4O2.2HCLl.lH2O; C, 54.47; H, 4.78; N, 9.77; Found: C, 54.10; H, 4.76; N, 9.65.

1, 3-Bis { [4-(2-imidazolyl)-2-methoxy)-phenoxy methyl] }-2-fluorobenzene dihydrochloride (DB 2555)

Reaction of 1,3-bis (bromomethyl)-2-fluorobenzene (1.4g, 5 mmol) and 4-hydroxy- 2- methoxybenzonitrile (1.37 g, 10 mmol) following Method A yielded 1, 3-Bis {(4-cyano-2- methoxy)-phenoxy methyl} -2-fluorobenzene as white solid (2.8 g, 71%); mp 185-7 °C; 'H NMR (DMSO-de): 7.59 (t, 2H,J = 7.2Hz), 7.45-7.41 (m, 4H), 731-7.27 (m 3H), 5.25 (s, 4H), 3.82 (s, 6H); ¹³ C NMR (DMSO-de): 159.2 (d, JC-F = 247Hz), 152.01, 149.59, 131.91(d, JC-F = 3Hz) 126.74, 125.02 (d, JC-F = 4.0Hz), 123.77 (d, JC-F = 14Hz),l 19.64, 115.22, 113.88, 103.69, 64.76, 56.41; MS: HRMS-ESI-POS.: calc for / a m/z 441.1226 (M ⁺ +Na), found m/z 441.1237.

Dinitrile (0.418 g, 1 mmol) was converted to di-imidazoline dihydrochloride as white solid (0.43 g, 70%) following Method D; mp. 237-9 °C; ¾ NMR (DMSO-de): 10.79 (s, 4H), 7.84 (d, 2H,J= 2.0 Hz), 7.77 (dd, 2H,J= 2.0 Hz,J= 8.4 Hz), 7.62 (t, 2H,J= 7.6Hz), 7.40 (d,J = 8.4Hz), 7.32 (t, 1H,J= 7.6Hz), 5.29 (s, 4H), 3.97 (s, 8H), 3.86 (s, 6H); ¹³ C NMR (DMSO-de): 164.1, 159.01 (d, JC-F =250HZ), 152.4, 148.9, 131.5 (d, JC-F = 3.0 Hz), 124.9 (d, JC-F = 4.0 Hz), 123.0 (d, JC-F = 15.0 Hz), 122.8, 114.4, 112.8, 112.1, 64.4 (d, JC-F = 3.5 Hz), 56.2, 44.1; MS: HRMS-ESI-POS.: calc for C28H30FN4O4 m/z 505.2246 (M ⁺ +1), found m/z 505.2248; analysis calc for C28H29F3N4O4.2HCI.I.85H2O; C, 54.83; H, 5.83; N, 8.90; Found: C, 55.01; H, 5.67; N, 9.02.

Example 2. Antibacterial Activity against E. coli

The sensitization fold of select compounds of the present invention was determined. E. coli bacteria were cultured in nutrient broth at 37 °C overnight prior to treatment. Bacteria were then incubated with various concentrations of erythromycin with or without the compounds shown below for 20 hours. Bacterial density was measured based on Oϋboo. Magnitude of the sensitization (sensitization fold) was calculated based on the IC90 of erythromycin using the following formula:

Sensitization fold (SF) = IC90 of erythromycin without compounds/IC9o of erythromycin with compounds

The cytotoxicity in H9c2 (ATCC®CRL-1446™) cells was also determined. The H9c2 cells were maintained in DMEM (Dulbecco’s Modified Eagle’s Medium) supplemented with 10% fetal bovine serum (MidSci; S01520HI) and 1% penicillin-streptomycin (Sigma-Aldrich; P4333) at 37 °C with 5% CO2. The H9c2 cells were seeded in 96-well plate one day before the experiment. Different concentrations of di-ami dine compounds were added into the H9c2 cells. The cells were then incubated with the compounds for 24 hours at 37 °C with 5% CCh.The cell viability was tested by the CCK-8. Specifically, after 24 hour incubation, 10 pL CCK-8 was added to each well. After 3 hours incubation at 37 °C, the absorbance at 450 nm was recorded by a plate reader. The results for the sensitization fold and cytotoxicity are shown in Table 1.

Table 1. MIC Sensitization Activity on E. coli

Example 3. Sensitization of Escherichia Coli (Gram Negative Bacterium) to Clarithromycin

The minimum inhibitory concentration (MIC) of clarithromycin on E. coli is 50 mcg/ml. Bacteria were cultured with clarithromycin at various concentrations in the presence or absence of the bacterial sensitizer, Compound D, for 24 hours at 37 °C. Then bacterial growth density was determined by measuring Oϋboo and the results are shown in Table 2.

Compound D Table 2. MIC of clarithromycin on E. coli with different concentrations.

Example 4. Sensitization of Escherichia Coli (Gram Negative Bacterium) to Novobiocin

The minimum inhibitory concentration (MIC) of novobiocin on E. coli is 100 mcg/ml. Bacteria were cultured with novobiocin at various concentrations in the presence or absence of bacterial sensitizer, Compound D, for 24 hours at 37 °C. Then bacterial growth density was determined by measuring Oϋboo and the results are shown in Table 3.

Table 3. MIC of novobiocin on E. coli with different concentrations. Example 5. Sensitization of Escherichia Coli (Gram Negative Bacterium) to Rifampicin

The minimum inhibitory concentration (MIC) of rifampicin on A. baumannii is 5 mcg/ml. Bacteria were cultured with the antibiotic at various concentrations in the presence or absence of bacterial sensitizer, Compound D, for 24 hours at 37 °C. Then bacterial growth density was determined by measuring Oϋboo and the results are shown in Table 4.

Table 4. MIC of rifampicin on baumannii with different concentrations. Example 6: Highly potent small molecule sensitizers of Gram-negative bacteria towards existing antibiotics

Instruments and reagents. All solvents were of reagent grade and were purchased from Fisher Scientific and Aldrich. Reagents and antibiotics were purchased from Aldrich, Oakwood, or VWR. The stationary phase of chromatographic purification is silica (230 ^c 400 mesh, Sorbtech). Silica gel TLC plate was purchased from Sorbtech. 'H-NMR (400 MHz) and ¹³ C-NMR (100 MHz) spectra were recorded on a Bruker Avance 400 MHz NMR spectrometer. Mass spectral analyses were performed on an ABI API 3200 (ESI-Triple Quadruple). HPLC was performed on a Shimadzu Prominence UFLC (column: Waters Cl 83.5 mM, 4.6* 100 mm). OD6OO and fluorescence intensity was recorded on Perkin Elmer Enspire UV/ Vis/Fluorescence plate reader

Bacteria strains: E.coli (ATCC 25922), baumannii (ATCC 17978), A. pneumoniae (43816), S. maltophilia (ATCC 31559), S. typhimurium (ATCC 14028), C. werkmanii (ATCC 51114), S. aureus (ATCC 12600) and methicillin-resistant staphylococcus aureus (MRSA, ATCC 33592) strains were purchased from ATCC. NR698 was provided.

Bacteria culture and MICs determination: Gram-negative bacteria were cultured in Mueller Hinton II cation-adjusted broth. Gram-positive bacteria were cultured in LB broth. Mycobacterium smegmatis was cultured in Middlebrook 7H9 Broth. MICs of antibiotics itself were determined by performing two-fold serial dilutions of antibiotics. MICs of antibiotics in the presence of bacterial sensitizers were determined by performing two-fold serial dilutions of antibiotics with or without a constant concentration of bacterial sensitizers. The MICs tests were performed on 96-well plates with a final volume of 200 pi Mueller Hinton II cation- adjusted broth in each well. Each well was inoculated with 5 x 10 ⁵ CFU/ml bacteria and was incubated for 24 h at 37 °C with continuous shaking of 200 rpm. The bacterial density was then determined by Oϋboo. Bacterial growth % = Oϋboo of antibiotic treatment group/ Oϋboo of antibiotic non-treatment group. MICs was determined as the concentrations that inhibit more than 90% of bacteria growth.

Sensitization fold determination and FIC index calculations: Sensitization fold = MIC of antibiotic only /MIC of antibiotic with bacterial sensitizer. For example, the MIC of rifampin on E.coli is 10 pg/ml, the MIC of rifampicin in the presence of 5 pg/ml MD-124 is measured to be 0.019 pg/ml, so the sensitization fold of 5 pg/ml MD-124 on E. coli towards rifampicin is 10 pg/ml/0.019 pg/ml = 512-fold. Since the MICs were determined by performing two-fold serial dilutions of antibiotic, so the sensitization fold can is the times of 2.

FIC index between compound a and b was calculated according to the formula below:

MIC of a in combination MIC of b in combination

FIC = FICa + FICb = +

MIC of a alone MIC of b alone

FIC < 0.5: Synergy; FIC between 0.5 and 1: Additive; FIC between 1 and 2: no interaction; FIC >4: antagonism.

Bacterial resistance frequency study: E. coli was grown overnight in Mueller Hinton II cation-adjusted broth medium and concentrated to ~5 ^c 10 ⁹ CFUs/ml in Mueller Hinton II cation-adjusted broth. Then a 200 mΐ volume of ~5 ^c 10 ⁹ CFUs/ml (equal to 1 x 10 ⁹ CFUs) was then transferred onto solid Mueller Hinton agar plates (100 mm Petri dishes) containing antibiotic 2- to 6-times the MIC, with or without 10 pg/ml MD-124. Then the plates were incubated at 37 °C for 48 h. Then the colonies formed on the plate were recorded and resistant frequency was calculated. Resistance frequency towards antibiotics or MD-124 and antibiotics combination were calculated by dividing the number of colonies formed after a 48 h by total CFUs inoculated on the plates initially. The resistance frequency calculation towards MD-124: For trovafloxacin and MD-124 combination, 2, 3 and 4 times of MIC of trovafloxacin was used and each combination has 3 replicates. So, for trovafloxacin and MD-124 combination, it is 3 combination conditions with each condition having 3 replicates, and the amount of CFUs tested is: 10 ⁹ CFUs per agar plates x 3 replicates per combination condition x 3 combination conditions = 9 x 10 ⁹ CFUs. The amount of CFUs tested for the novobiocin/MD-124 and clindamycin/MD-124 combination is the same. So, together 2.7 x 10 ¹⁰ CFUs were tested in the MD-124 and antibiotics combination. There are colonies that were resistant MD-124 and antibiotic combination. To find out whether those resistant strains are resistant to MD-124 or antibiotics, those colonies were then subjected to another antibiotic combination: MD-124 and rifampicin. It turned out that MD-124 was still able to sensitize those resistant strains towards rifampicin with the same potency on wild-type E. coli, which demonstrated those 6 combinational therapy resistant strains are not resistant to MD-124. No strain was found to be resistant to 10 pg/ml MD-124 out of 2.7 x 10 ¹⁰ CFUs.

The resistance frequency towards MD-124 was calculated to be:

< 1

< 3.7 x 10 -11

2.7 x 10 ¹⁰

Lysozyme assay to evaluate the disruption of Gram-negative bacteria out membrane by bacterial sensitizers. Lysozyme assay was performed based on literature reported method. E. coli was cultured in Mueller Hinton II cation-adjusted broth for overnight, centrifuged at 3000 g for 10 min, washed with HEPES buffer (pH = 7.2) and then centrifuged again to obtain bacteria pallet. The pallet was then gently resuspended in HEPES buffer with 5 mM NaCN to obtain an E. coli suspension with Oϋboo between 0.8-1.0. On a 96-well plate, each well was supplied with 100 pi lysozyme solution (100 pg/ml) containing 50 or 100 pg/ml bacterial sensitizers in HEPES buffer. To each well was added 100 mΐ E. coli suspension. The final concentration of lysozyme was 50 pg/ml. The plate was incubated at room temperature for 10 min and the Oϋboo was recorded. E. coli was also incubated with bacterial sensitizers in the absence of lysozyme to test if bacterial sensitizers would directly induce bacterial lysis. E. coli that was incubated with lysozyme alone or E. coli without any treatment were also used as negative control.

Evaluation of the influence of exogenous LPS and Mg ²⁺ on bacterial sensitizers.

The MICs of bacterial sensitizer and antibiotic combination in the presence of LPS (ranging from 0 to 40 mM) or Mg ²⁺ (ranging from 0 to 20 mM) was determined as described above (Bacteria culture and MICs determination section). Construction of MCR-1 and NDM-1 expressing E.coli strain. E. coli (ATCC 25922) was transformed with pGDP2 MCR-1 (Addgene, pGDP2 MCR-1, plasmid #118404) to generate colistin resistant strains. E. coli (ATCC 25922) was transformed with pGDPl NDM- 1 (Addgene, plasmid # 112883, pGDPl NDM-1) to generate strains that are resistant to a broad range of b-lactam antibiotics. The successful construction of the MCR-1 and NDM-1 over expression E.coli strains were validated by their increased resistance towards polymyxin B and b-lactam antibiotics (ampicillin, ceftazidime and meropenem) respectively.

Direct comparison of the antibiotic uptake in the presence and absence of MD-100 through HPLC study. E. coli (ATCC 25922) was cultured in Mueller Hinton II cation- adjusted broth for overnight at 37 °C to reach a density of OD6oo of 0.8 to 1.0. To 20 ml fresh Mueller Hinton II cation-adjusted broth was added 50 pi E. coli stock, 200 mΐ 5 mg/ml ( -CTT novobiocin and 100 mΐ 10 mM MD-100. In the other group, the same amount of E. coli stock, O-CH3 novobiocin was used in the absence of MD-100. Then E. coli was incubated for 20 h at 37 °C with continuous shaking of 200 rpm. After, the E. coli suspension was centrifuged at 3000 g for 10 min and the culture media was removed to obtain bacteria pallet. The pallets from the two groups was re-suspended in PBS to reach the same Oϋboo of 2.0. To this E. coli suspension was spiked with 10 mM internal standard. 1 ml A. coli from each group in PBS was lysed by sonication on ice for 15 min, followed by adding 2 ml MeOH, the mixture was then centrifuged at 3000 g for 5 min and the supernatant was analyzed by HPLC. 20 mΐ of each sample was injected into Shimadzu Prominence UFLC (column: Waters C18, 3.5 mM, 4.6x100 mm, injection loop volume: 20m1). The mobile phase was acetonitrile (ACNjTBO (with 0.05% trifluoroacetic acid in the aqueous) with ratios defined as: 20%~55% ACN, 0~10min; 55%~65% ACN, 10-20 min; 65%~20% ACN, 20-25 min. The internal standard used here is novobiocin because novobiocin have a very similar structure and chemical property compared with the analyte O-CH3 novobiocin.

Dansyl-PMBN displacement assay. Dansyl-PMBN was synthesized according to literature procedure. Dansyl-PMBN was dissolved in H2O to make 500 mM stock. Bacterial sensitizers were dissolved in ethanol to make 10 mM stock solutions. E. coli (ATCC 25922) was cultured in Mueller Hinton II cation-adjusted broth for overnight 37 °C. The E. coli stock was centrifuged at 3000 g for 10 min, washed with HEPES buffer (pH = 7.2) and then centrifuged again to obtain bacteria pallet. The pallet was then gently resuspended in HEPES buffer to obtain a E. coli suspension with Oϋboo about 0.3. The experiment was performed on 96-well plates. Each well was supplied with 100 mΐ coli suspension with 10 mM Dansyl-PMBN, then to each well, different concentrations of bacterial sensitizers were added to achieve a final concentration ranging from 0 to 200 mM. Then the mixture was incubated at room temperature for 3 min and the fluorescence intensities with different concentration of bacterial sensitizers were recorded (E _x = 340 nm; E _m = 520 nm).

Cytotoxicity test of bacterial sensitizers on mammalian cells. Cell viability was assessed by using Cell Counting Kit-8 (CCK-8, Dojindo, Japan). HEK293 or NIH3T3 cells were seeded in a 96-well plate one day before the experiment to reach 80% confluency. Cells were then incubated with various concentration of bacterial sensitizers at 37 °C with 5% CCh for 24 h, then 10 pL of CCK-8 solution was added to each well, and the plate was incubated for an additional at 37 °C 2 h with 5% CCh. The optical density at 450 nm was recorded by plate reader; and the results were calculated as a percentage of viability compared with the untreated control.

Development of Gram-Negative Bacteria Sensitizers

Compounds were synthesized and tested for their ability of sensitizing E.coli towards narrow-spectrum antibiotics (Tables 5A and 5B). Table 5A shows the structures of the compounds and Table 5B shows the activities, sensitization, and cytotoxicity of compounds.

Table 5A

Bacteria strains (as indicated in Table 5B) were cultured with rifampicin at various concentrations in the presence or absence of 10 mM of the indicated compound for 20 h at 37 °C. The MIC, sensitization, cytotoxicity, and MIC on mycobacteria were tested according to methods described herein. As described herein, the sensitization fold refers to the ability of the compound to lower the MIC of the antibiotic (e.g., rifampicin or erythromycin) on certain bacteria strains. The sensitization activities of compounds on B. subtilis were tested using erythromycin. The sensitization activities of compounds on MRSA were tested using rifampicin. The sensitization activities of compounds on E .coli were tested using rifampicin. The results are shown in Table 5B.

Table 5B

Select data from Table 5B are described below (Table 6). Sensitization fold of 10 mM compounds was tested on bacteria using rifampicin as the antibiotic; IC50 was tested on HEK293 cells. MD-129, 113,102,106 and 112 showed no sensitization activity at up to 10 mM.

Scheme 1. Structures of bacterial sensitizers synthesized and evaluated.

R D-100: X = O; Y = CH ₂ ; Ri = CH ₃ ; R ₂ = H

MD-100 ^' g ^NH2 MD-102 D-109: X = CH ₂ ; Y = O; R ₁ = CH ₃ ; R ₂ = H

NH D-103: X = O; Y = CH ₂ ; R ₁ = CH ₃ ; R ₂ =

MD-129 / W MD-112 CH ₃ D-126: X = CH ₂ ; Y = O; R ₁ = OCH ₃ ; R ₂ = H MD-106 D-124: X = CH ₂ ; Y = O; R ₁ = CF ₃ ; R ₂ = H D-120: X = O; Y = CH ₂ ; R ₁ = CH ₃ ; R ₂ = F

MD-125 D-108: X = CH ₂ ; Y = CH ₂ ; R ₁ = CH ₃ ; R ₂ = H

NH D-117: X = S; Y = CH ₂ ; R ₁ = CH ₃ ; R ₂ = H D-105: X = O; Y = CH ₂ ; R ₁ = t-butyl; R ₂ = H D-123: X = CH ₂ ; Y= O; R ₁ = n-butyl; R ₂ = H D-115: X = O; Y = CH ₂ ; R ₁ = t-butyl; R ₂ = F

E. coli was cultured with rifampicin at various concentrations in the presence or absence of 5 pg/ml MD-124 for 20 h at 37 °C. Then bacterial growth density was determined by measuring Oϋboo. Several compounds were capable of sensitizing E.coli towards narrow- spectrum antibiotics, with some by 32-fold at 10 pg/ml or less (Table 7).

Table 6

BW-MD-124 (MD-124) showed superior bacterial sensitization activities and was chosen for further biological evaluation (Figure 1A). MD-124 at a concentration of 5 pg/ml was able to sensitize E. coli toward rifampicin by 512-fold, lowering the MIC of rifampicin from 10 to 0.02 pg/ml (Figure IB). E. coli (5 ^c 10 ⁵ CFUs/ml) was then cultured in the absence and presence of 5 pg/ml MD-124 and OD6oo at different time points were recorded. MD-124 itself at the same concentration showed no effect on bacterial growth (Figure 1C). These results demonstrate that MD-124 has no direct bacteriostatic effect and works as adjuvant to other antibiotics. Table 7

A checkerboard assay shows that MD-124 sensitizes E. coli toward rifampicin in a concentration-dependent manner, reaching over 16,000-fold when ~10 pg/ml MD-124 was used with a MIC of rifampicin being 0.6 ng/ml (Figure ID). The fractional inhibitory concentration (FIC) index was calculated to be 0.09 based on the checkerboard assay (The MIC of MD-124 itself on E. coli is 50 pg/ml), indicating the strong synergistic effect between MD- 124 and rifampicin. The sensitization ability of MD-124 changed drastically in the range of 3 to 12 pg/ml, and as a result, a checkerboard assay of MD-124 varying from 0 to 10 pg/ml was performed (Figure IE). 5 pg/ml MD-124 sensitizes E. coli toward a broad range of existing antibiotics including narrow spectrum antibiotics such as clarithromycin (256-fold), erythromycin (128-fold), novobiocin (64-fold) and broad-spectrum antibiotics like trovafloxacin (32-fold), polymyxin B (32-fold) and chloramphenicol (8-fold) (Figure 1H and Table 8). A greater sensitization fold was achieved when MD-124 was used with narrow- spectrum antibiotics than broad-spectrums. When combined with MD-124, the MIC of various narrow-spectrum antibiotics tested was lowered to around 1 pg/ml or below, which is similar to the MIC with broad-spectrum antibiotics on E. coli (Figure 1H and Table 8). Compared with previously discovered bacterial sensitizers such as pentamidine and polymyxin B nonapeptide (PMBN), MD-124 showed much more potent sensitization activity (Figure 1G). For example, 20 pg/ml pentamidine and PMBN were shown to sensitize E.coli towards rifampicin by 4 and 16 -fold respectively, while 5 pg/ml MD-124 was able to sensitize by 512- fold. Besides E. coli, MD-124 also showed sensitization effect in various other Gram-negative bacterial strains such as A. baumannii, K. pneumoniae and S. typhimurium, the resistant strains of which are listed as WHO priority 1 pathogens in urgent need of new antibiotics (Figure IF).

Table 8

Resistance Frequency of MD- 124

Because bacteria can quickly develop resistance to new antimicrobial agents, the frequency of resistance development for ? coli towards MD-124 was evaluated. Briefly, E. coli was cultured with various concentrations of antibiotic (2 to 7-fold of MIC) in the presence and absence of 10 pg/ml MD-124. Then, the bacterial resistance frequency towards MD- 124/antibiotic combination and antibiotic itself was calculated (Figure 2D). E. coli showed 2 to 3 orders of magnitude lower resistance frequency towards MD-124/antibiotic combination than the antibiotic itself (Figure 2). For colonies that were resistant MD-124 and antibiotic combination, there is a need to determine whether the resistant strains were resistant to MD- 124 or antibiotics used in the combination. As a result, the combination therapy resistant colonies were then subjected to another antibiotic combination: MD-124 and rifampicin (Figure 2B). MD-124 was still effective in sensitizing those strains towards rifampicin with the same potency as on wild-type E. coli. Such results demonstrate that these resistant strains are not resistant to MD-124. No strain was found to be resistant to 10 pg/ml MD-124 out of 2.7 x 10 ¹⁰ CFUs, giving a resistant frequency of < 1/2.7 ^c 10 ¹⁰ (< 3.7 xlO ¹¹ ). The resistance frequency here is not defined based on direct inhibition/bactericidal effect like the case of traditional antibiotics but based on the sensitization effect of MD-124. These studies show: 1) MD-124 is able to lower the resistant frequency of bacteria towards antibiotics when used in combination; 2) bacteria show lower resistant frequency towards MD-124 than toward the antibiotic; and 3) even bacteria showing resistance towards one type of antibiotic/ MD-124 combination, a simple switch to another antibiotic/MD-124 combination would re-gain the sensitization effectiveness towards the resistant strains.

Mechanism of Bacterial Sensitization Activity

The mechanism of the bacterial sensitization activity was then investigated. Because MD-124 can sensitize Gram-negative bacterial towards a broad range of antibiotics and the outer membrane is the major barrier of antibiotic uptake, MD-124’s ability to disrupt bacterial outer membrane was determined (Figure 3A). MD-124 and MD-100 were used to study the sensitization mechanisms. MD-124 showed compromised ability to sensitize an outer membrane “leaky” mutant of E. coli strain NR698 (Figure 3B), which is already susceptible to narrow-spectrum antibiotics such as clarithromycin and erythromycin. MD-124 at a concentration of 5 pg/ml was shown to sensitize wild-type E. coli towards clarithromycin by 256-fold, andNR698 by 4-fold. The same phenomenon was observed when MD-100 was used on wild-type and NR698 E. coli (Figure 7). Such results demonstrate if a bacterial strain already has increased permeability because of compromised outer membrane integrity, the sensitization ability of MD-124 and MD-100 would be diminished. This is consistent with the sensitization mechanism of MD-124 being on the bacterial outer membrane. The disruption of bacterial outer membrane by MD-124 through the lysozyme assay was then determined. Briefly, lysozyme (14 KDa) can break down peptidoglycan and lead to bacterial lysis. However, lysozyme cannot penetrate intact Gram-negative bacterial outer membrane. With impaired Gram-negative bacterial membrane, lysozyme would be able to diffuse across the disrupted membrane and enzymatically cleave peptidoglycan, leading to bacterial lysis. In the presence of 25 pg/ml MD-124 or 50 pg/ml MD-100, lysozyme resulted in quick bacterial lysis while in the absence of the sensitizer, no cell lysis was observed (Figure 3C, left histogram in each pair). MD-124 and MD-100 themselves did not lead to bacterial lysis (Figure 3C, right histogram in each pair). These results indicate that MD-124 was able to disrupt membrane integrity. 25 pg/ml polymyxin B and 50 pg/ml pentamidine, which were used here as positive controls, also led to bacterial lysis when incubated together with lysozyme. 25 pg/ml MD-124 showed a similar potency as 25 pg/ml polymyxin B and was much more potent than 50 pg/ml pentamidine in disrupting bacterial outer membrane. The results also showed a positive correlation between the ability of the various bacterial sensitizers to disrupt outer membrane in the lysozyme assay and their ability to sensitize E. coli towards rifampicin (Figure 3D, the structure and sensitization fold of those bacterial sensitizers can be found in Scheme 1 and Table 6). Outer membrane disruption ability was based on lysozyme assay as described above and all bacterial sensitizer were used same concentration. 25 pg/ml bacterial sensitizers were used in the lysozyme assay. The bacterial sensitization activity was measured based on the sensitization fold on E.coli towards rifampicin, which was listed in detail in Table 1. MD- 102,106 and 129 fails to sensitize E.coli, thus the sensitization fold was determined as 1.

Next, the intracellular concentration of an antibiotic in the presence and absence of MD- 100 were compared to assess membrane permeabilization by MD-100. The concentration of antibiotic inside the bacteria was directly measured by analyzing bacterial lysates using HPLC after treatment with and without MD-100. As shown in Figure 3E, the relative intracellular concentration of an inactive novobiocin analog (0-methyl novobiocin, Scheme 2) was greatly increased in the presence MD-100. 0-Methyl novobiocin, which is inactive, was used in order to avoid bacterial killing after intracellular enrichment. Collectively, these results show that MD-124 sensitizes bacteria by permeabilizing membrane and allowing for increased antibiotic entry.

Scheme 2

Molecular Mechanistic Studies of Bacterial Sensitizers

Various experiments were then conducted to examine the molecular target(s). Adding extra LPS to the culture media abolished the sensitization effect of MD-124 and MD-100 (Figure 4A, Table 9 and Figure 7B). Briefly, E. coli was treated with 5 pg/ml MD-124 (about 10 mM) with varying concentrations of LPS (from 0 to 40 mM) for 20 h. Then Oϋboo was measured. The MIC of rifampicin only is 10 mg/ml.

Table 9

Mg ²⁺ dampened the bacterial sensitization activity of MD-124 on E. coli in a concentration dependent manner (Figure 4B, Table 10). Briefly, E.coli was treated with 5 pg/ml MD-124 (about 10 mM) with varying concentrations of Mg ²⁺ (from 0 to 15 mM) for 20 h. Then OD6oo was measured. The MIC of rifampicin only is 10 pg/ml.

Mg ²⁺ can bridge between adjacent lipid A and enhance the membrane integrity. Thus, high concentrations of this divalent cation may displace the diamidine and thus exert antagonistic effects against MD-124. This phenomenon was also observed on MD-100. The culture medium for E.coli is Muller Hinton Broth (Cation adjusted), which already has at least 0.5 mM Mg ²⁺ , so the “zero concentration point of Mg ²⁺ ” in Figure 4B represents the amount of exogenous Mg ²⁺ , not the total Mg ²⁺ in the culture medium. The free magnesium concentration in human blood is between 0.55-0.75 mM, indicating that physiological concentrations of Mg ²⁺ would not affect the sensitization ability of MD-124. A fluorescent conjugate of a polymyxin-B derivative (Dansyl-PMBN, Scheme 3), which would show increased fluorescent intensity after binding to the lipid A part of LPS, was used to further probe this issue. In the presence of another component that can also binding to lipid A, Dansyl- PMBN would be replaced, leading to decreased fluorescent intensity.

Table 10

Scheme 3

With the incremental addition of MD-124 to a mixture of E. coli and 10 mM Dansyl- PMBN, the fluorescent intensity of Dansyl-PMBN steadily decreased in a concentration dependent fashion, indicating binding of MD-124 to lipid A (Figure 4C). Pentamidine and MD-100 were also able to displace Dansyl-PMBN although not as much as MD-124. A mutant of the lipid A strain was constructed with an over-expression mobilized colistin resistance -1 ( mcr-1 ) gene, which would modify the phosphate group on lipid A, induce decreased negative charge density on Gram-negative bacteria outer membrane and lead to the resistance to colistin. ²⁶ · ²⁷ Two mcr-1 over-expressing strains, mcr-1 A and mcr-1 B were used to test the response of MD-124 towards the modified lipid A. The MIC of polymyxin B on these two strains were 10 and 30 pg/ml respectively, while the MIC on the wild type was 1.2 pg/ml (Table 11) Table 11

While 3 mg/ml MD-124 sensitized wild type E. coli towards rifampin by 16-fold, it was only able to sensitize mcr-1 B strain by 4-fold, and 5 pg/ml MD-124 were required to re-gain 32-fold sensitization on mcr-1 B strain (Figure 4E). This showed decreased activity for MD- 124 when lipid A was modified, supporting lipid A being the molecular target of MD-124. It is worth mentioning that 3 pg/ml MD-124 was still able to sensitize mcr-1 A (MIC 10 pg/ml) strains towards rifampin by 32-fold, which means mcr-1 stains with this level of resistance of polymyxin B did not achieve resistance towards MD-124 (Figure 4E). The clinical isolated mcr-1 over-expressing strains usually have a MIC of 10 pg/ml or below for polymyxin B, indicating MD-124’s effectiveness on clinical those strains. Even those mcr-1 strains that showed greater resistance towards polymyxin B (MIC 30 pg/ml) only induced mild resistance towards MD-124, raising the concentration required for 32-fold sensitization from 3 to 5 pg/ml. Collectively, these results not simply demonstrate that lipid A is the molecular target of MD- 124, but also suggest a therapeutic potential of MD-124 in the fight colistin resistant bacteria induced by mcr-1. MD-124 was also found to sensitize mcr-1 over-expressing stains towards many other antibiotics besides rifampicin (Table 16).

The sensitization effect of MD-124 on various clinically relevant strains and drug- resistant strains, especially the Gram-negative bacteria in ESKAPE category of pathogens, was then examined. Checkerboard assays revealed MD-124 was able to sensitize A. baumannii towards rifampicin, decreasing the MIC from 5 pg/ml to 0.04 and 0.01 pg/ml when 5 and 7 pg/ml of the sensitizer were used respectively (Figure 5A). The FIC index between MD-124 and rifampicin was calculated to be 0.14. Similar sensitization effect on A. baumannii was also observed with novobiocin through a checkerboard assay and the FIC index between MD-124 and novobiocin was determined to be 0.20 (Figure 5B). 5 pg/ml MD-124 also sensitized A. baumannii towards a variety of other antibiotics such as clarithromycin, fusidic acid and clindamycin, achieving 64, 128 and 8-fold sensitizations, respectively (Table 12). Table 12

Another ESKAPE pathogens - K. pneumoniae, was also susceptible to MD-124. As shown in Figure 5 C and D, MD-124 was able to sensitized pneumoniae towards rifampicin and clarithromycin by 512-fold or more; 10 pg/ml of MD-124 brought the MIC of rifampicin and clarithromycin from more than 20 pg/ml to 0.2 pg/ml or less. FIC index between MD-124 and rifampicin or clarithromycin was determined to be 0.15 and 0.16, respectively. Many other antibiotics can also be combined with 5 pg/ml MD-124 such as clindamycin, chloramphenicol, fusidic acid and novobiocin to inhibit d. pneumoniae growth (Table 13). Table 13

Carbapenem-resistant Enterobacteriaceae is causing rising concerns and is listed as WHO priority 1 pathogens for R&D of new antibiotics. To test the effect of MD-124 on carbapenem-resistant bacteria, NDM-1 expressing E. coli strain was constructed to induce carbapenem-resistance. Compared with wild-type, NDM-1 expressing E. coli strain showed a 30 to 100-fold increase of MIC towards b-lactam antibiotics such as ampicillin, ceftazidime and carbapenem antibiotics meropenem (Table 14 and Table 12).

Table 14 NDM-1 expressing E. coli strain did not show significant changes in MIC towards other family of antibiotics compared with the wild type (Table 15 vs Table 8). MD-124 was able to sensitize NDM-1 expressing E. coli strain with the same potency as for the wild-type E.coli. MD-124 sensitized NDM-1 expressing E. coli towards rifampicin in a concentration-dependent manner, decrease the MIC from 10 to 0.02 and 0.012 pg/ml when 5 and 10 pg/ml were used (Figure 5E). MD-124 also showed synergistic effect with rifampicin as the FIC index calculated to be 0.09. MD-124 sensitized carbapenem-resistant E. coli towards other narrow- spectrum antibiotics such as clarithromycin, novobiocin and broad-spectrum such as trovafloxacin, chloramphenicol (Table 15).

Table 15

Polymyxin and colistin-resistant strains induced by mcr-1 gene are threatening the last line of defense of antimicrobial treatment. It was observed that MD-124 sensitized mcr-1 expressing E. coli (MIC of polymyxin B is 30 pg/ml) towards rifampicin and several other antibiotics (Figure 5F, Table 16).

Table 16

MD-124 showed synergistic effect with rifampicin on mcr-1 expressing E. coli as the FIC index calculated to be 0.37. It is worth noting that compared with wild-type E. coli, MD- 124 showed slightly deceased sensitization ability on this mcr-1 expressing strain (Figure ID vs Figure 5F). However, 5 pg/ml MD-124 still brought the MIC of rifampicin and clarithromycin to 0.2 pg/ml or below on this mcr-1 induced polymyxin B resistant strain. Surprisingly, MD-124 sensitized this strain towards polymyxin B, bringing the MIC from 30 to 1 mg/ml. Such results mean that MD-124 was able to convert this polymyxin B resistant strain to a polymyxin B sensitive strain (Figure 8).

The effect of MD-124 in an ex vivo skin bum infection model was determined. To achieve topical application, compounds were formulated as hypromellose gel. Briefly, human skin (about 1cm ^c 1cm) was burnt with a soldering iron (95 °C) for 10 s; then 10 ⁵ CFU E. coli was inoculated to the burnt skin and was cultured at 37 °C for 1 hour. After that, skin was loaded with hypromellose gel with different antibiotics and cultured at 37 °C for 24 hours. After 24 hours incubation, the skin sample was homogenized and the supernatants were serially diluted and plated on agar plates, from which bacterial counts on the skin was calculated. While neither 4%o (w/w) novobiocin nor 1.5%o MD-124 themselves achieved significant E. coli growth inhibition, novobiocin and MD-124 combination effectively decreased the bacterial load when compared with vehicle group (Figure 6A). l%o polymyxin B hypromellose gel was used as positive control. To further investigate the scope and effectiveness of MD-124, a MD- 124 and clindamycin combination was tested on drug-resistant Gram-negative bacteria. MD- 124 and clindamycin can also effectively treat skin infection caused by NDM-1 expressing E. coli, which reduce the bacteria load for more than 1,000-fold than clindamycin alone (Figure 6B). The dosages used are comparable to or lower than the commonly used 0.5 ~ 2% antibiotics in ointment preparations.

MD-124 was shown to restore the effectiveness of polymyxin B towards E. coli expressing mcr-1. Specifically, it was investigated whether a MD- 124-polymyxin B combination would be effective in treating MCR-1 bacterial infection in this skin-bum model (Figure 6C). Polymyxin B alone (3%o, w/w) only had minor effects as compared with vehicle group (Figure 6C). In contrast, the MD- 124-polymyxin B combination (3%o (w/w) polymyxin B and 1.5%o (w/w)) reduced the bacterial load by ~ 200-fold (Figure 6C). Taken together, these results showed that the sensitization effect of MD-124 allows the use of narrow-spectrum antibiotics in treating Gram-negative bacterial infection and restores the sensitivity of drug- resistant strains towards tested certain antibiotics.

The effect of phosphatidylcholine on MD-124 sensitization activity was also determined. E. coli was treated with 10 mM MD-124 (about 5 pg/ml) and rifampicin combination with varying concentrations of phosphatidylcholine (from 0 to 320 mM) for 20 h at 37 °C, then the OD6oo was measured and the sensitization folds were calculated as mentioned above. The results are shown in Figure 9. Example 7. Antibacterial Activity against MRSA

The sensitization fold of select compounds described herein on Gram-positive bacteria was determined.

DB2560 (also refered as MD-100 herein and shown above) sensitizes Gram-positive bacteria such as B. subtilis towards traditional antibiotics. The MIC of DB2560 on wild type B. subtilis is 50 pg/ml. As shown in Figure 10A, 5.5 pg/ml of DB2560 alone (i.e., without any additional antibiotic) failed to significantly impact bacterial growth (80% growth density compared with the control (no treatment) group). The MIC of rifampicin on B. subtilis in the presence of 5.5 pg/ml of DB2560 was 0.037 pg/ml, a concentration at which rifampicin has litle inhibition effect. The sensitization fold and FIC index was calculated to be 256-fold and 0.11. The MIC of erythromycin in the presence of and absence of DB2560 was determined to be 1.5 and 50 pg/mL, which gave DB2560 a 32-fold sensitization and a FIC index of 0.14. A concentration of 5.5 pg/ml DB2560 sensitizes B. subtilis towards a wide range of antibiotics with distinct anti-microbial mechanisms, such as clindamycin (16-fold), clarithromycin (32- fold), novobiocin (4-fold), methicillin (4-fold), entrapenem (4-fold), trovafloxacin (8-fold).

The fact that DB2560 significantly sensitizes B. subtilis towards rifampicin, erythromycin and clindamycin indicates Gram-positive bacteria membrane are a very effective barrier for those antibiotics. DB2560, at a concentration of 2.7 pg/ml, sensitized MRSA towards existing antibiotics such as rifampicin (32-fold) (Figure 10B) and trovafloxacin (16- fold). Rifampicin is the first line of defense against MRSA and many MRSA strains become resistant to rifampicin through overexpression of efflux pumps and other mechanisms. The combination of the bacterial sensitizers as described herein, such as DB2560, and rifampicin can be used more as a more effective therapeutic against MRSA.

The MIC of many antibiotics such as erythromycin, rifampicin, and trovafloxacin on MRSA is significantly higher than wild type E. coli, which means even narrow-spectrum antibiotics such as rifampicin, a first-line of defense of MRSA, can cause severe collateral damage to benign Gram-negative bacteria like E. coli before it can kill MRSA. As a proof of concept, the relative ratio of E. coli and MRSA or B. subtilis and MRSA was measured with and without MD-108 (Figure 11A and B). Trovafloxacin (16 ng/ml) would prefer the inhibition of E. coli, leaving MRS A the dominant species (78% of the bacteria population). When supplied with 1.5 pg/ml MD-108 and 8 ng/ml trovafloxacin, the MRSA inhibition was achieved, leaving E. coli as the dominant species (89% of the bacteria population). Under 16 ng/ml trovafloxacin, the relative survival ratio between B. subtilis and MRSA is 1:1, while under 8 ng/ml trovafloxacin and 1.5 pg/ml MD-108, B. subtilis would dominate the composition (99.5 %).

Although the foregoing invention has been described in some detail by way of illustration and example for the purposes of clarity of understanding, it will be readily apparent to one of ordinary skill in the art in light of the teaching of this invention that certain changes and modifications may be made thereto without departing from the spirit and scope of the invention as defined in the appended.