RELATED APPLICATION

This application claims priority to U.S. Provisional Application No. 61/869,390, filed August 23, 2013, the entire content of which is herein incorporated by reference in its entirety.

BACKGROUND

Mycobacterial infections often manifest as diseases such as tuberculosis (TB).

Widespread misuse of existing antibiotics and poor compliance with prolonged, complex therapeutic regimens have given rise to mutations of the Mycobacterium tuberculosis.

Consequently, there exists an epidemic of drug resistance that threatens TB control worldwide. Treatments of drug-resistant M. tuberculosis strains, and latent tuberculosis infections, necessitate new anti-tuberculosis drugs that offer highly effective treatments with shortened regimens.

Capuramycin (Figure 1) and its congeners are considered important molecules for the development of a new drug for multidrug-resistant (MDR) M. tuberculosis infections. Extensive structure- activity relationship studies of capuramycin to improve the efficacy have been limited due to difficulty in selective chemical modifications of the desired position(s) of the natural product with biologically interesting functional groups. Therefore, there remains a need to establish a concise, convergent synthesis of capuramycin that is amenable to synthesis of analogs for structure-activity relationship (SAR) studies.

SUMMARY OF THE INVENTION

In one aspect, provided here in is a compound of Formula I:

Formula I or a pharmaceutically acceptable salt thereof. In another aspe

Formula or a pharmaceutically acceptable salt thereof.

In another aspect, provided herein are compounds of Formula X:

Formula X

or a pharmaceutically acceptable salt thereof.

In another aspect, provided herein is a process for preparing l -[5-0-[4,6-Dideoxy-6-oxo- 6-[[[(35)-hexahydro-2-oxo-lH-azepine]-3-yl]amino]- -L-erythro-4-hexenopyranosyl]-3-0- methyl 6-deoxy-6-amino-a-L-talofuranuronosyl]- 1 ,2,3,4-tetrahydro-2,4-dioxopyrimidine (capuramycin) or a compound of Formula I, wherein = represents a double bond; Q is N; R ¹ is

2 3

unsubstituted phenyl; R and R , when taken together, form a fused phenyl that is unsubstituted; R ⁴ , R ⁷ , and R ¹⁰ are Η; and R ⁵ , R ⁶ , R ⁸ , and R ⁹ are each, independently, Η or Ci ₆ -alkyl.

In yet another aspect, provided herein is a method for the treatment of a bacterial infection in a subject in need thereof, comprising administering to the subject a compound of Formula I, Formula II, or Formula X. In one embodiment, provided herein the bacterial infection is caused by Mycobacterium tuberculosis.

In still another aspect, provided herein is a method of treating tuberculosis in a subject in need thereof, comprising administering to the subject a compound of Formula I, Formula II, or Formula X.

In other aspects, provided herein are the intermediates having the Formula III; Formula

Ilia; or Formula IX. BRIEF DESCRIPTION OF THE FIGURES

Figure 1 shows the structures of Capuramycin (1) and UT-01309 (2).

Figure 2 shows an improved synthetic strategy for capuramycin analogs.

Figure 3 shows syntheses of the glycosyl donor 10 and acceptor 11.

Figure 4 shows the absolute configurations of compounds 28 and 29.

DETAILED DESCRIPTION OF THE INVENTION

The emergence of multidrug-resistant (MDR) strains of Mycobacterium tuberculosis (Mtb) seriously threatens tuberculosis (TB) control and prevention efforts (see a) K. Grenet, D. Guillemot, V. Jarlier, B. Moreau, S. Dubourdieu, R. Ruimy, L. Armand-Lefevre, P. Brau, A. Andremont, Emerg. Infect. Dis. 2004, 10, 1150-1153; b) Cohen, J. Science 2004, 306, 1872).

Moreover, people who are HIV- AIDS patients are susceptible to TB infection (Godfrey- Faussett, P. AIDS 2003, 17, 1079-1081). There are significant problems associated with treatment of AIDS and Mtb co-infected patients. Rifampicin and isoniazid [a key component of the DOTS (Directly Observed Treatment, Short-course) therapy] induce the cytochrome P450 3A4 enzyme in liver which shows significant interactions with protease inhibitors for HIV infections (see a) S. T. Cole, P. M. Alzari, Science 2005, 14, 214-215; b) C. K. Stover, P.

Warrener, D. R. van Devater, D. R. Sherman, T. M. Arain,. M. H. Langhorne, S. W. Anderson, J. A. Towell, Y. Yuan, D. N. McMurray, B. N. Kreiswirth, C. E. Barry, W. R. Baker, Nature 2000, 405, 962-966). In addition, rifampicin strongly interacts with non-nucleoside reverse transcriptase inhibitors. Thus, clinicians avoid starting Highly Active Antiretroviral Therapy (HAART), which consists of three or more highly potent reverse transcriptase inhibitors and protease inhibitors, until the TB infection has been cleared (see a) M. A. Wainberg, Scientifica 2012, 2012, 1-28; b) L. E. Connolly, P. H. Edelstein, L. Ramakrishnan, PLoS Med. 2007, 4, 435- 441 ; c) J. B. Nachega, M. Hislop, D. W. Dowdy, R. E. Chaisson, L. Regensberg, G. Maartens, Ann. Int. Med. 2007, 146, 564-573; d) W. J.; Burman, B. E. Jones, Am. J. Respir. Crit. Care Med. 2001, 164, 469-473). Thus, there are significant needs and interests in developing new TB drugs. However, over the last 40 years, only bedaquiline (SIRTURO), an ATP synthase inhibitor, was approved for the treatment of MDR-Mtb infections as a monotherapeutic agent in 2012 (see a) Diacon, A. H.; P. R. Donald, A. Pym, M. Grobusch, R. F. Patientia, R. Mahanyele, N. Bantubani, R. Narasimooloo, T. De Marez, R. van Heeswijk, N. Lounis, P. Meyvisch, K. Andries, D. F. McNeeley, Antimicrob. Agents Chemother. 2012, 56, 3271-3276; b) A. Matteelli, A. C. Carvalho, K. E. Carvalho, A. Kritski, Future Microbiol. 2010, 5, 849-858). The ultimate goal of the development of the treatment of MDR-Mtb strains is to find novel antibacterial agents which 1) interfere with unexploited bacterial molecular targets, 2) can shorten a TB drug regimen (one-month to three-month regimen), 3) can apply to combination TB chemotherapy, and 4) do not interfere with ability of HAART to treat HIV patients who are co-infected with Mtb.

Since peptidoglycan (PG) is an essential bacterial cell wall polymer, the machinery for PG biosynthesis provides a unique and selective target for antibiotic action. However, only a few enzymes in PG biosynthesis such as the penicillin binding proteins (PBPs) have been extensively studied (see G. D. Wright, Science 2007, 315, 1372-1373). Thus, the enzymes associated with the early PG biosynthesis enzymes [MurA, B, C, D, E, and F, MraY (phospho- MurNAc-pentapeptide translocase or translocase I), and MurG] are considered to be a source of unexploited drug targets (see a) P. Cudic, D. C. Behenna, M. K. Yu, R. G. Kruger, L. M.

Szwczuk, D. G. McCafferty, Bioorg. Med. Chem. Lett. 2001, 11, 3107-3110; b) J. S. Helm, Y. Hu, L. Chen, B. Gross, S. Walker, J. Am. Chem. Soc. 2003 J25, 11168-11169; c) A. Bachelier, R. Mayer, C. D. Klein, Bioorg. Med. Chem. Lett. 2006, 16, 5605-5609; d) S. Antane, C. E.

Caufield, W. Hu, D. Keeney, P. Labthavikul, K. Morris, S. M. Naughton, P. J. Petersen, B. A. Rasmussen, G. Singh, Y. Yang, Bioorg. Med. Chem. 2006, 16, 176-180; e) M. O. Taha, N. Atallah, A. G. Al-Bakri, C. Pradis-Bleau, H. Yonis, K. S. Levesque, Bioorg. Med. Chem. 2008, 16, 1218-1235; f) A. Bryskier, A. C. Dini, Antimicr. Agents: Antibacter. Antifung. 2005, 377- 400; g) M. Kotnik, J. Humljan, C. Contreras-Martel, M. Oblak, K. Kristan, M. Herve, D. Blanot, U. Urleb, S. Gobec, A. Dessen, T. Solmajer, J. Mol. Biol. 2007, 370, 107-115 ; h) A. Perdih, A. Kovac, G. Wolber, D. Blanot, S. Gobec, T. Solmajer, Bioorg. Med. Chem. Lett. 2009, 19, 2668- 2673; i) J. Humljan, M. Kotnik, C. Contreras-Martel, D. Blanot, U. Urleb, A. Dessen, T.

Solmajer, S. Gobec, J. Med. Chem. 2008, 51, 7486-7494). Recently, there has been significant interest in unexploited molecular targets related to PG biosynthesis is MraY (see T. D. H. Bugg, D. H. Timothy, A. J. Lloyd, D. I. Roper, Infect. Disorders: Drug Targets 2006, 6, 85-106), which catalyzes the transformation of UDP-N-acylmuramyl-L-alanyl-y-D-glutamyl-raeio- diaminopimelyl- D -alanyl- D -alanine (Park's nucleotide) to prenylpyrophosphoryl-N- acylmuramyl- L -Ala-γ- D -glu-m ro-DAP- D -Ala- D -Ala (lipid I) (see a) M. Kurosu, S.

Mahapatra, P. Narayanasamy, D. C. Crick, Tetrahedron Lett. 2007, 48, 799-803; b) M. ; Kurosu, P. Narayanasamy, D. C. Crick, Heterocycles 2007, 72, 339-352; c) M. Kurosu, K. Li, J. Org. Chem. 2008, 73, 9767-9770). MraY is inhibited by nucleoside-based complex natural products such as muraymycins (see L. Mcdonald, L. Barbieri, G. Carter, E. Lenoy, J. Lotvin, P. Petersen, M. Siegel, G. Singh, R. Williamson, J. Am. Chem. Soc. 2002, 124, 10260-10261), liposidomycin (see M. Ubukata, K. Kimura, K. Isono, C.C. Nelson, J. M. Gregson, J. A, J. Org. Chem. 1992, 57; 6392-6403), caprazamycin (see M. Igarashi, N. Nakagawa, N. Doi, S. Hattori, H. Naganawa, M. Hamada, J. Antibiot. 2003, 56, 580-583), pacidamycin (see P. B. Fernandes, R. N. Swanson, D. J. Hardy, C. W. Hanson, L. Coen, R. R. Rasmussen, R. H. Chen, J. Antibiot. 1989, 42, 521- 526), capuramycin (see H. Yamaguchi, S. Sato, S. Yoshida, K. Takada, M. Itoh, H. Seto, N. Otake, J. Antibiot. 1986, 39, 1047-1053). and other related natural products (see a) V. M.

Reddy, L. Einck, C. A. Nacy, Antimicro. Agents Chemother. 2008, 52, 719-721 ; b) S. Ichikawa, Chem. Pharm. Bull. 2008, 56, 1059-1072; c) C. D , Curr. Top. Med. Chem. 2005, 5, 1221- 1236; d) C. Dini, N. Drochon, S. Feteanu, J. C. Guillot, C. Peixoto, J. Aszodi, Bioorg. Med. Chem. Lett. 2001, 11 , 529-5231).

Capuramycin (1) and its analogs exhibited significant mycobacterial growth inhibitory activities in vitro and in vivo and very low toxicity in mice (see a) E. Bogatcheva, T. Dubuisson, M. Protopopova, L. Einck, C. A. Nacy, V. M. Reddy, J. Antimicro. Chemother. 2011, 66, 578- 587; b) V. M. Reddy, L. Einck, C. A. Nacy J. Antimicro. Chemother. 2008, 52, 719-721 ; c) T. oga, T. Fukuoka, T. Harasaki, H. Inoue, H. Hotoda, M. Kakuta, Y. Muramatsu, N. Yamamura, M. Hoshi, T. Hirota, J. Antimicro. Chemother. 2004, 54, 755-760). Moreover, capuramycin killed Mtb much faster than other first-line TB drugs (>90 % of the bacilli were killed within 48 h), and thus could dramatically reduce the time frame for effective anti-TB chemotherapy.

Since discovery of capuramycin as a specific spectrum antimycobacterial agent, extensive SAR studies of capuramycins have been limited because of difficulty in modifying the complex natural product at the desired position(s) with a wide range of functional groups.

Accordingly, it is essential to establish a concise and convergent synthesis of capuramycin that is amenable to synthesis of analogs for SAR studies.

Therefore, provided herein are compounds of Formula I and Formula II, which are useful for the treatment of infectious diseases, such as tuberculosis and other mycobacterial infections caused by mycobacteria. Also provided herein are processes for preparing l-[5-0-[4,6-Dideoxy- 6-oxo-6-[[[(35)-hexahydro-2-oxo-lH-azepine]-3-yl]amino]- -L-erythro-4-hexenopyranosyl]-3- O-methyl 6-deoxy-6-amino-a-L-talofuranuronosyl]-l ,2,3,4-tetrahydro-2,4-dioxopyrimidine (capuramycin, 1), analogues thereof, and intermediates useful therefore. Also provided herein are interemediates III, Ilia, and IX, which are useful in the process for preparing the capuramycin and/or a certain compound of Formula I, UT-01309 (2) (Figure 1) and derivatives thereof.

Compounds o f the Invention

In one aspect, provided here in is a compound of Formula I:

Formula I

or a pharmaceutically acceptable salt thereof;

wherein = represents a single bond or a double bond;

when = represents a single bond, Q is CH ₂ , NH, or O; or

when = represents a double bond, Q is CH or N;

R ¹ is H, halo, Ci _ 6-alkyl, aryl, heteroaryl, C3 _ 7-cycloalkyl, or C ₂ - 6-heterocycle, wherein aryl, heteroaryl, cycloalkyl, or heterocycle can be optionally, independently substituted one or more times;

R ² and R ³ together form a fused aryl, fused heteroaryl, fused C3_6-cycloalkyl, or fused heterocycle, wherein the fused aryl, fused heteroaryl, fused cycloalkyl, or fused heterocycle can be optionally, independently substituted one or more times;

R , R', and R are each, independently, H, Ci _ 6-alkyl, aryl, or OH; and

R ⁵ , R ⁶ , R ⁸ , and R ⁹ are each independently H, Ci - 6-alkyl, or aryl; or

R ⁵ and R ⁶ and/or R ⁸ and R ⁹ can be linked with (CH ₂ )i_3 to form a fused heterocycle.

In another aspect, provided herein is a compound of Formula II:

Formula II

or a pharmaceutically acceptable salt thereof;

wherein = represents a single bond or a double bond;

when = represents a single bond, Q is CH ₂ , NH, or O; or

when = represents a double bond, Q is CH or N;

R ¹ is H, halo, Ci _ 6-alkyl, aryl, heteroaryl, C3 _ 7-cycloalkyl, or C ₂ - 6-heterocycle, wherein aryl, heteroaryl, cycloalkyl, or heterocycle can be optionally, independently substituted one or more times;

2 3

R and R ^J are each, independently, H, Ci_ 6-alkyl, C3_6-cycloalkyl, aryl, halo, OH, 0(Ci_ 6-alkyl), OC(0)(Ci_ ₆ -alkyl), NH ₂ , NH(Ci_ ₆ -alkyl), N(Ci_ ₆ -alkyl) ₂ , or NHC(0)(Ci_ ₆ -alkyl), or heterocycle, wherein aryl, heteroaryl, cycloalkyl, or heterocycle can be optionally substituted one or more times; or

R ² and R ³ can, when taken together, form a fused aryl, fused heteroaryl, fused C3_6- cycloalkyl, or fused heterocycle, wherein the fused aryl, fused heteroaryl, fused cycloalkyl, or fused heterocycle can be optionally, independently, substituted one or more times;

R ⁴ is OH;

R ⁷ and R ¹⁰ are each, independently, H, Ci _ 6-alkyl, aryl, or OH; and

R ⁵ , R ⁶ , R ⁸ , and R ⁹ are each, independently, H, Ci _ 6-alkyl, or aryl; or

R ⁵ and R ⁶ and/or R ⁸ and R ⁹ can be linked with (CH ₂ )i_3 to form a fused heterocycle. In yet another aspect, la X:

Formula X

or a pharmaceutically acceptable salt thereof;

wherein

R ¹ is C ₃ -6-heterocycle or C(H)R ² (CH ₂ )i- ₆ -NHR ³ , each of which can be optionally substituted with (=0);

R ² is H, or Ci-6-alkyl-NH ₂ ;

R ³ is H, or OCi_ ₆ -alkyl;

R ⁷ and R ¹⁰ are each, independently, H, Ci _ 6-alkyl, aryl, or OH; and

R ³ , R , R , and R ^v are each, independently, H, Ci _ 6-alkyl, or aryl; or

R ⁵ and R ⁶ and/or R ⁸ and R ⁹ can be linked with (CH ₂ )i_ ₃ to form a fused heterocycle.

In one embodiment of Formula X, R ¹ is C(H)(CONH ₂ )(CH ₂ )i_ ₆ NH ₂ , (CH ₂ )i_ ₆ CONH ₂ , isoxazolidin-3-one, piperidine, or (CH ₂ )i_6C(0)N(H)OCi-3-alkyl.

In another embodiment of Formula X, R ⁵ and R ⁶ are each, independently, H or CH ₃ .

In one embodiment of Formula I or Formula II, = represents a single bond. In a certain embodiment, = represents a single bond and Q is CH ₂ . In another embodiment of Formula I or Formula II, = represents a double bond. In a certain embodiment, = represents a double bond and Q is N.

In one embodiment of Formula I or Formula II, R ¹ is H, halo, Ci _ 6-afkyl, aryl, heteroaryl, C3 _ 7-cycloalkyl, or C2 - 6-hetero cycle, wherein aryl, heteroaryl, cycloalkyl, or heterocycle can be substituted one or more times with Ci_6 alkyl, halogen, OH, Ci_6-primary alcohol, Ci-6-secondary alcohol, Ci_ ₆ -alkoxy, NH ₂ , C(0)-Ci_6 alkyl, C(0)(CH ₂ )i- 4X, C0 ₂ H, C0 ₂ -Ci_6 -alkyl, aryl, heteroaryl, or C ₂ _6 -heterocycle.

In some embodiments of Formula I or Formula II, R ¹ is H or unsubstituted phenyl. In certain embodiments of Formula I, R ¹ is unsubstituted phenyl. In certain embodiments of Formula II, R ¹ is H.

In one embodiment of Formula I, R ² and R ³ , when taken together, form a fused aryl, fused heteroaryl, fused C3_6-cycloalkyl, or fused heterocycle, wherein the fused aryl, fused heteroaryl, fused cycloalkyl, or fused heterocycle can be independently substituted one or more times with Ci_6 alkyl, halogen, OH, Ci_6 -primary alcohol, Ci_6-secondary alcohol, Ci_6-alkoxy, NH ₂ , (CH ₂ )i_4-NH ₂ , C(0)-C._6 alkyl, C0 ₂ -Ci_ ₆ -alkyl, aryl, heteroaryl, or C ₂ -6-heterocycle.

In another embodiment of Formula I, R ² and R ³ , when taken together, form a fused phenyl, wherein the fused phenyl can be optionally, independently substituted one or more times. In certain embodiments of Formula I, R ² and R ³ together form a fused phenyl, wherein the fused phenyl can be independently substituted one or more times with Ci_6 alkyl, halogen, OH, Ci_6- primary alcohol, Ci_6-secondary alcohol, Ci_6-alkoxy, NH ₂ , (CH ₂ )i 4-NH ₂ , C(0)-Ci_6 alkyl, C(0)(CH ₂ )i-4X, C0 ₂ H, In certain other embodiments of Formula I, R ² and R ³ together form a fused phenyl that is unsubstituted.

In certain embodiments of Formula II, R ² and R ³ are each, independently, H, Ci_ 6-alkyl,

C ₃ -6-cycloalkyl, aryl, halo, OH, 0(Ci_ 6-alkyl), OC(0)(Ci_ ₆ -alkyl), NH ₂ , NH(Ci_ ₆ -alkyl), N(Ci_ 6-alkyl) ₂ , or NHC(0)(Ci_ 6-alkyl), or heterocycle, wherein aryl, heteroaryl, cycloalkyl, or heterocycle can be optionally substituted one or more times with Ci_6 alkyl, halogen, OH, Ci_6- primary alcohol, Ci_6-secondary alcohol, Ci_6-alkoxy, NH ₂ , (CH ₂ )i ₄ -NH ₂ , C(0)-Ci_6 alkyl, C(0)(CH ₂ )i-4X, C0 ₂ H,

In certain embodiments of Formula II, one of R ² and R ³ is H; and one of R ² and R ³ is unsubstituted phenyl. In certain other embodiments, R ² and R ³ are H.

2 3

In one embodiment of Formula II, R and R , when taken together, form a fused aryl, fused heteroaryl, fused C3_6-cycloalkyl, or fused heterocycle, wherein the fused aryl, fused heteroaryl, fused cycloalkyl, or fused heterocycle can be independently substituted one or more times with Ci_6 alkyl, halogen, OH, Ci_6 -primary alcohol, Ci_6-secondary alcohol, Ci_6-alkoxy, NH ₂ , (CH ₂ ) _! _ ₄ -NH ₂ , C(0)-Ci_6 alkyl, C(0)(CH ₂ )^X, C0 ₂ H, (CH ₂ )^-C0 ₂ H, C0 ₂ -Ci_6 -alkyl, aryl, heteroaryl, or C ₂ _6-heterocycle.

2 3

In certain embodiments of Formula II, R and R together form a fused phenyl, wherein the fused phenyl can be independently substituted one or more times with Ci_6 alkyl, halogen, OH, Ci_6-primary alcohol, Ci_6-secondary alcohol, Ci_6-alkoxy, NH ₂ , (CH ₂ )i ₄ -NH ₂ , C(0)-Ci_6 alkyl, C(0)(CH ₂ )i_ ₄ X, C0 ₂ H, C0 ₂ -Ci_ ₆ -alkyl, aryl, heteroaryl, or CM-

2 3

heterocycle. In certain other embodiments of Formula II, R and R together form a fused phenyl that is unsubstituted.

As referred to above, variable X is halogen.

In one embodiment of Formula I, R ⁴ , R ⁷ , and R ¹⁰ are H.

In another embodiment of Formula I or Formula II, R ⁵ , R ⁶ , R ⁸ , and R ⁹ are each, independently, H or Ci _ 6 -alkyl. In a certain embodiment, R ⁵ , R ⁶ , R ⁸ , and R ⁹ are each, independently, H or CH ₃ .

In another embodiment of Formula I,

= represents a double bond;

Q is N;

R ¹ is unsubstituted phenyl;

R ² and R ³ , when taken together, form a fused phenyl that is unsubstituted;

R ⁴ , R ⁷ , and R ¹⁰ are H; and

R", R°, R , and R ^v are each, independently, H or Ci _ 6 -alkyl.

In still another embodiment of Formula I,

= represents a double bond;

Q is N;

R ¹ is unsubstituted phenyl;

R ² and R ³ , when taken together, form a fused phenyl that is unsubstituted;

R ⁴ , R ⁷ , and R ¹⁰ are H; and

R ⁵ , R ⁶ , R ⁸ , and R ⁹ are each, independently, H or CH ₃ .

In another embodiment of Formula II,

= represents a single bond;

Q is CH ₂ ;

R ¹ is H;

R ² and R ³ are H; R ⁴ is OH;

R ⁷ and R ¹⁰ are H; and

R ⁵ , R ⁶ , R ⁸ , and R ⁹ are each, independently, H or Ci _ 6-alkyl- In still another embodiment of Formula II,

= represents a single bond;

Q is CH ₂ ;

R ¹ is H;

R ² and R ³ are H;

R ⁴ is OH;

R ⁷ and R ¹⁰ are H; and

R ⁵ , R ⁶ , R ⁸ , and R ⁹ are each, independently, H or CH ₃ .

In one embodiment, the invention provides a pharmaceutical composition comprising a compound of Formula I, Formula II, or Formula X, or a pharmaceutically acceptable salt thereof, and at least one pharmaceutically acceptable carrier.

Preferred embodiments of Formula I (including pharmaceutically acceptable salts thereof) are shown in Table A and are considered to be "compounds of the invention."

Table A

11 Table B

Preferred embodiments of Formula X (including pharmaceutically acceptable salts thereof) are shown in Table C and also are considered to be "compounds of the invention".

Table C

Process for Preparing Compounds o f the Invention

Based on the synthetic sequences detailed in Schemes 1-3, Figure 2, and Figure 3, provided herein is a process for preparing l -[5-0-[4,6-Dideoxy-6-oxo-6-[[[(3S)-hexahydro-2- oxo-lH-azepine]-3-yl]amino]- -L-erythro-4-hexenopyranosyl]-3-0-methyl 6-deoxy-6-amino-a- L-talofuranuronosyl]-l ,2,3,4-tetrahydro-2,4-dioxopyrimidine (capuramycin, 1):

Capuramycin or a compound of Formula I, wherein = represents a double bond; Q is N; R ¹ is unsubstituted phenyl; R ² and R ³ , when taken together, form a fused phenyl that is unsubstituted; R ⁴ , R ⁷ , and R ¹⁰ are Η; and R ⁵ , R ⁶ , R ⁸ , and R ⁹ are each, independently, Η or Ci 6-alkyl;

the process comprising the steps of:

reacting a compound of Formula III:

III

wherein P ¹ and P ² are MTPM and MDPM, respectively,

with an appropriate hydrating reagent to provide an intermediate of Formula Ilia:

Ilia

deprotecting said intermediate with a suitable acid to provide a compound of Formula IV:

IV

reacting the compound of Formula IV with a series of oxidizing agents to provide a compound of Formula V:

V

coupling the compound of Formula VI with a compound of Formula V:

to provide a compound of Formula VII:

VII

or coupling the compound of Formula V with a compound of Formula VIII:

to provide a co

₃

IX

and reacting the compound of Formula VII or Formula IX with a suitable base to give capuramycin (1) or the aforesaid compound of Formula I, respectively.

In another aspect, provided herein is the compound of Formula III:

III

wherein P ¹ and P ² are MTPM and MDPM, respectively.

In another aspect, pro ided herein is the compound of Formula Ilia:

Ilia

wherein P ¹ and P ² are MTPM and MDPM, respectively.

In still another asp a IX:

IX

In certain embodiments, the compound of Formula II, Ila, or VIII are useful in the preparation of capuramycin and/or the aforesaid compound of Formula I.

Specific embodiments of these synthesis methods are provided below.

In one aspect, provided herein is a synthetic strategy to improve the syntheses of capuramycin (1) and capuramycin analog, UT-01309 (2), which is illustrated in Figure 2. Two protecting groups, (2,6-dichloro-4-methoxyphenyl)(2,4-dichlorophenyl)methyl

[monomethoxytetrachlorodiphenylmethyl (MTPM)] and (2,6-dichloro-4-methoxyphenyl)(2,4,6- O-diphenylmethyl trichloroacetimidateophenyl) methoxymethyl

[monomethoxydiphenylmethoxylmethyl (MDPM)] were implemented in the improved synthetic route for the uridine ureido nitrogen (3-position) and the primary alcohol (6"-position) (Figure 2). (5)-3- Amino- 1,4- benzodiazepin-2-one [(5)-13] is an important functional group to improve antimycobacterial activity of capuramycin. For SAR studies of the present capuramycin analogs, it was desirable to have a versatile resolution protocol of racemic amino acids, which were not available commercially.

Synthesis of (25)-uridyl-hydroxyacetonitrile 10 and mannosyl donor imidate 11:

In one embodiment, the uridine ureido nitrogen was protected with MDPMC1 (16) in the presence of DBU to afford the MDPM-protected uridine 9 in 95% yield (Figure 3). Selective alkylation of 9 at the secondary alcohol (3 '-position) was achieved via a SnCl ₂ -mediated methylation condition to yield the desired mono-methyl derivative in 60% yield (see A. R. Kore, G. Parmar, S. Reddy, Nucleos. Nucleot. Nucleic Acids 2006, 25, 307-314). Selective

chloroacetylation of the primary alcohol of the diol was performed with CICH ₂ CO ₂ H, EDCI, NaHC0 ₃ , and glyceroacetonide-Oxyma (17) in 5% H ₂ 0-CH ₃ CN to give rise to 18 in 98% yield (see Y. Wang, B. A. Aleiwi, Q. Wang, M. Kurosu, Org. Lett. 2012, 14, 4910-4913). The regiochemistry of 18 was unequivocally determined by extensive ^X H-NMR decoupling studies and the 2D NOESY experiments (see Appendix A: Supporting Information). Albeit the ordinal esterification conditions (e.g. C1CH ₂ C0 ₂ H, DCC, DMAP in CH ₂ C1 ₂ or ClCH ₂ COCl, pyridine in CH ₂ C1 ₂ ) provided a mixture of 18 and the over-reaction product, the formation of secondary alcohol ester under these conditions was not observed. Acetylation of the secondary alcohol of 18 followed by the removal of the chloroacetyl group with thiourea in MeOH afforded 19 in 95% overall yield (see L. Lazar, I. Bajza, Z. Jakab, A. Liptak, Synlett 2005, 14, 2242-2244). The primary alcohol of 19 was oxidized under Pfitzner-Moffatt conditions (DCC, C1 ₂ CHC0 ₂ H, DMS0-CH ₂ C1 ₂ ) to provide the corresponding aldehyde 20, which was utilized without purification (see a) R. S. Ranganathan, G. H. Jones, J. G. Moffatt, J. Org. Chem. 1974, 39, 290- 302; b) K. E. Pfitzner, J. G. Moffatt, J. Am. Chem. Soc. 1963, 85, 3026-3027).

Compound 19 was converted to 10 using water-catalyzed hydrocyanation with BzCN and the undesired stereochemistry of 21 was inverted via a modified Mitsunobu reaction [DIAD, TPP, C1CH ₂ C0 ₂ H, pyridine (1 :1 :1 :1)]. The chloroacetyl group of the ester was selectively deprotected with thiourea in MeOH. Thus, the synthesis of the mannosyl acceptor 10 was achieved in 7 steps from uridine (15) with 34% overall yield without the process of the inversion (21→10) or in 9 steps with 45% overall yield including the Mitsunobu reaction followed by deprotection. The mannosyl donor 11 was synthesized in 4 steps from oc-benzyl glycoside 22 (Figure 3). The primary acetate of 22 was selectively deprotected with [?Bu ₂ SnCl(OH)] ₂ (see A. Orita, Y. Hamada, T. Nakano, S. Toyoshima, J. Otera, Chem. Eur. J. 2001, 7, 3321-3327) and the generated alcohol was protected with MTPM-imidate 23 in the presence of TMSOTf to afford 24 in 93% overall yield (see a) Y. Wang, M. Kurosu, Tetrahedron 2012, 68, 4797-4804; b) M.

Kurosu, K. Li, Synthesis 2009, 21, 3633-3641 ;. c) M. Kurosu, K. Biswas, D. C. Crick, Org. Lett. 2007, 9, 1141-1144). Hydrogenolytic cleavage of the anomeric benzyl ether followed by the imidate-formation reaction provided 11 in 95% overall yield (see R. R. Schmidt, Angew. Chem. Int. Ed., 1986, 25, 212-235).

Mannosylation of the cyanohydrin 10 with 11:

In another embodiment, the NIS/AgBF ₄ promoted mannosylation of 5, which provided the orthoester 25 within 15 min, which subsequently underwent the rearrangement within 16 h to afford 7a exclusively in 90% yield (Scheme 1). The orthoester 25 could be distinguished from 7a in ^-NMR spectra of the crude reaction mixture; 25 showed a characteristic chemical shift of 1.78 ppm (CH ₃ ) (see A. H. Harreus, H. Kunz, Liebigs Ann. Chem. 1986, 717-730). All triflate ion associated-glycosylations with 6 (e.g. NIS/TfOH or NBS/TfOH) yielded a mixture of a- and β-mannosides (see a) K. Fukase, A. Hasuoka, I. Kinoshita, Y. Aoki, S. Kusumoto, Tetrahedron 1995, 51, 4923-4932; b) G. H. Yeeneman, S. H. van Leeuwen, J. H. van Boom, Tetrahedron Lett. 1990, 31, 1331-1334). Under the NIS/AgBF ₄ promoted conditions, mannosylation of the MDPM-protected 10 with the thioglycoside 26 did not provide the desired product 12. The acceptor 10 was stable under the NIS/AgBF ₄ conditions; however, the thioglycoside 26 was completely consumed to form the complex mixtures. Albeit mannosylation of 10 with a- mannopyranose 2,3,4,6-tetraacetate l-(2,2,2-trichloroethanimidate) (27) did not provide the desired product 7b, TMSOTf- and BF ₃ ^» OEt ₂ -cataryzed mannosylation of 10 with the imidate 11 afforded the desired product 12 in 45% and 75% yield, respectively. It is worth noting that the mannosylation with 11 could be achieved at high concentrations in short reaction times compared to the mannosylation of 5 with 6 under the conditions of NIS/AgBF4.

Scheme 1 Mannosylation of the cyanohyd

Resolution of racemic 3-amino-l,4-benzodiazepine-2-one:

In another embodiment, carbamate formation of (±)-13 with (5)-14 can be achieved by using P^NEt in a mixture of acetone and H ₂ O (3/1) (Scheme 2). The generated diastereomers could be purified by silica gel chromatography to afford 28 and 29 in 98% yield (approximately 49% each). Figure 4 depicts the absolute configurations of a wide range of amino acids can be determined by only analyzing the carbamate nitrogen protons of (5)-14 and (R)-14 derivatives in ^-NMR spectra. In all cases, the nitrogen protons of carbamates derived from L-amino acids and (5)-14 were shifted downfield relative to those obtained with L-amino acid-(R)-14

derivatives (see M. Kurosu, K. Li, Org. Lett. 2009, 11, 911-914). In ^-NMR, the chemical shifts of 29 should appear identical to those of the antipode of 29 (ent-29) (Figure 4). Thus, the A5(S-R) value of the N ^0, protons of 28 and ent-29 should determine the absolute stereochemistry of 28. The A6(N ^ct 28-N ^<X 29) value was +0.03 and thus the absolute stereochemistry of 28 was assigned to be L-configuration (R for 3-amino-l,4-benzodiazepine-2-one) as shown in Scheme 2. The diastereomeric excesses (des) of purified 28 and 29 were determined by HPLC to be >99.0%. Removal of the carbamate auxiliaries of 28 and 29 was achieved by 20% TFA in CH ₂ CI ₂ to afford (S)-13 and (R)-13 in >95% yields. The chiral auxiliary was recovered as racemic trifluoroacetate 30 in quantitative yield. The absolute configurations of (5)-13 and (R)- 13 were unequivocally confirmed by the comparison of optical rotations of those with the reported values for (5)-13 and (R)-13 (see B. E. Evans, K. E. Rittle, D. F. Veber, R. M.

Freidinger. J. Hirshfield, J. P. Springer, J. Org. Chem. 1987, 52, 3232-3232).

Scheme 2 Resolution of rac -3-amino-l,4-benzodiazepine-2-one. Syntheses of capuramycin and UT-01309:

In another embodiment, capuramycin (1) and UT-01309 (2) can be synthesized in 6 steps from 12. The improved scheme required only three purifications by column chromatography in the total number of synthetic steps (Scheme 3). The cyano group of 12 was hydrated using InCi ₃ -aldoxime in toluene, furnishing the corresponding primary amide (see E. S. Kim, H. S. Lee, S. H. Kim, J. Ν. Kim, Tetrahedron Lett. 2010, 51, 1589-1591). Without further purification, the primary amide was subjected to simultaneous deprotections of the MDPM and MPTM groups with 30% TFA in CH ₂ C1 ₂ to afford 8 in greater than 95% overall yield for two steps. Over 1 gram of 8 was synthesized via the new protecting group strategy summarized in Schemes 1-3, Figure 2, and Figure 3.

Oxidation-elimination reactions of 8 using S0 ₃ ^» pyridine in a biphasic solvent system

(DMSO/Et ₃ N = 3/1) provided the α,β-unsaturated aldehyde 31 (see D. M. Mackie, A. S. Perlin, Carbohydr. Res. 1972, 24, 67-85). The aldehyde 31 was oxidized to the corresponding carboxylic acid 32 by Pinnick oxidation (NaC10 ₂ , 2-methyl-2-butene) (see a) B. S. Bal, W. E. Childers, H. W. Pinnick, Tetrahedron 1981, 37, 2091 -2096; b) L. O. Bengt, N. Torsten, Acta Chem. Scand. 1973, 27, 888-890). The resulting crude carboxylic acid was coupled with (5)- aminocapro lactam (33) using an amide forming reaction in water media [glyceroacetonide- Oxyma (17), EDCI, NaHC0 ₃ in H ₂ 0] to yield 33 in 80-85% overall yield from 8 (see Q. Wang, Y. Wang, M. Kurosu, Org. Lett. 2012, 14, 3372-3375).

In the glyceroacetonide-Oxyma (17) / EDCI-mediated coupling reaction, simple basic and acidic aqueous work-up procedures could remove all reagents utilized in the reactions to afford the coupling product 34 in high yield with excellent purity. Saponification of 34 by using LiOH in THF-H ₂ O provided capuramycin (1) in greater than 95% yield. Similarly, UT-01309 (2) was synthesized using (5)-13 instead of 33 in the synthesis of 1 (Scheme 3). The purity of synthetic products, 1 and 2 were determined to be >99% by reverse-phase HPLC analyses.

Scheme 3 Synthesis of capuramycin and UT-01309.

Methods of Treatment

The present invention also provides methods for the treatment or of a disease caused by a microorganism comprising administering an effective amount of a compound of Formula I, Formula II, or Formula X to a subject in need thereof.

In one embodiment, the present invention provides methods for the treatment of a disease caused by a microorganism comprising administering an effective amount of a pharmaceutical composition comprising a compound of Formula I, Formula II, or Formula X.

In one embodiment, the invention provides a method for the treatment of a disease caused by the microorganism, M. tuberculosis. In another embodiment, a method for the treatment of a mycobacterial disease is provided. In another embodiment, a method for the treatment of a non- tuberculosis mycobacterial infection is provided.

The present invention further comprises methods and compositions effective for the treatment of infectious disease, including but not limited to those caused by bacterial, mycological, parasitic, and viral agents.

Definitions

As used herein, the terms "tuberculosis" and "TB" comprise disease states usually associated with infections caused by mycobacteria species comprising M. tuberculosis complex. The term "tuberculosis" is also associated with mycobacterial infections caused by mycobacteria other than M. tuberculosis (MOTT). Other mycobacterial species include M. avium- intracellular e, M. kansarii, M. fortuitum, M. chelonae, M. leprae, M. africanum, and M. microti, M. avium paratuberculosis, M. intracellular, M. scrofuhceum, M. xenopi, M. marinum, M. ulcer ans. In one embodiment, a method for the treatment of M. avium-intracellulare, M. kansarii, M. fortuitum, M. chelonae, M. leprae, M. africanum, and M. microti, M. avium paratuberculosis, M. intracellular, M. scrofiilaceum, M. xenopi, M. marinum, or M. ulcer ans with capuramycin analogues of the invention is provided.

"Subject" for the purposes of the present invention includes humans and other animals, particularly mammals, and other organisms. Thus the methods are applicable to both human therapy and veterinary applications. In some embodiments the patient is a mammal, and in a particular embodiment the patient is human.

The terms "effective amount" or "pharmaceutically effective amount" or "therapeutically effective amount" refer to a sufficient amount of an agent to provide the desired biological, therapeutic, and/or prophylactic result. That result can be reduction, amelioration, palliation, lessening, delaying, and/or alleviation of one or more of the signs, symptoms, or causes of a disease, or any other desired alteration of a biological system.

Unless otherwise indicated, "treating" or "treatment" of a disease, disorder, or syndrome, as used herein, means inhibiting the disease, disorder, or syndrome, that is, arresting its development; and relieving the disease, disorder, or syndrome, that is, causing regression of the disease, disorder, or syndrome. As is known in the art, in the context of treatment, adjustments for systemic versus localized delivery, age, body weight, general health, sex, diet, time of administration, drug interaction and the severity of the condition may be necessary, and will be ascertainable with routine experimentation by one of ordinary skill in the art.

"Pharmaceutical composition" means a mixture or solution containing at least one therapeutic agent to be administered to a subject (e.g., a mammal or human) in order to prevent or treat a particular disease or condition affecting the mammal.

"Pharmaceutically acceptable" means those compounds, materials, compositions, and/or dosage forms, which are, within the scope of sound medical judgment, suitable for contact with the tissues a subject (e.g., a mammal or human) without excessive toxicity, irritation allergic response and other problem complications commensurate with a reasonable benefit / risk ratio.

The terms "comprising" and "including" are used herein in their open-ended and non- limiting sense unless otherwise noted.

The terms "a" and "an" and "the" and similar references in the context of describing the invention (especially in the context of the following claims) are to be construed to cover both the singular and the plural, unless otherwise indicated herein or clearly contradicted by context. Where the plural form is used for compounds, salts, and the like, this is taken to mean also a single compound, salt, or the like.

As used herein, the terms "approximately" or "about" generally indicate a possible variation of no more than 10%, 5%, or 1 % of a value.

As used herein, the term "alkyl" refers to a fully saturated branched or unbranched hydrocarbon moiety. Preferably the alkyl comprises 1 to 20 carbon atoms, more preferably 1 to 16 carbon atoms, 1 to 10 carbon atoms, 1 to 7 carbon atoms, 1 to 6 carbons, 1 to 4 carbons, or 1 to 3 carbon atoms. Representative examples of alkyl include, but are not limited to, methyl, ethyl, n-propyl, so-propyl, «-butyl, sec-butyl, iso-butyl, tert-b tyl, «-pentyl, isopentyl, neopentyl, «-hexyl, 3-methylhexyl, 2,2- dimethylpentyl, 2,3-dimethylpentyl, «-heptyl, «-octyl, n- nonyl, «-decyl and the like. Furthermore, the expression "C _x -C _y -alkyl", wherein x is 1-5 and y is 2-10 indicates a particular alkyl group (straight- or branched -chain) of a particular range of carbons. For example, the expression Ci-C4-alkyl includes, but is not limited to, methyl, ethyl, propyl, butyl, isopropyl, tert-butyl and isobutyl.

As used herein, the term "cycloalkyl" refers to saturated or unsaturated monocyclic, bicyclic or tricyclic hydrocarbon groups of 3-12 carbon atoms, preferably 3-9, or 3-7 carbon atoms. Exemplary monocyclic hydrocarbon groups include, but are not limited to, cyclopropyl, cyclobutyl, cyclopentyl, cyclopentenyl, cyclohexyl and cyclohexenyl and the like. Exemplary bicyclic hydrocarbon groups include bornyl, indyl, hexahydroindyl, tetrahydronaphthyl, decahydronaphthyl, bicyclo[2.1.1]hexyl, bicyclo[2.2.1]heptyl, bicyclo[2.2.1 ]heptenyl, 6,6- dimethylbicyclo[3.1.1]heptyl, 2,6,6-trimethylbicyclo[3.1.1 ]heptyl, bicyclo[2.2.2]octyl and the like. Exemplary tricyclic hydrocarbon groups include adamantyl and the like.

The term "heteroalkyl," by itself or in combination with another term, means, unless otherwise stated, a stable straight or branched chain, or combinations thereof, consisting of the stated number of carbon atoms and from one to five heteroatoms, more preferably from one to three heteroatoms, selected from the group consisting of O, N, Si and S, and wherein the nitrogen and sulfur atoms may optionally be oxidized and the nitrogen heteroatom may optionally be quaternized. The heteroalkyl group is attached to the remainder of the molecule through a carbon atom or a heteroatom.

The term "aryl" includes aromatic monocyclic or multicyclic (e.g., tricyclic, bicyclic), hydrocarbon ring systems consisting only of hydrogen and carbon and containing from six to nineteen carbon atoms, or six to ten carbon atoms, where the ring systems may be partially saturated. Aryl groups include, but are not limited to, groups such as phenyl, tolyl, xylyl, anthryl, naphthyl and phenanthryl. Aryl groups can also be fused or bridged with alicyclic or heterocyclic rings which are not aromatic so as to form a polycycle (e.g., tetralin).

The term "heteroaryl," as used herein, represents a stable monocyclic or bicyclic ring of up to 7 atoms in each ring, wherein at least one ring is aromatic and contains from 1 to 4 heteroatoms selected from the group consisting of O, N and S. Heteroaryl groups within the scope of this definition include but are not limited to: acridinyl, carbazolyl, cinnolinyl, quinoxalinyl, pyrrazolyl, indolyl, benzotriazolyl, furanyl, thienyl, benzothienyl, benzofuranyl, quinolinyl, isoquinolinyl, oxazolyl, isoxazolyl, indolyl, pyrazinyl, pyridazinyl, pyridinyl, pyrimidinyl, pyrrolyl, tetrahydroquinoline. As with the definition of heterocycle below, "heteroaryl" is also understood to include the N-oxide derivative of any nitrogen-containing heteroaryl. In cases where the heteroaryl substituent is bicyclic and one ring is non-aromatic or contains no heteroatoms, it is understood that attachment is via the aromatic ring or via the heteroatom containing ring, respectively.

The term "heterocycle" or "heterocyclyl" refers to a five-member to ten-member, fully saturated or partially unsaturated nonaromatic heterocylic groups containing at least one heteroatom such as O, S or Ν. The most frequent examples are piperidinyl, morpholinyl, piperazinyl, pyrrolidinyl or pirazinyl. Attachment of a heterocyclyl substituent can occur via a carbon atom or via a heteroatom.

Moreover, the alkyl, alkenyl, cycloalkyl, cycloalkenyl, alkoxy, aryl, heteroaryl, and heterocycle groups described above can be "unsubstituted" or "substituted."

The term "substituted" is intended to describe moieties having substituents replacing a hydrogen on one or more atoms, e.g. C, O or N, of a molecule. Such substituents can independently include, for example, one or more of the following: straight or branched alkyl (preferably C ₁ -C5), cycloalkyl (preferably C3-C8), alkoxy (preferably Ci-Ce), thioalkyl

(preferably Ci-Ce), alkenyl (preferably C ₂ -C6), alkynyl (preferably C ₂ -C6), heterocyclic, carbocyclic, aryl (e.g., phenyl), aryloxy (e.g., phenoxy), aralkyl (e.g., benzyl), aryloxyalkyl (e.g., phenyloxyalkyl), arylacetamidoyl, alkylaryl, hetero aralkyl, alkylcarbonyl and arylcarbonyl or other such acyl group, heteroarylcarbonyl, or heteroaryl group, (CR'R")o- ₃ NR'R" (e.g., -NH ₂ ), (CR'R")o- ₃ CN (e.g., -CN), -N0 ₂ , halogen (e.g., -F, -CI, -Br, or -I), (CR'R")o- ₃ C(halogen) ₃ {e.g. , -CF ₃ ), (CR'R") ₀ - ₃ CH(halogen) ₂ , (CR'R") ₀ - ₃ CH ₂ (halogen), (CR'R") ₀ - ₃ CONR'R",

(CR'R")o- ₃ (CNH)NR'R", (CR'R")o ₃ S(0)i_ ₂ NR'R", (CR'R") ₀ - ₃ CHO, (CR'R") ₀ - ₃ O(CR'R") ₀ - ₃ H, (CR'R")o- ₃ S(0)o- ₃ R' (e.g., -S0 ₃ H, -OS0 ₃ H), (CR'R") ₀ - ₃ O(CR'R") ₀ - ₃ H (e.g., -CH ₂ OCH ₃ and -OCH ₃ ), (CR'R") ₀ - ₃ S(CR'R") ₀ - ₃ H (e.g., -SH and -SCH ₃ ), (CR'R") ₀ - ₃ OH (e.g., -OH), (CR'R")o- ₃ COR', (CR'R") ₀ - ₃ (substituted or unsubstituted phenyl), (CR'R") ₀ - ₃ (C ₃ -C ₈ cycloalkyl), (CR'R")o- ₃ C0 ₂ R' (e.g., -C0 ₂ H), or (CR'R") ₀ - ₃ OR' group, or the side chain of any naturally occurring amino acid; wherein R' and R" are each independently hydrogen, a C ₁ -C5 alkyl, C ₂ -C5 alkenyl, C ₂ -C5 alkynyl, or aryl group.

The term "optionally substituted" is used herein interchangeably with the phrase

"substituted or unsubstituted" or with the term "(un)substituted". Unless otherwise indicated, an optionally substituted group may have a substituent at each substitutable position of the group, and each substitution is independent of the other. An optionally substituted group also may have no substituents. Therefore the phrase "optionally substituted with one or more substituents" means that the number of substituents may vary from zero up to the number of available positions for substitution.

The term "suitable acid" is intended to describe acetic acid, trifluoro acetic acid, hydrochloric acid or mixtures thereof. In a particular embodiment, the suitable acid is trifluoro acetic acid.

The term "hydrating agent" is intended to describe a compound that hydrolyzes a functional group. In one embodiment, a nitrile is hydrated using InCl ₃ -aldoxime in toluene to furnish an amide.

The term "oxidizing agent" as referred to herein includes any suitable oxidizing agent including any substance, which will readily add or take on electrons. Oxidizing agents include inorganic and organic oxidizing agents, such as oxygen; peroxides, such as hydrogen peroxide and benzoyl peroxide; elemental halogen species, as well as oxygenated halogen species, such as hypochlorite ions and perchlorite species. In a certain embodiment, the suitable oxidizing agents are S0 ₃ -pyridine and NaC10 ₂ /2-methyl-2-butene.

The term "protecting group" refers to any functional group moiety that may be removed selectively under mild conditions. In certain embodiments, the protecting groups are selected from MTPM and MDPM,

The description of the disclosure herein should be construed in congruity with the laws and principals of chemical bonding. For example, it may be necessary to remove a hydrogen atom in order accommodate a substituent at any given location. Furthermore, it is to be understood that definitions of the variables (i.e., "R groups"), as well as the bond locations of the generic formula of the invention (i.e., Formula I, Formula II, or Formula X), will be consistent with the laws of chemical bonding known in the art. It is also to be understood that all of the compounds of the invention described above will further include bonds between adjacent atoms and/or hydrogens as required to satisfy the valence of each atom. That is, bonds and/or hydrogen atoms are added to provide the following number of total bonds to each of the following types of atoms: carbon: four bonds; nitrogen: three bonds; oxygen: two bonds; and sulfur: two-six bonds.

The compounds of this invention may include asymmetric carbon atoms. It is to be understood accordingly that the isomers arising from such asymmetry (e.g., all enantiomers, stereoisomers, rotamers, tautomers, diastereomers, or racemates) are included within the scope of this invention. Such isomers can be obtained in substantially pure form by classical separation techniques and by stereochemically controlled synthesis. Furthermore, the structures and other compounds and moieties discussed in this application also include all tautomers thereof.

Compounds described herein may be obtained through art recognized synthesis strategies.

It will also be noted that the substituents of some of the compounds of this invention include isomeric cyclic structures. It is to be understood accordingly that constitutional isomers of particular substituents are included within the scope of this invention, unless indicated otherwise. For example, the term "tetrazole" includes tetrazole, 2H-tetrazole, 3H-tetrazole, 4H- tetrazole and 5H-tetrazole. EXEMPLIFICATION

The invention is further illustrated by the following examples, which should not be construed as further limiting. The practice of the present invention will employ, unless otherwise indicated, conventional techniques of cell biology, cell culture, molecular biology, transgenic biology, microbiology and immunology, which are within the skill of the art.

Synthetic Procedures

General: All reagents and solvents were of commercial grade and were used as received without further purification unless otherwise noted. Tetrahydrofuran (THF) and diethyl ether (Et ₂ 0) were distilled from sodium benzophenone ketyl under an argon atmosphere prior to use. Methylene Chloride (CH2CI2), acetonitrile (CH3CN), benzene, toluene and triethylamine (Et3N) were distilled from calcium hydride under an Argon atmosphere. Flash chromatography was performed with Whatman silica gel (Purasil 60 A, 230-400 Mesh). Analytical thin- layer chromatography was performed with 0.25 mm coated commercial silica gel plates (EMD, Silica Gel 6OF ₂ 5 ₄ ) visualizing at 254 nm, or developed with eerie ammonium molybdate or

anisaldehyde solutions by heating on a hot plate. ^X H-NMR spectral data were obtained using 400, and 500 MHz instruments. ¹³ C-NMR spectral data were obtained using 100 andl25 MHz instruments. For all NMR spectra, δ values are given in ppm and J values in Hz.

(2,6-Dichloro-4-methoxyphenyl)(2,4,6-trichlorophenyl)-met hoxy methyl chloride (16): (2,6- Dichloro-4-methoxyphenyl)-(2,4,6-trichlorophenyl)-methoxymet hyl methyl sulfide was synthesized according to the procedure previously reported (see P. Cudic, D. C. Behenna, M. K. Yu, R. G. Krager, L. M. Szwczuk, D. G. McCafferty, Bioorg. Med. Chem. Lett. 2001, 11, 3107-3110). To a stirred solution of (2,6-dichloro-4-methoxyphenyl)-(2,4,6-trichlorophenyl)-metho xymethyl methyl sulfide (11.18 g, 25.0 mmol) in CH ₂ CI ₂ (63.0 mL) was added sulfuryl chloride (2.0 mL, 25.0 mmol) at rt. The reaction mixture was stirred for 1 h and all volatiles were evaporated to provide the crude product as oil which was pure enough for the next reaction (10.45 g, 96%). ^l H NMR (400 MHz, CDCI ₃ ): δ= 7.33 (s, 2H), 6.88 (s, 2H), 6.77 (s, 1H), 5.57 (q, J = 6.4 Hz, 2H), 3.80 (s, 3H); ¹³ C NMR (100 MHz, CDC1 ₃ ): δ= 159.6, 136.8, 136.6, 134.4, 131.7, 129.7, 124.3, 115.6, 80.1, 55.8; IR: ΰ = 3473, 1445, 1309 cm ^"1 ; elemental analysis calcd (%) for Ci5HioCi ₆ 0 ₂ : C, 41.42; H, 2.32; CI, 48.91. Found: C, 41.81 ; H, 2.41 ; CI, 48.97. 3-[(2,6-Dichloro-4-methoxy-phenyl)-(2,4,6-trichloro-phenyl)- methoxymethyl]-l-(3,4- dihydroxy-5-hydroxymethyl-tetrahydro-furan-2-yl)-lH-pyrimidi ne-2,4-dione(9): To a stirred solution of uridine (10.98 g, 45.0 mmol) in DMF (120 mL) at 0 °C, DBU (9.0 mL, 60.0 mmol) and 16 (13.08 g, 30.0 mmol) were added. After 1 h at 0 °C, the reaction was quenched by addition of MeOH (24 mL). All volatiles were evaporated in vacuo and the crude product was purified by silica gel chromatography with CHCVMeOH (95:5) to afford 9 as an oil (17.62 g, 95%). R _f = 0.3 (10% MeOH/CHCl ₃ ); H NMR (400 MHz, CDC1 ₃ ): δ= Ί .61 (d, J = 6.8 Hz, IH), 7.30 (d, J = 3.6 Hz, 2H), 6.83 (d, J = 4.8 Hz, 2H), 6.57 (s, IH), 5.77 (d, J = 8.4 Hz, IH), 5.59 (m, 3H), 4.32 (m, 2H), 4.24 (s, IH), 3.97 (d, J = 12.0 Hz, IH), 3.90 (s, IH), 3.83 (m, IH), 3.78 (s, 3H), 3.05 (s, IH), 2.20 (s, IH); ¹³ C NMR (100 MHz, CDC1 ₃ ): δ= 162.9, 159.4, 151.9, 140.1, 136.7, 134.1, 132.5, 129.5, 125.2, 115.5, 101.6, 93.2, 85.7, 77.9, 74.8, 70.4, 69.1, 61.7, 55.7, 36.6, 31.5; IR: ΰ = 3435, 1719, 1665, 1440, 1081 cm ^"1 ; HRMS (ESI ⁺ ) m/z calcd for

C ₂₄ H ₂₂ Ci ₅ N ₂ 0 ₈ : 640.9819; found: 640.9825.

Synthesis of 18: To a stirred solution of 9 (12.8 g, 20.0 mmol) in DMF (300 mL) was added SnCi ₂ (1.91 g, 10.0 mmol). The reaction mixture was heated to 50 °C followed by addition of CH ₂ N ₂ (150 mL, 60.0 mmol, 0.4 M in Et^O). After lh, all volatiles were evaporated in vacuo. The selectivity ratio and yield of the mono-methyl ethers were determined by ^X H-NMR analyses of the crude mixture to be 3:2 ratio in favor of the desired product. The crude product was dissolved in 5% H ₂ 0/MeCN (1.0 mL). Glyceroacetonide-Oxyma 17 (6.7 g, 30.0 mmol), EDCI (5.7 g, 30.0 mmol), chloroacetatic acid (3.72 g, 40.0 mmol), and NaHC0 ₃ (10.1 g, 120.0 mmol) were added to the reaction mixture. After 3 h, the reaction was quenched with aq. NaHCC>3. The aqueous layer was extracted with EtOAc (2x). The combined organic extracts were dried over Na ₂ S0 ₄ and concentrated in vacuo to yield the desired ester 18 (8.6 g, 59% over two steps) as a colorless liquid. R _f = 0.3 (30% hexanes/AcOEt); H NMR (500 MHz, CDC1 ₃ ): δ= 7.29 (d, J = 7.5 Hz, IH), 7.20 (s, 2H), 6.76, (s, 2H), 6.50 (s, IH), 5.71 (d, J = 7.5 Hz, IH), 5.50-5.46 (m, 3H), 4.45 (m, IH), 4.34 (m, 2H), 4.15 (m, IH), 4.04 (m, 2H), 3.96 (m, IH), 3.71 (s, 3H), 3.42 (s, 3H); ¹³ C NMR (100 MHz, CDC1 ₃ ): S= 166.9, 162.7, 159.3, 151.2, 140.3, 136.7, 134.0, 132.6, 129.5, 125.3, 115.5, 102.1 , 79.7, 78.9, 77.8, 72.7, 69.2, 65.0, 58.9, 55.7, 40.6; IR: ΰ = 3442, 1711 , 1660, 1445, 1309, 1070 cm ^"1 ; HRMS (ESI ⁺ ) m/z calcd for C ₂ 7H ₂₄ C ₆ N ₂ Na0 ₉ : 754.9481 ; found

754.9484.

Synthesis of 19: The ester 18 above was dissolved in pyridine/Ac ₂ 0 (2:1, 200 mL) and stirred at rt. Upon completion, all volatiles were evaporated in vacuo to afford the desired acetate. The crude material was dissolved in MeOH (200 mL) and thiourea (3.8 g, 50.0 mmol) was added. The reaction mixture was stirred at 50 °C for 4 h and cooled to rt. All volatiles were evaporated in vacuo. Purification by silica gel column chromatography with hexanes/AcOEt (1 :1) yielded the desired product 19 as an oil (7.8 g, 95% over two steps). R _f = 0.4 (30% hexanes/AcOEt); H NMR (500 MHz, CDC1 ₃ ): δ= 7.48 (d, 7 = 7.5 Hz, 1H), 7.30 (s, 2H), 6.83 (s, 2H), 6.57 (s, 1H), 5.77 (d, 7 = 7.5 Hz, 1H), 5.66 (s, 1H), 5.57 (bs, 2H), 5.44 (bs, 1H), 4.18 (bs, 1H), 4.11 (bs, 1H), 4.00 (d, J = 11.5 Hz, 1H), 3.80 (s, 1H), 3.77 (s, 3H), 3.41 (s, 3H), 2.25 (bs, 1H), 2.16 (s, 3H); ¹³ C NMR (100 MHz, CDC1 ₃ ): δ= 170.5, 162.6, 159.3, 151.4, 140.3, 136.7, 134.0, 132.6, 129.5, 125.3, 115.5, 102.3, 91.4, 83.0, 80.9, 77.8, 70.1, 69.2, 61.3, 59.0, 55.7, 20.8; IR: ΰ = 3445, 1719, 1665, 1440, 1302, 1081 cm ^"1 ; HRMS (ESf) m/z calcd for C ₂ 7H25Cl5N2Na0 ₉ : 720.9871 ; found 720.9875. Synthesis of 10: To a stirred solution of 19 (5.75 g, 8.0 mmol) in CH ₂ C1 ₂ /DMS0 (1 :1, 80 mL) at 0 °C was added DCC (4.0 g, 20.0 mmol) and dichloroacetic acid (1.02 g, 8.0 mmol). After 1 h at 0 °C, the reaction mixture was diluted with CH ₂ CI ₂ (60 mL) and washed with NaHCC>3 (aq.). The combined organic extracts were dried over Na ₂ S0 ₄ and concentrated in vacuo to give the crude aldehyde which was used directly in the next step after passing through a S1O ₂ pad. To a stirred solution of the crude aldehyde in DMSO/H ₂ 0 (4/1, 80 mL) was added BzCN (1.58 g, 12.0 mmol). After being stirred for 12 h at rt, NaHCC>3 (aq.) was added followed by AcOEt. The aqueous layer was extracted with EtOAc (2x). The combined organic extracts were dried over Na ₂ S0 ₄ and concentrated. The resulting crude material was purified by silica gel

chromatography with AcOEt/hexanes (2:3) to give 10 (3.7 g, 63%) and 21 (1.88 g, 32%). Data for 10: R _f = 0.4 (60% AcOEt/hexanes); ^l U NMR (500 MHz, CDCI3): δ= 7.31 (d, J = 7.5 Hz, 2H), 6.84 (d, J = 10.0 Hz, 2H), 6.56 (s, 1H), 5.83 (dd, J = 5.5 Hz, 1H), 5.58 (m, 1H), 5.40 (bs, 1H), 5.34 (bs, 1H), 5.23 (bs, 1H), 4.67 (d, J = 11.0 Hz, 1H), 4.55 (bs, 1H), 4.35 (s, 1H), 3.77 (s, 3H), 3.40 (s, 3H), 2.18 (s, 3H); ¹³ C NMR (100 MHz, CDCI3): δ= 170.2, 162.2, 159.4, 151.7, 142.2, 136.7, 134.2, 132.3, 129.6, 124.9, 117.2, 115.6, 103.1, 95.1 , 84.2, 78.5, 70.4, 69.3, 61.7, 59.3, 55.8, 43.1 , 21.9; IR: ΰ = 3378, 1755, 1724, 1676, 1463, 1238 cm ^"1 ; HRMS (ESI ⁺ ) m/z calcd for CzsHz _t ClsNsNaOo: 745.9823; found 745.9826. Data for 21 : R _f = 0.45 (60% AcOEt/hexanes); ^X H NMR (500 MHz, CDCI3): δ= 7.31 (d, J = 5.5 Hz, 2H), 6.83 (s, 2H), 6.55 (m, 1H), 5.81 (dd, J = 4.5 Hz, 1H), 5.69 (m, 0.5H), 5.57 (m, 2.5H), 5.49 (m, 0.5H), 5.42 (m, 0.5H), 4.77 (m, 1H), 4.71 (bs, 0.5H), 4.49 (bs, 0.5H), 4.36-4.29 (m, 2H), 3.77 (s, 3H), 3.45 (s, 1.5H), 3.43 (s, 1.5 H), 2.19 (s, 1.5H); 2.16 (s, 1.5 H); ¹³ C NMR (100 MHz, CDCI3): δ= 169.9, 162.7, 159.4, 151.4,

140.0, 136.7, 134.1 , 132.3, 129.5, 125.1, 117.3, 115.5, 102.7, 83.6, 81.1 , 77.9, 73.5, 61.4, 59.4, 55.7, 42.4, 23.4; IR: ΰ = 3378, 1755, 1724, 1676, 1463, 1238 cm ^"1 ; HRMS (ESI ⁺ ) m/z calcd for C28H24Ci5N3Na0 ₉ : 745.9823; found 745.9826. Synthesis of 10 via a Mitsunobu reaction: To a stirred solution of 21 (72.0 mg, 0.10 mmol), ClCHzCOOH (10.0 mg, 0.10 mmol), Ph ₃ P (26.0 mg, 0.10 mmol), and pyridine (8.0 μL·, 0.10 mmol) in toluene (1 mL) was added DIAD (22.0 mg, 0.10 mmol). After 4 h at rt, all volatiles were removed in vacuo and the crude ester was purified by silica gel chromatography. To a stirred solution of the ester in MeOH (2 mL), thiourea (38.0 mg, 0.50 mmol) was added and the reaction mixture was heated to 50 °C. After 4 h at 50 °C, the reaction was cooled down to rt and MeOH was evaporated in vacuo. The residue was purified by silica gel chromatography with hexanes/AcOEt (1 :1) to give 10 (68.0 mg, 90%) as a colorless oil. This reaction was performed for 21 (1.5 g, 2.01 mmol). Synthesis of 26: To a stirred solution of 6 (9.0 g, 20.0 mmol) in MeOH (200 mL), was added the ['Bu ₂ SnCl(OH)] ₂ (0.58 g, 1.0 mmol). Upon completion, the reaction mixture was concentrated in vacuo and filtered through a silica gel plug and concentrated to yield the free alcohol in quantitative yield. To the free alcohol in CH ₂ CI ₂ (400 mL) at 0 °C was added the imidate 23 (see J. S. Helm, Y. Hu, L. Chen, B. Gross, S. Walker, . Am. Chem. Soc. 2003J25, 11168-11169) (11.9 g, 24.0 mmol) and TMSOTf (1.0 mL, 12.0 mmol) was added. After 2 h at 0 °C, the reaction mixture was quenched with aq. sat. NaHC0 ₃ . The aqueous layer was extracted with CH ₂ CI ₂ (2x) and the combined organic extracts was washed with brine, dried over Na ₂ S0 ₄ and evaporated. Purification of the crude material by silica gel chromatography afforded 26 (13.7 g, 92% over two steps) as a colorless liquid. R _f = 0.5 (30% AcOEt/hexanes); ^X H NMR (500 MHz, CDCI3): 3= 7.83 (dd, J = 8.5 Hz, 1H), 7.37 (m, 2H), 7.18 (dd, J = 7.5 Hz, 1H), 7.00 (d, J = 8.0 Hz, 2H), 6.83 (d, J = 5.5 Hz, 2H), 6.21 (s, 0.5H), 6.15 (s, 0.5H), 5.47 (s, 1H), 5.39-5.23 (m, 3H), 4.63-4.55 (m, 1H), 3.78 (d, J = 6.5 Hz, 3H), 3.64 (m, 1H), 3.57 (d, 7 = 9.5 Hz, 1H), 2.32 (s, 1.5H), 2.13 (s, 1.5H), 2.07 (s, 1.5H), 2.01 (s, 1.5H), 2.00 (s, 1.5H), 1.97 (s, 3H); ¹³ C NMR (100 MHz, CDC1 ₃ ): S= 169.9, 159.5, 137.5, 137.2, 136.4, 133.4, 132.7, 132.4, 131.7, 131.6, 129.9, 129.8, 129.0, 126.1, 125.5, 125.0, 115.2, 86.0, 76.1, 71.2, 70.4, 69.7, 69.4, 68.2, 67.1, 55.7, 25.7; IR: ΰ = 3050, 1742, 1613, 1481 cm ^"1 ; HRMS (ESI ⁺ ) m/z calcd for C ₃ 3H32Cl4Na0 ₉ S: 769.0389; found

769.0387.

Synthesis of 24: To a stirred solution of 22 (13.2 g, 30.0 mmol) in MeOH (300 mL) was added the [ ^l Bu ₂ SnCl(OH)] ₂ catalyst (0.87 g, 1.5 mmol). Upon completion, the reaction mixture was concentrated in vacuo and filtered through a silica gel plug and concentrated to yield the free alcohol in 100% yield. To a stirred solution of the primary alcohol (12.0 g, 30.0 mmol) and the imidate 23 (see J. S. Helm, Y. Hu, L. Chen, B. Gross, S. Walker, . Am. Chem. Soc. 2003J25, 11168- 11169) (16.3 g, 33.0 mmol) in CH ₂ C1 ₂ (300 mL) at 0 °C was added TMSOTf (1.0 mL, 6.0 mmol) dropwise. After being stirred for 2 h, the reaction mixture was quenched with aq. sat. NaHCC>3. The aqueous layer was extracted with CH ₂ CI ₂ (2x) and the combined organic extract was washed with brine and dried over Na ₂ S0 ₄ . The evaporation of all volatiles in vacuo gave the crude product which was purified by silica gel chromatography to afford 24 (21.9 g, 98%) as a colorless liquid. R _f = 0.5 (30% AcOEt/hexanes); ^l U NMR (500 MHz, CDC1 ₃ ): δ= 7.91 (m, IH), 7.35-7.18 (m, 7H), 6.85 (s, 2H), 6.23 (d, J = 6.5 Hz, IH), 5.40-5.31 (m, 2H), 5.27 (s, IH), 5.22 (m, IH), 4.85 (d, J = 7.5 Hz, IH), 4.71 (m, IH), 4.52 (d, J = 11.5 Hz, IH), 4.06 (m, IH), 3.80 (s, 3H), 3.69-3.56 (m, 2H), 2.13 (s, 1.5H), 2.10 (s, 1.5H), 1.99 (s, 1.5H), 1.98 (s, 1.5H), 1.96 (s, 1.5H), 1.95 (s, 1.5H); ¹³ C NMR (100 MHz, CDC1 ₃ ): S= 170.1, 170.0, 169.9, 169.7, 159.5, 137.4, 137.2, 136.4, 133.5, 132.5, 131.6, 129.1, 128.5, 128.2, 126.1, 125.6, 125.1, 115.2, 96.4, 96.0, 76.9, 70.4, 69.7, 69.3, 69.0, 68.4, 67.6, 66.9, 60.4, 55.7, 20.8; IR: ΰ = 3055, 1744, 1615, 1484 cm ^"1 ; HRMS (ESf ) m/z calcd for C33H ₃ 2Ci4NaOio: 753.0618; found 753.0615.

Synthesis of 11: To a stirred solution of 24 (10.8 g, 15.0 mmol) in MeOH (600 mL) was added Pd/C (4.5 g, 10 wt %) under N ₂ . H ₂ gas was introduced via double-folded balloon and the reaction mixture was stirred for 4h under ¾. Upon completion, the solution was filtered through Celite and eluted with AcOEt. The organic solvent was evaporated to form the crude product which was used directly without further purification. The crude product was dissolved in dry CH ₂ CI ₂ followed by the addition of CC1 ₃ CN (15.0 mL) and DBU (0.45 mL). Upon completion, all volatiles were evaporated in vacuo. Purification by silica gel chromatography afforded the desired product 11 as colorless oil (11.2 g, 95%). R _f = 0.7 (30% AcOEt/hexanes); ^l U NMR (500 MHz, CDCI3): δ= 8.71 (s, IH), 7.87 (dd, J = 1Η)7.28-7.23 (m, 2H), 6.83 (s, 2H), 6.26 (d, J = 8.5 Hz, IH), 6.19 (s, IH), 5.48-5.40 (m, 3H), 4.23 (m, IH), 3.78 (s, 3H), 3.74 (m, IH), 3.64 (m, IH), 2.18 (s, 1.5H), 2.16 (s, 1.5H), 2.01 (s, 3H), 1.97 (s, 1.5H), 1.94 (s, 1.5H). ¹³ C NMR (100 MHz, CDCI ₃ ): δ= 169.9, 169.8, 169.4, 159.7, 159.5, 137.3, 136.4, 133.4, 132.3, 131.6, 131.4, 129.0,128.8, 126.1, 126.1, 125.8, 125.4, 125.0, 115.2, 94.6, 94.3, 90.6, 76.5, 75.8, 72.8, 71.8,

69.0, 68.2, 68.0, 67.1 , 66.0, 55.8, 55.6, 20.7; IR: ΰ = 3050, 1755, 1680, 1622, 1480 cm l ; HRMS (ESI ⁺ ) m/z calcd for CzsHzeClyN NaOi ₀ : 805.9245; found 805.9249.

Synthesis of 12: To a stirred solution of 10 (2.90 g, 4.0 mmol) and 11 (6.26 g, 8.0 mmol) in dry CH ₂ CI ₂ (50 mL) was added MS 3 A (10.0 g). The reaction was stirred for 30 min. at rt. The reaction mixture was cooled to -5 °C, followed by dropwise addition of BF ₃ ^» OEt ₂ (1.48 mL, 12.0 mmol). After being stirred for 3 h at -5 °C, the reaction was quenched with NaHCC>3 (aq.). The reaction mixture was passed through S1O ₂ pad and eluted with CH ₂ CI ₂ . The Organic layer was separated and dried over Na ₂ S0 ₄ and concentrated in vacuo. Purification by silica gel chromatography afforded 12 (4.04 g, 75%) as an oil. R _f = 0.45 (60% AcOEt/hexanes); ^l H NMR (500 MHz ,CDC1 ₃ ): δ= 7.98 (dd, J = 21 Hz, 1H), 7.30 (s, 4H), 7.25 (s, 1H), 6.84 (s, 4H), 6.56 (s, 1H), 6.27 (s, 0.5H), 6.17 (s, 0.5H), 5.94 (d, J = 7.5 Hz, 1H), 5.88 (m, 1H), 5.58 (m, 3H), 5.39 (bs, 1H), 5.25 (d, J = 10.5 Hz, 1H), 5.22 (s, 1H), 5.00 (d, J = 20.5 Hz, 1H), 4.60 (m, 1H), 4.38 (s, 1H), 4.19 (m, 1H), 3.82 (m, 1H), 3.79 (s, 3H), 3.78 (s, 3H), 3.66 (m, 1H), 3.45 (s, 3H), 2.20 (s, 3H), 2.18 (s, 1.5 H), 2.16 (s, 1.5H), 2.11 (s, 1.5H), 2.06 (s, 1.5H), 2.02 (s, 3H), 1.97 (s, 1.5H), 1.96 (s, 1.5H). ¹³ C NMR (100 MHz, CDC1 ₃ ): S= 169.6, 162.3, 159.6, 149.8, 137.1 , 136.9, 135.8, 134.4, 133.9, 133.0, 131.7, 131.1, 129.7, 129.3, 126.3, 125.1, 124.3, 115.4, 114.7, 103.8, 95.9, 89.7, 89.3, 80.9, 80.173.1, 72.1, 71.8, 68.9, 68.1, 65.7, 63.5, 59.2, 55.8, 29.7, 20.6; IR: ΰ = 3338, 2921, 2250, 1737, 1669, 1465, 1221 cm ^"1 ; HRMS (ESI ⁺ ) m/z calcd for

1367.9968; found 1367.9975.

Synthesis of 8: To a stirred solution of 12 (2.42 g, 1.8 mmol) in toluene (180 mL) was added InCi ₃ (0.4 g, 1.8 mmol) and acetaldoxime (0.67 mL, 10.8 mmol). The reaction mixture was heated at 70 °C for 4 h. Upon completion, the reaction was cooled to rt and all volatiles were evaporated. The crude material was passed through a short S1O ₂ pad. The amide was dissolved in TFA/CH ₂ CI ₂ (1 :2, 75 mL) and stirring was continued for 1 h at rt. The reaction mixture was concentrated in vacuo. The crude product was purified by silica gel chromatography to afford the product 8 as an amorphous solid (1.1 g, 96% over two steps). R _f = 0.3 (95% CHCl ₃ /MeOH); [a] _D ² ° = +75 (c = 0.4 in MeOH); ^l U NMR (500 MHz, CD ₃ OD): 3= 7.83 (d, J = 8.0 Hz, 1H), 5.98 (d, J = 1.5 Hz, 1H), 5.91 (d, 7 = 8.5 Hz, 1H), 5.52 (s, 1H), 5.40 (t, 7 = 5.0 Hz, 1H), 5.28 (m, 2H), 5.01 (s, 1H), 4.49 (d, J = 3.0 Hz, 1H), 4.40 (m, 1H), 4.20 (t, J = 4.0 Hz, 1H), 3.91 , (bs, 1H), 3.64- 3.58 (m, 3H), 3.40 (s, 3H), 2.13 (s, 6H), 2.04 (s, 3H), 2.00 (s, 3H); ¹³ C NMR (100 MHz, CD ₃ OD): S= 172.8, 172.0, 171.7, 171.6, 166.3, 152.2, 142.1 , 103.9, 98.2, 89.4, 83.8, 79.4, 76.7, 75.2, 73.9, 71.1 , 70.5, 67.2, 62.0, 59.4, 20.8, 20.6; IR: ΰ = 3413, 1710, 1680, 1223, 1066 cm ^"1 ; HRMS (ESI ⁺ ) m/z calcd for CzsHssNsNaOie: 654.1753; found 654.1746.

(2-Oxo-5-phenyl-2, 3-dihydro-lH-benzo[e][l,4]diazepin-3-yl)-carbamic acid (2,6-dichloro- 4-methoxy-phenyl)-(2,4-dichloro-phenyl)-methyl ester (28, 29): Racemic 3-amino-l,3- dihydro-5-phenyl-2H-l ,4-benzodiazepin-2-one [(±)-13] was synthesized according the reported procedure (see Η. Yamaguchi, S. Sato, S. Yoshida, K. Takada, M. Itoh, Η. Seto, N. Otake, . Antibiot. 1986, 39, 1047-1053). To a stirred solution of (±)-13 (25.0 mg, 0.10 mmol) in acetone/H ₂ 0 (3: 1, 3 mL) at rt was added (5)-(2,6-dichloro-4-methoxyphenyl)-(2,4-dichlorophenyl-methy l-N- succinimidyl carbonate (5)-14 (58.0 mg, 0.20 mmol) and Pr ₂ NEt (70.0 μί, 0.40 mmol). Upon completion after 4h, the reaction mixture was concentrated in vacuo to remove acetone. The crude material was partitioned between AcOEt (5 mL) and HC1 (1 N, 5 mL). The water phase was extracted with AcOEt (2x). The combined organic extracts was dried over Na ₂ S0 ₄ , and concentrated in vacuo. Purification by silica gel chromatography (hexanes/acetone = 1 :3) afforded the desired diastereomers 28 and 29 as an amorphous solid (31.0 mg each, 98% total yield). This reaction was performed with 1 gram of rac-13 to provide 28 (1.24 g). Data for 28: R _f = 0.34 (95% CHCl ₃ /MeOH); [a] _D ²⁰ = +77 (c = 0.2 in MeOH); ^X H NMR (400 MHz, CD ₃ OD): 3= 7.55-7.49 (m, 5H), 7.45 (m, 2H), 7.36 (m, 4H), 7.25-7.14 (m, 3H), 6.91 (s, 2H), 6.71 (m, 1H), 5.38 (d, J = 8.8 Hz, 1H), 3.82 (s, 3H); ¹³ C NMR (100 MHz, CDC1 ₃ ): 3= 168.6, 168.2, 160.0, 154.9, 138.6, 137.4, 134.5, 133.6, 132.4, 131.6, 130.9, 130.1 , 129.9, 128.5, 127.9, 126.7, 125.1 , 124.5, 121.6, 115.5 , 71.9, 69.5, 56.0; IR: ΰ = 3441 , 1936, 1711 , 1413, 1354, 1222, 1150 cm ^"1 ; HRMS (ESf) m/z calcd for C ₃ oH ₂ iCi ₄ N ₃ Na0 ₄ : 652.0154; found 652.0150; HPLC: retention time, 8.5 min (des >99%). Data for 29: R _f = 0.30 (95% CHCl ₃ :MeOH); [a] _D ²⁰ = +181 (c = 0.2 in MeOH); ^l U NMR (400 MHz, CD ₃ OD): 3= 7.48 (d, J = 16.8 Hz, 1 H), 7.46 (m, 4H), 7.40 (m, 1H), 7.38 (m, 5H), 7.20 (m, 2H), 7.12 (m, 1H), 6.86 (s, 2H), 6.82 (m, 1 H), 5.35 (d, J = 8.0 Hz, 1H), 3.78 (s, 3H); ¹³ C NMR (100 MHz, CDCI3): δ= 170.6, 168.1, 159.7, 154.7, 138.4, 137.2, 134.4, 133.4, 132.2, 131.5, 130.7, 129.9, 129.7, 128.3, 127.7, 126.4, 124.8, 124.3 , 121.3, 115.3, 71.7, 69.0, 55.7; IR: ΰ = 3441 , 1936, 1711 , 1413, 1354, 1222, 1150 cm ^"1 ; HRMS (ESI ⁺ ) m/z calcd for C ₃ oH ₂ iCi ₄ N ₃ Na0 ₄ : 652.0154; found 652.0151 ; HPLC: retention time, 8.0 min (des >99%).

(5)-3-Amino-l,3-dihydro-5-phenyl-2H-l,4-benzodiazepin-2-o ne [(5)-13] : The carbamate 28 (30.0 mg, 0.05 mmol) was dissolved in TFA/ CH ₂ C1 ₂ (1 :4, 2 mL) under N ₂ . After 1 h at rt, the reaction mixture was concentrated in vacuo. The residue was partitioned between NaHC0 ₃ (aq.) and CHCl ₃ /MeOH (10: 1). The aqueous layer was back extracted with CHCl ₃ /MeOH (10: 1). The combined organic extracts were dried over Na ₂ S0 ₄ and concentrated in vacuo. Purification of the crude material by silica gel chromatography afforded the desired product (5)-13 (12.0 mg, 95%) as an amorphous solid and the byproduct ester 29 (24.0 mg, 100%) as an oil. Data for (5)-13:

[a] _D ² ° = -220 (c = 0.2 in CH ₂ C1 ₂ ); ^l U NMR (400 MHz, DMSO-d6): 3= 10.74 (bs, 1H), 7.64 (m, 1H), 7.50 (m, 5H), 7.33 (m, 2H), 7.25 (m, 1H), 4.29 (s, 1H), 2.60 (bs, 2H); ¹³ C NMR (100 MHz, DMSO-d6): 3= 170.5, 164.7, 138.8, 138.6, 131.6, 130.1 , 129.3, 128.2, 126.6, 122.8, 121.2, 70.4; IR: ΰ = 3389, 2935, 1688, 1519, 1251 , 1081 cm ^"1 ; HRMS (ESI ⁺ ) m/z calcd for Ci ₅ Hi ₃ N ₃ NaO: 274.0956; found 274.0958. Data for 30: R _f = 0.6 (95% hexanes/AcOEt); ^l U NMR (500 MHz, CDC13): 3= 7.70 (s, 1H), 7.46 (s, 1H), 7.25 (s, 2H), 6.94 (s, 2H), 3.83 (s, 3H); 13C NMR (100 MHz, CDC13): 3= 172.0, 160.5, 136.8, 135.8, 134.7, 130.9, 126.9, 122.1 , 115.6, 74.3, 55.9; IR: ΰ = 1721, 1438, 1410, 1325 cm-1 ; HRMS (ESI+) mJz calcd for CieHgCLFsNaOs: 470.9126; found 470.9124.

Synthesis of 35: To a vigorously stirred solution of the alcohol 8 (0.20 g, 0.32 mmol) in dry DMSO (10 mL) and dry Et ₃ N (5 mL) was added a solution of S0 ₃ 'Py (0.252 g, 1.60 mmol) in dry DMSO (5 mL) at 20 °C under N ₂ . After 1 h at rt, the reaction mixture was quenched with water (0.1 mL). The DMSO and all volatiles were removed by evaporation in vacuo to give the crude aldehyde 31 which was used without purification in the next step. To a vigorously stirred solution of crude aldehyde 31 in iBuOH (0.8 mL) and 2-methyl-2-butene (0.60 mL) at rt was added a solution of NaH ₂ P0 ₄ (11.0 mg, 0.10 mmol) and NaC10 ₂ (9.0 mg 0.10 mmol) in H ₂ 0 (0.8 mL). After 1 h at rt, the reaction mixture was extracted with AcOEt, then CHCVMeOH (10:1). The combined organic extracts was dried over Na ₂ S0 ₄ and concentrated in vacuo to give the crude acid 32. To a stirred solution of the crude acid 32 (55.0 mg, 96.0 μιηοΐ) and (5)-13 (48.0 mg, 192.0 μιηοΐ) in DMF/H ₂ 0 (2:1, 3 mL) was added EDCI (90.0 mg, 0.48 mmol), glyceroacetonide-Oxyma 17 (0.114 g, 0.48 mmol) and NaHC0 ₃ (0.102 g, 1.20 mmol) sequentially. After 4 h at rt, all volatiles were evaporated and the resulting slurry was partitioned between AcOEt and NaHC0 ₃ (aq.), the aqueous layer was extracted with AcOEt (3x). The combined organic extracts were dried over Na ₂ S0 ₄ and concentrated in vacuo to give the crude product which was purified by silica gel chromatography to afford 35 (66.7 mg, 85% from 8) as an amorphous solid. [a] _D ²⁰ = +99 (c = 0.2 in MeOH); *H NMR (500 MHz, CD ₃ OD): 3= 7.91 (s, 1H), 7.86 (m, 1H), 7.61 (t, J = 7.5 Hz, 1H), 7.53 (m, 2H), 7.43 (m, 2H), 7.31 (m, 2H), 7.22 (m, 1H), 5.98 (s, 2H), 5.96 (s, 1H), 5.50 (s, 1H), 5.41 (s, 1H), 5.09 (m, 1H), 4.97 (m, 1H), 4.74 (m, 2H), 4.37 (s, 1H), 4.18 (m, 1H), 3.89 (m, 2H), 3.76 (m, 2H), 3.44 (s, 1H), 3.41 (s, 3H), 2.14 (s, 3H), 2.11 (s, 3H), 2.05 (s, 3H); ¹³ C NMR (100 MHz, CDC1 ₃ ): S= 172.3, 171.6, 169.3, 166.1, 152.1, 141.5, 140.1 , 133.4, 132.1, 131.8, 130.9, 129.4, 128.7, 124.7, 122.5, 104.0, 98.1 , 88.7, 82.3, 82.9, 79.5, 76.7, 75.9, 73.5, 71.8, 70.9, 70.4, 65.1 , 62.2, 59.5, 20.6; IR: ΰ = 3389, 2935, 1688, 1519, 1251, 1081cm ^"1 ; HRMS (ESI ⁺ ) m/z calcd for C ₃₈ H ₃₈ N ₆ NaOi ₅ : 841.2293; found 841.2296.

Synthesis of UT-01309 (2): To a stirred solution of 34 (13.0 mg, 16.0 μιηοΐ) in THF/H ₂ 0 (10:1 , 0.4 mL) at 0 °C was added LiOH (0.08 mL, 1 M in H ₂ 0). After being stirred for 1 h at 0 °C, the reaction mixture was quenched with THF/AcOH (10:1, 0.08 mL). All volatiles were evaporated in vacuo. Purification by silica gel PTLC (MeOH/CHCl ₃ , 1 :2) afforded 2 (10.60 mg, 95%) as an amorphous solid. R _f = 0.4 (70% CHCl ₃ /MeOH); [a] _D ² ° = +85 (c = 0.1 in MeOH); ^l U NMR (500 MHz, CD ₃ OD): 3= 7.88 (d, 7 = 8.5 Hz, 1H), 7.54 (t, 7 = 8.0 Hz, 1H), 7.41 (m, 3H), 7.33 (m, 2H), 7.26-7.17 (m, 3H), 6.00 (d, 7 = 4.0 Hz, 1H), 5.81 (d, 7 = 3.0, 1H), 5.64 (d, 7 = 8.5 Hz, 1H), 5.33 (s, 1H), 5.19 (d, 7 = 6.0 Hz, 1H), 4.67 (s, 1H), 4.43 (d, 7 = 6.5 Hz, 1H), 4.35 (d, 7 = 5.5 Hz, 1H), 4.3 (m, 1H), 3.89 (t, 7 = 5.5 Hz, 1H), 3.74 (t, 7 = 4.0 Hz, 1H), 3.40 (s, 3H); ¹³ C NMR (100 MHz, CD3OD): 3= 179.1, 173.8, 166.3, 164.9, 152.3, 142.0, 140.0, 133.6, 132.2, 131.9, 131.0, 129.4, 128.6, 124.8, 122.7, 102.7, 100.7, 91.1, 83.6, 80.0, 76.3, 75.8, 74.1, 72.7, 71.5, 70.6, 68.3, 62.8, 58.4; IR: ΰ = 3411 , 2933, 1696, 1515, 1279 cm ^"1 ; HRMS (ESI ⁺ ) m/z calcd for C ₃₂ H ₃₂ N ₆ NaOi ₂ : 715.1976; found 715.1972.

Synthesis of 34: To a stirred solution of the acid 32 (55.0 mg, 96.0 μηιοΐ) and 32 (31.0 mg, 192.0 μηιοΐ) in H ₂ 0 (1.0 mL) was added EDCI (90.0 mg, 0.48 mmol), glyceroacetonide-Oxyma 17 (0.114 g, 0.48 mmol) and NaHC0 ₃ (0.102 g, 1.20 mmol) sequentially. After being stirred for 4 h at rt, all volatiles were evaporated and the resulting slurry was partitioned between EtOAc and aq. NaHCC , the aqueous layer was extracted with AcOEt (3x). The combined organic extracts were dried over Na ₂ S0 ₄ and concentrated in vacuo to give the crude product. For data collections, a portion was purified by silica gel chromatography to afford 34 as an amorphous solid (57.0 mg, 85% from 8). [a] _D ²⁰ = +103 (c = 0.3 in CHCI ₃ ); *H NMR (500 MHz, CDC1 ₃ ): 3= 9.72 (broad, 1H), 7.96 (d, 7 = 6.8 Hz, 1H), 7.45 (d, 7 = 8.0 Hz, 1H), 7.39, (broad, 1H), 7.20 (broad, 1H), 6.23 (broad, 1H), 6.05 (d, 7 = 3.2 Hz, 1H), 5.80 (s, 1H), 5.69 (t, 7 = 3.6 Hz, 1H), 5.49 (s, 1H), 5.32-5.26 (m, 2H), 4.61 (dd, 7 = 7.2, 10.8 Hz, 1H), 4.55 (s, 1H), 4.39 (d, 7 = 5.6 Ηζ,ΙΗ), 4.01 (s, 1H), 3.30 (s, 2H), 3.25 (s, 3H), 2.11 (s, 6H), 2.06 (s, 3H), 1.86 (m, 2H), 1.60 (m, 3H), 1.40 (m, 1H); ¹³ C NMR (100 MHz, CDC1 ₃ ): 3= 176.1 , 170.3, 170.2, 170.12, 170.08, 169.03, 169.00, 163.5, 159.1 , 150.8, 144.5, 140.6, 104.1 , 103.8, 98.0, 82.0, 73.3, 65.2, 63.1 , 59.1, 52.0, 42.4, 31.6, 28.8, 20.95, 20.88, 20.83; IR: ΰ = 3379, 2930, 1691 , 1509, 1250, 1070 cm ^"1 ; HRMS (ESf) m/z calcd for C ₂ 9H ₈ N ₅ NaOi5: 718.2178; found 718.2186. Synthesis of Capuramycin (1): To a stirred solution of 34 (11.0 mg, 16.0 μιηοΐ) in THF/H ₂ 0 (10:1, 0.4 mL) at 0 °C was added LiOH (0.08 mL, 1 M in H ₂ 0). After being stirred for 1 h at 0 °C, the reaction mixture was quenched with THF/AcOH (10:1, 0.08 mL). All volatiles were evaporated in vacuo. Purification by silica gel PTLC (MeOH/CHCi ₃ , 1 :2) afforded the desired product 1 (8.60 mg, 95%) as an amorphous solid. R _f = 0.4 (70% CHCl ₃ /MeOH); [a] _D ² ° = +98 (c = 0.1 in H ₂ 0); ^X H NMR (400 MHz, CD ₃ OD): 3= 7.71 (d, 7 = 8.0 Hz, 1H), 5.97 (s, 1H), 5.82 (d, 7 = 8.0 Hz, 1H), 5.73 (s, 1H), 5.35 (s, 1H), 4.59 (d, 7 = 11.2 Hz, 2H), 4.47 (s, 1H), 4.44 (d, 7 = 4.8 Hz, 1H), 4.34 (s, 1H), 4.15 (s, 1H), 3.71 (t, 7 = 4.8 Hz, 1H), 3.26 (s, 3H), 1.94-1.57 (m, 6H), 1.32 (m, 2H). ¹³ C NMR (100 MHz, D ₂ 0): δ= 176.3, 173.0, 166.1, 161.4, 151.2, 141.5, 141.0, 109.4, 101.8, 99.3, 90.1 , 81.6, 78.1, 75.5, 71.9, 64.7, 61.7, 57.8, 52.2, 41.4, 30.3, 27.3; IR: ΰ = 3411 , 2933, 1696, 1515, 1279 cm ^"1 ; HRMS (ESf ) mJz calcd for C ₂ 3H3iN ₅ NaOi2: 592.1867; found 592.1864.

Biological Evaluation In vitro biological evaluation of UT-01309: UT-01309 (2) was identified by cell-based assays of a small optimized library of capuramycin analogs. In vitro biological activities of 2

synthesized here were evaluated against Mtb MraY (IC ₅₀ ) and a series of bacteria including Mycobacterium spp. The IC ₅₀ value of 2 against Mtb MraY was 5.5 nM (1: IC ₅₀ 18 nM against Mtb MraY). UT-01309 did not exhibit growth inhibitory activity against a series of Gram- positive and -negative bacteria including S. aureus, E. faecalis, E. coli, K. pneumonia, and P. aeruginosa even at 400 μg/mL concentrations. UT-01309 showed bactericidal activities specific to Mycobacterium spp. UT-01309 killed M. tuberculosis (H37Rv) completely at 2.5 μg/mL concentrations whereas capuramycin required 12.0 μg/mL. UT-01309 showed the MIC value of 6.5 μg/mL against M. smegmatis. Significantly, UT-01309 is active against drug-resistant M. tuberculosis (e.g. M. tuberculosis H37Rv INI Ir and M. tuberculosis H37Rv RFPr), and did not exhibit cytotoxicity against Vero monkey kidney cells and HepG2 human hepatoblastoma cells even at 250 μg/mL concentrations.

INCORPORATION BY REFERENCE

All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference.