CROSS-REFERENCE TO RELATED APPLICATIONS

[0001] The application claims the benefit of, and priority to, U.S.S.N. 63/246,118, filed September 20, 2021; the contents of which is incorporated herein by reference.

BACKGROUND

[0002] The Coronaviridae family of viruses are enveloped, single-stranded, positive-sense RNA viruses and include 141 species classified into four genera according to their phylogenetic relationships: a-, [3-, y-, and 5-coronavirus. Coronaviruses (CoVs) are zoonotic viruses that infect a variety of animals from whales to birds, bats, cats, and humans. Typically, CoV infection results in mild to moderate respiratory tract infections; however, some CoV species are extremely virulent and can result in widespread fatality. Severe acute respiratory syndrome coronavirus (SARS-CoV) is a human CoV responsible for the first pandemic of the 21 ^st century, infecting over 8,000 people with a 10% mortality rate. Middle East respiratory syndrome coronavirus (MERS-CoV) was identified in November 2012 and had since infected over 1,600 people in 26 countries with a 36% mortality rate. More recently, COVID-19 (SARS CoV2) coronaviruses have raised a global pandemic since first identified in late 2019. Therefore, it is important to identify coronavirus drug targets that can be utilized for the development of broadspectrum anti-coronaviral therapeutics to combat infections of existing and emerging coronaviruses.

[0003] All CoVs express a >800 kDa replicase polyprotein that contains either two or three cysteine proteases, the papain-like protease(s) (PLPpro, nsp3, or PLP1 and PLP2) and the SC- like protease (3CLpro, nsp5, or Mpro). These proteases process the CoV replicase polyprotein by cleaving it into 16 non-structural proteins, which are responsible for a variety of aspects of CoV replication. The CoV 3CLpro is responsible for processing 11 cleavage sites of within the replicase polyprotein and is essential for CoV replication, making it a highly valuable target for therapeutic development. The overall active site architecture and substrate recognition pockets are structurally conserved across CoV 3CLpros, increasing its attractiveness as a target for the development of broad-spectrum anti-CoV therapeutics. Moreover, high sequence conservation in the vicinity of active site among CoV 3CLpros from different coronavirus subclasses make them an excellent target for the development of broad-spectrum therapeutics for coronavirus infections. Accordingly, the development of CoV 3CLpro inhibitors is a promising path for the treatment of respiratory tract infections and related diseases.

[0004] Numerous studies on targeting the immediate zoonotic reservoirs of coronaviruses with small molecule inhibitors have helped inform structure -based design strategies aimed at creating molecular scaffolds that may aid in the development of therapeutic against coronaviral infection; however, small molecule antiviral agents or effective commercially available broadspectrum therapeutics have not yet been identified. There is a critical need for the development of broad-spectrum CoV therapeutics to overcome the challenges of traditional anti-CoV therapeutic development, as broad-spectrum therapeutics can be rapidly implemented upon zoonotic disease outbreak.

SUMMARY

[0005] The disclosure provides, for example, a process for the preparation of compounds which may be inhibitors of proteases, such as the 3C, CL- or 3CL-like protease.

[0006] In certain embodiments, provided herein is a process for the preparation of a compound of Formula I: Formula I.

DETAILED DESCRIPTION

[0007] The features and other details of the disclosure will now be more particularly described. Before further description of the present disclosure, certain terms employed in the specification, examples and appended claims are collected here. These definitions should be read in light of the remainder of the disclosure and as understood by a person of skill in the art. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by a person of ordinary skill in the art.

Definitions

[0008] The term “treating” includes any effect, e.g., lessening, reducing, modulating, or eliminating, that results in the improvement of the condition, disease, disorder and the like, including a reduction of viral shedding in asymptomatic individuals and prophylaxis of exposed individuals, independent of symptoms

[0009] The term “alkyl” as used herein refers to a saturated straight or branched hydrocarbon. Exemplary alkyl groups include, but are not limited to, straight or branched hydrocarbons of 1-6, 1-4, or 1-3 carbon atoms, referred to herein as Ci-ealkyl, Ci-4alkyl, and Cisalkyl, respectively. Exemplary alkyl groups include, but are not limited to, methyl, ethyl, propyl, isopropyl, 2-methyl-l -butyl, 3-methyl-2-butyl, 2-methyl-l -pentyl, 3 -methyl- 1 -pentyl, 4- methyl-1 -pentyl, 2 -methyl -2 -pentyl, 3-methyl-2-pentyl, 4-methyl-2-pentyl, 2,2-dimethyl-l -butyl, 3, 3 -dimethyl- 1 -butyl, 2 -ethyl- 1 -butyl, butyl, isobutyl, t-butyl, pentyl, isopentyl, neopentyl, hexyl, etc

[00010] The term “alkenyl” as used herein refers to an unsaturated straight or branched hydrocarbon having at least one carbon-carbon double bond. Exemplary alkenyl groups include, but are not limited to, a straight or branched group of 2-6 or 3-4 carbon atoms, referred to herein as Ci-Csalkenyl, Cb-Cealkcnyl. and C3-C4alkenyl, respectively. Exemplary alkenyl groups include, but are not limited to, vinyl, allyl, butenyl, pentenyl, etc.

[00011] The term “alkynyl” as used herein refers to an unsaturated straight or branched hydrocarbon having at least one carbon-carbon triple bond. Exemplary alkynyl groups include, but are not limited to, straight or branched groups of 2-6, or 3-6 carbon atoms, referred to herein as C2-ealkynyl, and Cvealkynyl. respectively. Exemplary alkynyl groups include, but are not limited to, ethynyl, propynyl, butynyl, pentynyl, hexynyl, methylpropynyl, etc.

[00012] The term “alkoxy” as used herein refers to a straight or branched alkyl group attached to oxygen (alkyl-O-). Exemplary alkoxy groups include, but are not limited to, alkoxy groups of 1-6 or 2-6 carbon atoms, referred to herein as Ci-Csalkoxy, Ci-Cealkoxy, and C2- Cealkoxy, respectively. Exemplary alkoxy groups include, but are not limited to methoxy, ethoxy, isopropoxy, etc. [00013] The term “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 electrons shared in a cyclic array) having 6-14 ring carbon atoms and zero heteroatoms provided in the aromatic ring system (“Ce-14 aryl”). In some embodiments, an aryl group has six ring carbon atoms (“Cearyl”; e.g., phenyl). In some embodiments, an aryl group has ten ring carbon atoms (“Cio aryl”; e.g., naphthyl such as 1-naphthyl and 2-naphthyl). In some embodiments, an aryl group has fourteen ring carbon atoms (“Ce aryl”; e.g., anthracyl). “Aryl” also includes ring systems wherein the aryl ring, as defined above, is fused with one or more carbocyclyl or heterocyclyl groups wherein the radical or 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. Typical aryl groups include, but are not limited to, groups derived from aceanthrylene, acenaphthylene, acephenanthrylene, anthracene, azulene, benzene, chrysene, coronene, fluoranthene, fluorene, hexacene, hexaphene, hexalene, as-indacene, s-indacene, indane, indene, naphthalene, octacene, octaphene, octalene, ovalene, penta-2,4-diene, pentacene, pentalene, pentaphene, perylene, phenalene, phenanthrene, picene, pleiadene, pyrene, pyranthrene, rubicene, triphenylene, and trinaphthalene. Particularly aryl groups include phenyl, naphthyl, indenyl, and tetrahydronaphthyl. Examples of representative substituted aryls include the following

[00015] wherein one of R ⁵⁶ and R ⁵⁷ may be hydrogen and at least one of R ⁵⁶ and R ⁵⁷ is each independently selected from Ci-Cs alkyl, Ci-Cs haloalkyl, 4-10 membered heterocyclyl, alkanoyl, Ci-Cs alkoxy, heteroaryloxy, alkylamino, arylamino, heteroarylamino, NR ⁵⁸ COR ⁵⁹ , NR ⁵⁸ SOR ⁵⁹ NR ⁵⁸ SO ₂ R ⁵⁹ , COOalkyl, COOaryl, CONR ⁵⁸ R ⁵⁹ , CONR ⁵⁸ OR ⁵⁹ , NR ⁵⁸ R ⁵⁹ , SO ₂ NR ⁵⁸ R ⁵⁹ , S-alkyl, SOalkyl, SO ₂ alkyl, Saryl, SOaryl, SO ₂ aryl; or R ⁵⁶ and R ⁵⁷ may be joined to form a cyclic ring (saturated or unsaturated) from 5 to 8 atoms, optionally containing one or more heteroatoms selected from the group N, O, or S. R ⁶⁰ and R ⁶¹ are each independently hydrogen, Ci-Cs alkyl, C1-C4 haloalkyl, C3-C10 cycloalkyl, 4-10 membered heterocyclyl, Ce-Cio aryl, substituted Ce-Cio aryl, 5-10 membered heteroaryl, or substituted 5-10 membered heteroaryl.

[00016] The term “carbonyl” as used herein refers to the radical -C(O)-. [00017] The term “cyano” as used herein refers to the radical -CN.

[00018] The terms “cycloalkyl” or a “carbocyclic group” as used herein refers to a saturated or partially unsaturated hydrocarbon group of, for example, 3-6, or 4-6 carbons, referred to herein as Cs-Ciocycloalkyl, Ci-ecycloalkyl or C4-6Cycloalkyl, respectively. Exemplary cycloalkyl groups include, but are not limited to, cyclohexyl, cyclopentyl, cyclopentenyl, cyclobutyl or cyclopropyl.

[00019] The terms “halo” or “halogen” as used herein refer to F, Cl, Br, or I.

[00020] The terms “haloalkyl” as used herein refers to an alkyl radical in which the alkyl group is substituted with one or more halogens. Typical haloalkyl groups include, but are not limited to, trifluoromethyl (i.e. CFs), difluoromethyl, fluoromethyl, chloromethyl, dichloromethyl, dibromoethyl, tribromomethyl, tetrafluoroethyl, and the like. Exemplary haloalkyl groups include, but are not limited to, straight or branched hydrocarbons of 1-6, 1-4, or 1-3 carbon atoms substituted with a halogen (i.e. Cl, F, Br and I), referred to herein as Ci- ehaloalkyl, Ci-4 haloalkyl, and Ci-shaloalkyl, respectively.

[00021] The term “hetero” when used to describe a compound or a group present on a compound means that one or more carbon atoms in the compound or group have been replaced by a nitrogen, oxygen, or sulfur heteroatom. Hetero may be applied to any of the hydrocarbyl groups described above such as alkyl, e.g., heteroalkyl, cycloalkyl, e.g., heterocyclyl, aryl, e.g,. heteroaryl, cycloalkenyl, e.g. cycloheteroalkenyl, and the like having from 1 to 5, and particularly from 1 to 3 heteroatoms.

[00022] The terms “heteroaryl” or “heteroaromatic group” as used herein refers to an aromatic 5-10 membered ring system containing one or more heteroatoms, for example one to three heteroatoms, such as nitrogen, oxygen, and sulfur. The term may also be used to refer to a 5-7 membered monocyclic heteroaryl or an 8-10 membered bicyclic heteroaryl. Where possible, said heteroaryl ring may be linked to the adjacent radical though carbon or nitrogen. Examples of heteroaryl rings include but are not limited to furan, thiophene, pyrrole, pyrrolopyridine, indole, thiazole, oxazole, isothiazole, isoxazole, imidazole, benzoimidazole, imidazopyridine, pyrazole, triazole, pyridine or pyrimidine, etc.

[00023] Examples of representative heteroaryls include the following:

[00024] wherein each Z is selected from carbonyl, N, NR ⁶⁵ , O, and S; and R ⁶⁵ is each independently hydrogen, Ci-Cs alkyl, C3-C10 cycloalkyl, 4-10 membered heterocyclyl, Ce-Cio aryl, or 5-10 membered heteroaryl.

[00025] The terms “heterocyclyl,” “heterocycle,” or “heterocyclic group” are art-recognized and refer to saturated or partially unsaturated 4-10 membered ring structures, whose ring structures include one to three heteroatoms, such as nitrogen, oxygen, and sulfur. Where possible, heterocyclyl rings may be linked to the adjacent radical through carbon or nitrogen. The term may also be used to refer to 4-10 membered saturated or partially unsaturated ring structures that are bridged, fused or spirocyclic ring structures, whose ring structures include one to three heteroatoms, such as nitrogen, oxygen, and sulfur. Examples of heterocyclyl groups include, but are not limited to, pyrrolidine, piperidine, morpholine, thiomorpholine, piperazine, oxetane, azetidine, tetrahydrofuran, dihydrofuran, dihydropyran, tetrahydropyran, etc. In some embodiments, the heterocycle is a spiro heterocycle (e.g., 2,8-diazaspiro[4.5]decane). In some embodiments, the heterocycle is a bridged heterocycle (e.g., octahydro-lH-4,7- methanoisoindole). "Spiro heterocyclyl," or “spiro heterocycle” refers to a polycyclic heterocyclyl with rings connected through one common atom (called a spiro atom), wherein the rings have one or more heteroatoms selected from the group consisting of N, O, and S(O) _m (wherein m is an integer of 0 to 2) as ring atoms. Representative examples of heterocyclyl include, for example:

[00026] The terms “hydroxy” and “hydroxyl” as used herein refers to the radical -OH.

[00027] The term “oxo” as used herein refers to the radical =0.

[00028] “Pharmaceutically or pharmacologically acceptable” include molecular entities and compositions that do not produce an adverse, allergic or other untoward reaction when administered to an animal, or a human, as appropriate. For human administration, preparations should meet sterility, pyrogenicity, and general safety and purity standards as required by FDA Office of Biologies standards.

[00029] The term “pharmaceutically acceptable carrier” or “pharmaceutically acceptable excipient” as used herein refers to any and all solvents, dispersion media, coatings, isotonic and absorption delaying agents, and the like, that are compatible with pharmaceutical administration. The use of such media and agents for pharmaceutically active substances is well known in the art. The compositions may also contain other active compounds providing supplemental, additional, or enhanced therapeutic functions.

[00030] The term “pharmaceutical composition” as used herein refers to a composition comprising at least one compound as disclosed herein formulated together with one or more pharmaceutically acceptable carriers.

[00031] ‘Individual,” “patient,” or “subject” are used interchangeably and include any animal, including mammals, preferably mice, rats, other rodents, rabbits, dogs, cats, swine, cattle, sheep, horses, or primates, and most preferably humans. The compounds of the disclosure can be administered to a mammal, such as a human, but can also be administered to other mammals such as an animal in need of veterinary treatment, e.g., domestic animals (e.g., dogs, cats, and the like), farm animals (e.g., cows, sheep, pigs, horses, and the like) and laboratory animals (e.g., rats, mice, guinea pigs, and the like). “Modulation” includes antagonism (e.g., inhibition), agonism, partial antagonism and/or partial agonism.

[00032] In the present specification, the term “therapeutically effective amount” means the amount of the subject compound that will elicit the biological or medical response of a tissue, system or animal, (e.g. mammal or human) that is being sought by the researcher, veterinarian, medical doctor or other clinician. The compounds of the disclosure are administered in therapeutically effective amounts to treat a disease. Alternatively, a therapeutically effective amount of a compound is the quantity required to achieve a desired therapeutic and/or prophylactic effect.

[00033] The term "pharmaceutically acceptable salt(s)" as used herein refers to salts of acidic or basic groups that may be present in compounds used in the compositions. Compounds included in the present compositions that are basic in nature are capable of forming a wide variety of salts with various inorganic and organic acids. The acids that may be used to prepare pharmaceutically acceptable acid addition salts of such basic compounds are those that form non-toxic acid addition salts, i.e., salts containing pharmacologically acceptable anions, including, but not limited to, malate, oxalate, chloride, bromide, iodide, nitrate, sulfate, bisulfate, phosphate, acid phosphate, isonicotinate, acetate, lactate, salicylate, citrate, tartrate, oleate, tannate, pantothenate, bitartrate, ascorbate, succinate, maleate, gentisinate, fumarate, gluconate, glucaronate, saccharate, formate, benzoate, glutamate, methanesulfonate, ethanesulfonate, benzenesulfonate, p-toluenesulfonate and pamoate (i.e., l,l'-methylene-bis-(2-hydroxy-3- naphthoate)) salts. Compounds included in the present compositions that are acidic in nature are capable of forming base salts with various pharmacologically acceptable cations. Examples of such salts include alkali metal or alkaline earth metal salts, particularly calcium, magnesium, sodium, lithium, zinc, potassium, and iron salts. Compounds included in the present compositions that include a basic or acidic moiety may also form pharmaceutically acceptable salts with various amino acids. The compounds of the disclosure may contain both acidic and basic groups; for example, one amino and one carboxylic acid group. In such a case, the compound can exist as an acid addition salt, a zwitterion, or a base salt.

[00034] The compounds of the disclosure may contain one or more chiral centers and, therefore, exist as stereoisomers. The term “stereoisomers” when used herein consist of all enantiomers or diastereomers. These compounds may be designated by the symbols “(+),” “R” or “S,” depending on the configuration of substituents around the stereogenic carbon atom, but the skilled artisan will recognize that a structure may denote a chiral center implicitly. The present disclosure encompasses various stereoisomers of these compounds and mixtures thereof. Mixtures of enantiomers or diastereomers may be designated “(±)” in nomenclature, but the skilled artisan will recognize that a structure may denote a chiral center implicitly. [00035] The compounds of the disclosure may contain one or more double bonds and, therefore, exist as geometric isomers resulting from the arrangement of substituents around a carbon-carbon double bond. The symbol — denotes a bond that may be a single, double or triple bond as described herein. Substituents around a carbon-carbon double bond are designated as being in the “Z” or “E” configuration wherein the terms “Z” and “E” are used in accordance with IUPAC standards. Unless otherwise specified, structures depicting double bonds encompass both the “E” and “Z” isomers. Substituents around a carbon-carbon double bond alternatively can be referred to as “cis” or “trans,” where “cis” represents substituents on the same side of the double bond and “trans” represents substituents on opposite sides of the double bond.

[00036] Compounds of the disclosure may contain a carbocyclic or heterocyclic ring and therefore, exist as geometric isomers resulting from the arrangement of substituents around the ring. The arrangement of substituents around a carbocyclic or heterocyclic ring are designated as being in the “Z” or “E” configuration wherein the terms “Z” and “E” are used in accordance with IUPAC standards. Unless otherwise specified, structures depicting carbocyclic or heterocyclic rings encompass both “Z” and “E” isomers. Substituents around a carbocyclic or heterocyclic rings may also be referred to as “cis” or “trans”, where the term “cis” represents substituents on the same side of the plane of the ring and the term “trans” represents substituents on opposite sides of the plane of the ring. Mixtures of compounds wherein the substituents are disposed on both the same and opposite sides of plane of the ring are designated “cis/trans.”

[00037] Individual enantiomers and diastereomers of compounds of the present disclosure can be prepared synthetically from commercially available starting materials that contain asymmetric or stereogenic centers, or by preparation of racemic mixtures followed by resolution methods well known to those of ordinary skill in the art. These methods of resolution are exemplified by (1) attachment of a mixture of enantiomers to a chiral auxiliary, separation of the resulting mixture of diastereomers by recrystallization or chromatography and liberation of the optically pure product from the auxiliary, (2) salt formation employing an optically active resolving agent, (3) direct separation of the mixture of optical enantiomers on chiral liquid chromatographic columns or (4) kinetic resolution using stereoselective chemical or enzymatic reagents. Racemic mixtures can also be resolved into their component enantiomers by well- known methods, such as chiral-phase liquid chromatography or crystallizing the compound in a chiral solvent. Stereoselective syntheses, a chemical or enzymatic reaction in which a single reactant forms an unequal mixture of stereoisomers during the creation of a new stereocenter or during the transformation of a pre-existing one, are well known in the art. Stereoselective syntheses encompass both enantio- and diastereoselective transformations, and may involve the use of chiral auxiliaries. For examples, see Carreira and Kvaemo, Classics in Stereoselective Synthesis, Wiley-VCH: Weinheim, 2009.

[00038] The compounds disclosed herein can exist in solvated as well as unsolvated forms with pharmaceutically acceptable solvents such as water, ethanol, and the like, and it is intended that the disclosure embrace both solvated and unsolvated forms. In one embodiment, the compound is amorphous. In one embodiment, the compound is a single polymorph. In another embodiment, the compound is a mixture of polymorphs. In another embodiment, the compound is in a crystalline form.

[00039] The disclosure also embraces isotopically labeled compounds of the disclosure which are identical to those recited herein, except that one or more atoms are replaced by an atom having an atomic mass or mass number different from the atomic mass or mass number usually found in nature. Examples of isotopes that can be incorporated into compounds of the disclosure include isotopes of hydrogen, carbon, nitrogen, oxygen, phosphorus, sulfur, fluorine and chlorine, such as ² H, ³ H, ¹³ C, ¹⁴ C, ¹⁵ N, ¹⁸ O, ¹⁷ 0, ³¹ P, ³² P, ³⁵ S, ¹⁸ F, and ³⁶ C1, respectively. For example, a compound of the disclosure may have one or more H atom replaced with deuterium.

[00040] Certain isotopically-labeled disclosed compounds (e.g., those labeled with ³ H and ¹⁴ C) are useful in compound and/or substrate tissue distribution assays. Tritiated (i.e., ³ H) and carbon- 14 (i.e., ¹⁴ C) isotopes are particularly preferred for their ease of preparation and detectability. Further, substitution with heavier isotopes such as deuterium (i.e., ² H) may afford certain therapeutic advantages resulting from greater metabolic stability (e.g., increased in vivo half-life or reduced dosage requirements) and hence may be preferred in some circumstances. Isotopically labeled compounds of the disclosure can generally be prepared by following procedures analogous to those disclosed in the examples herein by substituting an isotopically labeled reagent for a non-isotopically labeled reagent.

[00041] The term “prodrug” refers to compounds that are transformed in vivo to yield a disclosed compound or a pharmaceutically acceptable salt, hydrate or solvate of the compound. The transformation may occur by various mechanisms (such as by esterase, amidase, phosphatase, oxidative and or reductive metabolism) in various locations (such as in the intestinal lumen or upon transit of the intestine, blood or liver). Prodrugs are well known in the art (for example, see Rautio, Kumpulainen, et al, Nature Reviews Drug Discovery 2008, 7, 255). For example, if a compound of the disclosure or a pharmaceutically acceptable salt, hydrate or solvate of the compound contains a carboxylic acid functional group, a prodrug can comprise an ester formed by the replacement of the hydrogen atom of the acid group with a group such as (Ci-x)alkyl. (C2-i2)alkylcarbonyloxymethyl, l-(alkylcarbonyloxy)ethyl having from 4 to 9 carbon atoms, 1 -methyl- 1 -(alkylcarbonyloxy) -ethyl having from 5 to 10 carbon atoms, alkoxy carbonyloxymethyl having from 3 to 6 carbon atoms, 1 -(alkoxy carbonyloxy)ethyl having from 4 to 7 carbon atoms, 1 -methyl- 1 -(alkoxy carbonyloxy)ethyl having from 5 to 8 carbon atoms, N-(alkoxycarbonyl)aminomethyl having from 3 to 9 carbon atoms, l-(N-(alkoxycarbonyl)amino)ethyl having from 4 to 10 carbon atoms, 3-phthalidyl, 4-crotonolactonyl, gamma-butyrolacton-4-yl, di-N,N-(Ci-2)alkylamino(C2-3)alkyl (such as [3- dimethylaminoethyl), carbamoyl-(Ci-2)alkyl, N,N-di(Ci-2)alkylcarbamoyl-(Ci-2)alkyl and piperidino-, pyrrolidine- or morpholino(C2-3)alkyl.

[00042] Similarly, if a compound of the disclosure contains an alcohol functional group, a prodrug can be formed by the replacement of the hydrogen atom of the alcohol group with a group such as (Ci-6)alkylcarbonyloxymethyl, l-((Ci-6)alkylcarbonyloxy)ethyl, l-methyl-l-((Ci- 6)alkylcarbonyloxy)ethyl (Ci-6)alkoxycarbonyloxymethyl, N-(Ci-6)alkoxycarbonylaminomethyl, succinoyl, (Ci-e)alkylcarbonyl, a-amino(Ci-4)alkylcarbonyl, arylalkylcarbonyl and a- aminoalkylcarbonyl, or a-aminoalkylcarbonyl-a-aminoalkylcarbonyl, where each > - aminoalkylcarbonyl group is independently selected from the naturally occurring L-amino acids, P(O)(OH)2, -P(O)(O(Ci-e)alkyl)2or glycosyl (the radical resulting from the removal of a hydroxyl group of the hemiacetal form of a carbohydrate).

[00043] If a compound of the disclosure incorporates an amine functional group, a prodrug can be formed, for example, by creation of an amide or carbamate, an N-alkylcarbonyloxyalkyl derivative, an (oxodioxolenyl)methyl derivative, an N-Mannich base, imine or enamine. In addition, a secondary amine can be metabolically cleaved to generate a bioactive primary amine, or a tertiary amine can metabolically cleaved to generate a bioactive primary or secondary amine. For examples, see Simplicio, et al., Molecules 2008, 13, 519 and references therein.

[00044] The term "warhead" or "warhead group" as used herein refers to a functional group present on a compound wherein that functional group is capable of reversibly or irreversibly participating in a reaction with a protein, e.g., 3C or 3CL protease (e.g., with a cysteine on the protease such as Cys 145). Warheads may, for example, form covalent bonds with the protein, or may create stable transition states, or be a reversible or an irreversible alkylating agent. For example, the warhead moiety can be a functional group on an inhibitor that can participate in a bond-forming reaction, wherein a new covalent bond is formed between a portion of the warhead and a donor, for example an amino acid residue of a protein. In embodiments, the warhead is an electrophile and the “donor” is a nucleophile such as the side chain of a cysteine residue. As provided herein, a warhead may include a nitrile group. For example, nitriles may be reversible covalent warheads for cysteine protease inhibition. For example, where the mechanism of action may involve a formation of reversible covalent bond between the nitrile and the active cysteine to form a thioimidate adduct. Reaction of cysteine of glutathione or other proteins is generally reversible, while the reaction with cysteine or aminoethylthiols generally irreversibly forms a thiazolidine adduct. It can be appreciated that contemplated compounds herein may be a reversible or an irreversible inhibitor. It will be appreciated to one of skilled in the art that the compounds disclosed herein that include the warheads above also contemplate the precursors to those compounds, for example, where a cyano moiety involved in a warheads may be replaced with e.g., a halo moiety.

[00045] It will be appreciated to one of skilled in the art that the compounds disclosed herein can also irreversibly bind, or may otherwise inhibit e.g., a virus protein via any other mechanism of action.

[00046] The term "inhibitor" as used herein refers to a compound that binds to and /or inhibits a target protease with measurable affinity.

[00047] The term “reversible” or "reversible inhibitor" as used herein refers to a protease inhibitor that associates with a protease in such a way as to inhibit the activity of the protease while the protease and inhibitor are bound, but does not associate with a protease in such a way as to inhibit the activity of the protease when the protease and inhibitor are no longer bound. Reversible inhibitors can affect inhibition by competing with substrate for binding to the active site of the protease (competitive reversible inhibitor), or by associating with the protease bound to its substrate in a way to make the complex inactive (uncompetitive reversible inhibitor), or by associating with the protease and/or protease-substrate complex in a way that inhibits the activity of either and/or both.

[00048] As used herein, the term “irreversible” or “irreversible inhibitor” refers to an inhibitor (i.e., a compound) that can be covalently bonded to a target protease in a substantially non-reversible manner. An irreversible inhibitor will remain substantially bound to the target protease once covalent bond formation has occurred. Irreversible inhibitors usually display time dependency, whereby the degree of inhibition increases with the time with which the inhibitor is in contact with the enzyme. In certain embodiments, an irreversible inhibitor will remain substantially bound to target protease once covalent bond formation has occurred and will remain bound for a time period that is longer than the life of the protein.

[00049] As used herein and unless otherwise specified, the term “purity” or “pure” means one or more of the following: chiral purity, enantiomeric purity/enantiomerically pure, free of impurities (e.g., primary amide impurities, epimer impurities, and isomer impurities), substantially pure, and purity of any intermediates in the process of preparing a compound (for example, a compound of Formula I).

I. Viral Protease Inhibitor Compounds

[00050] Provided herein in part is a process for the preparation of a compound of Formula I:

[00051] In various embodiments, provided herein is a process for the preparation of a compound of Formula I: Formula I; comprising: providing a compound of Formula VI: Formula VI; coupling the compound of Formula VI with a compound of Formula VII, or a salt thereof:

Formula VIII: Formula VIII; amidating the compound of Formula VIII to produce a compound of Formula IX: Formula IX; and dehydrating the compound of Formula IX to provide the compound of Formula I; wherein R ¹ is selected from the group consisting of H, halogen, Ci-ealkyl, and Ci-ealkoxy; R ^2a , R ^2b , R ^2c , and R ^2d are independently, for each occurrence, selected from the group consisting of H, halogen, Ci- ealkyl, and Ci-ealkoxy; R ³ is selected from the group consisting of methyl, ethyl, propyl, and butyl; R ^l is independently, for each occurrence, H or Ci-ealkyl; or two R ^l may be taken, together with the carbon to which they are attached, to form a Cs-C locycloalkyl; and n is 0 or 1.

[00052] In various embodiments, provided herein is a process for the preparation of a compound of Formula I:

Formula I; comprising: coupling a compound of Formula VI with a compound of Formula VII, or a salt thereof:

F ormula VI F ormula VII ; thereby producing a compound of Formula VIII:

Formula VIII; amidating the compound of Formula VIII to produce a compound of Formula IX:

Formula IX; and dehydrating the compound of Formula IX to provide the compound of Formula I; wherein R ¹ is selected from the group consisting of H, halogen, Ci-ealkyl, and Ci-ealkoxy; R ^2a , R ^2b , R ^2C , and R ^2d are independently, for each occurrence, selected from the group consisting of H, halogen, Ci-ealkyl, and Ci-ealkoxy; R ³ is selected from the group consisting of methyl, ethyl, propyl, and butyl; R ^l is independently, for each occurrence, H or Ci-ealkyl; or two R ^l may be taken, together with the carbon to which they are attached, to form a Cs-Ciocycloalkyl; and n is 0 or 1.

[00053] In various embodiments, R ¹ is H.

[00054] In some embodiments, R ^2a , R ^2b , and R ^2c are H. In some embodiments, R ^2d is halogen. In some embodiments, R ^2a , R ^2b , and R ^2c are H; and R ^2d is chloro.

[00055] In various embodiments, R ³ is methyl.

[00056] In some embodiments, R ^l is H.

[00057] In some embodiments, R ^l is methyl. In some embodiments, R ^l selected from the group consisting of methyl, ethyl, propyl, and butyl.

[00058] In some embodiments, two R ^l are taken, together with the carbon to which they are attached, to form a cyclopropyl, cyclobutyl, or oxetanyl.

[00059] In various embodiments, n is 1. In various embodiments, n is 0.

[00060] In embodiments, providing the compound of Formula VI comprises: providing a compound of Formula IV : Formula IV; and activating the compound of Formula IV to provide the compound of Formula VI; wherein LG is a leaving group.

[00061] In embodiments, the compound of Formula VI is prepared by activating the compound of Formula IV to provide the compound of Formula VI; wherein LG is a leaving group.

[00062] In some embodiments, LG is halogen.

[00063] In some embodiments, LG is selected from the group consisting of fluoro, chloro, bromo, and pentafluorophenolate.

[00064] In some embodiments, LG is chloro.

[00065] In embodiments, providing the compound of Formula VI comprises: halogenating a compound of Formula III: Formula III; to produce a compound of Formula IV : Formula IV, wherein LG is a halogen; and amidating the compound of Formula IV to provide the compound of Formula VI.

[00066] In embodiments, the compound of Formula VI is prepared by halogenating a compound of Formula III: Formula III; to produce a compound of Formula IV : Formula IV, wherein LG is a halogen; and amidating the compound of Formula IV to provide the compound of Formula VI.

[00067] In embodiments, LG is selected from the group consisting of fluoro, bromo, and chloro.

[00068] In embodiments, coupling the compound of Formula VI with the compound of Formula VII, or a salt thereof, comprises contacting the compound of Formula VI with the compound of Formula VII, or a salt thereof, in the presence of a coupling reagent.

[00069] In some embodiments, the coupling reagent is 2-(lH-Benzotriazole-l-yl)-l, 1,3,3- tetramethylaminium tetrafluoroborate (TBTU).

[00070] In an embodiment, coupling the compound of Formula VI with the compound of Formula VII, or a salt thereof, further comprises a base.

[00071] In some embodiments, the salt of the compound of Formula VII is:

[00072] In some embodiments, the salt of the compound of Formula VII is: [00073] In some embodiments, the base is N,N-diisopropylethylamine (DIPEA).

[00074] In some embodiments, amidating the compound of Formula VIII comprises contacting the compound of Formula VIII with NHs. In some embodiments, amidating the compound of Formula VIII comprises contacting the compound of Formula VIII with NHs and 1 ,8-diazabicyclo(5.4.0)undec-7 -ene (DBU) .

[00075] In some embodiments, dehydrating the compound of Formula IX comprises contacting the compound of Formula IX with a trifluoroacetic acid anhydride; a propanephosphonic acid anhydride; or a propanephosphonic acid anhydride and N- methylmorpholine .

[00076] In some embodiments, dehydrating the compound of Formula IX comprises contacting the compound of Formula IX with a trifluoroacetic acid anhydride.

[00077] In some embodiments, dehydrating the compound of Formula IX comprises contacting the compound of Formula IX with a propanephosphonic acid anhydride. In some embodiments, dehydrating the compound of Formula IX comprises contacting the compound of Formula IX with A'-mc thy 1 morpholine. In some embodiments, dehydrating the compound of Formula IX comprises contacting the compound of Formula IX with a propanephosphonic acid anhydride and A'-mcthyl morpholine.

[00078] In some embodiments, halogenating the carboxylic acid represented by Formula III comprises contacting the compound of Formula III with (COC1)2 in the presence of a solvent and a co-solvent.

[00079] In embodiments, the solvent is dichloromethane. In embodiments, the solvent is tertbutyl methyl ether. In embodiments, the solvent is a mixture of dichloromethane and tert-butyl methyl ether.

[00080] In embodiments, the co-solvent is dimethylformamide.

[00081] In embodiments, amidating the compound of Formula IV comprises contacting the compound of Formula IV with (S)-2-amino-3-cyclopropylpropanoic acid in the presence of a base.

[00082] In some embodiments, the base is Na2COs.

[00083] In some embodiments, providing the compound of Formula III comprises: forming a salt of a compound of Formula III: Formula III; isolating the salt of the compound of Formula III; and contacting the salt of the compound of Formula III with an acid to produce a pure compound of Formula III.

[00084] In some embodiments, the compound of Formula III is prepared by isolating the salt of the compound of Formula III; and contacting the salt of the compound of Formula III with an acid to produce a pure compound of Formula III.

[00085] In some embodiments, forming the salt of the compound of Formula III comprises contacting the compound of Formula III with dicyclohexylamine.

[00086] In some embodiments, the acid is phosphoric acid.

[00087] In some embodiments, the compound of Formula I is provided in greater than about

99% purity.

[00088] In embodiments, the purity is chiral purity.

[00089] In some embodiments, the compound of Formula I is: the compound of Formula VI is: the compound of Formula VII, or salt thereof, is: the compound of Formula VIII is: the compound of Formula IX is:

[00090] In various embodiments, the compound of Formula I is

[00091] In embodiments, the compound of Formula I is provided in greater than about 99% purity.

[00092] In some embodiments, the purity is chiral purity. [00093] In some embodiments, the compound of Formula IV is:

[00094] In some embodiments, the compound of Formula III is:

[00095] Also provided herein, is a compound represented by: r pharmaceutically acceptable salt thereof, prepared by the process described herein.

[00096] Also provided herein, is a purified compound of Formula I: Formula I, prepared by the process described herein.

[00097] In some embodiments, the compound of Formula I is

[00098] In some embodiments, the compound has 98% or 99% purity. In some embodiments, the compound has 98%. In some embodiments, the compound has 99%.

[00099] In some embodiments, the compound has greater than 95% purity (e.g., greater than 96%, 97%, 98%, or 99% purity).

[000100] In some embodiments, the purity is chiral purity.

[000101] In some embodiments, an impurity is removed from the compound of any one of Formula I, Formula II, Formula III, Formula IV, Formula VI, Formula VII or salt thereof, Formula VIII, and Formula IX is purified prior to using the compound in any of the processes described herein. In some embodiments, water is removed from the compound of any one of Formula I, Formula II, Formula III, Formula IV, Formula VI, Formula VII or salt thereof, Formula VIII, and Formula IX is purified prior to using the compound in any of the processes described herein. In some embodiments, the compound of any one of Formula I, Formula II, Formula III, Formula IV, Formula VI, Formula VII or salt thereof, Formula VIII, and Formula IX is dried prior to using the compound in any of the processes described herein.

[000102] In some embodiments, the compound of any one of Formula I, Formula II, Formula III, Formula IV, Formula VI, Formula VII or salt thereof, Formula VIII, and Formula IX is purified prior to using the compound in any of the processes described herein. In some embodiments, purification comprises distillation, precipitation, crystallization, extraction, chromatography, or any combination thereof.

[000103] Procedures for making compounds described herein are provided below with reference to Schemes 1-7. In the reactions described below, it may be necessary to protect reactive functional groups (such as hydroxyl, amino, thio or carboxyl groups) to avoid their unwanted participation in the reactions. The incorporation of such groups, and the methods required to introduce and remove them are known to those skilled in the art (for example, see Greene, Wuts, Protective Groups in Organic Synthesis. 4th Ed. (2007)). The deprotection step may be the final step in the synthesis such that the removal of protecting groups affords compounds of Formula I, as disclosed herein. Starting materials used in the following schemes can be purchased or prepared by methods described in the chemical literature, or by adaptations thereof, using methods known by those skilled in the art. The order in which the steps are performed can vary depending on the groups introduced and the reagents used, but would be apparent to those skilled in the art.

EXAMPLES

[000104] The procedures disclosed herein can be conducted in a number of ways based on the teachings contained herein and synthetic procedures known in the art. In the description of the synthetic methods described below, it is to be understood that all proposed reaction conditions, including choice of solvent, reaction atmosphere, reaction temperature, duration of the experiment and workup procedures, can be chosen to be the conditions standard for that reaction, unless otherwise indicated. It is understood by one skilled in the art of organic synthesis that the functionality present on various portions of the molecule should be compatible with the reagents and reactions proposed. Substituents not compatible with the reaction conditions will be apparent to one skilled in the art, and alternate methods are therefore indicated. The starting materials for the examples are either commercially available or are readily prepared by standard methods from known materials.

[000105] At least some of the compounds identified as intermediates e.g., as part of a synthetic scheme disclosed herein are contemplated as compounds of the disclosure.

[000106] Chemical shifts in the ^J H NMR spectra are expressed in ppm relative to tetramethylsilane. The following abbreviations have been used: br = broad signal, s = singlet, d = doublet, dd = double doublet, dt = double triplet, ddd = double double doublet, t = triplet, td = triple doublet, tdd = triple double doublet, q = quartet, m = multiplet.

[000107] Abbreviations:

Example 1. A Process Description for the Preparation of 7-chloro-N-((S)-l-(((S)-l-cyano-2- ((S)-2-oxopiperidin-3-yl)ethyl)amino)-3-cyclopropyl-l-oxopro pan-2-yl)-lH-indole-2- carboxamide

Scheme 1

Synthesis of7-chloro-lH-indole-2-carbonyl chloride (12):

[000108] 7-Chloro- l//-indolc-2 -carboxylic acid was purified and used (Scheme 1, Step 1). 7-

Chloro- lH-indole-2 -carboxylic acid (10.0 kg) and dichloromethane (200 L) were charged into a reactor under N2 atmosphere at about 10-20 °C. Then, dimethylformamide (299g, 0.08 eq) was charged into the reactor under N2 at about 10-20 °C. (COC1)2 (13.0 kg, 2.00 eq) was charged into the reaction mixture drop-wise at about 5-10 °C in about 2-3 hours. After the addition, the mixture was stirred at about 10-20 °C for about another 6 hours. The mixture was filtered and the filter cake was rinsed with dichloromethane (20.0 L). The filtrate was concentrated to afford 7-chloro-lH-indole-2 -carbonyl chloride (11.0 kg). Synthesis of (S)-2-(7-chloro-lH-indole-2-carboxamido)-3-cyclopropylpropan oic acid (14):

[000109] Dichloromethane (88.0 L) and water (110 L) were charged into a reactor under N2 atmosphere at 10-20 °C. Then, Na2COs (21.8 kg, 4.00 eq) were charged into the reactor under N2 at about 10-20 °C. (S)-2-Amino-3-cyclopropylpropanoic acid (7.30 kg, 1.10 eq) was charged into the reactor under N2 at about 10-20 °C, and then the reaction mixture was cooled to about 0- 5 °C. The internal temperature of the reactor was kept at about 0-5 °C, and then a solution of 7- chloro- lH-indole-2 -carbonyl chloride (11.0 kg) in dichloromethane (88.0 L) was added dropwise into the reaction mixture over 3 hours. After the addition, the reaction mixture was stirred at about 0-5 °C for 1 hour. The reaction mixture was warmed to about 10-20 °C, and then water (22.0 L) was charged into the reaction mixture. The resulting mixture was stirred at about 10- 20 °C for 30 minutes, and then the mixture was settled for additional 30 minutes, thereby forming two layers. Extraction was performed by charging tetrahydrofuran (110 L) to the aqueous layer and charging HC1 (aq.) (3 mol/L) to adjust the pH to about 1 at a temperature of about 10-20 °C, and then the reaction mixture was stirred for 30 minutes. The resulting two layers were separated. The organic layer was concentrated to about 33.0 L, and the residue was charged to another reactor and heated to a temperature of about 70-80 °C. n-Heptane (66.0 L) was charged drop-wise into the reactor at about 70-80 °C, and then the reaction mixture was stirred at about 70-80 °C for 4 hours. The reaction mixture was cooled to 10-20 °C slowly over 8 hours, and then the mixture was stirred at about 10-20 °C for additional 12 hours. The filtrate cake was obtained after filtration of the reaction mixture, and then the filter cake was rinsed with water (110 L). The filter cake was dried under vacuum to obtain A)-2-(7-chloro- 1 H-indolc-2- carboxamido)-3 -cyclopropylpropanoic acid (13.0 kg).

Synthesis of methyl (S)-2-((S)-2-(7-chloro-l H-indole-2-carboxamido)-3- cyclopropylpropanamido)-3-( (S)-2-oxopiperidin-3-yl)propanoate (16)

[000110] Dichloromethane (260 L) and (S)-2-(7-chloro-l H-indole-2-carboxamido)-3- cyclopropylpropanoic acid (13.0 kg) were charged into a reactor under N2 atmosphere at about 10-20 °C. 2-(lH-Benzotriazole-l-yl)-l, 1, 3, 3-tetramethyluronium tetrafluoroborate (TBTU, 1.20 eq) was charged into the reactor under N2 at about 10-20 °C, and then methyl (S)-2-amino-3- ((S)-2-oxopiperidin-3-yl)propanoate ( 1. 18 eq) was charged into the reactor under N2 at about 10- 20 °C. The reactor was rinsed with dichloromethane (65.0 L) under N2 at 10-20 °C, and then the reaction mixture was cooled to about -5 to 5 °C. DIPEA (3.50 eq) was charged into the reaction mixture drop-wise over 3 hours, and then the reaction mixture was stirred at about -5 to 5 °C for additional 6 hours. 5 wt% NaHCOs solution (130 L) was charged into the reaction mixture at about -5 to 5 °C, and then the reaction mixture was warmed to about 10-20 °C. Dichloromethane (65.0 L) was charged into the mixture, and then the mixture was stirred at about 10-20 °C for 30 minutes and settled for additional 30 minutes. The resulting two layers were separated, and then about 0.6 mol/L HC1 (65.0 L) was charged into the organic layer. The mixture was stirred at about 10-20 °C for 30 minutes, and then settled for additional 30 minutes. The resulting two layers were separated, and the previous step was repeated. After separating the resulting two layers, a solution of about 10 wt% NaCl and 5 wt% NaHCOs (65.0 L) were charged into the organic layer, and then the mixture was stirred at 10-20 °C for 30 minutes and settled for additional 30 minutes. The resulting two layers were separated, and the organic layer was concentrated under vacuum (40-50 °C) to about 160 L. MeCN (260 L) was charged into the residue and the mixture was concentrated to about 160 L, and this step was repeated, followed by stirring of the mixture at about 15-25 °C for 4 hours. The mixture was filtered and the filter cake was rinsed with MeCN (39.0 L). The filter cake was dried under vacuum at about 40-45 °C to afford methyl (S)-2-((S)-2-(7-chloro- lH-indole-2-carboxamido)-3-cyclopropylpropanamido)-3- ((S)-2-oxopiperidin-3 -yl)propanoate .

Synthesis ofN-((S)-l-(((S)-l-amino-l-oxo-3-((S)-2-oxopiperidin-3-yl)pr opan-2-yl)amino)-3- cyclopropyl-l-oxopropan-2-yl)-7-chloro-lH-indole-2-carhoxami de (17) and 7-chloro-N-((S)-l- (((S)-l-cyano-2-((S)-2-oxopiperidin-3-yl)ethyl)amino)-3-cycl opropyl-l-oxopropan-2-yl)-lH- indole-2-carhoxamide (18)

[000111] Methyl (S)-2-((S)-2-(7-chloro-lH-indole-2-carboxamido)-3- cyclopropylpropanamido)-3-((S)-2-oxopiperidin-3-yl)propanoat e was reacted with NHs in methanol, and then purified to afford N-(/S)-l-(((S)-l-amino-l-oxo-3-((' _l S)-2-oxopiperidin-3- yl)propan-2-yl)amino)-3-cyclopropyl-l-oxopropan-2-yl)-7-chlo ro-lH-indole-2-carboxamide, which was treated with trifluoroacetic acid anhydride and triethyl amine in tetrahydrofuran, and then purified to afford 7-chloro-N-((S)-l-(((S)-l-cyano-2-((S)-2-oxopiperidin-3-yl)e thyl)amino)- 3 -cyclopropyl- 1 -oxopropan-2-yl)- 1 H-indole -2-carboxamide . Example 2. A Large-Scale Synthesis of 7-chloro-N-((S)-l-(((S)-l-cyano-2-((S)-2- oxopiperidin-3-yl)ethyl)amino)-3-cyclopropyl-l-oxopropan-2-y l)-lH-indole-2-carboxamide

Scheme 2

Example 3. A Large-Scale Synthesis of 7-chloro-N-((S)-l-(((S)-l-cyano-2-((S)-2- oxopiperidin-3-yl)ethyl)amino)-3-cyclopropyl-l-oxopropan-2-y l)-lH-indole-2-carboxamide

Scheme 3

Example 4. A Large-Scale Synthesis of 7-chloro-N-((S)-l-(((S)-l-cyano-2-((S)-2- oxopiperidin-3-yl)ethyl)amino)-3-cyclopropyl-l-oxopropan-2-y l)-lH-indole-2-carboxamide

Scheme 4

Example 5. Preparation of methyl (S)-2-((tert-butoxycarbonyl)amino)-3-((S)-2- oxopiperidin-3-yl)propanoate

Scheme 5

[000112] Charged a vessel with THL (10 L/kg) and dimethyl (tert-butoxycarbonyl)-L- glutamate (1.0 kg) and heat to 30 °C. Then added hexamethylphosphoramide (HMPA) (1.45 kg, 2.25 equiv.) and stir for about 10 minutes. The reaction mixture was then cooled to -77 ,5±7.5 °C and LiHMDS (IM in THL) (8.17 L/kg, 2.25 equiv.) was added slowly to the reaction mixture. After stirring for 30 minutes, 3 -bromopropionitrile (0.723 kg/kg, 1.5 equiv.) was added slowly over 2 hours at -77 ,5±7.5 °C. The reaction mixture was then stirred at -77 ,5±7.5 °C for 1 hour.

[000113] Then 5% citric acid monohydrate solution in water (5 L/kg) was added to the reaction mixturing while maintaining the temperature at -80 °C to -20 °C. The reaction mixture was then allowed to warm up to 25 °C and stirred for 1 hour at 25 °C. Ethyl acetate (10 L/kg) was added at 30 °C and then the mixture was stirred for about 10 minutes. Water (5 L/kg) was then added at 25 °C and the mixture was stirred for about 10 minutes. Once the layers settled, they were separated. The organic layer was washed with water (3X, 5 L/kg). All combined aqueous layers were extracted with ethyl acetate (4X, 5 L/kg). The combined organic layers were then concentrated and then azeotroped with methyl tertiary-butyl ether (aka tert-butyl methyl ether; MTBE) (3 L/kg). The crude product was then charged with MTBE (5 L/kg) and silica gel (230-400) (1.5 kg/kg) was added and stirred for 1 hour at 25 °C. The mixture was fdtered through celite bed. Celite bed washed with MTBE (3 L/kg).

[000114] Methanol (3 L/kg) was then added to the collected product and stirred for about 5 minutes. The methanol layer was washed with n-heptane (2X, 5 L/kg). Methanol layer was then concentrated to afford dimethyl (2S,4S)-2-((tert-butoxycarbonyl)amino)-4-(2- cyanoethyl)pentanedioate .

[000115] A first reaction vessel was then charged with Raney Nickel (0.7 kg/kg) under inert atmosphere. A second reaction vessel was charged with methanol (8 L/kg) and dimethyl (2S,4S)-2-((tert-butoxycarbonyl)amino)-4-(2-cyanoethyl)penta nedioate (1.0 kg/kg), which was then passed through CUNO filter and washed with methanol (2 L/kg). This solution was then added to the first reaction vessel. Then triethylamine (TEA) (0.46 kg/kg) was added to the reaction mixture. The reaction mixture was then degassed with argon, followed by hydrogen. Hydrogen pressure was applied at 70-73 psi with stirring at 25 °C. Then the reaction mixture was heated to 50 °C for at least 16 hours, maitaining 70-73 psi of hydrogen pressure.

[000116] The reaction mixture was then cooled to 25 °C and filtered. The bed was washed with methanol (2 L/kg). The filtrate was concentrated to about 3 vol of methanol and then washed with n-heptane (2X; 5 L/kg). The methanol layer was concentrated to afford methyl (S)- 2-((tert-butoxycarbonyl)amino)-3-((S)-2-oxopiperidin-3-yl)pr opanoate.

[000117] Yield: 2.0 kg of dimethyl (tert-butoxycarbonyl)-L-glutamate afforded 1.62 kg (68%) of crude dimethyl (2S,4S)-2-((tert-butoxycarbonyl)amino)-4-(2-cyanoethyl)penta nedioate.

[000118] Yield: 1.57 ,g of crude dimethyl (2S,4S)-2-((tert-butoxycarbonyl)amino)-4-(2- cyanoethyl)pentanedioate afforded 1.1 kg (77%) of crude methyl (S)-2-((tert- butoxycarbonyl)amino)-3-((S)-2-oxopiperidin-3-yl)propanoate.

[000119] Crude methyl (S)-2-((tert-butoxycarbonyl)amino)-3-((S)-2-oxopiperidin-3- yl)propanoate was purified as follows. First, the crude product was azeotroped with 2-methyl THF (3 L/kg). After diluting with 2-methyl THF (2.5 L/kg) under inert atmosphere, the reaction mixture was cooled to 5 °C. Then 4 N HCI was added and the reaction mixture was stirred for 1 hour. Then the reaction mixture was filtered under nitrogran atmosphere to obtain methyl HCI salt of (S)-2-((tert-butoxycarbonyl)amino)-3-((S)-2-oxopiperidin-3-y l)propanoate. This salt was then added to pre-cooled ethyl acetate (5 U/kg) at 5 °C. Then aqueous sodium bicarbonate was added and stirred for 30 minutes. The layers were separated, and the aqueous layer was extracted with ethyl acetate (2 U/kg; 5X). Then 10 w/w% silica gel was added to the organic layer and stirred for 30 minutes. This was then filtered and washed with ethyl acetate (5 U/kg). The organic layer was azeotroped with MTBE (2 L/kg; 2X). Then the concentrated product was dissolved in MTBE (2 L/kg), which was then stirred and then washed with n-heptane. The purified product was dried at 40 °C for 8 hours to afford purified methyl (S)-2-((tert- butoxycarbonyl)amino)-3-((S)-2-oxopiperidin-3-yl)propanoate.

[000120] Yield: 0.45 kg and 0.5 kg of crude methyl (S)-2-((tert-butoxycarbonyl)amino)-3- ((S)-2-oxopiperidin-3-yl)propanoate afforded 0.14 kg (35%) and 0.18 kg (36%, respectively, of purified methyl (S)-2-((tert-butoxycarbonyl)amino)-3-((S)-2-oxopiperidin-3-y l)propanoate.

Example 6. Preparation of HC1 salt of methyl (S)-2-amino-3-((S)-2-oxopiperidin-3- yl)propanoate (HC1 salt of 15)

Scheme 6

2 HCI salt of 15 HCI salt of 15

[000121] Under inert atmosphere, charged a vessel with methyl (S)-2-((tert- butoxycarbonyl)amino)-3-((S)-2-oxopiperidin-3-yl)propanoate (1.0 kg). Used mechanical stirrer, condenser, and temperature probe. Then added ethyl acetate (EtOAc) (4.51 kg, 5 U/kg, 5V) and began agitation. Then added 2 N HCI in ethyl acetate (12.5 L, 7.5 equiv.) to the reaction vessel at 25 °C. Stirred for a minimum of 4 hours at 25 °C. Then the reaction mixture was filtered under inert atmosphere, and the material was dried at 50 °C for 7-8 hours to obtain 2HC1 salt of methyl (S)-2-((tert-butoxycarbonyl)amino)-3-((S)-2-oxopiperidin-3-y l)propanoate (2HC1 salt of 15).

[000122] Yield: 100 g of methyl (S)-2-((tert-butoxycarbonyl)amino)-3-((S)-2-oxopiperidin-3- yl)propanoate afforded 79 g of 2HC1 salt of methyl (S)-2-((tert-butoxycarbonyl)amino)-3-((S)-2- oxopiperidin-3-yl)propanoate (2HC1 salt of 15) (86%).

[000123] Then under inert atmosphere at 0 °C, 2HC1 salt of methyl (S)-2-((tert- butoxycarbonyl)amino)-3-((S)-2-oxopiperidin-3-yl)propanoate (2HC1 salt of 15) and isopropanol: water (98.5: 1.5, 8V) were added to a vessel fitted with a mechanical stirrer, condenser, and temperature probe at 0 °C. The reaction mixture was stirred for 16 hours at 0 °C. Then the reaction mixture was filtered under inert atmosphere and washed with isopropanol (IPA):water (98.5: 1.5, IV). The isolated product was dried in vacuo at 45 °C for 12 hours to afford HC1 salt of methyl (S)-2-((tert-butoxycarbonyl)amino)-3-((S)-2-oxopiperidin-3- yl)propanoate (HC1 salt of 15).

[000124] Yield: 100 g of methyl (S)-2-((tert-butoxycarbonyl)amino)-3-((S)-2-oxopiperidin-3- yl)propanoate afforded 49 g of HC1 salt of methyl (S)-2-((tert-butoxycarbonyl)amino)-3-((S)-2- oxopiperidin-3-yl)propanoate (HC1 salt of 15) (62%).

Example 7. Preparation of 7-chloro-N-((S)-l-(((S)-l-cyano-2-((S)-2-oxopiperidin-3- yl)ethyl)amino)-3-cyclopropyl-l-oxopropan-2-yl)-lH-indole-2- carboxamide

Scheme 7

Synthesis of (S)-2-(7-chloro-lH-indole-2-carboxamido)-3-cyclopropylpropan oic acid (14)'.

[000125] 7 -Chloro- lH-indole-2 -carboxylic acid (10) was charged (100 g, 1.00 equivs. /parts)

(0.99 - 1.01 X) into a first vessel. Then MTBE (740 g, 7.4 parts) was added, followed by DMF (3.00 g, 0.030 parts). The temperature was adjusted to 15 °C. Then oxalyl chloride (84 g, 0.84 parts) was added dropwise at 15 °C for not less than 2 hours. Then the temperature was adjusted to 25 °C, and the first reaction mixture was stirred for 2 hours. [000126] A second vessel was charged with (S)-2-amino-3-cyclopropylpropanoic acid (13) (77 g, 0.77 X) and Na2COs (163 g, 1.63 parts). Then water (300 g, 3.0 parts) and MTBE (590 g, 5.9 parts) are added to the second vessel. The temperature was adjusted to 15 °C.

[000127] Then the reaction mixture from the first vessel was added to the second vessel at 15 °C dropwise. The resulting reaction mixture was stirred for 2 hours at 15 °C.

[000128] The reaction mixture was then cooled to 15 °C, and 3N HC1 (6-9X) was added to adjust the pH to 1. The reaction mixture was then stirred for 1 h at 15 °C. After letting stand for 30 minutes, the lower aqueous layer was discharged, and the organic layer was filtered through CUNO filter. Product was isolated by washing with ^-heptane. The product was mixed with water, heated, and stirred. Product was isolated by filtration, washed with water and dried in the oven in vacuo.

[000129] Yield: 100 g batch afforded 136 g (77%) of (S)-2-(7-chloro-lH-indole-2- carboxamido)-3 -cyclopropylpropanoic acid (14).

Synthesis of methyl (S)-2-((S)-2-(7-chloro-lH-indole-2-carboxamido)-3- cyclopropylpropanamido)-3-( (S)-2-oxopiperidin-3-yl)propcmoate (16):

[000130] Under nitrogen atmosphere at 20 °C, (S)-2-(7-chloro-lH-indole-2-carboxamido)-3- cyclopropylpropanoic acid (14) (1.0 kg) was added to a vessel fitted with a mechanical stirrer, a condenser, and a temperature probe. Then HC1 salt of methyl (S)-2-amino-3-((S)-2- oxopiperidin-3-yl)propanoate (HC1 salt of 15) (0.78 kg, 1.20 equiv) was added to reaction vessel at 20 °C. Then 2-(lH-Benzotriazole-l-yl)-l,l,3,3-tetramethylaminium tetrafluoroborate (TBTU) (1.25 kg, 1.20 equiv) and dichloromethane (DCM) (20.0 L, 20 L/kg) was added, and the reaction vessel was cooled to 7-12 °C. Then N,N- diisopropylethylamine (1.42 L, 2.47 equiv.) in dichloromethane (2.00 L, 2.0 L/kg) was added to the vessel at 7-12 °C over a minimum of 2.5 hours. The reaction was stirred for 3-3.5 hours.

[000131] Then 5% NaHCOs (5.0 L) was added to the reaction vessel while maintaining the termpature at 13-18 °C over 15 minutes. Then DCM (5 L) was added and the reaction mixture was warmed to 20-25 °C. The biphasic mixture was stirred for minimum 15 minutes. The organic and aqueous layers were separated. The organic layer was stirred with 0.6 M aqueous HC1 (5.0 L) and DCM (1.0 L). The layers were again separated, and the organic layer was again stirred with 0.6 M aq. HC1 (5 L). The layers were separated, and the organic layer was stirred with 1: 1 5% aq. NaHCOs and 28 % aq. NaCl (5 L). The layers were separated, and the organic layer was concentrated. To the concentrate was added acetonitrile (12 L), which was then cooled to 18 °C. This was concentrated, and the suspended solids were collected via filtration. The product was dried under vaccum at 40-45 °C.

[000132] Yield: 1 kg of (S)-2-(7-chloro-lH-indole-2-carboxamido)-3-cyclopropylpropan oic acid (14) afforded 1.43 kg (90%) of methyl (S)-2-((S)-2-(7-chloro-lH-indole-2-carboxamido)-3- cyclopropylpropanamido)-3-((S)-2-oxopiperidin-3-yl)propanoat e (16).

Synthesis ofN-((S)-l-(((S)-l-amino-l-oxo-3-((S)-2-oxopiperidin-3-yl)pr opan-2-yl)amino)-3- cyclopropyl-1 -oxopropan-2-yl)-7-chloro-lH-indole-2-carboxamide (17):

[000133] To an inert reactor at < 30 °C, charged methyl (S)-2-((S)-2-(7-chloro-lH-indole-2- carboxamido)-3-cyclopropylpropanamido)-3-((S)-2-oxopiperidin -3-yl)propanoate (16) (64.0 kg scale) to a vessel fitted with a mechanical stirrer, a condenser, and a temperature probe. Charged THF (227 kg, 5 L/kg) to the vessel at 20-25 °C, began agitation and held for 0.5 hours. Charged 7N NHs/MeOH (898 kg, 18 L/kg) to the vessel at 20-25 °C and rinsed forward with THF (29 kg, 0.5 L/kg). Charge l,8-diazabicyclo(5.4.0)undec-7-ene (DBU) (39.9 kg, 2.0 eq) to the vessel at 20-25 °C over 1.5 hours and rinsed forward with THF (29 kg, 0.5 L/kg). Heated the reaction mixture to 25-30 °C. Stirred the reaction for a minimum of 18 hours at 25-30 °C. Cooled reaction mixture to 10-15 °C and distilled under vacuum at < 35 °C until 11-12 L/kg (704-768 L) remained in vessel. Heated the reaction mixture to 45-50 °C with vigorous stirring for 1-2 hours to dislodge the solids stuck on the walls of the reactor. Cooled the mixture to 20-25 °C and then stirred the mixture for a minimum of 18 hours. Collected the suspended solid by filtration. Rinsed the residual solids in the vessel with methanol (152 kg, 3 L/kg). Washed the filter cake with the vessel rinse. Upon completion of the wash, maintain < 30 psi of nitrogen pressure on the filter for 6 h to de-liquor the solids. Dried the cake of product under vacuum at 40-45 °C until no further weight loss is observed.

[000134] Yield: 64 kg of methyl (S)-2-((S)-2-(7-chloro-lH-indole-2-carboxamido)-3- cyclopropylpropanamido)-3-((S)-2-oxopiperidin-3-yl)propanoat e (16) afforded 52.894 kg (85%) of N-((S)- 1 -(((S)- 1 -amino- 1 -oxo-3-((S)-2-oxopiperidin-3 -yl)propan-2-yl)amino)-3 -cyclopropyl - l-oxopropan-2-yl)-7-chloro-lH-indole-2-carboxamide (17). Synthesis of7-chloro-N-((S)-l-(((S)-l-cyano-2-((S)-2-oxopiperidin-3-yl )ethyl)amino)-3- cyclopropyl-l-oxopropan-2-yl)-lH-indole-2-carboxamide (18):

[000135] Under a nitrogen atmosphere at 28 °C, chargeed N-((S)-l-(((S)-l-amino-l-oxo-3- ((S)-2-oxopiperidin-3-yl)propan-2-yl)amino)-3-cyclopropyl-l- oxopropan-2-yl)-7-chloro-lH- indole-2 -carboxamide (17) (90 g) to a vessel fitted with a mechanical stirrer, a condenser, and a temperature probe. Charged 720 mb of anhydrous THF (8 V) and 270 m of EtOAc (3 V). Heated the reaction mixture to 28-32 °C. Charged JV-methylmorpholine (NMM) (96.1 g/104.4 mb, 5.0 equiv.) to the vessel at 28-32 °C over a minimum of 15 minutes followed by a line rinse of ethyl acetate (90 mb, 1.0 part). Heated the reaction mixture to 48-53 °C, target 50 °C. Charged propanephosphonic acid anhydride (TsP) as a 50% wt solution in EtOAc (423.2 g/395.5 mL, 3.5 equiv.) at 50-55 °C over 20 to 30 minutes followed by a line rinse of ethyl acetate (90 mb, 1.0 part) to the vessel at 50-55 °C. Stirred the reaction for 1.5 to 2 hours at 50-55 °C, target 53 °C.

[000136] Charged water (450 mL, 5V while maintaining the batch temperature at 20-43 °C. Stirred the biphasic mixture for a minimum of 15 minutes at 38-42 °C. Separated the layers. The lower aqueous layer was back extracted with EtOAC (360 mL, 4 V), agitated for 15-20 min at 20-43 °C. Separated the layers. Combined both organic layers at 38-43 °C. Charged 5% NaHCOs (450 mL, 5 V ) to the vessel maintaining temperature at 38-43 °C and stirred for 15-20 minutes. Separated the layers at 38-43 °C and discarded the lower aqueous layer. Charged 180 mL of EtOAC (2 V and 450 mL of water (5 parts) to the organic layer for 15-25 min at 38- 43 °C. Separated the layers. Kept the upper organic layer and discard the lower aqueous layer. Clarified the organic layer via polish filter. Washed the filter with prefiltered 180 mL of EtOAc (2 V) and combined with organic layer at 38-43 °C. Concentrated the batch to 900-990 mL (10- 1 IV) under reduced pressure at 38-43 °C. Charge dl350 mL (15 V) of prefiltered acetone while maintaining the temperature at 38-43 °C. Concentrated the batch to 900-990 mL (10-11 V) under reduced pressure at 38-43 °C. Charged 1350 mL (15 V) of prefiltered acetone while maintaining the temperature at 38-43 °C. Concentrated the batch to 900-990 mL (10-11 parts) under reduced pressure at 38-43 °C. Filtered. Washed the cake with 360 mL (4 V) of prefiltered acetone [000137] The product (75 g) was transferred to a flask fitted with a mechanical stirrer, thermometer, condenser and N2. Charged 75 mL of prefiltered acetic acid (I V) and 75 mL of prefiltered acetone (I V). Charged 675 mL of prefiltered acetone (9 V) at 20-25 °C. Heated the slurry to 53-58 °C and stir at 53-58 °C for 24-25 hours. Slurry was cooled to 20-25° C over 1.5- 2 hours and stired for a minimum of 3 hours. Filtered. Washed with 300 mL of prefiltered acetone (4 V). Dried the solids under vacuum at 50-55 °C for minimum of 15 hours. Transferred the solids to a flask fitted with stirrer, thermometer and N2. Charged 1190 mL of prefiltered process water (17 V) and stir the slurry at 20-25 °C. Charged 1.05 g of seeds (0.015 V) in 14 mL of prefiltered process water (0.2 V) and rinse forward with 35 mL of prefiltered process water (0.5 part) at 20-25 °C. Stirred solids at 68-73 °C for 24-25 hours. Cooled the solids to 20-25 °C over 2.5-3 hours and stirred for a minimum 22 hours. Filtered. Washed the cake with 280 mL of prefiltered process water (4 V). Dried the wet solids (looks like a paste) under vacuum at 58- 63 °C for a minimum of 24 hours.

[000138] Yield: 90 g of N-((S)-l-(((S)-l-amino-l-oxo-3-((S)-2-oxopiperidin-3-yl)prop an-2- yl)amino)-3-cyclopropyl-l-oxopropan-2-yl)-7-chloro-lH-indole -2-carboxamide (17) afforded 63.3 g (80%) of 7-chloro-N-((S)-l-(((S)-l-cyano-2-((S)-2-oxopiperidin-3-yl)e thyl)amino)-3- cyclopropyl- 1 -oxopropan-2-yl)- lH-indole-2 -carboxamide (18).

INCORPORATION BY REFERENCE

[000139] All publications and patents mentioned herein, including those items listed below, are hereby incorporated by reference in their entirety for all purposes as if each individual publication or patent was specifically and individually incorporated by reference. In case of conflict, the present application, including any definitions herein, will control.

EQUIVALENTS AND SCOPE

[000140] In the claims, articles such as “a,” “an,” and “the” may mean one or more than one unless indicated to the contrary or otherwise evident from the context. Claims or descriptions that include “or” between one or more members of a group are considered satisfied if one, more than one, or all of the group members are present in, employed in, or otherwise relevant to a given product or process unless indicated to the contrary or otherwise evident from the context. The invention includes embodiments in which exactly one member of the group is present in, employed in, or otherwise relevant to a given product or process. The invention includes embodiments in which more than one, or all of the group members are present in, employed in, or otherwise relevant to a given product or process.

[000141] Furthermore, the invention encompasses all variations, combinations, and permutations in which one or more limitations, elements, clauses, and descriptive terms from one or more of the listed claims is introduced into another claim. For example, any claim that is dependent on another claim can be modified to include one or more limitations found in any other claim that is dependent on the same base claim. Where elements are presented as lists, e.g., in Markush group format, each subgroup of the elements is also disclosed, and any element(s) can be removed from the group. It should it be understood that, in general, where the invention, or aspects of the invention, is/are referred to as comprising particular elements and/or features, certain embodiments of the invention or aspects of the invention consist, or consist essentially of, such elements and/or features. For purposes of simplicity, those embodiments have not been specifically set forth in haec verba herein. It is also noted that the terms “comprising” and “containing” are intended to be open and permits the inclusion of additional elements or steps. Where ranges are given, endpoints are included. Furthermore, unless otherwise indicated or otherwise evident from the context and understanding of one of ordinary skill in the art, values that are expressed as ranges can assume any specific value or sub-range within the stated ranges in different embodiments of the invention, to the tenth of the unit of the lower limit of the range, unless the context clearly dictates otherwise.

[000142] This application refers to various issued patents, published patent applications, journal articles, and other publications, all of which are incorporated herein by reference. If there is a conflict between any of the incorporated references and the instant specification, the specification shall control. In addition, any particular embodiment of the present invention that falls within the prior art may be explicitly excluded from any one or more of the claims. Because such embodiments are deemed to be known to one of ordinary skill in the art, they may be excluded even if the exclusion is not set forth explicitly herein. Any particular embodiment of the invention can be excluded from any claim, for any reason, whether or not related to the existence of prior art. [000143] Those skilled in the art will recognize or be able to ascertain using no more than routine experimentation many equivalents to the specific embodiments described herein. The scope of the present embodiments described herein is not intended to be limited to the above Description, but rather is as set forth in the appended claims. Those of ordinary skill in the art will appreciate that various changes and modifications to this description may be made without departing from the spirit or scope of the present invention, as defined in the following claims.