WO2022081984A1

WO2022081984A1 - Methods and compounds to treat sars infections

Info

Publication number: WO2022081984A1
Application number: PCT/US2021/055199
Authority: WO
Inventors: Tariq M. Rana
Original assignee: The Regents Of The University Of California
Priority date: 2020-10-16
Filing date: 2021-10-15
Publication date: 2022-04-21

Abstract

This disclosure features chemical entities (e.g., a compound (e.g., a compound of Formula (I), (II), (III), or (IV)), or a pharmaceutically acceptable salt, and/or hydrate, and/or cocrystal, and/or drug combination of the compound) that inhibit the main protease (MPro) of a coronavirus (e.g., SARS-CoV-2). Said chemical entities are useful, e.g., for treating a coronavirus infection (e.g., SARS-CoV-2 infection (e.g., COVID-19)) in a subject (e.g., a human). This disclosure also features compositions containing the same as well as methods of using and making the same.

Description

Methods and Compounds to Treat SARS Infections I. Federally Sponsored Research and Development This invention was made with Government support under grant No. DA039562 awarded by the National Institutes of Health. The Government has certain rights in the invention. II. BACKGROUND Coronavirus disease 2019 (COVID-19) is a transmissible respiratory disease caused by a novel severe acute respiratory syndrome coronavirus SARS-CoV-2. Since its emergence in December 2019, COVID-19 has rapidly spread worldwide spanning 216 countries. As of October 2020, there are more than 219 million confirmed cases and 4.55 million deaths (WHO COVID Pandemic). Reports indicate that COVID-19 patients present with a cluster of severe respiratory illness symptoms similar to SARS, with which the genome of SARS-CoV-2 shares approximately 80% identity. SARS-CoV-2 produces a spike protein that binds to host cell receptor ACE2 for entry. Upon entry, the positive genomic RNA of SARS-CoV-2 will attach directly to the host ribosome and translate two large polyproteins, which are then processed by proteolysis into components for packaging new virions. This proteolysis is controlled by two protease enzymes, the coronavirus main protease (M^pro) and the papain-like protease (PL^pro). An RNA-dependent RNA polymerase (RdRp) is also required to replicate the RNA genome. As such, there is a need for methods and compositions useful in the treatment of coronavirus infections, such as SARS-CoV-2 infection. III. SUMMARY This disclosure features chemical entities (e.g., a compound (e.g., a compound of Formula (I), (II), (III), or (IV) as defined herein) or a pharmaceutically acceptable salt, and/or hydrate, and/or cocrystal, and/or drug combination of the compound) that inhibit the main protease (M^Pro) of a coronavirus (e.g., SARS-CoV-2). Said chemical entities are useful, e.g., for treating a coronavirus infection (e.g., SARS-CoV-2 infection (e.g., COVID-19)) in a subject (e.g., a human). This disclosure also features compositions containing the same as well as methods of using and making the same. The term "halo" refers to fluoro (F), chloro (Cl), bromo (Br), or iodo (I). The term "alkyl" refers to a saturated acyclic hydrocarbon radical that may be a straight chain or branched chain, containing the indicated number of carbon atoms. For example, C_1-10 indicates that the group may have from 1 to 10 (inclusive) carbon atoms in it. Alkyl groups can either be unsubstituted or substituted with one or more substituents. Non-limiting examples include methyl, ethyl, iso-propyl, tert-butyl, n-hexyl. The term “saturated” as used in this context means only single bonds present between constituent carbon atoms and other available valences occupied by hydrogen and/or other substituents as defined herein. The term "haloalkyl" refers to an alkyl, in which one or more hydrogen atoms is/are replaced with an independently selected halo (e.g., -CF₃). The term "alkoxy" refers to an -O-alkyl radical (e.g., -OCH₃). The term “haloalkoxy” refers to an –O-haloalkyl radical (e.g., -OCF₃). The term “thioalkoxy” refers to an –S-alkyl radical (e.g., -SCH₃). The term "aryl" refers to a 6-20 carbon mono-, bi-, tri- or polycyclic group wherein at least one ring in the system is aromatic (e.g., 6-carbon monocyclic, 10-carbon bicyclic, or 14- carbon tricyclic aromatic ring system); and wherein 0, 1, 2, 3, or 4 atoms of each ring may be substituted by a substituent. Examples of aryl groups include phenyl, naphthyl, tetrahydronaphthyl, and the like. The term "cycloalkyl" as used herein refers to saturated or partially unsaturated (but not aromatic) cyclic hydrocarbon groups having 3 to 20 ring carbons, preferably 3 to 16 ring carbons, and more preferably 3 to 12 ring carbons or 3-10 ring carbons or 3-6 ring carbons, wherein the cycloalkyl group may be optionally substituted. Examples of cycloalkyl groups include, without limitation, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, and cyclooctyl. Cycloalkyl may include multiple fused and/or bridged rings. Non-limiting examples of fused/bridged cycloalkyl includes: bicyclo[1.1.0]butane, bicyclo[2.1.0]pentane, bicyclo[1.1.1]pentane, bicyclo[3.1.0]hexane, bicyclo[2.1.1]hexane, bicyclo[3.2.0]heptane, bicyclo[4.1.0]heptane, bicyclo[2.2.1]heptane, bicyclo[3.1.1]heptane, bicyclo[4.2.0]octane, bicyclo[3.2.1]octane, bicyclo[2.2.2]octane, and the like. Cycloalkyl also includes spirocyclic rings (e.g., spirocyclic bicycle wherein two rings are connected through just one atom). Non- limiting examples of spirocyclic cycloalkyls include spiro[2.2]pentane, spiro[2.5]octane, spiro[3.5]nonane, spiro[3.5]nonane, spiro[3.5]nonane, spiro[4.4]nonane, spiro[2.6]nonane, spiro[4.5]decane, spiro[3.6]decane, spiro[5.5]undecane, and the like. The term “heteroaryl”, as used herein, means a mono-, bi-, tri- or polycyclic group having 5 to 20 ring atoms, alternatively 5, 6, 9, 10, or 14 ring atoms; and having 6, 10, or 14 pi electrons shared in a cyclic array; wherein at least one ring in the system is aromatic (but does not have to be a ring which contains a heteroatom, e.g. tetrahydroisoquinolinyl, e.g., tetrahydroquinolinyl), and at least one ring in the system contains one or more heteroatoms independently selected from the group consisting of N, O, and S. Heteroaryl groups can either be unsubstituted or substituted with one or more substituents. Examples of heteroaryl include thienyl, pyridinyl, furyl, oxazolyl, oxadiazolyl, pyrrolyl, imidazolyl, triazolyl, thiodiazolyl, pyrazolyl, isoxazolyl, thiadiazolyl, pyranyl, pyrazinyl, pyrimidinyl, pyridazinyl, triazinyl, thiazolyl benzothienyl, benzoxadiazolyl, benzofuranyl, benzimidazolyl, benzotriazolyl, cinnolinyl, indazolyl, indolyl, isoquinolinyl, isothiazolyl, naphthyridinyl, purinyl, thienopyridinyl, pyrido[2,3-d]pyrimidinyl, pyrrolo[2,3-b]pyridinyl, quinazolinyl, quinolinyl, thieno[2,3-c]pyridinyl, pyrazolo[3,4-b]pyridinyl, pyrazolo[3,4-c]pyridinyl, pyrazolo[4,3- c]pyridine, pyrazolo[4,3-b]pyridinyl, tetrazolyl, chromane, 2,3-dihydrobenzo[b][1,4]dioxine, benzo[d][1,3]dioxole, 2,3-dihydrobenzofuran, tetrahydroquinoline, 2,3- dihydrobenzo[b][1,4]oxathiine, isoindoline, and others. In some embodiments, the heteroaryl is selected from thienyl, pyridinyl, furyl, pyrazolyl, imidazolyl, isoindolinyl, pyranyl, pyrazinyl, and pyrimidinyl. The term "heterocyclyl" refers to a mon-, bi-, tri-, or polycyclic saturated or partially unsaturated (but not aromatic) ring system with 3-16 ring atoms (e.g., 5-8 membered monocyclic, 8-12 membered bicyclic, or 11-14 membered tricyclic ring system) having 1-3 heteroatoms if monocyclic, 1-6 heteroatoms if bicyclic, or 1-9 heteroatoms if tricyclic or polycyclic, said heteroatoms selected from O, N, or S (e.g., carbon atoms and 1-3, 1-6, or 1-9 heteroatoms of N, O, or S if monocyclic, bicyclic, or tricyclic, respectively), wherein 0, 1, 2 or 3 atoms of each ring may be substituted by a substituent. Examples of heterocyclyl groups include piperazinyl, pyrrolidinyl, dioxanyl, morpholinyl, tetrahydrofuranyl, and the like. Heterocyclyl may include multiple fused and bridged rings. Non-limiting examples of fused/bridged heteorocyclyl includes: 2-azabicyclo[1.1.0]butane, 2-azabicyclo[2.1.0]pentane, 2-azabicyclo[1.1.1]pentane, 3-azabicyclo[3.1.0]hexane, 5-azabicyclo[2.1.1]hexane, 3- azabicyclo[3.2.0]heptane, octahydrocyclopenta[c]pyrrole, 3-azabicyclo[4.1.0]heptane, 7- azabicyclo[2.2.1]heptane, 6-azabicyclo[3.1.1]heptane, 7-azabicyclo[4.2.0]octane, 2- azabicyclo[2.2.2]octane, 3-azabicyclo[3.2.1]octane, 2-oxabicyclo[1.1.0]butane, 2- oxabicyclo[2.1.0]pentane, 2-oxabicyclo[1.1.1]pentane, 3-oxabicyclo[3.1.0]hexane, 5- oxabicyclo[2.1.1]hexane, 3-oxabicyclo[3.2.0]heptane, 3-oxabicyclo[4.1.0]heptane, 7- oxabicyclo[2.2.1]heptane, 6-oxabicyclo[3.1.1]heptane, 7-oxabicyclo[4.2.0]octane, 2- oxabicyclo[2.2.2]octane, 3-oxabicyclo[3.2.1]octane, and the like. Heterocyclyl also includes spirocyclic rings (e.g., spirocyclic bicycle wherein two rings are connected through just one atom). Non-limiting examples of spirocyclic heterocyclyls include 2-azaspiro[2.2]pentane, 4- azaspiro[2.5]octane, 1-azaspiro[3.5]nonane, 2-azaspiro[3.5]nonane, 7-azaspiro[3.5]nonane, 2- azaspiro[4.4]nonane, 6-azaspiro[2.6]nonane, 1,7-diazaspiro[4.5]decane, 7- azaspiro[4.5]decane 2,5-diazaspiro[3.6]decane, 3-azaspiro[5.5]undecane, 2- oxaspiro[2.2]pentane, 4-oxaspiro[2.5]octane, 1-oxaspiro[3.5]nonane, 2-oxaspiro[3.5]nonane, 7-oxaspiro[3.5]nonane, 2-oxaspiro[4.4]nonane, 6-oxaspiro[2.6]nonane, 1,7- dioxaspiro[4.5]decane, 2,5-dioxaspiro[3.6]decane, 1-oxaspiro[5.5]undecane, 3- oxaspiro[5.5]undecane, 3-oxa-9-azaspiro[5.5]undecane and the like. The term “inhibiting”, “inhibitor”, and/or “inhibits”, as used herein refers to ceasing biological and/or chemical activity, slowing biological and/or chemical activity, and/or reducing biological and/or chemical activity. For example, the inhibition of stress granule formation can include reducing the formation of stress granules, ceasing the formation of stress granules, and/or slowing the progression of stress granule formation. The term “pharmaceutically acceptable salts” is meant to include salts of the compounds that are prepared with relatively nontoxic acids or bases, depending on the particular substituents found on the compounds described herein. When compounds of the present disclosure contain relatively acidic functionalities, base addition salts can be obtained by contacting the neutral form of such compounds with a sufficient amount of the desired base, either neat or in a suitable inert solvent. Examples of pharmaceutically acceptable base addition salts include sodium, potassium, calcium, ammonium, organic amino, or magnesium salt, or a similar salt. When compounds of the present disclosure contain relatively basic functionalities, acid addition salts can be obtained by contacting the neutral form of such compounds with a sufficient amount of the desired acid, either neat or in a suitable inert solvent. Examples of pharmaceutically acceptable acid addition salts include those derived from inorganic acids like hydrochloric, hydrobromic, nitric, carbonic, monohydrogencarbonic, phosphoric, monohydrogenphosphoric, dihydrogenphosphoric, sulfuric, monohydrogensulfuric, hydriodic, or phosphorous acids and the like, as well as the salts derived from relatively nontoxic organic acids like acetic, propionic, isobutyric, maleic, malonic, benzoic, succinic, suberic, fumaric, lactic, mandelic, phthalic, benzenesulfonic, p-tolylsulfonic, citric, tartaric, oxalic, methanesulfonic, and the like. Also included are salts of amino acids such as arginate and the like, and salts of organic acids like glucuronic or galactunoric acids and the like (see, for example, Berge et al., “Pharmaceutical Salts”, Journal of Pharmaceutical Science, 1977, 66, 1-19). Certain specific compounds of the present disclosure contain both basic and acidic functionalities that allow the compounds to be converted into either base or acid addition salts. Certain compounds of the present disclosure can exist in unsolvated forms as well as solvated forms, including hydrated forms. In general, the solvated forms are equivalent to unsolvated forms and are encompassed within the scope of the present disclosure. Certain compounds of the present disclosure may exist in multiple crystalline or amorphous forms. In general, all physical forms are equivalent for the uses contemplated by the present disclosure and are intended to be within the scope of the present disclosure. “Pharmaceutically acceptable excipient” and “pharmaceutically acceptable carrier” refer to a substance that aids the administration of an active agent to and absorption by a subject and can be included in the compositions of the present disclosure without causing a significant adverse toxicological effect on the patient. Non-limiting examples of pharmaceutically acceptable excipients include water, NaCl, normal saline solutions, lactated Ringer’s, normal sucrose, normal glucose, binders, fillers, disintegrants, lubricants, coatings, sweeteners, flavors, salt solutions (such as Ringer's solution), alcohols, oils, gelatins, carbohydrates such as lactose, amylose or starch, fatty acid esters, hydroxymethycellulose, polyvinyl pyrrolidine, and colors, and the like. Such preparations can be sterilized and, if desired, mixed with auxiliary agents such as lubricants, preservatives, stabilizers, wetting agents, emulsifiers, salts for influencing osmotic pressure, buffers, coloring, and/or aromatic substances and the like that do not deleteriously react with the compounds of the disclosure. One of skill in the art will recognize that other pharmaceutical excipients are useful in the present disclosure. IV. BRIEF DESCRIPTION OF THE DRAWINGS FIG.1. Illustrates the structure of SARS-CoV-2 Main Protease (highly conserved with SARS M^pro). Catalysis is controlled by a dyad of reactive active site residues including His 41 and Cys 145, which follow covalent mechanism consistent with other Ser, Cys, and Thr proteases. FIG.2. Illustrates docking poses of Formula (I) compounds. A. Docking pose of compound 1 (ebselen) bound to the catalytic site of SARS-CoV-2 M^pro. A hydrogen bond is observed between the carbonyl oxygen atom of compound 1 and Glu 166. The benzoisoselenazole ring forms π-π stacking interactions with catalytic His 41. B. Docking pose of compound 19 bound to the catalytic site of SARS-CoV-2 M^pro. A hydrogen bond is observed between the carbonyl oxygen atom of compound 19 and Glu 166. The benzoisoselenazole ring forms π-π stacking interactions with catalytic His 41. The chlorine atom of compound 19 forms a halogen bond interaction with Gly 143. C. Docking pose of compound 20 bound to the catalytic site of SARS-CoV-2 M^pro. π-π stacking interactions are observed between the benzoisoselenazole ring of compound 20 and catalytic His 41. A hydrogen bond is observed between the carbonyl oxygen atom of compound 20 and Glu 166. D. Docking pose of compound 25 bound to the catalytic site of SARS-CoV-2 M^pro. A hydrogen bond is observed between the carbonyl oxygen atom of compound 25 and Glu 166. π-π stacking interactions are observed between the benzoisoselenazole ring of compound 25 and catalytic His 41. The nitrile group is observed to accept a hydrogen bond from Cys 44. FIG.3. Illustrates that ebselen and certain compounds described herein can covalently modify SARS-CoV-2 M^pro in the absence of reducing agents. A. compound 1 (ebselen) is a reversible covalent inhibitor of SARS-CoV-2 M^pro. The product formation over time was reduced approximately 65% relative to DMSO control (squares) by 1 µM of ebselen (dots) and by 89% by 10 µM of ebselen (inverted triangles) when added simultaneously with fluorogenic substrate. Upon 10x dilution in assay buffer without DTT, product formation of SARS-CoV-2 M^pro pre-incubated with 10 µM of ebselen (diamonds) is observed to reduce product formation by 91%, comparable to an undiluted concentration of 10 µM. When diluted in the presence of DTT, SARS-CoV-2 M^pro pre-incubated with 10 µM of ebselen (triangles) is observed to reduce product formation by 53% relative to DMSO control (squares), similar to that observed for a final concentration of 1 µM. These data indicate that ebselen can covalently modify SARS- CoV-2 M^pro, although this modification is reversible in the presence of strong reducing agents. B. compound 4 is a rapidly reversible inhibitor of SARS-CoV-2 M^pro. Upon 10x dilution, product formation of SARS-CoV-2 M^pro pre-incubated with 10 µM of compound 4 in the absence of DTT (diamonds) is observed to reduce product formation by 48% relative to DMSO control (squares), similar to that observed for a final concentration of 1 µM compound 4 (dots, 44% inhibition), while simultaneous addition of substrate and 10 µM compound 4 (inverted triangles) is observed to reduce product formation by 86%. Similar results are observed for SARS-CoV-2 M^pro pre-incubated with 10 µM of compound 4 in the presence of DTT (triangles,43% inhibition). C. compound 7 is a reversible covalent inhibitor of SARS-CoV-2 M^pro. D. compound 19 is a rapidly reversible inhibitor of SARS-CoV-2 M^pro. E. compound 20 is a reversible covalent inhibitor of SARS-CoV-2 M^pro. F. compound 25 is a reversible covalent inhibitor of SARS-CoV-2 M^pro. Upon 10x dilution, product formation of SARS-CoV- 2 M^pro pre-incubated with 10 µM of compound 25 in the absence of DTT (diamonds) is observed to reduce product formation by 64% relative to DMSO control (squares). Simultaneous addition of substrate and 10 µM 25 reduced product formation by 94%, while simultaneous addition of substrate and 1 µM compound 25 is observed to reduce product formation by 29%. These data suggest that while compound 25 may covalently modify SARS- CoV-2 M^pro, formation of the covalent adduct was incomplete after 30 minutes of incubation. FIG. 4. Illustrates that compound 1 (ebselen) and compound 4 are competitive inhibitors of SARS-CoV-2 main protease. A. M^pro exposed to varying concentrations of ebselen reaches a common Vmax at 30 µM substrate B. All ebselen conditions converge on a common y-intercept, indicating V_max is independent of inhibitor concentration, consistent with a competitive mechanism of inhibition. C. M^pro exposed to varying concentrations of compound 4 reaches a common V_max at 30 µM substrate D. All compound 4 conditions converge on a common y-intercept, indicating Vmax is independent of inhibitor concentration, consistent with a competitive mechanism of inhibition. FIG. 5. Illustrates antiviral activity of select Formula (I) compounds. Vero E6 cells were pre-treated with varying doses of compound then infected with SARS-CoV-2 to a multiplicity of infection (MOI) of 0.01. After 72 hours, cell proliferation was determined. Remdesivir is included as a positive control (EC₅₀ = 1.8 ± 1.2 µM). A. Dose-response curve for compound 1 (EC₅₀ = >20 µM). B. Dose-response curve for compound 4 (EC₅₀ = 11.2 ± 1.3 µM). C. Dose-response curve for compound 7 (EC₅₀ = 26.5 ± 1.2 µM). D. Dose-response curve for compound 18 (EC₅₀ = 6.5 ± 2.0 µM). E. Dose-response curve for compound 19 (EC₅₀ = 17.4 ± 3.5 µM). F. Dose-response curve for compound 20 (EC₅₀ = 18.2 ± 3.6 µM). G. Dose-response curve for compound 21 (EC₅₀ = 5.2 ± 1.2 µM). H. Dose-response curve for compound 24 (EC₅₀ = 0.8 ± 0.3 µM). I. Dose-response curve for compound 25 (EC₅₀ = 2.0 ± 1.1 µM). FIG. 6. Illustrates that compound 24 inhibits SARS-CoV-2 replication in infected human iPSC-deriv6 lung organoids. Sixty day old lung organoids were infected with SARS- CoV-2 USA-WA1/2020 virus at MOI of 2 and viral RNAs from A. supernatant, and B. cellular fractions quantified after 72 h of infection; mean ± SEM of n = 3 organoids cultured and infected in different wells; *p <0.05, by Student’s t test. FIG. 7. Illustrates that SARS-CoV-2 robustly replicates in human lung organoids and induces expression of genes involved in innate immunity and inflammation. Generation and characterization of iPSC-derived human lung organoids (LORGs). A. Representative phase contrast image of LORG at 60 Days (60D); scale bar represents 200 µm. B. Hematoxylin and Eosin staining of 60D LORG showing the alveolar like morphology; scale bars = 100 μm. C. Confocal images showing labelling for cells surrounding epithelial structures (ECAD) co- labelled with mesenchymal-cell-type marker vimentin (VIM). LORG is also co-labelled with SOX9 and FOXJ1 markers as well as with goblet cell marker MUC5AC and SOX9; scale bars = 100 μm and for enlarged image scale bar = 50 μm. D. Western blot analysis of 60D old organoid showing protein levels for ECAD, SOX9, FOXJ1, Mucin5AC. N=2 organoids. E. qRT-PCR analysis for 60D LORG shows expression of lung alveolar type 1 cell (AT1) genes AGER and HOPX; mean ± SEM of n = 3; *p < 0.05 and ***p < 0.001. F. qRT-PCR analysis for 60D LORG shows expression of lung alveolar type 2 cell (AT2) genes SFTPB, SFTPC, ABCA3 and SLC34A2; mean ± SEM of n = 3; *p < 0.05, **p < 0.01, and ***p < 0.001. G. LORGs express ACE2, TMPRSS2, DPP4, and Furin. qRT-PCR analysis for 60D LORG shows expression of ACE2, TMPRSS2, DPP4 and Furin; Data is presented as mean ± SEM of n=3; *p < 0.05 and **p < 0.01. Lung organoids are permissive to SARS-CoV-2 pseudovirus infection that is inhibited by Camostat, nafamostat, and EK1 peptide. H. Phase contrast and fluorescence imaging shows infection of SARS-CoV-2-GFP pseudovirus at 24h post infection at MOI=2; scale bars= 200 μm. I. SARS-CoV-2-Luciferase pseudovirus infection is blocked by viral entry inhibitors. Bar graph shows the luciferase activity in the presence and absence of TMPRSS2 inhibitor (Camostat mesylate), nafamostat, and a fusion inhibitor EK1 peptide to lung organoid infected with SARS-CoV-2 pseudovirus; SEM of n = 3; ***p < 0.001, by student t test. SARS-CoV-2 isolate USA-WA1/2020 robustly replicates in human lung organoids. Lung organoids were infected with SARS-CoV-2 USA-WA1/2020 virus at MOI of 2 and viral RNAs from J. supernatant and K. cellular; fractions were quantified at indicated times of infection; mean ± SEM of n = 2; **p < 0.01, and ***p < 0.001, by Student’s t test. L. SARS- CoV-2 isolate USA-WA1/2020 infection induces expression of immunity and inflammation genes. J. LORGs infected as above and gene expression of indicated genes was quantified by qRT-PCR at 72 hours post infection. Bar graph shows expression of immune response genes and cytokines. M. Organoids pre-treated with 25HC (5 µM) for 16h and infected with luciferase expressing SARS-CoV-2 pseudovirus at MOI =0.1 for 2 h and treated with fresh medium containing 5 µM 25HC. Luciferase activity was measured at 24h post-infection; mean ± SD of n = 3; ****p < 0.0001, by Student’s t test. V. DETAILED DESCRIPTION The disclosure is based, in part, on the finding that by targeting the main protease (M^pro) of a coronavirus (e.g., SARS-CoV-2), the replication of SARS-CoV-2 can be impeded. Accordingly, this disclosure features chemical entities (e.g., a compound or a pharmaceutically acceptable salt, and/or hydrate, and/or cocrystal, and/or drug combination of the compound) that inhibit the main protease (M^Pro) of a coronavirus (e.g., SARS-CoV-2). Said chemical entities are useful, e.g., for treating a coronavirus infection (e.g., SARS-CoV-2 infection (e.g., COVID-19)) in a subject (e.g., a human). This disclosure also features compositions containing the same as well as methods of using and making the same. Provided herein are compounds of Formula (I):

Formula (I) or a pharmaceutically acceptable salt thereof, wherein: R¹ is selected from the group consisting of: H, halo, C_1-6 alkyl, C_1-6 haloalkyl, C_1-6 alkoxy, and C_1-6 haloalkoxy; R² is phenyl, –CH₂-phenyl, or –C_4-10 alkyl, each optionally substituted with from 1-4 independently selected R^a; and each occurrence of R^a is independently selected from the group consisting of: halo; C_1- 10 alkyl; C_1-6 haloalkyl; cyano; C_1-6 alkoxy; C_1-6 haloalkoxy; C_1-6 thioalkoxy; and –OH. In some embodiments of Formula (I), one or both of (aa) and (bb) apply: (aa) R¹ is selected from the group consisting of: halo, C_1-6 alkyl, C_1-6 haloalkyl, C_1-6 alkoxy, and C_1-6 haloalkoxy; and/or (bb) R² is selected from the group consisting of: phenyl substituted with from 1-4 R^a; –CH₂-phenyl optionally substituted with from 1-4 independently selected R^a; and –C_4-10 alkyl optionally substituted with from 1-4 independently selected R^a. In some embodiments of Formula (I), when R¹ is H, R² is –CH₂-phenyl or –C_4-10 alkyl, each optionally substituted with from 1-4 independently selected R^a. In some embodiments of Formula (I), when R² is phenyl, R¹ is selected from the group consisting of: halo, C_1-6 alkyl, C_1-6 haloalkyl, C_1-6 alkoxy, and C_1-6 haloalkoxy. In some embodiments of Formula (I), R¹ is H. In some embodiments of Formula (I), R¹ is selected from the group consisting of: halo, C_1-3 alkyl, C_1-3 haloalkyl, C_1-3 alkoxy, and C_1-3 haloalkoxy. In some embodiments of Formula (I), R¹ is selected from the group consisting of: -F, - Cl, -CH₃, -CF₃, and –OCH₃. In some embodiments of Formula (I), R² is phenyl which is optionally substituted with from 1-4 independently selected R^a. In some embodiments of Formula (I), R² is phenyl substituted with from 1-4 independently selected R^a. In some embodiments of Formula (I), R² is phenyl substituted with from 1-2 independently selected R^a. In some embodiments of Formula (I), R² is ^a1

, wherein: R is selected from the group consisting of: H, F, Cl, CH₃, CF₃, OH, OCH₃, OCF₃, SCH₃, CN, C₂H₅, C₅H₁₁, C₇H₁₅, and C₈H₁₇; and R^a2 is selected from the group consisting of: H, F, Cl, CH₃, CF₃, OH, OCH₃, OCF₃, and SCH₃. In some embodiments of Formula (I), R² is , wherein R^a1 is an

independently selected R^a; and R^a2 is H or R^a. In some embodiments of Formula (I), R² is , wherein R^a1 is an cted R^a

independently sele ; and R^a2 is H or R^a. In some embodiments of Formula (I), R^a1 is selected from the group consisting of: -Br, -Cl, -F, cyano, C_1-3 alkyl, C_1-3 haloalkyl, and C_1-3 alkoxy. In some embodiments of Formula (I), R^a1 is selected from the group consisting of: -Br, -Cl, C_1-3 alkyl, and C_1-3 haloalkyl. In some embodiments of Formula (I), R^a1 is selected from the group consisting of –Br, -Cl, -CH₃, CH₂CH₃, and CF₃. In some embodiments of Formula (I), R^a2 is H or halo. In some embodiments of Formula (I), R² is C_4-10 alkyl optionally substituted with from 1-4 independently selected R^a. In some embodiments of Formula (I), R² is C_4-10 alkyl, such as linear C_4-10 alkyl. In some embodiments of Formula (I), R¹ is H, and R² is

, wherein: R^a1 is selected from the group consisting of: H, F, Cl, CH₃, CF₃, OH, OCH₃, OCF₃, SCH₃, CN, C₂H₅, C₅H₁₁, C₇H₁₅, and C8H17; and R^a2 is selected from the group consisting of: H, F, Cl, CH₃, CF₃, OH, OCH₃, OCF₃, and SCH₃. In some embodiments of Formula (I), R¹ is H, and R² is

, wherein R^a1 is an independently selected R^a; and R^a2 is H or R^a. In some embodiments of Formula (I), R¹ is H, and R² is

, wherein R^a1 is an independently selected R^a; and R^a2 is H or R^a. In some embodiments of Formula (I), R¹ is H, and R² is C_4-10 alkyl optionally substituted with from 1-4 independently selected R^a. In some embodiments of Formula (I), R¹ is H, and R² is C_4-10 alkyl, such as linear C_4-10 alkyl. In some embodiments of Formula (I), the compound is selected from the group consisting of the following:

or a pharmaceutically acceptable salt thereof. In some embodiments of Formula (I), the compound is selected from the group consisting of compounds 2-30, or a pharmaceutically acceptable salt thereof. In some embodiments of Formula (I), the compound is not compound 1, or a pharmaceutically acceptable salt thereof. In some embodiments of Formula (I), the compound is selected from the group consisting of the following:

or a pharmaceutically acceptable salt thereof. Also provided herein are compounds of Formula (II):

Formula (II) or a pharmaceutically acceptable salt thereof, wherein: Ar is:

or

; p, q, and r are independently 0, 1, 2, or 3; each R¹ is independently selected from the group consisting of: halo, C_1-6 alkyl, C_1-6 haloalkyl, C_1-6 alkoxy, C_1-6 haloalkoxy, C_1-6 thioalkoxy, -OH, cyano, and C(O)O(C_1-6 alkyl); and each R² is selected from the group consisting of: halo, C_1-6 alkyl, C_1-6 haloalkyl, C_1-6 alkoxy, C_1-6 haloalkoxy, C_1-6 thioalkoxy, -OH, and C(O)O(C_1-6 alkyl). In some embodiments of Formula (II), Ar is

In some embodiments of Formula (II), Ar is

In some embodiments of Formula (II), q is 1. In some embodiments of Formula (II), q is 2. In some embodiments of Formula (II), each R² is independently selected from the group consisting of: F, Cl, CN, CH₃, ^tBu, CF₃, OH, OCH₃, OCF₃, SCH₃, and C(O)OMe. In some embodiments of Formula (II), p is 0. In some embodiments of Formula (II), p is 1, 2, or 3. In some embodiments of Formula (II), R¹ is selected from the group consisting of: F, Cl, CH₃, CF₃, OH, OCH₃, OCF₃, SCH₃, CN, and C(O)OMe. In some embodiments of Formula (II), the compound is selected from the group consisting of:

or a pharmaceutically acceptable salt thereof. Also provided herein are compounds of Formula (III):

or a pharmaceutically acceptable salt thereof, wherein: X is halo; R¹ is selected from the group consisting of: º C1-15 alkyl optionally substituted with from 1-6 independently selected R^a; and º -L³-R³, wherein: o L³ is a bond or C_1-6 alkylene optionally substituted with from 1-6 independently selected R^a; and o R³ is selected from the group consisting of C_3-10 cycloalkyl, 4-10 membered heterocyclyl, C_6-10 aryl, and 5-10 membered heteroaryl, each of which is optionally substituted with from 1-4 independently selected R^b; and º -(Z¹-Z²)_m-Z³, wherein: o each Z¹ is independently C_1-6 alkylene optionally substituted with from 1-6 independently selected R^a; o each Z² is independently selected from the group consisting of: NH, N(C_1-3 alkyl), O, and S; and o Z³ is selected from the group consisting of: (i) C_1-6 alkyl optionally substituted with from 1-6 independently selected R^a; and (ii) –L³-R³; and o m is an integer from 1 to 10; R^1a is H or C_1-3 alkyl; or R^1a and R¹, taken together with the nitrogen atom to which each is attached forms a 4-8 membered heterocyclyl, wherein the heterocyclyl is optionally substituted with from 1-6 independently selected R^b; R^2a, R^2b, R^2c, and R^2d are independently selected from the group consisting of: halo, -OH, C_1-6 alkoxy, C_1-6 haloalkoxy, and nitro; each occurrence of R^a is independently selected from the group consisting of: halo, C_1-6 alkoxy, C_1-6 haloalkoxy, C_1-6 thioalkoxy, -OH, cyano, C(O)O(C_1-6 alkyl), C(O)(C_1-6 alkyl), S(O)_1-2C_1-6 alkyl, S(O)₂NR’R”, and C(O)NR’R”; each occurrence of R^b is independently selected from the group consisting of: halo, C_1-6 alkyl, C_1-6 haloalkyl, C_1-6 alkoxy, C_1-6 haloalkoxy, C_1-6 thioalkoxy, -OH, cyano, C(O)O(C_1-6 alkyl), C(O)(C_1-6 alkyl), S(O)_1-2C_1-6 alkyl, S(O)₂NR’R”, C(O)NR’R”, and –(L^c)_p-R^c; each p is independently 0, 1, 2, or 3; each L^c is independently selected from the group consisting of CH₂, C(=O), O, NH, N(C_1-3 alkyl), S, and S(O)_1-2; each R^c is independently selected from the group consisting of: C_3-10 cycloalkyl, C_6-10 aryl, 4-10 membered heterocyclyl, and 5-10 membered heteroaryl, each optionally substituted from 1-4 independently selected R^d; each occurrence of R^d is independently selected from the group consisting of: halo, C_1-6 alkyl, C_1-6 haloalkyl, C_1-6 alkoxy, C_1-6 haloalkoxy, C_1-6 thioalkoxy, -OH, cyano, and C(O)O(C_1-6 alkyl); and each occurrence of R’ and R” is independently H, C_1-6 alkyl, or C3-6 cycloalkyl. In some embodiments of Formula (III), R^2a is nitro. In some embodiments, R^2b, R^2c, and R^2d are each H. In some embodiments of Formula (III), R^2d is nitro. In some embodiments, R^2a, R^2b, and R^2c are each H. In some embodiments of Formula (III), R^2a and R^2d are –OH. In some embodiments, R^2b and R^2c are H. In some embodiments of Formula (III), R^1a is H. In some embodiments of Formula (III), R¹ is C_1-15 alkyl, such as C_4-15 alkyl (e.g., C_4-15 linear alkyl), optionally substituted with from 1-6 independently selected R^a. For example, R¹ can be selected from the group consisting of:

, ,

In some embodiments of Formula (III), R¹ is –R³ or –CH₂-R³. In some embodiments of Formula (III), R³ is selected from the group consisting of: C_3- 10 cycloalkyl and 4-10 membered heterocyclyl, each optionally substituted with from 1-4 independently selected R^b, optionally wherein one occurrence of R^b is –(L^c)_p-R^c. In some embodiments of Formula (III), R¹ is selected from the group consisting of: and

. In some embodiments of Formula (III), R³ is selected from the group consisting of: C_6- ₁₀ aryl and 5-10 membered heteroaryl, each optionally substituted with from 1-4 independently selected R^b, optionally wherein one occurrence of R^b is –(L^c)_p-R^c. In some embodiments of Formula (III), R¹ is selected from the group consisting of:

and

In some embodiments of Formula (III), R^1a and R¹, taken together with the nitrogen atom to which each is attached forms a 4-8 membered heterocyclyl, wherein the heterocyclyl is optionally substituted with from 1-6 independently selected R^b, such as wherein R^1a and R¹ taken together with the nitrogen atom to which each is attached forms

. In some embodiments of Formula (III), R¹ is -(Z¹-Z²)_m-Z³, optionally wherein Z¹ is CH₂CH₂; and Z² is –O-, such as wherein R¹ is

In some embodiments of Formula (III), the compound of selected from the group consisting of the following:

or a pharmaceutically acceptable sale thereof. In some embodiments of Formula (III), the compound is selected from the group consisting of:

or a pharmaceutically acceptable salt thereof. Also provided herein are compounds of Formula (IV):

Formula (IV) or a pharmaceutically acceptable salt thereof, wherein: R¹ is selected from the group consisting of: H, -OC_1-6 alkyl, -O(C_3-6 cycloalkyl), and NR’R”; R² is selected from the group consisting of: -C_1-6 alkyl, -C_1-6 haloalkyl, -NR’R”, -(C_1-6 alkylene)-NR’R”, -(C_1-6 haloalkylene)-NR’R”, -(C_1-6 alkylene)-NR’C(=W)R’, -(C_1-6 alkylene)-NR’C(=W)OR’, -(C_1-6 alkylene)-NR’C(=W)NR’R”, and

; R³ is selected from the group consisting of: -NHC(=O)R⁴ and -R⁵; R⁴ is selected from the group consisting of: C_1-6 alkyl, -(C_1-6 alkylene)-NR’R”, -(C_1-6 haloalkylene)-NR’R”, and –L⁶-R⁶; R⁵ is selected from the group consisting of: H, -NR’R”, -(C_1-6 alkylene)-NR’R”, -(C1- ₆ alkylene)-C(O)OH, -(C_1-6 alkylene)-C(O)O(C_1-6 alkyl), C_1-6 alkyl, C_1-6 haloalkyl, and -(C_1-6 alkylene)-OH; W is O, S, or NR’; -L⁶ is a bond or C_1-6 alkylene; -R⁶ is C_6-10 or 5-10 membered heteroaryl, each optionally substituted with from 1-4 substituents independently selected from the group consisting of: halo, cyano, C_1-6 alkyl, C_1-6 haloalkyl, C_1-6 alkoxy, and C_1-6 haloalkoxy; and each occurrence of R’ and R” is independently H, C_1-6 alkyl, or C_3-6 cycloalkyl. In some embodiments of Formula (IV), R¹ is H. In some embodiments of Formula (IV), R¹ is OC_1-6 alkyl, such as OMe. In some embodiments of Formula (IV), R¹ is NR’R” such as NHMe, or NH(C_3-6 cycloalkyl). In some embodiments of Formula (IV), R² is

In some embodiments of Formula (IV), R² is C_1-6 alkyl, such as isopropyl; or R² is C1- ₆ haloalkyl, such as CF₃ In some embodiments of Formula (IV), R² is -(C_1-6 alkylene)-NR’R”, such as – CH₂NHMe. In some embodiments of Formula (IV), R² is -(C_1-6 alkylene)NR’C(=W)NR’R”, such as –CH₂-NHC(=S)NH₂. In some embodiments of Formula (IV), R³ is -NHC(=O)R⁴. In some embodiments of Formula (IV), R³ is -NHC(=O)–L⁶-R⁶, such as wherein R³ is

. In some embodiments of Formula (IV), R³ is NHC(=O)R⁴; and R⁴ is C_1-6 alkyl such as methyl. In some embodiments of Formula (IV), R³ is NHC(=O)R⁴; and R⁴ is -(C_1-6 alkylene)- NR’R”, such as

In some embodiments of Formula (IV), R³ is NHC(=O)R⁴; and R⁴ is -(C_1-6 haloalkylene)-NR’R”, such as

In some embodiments of Formula (IV), R³ is –R⁵. In some embodiments of Formula (IV), R³ is NR’R”, -CH₂NR’R”, -C_1-3 alkyl, or – CH₂C(O)OH. In some embodiments of Formula (IV), R¹ is OMe, H, or NHMe; R² is isopropyl, CF₃, -NH₂, -CH₂NHMe, or –CH₂NH(C=S)NH₂; and R³ is NHC(=O)Me,

In some embodiments of Formula (IV), R¹ is OMe, H, or NHMe; R² is

; and R³ is NHC(=O)Me, methyl, NH₂, CH₂NH₂, or CH₂C(=O)OH. In some embodiments of Formula (IV), the compound has the following formula:

In some embodiments of Formula (IV), the compound is selected from the group consisting of:

wherein R” is C_1-6 alkyl or C_1-6 haloalkyl, such as wherein R” is C_1-6 alkyl, such as isopropyl. Also provided herein is a compound as shown in Table I. Table I. Compounds of Formula (I), (II), and (III).

Also provided herein are methods of treating a coronavirus infection in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of an inhibitor for the main protease of the coronavirus. In some embodiments, the method comprises administering to the subject one or more chemical entities generically or specifically described herein. In some embodiments, the method comprises administering to the subject a compound of Formula (I), Formula (II), Formula (III), Formula (IV), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition thereof as described herein. In some embodiments, the coronavirus infection is a betacoronavirus infection. In some embodiments, the coronavirus infection is selected from the group consisting of SARS-CoV-2, SARS-CoV, and MERS-CoV infection. In some embodiments, the coronavirus infection is a SARS-CoV-2 infection. For example, the coronavirus infections can be COVID-19. In some embodiments, the subject is human. Also provided herein are methods of treating a coronavirus infection in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of a compound of Formula (I), Formula (II), Formula (III), Formula (IV) as described anywhere herein, or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition thereof. In some embodiments, the coronavirus infection is a betacoronavirus infection. In some embodiments, the coronavirus infection is selected from the group consisting of SARS-CoV- 2, SARS-CoV, and MERS-CoV infection. In some embodiments, the coronavirus infection is a SARS-CoV-2 infection. For example, the coronavirus infections can be COVID-19. In some embodiments, the subject is human. VI. OTHER EMBODIMENTS It is to be understood that while the present disclosure has been described in conjunction with the detailed description thereof, the foregoing description is intended to illustrate and not limit the scope of the disclosure, which is defined by the scope of the appended claims. Other aspects, advantages, and modifications are within the scope of the following claims. VII. EXAMPLES It is understood that the examples and embodiments described herein are for illustrative purposes only and that various modifications or changes in light thereof will be suggested to persons skilled in the art and are to be included within the spirit and purview of this application and scope of the appended claims. All publications, patents, and patent applications cited herein are hereby incorporated by reference in their entirety for all purposes. Example 1. Compounds General Procedures. All reactions were performed in flame-dried round-bottomed or modified Schlenk flasks fitted with rubber septa under a positive pressure of argon, unless otherwise noted. Air- and moisture-sensitive liquids and solutions were transferred via syringe or stainless steel cannula. Solvents (methylene chloride, ether, tetrahydrofuran, benzene, and toluene) were purified using a Pure-Solv MD-5 Solvent Purification System (Innovative Technology). Where necessary, solvents were deoxygenated by sparging with nitrogen for at least 1 hour unless otherwise noted. All other reagents were used directly from the supplier without further purification unless otherwise noted. Organic solutions were concentrated by rotary evaporation at ~25 mbar in a water bath heated to 40 °C unless otherwise noted. Analytical thin-layer chromatography (TLC) was carried out using 0.2 mm commercial glass- coated silica gel plates (silica gel 60, F254, EMD chemical). Thin layer chromatography plates were visualized by exposure to ultraviolet light and/or exposure to iodine, or to an acidic solution of ceric ammonium molybdate, or a basic solution of potassium permanganate followed by heating on a hot plate. Gas chromatographs were measured using an Agilent 7820 GC. Mass spectra (MS) were obtained on a Karatos MS9, Autospec, or an Agilent 6150 and reported as m/z (relative intensity). Accurate masses are reported for the molecular ion [M+D]⁺. Nuclear magnetic resonance spectra (¹H NMR and ¹³C NMR) were recorded with a Varian Gemini (500 MHz, ¹H at 500 MHz, ¹³C at 125 MHz; or 600 MHz, ¹H at 600 MHz, ¹³C at 150 MHz). For CDCl₃, (CD₃)₂SO, and CD₃OD solutions, chemical shifts are reported as parts per million (ppm) referenced to residual protium or carbon of the solvent; CDCl₃ δ 7.26 (¹H) and 77.0 (¹³C) ppm, (CD₃)₂SO at δ 2.50 (¹H) and 39.5 (¹³C) ppm, CD₃OD δ at 3.31 (¹H) and 49.1 (¹³C)ppm. Coupling constants are reported in Hertz (Hz). Data for ¹H-NMR spectra are reported as follows: chemical shift (ppm, referenced to protium; (bs = broad singlet, s = singlet, br d = broad doublet, d = doublet, t = triplet, q = quartet, dd = doublet of doublets, td = triplet of doublets, ddd = doublet of doublet of doublets, m = multiplet, integration, and coupling constants (Hz)). HPLC was performed on an Agilent 1200 series HPLC with a Supelco Analytical Discovery® C18 (25 cm X 10 mm, 5µm) RP-HPLC column to quantify purity. Formula (I) Compounds Method A

The compounds described below were synthesized from commercially available acid chlorides and anilines in two steps. Step 1: Preparation of intermediates (I)-i1-30. A stirred solution of R²NH₂ (2 mmol) in DCM at 0 °C was treated with TEA (2 mmol), followed by the dropwise addition of corresponding acid chloride (I)-SM_1-30 (2 mmol) and the solution was stirred for 3 hours at room temperature. The reaction mixture was diluted in excess DCM, transferred to a separatory funnel, and extracted with water and brine solution. The organic layer was separated and concentrated under reduced pressure. The crude material was purified by column chromatography (hexane:ethyl acetate, 70:30) yield the intermediates (I)- i_1-30 as solids. Step 2: Preparation of compounds 1-30 A one-necked round-bottomed flask was fitted with a reflux condenser and with a magnetic stirrer. The flask was charged with corresponding intermediate (I)-i_1-30 (1 mmol), followed by the addition of Se powder (5 mmol) and tBuONa (2 mmol). The reaction mixture was left to stir at 130 °C for 12 hours. After completion of reaction, the reaction mixture was diluted with excess water and extracted with ethyl acetate. The organic layer was separate and concentrated under reduced pressure. The crude material was purified by column chromatography (hexane:ethyl acetate, 70:30) yielded compounds 1-30 as solids. Table A. Formula (I) compounds prepared by Method A.

Formula (II) Compounds Method B

Table B. Formula (II) compounds prepared by Method B.

Formula (III) Compounds Method C

To a stirred solution of 2,3-dichloro-5,8-didroxy-1,4-naphthoquinone[(III)-SM1, 50 mg, 193 μmol) or 2,3-dichloro-5-nitro-1,4-naphthoquinone([(III)-SM₂, 50 mg, 184 μmol) in DCM (1 mL), appropriate amine (R¹NHR^1a) (2 equiv.) in EtOH (1 mL) was added, and if the amine was hydrochloride 2 equiv. TEA was added to neutralize this hydrochloride. The reaction mixture changed the color immediately (for aliphatic amines) or slowly (for aromatic amines). Then another 3 mL of EtOH was added into the vigorously stirring system which was heated to 78˚С afterwards to reflux. The consumption of starting materials was followed and monitored by TLC. And after 30 min to 5 hours (the aromatic amine reaction time is longer than the aliphatic ones), the mixture was concentrated by rotary evaporator under reduced pressure. The final compounds were recrystallized in EtOH or purified by chromatographic silica gel column at yield 30-70%. Most of the final compounds are dark red solids. For the 5-nitro-1,4-naphthoquinone reactions, there are two new points in TLC which correspond to the 2-chloro and 3-chloro regioisomers. Compounds corresponding to the faster moving spot in TLC (the upper point) were isolated (only compound 97 is the regioisomer mixture) and determined to be the 3- chloro-position substituted products by NMR via 2D-HMBC. Table C. Formula (III) compounds prepared by Method C.

Example 2. In Silico Modeling of Selected Compounds with Schrödinger In silico modeling of selected compounds was performed using the Glide docking module of the Schrödinger 11.5 modeling software suite. A crystal structure of the SARS-CoV- 2 M^pro bound to N3 (PDB ID: 6UL7) was first refined using Prime (i. Jin, Z. et al, Nature 2020, 582, 289-293; ii. Jacobson, M. P. et al, J Mol Biol 2002, 320 (3), 597-608; iii. Jacobson, M. P. et al, Proteins 2004, 55 (2), 351-367). The Optimized Potentials for Liquid Simulations All- Atom (OPLS) force field and the Surface generalized Born (SGB) continuum solution model were used to optimize and minimize the crystal structure. The docking grid was generated as a 15 Å cube centered on N3 (x = -14, y = 17.7, z = 67.1). Ligprep was used to generate a minimized 3D structure for all antiviral compounds using the OPLS 2001 force field. Docking was performed with Glide XP (i. Friesner, R. A. et al, J Med Chem 2004, 47 (7), 1739-1749; ii. Halgren, T. A. et al, J Med Chem 2004, 47 (7), 1750-1759; iii. Friesner, R. A. et al, J Med Chem 2006, 49 (21), 6177-6196). Compounds were ranked by docking score and the docking poses were evaluated for interactions with key residues, such as the catalytic dyad His 41 and Cys 145. See, for example FIG.2. Example 3. SARS-CoV-2 Main Protease Protein Expression and Purification The GST-tagged SARS-CoV-2 main protease was expressed in E. Coli BL21 competent cells (New England Biolabs) transformed with pET41b plasmid by heat shock and spread on a LB Kanamycin agar plate, then incubated overnight at 37 °C. 2-3 colonies were picked and transferred to 5 mL of LB media treated with kanamycin (0.5 mg/mL final concentration), then grown overnight shaking at 37 °C. The overnight culture was then transferred to 2 L of LB kanamycin media and incubated at 37 °C until OD 0.8. The culture was cooled at 4 °C for 20 mins and induced with 0.5 mM isopropyl β-D-1- thiogalactopyranoside (IPTG), then grown shaken at 16 °C. Cell pellets were collected by centrifugation (5,000 g for 10 min at 4 °C) and the supernatant was discarded. The pellets were resuspended in lysis buffer (50 mM Tris-HCl pH 7.5, 500 mM NaCl, 1.0% Triton x-100, 0.5 mM EDTA, 1x Complete protease inhibitor cocktail, 1 mM β-mercaptoethanol in RNase-free water; 6 mL per gram) with DNase 1 (5U per mL, RNase-free) and incubated at 4 °C for 1 hour and sonicated. The suspension was centrifuged at 10,000 g for 20 min and the supernatant was transferred to a glutathione sepharose affinity resin column that had been pre-equilibrized with lysis buffer. The supernatant was incubated with the affinity resin column at 4 °C for 2 hours with end-over-end rotation. After incubation, the column was washed with 5 bed volumes of lysis buffer, 3 x 5 bed volumes of wash buffer (50 mM Tris-HCl pH 7.5, 500 mM NaCl, 0.1% Triton x-100, 0.5 mM EDTA, 1x Complete protease inhibitor cocktail, 1 mM β- mercaptoethanol in RNase-free water), and 5 bed volumes of pre-elution buffer (50 mM Tris- HCl pH 7.5, 100 mM NaCl in RNase-free water). The protease was eluted with elution buffer (50 mM Tris-HCl pH 7.5, 100 mM NaCl, 40 mM glutathione in RNase-free water) and collected in 1 mL fractions until no further protein was collected (3-5 bed volumes total). The purity of the fractions was determined by SDS-page and fractions of purified protein were collected and concentrated to 2 mg/mL. The GST-tagged purified protein was incubated with TEV protease at 37 °C for 4 hours to obtain the untagged SARS-CoV-2 protease. Excess GST and GST-TEV protease were removed by glutathione sepharose affinity column purification. The untagged proteases were eluted in 50 mM Tris-HCl pH 7.5, 100 mM NaCl in RNase-free water. The purity of the fractions was determined by SDS-page and fractions of purified protein were collected and concentrated to 5 µM. The protein solutions were transferred to a Slyde-A- Lyzer Dialysis Cassette (20,000 MWCO, Thermo Scientific) and dialyzed overnight at 4 °C against dialysis buffer (50 mM Tris-HCl pH 7.4, 200 mM NaCl, 1 mM EDTA, 1 mM DTT in RNase-free water). Example 4. FRET Protease Activity Assay Activity of the SARS-CoV-2 main proteases was determined using fluorescence resonance energy transfer (FRET) assay adapted from Muramatsu et al (Proc Natl Acad Sci U S A 2016, 113 (46), 12997-13002). The fluorogenic peptide Dabcyl-Val-Asn-Ser-Thr-Leu-Gln- Ser-Gly-Leu-Arg-Lys-EDANS was used as a substrate (AnaSpec Inc). All reactions were performed in a black 96-well plate with 200 µL assay buffer (50 mM Tris-HCl pH 7.4, 200 mM NaCl, 1 mM EDTA, 1 mM DTT in RNase-free water) with 25 nM SARS-CoV-2 protease and 3 µM substrate. Compounds were screened at a concentration of 10 µM. All inhibitors were dissolved in DMSO and added to a final concentration of 0.2% DMSO. Fluorescent readings were normalized to 200 µL assay buffer with 3 µM substrate and 10 µM of inhibitor with a final concentration of 0.2% DMSO. Cleavage between the Gln and Ser residues was monitored by a BioTek Synergy plate reader, with excitation at 380 nm and emission at 485 nm every 10 minutes for 1 hour. The relative rate for wild type protease and each inhibitor concentration was averaged from three assay results. The relative reaction rates were normalized to wild type protease, and the relative activity was reported as a percentage of the wild type protease activity in Table 1. Additionally, dose-response curves were generated for compounds that showed significant inhibition at 10 µM using the assay conditions described above. The dose-response curve for ebselen (compound 1) was also generated as a positive control. Inhibitors were screened at six concentrations ranging from 0.100-10 µM. As before, cleavage between the Gln and Ser residues was monitored by a BioTek Synergy plate reader, with excitation at 380 nm and emission at 485 nm every 10 minutes for 1 hour. The relative rate for wild type protease and each inhibitor concentration was averaged from three assay results. The relative reaction rates were normalized to wild type protease and dose-response curves were plotted in GraphPad Prism 6. Example curves for Formula (I) compounds are shown in FIG. 5. To determine if the compounds were covalent or rapid, reversible inhibitors of SARS- CoV-2 M^pro, pre-incubation dilution experiments were performed. In assay buffer, 250 nM protease was incubated on ice for 30 mins with 10 µM of either compound ebselen (compound 1), compounds 4, 7, 19, 20 or 25. The reaction mixture was then diluted 10-fold with assay buffer and the fluorogenic peptide substrate was added to a final concentration of 3 µM. The experiment was also repeated with assay buffer free of DTT to determine the effects of the reducing agent on the mechanism of inhibition. For each compound, the rate of product formation after preincubation-dilution was compared to the rate of product formation for M^pro with 0.2% DMSO, 1 µM, and 10 µM compound without dilution. Results are shown in FIG. 3. Example 5. logD Measurements logD values were measured at pH = 7.4 by the shake-flask method, according to the literature (Donovan, S. F. et al, J Chromatogr A 2002, 952 (1-2), 47-61; Box, K. et al, Anal Chem 2003, 75 (4), 883-892). Results are shown in Table 1. Example 6. Inhibition Mechanism The reaction velocities observed over a range of substrate (1.5, 3, 4.5, 6, 9, 15, 22.5, and 30 µM) and inhibitor concentrations (0, 0.5, 1, 5, and 10 µM) for either ebselen (compound 1) or compound 4 were globally fit to a generalized mixed-model of inhibition (See FIG. 4) represented by the following equilibrium reaction scheme: This mechanism allows for inhibitor binding to both the free enzyme and the enzyme-substrate complex with varying affinity described by the following rate equation:

The term Ki describes the affinity of the inhibitor for free enzyme. The mechanism can be evaluated by the term α. When α approaches 1, the inhibitor is considered non-competitive and when α approached infinity, the inhibitor is considered competitive.

Example 7. Antiviral Assays Approximately 2x10⁴ Vero E6 cells (ATCC) were plated in 100 μL of DMEM (Gibco) supplemented with 10% serum in each well of a 96-well flat bottom plate and allowed to adhere overnight. Cells were pre-treated with 0.10-20 μM test compound in 100 μL of the same media for 1 hr, washed, and infected with SARS-CoV-2 (USA_WA01/2020 [World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch]) in 50 μL of media at 0.01 MOI for 1.5 hrs. Cells were then washed, and test compounds reapplied at 0.10- 20 μM in 100 μL media and incubated at 37 °C in 5% CO2 for 72 hrs. Following incubation, 10 μL room temperature WST8 reagent was added to each well, mixed and incubated for an additional 3 hrs at 37 °C and 5% CO2. O.D. at 460 nm was read on a BioTek plate reader. For antiviral assays in Calu-3 human lung cells, approximately 1.5x10⁵ Calu-3 cells (ATCC) were plated in 500 μL of EMEM (Gibco) supplemented with 10% FBS, 2 mM L- glutamine, and 1% penicillin/streptomycin in each well of 24-well flat bottom plates and allowed to adhere overnight. Cells were pre-treated with 0.10-20 μM test compound in DMSO (0.2 % final v/v) of the same media for 1 hr, washed, and infected with SARS-CoV-2 (USA_WA01/2020) in reduced serum media (2-3%) at 0.1 MOI for 1.5 hrs. Cells were then washed with PBS, and test compounds reapplied at 0.10-20 μM in 500 μl media and incubated at 37 °C in 5% CO2 for 24 hrs. At 24 hours post-infection, supernatant and infected cells were collected and lysed using TRIzol and RNA was extracted using a Direct-zol RNA Kit (Zymo) and quantified by RT-qPCR using SARS-CoV-2 N primers, as previously described (Tiwari, S. K. et al, Stem Cell Reports 2021, 16 (3), 437-445; Li, N. et al, Cell Rep 2021, 35 (6), 109091; Wang, S. et al, EMBO J 2020, 39 (21), e106057). The primers are as follows: Forward: CACATTGGCACCCGCAATC; Reverse: GAGGAACGAGAAGAGGCTTG. Results are shown in Table 1. Table 1. Enzymatic and cellular anti-viral activity of Formula (I) compounds

Example 8. Lung organoid infection and treatment with compound 24 Human iPSC derived lung organoids were generated using previously published methods and characterized by expression of ACE2, TMPRSS2, and alveolar cell epithelial markers (SFTPC, SFTPB, HOPX). The 60D differentiated lung organoids were pretreated with 5 µM E24 for 2 h and infected with SARS-CoV-2 as described previously (Tiwari, S. K. et al, Stem Cell Reports 2021, 16 (3), 437-445). SARS-CoV-2 isolate USA-WA1/2020 was obtained from BEI Resources. SARS-CoV-2 was propagated, and infectious units quantified by plaque assay using Vero E6 cells. Human iPSC derived lung organoids, were infected with SARS- CoV-2 at MOI=2 for 2 h at 37 °C. Then cells were washed, and fresh medium was added. At 72 h post infection supernatant and infected organoids were collected and lysed using TRIzol and RNA was extracted using a Direct-zol RNA Kit (Zymo) and quantified by RT-qPCR using SARS-CoV-2 N primers. Results are shown in FIG. 6.

Claims

What is claimed is: 1. A compound of Formula (I):

Formula (I) or a pharmaceutically acceptable salt thereof, wherein: R¹ is selected from the group consisting of: H, halo, C_1-6 alkyl, C_1-6 haloalkyl, C_1-6 alkoxy, and C_1-6 haloalkoxy; R² is phenyl, –CH₂-phenyl, or –C_4-10 alkyl, each optionally substituted with from 1-4 independently selected R^a; and each occurrence of R^a is independently selected from the group consisting of: halo; C_1- 10 alkyl; C_1-6 haloalkyl; cyano; C_1-6 alkoxy; C_1-6 haloalkoxy; C_1-6 thioalkoxy; –OH; C(O)OC_1-6 alkyl; and C(O)C_1-6 alkyl.

2. The compound of claim 1, wherein one or both of (aa) and (bb) apply: (aa) R¹ is selected from the group consisting of: halo, C_1-6 alkyl, C_1-6 haloalkyl, C_1-6 alkoxy, and C_1-6 haloalkoxy; or (bb) R² is selected from the group consisting of: phenyl substituted with from 1-4 R^a; –CH₂-phenyl optionally substituted with from 1-4 independently selected R^a; and –C_4-10 alkyl optionally substituted with from 1-4 independently selected R^a.

3. The compound of claims 1 or 2, wherein R¹ is H.

4. The compound of claims 1 or 2, wherein R¹ is selected from the group consisting of: halo, C_1-3 alkyl, C_1-3 haloalkyl, C_1-3 alkoxy, and C_1-3 haloalkoxy.

5. The compound of any one of claims 1-4, wherein R¹ is selected from the group consisting of: -F, -Cl, -CH₃, -CF₃, and –OCH₃.

6. The compound of any one of claims 1-5, wherein R² is phenyl which is optionally substituted with from 1-4 independently selected R^a.

7. The compound of any one of claims 1-6, wherein R² is phenyl substituted with from 1-4 independently selected R^a.

8. The compound of any one of claims 1-7, wherein R² is phenyl substituted with from 1-2 independently selected R^a.

9. The compound of any one of claims 1-8, wherein R² is

, wherein: R^a1 is selected from the group consisting of: H, F, Cl, CH₃, CF₃, OH, OCH₃, OCF₃, SCH₃, CN, C₂H₅, C₅H11, C₇H₁₅, and C8H17; and R^a2 is selected from the group consisting of: H, F, Cl, CH₃, CF₃, OH, OCH₃, OCF₃, and SCH₃.

10. The compound of any one of claims 1-8, wherein R² is

, wherein R^a1 is an independently selected R^a; and R^a2 is H or R^a.

11. The compound of any one of claims 1-8, wherein R² is

, wherein R^a1 is an independently selected R^a; and R^a2 is H or R^a.

12. The compound of claims 10 or 11, wherein R^a1 is selected from the group consisting of: -Br, -Cl, -F, cyano, C_1-3 alkyl, C_1-3 haloalkyl, and C_1-3 alkoxy.

13. The compound of any one of claims 10-12, wherein R^a1 is selected from the group consisting of: -Br, -Cl, C_1-3 alkyl, and C_1-3 haloalkyl.

14. The compound of any one of claims 10-13, wherein R^a1 is selected from the group consisting of –Br, -Cl, -CH₃, CH₂CH₃, and CF₃.

15. The compound of any one of claims 10-14, wherein R^a2 is H or halo.

16. The compound of any one of claims 1-5, wherein R² is C_4-10 alkyl optionally substituted with from 1-4 independently selected R^a.

17. The compound of claim 16, wherein R² is C_4-10 alkyl, such as linear C_4-10 alkyl.

18. The compound of any one of claims 1-17, wherein the compound is selected from the group consisting of the following:

or a pharmaceutically acceptable salt thereof.

19. The compound of any one of claims 1-17, wherein the compound is selected from the group consisting of the following:

or a pharmaceutically acceptable salt thereof.

20. A compound of Formula (II):

Formula (II) or a pharmaceutically acceptable salt thereof, wherein: Ar is:

or

; p, q, and r are independently 0, 1, 2, or 3; each R¹ is independently selected from the group consisting of: halo, C_1-6 alkyl, C_1-6 haloalkyl, C_1-6 alkoxy, C_1-6 haloalkoxy, C_1-6 thioalkoxy, -OH, cyano, and C(O)O(C_1-6 alkyl); and each R² is selected from the group consisting of: halo, C_1-6 alkyl, C_1-6 haloalkyl, C_1-6 alkoxy, C_1-6 haloalkoxy, C_1-6 thioalkoxy, -OH, cyano, and C(O)O(C_1-6 alkyl).

21. The compound of claim 20, wherein Ar is

22. The compound of claim 20, wherein Ar is

23. The compound of any one of claims 20-22, wherein q is 1.

24. The compound of any one of claims 20-22, wherein q is 2.

25. The compound of any one of claims 20-24, wherein each R² is independently selected from the group consisting of: F, Cl, CN, CH₃, ^tBu, CF₃, OH, OCH₃, OCF₃, SCH₃, and C(O)OMe.

26. The compound of any one of claims 20-25, wherein p is 0.

27. The compound of any one of claims 20-25, wherein p is 1, 2, or 3.

28. The compound of any one of claims 20-25 or 27, wherein R¹ is selected from the group consisting of: F, Cl, CH₃, CF₃, OH, OCH₃, OCF₃, SCH₃, CN, and C(O)OMe.

29. The compound of any one of claims 20-28, wherein the compound is selected from the group consisting of:

or a pharmaceutically acceptable salt thereof.

30. A compound of Formula (III):

or a pharmaceutically acceptable salt thereof, wherein: X is halo (e.g., -Cl); R¹ is selected from the group consisting of: º -C_1-15 alkyl optionally substituted with from 1-6 independently selected R^a; and º -L³-R³, wherein: o -L³ is a bond or C_1-6 alkylene optionally substituted with from 1-6 independently selected R^a; and o -R³ is selected from the group consisting of: C_3-10 cycloalkyl, 4-10 membered heterocyclyl, C_6-10 aryl, and 5-10 membered heteroaryl, each of which is optionally substituted with from 1-4 independently selected R^b; and º -(Z¹-Z²)_m-Z³, wherein: o each Z¹ is independently C_1-6 alkylene optionally substituted with from 1-6 independently selected R^a; o each Z² is independently selected from the group consisting of: -NH-, - N(C_1-3 alkyl)-, -O-, and –S-; and o Z³ is selected from the group consisting of: (i) C_1-6 alkyl optionally substituted with from 1-6 independently selected R^a; and (ii) –L³-R³; and o m is an integer from 1 to 10; R^1a is H or C_1-3 alkyl; or R^1a and R¹, taken together with the nitrogen atom to which each is attached forms a 4- 8 membered heterocyclyl ring, wherein the heterocyclyl ring is optionally substituted with from 1-6 independently selected R^b; R^2a, R^2b, R^2c, and R^2d are independently selected from the group consisting of: H, halo, -OH, C_1-6 alkoxy, C_1-6 haloalkoxy, and nitro; each occurrence of R^a is independently selected from the group consisting of: halo, C1- ₆ alkoxy, C_1-6 haloalkoxy, C_1-6 thioalkoxy, -OH, cyano, C(O)O(C_1-6 alkyl), C(O)(C_1-6 alkyl), S(O)_1-2C_1-6 alkyl, S(O)₂NR’R”, -NR’R”, and C(O)NR’R”; each occurrence of R^b is independently selected from the group consisting of: halo, C_1- 6 alkyl, C_1-6 haloalkyl, C_1-6 alkoxy, C_1-6 haloalkoxy, C_1-6 thioalkoxy, -OH, cyano, C(O)O(C_1-6 alkyl), C(O)(C_1-6 alkyl), S(O)_1-2C_1-6 alkyl, S(O)₂NR’R”, -NR’R”, C(O)NR’R”, and –(L^c)_p-R^c; each p is independently 0, 1, 2, or 3; each L^c is independently selected from the group consisting of CH₂, C(=O), O, NH, N(C_1-3 alkyl), S, and S(O)1-2; each R^c is independently selected from the group consisting of: C_3-10 cycloalkyl, C_6-10 aryl, 4-10 membered heterocyclyl, and 5-10 membered heteroaryl, each optionally substituted from 1-4 independently selected R^d; each occurrence of R^d is independently selected from the group consisting of: halo, C_1- ₆ alkyl, C_1-6 haloalkyl, C_1-6 alkoxy, C_1-6 haloalkoxy, C_1-6 thioalkoxy, -OH, cyano, and C(O)O(C_1-6 alkyl); and each occurrence of R’ and R” is independently H, C_1-6 alkyl, C_3-6 cycloalkyl, C(O)C_1-6 alkyl, C(O)OC_1-6 alkyl, or S(O)_1-2C_1-6 alkyl.

31. The compound of claim 30, wherein R^2a is nitro.

32. The compound of claims 30 or 31, wherein R^2b, R^2c, and R^2d are each H.

33. The compound of claim 30, wherein R^2d is nitro.

34. The compound of claim 33, wherein R^2a, R^2b, and R^2c are each H.

35. The compound of claim 30, wherein R^2a and R^2d are –OH.

36. The compound of claim 35, wherein R^2b and R^2c are H.

37. The compound of any one of claims 30-36, wherein R^1a is H.

38. The compound of any one of claims 30-37, wherein R¹ is C_1-15 alkyl, such as C_4-15 alkyl (e.g., C_4-15 linear alkyl), optionally substituted with from 1-6 independently selected R^a.

39. The compound of any one of claims 30-38, wherein R¹ is selected from the group consisting of:

.

40. The compound of any one of claims 30-37, wherein R¹ is –R³ or –CH₂-R³.

41. The compound of any one of claims 30-37 or 40, wherein R³ is selected from the group consisting of: C_3-10 cycloalkyl and 4-10 membered heterocyclyl, each optionally substituted with from 1-4 independently selected R^b, optionally wherein one occurrence of R^b is –(L^c)_p-R^c.

42. The compound of any one of claims 30-37 or 41, wherein R¹ is selected from the group consisting of:

; ; ; ; and

43. The compound of any one of claims 30-37 or 40, wherein R³ is selected from the group consisting of: C_6-10 aryl and 5-10 membered heteroaryl, each optionally substituted with from 1-4 independently selected R^b, optionally wherein one occurrence of R^b is –(L^c)_p- R^c.

44. The compound of any one of claims 30-37, 40, or 43, wherein R¹ is selected from the group consisting of:

and

45. The compound of any one of claims 30-36, wherein R^1a and R¹, taken together with the nitrogen atom to which each is attached forms a 4-8 membered heterocyclyl, wherein the heterocyclyl is optionally substituted with from 1-6 independently selected R^b, such as wherein R^1a and R¹ taken together with the nitrogen atom to which each is attached forms

46. The compound of any one of claims 30-36, wherein R¹ is -(Z¹-Z²)_m-Z³, optionally wherein Z¹ is CH₂CH₂; and Z² is –O-, such as wherein R¹ is

47. The compound of any one of claims 30-46, wherein the compound of selected from the group consisting of the following:

or a pharmaceutically acceptable sale thereof.

48. The compound of any one of claims 30-47, wherein the compound is selected from the group consisting of:

or a pharmaceutically acceptable salt thereof.

49. A compound of Formula (IV):

R³ is selected from the group consisting of: -NHC(=O)R⁴ and -R⁵; R⁴ is selected from the group consisting of: C_1-6 alkyl, -(C_1-6 alkylene)-NR’R”, -(C_1-6 haloalkylene)-NR’R”, and –L⁶-R⁶; R⁵ is selected from the group consisting of: H, -NR’R”, -(C_1-6 alkylene)-NR’R”, -(C_1- ₆ alkylene)-C(O)OH, -(C_1-6 alkylene)-C(O)O(C_1-6 alkyl), C_1-6 alkyl, C_1-6 haloalkyl, and -(C_1-6 alkylene)-OH; W is O, S, or NR’; -L⁶ is a bond or C_1-6 alkylene; -R⁶ is C_6-10 or 5-10 membered heteroaryl, each optionally substituted with from 1-4 substituents independently selected from the group consisting of: halo, cyano, C_1-6 alkyl, C_1-6 haloalkyl, C_1-6 alkoxy, and C_1-6 haloalkoxy; and each occurrence of R’ and R” is independently H, C_1-6 alkyl, or C_3-6 cycloalkyl.

50. The compound of claim 49, wherein R¹ is H.

51. The compound of claim 49, wherein R¹ is OC_1-6 alkyl, such as OMe.

52. The compound of claim 49, wherein R¹ is NR’R” such as NHMe, or NH(C_3-6 cycloalkyl).

53. The compound of any one of claims 49-52, wherein R² is .

54. The compound of any one of claims 49-52, wherein R² is C_1-6 alkyl, such as isopropyl; or R² is C_1-6 haloalkyl, such as CF₃

55. The compound of any one of claims 49-52, wherein R² is -(C_1-6 alkylene)- NR’R”, such as –CH₂NHMe.

56. The compound of any one of claims 49-52, wherein R² is -(C_1-6 alkylene)NR’C(=W)NR’R”, such as –CH₂-NHC(=S)NH₂.

57. The compound of any one of claims 49-56, wherein R³ is -NHC(=O)R⁴.

58. The compound of any one of claims 49-57, wherein R³ is -NHC(=O)–L⁶-R⁶, such as wherein R³ is

59. The compound of any one of claims 49-57, wherein R³ is NHC(=O)R⁴; and R⁴ is C_1-6 alkyl such as methyl.

60. The compound of any one of claims 49-57, wherein R³ is NHC(=O)R⁴; and R⁴ is -(C_1-6 alkylene)-NR’R”, such a

61. The compound of any one of claims 49-57, wherein R³ is NHC(=O)R⁴; and R⁴ is -(C_1-6 haloalkylene)-NR’R”, such as

.

62. The compound of any one of claims 49-56, wherein R³ is –R⁵.

63. The compound of any one of claims 49-56 or 62, wherein R³ is NR’R”, - CH₂NR’R”, -C_1-3 alkyl, or –CH₂C(O)OH.

64. The compound of claim 49, wherein: R¹ is OMe, H, or NHMe; R² is isopropyl, CF₃, -NH₂, -CH₂NHMe, or –CH₂NH(C=S)NH₂; and R³ is NHC(=O)Me,

65. The compound of claim 49, wherein R¹ is OMe, H, or NHMe; R² is

; and R³ is NHC(=O)Me, methyl, NH₂, CH₂NH₂, or CH₂C(=O)OH.

66. The compound of any one of claims 49-63, wherein the compound has the following formula:

.

67. The compound of any one of claims 49-64, wherein the compound is selected from the group consisting of:

wherein R” is C_1-6 alkyl or C_1-6 haloalkyl, such as wherein R” is C_1-6 alkyl, such as isopropyl.

68. A compound selected from any one of compounds 1-103 as described herein, or a pharmaceutically acceptable salt thereof.

69. A pharmaceutical composition comprising a compound of any one of claims 1- 68 or a pharmaceutically acceptable salt thereof and one or more pharmaceutically acceptable excipients.

70. A method of treating a coronavirus infection in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of an inhibitor for the main protease of the coronavirus.

71. The method of claim 70, comprising administering one or more chemical entities generically or specifically described herein.

72. A method of treating a coronavirus infection in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of a compound of any one of claims 1-68, or a pharmaceutically acceptable salt thereof, or the pharmaceutical composition of claim 69.

73. The method of any one of claims 70-72, wherein the coronavirus infection is a betacoronavirus infection.

74. The method of any one of claims 70-73, wherein the coronavirus infection is selected from the group consisting of SARS-CoV-2, SARS-CoV, and MERS-CoV infection.

75. The method of any one of claims 70-74, wherein the coronavirus infection is a SARS-CoV-2 infection.

76. The method of any one of claims 70-75, wherein the coronavirus infections is COVID-19.

77. The method of any one of claims 70-76, wherein the subject is human.