WO2024102986A2 - Sars-cov-2 mpro inhibitors - Google Patents

Abstract

The present disclosure relates to certain molecules, pharmaceutical compositions containing them, and methods of using them to treat viral infections.

Description

SARS-COV-2 MPRO INHIBITORS RELATED APPLICATIONS [001] This application claims the benefit of U.S. Provisional Application No.63/424,293, filed November 10, 2022, the contents of each of which are fully incorporated by reference herein. TECHNICAL FIELD [002] The present disclosure relates to certain molecules, pharmaceutical compositions containing them, and methods of using them to treat viral infections. BACKGROUND [003] Coronaviruses (CoVs) are a group of related RNA viruses that cause diseases in a wide range of vertebrates including humans and domestic animals. Before 2003, there were only two CoVs, HCoV-229E and HCoV-OC43, known as human pathogens. The SARS pandemic in 2003 led to the revelation of SARS-CoV-1, a pathogen causing a severe respiratory infection. The subsequent surge in CoV research resulted in the discovery of two additional human CoVs, HCoV-NL63 and HCoV-HKU1, that are mildly pathogenic. One addition to this group was MERS-CoV that emerged in 2012 as a pathogen causing a severe respiratory infection. Although SARS-CoV-1 and MERS-CoV are highly lethal pathogens, the public health, social, and economic damages that they have caused are diminutive in comparison to that from SARS-CoV- 2, a newly emerged human CoV pathogen that causes COVID-19. Rival only to the 1918 influenza pandemic, the COVID-19 pandemic has led to catastrophic impacts worldwide. [004] As of August 23, 2022, the total number of confirmed global COVID-19 cases was over 597 million, of which 6.45 million succumbed to death (WHO data). To address this emergency, a large variety of drug repurposing research has been conducted to identify approved medications that might be potentially used as COVID-19 treatments. Significant part of this research has been targeting the SARS-CoV-2 main protease (MPro). MPro is a peptide fragment of two translation products pp1a and pp1ab of the SARS-CoV-2 RNA genome after the virus infects human cells. Both pp1a and pp1ab are very large polypeptides that need to undergo proteolytic hydrolysis to form 16 nonstructural proteins (nsps). These nsps are essential for the virus to replicate its genome in host cells, evade the host immune system, and package new virions for the infection of new host cells. Intervention of the proteolytic hydrolysis of pp1a and pp1ab is a viable approach to stop SARS-CoV-2 infection. There are two internal peptide fragments from pp1a and pp1b that function as cysteine proteases to hydrolyze all nsps. One is MPro and the other papain-like

protease (PLPro). As the major protease, MPro processes the majority of nsps. It is also more conserved than PLPro. MPro genes in SARS-CoV and SARS-CoV-2 share 96% sequence identity. [005] Targeting MPro for drug discovery has been demonstrated as a successful route for the development of SARS-CoV-2 antivirals by the U.S. FDA approval of the use of Pfizer PAXLOVID for the treatment COVID-19. Therefore, small molecule medicines that inhibit SARS-CoV-2 M^Pro (SC2M^Pro) are potentially effective treatment options for COVID-19. [006] In this disclosure, a series of new small molecules as potent SARS-CoV-2 MPro inhibitors were designed and synthesized. More importantly, these small molecules also showed promising antiviral activities against SARS-CoV-2, and many of the small molecules demonstrated superior antiviral activities in a head-to-head comparison with the FDA-approved COVID-19 drug PAXLOVID and nirmatrelvir. Although some treatment options are available, there is a continual need to develop small molecule medicines with improved efficacy and fewer side effects. SUMMARY [007] In one aspect, the disclosure relates to a compound of Formula I

[008] or a pharmaceutically acceptable salt thereof, wherein [009] X is -N(R⁵)- or -O-; [010] W is C1-C6 alkyl-(5-10 membered heteroaryl) or –NR⁶R⁷, wherein each hydrogen atom in C₁-C₆ alkyl is independently optionally substituted by an R^c and each hydrogen atom in (5-10 membered heteroaryl) is independently optionally substituted by an R^d; [011] R¹ is C₁-C₆ alkyl, 5-10 membered heteroaryl, -NR⁸R⁹, or -C₁-C₆ alkyl-NR⁸R⁹, wherein each hydrogen atom in C1-C6 alkyl and 5-10 membered heteroaryl is independently optionally substituted by an R^a; [012] each of R², R⁵, R¹⁰, and R¹¹ is independently H, deuterium, or C1-C6 alkyl; [013] each of R³ and R⁴ is independently H, deuterium, C₁-C₆ alkyl, C₂-C₆ alkenyl, C₆-C₁₀ aryl, or C3-C8 cycloalkyl, wherein each hydrogen atom in C1-C6 alkyl, C2-C6 alkenyl, C6-C10 aryl, and C₃-C₈ cycloalkyl is independently optionally substituted by an R^b; [014] each of R⁶, R⁷, R⁸, and R⁹ is independently H, deuterium, C1-C6 alkyl, C2-C6 alkenyl, C₃-C₈ cycloalkyl, -C(O)C₁-C₆ alkyl, -C₁-C₆ alkyl-C(O)NR¹⁰R¹¹, or -C₁-C₆ alkyl-C(O)OH, wherein each hydrogen atom in C1-C6 alkyl, C2-C6 alkenyl, and C3-C8 cycloalkyl is independently optionally substituted by R^e; 2 [015] each of R^a, R^b, R^c, R^d, and R^e, when present, is independently deuterium, halo, -CN, -OH, -NR⁸R⁹, -NR⁸C(O)C₁-C₆ alkyl, C₁-C₆ alkyl, C₂-C₆ alkenyl, C₃-C₈ cycloalkyl, C₁-C₆ alkoxy, C₆- C10 aryl, or 5-10 membered heteroaryl, wherein each hydrogen atom in C1-C6 alkyl, C2-C6 alkenyl, C₃-C₈ cycloalkyl, C₁-C₆ alkoxy, C₆-C₁₀ aryl, and 5-10 membered heteroaryl is independently optionally substituted by deuterium, halo, OH, -NH2, C1-C6 alkyl, C2-C6 alkenyl, C₁-C₆ alkoxy, 5-10 membered heteroaryl, C₆-C₁₀ aryl, C₂-C₆ alkenyl, or C₃-C₈ cycloalkyl; [016] each R^f, when present, is independently deuterium, halo, -OH, -NR⁸R⁹, -NR¹⁰C(O)C1-C6 alkyl, C₁-C₆ alkyl, C₂-C₆ alkenyl, C₁-C₆ alkoxy, 3-to 7-membered heterocycloalkyl, or C₃-C₈ cycloalkyl, wherein each hydrogen atom in C1-C6 alkyl, C2-C6 alkenyl, C1-C6 alkoxy or C3-C8 cycloalkyl is independently optionally substituted by deuterium, halo, -OH, -NR⁸R⁹, or C₁-C₆ alkyl; or two R^f combine together with the atom or atoms to which they are attached to form a C₃-C₈ cycloalkyl, wherein each hydrogen atom in C₃-C₈ cycloalkyl and 3-to 7-membered heterocycloalkyl is independently optionally substituted by deuterium, halo, -OH, -NR⁸R⁹, C1-C6 alkyl, C₂-C₆ alkenyl, or C₁-C₆ alkoxy; [017] n is 0 or 1; and [018] m is 0, 1, 2, or 3; [019] provided that when W is –NR⁶R⁷, then X is -N(R⁵)- and R¹ is CF3. [020] In another aspect, the disclosure relates to a compound of the Formula I

[021] or a pharmaceutically acceptable salt thereof, wherein [022] X is -N(R⁵)- or -O-; [023] W is C₁-C₆ alkyl-(5-10 membered heteroaryl) or –NR⁶R⁷, wherein each hydrogen atom in C1-C6 alkyl is independently optionally substituted by an R^c and each hydrogen atom in (5-10 membered heteroaryl) is independently optionally substituted by an R^d; [024] R¹ is C1-C6 alkyl, 5-10 membered heteroaryl, -NR⁸R⁹, or -C1-C6 alkyl-NR⁸R⁹, wherein each hydrogen atom in C₁-C₆ alkyl and 5-10 membered heteroaryl is independently optionally substituted by an R^a; [025] each of R², R⁵, R¹⁰, and R¹¹ is independently H, deuterium, or C₁-C₆ alkyl; [026] each of R³ and R⁴ is independently H, deuterium, C1-C6 alkyl, C2-C6 alkenyl, C6-C10 aryl, or C₃-C₈ cycloalkyl, wherein each hydrogen atom in C₁-C₆ alkyl, C₂-C₆ alkenyl, C₆-C₁₀ aryl, and C3-C8 cycloalkyl is independently optionally substituted by an R^b; 3

[027] each of R⁶, R⁷, R⁸, and R⁹ is independently H, deuterium, C1-C6 alkyl, C2-C6 alkenyl, C₃-C₈ cycloalkyl, -C(O)C₁-C₆ alkyl, -C₁-C₆ alkyl-C(O)NR¹⁰R¹¹, or -C₁-C₆ alkyl-C(O)OH, wherein each hydrogen atom in C1-C6 alkyl, C2-C6 alkenyl, and C3-C8 cycloalkyl is independently optionally substituted by R^e; [028] each of R^a, R^b, R^c, R^d, and R^e, when present, is independently deuterium, halo, -CN, -OH, -NR⁸R⁹, -NR⁸C(O)C₁-C₆ alkyl, C₁-C₆ alkyl, C₂-C₆ alkenyl, C₃-C₈ cycloalkyl, C₁-C₆ alkoxy, C₆- C10 aryl, or 5-10 membered heteroaryl, wherein each hydrogen atom in C1-C6 alkyl, C2-C6 alkenyl, C₃-C₈ cycloalkyl, C₁-C₆ alkoxy, C₆-C₁₀ aryl, and 5-10 membered heteroaryl is independently optionally substituted by deuterium, halo, OH, -NH2, C1-C6 alkyl, C2-C6 alkenyl, C₁-C₆ alkoxy, 5-10 membered heteroaryl, C₆-C₁₀ aryl, C₂-C₆ alkenyl, or C₃-C₈ cycloalkyl; [029] each R^f, when present, is independently deuterium, halo, -OH, -NR⁸R⁹, C1-C6 alkyl, C2- C₆ alkenyl, C₁-C₆ alkoxy or C₃-C₈ cycloalkyl, wherein each hydrogen atom in C₁-C₆ alkyl, C₂-C₆ alkenyl, C1-C6 alkoxy or C3-C8 cycloalkyl is independently optionally substituted by deuterium, halo, -OH, -NR⁸R⁹, or C₁-C₆ alkyl; or two R^f combine together with the atom or atoms to which they are attached to form a C3-C8 cycloalkyl, wherein each hydrogen atom in C3-C8 cycloalkyl is independently optionally substituted by deuterium, halo, -OH, -NR⁸R⁹, C₁-C₆ alkyl, C₂-C₆ alkenyl, or C1-C6 alkoxy; [030] n is 0 or 1; and [031] m is 1, 2, or 3; [032] provided that when W is –NR⁶R⁷, then X is -N(R⁵)- and R¹ is CF_3. [033] In another aspect, the disclosure provides compounds of the formula

[034] or a pharmaceutically acceptable salt thereof, wherein R¹, R^f, m, and W are as defined herein. [035] In another aspect, the disclosure provides compounds of the formula

[036] or a pharmaceutically acceptable salt thereof, wherein R¹, R², R³, R⁴, R^f, m, and W are as defined herein. [037] In another aspect, the disclosure provides compounds of the formula 4

[038] or a pharmaceutically acceptable salt thereof, wherein R¹, R², R³, R⁴, R⁶, R⁷, R^f, and m are as defined herein. [039] In another aspect, the disclosure provides compounds of the formula

[040] or a pharmaceutically acceptable salt thereof, wherein R^f, m, and W are as defined herein. [041] Additional embodiments, features, and advantages of the disclosure will be apparent from the following detailed description and through practice of the disclosure. The compounds of the present disclosure can be described as embodiments in any of the following enumerated clauses. It will be understood that any of the embodiments described herein can be used in connection with any other embodiments described herein to the extent that the embodiments do not contradict one another. [042] 1. A compound of Formula I

[043] or a pharmaceutically acceptable salt thereof, wherein [044] X is -N(R⁵)- or -O-; [045] W is C1-C6 alkyl-(5-10 membered heteroaryl) or –NR⁶R⁷, wherein each hydrogen atom in C1-C6 alkyl is independently optionally substituted by an R^c and each hydrogen atom in (5-10 membered heteroaryl) is independently optionally substituted by an R^d; [046] R¹ is C1-C6 alkyl, 5-10 membered heteroaryl, -NR⁸R⁹, or -C1-C6 alkyl-NR⁸R⁹, wherein each hydrogen atom in C1-C6 alkyl and 5-10 membered heteroaryl is independently optionally substituted by an R^a; [047] each of R², R⁵, R¹⁰, and R¹¹ is independently H, deuterium, or C1-C6 alkyl; [048] each of R³ and R⁴ is independently H, deuterium, C1-C6 alkyl, C2-C6 alkenyl, C6-C10 aryl, or C₃-C₈ cycloalkyl, wherein each hydrogen atom in C₁-C₆ alkyl, C₂-C₆ alkenyl, C₆-C₁₀ aryl, and C3-C8 cycloalkyl is independently optionally substituted by an R^b; [049] each of R⁶, R⁷, R⁸, and R⁹ is independently H, deuterium, C₁-C₆ alkyl, C₂-C₆ alkenyl, C3-C8 cycloalkyl, -C(O)C1-C6 alkyl, -C1-C6 alkyl-C(O)NR¹⁰R¹¹, or -C1-C6 alkyl-C(O)OH, wherein each hydrogen atom in C₁-C₆ alkyl, C₂-C₆ alkenyl, and C₃-C₈ cycloalkyl is independently optionally substituted by R^e; [050] each of R^a, R^b, R^c, R^d, and R^e, when present, is independently deuterium, halo, -CN, -OH, -NR⁸R⁹, -NR⁸C(O)C1-C6 alkyl, C1-C6 alkyl, C2-C6 alkenyl, C3-C8 cycloalkyl, C1-C6 alkoxy, C6- C₁₀ aryl, or 5-10 membered heteroaryl, wherein each hydrogen atom in C₁-C₆ alkyl, C₂-C₆ alkenyl, C3-C8 cycloalkyl, C1-C6 alkoxy, C6-C10 aryl, and 5-10 membered heteroaryl is independently optionally substituted by deuterium, halo, OH, -NH₂, C₁-C₆ alkyl, C₂-C₆ alkenyl, C1-C6 alkoxy, 5-10 membered heteroaryl, C6-C10 aryl, C2-C6 alkenyl, or C3-C8 cycloalkyl; [051] each R^f, when present, is independently deuterium, halo, -OH, -NR⁸R⁹, -NR¹⁰C(O)C₁-C₆ alkyl, C1-C6 alkyl, C2-C6 alkenyl, C1-C6 alkoxy, 3-to 7-membered heterocycloalkyl, or C3-C8 cycloalkyl, wherein each hydrogen atom in C₁-C₆ alkyl, C₂-C₆ alkenyl, C₁-C₆ alkoxy or C₃-C₈ cycloalkyl is independently optionally substituted by deuterium, halo, -OH, -NR⁸R⁹, or C1-C6 alkyl; or two R^f combine together with the atom or atoms to which they are attached to form a C3-C8 cycloalkyl, wherein each hydrogen atom in C3-C8 cycloalkyl and 3-to 7-membered heterocycloalkyl is independently optionally substituted by deuterium, halo, -OH, -NR⁸R⁹, C₁-C₆ alkyl, C2-C6 alkenyl, or C1-C6 alkoxy; [052] n is 0 or 1; and [053] m is 0, 1, 2, or 3; [054] provided that when W is –NR⁶R⁷, then X is -N(R⁵)- and R¹ is CF_3. [055] 2. A compound of Formula I

[056] or a pharmaceutically acceptable salt thereof, wherein [057] X is -N(R⁵)- or -O-; [058] W is C1-C6 alkyl-(5-10 membered heteroaryl) or –NR⁶R⁷, wherein each hydrogen atom in C₁-C₆ alkyl is independently optionally substituted by an R^c and each hydrogen atom in (5-10 membered heteroaryl) is independently optionally substituted by an R^d;

[059] R¹ is C1-C6 alkyl, 5-10 membered heteroaryl, -NR⁸R⁹, or -C1-C6 alkyl-NR⁸R⁹, wherein each hydrogen atom in C₁-C₆ alkyl and 5-10 membered heteroaryl is independently optionally substituted by an R^a; [060] each of R², R⁵, R¹⁰, and R¹¹ is independently H, deuterium, or C₁-C₆ alkyl; [061] each of R³ and R⁴ is independently H, deuterium, C1-C6 alkyl, C2-C6 alkenyl, C6-C10 aryl, or C₃-C₈ cycloalkyl, wherein each hydrogen atom in C₁-C₆ alkyl, C₂-C₆ alkenyl, C₆-C₁₀ aryl, and C3-C8 cycloalkyl is independently optionally substituted by an R^b; [062] each of R⁶, R⁷, R⁸, and R⁹ is independently H, deuterium, C₁-C₆ alkyl, C₂-C₆ alkenyl, C3-C8 cycloalkyl, -C(O)C1-C6 alkyl, -C1-C6 alkyl-C(O)NR¹⁰R¹¹, or -C1-C6 alkyl-C(O)OH, wherein each hydrogen atom in C₁-C₆ alkyl, C₂-C₆ alkenyl, and C₃-C₈ cycloalkyl is independently optionally substituted by R^e; [063] each of R^a, R^b, R^c, R^d, and R^e, when present, is independently deuterium, halo, -CN, -OH, -NR⁸R⁹, -NR⁸C(O)C1-C6 alkyl, C1-C6 alkyl, C2-C6 alkenyl, C3-C8 cycloalkyl, C1-C6 alkoxy, C6- C₁₀ aryl, or 5-10 membered heteroaryl, wherein each hydrogen atom in C₁-C₆ alkyl, C₂-C₆ alkenyl, C3-C8 cycloalkyl, C1-C6 alkoxy, C6-C10 aryl, and 5-10 membered heteroaryl is independently optionally substituted by deuterium, halo, OH, -NH₂, C₁-C₆ alkyl, C₂-C₆ alkenyl, C1-C6 alkoxy, 5-10 membered heteroaryl, C6-C10 aryl, C2-C6 alkenyl, or C3-C8 cycloalkyl; [064] each R^f, when present, is independently deuterium, halo, -OH, -NR⁸R⁹, -NR¹⁰C(O)C₁-C₆ alkyl, C1-C6 alkyl, C2-C6 alkenyl, C1-C6 alkoxy or C3-C8 cycloalkyl, wherein each hydrogen atom in C₁-C₆ alkyl, C₂-C₆ alkenyl, C₁-C₆ alkoxy or C₃-C₈ cycloalkyl is independently optionally substituted by deuterium, halo, -OH, -NR⁸R⁹, or C1-C6 alkyl; or two R^f combine together with the atom or atoms to which they are attached to form a C₃-C₈ cycloalkyl, wherein each hydrogen atom in C3-C8 cycloalkyl is independently optionally substituted by deuterium, halo, -OH, - NR⁸R⁹, C₁-C₆ alkyl, C₂-C₆ alkenyl, or C₁-C₆ alkoxy; [065] n is 0 or 1; and [066] m is 0, 1, 2, or 3; [067] provided that when W is –NR⁶R⁷, then X is -N(R⁵)- and R¹ is CF3. [068] 3. The compound or pharmaceutically acceptable salt of clause 1 or 2, wherein W is C1-C6 alkyl-(5-10 membered heteroaryl), wherein each hydrogen atom in C1-C6 alkyl is independently optionally substituted by an R^c and each hydrogen atom in (5-10 membered heteroaryl) is independently optionally substituted by an R^d. [069] 4. The compound or pharmaceutically acceptable salt of any one of clauses 1-3, wherein X is -N(R⁵)-. 7

[070] 5. The compound or pharmaceutically acceptable salt of any one of clauses 1-3, wherein X is -O-. [071] 6. The compound or pharmaceutically acceptable salt of any one of the preceding clauses, wherein W is C₁-C₆ alkyl-(5-10 membered heteroaryl), and one hydrogen atom in C₁-C₆ alkyl is substituted with an R^c. [072] 7. The compound or pharmaceutically acceptable salt of any one of the preceding clauses, wherein R^c, when present, is –CN. [073] 8. The compound or pharmaceutically acceptable salt of any one of the preceding clauses, wherein W is C1-C6 alkyl-(5-10 membered heteroaryl), and 5-10 membered heteroaryl is selected from

0, 1, 2, or 3. [074] 9. The compound or pharmaceutically acceptable salt of any one of the preceding clauses, wherein R^d, when present, is halo, -NHC(O)C1-C6 alkyl, or C1-C6 alkoxy, wherein each hydrogen atom in C1-C6 alkyl or C1-C6 alkoxy is independently optionally substituted by halo. [075] 10. The compound or pharmaceutically acceptable salt of any one of the preceding clauses, wherein R^d, when present, is fluoro or chloro. [076] 11. The compound or pharmaceutically acceptable salt of any one of the preceding clauses, wherein R^d, when present, is fluoro, -NHC(O)CF3, or OMe. [077] 12. The compound or pharmaceutically acceptable salt of clause 1 or 2, wherein W is -NR⁶R⁷. [078] 13. The compound or pharmaceutically acceptable salt of any one of clauses 1, 2, and 12, wherein one of R⁶ and R⁷ is -C(O)C1-C6 alkyl, and one of R⁶ and R⁷ is -C1-C6 alkyl- C(O)NR¹⁰R¹¹, wherein each hydrogen atom in C₁-C₆ alkyl is independently optionally substituted by R^e. [079] 14. The compound or pharmaceutically acceptable salt of any one of clauses 1, 2, and 12-13, wherein one of R⁶ and R⁷ is –C(O)CHCl2. [080] 15. The compound or pharmaceutically acceptable salt of any one of clauses 1, 2, and 12-14, wherein one of R⁶ and R⁷ is is –CH2CH2C(O)NH2. 8 [081] 16. The compound or pharmaceutically acceptable salt of any one of the preceding clauses, wherein n is 0. [082] 17. The compound or pharmaceutically acceptable salt of any one of the preceding clauses, wherein R¹ is 5-10 membered heteroaryl, wherein each hydrogen atom in 5-10 membered heteroaryl is independently optionally substituted by an R^a. [083] 18. The compound or pharmaceutically acceptable salt of any one of the preceding clauses, wherein R¹ is

, wherein p is 0, 1, 2, or 3. [084] 19. The compound or pharmaceutically acceptable salt of clause 18, wherein p is 1. [085] 20. The compound or pharmaceutically acceptable salt of any one of the preceding clauses, wherein each R^a, when present, is independently deuterium, halo, -CN, -OH, -NR⁸R⁹, C1-C6 alkyl, or C1-C6 alkoxy. [086] 21. The compound or pharmaceutically acceptable salt of any one of the preceding clauses, wherein R^a, when present, is -OCH3. [087] 22. The compound or pharmaceutically acceptable salt of any one of clauses 1 to 16, wherein R¹ is -CF3. [088] 23. The compound or pharmaceutically acceptable salt of clause 1 or 2, wherein the compound is of formula

. [089] 24. The compound or pharmaceutically acceptable salt of any one of clauses 1 to 15, wherein n is 1. [090] 25. The compound or pharmaceutically acceptable salt of clause 1 or 2, wherein the compound is of formula

. [091] 26. The compound or pharmaceutically acceptable of clause 1 or 2, wherein the compound is of formula

. [092] 27. The compound or pharmaceutically acceptable salt of any one of the preceding clauses, wherein R², when present, is H. [093] 28. The compound or pharmaceutically acceptable salt of any one of the preceding clauses, wherein R⁵, when present, is H. [094] 29. The compound or pharmaceutically acceptable salt of any one of clauses 1-15, wherein n is 1, one of R³ and R⁴ is H, and one of R³ and R⁴ is C1-C6 alkyl. [095] 30. The compound or pharmaceutically acceptable salt of any one of clauses 1-15 and 29, wherein one of R³ and R⁴ is H, and one of R³ and R⁴ is t-butoxy-ethyl or t-butyl. [096] 31. The compound or pharmaceutically acceptable salt of any one of the preceding clauses, wherein m is 2, and two R^f combine together with the atom or atoms to which they are attached to form a C₃-C₈ cycloalkyl. [097] 32. The compound or pharmaceutically acceptable salt of any one of clauses 1-31, wherein m is 2, and two R^f combine to form C₃-C₈ cycloalkyl substituted with one or more methyl or halo. [098] 33. The compound or pharmaceutically acceptable salt of any one of clauses 1-32, wherein m is 2, and two R^f combine to form cyclopropyl or a cyclopentyl. [099] 34. The compound or pharmaceutically acceptable salt of any one of clauses 1-32, wherein m is 2, and two R^f combine to form cyclopropyl or a cyclopentyl substituted with one or more methyl or halo. [0100] 35. The compound or pharmaceutically acceptable salt of any one of clauses 1-30, wherein m is 2, and two R^f combine together with the atom or atoms to which they are attached to form a 3-to 7-membered heterocycloalkyl. [0101] 36. The compound or pharmaceutically acceptable salt of any one of clauses 1-30, wherein m is 2, and two R^f combine together with the atom or atoms to which they are attached to form a 5-membered heterocycloalkyl, such as a dithiolane. [0102] 37. The compound or pharmaceutically acceptable salt of clause 1, wherein the compound is selected from the group consisting of: 1

13

[0103] or a pharmaceutically acceptable salt thereof. [0104] 38. A pharmaceutical composition comprising at least one compound of any one of clauses 1-37, or a pharmaceutically acceptable salt thereof, and optionally one or more pharmaceutically acceptable excipients. [0105] 39. A method of treating disease, such as a viral infection, comprising administering to a subject in need of such treatment an effective amount of a compound of any one of clauses 1-37, or a pharmaceutically acceptable salt thereof. BRIEF DESCRIPTIONS OF THE DRAWING [0106] Fig.1 shows in vivo efficacy of compounds 16 and 17 in SARS-CoV-2 infection in mice. [0107] Fig.2 shows pharmacokinetic profile of compounds 16 and 17 in mice. DETAILED DESCRIPTION [0108] Before the present disclosure is further described, it is to be understood that this disclosure is not limited to particular embodiments described, as such may, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to be limiting, since the scope of the present disclosure will be limited only by the appended claims. [0109] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as is commonly understood by one of ordinary skill in the art to which this disclosure belongs. All patents, applications, published applications and other publications referred to herein are incorporated by reference in their entireties. If a definition set forth in this section is contrary to or otherwise inconsistent with a definition set forth in a patent, application, or other 1

publication that is herein incorporated by reference, the definition set forth in this section prevails over the definition incorporated herein by reference. [0110] As used herein and in the appended claims, the singular forms “a,” “an,” and “the” include plural referents unless the context clearly dictates otherwise. It is further noted that the claims may be drafted to exclude any optional element. As such, this statement is intended to serve as antecedent basis for use of such exclusive terminology as “solely,” “only” and the like in connection with the recitation of claim elements, or use of a “negative” limitation. [0111] As used herein, the terms “including,” “containing,” and “comprising” are used in their open, non-limiting sense. [0112] To provide a more concise description, some of the quantitative expressions given herein are not qualified with the term “about.” It is understood that, whether the term “about” is used explicitly or not, every quantity given herein is meant to refer to the actual given value, and it is also meant to refer to the approximation to such given value that would reasonably be inferred based on the ordinary skill in the art, including equivalents and approximations due to the experimental and/or measurement conditions for such given value. Whenever a yield is given as a percentage, such yield refers to a mass of the entity for which the yield is given with respect to the maximum amount of the same entity that could be obtained under the particular stoichiometric conditions. Concentrations that are given as percentages refer to mass ratios, unless indicated differently. [0113] Except as otherwise noted, the methods and techniques of the present embodiments are generally performed according to conventional methods well known in the art and as described in various general and more specific references that are cited and discussed throughout the present specification. See, e.g., Loudon, Organic Chemistry, Fourth Edition, New York: Oxford University Press, 2002, pp. 360-361, 1084-1085; Smith and March, March's Advanced Organic Chemistry: Reactions, Mechanisms, and Structure, Fifth Edition, Wiley-Interscience, 2001. [0114] Chemical nomenclature for compounds described herein has generally been derived using the commercially-available ACD/Name 2014 (ACD/Labs) or ChemBioDraw Ultra 13.0 (Perkin Elmer). [0115] It is appreciated that certain features of the disclosure, which are, for clarity, described in the context of separate embodiments, may also be provided in combination in a single embodiment. Conversely, various features of the disclosure, which are, for brevity, described in the context of a single embodiment, may also be provided separately or in any suitable subcombination. All combinations of the embodiments pertaining to the chemical groups represented by the variables are specifically embraced by the present disclosure and are disclosed 1

herein just as if each and every combination was individually and explicitly disclosed, to the extent that such combinations embrace compounds that are stable compounds (i.e., compounds that can be isolated, characterized, and tested for biological activity). In addition, all subcombinations of the chemical groups listed in the embodiments describing such variables are also specifically embraced by the present disclosure and are disclosed herein just as if each and every such sub-combination of chemical groups was individually and explicitly disclosed herein. DEFINITIONS [0116] As used herein, the term “alkyl” includes a chain of carbon atoms, which is optionally branched and contains from 1 to 20 carbon atoms. It is to be further understood that in certain embodiments, alkyl may be advantageously of limited length, including C1-C12, C1-C10, C1-C9, C₁-C₈, C₁-C₇, C₁-C₆, and C₁-C₄, Illustratively, such particularly limited length alkyl groups, including C1-C8, C1-C7, C1-C6, and C1-C4, and the like may be referred to as “lower alkyl.” Illustrative alkyl groups include, but are not limited to, methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, sec-butyl, tert-butyl, pentyl, 2-pentyl, 3-pentyl, neopentyl, hexyl, heptyl, octyl, and the like. Alkyl may be substituted or unsubstituted. Typical substituent groups include cycloalkyl, aryl, heteroaryl, heteroalicyclic, hydroxy, alkoxy, aryloxy, mercapto, alkylthio, arylthio, cyano, halo, carbonyl, oxo (=O), thiocarbonyl, O-carbamyl, N-carbamyl, O-thiocarbamyl, N- thiocarbamyl, C-amido, N-amido, C-carboxy, O-carboxy, -NO2, and amino, or as described in the various embodiments provided herein. It will be understood that “alkyl” may be combined with other groups, such as those provided above, to form a functionalized alkyl. By way of example, the combination of an “alkyl” group, as described herein, with a “carboxy” group may be referred to as a “carboxyalkyl” group. Other non-limiting examples include hydroxyalkyl, aminoalkyl, and the like. [0117] As used herein, the term “alkenyl” includes a chain of carbon atoms, which is optionally branched, and contains from 2 to 20 carbon atoms, and also includes at least one carbon-carbon double bond (i.e., C=C). It will be understood that in certain embodiments, alkenyl may be advantageously of limited length, including C₂-C₁₂, C₂-C₉, C₂-C₈, C₂-C₇, C₂-C₆, and C₂-C₄. Illustratively, such particularly limited length alkenyl groups, including C2-C8, C2-C7, C2-C6, and C₂-C₄ may be referred to as lower alkenyl. Alkenyl may be unsubstituted, or substituted as described for alkyl or as described in the various embodiments provided herein. Illustrative alkenyl groups include, but are not limited to, ethenyl, 1-propenyl, 2-propenyl, 1-, 2-, or 3-butenyl, and the like. 1 [0118] As used herein, the term “alkynyl” includes a chain of carbon atoms, which is optionally branched, and contains from 2 to 20 carbon atoms, and also includes at least one carbon-carbon triple bond (i.e., C≡C). It will be understood that in certain embodiments, alkynyl may each be advantageously of limited length, including C₂-C₁₂, C₂-C₉, C₂-C₈, C₂-C₇, C₂-C₆, and C₂-C₄. Illustratively, such particularly limited length alkynyl groups, including C2-C8, C2-C7, C2-C6, and C₂-C₄ may be referred to as lower alkynyl. Alkynyl may be unsubstituted, or substituted as described for alkyl or as described in the various embodiments provided herein. Illustrative alkynyl groups include, but are not limited to, ethynyl, 1-propynyl, 2-propynyl, 1-, 2-, or 3-butynyl, and the like. [0119] As used herein, the term “aryl” refers to an all-carbon monocyclic or fused-ring polycyclic groups of 6 to 12 carbon atoms having a completely conjugated pi-electron system. It will be understood that in certain embodiments, aryl may be advantageously of limited size such as C₆- C10 aryl. Illustrative aryl groups include, but are not limited to, phenyl, naphthylenyl and anthracenyl. The aryl group may be unsubstituted, or substituted as described for alkyl or as described in the various embodiments provided herein. [0120] As used herein, the term “cycloalkyl” refers to a 3 to 15 member all-carbon monocyclic ring, including an all-carbon 5-member/6-member or 6-member/6-member fused bicyclic ring, or a multicyclic fused ring (a “fused” ring system means that each ring in the system shares an adjacent pair of carbon atoms with each other ring in the system) group, or a carbocyclic ring that is fused to another group such as a heterocyclic, such as ring 5- or 6-membered cycloalkyl fused to a 5- to 7- membered heterocyclic ring, where one or more of the rings may contain one or more double bonds but the cycloalkyl does not contain a completely conjugated pi-electron system. It will be understood that in certain embodiments, cycloalkyl may be advantageously of limited size such as C₃-C₁₂, C₃-C₉, C₃-C₈, C₃-C₆ and C₄-C₆. Cycloalkyl may be unsubstituted, or substituted as described for alkyl or as described in the various embodiments provided herein. Illustrative cycloalkyl groups include, but are not limited to, cyclopropyl, cyclobutyl, cyclopentyl, cyclopentenyl, cyclopentadienyl, cyclohexyl, cyclohexenyl, cycloheptyl, adamantyl, norbornyl, norbornenyl, 9H-fluoren-9-yl, and the like. Illustrative examples of cycloalkyl groups shown in graphical representations include the following entities, in the form of properly bonded moieties:

[0121] As used herein, the terms “heterocycloalkyl”, “heterocyclyl”, or “heterocycle” refers to a monocyclic or fused ring group having in the ring(s) from 3 to 12 ring atoms, in which at least one ring atom is a heteroatom, such as nitrogen, oxygen or sulfur, the remaining ring atoms being carbon atoms. Heterocycloalkyl may optionally contain 1, 2, 3 or 4 heteroatoms. A heterocycloalkyl group may be fused to another group such as another heterocycloalkyl, an aryl, or a heteroaryl group. Heterocycloalkyl may also have one of more double bonds, including double bonds to nitrogen (e.g., C=N or N=N) but does not contain a completely conjugated pi- electron system. It will be understood that in certain embodiments, heterocycloalkyl may be advantageously of limited size such as 3- to 7-membered heterocycloalkyl, 5- to 7-membered heterocycloalkyl, 3-, 4-, 5- or 6-membered heterocycloalkyl, and the like. Heterocycloalkyl may be unsubstituted, or substituted as described for alkyl or as described in the various embodiments provided herein. Illustrative heterocycloalkyl groups include, but are not limited to, oxiranyl, thianaryl, azetidinyl, oxetanyl, tetrahydrofuranyl, pyrrolidinyl, tetrahydropyranyl, piperidinyl, 1,4-dioxanyl, morpholinyl, 1,4-dithianyl, piperazinyl, oxepanyl, 3,4-dihydro-2H-pyranyl, 5,6-dihydro-2H-pyranyl, 2H-pyranyl, 1, 2, 3, 4-tetrahydropyridinyl, and the like. Illustrative examples of heterocycloalkyl groups shown in graphical representations include the following entities, in the form of properly bonded moieties:

[0122] As used herein, the term “aryl” refers to a monocyclic or fused ring group of 5 to 10 ring atoms, and also having a completely conjugated pi-electron system. It will be understood that in certain embodiments, aryl may be advantageously of limited size such as 6- to 10-membered aryl and the like. Aryl may be unsubstituted, or substituted as described for alkyl or as described in the various embodiments provided herein. Illustrative aryl groups include, but are not limited to, phenyl and naphthyl. [0123] As used herein, the term “heteroaryl” refers to a monocyclic or fused ring group of 5 to 10 ring atoms containing one, two, three or four ring heteroatoms selected from nitrogen, oxygen and sulfur, the remaining ring atoms being carbon atoms, and also having a completely conjugated pi-electron system. It will be understood that in certain embodiments, heteroaryl may be advantageously of limited size such as 3- to 7-membered heteroaryl, 5- to 7-membered heteroaryl, 5- to 10-membered heteroaryl and the like. Heteroaryl may be unsubstituted, or substituted as described for alkyl or as described in the various embodiments provided herein. In some embodiments, it will be understood that an atom exo to the heteroaryl ring atoms, such as an amino or a hydroxyl group, may contribute to the pi-electron system. For example, tautomeric hydroxyl-pyridine contains an -OH group, wherein the exo oxygen contributes to the pi-electron system, illustrated in the tautomeric 2-pyridone configuration. [0124] Illustrative heteroaryl groups include, but are not limited to, pyrrolyl, furanyl, thiophenyl, imidazolyl, oxazolyl, thiazolyl, pyrazolyl, pyridinyl, pyrimidinyl, quinolinyl, isoquinolinyl, purinyl, tetrazolyl, triazinyl, pyrazinyl, tetrazinyl, quinazolinyl, quinoxalinyl, thienyl, isoxazolyl, isothiazolyl, oxadiazolyl, thiadiazolyl, triazolyl, benzimidazolyl, benzoxazolyl, benzthiazolyl, benzisoxazolyl, benzisothiazolyl and carbazoloyl, and the like. Illustrative examples of heteroaryl groups shown in graphical representations, include the following entities, in the form of properly bonded moieties:

[0125] In a particular embodiment, the heteroaryl group is

. [0126] In a particular embodiment, the heteroaryl group is

. [0127] In a particular embodiment, the heteroaryl group is

. [0128] As used herein, “tautomer” refers each of two or more isomers of a compound which exist together in equilibrium, and are readily interchanged by migration of an atom or group within the molecule. In a particular embodiment, a tautomer can be either tautomer configuration of 2- pyridone, such as

. In a particular embodiment, a tautomer can be either tautomer configuration of pyrimidinedione, such as

. [0129] As used herein, “hydroxy” or “hydroxyl” refers to an -OH group. [0130] As used herein, “alkoxy” refers to both an -O-(alkyl) or an -O-(unsubstituted cycloalkyl) group. Representative examples include, but are not limited to, methoxy, ethoxy, propoxy, butoxy, cyclopropyloxy, cyclobutyloxy, cyclopentyloxy, cyclohexyloxy, and the like. [0131] As used herein, “halo” or “halogen” refers to fluorine, chlorine, bromine or iodine. [0132] As used herein, “cyano” refers to a -CN group. 2

[0133] The term “oxo” represents a carbonyl oxygen. For example, a cyclopentyl substituted with oxo is cyclopentanone. In another example, a hydroxy substituted aromatic compound may exist as an oxo substituted tautomer, such as hydroxyl-pyridine and pyridinone. In a particular embodiment, a hydroxy-substituted pyridine may be represented as an oxo tautomer, such as

H . In some embodiments, a hydroxy-substituted quinoline may be represented as an oxo tautomer, such as

. [0134] As used herein, “bond” refers to a covalent bond. [0135] The term “substituted” means that the specified group or moiety bears one or more substituents. The term “unsubstituted” means that the specified group bears no substituents. Where the term “substituted” is used to describe a structural system, the substitution is meant to occur at any valency-allowed position on the system. In some embodiments, “substituted” means that the specified group or moiety bears one or more substituents. It will be understood that in certain embodiments, substitutions may be advantageously limited in number. In some embodiments, “substituted” means that the specified group or moiety bears one to five substituents. In other embodiments, “substituted” means that the specified group or moiety bears one, two, or three substituents. In other embodiments, “substituted” means that the specified group or moiety bears one or two substituents. In still other embodiments, “substituted” means the specified group or moiety bears one substituent. [0136] As used herein, “optional” or “optionally” means that the subsequently described event or circumstance may but need not occur, and that the description includes instances where the event or circumstance occurs and instances in which it does not. For example, “wherein each hydrogen atom in C₁-C₆ alkyl, C₂-C₆ alkenyl, C₂-C₆ alkynyl, C₃-C₆ cycloalkyl, 3-to 7-membered heterocycloalkyl, C6-C10 aryl, or mono- or bicyclic heteroaryl is independently optionally substituted by C₁-C₆ alkyl” means that an alkyl may be but need not be present on any of the C1-C6 alkyl, C2-C6 alkenyl, C2-C6 alkynyl, C3-C6 cycloalkyl, 3-to 7-membered heterocycloalkyl, C₆-C₁₀ aryl, or mono- or bicyclic heteroaryl by replacement of a hydrogen atom for each alkyl group, and the description includes situations where the C1-C6 alkyl, C2-C6 alkenyl, C2-C6 alkynyl, C₃-C₆ cycloalkyl, 3-to 7-membered heterocycloalkyl, C₆-C₁₀ aryl, or mono- or bicyclic heteroaryl is substituted with an alkyl group and situations where the C1-C6 alkyl, C2-C6 alkenyl, C₂-C₆ alkynyl, C₃-C₆ cycloalkyl, 3-to 7-membered heterocycloalkyl, C₆-C₁₀ aryl, or mono- or bicyclic heteroaryl is not substituted with the alkyl group. 2

[0137] As used herein, “independently” means that the subsequently described event or circumstance is to be read on its own relative to other similar events or circumstances. For example, in a circumstance where several equivalent hydrogen groups are optionally substituted by another group described in the circumstance, the use of “independently optionally” means that each instance of a hydrogen atom on the group may be substituted by another group, where the groups replacing each of the hydrogen atoms may be the same or different. Or for example, where multiple groups exist all of which can be selected from a set of possibilities, the use of “independently” means that each of the groups can be selected from the set of possibilities separate from any other group, and the groups selected in the circumstance may be the same or different. [0138] As used herein, the phrase “taken together with the atoms to which they are attached” or “combine together with the atom to which they are attached” means that, for example, two substituents (e.g., two independent R^f groups) attached to two separate atoms or attached to the same atom form the groups that are defined by the claim, such as

. In particular, the phrase “combine together with the atoms to which they are attached” means, for example, two independent R^f groups on different ring atoms of

, such as carbon atom “1” and carbon atom “2” respectively, as shown in the structure below form a ring with those ring atoms.

[0139] For example, the phrase “two R^f combine together with the atoms to which they are attached combine to form” used in connection with the embodiments described herein includes the compounds represented as follows:

. [0140] Alternatively, the phrase can be directed to two substituents on the same atom. For example, the phrase “two R^f together with the atom to which they are attached combine to 2

form” used in connection with the embodiments described herein includes the compounds represented as follows:

. [0141] As used herein, the term “pharmaceutically acceptable salt” refers to those salts which counter ions which may be used in pharmaceuticals. See, generally, S.M. Berge, et al., “Pharmaceutical Salts,” J. Pharm. Sci., 1977, 66, 1-19. Preferred pharmaceutically acceptable salts are those that are pharmacologically effective and suitable for contact with the tissues of subjects without undue toxicity, irritation, or allergic response. A compound described herein may possess a sufficiently acidic group, a sufficiently basic group, both types of functional groups, or more than one of each type, and accordingly react with a number of inorganic or organic bases, and inorganic and organic acids, to form a pharmaceutically acceptable salt. Such salts include: [0142] (1) acid addition salts, which can be obtained by reaction of the free base of the parent compound with inorganic acids such as hydrochloric acid, hydrobromic acid, nitric acid, phosphoric acid, sulfuric acid, and perchloric acid and the like, or with organic acids such as acetic acid, oxalic acid, (D) or (L) malic acid, maleic acid, methane sulfonic acid, ethanesulfonic acid, p-toluenesulfonic acid, salicylic acid, tartaric acid, citric acid, succinic acid or malonic acid and the like; or [0143] (2) salts formed when an acidic proton present in the parent compound either is replaced by a metal ion, e.g., an alkali metal ion, an alkaline earth ion, or an aluminum ion; or coordinates with an organic base such as ethanolamine, diethanolamine, triethanolamine, trimethamine, N-methylglucamine, and the like. [0144] Pharmaceutically acceptable salts are well known to those skilled in the art, and any such pharmaceutically acceptable salt may be contemplated in connection with the embodiments described herein. Examples of pharmaceutically acceptable salts include sulfates, pyrosulfates, bisulfates, sulfites, bisulfites, phosphates, monohydrogen-phosphates, dihydrogenphosphates, metaphosphates, pyrophosphates, chlorides, bromides, iodides, acetates, propionates, decanoates, caprylates, acrylates, formates, isobutyrates, caproates, heptanoates, propiolates, oxalates, malonates, succinates, suberates, sebacates, fumarates, maleates, butyne-1,4-dioates, hexyne-1,6-dioates, benzoates, chlorobenzoates, methylbenzoates, dinitrobenzoates, hydroxybenzoates, methoxybenzoates, phthalates, sulfonates, methylsulfonates, propylsulfonates, besylates, xylenesulfonates, naphthalene-1-sulfonates, naphthalene-2-sulfonates, phenylacetates, phenylpropionates, phenylbutyrates, citrates, lactates, 2

γ-hydroxybutyrates, glycolates, tartrates, and mandelates. Lists of other suitable pharmaceutically acceptable salts are found in Remington's Pharmaceutical Sciences, 17th Edition, Mack Publishing Company, Easton, Pa., 1985. [0145] For a compound of Formula I that contains a basic nitrogen, a pharmaceutically acceptable salt may be prepared by any suitable method available in the art, for example, treatment of the free base with an inorganic acid, such as hydrochloric acid, hydrobromic acid, sulfuric acid, sulfamic acid, nitric acid, boric acid, phosphoric acid, and the like, or with an organic acid, such as acetic acid, phenylacetic acid, propionic acid, stearic acid, lactic acid, ascorbic acid, maleic acid, hydroxymaleic acid, isethionic acid, succinic acid, valeric acid, fumaric acid, malonic acid, pyruvic acid, oxalic acid, glycolic acid, salicylic acid, oleic acid, palmitic acid, lauric acid, a pyranosidyl acid, such as glucuronic acid or galacturonic acid, an alpha-hydroxy acid, such as mandelic acid, citric acid, or tartaric acid, an amino acid, such as aspartic acid or glutamic acid, an aromatic acid, such as benzoic acid, 2-acetoxybenzoic acid, naphthoic acid, or cinnamic acid, a sulfonic acid, such as laurylsulfonic acid, p-toluenesulfonic acid, methanesulfonic acid, or ethanesulfonic acid, or any compatible mixture of acids such as those given as examples herein, and any other acid and mixture thereof that are regarded as equivalents or acceptable substitutes in light of the ordinary level of skill in this technology. [0146] The disclosure also relates to pharmaceutically acceptable prodrugs of the compounds of Formula I, and treatment methods employing such pharmaceutically acceptable prodrugs. The term “prodrug” means a precursor of a designated compound that, following administration to a subject, yields the compound in vivo via a chemical or physiological process such as solvolysis or enzymatic cleavage, or under physiological conditions (e.g., a prodrug on being brought to physiological pH is converted to the compound of Formula I). A “pharmaceutically acceptable prodrug” is a prodrug that is non-toxic, biologically tolerable, and otherwise biologically suitable for administration to the subject. Illustrative procedures for the selection and preparation of suitable prodrug derivatives are described, for example, in “Design of Prodrugs”, ed. H. Bundgaard, Elsevier, 1985. [0147] The present disclosure also relates to pharmaceutically active metabolites of compounds of Formula I, and uses of such metabolites in the methods of the disclosure. A “pharmaceutically active metabolite” means a pharmacologically active product of metabolism in the body of a compound of Formula I, or salt thereof. Prodrugs and active metabolites of a compound may be determined using routine techniques known or available in the art. See, e.g., Bertolini et al., J. Med. Chem.1997, 40, 2011-2016; Shan et al., J. Pharm. Sci. 1997, 86 (7), 765-767; Bagshawe, Drug Dev. Res.1995, 34, 220-230; Bodor, Adv. Drug Res.1984, 13, 255-331; Bundgaard, Design 2 of Prodrugs (Elsevier Press, 1985); and Larsen, Design and Application of Prodrugs, Drug Design and Development (Krogsgaard-Larsen et al., eds., Harwood Academic Publishers, 1991). [0148] Any formula depicted herein is intended to represent a compound of that structural formula as well as certain variations or forms. For example, a formula given herein is intended to include a racemic form, or one or more enantiomeric, diastereomeric, or geometric isomers, or a mixture thereof. Additionally, any formula given herein is intended to refer also to a hydrate, solvate, or polymorph of such a compound, or a mixture thereof. For example, it will be appreciated that compounds depicted by a structural formula containing the symbol “

include both stereoisomers for the carbon atom to which the symbol

” is attached, specifically both the bonds “

” are encompassed by the meaning of “

”. [0149] Any formula given herein is also intended to represent unlabeled forms as well as isotopically labeled forms of the compounds. Isotopically labeled compounds have structures depicted by the formulas given herein except that one or more atoms are replaced by an atom having a selected atomic mass or mass number. Examples of isotopes that can be incorporated into compounds of the disclosure include isotopes of hydrogen, carbon, nitrogen, oxygen, phosphorous, fluorine, chlorine, and iodine, such as ²H, ³H, ¹¹C, ¹³C, ¹⁴C, ¹⁵N, ¹⁸O, ¹⁷O, ³¹P, ³²P, ³⁵S, ¹⁸F, ³⁶Cl, and ¹²⁵I, respectively. Such isotopically labelled compounds are useful in metabolic studies (preferably with ¹⁴C), reaction kinetic studies (with, for example ²H or ³H), detection or imaging techniques [such as positron emission tomography (PET) or single-photon emission computed tomography (SPECT)] including drug or substrate tissue distribution assays, or in radioactive treatment of patients. For example, isotope-labeled compounds and salts can be used as medicaments. Further, substitution with heavier isotopes such as deuterium (i.e., ²H) may afford certain therapeutic advantages resulting from greater metabolic stability, for example increased in vivo half-life or reduced dosage requirements. For example, deuterium (²H)-labeled compounds and salts may be therapeutically useful with potential therapeutic advantages over the non-²H-labeled compounds. Isotopically labeled compounds of this disclosure and prodrugs thereof can generally be prepared by carrying out the procedures disclosed in the schemes or in the examples and preparations described below by substituting a readily available isotopically labeled reagent for a non-isotopically labeled reagent. [0150] Any disubstituent referred to herein is meant to encompass the various attachment possibilities when more than one of such possibilities are allowed. For example, reference to disubstituent –A-B-, where A ≠ B, refers herein to such disubstituent with A attached to a first substituted member and B attached to a second substituted member, and it also refers to such 2

disubstituent with A attached to the second substituted member and B attached to the first substituted member. REPRESENTATIVE EMBODIMENTS [0151] In some embodiments, the compound is of Formula I

[0152] or a pharmaceutically acceptable salt thereof, wherein [0153] X is -N(R⁵)- or -O-; [0154] W is C₁-C₆ alkyl-(5-10 membered heteroaryl) or –NR⁶R⁷, wherein each hydrogen atom in C1-C6 alkyl is independently optionally substituted by an R^c and each hydrogen atom in (5-10 membered heteroaryl) is independently optionally substituted by an R^d; [0155] R¹ is C1-C6 alkyl, 5-10 membered heteroaryl, -NR⁸R⁹, or -C1-C6 alkyl-NR⁸R⁹, wherein each hydrogen atom in C₁-C₆ alkyl and 5-10 membered heteroaryl is independently optionally substituted by an R^a; [0156] each of R², R⁵, R¹⁰, and R¹¹ is independently H, deuterium, or C₁-C₆ alkyl; [0157] each of R³ and R⁴ is independently H, deuterium, C1-C6 alkyl, C2-C6 alkenyl, C6-C10 aryl, or C₃-C₈ cycloalkyl, wherein each hydrogen atom in C₁-C₆ alkyl, C₂-C₆ alkenyl, C₆-C₁₀ aryl, and C3-C8 cycloalkyl is independently optionally substituted by an R^b; [0158] each of R⁶, R⁷, R⁸, and R⁹ is independently H, deuterium, C₁-C₆ alkyl, C₂-C₆ alkenyl, C3-C8 cycloalkyl, -C(O)C1-C6 alkyl, -C1-C6 alkyl-C(O)NR¹⁰R¹¹, or -C1-C6 alkyl-C(O)OH, wherein each hydrogen atom in C₁-C₆ alkyl, C₂-C₆ alkenyl, and C₃-C₈ cycloalkyl is independently optionally substituted by R^e; [0159] each of R^a, R^b, R^c, R^d, and R^e, when present, is independently deuterium, halo, -CN, -OH, -NR⁸R⁹, -NR⁸C(O)C1-C6 alkyl, C1-C6 alkyl, C2-C6 alkenyl, C3-C8 cycloalkyl, C1-C6 alkoxy, C6- C₁₀ aryl, or 5-10 membered heteroaryl, wherein each hydrogen atom in C₁-C₆ alkyl, C₂-C₆ alkenyl, C3-C8 cycloalkyl, C1-C6 alkoxy, C6-C10 aryl, and 5-10 membered heteroaryl is independently optionally substituted by deuterium, halo, OH, -NH₂, C₁-C₆ alkyl, C₂-C₆ alkenyl, C1-C6 alkoxy, 5-10 membered heteroaryl, C6-C10 aryl, C2-C6 alkenyl, or C3-C8 cycloalkyl; [0160] each R^f, when present, is independently deuterium, halo, -OH, -NR⁸R⁹, -NR¹⁰C(O)C₁-C₆ alkyl, C1-C6 alkyl, C2-C6 alkenyl, C1-C6 alkoxy, 3-to 7-membered heterocycloalkyl, or C3-C8 cycloalkyl, wherein each hydrogen atom in C₁-C₆ alkyl, C₂-C₆ alkenyl, C₁-C₆ alkoxy or C₃-C₈ cycloalkyl is independently optionally substituted by deuterium, halo, -OH, -NR⁸R⁹, or C1-C6 2 alkyl; or two R^f combine together with the atom or atoms to which they are attached to form a C₃-C₈ cycloalkyl, wherein each hydrogen atom in C₃-C₈ cycloalkyl and 3-to 7-membered heterocycloalkyl is independently optionally substituted by deuterium, halo, -OH, -NR⁸R⁹, C1-C6 alkyl, C₂-C₆ alkenyl, or C₁-C₆ alkoxy; [0161] n is 0 or 1; and [0162] m is 0, 1, 2, or 3; [0163] provided that when W is –NR⁶R⁷, then X is -N(R⁵)- and R¹ is CF3. [0164] In some embodiments, the disclosure relates to a compound of the Formula I

[0165] or a pharmaceutically acceptable salt thereof, wherein [0166] X is -N(R⁵)- or -O-; [0167] W is C₁-C₆ alkyl-(5-10 membered heteroaryl) or –NR⁶R⁷, wherein each hydrogen atom in C1-C6 alkyl is independently optionally substituted by an R^c and each hydrogen atom in (5-10 membered heteroaryl) is independently optionally substituted by an R^d; [0168] R¹ is C1-C6 alkyl, 5-10 membered heteroaryl, -NR⁸R⁹, or -C1-C6 alkyl-NR⁸R⁹, wherein each hydrogen atom in C₁-C₆ alkyl and 5-10 membered heteroaryl is independently optionally substituted by an R^a; [0169] each of R², R⁵, R¹⁰, and R¹¹ is independently H, deuterium, or C₁-C₆ alkyl; [0170] each of R³ and R⁴ is independently H, deuterium, C1-C6 alkyl, C2-C6 alkenyl, C6-C10 aryl, or C₃-C₈ cycloalkyl, wherein each hydrogen atom in C₁-C₆ alkyl, C₂-C₆ alkenyl, C₆-C₁₀ aryl, and C3-C8 cycloalkyl is independently optionally substituted by an R^b; [0171] each of R⁶, R⁷, R⁸, and R⁹ is independently H, deuterium, C₁-C₆ alkyl, C₂-C₆ alkenyl, C3-C8 cycloalkyl, -C(O)C1-C6 alkyl, -C1-C6 alkyl-C(O)NR¹⁰R¹¹, or -C1-C6 alkyl-C(O)OH, wherein each hydrogen atom in C₁-C₆ alkyl, C₂-C₆ alkenyl, and C₃-C₈ cycloalkyl is independently optionally substituted by R^e; [0172] each of R^a, R^b, R^c, R^d, and R^e, when present, is independently deuterium, halo, -CN, -OH, -NR⁸R⁹, -NR⁸C(O)C1-C6 alkyl, C1-C6 alkyl, C2-C6 alkenyl, C3-C8 cycloalkyl, C1-C6 alkoxy, C6- C₁₀ aryl, or 5-10 membered heteroaryl, wherein each hydrogen atom in C₁-C₆ alkyl, C₂-C₆ alkenyl, C3-C8 cycloalkyl, C1-C6 alkoxy, C6-C10 aryl, and 5-10 membered heteroaryl is independently optionally substituted by deuterium, halo, OH, -NH₂, C₁-C₆ alkyl, C₂-C₆ alkenyl, C1-C6 alkoxy, 5-10 membered heteroaryl, C6-C10 aryl, C2-C6 alkenyl, or C3-C8 cycloalkyl; 2

[0173] each R^f, when present, is independently deuterium, halo, -OH, -NR⁸R⁹, C1-C6 alkyl, C2- C₆ alkenyl, C₁-C₆ alkoxy or C₃-C₈ cycloalkyl, wherein each hydrogen atom in C₁-C₆ alkyl, C₂-C₆ alkenyl, C1-C6 alkoxy or C3-C8 cycloalkyl is independently optionally substituted by deuterium, halo, -OH, -NR⁸R⁹, or C₁-C₆ alkyl; or two R^f combine together with the atom or atoms to which they are attached to form a C3-C8 cycloalkyl, wherein each hydrogen atom in C3-C8 cycloalkyl is independently optionally substituted by deuterium, halo, -OH, -NR⁸R⁹, C₁-C₆ alkyl, C₂-C₆ alkenyl, or C1-C6 alkoxy; [0174] n is 0 or 1; and [0175] m is 1, 2, or 3; [0176] provided that when W is –NR⁶R⁷, then X is -N(R⁵)- and R¹ is CF_3. [0177] In some embodiments, compounds described herein comprise a moiety of the formula I

[0178] or a pharmaceutically acceptable salt thereof, wherein R¹, R², R³, R⁴, R⁵, R⁶, R^f, n, m, X, and W are as defined herein. [0179] In some embodiments, the disclosure provides compounds of the formula

[0180] or a pharmaceutically acceptable salt thereof, wherein R¹, R^f, m, and W are as defined herein. [0181] In some embodiments, the disclosure provides compounds of the formula

[0182] or a pharmaceutically acceptable salt thereof, wherein R¹, R², R³, R⁴, R^f, m, and W are as defined herein. [0183] In some embodiments, the disclosure provides compounds of the formula 2

[0184] or a pharmaceutically acceptable salt thereof, wherein R¹, R², R³, R⁴, R⁶, R⁷, R^f, and m are as defined herein. [0185] In some embodiments, the disclosure provides compounds of the formula

[0186] or a pharmaceutically acceptable salt thereof, wherein R^f, m, and W are as defined herein. [0187] The compounds described and exemplified herein may comprise one or two amino acids. As used herein, the term “amino acid” may refer generally to beta, gamma, and longer amino acids, such as amino acids of the formula: -N(R)-(CR’R”)t-C(O)- where R is hydrogen, alkyl, acyl, or a suitable nitrogen protecting group, R’ and R” are hydrogen or a substituent, each of which is independently selected in each occurrence, and t is an integer such as 1, 2, 3, 4, or 5. Illustratively, R’ and/or R” independently correspond to, but are not limited to, hydrogen or the side chains present on naturally occurring amino acids, such as methyl, benzyl, hydroxymethyl, thiomethyl, carboxyl, carboxylmethyl, guanidinopropyl, and the like, and derivatives and protected derivatives thereof. The above described formula includes all stereoisomeric variations. In some embodiments, the stereoisomeric configuration is the L-configuration. For example, the amino acid may be selected from asparagine, aspartic acid, cysteine, glutamic acid, lysine, glutamine, arginine, serine, ornitine, threonine, and the like. In some embodiments, the amino acid may be threonine or a hydroxy-protected threonine. [0188] As used herein, the term “amino acid derivative” generally refers to an amino acid as defined herein where either, or both, the amino group and/or the side chain is substituted or a non- naturally occurring amino acid. Illustrative amino acid derivatives include prodrugs and protecting groups of the amino group and/or the side chain, such as amine, amide, hydroxy, carboxylic acid, and thio prodrugs and protecting groups. Additional illustrative amino acid derivatives include substituted variations of the amino acid as described herein, such as, but not limited to, ethers and esters of hydroxy groups, amides, carbamates, and ureas of amino groups, esters, amides, and cyano derivatives of carboxylic acid groups, and the like. In some embodiments, the amino acid derivative comprises a a sidechain that is not naturally occurring. 2 In some embodiments, the side chain is t-butyl, methyl-cyclohexyl, hydroxy-protected threonines, methyl-pyrrolidone, etc. for example. [0189] In some embodiments, X is -N(R⁵)-. In some embodiments, X is -N(R⁵), wherein R⁵ is H, deuterium, or C₁-C₆ alkyl. In some embodiments, X is -N(R⁵), wherein R⁵ is H. In certain preferred embodiments, X is –NH. [0190] In some embodiments, X is -O-. [0191] In some embodiments, W is C1-C6 alkyl-(5-10 membered heteroaryl) wherein each hydrogen atom in C₁-C₆ alkyl is independently optionally substituted by an R^c and each hydrogen atom in (5-10 membered heteroaryl) is independently optionally substituted by an R^d. [0192] In some embodiments, W is C₁-C₆ alkyl-(5-10 membered heteroaryl), and 0, 1, 2, or 3 hydrogen atoms in C1-C6 alkyl are independently substituted with an R^c. In some embodiments, W is C₁-C₆ alkyl-(5-10 membered heteroaryl), and 1 or 2 hydrogen atoms in C₁-C₆ alkyl are independently substituted with an R^c. In some embodiments, W is C1-C6 alkyl-(5-10 membered heteroaryl), and a hydrogen atom in C₁-C₆ alkyl is substituted with an R^c. In some embodiments, W is CH2-(5-10 membered heteroaryl), CHR^c-(5-10 membered heteroaryl), or C(R^c)2-(5-10 membered heteroaryl). [0193] In some embodiments, each R^c, when present, is independently halo, -OH, or -CN. In some embodiments, R^c is halo. In some embodiments, R^c is -CN. In certain preferred embodiments, R^c is -CN. In some embodiments, two R^c, are taken together to form an oxo. In some embodiments, two R^c are taken together on the carbon to which they are attached to form an oxo. [0194] In some embodiments, W is C₁-C₆ alkyl-(5-10 membered heteroaryl), and 0, 1, 2, or 3 hydrogen atoms in (5-10 membered heteroaryl) are independently optionally substituted by an R^d. In some embodiments, W is C₁-C₆ alkyl-(5-10 membered heteroaryl), and 0, 1, or 2 hydrogen atoms in (5-10 membered heteroaryl) are independently optionally substituted by an R^d. [0195] In some embodiments, each R^d, when present, is independently halo, -NR⁸C(O)C₁-C₆ alkyl, or C1-C6 alkoxy, wherein each hydrogen atom in C1-C6 alkyl or C1-C6 alkoxy is independently optionally substituted by halo. In some embodiments, each R^d, when present, is independently halo, -OH, -NR⁸C(O)C1-C6 alkyl, or C1-C6 alkoxy, wherein each hydrogen atom in C₁-C₆ alkyl or C₁-C₆ alkoxy is independently optionally substituted by halo. In some embodiments, R^d is halo. In some embodiments, R^d is fluoro or chloro. In some embodiments, R^d is -OH. For example, if R^d is –OH on a heteroaryl, the –OH substituted heteroaryl may be a tautomer represented as an oxo tautomer. In some embodiments, R^d is –NR⁸C(O)C1-C6 alkyl, wherein R⁵ is H. In some embodiments, R^d is –NR⁸C(O)C₁-C₆ alkyl, wherein each hydrogen atom 3 in C1-C6 alkyl is independently optionally substituted by halo. In some embodiments, R^d is - NHC(O)Me. In some embodiments, R^d is -NHC(O)CF₃. In some embodiments, R^d is C₁-C₆ alkoxy. In some embodiments, R^d is methoxy. [0196] In some embodiments, W is C₁-C₆ alkyl-(5-10 membered heteroaryl), wherein the (5-10 membered heteroaryl) is selected from pyridine, pyrimidine, pyrimidinedione, pyridone, quinoline, quinolone, isoquinoline, or isoquinolone. In some embodiments, W is C₁-C₆ alkyl-(5- 10 membered heteroaryl), wherein the (5-10 membered heteroaryl) is pyridine. In some embodiments, W is C₁-C₆ alkyl-(5-10 membered heteroaryl), wherein the (5-10 membered heteroaryl) is pyridone. In some embodiments, W is C1-C6 alkyl-(5-10 membered heteroaryl), wherein the (5-10 membered heteroaryl) is pyrimidinedione. In some embodiments, W is C₁-C₆ alkyl-(5-10 membered heteroaryl), wherein the (5-10 membered heteroaryl) is isoquinoline. In some embodiments, W is C₁-C₆ alkyl-(5-10 membered heteroaryl), wherein the (5-10 membered heteroaryl) is quinoline. In some embodiments, W is C1-C6 alkyl-(5-10 membered heteroaryl), wherein the (5-10 membered heteroaryl) is quinolinone. In some embodiments, W is C₁-C₆ alkyl- (5-10 membered heteroaryl), wherein the 5-10 membered heteroaryl is selected from

0, 1, 2, or 3. In some embodiments, W is C1-C6 alkyl-(5-10 membered heteroaryl), and 5-10 membered heteroaryl is selected from

and wherein q is 0, 1, 2, or 3. In some embodiments, W is C1-C6 alkyl-(5-10

membered heteroaryl), and 5-10 membered heteroaryl is selected from

3

, , , and , wherein q is 0, 1, 2, or 3. [0197] In some embodiments, R^d is –OH, and W is

, , In some embodiments, R^d is halo, and W is

, , , ,

[0198] In some embodiments, q is 0, 1 or 2. In some embodiments, q is 0. In some embodiments, q is 1. In some embodiments, q is 2. In some embodiments, q is 0 or 1. [0199] In some embodiments, W is

. [0200] In some embodiments, W is 3

, , , , o , and is preferably

[0201] In some embodiments, W is

[0202] In some embodiments, W is

, , , , ,

, , , , , and is preferably

[0203] In some embodiments, W is

[0204] In some embodiments, W is 3

[0205] In some embodiments, W is

[0206] In some embodiments, W is

[0207] In certain preferred embodiments, W is 3

, or . [0208] In certain preferred embodiments, W is

, , , , and is more preferably

[0209] In certain preferred embodiments, W is

such as

, , ,

[0210] In some embodiments, W is -NR⁶R⁷. [0211] In some embodiments, each of R⁶ and R⁷ is independently -C(O)C₁-C₆ alkyl or -C₁-C₆ alkyl-C(O)NR¹⁰R¹¹, wherein each hydrogen atom in C1-C6 alkyl is independently optionally substituted by R^e. In some embodiments, one of R⁶ and R⁷ is -C(O)C₁-C₆ alkyl and the other of R⁶ and R⁷ is -C1-C6 alkyl-C(O)NR¹⁰R¹¹, wherein each hydrogen atom in C1-C6 alkyl is independently optionally substituted by R^e. In some embodiments, each of R⁶ and R⁷ is independently -C(O)C1-C6 alkyl or -C1-C6 alkyl-C(O)NR¹⁰R¹¹, wherein 0, 1, 2, or 3 hydrogen 3

atoms in C1-C6 alkyl are independently optionally substituted by R^e. In some embodiments, each of R⁶ and R⁷ is independently -C(O)C₁-C₆ alkyl or -C₁-C₆ alkyl-C(O)NR¹⁰R¹¹, wherein 0 hydrogen atoms in C1-C6 alkyl are independently optionally substituted by R^e. In some embodiments, each of R⁶ and R⁷ is independently -C(O)C₁-C₆ alkyl or -C₁-C₆ alkyl-C(O)NR¹⁰R¹¹, wherein 1 hydrogen atoms in C1-C6 alkyl are independently optionally substituted by R^e. In some embodiments, each of R⁶ and R⁷ is independently -C(O)C₁-C₆ alkyl or -C₁-C₆ alkyl-C(O)NR¹⁰R¹¹, wherein 2 hydrogen atoms in C1-C6 alkyl are independently optionally substituted by R^e. In some embodiments, each of R⁶ and R⁷ is independently -C(O)C₁-C₆ alkyl or -C₁-C₆ alkyl-C(O)NR¹⁰R¹¹, wherein 3 hydrogen atoms in C1-C6 alkyl are independently optionally substituted by R^e. [0212] In some embodiments, each R^e, when present, is independently halo. In some embodiments, R⁶ or R⁷ is -C(O)C1-C6 alkyl and -C(O)C1-C6 alkyl is –C(O)CH2R^e, –C(O)CHR^e2, or –C(O)CR^e ₃. In some embodiments, -C(O)C₁-C₆ alkyl is C(O)CHCl₂. In some embodiments, R⁶ or R⁷ is -C1-C6 alkyl-C(O)NR¹⁰R¹¹, and -C1-C6 alkyl-C(O)NR¹⁰R¹¹ is –CH2C(O)NH2, – CH₂CH₂C(O)NH₂, or –CH₂CH₂CH₂C(O)NH₂. In some embodiments, -C₁-C₆ alkyl-C(O)NR¹⁰R¹¹ is –CH2CH2C(O)NH2. [0213] In some embodiments, each of R¹⁰ and R¹¹ are independently H. [0214] In some embodiments, R¹ is C1-C6 alkyl, wherein each hydrogen atom in C1-C6 alkyl is independently optionally substituted by an R^a. In some embodiments, R¹ is methyl, ethyl, or propyl, wherein each hydrogen atom is independently optionally substituted by an R^a. [0215] In some embodiments, R^a, when present, is halo. In some embodiments, R^a, when present, is fluoro. In some embodiments, R¹ is methyl, wherein each hydrogen atom is independently optionally substituted by an R^a. In certain preferred embodiments embodiments, R¹ is -CF₃. [0216] In some embodiments, R¹ is 5-10 membered heteroaryl, wherein each hydrogen atom in 5-10 membered heteroaryl is independently optionally substituted by an R^a. In some embodiments, the 5-10 membered heteroaryl is indole, quinolone, or isoquinoline, wherein each hydrogen atom is independently optionally substituted by an R^a. In some embodiments, the 5-10 membered heteroaryl is indole. In some embodiments, R¹ is

, wherein p is 0, 1, 2, or 3. In some embodiments, p is 0. In some embodiments, p is 1. In some embodiments, p is 2. 3

[0217] In some embodiments, each R^a, when present, is independently halo or C1-C6 alkoxy. In some embodiments, R^a, when present, is -OCH3. In some embodiments,

. [0218] In some embodiments, n is 0 or 1. In some embodiments, n is 0. In certain preferred embodiments, n is 1. [0219] In some embodiments,

[0220] In some embodiments, R² is H, deuterium, or C1-C6 alkyl. In certain preferred embodiments, R² is H. In some embodiments, R² is C₁-C₆ alkyl. [0221] In some embodiments, each of R³ and R⁴ is independently H or C1-C6 alkyl, each hydrogen atom in C₁-C₆ alkyl is independently optionally substituted by an R^b. In some embodiments, one of R³ and R⁴ is H, and one of R³ and R⁴ is C1-C6 alkyl. In some embodiments, one of R³ and R⁴ is H, and one of R³ and R⁴ is tert-butyl, wherein each hydrogen atom is optionally substituted by an R^b. In some embodiments, one of R³ and R⁴ is H, and one of R³ and R⁴ is ethyl, wherein each hydrogen atom is optionally substituted by an R^b. In certain preferred embodiments, one of R³ and R⁴ is H and the otheris tert-butyl, such

[0222] In some embodiments, each R^b, when present, is independently C₁-C₆ alkoxy. In some embodiments, R^b is tert-butoxy. In some embodiments, one of R³ and R⁴ is H, and one of R³ and R⁴ is t-butoxy-ethyl. [0223] In some embodiments, two R^f combine together with the atom or atoms to which they are attached to form a C₃-C₈ cycloalkyl, wherein each hydrogen atom in C₃-C₈ cycloalkyl is independently optionally substituted by halo or C1-C6 alkyl. In some embodiments, two R^f combine together to form

. In some embodiments, two R^f combine together to form

some embodiments, 0, 1, 2, or 3 hydrogen atoms in C₃-C₈ cycloalkyl are substituted by halo or C1-C6 alkyl. In some embodiments, 0, 1, or 2 hydrogen atoms in C3-C8 cycloalkyl are 3 independently substituted by halo or C1-C6 alkyl. In some embodiments, 0 hydrogen atoms in C3- C₈ cycloalkyl are independently substituted by halo or C₁-C₆ alkyl. In some embodiments, 1 hydrogen atoms in C3-C8 cycloalkyl are independently substituted by halo or C1-C6 alkyl. In some embodiments, 2 hydrogen atoms in C₃-C₈ cycloalkyl are independently substituted by halo or C1-C6 alkyl. In some embodiments, 2 hydrogen atoms in C3-C8 cycloalkyl are independently substituted by halo. In some embodiments, 2 hydrogen atoms in C₃-C₈ cycloalkyl are independently substituted by chloro. In some embodiments, two R^f combine together to form

some embodiments, 2 hydrogen atoms in C3-C8 cycloalkyl are independently substituted by C₁-C₆ alkyl. In some embodiments, 2 hydrogen atoms in C₃-C₈ cycloalkyl are independently substituted by methyl. In some embodiments, two R^f combine together to form

. In certain preferred embodiments, two R^f combine together t

such a

[0224] In some embodiments, two R^f combine together with the atom or atoms to which they are attached to form 3-to 7-membered heterocycloalkyl, for example a spiro heterocycloalkyl, wherein each hydrogen atom in 3-to 7-membered heterocycloalkyl is independently optionally substituted by halo or C1-C6 alkyl. In some embodiments, 1 hydrogen atom in 3-to 7-membered heterocycloalkyl is independently substituted by halo or C₁-C₆ alkyl. In some embodiments, two R^f combine together to form a dithiolane (e.g., 1,3-dithiolane), such as a spiro 1,3-dithiolane (e.g.,

[0225] In some embodiments, a pharmaceutical composition comprises at least one compound of Formula I, or a pharmaceutically acceptable salt thereof, and optionally one or more pharmaceutically acceptable excipients. [0226] In some embodiments, a method of treating disease, such as a viral infection, comprises administering to a subject in need of such treatment an effective amount of a compound of Formula I, or a pharmaceutically acceptable salt thereof. [0227] ALTERNATIVE EMBODIMENTS [0228] 1. A compound of Formula

or a pharmaceutically acceptable salt thereof, wherein X is -N(R⁵)- or -O-; W is C1-C6 alkyl-(5-10 membered heteroaryl) or –NR⁶R⁷, wherein each hydrogen atom in C1-C6 alkyl is independently optionally substituted by an R^c and each hydrogen atom in (5-10 membered heteroaryl) is independently optionally substituted by an R^d; R¹ is C1-C6 alkyl, 5-10 membered heteroaryl, -NR⁸R⁹, or -C1-C6 alkyl-NR⁸R⁹, wherein each hydrogen atom in C₁-C₆ alkyl and 5-10 membered heteroaryl is independently optionally substituted by an R^a; each of R², R⁵, R¹⁰, and R¹¹ is independently H, deuterium, or C₁-C₆ alkyl; each of R³ and R⁴ is independently H, deuterium, C1-C6 alkyl, C2-C6 alkenyl, C6-C10 aryl, or C₃-C₈ cycloalkyl, wherein each hydrogen atom in C₁-C₆ alkyl, C₂-C₆ alkenyl, C₆-C₁₀ aryl, and C3-C8 cycloalkyl is independently optionally substituted by an R^b; each of R⁶, R⁷, R⁸, and R⁹ is independently H, deuterium, C₁-C₆ alkyl, C₂-C₆ alkenyl, C3-C8 cycloalkyl, -C(O)C1-C6 alkyl, -C1-C6 alkyl-C(O)NR¹⁰R¹¹, or -C1-C6 alkyl-C(O)OH, wherein each hydrogen atom in C₁-C₆ alkyl, C₂-C₆ alkenyl, and C₃-C₈ cycloalkyl is independently optionally substituted by R^e; each of R^a, R^b, R^c, R^d, and R^e, when present, is independently deuterium, halo, -CN, -OH, -NR⁸R⁹, -NR⁸C(O)C1-C6 alkyl, C1-C6 alkyl, C2-C6 alkenyl, C3-C8 cycloalkyl, C1-C6 alkoxy, C6- C₁₀ aryl, or 5-10 membered heteroaryl, wherein each hydrogen atom in C₁-C₆ alkyl, C₂-C₆ alkenyl, C3-C8 cycloalkyl, C1-C6 alkoxy, C6-C10 aryl, and 5-10 membered heteroaryl is independently optionally substituted by deuterium, halo, OH, -NH₂, C₁-C₆ alkyl, C₂-C₆ alkenyl, C1-C6 alkoxy, 5-10 membered heteroaryl, C6-C10 aryl, C2-C6 alkenyl, or C3-C8 cycloalkyl; each R^f, when present, is independently deuterium, halo, -OH, -NR⁸R⁹, C₁-C₆ alkyl, C₂- C6 alkenyl, C1-C6 alkoxy or C3-C8 cycloalkyl, wherein each hydrogen atom in C1-C6 alkyl, C2-C6 alkenyl, C₁-C₆ alkoxy or C₃-C₈ cycloalkyl is independently optionally substituted by deuterium, 3

halo, -OH, -NR⁸R⁹, or C1-C6 alkyl; or two R^f combine together with the atom or atoms to which they are attached to form a C₃-C₈ cycloalkyl, wherein each hydrogen atom in C₃-C₈ cycloalkyl is independently optionally substituted by deuterium, halo, -OH, -NR⁸R⁹, C1-C6 alkyl, C2-C6 alkenyl, or C₁-C₆ alkoxy; n is 0 or 1; and m is 0, 1, 2, or 3; provided that when W is –NR⁶R⁷, then X is -N(R⁵)- and R¹ is CF3. [0229] 2. The compound or pharmaceutically acceptable salt of embodiment 1, wherein W is C₁- C6 alkyl-(5-10 membered heteroaryl), wherein each hydrogen atom in C1-C6 alkyl is independently optionally substituted by an R^c and each hydrogen atom in (5-10 membered heteroaryl) is independently optionally substituted by an R^d. [0230] 3. The compound or pharmaceutically acceptable salt of embodiment 1 or 2, wherein X is -N(R⁵)-. [0231] 4. The compound or pharmaceutically acceptable salt of embodiment 1 or 2, wherein X is -O-. [0232] 5. The compound or pharmaceutically acceptable salt of any one of the preceding embodiments, wherein W is C1-C6 alkyl-(5-10 membered heteroaryl), and one hydrogen atom in C₁-C₆ alkyl is substituted with an R^c. [0233] 6. The compound or pharmaceutically acceptable salt of any one of the preceding embodiments, wherein R^c, when present, is –CN. [0234] 7. The compound or pharmaceutically acceptable salt of any one of the preceding embodiments, wherein W is C₁-C₆ alkyl-(5-10 membered heteroaryl), and 5-10 membered heteroaryl is selected from

[0235] 8. The compound or pharmaceutically acceptable salt of any one of the preceding claims, wherein R^d, when present, is halo, -NHC(O)C1-C6 alkyl, or C1-C6 alkoxy, wherein each hydrogen atom in C₁-C₆ alkyl or C₁-C₆ alkoxy is independently optionally substituted by halo. [0236] 9. The compound or pharmaceutically acceptable salt of any one of the preceding claims, wherein R^d, when present, is fluoro or chloro. [0237] 10. The compound or pharmaceutically acceptable salt of any one of the preceding claims, wherein R^d, when present, is -NHC(O)CF₃, -NHC(O)CF₃, or OMe. 4 [0238] 11. The compound or pharmaceutically acceptable salt of embodiment 1, wherein W is -NR⁶R⁷. [0239] 12. The compound or pharmaceutically acceptable salt of any one of the preceding embodiments, wherein R¹ is 5-10 membered heteroaryl, wherein each hydrogen atom in 5-10 membered heteroaryl is independently optionally substituted by an R^a. [0240] 13. The compound or pharmaceutically acceptable salt of any one of any one of the preceding embodiments, wherein R¹ is

, wherein p is 0, 1, 2, or 3. [0241] 14. The compound or pharmaceutically acceptable salt of embodiment 13, wherein p is 1. [0242] 15. The compound or pharmaceutically acceptable salt of any one of the preceding embodiments, wherein each R^a, when present, is independently deuterium, halo, -CN, -OH, - NR⁸R⁹, C1-C6 alkyl, or C1-C6 alkoxy. [0243] 16. The compound or pharmaceutically acceptable salt of any one of the preceding embodiments, wherein R^a, when present, is -OCH3. [0244] 17. The compound or pharmaceutically acceptable salt of any one of embodiments 1 to 4, wherein R¹ is -CF3. [0245] 18. The compound or pharmaceutically acceptable salt of embodiment 1 or 17, wherein one of R⁶ and R⁷ is -C(O)C1-C6 alkyl, and one of R⁶ and R⁷ is -C1-C6 alkyl-C(O)NR¹⁰R¹¹, wherein each hydrogen atom in C₁-C₆ alkyl is independently optionally substituted by R^e. [0246] 19. The compound or pharmaceutically acceptable salt of embodiment 18, wherein -C(O)C₁-C₆ alkyl is –C(O)CHCl₂. [0247] 20. The compound or pharmaceutically acceptable salt of embodiment 18 or 19, wherein is -C₁-C₆ alkyl-C(O)NR¹⁰R¹¹ is –CH₂CH₂C(O)NH₂. [0248] 21. The compound or pharmaceutically acceptable salt of any one of the preceding embodiments, wherein n is 0. [0249] 22. The compound or pharmaceutically acceptable salt of embodiment 21, wherein the compound is of formula

. [0250] 23. The compound or pharmaceutically acceptable salt of any one of embodiments 1 to 20, wherein n is 1.

[0251] 24. The compound or pharmaceutically acceptable of embodiment 23, wherein the compound is of formula

. [0252] 25. The compound or pharmaceutically acceptable of embodiment 23, wherein the compound is of formula

. [0253] 26. The compound or pharmaceutically acceptable salt of any one of the preceding embodiments, wherein R², when present, is H. [0254] 27. The compound or pharmaceutically acceptable salt of any one of the preceding embodiments, wherein R⁵, when present, is H. [0255] 28. The compound or pharmaceutically acceptable salt of any one of the preceding embodiments, wherein n is 1, one of R³ and R⁴ is H, and one of R³ and R⁴ is C₁-C₆ alkyl. [0256] 29. The compound or pharmaceutically acceptable salt embodiment 28, wherein one of R³ and R⁴ is H, and one of R³ and R⁴ is t-butoxy-ethyl or t-butyl. [0257] 30. The compound or pharmaceutically acceptable salt of any one of the preceding embodiments, wherein m is 2, and two R^f combine together with the atom or atoms to which they are attached to form a C3-C8 cycloalkyl. [0258] 31. The compound or pharmaceutically acceptable salt of embodiment 30, wherein the C3-C8 cycloalkyl is a cyclopropyl or a cyclopentyl. [0259] 32. The compound or pharmaceutically acceptable salt of embodiment 30 or 31, wherein the C3-C8 cycloalkyl is substituted with one or more methyl or halo. [0260] 33. A compound selected from the group consisting of: 4

. [0261] 34. A pharmaceutical composition comprising at least one compound of embodiment 1, or a pharmaceutically acceptable salt thereof, and optionally one or more pharmaceutically acceptable excipients. [0262] 35. A method of treating disease, such as a viral infection, comprising administering to a subject in need of such treatment an effective amount of a compound of embodiment 1, or a pharmaceutically acceptable salt thereof. [0263] The following represent illustrative embodiments of compounds of the Formula I: [0264] Table A:

4

4

4

47

49

50

5

[0265] Those skilled in the art will recognize that the species listed or illustrated herein are not exhaustive, and that additional species within the scope of these defined terms may also be selected. [0266] Pharmaceutical Compositions [0267] For treatment purposes, pharmaceutical compositions comprising the compounds described herein may further comprise one or more pharmaceutically-acceptable excipients. A pharmaceutically-acceptable excipient is a substance that is non-toxic and otherwise biologically suitable for administration to a subject. Such excipients facilitate administration of the 5

compounds described herein and are compatible with the active ingredient. Examples of pharmaceutically-acceptable excipients include stabilizers, lubricants, surfactants, diluents, anti- oxidants, binders, coloring agents, bulking agents, emulsifiers, or taste-modifying agents. In preferred embodiments, pharmaceutical compositions according to the invention are sterile compositions. Pharmaceutical compositions may be prepared using compounding techniques known or that become available to those skilled in the art. [0268] Sterile compositions are also contemplated by the invention, including compositions that are in accord with national and local regulations governing such compositions. [0269] The pharmaceutical compositions and compounds described herein may be formulated as solutions, emulsions, suspensions, or dispersions in suitable pharmaceutical solvents or carriers, or as pills, tablets, lozenges, suppositories, sachets, dragees, granules, powders, powders for reconstitution, or capsules along with solid carriers according to conventional methods known in the art for preparation of various dosage forms. Pharmaceutical compositions of the invention may be administered by a suitable route of delivery, such as oral, parenteral, rectal, nasal, topical, or ocular routes, or by inhalation. Preferably, the compositions are formulated for intravenous or oral administration. [0270] For oral administration, the compounds the invention may be provided in a solid form, such as a tablet or capsule, or as a solution, emulsion, or suspension. To prepare the oral compositions, the compounds of the invention may be formulated to yield a dosage of, e.g., from about 0.1 mg to 1 g daily, or about 1 mg to 50 mg daily, or about 50 to 250 mg daily, or about 250 mg to 1 g daily. Oral tablets may include the active ingredient(s) mixed with compatible pharmaceutically acceptable excipients such as diluents, disintegrating agents, binding agents, lubricating agents, sweetening agents, flavoring agents, coloring agents and preservative agents. Suitable inert fillers include sodium and calcium carbonate, sodium and calcium phosphate, lactose, starch, sugar, glucose, methyl cellulose, magnesium stearate, mannitol, sorbitol, and the like. Exemplary liquid oral excipients include ethanol, glycerol, water, and the like. Starch, polyvinyl-pyrrolidone (PVP), sodium starch glycolate, microcrystalline cellulose, and alginic acid are exemplary disintegrating agents. Binding agents may include starch and gelatin. The lubricating agent, if present, may be magnesium stearate, stearic acid, or talc. If desired, the tablets may be coated with a material such as glyceryl monostearate or glyceryl distearate to delay absorption in the gastrointestinal tract, or may be coated with an enteric coating. [0271] Capsules for oral administration include hard and soft gelatin capsules. To prepare hard gelatin capsules, active ingredient(s) may be mixed with a solid, semi-solid, or liquid diluent. Soft gelatin capsules may be prepared by mixing the active ingredient with water, an oil, such as 5

peanut oil or olive oil, liquid paraffin, a mixture of mono and di-glycerides of short chain fatty acids, polyethylene glycol 400, or propylene glycol. [0272] Liquids for oral administration may be in the form of suspensions, solutions, emulsions, or syrups, or may be lyophilized or presented as a dry product for reconstitution with water or other suitable vehicle before use. Such liquid compositions may optionally contain: pharmaceutically-acceptable excipients such as suspending agents (for example, sorbitol, methyl cellulose, sodium alginate, gelatin, hydroxyethylcellulose, carboxymethylcellulose, aluminum stearate gel and the like); non-aqueous vehicles, e.g., oil (for example, almond oil or fractionated coconut oil), propylene glycol, ethyl alcohol, or water; preservatives (for example, methyl or propyl p-hydroxybenzoate or sorbic acid); wetting agents such as lecithin; and, if desired, flavoring or coloring agents. [0273] For parenteral use, including intravenous, intramuscular, intraperitoneal, intranasal, or subcutaneous routes, the agents of the invention may be provided in sterile aqueous solutions or suspensions, buffered to an appropriate pH and isotonicity or in parenterally acceptable oil. Suitable aqueous vehicles include Ringer's solution and isotonic sodium chloride. Such forms may be presented in unit-dose form such as ampoules or disposable injection devices, in multi- dose forms such as vials from which the appropriate dose may be withdrawn, or in a solid form or pre-concentrate that can be used to prepare an injectable formulation. Illustrative infusion doses range from about 1 to 1000 μg/kg/minute of agent admixed with a pharmaceutical carrier over a period ranging from several minutes to several days. [0274] For nasal, inhaled, or oral administration, the inventive pharmaceutical compositions may be administered using, for example, a spray formulation also containing a suitable carrier. The inventive compositions may be formulated for rectal administration as a suppository. [0275] For topical applications, the compounds of the present invention are preferably formulated as creams or ointments or a similar vehicle suitable for topical administration. For topical administration, the inventive compounds may be mixed with a pharmaceutical carrier at a concentration of about 0.1% to about 10% of drug to vehicle. Another mode of administering the agents of the invention may utilize a patch formulation to effect transdermal delivery. [0276] As used herein, the terms “treat” or “treatment” encompass both “preventative” and “curative” treatment. “Preventative” treatment is meant to indicate a postponement of development of a disease, a symptom of a disease, or medical condition, suppressing symptoms that may appear, or reducing the risk of developing or recurrence of a disease or symptom. “Curative” treatment includes reducing the severity of or suppressing the worsening of an existing disease, symptom, or condition. Thus, treatment includes ameliorating or preventing the 5

worsening of existing disease symptoms, preventing additional symptoms from occurring, ameliorating or preventing the underlying systemic causes of symptoms, inhibiting the disorder or disease, e.g., arresting the development of the disorder or disease, relieving the disorder or disease, causing regression of the disorder or disease, relieving a condition caused by the disease or disorder, or stopping the symptoms of the disease or disorder. [0277] The term “subject” refers to a mammalian patient in need of such treatment, such as a human. [0278] Exemplary diseases include those caused by SARS-CoV-2, SARS-CoV, MERS-CoV, Ebola virus, Paramyxoviruses, Bunyaviruses (Bunyavirales), Togaviruses, Filoviruses, Picornaviruses, Flaviviruses. In some example, the disease is caused by SARS-CoV-2. [0279] In one aspect, the compounds and pharmaceutical compositions of the invention specifically target SC2M^Pro. Thus, these compounds and pharmaceutical compositions can be used to prevent, reverse, slow, or inhibit the activity of this protease. In preferred embodiments, methods of treatment include treating viral infections. In other embodiments, methods are for treating viral infections caused by COVID-19. [0280] In the inhibitory methods of the invention, an “effective amount” means an amount sufficient to inhibit the target protein. Measuring such target modulation may be performed by routine analytical methods such as those described below. Such modulation is useful in a variety of settings, including in vitro assays. [0281] In treatment methods according to the invention, an “effective amount” means an amount or dose sufficient to generally bring about the desired therapeutic benefit in subjects needing such treatment. Effective amounts or doses of the compounds of the invention may be ascertained by routine methods, such as modeling, dose escalation, or clinical trials, taking into account routine factors, e.g., the mode or route of administration or drug delivery, the pharmacokinetics of the agent, the severity and course of the infection, the subject’s health status, condition, and weight, and the judgment of the treating physician. An exemplary dose is in the range of about from about 0.1 mg to 1 g daily, or about 1 mg to 50 mg daily, or about 50 to 250 mg daily, or about 250 mg to 1 g daily. The total dosage may be given in single or divided dosage units (e.g., BID, TID, QID). [0282] Once improvement of the patient’s disease has occurred, the dose may be adjusted for preventative or maintenance treatment. For example, the dosage or the frequency of administration, or both, may be reduced as a function of the symptoms, to a level at which the desired therapeutic or prophylactic effect is maintained. Of course, if symptoms have been alleviated to an appropriate level, treatment may cease. Patients may, however, require 5

intermittent treatment on a long-term basis upon any recurrence of symptoms. Patients may also require chronic treatment on a long-term basis. [0283] Drug Combinations [0284] The inventive compounds described herein may be used in pharmaceutical compositions or methods in combination with one or more additional active ingredients in the treatment of the diseases and disorders described herein. Further additional active ingredients include other therapeutics or agents that mitigate adverse effects of therapies for the intended disease targets. Such combinations may serve to increase efficacy, ameliorate other disease symptoms, decrease one or more side effects, or decrease the required dose of an inventive compound. The additional active ingredients may be administered in a separate pharmaceutical composition from a compound of the present invention or may be included with a compound of the present invention in a single pharmaceutical composition. The additional active ingredients may be administered simultaneously with, prior to, or after administration of a compound of the present invention. [0285] Combination agents include additional active ingredients are those that are known or discovered to be effective in treating the diseases and disorders described herein, including those active against another target associated with the disease. For example, compositions and formulations of the invention, as well as methods of treatment, can further comprise other drugs or pharmaceuticals, e.g., other active agents useful for treating or palliative for the target diseases or related symptoms or conditions. For viral infections, additional such agents include, but are not limited to, remdesivir, favipiravir, ribavirin, monoclonal antibodies, dexamethasone, interferon, umifenovir, oseltamivir, lopinavir, and ritonavir. The pharmaceutical compositions of the invention may additionally comprise one or more of such active agents, and methods of treatment may additionally comprise administering an effective amount of one or more of such active agents. [0286] Chemical Synthesis [0287] Exemplary chemical entities useful in methods of the description will now be described by reference to illustrative synthetic schemes for their general preparation below and the specific examples that follow. Artisans will recognize that, to obtain the various compounds herein, starting materials may be suitably selected so that the ultimately desired substituents will be carried through the reaction scheme with or without protection as appropriate to yield the desired product. Alternatively, it may be necessary or desirable to employ, in the place of the ultimately desired substituent, a suitable group that may be carried through the reaction scheme and replaced as appropriate with the desired substituent. Furthermore, one of skill in the art will recognize that 5

the transformations shown in the schemes below may be performed in any order that is compatible with the functionality of the particular pendant groups. [0288] Abbreviations [0289] The examples described herein use materials, including but not limited to, those described by the following abbreviations known to those skilled in the art:

5

[0290] The following represent intermediate compounds used in the chemical synthesis to prepare compounds of the Formula I: [0291] Table B: Commercially available representative intermediate compounds

[0292] Representative Synthetic Procedure I

[0293] Scheme S1. The synthesis of compounds 1, 2, 3, 14, 15, 16, 17, 18, and 19. Reaction conditions: (a) triflic anhydride, Et3N, DMAP, DCM, -23°C, 22h; (b) 2-formyl boronic acid, AsPh3, Pd(BnCN)2Cl2, Cs2CO3, DMF/THF/H2O; (c) O-methylhydroxylamine·HCl, pyridine, 4 Å molecular sieves; (d) DCB, 130 °C; (e) i) TMS-CN, AcOH, THF, ii) NH₄Cl, NH₃; (f) Intermediate A, COMU, DIPEA, DCM.

[0294] 2-amino-2-(isoquinolin-4-yl)acetonitrile: [0295] ¹H NMR (400 MHz, CDCl₃) δ 9.21 (s, 1H), 8.70 (s, 1H), 8.12 (d, J = 8.5 Hz, 1H), 7.98 (d, J = 8.2 Hz, 1H), 7.76 (t, J = 7.7 Hz, 1H), 7.62 (t, J = 7.5 Hz, 1H), 5.43 (s, 1H), 2.07 (d, J = 8.2 Hz, 2H).¹³C NMR (101 MHz, CDCl₃) δ 154.71, 141.52, 132.79, 131.56, 128.71, 128.56, 127.85, 125.34, 122.39, 120.11, 43.74.

[0296] Compounds 1-3 [0297] (1R,2S,5S)-N-(cyano(isoquinolin-4-yl)methyl)-3-((S)-3,3-dimethyl-2-(2,2,2- trifluoroacetamido)butanoyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide (Mixture): ¹H NMR (400 MHz, CDCl3) δ 9.22 (s, 0.45H), 9.16 (s, 0.55H), 8.74 (s, 0.45H), 8.72 (s, 0.55H), 8.20 (d, J = 8.7 Hz, 0.45H), 8.14 (d, J = 8.9 Hz, 0.55H), 8.01 (d, J = 8.2 Hz, 0.45H), 7.96 – 7.58 (m, 3.55H), 6.93 (d, J = 9.4 Hz, 0.45H), 6.83 (d, J = 9.4 Hz, 0.55H), 6.70 (d, J = 8.7 Hz, 0.55H), 6.65 (d, J = 8.8 Hz, 0.45H), 4.50 (d, J = 9.4 Hz, 0.45H), 4.38 – 4.32 (m, 1.55H), 3.89 (dd, J = 10.4, 4.9 Hz, 0.45H), 3.82 (d, J = 10.5 Hz, 0.45H), 3.79 – 3.67 (m, 1.10H), 1.73 (d, J = 7.7 Hz, 0.55H), 1.62 – 1.49 (m, 1.45H), 1.07 – 0.93 (m, 7H), 0.73 (s, 3H), 0.53 (s, 5H). [0298] (Top isomer based on TLC): ¹H NMR (400 MHz, CDCl₃) δ 9.20 (s, 1H), 8.78 (s, 1H), 8.02 – 7.85 (m, 3H), 7.77 (ddd, J = 8.4, 6.9, 1.3 Hz, 1H), 7.71 – 7.61 (m, 1H), 6.69 (dd, J = 9.0, 5.4 Hz, 2H), 4.38 – 4.29 (m, 2H), 3.75 – 3.65 (m, 2H), 1.77 (d, J = 7.7 Hz, 1H), 1.54 (ddd, J = 7.7, 4.1, 1.9 Hz, 1H), 1.02 (s, 3H), 0.73 (s, 3H), 0.47 (s, 9H). [0299] (Bottom isomer based on TLC): ¹H NMR (400 MHz, CDCl₃) δ 9.27 (s, 1H), 8.78 (s, 1H), 8.04 (dd, J = 8.1, 1.2 Hz, 1H), 7.92 – 7.85 (m, 2H), 7.85 – 7.73 (m, 1H), 7.73 – 7.61 (m, 1H), 6.80 (d, J = 9.3 Hz, 1H), 6.63 (d, J = 8.8 Hz, 1H), 4.50 (d, J = 9.4 Hz, 1H), 4.35 (d, J = 3.9 5 Hz, 1H), 3.90 – 3.79 (m, 2H), 1.69 (d, J = 7.7 Hz, 1H), 1.61 – 1.50 (m, 1H), 0.97 (s, 10.5H), 0.73 (d, J = 1.7 Hz, 3H), 0.46 (s, 1.5H).

[0300] 8-fluoroisoquinoline-4-carbaldehyde: [0301] ¹H NMR (400 MHz, DMSO) δ 10.44 (s, 1H), 9.76 (s, 1H), 9.21 (s, 1H), 8.89 (d, J = 8.6 Hz, 1H), 8.04 (td, J = 8.2, 6.0 Hz, 1H), 7.67 (dd, J = 10.5, 8.0 Hz, 1H).

[0302] 2-amino-2-(8-fluoroisoquinolin-4-yl) acetonitrile: [0303] ¹H NMR (400 MHz, DMSO) δ 9.44 (s, 1H), 8.74 (s, 1H), 8.04 (d, J = 8.6 Hz, 1H), 7.84 (td, J = 8.1, 5.9 Hz, 1H), 7.50 (dd, J = 10.5, 7.9 Hz, 1H), 5.71 (s, 1H), 3.01 (d, J = 6.6 Hz, 2H). [0304] ¹³C NMR (101 MHz, DMSO) δ 160.29, 157.76, 146.87, 142.70, 134.23, 132.43, 132.34, 127.36, 121.84, 120.01, 118.68, 112.15, 43.15.

[0305] Compound 17 [0306] (1R,2S,5S)-N-(cyano(8-fluoroisoquinolin-4-yl)methyl)-3-((S)-3,3-dimethyl-2-(2,2,2- trifluoroacetamido)butanoyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide: [0307] ¹H NMR (400 MHz, DMSO) δ 9.65 (d, J = 7.8 Hz, 1H), 9.58 (s, 1H), 9.36 (d, J = 8.2 Hz, 1H), 8.89 – 8.81 (m, 1H), 7.88 – 7.78 (m, 2H), 7.67 – 7.56 (m, 1H), 6.92 (t, J = 7.9 Hz, 1H), 4.39 (t, J = 8.6 Hz, 1H), 4.23 (d, J = 13.2 Hz, 1H), 3.94 (dd, J = 10.2, 5.4 Hz, 1H), 3.70 (t, J = 13.6 Hz, 1H), 1.60 (dd, J = 14.4, 7.3 Hz, 1H), 1.36 (d, J = 7.6 Hz, 1H), 1.04 (s, 3H), 1.00 (s, 9H), 0.91 (d, J = 22.9 Hz, 1H), 0.82 (s, 3H). 6

[0308] 2-(2,2-dimethyl-4H-1,3-dioxin-5-yl)-5-fluorobenzaldehyde: [0309] ¹H NMR (400 MHz, CDCl3) δ 10.16 (d, J = 3.0 Hz, 1H), 7.60 (dd, J = 8.8, 2.8 Hz, 1H), 7.34 (dd, J = 8.6, 5.2 Hz, 1H), 7.31 – 7.27 (m, 1H), 6.37 (t, J = 1.6 Hz, 1H), 4.46 (d, J = 1.6 Hz, 2H), 1.57 (s, 6H).

[0310] (E)-2-(2,2-dimethyl-4H-1,3-dioxin-5-yl)-5-fluorobenzaldehyde O-methyl oxime: [0311] ¹H NMR (400 MHz, CDCl3) δ 8.16 (d, J = 1.8 Hz, 1H), 7.50 (dd, J = 9.8, 2.8 Hz, 1H), 7.10 (dd, J = 8.5, 5.6 Hz, 1H), 6.97 (td, J = 8.3, 2.8 Hz, 1H), 6.27 (t, J = 1.6 Hz, 1H), 4.24 (d, J = 1.7 Hz, 2H), 3.91 (s, 3H), 1.48 (s, 6H).¹³C NMR (101 MHz, CDCl3) δ 163.19, 160.73, 146.36, 146.34, 140.81, 132.96, 132.88, 131.81, 131.78, 131.70, 131.62, 116.94, 116.72, 112.85, 112.62, 109.36, 98.73, 62.19, 24.41.

[0312] 7-fluoroisoquinoline-4-carbaldehyde: [0313] ¹H NMR (400 MHz, DMSO) δ 10.40 (s, 1H), 9.59 (d, J = 0.8 Hz, 1H), 9.14 (dd, J = 9.4, 5.4 Hz, 1H), 9.09 (s, 1H), 8.14 (dd, J = 9.1, 2.8 Hz, 1H), 7.95 (td, J = 9.1, 2.8 Hz, 1H).¹³C NMR (101 MHz, DMSO) δ 194.63, 162.25, 159.78, 158.23, 158.18, 152.46, 152.44, 129.78, 129.69, 129.14, 127.47, 127.39, 124.69, 124.67, 124.29, 124.04, 112.71, 112.50.

[0314] Compound 16 [0315] (1R,2S,5S)-N-(cyano(7-fluoroisoquinolin-4-yl)methyl)-3-((S)-3,3-dimethyl-2-(2,2,2- trifluoroacetamido)butanoyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide (top isomer): [0316] Top Isomer based on TLC: [0317] ¹H NMR (400 MHz, DMSO) δ 9.62 (d, J = 7.9 Hz, 1H), 9.41 (d, J = 3.3 Hz, 1H), 9.34 (d, J = 8.2 Hz, 1H), 8.72 (d, J = 6.9 Hz, 1H), 8.14 – 8.04 (m, 2H), 7.70 (td, J = 8.9, 2.7 Hz, 1H), 6.95 (d, J = 7.9 Hz, 1H), 4.40 (d, J = 8.4 Hz, 1H), 4.19 (s, 1H), 3.94 (dd, J = 10.3, 5.4 Hz, 1H), 3.72 (d, J = 10.4 Hz, 1H), 1.61 (dd, J = 7.6, 5.3 Hz, 1H), 1.36 (d, J = 7.6 Hz, 1H), 1.04 (s, 3H), 1.01 (s, 9H), 0.82 (s, 3H). [0318] Bottom Isomer based on TLC (impure): [0319] ¹H NMR (400 MHz, DMSO) δ 9.56 (d, J = 7.9 Hz, 1H), 9.45 (d, J = 9.1 Hz, 2H), 8.76 (s, 1H), 8.14 (ddd, J = 9.2, 6.0, 3.9 Hz, 2H), 7.95 (td, J = 8.9, 2.8 Hz, 1H), 6.96 (d, J = 7.8 Hz, 1H), 4.43 (d, J = 8.4 Hz, 1H), 4.29 (s, 1H), 3.99 (dt, J = 10.3, 5.2 Hz, 1H), 3.73 (d, J = 10.4 Hz, 1H), 1.61 (dd, J = 7.6, 5.4 Hz, 1H), 1.19 (d, J = 7.6 Hz, 1H), 1.08 (d, J = 12.1 Hz, 3H), 0.99 (d, J = 6.6 Hz, 9H), 0.87 (d, J = 6.4 Hz, 3H). [0320] Isomer Mixture: [0321] ¹H NMR (400 MHz, DMSO) δ 9.62 (d, J = 7.9 Hz, 0.5H), 9.51 (d, J = 7.9 Hz, 0.5H), 9.44 – 9.31 (m, 2H), 8.72 (d, J = 6.9 Hz, 1H), 8.14 – 8.04 (m, 2H), 7.89 (td, J = 8.9, 2.8 Hz, 0.5H), 7.70 (td, J = 9.0, 2.7 Hz, 0.5H), 6.93 (dd, J = 17.0, 7.9 Hz, 1H), 4.39 (dd, J = 10.4, 8.3 Hz, 1H), 4.24 (s, 0.5H), 4.19 (s, 0.5H), 3.94 (dt, J = 10.3, 5.2 Hz, 1H), 3.69 (dd, J = 17.3, 10.4 Hz, 1H), 1.61 (dd, J = 7.6, 5.3 Hz, 0.5H), 1.56 (dd, J = 7.6, 5.4 Hz, 0.5H), 1.36 (d, J = 7.6 Hz, 0.5H), 1.14 (d, J = 7.6 Hz, 0.5H), 1.02 (d, J = 12.1 Hz, 6H), 0.93 (d, J = 6.5 Hz, 6H), 0.82 (d, J = 6.4 Hz, 3H).

[0322] 6-fluoroisoquinoline-4-carbaldehyde: [0323] ¹H NMR (400 MHz, DMSO) δ 10.39 (s, 1H), 9.62 (d, J = 0.9 Hz, 1H), 9.13 (d, J = 0.9 Hz, 1H), 8.74 (dd, J = 11.1, 2.6 Hz, 1H), 8.45 (dd, J = 9.1, 6.0 Hz, 1H), 7.77 (td, J = 8.9, 2.6 Hz, 1H).¹³C NMR (101 MHz, DMSO) δ 194.56, 166.53, 164.02, 158.56, 153.85, 133.66 (q), 125.96, 124.45, 119.32 (d), 108.19 (d). 6

[0324] 2-amino-2-(6-fluoroisoquinolin-4-yl)acetonitrile: [0325] ¹H NMR (400 MHz, DMSO) δ 9.51 (d, J = 0.8 Hz, 1H), 8.86 (s, 1H), 8.55 – 8.39 (m, 1H), 8.18 (dd, J = 11.1, 2.5 Hz, 1H), 7.83 (td, J = 8.9, 2.5 Hz, 1H), 5.89 (d, J = 10.2 Hz, 1H), 3.25 (brs, 2H). ¹³C NMR (101 MHz, DMSO) δ 164.54, 162.06, 153.71, 142.39, 134.55 (q), 127.48 (d), 125.94, 121.84, 118.57 (d), 107.86 (d), 43.09.

[0326] Compound 15 [0327] (1S,2S,5S)-N-(cyano(6-fluoroisoquinolin-4-yl)methyl)-3-((S)-3,3-dimethyl-2-(2,2,2- trifluoroacetamido)butanoyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide: [0328] ¹H NMR (400 MHz, DMSO) δ 9.64 – 9.29 (m, 3H), 8.74 (d, J = 7.4 Hz, 1H), 8.38 (dt, J = 9.7, 5.9 Hz, 1H), 7.79 – 7.64 (m, 2H), 6.88 (dd, J = 25.6, 8.0 Hz, 1H), 4.38 (dd, J = 13.1, 8.3 Hz, 1H), 4.21 (d, J = 23.8 Hz, 1H), 3.94 (dd, J = 10.4, 5.5 Hz, 1H), 3.69 (dd, J = 24.8, 10.4 Hz, 1H), 1.58 (ddd, J = 23.6, 7.6, 5.5 Hz, 1H), 1.38 – 1.22 (m, 1H), 1.07 – 0.78 (m, 15H). [0329] Representative Synthetic Procedure II

[0330] Scheme S2. The synthesis of compounds 4, 5, 6, 9, and 10. Reaction conditions: (a) i) TMS-CN, AcOH, THF, ii) NH4Cl, NH3; (b) Intermediate A, COMU, DIPEA, DCM.

[0331] 2-amino-2-(5-chloropyridin-3-yl)acetonitrile: 6

[0332] To a solution of Trimethylsilyl cyanide (1.68 g, 17.02 mmol) was added 5- chloronicotinaldehyde (2.0 g, 14.18 mmol) in THF (20 mL) and water (20 mL) over 30 min at 5- 10 °C. To the reaction mixture was added acetic acid (1.02 g, 17.02 mmol) over 30 min at 5-10 °C. The reaction mixture was stirred at room temperature for a further 12 h and then cooled to 5 °C. The 2-(5-chloropyridin-3-yl)-2-hydroxyacetonitrile product was collected by filtration and washed with water, and the crystals were used immediately after drying. The cyanohydrin product (2.1 g, 12.5 mmol) was added slowly, at room temperature, to a solution of ammonium chloride (3.9 g, 75 mmol) in 25% aqueous ammonia (21 mL). The reaction mixture was stirred at room temperature for 12 h and then extracted with methylene chloride (3 X 30 mL). The organic phases were dried and evaporated to give the title compound as a colorless solid (1.05 g, 53%). [0333] ¹H NMR (400 MHz, CDCl3) δ 8.63 (d, J = 2.0 Hz, 1H), 8.54 (d, J = 2.3 Hz, 1H), 7.86 (td, J = 2.2, 0.8 Hz, 1H), 4.91 (t, J = 7.7 Hz, 1H), 1.97 (d, J = 8.2 Hz, 2H).¹³C NMR (101 MHz, CDCl3) δ 149.45, 146.01, 134.27, 133.17, 132.47, 119.46, 44.65.

[0334] Compounds 4-6 [0335] To a stirred solution of Intermediate A (0.27 mmol, 100 mg) and 2-amino-2-(5- chloropyridin-3-yl)acetonitrile (0.32 mmol, 55 mg) in anhydrous DCM (5 mL) at 0 °C was added COMU (0.38 mmol, 164 mg). After 15 min, NMM (0.82 mmol, 90.6 µL) was added, and the mixture was stirred at same temperature for 1 h. After completion of reaction, the reaction mixture was diluted with DCM (2×10 mL) and H2O (10 mL) and washed with saturated brine solution (2×10 mL) sequentially. The organic layer was dried over anhydrous Na2SO4 and then concentrated in vacuo. The residue was then purified with flash chromatography (0-50% EtOAc in Hexanes as the eluent) to afford Compound 4 (1:2 diastereomeric mixture) as a white solid (40 mg, 28%). [0336] (1R,2S,5S)-N-((5-chloropyridin-3-yl)(cyano)methyl)-3-((S)-3,3-dimethyl-2-(2,2,2- trifluoroacetamido)butanoyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide (Top isomer) [0337] ¹H NMR (400 MHz, CDCl₃) δ 8.55 (dd, J = 15.6, 1.9 Hz, 2H), 7.86 (d, J = 8.7 Hz, 1H), 7.76 (t, J = 1.9 Hz, 1H), 6.82 (t, J = 12.6 Hz, 1H), 6.14 (d, J = 8.7 Hz, 1H), 4.48 – 4.36 (m, 1H), 6

4.37 – 4.22 (m, 1H), 3.87 – 3.75 (m, 2H), 1.69 – 1.60 (m, 1H), 1.56 (dd, J = 7.1, 4.9 Hz, 1H), 1.06 – 0.98 (m, 3H), 0.96 (d, J = 11.0 Hz, 3H), 0.80 (d, J = 8.4 Hz, 9H). [0338] (1R,2S,5S)-N-((5-chloropyridin-3-yl)(cyano)methyl)-3-((S)-3,3-dimethyl-2-(2,2,2- trifluoroacetamido)butanoyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide (Bottom isomer) [0339] ¹H NMR (400 MHz, CDCl₃) δ 8.57 (d, J = 8.0 Hz, 2H), 7.89 (d, J = 8.5 Hz, 1H), 7.75 (dd, J = 6.7, 4.8 Hz, 1H), 6.70 (dd, J = 27.4, 8.9 Hz, 1H), 6.08 (dd, J = 35.1, 8.7 Hz, 1H), 4.50 (d, J = 9.4 Hz, 1H), 4.42 (d, J = 8.5 Hz, 1H), 3.90 – 3.75 (m, 2H), 1.73 (dd, J = 24.8, 7.7 Hz, 1H), 1.55 (dd, J = 7.6, 4.9 Hz, 1H), 1.02 (d, J = 2.4 Hz, 3H), 0.98 (s, 6H), 0.78 (d, J = 2.6 Hz, 6H).

[0340] 2-amino-2-(5-fluoropyridin-3-yl)acetonitrile: [0341] ¹H NMR (400 MHz, DMSO) δ 8.62 – 8.57 (m, 2H), 7.90 – 7.83 (m, 1H), 5.30 – 5.14 (m, 1H), 3.05 (d, J = 23.1 Hz, 2H).

[0342] Compound 10 [0343] Compound 10 was prepared according to the methods preparing compounds 4-6, using 2- amino-2-(5-fluoropyridin-3-yl)acetonitrile. [0344] (1R,2S,5S)-N-(cyano(5-fluoropyridin-3-yl)methyl)-3-((S)-3,3-dimethyl-2-(2,2,2- trifluoroacetamido)butanoyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide (Top isomer) [0345] ¹H NMR (400 MHz, CDCl₃) δ 8.59 – 8.29 (m, 2H), 7.99 – 7.78 (m, 1H), 7.49 (t, J = 10.7 Hz, 1H), 6.97 – 6.73 (m, 1H), 6.29 – 6.02 (m, 1H), 4.55 – 4.36 (m, 1H), 4.37 – 4.23 (m, 1H), 3.92 – 3.70 (m, 2H), 1.63 – 1.52 (m, 2H), 1.06 – 0.98 (m, 3H), 0.82 (s, 9H), 0.80 – 0.76 (m, 3H). [0346] (1R,2S,5S)-N-(cyano(5-fluoropyridin-3-yl)methyl)-3-((S)-3,3-dimethyl-2-(2,2,2- trifluoroacetamido)butanoyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide (Isomer Mixture) [0347] ¹H NMR (400 MHz, CDCl₃) δ 8.53 (s, 1H), 8.47 (dd, J = 11.6, 2.3 Hz, 1H), 7.66 (ddd, J = 68.9, 14.4, 7.4 Hz, 2H), 6.72 (dd, J = 26.1, 9.3 Hz, 1H), 6.12 (dd, J = 36.5, 8.6 Hz, 1H), 4.46 6

(dd, J = 31.1, 9.4 Hz, 1H), 4.41 – 4.30 (m, 1H), 3.87 – 3.77 (m, 2H), 1.70 (dd, J = 23.0, 7.7 Hz, 1H), 1.56 (dd, J = 11.6, 5.1 Hz, 1H), 1.02 (d, J = 3.7 Hz, 3H), 0.97 (s, 3H), 0.78 (s, 9H).

[0348] 2-amino-2-(5-methoxypyridin-3-yl)acetonitrile: [0349] ¹H NMR (400 MHz, DMSO) δ 8.34 (dd, J = 6.3, 1.5 Hz, 1H), 8.31 (d, J = 2.8 Hz, 1H), 7.61 – 7.50 (m, 1H), 5.17 (d, J = 13.3 Hz, 1H), 3.89 – 3.86 (m, 3H), 2.98 (s, 2H).¹³C NMR (101 MHz, DMSO) δ 155.84, 140.44, 137.75, 135.42, 122.07, 119.20, 56.08, 44.60.

[0350] Compound 9 [0351] (1R,2S,5S)-N-(cyano(5-methoxypyridin-3-yl)methyl)-3-((S)-3,3-dimethyl-2-(2,2,2- trifluoroacetamido)butanoyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide: [0352] To a stirred solution of Intermediate A (0.27 mmol, 100 mg) and 2-amino-2-(5- methoxypyridin-3-yl)acetonitrile (0.32 mmol, 54 mg) in anhydrous DCM (5 mL) ) at 0 °C was added COMU (0.38 mmol, 164 mg). After 15 min, NMM (0.82 mmol, 90.6 µL) was added, and the mixture was stirred at same temperature for 1 h. After completion of reaction, The reaction mixture was diluted with DCM (2×10 mL) and H2O (10 mL). washed with saturated brine solution (2×10 mL) sequentially. The organic layer was dried over anhydrous Na₂SO₄ and then concentrated on vacuo. The residue was then purified with flash chromatography (0-50% EtOAc in Hexanes as the eluent) to afford Compound 9 (1:2 diastereomeric mixture) as a white solid (60 mg, 43%). [0353] ¹H NMR (400 MHz, CDCl₃) δ 8.29 (dd, J = 15.0, 12.5 Hz, 2H), 7.92 – 7.56 (m, 1H), 7.31 (t, J = 12.8 Hz, 1H), 6.76 (dd, J = 27.7, 9.1 Hz, 1H), 6.07 (dd, J = 37.4, 8.5 Hz, 1H), 4.52 – 4.40 (m, 1H), 4.40 – 4.29 (m, 2H), 3.84 (d, J = 7.6 Hz, 3H), 3.79 (d, J = 4.0 Hz, 1H), 1.67 (t, J = 5.7 Hz, 1H), 1.55 (dd, J = 7.5, 4.1 Hz, 1H), 1.01 (d, J = 4.6 Hz, 3H), 0.97 (s, 3H), 0.78(s, 9H). [0354] Representative Synthetic Procedure III 6

[0355] Scheme S3. The synthesis of compound 13. Reaction conditions: (a) 2-amino-2- (isoquinolin-4-yl)acetonitrile, COMU, DIPEA, DCM, 0°C; (b) 2,2,2-TFE, TMS-Cl; (c) Intermediate B, COMU, DIPEA, DCM.

[0356] tert-butyl 3-((cyano(isoquinolin-4-yl)methyl)carbamoyl)-2-azaspiro[4.4]nonane-2- carboxylate: [0357] 2-(tert-butoxycarbonyl)-2-azaspiro[4.4]nonane-3-carboxylic acid (150mg, 0.55 mmol) and 2-amino-2-(isoquinolin-4-yl)acetonitrile (122 mg, 0.66 mmol) were dissolved in DCM (6.0 ml) and COMU (360 mg, 0.83 mmol) was added at 0 °C. The reaction mixture was stirred at room temperature for 5 min and Hunig's base (DIPEA) (0.14 mL, 0.83 mmol) was added. The solution was stirred for 2 hours. The mixture was poured onto an aqueous sodium hydrogen carbonate (saturated, 20 ml) and water (20 ml). The mixture was stirred in an Erlenmeyer flask for 10 min. The aqueous layer was extracted with DCM. The organic layer was washed with brine, dried on MgSO4. It was concentrated under reduced pressure. The crude product was purified by flash (eluted with 25:75 to 50:50 EtOAc/ hexanes) to give tert-butyl 3- ((cyano(isoquinolin-4-yl)methyl)carbamoyl)-2-azaspiro[4.4]nonane-2-carboxylate as a colorless solid (180 mg, 75%). [0358] ¹H NMR (400 MHz, DMSO) δ 9.39 (dd, J = 16.1, 7.4 Hz, 2H), 8.83 – 8.61 (m, 1H), 8.25 (dd, J = 8.2, 4.5 Hz, 1H), 8.14 – 7.95 (m, 1H), 7.95-7.84 (m, 1H), 7.82-7.73 (m, 1H), 6.93-6.84 6 (m, 1H), 4.11 (q, J = 7.7 Hz, 1H), 3.31 – 3.16 (m, 2H), 1.99 (q, J = 7.5 Hz, 1H), 1.56 (dt, J = 7.1, 3.7 Hz, 4H), 1.42 – 1.31 (m, 6H), 1.22 (d, J = 21.1 Hz, 9H).

[0359] Compound 13 [0360] N-(cyano(isoquinolin-4-yl)methyl)-2-(4-methoxy-1H-indole-2-carbonyl)-2- azaspiro[4.4]nonane-3-carboxamide: [0361] tert-butyl 3-((cyano(isoquinolin-4-yl)methyl)carbamoyl)-2-azaspiro[4.4]nonane-2- carboxylate (170 mg, 1.11 mmol) was dissolved in anhydrous trifluoroethanol (5 mL). The stirred solution is cooled in an ice bath and TMSCl (0.2 mL) is added dropwise. The mixture is the same temperature until the reaction completion. After completely removing the solvent by rotavapor, crude N-(cyano(isoquinolin-4-yl)methyl)-2-azaspiro[4.4]nonane-3-carboxamide hydrochloride is directly used for the next step. Intermediate B, 4-methoxy-1H-indole-2-carboxylic acid (50mg, 0.26 mmol), and N-(cyano(isoquinolin-4-yl)methyl)-2-azaspiro[4.4]nonane-3-carboxamide hydrochloride (80 mg, 0.21 mmol) were dissolved in DCM (6.0 ml) and COMU (138 mg, 0.31 mmol) was added at 0 °C. The reaction mixture was stirred at room temperature for 5 min and Hunig's base (0.10 mL 0.63 mmol) was added. The solution was stirred for 2 hours. The mixture was poured onto an aqueous sodium hydrogen carbonate (saturated, 20 ml) and water (20 ml). The mixture was stirred in an Erlenmeyer flask for 10 min. The aqueous layer was extracted with DCM. The organic layer was washed with brine and dried on MgSO4. It was concentrated under reduced pressure. The crude product was purified by flash (eluted with 10:90 to 75:25 EtOAc/ hexanes) to give the title compound 13 as a colorless solid (72 mg, 66%): [0362] ¹H NMR (400 MHz, DMSO) δ 11.60 (dd, J = 30.6, 2.3 Hz, 1H), 9.57 – 9.25 (m, 2H), 8.75 (d, J = 14.6 Hz, 1H), 8.30 – 8.21 (m, 1H), 8.07 (dd, J = 42.9, 8.5 Hz, 1H), 7.96-7.87 (m, 1H), 7.80 (q, J = 7.4 Hz, 1H), 7.14 (td, J = 7.9, 1.3 Hz, 1H), 7.06 (d, J = 8.2 Hz, 1H), 6.95 (dd, J = 4.4, 2.3 Hz, 1H), 6.85 (dd, J = 12.2, 7.6 Hz, 1H), 6.53 (d, J = 7.6 Hz, 1H), 4.64 – 4.47 (m, 1H), 3.89 (s, 3H), 3.84 (d, J = 8.7 Hz, 2H), 2.23 – 1.91 (m, 1H), 1.86 – 1.67 (m, 2H), 1.63 – 1.37 (m, 7H). ¹³C NMR (101 MHz, DMSO) δ 171.87, 161.05, 161.03, 154.65, 154.15, 141.90, 137.80, 132.71, 132.31, 129.46, 129.08, 128.64, 128.44, 125.29, 124.23, 123.99, 123.21, 122.82, 118.67, 118.63, 118.34, 118.21, 105.81, 103.12, 99.64, 61.34, 61.11, 60.48, 60.39, 55.40, 50.27, 50.23, 41.17, 41.03, 37.41, 35.64, 35.51, 24.84, 24.80.

[0363] Representative Synthetic Procedure IV

[0364] Scheme S4. The synthesis of compound 12. Reaction conditions: (a) methyl 2-((tert- butoxycarbonyl)amino)-2-(dimethoxyphosphoryl)acetate, DBU, DCM; (b) Pd/C, H₂, MeOH; (c) NH3 in MeOH, 70 °C; (d) cyanuric chloride, DMF, 0°C to RT; (e) TFA, DCM; (f) 2-(tert- butoxycarbonyl)-2-azaspiro[4.4]nonane-3-carboxylic acid, COMU, DIPEA, DCM, 0°C; (g) 2,2,2-TFE, TMS-Cl; (h) Intermediate B, COMU, DIPEA, DCM.

[0365] tert-butyl (1-amino-1-oxo-3-(2-oxo-1,2-dihydropyridin-3-yl)propan-2-yl)carbamate: [0366] Into a 60 mL sealed tube was placed a solution of methyl 2-((tert-butoxycarbonyl)amino)- 3-(2-oxo-1,2-dihydropyridin-3-yl)propanoate (1.5 g, 5.06 mmol) in NH3 in MeOH (30 mL). The resulting solution was stirred for 16 h at 70 °C. The reaction was concentrated under vacuum and the obtained crude material was crystallized by hexane and pentane to afford 1.1 g (63.32%) of tert-butyl (1-amino-1-oxo-3-(2-oxo-1,2-dihydropyridin-3-yl)propan-2-yl)carbamate as a white solid.¹H NMR (400 MHz, DMSO) δ 7.40 – 7.12 (m, 3H), 7.03 (d, J = 7.8 Hz, 1H), 6.94 (s, 1H), 6.13 (t, J = 6.6 Hz, 1H), 4.05 (td, J = 8.7, 4.3 Hz, 1H), 2.79 (dd, J = 13.8, 4.2 Hz, 1H), 2.57 (dd, 6

J = 13.7, 9.5 Hz, 1H), 1.33 (s, 9H). ¹³C NMR (101 MHz, DMSO) δ 174.05, 163.61, 155.63, 139.72, 134.01, 129.07, 105.50, 78.34, 54.71, 33.33, 28.62.

[0367] tert-butyl (1-cyano-2-(2-oxo-1,2-dihydropyridin-3-yl)ethyl)carbamate: [0368] To a solution of tert-butyl (1-amino-1-oxo-3-(2-oxo-1,2-dihydropyridin-3-yl)propan-2- yl)carbamate (1.0 g, 3.55 mmol) in DMF (anhydrous, 15 mL) was added 2,4,6-trichloro-1,3,5- triazine (980 mg, 5.31 mmol) at 0°C. The reaction was stirred at room temperature for 2 hrs. The reaction was poured into water (30 mL), and the mixture was extracted with ethyl acetate (25 mL*3). The combined organic layers were washed with water and brine, dried over Na2SO4, filtered, and concentrated to give a residue, which was purified by silica gel chromatography (Dichloromethane: MeOH = 10: 1) to give tert-butyl (1-cyano-2-(2-oxo-1,2-dihydropyridin-3- yl)ethyl)carbamate (0.62 g, 66 % yield) as a colorless solid. [0369] ¹H NMR (400 MHz, DMSO) δ 7.83 (d, J = 7.9 Hz, 1H), 7.42-7.33 (m, 2H), 6.20 (t, J = 6.6 Hz, 1H), 4.80 (q, J = 7.6 Hz, 1H), 2.89 – 2.75 (m, 2H), 1.38 (s, 9H). ¹³C NMR (101 MHz, DMSO) δ 155.10, 150.39, 141.17, 135.05, 126.18, 119.86, 105.52, 79.77, 49.06, 34.20, 28.46.

[0370] tert-butyl-3-((1-cyano-2-(2-oxo-1,2-dihydropyridin-3-yl)ethyl)carbamoyl)-2- azaspiro[4.4]nonane-2-carboxylate: [0371] A solution of TFA (1 ml) was added to a solution of tert-butyl (1-cyano-2-(2-oxo-1,2- dihydropyridin-3-yl)ethyl)carbamate (350 mg, 1.33 mmol) in dichloromethane (10 ml), and the reaction mixture was stirred at 25 °C for 6 h. Removal of solvents afforded TFA salt of 2-amino- 3-(2-oxo-1,2-dihydropyridin-3-yl)propanenitrile as a white solid (250 mg). This material was used directly in the following step. 2-(tert-butoxycarbonyl)-2-azaspiro[4.4]nonane-3-carboxylic acid (160 mg, 0.59 mmol) and 2-amino-3-(2-oxo-1,2-dihydropyridin-3-yl)propanenitrile (230 mg, 0.88 mmol) were dissolved in DCM (6.0 ml) and COMU (380 mg, 0.88 mmol) was added at 0 °C. The reaction mixture was stirred at room temperature for 5 min and Hunig's base (DIPEA) (0.50 mL 2.95 mmol) was added. The solution was stirred for 2 hours. The mixture was poured onto an aqueous sodium hydrogen carbonate (saturated, 20 ml) and water (20 ml). The mixture was stirred in an Erlenmeyer flask for 10 min. The aqueous layer was extracted with DCM. The 7

organic layer was washed with brine and dried on MgSO4. It was concentrated to give a residue, which was purified by silica gel chromatography (Dichloromethane: MeOH = 10: 1) to give tert- butyl-3-((1-cyano-2-(2-oxo-1,2-dihydropyridin-3-yl)ethyl)carbamoyl)-2-azaspiro[4.4]nonane-2- carboxylate (0.14 g, 56 % yield) as a colorless solid. ¹H NMR (400 MHz, DMSO) δ 11.71 (s, 1H), 8.52 (dd, J = 45.1, 6.9 Hz, 1H), 7.34 (dd, J = 37.5, 6.5 Hz, 2H), 6.23 – 6.04 (m, 1H), 4.85 – 4.62 (m, 2H), 4.11 – 3.92 (m, 1H), 3.26 (d, J = 10.5 Hz, 1H), 3.15 – 3.03 (m, 1H), 2.93 (ddd, J = 13.3, 8.4, 4.9 Hz, 1H), 2.74 – 2.64 (m, 1H), 2.10 – 1.94 (m, 1H), 1.68 – 1.47 (m, 6H), 1.30 (dd, J = 50.3, 20.2 Hz, 11H).

[0372] Compound 12 [0373] N-(1-cyano-2-(2-oxo-1,2-dihydropyridin-3-yl)ethyl)-2-(4-methoxy-1H-indole-2- carbonyl)-2-azaspiro[4.4]nonane-3-carboxamide: [0374] tert-butyl-3-((1-cyano-2-(2-oxo-1,2-dihydropyridin-3-yl)ethyl)carbamoyl)-2- azaspiro[4.4]nonane-2-carboxylate (130 mg, 0.31mmol) dissolved in anhydrous trifluoroethanol (5 mL). The stirred solution is cooled in an ice bath and TMSCl (0.2 mL) is added dropwise. The mixture is at the same temperature until the reaction completion. After completion removes solvent by rotavapor, and crude N-(1-cyano-2-(2-oxo-1,2-dihydropyridin-3-yl)ethyl)-2- azaspiro[4.4]nonane-3-carboxamide directly used for the next step. 4-methoxy-1H-indole-2- carboxylic acid Intermediate B (40 mg, 0.20 mmol) and N-(1-cyano-2-(2-oxo-1,2- dihydropyridin-3-yl)ethyl)-2-azaspiro[4.4]nonane-3-carboxamide (80 mg, 0.24 mmol) were dissolved in DCM (6.0 ml) and COMU (134 mg, 0.30 mmol) was added at 0 °C. The reaction mixture was stirred at room temperature for 5 min and Hunig's base (0.10 mL 0.60 mmol) was added. The solution was stirred for 2 hours. The mixture was poured onto an aqueous sodium hydrogen carbonate (saturated, 20 ml) and water (20 ml). The mixture was stirred in an Erlenmeyer flask for 10 min. The aqueous layer was extracted with DCM. The organic layer was washed with brine and dried on MgSO4. It was concentrated to give a residue, which was purified by silica gel chromatography (Dichloromethane: MeOH = 10: 1) to give Compound 12 (17 mg, 17 % yield) as a colorless solid. [0375] ¹H NMR (400 MHz, DMSO) δ 11.76 – 11.30 (m, 2H), 8.56 (dd, J = 43.1, 6.9 Hz, 1H), 7.19 (d, J = 6.7 Hz, 1H), 7.05 (q, J = 7.1 Hz, 1H), 6.97 (d, J = 8.3 Hz, 1H), 6.88 (d, J = 2.2 Hz, 1H), 6.45 (d, J = 7.6 Hz, 1H), 5.93 (t, J = 6.6 Hz, 1H), 4.65 (q, J = 9.1 Hz, 2H), 4.55 – 4.37 (m, 71

2H), 3.78 (d, J = 34.1 Hz, 4H), 2.91 (dd, J = 13.4, 4.6 Hz, 1H), 2.58 (dd, J = 13.5, 8.6 Hz, 1H), 1.97 (dd, J = 12.4, 7.8 Hz, 1H), 1.70 – 1.31 (m, 8H), 1.23 – 1.14 (m, 1H). [0376] Representative Synthetic Procedure V

[0377] Scheme S5. The synthesis of compounds 7 and 8. Reaction conditions: (a) 2-amino-2- (5-chloropyridin-3-yl)acetonitrile, COMU, DIPEA, DCM; (b) 2-amino-2-(isoquinolin-4- yl)acetonitrile, COMU, DIPEA, DCM.

[0378] Compound 7 [0379] (1R,2S,5S)-3-(O-(tert-butyl)-N-(2,2,2-trifluoroacetyl)-L-threonyl)-N-((5- chloropyridin-3-yl)(cyano)methyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2- carboxamide: [0380] ¹H NMR (400 MHz, CDCl₃) δ 8.55 (ddd, J = 15.7, 13.1, 2.1 Hz, 2H), 7.74 (dt, J = 4.3, 2.2 Hz, 1.55H), 7.54 (d, J = 8.7 Hz, 0.45H), 7.10 (d, J = 7.1 Hz, 0.55H), 6.97 (d, J = 7.2 Hz, 0.45H), 6.31 (d, J = 8.8 Hz, 0.45H), 6.18 (d, J = 8.2 Hz, 0.55H), 4.57 (d, J = 6.1 Hz, 2H), 3.99 (dp, J = 34.8, 5.9 Hz, 2H), 3.63 (d, J = 10.5 Hz, 1H), 1.66 (d, J = 7.5 Hz, 0.45H), 1.59 (d, J = 7.4 Hz, 0.55H), 1.49 (dt, J = 7.5, 5.6 Hz, 1H), 1.19 (s, 4H), 1.10 (s, 5H), 1.04 (dd, J = 10.6, 5.8 Hz, 4.7H), 0.85 (d, J = 6.8 Hz, 3H), 0.56 (d, J = 6.4 Hz, 1.3H) 7

[0381] Compound 8 [0382] (1R,2S,5S)-3-(O-(tert-butyl)-N-(2,2,2-trifluoroacetyl)-L-threonyl)-N- (cyano(isoquinolin-4-yl)methyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide: [0383] ¹H NMR (400 MHz, CDCl3) δ 9.25 (s, 1H), 8.81 (d, J = 61.0 Hz, 1H), 8.07 – 7.94 (m, 1H), 7.93 – 7.63 (m, 3.5H), 7.53 (d, J = 9.0 Hz, 0.5H), 7.15 (d, J = 7.2 Hz, 0.5H), 6.89 (d, J = 9.0 Hz, 0.5H), 6.73 (dd, J = 8.0, 3.5 Hz, 1H), 4.57 (d, J = 1.4 Hz, 1H), 4.52 – 4.35 (m, 1H), 4.07 – 3.86 (m, 2H), 3.76 – 3.65 (m, 1H), 3.55 (dd, J = 10.8, 4.8 Hz, 1H), 1.66 (dd, J = 41.3, 7.5 Hz, 1H), 1.50 – 1.37 (m, 1H), 1.15 (s, 4H), 1.02 (d, J = 14.6 Hz, 3H), 0.92 (d, J = 5.8 Hz, 7H), 0.82 (d, J = 8.8 Hz, 3H), -0.35 (d, J = 6.4 Hz, 1H). [0384] Representative Synthetic Procedure VI

[0385] Scheme S6. The synthesis of compound 11. Reaction conditions: (a) 2-amino-2-(5- chloropyridin-3-yl)acetonitrile, COMU, DIPEA, DCM, 0°C; (b) 2,2,2-TFE, TMS-Cl; (c) Intermediate B, COMU, DIPEA, DCM.

[0386] tert-butyl 3-(((5-chloropyridin-3-yl)(cyano)methyl)carbamoyl)-2- azaspiro[4.4]nonane-2-carboxylate (31): [0387] ¹H NMR (400 MHz, CDCl3) δ 8.59 – 8.48 (m, 2H), 7.78 (t, J = 2.1 Hz, 1H), 6.13 (s, 1H), 4.38 – 4.20 (m, 1H), 3.44 – 3.15 (m, 1H), 3.13 – 2.97 (m, 1H), 1.70 – 1.15 (m, 14H).

[0388] Compound 11 [0389] N-((5-chloropyridin-3-yl)(cyano)methyl)-2-(4-methoxy-1H-indole-2-carbonyl)-2- azaspiro[4.4]nonane-3-carboxamide: [0390] ¹H NMR (400 MHz, DMSO) δ 11.59 (dd, J = 9.2, 2.3 Hz, 1H), 9.46 (dd, J = 28.7, 8.0 Hz, 1H), 8.76 – 8.51 (m, 2H), 7.98 (dt, J = 19.6, 2.3 Hz, 1H), 7.13 (td, J = 7.9, 1.5 Hz, 1H), 7.08 – 7.02 (m, 1H), 6.96 (t, J = 2.5 Hz, 1H), 6.53 (d, J = 7.6 Hz, 1H), 6.38 (dd, J = 8.0, 4.5 Hz, 1H), 4.56 (td, J = 8.3, 2.8 Hz, 1H), 3.89 (s, 3H), 3.85 (d, J = 2.6 Hz, 2H), 2.17 (dt, J = 12.1, 7.7 Hz, 1H), 1.88 – 1.73 (m, 2H), 1.66 – 1.42 (m, 7H). [0391] Representative Synthetic Procedure VII

[0392] Scheme S7. The synthesis of compound 25. Reaction conditions: 2-amino-2-(7- fluoroisoquinolin-4-yl)acetonitrile, COMU, DIPEA, DCM.

[0393] Compound 25 [0394] (3S)-N-(cyano(7-fluoroisoquinolin-4-yl)methyl)-2-((S)-3,3-dimethyl-2-(2,2,2- trifluoroacetamido)butanoyl)-2-azaspiro[4.4]nonane-3-carboxamide: [0395] ¹H NMR (400 MHz, DMSO) δ 9.49 – 9.29 (m, 2H), 9.25 – 9.10 (m, 1H), 8.64 (d, J = 16.3 Hz, 1H), 8.10 – 7.92 (m, 2H), 7.81 (td, J = 8.9, 2.7 Hz, 0.5H), 7.65 (td, J = 9.0, 2.8 Hz, 0.5H), 6.84 (dd, J = 8.0, 6.1 Hz, 1H), 4.40 (d, J = 7.6 Hz, 1H), 4.25 – 4.10 (m, 1H), 3.69 – 3.59 (m, 1H), 7 3.35 – 3.31 (m, 1H), 2.04 – 1.90 (m, 0.5H), 1.83 (dd, J = 12.1, 7.7 Hz, 0.5H), 1.73 (dd, J = 12.1, 9.6 Hz, 0.5H), 1.62 – 1.36 (m, 5.5H), 1.29 – 1.15 (m, 3H), 0.93 (d, J = 16.8 Hz, 9H). [0396] Representative Synthetic Procedure VIII

[0397] Scheme S8. The synthesis of compound 26. Reaction conditions: 2-amino-2-(7- fluoroisoquinolin-4-yl)acetonitrile, COMU, DIPEA, DCM.

[0398] Compound 26 [0399] (8S)-N-(cyano(7-fluoroisoquinolin-4-yl)methyl)-7-((S)-3,3-dimethyl-2-(2,2,2- trifluoroacetamido)butanoyl)-1,4-dithia-7-azaspiro[4.4]nonane-8-carboxamide: [0400] ¹H NMR (400 MHz, DMSO) δ 9.61 – 9.37 (m, 1H), 9.37 – 9.24 (m, 2H), 8.64 (d, J = 15.1 Hz, 1H), 8.13 – 7.92 (m, 2H), 7.85 – 7.60 (m, 1H), 6.84 (t, J = 7.6 Hz, 1H), 4.44 (d, J = 8.5 Hz, 1H), 4.36 – 4.19 (m, 1H), 4.11 (t, J = 9.9 Hz, 1H), 3.87 (dd, J = 11.0, 5.2 Hz, 1H), 3.39 – 3.27 (m, 2H), 2.62 – 2.50 (m, 1H), 2.32 – 2.13 (m, 1H), 0.89 (d, J = 19.7 Hz, 9H). [0401] Representative Synthetic Procedure IX

[0402] Scheme S9. The synthesis of compounds 27, 28, and 41. Reaction conditions: (a) 2- amino-2-(2,7-naphthyridin-4-yl)acetonitrile, COMU, DIPEA, DCM; (b) 2 2-amino-2-(1,6- naphthyridin-8-yl)acetonitrile, COMU, DIPEA, DCM; (c) 2-amino-2-(2-oxo-1,2- dihydroquinolin-4-yl)acetonitrile, COMU, DIPEA, DCM.

[0403] Compound 27 [0404] (1R,2S,5S)-N-(cyano(2,7-naphthyridin-4-yl)methyl)-3-((S)-3,3-dimethyl-2-(2,2,2- trifluoroacetamido)butanoyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide: [0405] 'H NMR (400 MHz, DMSO) 9.65 - 9.50 (m, 2H), 9.32 - 9.19 (m, 1H), 8.90- 8.50 (m, 2H), 8.02 - 7.91 (m, 1H), 6.53 - 6.38 (m, 2H), 4.94 (s, 1H), 4.51 (s, 1H), 4.03 - 3.95 (m, 1H), 3.88 (m, 1H), 1.71 - 1.52 (m, 2H), 1.07 - 1.04 (m, 3H), 1.02 (s, 9H), 0.92 - 0.90 (m, 3H).

[0406] Compound 28 [0407] (1R,2S,5S)-N-(cyano(1,6-naphthyridin-8-yl)methyl)-3-((S)-3,3-dimethyl-2-(2,2,2- trifluoroacetamido)butanoyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide: [0408] ¹H NMR (400 MHz, DMSO) δ 9.71 – 9.49 (m, 2H), 9.49 – 9.38 (m, 1H), 9.36 – 9.27 (m, 1H), 9.01 (d, J = 8.1 Hz, 1H), 8.79-8.74 (m, 1H), 7.94-7.98 (m, 1H), 6.94-6.86 (m, 1H), 4.51 – 4.36 (m, 2H), 3.98-3.92 (m, 1H), 3.80-3.73 (m, 1H), 1.67 – 1.56 (m, 1H), 1.51 – 1.29 (m, 1H), 1.12 – 1.01 (m, 8H), 0.96 – 0.88 (m, 7H).

[0409] Compound 41 [0410] (1R,2S,5S)-N-(cyano(2-oxo-1,2-dihydroquinolin-4-yl)methyl)-3-((S)-3,3-dimethyl-2- (2,2,2-trifluoroacetamido)butanoyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2- carboxamide: [0411] ¹H NMR (400 MHz, DMSO) δ 12.00 (d, J = 8.8 Hz, 1H), 9.56 (dd, J = 44.0, 8.2 Hz, 1H), 9.39 (dd, J = 8.3, 4.7 Hz, 1H), 7.66 – 7.50 (m, 2H), 7.38 (t, J = 7.0 Hz, 1H), 7.26 – 7.09 (m, 1H), 6.77 – 6.65 (m, 2H), 4.40 (dd, J = 8.3, 3.6 Hz, 1H), 4.24 (d, J = 9.2 Hz, 1H), 3.94 (dd, J = 10.3, 5.5 Hz, 1H), 3.71 (t, J = 10.6 Hz, 1H), 1.59 (dt, J = 11.8, 6.7 Hz, 1H), 1.38 – 1.27 (m, 1H), 1.08 – 0.92 (m, 12H), 0.83 (d, J = 6.4 Hz, 3H). [0412] Biological Examples [0413] M^Pro Expression and Purification. [0414] The expression plasmid pET28a-His-SUMO-M^Pro was constructed and used to transform E. coli BL21(DE3) cells. A single colony grown on a LB plate containing 50 µg/mL kanamycin was picked and grown in 5 mL LB media supplemented with 50 µg/mL kanamycin overnight. This overnight culture was inoculated to 6 L 2YT media with 50 µg/mL kanamycin. Cells were grown to OD₆₀₀ as 0.8. At this point, 1 mM IPTG was added to induce the expression of His- 7 SUMO-M^Pro. Induced cells were let grown for 3 h and then harvested by centrifugation at 12,000 rpm, 4 °C for 30 min. Cell pellets we resuspended in 150 mL lysis buffer (20 mM Tris-HCl, 100 mM NaCl, 10 mM imidazole, pH 8.0) and lysed the cells by sonication on ice. The lysate was clarified by centrifugation at 16,000 rpm, 4 °C for 30 min. The supernatant was decantedand mixed with Ni-NTA resins (GenScript). The resins were loaded to a column, washed the resins with 10 volumes of lysis buffer, and eluted the bound protein using elution buffer (20 mM Tris- HCl, 100 mM NaCl, 250 mM imidazole, pH 8.0). Buffer of the elute was exchanged to another buffer (20 mM Tris-HCl, 100 mM NaCl, 10 mM imidazole, 1 mM DTT, pH 8.0) using a HiPrep 26/10 desalting column (Cytiva) and digested the elute using 10 units SUMO protease overnight at 4 °C. The digested elute was subjected to Ni-NTA resins in a column to remove His-tagged SUMO protease, His-tagged SUMO tag, and undigested His-SUMO-M^Pro. The flow-through was loaded onto a Q-Sepharose column and purified M^Pro using FPLC by running a linear gradient from 0 to 500 mM NaCl in a buffer (20 mM Tris-HCl, 1 mM DTT, pH 8.0). Fractions eluted from the Q-Sepharose column was concentrated and loaded onto a HiPrep 16/60 Sephacryl S-100 HR column and purified using a buffer containing 20 mM Tris-HCl, 100 mM NaCl, 1 mM DTT, and 1 mM EDTA at pH 7.8. The final purified was concentrated and stored in a -80 °C freezer. [0415] In Vitro M^Pro Inhibition Potency Characterizations. [0416] The assay was conducted using 20 nM M^Pro and 10 µM Sub3. For all synthesized compounds, 10 nM M^Pro was used. All compounds are dissolved in DMSO as 10 mM stock solutions. Sub3 is dissolved in DMSO as a 1 mM stock solution and diluted 100 times in the final assay buffer containing 10 mM NaxHyPO4, 10 mM NaCl, 0.5 mM EDTA, and 1.25% DMSO at pH 7.6. M^Pro and the compounds are incubated in the final assay buffer for 30 min before adding the substrate to initiate the reaction catalyzed by M^Pro. The production format is monitored in a fluorescence plate reader with excitation at 336 nm and emission at 455 nm. [0417] In cellulo M^Pro Inhibition Potency Characterizations. [0418] HEK 293T/17 cells are grown in high-glucose DMEM with GlutaMAX supplement and 10% FBS in 10 cm culture plates under 37 °C and 5% CO2 to 80-90% confluency and then transfected cells with the pLVX-M^Pro-eGFP-2 plasmid. 30 mg/mL polyethyleneimine and the total of 8 µg of the plasmid in 500 µL opti-MEM media are used for transfection. Transfected cells are incubated overnight. On the second day, cells are collected using 0.05% trypsin-EDTA to detach them from plates, resuspended collected cells in the original growth media, adjusted the cell density to 5x10⁵ cells/mL, added 500 µL adjusted cells to each well of a 48-well plate, and then added 100 µL of a drug solution in DMEM. Treated cells are incubated under 37 °C and 5% CO₂ for 72 h. After 72 h incubation, cells are collected using trypsinization and centrifugation.

Collected cells are resuspended in 200 µL PBS and analyzed cells with fluorescence using a Cytoflex Research Flow Cytometer based on the size scatters (SSC-A and SSC-H) and forward scatter (FSC-A). Cells are gated based on SSC-A and FSC-A then with SSC-A and SSC-H. Fluorescence is detected with excitation at 488 nm and emission at 525 nm. All collected data are converted to csv files and analyzed using a self-prepared MATLAB script for massive data processing. The FITC-A column is sorted from lowest to highest. A 10⁶ cutoff is set to separate the column to two groups with higher than 10⁶ as positive and lower than 10⁶ as negative. The positive group is integrated and divided the total integrated fluorescence intensity by the total cell positive cell counts. The standard deviation of positive fluorescence is calculated as well. All processed data are plotted and fitted to a four-parameter Hill equation in GraphPad 9.0 to obtain determined EC50 values. [0419] Cell-based Assay for SARS-CoV-2 Inhibition Potency Characterizations. [0420] A slightly modified cytopathic effect (CPE)-based microneutralization assay is used to evaluate the drug efficacy against SARS-CoV-2 infection. Briefly, confluent african green monkey kidney cells (Vero E6) or human alveolar epithelial A549 cells stably expressing human ACE2 viral receptor, designated A549/hACE2, grown in 96-wells microtiter plates are pre-treated with serially 2-folds diluted individual drugs for two hours before infection with 100 or 500 infectious SARS-CoV-2 (USA-WA1/2020) particles in 100 μl EMEM supplemented with 2% FBS, respectively. Cells pre-treated with parallelly diluted dimethyl sulfoxide (DMSO) with or without virus are included as positive and negative controls, respectively. After cultivation at 37 °C for 3 days, individual wells are observed under the microcopy for the status of virus-induced formation of CPE. The efficacy of individual drugs is calculated and expressed as the lowest concentration capable of completely preventing virus-induced CPE in 100% (EC100) or 50% (EC50) of the wells. All compounds are dissolved in 100% DMSO as 10 mM stock solutions before subjecting to dilutions with culture media. [0421] The following represent biological data of compounds of the Formula I: [0422] Table C:

79

8

[0423] In vivo efficacy of compounds 16 and 17 in SARS-CoV-2 infection in mice.Groups (n=5 per group) of 8- to 10-week-old Balb/c mice were intranasally infected with 10⁴ PFU mouse-adapted SARS-CoV-2 CMA3P20. At 0, 12, 24, and 36 hours post-infection, each group of mice was treated with vehicle (comprising DMSO/PEG400/deionized water at ratio 10/30/60, v/v/v), nirmatrelvir (100 mg/kg), and selected compounds (100 mg/kg) (compounds 16 and 17), respectively. At 48 h post-infection, the mice were euthanized, and lung tissues were harvested. Viral loads in the lung were quantified by a plaque assay. [0424] A comparative in vivo efficacy study involving nirmatrelvir abd selected compounds (compounds 16 and 17) was carried out. When administered orally at a dosage of 100 mg/kg, compared to the vehicle control, compounds 16 and 17 markedly reduced the viral load in the lungs of infected hACE2+ mice, approximately by a factor of 120 and 74, respectively. In contrast, nirmatrelvir only lowered the viral load by roughly threefold. Hence, compounds 16 and 17 demonstrated markedly superior in vivo potency compared to nirmatrelvir in animal studies. In addition, histochemistry analysis shows that compound 16 reduces the lung tissue damage on day 2 post-infection.100 mg/kg compound 16 treatment worked as well when the treatment started at 6 h and 12 h post-infection.

Claims

WHAT IS CLAIMED IS: 1. A compound of Formula I

or a pharmaceutically acceptable salt thereof, wherein X is -N(R⁵)- or -O-; W is C1-C6 alkyl-(5-10 membered heteroaryl) or –NR⁶R⁷, wherein each hydrogen atom in C1-C6 alkyl is independently optionally substituted by an R^c and each hydrogen atom in (5-10 membered heteroaryl) is independently optionally substituted by an R^d; R¹ is C1-C6 alkyl, 5-10 membered heteroaryl, -NR⁸R⁹, or -C1-C6 alkyl-NR⁸R⁹, wherein each hydrogen atom in C1-C6 alkyl and 5-10 membered heteroaryl is independently optionally substituted by an R^a; each of R², R⁵, R¹⁰, and R¹¹ is independently H, deuterium, or C1-C6 alkyl; each of R³ and R⁴ is independently H, deuterium, C₁-C₆ alkyl, C₂-C₆ alkenyl, C₆-C₁₀ aryl, or C3-C8 cycloalkyl, wherein each hydrogen atom in C1-C6 alkyl, C2-C6 alkenyl, C6-C10 aryl, and C₃-C₈ cycloalkyl is independently optionally substituted by an R^b; each of R⁶, R⁷, R⁸, and R⁹ is independently H, deuterium, C1-C6 alkyl, C2-C6 alkenyl, C₃-C₈ cycloalkyl, -C(O)C₁-C₆ alkyl, -C₁-C₆ alkyl-C(O)NR¹⁰R¹¹, or -C₁-C₆ alkyl-C(O)OH, wherein each hydrogen atom in C1-C6 alkyl, C2-C6 alkenyl, and C3-C8 cycloalkyl is independently optionally substituted by R^e; each of R^a, R^b, R^c, R^d, and R^e, when present, is independently deuterium, halo, -CN, -OH, -NR⁸R⁹, -NR⁸C(O)C₁-C₆ alkyl, C₁-C₆ alkyl, C₂-C₆ alkenyl, C₃-C₈ cycloalkyl, C₁-C₆ alkoxy, C₆- C10 aryl, or 5-10 membered heteroaryl, wherein each hydrogen atom in C1-C6 alkyl, C2-C6 alkenyl, C₃-C₈ cycloalkyl, C₁-C₆ alkoxy, C₆-C₁₀ aryl, and 5-10 membered heteroaryl is independently optionally substituted by deuterium, halo, OH, -NH2, C1-C6 alkyl, C2-C6 alkenyl, C₁-C₆ alkoxy, 5-10 membered heteroaryl, C₆-C₁₀ aryl, C₂-C₆ alkenyl, or C₃-C₈ cycloalkyl; each R^f, when present, is independently deuterium, halo, -OH, -NR⁸R⁹, -NR¹⁰C(O)C1-C6 alkyl, C₁-C₆ alkyl, C₂-C₆ alkenyl, C₁-C₆ alkoxy,

3-to 7-membered heterocycloalkyl, or C₃-C₈ cycloalkyl, wherein each hydrogen atom in C1-C6 alkyl, C2-C6 alkenyl, C1-C6 alkoxy or C3-C8 cycloalkyl is independently optionally substituted by deuterium, halo, -OH, -NR⁸R⁹, or C₁-C₆ alkyl; or two R^f combine together with the atom or atoms to which they are attached to form a C₃-C₈ cycloalkyl, wherein each hydrogen atom in C₃-C₈ cycloalkyl and 3-to 7-membered 8

heterocycloalkyl is independently optionally substituted by deuterium, halo, -OH, -NR⁸R⁹, C1-C6 alkyl, C₂-C₆ alkenyl, or C₁-C₆ alkoxy; n is 0 or 1; and m is 0, 1, 2, or 3; provided that when W is –NR⁶R⁷, then X is -N(R⁵)- and R¹ is CF3. 2. A compound of Formula I

or a pharmaceutically acceptable salt thereof, wherein X is -N(R⁵)- or -O-; W is C1-C6 alkyl-(5-10 membered heteroaryl) or –NR⁶R⁷, wherein each hydrogen atom in C₁-C₆ alkyl is independently optionally substituted by an R^c and each hydrogen atom in (5-10 membered heteroaryl) is independently optionally substituted by an R^d; R¹ is C₁-C₆ alkyl, 5-10 membered heteroaryl, -NR⁸R⁹, or -C₁-C₆ alkyl-NR⁸R⁹, wherein each hydrogen atom in C1-C6 alkyl and 5-10 membered heteroaryl is independently optionally substituted by an R^a; each of R², R⁵, R¹⁰, and R¹¹ is independently H, deuterium, or C1-C6 alkyl; each of R³ and R⁴ is independently H, deuterium, C₁-C₆ alkyl, C₂-C₆ alkenyl, C₆-C₁₀ aryl, or C3-C8 cycloalkyl, wherein each hydrogen atom in C1-C6 alkyl, C2-C6 alkenyl, C6-C10 aryl, and C₃-C₈ cycloalkyl is independently optionally substituted by an R^b; each of R⁶, R⁷, R⁸, and R⁹ is independently H, deuterium, C1-C6 alkyl, C2-C6 alkenyl, C₃-C₈ cycloalkyl, -C(O)C₁-C₆ alkyl, -C₁-C₆ alkyl-C(O)NR¹⁰R¹¹, or -C₁-C₆ alkyl-C(O)OH, wherein each hydrogen atom in C1-C6 alkyl, C2-C6 alkenyl, and C3-C8 cycloalkyl is independently optionally substituted by R^e; each of R^a, R^b, R^c, R^d, and R^e, when present, is independently deuterium, halo, -CN, -OH, -NR⁸R⁹, -NR⁸C(O)C₁-C₆ alkyl, C₁-C₆ alkyl, C₂-C₆ alkenyl, C₃-C₈ cycloalkyl, C₁-C₆ alkoxy, C₆- C10 aryl, or 5-10 membered heteroaryl, wherein each hydrogen atom in C1-C6 alkyl, C2-C6 alkenyl, C₃-C₈ cycloalkyl, C₁-C₆ alkoxy, C₆-C₁₀ aryl, and 5-10 membered heteroaryl is independently optionally substituted by deuterium, halo, OH, -NH2, C1-C6 alkyl, C2-C6 alkenyl, C₁-C₆ alkoxy, 5-10 membered heteroaryl, C₆-C₁₀ aryl, C₂-C₆ alkenyl, or C₃-C₈ cycloalkyl; each R^f, when present, is independently deuterium, halo, -OH, -NR⁸R⁹, -NR¹⁰C(O)C1-C6 alkyl, C₁-C₆ alkyl, C₂-C₆ alkenyl, C₁-C₆ alkoxy or C₃-C₈ cycloalkyl, wherein each hydrogen atom 8 in C1-C6 alkyl, C2-C6 alkenyl, C1-C6 alkoxy or C3-C8 cycloalkyl is independently optionally substituted by deuterium, halo, -OH, -NR⁸R⁹, or C₁-C₆ alkyl; or two R^f combine together with the atom or atoms to which they are attached to form a C3-C8 cycloalkyl, wherein each hydrogen atom in C₃-C₈ cycloalkyl is independently optionally substituted by deuterium, halo, -OH, - NR⁸R⁹, C1-C6 alkyl, C2-C6 alkenyl, or C1-C6 alkoxy; n is 0 or 1; and m is 0, 1, 2, or 3; provided that when W is –NR⁶R⁷, then X is -N(R⁵)- and R¹ is CF_3. 3. The compound or pharmaceutically acceptable salt of claim 1 or 2, wherein W is C₁-C₆ alkyl-(5-10 membered heteroaryl), wherein each hydrogen atom in C₁-C₆ alkyl is independently optionally substituted by an R^c and each hydrogen atom in (5-10 membered heteroaryl) is independently optionally substituted by an R^d.

4. The compound or pharmaceutically acceptable salt of any one of claims 1-3, wherein X is -N(R⁵)-.

5. The compound or pharmaceutically acceptable salt of any one of claims 1-3, wherein X is -O-.

6. The compound or pharmaceutically acceptable salt of any one of the preceding claims, wherein W is C₁-C₆ alkyl-(5-10 membered heteroaryl), and one hydrogen atom in C₁-C₆ alkyl is substituted with an R^c.

7. The compound or pharmaceutically acceptable salt of any one of the preceding claims, wherein R^c, when present, is –CN.

8. The compound or pharmaceutically acceptable salt of any one of the preceding claims, wherein W is C1-C6 alkyl-(5-10 membered heteroaryl), and 5-10 membered heteroaryl is selected from

9. The compound or pharmaceutically acceptable salt of any one of the preceding claims, wherein R^d, when present, is halo, -NHC(O)C₁-C₆ alkyl, or C₁-C₆ alkoxy, wherein each hydrogen atom in C1-C6 alkyl or C1-C6 alkoxy is independently optionally substituted by halo.

10. The compound or pharmaceutically acceptable salt of any one of the preceding claims, wherein R^d, when present, is fluoro or chloro.

11. The compound or pharmaceutically acceptable salt of any one of the preceding claims, wherein R^d, when present, is fluoro, -NHC(O)CF3, or OMe.

12. The compound or pharmaceutically acceptable salt of claim 1 or 2, wherein W is -NR⁶R⁷.

13. The compound or pharmaceutically acceptable salt of any one of claims 1, 2, and 12, wherein one of R⁶ and R⁷ is -C(O)C1-C6 alkyl, and one of R⁶ and R⁷ is -C1-C6 alkyl- C(O)NR¹⁰R¹¹, wherein each hydrogen atom in C₁-C₆ alkyl is independently optionally substituted by R^e.

14. The compound or pharmaceutically acceptable salt of any one of claims 1, 2, and 12-13, wherein one of R⁶ and R⁷ is –C(O)CHCl2.

15. The compound or pharmaceutically acceptable salt of any one of claims 1, 2, and 12-14, wherein one of R⁶ and R⁷ is is –CH2CH2C(O)NH2.

16. The compound or pharmaceutically acceptable salt of any one of the preceding claims, wherein n is 0.

17. The compound or pharmaceutically acceptable salt of any one of the preceding claims, wherein R¹ is 5-10 membered heteroaryl, wherein each hydrogen atom in 5-10 membered heteroaryl is independently optionally substituted by an R^a.

18. The compound or pharmaceutically acceptable salt of any one of the preceding claims, wherein R¹ is

, wherein p is 0, 1, 2, or 3.

19. The compound or pharmaceutically acceptable salt of claim 18, wherein p is 1.

20. The compound or pharmaceutically acceptable salt of any one of the preceding claims, wherein each R^a, when present, is independently deuterium, halo, -CN, -OH, -NR⁸R⁹, C₁-C₆ alkyl, or C₁-C₆ alkoxy.

21. The compound or pharmaceutically acceptable salt of any one of the preceding claims, wherein R^a, when present, is -OCH₃.

22. The compound or pharmaceutically acceptable salt of any one of claims 1 to 16, wherein R¹ is -CF₃. 8

23. The compound or pharmaceutically acceptable salt of claim 1 or 2, wherein the compound is of formula

.

24. The compound or pharmaceutically acceptable salt of any one of claims 1 to 15, wherein n is 1.

25. The compound or pharmaceutically acceptable salt of claim 1 or 2, wherein the compound is of formula

.

26. The compound or pharmaceutically acceptable of claim 1 or 2, wherein the compound is of formula

.

27. The compound or pharmaceutically acceptable salt of any one of the preceding claims, wherein R², when present, is H.

28. The compound or pharmaceutically acceptable salt of any one of the preceding claims, wherein R⁵, when present, is H.

29. The compound or pharmaceutically acceptable salt of any one of claims 1-15, wherein n is 1, one of R³ and R⁴ is H, and one of R³ and R⁴ is C1-C6 alkyl.

30. The compound or pharmaceutically acceptable salt of any one of claims 1-15 and 29, wherein one of R³ and R⁴ is H, and one of R³ and R⁴ is t-butoxy-ethyl or t-butyl.

31. The compound or pharmaceutically acceptable salt of any one of the preceding claims, wherein m is 2, and two R^f combine together with the atom or atoms to which they are attached to form a C₃-C₈ cycloalkyl.

32. The compound or pharmaceutically acceptable salt of any one of claims 1-31, wherein m is 2, and two R^f combine to form C₃-C₈ cycloalkyl substituted with one or more methyl or halo. 8

33. The compound or pharmaceutically acceptable salt of any one of claims 1-32, wherein m is 2, and two R^f combine to form cyclopropyl or a cyclopentyl.

34. The compound or pharmaceutically acceptable salt of any one of claims 1-32, wherein m is 2, and two R^f combine to form cyclopropyl or a cyclopentyl substituted with one or more methyl or halo.

35. The compound or pharmaceutically acceptable salt of any one of claims 1-30, wherein m is 2, and two R^f combine together with the atom or atoms to which they are attached to form a 3-to 7-membered heterocycloalkyl.

36. The compound or pharmaceutically acceptable salt of any one of claims 1-30, wherein m is 2, and two R^f combine together with the atom or atoms to which they are attached to form a 5-membered heterocycloalkyl, such as a dithiolane.

37. The compound or pharmaceutically acceptable salt of claim 1, wherein the compound is selected from the group consisting of:

F

or a pharmaceutically acceptable salt thereof.

38. A pharmaceutical composition comprising at least one compound of any one of claims1-37, or a pharmaceutically acceptable salt thereof, and optionally one or more pharmaceutically acceptable excipients.

39. A method of treating disease, such as a viral infection, comprising administering to a subject in need of such treatment an effective amount of a compound of any one of claims 1- 37, or a pharmaceutically acceptable salt thereof.