A Quick Route to Multiple Highly Potent SARS‐CoV‐2 Main Protease Inhibitors

• Published in: ChemMedChem Vol. 16; no. 6; pp. 942 - 948
• Main Authors: Yang, Kai S., Ma, Xinyu R., Ma, Yuying, Alugubelli, Yugendar R., Scott, Danielle A., Vatansever, Erol C., Drelich, Aleksandra K., Sankaran, Banumathi, Geng, Zhi Z., Blankenship, Lauren R., Ward, Hannah E., Sheng, Yan J., Hsu, Jason C., Kratch, Kaci C., Zhao, Baoyu, Hayatshahi, Hamed S., Liu, Jin, Li, Pingwei, Fierke, Carol A., Tseng, Chien‐Te K., Xu, Shiqing, Liu, Wenshe Ray
• Format: Journal Article
• Language: English
• Published: WEINHEIM Wiley 18.03.2021; Wiley Subscription Services, Inc; ChemPubSoc Europe
• Subjects: 3C-like protease; 60 APPLIED LIFE SCIENCES; A549 Cells; ACE2; Alanine - analogs & derivatives; Alanine - metabolism; Alanine - pharmacology; Angiotensin-converting enzyme 2; Animals; Antiviral Agents - chemical synthesis; Antiviral Agents - metabolism; Antiviral Agents - pharmacology; Antiviral drugs; antivirals; Catalytic Domain; Chemical bonds; Chemistry, Medicinal; Chlorocebus aethiops; Coronavirus 3C Proteases - antagonists & inhibitors; Coronavirus 3C Proteases - chemistry; Coronavirus 3C Proteases - metabolism; Covalent bonds; COVID-19; Crystallography; Cysteine - chemistry; Cysteine Proteinase Inhibitors - chemical synthesis; Cysteine Proteinase Inhibitors - metabolism; Cysteine Proteinase Inhibitors - pharmacology; Humans; Life Sciences & Biomedicine; main protease; Microbial Sensitivity Tests; Pathogenesis; Pharmacology & Pharmacy; Polypeptides; Protease; Protease inhibitors; Protein Binding; Proteinase inhibitors; Proteolysis; Pyrrolidinones - chemical synthesis; Pyrrolidinones - metabolism; Pyrrolidinones - pharmacology; reversible covalent inhibitors; SARS-CoV-2; SARS-CoV-2 - drug effects; SARS-CoV-2 - enzymology; Science & Technology; Severe acute respiratory syndrome; Severe acute respiratory syndrome coronavirus 2; Vero Cells; Viral diseases; Viruses; COVID-19; 3C-like protease; antivirals; reversible covalent inhibitors; SARS-CoV-2; EFFICACY; main protease; IDENTIFICATION; CORONAVIRUS
• ISSN: 1860-7179; 1860-7187; 1860-7187
• DOI: 10.1002/cmdc.202000924

The COVID‐19 pathogen, SARS‐CoV‐2, requires its main protease (SC2MPro) to digest two of its translated long polypeptides to form a number of mature proteins that are essential for viral replication and pathogenesis. Inhibition of this vital proteolytic process is effective in preventing the virus from replicating in infected cells and therefore provides a potential COVID‐19 treatment option. Guided by previous medicinal chemistry studies about SARS‐CoV‐1 main protease (SC1MPro), we have designed and synthesized a series of SC2MPro inhibitors that contain β‐(S‐2‐oxopyrrolidin‐3‐yl)‐alaninal (Opal) for the formation of a reversible covalent bond with the SC2MPro active‐site cysteine C145. All inhibitors display high potency with Ki values at or below 100 nM. The most potent compound, MPI3, has as a Ki value of 8.3 nM. Crystallographic analyses of SC2MPro bound to seven inhibitors indicated both formation of a covalent bond with C145 and structural rearrangement from the apoenzyme to accommodate the inhibitors. Virus inhibition assays revealed that several inhibitors have high potency in inhibiting the SARS‐CoV‐2‐induced cytopathogenic effect in both Vero E6 and A549/ACE2 cells. Two inhibitors, MPI5 and MPI8, completely prevented the SARS‐CoV‐2‐induced cytopathogenic effect in Vero E6 cells at 2.5–5 μM and A549/ACE2 cells at 0.16–0.31 μM. Their virus inhibition potency is much higher than that of some existing molecules that are under preclinical and clinical investigations for the treatment of COVID‐19. Our study indicates that there is a large chemical space that needs to be explored for the development of SC2MPro inhibitors with ultra‐high antiviral potency. Small but strong: A series of SARS‐CoV‐2 MPro covalent inhibitors exhibit excellent activity. Protein crystallography analysis and a live virus‐based microneutralization assay found two of the most potent anti‐SARS‐CoV‐2 small molecules so far. Due to the urgent matter of the COVID‐19 pandemic, these two inhibitors could be quickly advanced to preclinical and clinical tests for COVID‐19.