Discovery of Chlorofluoroacetamide-Based Covalent Inhibitors for SARS-CoV-2 3CL Protease

Hirose, Y.; Shindo, N.; Mori, M.; Onitsuka, S.; Isogai, H.; Hamada, R.; Hiramoto, T.; Ochi, J.; Takahashi, D.; Ueda, T.; Caaveiro, J. M. M.; Yoshida, Y.; Ohdo, S.; Matsunaga, N.; Toba, S.; Sasaki, M.; Orba, Y.; Sawa, H.; Sato, A.; Kawanishi, E.; Ojida, A.

doi:10.1101/2022.06.05.494897

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bioRxiv · 10.1101/2022.06.05.494897

Discovery of Chlorofluoroacetamide-Based Covalent Inhibitors for SARS-CoV-2 3CL Protease

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Abstract

The pandemic of coronavirus disease 2019 (COVID-19) has urgently necessitated the development of antiviral agents against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The 3C-like protease (3CLpro) is a promising target for COVID-19 treatment. Here, we report the new class of covalent inhibitors for 3CLpro possessing chlorofluoroacetamide (CFA) as a cysteine reactive warhead. Based on the aza-peptide scaffold, we synthesized the series of CFA derivatives in enantiopure form and evaluated their biochemical efficiencies. The data revealed that 8a (YH-6) with R configuration at the CFA unit strongly blocks the SARS-CoV-2 replication in the infected cells and this potency is comparable to that of nirmatrelvir. The X-ray structural analysis shows that 8a (YH-6) forms a covalent bond with Cys145 at the catalytic center of 3CLpro. The strong antiviral activity and sufficient pharmacokinetics property of 8a (YH-6) suggest its potential as a lead compound for treatment of COVID-19.

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Hirose, Y., Shindo, N., Mori, M., Onitsuka, S., Isogai, H., Hamada, R., Hiramoto, T., Ochi, J., Takahashi, D., Ueda, T., Caaveiro, J. M. M., Yoshida, Y., Ohdo, S., Matsunaga, N., Toba, S., Sasaki, M., Orba, Y., Sawa, H., Sato, A., Kawanishi, E., Ojida, A.. 2022-06-06. Discovery of Chlorofluoroacetamide-Based Covalent Inhibitors for SARS-CoV-2 3CL Protease. https://doi.org/10.1101/2022.06.05.494897

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