Journal Article

A novel, covalent broad-spectrum inhibitor targeting human coronavirus M pro

Ding, Xiaoyu, Peng, Guilin, Zheng, Jie, Wang, Dong, Yang, Minglei, Zhao, Jincun, Malkov, Maxim N, Yuan, Bin, Zhong, Nanshan, Peng, Jingjing, Liang, Xing, Polykovskiy, Daniil A, Chen, Xinwen, Su, Jingyi, Li, Taotao, Zhavoronkov, Alex, Zhao, Jingxian, Chen, Zhao, Ivanenkov, Yan A, Zhu, Qingsong, Sun, Deheng, Wei, Peilan, Zhu, Airu, Fan, Yaya, Li, Rong, Malyshev, Alexander S, Xie, Zhanhong, Tang, Jielin, Zhang, Man, Yuan, Jinwei, Ding, Xiao, He, Yiyun, Aliper, Alex, Cai, Xin, Ren, Feng, Wang, Ling, Bezrukov, Dmitry S, Guo, Hu, Li, Zhun, Hu, Xiaoyu, Zagribelnyy, Bogdan A, Yang, Qi, Liu, Sang, Terentiev, Victor A, Sun, Jing, Aspuru-Guzik, Alán, Guan, Xin

2025

Overview

Human coronaviruses (CoV) cause respiratory infections that range from mild to severe. CoVs are a large family of viruses with considerable genetic heterogeneity and a multitude of viral types, making preventing and treating these viruses difficult. Comprehensive treatments that inhibit CoV infections fulfill a pressing medical need and may be immensely valuable in managing emerging and endemic CoV infections. As the main protease (M ) is highly conserved across many CoVs, this protease has been identified as a route for broad CoV inhibition. We utilize the advanced generative chemistry platform Chemistry42 for de novo molecular design and obtained novel small-molecule, non-peptide-like inhibitors targeting the SARS-CoV-2 M . ISM3312 is identified as an irreversible, covalent M inhibitor from extensive virtual screening and structure-based optimization efforts. ISM3312 exhibits low off-target risk and outstanding antiviral activity against multiple human coronaviruses, including SARS-CoV-2, MERS-CoV, 229E, OC43, NL63, and HKU1 independent of P-glycoprotein (P-gp) inhibition. Furthermore, ISM3312 shows significant inhibitory effects against Nirmatrelvir-resistant M mutants, suggesting ISM3312 may contribute to reduced viral escape in these settings. Incorporating ISM3312 and Nirmatrelvir into antiviral strategy could improve preparedness and reinforce defenses against future coronavirus threats.

• Subject: Antiviral Agents - chemistry / Antiviral Agents - pharmacology / Coronavirus 3C Proteases - antagonists & inhibitors / Coronavirus 3C Proteases - chemistry / Coronavirus 3C Proteases - metabolism / COVID-19 - virology / COVID-19 Drug Treatment / Humans / Middle East Respiratory Syndrome Coronavirus - drug effects / Middle East Respiratory Syndrome Coronavirus - enzymology / Protease Inhibitors - chemistry / Protease Inhibitors - pharmacology / SARS-CoV-2 - drug effects / SARS-CoV-2 - enzymology