Alkyne as a Latent Warhead to Covalently Target SARS-CoV-2 Main Protease
Chau Ngo, William Fried, Saba R. Aliyari, Joshua Feng, Chao Qin, Shilei Zhang, Hanjing Yang, Jean Shanaa, Pinghui Feng, Genhong Cheng, Xiaojiang S. Chen, Chao Zhang
Abstract
High Resolution Image Download MS PowerPoint Slide There is an urgent need for improved therapy to better control the ongoing COVID-19 pandemic. The main protease M pro plays a pivotal role in SARS-CoV-2 replications, thereby representing an attractive target for antiviral development. We seek to identify novel electrophilic warheads for efficient, covalent inhibition of M pro . By comparing the efficacy of a panel of warheads installed on a common scaffold against M pro, we discovered that the terminal alkyne could covalently modify M pro as a latent warhead. Our biochemical and X-ray structural analyses revealed the irreversible formation of the vinyl-sulfide linkage between the alkyne and the catalytic cysteine of M pro . Clickable probes based on the alkyne inhibitors were developed to measure target engagement, drug residence time, and off-target effects. The best alkyne-containing inhibitors potently inhibited SARS-CoV-2 infection in cell infection models. Our findings highlight great potentials of alkyne as a latent warhead to target cystine proteases in viruses and beyond.