Potent Noncovalent Inhibitors of the Main Protease of SARS-CoV-2 from Molecular Sculpting of the Drug Perampanel Guided by Free Energy Perturbation Calculations

Zhang, Chun-Hui; Stone, Elizabeth A.; Deshmukh, Maya; Ippolito, Joseph A.; Ghahremanpour, Mohammad M.; Tirado-Rives, Julian; Spasov, Krasimir A.; Zhang, Shuo; Takeo, Yuka; Kudalkar, Shalley N.; Liang, Zhuobin; Isaacs, Farren; Lindenbach, Brett; Miller, Scott J.; Anderson, Karen S.; Jorgensen, William L.

[Image: see text] Starting from our previous finding of 14 known drugs as inhibitors of the main protease (M(pro)) of SARS-CoV-2, the virus responsible for COVID-19, we have redesigned the weak hit perampanel to yield multiple noncovalent, nonpeptidic inhibitors with ca. 20 nM IC(50) values in a kinetic assay. Free-energy perturbation (FEP) calculations for M(pro)-ligand complexes provided valuable guidance on beneficial modifications that rapidly delivered the potent analogues. The design efforts were confirmed and augmented by determination of high-resolution X-ray crystal structures for five analogues bound to M(pro). Results of cell-based antiviral assays further demonstrated the potential of the compounds for treatment of COVID-19. In addition to the possible therapeutic significance, the work clearly demonstrates the power of computational chemistry for drug discovery, especially FEP-guided lead optimization.