Expedited Approach toward the Rational Design of Noncovalent SARS-CoV-2 Main Protease Inhibitors.
Kitamura N, Sacco MD, Ma C, Hu Y, Townsend JA, Meng X, Zhang F, Zhang X, Ba M, Szeto T, Kukuljac A, Marty MT, Schultz D, Cherry S, Xiang Y, Chen Y, Wang J.
The main protease (M<sup>pro</sup>) of SARS-CoV-2 is a validated antiviral drug target. Several M<sup>pro</sup> inhibitors have been reported with potent enzymatic inhibition and cellular antiviral activity, including <b>GC376</b>, <b>boceprevir</b>, <b>calpain inhibitors II</b>, and <b>XII</b>, with each containing a reactive warhead that covalently modifies the catalytic Cys145. Coupling structure-based drug design with the one-pot Ugi four-component reaction, we discovered one of the most potent noncovalent inhibitors, <b>23R</b> (<b>Jun8-76-3A</b>) that is structurally distinct from the canonical M<sup>pro</sup> inhibitor <b>GC376</b>. Significantly, <b>23R</b> is highly selective compared with covalent inhibitors such as <b>GC376</b>, especially toward host proteases. The cocrystal structure of SARS-CoV-2 M<sup>pro</sup> with <b>23R</b> revealed a previously unexplored binding site located in between the S2 and S4 pockets. Overall, this study discovered <b>23R</b>, one of the most potent and selective noncovalent SARS-CoV-2 M<sup>pro</sup> inhibitors reported to date, and a novel binding pocket in M<sup>pro</sup> that can be explored for inhibitor design.