Structure-based inhibitor optimization for the Nsp3 Macrodomain of SARS-CoV-2.
Gahbauer S., Correy GJ., Schuller M., Ferla MP., Doruk YU., Rachman M., Wu T., Diolaiti M., Wang S., Neitz RJ., Fearon D., Radchenko D., Moroz Y., Irwin JJ., Renslo AR., Taylor JC., Gestwicki JE., von Delft F., Ashworth A., Ahel I., Shoichet BK., Fraser JS.
The nonstructural protein 3 (NSP3) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) contains a conserved macrodomain enzyme (Mac1) that is critical for pathogenesis and lethality. While small molecule inhibitors of Mac1 have great therapeutic potential, few have been described. Here, we report the structure-based development of several chemical scaffolds exhibiting low- to sub-micromolar affinity for Mac1 through iterations of computer-aided design, structural characterization by ultra-high resolution X-ray protein crystallography, and binding evaluation with in-solution assays. Potent scaffolds were designed with in silico linkage of previously obtained fragment hits and ultra-large library docking screens of more than 450 million molecules. In total, 160 hits comprising 119 different scaffolds were discovered and 152 Mac1-ligand complex crystal structures were determined, typically to 1 Ã… resolution or better. The structure-activity-relationships emerging from this study may template future drug development against Mac1. Summary: Computational fragment-linking and ultra-large library docking identifies potent inhibitors of the SARS-CoV-2 macrodomain.