To identify starting points for therapeutics targeting SARS-CoV-2, the Paul Scherrer Institute and Idorsia decided to collaboratively perform an X-ray crystallographic fragment screen against its main protease. Fragment-based screening was carried out using crystals with a pronounced open conformation of the substrate-binding pocket. Of 631 soaked fragments, a total of 29 hits bound either in the active site (24 hits), a remote binding pocket (three hits) or at crystal-packing interfaces (two hits). Notably, two fragments with a pose that was sterically incompatible with a more occluded crystal form were identified. Two isatin-based electrophilic fragments bound covalently to the catalytic cysteine residue. The structures also revealed a surprisingly strong influence of the crystal form on the binding pose of three published fragments used as positive controls, with implications for fragment screening by crystallography.

PDB references: SARS-CoV-2 main protease, complex with cpd-1, 7gre; complex with cpd-2, 7grf; complex with cpd-3, 7grg; complex with cpd-4, 7grh; complex with cpd-5, 7gri; complex with cpd-6, 7grj; complex with cpd-7, 7grk; complex with cpd-8, 7grl; complex with cpd-9, 7grm; complex with cpd-10, 7grn; complex with cpd-11, 7gro; complex with cpd-12, 7grp; complex with cpd-13, 7grq; complex with cpd-14, 7grr; complex with cpd-15, 7grs; complex with cpd-16, 7grt; complex with cpd-17, 7gru; complex with cpd-18, 7grv; complex with cpd-19, 7grw; complex with cpd-20, 7grx; complex with cpd-21, 7gry; complex with cpd-22, 7grz; complex with cpd-23, 7gs0; complex with cpd-24, 7gs1; complex with cpd-25, 7gs2; complex with cpd-26, 7gs3; complex with cpd-27, 7gs4; complex with cpd-28, 7gs5; complex with cpd-29, 7gs6