Fragment‐based screening targeting an open form of the SARS‐CoV‐2 main protease binding pocket

• Published in: Acta crystallographica. Section D, Biological crystallography. Vol. 80; no. 2; pp. 123 - 136
• Main Authors: Huang, Chia-Ying, Metz, Alexander, Lange, Roland, Artico, Nadia, Potot, Céline, Hazemann, Julien, Müller, Manon, Dos Santos, Marina, Chambovey, Alain, Ritz, Daniel, Eris, Deniz, Meyer, Solange, Bourquin, Geoffroy, Sharpe, May, Mac Sweeney, Aengus
• Format: Journal Article
• Language: English
• Published: 5 Abbey Square, Chester, Cheshire CH1 2HU, England International Union of Crystallography 01.02.2024; Wiley Subscription Services, Inc
• Subjects: 3CLpro; Binding; Catalytic Domain; Conformation; Coronavirus 3C Proteases; covalent binders; COVID-19; Crystallography; Crystallography, X-Ray; Crystals; fragment screening; Fragments; Humans; Protease; SARS-CoV-2; Screening; Severe acute respiratory syndrome coronavirus 2; Substrates; surface plasmon resonance; X‐ray crystallography; X-ray crystallography; SARS-CoV-2; 3CLpro; covalent binders; surface plasmon resonance; fragment screening
• ISSN: 2059-7983; 0907-4449; 2059-7983; 1399-0047
• DOI: 10.1107/S2059798324000329

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. X‐ray crystallographic screening of SARS‐CoV‐2 3CL protease resulted in 29 fragment hits, including two isatin‐based reversible covalent binders, and revealed a strong influence of the crystal form used for fragment soaking on the bound conformations of three additional reference fragments.