NMR spectroscopy of the main protease of SARS‐CoV‐2 and fragment‐based screening identify three protein hotspots and an antiviral fragment

François-Xavier Cantrelle (1, 2) , Emmanuelle Boll (1, 2) , Lucile Brier (3) , Danai Moschidi (1, 2) , Sandrine Belouzard (4) , Valérie Landry (3) , Florence B Leroux (3) , Frédérique Dewitte (1, 2) , Isabelle Landrieu (1, 2) , Jean Dubuisson (4) , Benoit Deprez (3) , Julie Charton (3) , Xavier Hanoulle (1, 2)

1 RID-AGE - Facteurs de Risque et Déterminants Moléculaires des Maladies liées au Vieillissement - U 1167
2 ERL 9002 - BSI - Biologie Structurale Intégrative
3 M2SV - Médicaments et molécules pour agir sur les Systèmes Vivants - U 1177
4 CIIL - Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204

The main protease (3CLp) of the SARS-CoV-2, the causative agent for the COVID-19 pandemic, is one of the main targets for drug development. To be active, 3CLp relies on a complex interplay between dimerization, active site flexibility, and allosteric regulation. The deciphering of these mechanisms is a crucial step to enable the search for inhibitors. In this context, using NMR spectroscopy, we studied the conformation of dimeric 3CLp from the SARS-CoV-2 and monitored ligand binding, based on NMR signal assignments. We performed a fragment-based screening that led to the identification of 38 fragment hits. Their binding sites showed three hotspots on 3CLp, two in the substrate binding pocket and one at the dimer interface. F01 is a non-covalent inhibitor of the 3CLp and has antiviral activity in SARS-CoV-2 infected cells. This study sheds light on the complex structure-function relationships of 3CLp, and constitutes a strong basis to assist in developing potent 3CLp inhibitors.

Domaines: Biologie structurale [q-bio.BM]; Chimie thérapeutique; Virologie

François-Xavier Cantrelle, Emmanuelle Boll, Lucile Brier, Danai Moschidi, Sandrine Belouzard, et al.. NMR spectroscopy of the main protease of SARS‐CoV‐2 and fragment‐based screening identify three protein hotspots and an antiviral fragment. Angewandte Chemie International Edition, In press, 60 (48), pp.25428-25435. ⟨10.1002/anie.202109965⟩. ⟨hal-03363607⟩