Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease

A Douangamath ,Martin A Walsh,Peter O’Brien,M.e.m Noble ,Gemma Davison,Nir London,R Skyner ,M Snee ,C Wild ,P Lukacik ,A.j Powell ,Rambabu N Reddi,A Aimon ,Michael J Waring,T Krojer ,E Resnick ,P Gehrtz ,György M Keserű ,James D Firth,M Fairhead ,F Von Delft ,Claire Strain-Damerell,D Fearon ,Simon P Jones ,Thomas D Downes,L Dunnett ,A Carbery ,Péter Ábrányi‐Balogh ,A Dias ,Aaron Keeley,Mathew P Martin,Hanna F Klein,J Brandão-Neto ,C.d Owen

doi:10.1038/s41467-020-18709-w

Abstract

COVID-19, caused by SARS-CoV-2, lacks effective therapeutics. Additionally, no antiviral drugs or vaccines were developed against the closely related coronavirus, SARS-CoV-1 or MERS-CoV, despite previous zoonotic outbreaks. To identify starting points for such therapeutics, we performed a large-scale screen of electrophile and non-covalent fragments through a combined mass spectrometry and X-ray approach against the SARS-CoV-2 main protease, one of two cysteine viral proteases essential for viral replication. Our crystallographic screen identified 71 hits that span the entire active site, as well as 3 hits at the dimer interface. These structures reveal routes to rapidly develop more potent inhibitors through merging of covalent and non-covalent fragment hits; one series of low-reactivity, tractable covalent fragments were progressed to discover improved binders. These combined hits offer unprecedented structural and reactivity information for on-going structure-based drug design against SARS-CoV-2 main protease.

Highlights

COVID-19, caused by SARS-CoV-2, lacks effective therapeutics
The polyproteins are processed by two viral cysteine proteases: a papain-like protease (PLpro) which cleaves three sites, releasing non-structural proteins nsp[1,2,3] and a 3C-like protease, referred to as the main protease (Mpro), that cleaves at 11 sites to release non-structural proteins
Mpro crystallizes in a ligand-free form that diffracts to nearatomic resolution

Summary

Introduction

COVID-19, caused by SARS-CoV-2, lacks effective therapeutics. no antiviral drugs or vaccines were developed against the closely related coronavirus, SARS-CoV-1 or MERS-CoV, despite previous zoonotic outbreaks. Our crystallographic screen identified 71 hits that span the entire active site, as well as 3 hits at the dimer interface These structures reveal routes to rapidly develop more potent inhibitors through merging of covalent and non-covalent fragment hits; one series of low-reactivity, tractable covalent fragments were progressed to discover improved binders. These combined hits offer unprecedented structural and reactivity information for on-going structure-based drug design against SARS-CoV-2 main protease. Other studies have taken the popular approach of high-throughput screens (HTS) Despite these efforts, drugs remain elusive that directly target SARS-CoV-2 (rather than disease symptoms) and are verified by clinical trials. Their promise is that potency can be achieved with high efficiency, simplifying the progression of molecules to biological or clinical impact

Methods

Results

Conclusion