An in-solution snapshot of SARS-COV-2 main protease maturation process and inhibition

DOI: 10.1038/s41467-023-37035-5

Authors: Gabriela Dias Noske (University of Sao Paulo) , Yun Song (Diamond Light Source) , Rafaela Sachetto Fernandes (University of Sao Paulo) , Rod Chalk (University of Oxford) , Haitem Elmassoudi (University of Oxford) , Lizbe Koekemoer (University of Oxford) , C. David Owen (Diamond Light Source) , Tarick J. El-Baba (University of Oxford; The Kavli Institute for Nanoscience Discovery) , Carol V. Robinson (University of Oxford; The Kavli Institute for Nanoscience Discovery) , Glaucius Oliva (University of Sao Paulo) , Andre Schutzer Godoy (University of Sao Paulo)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: Nature Communications , VOL 14

State: Published (Approved)
Published: March 2023
Diamond Proposal Number(s): 27083 , 29349

Abstract: The main protease from SARS-CoV-2 (Mpro) is responsible for cleavage of the viral polyprotein. Mpro self-processing is called maturation, and it is crucial for enzyme dimerization and activity. Here we use C145S Mpro to study the structure and dynamics of N-terminal cleavage in solution. Native mass spectroscopy analysis shows that mixed oligomeric states are composed of cleaved and uncleaved particles, indicating that N-terminal processing is not critical for dimerization. A 3.5 Å cryo-EM structure provides details of Mpro N-terminal cleavage outside the constrains of crystal environment. We show that different classes of inhibitors shift the balance between oligomeric states. While non-covalent inhibitor MAT-POS-e194df51-1 prevents dimerization, the covalent inhibitor nirmatrelvir induces the conversion of monomers into dimers, even with intact N-termini. Our data indicates that the Mpro dimerization is triggered by induced fit due to covalent linkage during substrate processing rather than the N-terminal processing.

Journal Keywords: Cryoelectron microscopy; Drug discovery; Proteases; SARS-CoV-2

Diamond Keywords: COVID-19; Viruses

Subject Areas: Biology and Bio-materials, Medicine

Diamond Offline Facilities: Electron Bio-Imaging Centre (eBIC)
Instruments: Krios II-Titan Krios II at Diamond

Added On: 29/03/2023 14:38

Documents:
s41467-023-37035-5.pdf

Discipline Tags:

Pathogens Infectious Diseases Health & Wellbeing Structural biology Drug Discovery Life Sciences & Biotech

Technical Tags:

Microscopy Electron Microscopy (EM) Cryo Electron Microscopy (Cryo EM)