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TitleAn in-solution snapshot of SARS-COV-2 main protease maturation process and inhibition.
Journal, issue, pagesNat Commun, Vol. 14, Issue 1, Page 1545, Year 2023
Publish dateMar 20, 2023
AuthorsGabriela Dias Noske / Yun Song / Rafaela Sachetto Fernandes / Rod Chalk / Haitem Elmassoudi / Lizbé Koekemoer / C David Owen / Tarick J El-Baba / Carol V Robinson / / Glaucius Oliva / Andre Schutzer Godoy /
PubMed AbstractThe main protease from SARS-CoV-2 (M) is responsible for cleavage of the viral polyprotein. M self-processing is called maturation, and it is crucial for enzyme dimerization and activity. Here we use ...The main protease from SARS-CoV-2 (M) is responsible for cleavage of the viral polyprotein. M self-processing is called maturation, and it is crucial for enzyme dimerization and activity. Here we use C145S M 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 M 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 M dimerization is triggered by induced fit due to covalent linkage during substrate processing rather than the N-terminal processing.
External linksNat Commun / PubMed:36941262 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution1.738 - 3.5 Å
Structure data

28666

8ey2

EMDB-28666, PDB-8ey2:
Cryo-EM structure of SARS-CoV-2 Main protease C145S in complex with N-terminal peptide
Method: EM (single particle) / Resolution: 3.5 Å

PDB-8eyj:
Crystal Structure of uncleaved SARS-CoV-2 Main Protease C145S mutant in complex with Nirmatrelvir
Method: X-RAY DIFFRACTION / Resolution: 1.738 Å

Chemicals

ChemComp-4WI:
(1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide / medication, antivirus, protease inhibitor*YM / Nirmatrelvir

ChemComp-HOH:
WATER / Water

Source
  • severe acute respiratory syndrome coronavirus 2
KeywordsVIRAL PROTEIN / covid19 / mpro / main protease / cryo-Em / 3cl / sars-cov-2 / complex / Nirmatrelvir

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