8B2T

SARS-CoV-2 Main Protease (Mpro) in complex with nirmatrelvir alkyne

Summary for 8B2T

• Entry DOI: 10.2210/pdb8b2t/pdb
• Descriptor: 3C-like proteinase nsp5, Nirmatrelvir (reacted form) (3 entities in total)
• Functional Keywords: inhibitor, complex, covalent, viral protein
• Biological source: Severe acute respiratory syndrome coronavirus 2
• Total number of polymer chains: 1
• Total formula weight: 34197.97

Authors

Owen, C.D.,Crawshaw, A.D.,Warren, A.J.,Trincao, J.,Zhao, Y.,Brewitz, L.,Malla, T.R.,Salah, E.,Petra, L.,Strain-Damerell, C.,Schofield, C.J.,Walsh, M.A. (deposition date: 2022-09-14, release date: 2023-02-22, Last modification date: 2024-11-13)

Primary citation

Brewitz, L.,Dumjahn, L.,Zhao, Y.,Owen, C.D.,Laidlaw, S.M.,Malla, T.R.,Nguyen, D.,Lukacik, P.,Salah, E.,Crawshaw, A.D.,Warren, A.J.,Trincao, J.,Strain-Damerell, C.,Carroll, M.W.,Walsh, M.A.,Schofield, C.J.
Alkyne Derivatives of SARS-CoV-2 Main Protease Inhibitors Including Nirmatrelvir Inhibit by Reacting Covalently with the Nucleophilic Cysteine.
J.Med.Chem., 66:2663-2680, 2023

PubMed Abstract: Nirmatrelvir (PF-07321332) is a nitrile-bearing small-molecule inhibitor that, in combination with ritonavir, is used to treat infections by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Nirmatrelvir interrupts the viral life cycle by inhibiting the SARS-CoV-2 main protease (M), which is essential for processing viral polyproteins into functional nonstructural proteins. We report studies which reveal that derivatives of nirmatrelvir and other M inhibitors with a nonactivated terminal alkyne group positioned similarly to the electrophilic nitrile of nirmatrelvir can efficiently inhibit isolated M and SARS-CoV-2 replication in cells. Mass spectrometric and crystallographic evidence shows that the alkyne derivatives inhibit M by apparent irreversible covalent reactions with the active site cysteine (Cys145), while the analogous nitriles react reversibly. The results highlight the potential for irreversible covalent inhibition of M and other nucleophilic cysteine proteases by alkynes, which, in contrast to nitriles, can be functionalized at their terminal position to optimize inhibition and selectivity, as well as pharmacodynamic and pharmacokinetic properties.

PubMed: 36757959
DOI: 10.1021/acs.jmedchem.2c01627

Experimental method

X-RAY DIFFRACTION (1.893 Å)