8B2T image
Deposition Date 2022-09-14
Release Date 2023-02-22
Last Version Date 2024-11-13
Entry Detail
PDB ID:
8B2T
Keywords:
Title:
SARS-CoV-2 Main Protease (Mpro) in complex with nirmatrelvir alkyne
Biological Source:
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.89 Å
R-Value Free:
0.22
R-Value Work:
0.18
Space Group:
P 21 21 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:3C-like proteinase nsp5
Gene (Uniprot):rep
Chain IDs:A
Chain Length:305
Number of Molecules:1
Biological Source:Severe acute respiratory syndrome coronavirus 2
Ligand Molecules
Primary Citation
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)
PMID: 36757959 DOI: 10.1021/acs.jmedchem.2c01627

Abstact

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 (Mpro), which is essential for processing viral polyproteins into functional nonstructural proteins. We report studies which reveal that derivatives of nirmatrelvir and other Mpro inhibitors with a nonactivated terminal alkyne group positioned similarly to the electrophilic nitrile of nirmatrelvir can efficiently inhibit isolated Mpro and SARS-CoV-2 replication in cells. Mass spectrometric and crystallographic evidence shows that the alkyne derivatives inhibit Mpro 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 Mpro 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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures