Pro108Ser mutation of SARS-CoV-2 3CLpro reduces the enzyme activity and ameliorates the clinical severity of COVID-19

Abstract

Recently, an international randomized controlled clinical trial showed that patients with SARS-CoV-2 infection treated orally with the 3-chymotrypsin-like protease (3CLpro) inhibitor PF-07321332 within three days of symptom onset showed an 89% lower risk of COVID-19-related hospital admission/ death from any cause as compared with the patients who received placebo. Lending support to this critically important result of the aforementioned trial, we demonstrated in our study that patients infected with a SARS-Cov-2 sub-lineage (B.1.1.284) carrying the Pro108Ser mutation in 3CLpro tended to have a comparatively milder clinical course (i.e., a smaller proportion of patients required oxygen supplementation during the clinical course) than patients infected with the same sub-lineage of virus not carrying the mutation. Characterization of the mutant 3CLpro revealed that the Kcat/Km of the 3CLpro enzyme containing Ser108 was 58% lower than that of Pro108 3CLpro. Hydrogen/deuterium-exchange mass spectrometry (HDX-MS) revealed that the reduced activity was associated with structural perturbation surrounding the substrate-binding region of the enzyme, which is positioned behind and distant from the 108th amino acid residue. Our findings of the attenuated clinical course of COVID-19 in patients infected with SARS-CoV-2 strains with reduced 3CLpro enzymatic activity greatly endorses the promising result of the aforementioned clinical trial of the 3CLpro inhibitor.

Naturally occurring mutations of SARS-CoV-2 main protease confer drug resistance to nirmatrelvir

“…Recent sequence analysis of SARS-CoV-2 M pro revealed multiple prevalent mutations including G15S (C.37 Lambda), T21I (B.1.1.318), L89F (B.1.2), K90R (B.1.351 Beta), P108S (B.1.1.284), P132H (B.1.1.529 Omicron), and L205V (P.2 Zeta) (7)(8)(9). All these mutants are located outside the nirmatrelvir binding site (Fig.…”

The SARS‐CoV‐2 main protease (Mpro): Structure, function, and emerging therapies for COVID‐19

“…3CL pro is approximately 34.21 kDa per monomer (average molecular weight of monomeric deposited models). 3CL pro is matured in a dimeric form, and the individual monomers are enzymatically less active, where the monomers consist of three domains, including domain I, domain II, and domain III 60,61 . Among them, domain III is an extra helix domain, whose aggregation initiates the dimerization of 3CL pro 16,22,36,62 .…”

Potential medicinal plants involved in inhibiting 3CLpro activity: A practical alternate approach to combating COVID-19

“…Recently, results of a clinical trial revealed that SARS-CoV-2-infected patients, when treated orally with the 3CL pro inhibitor nirmatrelvir (PF-07321332) during the first three days of infection, showed an 89% lower risk of COVID-19-related hospital admission or death [25] . In line with this important result, a group of Japanese scientists reported that patients infected with a SARS-CoV-2 sub-lineage (B.1.1.284) containing the Pro108Ser mutation in 3CL pro required a milder clinical treatment compared to the patients infected with the same sub-lineage of virus without the mutation [26] . Moreover, Abdelnabi et al [27] also reported that PF-07321332 exerted potent inhibition of 3CL pro activity within different variants of SARS-CoV-2.…”