Mutation-Induced Resistance of SARS-CoV-2 Mpro to WU-04 Revealed by Multi-Scale Modeling

TL;DR

This study uses advanced modeling to show how mutations in the SARS-CoV-2 protease can reduce the effectiveness of a drug called WU-04 and suggests ways to design more resilient drugs.

Contribution

The paper introduces a novel multi-scale modeling approach combining molecular dynamics and network analysis to assess mutation-induced drug resistance in SARS-CoV-2 Mpro.

Findings

Single mutations at positions 49, 165, and 301 reduce WU-04 binding affinity by up to ~12 kcal/mol.

The M49K/S301P double mutant partially restores drug binding through re-established hydrophobic and hydrogen-bond interactions.

Residue 301 is part of a communication network linking distant domains, and its mutation rewires interactions to compensate for local disruptions.

Abstract

The clinical durability of SARS-CoV-2 main protease (Mpro) inhibitors depends on their resilience to emerging resistance mutations. Recent genomic surveillance and functional reports have highlighted substitutions at positions 49, 165, and 301, raising questions about the robustness of the noncovalent inhibitor WU-04 in variant backgrounds. Here, we combined μs-scale, triplicate molecular dynamics simulations with end-state binding free energy estimates and a network-rewiring inference (NRI) framework that maps long-range dynamical communication across the full protease dimer. We evaluated wild type (WT), single mutants M49K, M165V, S301P, and selected double mutants (M49K & M165V, M49K & S301P). Relative to WT, single substitutions produced reductions in computed binding affinity of up to ~12kcal/mol, accompanied by loss or reshaping of the S2 subsite and altered ligand burial. Notably, the M49K/S301P double mutant partially restored WU-04 engagement, narrowing the ΔΔGrestore gap to within ΔΔGrestore of WT and re-establishing key hydrophobic and hydrogen-bond contacts. NRI analysis revealed that distal residue 301 participates in a communication corridor linking the C-terminal helical domain to the active-site cleft; its substitution rewires inter-domain coupling that can compensate for local disruptions at residue 49. Together, these results identify structural hotspots and network pathways that may inform the design of next-generation Mpro inhibitors with improved mutation tolerance—specifically by strengthening interactions that do not rely solely on the mutable S2 pocket and by engaging conserved backbone features near the 165–166 region.

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