Bioinformatics-Guided Analysis of MLH1 Gene Variants: Structural Modeling, Dynamics, and Drug Interaction Studies

Background and Objective: The MLH1 gene encodes a key protein of the DNA mismatch repair (MMR) system responsible for maintaining genomic stability. Mutations in MLH1 can disrupt DNA repair, leading to microsatellite instability and an increased risk of hereditary cancers such as Lynch syndrome and colorectal cancer. This study aimed to identify deleterious missense variants of the MLH1 gene and evaluate their structural, dynamic, and therapeutic implications using integrated bioinformatics analysis, Normal Mode Analysis (iMODS), and molecular docking studies. Materials and Methods: Missense variants were screened using twelve in silico prediction tools to identify potentially damaging nsSNPs. Mutation3D was used to analyze the spatial clustering of variants. A full-length three-dimensional structure of MLH1 (756 amino acids) was predicted using AlphaFold and validated using QMEAN and ProSA scores. Structural dynamics were examined using iMODs server. Molecular docking was performed in PyRx to assess interactions between wild-type and mutant MLH1 proteins and selected FDA-approved anticancer drugs. Results: Twenty-six nsSNPs were predicted to be highly deleterious, with eight variants located in structurally important regions. Structural validation of the MLH1 model yielded a QMEAN Z-score of -4.17 and a ProSA Z-score of -7.15. Four variants (L11V, R27Q, I115T, and E319K) showed notable structural deviations from the wild-type protein. Normal Mode Analysis indicated that the L11V variant exhibited slightly increased rigidity compared with the wild type, while R27Q, I115T, and E319K showed marginally increased flexibility. Docking analysis revealed stable interactions between MLH1 proteins and several anticancer drugs, including Cabozantinib, Irinotecan, Crizotinib, and Olaparib, although mutations altered binding orientations and interaction patterns. Conclusion: The findings highlight the structural and dynamic effects of MLH1 missense mutations and their potential influence on therapeutic interactions. This study provides insights into MLH1 variant pathogenicity and may support future experimental validation and targeted therapeutic strategies for colorectal cancer.