Structural and dynamic implications of the R136H mutation in DNA GyrB: insights into antimicrobial resistance and novobiocin efficacy

Abstract

Antimicrobial resistance, driven by the overuse and misuse of antibiotics, represents a critical global health concern. This study explores the molecular mechanisms underlying resistance associated with the R136H point mutation in DNA gyrase, a key bacterial enzyme targeted by antibiotics such as novobiocin. Using molecular dynamics (MD) simulations, we evaluated the impact of this mutation on the binding affinity, structural stability, and dynamic behavior of the protein–novobiocin complex. The results reveal that the R136H mutation induces measurable structural changes in protein flexibility, as quantified by RMSF, inter-residue interaction networks, and secondary-structure stability, observed in both apo and novobiocin-bound states. These structural alterations correlate with the experimentally reported reduction in novobiocin's antibacterial efficacy against the R136H mutant. MM-PBSA binding energy calculations support this observation, showing a less favorable binding profile for the mutant (ΔG = −23.92 kcal mol⁻¹) compared to the wild type (ΔG = −32.64 kcal mol⁻¹). Regions spanning Val97–Val120 and Thr32–Arg316 exhibited the most pronounced structural perturbations, suggesting these segments play key roles in maintaining the wild-type binding site architecture. Collectively, these structural insights into R136H-mediated resistance provide a foundation for designing next-generation antibiotics that could mitigate mutation-induced binding impairments.