The Effects of One-Point Mutation on the New Delhi Metallo Beta-Lactamase-1 Resistance toward Carbapenem Antibiotics and β-Lactamase Inhibitors: An In Silico Systematic Approach

• Published in: International journal of molecular sciences Vol. 23; no. 24; p. 16083
• Main Authors: Tran, Van-Thanh, Tran, Viet-Hung, Nguyen, Dac-Nhan, Do, Tran-Giang-Son, Vo, Thanh-Phuong, Nguyen, Thi-Thao-Nhung, Huynh, Phuong Nguyen Hoai, Thai, Khac-Minh
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 16.12.2022; MDPI
• Subjects: alternative one-point mutation; Amides; Anti-Bacterial Agents - chemistry; Anti-Bacterial Agents - pharmacology; Antibiotic resistance; Antibiotics; Bacteria; Bacteria - metabolism; beta-Lactamase Inhibitors - chemistry; beta-Lactamase Inhibitors - pharmacology; beta-Lactamases - metabolism; Binding; Captopril; Carbapenems; Carbapenems - chemistry; Carbapenems - pharmacology; Drug resistance; Enzymes; Free energy; Hydrogen bonds; Hydrolysis; Imipenem; in silico; Inhibitors; Ligands; Meropenem; Metallography; Microbial Sensitivity Tests; molecular docking; Molecular dynamics; molecular dynamics simulation; Mutants; Mutation; New Delhi Metallo beta-lactamase-1 enzyme; Point Mutation; Proteins; Simulation; Software; Thiorphan; β Lactamase; β-Lactam antibiotics; alternative one-point mutation; molecular docking; in silico; New Delhi Metallo beta-lactamase-1 enzyme; molecular dynamics simulation
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms232416083

Antibiotic resistance has been becoming more and more critical due to bacteria's evolving hydrolysis enzymes. The NDM-1 enzyme could hydrolyze not only carbapenems but also most of β-lactam's antibiotics and inhibitors. In fact, variant strains could impose a high impact on the resistance of bacteria producing NDM-1. Although previous studies showed the effect of some variants toward antibiotics and inhibitors binding, there has been no research systematically evaluating the effects of alternative one-point mutations on the hydrolysis capacity of NDM-1. This study aims to identify which mutants could increase or decrease the effectiveness of antibiotics and β-lactamase inhibitors toward bacteria. Firstly, 35 different variants with a high probability of emergence based on the PAM-1 matrix were constructed and then docked with 5 ligands, namely d-captopril, l-captopril, thiorphan, imipenem, and meropenem. The selected complexes underwent molecular dynamics simulation and free energy binding estimation, with the results showing that the substitutions at residues 122 and 124 most influenced the binding ability of NDM-1 toward inhibitors and antibiotics. The H122R mutant decreases the binding ability between d-captopril and NDM-1 and diminishes the effectiveness of this antibiotic toward Enterobacteriaceae. However, the H122R mutant has a contrary impact on thiorphan, which should be tested in vitro and in vivo in further experiments.