Chauhan Shweta Singh, Jamal Tanya, Gupta Anshika, Parthasarathi Ramakrishnan
REACT-Computational Toxicology Group, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow, 226001, Uttar Pradesh, India.
Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India.
Mol Divers. 2025 Apr 27. doi: 10.1007/s11030-025-11204-8.
The rise of antimicrobial resistance (AMR) of the routinely used antibiotics is ineffective against drug-resistant pathogenic strains of Escherichia coli, set off with limited treatment choices, costs, and increasing mortality rates. Multidrug efflux pumps have been identified as crucial determinants of AMR, flushing numerous antibiotics from cells in a non-specific way, and have emerged as promising drug targets to overcome AMR. Herein, the work focuses on determining structural and mutational insights of tripartite efflux pump subunit AcrB by executing multiple sequence alignment (MSA); the residues 615 and 617 at the substrate-binding site were identified mutated from an aromatic amino acid, phenylalanine, to an aliphatic amino acid, alanine. The study proceeded with the co-development of AcrB antagonist's by applying pharmacokinetic parameters filters to 40,613 natural compounds and molecular docking of single compounds, multiple ligand simultaneous docking (MLSD), molecular dynamics (MD) simulations, principal component analysis (PCA), and free energy landscape (FEL) analysis by considering resistant antibiotics. The identified mutations in the AcrB subunit are responsible for upregulating the activity of the AcrAB-TolC efflux pump and leading to a reduced concentration of antibiotics in the bacterial cytoplasm, ultimately increasing antibiotic resistance. Furthermore, based upon compound screening against target AcrB, 3-Hydroxyfumiquinazoline A shows competitive interaction with the antibiotic Erythromycin. A similar interaction pattern was observed between Sungucine and Cheatoglobosin D with Novobiocin while Procheatoglobosin I and Chaetoglobosin Q with Fusidic acid. Our findings highlight a novel class of efflux pump inhibitors (EPIs) that effectively antagonize the AcrB subunit and could serve as novel adjuvant alternatives for reviving antibiotic activity in resistant bacteria.
常规使用的抗生素的抗菌耐药性（AMR）不断上升，对耐药性大肠杆菌致病菌株无效，导致治疗选择有限、成本增加且死亡率上升。多药外排泵已被确定为AMR的关键决定因素，它以非特异性方式将多种抗生素从细胞中排出，已成为克服AMR的有前景的药物靶点。在此，这项工作聚焦于通过进行多序列比对（MSA）来确定三方外排泵亚基AcrB的结构和突变见解；底物结合位点的615和617位残基被确定从芳香族氨基酸苯丙氨酸突变为脂肪族氨基酸丙氨酸。该研究通过将药代动力学参数过滤器应用于40613种天然化合物，并对单一化合物进行分子对接、多配体同时对接（MLSD）、分子动力学（MD）模拟、主成分分析（PCA）以及考虑耐药性抗生素的自由能景观（FEL）分析，共同开发AcrB拮抗剂。在AcrB亚基中鉴定出的突变导致AcrAB - TolC外排泵的活性上调，并导致细菌细胞质中抗生素浓度降低，最终增加抗生素耐药性。此外，基于针对靶标AcrB的化合物筛选，3 - 羟基烟曲霉喹唑啉A显示出与抗生素红霉素的竞争性相互作用。在Sungucine和Cheatoglobosin D与新生霉素之间以及Procheatoglobosin I和Chaetoglobosin Q与夫西地酸之间观察到类似的相互作用模式。我们的研究结果突出了一类新型的外排泵抑制剂（EPI），它们能有效拮抗AcrB亚基，并可作为恢复耐药细菌中抗生素活性的新型辅助替代品。
