Pharmacy and Bioengineering of Technology, Chongqing University of Technology, Chongqing, 400054, China.
Chongqing Municipal Key Laboratory of Institutions of Higher Education of Target Based Drug Screening and Activity Evaluation, Chongqing, 400054, China.
Amino Acids. 2023 Oct;55(10):1317-1331. doi: 10.1007/s00726-023-03307-z. Epub 2023 Sep 5.
The emergence of drug-resistant superbugs has necessitated a pressing need for innovative antibiotics. Antimicrobial peptides (AMPs) have demonstrated broad-spectrum antibacterial activity, reduced susceptibility to resistance, and immunomodulatory effects, rendering them promising for combating drug-resistant microorganisms. This study employed computational simulation methods to screen and design AMPs specifically targeting ESKAPE pathogens. Particularly, AMPs were rationally designed to target the BamA and obtain novel antimicrobial peptide sequences. The designed AMPs were assessed for their antibacterial activities, mechanisms, and stability. Molecular docking and dynamics simulations demonstrated the interaction of both designed AMPs, 11pep and D-11pep, with the β1, β9, β15, and β16 chains of BamA, resulting in misfolding of outer membrane proteins and antibacterial effects. Subsequent antibacterial investigations confirmed the broad-spectrum activity of both 11pep and D-11pep, with D-11pep demonstrating higher potency against resistant Gram-negative bacteria. D-11pep exhibited MICs of 16, 8, and 32 μg/mL against carbapenem-resistant Escherichia coli, carbapenem-resistant Pseudomonas aeruginosa, and multi-drug-resistant Acinetobacter baumannii, respectively, with a concomitant lower resistance induction. Mechanism of action studies confirmed that peptides could disrupt the bacterial outer membrane, aligning with the findings of molecular dynamics simulations. Additionally, D-11pep demonstrated superior stability and reduced toxicity in comparison to 11pep. The findings of this study underscore the efficacy of rational AMP design that targets BamA, along with the utilization of D-amino acid replacements as a strategy for developing AMPs against drug-resistant bacteria.
耐药超级细菌的出现迫切需要创新的抗生素。抗菌肽（AMPs）具有广谱抗菌活性、降低耐药性的潜力以及免疫调节作用，因此有望用于对抗耐药微生物。本研究采用计算模拟方法筛选和设计专门针对 ESKAPE 病原体的 AMPs。特别是，合理设计 AMP 以靶向 BamA 并获得新的抗菌肽序列。评估了设计的 AMP 的抗菌活性、机制和稳定性。分子对接和动力学模拟表明，两种设计的 AMP（11pep 和 D-11pep）与 BamA 的 β1、β9、β15 和 β16 链相互作用，导致外膜蛋白错误折叠和抗菌作用。随后的抗菌研究证实了 11pep 和 D-11pep 的广谱活性，D-11pep 对耐碳青霉烯类革兰氏阴性菌的活性更高。D-11pep 对耐碳青霉烯类大肠埃希菌、耐碳青霉烯类铜绿假单胞菌和多药耐药鲍曼不动杆菌的 MIC 值分别为 16、8 和 32μg/mL，同时诱导耐药性较低。作用机制研究证实肽可以破坏细菌的外膜，这与分子动力学模拟的结果一致。此外，与 11pep 相比，D-11pep 具有更好的稳定性和更低的毒性。本研究结果强调了针对 BamA 的合理 AMP 设计的有效性，以及使用 D-氨基酸替换作为开发针对耐药细菌的 AMP 的策略。
