Ma Wendong, Jiang Xukai, Mu Kaijie, Tian Sixin, Yu Heidi H, Wickremasinghe Hasini, Velkov Tony, Roberts Kade D, Patil Nitin A, Li Jian
Biomedicine Discovery Institute, Infection Program, Department of Microbiology, Monash University, Melbourne, VIC 3800, Australia.
National Glycoengineering Research Center, Shandong University, Qingdao 266237, Shandong, China.
JACS Au. 2025 Sep 18;5(10):4714-4727. doi: 10.1021/jacsau.5c00587. eCollection 2025 Oct 27.
Multidrug-resistant Gram-negative bacteria have caused a serious threat to global health, and polymyxins are an important last-line therapy. As resistance to polymyxins is emerging, understanding the structure-activity relationship (SAR) of the polymyxins can facilitate the discovery of novel antimicrobial lipopeptides with improved antibacterial activity. However, l-2,4-diaminobutyric acid (Dab) is a key amino acid for the antibacterial activity of polymyxins, and the SAR of five Dab residues has not been well studied. Here, we employed an all-atom molecular dynamics simulation approach by integrating a lipidomics-informed outer membrane (OM)-based model and systematically investigated the SAR of the five Dab residues, specifically the length of their side chains. The impact of the length of the Dab side chain on three activity-related aspects, namely, the conformation of polymyxins, OM penetration ability, and membrane deformation, was systematically examined at the atomic level and compared with antimicrobial activity results. We uncovered that altering the side chain length of the Dab residues at different positions significantly affected the antibacterial activity via distinct mechanisms. Longer side chains of Dab residues in the linear tripeptide segment (Dab and Dab) and shorter side chains in the heptapeptide ring (Dab, Dab, and Dab) resulted in marked changes in OM deformation. Importantly, polymyxin activity is governed by the interplay of multiple structural and functional factors. Our mechanism-based SAR model predicted how these position-specific modifications in Dab side chains modulate polymyxin activity, as supported by experimental validation. Specifically, elongation of the Dab and Dab side chains led to significantly reduced antibacterial activity, while shortening of the Dab side chain enhanced activity. Collectively, the atomic-level SAR of polymyxins centered on the Dab residues will help expedite the rational design of new-generation antimicrobial lipopeptides, and our transferable framework provides broad implications for advancing membrane-active therapeutic agents.
多重耐药革兰氏阴性菌已对全球健康构成严重威胁，而多粘菌素是重要的最后一线治疗药物。随着对多粘菌素耐药性的出现，了解多粘菌素的构效关系（SAR）有助于发现具有改善抗菌活性的新型抗菌脂肽。然而，L-2,4-二氨基丁酸（Dab）是多粘菌素抗菌活性的关键氨基酸，五个Dab残基的构效关系尚未得到充分研究。在此，我们采用全原子分子动力学模拟方法，结合基于脂质组学信息的外膜（OM）模型，系统地研究了五个Dab残基的构效关系，特别是它们侧链的长度。在原子水平上系统地研究了Dab侧链长度对三个与活性相关方面的影响，即多粘菌素的构象、OM穿透能力和膜变形，并与抗菌活性结果进行了比较。我们发现，改变不同位置Dab残基的侧链长度会通过不同机制显著影响抗菌活性。线性三肽段（Dab和Dab）中Dab残基的较长侧链和七肽环（Dab、Dab和Dab）中较短的侧链导致OM变形发生显著变化。重要的是，多粘菌素活性受多种结构和功能因素相互作用的支配。我们基于机制的构效关系模型预测了Dab侧链中这些位置特异性修饰如何调节多粘菌素活性，实验验证也支持了这一点。具体而言，Dab和Dab侧链的延长导致抗菌活性显著降低，而Dab侧链的缩短则增强了活性。总体而言，以Dab残基为中心的多粘菌素原子水平构效关系将有助于加快新一代抗菌脂肽的合理设计，我们的可转移框架为推进膜活性治疗药物具有广泛意义。
