School of Chemistry, University of Southampton, Southampton, UK; Bioinformatics Institute (BII), Agency for Science, Technology and Research (A∗STAR), Singapore, Republic of Singapore.
Bioinformatics Institute (BII), Agency for Science, Technology and Research (A∗STAR), Singapore, Republic of Singapore.
J Biol Chem. 2024 Oct;300(10):107754. doi: 10.1016/j.jbc.2024.107754. Epub 2024 Sep 10.
The rise in multi-drug resistant Gram-negative bacterial infections has led to an increased need for "last-resort" antibiotics such as polymyxins. However, the emergence of polymyxin-resistant strains threatens to bring about a post-antibiotic era. Thus, there is a need to develop new polymyxin-based antibiotics, but a lack of knowledge of the mechanism of action of polymyxins hinders such efforts. It has recently been suggested that polymyxins induce cell lysis of the Gram-negative bacterial inner membrane (IM) by targeting trace amounts of lipopolysaccharide (LPS) localized there. We use multiscale molecular dynamics (MD), including long-timescale coarse-grained (CG) and all-atom (AA) simulations, to investigate the interactions of polymyxin B1 (PMB1) with bacterial IM models containing phospholipids (PLs), small quantities of LPS, and IM proteins. LPS was observed to (transiently) phase separate from PLs at multiple LPS concentrations, and associate with proteins in the IM. PMB1 spontaneously inserted into the IM and localized at the LPS-PL interface, where it cross-linked lipid headgroups via hydrogen bonds, sampling a wide range of interfacial environments. In the presence of membrane proteins, a small number of PMB1 molecules formed interactions with them, in a manner that was modulated by local LPS molecules. Electroporation-driven translocation of PMB1 via water-filled pores was favored at the protein-PL interface, supporting the 'destabilizing' role proteins may have within the IM. Overall, this in-depth characterization of PMB1 modes of interaction reveals how small amounts of mislocalized LPS may play a role in pre-lytic targeting and provides insights that may facilitate rational improvement of polymyxin-based antibiotics.
革兰氏阴性菌耐药性的增加导致对多粘菌素等“最后手段”抗生素的需求增加。然而，多粘菌素耐药菌株的出现威胁着后抗生素时代的到来。因此，需要开发新的多粘菌素类抗生素，但由于对多粘菌素作用机制的了解不足，阻碍了这方面的努力。最近有人提出，多粘菌素通过靶向局部存在的痕量脂多糖（LPS）来诱导革兰氏阴性菌内膜（IM）的细胞裂解。我们使用多尺度分子动力学（MD），包括长时间粗粒度（CG）和全原子（AA）模拟，研究了多粘菌素 B1（PMB1）与含有磷脂（PL）、少量 LPS 和 IM 蛋白的细菌 IM 模型的相互作用。在多个 LPS 浓度下，观察到 LPS 与 PL 发生（瞬时）相分离，并与 IM 中的蛋白质结合。PMB1 自发插入 IM 并定位于 LPS-PL 界面，通过氢键与脂质头基交联，在广泛的界面环境中进行采样。在膜蛋白存在的情况下，少量 PMB1 分子与它们形成相互作用，这种相互作用受到局部 LPS 分子的调节。水填充孔驱动的 PMB1 通过电穿孔易位在蛋白质-PL 界面处有利，这支持了蛋白质在 IM 中可能具有“破坏稳定”的作用。总的来说，对 PMB1 相互作用模式的深入表征揭示了少量定位错误的 LPS 如何在预溶菌靶向中发挥作用，并提供了可能有助于合理改进多粘菌素类抗生素的见解。
