Science Program, School of Chemical Engineering and Science, Faculty of Engineering, Computing and Science, Swinburne University of Technology Sarawak, Kuching 93350, Malaysia.
Department of Biotechnology & Microbiology, Kannur University, Kannur 670 661, Kerala, India.
J Chem Inf Model. 2022 May 23;62(10):2586-2599. doi: 10.1021/acs.jcim.2c00300. Epub 2022 May 9.
Lipoteichoic acid synthase (LtaS) is a key enzyme for the cell wall biosynthesis of Gram-positive bacteria. Gram-positive bacteria that lack lipoteichoic acid (LTA) exhibit impaired cell division and growth defects. Thus, LtaS appears to be an attractive antimicrobial target. The pharmacology around LtaS remains largely unexplored with only two small-molecule LtaS inhibitors reported, namely "compound " and the Congo red dye. Structure-based drug discovery efforts against LtaS remain unattempted due to the lack of an inhibitor-bound structure of LtaS. To address this, we combined the use of a molecular docking technique with molecular dynamics (MD) simulations to model a plausible binding mode of compound to the extracellular catalytic domain of LtaS (eLtaS). The model was validated using alanine mutagenesis studies combined with isothermal titration calorimetry. Additionally, lead optimization driven by our computational model resulted in an improved version of compound , namely, compound which showed greater affinity for binding to eLtaS than compound in biophysical assays. Compound reduced LTA production in dose-dependently, induced aberrant morphology as seen for LTA-deficient bacteria, and significantly reduced bacteria titers in the lung of mice infected with . Analysis of our MD simulation trajectories revealed the possible formation of a transient cryptic pocket in eLtaS. Virtual screening (VS) against the cryptic pocket led to the identification of a new class of inhibitors that could potentiate β-lactams against methicillin-resistant . Our overall workflow and data should encourage further drug design campaign against LtaS. Finally, our work reinforces the importance of considering protein conformational flexibility to a successful VS endeavor.
脂磷壁酸合成酶（LtaS）是革兰氏阳性菌细胞壁生物合成的关键酶。缺乏脂磷壁酸（LTA）的革兰氏阳性菌表现出细胞分裂受损和生长缺陷。因此，LtaS 似乎是一个有吸引力的抗菌靶标。围绕 LtaS 的药理学仍在很大程度上未被探索，仅报道了两种小分子 LtaS 抑制剂，即“化合物”和刚果红染料。由于缺乏 LtaS 的抑制剂结合结构，针对 LtaS 的基于结构的药物发现工作仍未尝试。为了解决这个问题，我们结合使用分子对接技术和分子动力学（MD）模拟来模拟化合物与 LtaS 细胞外催化结构域（eLtaS）的合理结合模式。该模型通过结合使用丙氨酸突变研究和等温滴定量热法进行了验证。此外，我们的计算模型驱动的先导化合物优化导致了化合物的改进版本，即化合物，其在生物物理测定中比化合物对 eLtaS 的结合亲和力更高。化合物以剂量依赖性方式降低 LTA 的产生，诱导 LTA 缺陷细菌的异常形态，并显著降低感染的小鼠肺部中的细菌滴度。对我们的 MD 模拟轨迹的分析揭示了 eLtaS 中可能形成瞬态隐匿口袋。针对隐匿口袋的虚拟筛选导致鉴定出一类新的抑制剂，可增强β-内酰胺类药物对耐甲氧西林的作用。我们的整体工作流程和数据应鼓励针对 LtaS 进行进一步的药物设计活动。最后，我们的工作强调了考虑蛋白质构象灵活性对于成功的虚拟筛选工作的重要性。
