Molecular interaction studies of thymol via molecular dynamic simulations and free energy calculations using multi-target approach against <i>Aedes aegypti</i> proteome to decipher its role as mosquito repellent

<i>Aedes aegypti</i> (<i>A. aegypti</i>) is the principal vector for several diseases and despite having synthetic repellents to curb its feeding and transmission, they pose a threat to humans upon chronic use. Therefore, this study explores natural alternative thymol, via both structural and molecular binding properties against whole proteome targets of <i>A.</i> using a multi-target approach<i>.</i> Properties of thymol were studied using ProTox-II to determine the toxicity class. A preliminary screening of the proteome of <i>A. aegypti</i> was performed using existing microarray data analysis, conserved domain studies and protein modelling to narrow down the target categories. RaptorX standalone high-computing server was utilised for 309 protein structure modelling. Molecular docking was performed for 20 shortlisted protein categories against thymol, and top three docked complexes were simulated at 100 ns. Results showed that thymol belonged to class 4 low-toxicity, and molecular docking and 100 ns simulations in dynamic environment revealed stable complexes of thymol with glutathione-S-transferase (GST), octopamine receptor and glutamate-gated chloride channels (GGCC). Free energy binding via molecular mechanics revealed thymol with GST and GGCC to be stable. Our multi-target study presents insights into the molecular binding events that take place when thymol binds to newly identified <i>A. aegypti</i> targets.埃及伊蚊（Aedes aegypti，简称A. aegypti）是多种疾病的主要传播媒介。尽管目前已有合成驱避剂可抑制其吸血行为与疾病传播，但长期使用该类药剂会对人类健康构成威胁。为此，本研究以天然替代物百里酚（thymol）为研究对象，采用多靶点策略，从结构特性与分子结合特性层面探究其针对埃及伊蚊全蛋白质组靶点的作用效果。研究人员通过ProTox-II工具分析百里酚的相关性质，以确定其毒性等级；利用现有微阵列数据分析、保守结构域研究及蛋白质建模技术，对埃及伊蚊蛋白质组进行初步筛选，以缩小候选靶点的类别范围。本研究借助RaptorX独立高性能计算服务器完成了309个蛋白质的结构建模；针对筛选出的20个蛋白质类别开展百里酚分子对接实验，并选取排名前三的对接复合物进行100纳秒的分子动力学模拟。实验结果显示，百里酚属于4级低毒性物质；分子对接与100纳秒动态环境下的分子动力学模拟结果表明，百里酚可与谷胱甘肽S-转移酶（GST）、章鱼胺受体及谷氨酸门控氯离子通道（GGCC）形成稳定复合物。分子力学结合自由能分析进一步证实，百里酚与GST及GGCC的结合稳定性优异。本多靶点研究揭示了百里酚与新发现的埃及伊蚊靶点结合时的分子结合过程与机制。