Screening of potential lead molecules against prioritised targets of multi-drug-resistant-Acinetobacter baumannii – insights from molecular docking, molecular dynamic simulations and in vitro assays

Acinetobacter baumannii, an opportunistic pathogen, has become multi-drug resistant (MDR) to major classes of antibacterial and poses grave threat to public health. The current study focused to screen novel phytotherapeutics against prioritised targets of Acinetobacter baumannii by computational investigation. Fourteen potential drug targets were screened based on their functional role in various biosynthetic pathways and the 3D structures of 9 targets were retrieved from Protein Data Bank and others were computationally predicted. By extensive literature survey, 104 molecules from 48 herbal sources were screened and subjected to virtual screening. Ten clinical isolates of A. baumannii were tested for antibiotic susceptibility towards clinafloxacin, imipenem and polymyxin-E. Computational screening suggested that Ajmalicine ((19α)-16, 17-didehydro-19-methyloxayohimban-16-carboxylic acid methyl ester from Rauwolfia serpentina), Strictamin (Akuammilan-17-oic acid methyl ester from Alstonia scholaris) and Limonin (7, 16-dioxo-7, 16-dideoxylimondiol from Citrus sps) exhibited promising binding towards multiple drug targets of A. baumannii in comparison with the binding between standard drugs and their targets. Limonin displayed promising binding potential (binding energy −9.8 kcal/mol) towards diaminopimelate epimerase (DapF) and UDP-N-acetylglucosamine 1-carboxyvinyltransferase (MurA). Ajmalicine and Strictamin demonstrated good binding potential (−9.5, −8.5 kcal/mol, respectively) towards MurA and shikimate dehydrogenase (−7.8 kcal/mol). Molecular dynamic simulations further validated the docking results. In vitro assay suggested that the tested isolates exhibited resistance to clinafloxacin, imipenem and polymyxin-E and the herbal preparations (crude extract) demonstrated a significant antibacterial potential (p ≤ .05). The study suggests that the aforementioned lead candidates and targets can be used for structure-based drug screening towards MDR A. baumannii.

鲍曼不动杆菌（Acinetobacter baumannii）作为一种机会致病菌，现已对主要类别抗菌药物产生多重耐药性（multi-drug resistant, MDR），对公共卫生构成严重威胁。本研究采用计算生物学研究手段，针对鲍曼不动杆菌的优先靶点筛选新型植物源治疗药物。研究基于14个潜在药物靶点在各类生物合成通路中的功能作用完成筛选，其中9个靶点的三维结构从蛋白质数据库（Protein Data Bank, PDB）中获取，剩余靶点通过计算预测获得。通过广泛的文献调研，从48种植物来源中筛选得到104个小分子化合物，并开展虚拟筛选。选取10株鲍曼不动杆菌临床分离株，检测其对克林沙星、亚胺培南及多粘菌素E的抗生素敏感性。虚拟筛选结果显示，与标准药物与其靶点的结合作用相比，阿义马林（Ajmalicine，(19α)-16,17-二脱氢-19-甲氧基育亨宾-16-羧酸甲酯，来源于蛇根木（Rauwolfia serpentina））、司曲他明（Strictamin，阿枯米灵-17-羧酸甲酯，来源于鸡骨常山（Alstonia scholaris））以及柠檬苦素（Limonin，7,16-二氧代-7,16-二脱氧柠檬苦二醇，来源于柑橘属植物（Citrus sps））可与鲍曼不动杆菌的多个药物靶点展现出优异的结合活性。其中，柠檬苦素对二氨基庚二酸表异构酶（diaminopimelate epimerase, DapF）以及UDP-N-乙酰葡糖胺1-羧基乙烯基转移酶（UDP-N-acetylglucosamine 1-carboxyvinyltransferase, MurA）展现出优异的结合潜能，结合能为-9.8 kcal/mol；阿义马林与司曲他明分别对MurA以及莽草酸脱氢酶（shikimate dehydrogenase）展现出良好的结合潜能，结合能分别为-9.5 kcal/mol与-7.8 kcal/mol。分子动力学模拟进一步验证了该分子对接结果。体外实验结果显示，受试分离株对克林沙星、亚胺培南及多粘菌素E均产生耐药性，而植物粗提物展现出显著的抗菌活性（p ≤ 0.05）。本研究表明，上述候选化合物与靶点可用于针对多重耐药鲍曼不动杆菌的基于结构的药物筛选。