Nargotra Amit, Ali Shakir, Koul Surrinder
Discovery Informatics Unit, Indian Institute of Integrative Medicine, Canal Road, Jammu - 180001, India.
Curr Comput Aided Drug Des. 2014;10(3):226-36. doi: 10.2174/157340991003150302230455.
Efflux pump--a membrane protein belonging to Major Facilitator (MF) family and associated with Multi Drug Resistance (MDR) has been a major factor in drug resistance of bacteria. In the era when no new effective antibiotic had been reported for years, the detailed study of these membrane proteins became imperative in order to improve the efficacy of existing drugs. The Bacillus subtilis membrane protein Bmr belongs to the super family of major facilitator proteins and is one of the first-discovered bacterial multidrug-efflux transporters. Development of Bmr inhibitors (B. subtilis) for least resistance, better drug sustainability and effective cellular activity requires three dimensional structure of this protein which has not yet been determined. In this communication structural characterization of this important efflux pump has been attempted using in silico approaches. The modeled structure of Bmr has been found to have 12 main helical segments interspersed by loops of variable lengths at regular intervals with both N- and C-termini on the same side of membrane. Docking of the known inhibitor reserpine on to the predicted structure of Bmr and its mutants signified the importance of the residues Phe143, Val286 and Phe306 in the interaction with the ligand. Besides this, the role of Arg313 and Phe309 in the H-bond formation and π-π interaction respectively, with reserpine was the new significant finding based on the interaction studies. The structure elucidation of Bmr and the role of these residues in binding to the ligand are expected to have a great impact on the efflux pump inhibition studies around the world and hence in the efficiency of the existing antibiotic drugs.
外排泵——一种属于主要易化子（MF）家族且与多药耐药性（MDR）相关的膜蛋白，一直是细菌耐药性的主要因素。在多年未报告有新的有效抗生素的时代，为提高现有药物的疗效，对这些膜蛋白进行详细研究变得势在必行。枯草芽孢杆菌膜蛋白Bmr属于主要易化子蛋白超家族，是最早发现的细菌多药外排转运蛋白之一。开发具有最低耐药性、更好的药物可持续性和有效细胞活性的Bmr抑制剂（枯草芽孢杆菌）需要该蛋白的三维结构，而其三维结构尚未确定。在本通讯中，已尝试使用计算机方法对这种重要的外排泵进行结构表征。已发现Bmr的模拟结构有12个主要螺旋段，以规则间隔穿插着不同长度的环，N端和C端都在膜的同一侧。已知抑制剂利血平与Bmr及其突变体的预测结构对接表明，苯丙氨酸143、缬氨酸286和苯丙氨酸306残基在与配体相互作用中的重要性。除此之外，基于相互作用研究，精氨酸313和苯丙氨酸309分别在与利血平形成氢键和π-π相互作用中的作用是新的重要发现。Bmr的结构阐明以及这些残基在与配体结合中的作用预计将对全球的外排泵抑制研究产生重大影响，从而影响现有抗生素药物的效率。
