Bhaskar Baki Vijaya, Babu Tirumalasetty Muni Chandra, Reddy Netala Vasudeva, Rajendra Wudayagiri
Division of Molecular Biology, Department of Zoology.
Department of Biotechnology, Sri Venkateswara University, Tirupati, Andhra Pradesh, India.
Drug Des Devel Ther. 2016 Oct 3;10:3237-3252. doi: 10.2147/DDDT.S113556. eCollection 2016.
Emerging drug resistance in clinical isolates of might be implicated to the overexpression of NorA efflux pump which is capable of extruding numerous structurally diverse compounds. However, NorA efflux pump is considered as a potential drug target for the development of efflux pump inhibitors. In the present study, NorA model was constructed based on the crystal structure of glycerol-3-phosphate transporter (PDBID: 1PW4). Molecular dynamics (MD) simulation was performed using NAMD2.7 for NorA which is embedded in the hydrated lipid bilayer. Structural design of NorA unveils amino (N)- and carboxyl (C)-terminal domains which are connected by long cytoplasmic loop. N and C domains are composed of six transmembrane α-helices (TM) which exhibits pseudo-twofold symmetry and possess voluminous substrate binding cavity between TM helices. Molecular docking of reserpine, totarol, ferruginol, salvin, thioxanthene, phenothiazine, omeprazole, verapamil, nalidixic acid, ciprofloxacin, levofloxacin, and acridine to NorA found that all the molecules were bound at the large hydrophobic cleft and indicated significant interactions with the key residues. In addition, structure-based virtual screening was employed which indicates that 14 potent novel lead molecules such as CID58685302, CID58685367, CID5799283, CID5578487, CID60028372, ZINC12196383, ZINC72140751, ZINC72137843, ZINC39227983, ZINC43742707, ZINC12196375, ZINC66166948, ZINC39228014, and ZINC14616160 have highest binding affinity for NorA. These lead molecules displayed considerable pharmacological properties as evidenced by Lipinski rule of five and prophecy of toxicity risk assessment. Thus, the present study will be helpful in designing and synthesis of a novel class of NorA efflux pump inhibitors that restore the susceptibilities of drug compounds.
临床分离株中出现的耐药性可能与诺氟沙星外排泵的过表达有关，该泵能够排出多种结构不同的化合物。然而，诺氟沙星外排泵被认为是开发外排泵抑制剂的潜在药物靶点。在本研究中，基于甘油-3-磷酸转运蛋白的晶体结构（PDBID: 1PW4）构建了诺氟沙星模型。使用NAMD2.7对嵌入水合脂质双层的诺氟沙星进行分子动力学（MD）模拟。诺氟沙星的结构设计揭示了由长细胞质环连接的氨基（N）端和羧基（C）端结构域。N和C结构域由六个跨膜α-螺旋（TM）组成，呈现假二重对称，并且在TM螺旋之间具有大量的底物结合腔。利血平、托塔罗醇、铁杉醇、萨尔文、噻吨、吩噻嗪、奥美拉唑、维拉帕米、萘啶酸、环丙沙星、左氧氟沙星和吖啶与诺氟沙星的分子对接发现，所有分子都结合在大的疏水裂缝处，并与关键残基有显著相互作用。此外，采用基于结构的虚拟筛选，结果表明14种有效的新型先导分子，如CID58685302、CID58685367、CID5799283、CID5578487、CID60028372、ZINC12196383、ZINC72140751、ZINC72137843、ZINC39227983、ZINC43742707、ZINC12196375、ZINC66166948、ZINC39228014和ZINC14616160对诺氟沙星具有最高的结合亲和力。这些先导分子表现出相当的药理特性，这由Lipinski五规则和毒性风险评估预测所证明。因此，本研究将有助于设计和合成一类新型的诺氟沙星外排泵抑制剂，恢复药物化合物的敏感性。
