Analysis of P-glycoprotein structure and binding sites

Multidrug resistance is one of the major causes for the failure to successful chemotherapy. Although there are many mechanisms responsible for MDR, classic MDR is associated with the over expression of P-glycoprotein (P-gp), resulting in increased efflux of chemotherapy from cancer cells. It is proposed to operate as a “hydrophobic vacuum cleaner”, expelling non-polar compounds from the membrane bilayer to the exterior, driven by the energy of ATP hydrolysis. Usually, its efflux function can be inhibited by various reverse agents. Structure diversity is a hallmark of P-gp reverse agents, thus a structural description of poly-specific drug-binding is important for the rational design of MDR inhibitors. In this study, the analysis of structure and binding sites of P-gp was carried out based on the crystal structure of mouse P-gp (ABCB1). There were 10 pockets with the volume larger than Ǻ 3 were found with the online tool of Q-SiteFinder. The docking of typical P-gp efflux pump inhibitors such as XR9576 and OC144-093 were carried out and analyzed with Accelrys Discovery Studio. XR9576 and OC144-093 may bind to the nucleotide-binding domain (NBD) and the pocket at the entrance of the transporting site respectively according to the docking results.