Homology modeling and substrate binding studies of human P-glycoprotein

Abstract

Multidrug-resistance (MDR) in cancer cells often relates to the overexpression of P-glycoprotein (P-gp), resulting in increased efflux of chemotherapy from cancer cells. A clear understanding of P-gp substrate binding will lead to the development of selective P-gp inhibitors, which resensitize cancer cells to standard chemotherapy. Unfortunately, the three-dimensional structure of human P-glycoprotein has not yet been available. In this investigation, homology model of human P-gp was developed based on a recent refined structure of mouse P-gp (PDB: 4M1M). The models were further assessed by Ramachandran plot in PROCHECK, ProSA-web Z-score and QMEAN score. The results indicated that the proposed models were reliable for further binding site and docking studies. Using AutoDock-based blind docking protocol, the probable binding sites for the known substrates rhodamine B, daunorubicin, colchicine, and Hoechst 33342 were identified and in very good agreement with the available side-directed mutagenesis studies. The binding location of the cytotoxic drug vinblastine was identified and characterized. The docking result indicated that vinblastin and verapamil shared overlapping sites on P-gp, composed of residue Leu65, Met69, Ile340, Phe983, Tyr953, and Met986. This might aid in understanding how verapamil, an inhibitor of P-gp, effectively enhanced cytotoxicity of vinblastine against P-gp-mediated MDR. Our observations suggested that human P-gp model derived from 4M1M could better explain the binding of human P-gp substrates/ inhibitors. This model served as a starting point to gain knowledge of P-gp drug-binding region(s) and to identify novel P-gp inhibitors that might have a potential to overcome MDR in cancer therapy.

Search for ABCB1 Modulators Among 2-Amine-5-Arylideneimidazolones as a New Perspective to Overcome Cancer Multidrug Resistance

“…As a reference for further investigations, one of the top-ranked poses (with a docking score −7.471 for the neutral form of verapamil) was chosen for its very good agreement with experimental data. The binding mode of verapamil in this pose follows the pattern of protein-ligand interactions predicted by other authors [32,34,[39][40][41]. The molecule of the ligand is located in the surroundings, including mostly hydrophobic residues: Met 69, Phe 72, Ile 306, Phe 335, Phe 336, Leu 339, Leu 724, Phe 728, Phe 732, Leu 762, Phe 957, Leu 975, Phe 978, Phe 983, and Met 986 ( Figure 4).…”

5-Arylidenerhodanines as P-gp Modulators: An Interesting Effect of the Carboxyl Group on ABCB1 Function in Multidrug-Resistant Cancer Cells

“…The binding sites of 11 and verapamil in hP-gp predicted by IFD were located in the upper part of the internal binding cavity (Figure 3A,B), similarly to other P-gp inhibitors seen in X-ray or cryo-EM complexes [33][34][35]. For verapamil, the binding modes found in docking to the homology model and to the cryo-EM structure were similar and followed the protein-ligand interaction pattern reported for verapamil by other authors (Figure 4A,B) [37][38][39]. The top-ranked docking poses of verapamil in both protein structures formed hydrogen bonds with Tyr307 and Tyr953 as well as aromatic π-π interactions with Phe983.…”