title: In silico model for P-glycoprotein substrate prediction: insights from molecular dynamics and in vitro studies.
abstract: P-glycoprotein (P-gp) is a plasma membrane efflux transporter belonging to ATP-binding cassette superfamily, responsible for multidrug resistance in tumor cells. Over-expression of P-gp in cancer cells limits the efficacy of many anticancer drugs. A clear understanding of P-gp substrate binding will be advantageous in early drug discovery process. However, substrate poly-specificity of P-gp is a limiting factor in rational drug design. In this investigation, we report a dynamic trans-membrane model of P-gp that accurately identified the substrate binding residues of known anticancer agents. The study included homology modeling of human P-gp based on the crystal structure of C. elegans P-gp, molecular docking, molecular dynamics analyses and binding free energy calculations. The model was further utilized to speculate substrate propensity of in-house anticancer compounds. The model demonstrated promising results with one anticancer compound (NSC745689). As per our observations, the molecule could be a potential lead for anticancer agents devoid of P-gp mediated multiple drug resistance. The in silico results were further validated experimentally using Caco-2 cell lines studies, where NSC745689 exhibited poor permeability (P app 1.03 ± 0.16 × 10(-6) cm/s) and low efflux ratio of 0.26.
authors.affiliation: Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Sector-67, S.A.S. Nagar, 160 062, Punjab, India.
authors.forename: Rameshwar
authors.initials: R
authors.lastname: Prajapati
authors.forename: Udghosh
authors.initials: U
authors.lastname: Singh
authors.forename: Abhijeet
authors.initials: A
authors.lastname: Patil
authors.forename: Kailas S
authors.initials: KS
authors.lastname: Khomane
authors.forename: Pravin
authors.initials: P
authors.lastname: Bagul
authors.forename: Arvind K
authors.initials: AK
authors.lastname: Bansal
authors.forename: Abhay T
authors.initials: AT
authors.lastname: Sangamwar
mesh_terms: D020168:ATP Binding Cassette Transporter, Subfamily B, Member 1 / Q000737:chemistry / Q000378:metabolism*; D000818:Animals; D000970:Antineoplastic Agents / Q000378:metabolism* / Q000493:pharmacokinetics / Q000494:pharmacology*; D018938:Caco-2 Cells; D017173:Caenorhabditis elegans / Q000737:chemistry / Q000378:metabolism; D029742:Caenorhabditis elegans Proteins / Q000378:metabolism; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D019008:Drug Resistance, Neoplasm; D006801:Humans; D008954:Models, Biological; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D009369:Neoplasms / Q000188:drug therapy*; D040681:Structural Homology, Protein; D013379:Substrate Specificity; D013816:Thermodynamics
chemical_list: D020168:ATP Binding Cassette Transporter, Subfamily B, Member 1; D000970:Antineoplastic Agents; D029742:Caenorhabditis elegans Proteins