title: Quantitative structure--activity relationship analysis and molecular dynamics simulation to functionally validate nonsynonymous polymorphisms of human ABC transporter ABCB1 (P-glycoprotein/MDR1).
abstract: Several preclinical and clinical studies suggest the importance of naturally occurring polymorphisms of drug transporters in the individual difference of drug response. To functionally validate the nonsynonymous polymorphisms of ABCB1 (P-glycoprotein/MDR1) in vitro, we generated SNP variant forms (i.e., S400N, R492C, R669C, I849M, A893P, A893S, A893T, M986V, A999T, P1051A, and G1063A) and expressed them in Sf9 cells. The kinetic properties (Km and Vmax) of those variants were analyzed by measuring the ATPase activity to obtain the ATPase profile for each variant toward structurally unrelated substrates. On the basis of the experimental data, we determined the substrate specificity of ABCB1 WT and its variants by the quantitative structure-activity relationship (QSAR) analysis method. While several SNP variants appeared to influence the substrate specificity of ABCB1, the nonsynonymous polymorphisms of 2677G > T, A, or C at amino acid position 893 (Ala > Ser, Thr, or Pro) have great impacts on both the activity and the substrate specificity of ABCB1. The A893P variant (2677G > C), a rare mutation, exhibited markedly high activity of ATPase toward different test compounds. Molecular dynamics (MD) simulation based on a three-dimensional structural model of human ABCB1 revealed that multiple kinks are formed in the intracellular loop between transmembrane domains 10 and 11 of the A893P variant (2677G > C) protein. The polymorphisms of 2677G, 2677T, and 2677A exhibit wide ethnic differences in the allele frequency, and these nonsynonymous polymorphisms are suggested to be clinically important because of their altered ATPase activity and substrate specificity toward different drugs.
authors.affiliation: Department of Biomolecular Engineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan.
authors.forename: Aki
authors.initials: A
authors.lastname: Sakurai
authors.forename: Yuko
authors.initials: Y
authors.lastname: Onishi
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Hirano
authors.forename: Michel
authors.initials: M
authors.lastname: Seigneuret
authors.forename: Kazuya
authors.initials: K
authors.lastname: Obanayama
authors.forename: Gunwoo
authors.initials: G
authors.lastname: Kim
authors.forename: Ei Leen
authors.initials: EL
authors.lastname: Liew
authors.forename: Toshiyuki
authors.initials: T
authors.lastname: Sakaeda
authors.forename: Koh-Ichiro
authors.initials: K
authors.lastname: Yoshiura
authors.forename: Norio
authors.initials: N
authors.lastname: Niikawa
authors.forename: Minoru
authors.initials: M
authors.lastname: Sakurai
authors.forename: Toshihisa
authors.initials: T
authors.lastname: Ishikawa
mesh_terms: D018435:ATP Binding Cassette Transporter, Subfamily B; D020168:ATP Binding Cassette Transporter, Subfamily B, Member 1 / Q000235:genetics* / Q000378:metabolism; D000251:Adenosine Triphosphatases / Q000378:metabolism; D000595:Amino Acid Sequence; D000818:Animals; D003198:Computer Simulation; D005787:Gene Frequency; D006801:Humans; D007700:Kinetics; D009529:Nicardipine / Q000494:pharmacology; D011110:Polymorphism, Genetic; D020641:Polymorphism, Single Nucleotide; D021281:Quantitative Structure-Activity Relationship; D017386:Sequence Homology, Amino Acid; D018411:Spodoptera; D013379:Substrate Specificity; D014700:Verapamil / Q000494:pharmacology
chemical_list: C513055:ABCB1 protein, human; D018435:ATP Binding Cassette Transporter, Subfamily B; D020168:ATP Binding Cassette Transporter, Subfamily B, Member 1; D014700:Verapamil; D009529:Nicardipine; D000251:Adenosine Triphosphatases