Homology modelling of human P-glycoprotein

Biochemical Society Transactions

Volumn 43, Issue , 2015, Pages 952-958

  Domicevica, Laura ^a   Biggin, Philip C ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

ATP binding cassette (ABC) transporters; Computational; Export pump; Molecular dynamics; Multi drug resistance; Simulation

Indexed keywords

MULTIDRUG RESISTANCE PROTEIN; DRUG; LIPID BILAYER;

ARTICLE; HUMAN; MOLECULAR DYNAMICS; PRIORITY JOURNAL; SEQUENCE HOMOLOGY; BINDING SITE; CHEMISTRY; LIPID BILAYER; METABOLISM; MULTIDRUG RESISTANCE; PROTEIN CONFORMATION; TRANSPORT AT THE CELLULAR LEVEL; X RAY CRYSTALLOGRAPHY;

BINDING SITES; BIOLOGICAL TRANSPORT; CRYSTALLOGRAPHY, X-RAY; DRUG RESISTANCE, MULTIPLE; HUMANS; LIPID BILAYERS; MOLECULAR DYNAMICS SIMULATION; P-GLYCOPROTEINS; PHARMACEUTICAL PREPARATIONS; PROTEIN CONFORMATION;

EID: 84947211368     PISSN: 03005127     EISSN: 14708752     Source Type: Journal    
DOI: 10.1042/BST20150125     Document Type: Article

References (54)

1. Wong, K., Ma, J., Rothnie, A., Biggin, P.C. and Kerr, I.D. (2014) Towards understanding promiscuity in multidrug efflux pumps. Trends Biochem. Sci. 39, 8-16 CrossRef PubMed
2. Ferreira, R.J., Ferreira, M.-J.U. and dos Santos, D.J.V.A. (2015) Reversing cancer multidrug resistance: insights into the efflux by ABC transports from in silico studies. Wiley Interdiscip. Rev. Comp. Mol. Sci. 5, 27-55 CrossRef
3. Chen, L., Li, Y., Yu, H., Zhang, L. and Hou, T. (2012) Computational models for predicting substrates or inhibitors of P-glycoprotein. Drug Discov. Today 17, 343-351 CrossRef PubMed
4. Dawson, R.J.P. and Locher, K.P. (2006) Structure of a bacterial multidrug ABC transporter. Nature 443, 180-185 CrossRef PubMed
5. Dawson, R.J.P. and Locher, K.P. (2007) Structure of the multidrug ABC transporter Sav1866 from Staphylococcus aureus in complex with AMP-PNP. FEBS Lett. 581, 935-938 CrossRef PubMed
6. Ward, A., Reyes, C.L., Yu, J., Roth, C.B. and Chang, G. (2007) Flexibility in the ABC transporter MsbA: alternating access with a twist. Proc. Natl. Acad. Sci. U.S.A. 104, 19005-19010 CrossRef PubMed
7. Jin, M.S., Oldham, M.L., Zhang, Q. and Chen, J. (2012) Crystal structure of the multidrug transporter P-glycoprotein from Caenorhabditis elegans. Nature 490, 566-569 CrossRef PubMed
8. Loo, T.W. and Clarke, D.M. (2013) Drug rescue distinguishes between different structural models of human P-glycoprotein. Biochemistry 52, 7167-7169 CrossRef PubMed
9. Szewczyk, P., Tao, H., McGrath, A.P., Villaluz, M., Rees, S.D., Lee, S.C., Doshi, R., Urbatsch, I.L., Zhang, Q. and Chang, G. (2015) Snapshots of ligand entry, malleable binding and induced helical movement in P-glycoprotein. Acta Cryst. D 71, 732-741 CrossRef
10. Ward, A.B., Szewczyk, P., Grimard, V., Lee, C.-W., Martinez, L., Doshi, R., Caya, A., Villaluz, M., Pardon, E., Cregger, C. et al. (2013) Structures of P-glycoprotein reveal its conformational flexibility and an epitope on the nucleotide-binding domain. Proc. Natl. Acad. Sci. U.S.A. 110, 13386-13391 CrossRef PubMed
11. Li, J., Jaimes, K.F. and Aller, S.G. (2014) Refined structures of mouse P-glycoprotein. Protein Sci 23, 34-46 CrossRef PubMed
12. Chufan, E.E., Kapoor, K., Sim, H.-M., Singh, S., Talele, T.T., Durell, S.R. and Ambudkar, S.V. (2013) Multiple transport-active binding sites are available for a single substrate on human P-Glycoprotein (ABCB1). PLoS One 8, e82463 CrossRef PubMed
13. Ma, J. and Biggin, P.C. (2013) Substrate versus inhibitor dynamics of P-glycoprotein. Prot. Struc. Func. Gen. 81, 1653-1668 CrossRef
14. O'Mara, M.L. and Mark, A.E. (2012) The effect of environment on the structure of a membrane protein: P-glycoprotein under physiological conditions. J. Chem. Theory Comput. 8, 3964-3976 CrossRef
15. Hrycyna, C.A., Airan, L.E., Germann, U.A., Ambudkar, S.V., Pastan, I. and Gottesman, M.M. (1998) Structural flexibility of the linker region of human P-glycoprotein permits ATP hydrolysis and drug transport. Biochemistry 37, 13660-13673 CrossRef PubMed
16. Sato, T., Kodan, A., Kimura, Y., Ueda, K., Nakatsu, T. and Kato, H. (2009). Functional role of the linker region in purified human P-glycoprotein. FEBS J 276, 3504-3516 CrossRef PubMed
17. Ferreira, R.J., Ferreira, M.-J.U. and dos Santos, D.J.V.A. (2013) Assessing the stabilization of p-glycoprotein's nucleotide-binding domains by the linker, using molecular dynamics. Mol. Inform. 32, 529-540 CrossRef
18. Moradi, M. and Tajkhorshid, E. (2013) Mechanistic picture for conformational transition of a membrane transporter at atomic resolution. Proc. Natl. Acad. Sci. U.S.A. 110, 18916-18921 CrossRef PubMed
19. Aittoniemi, J., de Wet, H., Ashcroft, F.M. and Sansom, M.S.P. (2010). Asymmetric switching in a homodimeric ABC transporter: a simulation study. PLoS Comp. Biol. 6, e1000762 CrossRef
20. Becker, J.-P., Van Bambeke, F.o., Tulkens, P.M. and Pré vost, M. (2010). Dynamics and structural changes induced by ATP binding in SAV1866, a bacterial ABC exporter. J. Phys. Chem. B. 114, 15948-15957 CrossRef PubMed
21. Gyimesi, G., Ramachandran, S., Kota, P., Dokholyan, N.V., Sarkadi, B. and Hegeds, T. (2011) ATP hydrolysis at one of the two sites in ABC transporters initiates transport related conformational transitions. Biochim. Biophys. Acta 1808, 2954-2964 CrossRef PubMed
22. Jones, P.M. and George, A.M. (2011) Molecular-dynamics simulations of the ATP/apo state of a multidrug ATP-Binding Cassette transporter provide a structural and mechanistic basis for the asymmetric occluded state. Biophys. J. 100, 3025-3034 CrossRef PubMed
23. Oliveira, A.S., Baptista, A.M. and Soares, C.M. (2011) Conformational changes induced by ATP-hydrolysis in an ABC transporter: a molecular dynamics study of the Sav1866 exporter. Proteins 79, 1977-1990 CrossRef PubMed
24. St-Pierre, J.-F., Bunker, A., Róg, T., Karttunen, M. and Mousseau, N. (2012) Molecular dynamics simulations of the bacterial ABC transporter SAV1866 in the closed form. J. Phys. Chem. B 116, 2934-2942 CrossRef PubMed
25. Pajeva, I.K., Globisch, C. and Wiese, M. (2009) Comparison of the inward- and outward-open homology models and ligand binding of human P-glycoprotein. FEBS J 276, 7016-7026 CrossRef PubMed
26. Pajeva, I.K., Globisch, C. and Wiese, M. (2009) Combined pharmacophore modeling, docking, and 3D QSAR studies of ABCB1 and ABCC1 transporter inhibitors. ChemMedChem 4, 1883-1896 CrossRef PubMed
27. Palmeira, A., Vasconcelos, M.H., Paiva, A., Fernandes, M.X., Pinto, M. and Sousa, E. (2012) Dual inhibitors of P-glycoprotein and tumor cell growth: (Re)discovering thioxanthones. Biochem. Pharm. 83, 57-68 CrossRef
28. Yamaguchi, H., Kidachi, Y., Kamiie, K., Noshita, T. and Umetsu, H. (2012). Homology modeling and structural analysis of human P-glycoprotein. Bioinformation 8, 1066-1074 CrossRef PubMed
29. Tajima, Y., Nakagawa, H., Tamura, A., Kadioglu, O., Satake, K., Mitani, Y., Murase, H., Regasini, L.O., da Silva Bolzani, V., Ishikawa, T. et al. (2014). Nitensidine A, a guanidine alkaloid from Pterogyne nitens, is a novel substrate for human ABC transporter ABCB1. Phytomed. 21, 323-332 CrossRef
30. Klepsch, F., Chiba, P. and Ecker, G.F. (2011) Exhaustive sampling of docking poses reveals binding hypotheses for propafenone type inhibitors of P-glycoprotein. PLoS Comput. Biol. 7, e1002036 CrossRef PubMed
31. Jabeen, I., Wetwitayaklung, P., Klepsch, F., Parveen, Z., Chiba, P. and Ecker, G.F. (2011) Probing the stereoselectivity of P-glycoprotein-synthesis, biological activity and ligand docking studies of a set of enantiopure benzopyrano[3,4-b][1,4]oxazines. Chem. Commun. 47, 2586-2588 CrossRef
32. Jabeen, I., Pleban, K., Rinner, U., Chiba, P. and Ecker, G.F. (2012). Structure-activity relationships, ligand efficiency, and lipophilic efficiency profiles of benzophenone-type inhibitors of the multidrug transporter P-Glycoprotein. J. Med. Chem. 55, 3261-3273 CrossRef PubMed
33. Pajeva, I.K., Sterz, K., Christlieb, M., Steggemann, K., Marighetti, F. and Wiese, M. (2013) Interactions of the multidrug resistance modulators tariquidar and elacridar and their analogues with P-glycoprotein. ChemMedChem 8, 1701-1713 CrossRef PubMed
34. Jara, G.E., Vera, D.M.A. and Pierini, A.B. (2013) Binding of modulators to mouse and human multidrug resistance P-glycoprotein. A computational study. J. Mol. Graph. Model. 46, 10-21 CrossRef PubMed
35. Singh, D., Godbole, M. and Misra, K. (2013) A plausible explanation for enhanced bioavailability of P-gp substrates in presence of piperine: simulation for next generation of P-gp inhibitors. J. Mol. Model. 19, 227-238 CrossRef PubMed
36. Xu, X., Li, R., Ma, M., Wang, X., Wang, Y. and Zou, H. (2012) Multidrug resistance protein P-glycoprotein does not recognize nanoparticle C60: experiment and modeling. Soft Matter 8, 2915-2923 CrossRef
37. Zhang, J., Sun, T., Liang, L., Wu, T. and Wang, Q. (2014) Drug promiscuity of P-glycoprotein and its mechanism of interaction with paclitaxel and doxorubicin. Soft Matter 10, 438-445 CrossRef PubMed
38. Prajapati, R., Singh, U., Patil, A., Khomane, K., Bagul, P., Bansal, A. and Sangamwar, A. (2013) In silico model for P-glycoprotein substrate prediction: insights from molecular dynamics and in vitro studies. J. Comp. Aided Mol. Des. 27, 347-363 CrossRef
39. O'Mara, M.L. and Tieleman, D.P. (2007) P-glycoprotein models of the apo and ATP-bound states based on homology with Sav1866 and MalK. FEBS Lett 581, 4217-4222 CrossRef PubMed
40. Wise, J.G. (2012) Catalytic transitions in the human MDR1 P-glycoprotein drug binding sites. Biochemistry 51, 5125-5141 CrossRef PubMed
41. Brewer, F.K., Follit, C.A., Vogel, P.D. and Wise, J.G. (2014) In silico screening for inhibitors of P-glycoprotein that target the nucleotide binding domains. Mol. Pharm. 86, 716-726 CrossRef
42. Pajeva, I.K., Hanl, M. and Wiese, M. (2013) Protein contacts and ligand binding in the inward-facing model of human P-Glycoprotein. ChemMedChem 8, 748-762 CrossRef PubMed
43. Zeino, M., Saeed, M.M., Kadioglu, O. and Efferth, T. (2014) The ability of molecular docking to unravel the controversy and challenges related to P-glycoprotein - a well-known, yet poorly understood drug transporter. Invest. New Drugs 32, 618-625 CrossRef PubMed
44. Pan, L. and Aller, S.G. (2015) Equilibrated atomic models of outward-facing p-glycoprotein and effect of ATP binding on structural dynamics. Sci. Rep. 5, 7880 CrossRef PubMed
45. Subramanian, N., Condic-Jurkic, K., Mark, A.E. and O'Mara, M.L. (2015). Identification of possible binding sites for morphine and nicardipine on the multidrug transporter P-glycoprotein using umbrella sampling techniques. J. Chem. Inf. Model. 55, 1202-1217 CrossRef PubMed
46. Klappe, K., Hummel, I., Hoekstra, D. and Kok, J.W. (2009) Lipid dependence of ABC transporter localization and function. Chem. Phys. Lipids 161, 57-64 CrossRef PubMed
47. Shen, M.Y. and Sali, A. (2006) Statistical potential for assessment and prediction of protein structures. Protein Sci 15, 2507-2524 CrossRef PubMed
48. Benkert, P., Biasini, M. and Schwede, T. (2011) Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics 27, 343-350 CrossRef PubMed
49. Kodan, A., Yamaguchi, T., Nakatsu, T., Sakiyama, K., Hipolito, C.J., Fujioka, A., Hirokane, R., Ikeguchi, K., Watanabe, B., Hiratake, J. et al. (2014). Structural basis for gating mechanisms of a eukaryotic P-glycoprotein homolog. Proc. Natl. Acad. Sci. U.S.A. 111, 4049-4054 CrossRef PubMed
50. Wen, P.-C., Verhalen, B., Wilkens, S., McHaourab, H.S. and Tajkhorshid, E. (2013) On the origin of large flexibility of P-glycoprotein in the inward-facing state. J. Biol. Chem. 288, 19211-19220 CrossRef PubMed
51. Aller, S.G., Yu, J., Ward, A., Weng, Y., Chittaboina, S., Zhuo, R., Harrell, P.M., Trinh, Y.T., Zhang, Q., Urbatsch, I.L. and Chang, G. (2009) Structure of P-glycoprotein reveals a molecular basis for poly-specific drug binding. Science 323, 1718-1722 CrossRef PubMed
52. Hohl, M., Briand, C., Grütter, M.G. and Seeger, M.A. (2012) Crystal structure of a heterodimeric ABC transporter in its inward-facing conformation. Nat. Struct. Mol. Biol. 19, 395-402 CrossRef PubMed
53. Shintre, C.A., Pike, A.C.W., Li, Q., Kim, J.-I., Barr, A.J., Goubin, S., Shrestha, L., Yang, J., Berridge, G., Ross, J. et al. (2013) Structures of ABCB10, a human ATP-binding cassette transporter in apo- and nucleotide-bound states. Proc. Natl. Acad. Sci. U.S.A. 110, 9710-9715 CrossRef PubMed
54. Choudhury, H.G., Tong, Z., Mathavan, I., Li, Y., Iwata, S., Zirah, S., Rebuffat, S., van Veen, H.W. and Beis, K. (2014) Structure of an antibacterial peptide ATP-binding cassette transporter in a novel outward occluded state. Proc. Natl. Acad. Sci. U.S.A. 111, 9145-9150 CrossRef PubMed