Computational models for predicting the interaction with ABC transporters

Drug Discovery Today: Technologies

Volumn 12, Issue , 2014, Pages

  Pinto, Marta ^a   Digles, Daniela ^a   Ecker, Gerhard F ^a  

^a UNIVERSITY OF VIENNA   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

ABC TRANSPORTER; BILE SALT EXPORT PUMP; BREAST CANCER RESISTANCE PROTEIN; LIGAND; MULTIDRUG RESISTANCE ASSOCIATED PROTEIN 1; MULTIDRUG RESISTANCE ASSOCIATED PROTEIN 2; MULTIDRUG RESISTANCE ASSOCIATED PROTEIN 3; MULTIDRUG RESISTANCE ASSOCIATED PROTEIN 6; MULTIDRUG RESISTANCE PROTEIN 1; DRUG; XENOBIOTIC AGENT;

ARTICLE; COMPARATIVE MOLECULAR FIELD ANALYSIS; HUMAN; MOLECULAR INTERACTION; MOLECULAR MODEL; PHARMACOPHORE; ANIMAL; BIOLOGICAL MODEL; BIOLOGY; CHEMISTRY; ENZYME SPECIFICITY; FORECASTING; METABOLISM; PROCEDURES; QUANTITATIVE STRUCTURE ACTIVITY RELATION;

ANIMALS; ATP-BINDING CASSETTE TRANSPORTERS; COMPUTATIONAL BIOLOGY; FORECASTING; HUMANS; LIGANDS; MODELS, BIOLOGICAL; PHARMACEUTICAL PREPARATIONS; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; SUBSTRATE SPECIFICITY; XENOBIOTICS;

EID: 84901191208     PISSN: None     EISSN: 17406749     Source Type: Journal    
DOI: 10.1016/j.ddtec.2014.03.007     Document Type: Review

References (54)

1. W. Saurin, M. Hofnung, and E. Dassa Getting in or out: early segregation between importers and exporters in the evolution of ATP-binding cassette (ABC) transporters J. Mol. Evol. 48 1999 22 24
2. M. Dean, A. Rzhetsky, and R. Allikmets The human ATP-binding cassette (ABC) transporter superfamily Genome Res. 11 2001 1156 1166
3. K.F. Ejendal, and C.A. Hrycyna Multidrug resistance and cancer: the role of the human ABC transporter ABCG2 Current Protein Pept. Sci. 3 2002 503 511
4. L.Z. Benet, T. Izumi, Y. Zhang, J.A. Silverman, and V.J. Wacher Intestinal MDR transport proteins and P-450 enzymes as barriers to oral drug delivery J. Control Release 62 1999 25 31
5. M.V. Varma, K. Sateesh, and R. Panchagnula Functional role of P-glycoprotein in limiting intestinal absorption of drugs: contribution of passive permeability to P-glycoprotein mediated efflux transport Mol. Pharm. 2 2005 12 21
6. A.H. Schinkel, and J.W. Jonker Mammalian drug efflux transporters of the ATP binding cassette (ABC) family: an overview Adv. Drug Deliv. Rev. 55 2003 3 29
7. http://www.fda.gov/Drugs/DevelopmentApprovalProcess/DevelopmentResources/ DrugInteractionsLabeling/ucm093664.htm#PgpTransport (accessed 16.01.14)
8. M.J. Zamek-Gliszczynski, K.A. Hoffmaster, D.J. Tweedie, K.M. Giacomini, and K.M. Hillgren Highlights from the International Transporter Consortium Second Workshop Clin. Pharmacol. Therap. 92 2012 553 556
9. R.J. Dawson, and K.P. Locher Structure of a bacterial multidrug ABC transporter Nature 443 2006 180 185
10. A. Ward, C.L. Reyes, J. Yu, C.B. Roth, and G. Chang Flexibility in the ABC transporter MSBA: alternating access with a twist Proc. Natl. Acad. Sci. U. S. A. 104 2007 19005 19010
11. S.G. Aller, J. Yu, A. Ward, Y. Weng, S. Chittaboina, and R. Zhuo et al. Structure of P-glycoprotein reveals a molecular basis for poly-specific drug binding Science 323 2009 1718 1722
12. M.S. Jin, M.L. Oldham, Q. Zhang, and J. Chen Crystal structure of the multidrug transporter P-glycoprotein from Caenorhabditis elegans Nature 490 2012 566 569
13. C.A. Shintre, A.C. Pike, Q. Li, J.I. Kim, A.J. Barr, and S. Goubin et al. Structures of ABCB10, a human ATP-binding cassette transporter in apo-and nucleotide-bound states Proc. Natl. Acad. Sci. U. S. A. 110 2013 9710 9715
14. L.M. Chan, S. Lowes, and B.H. Hirst The ABCs of drug transport in intestine and liver: efflux proteins limiting drug absorption and bioavailability Eur. J. Pharm. Sci. 21 2004 25 51
15. P. Borst, R. Evers, M. Kool, and J. Wijnholds A family of drug transporters: the multidrug resistance-associated proteins J. Natl. Cancer Inst. 92 2000 1295 1302
16. L. Chen, Y. Li, H. Yu, L. Zhang, and T. Hou Computational models for predicting substrates or inhibitors of P-glycoprotein Drug Discov. Today 17 2012 343 351
17. F. Brocatelli, E. Carosati, A. Neri, M. Frosini, L. Goracci, and T.I. Oprea et al. A novel approach for predicting P-glycoprotein (ABCB1) inhibition using molecular interaction fields J. Med. Chem. 54 2011 1740 1751
18. V. Poongavanam, N. Haider, and G.F. Ecker Fingerprint-based in silico models for the prediction of P-glycoprotein substrates and inhibitors Bioorg. Med. Chem. 20 2012 5388 5395
19. W. Tan, H. Mei, L. Chao, T. Liu, X. Pan, and M. Shu et al. Combined QSAR and molecule docking studies on predicting P-glycoprotein inhibitors J. Comput. Aided Mol. Des. 27 2013 1067 1073
20. F. Klepsch, P. Vasanthanathan, and G.F. Ecker Ligand and structure-based classification models for prediction of P-glycoprotein inhibitors J. Chem. Inf. Model. 54 2014 218 229
21. Z. Bikadi, I. Hazai, D. Malik, K. Jemnitz, Z. Veres, and P. Hari et al. Predicting P-glycoprotein-mediated drug transport based on Support Vector Machine and three-dimensional crystal structure of P-glycoprotein PLoS ONE 6 2011 e25815
22. J.Y. Joung, H. Kim, H.M. Kim, S.K. Ahn, K.Y. Nam, and K.T. No Prediction models of P-glycoprotein substrates using simple 2D and 3D descriptors by recursive partitioning approach Bull. Korean Chem. Soc. 33 2012 1123 1127
23. F. Broccatelli QSAR models for P-glycoprotein transport based on a highly consistent data set J. Chem. Inf. Model. 52 2012 2462 2470
24. S. Childs, R.L. Yeh, E. Georges, and V. Ling Identification of a sister gene to P-glycoprotein Cancer Res. 55 1995 2029 2034
25. R. Thompson, and S. Strautnieks BSEP: function and role in progressive familial intrahepatic cholestasis Semin. Liver Dis. 21 1995 545 550
26. P.J. Meier, and B. Stieger Bile salt transporters Annu. Rev. Physiol. 64 2002 635 661
27. P.L.M. Jansen, M. Müller, and E. Sturm Genes and cholestasis Hepatology 34 2003 1067 1074
28. C. Pauli-Magnus, T. Lang, Y. Meier, T. Zodan-Marin, D. Jung, and C. Breymann et al. Sequence analysis of bile salt export pump (ABCB11) and multidrug resistance p-glycoprotein 3 (ABCB4, MDR3) in patients with intrahepatic cholestasis of pregnancy Pharmacogenetics 14 2004 91 102
29. H. Hirano, A. Kurata, Y. Onishi, A. Sakurai, H. Saito, and H. Nakagawa et al. High-speed screening and QSAR analysis of human ATP-binding cassette transporter ABCB11 (bile salt export pump) to predict drug-induced intrahepatic cholestasis Mol. Pharm. 3 2006 252 265
30. D.J. Warner, H. Chen, L.D. Cantin, J.G. Kenna, S. Stahl, and C.L. Walker et al. Mitigating the inhibition of human bile salt export pump by drugs: opportunities provided by physicochemical property modulation, in-silico modeling and structural modification Drug Metab. Dispos. 40 2012 2332 2341
31. J.M. Pedersen, P. Matsson, C.A. Bergström, J. Hoogstraate, A. Norén, and E.L. LeCluyse et al. Early identification of clinically relevant drug interactions with the human bile salt export pump (BSEP/ABCB11) Toxicol. Sci. 136 2013 328 343
32. J.M. Pedersen, P. Matsson, C.A. Bergström, J. Hoogstraate, A. Norén, and E.L. LeCluyse et al. Tissue distribution of the multidrug resistance protein 1 Am. J. Pathol. 148 1996 1237 1247
33. E. Bakos, T. Hegedüs, Z. Holló, E. Welker, G.E. Tusnády, and G.J. Zaman et al. Membrane topology and glycosylation of the human multidrug resistance-associated protein J. Chem. Biol. 2741 1997 12322 12326
34. G. Jedlitschky, I. Leier, U. Buchholz, K. Barnouin, G. Kurz, and D. Keppler Transport of glutathione, glucuronate, and sulfate conjugates by the MRP gene-encoded conjugate export pump Cancer Res. 56 1996 988 994
35. J.J. van Zanden, H.M. Wortelboer, S. Bijlsma, A. Punt, M. Usta, and P.J. Bladeren et al. Quantitative structure activity relationship studies on the flavonoid mediated inhibition of multidrug resistance proteins 1 and 2 Biochem. Pharmacol. 69 2005 699 708
36. C. Chang, S. Ekins, P. Bahadduri, and P.W. Swaan Pharmacophore-based discovery of ligands for drug transporters Adv. Drug Deliv. Rev. 58 2006 1431 1450
37. N.R. Tawari, S. Bag, and M.S. Degani Pharmacophore mapping of a series of pyrrolopyrimidines, indolopyrimidines and their congeners as multidrug-resistance-associated protein (MRP1) modulators J. Mol. Model. 14 2008 911 921
38. I.K. Pajeva, C. Globisch, and M. Wiese Combined pharmacophore modeling, docking, and 3D QSAR studies of ABCB1 and ABCC1 transporter inhibitors ChemMedChem 4 2009 1883 1896
39. D. Keppler, J. König, and M. Büchler The canalicular multidrug resistance protein, cMRP/MRP2, a novel conjugate export pump expressed in the apical membrane of hepatocytes Adv. Enzyme Regul. 37 1997 321 333
40. C.C. Paulusma, M. Kool, P.J. Bosma, G.L. Scheffer, F. ter Borg, and R.J. Scheper et al. A mutation in the human canalicular multispecific organic anion transporter gene causes the Dubin-Johnson syndrome Hepatology 25 1997 1539 1542
41. L. Xing, Y. Hu, and Y. Lai Advancement of structure-activity relationship of multidrug resistance-associated protein 2 interactions AAPS J. 11 2009 406 413
42. Y. Lai, L. Xing, G.I. Poda, and Y. Hu Structure-activity relationships for interaction with multidrug resistance protein 2 (ABCC2/MRP2): the role of torsion angle for a series of biphenyl-substituted heterocycles Drug Metab. Dispos. 35 2007 937 945
43. J.M. Pedersen, P. Matsson, C.A. Bergström, U. Norinder, J. Hoogstraate, and P. Artursson Prediction and identification of drug interactions with the human ATP-binding cassette transporter multidrug-resistance associated protein 2 (MRP2; ABCC2) J. Med. Chem. 51 2008 3275 3287
44. H. Zhang, M.L. Xiang, Y.L. Zhao, Y.Q. Wei, and S.Y. Yang Support vector machine and pharmacophore-based prediction models of multidrug-resistance protein 2 (MRP2) inhibitors Eur. J. Pharm. Sci. 36 2009 451 457
45. M. Pinto, M. Trauner, and G.F. Ecker An in silico classification model for putative ABCC2 substrates Mol. Inf. 31 2012 547 553
46. M. Maliepaard, G.L. Scheffer, I.F. Faneyte, M.A. van Gastelen, A.C. Pijnenborg, and A.H. Schinkel et al. Subcellular localization and distribution of the breast cancer resistance protein transporter in normal human tissues Cancer Res. 61 2001 3458 3464
47. R.W. Robey, K.K. To, O. Polgar, M. Dohse, P. Fetsch, and M. Dean et al. ABCG2: a perspective Adv. Drug Deliv. Rev. 61 2009 3 13
48. Y.A. Ghandi, and M.E. Morris Structure-activity relationships and quantitative structure-activity relationships for breast cancer resistance protein (ABCG2) AAPS J. 11 2009 541 552
49. E. Nicolle, J. Boccard, D. Guilet, M.G. Dijoux-Franca, F. Zelefac, and S. Macalou et al. Breast cancer resistance protein (BCRP/ABCG2): new inhibitors and QSAR studies by a 3D linear solvation energy approach Eur. J. Pharm. Sci. 38 2009 39 46
50. A. Pick, H. Müller, R. Mayer, B. Haenisch, I.K. Pajeva, and M. Weigt et al. Structure-activity relationships of flavonoids as inhibitors of breast cancer resistance protein (BCRP) Bioorg. Med. Chem. 19 2011 2090 2102
51. F. Marighetti, K. Steggemann, M. Hanl, and M. Wiese Synthesis and quantitative structure-activity relationships of selective BCRP inhibitors ChemMedChem 8 2013 125 135
52. Y. Pan, P.P. Chothe, and P.W. Swaan Identification of novel breast cancer resistance protein (BCRP) inhibitors by virtual screening Mol. Pharm. 10 2013 1236 1248
53. M.E. Gantner, M.E. Di Ianni, M.E. Ruiz, A. Talevi, and L.E. Bruno-Blanch Development of Conformation Independent Computational Models for the Early Recognition of Breast Cancer Resistance Protein Substrates 2013 BioMed Research International 12 Article ID 863592
54. E. Hazai, I. Hazai, I. Ragueneau-Majlessi, S.P. Chung, Z. Bikadi, and Q. Mao Predicting substrates of the human breast cancer resistance protein using a support vector machine method BMC Bioinform. 14 2013 130