Predicting binding to P-glycoprotein by flexible receptor docking

PLoS Computational Biology

Volumn 7, Issue 6, 2011, Pages

  Dolghih, Elena ^a   Bryant, Clifford ^a   Renslo, Adam R ^a   Jacobson, Matthew P ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; CANCER CELLS; CRYSTAL STRUCTURE; FORECASTING; GLYCOPROTEINS; LIGANDS; PEPTIDES;

BARRIER PENETRATION; BLOOD-BRAIN BARRIER; CANCER CELLS; CRYSTALS STRUCTURES; EFFLUX PUMPS; ENTRY POINT; MULTIDRUG RESISTANCE; OVEREXPRESSIONS; P-GLYCOPROTEIN; TRANSPORT PROTEINS;

BINDING SITES;

CALCEIN; CYCLOPEPTIDE; CYSTEINE PROTEINASE INHIBITOR; GLYCOPROTEIN P; ABCB1 PROTEIN, HUMAN;

ARTICLE; BINDING SITE; CELL METABOLISM; CONTROLLED STUDY; CRYSTAL STRUCTURE; HYDROPHOBICITY; MOLECULAR DOCKING; MOLECULAR DYNAMICS; MOLECULAR MODEL; PHYSICAL CHEMISTRY; PREDICTION; PROTEIN BINDING; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN TRANSPORT; STRUCTURE ANALYSIS; ALGORITHM; ANIMAL; CELL LINE; CHEMISTRY; DOG; DRUG DEVELOPMENT; HUMAN; METABOLISM; MOUSE; PHARMACOKINETICS; PLIABILITY; RECEIVER OPERATING CHARACTERISTIC;

ALGORITHMS; ANIMALS; BINDING SITES; CELL LINE; CYSTEINE PROTEINASE INHIBITORS; DOGS; DRUG DISCOVERY; HUMANS; MICE; MOLECULAR DYNAMICS SIMULATION; P-GLYCOPROTEIN; PHARMACOKINETICS; PLIABILITY; PROTEIN BINDING; ROC CURVE;

EID: 79959833862     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1002083     Document Type: Article

References (53)

1. Thiebaut F, Tsuruo T, Hamada H, Gottesman MM, Pastan I, et al. (1987) Cellular localization of the multidrug-resistance gene product P-glycoprotein in normal human tissues. Proc Natl Acad Sci U S A 84: 7735-7738.
2. Szakacs G, Varadi A, Ozvegy-Laczka C, Sarkadi B, (2008) The role of ABC transporters in drug absorption, distribution, metabolism, excretion and toxicity (ADME-Tox). Drug Discov Today 13: 379-393.
3. Schinkel AH, Wagenaar E, Mol CA, van Deemter L, (1996) P-glycoprotein in the blood-brain barrier of mice influences the brain penetration and pharmacological activity of many drugs. J Clin Invest 97: 2517-2524.
4. Ambudkar SV, Dey S, Hrycyna CA, Ramachandra M, Pastan I, et al. (1999) Biochemical, cellular, and pharmacological aspects of the multidrug transporter. Annu Rev Pharmacol Toxicol 39: 361-398.
5. Fletcher JI, Haber M, Henderson MJ, Norris MD, (2010) ABC transporters in cancer: more than just drug efflux pumps. Nat Rev Cancer 10: 147-156.
6. Ayrton A, Morgan P, (2008) Role of transport proteins in drug discovery and development: a pharmaceutical perspective. Xenobiotica 38: 676-708.
7. Hochman JH, Yamazaki M, Ohe T, Lin JH, (2002) Evaluation of drug interactions with P-glycoprotein in drug discovery: in vitro assessment of the potential for drug-drug interactions with P-glycoprotein. Curr Drug Metab 3: 257-273.
8. Polli JW, Wring SA, Humphreys JE, Huang L, Morgan JB, et al. (2001) Rational use of in vitro P-glycoprotein assays in drug discovery. J Pharmacol Exp Ther 299: 620-628.
9. Feng B, Mills JB, Davidson RE, Mireles RJ, Janiszewski JS, et al. (2008) In vitro P-glycoprotein assays to predict the in vivo interactions of P-glycoprotein with drugs in the central nervous system. Drug Metab Dispos 36: 268-275.
10. Li WX, Li L, Eksterowicz J, Ling XB, Cardozo M, (2007) Significance analysis and multiple pharmacophore models for differentiating P-glycoprotein substrates. J Chem Inf Model 47: 2429-2438.
11. Mahar Doan KM, Humphreys JE, Webster LO, Wring SA, Shampine LJ, et al. (2002) Passive permeability and P-glycoprotein-mediated efflux differentiate central nervous system (CNS) and non-CNS marketed drugs. J Pharmacol Exp Ther 303: 1029-1037.
12. Wang Q, Rager JD, Weinstein K, Kardos PS, Dobson GL, et al. (2005) Evaluation of the MDR-MDCK cell line as a permeability screen for the blood-brain barrier. Int J Pharm 288: 349-359.
13. Gombar VK, Polli JW, Humphreys JE, Wring SA, Serabjit-Singh CS, (2004) Predicting P-glycoprotein substrates by a quantitative structure-activity relationship model. J Pharm Sci 93: 957-968.
14. Crivori P, Reinach B, Pezzetta D, Poggesi I, (2006) Computational models for identifying potential P-glycoprotein substrates and inhibitors. Mol Pharm 3: 33-44.
15. Summerfield SG, Read K, Begley DJ, Obradovic T, Hidalgo IJ, et al. (2007) Central nervous system drug disposition: the relationship between in situ brain permeability and brain free fraction. J Pharmacol Exp Ther 322: 205-213.
16. Seelig A, (1998) A general pattern for substrate recognition by P-glycoprotein. Eur J Biochem 251: 252-261.
17. Ueda K, Cardarelli C, Gottesman MM, Pastan I, (1987) Expression of a full-length cDNA for the human "MDR1" gene confers resistance to colchicine, doxorubicin, and vinblastine. Proc Natl Acad Sci U S A 84: 3004-3008.
18. Loo TW, Clarke DM, (1994) Mutations to amino acids located in predicted transmembrane segment 6 (TM6) modulate the activity and substrate specificity of human P-glycoprotein. Biochem 33: 14049-14057.
19. Shapiro AB, Ling V, (1997) Positively cooperative sites for drug transport by P-glycoprotein with distinct drug specificities. Eur J Biochem 250: 130-137.
20. Garrigues A, Loiseau N, Delaforge M, Ferte J, Garrigos M, et al. (2002) Characterization of two pharmacophores on the multidrug transporter P-glycoprotein. Mol Pharmacol 62: 1288-1298.
21. Penzotti JE, Lamb ML, Evensen E, Grootenhuis PD, (2002) A computational ensemble pharmacophore model for identifying substrates of P-glycoprotein. J Med Chem 45: 1737-1740.
22. de Cerqueira Lima P, Golbraikh A, Oloff S, Xiao Y, Tropsha A, (2006) Combinatorial QSAR modeling of P-glycoprotein substrates. J Chem Inf Model 46: 1245-1254.
23. Huang J, Ma G, Muhammad I, Cheng Y, (2007) Identifying P-glycoprotein substrates using a support vector machine optimized by a particle swarm. J Chem Inf Model 47: 1638-1647.
24. Cabrera MA, Gonzalez I, Fernandez C, Navarro C, Bermejo M, (2006) A topological substructural approach for the prediction of P-glycoprotein substrates. J Pharm Sci 95: 589-606.
25. Dey S, Ramachandra M, Pastan I, Gottesman MM, Ambudkar SV, (1997) Evidence for two nonidentical drug-interaction sites in the human P-glycoprotein. Proc Natl Acad Sci U S A 94: 10594-10599.
26. Loo TW, Bartlett MC, Clarke DM, (2003) Methanethiosulfonate derivatives of rhodamine and verapamil activate human P-glycoprotein at different sites. J Biol Chem 278: 50136-50141.
27. Martin C, Berridge G, Higgins CF, Mistry P, Charlton P, et al. (2000) Communication between multiple drug binding sites on P-glycoprotein. Mol Pharmacol 58: 624-632.
28. Ayesh S, Shao YM, Stein WD, (1996) Co-operative, competitive and non-competitive interactions between modulators of P-glycoprotein. Biochim Biophys Acta 1316: 8-18.
29. Aller SG, Yu J, Ward A, Weng Y, Chittaboina S, et al. (2009) Structure of P-glycoprotein reveals a molecular basis for poly-specific drug binding. Science 323: 1718-1722.
30. Loo TW, Bartlett MC, Clarke DM, (2003) Simultaneous binding of two different drugs in the binding pocket of the human multidrug resistance P-glycoprotein. J Biol Chem 278: 39706-39710.
31. Sherman W, Day T, Jacobson MP, Friesner RA, Farid R, (2006) Novel procedure for modeling ligand/receptor induced fit effects. J Med Chem 49: 534-553.
32. Friesner RA, Murphy RB, Repasky MP, Frye LL, Greenwood JR, et al. (2006) Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. J Med Chem 49: 6177-6196.
33. Ghosh A, Rapp CS, Friesner RA, (1998) Generalized born model based on a surface integral formulation. J Phys Chem B 102: 10983-10990.
34. Huang N, Kalyanaraman C, Irwin JJ, Jacobson MP, (2006) Physics-based scoring of protein-ligand complexes: enrichment of known inhibitors in large-scale virtual screening. J Chem Inf Model 46: 243-253.
35. Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
36. Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, et al. (2004) Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 47: 1739-1749.
37. Kaminski GA, Friesner RA, Tirado-Rives J, Jorgensen WL, (2001) Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J Phys Chem B 105: 6474-6487.
38. Jorgensen WL, Tiradorives J, (1988) The Opls Potential Functions for Proteins- Energy Minimizations for Crystals of Cyclic-Peptides and Crambin. J Am Chem Soc 110: 1657-1666.
39. Jacobson MP, Friesner RA, Xiang Z, Honig B, (2002) On the role of the crystal environment in determining protein side-chain conformations. J Mol Biol 320: 597-608.
40. Wishart DS, Knox C, Guo AC, Cheng D, Shrivastava S, et al. (2008) DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res 36: D901-D906.
41. Hennessy M, Spiers JP, (2007) A primer on the mechanics of P-glycoprotein the multidrug transporter. Pharmacol Res 55: 1-15.
42. Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M, (2010) KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res 38: D355-360.
43. Palmer JT, Bryant C, Wang DX, Davis DE, Setti EL, et al. (2005) Design and synthesis of tri-ring P3 benzamide-containing aminonitriles as potent, selective, orally effective inhibitors of cathepsin K. J Med Chem 48: 7520-7534.
44. Pansare SV, Huyer G, Arnold LD, Vederas JC, (1998) Synthesis of N-protected alpha-Amino acids from N-(benzyloxycarbonyl)-L-serine via its beta-lactone: N-(benzyloxycarbonyl)-beta-(pyrazol-1-yl)-L-alanine. Organic Syntheses Vol. 9: 58.
45. Arnold LD, Kalantar TH, Vederas JC, (1985) Conversion of Serine to Stereochemically Pure Beta-Substituted Alpha-Amino-Acids Via Beta-Lactones. J Am Chem Soc 107: 7105-7109.
46. Loo TW, Clarke DM, (2002) Location of the rhodamine-binding site in the human multidrug resistance P-glycoprotein. J Biol Chem 277: 44332-44338.
47. Mitchell AM, Tom M, Mortimer RH, (2005) Thyroid hormone export from cells: contribution of P-glycoprotein. J Endocrinol 185: 93-98.
48. Fan J, Liu S, Du Y, Morrison J, Shipman R, et al. (2009) Up-regulation of transporters and enzymes by the vitamin D receptor ligands, 1alpha,25-dihydroxyvitamin D3 and vitamin D analogs, in the Caco-2 cell monolayer. J Pharmacol Exp Ther 330: 389-402.
49. Yang CP, DePinho SG, Greenberger LM, Arceci RJ, Horwitz SB, (1989) Progesterone interacts with P-glycoprotein in multidrug-resistant cells and in the endometrium of gravid uterus. J Biol Chem 264: 782-788.
50. Wang E, Casciano CN, Clement RP, Johnson WW, (2000) Cholesterol interaction with the daunorubicin binding site of P-glycoprotein. Biochem Biophys Res Commun 276: 909-916.
51. Lee JS, Paull K, Alvarez M, Hose C, Monks A, et al. (1994) Rhodamine efflux patterns predict P-glycoprotein substrates in the National Cancer Institute drug screen. Mol Pharmacol 46: 627-638.
52. Rezai T, Bock JE, Zhou MV, Kalyanaraman C, Lokey RS, et al. (2006) Conformational flexibility, internal hydrogen bonding, and passive membrane permeability: successful in silico prediction of the relative permeabilities of cyclic peptides. J Am Chem Soc 128: 14073-14080.
53. Kalyanaraman C, Jacobson MP, (2007) An atomistic model of passive membrane permeability: application to a series of FDA approved drugs. J Comput Aided Mol Des 21: 675-679.