Development of a highly specific ensemble of topological models for early identification of P-glycoprotein substrates

Journal of Chemometrics

Volumn 25, Issue 6, 2011, Pages 313-322

  Di Ianni, Mauricio ^a   Talevi, Alan ^a   Castro, Eduardo A ^b   Bruno Blanch, Luis E ^a  

^a FACULTAD DE CIENCIAS EXACTAS   (Argentina)

^b INSTITUTO DE INVESTIGACIONES FISICOQUÍMICAS TEÓRICAS Y APLICADAS INIFTA   (Argentina)

Author keywords

Data fusion; Pgp; Topological models

Indexed keywords

BIOCHEMISTRY; DIAGNOSIS; GLYCOPROTEINS; TOPOLOGY;

BLOOD-BRAIN BARRIER; CHEMOTHERAPEUTIC AGENTS; CLASSIFIER MODELS; DRUG DEVELOPMENT CYCLE; EFFLUX TRANSPORTER; MULTIDRUG RESISTANCE; P-GLYCOPROTEIN; TOPOLOGICAL MODELS; TRANSPORTER PROTEINS; VIRTUAL SCREENING;

DATA FUSION;

EID: 79959739206     PISSN: 08869383     EISSN: 1099128X     Source Type: Journal    
DOI: 10.1002/cem.1376     Document Type: Article

References (39)

1. Schuster D, Laggner C, Langer T.Why drugs fail-a study on side effects in nximahemical entities.Curr. Pharm. Des. 2005;11:3545-3559.
2. Kola I, Landis J.Can the pharmaceutical industry reduce attrition rates?Nat. Rev. Drug Discov. 2004;3:711-715.
3. Hop C, Cole M, Davidson R, Duignan D, Federico J, Janisewski J, Jenkins K, Krueger S, Lebowitz R, Liston T, Mitchell W, Snyder M, Steyn S, Soglia J, Taylor C, Troutman M, Umland J, West M, Whalen K, Zelesky V, Zhao S.High throughput ADME screening: practical considerations, impact on the portfolio and enabler of in silico ADME models.Curr. Dru. Metab. 2008;9:847-853.
4. Fromm M.Importance of P-glycoprotein at blood-tissue barriers.Trends Pharmacol. Sci. 2005;25:423-429.
5. Taft R.Drug excretion. InPharmacology: Principles and Practice, Hacker M, Messer WS, Bachmann KA (eds).Academic Press: San Diego, USA, 2009;175-201.
6. Siddiqui A, Kerb R, Weale M, Brinkmann U, Smith A, Goldstein D, Wood N, Sisodiya S.Association of multi-drug resistance in epilepsy with a polymorphism in the drug-transporter gene.N. Engl. J. Med. 2003;348:1442-1448.
7. Volk H, Burkhardt K, Potschka H, Chen J, Becker A, Löscher W.Neuronal expression of the drug efflux transporter P-glycoprotein in the rat hippocampus after limbic seizures.Neurosciene 2004;123:751-759.
8. Bauer B, Hartz A, Fricker G, Miller D.Pregnane X receptor up-regulation of P-glycoprotein expression and transport function at the blood-brain barrier.Mol. Pharmacol. 2004;66:413-419.
9. Thomas H, Coley H.Overcoming multi-drug resistance in cancer: an update on the clinical strategy of inhibitin p-glycoprotein.Cancer Control 2003;10:159-165.
10. Kim R, Fromm M, Wandel C, Leake B, Wood A, Roden D, Wilkinson G.The drug transporter P-glycoprotein limits oral absorption and brain entry of HIV-1 protease inhibitors.J. Clin. Invest. 1998;101:289-294.
11. Löscher W, Potschka H.Role of drug efflux transporters in the brain for drug disposition and treatment of brain diseases.Prog. Neurobiol. 2005;76:22-76.
12. Penzotti J, Lamb M, Evensen E, Grootenhuis P.A computational ensemble pharmacophore model for identifying substrates of P-glycoprotein.J. Med. Chem. 2002;45:1737-1740.
13. Xue Y, Yap C, Sun L, Cao Z, Wang J, Chen Y.Prediction of P-glycoprotein substrates by a support vector machine approach.J. Chem. Inf. Comput. Sci. 2004;44:1497-1505.
14. Cerqueira Lima P, Golbraikh A, Oloff S, Xiao Y, Tropsha A.Combinatorial QSAR modeling of P-glycoprotein substrates.J. Chem. Inf. Model. 2006;46:1245-1254.
15. Cianchetta G, Singleton R, Zhang M, Wildgoose M, Giesing D, Fravolini A, Cruciani G, Vaz R.A pharmacophore hypothesis for P-glycoprotein substrate recognition using GRIND-based 3D-QSAR.J. Med. Chem. 2005;48:2927-2935.
16. Zhang L, Balimane P, Johnson S, Chong S.Development of an in silico model for predicting efflux substrates in Caco-2 cells.Int. J. Pharm. 2007;343:98-105.
17. Li W, Li L, Eksterowicz J, Ling X, Cardozo M.Significance analysis and multiple pharmacophore models for differentiating P-glycoprotein substrates.J. Chem. Inf. Model. 2007;47:2429-2438.
18. Chang C, Bahadduri P, Polli J, Swaan P, Ekins S.Rapid identification of P-glycoprotein substrates and inhibitors.Drug Metab. Dispos. 2006;34:1876-1984.
19. Ekins S, Kim R, Leake B, Dantzig A, Schuetz E, Lan L, Yasuda K, Shepard R, Winter M, Schuetz J, Wikel J, Wrigton S.Application of three-dimensional quantitative structure-activity relationships of P-glycoprotein inhibitors and substrates.Mol. Pharmacol. 2002;61:974-981.
20. Wang R, Kuo C, Lien L, Lien E.Structure-activity relationship: analyses of p-glycoprotein substrates and inhibitors.J. Clin. Pharm. Ther. 2003;28:203-228.
21. Boccard J, Bajot F, Di Pietro A, Rudaz S, Boumendjel A, Nicolle E, Carrupt P.A 3D linear solvatation energy model to quantify the affinity of flavonoid derivatives toward p-glycoprotein.Eur. J. Pharm. Sci. 2009;36:254-264.
22. Zalloum H, Taha M.Development of predictive in silico model for cyclosporine- and aureobasidin-based P-glycoprotein inhibitors employing receptor surface analysis.J. Mol. Graph. Model. 2008;27:439-451.
23. Müller H, Pajeva I, Globisch C, Wiese M.Functional assay and structure-activity relationships of new third-generation P-glycoprotein inhibitors.Bioorg. Med. Chem. 2008;16:2448-2462.
24. Huang J, Ma G, Muhammad I, Cheng Y.Identifying P-glycoprotein substrates using a support vector machine optimized by a particle swarn.J. Chem. Inf. Model. 2007;47:1638-1647.
25. Cabrera M, González I, Fernández C, Navarro C, Bermejo M.A topological substructural approach for the prediction of P-glycoprotein substrates.J. Pharm. Sci. 2006;95:589-606.
26. Bohacek R, Mc Martin C, Guida W.The art and practice of structure-based drug design: a molecular modeling perspective.Med. Res. Rev. 1996;16:3-50.
27. Schneider G, So S.Adaptive Systems in Drug Design.Landes Bioscience: Georgetown, USA, 2003.
28. Talevi A, Gavernet L, Bruno-Blanch L.Combined virtual screening strategies.Curr. Comput. Aided Drug Des. 2009;5:23-37.
29. Seddon A, Curnow P, Booth P.Membrane proteins, lipids and detergents: not just soap opera.Biochim. Biophys. Acta 2006;1666:105-117.
30. Aller S, Ward A, Weng Y, Chittaboina S, Zhuo R, Harrell P, Trinh Y, Zhang Q, Urbatsch I, Chang G.Structure of P-glycoprotein reveals a molecular basis for poly-specific drug binding.Science 2009;323:1718-1722.
31. Mahar Doan K, Humphreys J, Webster L, Wring S, Shampine L, Serabjit-Singh C, Adkison K, Polli J.Passive permeability and P-glycoprotein-mediated efflux differentiate central nervous system (CNS) and non-CNS marketed drugs.J. Pharmacol. Exp. Ther. 2002;303:1029-1037.
32. Talevi A, Bellera C, Castro E, Bruno-Blanch L.Optimal partition of datasets of QSPR studies: a sampling problem.MATCH Commun. Math. Comput. Chem. 2010;63:585-599.
33. Srinivas E, Narashima Murthy J, Raghu Ram Rao R, Narahari Sastry G.Recent advances in molecular modeling and medicinal chemistry aspects of phospho-glycoprotein.Curr. Drug Metab. 2006;7:205-217.
34. Raub T.P-glycoprotein recognition of substrates and circumvention through rational drug design.Mol. Pharm. 2005;3:3-25.
35. Wiese M, Pajeva I.Structure-activity relationships of multidrug resistance reversers.Curr. Med. Chem. 2001;8:685-713.
36. Triballeau N, Acher F, Brabet I, Pin J, Bertrand H.Virtual screening workflow development guided by the 'Receiver Operating Characteristic' Curve approach. Application to high-throughput docking on metabotropic glutamate receptor subtype 4.J. Med. Chem. 2005;48:2534-2547.
37. Neyman J, Pearson E.On the problem of the most efficient tests of statistical hypothesis.Philos. Trans. R. Soc. Lond. A 1933;231:289-337.
38. Hubbard R, Bayarri M.Confusion over measures of evidence (p's) versus errors (alphas's) in classical statistical testing.Am. Stat. 2003;57:171-178.
39. Shapiro A, Fox K, Lam P, Ling V.Stimulation of P-glycoprotein-mediated transport by prazosin and progesterone. Evidence for a third site.Eur. J. Biochem. 1999;259:841-850.