Accounting of ligand-receptor interactions to explore and design novel architecture for PTP 1B inhibition: A legitimate approach

Journal of Chemometrics

Volumn 26, Issue 11-12, 2012, Pages 576-584

  Malla, Priyanka ^a   Kumar, Rajnish ^a   Kumar, Manoj ^a  

^a PANJAB UNIVERSITY   (India)

Author keywords

Diabetes; Docking; Partial least square; Pharmacokinetics; Pharmacophore hypothesis

Indexed keywords

AMINO ACIDS; HYDROGEN BONDS; LIGANDS;

ANTIDIABETIC ACTIVITY; BIPHENYL DERIVATIVES; COMPUTER AIDED DRUG DESIGN; DOCKING; LIGAND-RECEPTOR INTERACTIONS; NOVEL ARCHITECTURE; PARTIAL LEAST-SQUARES; PHARMACOPHORE HYPOTHESIS; PHARMACOPHORES; PROTEIN-TYROSINE PHOSPHATASE 1B;

PHARMACOKINETICS;

EID: 84871446151     PISSN: 08869383     EISSN: 1099128X     Source Type: Journal    
DOI: 10.1002/cem.2480     Document Type: Article

References (49)

1. Heydari I, Radi V, Razmjou S, Amiri A. Chronic complications of diabetes mellitus in newly diagnosed patients. Int. J. Diabetes Mellitus 2010; 2: 61-63.
2. Whiting DR, Guariguata L, Weil C, Shaw J. IDF Diabetes Atlas: global estimates of the prevalence of diabetes for 2011 and 2030. Diabetes Res. Clin. Pract. 2011; 94: 311-321.
3. Shaw JE, Sicree RA, Zimmet PZ. Global estimates of the prevalence of diabetes for 2010 and 2030. Diabetes Res. Clin. Pract. 2010; 87: 4-14.
4. Danaie G, Finucane MM, Lu Y, Singh GM, Cowan MJ, Paciorek CJ, Lin JK, Farzadfar F, Khang Y-H, Stevens GA, Rao M, Ali MK, Riley LM, Robinson CA, Ezzati M. National, regional, and global trends in fasting plasma glucose and diabetes prevalence since 1980: systematic analysis of health examination surveys and epidemiological studies with 370 country- years and 2.7 million participants. Lancet 2011; 378: 31-40.
5. Guariguata L, Whiting D, Weil C, Unwin N. The International Diabetes Federation Diabetes Atlas methodology for estimating global and national prevalence of diabetes in adults. Diabetes Res. Clin. Pract. 2011; 94: 322-332.
6. Diagnosis and classification of diabetes mellitus. Diabetes Care 2004; 27: S5-S10.
7. Murthy VS, Kulkarni VM. Molecular modeling of protein tyrosine phosphatase 1B (PTP 1B) inhibitors. Bioorg. Med. Chem. 2002; 10: 897-906.
8. Grundy SM. Drug therapy of the metabolic syndrome: minimizing the emerging crisis in polypharmacy. Nat. Rev. Drug Discov. 2006; 5: 295-309.
9. Sotiropoulos KB, Clermont A, Yasuda Y, Rask-Madsen C, Matsumoto M, Takahashi J, Vecchia KD, Kondo T, Aiello LP, King GL. Adipose-specific effect of rosiglitazone on vascular permeability and protein kinase C activation: novel mechanism for PPAR-γ agonists effects on edema and weight gain. FASEB J. 2006; 20: 1203-1205.
10. Scheen AJ, Gaal V. Sitagliptine (Januvia): incretin enhancer potentiating insulin secretion for the treatment of type 2 diabetes. Rev. Med. Liege 2008; 63: 105-109.
11. Johnson TO, Ermolieff J, Jirousek MR. Protein tyrosine phosphatase 1B inhibitors for diabetes. Nat. Rev. Drug Discov. 2002; 1: 696-709.
12. Ahmad F, Li PM, Meyerovitch J, Goldstein BJ, Chernoff J, Gustafson TA, Kusari J. Osmotic loading of neutralizing antibodies demonstrates a role for protein tyrosine phosphatase 1B in negative regulation of the insulin action pathway. J. Biol. Chem. 1995; 270: 20503-20508.
13. Bandyopadhyay D, Kusari A, Kenner KA, Liu F, Chernoff J, Gustafson TA, Kusari J. Protein tyrosine phosphatase 1B complexes with the insulin receptor in vivo and is tyrosine-phosphorylated in the presence of insulin. J. Biol. Chem. 1997; 272: 1639-1645.
14. Kusari J, Kenner KA, Shu KI, Hill DE, Henry RR. Skeletal muscle protein tyrosine phosphatase activity and tyrosine phosphatase 1B protein content are associated with insulin action and resistance. J. Clin. Invest. 1994; 93: 1156-1162.
15. Adams DR, Abraham A, Asano J, Breslin C, Dick AJC, Ixkes U, Johnston BF, Johnston D, Kewnay J, Mackay SP, MacKenzie SJ, McFarlane M, Mitchell L, Spinks D, Takano Y. 2-Aryl-3, 3, 3-trifluoro-2-hydroxypropionic acids: a new class of protein tyrosine phosphatase 1B inhibitors. Bioorg. Med. Chem. Lett. 2007; 17: 6579-6583.
16. Yue EW, Wayland B, Douty B, Crawley ML, McLaughlin E, Takvorian A, Wasserman Z, Bower MJ, Wei M, Li Y, Ala PJ, Gonneville L, Wynn R, Burn TC, Liu PCC, Combs AP. Isothiazolidinone heterocycles as inhibitors of protein tyrosine phosphatases: synthesis and structure-activity relationships of a peptide scaffold. Bioorg. Med. Chem. 2006; 14: 5833-5849.
17. Cho SY, Baek JY, Han SS, Kang SK, Ha JD, Ahn JH, Lee JD, Kim KR, Cheon HG, Rhee SD, Yang SD, Yon GH, Pak CS, Choi JK. PTP-1B inhibitors: cyclopenta[d][1, 2]-oxazine derivatives. Bioorg. Med. Chem. Lett. 2006; 16: 499-502.
18. Kumar A, Ahmad P, Maurya RA, Singh AB, Srivastava AK. Novel 2-aryl-naphtho[1, 2-d]oxazole derivatives as potential PTP-1B inhibitors showing antihyperglycemic activities. Eur. J. Med. Chem. 2009; 44: 109-116.
19. Cheng Y, Zhou M, Tung CH, Ji M, Zhang F. Studies on two types of PTP1B inhibitors for the treatment of type 2 diabetes: hologram QSAR for OBA and BBB analogues. Bioorg. Med. Chem. Lett. 2010; 20: 3329-3337.
20. Barford D, Flint AJ, Tonks NK. Crystal structure of human protein tyrosine phosphatase 1B. Science 1994; 263: 1397-1404.
21. Combs AP, Yue EW, Bower M, Ala PJ, Wayland B, Douty B, Takvorian A, Polam P, Wasserman Z, Zhu W, Crawley ML, Pruitt J, Sparks R, Glass B, Modi D, McLaughlin E, Bostrom L, Li M, Galya L, Blom K, Hillman MI, Gonneville L, Reid BG, Wei M, Becker-Pasha M, Klabe R, Huber R, Li Y, Hollis G, Burn TC, Wynn R, Liu P, Metcalf B. Structure-based design and discovery of protein tyrosine phosphatise inhibitors incorporating novel isothiazolidinone heterocyclic phosphotyrosine mimetics. J. Med. Chem. 2005; 48: 6544-6548.
22. Groves MR, Yao ZJ, Roller PP, Burke TR, Barford D. Structural basis for inhibition of the protein tyrosine phosphatase 1B by phosphotyrosine peptide mimetics. Biochemistry 1998; 37: 17773-17783.
23. Huang P, Ramphal J, Wei JC, Liang W, Jallal B, McMahon G, Tang C. Structure-based design and discovery of novel inhibitors of protein tyrosine phosphatises. Bioorg. Med. Chem. 2003; 11: 1835-1849.
24. Puius YA, Zhao Y, Sullivan M, Lwarence DS, Almo SC, Zhang ZY. Identification of a second aryl phosphate-binding site in protein tyrosine phosphatase 1B: a paradigm for inhibitor design. Proc. Natl. Acad. Sci. U.S.A. 1997; 94: 13420-13425.
25. Zhang X, Li X, Wang R. Interpretation of the binding affinities of PTP1B Inhibitors with the MM-GB/SA method and the X-score scoring function. J. Chem. Inf. Model. 2009; 49: 1033-1048.
26. Ramírez-Espinosa JJ, Yolanda Rios M, López-Martínez S, López-Vallejo F, Medina-Franco JL, Paoli P, Camici G, Navarrete-Vázquez G, Ortiz-Andrade R, Estrada-Soto S. Antidiabetic activity of some pentacyclic acid triterpenoids, role of PTP 1B: in vitro, in silico, and in vivo approaches. Eur. J. Med. Chem. 2011; 46: 2243-2251.
27. Thareja S, Aggarwal S, Bhardwaj TR, Kumar M. Protein tyrosine phosphatase 1B inhibitors: a molecular level legitimate approach for the management of diabetes mellitus. Med. Res. Rev. 2012; 32: 459-517.
28. Forghieri M, Laggner C, Paoli P, Langer T, Manao G, Camici G, Bondioli L, Prati F, Costantino L. Synthesis, activity and molecular modeling of a new series of chromones as low molecular weight protein tyrosine phosphatase inhibitors. Bioorg. Med. Chem. 2009; 17: 2658-2672.
29. Malamas MS, Sredy J, Moxham C, Katz A, Xu W, McDevitt R, Adebayo FO, Sawicki DR, Seestaller L, Sullivan D, Taylor JR. Novel benzofuran and benzothiophene biphenyls as inhibitors of protein tyrosine phosphatase 1B with antihyperglycemic properties. J. Med. Chem. 2000; 43: 1293-1310.
30. Shim YS, Kim KC, Chi DY, Lee KH, Cho H. Formylchromone derivatives as a novel class of protein tyrosine phosphatase 1B inhibitors. Bioorg. Med. Chem. Lett. 2003; 13: 2561-2563.
31. Arabaci G, Yi T, Fu H, Porter ME, Beebe KD, Pei D. α-Bromoacetophenone derivatives as neutral protein tyrosine phosphatase inhibitors: structure-activity relationship. Bioorg. Med. Chem. Lett. 2002; 12: 3047-3050.
32. Xie J, Tian J, Sua L, Huang M, Zhu X, Ye F, Wana Y. Pyrrolo[2, 3-c]azepine derivatives: a new class of potent protein tyrosine phosphatase 1B inhibitors. Bioorg. Med. Chem. Lett. 2011; 21: 4306-4309.
33. Black E, Breed J, Breeze AL, Embrey K, Garcia R, Gero TW, Godfrey L, Kenny PW, Morley AD, Minshull CA, Pannifer AD, Read J, Rees A, Russell DJ, Toader D, Tucker J. Structure-based design of protein tyrosine phosphatase-1B inhibitors. Bioorg. Med. Chem. Lett. 2005; 15: 2503-2507.
34. Phase, version 3.4, Schrödinger, LLC, New York, NY, 2012.
35. QikProp, version 3.5, Schrödinger, LLC, New York, NY, 2012.
36. Kaminski GA, Friesner RA, Tirado-Rives J, Jorgensen WL. Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J. Phys. Chem. B 2001; 105: 6474-6487.
37. Dixon SL, Smondyrev AM, Knoll EH, Rao SN, Shaw DE, Friesner RA. PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results. J. Comput. Aided Mol. Des. 2006; 20: 647-671.
38. Reeetu Kumar V. Computer aided design of selective calcium channel blockers: using pharmacophore based and docking simulations. Int. J. Pharm. Sci. Res. 2012; 3: 805-810.
39. Muňoz C, Adasme F, Alzate-Morales JH, Vergara-Jaque A, Kniess T, Caballero J. Study of differences in the VEGFR2 inhibitory activities between semaxanib and SU5205 using 3D-QSAR, docking, and molecular dynamics simulations. J. Mol. Graph Model 2012; 32: 39-48.
40. Glide, version 5.8, Schrödinger, LLC, New York, NY, 2012.
41. Available at URL: http://www.pdb.org/pdb/explore/explore.do?structureId=1ecv.
42. Liaison, version 5.8, Schrödinger, LLC, New York, NY, 2012.
43. MacroModel, version 9.9, Schrödinger, LLC, New York, NY, 2011.
44. Lipinski CA, Lombardo F, Dominy BW, Feeney P. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. J. Adv. Drug Deliv. Rev. 2001; 46: 3-26.
45. Goldstein BJ, Bitter-Kowalczyk A, White MF, Harbeck M. Tyrosine dephosphorylation and deactivation of insulin receptor substrate-1 by protein tyrosine phosphatase 1B. J. Biol. Chem. 2000; 275: 4283-4289.
46. Dureja H, Kumar V, Gupta S, Madan AK. Topochemical models for the prediction of lipophilicity of 1, 3-disubstituted propan-2-one analogs. J. Theor. Comput. Chem. 2007; 6: 435-448.
47. Wold S. Validation of QSAR's. Quant. Struct. Act. Relat. 1991; 10: 191-193.
48. SiteMap, version 2.6, Schrödinger, LLC, New York, NY, 2012.
49. Pawar P, Lokwani D, Bhandari S, Mitra D, Sabde S, Bothara K, Madgulkar A. Design of potential reverse transcriptase inhibitor containing Isatin nucleus using molecular modeling studies. Bioorg. Med. Chem. 2010; 18: 3198-3211.