Induced fit docking, pharmacophore modeling, and molecular dynamic simulations on thiazolidinedione derivatives to explore key interactions with Tyr48 in polyol pathway

Journal of Molecular Modeling

Volumn 20, Issue 7, 2014, Pages

  Vijjulatha, Manga ^a   Lingala, Yamini ^a   Merugu, Raviraja Tejaswi ^a  

^a OSMANIA UNIVERSITY   (India)

Author keywords

ALR aldose reductase; Diabetes mellitus; IFD induced fit docking; MD molecular dynamics; Pharmacophore modeling; PLS Partial least square analysis; Polyol pathway

Indexed keywords

2,4 THIAZOLIDINEDIONE DERIVATIVE; ALDEHYDE REDUCTASE; NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE; OXIDOREDUCTASE INHIBITOR; POLYOL; ANTIDIABETIC AGENT; ENZYME INHIBITOR; LIGAND; POLYMER; PROTEIN BINDING; TYROSINE;

AMINO ACID SEQUENCE; ARTICLE; BINDING AFFINITY; BINDING SITE; CRYSTAL STRUCTURE; ENZYME INHIBITOR COMPLEX; HYDROGEN BOND; INDUCED FIT DOCKING; MOLECULAR DOCKING; MOLECULAR DYNAMICS; PHARMACOPHORE; PRIORITY JOURNAL; PROTEIN STRUCTURE; QUANTITATIVE STRUCTURE ACTIVITY RELATION; THREE DIMENSIONAL QUANTITATIVE STRUCTURE ACTIVITY RELATIONSHIP; ANTAGONISTS AND INHIBITORS; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER AIDED DESIGN; DRUG DESIGN; METABOLISM; MOLECULAR GENETICS; PROTEIN CONFORMATION; STRUCTURE ACTIVITY RELATION;

ALDEHYDE REDUCTASE; AMINO ACID SEQUENCE; BINDING SITES; COMPUTER-AIDED DESIGN; DRUG DESIGN; ENZYME INHIBITORS; HYDROGEN BONDING; HYPOGLYCEMIC AGENTS; LIGANDS; MOLECULAR DOCKING SIMULATION; MOLECULAR DYNAMICS SIMULATION; MOLECULAR SEQUENCE DATA; MOLECULAR STRUCTURE; NADP; POLYMERS; PROTEIN BINDING; PROTEIN CONFORMATION; STRUCTURE-ACTIVITY RELATIONSHIP; THIAZOLIDINEDIONES; TYROSINE;

EID: 84903256337     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-014-2348-8     Document Type: Article

References (65)

1. Brownlee M (2001) Biochemistry and molecular cell biology of diabetic complications. Nature 414:813-20
2. Koukoulitsa C, Zika C, Geromichalos GD, Demopoulos VJ, Skaltsa H (2006) Evaluation of aldose reductase inhibition and docking studies of some secondary metabolites isolated from Origanum vulgare L. ssp. Hirtum Bioorg Med Chem 14:1653-59 (Pubitemid 43120300)
3. Zimmet P, Alberti KGMM, Shaw J (2001) Global and societal implications of the diabetes epidemic. Nature 414:782-87 (Pubitemid 34000780)
4. International Diabetes Federation (2011) Diabetes Atlas (5th ed). Retrived from http://www.idf.org/diabetesatlas/5e/the-global-burden
5. Calcutt NA, Freshwater JD, Mizisin AP (2004) Prevention of sensory disorders in diabetic Sprague-Dawley rats by aldose reductase inhibition or treatment with ciliary neurotrophic factor. Diabetologia 47:718-24 (Pubitemid 38658374)
6. Cameron NE, Cotter MA, Basso M, Hohman TC (1997) Comparison of the effects of inhibitors of aldose reductase and sorbitol dehydrogenase on neurovascular function, nerve conduction and tissue polyol pathway metabolites in streptozotocin-diabetic rats. Diabetologia 40:271-81 (Pubitemid 27096550)
7. Hotta N (1995) New approaches for treatment in diabetes: aldose reductase inhibitors. Biomed Pharmacother 49:232-43
8. Ishii H, Tada H, Isogai S (1998) An aldose reductase inhibitor prevents glucose-induced increase in transforming growth factor-β and protein kinase C activity in cultured human mesangial cells. Diabetologia 41:362-64 (Pubitemid 28254833)
9. Kasuya Y, Ito M, Nakamura J, Hamada Y, Nakayama M, Chaya S, Komori T, Naruse K, Nakashima E, Kato K, Koh N, Hotta N (1999) An aldose redutase inhibitor prevents the intimal thickening in coronary arteries of galactose-fed beagle dogs. Diabetologia 42:1404-09 (Pubitemid 30012310)
10. Petrash JM (2004) All in the family: aldose reductase and closely related aldo-keto reductases. Cell Mol Life Sci 61:737-49
11. Settimo FD, Primofiore G, Motta CL, Salerno S, Novellino E, Greco G, Lavecchia A, Laneri S, Boldrini E (2005) Spirohydantoin derivatives of thiopyrano [2,3-b] pyridin-4 (4H)-one as potent in vitro and in vivo aldose reductase inhibitors. Bioorg Med Chem 13:491-99 (Pubitemid 39642932)
12. El-Kabbani O, Ruiz F, Darmanin C, Chung RPT (2004) Aldose reductase structures: implications for mechanism and inhibition. Cell Mol Life Sci 61:750-762 (Pubitemid 38650996)
13. Howard EI, Sanishvili R, Cachau RE, Mitschler A, Chevrier B, Barth P, Lamour V, Van Zandt M, Sibley E, Bon C, Moras D, Schneider TR, Joachimiak A, Podjarny A (2004) Ultrahigh resolution drug design I: details of interactions in human aldose reductase-inhibitor complex at 0.66 A. Proteins Struct Funct Genet Bioinforma 55:792-804 (Pubitemid 38702939)
14. Gabbay KH (1973) The sorbitol pathway and the complications of diabetes. New Engl J Med 288:831-36
15. Blakeley MP, Ruiz F, Cachau R, Hazemann I, Meilleur F, Mitschler A, Ginell S, Afonine P, Ventura ON, Cousido-Siah A, Haertlein M, Joachimiak A, Myles D, Podjarny A (2008) Quantum model of catalysis based on a mobile proton revealed by subatomic x-ray and neutron diffraction studies of h-aldose reductase. Proc Natl Acad Sci U S A 105(6):1844-48 (Pubitemid 351439427)
16. Fernández M, Caballero J, Helguera AM, Castro EA, González MP (2005) Quantitative structure-activity relationship to predict differential inhibition of aldose reductase by flavonoid compounds. Bioorg Med Chem 13:3269-77
17. Hu L, Chen G, Chau RMW (2006) A neural networks-based drug discovery approach and its application for designing aldose reductase inhibitors. J Mol Graph Model 24:244-53 (Pubitemid 41786038)
18. Prabhakar YS, Gupta MK, Roy N, Venkateswarlu Y (2006) A high dimensional QSAR study on the aldose reductase inhibitory activity of some flavones: topological descriptors in modeling the activity. J Chem Inf Model 46:86-92 (Pubitemid 43282102)
19. Ko K, Won Y (2005) Quantitative structure and aldose reductase inhibitory activity relationship of 1,2,3,4-tetrahydropyrrolo [1,2-a] pyrazine-4-spiro- 3′-pyrrolidine-1,2′,3,5′-tetrone derivatives. Bioorg Med Chem 13:1445-52 (Pubitemid 40215231)
20. Ko K, Won H, Won Y (2006) Quantitative structure-activity relationship of spirosuccinimide type aldose reductase inhibitors diminishing sorbitol accumulation in vivo. Bioorg Med Chem 14:3090-97
21. Bruno G, Costantino L, Curinga C, Maccari R, Monforte F, Nicoló F, Ottanà R, Vigorita MG (2002) Synthesis and aldose reductase inhibitory activity of 5-arylidene-2,4-thiazolidinediones. Bioorg Med Chem 10:1077-84 (Pubitemid 34139922)
22. Maccari R, Ottanà R, Ciurleo R, Vigorita MG, Rakowitz D, Steindl T, Langer T (2007) Evaluation of in vitro aldose redutase inhibitory activity of 5-arylidene-2, 4-thiazolidinediones. Bioorg Med Chem Lett 17:3886-93 (Pubitemid 46924830)
23. Maccari R, Ottanà R, Curinga C, Vigorita MG, Rakowitz D, Steindl T, Langer T (2005) Structure-activity relationships and molecular modelling of 5-arylidene-2,4-thiazolidinediones active as aldose reductase inhibitors. Bioorg Med Chem 13:2809-23 (Pubitemid 40387491)
24. Rakowitz D, Maccari R, Ottanà R, Vigorita MG (2006) In vitro aldose reductase inhibitory activity of 5-benzyl-2, 4-thiazolidinediones. Bioorg Med Chem 14:567-74 (Pubitemid 41767617)
25. Sambasivarao SV, Soni LK, Gupta AK, Hanumantharao P, Kaskhedikar SG (2006) Quantitative structure-activity analysis of 5-arylidene-2,4- thiazolidinediones as aldose reductase inhibitors. Bioorg Med Chem Lett 16:512-20 (Pubitemid 43014828)
26. Abhinit M, Ghodke M, Pratima NA (2009) Exploring potential of 4-thiazolidinone: a brief review. Inter J Phar and Pharceu Sci 1:47-64
27. OMoore-Sullivan TM, Prins JB (2002) Thiazolidinediones and type 2 diabetes: new drugs for an old disease. Med J Aust 176:381-6
28. Pan HJ, Lin Y, Chen YE, Vance DE, Leiter EH (2006) Adverse hepatic and cardiac responses to rosiglitazone in a new mouse model of type 2 diabetes: relation to dysregulated phosphatidylcholine metabolism. Vasc Pharmacol 45:65-71 (Pubitemid 43963486)
29. Cromlish JA, Flynn TG (1983) Purification and characterization of two aldose reductase isoenzymes from rabbit muscle. J Biol Chem 256(5):3416-3424
30. Sharma SR, Sharma N (2008) Epalrestat, an aldose reductase inhibitor, in diabetic neuropathy: an Indian perspective. Ann Indian Acad Neurol 11(4):231-235
31. Zhu C (2013) In: Oluwafemi Oguntibeju (ed.) Aldose reductase inhibitors as potential therapeutic drugs of diabetic complications, diabetes mellitus - insights and perspectives. DOI:10.5772/54642.
32. Dixon SL, Smondyrev AM, Knoll EH, Rao SN, Shaw DE, Friesner RA (2006) 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 20:647-71 (Pubitemid 46023928)
33. Schrödinger (2012) Ligprep, version 2.3. Schrödinger LLC, New York
34. Jorgensen WL, Maxwell DS, Tirado-Rives J (1996) Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 118:11225-36 (Pubitemid 26399746)
35. Magrane M, UniProt consortium, (2011) UniProt Knowledgebase: a hub of integrated protein data Database, 2011
36. Johnson M, Zaretskaya I, Raytselis Y, Merezhuk Y, McGinnis S, Madden TL (2008) NCBI BLAST: a better web interface. Nucl Acids Res 25:W5-W9
37. Ramu C, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD (2003) Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res 31:3497-500 (Pubitemid 37442184)
38. Marti-Renom MA, Stuart AC, Fiser A, Sanchez R, Melo F, Sali A (2000) Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct 29:291-325 (Pubitemid 30599596)
39. Sali A, Blundell TL (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234:779-815 (Pubitemid 24007801)
40. Laskowski RA, Mac Arthur MW, Moss DS, Thornton JM (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Cryst 26:283-91
41. Eisenberg D, Lüthy R, Bowie JU (1997) VERIFY3D: assessment of protein models with three-dimensional profiles. Methods Enzymol 277:396-404
42. Wiederstein M, Sippl MJ (2007) ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res 35:W407-W410
43. Sali A, Kuriyan J (1999) Challenges at the frontiers of structural biology. Trends Cell Biol 12:M20-M24
44. Rarey M, Kramer B, Lengauer T, Kleb GA (1996) A fast flexible docking method using an incremental construction algorithm. J Mol Biol 261:470-89 (Pubitemid 26335901)
45. Schrödinger (2012) Glide, version 5.5. Schrödinger LLC, New York
46. Leach R (1996) Molecular modelling, principles and applications, 2nd edn. Harlow, Essex, England, Longman
47. Schrödinger (2009) Prime, version 2.1. Schrödinger LLC. New York, NY
48. Tarle I, Borhani DW, Wilson DK, Quiochol FA, Petrash JM (1993) Probing the active site of human aldose reductase. Site-directed mutagenesis of Asp-43, Tyr-48, Lys-77, and His-110. J Biol Chem 268:25687-93 (Pubitemid 23358181)
49. Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT, Repasky MP, Knoll EH, Shelly M, Perry JK, Shaw DE, Francis P, PS S k (2004) Glide: a new approach for rapid, accurate docking and scoring. 1. method and assessment of docking accuracy. J Med Chem 47:1739-49 (Pubitemid 38380917)
50. Yamini L, Vijjulatha M (2008) Inhibitors of human dihydrofolate reductase: a computational design and docking studies Using glide. E J Chem 5:263-70
51. Friesner RA, Murphy RB, Repasky MP, Frye LL, Greenwood JR, Halgren TA, Sanschagrin PC, Mainz DT (2006) Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. J Med Chem 49:6177-96 (Pubitemid 44595196)
52. Hess B, Kutzner C, Spoel DV, Lindahl E (2008) GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput 4:435-47
53. Spoel DV, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJ (2005) GROMACS: fast, flexible, and free. J Comput Chem 26:1701-18 (Pubitemid 43076182)
54. Schüttelkopf AW, van Aalten DMF (2004) PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr D60:1355-63 (Pubitemid 41079731)
55. Oostenbrink C, Villa A, Mark AE, van Gunsteren WF (2004) A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6. J Comput Chem 13:1656-76
56. Gunsteren WFV, Billeter SR, Eising AA, Hunenberger PH, Kruger P, Mark AE, Scott WRP, Tironi IG, "Biomolecular Simulation: The GROMOS96 Manual and User Guide." VdF: Hochschulverlag AG an der ETH Zurich and BIOMOS b.v, Zurich, Gronigen (1996). ISBN 3 7281 2422 2.
57. Darden T, York D, Pedersen L (1993) Particlemesh Ewald: An N-log (N) method for Ewald sums in large systems. J Chem Phys 98:10089-92
58. Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen H (1995) A smooth particle mesh Ewald method. J Chem Phys 103:8577-93
59. Berendsen HJC, Postma JP, Gunsteren WFV, DiNola A, Haak JR (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81:3684-90
60. Berendsen HJC, Grigera JR, Straatsma TP (1987) The missing term in effective pair potentials. J Phys Chem 91:6269-71
61. Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14:33-38 (Pubitemid 26152973)
62. Mercader AG, Pomilio AB (2012) 2D- and 3D-QSAR studies of flavonoids, biflavones and chalcones: antiviral, antibacterial, antifungal, and antimycobacterial activities. Anti-Infect Agents 10:41-54
63. Pasha FA, Muddassar M, Jung H, Yang BS, Lee C, Oh JS, Cho SJ, Cho H (2008) QM and pharmacophore based 3D-QSAR of MK886 analogues against mPGES-1. Bull Korean Chem Soc 29:647-55 (Pubitemid 351468670)
64. Yadav DK, Khan F, Negi AS (2012) Pharmacophore modeling, molecular docking, QSAR, and in silico ADMET studies of gallic acid derivatives for immunomodulatory activity. J Mol Model 18:2513-25
65. Colovos C, Yeates TO (1993) Verification of protein structures: patterns of non-bonded atomic interactions. Protein Sci 2:1511-19 (Pubitemid 23262844)