Prediction of a new surface binding pocket and evaluation of inhibitors against huntingtin interacting protein 14: An insight using docking studies

Journal of Molecular Modeling

Volumn 17, Issue 12, 2011, Pages 3047-3056

  Gupta, Shipra ^a   Misra, Gauri ^a   Pant, Mohan C ^b   Seth, Prahlad Kishor ^a  

^a Biotech Park   (India)

^b KING GEORGE'S MEDICAL UNIVERSITY   (India)

Author keywords

Huntingtin interacting protein; Huntingtin protein; Molecular docking; Molecular interactions

Indexed keywords

AGENTS INTERACTING WITH TRANSMITTER, HORMONE OR DRUG RECEPTORS; AMANTADINE; BINDING PROTEIN; CID 14052; CID 2130; CID 2915; CID 3446; CID 4054; CID 4059; CID 4171; CID 4205; CID 42396; CID 43815; CID 5984; CID 6037; CID 61503; CID 6251; CID 62923; CID 64953; CID 6503; CID 6518; CID 68614; CID 753; CID 82170; CID 91536; CID 9303; CID 94423; CYSTAMINE; DIODONE; DOCKING PROTEIN; ETHAMBUTOL; FLUORODEOXYGLUCOSE F 18; FOLIC ACID; FRUCTOSE; GABAPENTIN; GLYCEROL; HALOPERIDOL; HUNTINGTIN INTERACTING PROTEIN 14; LACTIC ACID; MANNITOL; MEGLUMINE ANTIMONATE; MEMANTINE; MEPHENESIN; METOPROLOL; MINOCYCLINE; MIRTAZAPINE; OXPRENOLOL; PAROXETINE; PENTAERYTHRITYL TETRANITRATE; PRENALTEROL; PROPRANOLOL; SORBITOL; TROMETAMOL; UNCLASSIFIED DRUG; VENLAFAXINE;

ARTICLE; DRUG PROTEIN BINDING; DRUG STRUCTURE; HYDROGEN BOND; MOLECULAR DOCKING; POLAR SURFACE AREA; PREDICTION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION; SURFACE PROPERTY;

ACYLTRANSFERASES; ADAPTOR PROTEINS, SIGNAL TRANSDUCING; BINDING SITES; ENZYME INHIBITORS; FLUORODEOXYGLUCOSE F18; HUMANS; HUNTINGTON DISEASE; HYDROGEN BONDING; METOPROLOL; MINOCYCLINE; MODELS, MOLECULAR; NERVE TISSUE PROTEINS; NUCLEAR PROTEINS; PEPTIDES; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; TETRACYCLINE; THERMODYNAMICS;

EID: 84855701993     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-011-1005-8     Document Type: Article

References (30)

1. Huang KYA, Kang R, Arstikaitis P, Singaraja RR, Metzler M et al (2004) Huntingtin interacting protein HIP14, is a palmitoyl transferase involved in palmitoylation and trafficking of multiple neuronal proteins. Neuron 44:977-986 (Pubitemid 39643093)
2. Yanai A, Huang K, Kang R, Singaraja RR, Arstikaitis P, Gan L et al (2006) Palmitoylation of huntingtin by HIP14 is essential for its trafficking and function. Nat Neurosci 9:824-831
3. Singaraja RR, Hadano S, Metzler M, Givan S, Wellington CL, Warby S et al (2002) HIP14, a novel ankyrin domain-containing protein, links huntingtin to intracellular trafficking and endocytosis. Hum Mol Genet 11:2815-2828 (Pubitemid 35331814)
4. SEM DCE, French KJ, Upson JJ, Smith CD (2004) Huntingtin interacting protein 14 is an oncogenic human protein: Palmitoyl 9230-9237acyltransferase. Oncogene 23:9230-9237 (Pubitemid 40069693)
5. Ghose AK, Viswanadhan VN, Wendoloski JJ (1999) A knowledge-based approach in designing combinatorial or medicinal chemistry libraries for drug discovery. 1. A qualitative and quantitative characterization of known drug databases. J Comb Chem 1:55-68
6. Gao T, Collins RE, Horton JR, Zhang X, Zhang R, Dhayalan A et al (2009) The ankyrin repeat domain of Huntingtin interacting protein 14 contains a surface aromatic cage, a potential site for methyl-lysine binding. Proteins 76:772-777
7. Berman HM,Westbrook J, Feng Z, Gilliland G, Bhat TN,Weissig H et al (2000) The Protein Data Bank. Nucleic Acids Res 28:235-242 (Pubitemid 30047768)
8. SYBYL-X 1.1, Tripos International. (1699) South Hanley Rd, St Louis, Missouri, 63144, USA
9. Bikadi Z, Hazai E (2009) Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDock. J Cheminformatics 1:15
10. Labute P (2007) Protonate 3D: Assignment of Macromolecular Protonation State and Geometry. Chemical Computing Group Inc.
11. Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK et al (1998) Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem 19:1639-1662 (Pubitemid 128590223)
12. Mark HEF, Geoffrey H, Bernhard P, Peter R, Ian HW (2009) The WEKAData Mining Software:AnUpdate. SIGKDDExplor 11:10-18
13. Guha R, Howard MT, Hutchison GR, Murray-Rust P, Rzepa H, Steinbeck C et al (2006) The Blue Obelisk-interoperability in chemical informatics. J Chem Inf Model 46:991-998
14. Schneidman-Duhovny D, Inbar Y, Nussinov R, Wolfson HJ (2005) PatchDock and SymmDock: Servers for rigid and symmetric docking. Nucleic Acids Res 33:W363-367 (Pubitemid 44529944)
15. Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS et al (2009) AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem 30:2785-2791
16. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC et al (2004) UCSF Chimera-a visualization system for exploratory research and analysis. J Comput Chem 25:1605-1612
17. Shaikh SA, Ahmed SR, Jayaram B (2004) A molecular thermodynamic view of DNA-drug interactions: A case study of 25 minor-groove binders. Arch Biochem Biophys 429:81-99 (Pubitemid 39013384)
18. Sikic M, Tomic S, Vlahovicek K (2009) Prediction of proteinprotein interaction sites in sequences and 3D structures by random forests. PLoS Comput Biol 5:e1000278
19. Egan WJ, Lauri G (2003). Prediction of molecular polar surface area and bioabsorption. Pharmacopeia, Inc.
20. Sarah LK NL, Nancy B, Peter JT, Lei X, Philip EB (2009) Drug Discovery Using Chemical Systems Biology:Repositioning the Safe Medicine Comtan to Treat Multi-Drug and Extensively Drug Resistant Tuberculosis. PLoS Comput Biol 5
21. KAKR SVK, Singh RK, Singh PP (2008) Hydrophobic, Polar and Hydrogen Bonding Based Drug-Receptor Interaction of Tetrahydroimidazobenzodiazepinones. Am J Immunol 4:33-42
22. Thomas M, Ashizawa T, Jankovic J (2004) Minocycline in Huntington's disease: A pilot study. Mov Disord 19:692-695 (Pubitemid 39173025)
23. Sonnhammer Erik LLHV (2005) Scoredist: A simple and robust protein sequence distance estimator. BMC Bioinformatics 6
24. YF AFR, Linyi C, Nicholas GD (2002) US Patent 6522975- Prediction of molecular polar surface area and bioabsorption. J Cell Biol 159:23-28
25. Jain AN (2000) Scoring Functions for Protein-Ligand Docking. Curr Protein Pept Sci 7:407-20
26. Heron DE, Ferris RL, Karamouzis M, Andrade RS, Deeb EL, Burton S et al (2009) Stereotactic body radiotherapy for recurrent squamous cell carcinoma of the head and neck: Results of a phase I dose-escalation trial. Int J Radiat Oncol Biol Phys 75:1493-1500
27. Mazziotta JC, Phelps ME, Pahl JJ, Huang SC, Baxter LR, Riege WH et al (1987) Reduced cerebral glucose metabolism in asymptomatic subjects at risk for Huntington's disease. N Engl J Med 316:357-362 (Pubitemid 17034259)
28. Lai RC, Xu MX, Huang WQ,Wang XD, ZengWA, Lin WQ (2006) Beneficial effects of metoprolol on perioperative cardiac function of elderly esophageal cancer patients. Ai Zheng 25:609-613
29. JMP KK, Andrew JN,McDonald JT, Sun Y,Micewicz E et al (2009) High-Throughput Screening Identifies Two Classes of Antibiotics as Radioprotectors: Tetracyclines and Fluoroquinolones. Clin Cancer Res 15:7238-7245
30. Fandos R, Fernandez-Gallardo J, Otero A, Rodriguez A, Ruiz MaJ (2010) nfluence of Hydrogen Bonds on the Stability of Some Cationic Monoaminocarbene Tantalum Complexes Containing Tridentate Bis(phenolato) [OSO]-Type Ligands. Organometallics 29:5834-5840