Homology modeling, molecular dynamics, and molecular docking studies of Trichomonas vaginalis carbamate kinase

Medicinal Chemistry Research

Volumn 21, Issue 8, 2012, Pages 2105-2116

  Kirubakaran, Palani ^a   Muthusamy, Karthikeyan ^a   Singh, Kh Dhanachandra ^a   Nagamani, Selvaraman ^a  

^a ALAGAPPA UNIVERSITY   (India)

Author keywords

Carbamate kinase; Molecular dynamics and molecular docking; Three dimensional model; Trichomonas vaginalis

Indexed keywords

ANTIPROTOZOAL AGENT; CARBAMATE KINASE; CARBAMATE KINASE INHIBITOR; ENZYME INHIBITOR; SILICON; UNCLASSIFIED DRUG;

ANIMAL CELL; ARTICLE; BINDING SITE; COMPUTER PROGRAM; DATA BASE; DRUG ABSORPTION; DRUG BINDING; DRUG DISTRIBUTION; DRUG EXCRETION; DRUG METABOLISM; HIGH THROUGHPUT SCREENING; MOLECULAR DOCKING; MOLECULAR DYNAMICS; MOLECULAR MODEL; NONHUMAN; SEQUENCE HOMOLOGY; STEREOCHEMISTRY; TRICHOMONAS VAGINALIS;

EID: 84866055935     PISSN: 10542523     EISSN: 15548120     Source Type: Journal    
DOI: 10.1007/s00044-011-9719-9     Document Type: Article

References (33)

1. Anne Marie J, Sid T (2008) Driving forces for ligand migration in the leucine transporter. Chem Biol Drug Des 72(4):265-272
2. Bowers KJ, Dror RO, Shaw DE (2006) The midpoint method for parallelization of particle simulations. J Chem Phys 124(18): 184109-184111
3. Combet C, Jambon M, Deleage G, Geourjon C (2002) Geno3D: automatic comparative molecular modelling of protein. Bioinformatics 18(1):213-214
4. Edwards MR, Schofield PJ, O'Sullivan WJ, Costello M (1992) Arginine metabolism during culture of Giardia intestinalis. Mol Biochem Parasitol 53(1-2):97-103
5. Eric FP, Thomas DG, Conrad CH, Gregory SC, Daniel MG, Elaine CM, Thomas EF (2004) UCSF Chimera-a visualization system for exploratory research and analysis. J Comput Chem 25(13): 1605-1612
6. Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT, Repasky MP, Knoll EH, Shelley M, Perry JK, Shaw DE, Francis P, Shenkin PS (2004) Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 47(7):1739-1749
7. Galkin A, Kulakova L, Wu R, Nash TE, Dunaway-Mariano D, Herzberg O (2010) X-ray structure and characterization of carbamate kinase from the human parasite Giardia lamblia. Acta Crystallogr Sect F 66(4):386-390
8. Geronikaki AA, Dearden JC, Filimonov D, Galaeva I, Garibova TL, Gloriozova T, Krajneva V, Lagunin A, Macaev FZ, Molodavkin G, Poroikov VV, Pogrebnoi SI, Shepeli F, Voronina TA, Tsitlakidou M, Vlad L (2004) Design of new cognition enhancers: from computer prediction to synthesis and biological evaluation. J Med Chem 47(11):2870-2876
9. Geronikaki AA, Lagunin AA, Hadjipavlou-Litina DI, Eleftheriou PT, Filimonov DA, Poroikov VV, Alam I, Saxena AK (2008) Computer-aided discovery of anti-inflammatory thiazolidinones with dual cyclooxygenase/lipoxygenase inhibition. J Med Chem 51(6):1601-1609
10. Jorgensen WL, Duffy EM (2000) Prediction of drug solubility from Monte Carlo simulations. Bioorg Med Chem Lett 10(11): 1155-1158
11. 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(45):11225-11236
12. 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(28):6474-6487
13. Kevin JB, Edmond C, Huafeng X, Ron OD,Michael PE, Brent AG, John LK, IstvanK,Mark AM, FedericoDS, JohnKS, Yibing S,DavidES (2006) Scalable algorithms for molecular dynamics simulations on commodity clusters. In Proceedings of the 2006 ACM/IEEE conference on Supercomputing Tampa. ACM, Florida
14. Kevin JB, Ron OD, David ES (2007) Zonal methods for the parallel execution of range-limited N-body simulations. J Comput Phys 221(1):303-329
15. Kroemer RT, Doughty SW, Robinson AJ, Richards WG (1996) Prediction of the three-dimensional structure of human interleukin-7 by homology modeling. Protein Eng 9(6):493-498
16. Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr 26(2):283-291
17. Linstead D, Cranshaw MA (1983) The pathway of arginine catabolism in the parasitic flagellate Trichomonas vaginalis. Mol Biochem Parasitol 8(3):241-252
18. Manfred JS (1993) Recognition of errors in three-dimensional structures of proteins. Proteins 17(4):355-362
19. Markus C, Philippe HH, Dirk B, Riccardo B, Roland B, Daan PG, Tim NH, Mika AK, Vincent K, Chris O, Christine P, Daniel T, Wilfred FvG (2005) The GROMOS software for biomolecular simulation: GROMOS05. J Comput Chem 26(16):1719-1751
20. McGuffin LJ, Jones DT (2003) Improvement of the GenTHREADER method for genomic fold recognition. Bioinformatics 19(7): 874-881
21. Nabuurs SB, Wagener M, de Vlieg J (2007) A flexible approach to induced fit docking. J Med Chem 50(26):6507-6518
22. Navarrete-Vazquez G, Rojano-Vilchis MdM, Yepez-Mulia L, Melendez V, Gerena L, Hernandez-Campos A, Castillo R, Hernandez-Luis F (2006) Synthesis and antiprotozoal activity of some 2-(trifluoromethyl)-1H-benzimidazole bioisosteres. Eur J Med Chem 41(1):135-141
23. Navarrete-Vázquez G, Yépez L, Hernández-Campos A, Tapia A, Hernández-Luis F, Cedillo R, González J, Martínez-Fernández A, Martínez-Grueiro M, Castillo R (2003) Synthesis and antiparasitic activity of albendazole and mebendazole analogues. Bioorg Med Chem 11(21):4615-4622
24. Nicolas G, Manuel CP (1997) SWISS-MODEL and the Swiss-Pdb Viewer: an environment for comparative protein modeling. Electrophoresis 18(15):2714-2723
25. Poroikov VV, Filimonov DA, Ihlenfeldt WD, Gloriozova TA, Lagunin AA, Borodina YV, Stepanchikova AV, Nicklaus MC (2002) PASS biological activity spectrum predictions in the enhanced open NCI database browser. J Chem Inf Model 43(1):228-236
26. Sali A, Blundell TL (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234(3):779-815
27. Sali A, Potterton L, Yuan F, van Vlijmen H, Karplus M (1995) Evaluation of comparative protein modeling by MODELLER. Proteins 23:318-326
28. Schofield PJ, Edwards MR, Matthews J, Wilson JR (1992) The pathway of arginine catabolism in Giardia intestinalis. Mol Biochem Parasitol 51(1):29-36
29. Schrädinger Suite 2009 Virtual Screening Workflow; Glide version 5.5, Schrädinger, LLC, New York, NY, 2009; LigPrep version 2.3, Schrädinger, LLC, New York, NY, 2009; QikProp version 3.2 (2009) Schrädinger, LLC, New York, NY
30. Schwede T, Kopp J, Guex N, Peitsch MC (2003) SWISS-MODEL: an automated protein homology-modeling server. Nucl Acids Res 31(13):3381-3385
31. Shaw DE (2005) A fast, scalable method for the parallel evaluation of distance-limited pairwise particle interactions. J Comput Chem 26(13):1318-1328
32. Sherman W, Day T, Jacobson MP, Friesner RA, Farid R (2005) Novel procedure for modeling ligand/receptor induced fit effects. J Med Chem 49(2):534-553
33. Wendel Karen A, Workowski Kimberly A (2007) Trichomoniasis: challenges to appropriate management. Clin Infect Dis 44(S3): S123-S129