Probing the structure of Leishmania donovani chagasi DHFR-TS: Comparative protein modeling and protein-ligand interaction studies

Journal of Molecular Modeling

Volumn 16, Issue 9, 2010, Pages 1539-1547

  Maganti, Lakshmi ^a   Manoharan, Prabu ^a   Ghoshal, Nanda ^a  

^a INDIAN INSTITUTE OF CHEMICAL BIOLOGY   (India)

Author keywords

Docking; Homology modeling; Leishmanial DHFR TS; Methotrexate

Indexed keywords

DIHYDROFOLATE REDUCTASE; DIHYDROFOLIC ACID; FOLIC ACID; TETRAHYDROFOLIC ACID;

AMINO ACID SEQUENCE; CRYSTAL STRUCTURE; LEISHMANIA DONOVANI; LEISHMANIA DONOVANI CHAGASI; MOLECULAR DOCKING; MOLECULAR DYNAMICS; MOLECULAR MODEL; NONHUMAN; NOTE; NUCLEOTIDE METABOLISM; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; SEQUENCE ALIGNMENT; VISCERAL LEISHMANIASIS;

AMINO ACID SEQUENCE; BINDING SITES; BIOCATALYSIS; HYDROGEN BONDING; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; LEISHMANIA INFANTUM; LIGANDS; METHOTREXATE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MULTIENZYME COMPLEXES; REPRODUCIBILITY OF RESULTS; SEQUENCE ALIGNMENT; STRUCTURAL HOMOLOGY, PROTEIN; TETRAHYDROFOLATE DEHYDROGENASE; THYMIDYLATE SYNTHASE;

BACTERIA (MICROORGANISMS); LEISHMANIA DONOVANI CHAGASI; LEISHMANIA MAJOR; TRYPANOSOMA CRUZI;

EID: 77955341067     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-010-0649-0     Document Type: Note

References (34)

1. AM Cunha E Chagas 1937 New species of protozoa of the genus Leishmania pathogenic to man Leishmania chagasi n. sp previous note O Hospital 11 3 9
2. SL Croft GH Coombs 2003 Leishmaniasis-current chemotherapy and recent advances in the search for novel drugs Trends Parasitol 19 502 508 10.1016/j.pt.2003.09.008 10.1016/j.pt.2003.09.008 1:CAS:528:DC%2BD3sXosVyisL0%3D (Pubitemid 37329659)
3. PJ Guerin P Olliaro S Sundar M Boelaert Sl Croft P Desjeux MK Wasunna ADM Bryceson 2002 Visceral leishmaniasis: current status of control, diagnosis, and treatment, and a proposed research and development agenda Lancet Infect Dis 2 494 501 10.1016/S1473-3099(02)00347-X 10.1016/S1473-3099(02)00347-X (Pubitemid 34826855)
4. CR Davies P Kaye SL Croft S Sunder 2003 Leishmaniasis: new approaches to disease control BMJ 326 377 382 10.1136/bmj.326.7385.377 10.1136/bmj.326.7385. 377
5. P Desjeux 2001 Worldwide increasing risk factors for leishmaniasis Med Microbiol Immunol 190 77 79 10.1007/s004300100085 1:STN:280: DC%2BD38%2Fkt1yltg%3D%3D (Pubitemid 33079364)
6. World Health Organization (2000) The Leishmaniasis and Leishmania/HIV co-infections. Fact Sheet Number 116. WHO, Geneva, Switzerland
7. FC Shafinaz VB Villamor RH Guerrero I Leal R Brun SL Croft JM Goodman L Maes LM Ruiz-Perez DG Pacanowska IH Gilbert 1999 Design, synthesis, and evaluation of inhibitors of trypanosomal and leishmanial dihydrofolate reductase J Med Chem 42 4300 4312 10.1021/jm981130+ 10.1021/jm981130+ (Pubitemid 29504134)
8. R Decampo 2001 Recent developments in the chemotherapy of Cha-gas' disease Curr Pharm Des 7 1157 1164 10.2174/1381612013397546 10.2174/ 1381612013397546 (Pubitemid 32640575)
9. K McLuskey F Gibellini P Carvalho MA Avery WN Huntera 2004 Inhibition of Leishmania major pteridine reductase by 2, 4, 6-triaminoquinazoline: structure of the NADPH ternary complex Acta Cryst 60 1780 1785 10.1107/S0907444904018955 (Pubitemid 41079699)
10. R Ferone S Roland 1980 Dihydrofolate reductase: thymidylate synthase, a bifunctional polypeptide from Crithidia fasciculata Proc Natl Acad Sci USA 77 5802 5806 10.1073/pnas.77.10.5802 1:CAS:528:DyaL3MXhsGn (Pubitemid 11206407)
11. CE Garrett JA Coderre TD Meek EP Garvey DM Claman SM Beverly DV Santhi 1984 A Bifunctional thymidylate synthase-dihydrofolate reductase in protozoa Mol Biochem Parasitol 11 257 265 10.1016/0166-6851(84)90070-7 10.1016/0166-6851(84) 90070-7 1:CAS:528:DyaL2cXkvVOjt78%3D
12. KM Ivanetich DV Santhi 1990 Bifunctional thymidylate synthase- dihydrofolate reductase in protozoa FASEB J 4 1591 1597 0892-6638/90/0004-1591/ $O1.50 1:CAS:528:DyaK3cXktVejs7Y%3D
13. A Bermingham JP Derrick 2002 The folic acid biosynthesis pathway in bacteria: evaluation of potential for antibacterial drug discovery BioEssays 24 637 648 10.1002/bies.10114 10.1002/bies.10114 1:CAS:528:DC%2BD38XlvVSntr8%3D (Pubitemid 34780351)
14. C Walsh 2003 Antibiotics: actions, origins, resistance ASM Washington 10.1110/ps.041032204
15. Walsh C (2003) Antibiotics: actions, origins, resistance. ASM, Washington. doi: 10.1110/ps.041032204
16. RL Then 2004 Antimicrobial dihydrofolate reductase inhibitors- achievements and future options: review J Chemother 16 3 12 1:CAS:528: DC%2BD2cXjs1yjsbg%3D
17. QC Zheng ZS Li M Sun Y Zhang CC Sun 2005 Homology modeling and substrate binding study of nudix hydrolase Ndx1 from Thermos thermophilus HB8 Biochem Biophys Res Commun 333 881 887 10.1016/j.bbrc.2005.05.169 1:CAS:528: DC%2BD2MXlvVentL0%3D (Pubitemid 40854241)
18. W Xu P Cai M Yan L Xu PK Ouyang 2007 Molecular docking of xylitol and xylose isomerase from Thermus thermophilus and model analysis Chem J Chin Univ 28 971 973 1:CAS:528:DC%2BD2sXmtVygurw%3D
19. YP He HR Hu LS Xu 2005 Structure-activity relationship studies on 6-naphthylmethyl substituted HEPT derivatives as nonnucleoside reverse transcriptase inhibitors based on molecular docking Chem J Chin Univ 26 254 258 1:CAS:528:DC%2BD2MXhs1yksb4%3D
20. DR Knighton CC Kan E Howland CA Janson Z Hostomska KM Welsh DA Matthews 1994 Structure of and kinetic channelling in bifunctional dihydrofolate reductase-thymidylate synthase Nat Struct Biol 1 186 194 10.1038/nsb0394-186 10.1038/nsb0394-186 1:CAS:528:DyaK2cXkslOitLo%3D
21. O Senkovich N Schormann D Chattopadhyay 2009 Structures of dihydrofolate reductase-thymidylate synthase of Trypanosoma cruzi in the folate-free state and in complex with two antifolate drugs, trimetrexate and methotrexate Acta Cryst 65 704 716 10.1107/S090744490901230X
22. InsightII (2007) Accelrys, San Diego
23. GOLD (2006) CCDC, Cambridge
24. http://www.pymol.org
25. SB Needleman CD Wunsch 1970 A general method applicable to the search for similarities in the amino acid sequence of two proteins J Mol Biol 48 443 453 10.1016/0022-2836(70)90057-4 10.1016/0022-2836(70)90057-4 1:CAS:528: DyaE3cXktVShu74%3D
26. L Jaroszewski K Pawlowski A Godzik 1998 Multiple model approach: exploring the limits of comparative modeling J Mol Model 4 294 309 10.1007/s008940050087 10.1007/s008940050087 1:CAS:528:DyaK1cXnsFGrtbo%3D
27. R Luthy JU Bowie D Eisenberg 1992 Assessment of protein models with three-dimensional profiles Nature 356 83 85 10.1038/356083a0 10.1038/356083a0 1:STN:280:DyaK387mvVWluw%3D%3D
28. C Colovos TO Yeates 1993 Verification of protein structures: patterns of nonbonded atomic interactions Protein Sci 2 1511 1519 10.1002/pro.5560020916 10.1002/pro.5560020916 1:CAS:528:DyaK2cXhvVKltbk%3D
29. RWW Hooft G Vriend C Sander EE Abola 1996 Errors in protein structures Nature 381 272 272 10.1038/381272a0 10.1038/381272a0 1:CAS:528: DyaK28XjtFOmsro%3D
30. MJ Sippl 1993 Boltzmann's principle, knowledge-based mean fields and protein folding J Comput Aided Mol Des 7 473 501 10.1007/BF02337562 10.1007/BF02337562 1:CAS:528:DyaK2cXhvVKgtr4%3D
31. RA Laskowski MW Macarthur DS Moss JM Thornton 1993 PROCHECK a program to check the stereo chemical quality of protein structure J Appl Cryst 26 283 291 10.1107/S0021889892009944 10.1107/S0021889892009944 1:CAS:528:DyaK3sXit12lurY%3D
32. N Guex MC Peitsch 1997 SWISS MODEL and the Swiss pdb viewer: an environment for comparative protein modeling Electrophoresis 18 2714 2723 10.1093/nar/gkg520 10.1002/elps.1150181505 1:CAS:528:DyaK1cXhvFaks70%3D
33. Cerius2 (2006) Accelrys, San Diego
34. AC Wallace RA Laskowski JM Thornton 1995 LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions Protein Eng 8 127 134 10.1093/protein/8.2.127 10.1093/protein/8.2.127 1:CAS:528:DyaK2MXltVCgtLc%3D