Modeling the interactions of herbal drugs to β-ketoacyl acp synthase of mycobacterium tuberculosis h37rv

Journal of Biomolecular Structure and Dynamics

Volumn 25, Issue 5, 2008, Pages 481-493

  Ramesh, K V ^a   Purohit, Mitali ^a   Mekhala, K ^a   Krishnan, Mrinalini ^a   Wagle, Kaushiki ^a   Deshmukh, Sudha ^a  

^a JAIN UNIVERSITY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

3 OXOACYL ACYL CARRIER PROTEIN SYNTHASE; ACTEOSIDE; ALLOCUSPAREINE; ALOE EMODIN; BETA AMYRIN; CATECHIN; CERULENIN; CITRIC ACID; CYSTEINE; HERBACEOUS AGENT; HISTONE; ISOHARMINE; LAURIC ACID; LEUCOGEN; LUTEOLIN; NIMBIN; PURPURIN; QUERCETIN; THIOLACTOMYCIN; TOTAROL; TUBERCULOSTATIC AGENT; UNCLASSIFIED DRUG; URSOLIC ACID;

ARTICLE; CATALYSIS; DATA BASE; DRUG BINDING; ENZYME STRUCTURE; GENETIC CODE; GENETIC CONSERVATION; HERBAL MEDICINE; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; OPEN READING FRAME; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DOMAIN; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; TUBERCULOSIS;

3-OXOACYL-(ACYL-CARRIER-PROTEIN) SYNTHASE; ALGORITHMS; AMINO ACID SEQUENCE; ANTITUBERCULAR AGENTS; BACTERIAL PROTEINS; BINDING SITES; HUMANS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MYCOBACTERIUM TUBERCULOSIS; OPEN READING FRAMES; PLANT PREPARATIONS; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT; SOFTWARE;

ALOE; MYCOBACTERIUM TUBERCULOSIS;

EID: 41049094654     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2008.10507195     Document Type: Article

References (65)

1. http://www.who.int/mediacenter/factsheets/fs04/en/WHO Tuberculosis Fact sheet No. 104
2. Chan, E. D., and Iseman, M. D., 2002. Br Med J, 325:1282–1286.
3. Michison, D. A., 1998. Mycobacteria II Chemotherapy Edited by:Gangadharam, P. R. J., and Jenkins, P. A., 15–50. New York:Chapman and Hall.
4. Kolattukudy, P. E., Fernandez, N. D., Azad, A. K., Fitzmaurice, A. M., and Sirakova, T. D., 1997. Mol Microbiol, 24:263–270.
5. Ratledge, C. R., 1982. The Biology of Mycobacteria Edited by:Ratledge and Stanford. 53–94. San Diego:Academic.
6. Mdluli, K., Slayden, R. A., Zhu, Y., Ramaswamy, S., Pan, X., Mead, D., Crane, D. D., Musser, J. M., and Barry, C. E., III. 1998. Science, 280:1607–1610.
7. Goulding, C. W., Apostol, M., Anderson, H. D., and Harindarpal, S. Gill. 2002. The TB Structural Genomics Consortium:Providing a Structural Foundation for Drug Discovery. Current Drug Targets-Infectious Disorders. other
8. Roswarski, D. A., Vilchezes, C., Sugantino, M., Bittman, R., and Sacchettini, J. C., 1999. J Biol Chem, 274:15582–15589.
9. Roswarski, D. A., Grant, G. A., Barton, D. H. R., Jacobs, W. R., Jr. and Sacchettini, J. C., 1998. Science, 279:98–102.
10. Price, A. C., Choi, K. W., Heath, R. J., Li, Z., White, S. W., and Rock, C. O., 2001. J Biol Chem, 276:6551–6559.
11. Kim, P., Zhang, Y. M., Shenoy, G., Nguyen, Q., Boshoff, H. I., Manjunatha, U. H., Goodwin, M., Lonsdale, J., Price, A. C., Darcie, J., Miller Duncan, K., White, S. W., Rock, C. O., Clifton, E., Barry and Dowd, C. S., 2006. J Med Chem, 12:159–171.
12. http://www.doe-mbi-ucla.edu/TB/index.php.
13. Sabnis, Y., Rosenthal, P. J., Desai, P., and Avery, M. A., 2002. J Biomol Struct Dyn, 19:765–774.
14. Goldberg, D. E., 1989. Genetic Algorithms in Search, Optimization and Machine Learning. Reading, MA:Ad-dison-Wesley.
15. Pedersen, J. T., and Moult, J., 1997. J Mol Biol, 269:240–259.
16. Sun, Z., Xia, X., Guo, Q., and Xu, D., 1999. J Protein Chem, 18:39–46.
17. Pegg, S. C., Haresco, J. J., and Kuntz, I. D., 2001. J Comput Aided Mol Dis, 15:911–933.
18. Notredame, C., and Higgins, D. G., 1996. Nucleic Acids Res, 24:1515–1524.
19. Ramesh, K. V., Kaushiki, W., and Sudha, D., 2007. J Biomol Struct Dyn, 24:303–428.
20. De Smet, P. A., 2002. N Engl J Med, 347:2046–2056.
21. Dixon, R. A., 2001. Nature, 411:843–847.
22. http://www.ncbi.nlm.nih.gov
23. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. J., 1987. Nuc Acids Res, 25:3389–3402.
24. Sali and Blundell, T. L., 1993. J Mol Biol, 234:779–815.
25. Thompson, J. D., Higgins, D. G., and Gibson, T. J., 1994. Nuc Acids Res, 22:4673–4680.
26. Fiser, A., and Sali, A., 2003. Methods in Enzymology Edited by:Carter, C. W., and Sweet, R. M., 374San Diego:Academic Press. 463–493
27. http://www.expasy.org/spdbv/
28. Guex, N., and Peitsch, M. C., 1997. Electrophoresis, 18:2714–2723.
29. Shen, M. Y., and Sali, A., 2006. Protein Sci, 15:2507–2524.
30. John, B., and Sali, A., 2003. Nuc Acid Res, 14:3982–3992.
31. Brown, A. K., Sridharan, S., Kremer, L., Lindenberg, S., Dover, L. G., Sacchettini, J. C., and Besra, G. S., 2005. J Biol Chem, 280:32539–32547.
32. Bagaupdinov et al. unpublished.
33. http://www.vakser.bionformatics.ku.edu/resources/gramm/grammx
34. Tovchigrechko1, A., and Vakser, I. A., 2006. Nucleic Acids Research 34. W310–314. Web Server issue
35. Laskowski, R. A., McArthur, M. W., Moss, M. D., and Thornton, J. M., 1998. J Appl Cryst, 26:283–291.
36. Luthy, R., Bowie, J. U., and Eisenberg, D., 1992. Nature, 356:83–85.
37. Hooft, R. W., Vreind, G., Sander, C., and Abola, E. E., 1996. Nature, 381:272–272.
38. Kleywegt, G. J., and Jones, T. A., 1996. Structure, 4:1395–1400.
39. Jogl, G., and Tong, L., 2003. Cell, 112:113–122.
40. Price, A. C., Choi, K. W., Heath, R. J., Li, Z., White, S. W., and Rock, C. O., 2001. J Biol Chem, 276:6551–6559.
41. Moche, M., Schneider, G., Edwards, P., Dehesh, K., and Lindqvist, Y., 1999. J Biol Chem, 274:6031–6034.
42. Rukachaisirikul, T., Prabpai, S., Kongsaeree, P., and Suksamrarn, A., 2004. Chem Pharm Bull, 52:760–761.
43. Hatano, T., Uebayashi, H., Ito, H., Shiota, S., Tsuchiya, T., and Yoshida, T., 1999. Chem Pharm Bull, 47:1121–1127.
44. Basu, S., Ghosh, A., and Hazra, B., 2005. Phytother Res, 19:888–894.
45. Sanches, N. R., Cortez, D. A. G., Schiavini, M. S., Nakamura, C. V., and Filho, B. P., 2005. Brazilian Archives of Biology and Technology, 48:429–436.
46. Zhang, Y. M., and Rock, C. O., 2004. J Biol Chem, 279:30994–31001.
47. Ayoub, M., and Rashan, L. J., 1991. Phytochemistry, 30:1046–1047.
48. Narayanan, V., and Seshadri, T. R., 1972. Indian J Chem, 10:379–381.
49. Sevda, S., Ali, H. M., Houghtonb, P. J., and Cubukcu, B., 2005. Fitoterapia, 76:269–272.
50. Lodhi, S., Pawar, R. S., Jain, A. P., and Singhai, A. K., 2006. J Ethnopharmacol, 108:204–210.
51. Siddiqui, S., Faizi, S., Siddiqui, B. S., and Ghiasuddin, J., 1992. Nat Prod, 55:303–310.
52. Mossa, J. S., Farouk, S., El-Feraly and Ilias, M., 2004. Phytother Res, 18:934–937.
53. Gua, J. Q., Wang, Y., Franzblau, S. G., Montenegro, G., and Timmermann, B. N., 2004. Z Naturforsch [C], 59:797–802.
54. Hasan, K., Calis, I., Perozzo, R., Brun, R., Donmez, A. A., Linden, A., Ruedi, P., and Tasdemir, D., 2004. Planta Med, 70:711–717.
55. http://www.mdli.com
56. Kuntz, I. D., Blaney, J. M., Oatley, S. J., Langridge, R., and Ferrin, T. E., 1982. J Mol Biol, 161:269–288.
57. Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., and Ferrin, T. E., 2004. J Comput Chem, 25:1605–1612.
58. DeLano, W. L., 2002. The PyMOL Molecular Graphics System. Palo Alto, CA, USA:DeLano Scientific.
59. Rie, Y., Knowles, P. W., and Wada, H., 2004. J Biol Chem, 279:8242–8251.
60. Sanchez, R., and Sali, A., 1997. Proteins (Suppl),:50–58.
61. Fiser, A., and Sali, A., http://www.salilab.org/pdf/086_FiserDekker2000.pdf
62. Olsen, J. G., Kadziola, A., von Wettstein-Knowles, P., Siggaard, A. M., and Larsen, S., 2001. Structure, 9:233–243.
63. Siggaard, A. M., Bangera, G., Olsen, J. G., and von Wettstein-Knowles, P., 1998. Advances in Plant Lipid Research Edited by:Sanchez, J., Cerda Olmedo, E., and Martinez-Force, E., 67–70. Sevilla:Universidad de sevilla, Secretariado de Publicaciones.
64. Witkowski, A., Joshi, A. K., and Smith, S., 2002. Biochemistry, 41:10877–10887.
65. Berg, J. M., Tymoczko, J. L., and Stryer, L., Biochemistry (6th edn), Freeman and Co., New York