Entamoeba histolytica: Computer-assisted modeling of phosphofructokinase for the prediction of broad-spectrum antiparasitic agents

Experimental Parasitology

Volumn 87, Issue 3, 1997, Pages 194-202

  Byington, Carrie L ^a   Dunbrack Jr , Roland L ^b   Whitby, Frank G ^a   Cohen, Fred E ^b   Agabian, Nina ^b  

^a UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

6 PHOSPHOFRUCTOKINASE; ALENDRONIC ACID; ANTIPARASITIC AGENT; BA 49280E; METRONIDAZOLE; PAMIDRONIC ACID; PAROMOMYCIN; PROTEINASE INHIBITOR; UNCLASSIFIED DRUG;

ARTICLE; COMPUTER ANALYSIS; CONTROLLED STUDY; ENTAMOEBA HISTOLYTICA; GROWTH INHIBITION; MODEL; NONHUMAN; PREDICTION; PRIORITY JOURNAL;

ENTAMOEBA HISTOLYTICA; GEOBACILLUS STEAROTHERMOPHILUS; GIARDIA INTESTINALIS; NAEGLERIA FOWLERI; PROTISTA; RUMEX; TOXOPLASMA GONDII; TRICHOMONAS VAGINALIS;

EID: 0031282558     PISSN: 00144894     EISSN: None     Source Type: Journal    
DOI: 10.1006/expr.1997.4224     Document Type: Article

References (25)

1. Bower, M. J., Cohen, F. E., and Dunbrack, R. L., Jr. 1997. Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: A new homology modeling tool. Journal of Molecular Biology 267, 1268-1282.
2. Bruchhaus, I., Jacobs, T., Dennart, M., and Tannich, E. 1996. Pyrophosphate-dependent phosphofructokinase of Entamoeba histolytica: Molecular cloning, recombinant expression, and inhibition by pyrophosphate analogs. Biochemical Journal 316, 57-63.
3. Chothia, C., and Lesk, A. M. 1986. The relation between the divergence of sequences and structure in proteins. EMBO Journal 5(4), 823-826.
4. Cohen, F. E., Gregoret, L. M., Amiri, P., Aldape, K., Railey, J., and McKerrow J. H. 1991. Arresting tissue invasion of a parasite by protease inhibitors chosen with the aid of computer modeling. Biochemistry 30, 11221-11229.
5. Cramer, C. J., Hawkins, G. D., Lynch, G. C., Geisen, D. J., Truhlar, D. J., and Liotard, D. 1994. AMSOL - Version 4.5. QCPE Bulletin 14, 55-57.
6. DesJarlais, R. L., Seibel, G. L., Kuntz, I. D., Furth, P. S., Alvarez, J. C., Ortiz, de Montellano, P. R., DeCamp, D. L., Babe, L. M., and Craik, C. S. 1990. Structure-based design of nonpeptide inhibitors specific for the human immunodeficiency virus 1 protease. Proceedings of the National Academy of Sciences of the United States of America 87(17), 6644-6648.
7. Dunbrack, R. L., Jr., and Cohen, F. E. 1997. Bayesian statistical analysis of the backbone-dependent rotamer preferences of protein sidechains. Protein Science 6, 1661-1681.
8. Dunbrack, R. L., Jr., Gerloff, D. L., Bower, M., Chen, X., Lichtarge, O., and Cohen, F. E. 1997. Meeting review: The second meeting on the critical assessment of techniques for protein structure prediction (CASP2), Asilomar, CA, December 13-16, 1996. Folding and Design 2, R27-R42.
9. Dunbrack, R. L., Jr., and Karplus, M. 1994. Conformational analysis of the backbone dependent rotamer preferences of side chains. Nature Structural Biology 1, 334-340.
10. Dunbrack, R. L., Jr., and Karplus, M. 1993. Backbone-dependent rotamer library for proteins: Application to side chain prediction. Journal of Molecular Biology 230, 543-574.
11. Evans, P. R., Farrants, G. W., and Hudson, P. J. 1981. Phosphofructokinase: Structure and control. Philosophical Transactions of the Royal Society of London, Series B 293, 53.
12. Licata, A. A. 1997. Bisphosphonate therapy. American Journal of the Medical Sciences 313(1), 17-22.
13. Meng, E. C., Gschwend, D. A., Blaney, J. M., and Kuntz, I. D. 1993. Orientational sampling and rigid-body minimization in molecular docking. Proteins 17, 266-278.
14. Navia, M. A., and Peattie, D. A. 1993. Structure-based drug design: applications in immunopharmacology and immune suppression. Trends in Pharmacologic Science 14(5), 189-195.
15. Pearlman, D. A., Case, D. A., Caldwell, J. W., Ross, W. S., Cheatham, T. E., Ferguson, D. M., Seibel, G. L., Singh, U. C., Weiner, P. K., and Kollman, P. A. 1995. AMBER 4.1, University of California at San Francisco, San Francisco, CA.
16. Peng, Z. Y., Mansour, J. M., Araujo, F., Ju, J. Y., McKenna, C. E., and Mansour, T. E. 1995. Some phosphonic acid analogs as inhibitors of pyrophosphate-dependent phosphofructokinase, a novel target in Toxoplasma gondii. Biochemical Pharmacology 49(1), 105-113.
17. Ravdin, J. I. 1995. Amebiasis. Clinical Infectious Diseases 20, 1453-1466.
18. Reeves, R. 1968. A new enzyme with the glycolytic function of pyruvate kinase. Journal of Biological Chemistry 234, 3202-3204.
19. Ring, C. S., Sun, E., McKerrow, J. H., Garson, K. L., Rosenthal, P. J., Kuntz, I. D., and Cohen, F. E. 1993. Structure based inhibitor design by using protein models for the development of antiparasitic agents. Proceedings of the National Academy of Sciences, USA 90, 3583-3587.
20. Rost, B. 1996. PHD: Predicting one-dimensional protein structure by profile based neural networks. Methods in Enzymology 364, 164-168.
21. Shirakihara, Y., and Evans, P. R. 1988. Crystal structure of the complex of phosphofructokinase from Escherichia coli with its reaction products. Journal of Molecular Biology 204(4), 973-994.
22. Summers, N. L., Carlson, W. D., and Karplus, M. 1987. Analysis of side-chain orientations in homologous proteins. Journal of Molecular Biology 196(1), 175-198.
23. "The Medical Letter on Drugs and Therapeutics." (M. Abramowicz, Ed.), Drugs for Parasitic Infections. 1993: 35 (911), 111-22.
24. "The Physician's Desk Reference." 1997 (Ronald Arky, medical consultant) Didronel® I.V. infusion (etidronate disodium). pp. 1545-46. Medical Economics, Montvale, NJ.
25. Thompson, J. D., Higgins, D. G., and Gibson, T. J. 1994. CLUSTALW: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties, and weight matrix choice. Nucleic Acids Research 22, 4673-4680.