A computational tool to optimize ligand selectivity between two similar biomacromolecular targets

Journal of Computer-Aided Molecular Design

Volumn 19, Issue 2, 2005, Pages 69-82

  Chen, Deliang L ^a   Kellogg, Glen E ^a  

^a VIRGINIA COMMONWEALTH UNIVERSITY   (United States)

Author keywords

Binding specificity; Hydropathic analysis; Selectivity

Indexed keywords

BINDING ENERGY; ENZYMES; HYDROGEN BONDS; LEAD COMPOUNDS; MAMMALS;

BINDING AFFINITIES; BINDING SPECIFICITIES; COMPUTATIONAL TOOLS; FUNCTIONAL MODIFICATION; HYDROPATHIC ANALYSE; IN-SILICO; LIGAND-RECEPTOR; RELATIVE BINDING; SELECTIVITY; STERICS;

LIGANDS;

10 PROPARGYL 5,8 DIDEAZAFOLIC ACID; 4 HYDROXYPHENYLPYRUVATE DIOXYGENASE; THYMIDYLATE SYNTHASE;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; ATOM; BACTERIUM MUTANT; BINDING AFFINITY; COMPUTER AIDED DESIGN; COMPUTER MODEL; COMPUTER PROGRAM; DRUG STRUCTURE; HYDROGEN BOND; HYDROPHOBICITY; LACTOBACILLUS CASEI; LIGAND BINDING; MATHEMATICAL COMPUTING; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN TARGETING; STEREOSPECIFICITY; STRUCTURE ANALYSIS; WILD TYPE;

EID: 22144451813     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-005-1485-7     Document Type: Article

References (34)

1. (a) Li, A.P., Curr. Top. Med. Chem., 4 (2004) 701
2. (b) Lin, J., Sahakian, D.C., de Morais, S.M., Xu, J.J., Polzer, R.J. and Winter, S.M., Curr. Top. Med. Chem., 3 (2003) 1125
3. R.J. Riley and J.G. Kenna 2004 Curr. Opin. Drug. Discov. Devel. 7 86 1:CAS:528:DC%2BD2cXpvFOnur8%3D 14982152
4. (a) Cheng, A. and Merz, K.M., Jr., J. Med. Chem., 46 (2003) 3572
5. (b) Gombar, V.K., Silver, I.S. and Zhao, Z., Curr. Top. Med. Chem., 3 (2003) 1205
6. (c) Vermeulen, N.P., Curr. Top. Med. Chem., 3 (2003) 1227
7. (d) Krejsa, C.M., Horvath, D., Rogalski, S.L., Penzotti, J.E., Mao, B., Barbosa, F. and Migeon, J.C., Curr. Opin. Drug Discov. Devel., 6 (2003) 470
8. (e) Stouch, T.R., Kenyon, J.R., Johnson, S.R., Chen, X.Q., Doweyko, A. and Li, Y., J. Comput. Aided Mol. Des., 17 (2003) 83
9. (a) Cashman, D.J. and Kellogg, G.E., J. Med. Chem., 47 (2004) 1360
10. (b) Cashman, D.J., Scarsdale, J.N. and Kellogg, G.E., Nucleic Acids Res., 31 (2003) 4410
11. (a) He, X., Reeve, A.M., Desai, U., Kellogg, G.E. and Reynolds, K.A., Antimicrob. Agents Chemother., 48 (2004) 3093
12. (b) He, X. and Reynolds, K.A., Antimicrob. Agents Chemother. 46 (2002) 1310
13. (c) Scarsdale, J.N., Kazanina, G., He, X., Reynolds, KA. and Wright, H.T., J. Biol. Chem., 276 (2001) 20516
14. (a) Kellogg, G.E. and Abraham, D.J., Eur. J. Med. Chem., 35 (2000) 651
15. (b) Burnett, J.C., Kellogg, G.E. and Abraham, D.J., Biochemistry, 39 (2000) 1622
16. (c) Cozzini, P., Fornabaio, M., Marabotti, A., Abraham, D.J., Kellogg, G. E. and Mozzarelli A., J. Med. Chem., 45 (2002) 2469
17. (d) Fornabaio, M., Cozzini, P., Mozzarelli, A., Abraham, D.J. and Kellogg, G. E., J. Med. Chem., 46 (2003) 4487
18. (e) Fornabaio, M., Spyrakis, F, Mozzarelli, A., Cozzini, P., Abraham, D.J. and Kellogg, G. E., J. Med. Chem., 47 (2004) 4507
19. (a) Kellogg, G.E., Fornabaio, M., Chen, D.L. and Abraham, D.J., J. Chem. Info. Comput. Sci. (submitted)
20. (b) Kellogg, G.E; eduSoft LC Programmers' Toolkit Manual. http://www.edusoft-lc.com/toolkits/manuals
21. F.M. Richards 1977 Ann. Rev. Biophs. Bioeng. 6 151 10.1146/ annurev.bb.06.060177.001055 1:CAS:528:DyaE2sXks1CisrY%3D
22. G.E. Kellogg and D.L. Chen 2004 Chem. & Biodivers. 1 98
23. (a) Fersht, A.R., Shi, J.P., Knill-Jones, J., Lowe, D.M., Wilkinson, A.J., Blow, D.M., Brick, P., Carter, P, Waye, M M.Y. and Wiinter, G., Nature, 314 (1985) 235
24. (b) Jencks, W.P., Catalysis in Chemistry and Enzymology, McGraw-Hill, New York, 1969
25. (a) Lipinski, C.A., Lombardo, F., Dominy, B.W. and Feeney, P.J., Adv. Drug Deliv. Rev., 46 (2001) 3
26. (b) Oprea, T. I., J. Comput. Aided Mol. Des., 14 (2000) 251-264
27. (a) van Laar, J.A., Rustum, Y.M., Ackland, S.P., van Groeningen, C.J. and Peters, G.J., Eur. J. Cancer, 34 (1998) 296-306
28. (b) Finer-Moore, J., Fauman, E.B., Foster, P.G., Perry, K.M., Santi, D.V. and Stroud, R.M., J. Mol. Biol., 232 (1993) 1101-1116
29. (c) Birdsall, D.L., Finer-Moore, J. and Stroud, R.M., J. Mol. Biol., 255 (1996) 522-535
30. C. Yang J.W. Pflugrath D.L. Camper M.L. Foster D.J. Pernich and T.A. Walsh 2004 Biochemistry 43 10414-10423 10.1021/bi049323o 1:CAS:528:DC%2BD2cXlslKls7c%3D 15301540
31. H.J. Bohm 1995 Persp. Drug. Discov. Design 3 21-33
32. Tripos, Inc., St. Louis, MO, USA
33. (a) Lauri, G. and Bartlett, P.A., J. Comput.-Aided Mol. Design, 8 (1994) 51-66
34. (b) Bartlett, P.A., In Chatgilialoglu, C. and Snieckus, V. (Eds.), Organic Synthesis, From Gnosis to Prognosis (NATO Advanced Study Institute), Kluwer, Dordrecht, 1986, pp. 137-173