Ligand-based computer-aided pesticide design. A review of applications of the CoMFA and CoMSIA methodologies

Pest Management Science

Volumn 59, Issue 4, 2003, Pages 393-400

  Bordás, Barna ^a   Kömíves, Tamás ^a   Lopata, Antal ^b  

^a INSTITUTE OF EXPERIMENTAL MEDICINE   (Hungary)

^b CheMicro Ltd   (Hungary)

Author keywords

CoMFA; CoMSIA; Fungicide; Herbicide; Insecticide; QSAR; Receptor; Safener

Indexed keywords

ACETAMIDE DERIVATIVE; AGRICULTURAL CHEMICAL; BIOPOLYMER; DICHLOROACETAMIDE; FUNGICIDE; HERBICIDE; INSECTICIDE; LIGAND; UNCLASSIFIED DRUG;

AGROCHEMICAL; FUNGICIDE; HERBICIDE; INSECTICIDE; MOLECULAR ANALYSIS;

ANALYTIC METHOD; BINDING SITE; CHEMICAL ANALYSIS; CHEMICAL INTERACTION; CHEMICAL STRUCTURE; COMPUTER AIDED DESIGN; LIGAND BINDING; QUANTITATIVE STRUCTURE ACTIVITY RELATION; REVIEW;

COMPUTER-AIDED DESIGN; LIGANDS; MODELS, MOLECULAR; PESTICIDES; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 0242584957     PISSN: 1526498X     EISSN: None     Source Type: Journal    
DOI: 10.1002/ps.614     Document Type: Review

References (49)

1. Kohl P, Noble D, Winslow RL and Hunter PJ, Computational modelling of biological systems: tools and visions. Phil Trans Royal Soc London Ser A - Math Phys Eng Sci 358:579-610 (2000).
2. Leach AR and Hann MM, The in silico world of virtual libraries. Drug Discovery Today 5:326-336 (2000).
3. Horvath D and Jeandenans C, Molecular similarity and virtual screening. In silico methods to retrieve active analogs in the context of discovering therapeutic compounds. Actual Chim 9:64-67 (2000).
4. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN and Bourne PE, The Protein Data Bank. Nucleic Acid Res 28:235-242 (2000).
5. Reiss T, Drug discovery of the future: the implications of the human genome project. Trends Biotechnol 19:496-499 (2001).
6. Anon, Analysis of the genome sequence of the flowering plant Arabidobsis thaliana. Nature (London) 408:796-815 (2000).
7. Dean PM and Zanders ED, The use of chemical design tools to transform proteomics data into drug candidates. Biotechnology 32(Suppl):28-33 (2002).
8. Tice CM, Selecting the right compounds for screening: does Lipinski's Rule of 5 for pharmaceuticals apply to agrochemicals? Pest Manag Sci 57:3-16 (2001).
9. Marshall GR, Barry CD, Bosshard HE, Dammkoehler RA and Dunn DA, The conformational parameter in drug design: the active analog approach, in Computer-assisted drug design, ed by Olson EC and Christofferse RE, ACS Symposium Series No 112, American Chemical Society, Washington, DC, pp 205-226 (1979).
10. Josien H, Convert O, Berlose J-P, Sagan S, Brunissen A, Lavielle S and Chassaing G, Topographic analysis of the S7 binding subsite of the tachikinin neurokinin receptor. Biopolymers 39:133-147 (1996).
11. Martin Y, Bures M, Danaher E, DeLazzer J, Lico I and Pavlik PA, A fast new approach to pharmacophore mapping and its application to dopaminergic and benzodiazepine agonist. J Comp-Aided Mol Design 7:83-102 (1993).
12. Jones G, Willett P and Glen RC, A genetic algorithm for flexible molecular overlay and pharmacophore elucidation. J Comp-Aided Mol Design 9:532-549 (1995).
13. Hurst T and Heritage T, HQSAR - A highly predictive QSAR technique based on Molecular Holograms, Abstracts of Papers of the American Chemical Society, Vol 213, 19-CINF, Part 1, Apr 13 (1997).
14. Wold H, Partial Least Squares, in Encyclopedia of statistical sciences, Vol 6, ed by Kotz S and Johnson NL, Wiley, New York, pp 581-591 (1985).
15. Clark M and Cramer IIIRD, The probability of chance correlation using partial least squares (PLSR). Quant Struct-Act Relat 12:137-145 (1993).
16. Cramer RD, DePriest SA, Patterson DE and Hecht P, The developing practice of comparative molecular field analysis, in 3D QSAR in drug design: theory, methods and applications, ed by Kubinyi H, Escom, Leiden, pp 443-485 (1993).
17. Klebe G, Abraham U and Mietzner T, Molecular similarity indices in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity. J Med Chem 37:4130-4146 (1994).
18. Rarey M, Kramer B, Lengauer T and Klebe G, A fast flexible docking method using an incremental construction algorithm. J Mol Biol 261:470-489 (1996).
19. Meng EC, Shoichet BK and Kuntz ID, Automated docking with grid-based energy evaluation. J Comp Chem 13:505-524 (1992).
20. Jordan DB, Basarab GS, Liao D-I, Johnson WMP, Winzenberg KN and Winkler DA, Structure-based design of inhibitors of the rice blast fungal enzyme trihydroxynaphthalene reductase. J Mol Graphics Model 19:434-447 (2001).
21. Nakagawa Y, Wheelock CE, Morisseau C, Goodrow MH, Hammock BG and Hammock BD, 3-D QSAR analysis of inhibition of murine soluble epoxide hydrolase (MsEH) by benzoylureas, arylureas, and their analogues. Bioorg Med Chem 8:2663-2673 (2000).
22. Nakagawa Y, Hattori K, Shimizu B, Akamatsu M, Miyagawa H and Ueno T, Quantitative structure-activity studies of insect growth regulators XIV. Three-dimensional quantitative structure-activity relationship of ecdysone agonists including dibenzoylhydrazine analogs. Pestic Sci 53:267-277 (1998).
23. Nakagawa Y, Shimizu B, Oikawa N, Akamatsu M, Nishimura K, Kurihara N, Ueno T and Fujita T, Three-dimensional quantitative structure-activity analysis of steroidal and dibenzoylhydrazine-type ecdysone agonists, in Classical and three-dimensional QSAR in agrochemistry, ed by Hansch C and Fujita T, ACS Symposium Series, No 606, American Chemical Society, Washington, DC, pp 288-301 (1995).
24. Okazawa A, Akamatsu M, Ohoka A, Nishiwaki H, Cho W-J, Nakagawa Y, Nishimura K and Ueno T, Prediction of the binding mode of imidacloprid and related compounds to house-fly head acetylcholine receptors using three-dimensional QSAR analysis. Pestic Sci 54:134-144 (1998).
25. Okazawa A, Akamatsu M, Nishiwaki H, Nakagawa Y, Miyagawa H, Nishimura K and Ueno T, Three-dimensional quantitative structure-activity relationship analysis of acyclic and cyclic chloronicotinyl insecticides. Pest Manag Sci 56:509-515 (2000).
26. Akamatsu M and Ozoe Y, Structural differences between antagonist binding sites on GABA receptors of insects and mammals: Approach by 3D-QSAR. Nihon Noyaku Gakkaishi (J Pestic Sci) 23:344-348 (1998).
27. Akamatsu M, Ozoe Y, Ueno T, Fujita T, Mochida K, Nakamura T and Matsumura F, Sites of action of noncompetitive GABA antagonists in houseflies and rats: three-dimensional QSAR analysis. Pestic Sci 49:319-332 (1997).
28. Ozoe Y, Akamatsu M, Higata T, Ikeda I, Mochida K, Koike K, Ohmoto T and Nikaido T, Picrodendrin and related terpenoid antagonists reveal structural differences between ionotropic GABA receptors of mammals and insects. Bioorg Med Chem 6:481-492 (1998).
29. Kuriyama T, Schmidt TJ, Okuyama E and Ozoe Y, Structure-activity relationships of seco-prezizaane terpenoids in gamma-aminobutyric acid receptors of houseflies and rats. Bioorg Med Chem 10:1873-1881 (2002).
30. Ju XL and Ozoe Y, Bicyclophosphorothionate antagonists exhibiting selectivity for housefly GABA receptors. Pestic Sci 55:971-982 (1999).
31. Dinan L, Hormann RE and Fujimoto T, An extensive ecdysteroid CoMFA. J Comput-Aided Mol Design 13:185-207 (1999).
32. Ujváry I, Nicotine and other insecticidal alkaloids, in Nicotinoid insecticides and the nicotinic acetylcholine receptor, ed by Yamamoto I and Casida JE, Springer-Verlag, Tokyo, pp 29-69 (1999).
33. Sutko JL, Airey JA, Welch W and Ruest L, The pharmacology of ryanodine and related compounds. Pharm Rev 49:53-98 (1997).
34. Yang GF, Jiang XH, Ding Y and Yang HZ, Three dimensional quantitative structure-activity relationships of novel 2-heteroaryl-4-chromanone derivatives. Acta Chim Sin 60:134-138 (2002).
35. Chuman H, Karasawa M and Fujita T, A novel three-dimensional QSAR procedure: Voronoi field analysis. Quant Struct-Act Relat 17:313-326 (1998).
36. Zhou WH, Wen X, Sun M, Yang X, Liu XL and Miao FM, Comparative molecule field analysis of photosystem II inhibitors. Chinese J Org Chem 20:564-569 (2000).
37. Jalaie M and Erickson JA, Homology model directed alignment selection for comparative molecular field analysis: Application to photosystem II inhibitors. J Comput-Aided Mol Design 14:181-197 (2000).
38. Dayan FE and Allen SN, Predicting the activity of the natural phytotoxic diphenyl ether cyperine using Comparative Molecular Field Analysis. Pest Manag Sci 56:717-722 (2000).
39. Durst GL, Comparative molecular field analysis (CoMFA) of herbicidal protoporphyrinogen oxidase inhibitors using standard steric and electrostatic fields and an alternative LUMO field. Quant Struct-Act Relat 17:419-426 (1998).
40. Clark RD, Synthesis and QSAR of herbicidal 3-pyrazolyl α,α,α-trifluorotolyl ethers. J Agric Food Chem 44:3643-3652 (1996).
41. Hou TJ, Li ZM, Li Z, Liu J and Xu XJ, Three-dimensional quantitative structure-activity relationship analysis of the new potent sulfonylureas using comparative molecular similarity indices analysis. J Chem Inf Comput Sci 40:1002-1009 (2000).
42. Yang G, Liu H and Yang H, QSAR and 3D-QSAR analysis of structurally diverse ALS inhibitors: sulfonylureas and triazolopyrimidine-2-sulfonamides. Pesict Sci 55:1143-1150 (1999).
43. Yang GF, Liu HY, Yang XF and Yang HZ, Design, syntheses and biological activity of novel herbicides targeting ALS - VIII. Studies on structure-activity relationships of fused heterocyclic sulfonamide herbicides by combined Hansch analyses and CoMFA method. Acta Chim Sin 57:706-711 (1999).
44. Bargar TM, Secor J, Markley LD, Shaw BA and Erickson JA, A comparative molecular field analysis study of obtusifoliol 14α-methyl demethylase inhibitors. Pestic Sci 55:1059-1069 (1999).
45. Webb SR, Durst GL, Pernich D and Hall JC, Interaction of cyclohexanediones with acetyl coenzyme-A carboxylase and an artificial target-site antibody mimic: a comparative molecular field analysis. J Agric Food Chem 48:2506-2511 (2000).
46. Martinez A, Ochoa C, Rodriguez J, Rodriguez M, Castro A, Gonzalez M and Martinez MM, Comparative molecular field analysis (CoMFA) on [6]+[6] fused pyrazines with nematocide properties. Quant Struct-Act Rel 16:327-376 (1997).
47. Bordás B, Kömíves T, Szántó Z and Lopata A, Comparative three-dimensional quantitative structure-activity relationship study of safeners and herbicides. J Agric Food Chem 48:926-931 (2000).
48. Dutka F and Kömíves T, MG-191, a new selective herbicide antidote, in Pesticide science and biotechnology, ed by Greenhalgh R and Roberts TR, Blackwell, Oxford, UK, pp 201-204 (1987).
49. Walton JD and Casida JE, Specific binding of a dichloroacetamide safener in maize at a site that also binds thiocarbamate and chloroacetanilide herbicides. Plant Physiol 109:213-219 (1995).