Development of new agrochemicals by quantitative structure-activity relationship (QSAR) methodology. III. 3D QSAR methodologies and computer-assisted molecular design (CAMD)

정량적인 구조-활성상관 (QSAR) 기법에 의한 새로운 농약의 개발. III. 3D QSAR 기법들과 컴퓨터를 이용한 분자설계(CAMD)

  • Sung, Nack-Do (Dividion of Applied Biology & Chemistry, College of Agriculture & Life Sciences, Chungnam National University)
  • 성낙도 (충남대학교 농업생명과학대학 응용생물화학부)
  • Published : 2003.03.27

Abstract

Acoording to improvement of HTOS (high throughput organic synthesis) and HTS (high throughput screening) technique, the CoMFA (comparative molecular field analysis), CoMSIA (comparative molecular similarity indeces analysis) and molecular HQSAR (hologram quantitative structure-activity relationship) analysis techniques as methodology of computer assisted molecular design (CAMD) were introduced generally and summarized for some application cases.

새로운 농약을 탐색하고 개발하는데 있어서 고효율 유기함성 (HTOS) 기술과 고효율 검색 (HTS) 기술 등의 발전과 더불어 컴퓨터 화학을 이용한 분자설계 (CAMD) 방법으로 보편화되고 있는 비교 분자장 분석(CoMFA)과 비교 분자 유사성 지수분석(CoMSIA) 등, 3D QSAR 기법들을 위시하여 분자 홀로그램 구조 - 활성관계 (HQSAR) 분석방법 등, QSAR 기법들을 요약하고 그 활용 사례들을 간략하게 소개하였다.

Keywords

References

  1. Accelrys : www.accelrys.com. 200 Wheeler Rd., S. tower, Burlington, MA. U. S. A.
  2. Borher, D. C., D. S. Fullertoton and K. Yoshioka (1997) Computer-assisted drug design, ACS symposium series 112. pp. 259. American chemical society, Washington, DC
  3. CMC (1996) Computational medicinal chemistry, CMC modeling guide, Computer aided molecular design, QSAR, Faculty of pharmacy Utrecht university; www:cmc.pharm.uu.nl, Netherlands
  4. Cramer, R. D., D. E. Patterson and J. D. Bunce (1988a) Comparative molecular field analysis (CoMFA), I. Effect of shape on binding of steroids to carrier proteins, J. Am. Chem. Soc., 110:5959-5967
  5. Cramer, R. D. III., J. D. Bunce and D. E Patterson (1988b) Cross-validation, bootstrapping, and partial least squares compared with multiple regression in conventional qsar studies. Quant. Struct. Act. Relat. 7:18-25
  6. David, R. and A. J. Hofinger (1994) Application of genetic function approximation to quantitative structureactivity relationships and quantitative structure-property relationships. J. Chem. Inf. Comput. Sci. 34:854-866
  7. Dillon, W. R. and M. Goldsten (1984) Multivariate analysis: Methods and applications. pp.209., John iley & Sons, New York
  8. Eto, M. (1992) Rational approaches to finding agrochemical leads, Ch. 4, In Rational Approaches to Structure, Activity, and Ecotoxicology of Agrochemicals (ed. Draber, W. and T. Fujita) CRC Press, London
  9. Free, S. M. and J. W. Wilson (1964) A mathematical contribution to structure-activity studies. J. Med. Chem 7:359-366
  10. Gallop, M. A, R. W. Barrett, W. Dow., S. P. A Fodor and E. M. Gorden (1994) Applications of combinatoridal technologies to drug discovery. 1. Back ground and peptide combinatorial libraries, J. Med. Chem 37:1233 -1251
  11. Gasteiger, J. and M. Marsili (1980) Iterative partial equalization of orbital electro-negativity; a rapid access to atomic charges. Tetrahedron, 36:3219-3228 https://doi.org/10.1016/0040-4020(80)80168-2
  12. Ghose, A. K., V. N. Viswanadhan, J. J. Wendoloski (1999) A knowledge-based approach in designing combinatorial or medicinal chemistry libraries for drug discovery. 1. A qualitative and quantitative characterization of known drug databases. J. Comb. Chem. 1:55-68
  13. Hansch, C. and A. Leo (1995) Exploring QSAR: Fundamentals and Applications in Chemistry and Biologt. ACS Professional Reference Book, American Chemical Society, Washington, D.C
  14. Heritage T. W. and D. R. Lowis (1999) Molecular hologram QSAR. Ch. 4., In Rational drug design: Novel Methodology and Practical Applications (ed. Parrill, A. L. and M. R. Reddy), ACS Symposium Series 719, American Chemical Society. Washington, D.C
  15. Hopjinger, A. J., S. Wang, J. S. Tokarski, B. Jin, M. Albuquer, P. J. Madhav and C. Duraiswami (1997) Construction of 3D QSAR models using the 3D QSAR analysis formalim. J. Am. Chem. Soc. 119:10509-10524
  16. Keer, I. D., R. Sankararamakrishnan, O. S. Smart and M. S. P. Sansom (1994) Parallel helix bundles and ionchannels: molecular modeling via simulated annealing and restrained molecular dynamics, Biophysical J. 67:1501-1515
  17. Kim, K. H. (1993) Comparison of classical and 3D QSAR. pp.619-642, In 3D QSAR Drug Design Theory, Methods and Applications (ed. Kubinyi, H.) ESCOM. Leiden
  18. Klebe, G., U. Abraham and T. Mietzner (1994) Molecu-lar similarity indices in a comparative analysis(CoMSIA) of drug molecules to correlate and predict their biological activity, J. Moo. Chem. 37:4130-4146
  19. Klebe, G. (1998) Comparative molecular similarity indices analysis: CoMSIA Perspect, Drug Discovery Des. 12:87-104
  20. Kubinyi, H. (1993a) QSAR, Hausch analysis and related approaches, In Methods and Principles in Medcinal Chemistry(ed. Mannhold, R., L. P. Krogsgaard and H. Timmerman), Vol. 1., VCH, Weinheim
  21. Kubinyi, H. (1993b) 3D QSAR in Drug Design; Theory, Methods and Applications. ESCOM, Leiden. Lowis, D. R. (1997) HQSAR. A new, highly predictive QSAR technique. Tripos Technical Notes, Vol. 1, No.5
  22. Malinowski, E. R. and D. G. Howery (1980) Factor Analyses in Chemistry. Wiely, New York
  23. Reddy, M. R. and A. L. Parrill (1999) Overview of rational drug design. In Rational Drug Design(ed. Reddy, M. R. and Parrill). Ch. 1., ACS Symposium Series 719, American Chemical Society, Washington, DC
  24. Reddy, M. R. and A. L. Parrill (1999) Overview of rational drug design. In Rational Drug Design(ed. Reddy, M. R. and Parrill). Ch. 1., ACS Symposium Series 719, American Chemical Society, Washington, DC
  25. Silverman, B. D. and D. E. Platt (1996) Comparative molecular moment analysis (CoMMA): 3D-QSAR with out molecular superposition. J. Med. Chem. 39:2129-2140
  26. Stahle, L. and S. Wold (1988) Multivariate data analysis and experimental design in biomedical reearch. Progr. Med. Chem. 25:292-334
  27. Tong, W., D. R. Lowis, R. Perkins, Y. Chen, W. J. Welsh,, D. W. Goddette, T. W. Heritage and D. M. Sheehan (1998) Exaluation of quantitative structureactivity relationship methods for large-scale prediction of chemicals binding to the estrogen receptor. J. Chem. Inf. Comput. Sci. 38:669-677
  28. Tripos: www.tripos.com. Sybyl program (Ver. 6.9). 1699, S. Hanely Rd., Suite 303, S1. Louis, MO. 63144, U. S. A
  29. Yu, S. J. and N. D. Sung (2002) Comparative molecular field analysis (CoMFA) on the farnesy1 protein transferase (FPTase) inhibition activity of bis-aromatic $\alpha$,$\beta$-unsaturated ketones. Agric. Chem. Biotechnol. 45 (1):1-6
  30. Vedani, A. and M. Dobler (2002) 5D-QSAR: The key for simulating induced fit. J. Med. Chem., 45:2139-2149
  31. Waterbeemd, H. V. D. (1992) The history of drug research: From Hansch to the present, Quant. Struct. Act. Relat. 11:200-204
  32. Waterbeemd, H. V. D. (1996) Design of bioactive compounds, Ch.1., In Structure-Property Correlations in Drug Research (ed. Waterbeemd, H. V. D.). Academic Press, R. G. Landes Co. Austin
  33. Wexler, R. R., W. J. Greenlee, J. D. Irvin, M. R. Goldberg, K. Prendergast, R. D. Smith and P. B. Timmermans (1996) Nonpeptide angiotensin II receptor antagonists: The next generation in antihypertensive tberaphy, J. Med Chem, 39:625~56
  34. Wise, M., R. D. Cramer, D. Smith and I. Exman (1983) Progress in three-dimensional drug design: The use of real tine colour graphics and computer postulation of bioactive molecules in DYLOMMS. pp.145-146. In Quantitative Approaches to Drug Design (ed. Dearden, J. C), Elsevier, Armsterdam
  35. Wold, S., C. Albano, W. J. I. Dunn, U. Edlund,, K. Esbensen, P. Geladi, S. Hellberg, E. Johannson, W. Lindberg and M. Sjostrom (1984) Multivariate data analysis in chemistry. In Chemometrics: Mathematics and Statistics in Chemistry (ed Kowalskl, B.) Reidel, Dordrecht, Netherlands
  36. 성낙도, 유성재, 임치환, 赤松美紀(1998) 비스 방향족$\alpha$,$\beta$-불포화 케톤 유도체 중 2- thienyl 및 2-furyl 치환체의 항균활성에 관한 비교분자장 분석(CoMFA), 한국농약과학회지 2(2):16-21
  37. 성낙도, 김기현 (2002a) 고추역 병균에 대한 2-N-benzyl-5-phenoxy-3-isothiazolone 유도체의 살균활성 에 관한 비교분자 유사성 지수분석 (CoMSIA)과 홀로그램 구조-활성관계 (HQSAR) . 한국농약과학회지 6(3):209-217
  38. 성낙도, 이희철 (2002b) 고추 역병균에 대한 3-pheny1-isoxazole과 3-pheny1-2,5-dihydrois-oxazol-5-one 유도체의 살균활성에 관한 비교 분자장 분석(CoMFA). 한국농약과학회지 6(2):72-79
  39. 성낙도, 옥환석, 송종환, 이용구 (2003a) N-치환 pheny1-3,4,5,6-tetrahydrophthalimide와 N-치환 pheny1-3,4-dimethylmaleimide 유도체의 생장 저해 활성에 관한 비교 분자장 분석(CoMFA). 한국농약과학회지 투고 중
  40. 성낙도, 이상호, 송종환, 김형래(2003b) 제초성 3-pheny1-5-(3,7-dichloro-8-quinolinyl)-1,2,4-oxadiazole 유도체들의 생장 저해활성에 관한 비교 분자장 분석(CoMFA)과 분자 홀로그램 구조-활성관계(HQSAR). 한국농약과학회지 투고 중