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Computer Modelling and Information Technology

  • David Bawden
  • Michael S. Tute
  • John C. Dearden
Chapter

Abstract

The computer modelling of relationships between structure and biological response was considered by the FRAME Toxicity Committee in 1982 (1). This is an update of that first report.

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REFERENCES

  1. 1.
    Tute, M.S. (1983). Mathematical modelling. In Animals and Alternatives in Toxicity Testing (ed. M. Balls, R.J. Riddell & A.N. Worden), pp. 137–151. London: Academic Press.Google Scholar
  2. 2.
    Hansch, C. (1985). The QSAR paradigm in the design of less toxic molecules. Drug Metabolism Reviews 15, 1279–1294.CrossRefGoogle Scholar
  3. 3.
    Anon. (1986). ECETOC Monograph No. 8: Structure-activity relationships in toxicology and ecotoxicology: an assessment. Brussels: ECETOC.Google Scholar
  4. 4.
    Bawden, D. & Blakeman, K.H. (1990). IT Strategies for Information Management. London: Butterworths.Google Scholar
  5. 5.
    Wexler, P. (1988). Information Resources in Toxicology, 2nd edn. Amsterdam: Elsevier.Google Scholar
  6. 6.
    Hansch, C. (1981). The physicochemical approach to drug design and discovery (QSAR). Drug Development Research 1, 267–309.CrossRefGoogle Scholar
  7. 7.
    Franke, R. (1984). Theoretical Drug Design Methods, 382–384. Amsterdam: Elsevier.Google Scholar
  8. 8.
    Warr, W.A., ed. (1988). Chemical StructuresThe International Language of Chemistry. Berlin: Springer-Verlag.CrossRefGoogle Scholar
  9. 9.
    Armstrong, C.J. & Large, J. A., eds (1988). Manual of Online Search Strategies. Aldershot: Gower.Google Scholar
  10. 10.
    Anon. (1988). Toxicology Newsletter 8. Health Designs, Inc.Google Scholar
  11. 11.
    Cramer, R.D., Bunce, J.D. & Patterson, D.E. (1988). Cross-validation, bootstrapping and partial least squares compared with multiple regression in conventional QSAR studies. Quantitative Structure-activity Relationships 7, 18–25.CrossRefGoogle Scholar
  12. 12.
    Komatsu, K., Hirono, S. & Moriguchi, I. (1985). Aquatic toxicity: a predictive structure-activity model. Chemical and Pharmaceutical Bulletin 33, 4081–4084.PubMedCrossRefGoogle Scholar
  13. 13.
    Overton, E. (1987). Osmotic properties of cells and their bearing on toxicology and pharmacology. Z. Physik. Chem. 22, 189.Google Scholar
  14. 14.
    Hansch, C. (1971). Quantitative structure-activity relationships in drug design. In Drug Design (ed. E.J. Ariens), pp. 271–342. New York: Academic Press.Google Scholar
  15. 15.
    Topliss, J.G. & Edwards, R.P. (1979). Chance factors in studies of quantitative structure-activity relationships. Journal of Medical Chemistry 22, 1238–1244.CrossRefGoogle Scholar
  16. 16.
    Lipnick, R.L., Pritzker, C.S. & Bentley, D.L. (1987). In QSAR in Drug Design and Toxicology (ed. D. Hadzi & B. Jerman-Blazic), p. 301. Amsterdam: Elsevier.Google Scholar
  17. 17.
    Enslein, K., Lander, T.R., Tomb, M.E. & Craig, P.N. (1983). Benchmark Papers in Toxicology. Princeton, NJ, USA: Princeton Scientific Publishers.Google Scholar
  18. 18.
    Enslein, K. (1988). An overview of structure-activity relationships as an alternative to testing in animals for carcinogenicity, mutagenicity, dermal and eye irritation, and acute oral toxicity. Toxicology and Industrial Health 4, 479–498.PubMedCrossRefGoogle Scholar
  19. 19.
    von Szentpaly, L.V. (1984). Carcinogenesis by polycyclic aromatic hydrocarbons: a multilinear regression on new type PMO indices. Journal of the American Chemical Society 106, 6021–6028.CrossRefGoogle Scholar
  20. 20.
    Li, R., Hansch, C., Matthews, D., Blaney, J.M., Langridge, R., Delchamp, T.J., Susten, S.S. & Freidsheim, J.H. (1982). A comparison by QSAR crystallography and computer graphics of the inhibition of various dihydrofolate reductases by 5-(X-benzyl)-2,4-diamino-pyrimidines. Quantitative Structure-activity Relationships 1, 1–7.CrossRefGoogle Scholar
  21. 21.
    Hansch, C., Li, R., Blaney, J.M. & Langridge, R. (1982). Comparison of the inhibition of Eschericia coli and Lactobacillus casei DHFR by 2,4-diamino-5-(substituted-benzyl)pyrimidines: quantitative structure-activity relationships, X-ray crystallography, and computer graphics in structure-activity analysis. Journal of Medical Chemistry 25, 777–784.CrossRefGoogle Scholar
  22. 22.
    Lipnick, R.L. (1985). A perspective on quantitative structure-activity relationships in ecotoxicology. Environmental Toxicology and Chemistry 4, 255–257.CrossRefGoogle Scholar
  23. 23.
    Janardan, S.K., Olson, C.S. & Schaeffer, D.J. (1984). Quantitative comparison of acute toxicity of organic chemicals to rat and fish. Ecotoxicology and Environmental Safety 8, 531–539.PubMedCrossRefGoogle Scholar
  24. 24.
    Enslein, K., Tuzzeo, T.M., Borgstedt, H.H., Blake, B.W. & Hart, J.B. (1987). Prediction of rat oral LD50 from Daphnia magna LC50 and chemical structure. In QSAR in Environmental Toxicology (ed. K.L.E. Kaiser), 2nd edn, p. 91. Dordrecht: Reidel.CrossRefGoogle Scholar
  25. 25.
    Veith, G.D., Call, D.J. & Brooks, L.T. (1983). Structure-toxicity relationships for the fathead minnow, Pimephales promelas: narcotic industrial chemicals. Canadian Journal of Fish and Aquatic Sciences 40, 743–748.CrossRefGoogle Scholar
  26. 26.
    McKim, J.M., Schmieder, P.K., Carlson, R.W., Hunt, E.P. & Niemi, G.J. (1987). Use of repiratory-cardiovascular responses of rainbow trout (Salmo gairdneri) in identifying acute toxicity sundromes in fish. I. Pentachlorophenol, 2,4-dinitrophenol, tricaine methanesulfonate and 10-octanol. Environmental Toxicology and Chemistry 6, 295–312.CrossRefGoogle Scholar
  27. 27.
    Lipnick, R.L. (1989). Narcosis, electrophile and proelectrophile toxicity mechanisms: application of SAR and OSAR. Environmental Toxicology and Chemistry 8, 1–12.Google Scholar
  28. 28.
    Hermens, J., Busser, F., Leeuwangh, P. & Musch, A. (1985). Quantitative correlation studies between the acute lethal toxicity of 15 organic halides in the guppy (Poecilla reticulata) and chemical reactivity towards 4-nitro benzylpyridine. Toxicology and Environmental Chemistry 9, 219–236.CrossRefGoogle Scholar
  29. 29.
    Schultz, T.W. (1987). Relative toxicity of para-substituted phenols: log Kow and pKa-dependent structure-activity relatinships. Bulletin of Environmental Contamination and Toxicology 38, 994–999.PubMedCrossRefGoogle Scholar
  30. 30.
    Dearden, J.C. & Nicholson, R.M. (1986). The prediction of biodegradability by the use of quantitative structure-activity relationships: correlation of biological oxygen demand with atomic charge difference. Pesticide Science 17, 305–310.CrossRefGoogle Scholar
  31. 31.
    Esser, H.O. (1986). A review of the correlation between physicochemical properties and bioaccumulation. Pesticide Science 17, 265–276.CrossRefGoogle Scholar
  32. 32.
    Broderius, S. & Kahl, M. (1985). Acute toxicity of organic chemical mixtures to the fathead minnow. Aquatic Toxicology 6, 307–322.CrossRefGoogle Scholar
  33. 33.
    Konemann, H. (1981). Quantitative structure-activity relationships in fish toxicity studies. I. Relationship for 50 industrial pollutants. Toxicology 19, 209–221.PubMedCrossRefGoogle Scholar
  34. 34.
    34.Hermens, J. & de Bruijn, J. (1987). A QSAR study for fish toxicity data of organophos-phorus compounds. In QSAR in Drug Design and Toxicology (ed. D. Hadzi & B. Jerman-Blazic), pp. 343–345. Amsterdam: Elsevier.Google Scholar
  35. 35.
    Koch, R. (1982). Chemical and structural properties and trace elements in aqueous ecosystems. Acta Hydrochimica et Hydrobiologica 10, 535–549.CrossRefGoogle Scholar
  36. 36.
    Kwasniewska, K. & Kaiser, K.L.E. (1983). Toxicities of selected phenols to fermentative and oxidative yeasts. Bulletin og Environmental Contamination and Toxicology 31, 188–194.CrossRefGoogle Scholar
  37. 37.
    Hall, L.H. & Kier, L.B. (1984). A molecular connectivity study of phenols and their toxicity to fish. In QSAR of Bioactive Compounds (ed. M. Kuchar), pp. 53–59. Barcelona: J.R. Prous.Google Scholar
  38. 38.
    Dunn, W.J. (1988). QSAR approaches to predicting toxicity. Toxicology Letters 43, 277–283.PubMedCrossRefGoogle Scholar
  39. 39.
    Niemi, G.J., Veith, G.D., Regal, R.R. & Vaishnav, D.D. (1987). Structural features associated with degradable and persisten chemicals. Environmental Toxicology and Chemistry 6, 515–527.CrossRefGoogle Scholar
  40. 40.
    Benigni, R., Andreoli, C. & Giuliani, A. (1989). Inter-relationships among carcinogenicity, mutagenicity, acute toxicity and chemical structure in a genotoxicity database. Journal of Toxicology and Environmental Health 27, 1–20.PubMedCrossRefGoogle Scholar
  41. 41.
    Albano, C., Dunn, W.J., Edlund, U., Johansson, E., Norden, R., Sjöström, M. & Wold, S. (1978). Four levels of pattern recognition. Analytica Chimica Acta 103, 429–443.CrossRefGoogle Scholar
  42. 42.
    Dunn, W.J., Wold, S., Edlund, U., Hellberg, S. & Gasteiger, J. (1984). Multivariate structure-activity relationships between data from a battery of biological tests and an ensemble of structure descriptors: the PLS method. Quantitative structure-activity relationships 3, 131–137.CrossRefGoogle Scholar
  43. 43.
    Hellberg, S., Wold, S., Dunn, W.J., Gasteiger, J. & Hutchings, M.G. (1985). The anaesthetic activity and toxicity of halogenated methyl ethers: a multivariate QSAR modelled by PLS. Quantitative Structure-activity Relationships 4, 1–11.CrossRefGoogle Scholar
  44. 44.
    Rosenkrantz, H.S. & Klopman, G. (1988). CASE, the computer-automated structure evaluation system, as an alternative to extensive animal testing. Toxicology and Industrial Health 4, 533–540.CrossRefGoogle Scholar
  45. 45.
    Hansch, C. & Klein, T.E. (1986). Molecular graphics and QSAR in the study of enzyme-ligand interactions: on the definition of bioreceptors. Ace. Chem. Res. 19, 392–400.CrossRefGoogle Scholar
  46. 46.
    Kuyper, L.F., Roth, B., Baccanari, D.P., Ferone, R., Beddell, CR., Champness, J.N., Dann, J.G., Norrington, F.E.A., Baker, D.J. & Goodford, P. (1982). Receptor-based design of dihydrofolate reductase inhibitors: comparison of crystallographically determined enzyme binding with enzyme affinity in a series of carboxy-substituted trimethoprim analogues. Journal of Medical Chemistry 25, 1120–1122.CrossRefGoogle Scholar
  47. 47.
    Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer, E.F., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T. & Tasumi, M. (1977). The protein data bank: a computer-based archival file for macromolecular structures. Journal of Molecular Biology 112, 535–542.PubMedCrossRefGoogle Scholar
  48. 48.
    Allen, F.H., Kennard, O. & Taylor, R. (1983). Systematic analysis of structural data as a research technique in organic chemistry. Acc. Chem. Res. 16, 146–153.CrossRefGoogle Scholar
  49. 49.
    Vinter, J.G. (1985). Molecular graphics for the medicinal chemist. Chemistry in Britain, January 1985, p. 32.Google Scholar
  50. 50.
    Goodford, P.J. (1985). A computational procedure for determining energetically favourable binding sites on biologically important macromolecules. Journal of Medical Chemistry 28, 849–857.CrossRefGoogle Scholar
  51. 51.
    Sternberg, M.J.E. (1986). Prediction of protein structure from amino acid sequence. Anti-cancer Drug Design 1, 169–178.PubMedGoogle Scholar
  52. 52.
    Lapatto, R., Blundell, T., Hemmings, A., Overington, J., Wilderspin, A., Wood, S., Merson, J.R., Whittle, P.J., Danley, D.E., Geoghegan, K.F., Hawrylik, S.J., Lee, S.E., Scheid, K.G. & Hobart, P.M. (1989). X-ray analysis of HIV-1 proteinase at 2.7 angstrom resolution confirms structural homology among retroviral enzymes. Nature 342, 299–302.PubMedCrossRefGoogle Scholar
  53. 53.
    Bedell, C.R., Goodford, P.J., Kneen, G., White, R.D., Wilkinson, S. & Wootton, R. (1984). Substituted benzaldehydes designed to increase the oxygen affinity of human haemoglobin and inhibit the sickling of sickle erythrocytes. British Journal of Pharmacology 82, 397–407.CrossRefGoogle Scholar
  54. 54.
    Hassall, C.H., Kohn, A., Moody, C.J. & Thomas, W.A. (1982). The design of a new group of angiotensin-converting enzyme inhibitors. FEBS Letters 147, 175–179.PubMedCrossRefGoogle Scholar
  55. 55.
    Rossmann, M.G. (1989). The structure of antiviral agents that inhibit uncoating when complexed with viral capsids. Antiviral Research 11, 3–13.PubMedCrossRefGoogle Scholar
  56. 56.
    Boyle, F.T., Gilman, D.J., Gravestock, M.B. & Wardleworth, J.M. (1988). Synthesis and structure-activity relationships of a novel antifungal agent, ICI-195,739. Annals of the New York Academy of Sciences 544, 86–100.PubMedCrossRefGoogle Scholar
  57. 57.
    Czaplinsky, K.H., Kansy, M., Seydel, J.K. & Haller, R. (1987). Design of a new substituted 2,4-diamino-5-benzylpyrimidine as inhibitor of bacterial dihydrofolate reductase assisted by molecular graphics. Quantitative Structure-activity Relationships 6, 70–72.CrossRefGoogle Scholar
  58. 58.
    Lumley, C.E. (1989). The value of a toxicology computerised database for challenging regulatory guidelines. Journal of Human Toxicology, in press.Google Scholar
  59. 59.
    Lumley, C.E. & Walker, S.R. (1985). The value of chronic animal toxicology studies of pharmaceutical compounds: a retrospective analysis. Fundamental and Applied Toxicology 5, 1007–1024.PubMedCrossRefGoogle Scholar
  60. 60.
    Lumley, C.E. & Walker, S.R. (1986). A critical appraisal of the duration of chronic animal toxicity studies. Regulatory Toxicology and Pharmacology 6, 66–72.PubMedCrossRefGoogle Scholar
  61. 61.
    Richards, W.G. (1988). Computer-aided molecular design. Science Programme, Oxford 72, 481–492.Google Scholar
  62. 62.
    Bash, P.A., Singh, U.C., Brown, F.K., Langridge, R. & Kollman, P.A. (1987). Calculation of the relative change in binding free energy of a protein-inhibitor complex. Science 235, 574–576.PubMedCrossRefGoogle Scholar
  63. 63.
    Kuntz, I.D., Blaney, J.M., Oatley, J.S., Langridge, R. & Ferrin, T.E. (1982). A geometric approach to macromolecule-ligand interactions. Journal of Molecular Biology 161, 269–288.PubMedCrossRefGoogle Scholar
  64. 64.
    DesJarlais, R.L., Sheridan, R.P., Dixon, J.S., Kuntz, I.D. & Venkataraghavan, R. (1986). Docking flexible ligands to macromolecular receptors by molecular shape. Journal of Medical Chemistry 29, 2149–2153.CrossRefGoogle Scholar
  65. 65.
    Cramer, R.D., Patterson, D.E. & Bunce, J.D. (1988). Comparative molecular field analysis (CoMFA). I. Effect of shape on binding of steroids to carrier proteins. Journal of the American Chemistry Society 110, 5959–5967.CrossRefGoogle Scholar
  66. 66.
    Doweyko, A.M. (1988). The hypothetical active site lattice: an approach to modelling active sites from data on inhibitor molecules. Journal of Medical Chemistry 31, 1396–1406.CrossRefGoogle Scholar
  67. 67.
    Walker, J.R. (1983). Computer simulation of animal systems in the medical school laboratory. ATLA 11, 47–54.Google Scholar
  68. 68.
    Hughes, I.E. (1984). The use of computers to simulate animal preparations in the teaching of practical pharmacology. ATLA 11, 204–213.Google Scholar
  69. 69.
    Dickinson, C.J., Ingram, D. & Ahmed, K. (1985). The Mac family of physiological models. ATLA 1, 107–116.Google Scholar
  70. 70.
    Dewhurst, D.G., Brown, G.J. & Meehan, A.S. (1988). Microcomputer simulations of laboratory experiments in physiology. ATLA 15, 280–289.Google Scholar
  71. 71.
    Brown, G.J., Collins, G.G.S., Dewhurst, D.G. & Hughes, I.E. (1988). Computer simulations of laboratory experiments in physiology. ATLA 16, 163.Google Scholar
  72. 72.
    Mahmoudian, M. (1987). A program for simulation of the effects of drugs on the blood pressure of laboratory animals. ATLA 15, 147–148.Google Scholar
  73. 73.
    Mahmoudian, M. (1989). A programe for simulation of the effects of drugs on the performance of the normal heart and in congestive heart failure. ATLA 16, 297–298.Google Scholar
  74. 74.
    Lovell, D.P. (1986). Risk assessment: general principles. In Toxic Hazard Assessment of Chemicals (ed. M.L. Richardson), pp. 207–222. London: Royal Society of Chemistry.Google Scholar
  75. 75.
    Park, C.N. (1989). Mathematical models in quantitative assessment of carcinogenic risk. Regulatory Toxicology and Pharmacology 9, 236–243.PubMedCrossRefGoogle Scholar
  76. 76.
    Gaylor, D.W. (1988). Applicability of cancer risk assessment techniques to other toxic effects. Toxicology and Industrial Health 4, 453–459.PubMedCrossRefGoogle Scholar
  77. 77.
    Travis, C.C. (1987). Interspecies extrapolations in risk analysis. Toxicology 47, 3–13.PubMedCrossRefGoogle Scholar
  78. 78.
    Kodell, R.L. & Gaylor, D.W. (1989). On the additive and multiplicative models of relative risk. Biometrical Journal 31, 359–370.CrossRefGoogle Scholar
  79. 79.
    Gaylor, D.W. (1989). Quantitative risk analysis for quantal reproductive and developmental effects. Environmental Health perspectives 79, 243–246.PubMedPubMedCentralCrossRefGoogle Scholar
  80. 80.
    Kimmell, C.A. & Gaylor, D.W. (1988). Issues in qualitative and quantitative risk analysis for developmental toxicology. Risk Analysis 8, 15–20.CrossRefGoogle Scholar
  81. 81.
    Flamm, W.G. (1989). Critical assessment of carcinogenic risk policy. Regulatory Toxicology and Pharmacology 9, 216–224.PubMedCrossRefGoogle Scholar
  82. 82.
    Lovell, D.P. (1986). Risk assessment: general principles. In Toxic Hazard Assessment of Chemicals (ed. M.C. Richardson). London: Royal Society of Chemistry.Google Scholar
  83. 83.
    US Congress, Office of Technology Assessment (1986). Alternatives to Animal Use in Research, Testing and Education, 441 pp. Washington, DC: US Congress, Office of Technology Assessment.Google Scholar
  84. 84.
    Bawden, D. (1987). Information resources and computer systems as alternatives (review of OTA Report, Chapter 9). ATLA 14, 344–352.Google Scholar
  85. 85.
    Bawden, D. (1989). Computers in toxicology (Conference Report). ATLA 17, 29–30.Google Scholar
  86. 86.
    Oxborrow, E. (1986). Databases and Database Systems. Bromley: Chartwell-Bratt.Google Scholar
  87. 87.
    Ashford, J.H. & Willett, P. (1989). Text Retrieval and Document Databases. Bromley: Chartwell-Bratt.Google Scholar
  88. 88.
    Kissman, H.M. & Wexler, P. (1986). Toxicology information systems: a historical perspective. Journal of Chemical Information and Computer Sciences 12, 143–151.Google Scholar
  89. 89.
    Bawden, D. & Robinson, L. (1989). Databases and data banks. Journal of Human Toxicology, in press.Google Scholar
  90. 90.
    Bawden, D. (1988). Chemical toxicology data banks. Aslib Proceedings 40, 79–85.CrossRefGoogle Scholar
  91. 91.
    Pantry, S. (1989). Occupational health and safety information services. Occuptional Health, pp. 249–251.Google Scholar
  92. 92.
    Jameson, A. (1987). Downloading and Uploading in Online Information Retrieval. Bradford: MCB University Press.Google Scholar
  93. 93.
    Straube, K. and Antoniewicz, C.M. (1989). Teaching end-users how to search the National Library of Medicine’s toxicology databases. Medical Reference Services Quarterly 7, 31–39.CrossRefGoogle Scholar
  94. 94.
    Mitchell, J. & Harrison, J., eds (1990). CD-ROM Directory. London: TFPL Publishing.Google Scholar
  95. 95.
    Emard, K-P. (1989). CD-ROMs in Print 19891990. New York: Meckler Publishing.Google Scholar
  96. 96.
    Bawden, D. & Brock, A.M. (1985). Chemical toxicology searching: a comparative study of online databases. Journal of Chemical Information and Computer Sciences 25, 31–35.PubMedGoogle Scholar
  97. 97.
    Costigan, A. et al. (1985). Comparison of search techniques (printed and computerised) with specific reference to the RTECS Data Bank. Journal of Information Science 10, 79–86.CrossRefGoogle Scholar
  98. 98.
    Cassidy, A.L. & Kostrewski, B.J. (1986). An evaluation of information sources in household product poisoning. Journal of Information Science 12, 143–151.CrossRefGoogle Scholar
  99. 99.
    Weininger, D., Weininger, A. & Leo, A.J. (1987). MedChem Software Manual, Release 3.52, Medicinal Chemistry Project, Pomona College, Claremont, CA.Google Scholar
  100. 100.
    Martin, Y.C., Danaher, E.B., May, C.S. & Weininger, D. (1988). MENTHOR, a database system for the storage and retrieval of 3-dimensional molecular structures and associated data searchable by substructural, biologic, physical or geometric properties. Journal of Computer-aided Molecular Design 2, 15–29.PubMedCrossRefGoogle Scholar
  101. 101.
    Jakes, S.E., Watts, N., Willett, P., Bawden, D. & Fisher, J.D. (1987). Pharmacophoric pattern matching in files of 3D chemical structures. Journal of Molecular Graphics 5, 41–48.CrossRefGoogle Scholar
  102. 102.
    Lumley, C.E. (1989). The value of a toxicology computerised database for challenging regulatory guidelines. Journal of Human Toxicology, in press.Google Scholar
  103. 103.
    Lumley, C.E. & Walker, S.R. (1985). The value of chronic animal toxicology studies of pharmaceutical compounds: a retrospective analysis. Fundamental and Applied Toxicology 5, 1007–1024.PubMedCrossRefGoogle Scholar

Copyright information

© FRAME 1991

Authors and Affiliations

  • David Bawden
    • 1
  • Michael S. Tute
    • 2
  • John C. Dearden
    • 3
  1. 1.Department of Information ScienceThe City UniversityLondonUK
  2. 2.Pfizer Central ResearchSandwichUK
  3. 3.School of Health SciencesLiverpool PolytechnicLiverpoolUK

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