Skip to main content

A Discussion of Various Computational Methods for Drug Design

  • Chapter
Molecular Modelling and Drug Design

Part of the book series: Topics in Molecular and Structural Biology ((TMSB))

Abstract

Our understanding of the specificity of biological function is based on the principles of molecular recognition.1 The binding and actions of a drug are controlled by the patterns of molecular fields found in the vicinity of the contact surface of the receptor. The goal of drug design is to rationalize observations of the patterns of structure-activity relationships and of ligand-receptor interactions, and to use this knowledge to design novel ligands. Computational methods now play a crucial role in the process of drug design. This review will concentrate on two main topics: the construction of pharmacophoric models (building on structure-activity relationships) and the generation of lead compounds from models of the target receptor site (building on ligand-receptor interactions). There have been significant advances in both areas over the past few years, and it is now timely to examine the progress that has been made, and to look to the future.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Dean, P. M. (1987). Molecular Foundations of Drug-Receptor Interaction, Cambridge University Press, Cambridge

    Google Scholar 

  2. Lewis, R. A. (1991). Meth. Enzymol., 202, 127–156, and references therein

    Google Scholar 

  3. Jencks, W. P. (1980). In Chemical Recognition in Biology, ed. Chapeville, F. and Haenni, A.-L., Springer-Verlag, Berlin, p. 3

    Chapter  Google Scholar 

  4. Sharpe, K., Fine, R. and Honig, B. (1987). Science, 236, 1460–1463

    Article  Google Scholar 

  5. Rullmann, J. A. C. and van Duijnen, P. T. (1990). Reports in Molecular Theory, 1, 1–21

    CAS  Google Scholar 

  6. Taylor, R. and Kennard, O. (1984). Acc. Chem. Res., 17, 320–326

    Article  CAS  Google Scholar 

  7. Legon, A. C. and Milien, D. J. (1992). Chem. Soc. Rev., 21, 71–78

    Article  CAS  Google Scholar 

  8. Mitchell, J. B. O. and Price, S. L. (1989). Chem. Phys. Lett., 154, 267–272

    Article  CAS  Google Scholar 

  9. Fersht, A. R. (1984). Proc. Roy. Soc. Lond. B, 187, 397–407

    Article  Google Scholar 

  10. 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 Winter, G. (1985). Nature, 314, 235–238

    Article  PubMed  CAS  Google Scholar 

  11. Horovitz, A., Serrano, L., Avron, B., Bycroft, M. and Fersht, A. R. (1990). J. Mol. Biol., 216, 1031–1044

    Article  PubMed  CAS  Google Scholar 

  12. Doig, A. J. and Williams, D. H. (1992). J. Am. Chem. Soc., 114, 338–343

    Article  CAS  Google Scholar 

  13. Chau, P.-L. (1991). PhD Thesis, University of Cambridge

    Google Scholar 

  14. Grootenhuis, P. D. J. and Kollman, P. A. (1989). J. Am. Chem. Soc., 111, 2152–2158

    Article  CAS  Google Scholar 

  15. Fersht, A. R. and Sternberg, M. J. E. (1989). Prot. Eng., 2, 527–530

    Article  CAS  Google Scholar 

  16. Harvey, S. C. (1989). Proteins, 5, 78–92

    Article  PubMed  CAS  Google Scholar 

  17. Warwicker, J. and Watson, H. C. (1982). J. Mol. Biol., 157, 671–679

    Article  PubMed  CAS  Google Scholar 

  18. Sharp, K. A. and Honig, B. (1990). Ann. Rev. Biophys. Biophys. Chem., 19, 301–332

    Article  CAS  Google Scholar 

  19. Gilson, M. K., Sharp, K. A. and Honig, B. (1987). J. Comp. Chem., 9, 327–335

    Article  Google Scholar 

  20. Russell, S. T. and Warshel, A. (1985). J. Mol. Biol., 185, 389–404

    Article  PubMed  CAS  Google Scholar 

  21. Warshel, A. and Åqvist, J. (1991). Ann. Rev. Biophys. Biophys. Chem., 20, 267–298

    Article  CAS  Google Scholar 

  22. Schaefer, M. and Froemmel, C. (1990). J. Mol. Biol., 216, 1045–1066

    Article  PubMed  CAS  Google Scholar 

  23. Eisenberg, D. and McLachlan, A. D. (1986). Nature, 319, 199–203

    Article  PubMed  CAS  Google Scholar 

  24. Sharp, K. A., Nicholls, A., Friedman, R. and Honig, B. (1991). Biochemistry, 30, 9686–9697

    Article  PubMed  CAS  Google Scholar 

  25. Ben-Naim, A. (1980). Hydrophobie Interactions, Plenum Press, New York

    Book  Google Scholar 

  26. Dill, K. A. (1985). Biochemistry, 24, 1501–1509

    Article  PubMed  CAS  Google Scholar 

  27. Chan, H. S. and Dill, K. A. (1990). Proc. Natl Acad. Sci. USA, 87, 6388–6392

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  28. Fersht, A. R. (1985). Enzyme Structure and Mechanism, 2nd edn, Freeman, New York

    Google Scholar 

  29. Hollenberg, M. D. (1990) J. Med. Chem., 5, 1275–1281

    Article  Google Scholar 

  30. Warshel, A., Åqvist, J. and Creighton, S. (1989). Proc. Natl Acad. Sci. USA, 86, 5820–5824

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  31. Sciortino, F., Geiger, A. and Stanley, H. E. (1991). Nature, 354, 218–221

    Article  CAS  Google Scholar 

  32. Quiocho, F. A., Wilson, D. K. and Vyas, N. K. (1989). Nature, 340, 404–407

    Article  PubMed  CAS  Google Scholar 

  33. Blundell, T. L., Sibanda, B. L., Sternberg, M. J. E. and Thornton, J. M. (1987). Nature, 326, 347–352

    Article  PubMed  CAS  Google Scholar 

  34. Marshall, G. R. (1987). Ann. Rev. Pharmacol. Toxicol., 27, 193–213, and references therein

    Article  CAS  Google Scholar 

  35. Cohen, N. C. (1985). Adv. Drug Res., 14, 42–145

    Google Scholar 

  36. Diana, G. D., Treasurywala, A. M., Bailey, T. R., Oglesby, R. C., Pevear, D. C. and Dutko, F. J. (1990). J. Med. Chem., 33, 1306–1311

    Article  PubMed  CAS  Google Scholar 

  37. Wold, S., Albano, C., Dunn, W. J., Edlund, U., Esbensen, K., Geladi, P., Hellberg, S., Johansson, E., Lindberg, W. and Sjostrom, M. (1984). In Chemometrics, ed. Kowlaski, B. R., Reidel, Dordrecht, pp. 17–96

    Chapter  Google Scholar 

  38. Liu, R. S. H., Asato, A. E., Denny, M. and Mead, D. (1984). J. Am. Chem. Soc., 106, 8298–8300

    Article  CAS  Google Scholar 

  39. Liu, R. S. H. and Mirzadegan, T. (1988). J. Am. Chem. Soc., 110, 8617–8623

    Article  CAS  Google Scholar 

  40. Hansch, C. (1969). Acc. Chem. Res., 2, 232–239

    Article  CAS  Google Scholar 

  41. Andrea, T. A. and Kalayeh, H. (1991). J. Med. Chem., 34, 2824–2836

    Article  PubMed  CAS  Google Scholar 

  42. King, R. D., Muggleton, S., Lewis, R. A. and Sternberg, M. J. E. (1993). Proc. Natl Acad. Sci. USA, 89, 11322–11326

    Article  Google Scholar 

  43. Muggleton, S. (1991). New Generation Computing, 8, 295–318

    Article  Google Scholar 

  44. Hansch, C., Ren-Li, L., Blaney, J. M. and Langridge, R. (1982). J. Med. Chem., 25, 777–784

    Article  PubMed  CAS  Google Scholar 

  45. Matthews, D. A., Bolin, J. T., Burridge, J. M., Filman, D. J., Volz, K. W., Kaufman, B. T., Beddell, C. R., Champness, J. N., Stammers, D. K. and Kraut, J. (1985). J. Biol. Chem., 260, 381–391

    PubMed  CAS  Google Scholar 

  46. Champness, J. N., Stammers, D. K. and Beddell, C. R. (1986). FEBS Lett., 199, 61–67

    Article  PubMed  CAS  Google Scholar 

  47. Crippen, G. M. (1987). J. Comp. Chem., 8, 943–955

    Article  CAS  Google Scholar 

  48. Sheridan, R. P., Nilakantan, R., Dixon, J. S. and Venkataraghavan, R. (1986). J. Med. Chem., 29, 899–906

    Article  PubMed  CAS  Google Scholar 

  49. Martin, Y. C. (1992). J. Med. Chem., 35, 2145–2154

    Article  PubMed  CAS  Google Scholar 

  50. Guner, O. F., Henry, D. R. and Pearlman, R. S. (1992). J. Chem. Inf. Comp. Sci., 32, 101–109

    Article  CAS  Google Scholar 

  51. Jakes, S. E. and Willett, P. (1986). J. Mol. Graph., 4, 12–20

    Article  CAS  Google Scholar 

  52. Murrall, N. W. and Davies, E. K. (1990). J. Chem. Inf. Comp. Sci., 30, 312–316

    Article  CAS  Google Scholar 

  53. Clark, D. E., Willett, P. and Kenny, P. W. (1992). J. Mol. Graph., 10, 194–204

    Article  PubMed  CAS  Google Scholar 

  54. Crippen, G. M. (1981). Distance Geometry and Conformational Calculations, Research Studies Press, Wiley, Chichester

    Google Scholar 

  55. Cramer, R. D. (1988). J. Am. Chem. Soc., 110, 5959–5967

    Article  PubMed  CAS  Google Scholar 

  56. Marshall, G. R. and Cramer, R. D. (1988). Trends Pharm. Sci., 9, 285–289

    Article  PubMed  CAS  Google Scholar 

  57. Maggiora, G. and Johnson, M. (1990). Concepts and Applications of Molecular Similarity, Wiley, New York

    Google Scholar 

  58. Dean, P. M., Callow, P. and Chau, P. L. (1988). J. Mol. Graph., 6, 28–34

    Article  CAS  Google Scholar 

  59. Barakat, M. T. and Dean, P. M. (1990). J. Comp.-Aided Mol. Design, 4, 295–316

    Article  CAS  Google Scholar 

  60. Barakat, M. T. and Dean, P. M. (1990). J. Comp.-Aided Mol. Design, 4, 317–330

    Article  CAS  Google Scholar 

  61. Cohen, N. C., Blaney, J. M., Humblet, C., Gund, P. and Barry, D. C. (1990). J. Med. Chem., 33, 883–894

    Article  PubMed  CAS  Google Scholar 

  62. Goodford, P. J. (1985). J. Med. Chem., 28, 849–857

    Article  PubMed  CAS  Google Scholar 

  63. Boobbyer, D. N. A., Goodford, P. J., McWhinnie, P. M. and Wade, R. C. (1989). J. Med. Chem., 32, 1083–1094

    Article  PubMed  CAS  Google Scholar 

  64. Danziger, D. J. and Dean, P. M. (1989). Proc. Roy. Soc. Lond. B, 236, 115–124

    Article  CAS  Google Scholar 

  65. Busetta, B., Tickle, I. J. and Blundell, T. L. (1983). J. Appl. Cryst., 16, 432–437

    Article  CAS  Google Scholar 

  66. Pattabiraman, N., Levitt, M., Ferrin, T. E. and Langridge, R. (1985). J. Comp. Chem., 6, 432–436

    Article  CAS  Google Scholar 

  67. Tomioka, N., Itai, A. and Iitaka, Y. (1987). J. Comp.-Aided Mol. Design, 1, 197–210

    Article  CAS  Google Scholar 

  68. Kuntz, I. D., Blaney, J. M., Oatley, S. J., Langridge, R. and Ferrin, T. E. (1982). J. Mol. Biol., 161, 269–288

    Article  PubMed  CAS  Google Scholar 

  69. DesJarlais, R. L., Sheridan, R. P., Dixon, J. S., Kuntz, I. D. and Venkataraghavan, R. (1986). J. Med. Chem., 29, 2149–2153

    Article  PubMed  CAS  Google Scholar 

  70. DesJarlais, R. L., Sheridan, R. P., Scibel, G. L., Kuntz, I. D. and Venkataraghavan, R. (1988). J. Med. Chem., 31, 722–729

    Article  PubMed  CAS  Google Scholar 

  71. Meng, E. C., Shoichet, B. K. and Kuntz, I. D. (1993). J. Comp. Chem., 13, 505–524

    Article  Google Scholar 

  72. Lawrence, M. C. and Davis, P. C. (1992). Proteins, 12, 31–41

    Article  PubMed  CAS  Google Scholar 

  73. van Gunsteren, W. F. and Berendsen, H. J. C. (1987). J. Comp.-Aided Mol. Design, 1, 171–176

    Article  Google Scholar 

  74. McCammon, J. A. (1987). Science, 238, 486–491

    Article  PubMed  CAS  Google Scholar 

  75. Brooks, C. L., Karplus, M. and Pettitt, B. M. (1988). Proteins, Wiley, New York

    Google Scholar 

  76. McCammon, J. A. and Harvey, S. C. (1987). Dynamics of Proteins and Nucleic Acids, Cambridge University Press, Cambridge

    Book  Google Scholar 

  77. Deleted in proof

    Google Scholar 

  78. Jian, F. and Kim, S.-H. (1991). J. Mol. Biol., 219, 79–102

    Article  Google Scholar 

  79. Shoichet, B. K. and Kuntz, I. D. (1991). J. Mol. Biol., 221, 327–346

    Article  PubMed  CAS  Google Scholar 

  80. Shoichet, B. K., Bodian, D. L. and Kuntz, I. D. (1992). J. Comp. Chem., 13, 380–397

    Article  CAS  Google Scholar 

  81. Goodsell, D. S. and Olson, A. J. (1990). Proteins, 8, 195–202

    Article  PubMed  CAS  Google Scholar 

  82. Weiner, S. J., Kollman, P. A., Case, D. A., Singh, U. C., Ghio, C., Alagona, G., Profeta, S. and Weiner, P. (1984). J. Am. Chem. Soc., 106, 765–784

    Article  CAS  Google Scholar 

  83. Smellie, A. S., Crippen, G. M. and Richards, W. G. (1991). J. Chem. Inf. Comp. Sci., 31, 386

    Article  CAS  Google Scholar 

  84. Leach, A. R. and Kuntz, I. D. (1992). J. Comp. Chem., 13, 730–748

    Article  CAS  Google Scholar 

  85. Leach, A. R. and Prout, K. (1990). J. Comp. Chem., 11, 1193

    Article  CAS  Google Scholar 

  86. Lewis, R. A. and Dean, P. M. (1989). Proc. Roy. Soc. Lond. B, 236, 125–140

    Article  CAS  Google Scholar 

  87. Lewis, R. A. and Dean, P. M. (1989). Proc. Roy. Soc. Lond. B, 236, 141–162

    Article  CAS  Google Scholar 

  88. Adamson, G. W., Creasey, S. E., Eakins, J. P. and Lynch, M. F. (1973). J. Chem. Soc. Perkin Trans. I, 1973, 2071–2076

    Google Scholar 

  89. Lewis, R. A. (1990). J. Comp.-Aided Mol. Design, 4, 205–210

    Article  CAS  Google Scholar 

  90. Lewis, R. A. (1989). Sixth European Seminar on Computer-Aided Molecular Design, London

    Google Scholar 

  91. Lewis, R. A. (1990). In Proceedings of Scientific Computing and Automation, ed. Karjalainen, E. J., Elsevier, Amsterdam

    Google Scholar 

  92. Lewis, R. A., Roe, D. C., Huang, C., Ferrin, T. E., Langridge, R. and Kuntz, I. D. (1992). J. Mol. Graph., 10, 66–78

    Article  PubMed  CAS  Google Scholar 

  93. Moon, J. B. and Howe, W. J. (1991). Proteins, 11, 314–328

    Article  PubMed  CAS  Google Scholar 

  94. Nishibata, Y. and Itai, A. (1991). Tetrahedron, 47, 8985–8990

    Article  CAS  Google Scholar 

  95. Nilakantan, R., Bauman, N. and Venkataraghavan, R. (1991). J. Chem. Inf. Comp. Sci., 31, 527–530

    Article  CAS  Google Scholar 

  96. Bohm, H.-J. (1992). J. Comp.-Aided Mol. Design, 6, 61–78

    Article  CAS  Google Scholar 

  97. Lewis, R. A. (1992). J. Mol. Graph., 10, 131–143

    Article  PubMed  CAS  Google Scholar 

  98. Go, N. and Scheraga H. A. (1970). Macromolecules, 3, 178–187

    Article  CAS  Google Scholar 

  99. Bruccoleri, R. E. and Karplus, M. (1985). Macromolecules, 18, 2767–2773

    Article  CAS  Google Scholar 

  100. Bruccoleri, R. E. and Karplus, M. (1987). Biopolymers, 26, 137–168

    Article  PubMed  CAS  Google Scholar 

  101. Bruccoleri, R. E., Haber, E. and Novotny, J. (1988). Nature, 335, 564–568

    Article  PubMed  CAS  Google Scholar 

  102. Hassall, C. H., Krohn, A., Moody, C. J. and Thomas, W. A. (1984). J. Chem. Soc. Perkin Trans. I, 155–164

    Google Scholar 

  103. Huff, J. R. (1991). J. Med. Chem., 34, 2305–2314

    Article  PubMed  CAS  Google Scholar 

  104. Miller, M., Schneider, J., Sathyanarayana, B. K., Toth, M. V., Marshall, G. R., Clawson, L., Selk, L., Kent, S. B. H. and Wlodawer, A. (1989). Science, 246, 1149–1152

    Article  PubMed  CAS  Google Scholar 

  105. Erickson, J., Neidhart, D. J., VanDrie, J., Kempf, D. J., Wang, X. C., Norbeck, D. W., Plattner, J. J., Rittenhouse, J. W., Turon, M., Wideburg, N., Kohlbrenner, W. E., Simmer, R., Helfrich, R., Paul, D. A. and Knigge, M. (1990). Science, 249, 527–533

    Article  PubMed  CAS  Google Scholar 

  106. Thompson, W. S., Fitzgerald, P. M. D., Holloway, M. K., Emini, E. A., Darke, P. L., McKeever, B. M., Schleif, W. A., Quintero, J. C., Zugay, J. A., Tucker, T. J., Schwering, J. E., Homnick, C. F., Nunberg, J., Springer, J. P. and Huff, J. R. (1992). J. Med. Chem., 35, 1685–1701

    Article  PubMed  CAS  Google Scholar 

  107. DesJarlais, R. L., Scibel, 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). Proc. Natl Acad. Sci. USA, 87, 6644–6648

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  108. Brinkworth, R. L, Woon, T. C. and Fairlie, D. P. (1991). Biochem. Biophys. Res. Commun., 176, 241–246

    Article  PubMed  CAS  Google Scholar 

  109. Matthews, D. A., Appelt, K., Oatley, S. J. and Xuong, N. H. (1990). J. Mol. Biol., 214, 923–936

    Article  PubMed  CAS  Google Scholar 

  110. Appelt, K., Bacquet, R. J., Bartlett, C. A., Booth, C. L. J., Freer, S. T., Fuhry, M. A. M., Gehring, M. R., Herrmann, S. M., Howland, E. F., Janson, C. A., Jones, T. A., Kan, C.-C., Kathadekar, V., Lewis, K. K., Marzoni, G. P., Matthews, D. A., Mohr, C., Moomaw, E. W., Morse, C. A., Oatley, S. J., Ogden, R. C., Reddy, M. R., Reich, S. H., Schoettlin, W. S., Smith, W. W., Varney, M. D., Villafrance, J. E., Ward, R. W., Webber, S., Webber, S. E., Welsh, K. M. and White, J. (1991). J. Med. Chem., 34, 1925–1934

    Article  PubMed  CAS  Google Scholar 

  111. Matthews, D. A., Villafranca, T. E., Janson, C. A., Smith, W. W., Welsh, K. and Freer, S. (1990). J. Mol. Biol., 214, 937–948

    Article  PubMed  CAS  Google Scholar 

Download references

Authors

Editor information

J. G. Vinter Mark Gardner

Copyright information

© 1994 J. G. Vinter and M. Gardner

About this chapter

Cite this chapter

Lewis, R.A., Meng, E.C. (1994). A Discussion of Various Computational Methods for Drug Design. In: Vinter, J.G., Gardner, M. (eds) Molecular Modelling and Drug Design. Topics in Molecular and Structural Biology. Palgrave, London. https://doi.org/10.1007/978-1-349-12973-7_5

Download citation

  • DOI: https://doi.org/10.1007/978-1-349-12973-7_5

  • Publisher Name: Palgrave, London

  • Print ISBN: 978-1-349-12975-1

  • Online ISBN: 978-1-349-12973-7

  • eBook Packages: EngineeringEngineering (R0)

Publish with us

Policies and ethics