Skip to main content
SpringerLink
Log in
Book cover

3D QSAR in Drug Design pp 225–252Cite as

Similarity and Dissimilarity: A Medicinal Chemist’s View

  • Chapter

Part of the book series: Three-Dimensional Quantitative Structure Activity Relationships ((QSAR,volume 2))

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

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   169.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Böhm, H.-J., Klebe, G. and Kubinyi, H., Wirkstoffdesign. Der Weg zum Arzneimittel, Spektrum Akademischer Verlag, Heidelberg, 1996.

    Google Scholar 

  2. Wermuth, C.G. (Ed.), The Practice of Medicinal Chemistry, Academic Press, London, 1996.

    Google Scholar 

  3. Wolff, M.E. (Ed.), Burger’s Medicinal Chemistry, 5th Ed., Vol. 1, John Wiley, New York, 1995.

    Google Scholar 

  4. Weber, L., Wallbaum, S., Broger, C. and Gubernator, K., Optimization of the biological activity of combinatorial compound libraries by a genetic algorithm, Angew. Chem., 107 (1995) 2452–2154; Angew. Chem. Intern. Ed., 34 (1995) 2280–2282.

    Google Scholar 

  5. Singh, J., Ator, MA., Jaeger, E.P., Allen, M.P., Whipple. D.A., Soloweij, J.E., Chowdhary, S. and Treasurywala, A.M., Application of genetic algorithms to combinatiorial synthesis: a computational approach to lead identification and lead optimization, J. Am. Chem. Soc., 118 (1996), 1669–1676.

    CAS  Google Scholar 

  6. Morgan. B.P., Holland D.R., Matthews, B.W, and Barlelt, P.A., Structure-based design of an inhibitor of the zinc peptidase thermolysin, J. Am. Chem. Soc., 116 (1994) 3251–3260.

    Article  CAS  Google Scholar 

  7. Kaminski, J.J., Wallmark, B., Briving, C. and Anderson, B.-M., Antiulcer agents: 5. inhibition of gastric H+/K+-ATPase by substituted Imidazo[1,2-a]pyridines and related analogs andits implications in modeling the high affinity potassium ion binding site of the gastric proton pump enzyme, J. Med. Chem., 34 (1991) 513–541.

    Article  Google Scholar 

  8. Lauri, G. and Barlett, P.A., CAVEAT: A program to facilitate the design of organic molecules J. Comput.-Aided Mol. Design, 8 (1994) 51–66.

    Article  CAS  Google Scholar 

  9. Kaplan, A.P, and Barlelt, P.A., Synthesis and evaluation of tin inhibitor of carboxypeptidase A with a Kivalue in the femtomolar range, Biochemistry. 30 (1991) 8165–8170.

    Article  CAS  Google Scholar 

  10. Barlett, PA. and Marlowe, C.K., Evaluation of intrinsic bindingenergy from a hydrogen bonding group in an enzyme inhibitor, Science. 235 (1987) 569–571.

    Google Scholar 

  11. Morgan, B.P., Scholtz, J.M., Ballinger, M.D., Zipkin, I.D. and Barlett, PA., Differential binding energy: A detailed evaluation of the infleunce of hydrogen-bonding and hydrophobic groups on the inhibition of thermolysin by phosphorous inhibitors, J. Am. Chem. Soc., 113 (1991) 297–307.

    CAS  Google Scholar 

  12. Merz, K.M. and Kollman, PA., Free energy perturbation of the inhibition of thermolysin: Prediction of the free energy of binding of a new inhibitor, J. Am. Chem. Soc., 111 (1989) 5649–5655.

    CAS  Google Scholar 

  13. Shuman, R.T., Rothenberger, R.B., Campbell, C.S., Smith. G.F., Gifford-Moore, D.S. and Gesellchen, P.D., A series of highly selective thrombin inhibitors, In Smith, J.A, and Rivier, J.E. (Eds) Peptides—chemistry and biology proceedings of the 12th American Peptide Symposium. Cambridge. MA, U.S.A., 1991, ESCOM Science Publishers R.V., Leiden, 1992. pp. 801–802.

    Google Scholar 

  14. Stanton, J.L., Ksander, G.M., de Jesus, R. and Sperbeck, D.M., The effect of heteroatom substitution on a series of phosphonate inhibitors of neutral endopeptidase 24.11, Bioorg. Med. Chem. Lett., 4 (1994) 539–542.

    Article  CAS  Google Scholar 

  15. Weber, A.E., Steiner, M.G., Krieter, PA., Colletti, A.E., Tata, J.R., Halgren, T.A., Ball. R.G., Doyle, J.J., Schorn, T.W., Stearns, R.A., Miller, R.R., Siegl, P.K.S., Greenlee, W.J. and Patchett, A.A., Highly potent. orally active diester macrocyclic human renin inhibitors, J. Med. Chem. 35 (1992) 3755–3773.

    Article  CAS  Google Scholar 

  16. Wolfenden, R. and Kati, W.M., Testing the limits of protein-ligand binding discrimination with transition-state analogue inhibitors, Acc. Chem. Res., 24 (1991) 209–215.

    Article  CAS  Google Scholar 

  17. Xiang, S., Short, S.A., Wolfenden. R. and Carter, C.W., Transition-state selectivity a single hydroxyl group during catalysis by cytidine deaminase, Biochemistry, 34 (1995) 4516–4523.

    Article  CAS  Google Scholar 

  18. Parker. E.M., Grisel, D.A., Iben, L.G. and Shapiro, R.S., A single amino acid difference accounts for the pharmacological distinctions between the ral and human 5-Hydroxytryptamine1Breceptors, J. Neurochem., 60 (1993) 380–383.

    CAS  Google Scholar 

  19. Clozel, J.-P. and Fischli, W., Discovery of reremikiren as the first orally active renin inhihitor. Arzneim.-Forsch. (Drug Research). 43 (1993) 260–262.

    CAS  Google Scholar 

  20. Li, R.-L., Hansch, C., Matthews, D., Blaney, J.M., Langridge, R., Delcamp. T.J., Susten, S.S. and Freisheim, J.H., A comparason by QSAR. crystallography, and computer graphics of the inhibition of various dihydrofolate reductases by 5-(X-Benzyl)-2,4-diaminopyrimidines, Quant. Struct.-Act. Relal., 1 (1982) 1–7.

    CAS  Google Scholar 

  21. Li, Z., Nguyen, D.T., Kitson, D.H., Bajorath, J., Kraut, J and Hagler, A.T., Origin of trimethoprim’s pharmacologic activity and differential binding to E. coli and chicken liver dihydrofolate reductases: Long-range electrostatic non-‘lock and key’ specificity, Abstract of Presentations, Scientific Seminar Tour 1993, BIOSYM. San Diego, CA, U.S.A., 1993, pp. 14–19

    Google Scholar 

  22. Roques, B.P., Nobel, F., Daugé, V., Fournié-Zaluski, M. and Beaumont, A., Neutral endopeptidase 24.1I: Structure, inhibition and experimental and clinical pharmacology, Pharmacol. Rev., 45 (1993) 87–146.

    CAS  Google Scholar 

  23. Roderick, S.L., Fournié-Zaluski, MC., Roques, B.P and Mathews, B.W., Thiorphan and retrothiorphan display equivalent interactions when bound to crystalline thermolsin. Biochemistry, 28 (1989) 1493–1497.

    Article  CAS  Google Scholar 

  24. Slusarchyk, W.A., Robl, J.A., Taunk, P.C., Asaad, M.M., Bird, J.E., DiMarco, J. and Pan. Y., Dual metalloprotease inhibitors: V. Utilization of bicyclic azepinothiazolidines and azepinonetetrahydrothiazenes in constrained peptidomimetics of mercaptoacyl dipeptides, Bioorg. Med. Chem. Lett., 7 (1995) 753–758.

    Google Scholar 

  25. Hofmann, A., LSD—mein Sorgenkind. dtv/Klett-Cotta, Munich, 1993.

    Google Scholar 

  26. Hanson, D.J., Dioxin toxicity: New studies prompt debate, regulatory action, Chem. Eng. News, 12 August 1991. 7–14.

    Google Scholar 

  27. Mattos, C. and Ringe, D., Multiple binding modes, In Kubinyi, H. (Ed.) 3D QSAR in drug design: Theory methods and applications, ESCOM Science Publishers B.V., Leiden, 1993 pp. 226–254.

    Google Scholar 

  28. Meyer, E.F., Botos, I., Scapozza, L. and Zhang, D., Backward binding and other structural surprises, Persp. Drug Discov. Design, 3 (1993) 168–195.

    Google Scholar 

  29. Böhm, H.-J. and Klebe, G., What can we learn from molecular recognition in protein-ligand complexes for the design of new drug?, Angew. Chem., 108 (1996) 2750–2778: Angew. Chem. Intern. Edit., 35 (1996), 2588–2614.

    Google Scholar 

  30. Montgomery, J.A. and Niwas, S., Stucture-based drug design, Chemtech. 23 (1993) 30–37.

    CAS  Google Scholar 

  31. Montgomery, J.A., and Secrist III, J.A., PNP Inhibitors, Persp. Drug Discov. Design, 2 (1994) 205–220

    CAS  Google Scholar 

  32. Kester, W.R., and Matthew.;, B.W., Cystallographic study of the binding of dipeptide inhibitors to thermolysin: Implications for the mechanism of catalysis, Biochemistry, 16 (1977) 2506–2516.

    Article  CAS  Google Scholar 

  33. Badger, J., Minor, I., Kremer, M.J., Oliveira, MA., Smith, T.J., Griffith, J.P., Guerin, D.M.A., Krishnaswamy, S., Luo, M., Rossmann, M.G., McKinlay. M.A., Diana, G.D., Dutko, F.J., Fancher, M., Ruechert, R.R. and Heinz, B.A., Structural analysis of a series of antiviral agents complexed with human rhinovirus 14, Proc. Natl. Acad. Sci. USA, 85 (1988) 3304–3308.

    CAS  Google Scholar 

  34. Diana, G.D., Treasurywala, A.M., Bailey, T.R., Oglesby, R.C., Pevear, D.C. and Dutko, F.J., A model for compuonds active against human rhinovirus-14 based on X-ray cystallography data, J. Med. Chem., 33 (1990) 1306–1311.

    Article  CAS  Google Scholar 

  35. Bystroff, C., Oatley, S.J. and Kraut, J., Crystal structures of Eschericha coli dihydrofolate reductase The NAPD+holoenzyme and the folate NADP+ternary complex: Substrate binding and a model for the transition state Biochemistry. 29 (1990) 3263–3277

    Article  CAS  Google Scholar 

  36. Bolin, J.T., Filman, D.J., Matthews, D.A., Hamlin R.C. and Kraut, J., Crystal structure of Eschericha coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 Å resolution, J. Biol. Chem., 257 (1982) 13650–13662.

    CAS  Google Scholar 

  37. Poulos, T.L, and Howard, A.J., Crystal structures of metyrapone-and phenylimidazole-inhibited complexes of cytochrome P-450cam, Biochemistry, 26 (1987) 8165–8174.

    Article  CAS  Google Scholar 

  38. Mattos, C., Rasmussen, B., Ding, X., Petsko, G.A. and Ringe, D., Analogous inhibitors of elastase do not always bind analogously, Nature. Struct. Biol., 1 (1994) 55–58.

    Article  CAS  Google Scholar 

  39. Massumoto, O., Taga, T., Matsushima, M., Higashi, T. and Machida, K., Multiple binding of inhibitors in the complex formed by bovine tryosin and fragments of a synthetic inhibitor, Chem. Pharm. Bull., 38 (1990) 2253–2255.

    Google Scholar 

  40. Underwood, D.J., Strader, C.D., Rivero, R., Patchett, A.A., Greenlee, W. and Predergast, K., Structural model of antagonist and agonist binding lo the angiotensin II, AT1subtype G protein coupled receptor, Chem. Biol., 1 (1994) 211–221.

    Article  CAS  Google Scholar 

  41. Aquino, C.J., Armour, D.R., Bermann, J.M., Birkemo, L.S., Carr, R.A.E., Croom, D.K., Dezube, M., Dougherty, Jr., R.W. Ervin, G.N., Grizzle, M.K., Head, J.E., Hirst, G.C., James, M.K., Johnson, M.F., Miller, L.J., Queen, K.L., Rimele, T.J., Smith, D.N. and Sugg, E.E., Discovery of 1,5-Benzodiazepines with peripheral cholecystokinin (CCK-A) receptor agonist activity: I. optimization of the Agonist ‘Tigger’, J. Riled. Chem., 39 (1996) 562–569.

    CAS  Google Scholar 

  42. Hirst, G.C., Queen, K.L., Sugg, E.E. and Willson, T.M., Conversion acyclic nonpeptide CCK antagonist into CCK agonists. Bioorg, Med. Chem. Lett., 7 (1997) 511–514.

    Article  CAS  Google Scholar 

  43. Samanen, J., GPVIIb/IIIa antagonist, Ann. Rep. Med. Chem., 31 (1996) 91–100.

    CAS  Google Scholar 

  44. Engleman, V.W., Kellogg, M.S. and Rogers, T.E., Cell adhesion integrins us pharmaceutical targets, Ann. Rep. Med. Chem., 31 (1996) 191–200.

    CAS  Google Scholar 

  45. Aumailley, M., Gurrath, M., Müller, G., Calvete, J., Timpl, R. and Kessler, II., Arg-Glv-Asp constrained within cyclic pentapeptides: Strong and selective inhibitors of cell adhesion to vitronectin and laminun fragment P1. FEBS Lett. 291 (1991) 50–54.

    Article  CAS  Google Scholar 

  46. Keenan, R., Miller, W., Ali, F., Barton, L., Bondinell, J., Burgess, J., Callahan, J., Calvo, R.. Cousins, R., Gowen, M., Huffman, W., Hwang, S., Jakas, D., Ku, T., Kwon, C., Lago, A., Mombouyran, V., Nguyen, T., Ross, S., Samanen, J., Takata, D., Uzinskas, I., Venslavsky, J., Wong, A., Yellin, T. and Yuan, C., Nonpeptide vitronectin receptor antagonists, Abstract MEDl 236, 211th ACS National Meeting, 1996.

    Google Scholar 

  47. Ariêns, E.J., Wuis, E.W. and Vetinga, E.J., Stereosselectivity of bioactive xenobiotics: A pre-Pasteur attitude in meficinal chemistry, pharmacokinetics and clinical pharmacology, Biochem, Pharmacol., 37 (1998) 9–18.

    Google Scholar 

  48. Friedman, L. and Miller, J.G., Odor incongruity and chirality, Science. 172 (1971) 1044–1046.

    CAS  Google Scholar 

  49. Höltje, H.-D. and Marrer, S., A molecular graphics study on structure-action relationships of calcium-antagonistic and agonistic 1,4-dihydropyridines, J. Comput.-Aided Mol. Design, 1 (1987) 23–30.

    Google Scholar 

  50. Kubinyi, H., QSAR: Hanseh analysis and related approaches. VCH, Weinheim, 1993.

    Google Scholar 

  51. Böhm, H.-J., The development of a simple empirical scoring function to estimate the binding constant for (a protein-ligand c complex of known three-dimensional structure, J. Cornput.-Aided Mol. Design, 8 (1994) 243–256.

    Google Scholar 

  52. Rum, G. and Herndon, W.C., Molecular similarity concepts: 5. Analysis of steroid-protein binding constants, J. Am. Chem. Soc., 113 (1991) 9055–9060.

    Article  CAS  Google Scholar 

  53. Good, A.C., Peterson, S.J. and Richards, W.G., QSAR’s, from similarity matrices: Technique validation and application in the comparison of different similarity evaluation methods, J. Med. Chem., 36 (1993). 2929–2937.

    CAS  Google Scholar 

  54. Good, A.C., 3D molecular similarity indices and their application in QSAR studies, In: Dean, P. (Ed.) Molecular similarity in drug design, Chapman and Hall. New York, 1995, pp. 23–56.

    Google Scholar 

  55. Martin, Y.C., Lin, C.T., Hetti, C. and DeLazzer, J., PLS analysis to detect nonlinear relationships between biological potency and molecular properties. J. Med. Chem., 38 (1995) 3009–3015.

    CAS  Google Scholar 

  56. Kubinyi, H., A General View on Similarity and QSAR Studies, In Computer-assisted lead finding and optimization, Proceedings of the 11th European Symposium on Quantitative Structure-Activity Relationships. Lausanne, Switzerland, 1996: van der Waterbeemd, H., Testa, B. and Folkers, G. (Eds.): Verlag Helvetica Chimica Acta and VCH: Basel, Weinheim, 1997. pp. 7–28.

    Google Scholar 

  57. Klebe, G., Abraham. U and Mietzner, T, Molecular similarity indies in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological potency, J. Med. Chem., 37 (1994) 4130–4146

    Article  CAS  Google Scholar 

  58. Kubinyi, H., Hamprecht, F.A. and Mietzner, T., Three-dimensional quantitative similarity-activity relationships (3D QSiAR), from SEAL similarity matrices, manuscript submitted for publication.

    Google Scholar 

  59. Kearsley, S.K. and Smith, G.M., An alternative method for the alignment of molecular structures: Maximizing electrostatic and steric overlap, Tetrahedron Comp. Methodol., 3 (1990) 615–633.

    CAS  Google Scholar 

  60. Klebe, G., Mietzner, T. and Weber, F. Different approaches toward an automatic alignment of drug molecules: application to sterol mimics, thrombin and thermolysin inhibitors, J. Comput.-Aided Mol. Design, 8 (1994) 751–778.

    CAS  Google Scholar 

  61. Cho, S.J. and Tropsha, A., Cross-validated R2guided region selection for comparative molecular field analysis (CoMFA): Asimple methodto achieve consistent results, J. Med. Chem., 38 (1995) 1060–1066.

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Drug Design, BASF AG, 0-67056, Ludwigshalfen, Germany

    Hugo Kubinyi

Authors
  1. Hugo Kubinyi
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. ZHF/G, A30, BASF AG, D-67056, Ludwigshafen, Germany

    Hugo Kubinyi

  2. Department Pharmazie, ETH-Zürich, Winterthurer Strasse 190, CH-8057, Zürich, Switzerland

    Gerd Folkers

  3. Abbott Laboratories, Pharmaceutical Products Division, 100 Abbott Park Rd., Abbott Park, IL, 60064-3500, USA

    Yvonne C. Martin

Rights and permissions

Reprints and permissions

Copyright information

© 2002 Kluwer Academic Publishers

About this chapter

Cite this chapter

Kubinyi, H. (2002). Similarity and Dissimilarity: A Medicinal Chemist’s View. In: Kubinyi, H., Folkers, G., Martin, Y.C. (eds) 3D QSAR in Drug Design. Three-Dimensional Quantitative Structure Activity Relationships, vol 2. Springer, Dordrecht. https://doi.org/10.1007/0-306-46857-3_13

Download citation

  • DOI: https://doi.org/10.1007/0-306-46857-3_13

  • Publisher Name: Springer, Dordrecht

  • Print ISBN: 978-0-7923-4790-3

  • Online ISBN: 978-0-306-46857-5

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation