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References
Böhm, H.-J., Klebe, G. and Kubinyi, H., Wirkstoffdesign. Der Weg zum Arzneimittel, Spektrum Akademischer Verlag, Heidelberg, 1996.
Wermuth, C.G. (Ed.), The Practice of Medicinal Chemistry, Academic Press, London, 1996.
Wolff, M.E. (Ed.), Burger’s Medicinal Chemistry, 5th Ed., Vol. 1, John Wiley, New York, 1995.
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.
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.
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.
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.
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.
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.
Barlett, PA. and Marlowe, C.K., Evaluation of intrinsic bindingenergy from a hydrogen bonding group in an enzyme inhibitor, Science. 235 (1987) 569–571.
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.
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.
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.
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.
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.
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.
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.
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.
Clozel, J.-P. and Fischli, W., Discovery of reremikiren as the first orally active renin inhihitor. Arzneim.-Forsch. (Drug Research). 43 (1993) 260–262.
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.
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
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.
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.
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.
Hofmann, A., LSD—mein Sorgenkind. dtv/Klett-Cotta, Munich, 1993.
Hanson, D.J., Dioxin toxicity: New studies prompt debate, regulatory action, Chem. Eng. News, 12 August 1991. 7–14.
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.
Meyer, E.F., Botos, I., Scapozza, L. and Zhang, D., Backward binding and other structural surprises, Persp. Drug Discov. Design, 3 (1993) 168–195.
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.
Montgomery, J.A. and Niwas, S., Stucture-based drug design, Chemtech. 23 (1993) 30–37.
Montgomery, J.A., and Secrist III, J.A., PNP Inhibitors, Persp. Drug Discov. Design, 2 (1994) 205–220
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.
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.
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.
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
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.
Poulos, T.L, and Howard, A.J., Crystal structures of metyrapone-and phenylimidazole-inhibited complexes of cytochrome P-450cam, Biochemistry, 26 (1987) 8165–8174.
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.
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.
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.
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.
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.
Samanen, J., GPVIIb/IIIa antagonist, Ann. Rep. Med. Chem., 31 (1996) 91–100.
Engleman, V.W., Kellogg, M.S. and Rogers, T.E., Cell adhesion integrins us pharmaceutical targets, Ann. Rep. Med. Chem., 31 (1996) 191–200.
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.
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.
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.
Friedman, L. and Miller, J.G., Odor incongruity and chirality, Science. 172 (1971) 1044–1046.
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.
Kubinyi, H., QSAR: Hanseh analysis and related approaches. VCH, Weinheim, 1993.
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.
Rum, G. and Herndon, W.C., Molecular similarity concepts: 5. Analysis of steroid-protein binding constants, J. Am. Chem. Soc., 113 (1991) 9055–9060.
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.
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.
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.
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.
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
Kubinyi, H., Hamprecht, F.A. and Mietzner, T., Three-dimensional quantitative similarity-activity relationships (3D QSiAR), from SEAL similarity matrices, manuscript submitted for publication.
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.
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.
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.
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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
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