Three-dimensional quantitative structure-activity relationships from molecular similarity matrices and genetic neural networks. 2. Applications

Journal of Medicinal Chemistry

Volumn 40, Issue 26, 1997, Pages 4360-4371

  So, Sung Sau ^a   Karplus, Martin ^b  

^a HARVARD UNIVERSITY   (United States)

^b UNIVERSITÉ DE STRASBOURG   (France)

Author keywords

[No Author keywords available]

Indexed keywords

1 BENZYLIMIDAZOLE; AMIDINE; AROMATIC HYDROCARBON RECEPTOR; BENZODIAZEPINE RECEPTOR; BENZODIAZEPINE RECEPTOR AFFECTING AGENT; BENZOIC ACID DERIVATIVE; BETA CARBOLINE DERIVATIVE; CHOLINESTERASE INHIBITOR; DOPAMINE BETA MONOOXYGENASE; ENZYME INHIBITOR; GLYCOGEN PHOSPHORYLASE; HALOGENATED HYDROCARBON; IMIDAZOLE DERIVATIVE;

ARTICLE; ARTIFICIAL NEURAL NETWORK; BINDING AFFINITY; COMPUTER PROGRAM; DRUG RECEPTOR BINDING; ELECTRIC FIELD; MOLECULAR MODEL; PHYSICAL CHEMISTRY; PKA; QUANTITATIVE STRUCTURE ACTIVITY RELATION; STEREOCHEMISTRY;

CHOLINESTERASE INHIBITORS; DOPAMINE BETA-HYDROXYLASE; DRUG DESIGN; ELECTROSTATICS; ENZYME INHIBITORS; MOLECULAR CONFORMATION; MOLECULAR STRUCTURE; NEURAL NETWORKS (COMPUTER); PHOSPHORYLASES; RECEPTORS, ARYL HYDROCARBON; RECEPTORS, GABA-A; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 0031466773     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm970488n     Document Type: Article

References (54)

1. So, S.-S.; Karplus, M. Three-dimensional quantitative structure-activity relationships from molecular similarity matrices and genetic neural networks. 1. Method and validations, J. Med. Chem. 1997, 40, 4347-4359.
2. So, S.-S.; Karplus, M. Evolutionary optimization in quantitative structure-activity relationship: an application of genetic neural network. J. Med. Chem. 1996, 39, 1521-1530.
3. A receptors. J. Med. Chem. 1996, 39, 5246-5256.
4. Watson, K. A.; Mitchell, E. P.; Johnson, L. N.; Cruciani, G.; Son, J. C.; Bichard, C. J. F.; Fleet, G. W. J.; Oikonomakos, N. G.; Kontou, M.; Zographos, S. E. Glucose analogue inhibitors of glycogen phosphorylase: from crystallographic analsysis to drug prediction using GRID force-field and GOLPE variable selection. Acta Crystallogr. 1995, D51, 458-472.
5. Martin, J. L.; Johnson, L. N.; Withers, S. G. Comparison of the binding of glucose and glucose 1-phosphate derivatives to T-state glycogen phosphoryiase b. Biochemistry 1990, 29, 10745-10757.
6. Martin, J. L.; Veluraja, K,; ROSS, K.; Johnson, L. N.; Fleet, G. W.; Ramsden, N. G.; Bruce, I.; Orchard, M. G.; Oikonomakos, N. G.; Papageorgiou, A. C. Glucose analogue inhibitors of glycogen phosphoryiase: the design of potential drugs for diabetes. Biochemistry 1991, 30, 10101-10116.
7. Johnson, L. N.; Snape, P.; Martin, J. L.; Acharya, K. R.; Barford, D,; Oikonomakos, N. G. Crystallographic binding studies on the allosteric inhibitor glucose-6-phosphate to T state glycogen phosphoryiase b. J. Mol. Biol. 1993, 232, 253-267.
8. Oikonomakos, N. G.; Kontou, M.; Zographos, S. E.; Tsitoura, H. S.; Johnson, L. N.; Watson, K. A.; Mitchell, E. P.; Fleet, G. W.; Son, J. C.; Bichard, C. J.; et al. The design of potential antidiabetic drugs: experimental investigation of a number of beta-D-glucose analogue inhibitors of glycogen phosphorylase. Eur. J. Drug Metab. Pharmacokinet. 1994, 19, 185-192.
9. Oikonomakos, N. G.; Kontou, M.; Zographos, S. E.; Watson, K. A.; Johnson, L. N.; Bichard, C. J.; Fleet, G. W.; Acharya, K. R. N-Acetyl-beta-D-glucopyranosylamine: a potent T-state inhibitor of glycogen phosphoryiase. A comparison with alpha-D-glucose. Protein Sci. 1995, 4, 2469-2477.
10. Watson, K. A.; Mitchell, E. P.; Johnson, L. N.; Son, J. C.; Bichard, C. J.; Orchard, M. G.; Fleet, G. W.; Oikonomakos, N. G.; Leonidas, D. D.; Kontou, M. Design of inhibitors of glycogen phosphoryiase: a study of alpha- and beta-C-glucosides and 1-thio-beta-D-glucose compounds. Biochemistry 1994, 33, 5745-5758.
11. Oikonomakos, N. G.; Zographos, S. E.; Johnson, L. N.; Papageorgiou, A. C.; Acharya, K. R. The binding of 2-deoxy-D-glucose 6-phosphate to glycogen phosphoryiase b: kinetic and crystallographic studies, J. Mol. Biol. 1995, 254, 900-917.
12. Cruciani, G.; Watson, K. A. Comparative molecular field analysis using GRID force-field and GOLPE variable selection methods in a study of inhibitors of glycogen phosphoryiase b. J. Med. Chem. 1994, 37, 2589-2601.
13. a's) of clonidine-like imidazolines, 2-substituted imidazoles, and l-methyl-2-substituted-imidazoles from 3D structures using a comparative molecular field analysis (CoMFA) approach. J. Med. Chem. 1991, 34, 2056-2060.
14. Kim, K. H.; Martin, Y. C. Direct prediction of linear free energy substituent effects from 3D structures using comparative molecular field analysis. 1. Electronic effects of substituted benzoic acids. J. Org. Chem. 1991, 56, 2723-2729.
15. Good, A. C.; Peterson, S. J.; Richards, W. G. QSAR's from similarity matrices. Technique validation and application in the comparison of different similarity evaluation methods. J. Med. Chem. 1993, 36, 2929-2937.
16. Martin, Y. C.; Lin, C. T.; Hetti, C.; DeLazzer, J. PLS analysis of distance matrices to detect nonlinear relationships between biological potency and molecular properties. J. Med. Chem. 1995, 38, 3009-3015.
17. Silverman, B. D.; Platt, D. E. Comparative molecular moment analysis (CoMMA): 3D-QSAR without molecular superposition. J. Med. Chem. 1996, 39, 2129-2140.
18. Waller, C. L.; McKinney, J. D. Comparative molecular field analysis of polyhalogenated dibenzo-p-dioxins, dibenzofurans, and biphenyls. J. Med. Chem. 1992, 35, 3660-3666.
19. Wagener, M.; Sadowski, J.; Gasteiger, J. Autocorrelation of molecular surface properties for modeling corticosteroid binding globulin and cytosolic Ah receptor activity by neural networks. J. Am. Chem. Soc. 1995, 117, 7769-7775.
20. Burke, B. J.; Hopfinger, A. J. 1-(Substituted-benyzl)imidazole2(3H)-thione inhibitors of dopamine β-hydroxylase. J. Med. Chem. 1990, 33, 274-281.
21. Hahn, M.; Rogers, D. Receptor surface models. 2. Application to quantitative structure-activity relationships studies. J. Med. Chem. 1995, 38, 2091-2102.
22. Allen, M. S.; Tan, Y.-C.; Trudell, M. L.; Narayanan, K.; Schindler, L. R.; Martin, M. J.; Schultz, C.; Hagen, T. J.; Koehler, K. F.; Codding, P. W.; Skolnick, P.; Cook, J. M. Synthetic and computer-assisted analyses of the pharmacophore for the benzodiazepine receptor inverse agonist site. J. Med. Chem. 1990, 33, 2343-2357.
23. Allen, M. S.; LaLoggia, A. J.; Dorn, L. J.; Martin, M. J.; Costantino, G.; Hagen, T. J.; Koehler, K. F.; Skolnick, P.; Cook, J. M. Predictive binding of beta-carboline inverse agonists and antagonists via the CoMFA/GOLPE approach. J. Med. Chem. 1992, 35, 4001-4010.
24. Kroemer, R. T.; Hecht, P.; Liedl, K. R. Different electrostatic descriptors in comparative molecular field analysis: a comparison of molecular electrostatic and Coulomb potentials. J. Comput. Chem. 1996, 17, 1296-1308.
25. Cho, S. J.; Garsia, M. L. S.; Bier, J.; Tropsha, A. Structure-based alignment and comparative molecular field analysis of acetylcholinesterase inhibitors. J. Med. Chem. 1996, 39, 5064-5071.
26. Montanari, C. A.; Tute, M. S.; Beezer, A. E.; Mitchell, J. C. Determination of receptor-bound drug conformations by QSAR using flexible fitting to derive a molecular similarity index. J. Comput.-Aided Mol. Des. 1996, 10, 67-73.
27. Cerius2, Version 2.0; Molecular Simulations Inc., San Diego, CA.
28. Rappé, A. K.; Casewit, C. J.; Colwell, K. S.; Goddard, W. A., III; Skiff, W. M. UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations. J. Am. Chem. Soc. 1992, 114, 5832-5842.
29. Stewart, J. J. P. MOPAC: A semiempirical molecular orbital program. J. Comput.-Aided Mol. Des. 1990, 4, 1-105.
30. Hodgkin, E. E.; Richards, W. G. Molecular similarity based on electrostatic potential and electric field. Int. J. Quantum Chem., Quantum Biol. Symp. 1987, 14, 105-110.
31. Meyer, A. M.; Richards, W. G. Similarity of molecular shape. J. Comput.-Aided Mol. Des. 1991.
32. Kubinyi, H.; Abraham, U. Practical problems in PLS analyses. In 3D QSAR in Drug Design: Theory, Methods and Applications; Kubinyi, H., Ed.; ESCOM Science Publishers B.V.: Leiden, The Netherlands, 1993; pp 717-728.
33. Andrea, T. A.; Kalayeh, H. Applications of neural networks in quantitative structure-activity relationships of dihydrofolate reductase inhibitors. J. Med. Chem. 1991, 34, 2824-2836.
34. So, S.-S.; Richards, W. G. Application of neural networks: quantitative structure-activity relationships of the derivatives of 2,4-diamino-5-(substituted-benzyl)pyrimidines as DHFR inhibitors. J. Med. Chem. 1992, 35, 3201-3207.
35. Manallack, D. T.; Ellis, D. D.; Livingstone, D. J. Analysis of linear and nonlinear QSAR data using neural networks. J. Med. Chem. 1994, 37, 3758-3767.
36. Bandiera, S.; Safe, S.; Okey, A. B. Binding of polychlorinated biphenyls classified as either phenobarbitone-, 3-methylchol-anthrene- or mixed-type inducers to cytosolic Ah receptor. Chem.-Biol. Interact. 1982, 39, 259-277.
37. Safe, S. H. Comparative toxicology and mechanism of action of polychlorinated dibenzo-p-dioxins and dibenzofurans. Annu. Rev. Pharmacol. Toxicol. 1986, 26, 371-399.
38. Safe, S. H. Polychlorinated biphenyls (PCBs), dibenzo-p-dioxins (PCDDs), dibenzofurans (PCDFs), and related compounds: environmental and mechanistic considerations which support the development of toxic equivalency factors (TEFs). Crit. Rev. Toxicol. 1990, 21, 51-88.
39. Dammkoeler, R. A.; Karasek, S. F.; Shands, E. F. B.; Marshall, G. R., Constrained search of con formational hyperspace. J. Comput.-Aided Mol. Des. 1989, 3, 3-21.
40. Hahn, M. Receptor surface models. 1. Definition and construction. J. Med. Chem. 1995, 38, 2080-2090.
41. 2-guided region selection for comparative molecular field analysis: a simple method to achieve consistent results. J. Med. Chem. 1995, 38, 1060-1066.
42. 2-GRS approach. J. Med. Chem. 1996, 39, 1383-1395.
43. Lowe, P. R.; Sansom, C. E.; Schwalbe, C. H.; Stevens, M. F. G. Crystal structure and molecular modelling of the antimicrobial drug pentamidine. J. Chem. Soc., Chem. Commun. 1989, 1164-1165.
44. Donkor, I. O.; Tidwell, R. R.; Jones, S. K. Pentamidine congeners. 2. 2-Butene-bridged aromatic diamidines and diimidazolines as potential anti-Pneumocystis carinii pneumonia agents. J. Med. Chem. 1994, 37, 4554-4557.
45. Bichard, C. J. F.; Mitchell, E. P.; Wormald, M. R.; Watson, K. A.; Johnson, L. N.; Zographos, S. E.; Koutra, D. D.; Oikonomakos, N. G.; Fleet, G. W. J. Potent inhibition of glycogen phosphorylase by a spirohydantoin of glucopyranose: first pyranose analogues of hydantocidin. Tetrahedron Lett. 1995, 30, 2145-2148.
46. Krülle, T. M.; Watson, K. A.; Gregoriou, M.; Johnson, L. N.; Crook, S.; Watkin, D. J.; Griffiths, R. C.; Nash, R. J.; Tsitsanou, K. E.; Zographos, S. E.; Oikonomakos, N. G.; Fleet, G. W. J. Specific inhibition of glycogen phosphorylase by a spirodiketo-piperazine at the anomeric position of glucopyranose. Tetrahedron Lett. 1995, 36, 8281-8294.
47. Goodford, P. J. A computational procedure for determining energetically favorable binding sites on biologically important molecules. J. Med. Chem. 1985, 28, 849-857.
48. Cruciani, G.; Clementi, S. GOLPE: philosophy and applications in 3D QSAR. In Advanced Computer-Assisted Techniques in Drug Discovery; van de Waterbeemd, H., Ed.; VCH Publishers, Inc.: New York, 1994; Vol. 3, pp 61-88.
49. Jurs, P. C.; Dixon, S. L.; Egolf, L. M. Molecular concepts; representations of molecules. In Chemometric Methods in Molecular Design; van de Waterbeemd, H., Ed.; VCH Publishers, Inc.: New York, 1995; Vol. 2, pp 15-38.
50. Hansch, C.; Leo, A. Substituent Constants for Correlation Analysis in Chemistry and Biology; John Wiley & Sons, Inc.: New York, 1979.
51. Sotomatsu, T.; Murata, Y.; Fujita, T. Correlation analysis of substituent effects on the acidity of benzoic acids by the AMI method. J. Comput. Chem. 1989, 10, 94-98.
52. Wold, S.; Eriksson, L. Statistical validation of QSAR results. In Chemometric Methods in Molecular Design; van de Waterbeemd, H., Ed.; VCH Publishers, Inc.: New York, 1995; Vol. 2, pp 309- 318.
53. Topliss, J. G.; Edwards, R. P. Chance factors in studies of quantitative structure-activity relationships. J. Med. Chem. 1979, 22, 1238-1244.
54. So, S.-S.; Karplus, M. Manuscript in preparation.