Building predictive models for protein tyrosine phosphatase 1B inhibitors based on discriminating structural features by reassembling medicinal chemistry building blocks

Journal of Medicinal Chemistry

Volumn 47, Issue 24, 2004, Pages 5984-5994

  Yang, Chihae ^a   Cross, Kevin ^a   Myatt, Glenn J ^a   Blower, Paul E ^a   Rathman, James F ^b  

^a Leadscope Inc   (United States)

^b Ohio State University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BENZOFURAN DERIVATIVE; BENZOTHIOPHENE DERIVATIVE; BIPHENYL DERIVATIVE; PROTEIN TYROSINE PHOSPHATASE 1B; PROTEIN TYROSINE PHOSPHATASE 1B INHIBITOR;

ALGORITHM; ARTICLE; COMPARATIVE MOLECULAR FIELD ANALYSIS; DRUG DESIGN; DRUG STRUCTURE; ENZYME INHIBITION; MOLECULAR MODEL; PREDICTION; REGRESSION ANALYSIS;

MODELS, MOLECULAR; MOLECULAR STRUCTURE; PROTEIN-TYROSINE-PHOSPHATASE; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 8644248268     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm0497242     Document Type: Article

References (24)

1. Cramer, R. D. I.; Patterson, D. E.; Bunce, J. D. Comparative Molecular Field Analysis (CoMFA). 1. The Effect of Shape on Binding of Steroids to Carrier Proteins. J. Am. Chem. Soc. 1988, 110, 5959-5967.
2. Mason, J. S.; Morize, I.; Menard, P. R.; Cheney, D. L.; Hulme, C.; Labaudiniere, R. F. New 4-point pharmacophore method for molecular similarity and diversity applications: overview of the method and applications, including a novel approach to the design of combinatorial libraries containing privileged substructures. J. Med. Chem. 1999, 42, 3251-3264.
3. Martin, Y. C. Pharmacophore Mapping. In Designing Bioactiue Molecules: Three-Dimensional Techniques and Applications; Martin, Y. C., Willett, P., Eds.; American Chemical Society: Washington DC, 1998; pp 121-148.
4. Barnard, J. M.; Downs, G. M. Clustering of Chemical Structures on the Basis of Two-Dimensional Similarity Measures. J. Chem. Inf. Comput. Sci. 1992, 32, 644-649.
5. Willett, P.; Barnard, J. M.; Downs, G. M. Chemical Similarity Searching. J. Chem. Inf. Comput. Sci. 1998, 38, 983-996.
6. Cross, K. P.; Myatt, G. J.; Yang, C.; Fligner, M. A.; Verducci, J. S.; Blower, P. E., Jr. Finding Discriminating Structural Features by Reassembling Common Building Blocks. J. Med. Chem. 2003, 46, 4770-4775.
7. Saltiel, A. R.; Kahn, C. R. Insulin signaling and the regulation of glucose and lipid metabolism. Nature 2001, 414, 799.
8. Murthy, V. S.; Kulkarni, V. M. 3D-QSAR CoMFA and CoMSIA on Protein Tyrosine Phosphatase 1B Inhibitors. Bioorg. Med. Chem. 2002, 10, 2267-2282.
9. Sippl, W. Development of biologically active compounds by combining 3D QSAR and structure-based design methods. J. Comput.-Aided Mol. Des. 2002, 16, 825-830.
10. Patankar, S. J.; Jurs, P. C. Classification of Inhibitors of Protein Tyrosine Phosphatase 1B Using Molecular Structure Based Descriptors. J. Chem. Inf. Comput. Sci. 2003, 43, 885-899.
11. Malamas, M. S.; Sredy, J.; Gunawan, I.; Mihan, B.; Sawicki, D. R.; Seestaller, L.; Sullivan, S.; Flam, B. R. New azolidinediones as inhibitors of protein tyrosine phosphatase 1B with antihyperflycemic properties. J. Med. Chem. 2000, 43, 995-1010.
12. Malamas, M. S.; Sredy, J.; Moxham, C.; Klatz, A.; Xu, W.; McDevitt, R.; Adebayo, F. O.; Sawicki, D. R.; Seestaller, L.; Sullivan, D.; Taylor, J. R. Novel benzofuran and benzothiophene biphenyls as inhibitors of protein tyrosine phosphatase 1B with antihyperglycemic properties. J. Med. Chem. 2000, 43, 1293-1310.
13. Roberts, G.; Myatt, G. J.; Johnson, W. P.; Cross, K. P.; Blower, P. E., Jr. Leadscope: software for exploring large sets of screening data. J. Chem. Inf. Comput. Sci. 2000, 40, 1302-1314.
14. Wildman, S. A.; Crippen, G. M. Prediction of Physicochemical Parameters by Atomic Contributions. J. Chem. Inf. Comput. Sci. 1999, 39, 868-873.
15. Ertl, P.; Rohde, B.; Selzer, P. Fast Calculation of Molecular Polar Surface Area as a Sum of Fragment-Based Contributions and Its Application to the Prediction of Drug Transport Properties. J. Med. Chem. 2000, 43, 3714-3717.
16. Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J. Experimental and computational approaches to estimate solubility and permeability in drug discovery and developmental settings. Adv. Drug Delivery Rev. 1997, 23, 3-25.
17. Nguyen, D. V.; Rocke, D. M. Tumor classification by partial least squares using microarray gene expression data. Bioinformatics 2002, 18, 39-50.
18. Geladi Geladi, P.; Kowalski, B. Partial least squares regression: A tutorial. Anal. Chim. Acta 1988, 185, 1-17.
19. Burke, T. R.; Kole, H. K.; Roller, P. P. Potent inhibition of insulin receptor dephosphorylation by a hexamer peptide containing the phosphotyrosyl mimetic F2Pmp. Biochem. Biophys. Res. Commun. 1994, 204, 129-134.
20. Liu, D. G.; Gao, Y.; Voigt, J. H.; Lee, K.; Nicklaus, M. C.; Wu, L.; Zhang, Z. Y.; Burke, T. R., Jr. Acylsulfonamide-Containing PTP1B Inhibitors Designed to Mimic an Enzyme-Bound Water of Hydration. Bioorg. Med. Chem. Lett. 2003, 13, 3005-3007.
21. Xin, Z.; Oost, T. K.; Abad-Zapatero, C.; Hajduk, P. J.; Pei, Z.; Szczepankiewicz, B. G.; Hutching, C. W.; Ballaron, S. J.; Stashko, M. A.; Lubben, T.; Trevillyan, J. M.; Jirousek, M. R.; Liu, G. Potent, Selective Inhibitors of Protein Tyrosine Phosphatase 1B. Bioorg. Med. Chem. Lett. 2003, 13, 1887-1890.
22. Liu, G.; Xin, Z.; Liang, H.; Abad-Zapatero, C.; Hajduk, P. J.; Janowick, D. A.; Szczepankiewicz, B. G.; Pei, Z.; Hutchins, C. W.; Ballaron, S. J.; Stashko, M. A.; Lubben, T. H.; Berg, C. E.; Rondinone, C. M.; Trevillyan, J. M.; Jirousek, M. R. Selective Protein Tyrosine Phosphatase1B Inhibitors: Targeting the Second Phosphotyrosine Binding Site with Non-Carboxylic Acid-Containing Ligands. J. Med. Chem. 2003, 46, 3437-3440.
23. Seidler, J.; McGovern, S. L.; Doman, T. N.; Shoichet, B. K. Identification and Prediction of Promiscuous Aggregating Inhibitors among Known Drugs. J. Med. Chem. 2003, 46, 4477-4486.
24. Sammon, J. W., Jr. A nonlinear mapping for data structure analysis. IEEE Trans. Comput. 1969, 18, 401-409.