Generation of new synthetic scaffolds using framework libraries selected and refined via medicinal chemist synthetic expertise

Journal of Chemical Information and Modeling

Volumn 48, Issue 4, 2008, Pages 882-888

  Webb, Thomas R ^a,d   Venegas, Ruben E ^b   Wang, Jian ^a   Deschenes, Alain ^c  

^a ChemBridge Research Labs Inc ^*  (United States)

^b ChemBridge Corporation   (United States)

^c Chemical Computing Group   (Canada)

^d ST JUDE CHILDREN S RESEARCH HOSPITAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOACTIVITY; CONFORMATIONS; LIGANDS; PROTEINS;

PROTEIN FAMILIES; SYNTHETIC SCAFFOLDS; VIRTUAL FRAMEWORK;

MEDICINE;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; DRUG DESIGN;

CHEMISTRY, PHARMACEUTICAL; DRUG DESIGN; MODELS, MOLECULAR; MOLECULAR CONFORMATION;

EID: 44449096689     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci7001928     Document Type: Article

References (27)

1. Schneider, G.; Fechner, U. Computer-based De Novo Design of Drug-like Molecules. Nat. Rev. Drug Disc. 2005, 8, 649-663.
2. Perez, J. J.; Corcho, F.; Llorens, O. Molecular Modeling in the Design of Peptidomimetics and Peptide Surrogates. Curr. Med. Chem. 2002, 24, 2209-29.
3. Goodman, M.; To, S. Peptidomimetics for drug design, In Burger's Medicinal Chemistry and Drug Discovery, 5th ed.; Wolf, M. E., Eds.; John Wiley and Sons: New York, 1995; Vol. 1, pp 803-861.
4. (a) Ball, J. B.; Alewood, P. R. Conformational Constraints: Nonpeptide β-Turn Mimics. J. Mol. Rec. 1990, 2, 55-64.
5. (b) Olson, G. L.; Bolin, D. R.; Bonner, M. P.; Bos, M.; Cook, C. M.; Fry, D.; Graves, B. J.; Hatada, M.; Hill, D. E.; Kahn, M.; Madison, V. S.; Rusiecki, V. K.; Sarabu, R.; Sepinwall, J.; Vincent, G. P.; Voss, M. E. Concepts and Progress in the Development of Peptide Mimetics. J. Med. Chem. 1993, 21, 3041-3049.
6. (c) Adang, A. E. P.; Hermkens, P. H. H.; Linders, J. T. M.; Ottenheijm, H. C. J.; van Staveren, C. J. Case Histories of Peptidomimetics: Progression from Peptides to Drugs. Recl. Trav. Chem. Pays-Bas. 1994, 113, 63-78.
7. Sebhat, I. K.; Martin, W. J.; Ye, Z.; Barakat, K.; Mosley, R. T.; Johnston, D. B. R.; Bakshi, R.; Palucki, B.; Weinberg, D. H.; MacNeil, T.; Kalyani, R. N.; Tang, R.; Stearns, R. A.; Miller, R. R.; Tamvakopoulos, C.; Strack, A. M.; McGowan, E.; Cashen, D. E.; Drisko, J. E.; Hom, G. H.; Howard, A. D.; MacIntyre, D. E.; van der Ploeg, L. H. T.; Patchett, A. A.; Nargund, R. P. Design and Pharmacology of N-[(3R)-1,2,3,4-tetrahydroisoquinolinium-3-ylarboyl]- (1R)-1-(4-chloro-benzyl)-2-[4-cyclohexyl-4-(1H-1,2,4-triazol-1-ylmethyl) -piperi-din-1-yl]-2-oxoethylamine (1), a Potent, Selective, Melanocortin Subtype-4 Receptor Agonist. J. Med. Chem. 2002, 45, 4589-4893.
8. Nargund, R. P.; Patchett, A. A.; Bach, M. A.; Murphy, M. G.; Smith, R. Peptidomimetic Growth Hormone Secretagogues. Design Considerations and Therapeutic Potential. J. Med. Chem. 1998, 41, 3103-3127.
9. Liao, S.; Alfaro-Lopez, J.; Shenderovich, M. D.; Hosohata, K.; Lin, J.; Li, X.; Stropova, D.; Davis, P.; Jernigan, K. A.; Porreca, F.; Yamamura, H. I.; Hruby, V. J. De novo Design, Synthesis, and Biological Activities of High-affinity and Selective Non-Peptide Agonists of the δ-opioid Receptor. J. Med. Chem. 1998, 41, 4767-4776.
10. Okayama, T.; Wei, H.; Davis, P.; Porreca, F.; Yamamura, H. I.; Hruby, V. J. Lead Development of SL-3111; Exploration of a Second Generation of Non-peptide Peptide Mimetics for Potent and Selective δ-opioid Receptor Agonists. Pep. Sci. 2000, 349-352.
11. Croston, G. E.; Olsson, R.; Currier, E. A.; Burstein, E. S.; Weiner, D.; Nash, N.; Severance, D.; Allenmark, S. G.; Thunberg, L.; Ma, J.-N.; Mohell, N.; O'Dowd, B.; Brann, M. R.; Hacksell, U. Discovery of the First Nonpeptide Agonist of the GPR14/urotensin-II Receptor: 3-(4-Chlorophenyl)-3-(-2-dimethylamino- ethyl)isochroman-1-one (AC-7954). J. Med. Chem. 2002, 45, 4950-4953.
12. Rohrer, S. P.; Birzin, E. T.; Mosley, R. T.; Berk, S. C.; Hutchins, S. M.; Shen, D.-M.; Xiong, Y.; Hayes, E. C.; Parmar, R. M.; Foor, F.; Mitra, S. W.; Degrado, S. J.; Shu, M.; Klopp, J. M.; Cai, S.-J.; Blake, A.; Chan, W. W. S.; Pasternak, A.; Yang, L.; Patchett, A. A.; Smith, R. G.; Chapman, K. T.; Schaeffer, J. M. Rapid Identification of Subtype-selective Agonists of the Somatostatin Receptor Through Combinatorial Chemistry. Science 1998, 282, 737-740.
13. Yang, L.; Berk, S. C.; Rohrer, S. P.; Mosley, R. T.; Guo, L.; Underwood, D. J.; Arsion, B. H.; Birzin, E. T.; Hayes, E. C.; Mitra, S. W.; Parmar, R. M.; Cheng, K.; Wu, T.-J.; Butler, B. S.; Foor, F.; Pasternak, A.; Pan, Y.; Silva, M.; Freidinger, R. M.; Smith, R. G.; Chapman, K.; Schaeffer, J. M.; Patchett, A. A. Synthesis and Biological Activities of Potent Peptidomimetics Selective for Somatostatin Receptor Subtype 2. Proc. Natl. Acad. Sci. USA 1998, 95, 10836-10841.
14. Lipinski, C. A. Drug-like Properties and the Causes of Poor Solubility and Poor Permeability. J. Pharmacol. Toxicol. Methods 2000, 44, 235-249.
15. Hirschmann, R.; Nicolaou, K. C.; Pietranico, S.; Leahy, E. M.; Salvino, J.; Arison, B.; Cichy, M. A.; Spoors, P. G.; Shakespeare, W. C.; Sprengler, P. A.; Hamley, P.; Smith, A. B., III; Reisine, T.; Raynor, K.; Maechler, L.; Donaldson, C.; Vale, W.; Freidinger, R. M.; Cascieri, M. R.; Strader, C. D. De novo design and synthesis of somatostatin non-peptide peptidomimetics utilizing beta-D-glucose as a novel scaffolding. J. Am. Chem. Soc. 1993, 115, 12550-12568.
16. Chianelli, D.; Kim, Y.-C.; Lvovskiy, D.; Webb, T. R. Application of a Novel Design Paradigm to Generate General Nonpeptide Combinatorial Scaffolds Mimicking Beta Turns: Dynthesis of Ligands for Domatostatin Receptors. Bioorg. Med. Chem. 2003, 11 (23), 5059-5068.
17. Im, I.; Webb, T. R.; Gong, Y.-D.; Kim, J.-I.; Kim, Y.-C. Solid-phase Synthesis of Tetrahydro-1,4-benzodiazepine-2-one Derivatives as a β-turn Peptidomimic Library. J. Comb. Chem. 2004, 6, 207-213.
18. Webb, T. R.; Jiang, L.; Sviridov, S.; Venegas, R. E.; Vlaskina, A. V.; McGrath, D.; Tucker, J.; Wang, J.; Deschenes, A.; and Li, R. Application of a Novel Design Paradigm to Generate General Nonpeptide Combinatorial Templates Mimicking Beta Turns: Part II, Synthesis of Ligands for Melanocortin Receptors. J. Comb. Chem 2007, 9, 704-710.
19. α atom analysis. J. Comput. Aided Mol. Des. 1999, 13, 469-483.
20. Webb, T. R. Some principles related to chemogenomics in compound library and template design for GPCRs. In Chemogenomics in Drug Discovery - A Medicinal Chemistry Perspective, 1st ed.; Kubinyi, H., Müller, G., Eds.; Wiley-VCH: Weinheim, Germany, 2004, Vol. 22, pp 313-324.
21. MOE (The Molecular Operating Environment), version 2005.06; Chemical Computing Group Inc.: Montreal, Canada, 2005.
22. Russell, S. J.; Blandl, T.; Skelton, N. J.; Cochran, A. G. Stability of Cyclic β-Hairpins: Asymmetric Contributions from Side Chains of a Hydrogen-Bonded Cross-Strand Residue Pair. J. Am. Chem. Soc. 2003, 125, 388-395.
23. Bohl, M.; Loeprecht, B.; Wendt, B.; Heritage, T. Unsupervised 3D Ring Template Searching as an Ideas Generator for Scaffold Hopping: Use of the LAMDA, RigFit, and Field-Based Similarity Search (FBSS) Methods. J. Chem. Inf. Model. 2006, 46, 1882-1890.
24. Vassilev, L. T. p53 Activation by Small Molecules: Application in Oncology. J. Med. Chem. 2005, 48, 4491-4499.
25. Lameijer, E. W.; Kok, J. N.; Back, T.; IJzerman, A. P. The Molecule Evoluator. An Interactive Evolutionary Algorithm for the Design of Drug-Like Molecules. J. Chem. Inf. Model. 2006, 46, 545-552.
26. Lameijer, E.-W.; Tromp, R. A.; Spanjersberg, R. F.; Brussee, J.; IJzerman, A. P. Designing Active Template Molecules by Combining Computational De Novo Design and Human Chemist's Expertise. J. Med Chem. 2007, 50, 1925-1932.
27. Yang, Y.; Nesterenko, D. V.; Trump, R. P.; Yamaguchi, K.; Bartlett, P. A.; Drueckhammer, D. G. Virtual hydrocarbon and combinatorial databases for use with CAVEAT. J. Chem. Inf. Model. 2005, 45, 1820-1823.