Validation of Molecular Docking Calculations Involving FGF-1 and FGF-2

Journal of Medicinal Chemistry

Volumn 47, Issue 7, 2004, Pages 1683-1693

  Bytheway, Ian ^a   Cochran, Siska ^a  

^a Progen Pharmaceuticals Limited   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

FIBROBLAST GROWTH FACTOR 1; FIBROBLAST GROWTH FACTOR 2; LIGAND;

ARTICLE; BINDING AFFINITY; BINDING SITE; CALCULATION; CORRELATION ANALYSIS; MATHEMATICAL ANALYSIS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN FUNCTION; SCORING SYSTEM; VALIDATION PROCESS;

BINDING SITES; FIBROBLAST GROWTH FACTOR 1; FIBROBLAST GROWTH FACTOR 2; LIGANDS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; OLIGOSACCHARIDES; PROTEIN BINDING;

EID: 1642383510     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm030447t     Document Type: Article

References (57)

1. Folkman, J. Tumor Angiogenesis: Therapeutic Implications. N. Engl. J. Med. 1971, 285, 1182-1186.
2. Liekens, S.; Leali, D.; Neyts, J.; Esnouf, R.; Rusnati, M.; Dell'Era, P. ; Maudgal, P. C.; De Clercq, E.; Presta, M. Modulation of Fibroblast Growth Factor-2 Receptor Binding, Signaling, and Mitogenic Activity by Heparin-Mimicking Polysulfonated Compounds. Mol. Pharmacol. 1999, 56, 204-213.
3. Sola, F.; Farao, M.; Pesenti, E.; Marsiglio, A.; Mongelli, N.; Grandi, M. Antitumor Activity of FCE 26644 a New Growth-Factor Complexing Molecule. Cancer Chemother. Pharmacol. 1995, 36, 217-222.
4. Foxall, C.; Wei, Z.; Schaefer, M. E.; Casabonne, M.; Fugedi, P.; Peto, C.; Castellot, J. J.; Brandley, B. K. Sulfated Malto-Oligosaccharides Bind to Basic FGF, Inhibit Endothelial Cell Proliferation, and Disrupt Endothelial Cell Tube Formation. J. Cell. Physiol. 1996, 168, 657-667.
5. Parish, C. R.; Freeman, C.; Brown, K. J.; Francis, D. J.; Cowden, W. B. Identification of Sulfated Oligosaccharide-Based Inhibitors of Tumor Growth and Metastasis Using Novel in Vitro Assays for Angiogenesis and Heparanase Activity. Cancer Res. 1999, 59, 3433-3441.
6. Murphy, P. V.; Pitt, N.; O'Brien, A.; Enright, P. M.; Dunne, A.; Wilson, S. J.; Duane, R. M.; O'Boyle, K. M. Identification of Novel Inhibitors of Fibroblast Growth Factor (FGF-2) Binding to Heparin and Endothelial Cell Survival from a Structurally Diverse Carbohybrid Library. Bioorg. Med. Chem. Lett. 2002, 12, 3287-3290.
7. Fernández-Tornero, C.; Lozano, R. M.; Redondo-Horcajo, M.; M. Gómez, A.; López, J. C.; Quesada, E.; Uriel, C.; Valverde, S.; Cuevas, P.; Romero, A.; Giménez-Gallego, G. Leads for Development of New Naphthalenesulfonate Derivatives with Enhanced Antiangiogenic Activity: Crystal Structure of Acidic Fibroblast Growth Factor in Complex with 5-amino-2-naphthalenesulfonate. J. Biol. Chem. 2003, 278, 21774-21781.
8. Yayon, A.; Klagsbrun, M.; Esko, J. D.; Leder, P.; Ornitz, D. M. Cell Surface, Heparin-Like Molecules are Required for Binding of Basic Fibroblast Growth Factor to its High Affinity Receptor. Cell 1991, 64, 841-848.
9. Rapraeger, A. C.; Krufka, A.; Olwin, B. B. Requirement of Heparan Sulfate for bFGF-Mediated Fibroblast Growth and Myoblast Differentiation. Science 1991, 252, 1705-1708.
10. Ornitz, D. M.; Yayon, A.; Flanagan, J. G.; Svahn, C. M.; Levi, E.; Leder, P. Heparin is Required for Cell-Free Binding of Basic Fibroblast Growth Factor to a Soluble Receptor and for Mitogenesis in Whole Cells. Mol. Cell. Biol. 1992, 12, 240-247.
11. Coltrini, D.; Rusnati, M.; Zoppetti, G.; Oreste, P.; Grazioli, G.; Naggi, A.; Presta, M. Different Effects of Mucosal, Bovine Lung and Chemically Modified Heparin on Selected Biological Properties of Basic Fibroblast Growth Factor. Biochem. J. 1994, 303, 583-590.
12. Schlessinger, J.; Plotnikov, A. N.; Ibrahimi, O. A.; Eliseenkova, A. V.; Yeh, B. K.; Yayon, A.; Linhardt, R. J.; Mohammadi, M. Crystal Structure of a Ternary FGF-FGFR-Heparin Complex Reveals a Dual Role for Heparin in FGFR Binding and Dimerization. Mol. Cell 2000, 6, 743-750.
13. Pellegrini, L.; Burke, D. F.; von Delft, F.; Mulloy, B.; Blundell, T. L. Crystal Structure of Fibroblast Growth Factor Receptor Ectodomain Bound to Ligand and Heparin. Nature 2000, 407, 1029-1034.
14. Rabenstein, D. L. Heparin and Heparan Sulfate: Structure and Function. Nat. Prod. Rep. 2002, 19, 312-331.
15. Capila, I.; Linhardt, R. J. Heparin-Protein Interactions. Angew. Chem., Int. Ed. 2002, 41, 391-412.
16. Zhu, X.; Hsu, B. T.; Rees, D. C. Structural Studies of the Binding of the Anti-Ulcer Drug Sucrose Octasulfate to Acidic Fibroblast Growth Factor. Structure 1993, 1, 27-34.
17. Yeh, B. K.; Eliseenkova, A. V.; Plotnikov, A. N.; Green, D.; Pinnell, J. ; Polat, T.; Gritli-Linde, A.; Linhardt, R. J.; Mohammadi, M. Structural Basis for Activation of Fibroblast Growth Factor Signaling by Sucrose Octasulfate. Mol. Cell. Biol. 2002, 22, 7184-7192.
18. Lozano, R. M.; Jiménez, M. Á.; Santoro, J.; Rico, M.; Giménez-Gallego, G. Solution Structure of Acidic Fibroblast Growth Factor Bound to 1,3,6-naphthalenetrisulfonate: A Minimal Model for the Anti-tumoral Action of Suramins and Suradistas. J. Mol. Biol. 1998, 281, 899-915.
19. DiGabriele, A. D.; Lax, I.; Chen, D. I.; Svahn, C. M.; Jaye, M.; Schlessinger, J.; Hendrickson, W. A. Structure of a Heparin-Linked Biologically Active Dimer of Fibroblast Growth Factor. Nature 1998, 393, 812-817.
20. Thompson, L. D.; Pantoliano, M. W.; Springer, B. A. Energetic Characterization of the Basic Fibroblast Growth Factor-Heparin Interaction: Identification of the Heparin Binding Domain. Biochemistry 1994, 33, 3831-3840.
21. Pantoliano, M. W.; Horlick, R. A.; Springer, B. A.; Van Dyk, D. E.; Tobery, T.; Wetmore, D. R.; Lear, J. D.; Nahapetian, A. T.; Bradley, J. D.; Sisk, W. P. Multivalent Ligand-Receptor Binding Interactions in the Fibroblast Growth Factor System Produce a Cooperative Growth Factor and Heparin Mechanism for Receptor Dimerization. Biochemistry 1994, 33, 10229-10248.
22. Kunou, M.; Koizumi, M.; Shimizu, K.; Kawase, M.; Hatanaka, K. Synthesis of Sulfated Colominic Acids and their Interaction with Fibroblast Growth Factors. Biomacromolecules 2000, 1, 451-458.
23. Mulloy, B.; Forster, M. J. Conformation and Dynamics of Heparin and Heparan Sulfate. Glycobiology 2000, 10, 1147-1156.
24. Sadir, R.; Baleux, F.; Grosdidier, A.; Imberty, A.; Lortat-Jacob, H. Characterization of the Stromal Cell-Derived Factor-αa-Heparin Complex. J. Biol. Chem. 2001, 276, 8288-8296.
25. Lortat-Jacob, H.; Grosdidier, A.; Imberty, A. Structural Diversity of Heparan Sulfate Binding Domains in Chemokines. Proc. Natl Acad. Sci. U.S.A. 2002, 99, 1229-1234.
26. Bitomsky, W.; Wade, R. C. Docking of Glycosaminoglycans to Heparin-Binding Proteins: Validation for aFGF, bFGF, and Antithrombin and Application to IL-8. J. Am. Chem. Soc. 1999, 121, 3004-3013.
27. Ornitz, D. M.; Herr, A. B.; Nilsson, M.; Westman, J.; Svahn, C. M.; Waksman, G. FGF Binding and FGF Receptor Activation by Synthetic Heparan-Derived Di- and Trisaccharides. Science 1995, 268, 432-436.
28. Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J. Experimental and Computational Approaches to Estimate Solubility and Permeability in Drug Discovery and Development Settings. Adv. Drug Delivery Rev. 1997, 23, 3-25.
29. Veber, D. F.; Johnson, S. R.; Cheng, H.-Y.; Smith, B. R.; Ward, K. W.; Kopple, K. D. Molecular Properties that Influence the Oral Bioavailability of Drug Candidates. J. Med. Chem. 2002, 45, 2615-2623.
30. Qasba, P. K. Involvement of Sugars in Protein-Protein Interactions. Carbohydr. Polym. 2000, 41, 293-309.
31. Nissink, J. W. M.; Murray, C.; Hartshorn, M.; Verdonk, M. L.; Cole, J. C.; Taylor, R. A New Test for Validating Predictions of Protein-Ligand Interactions. Proteins 2002, 49, 457-471.
32. Wang, R.; Lu, Y.; Wang, S. Comparative Evaluation of 11 Scoring Functions for Molecular Docking. J. Med. Chem. 2003, 46, 2287-2303.
33. Faham, S.; Hileman, R. E.; Fromm, J. R.; Linhardt, R. J.; Rees, D. C. Heparin Structure and Interactions with Basic Fibroblast Growth Factor. Science 1996, 271, 1116-1120.
34. Banks, J.; Cao, Y.; Damm, W.; Friesner, R.; Gallichio, E.; Halgren, T.; Levy, R.; Mainz, D.; Murphy, R. Impact 2.5; Schrödinger LLC: Portland.
35. Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. Development and Testing of the Opls All Atom Force Field on Conformational Energetics and Properties of Organic Liquids. J. Am. Chem. Soc. 1996, 118, 11225-11236.
36. Eldridge, M. D.; Murray, C. W.; Auton, T. R.; Paolini, G. V.; Mee, R. V. Empirical Scoring Functions: I. The Development of a Fast Empirical Scoring Function to Estimate the Binding Affinity of Ligands in Receptor Complexes. J. Comput.-Aided Mol. Des. 1997, 11, 425-445.
37. Schrödinger LLC. First Discovery Technical Notes; Schrödinger Press: Portland, 2003.
38. Fairweather, J. K.; Ferro, V. Unpublished results.
39. Liu, L.; Ferro, V. Unpublished results.
40. Cochran, S.; Li, C.; Fairweather, J. K.; Kett, W. C.; Coombe, D. R.; Ferro, V. Probing the Interactions of Phosphosulfomannans with Angiogenic Growth Factors by Surface Plasmon Resonance. J. Med. Chem. 2003, 46, 4601-4608.
41. Li, C.; Cochran, S.; Ferro, V. Unpublished results.
42. Stahl, M.; Rarey, M. Detailed Analysis of Scoring Functions for Virtual Screening. J. Med. Chem. 2001, 44, 1035-1042.
43. Schulz-Gasch, T.; Stahl, M. Binding Site Characteristics in Structure-Based Virtual Screening: Evaluation of Current Docking Tools. J. Mol. Mod. 2003, 9, 47-57.
44. Smith, R.; Hubbard, R. E.; Gschwend, D. A.; Leach, A. R.; Good, A. C. Analysis and Optimization of Structure-Based Virtual Screening Protocols. (3). New Methods and Old Problems in Scoring Function Design. J. Mol. Graph. Model. 2003, 22, 41-53.
45. Boström, J. Reproducing the Conformations of Protein-Bound Ligands: A Critical Evaluation of Several Popular Conformational Searching Tools. J. Comput.-Aided Mol. Des. 2001, 15, 1137-1152.
46. Good, A. C.; Cheney, D. L. Analysis and Optimization of Structure-Based Virtual Screening Protocols (1): Exploration of Ligand Conformational Sampling Techniques. J. Mol. Graph. Model. 2003, 22, 23-30.
47. Chang, G. G., W. C.; Still, W. C. An Internal Coordinate Monte Carlo Method for Searching Conformational Space. J. Am. Chem. Soc. 1989, 111, 4379-4386.
48. Still, W. C.; Tempczyk, A.; Hawley, R. C.; Hendrickson, T. Semianalytical Treatment of Solvation for Molecular Mechanics and Dynamics. J. Am. Chem. Soc. 1990, 112, 6127-6129.
49. Mohamadi, F. R.; Richards, N. G. J.; Guida, W. C.; Liskamp, R.; Lipton, M.; Caufield, C.; Chang, G.; Hendrickson, T.; Still, W. C. MacroModel-an Integrated Software System for Modeling Organic and Bioorganic Molecules Using Molecular Mechanics. J. Comput. Chem. 1990, 11, 440-467.
50. Shenkin, P. S.; McDonald, D. Q. Cluster Analysis of Molecular Conformations. J. Comput. Chem. 1994, 15, 899-916.
51. Wang, J.; Kollman, P. A.; Kuntz, I. D. Flexible Ligand Docking: A Multistep Strategy Approach. Proteins 1999, 36, 1-19.
52. Zabell, A. P.; Post, C. B. Docking Multiple Conformations of a Flexible Ligand into a Protein Binding Site Using NMR Restraints. Proteins 2002, 46, 295-307.
53. Clare, B. W. MARTHA; University of Western Australia: Crawley. Program available from the site http://www.chem.uwa.edu.au/research/bclare.
54. Clare, B. W. Qsar of Benzene Derivatives: Comparison of Classical Descriptors, Quantum Theoretic Parameters and Flip Regression, Exemplified by Phenylalkylamine Hallucinogens. J. Comput.-Aided Mol. Des. 2002, 16, 611-633.
55. Leach, A. R. Molecular Modelling. Principles and Applications; Pearson Educational Ltd: Harlow, 2001.
56. Spiegel, M. R.; Liu, J. Mathematical Handbook of Formulas and Tables, 2nd ed.; McGraw-Hill: Singapore, 1999.
57. Pellegrini, L. Role of Heparan Sulfate in Fibroblast Growth Factor Signaling: A Structural View. Curr. Opin. Struct. Biol. 2001, 11, 629-634.