Theoretical study of inhibition of adenosine deaminase by (8R)-coformycin and (8R)-deoxycoformycin

Journal of Medicinal Chemistry

Volumn 39, Issue 1, 1996, Pages 277-284

  Marrone, Tami J ^a   Straatsma, T P ^b   Briggs, James M ^a   Wilson, David K ^c   Quiocho, Florante A ^c   McCammon, J Andrew ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

^c BAYLOR COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE DEAMINASE; AMINO ACID; AMMONIA; ASPARTIC ACID; COFORMYCIN; DEOXYRIBOSE; ENZYME INHIBITOR; HISTIDINE; HYDROGEN; HYDROXYL GROUP; INOSINE; PENTOSTATIN; PROTEIN; PURINE NUCLEOSIDE; RIBONUCLEOSIDE; RIBOSE; WATER;

ARTICLE; BINDING SITE; CRYSTAL STRUCTURE; DRUG BINDING; ENERGY; ENZYME INHIBITION; HUMAN IMMUNODEFICIENCY VIRUS; HYDROGEN BOND; MOLECULAR DYNAMICS; SIMULATION;

ADENOSINE DEAMINASE; BINDING SITES; COFORMYCIN; DEOXYRIBOSE; ENZYME INHIBITORS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MOLECULAR STRUCTURE; PENTOSTATIN; PROTEIN BINDING; RIBOSE; THERMODYNAMICS; WATER;

EID: 0030020948     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm9505674     Document Type: Article

References (28)

1. Kredich, N. M.; Hershfield, M. S. In The Metabolic Basis of Inherited Disease; Scrivner, R., et al., Eds.; McGraw-Hill: New York, 1989; Vol. 6, pp 1045-1075.
2. Goodchild, J. The Biochemistry of Nucleoside Antibiotics. In Topics in Antibiotic Chemistry; Sammes, P. G., Ed.; John Wiley & Sons: New York, 1982; Vol. 6, pp 99-227.
3. Barchi, J. J., Jr.; Marquez, V. E.; Driscoll, J. S.; Ford, H., Jr.; Mitsuya, H.; Shirasaka, T.; Aoki, S.; Kelly, J. Potential Anti-AIDS Drugs. Lipohilic, Adenosine Deaminase-Activated Prodrugs. J. Med. Chem. 1991, 34, 1647-1655.
4. Ford, H., Jr.; Siddiqui, M. A.; Driscoll, J. S.; Marquez, V. E.; Kelley, J. A.; Mitsuya, H.; Shirasaka, T. Lipohilic, Acid-Stable, Adenosine-Deaminase-Activated Anti-HIV Prodrugs for Central Nervous System Delivery. 2. 6-Halo and 6-Alkoxy Prodrugs of 2′-B-Fluoro-2′,3′-dideoxyinosine J. Med. Chem. 1995, 38, 1189-1195
5. Cha, S.; Agarwal, R. P.; Parks, R. E., Jr. Tight-Binding Inhibitors-II Non-Steady State Nature of Inhibition of Milk Xanthine Oxidase by Allopurinol and Alloxanthine and of Human Erythrocytic Adenosine Deaminase by Coformycin. Biochem. Pharmacol. 1975, 24, 2187-2197.
6. Agerwal, R. P.; Spector, T.; Parks, R. E., Jr. Tight-Binding Inhibitors-IV Inhibition of Adenosine Deaminases by Various Inhibitors. Biochem. Pharmacol. 1977, 26, 359-367.
7. Wolfenden, R.; Wentworth, D. F.; Mitchell, G. N. Influence of Substituent Ribose on Transition State Affinity in Reactions Catalyzed by Adenosine Deaminase. Biochemistry 1977, 16, 5071-5077.
8. Wilson, D. K.; Quiocho, F. A. Unpublished results.
9. Wilson, D. K.; Rudolph, F. B.; Quiocho, F. A. Atomic Structure of Adenosine Deaminase Complexed with a ransition State Analog: Understanding Catalysis and Immunodeficiency Mutations. J. Chem. Phys. 1991, 91, 3631-3637.
10. Frisch, M. J.; Trucks, G. W.; Head-Gordon, M.; Gill, P. M. W.; Wongand, M. W.; Foresman, J. B.; Johnson, B. G.; Schlegel, H. B.; Robb, M. A.; Replogle, E. S.; Gomperts, R.; Andres, J. L.; Raghavachari, K.; Binkley, J. S.; Gonzalez, C.; Martin, R. L.; Fox, D. J.; Defrees, D. J.; Baker, J.; Stewart, J. J. P.; Pople, J. A. Gaussian92, Revision E.2; Gaussian Inc.: Pittsburgh, PA, 1992.
11. Dunning, J.; Hay, P. J. In Methods of Electronic Structure Theory; Schaeffer, H. F., III, Ed.; Plenum Press: New York, 1977; pp 1-28.
12. Hay, P. J.; Wadt, W. R. Ab initio Effective Core Potentials for Molecular Calculations. Potentials for the Transition Metal Atoms Sc to Hg. J. Chem. Phys. 1985, 82, 270-283.
13. Breneman, C. M.; Wiberg, K. B. Determining Atom-centered Monopoles from Molecular Electrostatic Potentials- The Need for High Sampling Density in Formamide Conformational Analysis. J. Comput. Chem. 1990, 11, 361.
14. Hoops, S. C.; Anderson, K. W.; Merz, K. M., Jr. Force Field Design of Metalloproteins. J. Am. Chem. Soc. 1991, 113, 8262-8270.
15. Jorgensen, W. L. BOSS 31. Yale University: New Haven, CT, 1991.
16. Jorgensen, W. L.; Tirado-Rives, J. The OPLS Potential Functions for Proteins. Energy Minimizations for Crystals of Cyclic Peptides and Crambin. J. Am. Chem. Soc. 1988, 110, 1657-1666.
17. Weiner, S. J.; Kollman, P. A.; Nguyen, D. T.; Case, D. A. An All Atom Force Field for Simulation of Proteins and Nucleic Acids. J. Comput. Chem. 1986, 7, 230-252.
18. Tirado-Rives, J. Personal communication.
19. Smith, P. E.; Dang, L. X.; Pettitt, B. M. Simulation of the Structure and Dynamics of the Bis(Penicillamine) Enkephalin-Zwitterion. J. Am. Chem. Soc. 1991, 113, 67-73.
20. Antosiewicz, J.; McCammon, J. A.; Gilson, M. K. Prediction of PH-Dependent Properties of Proteins. J. Mol. Biol. 1994, 238, 415-436.
21. Davis, M. E.; Madura, J. D.; Luty, B. A.; McCammon, J. A. Electrostatics and Diffusion of Molecules in Solution with the University of Houston Brownian Dynamics Program. Comput. Phys. Commun. 1991, 62, 187-197.
22. Straatsma, T. P.; McCammon, J. A. Computational Alchemy. Annu. Rev. Phys. Chem. 1992, 43, 407-435.
23. Straatsma, T. P.; McCammon, J. A. Multiconfiguration Thermodynamic Integration. J. Chem. Phys. 1991, 91, 3631-3637.
24. Straatsma, T. P.; McCammon, J. A. Argos, A Vectorized General Molecular Dynamics Program. J. Comput. Chem. 1990, 11, 943-951.
25. Berendsen, H. J. C.; Grigera, J. E.; Straatsma, T. P. The Missing Term in Effective Pair Potentials. J. Phys. Chem. 1987, 91, 6269.
26. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F ; DiNola, A.; Haak, J. R. Molecular Dynamics with Coupling to an External Heat Bath. J. Chem. Phys. 1984, 81, 3684.
27. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes. J. Comput. Phys. 1977, 23, 327.
28. Suzuki, S. S.; Green, P. G.; Bumgarner, R. E.; Dasgupta, S.; Goddard, W. A., III; Blake, G. A. Benzene Forms Hydrogen Bonds with Water. Science 1992, 257, 942-945.