Summary
Molecular dynamics simulation and free energy perturbation techniques have been used to study the relative binding free energies of 8-methylpterins and 8-methyl-N5-deazapterins to dihydrofolate reductase (DHFR). Methyl-substitution at the 5, 6 and 7 positions in the N-heterocyclic ring gives rise to a variety of ring substituent patterns and biological activity: several of these methyl derivatives of the 8-methyl parent compounds (8-methylpterin and 8-methyl-N5-deazapterin) have been identified as substrates or inhibitors of vertebrate DHFR in previous work. The calculated free energy differences reveal that the methyl-substituted compounds are thermodynamically more stable than the primary compounds (8-methylpterin and 8-methyl-N5-deazapterin) when bound to the enzyme, due largely to hydrophobic hydration phenomena. Methyl substitution at the 5 and/or 7 positions in the 6-methyl-substituted compounds has only a small effect on the stability of ligand binding. Furthermore, repulsive interactions between the 6-methyl substituent and DHFR are minimal, suggesting that the 6-methyl position is optimal for binding. The results also show that similarly substituted 8-methylpterins and 8-methyl-N5-deazapterins have very similar affinities for binding to DHFR. The computer simulation predictions are in broad agreement with experimental data obtained from kinetic studies, i.e. 6,8-dimethylpterin is a more efficient substrate than 8-methylpterin and 6,8-dimethyl-N5-deazapterin is a better inhibitor than 8-methyl-N5-deazapterin.
Similar content being viewed by others
References
Blakley, R.L., In Blakley, R.L. and Benkovic, S.J. (Eds.) Folates and Pterins-Chemistry and Biochemistry of Folates, Vol. 1, Wiley, New York, 1984, pp. 191–253.
Kraut, J. and Matthews, D.A., In Jurnak, F.A. and McPherson, A. (Eds.) Biological Macromolecules and Assemblies, Vol. 3, Wiley, New York, 1987, pp. 1–72.
Thibault, V., Koen, M.J. and Gready, J.E., Biochemistry 28 (1989) 6042.
Gready, J.E., In Curtius, H.-Ch., Ghisla, S. and Blau, N. (Eds.) Chemistry and Biology of Pteridines 1989, de Gruyter, Berlin, 1990, pp. 23–30.
Koen, M.J., Haynes, R.K., Gready, J.E. and Pilling, P.A., In Curtius, H.-Ch., Ghisla, S. and Blau, N. (Eds.) Chemistry and Biology of Pteridines 1989, de Gruyter, Berlin, 1990, pp. 94–97.
Cummins, P.L. and Gready, J.E., Proteins: Struct. Funct. Genet., in press.
Jeong, S.S., Wormell, P. and Gready, J.E., In Blau, N., Curtius, H.-Ch., Levine, R. and Yim, J. (Eds.) Pteridines and Related Biogenic Amines and Folates, Hanrim, Seoul, 1992, pp. 277–292.
Gready, J.E., Ivery, M.T.G., Koen, M.J. and Yang, H.J., In Blau, N., Curtius, H.-Ch., Levine, R. and Yim, J. (Eds.) Pteridines and Related Biogenic Amines and Folates, Hanrim, Seoul, 1992, pp. 265–276.
Koen, M.J. and Gready, J.E., J. Org. Chem., 58 (1993) 1104.
Gready, J.E., J. Comput. Chem., 6 (1985) 377.
Gready, J.E., Biochemistry 24 (1985) 4761.
Williams, M.L. and Gready, J.E., J. Comput. Chem., 10 (1989) 35.
Jordan, M.J. and Gready, J.E., J. Comput. Chem. 10 (1989) 186.
Brown, D.J. and Jacobsen, N.W., J. Chem. Soc., (1961) 4413.
Pfleiderer, W., In Blakley, R.L. and Benkovic, S.J. (Eds.) Folates and Pterins-Chemistry and Biochemistry of Pterins, Vol. 2, Wiley, New York, 1985, pp. 43–114.
Gready, J.E., to be published.
Stone, S.R., Montgomery, J.A. and Morrison, J.F., Biochem. Pharmacol., 33 (1984) 175.
Davies, J.F., Delcamp, T.J., Prendergast, N.J., Ashford, V.A., Freisheim, J.H. and Kraut, J., Biochemistry, 29 (1990) 9467.
Ivery, M.T.G. and Gready, J.E., In Ayling, J.E., Nair, M.G. and Baugh, C.M. (Eds.) Chemistry and Biology of Pteridines and Folates, Plenum Press, New York, 1993, in press.
Tembe, B.L. and McCammon, J.A., Comput. Chem., 8, (1984) 281.
Singh, U.C., Brown, F.K., Bash, P.A. and Kollman, P.A., J. Am. Chem. Soc., 109 (1987) 1607.
Singh, U.C., Proc. Natl. Acad. Sci. USA, 85, (1988) 4280.
Singh, U.C. and Benkovic, S.J., Proc. Natl. Acad. Sci. USA, 85 (1988) 9519.
Brooks, C.L., Int. J. Quantum Chem. Quantum Biol. Symp., 15 (1988) 221.
Brooks, C.L., and Fleischman, S.H., J. Am. Chem. Soc., 112, (1990) 3307.
Fleischman, S.H. and Brooks, C.L., Proteins: Struct. Funct. Genet., 7 (1990) 52.
McDonald, J.J. and Brooks, C.L., J. Am. Chem. Soc., 113 (1991) 2295.
Volz, K.W., Matthews, D.A., Alden, R.A., Freer, S.T., Hansch, C., Kaufman, B.T. and Kraut, J., J. Biol. Chem., 257 (1982) 2528.
Matthews, D.A., Bolin, T.J., Burridge, J.M., Filman, D.J., Volz, K.N., Kaufman, B.T., Beddell, C.R., Champness, J.N., Stammers, D.K. and Kraut, J., J. Biol. Chem., 260 (1985) 381.
Matthews, D.A., Oatley, S.J. and Kraut, J., unpublished results for clDHFR·NADP+·biopterin complex.
McTigue, M.A., DaviesII, J.F., Kaufman, B.T. and Kraut, J., Biochemistry, 31 (1992) 7264.
VanGunsteren, W.F., Prot. Eng., 2 (1988) 5.
VanGunsteren, W.F., In vanGunsteren, W.F. and Weiner, P.K. (Eds.) Computer Simulation of Biomolecular Systems, ESCOM, Leiden, 1989, pp. 27–59.
Pettitt, B.M., In vanGunsteren, W.F. and Weiner, P.K. (Eds.) Computer Simulation of Biomolecular Systems, ESCOM, Leiden, 1989, pp. 94–100.
Pearlman, D.A. and Kollman, P.A., In vanGunsteren, W.F. and Weiner, P.K. (Eds.) Computer Simulation of Biomolecular Systems, ESCOM, Leiden, 1989, pp. 101–119.
Pearlman, D.A. and Kollman, P.A., J. Am. Chem. Soc., 113 (1991) 7167.
Weiner, S.J., Kollman, P.A., Nguyen, D.T. and Case, D.A., J. Comput. Chem., 7 (1986) 230.
Weiner, S.J., Kollman, P.A., Case, D.A., Singh, U.C., Ghio, C., Alagona, G., Profeta, S. and Weiner, P.K., J. Am. Chem. Soc., 106 (1984) 765.
Cummins, P.L., Ramnarayan, K., Singh, U.C. and Gready, J.E., J. Am. Chem. Soc., 113 (1991) 8247.
Jorgensen, W.L., Chandrasekhar, J., Madura, J.D., Impey, R.W. and Klein, M.L., J. Chem. Phys., 79 (1983) 926.
Dewar, M.J.S., Zoebisch, E.G., Healy, E.F. and Stewart, J.J.P., J. Am. Chem. Soc., 107 (1985) 3902.
Cummins, P.L. and Gready, J.E., Chem. Phys. Lett., 174 (1990) 355.
Hagler, A.T., Maple, J.R., Thacher, T.S., Fitzgerald, G.B. and Dinur, U., In vanGunsteren, W.F. and Weiner, P.K. (Eds.) Computer Simulation of Biomolecular Systems, ESCOM, Leiden, 1989, pp. 149–167.
Mezei, M. and Beveridge, D.L., Ann. N.Y. Acad. Sci., 482 (1986) 1.
Singh, U.C., Weiner, P.K., Caldwell, J.W. and Kollman, P.A., AMBER (Version 3.2), Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 1988.
Rao, B.G. and Singh, U.C., J. Am. Chem. Soc., 111 (1989) 3125.
VanGunsteren, W.F. and Berendsen, H.J.C., Mol. Phys., 34 (1977) 1311.
Brooks, C.L., Brunger, A. and Karplus, M., Biopolymers, 24 (1985) 843.
This version of NEWTON has been locally modified to perform direct averaging of coordinates.
Ferrin, T., Huang, C., Pettersen, E.F., Couch, G.S. and Jarvis, L., MidasPlus program, Computer Graphics Laboratory, University of California, San Francisco, CA, 1989.
Bystroff, C., Oatley, S.J. and Kraut, J., Biochemistry, 29, (1990) 3263.
Mezei, M., J. Comput. Phys., 68 (1987) 237.
Solmajer, T. and Mehler, E.L., Prot. Eng. 4 (1991) 911.
Solmajer, T. and Mehler, E.L., Int. J. Quantum Chem., 44 (1992) 291.
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Cummins, P.L., Gready, J.E. Computer-aided drug design: A free energy perturbation study on the binding of methyl-substituted pterins and N5-deazapterins to dihydrofolate reductase. J Computer-Aided Mol Des 7, 535–555 (1993). https://doi.org/10.1007/BF00124361
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1007/BF00124361