Abstract
We report a new structure-based strategy for the identification of novel inhibitors. This approach has been applied to Bacillus stearothermophilus alanine racemase (AlaR), an enzyme implicated in the biosynthesis of the bacterial cell wall. The enzyme catalyzes the racemization of l- and d-alanine using pyridoxal 5′-phosphate (PLP) as a cofactor. The restriction of AlaR to bacteria and some fungi and the absolute requirement for d-alanine in peptidoglycan biosynthesis make alanine racemase a suitable target for drug design. Unfortunately, known inhibitors of alanine racemase are not specific and inhibit the activity of other PLP-dependent enzymes, leading to neurological and other side effects.
This article describes the development of a receptor-based pharmacophore model for AlaR, taking into account receptor flexibility (i.e. a `dynamic' pharmacophore model). In order to accomplish this, molecular dynamics (MD) simulations were performed on the full AlaR dimer from Bacillus stearothermophilus (PDB entry, 1sft) with a d-alanine molecule in one active site and the non-covalent inhibitor, propionate, in the second active site of this homodimer. The basic strategy followed in this study was to utilize conformations of the protein obtained during MD simulations to generate a dynamic pharmacophore model using the property mapping capability of the LigBuilder program. Compounds from the Available Chemicals Directory that fit the pharmacophore model were identified and have been submitted for experimental testing.
The approach described here can be used as a valuable tool for the design of novel inhibitors of other biomolecular targets.
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Roe, D.C. and Kuntz, I.D., J. Comp. Aid. Mol. Des., 9 (1995) 269.
Böhm, H.-J., J. Comp. Aid. Mol. Des., 10 (1996) 265.
Kick, E.K., Roe, D.C., Skillman, A.G., Liu, G.C., Ewing, T.J.A., Sun, Y., Kuntz, I.D. and Ellman, J.A., Chem. Biol., 4 (1997) 297.
Klebe, G., J. Mol. Med. 78 (2000) 269.
Helmy, B., Scand. J. Respir. Dis. 71S (1970) 220.
Shaw, J.P., Petsko, G.A. and Ringe, D., Biochemistry 36 (1997) 1329.
Stamper, C.G.F., Morollo, A.A. and Ringe, D., Biochemistry 37 (1998) 10438.
Morollo, A.A., Petsko, G.A. and Ringe, D., Biochemistry 38 (1999) 3293.
Watanabe, A., Yoshimura, T., Mikami, B., Hayashi, H., Kagamiyama, H. and Esaki, N., J. Biol. Chem. (2002) in press.
Carlson, H.A., Masukawa, K.M., Rubins, K., Bushman, F.D., Jorgensen, W.L., Lins, R.D., Briggs, J.M. and McCammon, J.A., J. Med. Chem. 43 (2000) 2100.
Jorgensen, W.L., BOSS Version 3.8 (1997), Yale University, New Haven, CT.
Lipinski, C.A., Lombardo, F., Dominy, B.W. and Feeney, P., Advanced Drug Delivery Reviews 23 (1997) 3.
Wang, R., Gao, Y. and Lai, L., J. Mol. Model. 6 (2000) 498.
ACD: Available Chemicals Directory; Version 2000, Accelrys Inc., http://www.accelrys.com.
CATALYST, Accelrys Inc., San Diego, CA, http://www.accelrys.com.
Strych, U., Benedik, M.J., J. Bact. 184, Vol. 1 (2002) 4321.
MacKerell, A.D., Bashford, D., Bellott, M., Dunbrack, R.L., Evanseck, J.D., Field, M.J., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph-McCarthy, D., Kuchnir, L., Kuczera, K., Lau, F.T.K., Mattos, C., Michnick, S., Ngo, T., Nguyen, D.T., Prodhom, B., Reiher, W.E., Roux, B., Schlenkrich, M., Smith, J.C., Stote, R., Straub, J., Watanabe, M., Wiorkiewicz-Kuczera, J., Yin, D., Karplus, M., J. Phys. Chem. 102 (1998) 586.
Gaussian98, Gaussian, Inc., Pittsburgh, PA, 1998, http://www.gaussian.com.
Antosiewicz, J., Briggs, J.M., Elcock, A.H., Gilson, M.K., McCammon, J.A., J. Comput. Chem. 17 (1996) 1633.
Madura, J.D., Briggs, J.M., Wade, R.C., Davis, M.E., Lutty, B.A., Ilin, A., Antosiewicz, J., Gilson, M.K., Bagheri, B., Scott, L.R., and McCammon, J.A. Comp. Phys. Comm. 91 (1995) 57.
Ondrechen, M.J., Briggs, J.M. and McCammon, J.A., J. Am. Chem. Soc. 123 (2001) 2830.
Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S. and Karplus, M., J. Comp. Chem. 4 (1983) 187.
Kalé, L., Skeel, R., Bhandarkar, M., Brunner, R., Gursoy, A., Krawetz, N., Phillips, J., Shinozaki, A., Varadarajan, K. and Schulten, K., J. Comput. Phys. 151 (1999) 283.
Berendsen, H.J.C., Postma, J.P.M., van Gusteren, N.F., Di Nola, A. and Haak, J.R., J. Chem. Phys. 81 (1984) 3684.
Jorgensen, W.L., Chandresekhar, J., Madura, J., Impey, R., Klein, M.J., Chem. Phys. 79 (1983) 926.
Ryckaert, J.P., Cicotti, G. and Berendsen, H.J.C., J. Comp. Phys. 23 (1977) 327.
Allen, M.P. and Tildesley, D.J., Computer Simulations of Liquids, Oxford University Press, New York, 1987.
SAS 8.1, SAS Institute Inc., Cary, NC 27513, USA, http://www.sas.com.
Barnum, D., Greene, J., Smellie, A., Sprague, P., J. Chem. Inf. Comput. Sci. 36 (1996) 563.
Wang, R., Gao, Y. and Lai, L., Perspectives in Drug Discovery and Design 19 (2000) 47.
InsightII, Accelrys Inc., http://www.accelrys.com.
Bondi, A., J. Phys. Chem 68 (1964) 441.
Smelie, A., Teig, S., Towbin, P., J. Comp. Chem. 16 (1995) 171.
Hansch, C., Bjorkroth, J.P. and Leo, A., J. Pharm. Sci. 76 (1987) 663.
Bozler, G. and Schmid, J, Martin, Y.C., Kutter, E. and Austel, V. (Eds.), Principles of Pharmacokinetics and Drug Metabolism, Modern Drug Research - Path to Better and Safer Drugs, Marcel Dekker, Inc., New York, NY, U.S.A., 1989, pp. 77-160.
Wang, E. and Walsh, C., Biochemistry 17 (1978) 1313.
Roze, U., Strominger, J.L., Mol. Pharmacol. 2 (1966) 92.
Neuhas, F.C., Gotlich, P.L., Shaw (Eds.), Antibiotics, vol. 1, Springer-Verlag, Heidelberg, Germany, 1967, pp. 40.
Hünenberger, P.H., Mark, A.E., van Gunsteren, W.F., J. Mol. Biol. 252 (1995) 492.
Stocker, U., Spiegel, K., van Gunsteren, W.F, J. Biomol. NMR 18 (2000) 1.
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Mustata, G.I., Briggs, J.M. A structure-based design approach for the identification of novel inhibitors: application to an alanine racemase. J Comput Aided Mol Des 16, 935–953 (2002). https://doi.org/10.1023/A:1023875514454
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DOI: https://doi.org/10.1023/A:1023875514454