Identification and energetic ranking of possible docking sites for pterin on dihydrofolate reductase

• Published in: Journal of computer-aided molecular design Vol. 12; no. 4; pp. 325 - 333
• Main Authors: Bliznyuk, A A, Gready, J E
• Format: Journal Article
• Language: English
• Published: Netherlands Springer Nature B.V 01-07-1998
• Subjects: Binding; Binding Sites; Computer Simulation; Crystal structure; Docking; Enzymes; Failure; Fourier Analysis; Ligands; Mathematical analysis; Models, Molecular; Molecular structure; Poisson equation; Protein Conformation; Pterins - chemistry; Pterins - metabolism; Reductases; Solvation; Tetrahydrofolate Dehydrogenase - chemistry; Tetrahydrofolate Dehydrogenase - metabolism; Thermodynamics
• ISSN: 0920-654X; 1573-4951
• DOI: 10.1023/A:1008039000355

The reliability of new methodology for detecting sites for ligand binding on the surfaces of proteins has been tested using a range of dihydrofolate reductase (DHFR) crystal structures. Docking of the pterin molecule to ten such DHFR structures has been examined. Initial docking sites were selected using the VDW-FFT method we have developed recently. This procedure was followed by rigid geometry optimization and solvation energy calculations using our parametrized reaction field multipoles (PRFM) method and the finite difference solution of the Poisson equation (FDPB) method. Two different sets of MM parameters, from the OPLS and Amber94 force fields, have been used. In eight cases the energy of the complexes with pterin bound at the active site was the lowest with the recent Amber94 parameters. In one case the spurious first-ranked site was only 1.8 kcal/mol lower in energy compared with the active site. The other 'failure' of the method may, in fact, represent a valid initial binding site. The calculations with the old OPLS parameters gave slightly worse results.