Calculation of the Reaction Pathway for the Aromatic Ring Flip in Methotrexate Complexed to Dihydrofolate Reductase

Chandra S. Verma,*^a  Stefan Fischer,*^b  Leo S. D. Caves,^a Gordon C. K. Roberts,^c and Roderick E. Hubbard^a

^aDepartment of Chemistry, University of York, York YO1 5DD, U.K.,  ^bLaboratoire de Chimie Biophysique, Institut Le Bel, Université Louis Pasteur, 4 Rue Blaise Pascal, 67000 Strasbourg, France, and ^cDepartment of Biochemistry and Biological NMR Centre, University of Leicester, Leicester LE1 9HN, U.K.

Received: September 1, 1995

In Final Form: November 3, 1995

Abstract:

The rotation of the benzoyl ring of methotrexate has been modeled in its complexes with dihydrofolate reductase (DHFR). The conjugate peak refinement method (Fischer, S.; Karplus, M. Chem. Phys. Lett. 1992, 194, 252) was used to generate conformational reaction paths and to locate transition states for the 180 degrees ring-flip process. The computed energy barriers for the 3',5'-fluoro-substituted benzoyl ring of methotrexate (F₂MTX) are 11.3 and 10.1 kcal/mol for the binary and ternary (with cofactor NADPH) complexes, respectively, which compare well with the experimental enthalpies of activation of 11.5 (binary) and 9.9 kcal/mol (ternary) from¹⁹F-nmr spectroscopy (Clore, G. M.; Gronenborn, A. M.; Birdsall, B.; Feeney, J.; Roberts, G. C. K. Biochem. J. 1984, 217, 659). The pathways for the hydrogen-substituted isomer (H₂MTX) are found to be similar, although the computed barrier heights are lower (6.5 and 5.0 kcal/mol, respectively). The process is characterized by an asynchronous transition of the two dihedral angles adjacent to the benzoyl ring and by a twin gating of the ring flip by four residues (Leu27, Phe30, Phe49, and Pro50), which form a "hydrophobic quadrant" around the ring. Perturbations of the protein up to 8 Å from the active site (which expands by 1.6 Å) make contributions to the energetics of the process. The local and global characteristics of the path and the effects of structural (crystallographic) solvent and the cofactor are discussed.