A molecular dynamics study of the inhibition of chicken dihydrofolate reductase by a phenyl triazine

Abstract

AbstractMolecular dynamics simulations have been used to investigate the ternary complex formed between chicken liver dihydrofolate reductase, a phenyl triazine inhibitor, and reduced nicotinamide adenine dinucleotide phosphate (NADPH). The solvent was represented by a sphere of water molecules encompassing the system. We report the results of quantum mechanical calculations of the rotational barrier in the pyrophosphate link and the barrier to inversion of the triazine ring. AMBER parameters for NADPH and the triazine are provided. Over the course of a 300‐ps molecular dynamics simulation of the ternary complex in water, the triazine inhibitor maintains the same hydrogen bonding and hydrophobic interactions with the enzyme that are observed in the X‐ray crystal structure. Despite the low calculated barrier to inversion of the triazine ring, a single puckered conformation is observed throughout the simulation. It is proposed that this is primarily due to interactions with Phe34, which maintains an approximately parallel orientation to the triazine ring. The nicotinamide portion of NADPH maintains the interactions observed in the crystal structure, but more conformational change is observed at the adenine end together with associated changes in the protein. Two conformations for the sidechain of Tyr31 are present in the X‐ray structure. The main simulation reported here corresponds to the conformation characterized by (χ1 = − 161°, χ2 = − 103°). A separate simulation was also performed in which the sidechain of Tyr31 was initially set to the other conformation present in the crystal structure (χ1 = 139°, χ2 = −99°). During this simulation, χ1 of this sidechain gradually changed until it occupied the region characterized by χ1 = −160°, thereby suggesting that this is the preferred conformation for this residue. The simulation required 200 ps to reach structural equilibrium (as measured by the root mean square, rms, deviation from the initial crystal structure), thus reinforcing the view that simulations of at least several hundreds of picoseconds are desirable when studying such systems. © 1995 John Wiley & Sons, Inc.