Structural characteristics of antifolate dihydrofolate reductase enzyme interactions

Abstract

The ubiquitous enzyme dihydrofolate reductase (DHFR) is responsible for the reduction of 5,6-dihydrofolate to 5,6,7,8-tetrahydrofolate in an NADPH-dependent manner. It is also a key pharmacological target for the treatment of cancer, as well as bacterial and opportunistic pathogenic infections. Interest in the design of potent and selective antifolate inhibitors has made DHFR one of the most studied enzymes, in particular its structural and biochemical properties. This review surveys more than 129 DHFR solution and crystal structures currently (02/07) reported in the Protein Data Bank representing 15 species of enzyme. Comparison of these DHFR sequences shows that while there is a high sequence homology among vertebrate species (75-95%), there is only about 30% homology between vertebrate and bacterial species. Despite the highly conserved nature of the ligand and cofactor binding sites, DHFR can bind a wide range of compounds that can have a high degree of flexibility. The enzyme itself can also undergo ligand-induced conformational changes that reflect its catalytic mechanism of action. Mechanistic questions can now be addressed with the structural data available for atomic resolution enzyme complexes as well as from neutron diffraction data that have recently become available. These data provide new insight into the design of novel inhibitors that can target specific species with high selectivity of binding.

Kinetic and Structural Analysis for Potent Antifolate Inhibition of Pneumocystis jirovecii, Pneumocystis carinii, and Human Dihydrofolate Reductases and Their Active-Site Variants

“…S1 in the supplemental material). The pyrido [2,3-d]pyrimidine ring orientation of OAAG324 is similar to that observed for other pyridopyrimidines (14,27).…”

“…5) (18). As observed in many pcDHFR crystal structures (27), residues 1 to 4 are not observed in the electron density and the region between residues 83 to 89 is disordered.…”

“…1), as well as the trimethoxybenzyl groups adopting an in-plane or out-of-plane conformation. Analysis of the TMP conformations observed in DHFR structures shows that they cluster in two broad torsion angle ranges, 180 to 210°/50 to 90°and 260 to 280°/95 to 105°for 1 and 2, respectively (14,17,27). The cluster near 260 to 280°/95 to 105°is less populated, with only a few outliers with 2 near 50 to 65°for the two bridge angles.…”

Dihydrofolate reductase (DHFR) inhibition and molecular modeling study of some 6-bromo- or 6,8-dibromo-quinazolin-4(3H)-ones

“…Their geometry was optimized by using the MMFF94 forcefield followed by a flexible alignment using systematic conformational search. Lowest energy aligned conformation(s) were identified [35]. …”

“…To show similarity between the 3-D structures of the most active 22 and 20, from one side and the inactive 24 from the other side, flexible alignment [35] was employed. The top scoring alignment with the least strain energy is shown in (Fig.…”