Receptor-based design of dihydrofolate reductase inhibitors: comparison of crystallographically determined enzyme binding with enzyme affinity in a series of carboxy-substituted trimethoprim analogs

Abstract

By the use of molecular models of Escherichia coli dihydrofolate reductase (DHFR), analogues of trimethoprim (TMP) were designed which incorporated various 3'-carboxyalkoxy moieties in order to acquire ionic interactions with positively charged active-site residues. Certain of these compounds have shown exceptionally high affinity for this enzyme. For example, the 3'-(carboxypentyl)oxy analogue was found to be 55-fold more inhibitory than TMP toward E. coli DHFR (Ki = 0.024 nM vs. 1.32 nM for TMP). X-ray crystallographic studies of E. coli DHFR in binary complexes with TMP and two members of this acid-containing series of compounds defined the binding of these inhibitors and showed the carboxyl group of the latter two inhibitors to be ionically bound to Arg-57. These observations were in agreement with postulated binding modes that were based on receptor modeling.

Malarial dihydrofolate reductase as a paradigm for drug development against a resistance-compromised target

“…Joining these chemical groups with a flexible linker could also reduce the possibility of resistance resulting from amino acid mutations. DHFR inhibitors designed to interact with the conserved Arg have previously been reported by other groups (25,26). Although Arg122 is identically conserved in all chromosomally encoded DHFRs, comparison of structures for Pf and human DHFRs shows species-dependent amino acid differences for several residues in the vicinity of the conserved Arg.…”

A 1H n.m.r. study of the role of the glutamate moiety in the binding of methotrexate to Lactobacillus casei dihydrofolate reductase

“…These estimates indicate that the x-carboxylateArg 57 interaction and the y-carboxylate-His 28 interaction make roughly equal contributions to the overall binding energy. Some support for the estimate of the cx-carboxylate-Arg 57 interaction energy comes from the work of Kuyper et al (1982), who have prepared a series of trimethoprim analogues bearing a carboxylate group attached by a short alkyl chain. When the alkyl chain was of the appropriate length, the carboxylate was shown crystallographically to interact with Arg 57 of the E. coli enzyme, and the additional interaction energy (over that of trimethoprim itself, in the binary complex) amounted to 6.8 kJ.mol-t.…”

Electrostatic Lock-and-Key Model for the Study of Biological Isosterism: Role of Structural Water in the Binding of Basic Pancreatic Trypsin Inhibitor to ß-Trypsin

“…H-OH vs. \ 379 pm to about 260 pm, as it is indicated by X-ray diffraction data [13]. The importance of the reduction of the distance between charged groups of the enzyme and its inhibi tor in enhancing the Gibbs free energy of binding was also stressed by Kuyper et al [16].…”

“…ligand binding [1,9,16,18]. However, at least two further requirements, electrostatic complementarity [17,33] and matching of nonpolar regions, should be met in order to ensure optimum binding.…”