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

• Published in: Journal of medicinal chemistry 1985-03, Vol.28 (3), p.303-311
• Main Authors: Kuyper, Lee F, Roth, Barbara, Baccanari, David P, Ferone, Robert, Beddell, Christopher R, Champness, John N, Stammers, David K, Dann, John G, Norrington, Frank E. A
• Format: Article
• Language: English
• Subjects: Analytical, structural and metabolic biochemistry; Binding Sites; Biological and medical sciences; Enzymes and enzyme inhibitors; Escherichia coli; Folic Acid Antagonists; Fundamental and applied biological sciences. Psychology; Kinetics; Methotrexate - pharmacology; Microbial Sensitivity Tests; Models, Molecular; Oxidoreductases; Protein Conformation; Structure-Activity Relationship; tetrahydrofolate dehydrogenase; trimethoprim; Trimethoprim - analogs & derivatives; Trimethoprim - pharmacology; X-Ray Diffraction
• ISSN: 0022-2623; 1520-4804
• DOI: 10.1021/jm00381a008

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.