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Title: X-ray structure of the ternary MTX·NADPH complex of the anthrax dihydrofolate reductase: A pharmacophore for dual-site inhibitor design

Abstract

For reasons of bioterrorism and drug resistance, it is imperative to identify and develop new molecular points of intervention against anthrax. Dihydrofolate reductase (DHFR) is a highly conserved enzyme and an established target in a number of species for a variety of chemotherapeutic programs. Recently, the crystal structure of B. anthracis DHFR (baDHFR) in complex with methotrexate (MTX) was determined and, based on the structure, proposals were made for drug design strategies directed against the substrate binding site. However, little is gleaned about the binding site for NADPH, the cofactor responsible for hydride transfer in the catalytic mechanism. In the present study, X-ray crystallography at 100 K was used to determine the structure of baDHFR in complex with MTX and NADPH. Although the NADPH binding mode is nearly identical to that seen in other DHFR ternary complex structures, the adenine moiety adopts an off-plane tilt of nearly 90 deg. and this orientation is stabilized by hydrogen bonds to functionally conserved Arg residues. A comparison of the binding site, focusing on this region, between baDHFR and the human enzyme is discussed, with an aim at designing species-selective therapeutics. Indeed, the ternary model, refined to 2.3{angstrom} resolution, provides an accurate template formore » testing the feasibility of identifying dual-site inhibitors, compounds that target both the substrate and cofactor binding site. With the ternary model in hand, using in silico methods, several compounds were identified which could potentially form key bonding contacts in the substrate and cofactor binding sites. Ultimately, two structurally distinct compounds were verified that inhibit baDHFR at low {mu}M concentrations. The apparent K{sub d} for one of these, (2-(3-(2-(hydroxyimino)-2-(pyridine-4-yl)-6,7-dimethylquinoxalin-2-yl)-1-(pyridine-4-yl)ethanone oxime), was measured by fluorescence spectroscopy to be 5.3 {mu}M.« less

Authors:
; ; ; ;
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1005557
Resource Type:
Journal Article
Journal Name:
J. Struct. Biol.
Additional Journal Information:
Journal Volume: 166; Journal Issue: (2) ; 05, 2009; Journal ID: ISSN 1047-8477
Country of Publication:
United States
Language:
ENGLISH
Subject:
36 MATERIALS SCIENCE; 45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEFENSE; 99 GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE; ADENINES; ADMINISTRATIVE PROCEDURES; BIOLOGICAL WARFARE AGENTS; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; DESIGN; DRUGS; ENZYMES; FLUORESCENCE SPECTROSCOPY; HUMAN POPULATIONS; HYDRIDES; HYDROGEN; METHOTREXATE; ORIENTATION; OXIDOREDUCTASES; RESIDUES; RESOLUTION; SUBSTRATES; TESTING

Citation Formats

Bennett, Brad C, Wan, Qun, Ahmad, Md Faiz, Langan, Paul, Dealwis, Chris G, Case Western), and LANL). X-ray structure of the ternary MTX·NADPH complex of the anthrax dihydrofolate reductase: A pharmacophore for dual-site inhibitor design. United States: N. p., 2009. Web. doi:10.1016/j.jsb.2009.01.001.
Bennett, Brad C, Wan, Qun, Ahmad, Md Faiz, Langan, Paul, Dealwis, Chris G, Case Western), & LANL). X-ray structure of the ternary MTX·NADPH complex of the anthrax dihydrofolate reductase: A pharmacophore for dual-site inhibitor design. United States. https://doi.org/10.1016/j.jsb.2009.01.001
Bennett, Brad C, Wan, Qun, Ahmad, Md Faiz, Langan, Paul, Dealwis, Chris G, Case Western), and LANL). Wed . "X-ray structure of the ternary MTX·NADPH complex of the anthrax dihydrofolate reductase: A pharmacophore for dual-site inhibitor design". United States. https://doi.org/10.1016/j.jsb.2009.01.001.
@article{osti_1005557,
title = {X-ray structure of the ternary MTX·NADPH complex of the anthrax dihydrofolate reductase: A pharmacophore for dual-site inhibitor design},
author = {Bennett, Brad C and Wan, Qun and Ahmad, Md Faiz and Langan, Paul and Dealwis, Chris G and Case Western) and LANL)},
abstractNote = {For reasons of bioterrorism and drug resistance, it is imperative to identify and develop new molecular points of intervention against anthrax. Dihydrofolate reductase (DHFR) is a highly conserved enzyme and an established target in a number of species for a variety of chemotherapeutic programs. Recently, the crystal structure of B. anthracis DHFR (baDHFR) in complex with methotrexate (MTX) was determined and, based on the structure, proposals were made for drug design strategies directed against the substrate binding site. However, little is gleaned about the binding site for NADPH, the cofactor responsible for hydride transfer in the catalytic mechanism. In the present study, X-ray crystallography at 100 K was used to determine the structure of baDHFR in complex with MTX and NADPH. Although the NADPH binding mode is nearly identical to that seen in other DHFR ternary complex structures, the adenine moiety adopts an off-plane tilt of nearly 90 deg. and this orientation is stabilized by hydrogen bonds to functionally conserved Arg residues. A comparison of the binding site, focusing on this region, between baDHFR and the human enzyme is discussed, with an aim at designing species-selective therapeutics. Indeed, the ternary model, refined to 2.3{angstrom} resolution, provides an accurate template for testing the feasibility of identifying dual-site inhibitors, compounds that target both the substrate and cofactor binding site. With the ternary model in hand, using in silico methods, several compounds were identified which could potentially form key bonding contacts in the substrate and cofactor binding sites. Ultimately, two structurally distinct compounds were verified that inhibit baDHFR at low {mu}M concentrations. The apparent K{sub d} for one of these, (2-(3-(2-(hydroxyimino)-2-(pyridine-4-yl)-6,7-dimethylquinoxalin-2-yl)-1-(pyridine-4-yl)ethanone oxime), was measured by fluorescence spectroscopy to be 5.3 {mu}M.},
doi = {10.1016/j.jsb.2009.01.001},
url = {https://www.osti.gov/biblio/1005557}, journal = {J. Struct. Biol.},
issn = {1047-8477},
number = (2) ; 05, 2009,
volume = 166,
place = {United States},
year = {2009},
month = {11}
}