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Bourne CR, Bunce RA, Bourne PC, Berlin KD, Barrow EW, Barrow WW. Crystal structure of Bacillus anthracis dihydrofolate reductase with the dihydrophthalazine-based trimethoprim derivative RAB1 provides a structural explanation of potency and selectivity. Antimicrob Agents Chemother 2009; 53:3065-73. [PMID: 19364848 PMCID: PMC2704665 DOI: 10.1128/aac.01666-08] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2008] [Revised: 02/03/2009] [Accepted: 04/06/2009] [Indexed: 11/20/2022] Open
Abstract
Bacillus anthracis possesses an innate resistance to the antibiotic trimethoprim due to poor binding to dihydrofolate reductase (DHFR); currently, there are no commercial antibacterials that target this enzyme in B. anthracis. We have previously reported a series of dihydrophthalazine-based trimethoprim derivatives that are inhibitors for this target. In the present work, we have synthesized one compound (RAB1) displaying favorable 50% inhibitory concentration (54 nM) and MIC (< or =12.8 microg/ml) values. RAB1 was cocrystallized with the B. anthracis DHFR in the space group P2(1)2(1)2(1), and X-ray diffraction data were collected to a 2.3-A resolution. Binding of RAB1 causes a conformational change of the side chain of Arg58 and Met37 to accommodate the dihydrophthalazine moiety. Unlike the natural substrate or trimethoprim, the dihydrophthalazine group provides a large hydrophobic anchor that embeds within the DHFR active site and accounts for its selective inhibitory activity against B. anthracis.
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Affiliation(s)
- Christina R Bourne
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK 74078, USA.
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Kasam V, Salzemann J, Botha M, Dacosta A, Degliesposti G, Isea R, Kim D, Maass A, Kenyon C, Rastelli G, Hofmann-Apitius M, Breton V. WISDOM-II: screening against multiple targets implicated in malaria using computational grid infrastructures. Malar J 2009; 8:88. [PMID: 19409081 PMCID: PMC2691744 DOI: 10.1186/1475-2875-8-88] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2008] [Accepted: 05/01/2009] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Despite continuous efforts of the international community to reduce the impact of malaria on developing countries, no significant progress has been made in the recent years and the discovery of new drugs is more than ever needed. Out of the many proteins involved in the metabolic activities of the Plasmodium parasite, some are promising targets to carry out rational drug discovery. MOTIVATION Recent years have witnessed the emergence of grids, which are highly distributed computing infrastructures particularly well fitted for embarrassingly parallel computations like docking. In 2005, a first attempt at using grids for large-scale virtual screening focused on plasmepsins and ended up in the identification of previously unknown scaffolds, which were confirmed in vitro to be active plasmepsin inhibitors. Following this success, a second deployment took place in the fall of 2006 focussing on one well known target, dihydrofolate reductase (DHFR), and on a new promising one, glutathione-S-transferase. METHODS In silico drug design, especially vHTS is a widely and well-accepted technology in lead identification and lead optimization. This approach, therefore builds, upon the progress made in computational chemistry to achieve more accurate in silico docking and in information technology to design and operate large scale grid infrastructures. RESULTS On the computational side, a sustained infrastructure has been developed: docking at large scale, using different strategies in result analysis, storing of the results on the fly into MySQL databases and application of molecular dynamics refinement are MM-PBSA and MM-GBSA rescoring. The modeling results obtained are very promising. Based on the modeling results, In vitro results are underway for all the targets against which screening is performed. CONCLUSION The current paper describes the rational drug discovery activity at large scale, especially molecular docking using FlexX software on computational grids in finding hits against three different targets (PfGST, PfDHFR, PvDHFR (wild type and mutant forms) implicated in malaria. Grid-enabled virtual screening approach is proposed to produce focus compound libraries for other biological targets relevant to fight the infectious diseases of the developing world.
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Affiliation(s)
- Vinod Kasam
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), 53754 Sankt Augustin, Germany
- LPC Clermont-Ferrand, Campus des Cézeaux, 63177 Aubière Cedex, France
| | - Jean Salzemann
- LPC Clermont-Ferrand, Campus des Cézeaux, 63177 Aubière Cedex, France
| | - Marli Botha
- CSIR Biosciences, Modderfontein, Johannesburg, 1645, South Africa
| | - Ana Dacosta
- LPC Clermont-Ferrand, Campus des Cézeaux, 63177 Aubière Cedex, France
| | - Gianluca Degliesposti
- Dipartimento di Scienze Farmaceutiche, Università di Modena e Reggio Emilia. Via Campi 183, 41100 Modena Italy
| | - Raul Isea
- Fundacion IDEA, Centro de Biociencias, Hoyo de la Puerta, Baruta 1080, Venezuela
| | - Doman Kim
- School of Biological Sciences and Technology, Chonnam National University, Gwang-Ju, South Korea
| | - Astrid Maass
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), 53754 Sankt Augustin, Germany
| | - Colin Kenyon
- CSIR Biosciences, Modderfontein, Johannesburg, 1645, South Africa
| | - Giulio Rastelli
- Dipartimento di Scienze Farmaceutiche, Università di Modena e Reggio Emilia. Via Campi 183, 41100 Modena Italy
| | - Martin Hofmann-Apitius
- Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), 53754 Sankt Augustin, Germany
| | - Vincent Breton
- LPC Clermont-Ferrand, Campus des Cézeaux, 63177 Aubière Cedex, France
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Mutational 'hot-spots' in mammalian, bacterial and protozoal dihydrofolate reductases associated with antifolate resistance: sequence and structural comparison. Drug Resist Updat 2009; 12:28-41. [PMID: 19272832 DOI: 10.1016/j.drup.2009.02.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2008] [Revised: 12/24/2008] [Accepted: 02/04/2009] [Indexed: 12/16/2022]
Abstract
Human dihydrofolate reductase (DHFR) is a primary target for antifolate drugs in cancer treatment, while DHFRs from Plasmodium falciparum, Plasmodium vivax and various bacterial species are primary targets in the treatment of malaria and bacterial infections. Mutations in each of these DHFRs can result in resistance towards clinically relevant antifolates. We review the structural and functional impact of active-site mutations with respect to enzyme activity and antifolate resistance of DHFRs from mammals, protozoa and bacteria. The high structural homology between DHFRs results in a number of cross-species, active-site 'hot-spots' for broad-based antifolate resistance. In addition, we identify mutations that confer species-specific resistance, or antifolate-specific resistance. This comparative review of antifolate binding in diverse species provides new insights into the relationship between antifolate design and the development of mutational resistance. It also presents avenues for designing antifolate-resistant mammalian DHFRs as chemoprotective agents.
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54
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Fogel GB, Cheung M, Pittman E, Hecht D. In silico screening against wild-type and mutant Plasmodium falciparum dihydrofolate reductase. J Mol Graph Model 2008; 26:1145-52. [DOI: 10.1016/j.jmgm.2007.10.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2007] [Revised: 10/11/2007] [Accepted: 10/11/2007] [Indexed: 12/21/2022]
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55
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Hecht D, Cheung M, Fogel GB. QSAR using evolved neural networks for the inhibition of mutant PfDHFR by pyrimethamine derivatives. Biosystems 2008; 92:10-5. [DOI: 10.1016/j.biosystems.2007.10.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2007] [Revised: 10/25/2007] [Accepted: 10/29/2007] [Indexed: 10/22/2022]
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56
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Breton V, Jacq N, Kasam V, Hofmann-Apitius M. Grid-Added Value to Address Malaria. ACTA ACUST UNITED AC 2008; 12:173-81. [DOI: 10.1109/titb.2007.895930] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - N. Jacq
- Univ. Blaise Pascal, Aubiere
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57
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Modeling the inhibition of quadruple mutant Plasmodium falciparum dihydrofolate reductase by pyrimethamine derivatives. J Comput Aided Mol Des 2007; 22:29-38. [DOI: 10.1007/s10822-007-9152-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2007] [Accepted: 11/15/2007] [Indexed: 11/27/2022]
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58
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Bennett BC, Xu H, Simmerman RF, Lee RE, Dealwis CG. Crystal structure of the anthrax drug target, Bacillus anthracis dihydrofolate reductase. J Med Chem 2007; 50:4374-81. [PMID: 17696333 DOI: 10.1021/jm070319v] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Spores of Bacillus anthracis are the infectious agent of anthrax. Current antibiotic treatments are limited due to resistance and patient age restrictions; thus, additional targets for therapeutic intervention are needed. One possible candidate is dihydrofolate reductase (DHFR), a biosynthetic enzyme necessary for anthrax pathogenicity. We determined the crystal structure of DHFR from B. anthracis (baDHFR) in complex with methotrexate (MTX; 1) at 2.4 Angstrom resolution. The structure reveals the crucial interactions required for MTX binding and a putative molecular basis for how baDHFR has natural resistance to trimethoprim (TMP; 2). The structure also allows insights for designing selective baDHFR inhibitors that will have weak affinities for the human enzyme. Additionally, we have found that 5-nitro-6-methylamino-isocytosine (MANIC; 3), which inhibits another B. anthracis folate synthesis enzyme, dihydropteroate synthase (DHPS), can also inhibit baDHFR. This provides a starting point for designing multi-target inhibitors that are less likely to induce drug resistance.
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Affiliation(s)
- Brad C Bennett
- Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
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59
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Djapa LY, Zelikson R, Delahodde A, Bolotin-Fukuhara M, Mazabraud A. Plasmodium vivax dihydrofolate reductase as a target of sulpha drugs. FEMS Microbiol Lett 2007; 256:105-11. [PMID: 16487326 DOI: 10.1111/j.1574-6968.2005.00095.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Sulpha drugs act as competitive inhibitors of p-amino benzoic acid, an intermediate in the de novo folate pathway. Dihydropteroate synthase condenses sulpha drugs into sulpha-dihydropteroate (sulpha-DHP), which competes with dihydrofolate, the dihydrofolate reductase (DHFR) substrate. This designates DHFR as a possible target of sulpha-DHP. We suggest here that Plasmodium vivax DHFR is indeed the in vivo target of sulpha drugs. The wild-type DHFR expressed in Saccharomyces cerevisiae leads to cell growth inhibition, while sensitivity to the drug is exacerbated in the mutants. Contrary to what is observed with sulphanilamide, methotrexate is less effective on P. vivax-DHFR mutants than on wild-type mutant.
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Affiliation(s)
- Liselotte Yimga Djapa
- Institut de Génétique et de Microbiologie, CNRS UMR 8621, Université Paris-Sud, Orsay Cedex, France
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Hawkins VN, Joshi H, Rungsihirunrat K, Na-Bangchang K, Sibley CH. Antifolates can have a role in the treatment of Plasmodium vivax. Trends Parasitol 2007; 23:213-22. [PMID: 17368986 DOI: 10.1016/j.pt.2007.03.002] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2006] [Revised: 02/01/2007] [Accepted: 03/06/2007] [Indexed: 12/14/2022]
Abstract
Plasmodium vivax is a serious health concern in many regions and is sometimes inadvertently treated with sulfadoxine-pyrimethamine (SP). Mutations in the genes that encode dihydrofolate reductase (DHFR) and dihydropteroate synthase (DHPS) confer resistance to pyrimethamine and sulfadoxine, respectively. Numerous studies have examined the prevalence and diversity of mutations in P. vivax dhfr and some have assessed the relationship between dhfr genotype and clinical or in vitro response to pyrimethamine. Other studies have examined the impact of dhps genotype on response to sulfadoxine. These data indicate that, under certain circumstances, SP could be a valuable tool in the fight against P. vivax.
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Affiliation(s)
- Vivian N Hawkins
- Department of Genome Sciences, University of Washington, Box 355065, Seattle, WA 98195, USA
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Cody V, Pace J, Chisum K, Rosowsky A. New insights into DHFR interactions: analysis of Pneumocystis carinii and mouse DHFR complexes with NADPH and two highly potent 5-(omega-carboxy(alkyloxy) trimethoprim derivatives reveals conformational correlations with activity and novel parallel ring stacking interactions. Proteins 2007; 65:959-69. [PMID: 17019704 DOI: 10.1002/prot.21131] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Structural data are reported for two highly potent antifolates, 2,4-diamino-5-[3',4'-dimethoxy-5'-(5-carboxy-1-pentynyl)]benzylpyrimidine (PY1011), with 5000-fold selectivity for Pneumocystis carinii dihydrofolate reductase (pcDHFR), relative to rat liver DHFR, and 2,4-diamino-5-[2-methoxy-5-(4-carboxybutyloxy)benzyl]pyrimidine (PY957), that has 80-fold selectivity for pcDHFR. Crystal structures are reported for NADPH ternary complexes with PY957 and pcDHFR, refined to 2.2 A resolution; with PY1011 and pcDHFR, refined to 2.0 A resolution; and with PY1011 and mouse DHFR (mDHFR), refined to 2.2 A resolution. These results reveal that the carboxylate of the omega-carboxyalkyloxy side chain of these inhibitors form ionic interactions with the conserved Arg in the substrate binding pocket of DHFR. These data suggest that the enhanced inhibitory activity of PY1011 compared with PY957 is, in part, due to the favorable contacts with Phe69 of pcDHFR by the methylene carbons of the inhibitor side chain that are oriented by the triple bond of the 1-pentynyl side chain. These contacts are not present in the PY957 pcDHFR complex, or in the PY1011 mDHFR complex. In the structure of mDHFR the site of Phe69 in pcDHFR is occupied by Asn64. These data also revealed a preference for an unusual parallel ring stacking interaction between Tyr35 of the active site helix and Phe199 of the C-terminal beta sheet in pcDHFR and by Tyr33 and Phe179 in mDHFR that is independent of bound ligand. A unique His174-His187 parallel ring stacking interaction was also observed only in the structure of pcDHFR. These ring stacking interactions are rarely found in any other protein families and may serve to enhance protein stability.
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Affiliation(s)
- Vivian Cody
- Department of Structural Biology, Hauptman-Woodward Medical Research Institute, Buffalo, New York 14203, USA.
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Abstract
Synthesis de novo, acquisition by salvage and interconversion of purines and pyrimidines represent the fundamental requirements for their eventual assembly into nucleic acids as nucleotides and the deployment of their derivatives in other biochemical pathways. A small number of drugs targeted to nucleotide metabolism, by virtue of their effect on folate biosynthesis and recycling, have been successfully used against apicomplexan parasites such as Plasmodium and Toxoplasma for many years, although resistance is now a major problem in the prevention and treatment of malaria. Many targets not involving folate metabolism have also been explored at the experimental level. However, the unravelling of the genome sequences of these eukaryotic unicellular organisms, together with increasingly sophisticated molecular analyses, opens up possibilities of introducing new drugs that could interfere with these processes. This review examines the status of established drugs of this type and the potential for further exploiting the vulnerability of apicomplexan human pathogens to inhibition of this key area of metabolism.
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Affiliation(s)
- John E Hyde
- Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7ND, UK.
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63
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Bunyarataphan S, Leartsakulpanich U, Taweechai S, Tarnchompoo B, Kamchonwongpaisan S, Yuthavong Y. Evaluation of the activities of pyrimethamine analogs against Plasmodium vivax and Plasmodium falciparum dihydrofolate reductase-thymidylate synthase using in vitro enzyme inhibition and bacterial complementation assays. Antimicrob Agents Chemother 2006; 50:3631-7. [PMID: 16954316 PMCID: PMC1635237 DOI: 10.1128/aac.00448-06] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pyrimethamine analogs were examined as potential agents against vivax malaria using a bacterial surrogate system carrying Plasmodium vivax dihydrofolate reductase-thymidylate synthase (PvDHFR-TS), in which the PvDHFR complemented chemically knocked out host dihydrofolate reductase. The system was initially tested with P. falciparum dihydrofolate reductase-thymidylate synthase and was found to have good correlation with the parasite-based system. The 50% inhibitory concentrations derived from PvDHFR-TS-dependent bacteria were correlated with their corresponding inhibition constants (Ki) from an enzyme inhibition assay, pointing to the likelihood that the potent enzyme inhibitors will also have potent antimalarial activities. Active compounds against both wild-type and S58R S117N (SP21) double-mutant P. vivax include analogs with structures which can avert a steric clash with the asparagine (S117N) side chain of the mutant, similar to those found for homologous Plasmodium falciparum mutants, raising the possibility that the same compounds can be developed against both types of antifolate-resistant malaria. This rapid and convenient drug screening system should be useful for development of new antifolates against P. vivax, for which a continuous culture system is not yet available.
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Affiliation(s)
- Sasinee Bunyarataphan
- National Center for Genetic Engineering and Biotechnology, 113 Paholyothin Rd., Klong 1, Klong Luang, Pathumthani 12120, Thailand
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64
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Yuthavong Y, Kamchonwongpaisan S, Leartsakulpanich U, Chitnumsub P. Folate metabolism as a source of molecular targets for antimalarials. Future Microbiol 2006; 1:113-25. [PMID: 17661690 DOI: 10.2217/17460913.1.1.113] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Folate metabolism of the malaria parasites provides two targets for current antimalarials: dihydrofolate reductase and dihydropteroate synthase. Dihydrofolate reductase inhibitors have been used as antimalarials over the past few decades, often in combination with dihydropteroate synthase inhibitors. Resistance to these antifolate drugs developed through mutations in both target enzymes. However, limited mutation possibilities gave opportunities for the development of new drugs. Furthermore, other enzymes in the folate and related pathways are potential new targets that remain to be exploited. These include thymidylate synthase, an enzyme fused with dihydrofolate reductase in the same protein chain, serine hydroxymethyltransferase, methylene tetrahydrofolate dehydrogenase, methionine synthase and enzymes in the glycine cleavage pathway.
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65
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Argyrou A, Vetting MW, Aladegbami B, Blanchard JS. Mycobacterium tuberculosis dihydrofolate reductase is a target for isoniazid. Nat Struct Mol Biol 2006; 13:408-13. [PMID: 16648861 DOI: 10.1038/nsmb1089] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2005] [Accepted: 03/24/2006] [Indexed: 11/08/2022]
Abstract
Isoniazid is a key drug used in the treatment of tuberculosis. Isoniazid is a pro-drug, which, after activation by the katG-encoded catalase peroxidase, reacts nonenzymatically with NAD(+) and NADP(+) to generate several isonicotinoyl adducts of these pyridine nucleotides. One of these, the acyclic 4S isomer of isoniazid-NAD, targets the inhA-encoded enoyl-ACP reductase, an enzyme essential for mycolic acid biosynthesis in Mycobacterium tuberculosis. Here we show that the acyclic 4R isomer of isoniazid-NADP inhibits the M. tuberculosis dihydrofolate reductase (DHFR), an enzyme essential for nucleic acid synthesis. This biologically relevant form of the isoniazid adduct is a subnanomolar bisubstrate inhibitor of M. tuberculosis DHFR. Expression of M. tuberculosis DHFR in Mycobacterium smegmatis mc(2)155 protects cells against growth inhibition by isoniazid by sequestering the drug. Thus, M. tuberculosis DHFR is the first new target for isoniazid identified in the last decade.
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Affiliation(s)
- Argyrides Argyrou
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA
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