1
|
Xie ZT, Mi BQ, Lu YJ, Chen MT, Ye ZW. Research progress on carotenoid production by Rhodosporidium toruloides. Appl Microbiol Biotechnol 2024; 108:7. [PMID: 38170311 DOI: 10.1007/s00253-023-12943-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 11/09/2023] [Accepted: 11/15/2023] [Indexed: 01/05/2024]
Abstract
Carotenoids are natural lipophilic pigments, which have been proven to provide significant health benefits to humans, relying on their capacity to efficiently scavenge singlet oxygen and peroxyl radicals as antioxidants. Strains belonging to the genus Rhodosporidium represent a heterogeneous group known for a number of phenotypic traits including accumulation of carotenoids and lipids and tolerance to heavy metals and oxidative stress. As a representative of these yeasts, Rhodosporidium toruloides naturally produces carotenoids with high antioxidant activity and grows on a wide variety of carbon sources. As a result, R. toruloides is a promising host for the efficient production of more value-added lipophilic compound carotenoids, e.g., torulene and torularhodin. This review provides a comprehensive summary of the research progress on carotenoid biosynthesis in R. toruloides, focusing on the understanding of biosynthetic pathways and the regulation of key enzymes and genes involved in the process. Moreover, the relationship between the accumulation of carotenoids and lipid biosynthesis, as well as the stress from diverse abiotic factors, has also been discussed for the first time. Finally, several feasible strategies have been proposed to promote carotenoid production by R. toruloides. It is possible that R. toruloides may become a critical strain in the production of carotenoids or high-value terpenoids by genetic technologies and optimal fermentation processes. KEY POINTS: • Biosynthetic pathway and its regulation of carotenoids in Rhodosporidium toruloides were concluded • Stimulation of abiotic factors for carotenoid biosynthesis in R. toruloides was summarized • Feasible strategies for increasing carotenoid production by R. toruloides were proposed.
Collapse
Affiliation(s)
- Zhuo-Ting Xie
- College of Food Science, South China Agricultural University, Guangzhou, 510642, China
- Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou, 510642, China
| | - Bing-Qian Mi
- College of Food Science, South China Agricultural University, Guangzhou, 510642, China
| | - Yong-Jun Lu
- College of Food Science, South China Agricultural University, Guangzhou, 510642, China
| | - Mou-Tong Chen
- College of Food Science, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China.
| | - Zhi-Wei Ye
- College of Food Science, South China Agricultural University, Guangzhou, 510642, China.
- Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou, 510642, China.
| |
Collapse
|
2
|
Bague D, Wang R, Hodge D, Mikati MO, Roma JS, Boshoff HI, Dailey AL, Girma M, Couch RD, Odom John AR, Dowd CS. Inhibition of DXR in the MEP pathway with lipophilic N-alkoxyaryl FR900098 analogs. RSC Med Chem 2024; 15:2422-2439. [PMID: 39026652 PMCID: PMC11253873 DOI: 10.1039/d3md00642e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 05/22/2024] [Indexed: 07/20/2024] Open
Abstract
In Mycobacterium tuberculosis (Mtb) and Plasmodium falciparum (Pf), the methylerythritol phosphate (MEP) pathway is responsible for isoprene synthesis. This pathway and its products are vital to bacterial/parasitic metabolism and survival, and represent an attractive set of drug targets due to their essentiality in these pathogens but absence in humans. The second step in the MEP pathway is the conversion of 1-deoxy-d-xylulose-5-phosphate (DXP) to MEP and is catalyzed by 1-deoxy-d-xylulose-5-phosphate reductoisomerase (DXR). Natural products fosmidomycin and FR900098 inhibit DXR, but are too polar to reach the desired target inside some cells, such as Mtb. Synthesized FR900098 analogs with lipophilic substitution in the position α to the phosphorous atom showed promise, resulting in increased activity against Mtb and Pf. Here, an α substitution, consisting of a 3,4-dichlorophenyl substituent, in combination with various O-linked alkylaryl substituents on the hydroxamate moiety is utilized in the synthesis of a novel series of FR900098 analogs. The purpose of the O-linked alkylaryl substituents is to further enhance DXR inhibition by extending the structure into the adjacent NADPH binding pocket, blocking the binding of both DXP and NADPH. Of the initial O-linked alkylaryl substituted analogs, compound 6e showed most potent activity against Pf parasites at 3.60 μM. Additional compounds varying the phenyl ring of 6e were synthesized. The most potent phosphonic acids, 6l and 6n, display nM activity against PfDXR and low μM activity against Pf parasites. Prodrugs of these compounds were less effective against Pf parasites but showed modest activity against Mtb cells. Data from this series of compounds suggests that this combination of substituents can be advantageous in designing a new generation of antimicrobials.
Collapse
Affiliation(s)
- Darean Bague
- Department of Chemistry, George Washington University Washington D.C. 20052 USA
| | - Ruiqin Wang
- Department of Chemistry, George Washington University Washington D.C. 20052 USA
| | - Dana Hodge
- Division of Infectious Diseases, Children's Hospital of Philadelphia Philadelphia PA 19104 USA
| | - Marwa O Mikati
- Department of Molecular Microbiology, Washington University School of Medicine St. Louis MO 63110 USA
| | - Jose S Roma
- Tuberculosis Research Section, LCIM, NIAID/NIH Bethesda MD 20892 USA
| | - Helena I Boshoff
- Tuberculosis Research Section, LCIM, NIAID/NIH Bethesda MD 20892 USA
| | - Allyson L Dailey
- Department of Chemistry and Biochemistry, George Mason University Fairfax VA 22030 USA
| | - Misgina Girma
- Department of Chemistry and Biochemistry, George Mason University Fairfax VA 22030 USA
| | - Robin D Couch
- Department of Chemistry and Biochemistry, George Mason University Fairfax VA 22030 USA
| | - Audrey R Odom John
- Division of Infectious Diseases, Children's Hospital of Philadelphia Philadelphia PA 19104 USA
- Department of Molecular Microbiology, Washington University School of Medicine St. Louis MO 63110 USA
| | - Cynthia S Dowd
- Department of Chemistry, George Washington University Washington D.C. 20052 USA
| |
Collapse
|
3
|
Shin D, Kim S, Lee DH, Han SJ. Synthetic Strategies toward Ortho-3-propanoate Substituted Aryl Phosphonates by Three-Component Coupling Reactions of Arynes, Phosphites, and Acrylates. J Org Chem 2024. [PMID: 38803278 DOI: 10.1021/acs.joc.4c00672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Mild, metal-free, and operationally simple three-component coupling reactions involving arynes, phosphites, and acrylates have been achieved. The reaction proceeded well with α- or β-substituted acrylates. Additionally, various functional groups were tolerated under these reaction conditions, resulting in diverse ortho-3-propanoate-substituted aryl phosphonates. Moreover, the reaction can be used to synthesize a range of organophosphorus compounds present in natural products, materials, and biologically active compounds.
Collapse
Affiliation(s)
- Donghwa Shin
- Chemical and Biological Integrative Research Center, Korea Institute of Science and Technology, 5 Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Seoul 04107, Republic of Korea
| | - Soomin Kim
- Chemical and Biological Integrative Research Center, Korea Institute of Science and Technology, 5 Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Duck-Hyung Lee
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Seoul 04107, Republic of Korea
| | - Seo-Jung Han
- Chemical and Biological Integrative Research Center, Korea Institute of Science and Technology, 5 Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea
- Division of Bio-Medical Science and Technology, KIST School, University of Science and Technology, Seoul 02792, Republic of Korea
| |
Collapse
|
4
|
Wu X, Bu M, Yang Z, Ping H, Song C, Duan J, Zhang A. Design and synthesis of fosmidomycin analogs containing aza-linkers and their biological activity evaluation. PEST MANAGEMENT SCIENCE 2024; 80:846-856. [PMID: 37794283 DOI: 10.1002/ps.7810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 10/02/2023] [Accepted: 10/05/2023] [Indexed: 10/06/2023]
Abstract
BACKGROUND The enzymes involved in the 2-C-methyl-d-erythritol 4-phosphate (MEP) pathway are attractive targets of a new mode of action for developing anti-infective drugs and herbicides, and inhibitors against 1-deoxy-d-xylulose 5-phosphate reductoisomerase (IspC), the second key enzyme in the pathway, have been intensively investigated; however, few works are reported regarding IspC inhibitors designed for new herbicide discovery. RESULTS A series of fosmidomycin (FOS) analogs were designed with nitrogen-containing linkers replacing the trimethylene linker between the two active substructures of FOS, phosphonic acid and hydroxamic acid. Synthesis followed a facile three-step route of sequential aza-Michael addition of α-amino acids to dibenzyl vinylphosphonate, amidation of the amino acid carboxyl with O-benzyl hydroxylamine, and simultaneous removal of the benzyl protective groups. Biological activity evaluation of IspC and model plants revealed that some compounds had moderate enzyme and model plant growth inhibition effects. In particular, compound 10g, which has a N-(4-fluorophenylethyl) nitrogen-containing linker, exhibited the best plant inhibition activities, superior to the control FOS against the model plants Arabidopsis thaliana, Brassica napus L., Amaranthus retroflexus and Echinochloa crus-galli. A dimethylallyl pyrophosphate rescue assay on A. thaliana confirmed that both 10g and FOS exert their herbicidal activity by blocking the MEP pathway. This result consistent with molecular docking, which confirmed 10g and FOS binding to the IspC active site in a similar way. CONCLUSION Compound 10g has excellent herbicidal activity and represents the first herbicide lead structure of a new mode of action that targets IspC enzyme in the MEP pathway. © 2023 Society of Chemical Industry.
Collapse
Affiliation(s)
- Xin Wu
- National Key Laboratory of Green Pesticide, College of Chemistry, Central China Normal University, Wuhan, China
| | - Mengwei Bu
- National Key Laboratory of Green Pesticide, College of Chemistry, Central China Normal University, Wuhan, China
| | - Zili Yang
- National Key Laboratory of Green Pesticide, College of Chemistry, Central China Normal University, Wuhan, China
| | - Hongrui Ping
- National Key Laboratory of Green Pesticide, College of Chemistry, Central China Normal University, Wuhan, China
| | - Chunlin Song
- National Key Laboratory of Green Pesticide, College of Chemistry, Central China Normal University, Wuhan, China
| | - Jiang Duan
- National Key Laboratory of Green Pesticide, College of Chemistry, Central China Normal University, Wuhan, China
| | - Aidong Zhang
- National Key Laboratory of Green Pesticide, College of Chemistry, Central China Normal University, Wuhan, China
| |
Collapse
|
5
|
Over 40 Years of Fosmidomycin Drug Research: A Comprehensive Review and Future Opportunities. Pharmaceuticals (Basel) 2022; 15:ph15121553. [PMID: 36559004 PMCID: PMC9782300 DOI: 10.3390/ph15121553] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/01/2022] [Accepted: 12/05/2022] [Indexed: 12/15/2022] Open
Abstract
To address the continued rise of multi-drug-resistant microorganisms, the development of novel drugs with new modes of action is urgently required. While humans biosynthesize the essential isoprenoid precursors isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) via the established mevalonate pathway, pathogenic protozoa and certain pathogenic eubacteria use the less well-known methylerythritol phosphate pathway for this purpose. Important pathogens using the MEP pathway are, for example, Plasmodium falciparum, Mycobacterium tuberculosis, Pseudomonas aeruginosa and Escherichia coli. The enzymes of that pathway are targets for antiinfective drugs that are exempt from target-related toxicity. 2C-Methyl-D-erythritol 4-phosphate (MEP), the second enzyme of the non-mevalonate pathway, has been established as the molecular target of fosmidomycin, an antibiotic that has so far failed to be approved as an anti-infective drug. This review describes the development and anti-infective properties of a wide range of fosmidomycin derivatives synthesized over the last four decades. Here we discuss the DXR inhibitor pharmacophore, which comprises a metal-binding group, a phosphate or phosphonate moiety and a connecting linker. Furthermore, non-fosmidomycin-based DXRi, bisubstrate inhibitors and several prodrug concepts are described. A comprehensive structure-activity relationship (SAR) of nearly all inhibitor types is presented and some novel opportunities for further drug development of DXR inhibitors are discussed.
Collapse
|
6
|
Anthony WE, Wang B, Sukhum KV, D'Souza AW, Hink T, Cass C, Seiler S, Reske KA, Coon C, Dubberke ER, Burnham CAD, Dantas G, Kwon JH. Acute and persistent effects of commonly used antibiotics on the gut microbiome and resistome in healthy adults. Cell Rep 2022; 39:110649. [PMID: 35417701 PMCID: PMC9066705 DOI: 10.1016/j.celrep.2022.110649] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 01/07/2022] [Accepted: 03/17/2022] [Indexed: 02/09/2023] Open
Abstract
Antibiotics are deployed against bacterial pathogens, but their targeting of conserved microbial processes means they also collaterally perturb the commensal microbiome. To understand acute and persistent effects of antibiotics on the gut microbiota of healthy adult volunteers, we quantify microbiome dynamics before, during, and 6 months after exposure to 4 commonly used antibiotic regimens. We observe an acute decrease in species richness and culturable bacteria after antibiotics, with most healthy adult microbiomes returning to pre-treatment species richness after 2 months, but with an altered taxonomy, resistome, and metabolic output, as well as an increased antibiotic resistance burden. Azithromycin delays the recovery of species richness, resulting in greater compositional distance. A subset of volunteers experience a persistent reduction in microbiome diversity after antibiotics and share compositional similarities with patients hospitalized in intensive care units. These results improve our quantitative understanding of the impact of antibiotics on commensal microbiome dynamics, resilience, and recovery.
Collapse
Affiliation(s)
- Winston E Anthony
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Bin Wang
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kimberley V Sukhum
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Alaric W D'Souza
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Tiffany Hink
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Candice Cass
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Sondra Seiler
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kimberly A Reske
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Christopher Coon
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Erik R Dubberke
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Carey-Ann D Burnham
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA.
| | - Jennie H Kwon
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
| |
Collapse
|
7
|
Dreneau A, Krebs FS, Munier M, Ngov C, Tritsch D, Lièvremont D, Rohmer M, Grosdemange-Billiard C. α,α-Difluorophosphonohydroxamic Acid Derivatives among the Best Antibacterial Fosmidomycin Analogues. Molecules 2021; 26:molecules26165111. [PMID: 34443699 PMCID: PMC8397956 DOI: 10.3390/molecules26165111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/19/2021] [Accepted: 08/22/2021] [Indexed: 11/17/2022] Open
Abstract
Three α,α-difluorophosphonate derivatives of fosmidomycin were synthesized from diethyl 1,1-difluorobut-3-enylphosphonate and were evaluated on Escherichia coli. Two of them are among the best 1-deoxy-d-xylulose 5-phosphate reductoisomerase inhibitors, with IC50 in the nM range, much better than fosmidomycin, the reference compound. They also showed an enhanced antimicrobial activity against E. coli on Petri dishes in comparison with the corresponding phosphates and the non-fluorinated phosphonate.
Collapse
|
8
|
|
9
|
Non-hydroxamate inhibitors of 1-deoxy-d-xylulose 5-phosphate reductoisomerase (DXR): A critical review and future perspective. Eur J Med Chem 2020; 213:113055. [PMID: 33303239 DOI: 10.1016/j.ejmech.2020.113055] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/18/2020] [Accepted: 11/21/2020] [Indexed: 12/22/2022]
Abstract
1-deoxy-d-xylulose 5-phosphate reductoisomerase (DXR) catalyzes the second step of the non-mevalonate (or MEP) pathway that functions in several organisms and plants for the synthesis of isoprenoids. DXR is essential for the survival of multiple pathogenic bacteria/parasites, including those that cause tuberculosis and malaria in humans. DXR function is inhibited by fosmidomycin (1), a natural product, which forms a chelate with the active site divalent metal (Mg2+/Mn2+) through its hydroxamate metal-binding group (MBG). Most of the potent DXR inhibitors are structurally similar to 1 and retain hydroxamate despite the unfavourable pharmacokinetic and toxicity profile of the latter. We provide our perspective on the lack of non-hydroxamate DXR inhibitors. We also highlight the fundamental flaws in the design of MBG in these molecules, primarily responsible for their failure to inhibit DXR. We also suggest that for designing next-generation non-hydroxamate DXR inhibitors, approaches followed for other metalloenzymes targets may be exploited.
Collapse
|
10
|
Adeyemi CM, Hoppe HC, Isaacs M, Mnkandhla D, Lobb KA, Klein R, Kaye PT. Synthesis and anti-parasitic activity of N-benzylated phosphoramidate Mg 2+-chelating ligands. Bioorg Chem 2020; 105:104280. [PMID: 33152647 DOI: 10.1016/j.bioorg.2020.104280] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 09/11/2020] [Accepted: 09/12/2020] [Indexed: 11/16/2022]
Abstract
A series of N-benzylated phosphoramidate esters, containing a 3,4-dihydroxyphenyl Mg2+-chelating group, has been synthesised in five steps as analogues of fosmidomycin, a Plasmodium falciparum 1-deoxy-1-d-xylulose-5-phosphate reductoisomerase (PfDXR) inhibitor. The 3,4-dihydroxyphenyl group effectively replaces the Mg2+-chelating hydroxamic acid group in fosmidomycin. The compounds showed very encouraging anti-parasitic activity with IC50 values of 5.6-16.4 µM against Plasmodium falciparum parasites and IC50 values of 5.2 - 10.2 µM against Trypanosoma brucei brucei (T.b.brucei). Data obtained from in silico docking of the ligands in the PfDXR receptor cavity (3AU9)5 support their potential as PfDXR inhibitors.
Collapse
Affiliation(s)
- Christiana M Adeyemi
- Department of Chemistry, Rhodes University, Grahamstown 6140, South Africa; Department of Biochemistry and Microbiolgy, Rhodes University, Grahamstown 6140, South Africa
| | - Heinrich C Hoppe
- Department of Biochemistry and Microbiolgy, Rhodes University, Grahamstown 6140, South Africa; Centre for Chemico- and Biomedicinal Research, Rhodes University, Grahamstown 6140, South Africa
| | - Michelle Isaacs
- Department of Biochemistry and Microbiolgy, Rhodes University, Grahamstown 6140, South Africa; Centre for Chemico- and Biomedicinal Research, Rhodes University, Grahamstown 6140, South Africa
| | - Dumisani Mnkandhla
- Department of Biochemistry and Microbiolgy, Rhodes University, Grahamstown 6140, South Africa; Centre for Chemico- and Biomedicinal Research, Rhodes University, Grahamstown 6140, South Africa
| | - Kevin A Lobb
- Department of Chemistry, Rhodes University, Grahamstown 6140, South Africa; Department of Biochemistry and Microbiolgy, Rhodes University, Grahamstown 6140, South Africa; Centre for Chemico- and Biomedicinal Research, Rhodes University, Grahamstown 6140, South Africa
| | - Rosalyn Klein
- Department of Chemistry, Rhodes University, Grahamstown 6140, South Africa; Department of Biochemistry and Microbiolgy, Rhodes University, Grahamstown 6140, South Africa; Centre for Chemico- and Biomedicinal Research, Rhodes University, Grahamstown 6140, South Africa
| | - Perry T Kaye
- Department of Chemistry, Rhodes University, Grahamstown 6140, South Africa; Department of Biochemistry and Microbiolgy, Rhodes University, Grahamstown 6140, South Africa; Centre for Chemico- and Biomedicinal Research, Rhodes University, Grahamstown 6140, South Africa.
| |
Collapse
|
11
|
A computational study of the molecular basis of antibiotic resistance in a DXR mutant. J Comput Aided Mol Des 2019; 33:927-940. [DOI: 10.1007/s10822-019-00229-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 09/28/2019] [Indexed: 10/25/2022]
|
12
|
Steigenberger B, Pieters RJ, Heck AJR, Scheltema RA. PhoX: An IMAC-Enrichable Cross-Linking Reagent. ACS CENTRAL SCIENCE 2019; 5:1514-1522. [PMID: 31572778 PMCID: PMC6764163 DOI: 10.1021/acscentsci.9b00416] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Indexed: 05/02/2023]
Abstract
Chemical cross-linking mass spectrometry is rapidly emerging as a prominent technique to study protein structures. Structural information is obtained by covalently connecting peptides in close proximity by small reagents and identifying the resulting peptide pairs by mass spectrometry. However, substoichiometric reaction efficiencies render routine detection of cross-linked peptides problematic. Here, we present a new trifunctional cross-linking reagent, termed PhoX, which is decorated with a stable phosphonic acid handle. This makes the cross-linked peptides amenable to the well-established immobilized metal affinity chromatography (IMAC) enrichment. The handle allows for 300× enrichment efficiency and 97% specificity. We exemplify the approach on various model proteins and protein complexes, e.g., resulting in a structural model of the LRP1/RAP complex. Almost completely removing linear peptides allows PhoX, although noncleavable, to be applied to complex lysates. Focusing the database search to the 1400 most abundant proteins, we were able to identify 1156 cross-links in a single 3 h measurement.
Collapse
Affiliation(s)
- Barbara Steigenberger
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet
Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences,
Utrecht University, Padualaan 8, 3584 CH Utrecht,
The Netherlands
- Netherlands Proteomics
Centre, Padualaan 8, 3584 CH Utrecht, The
Netherlands
- Department of Chemical Biology & Drug Discovery,
Utrecht Institute for Pharmaceutical Sciences, Utrecht
University, P.O. Box 80082, 3508 TB Utrecht, The
Netherlands
| | - Roland J. Pieters
- Department of Chemical Biology & Drug Discovery,
Utrecht Institute for Pharmaceutical Sciences, Utrecht
University, P.O. Box 80082, 3508 TB Utrecht, The
Netherlands
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet
Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences,
Utrecht University, Padualaan 8, 3584 CH Utrecht,
The Netherlands
- Netherlands Proteomics
Centre, Padualaan 8, 3584 CH Utrecht, The
Netherlands
- Phone: +31 30 253 6797. Fax: +31 30
253 69 18. E-mail:
| | - Richard A. Scheltema
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet
Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences,
Utrecht University, Padualaan 8, 3584 CH Utrecht,
The Netherlands
- Netherlands Proteomics
Centre, Padualaan 8, 3584 CH Utrecht, The
Netherlands
- Phone: +31 30 253 45 64. Fax: +31 30
253 69 18. E-mail:
| |
Collapse
|
13
|
Chen AY, Adamek RN, Dick BL, Credille CV, Morrison CN, Cohen SM. Targeting Metalloenzymes for Therapeutic Intervention. Chem Rev 2019; 119:1323-1455. [PMID: 30192523 PMCID: PMC6405328 DOI: 10.1021/acs.chemrev.8b00201] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metalloenzymes are central to a wide range of essential biological activities, including nucleic acid modification, protein degradation, and many others. The role of metalloenzymes in these processes also makes them central for the progression of many diseases and, as such, makes metalloenzymes attractive targets for therapeutic intervention. Increasing awareness of the role metalloenzymes play in disease and their importance as a class of targets has amplified interest in the development of new strategies to develop inhibitors and ultimately useful drugs. In this Review, we provide a broad overview of several drug discovery efforts focused on metalloenzymes and attempt to map out the current landscape of high-value metalloenzyme targets.
Collapse
Affiliation(s)
- Allie Y Chen
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Rebecca N Adamek
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Benjamin L Dick
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Cy V Credille
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Christine N Morrison
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Seth M Cohen
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| |
Collapse
|
14
|
Stenzel K, Hamacher A, Hansen FK, Gertzen CGW, Senger J, Marquardt V, Marek L, Marek M, Romier C, Remke M, Jung M, Gohlke H, Kassack MU, Kurz T. Alkoxyurea-Based Histone Deacetylase Inhibitors Increase Cisplatin Potency in Chemoresistant Cancer Cell Lines. J Med Chem 2017; 60:5334-5348. [DOI: 10.1021/acs.jmedchem.6b01538] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Katharina Stenzel
- Institut
für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Alexandra Hamacher
- Institut
für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Finn K. Hansen
- Institut
für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
- Pharmaceutical/Medicinal
Chemistry, Institute of Pharmacy, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany
| | - Christoph G. W. Gertzen
- Institut
für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Johanna Senger
- Institut
für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Viktoria Marquardt
- Institut
für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
- Department
of Pediatric Oncology, Hematology, and Clinical Immunology, Medical
Faculty, Heinrich-Heine-University, Moorenstraße 5, 40225 Düsseldorf, Germany
- Department
of Neuropathology, Medical Faculty, Heinrich-Heine-University, Moorenstraße 5, 40225 Düsseldorf, Germany
- Division of Pediatric
Neuro-Oncogenomics, German Cancer Consortium (DKTK) and German Cancer
Research Center (DKFZ), Moorenstraße
5, 40225 Düsseldorf, Germany
| | - Linda Marek
- Institut
für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Martin Marek
- Département
de Biologie Structurale Intégrative, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UDS), CNRS, INSERM, 1 Rue Laurent Fries, 67404 Illkirch Cedex, France
| | - Christophe Romier
- Département
de Biologie Structurale Intégrative, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UDS), CNRS, INSERM, 1 Rue Laurent Fries, 67404 Illkirch Cedex, France
| | - Marc Remke
- Department
of Pediatric Oncology, Hematology, and Clinical Immunology, Medical
Faculty, Heinrich-Heine-University, Moorenstraße 5, 40225 Düsseldorf, Germany
- Department
of Neuropathology, Medical Faculty, Heinrich-Heine-University, Moorenstraße 5, 40225 Düsseldorf, Germany
- Division of Pediatric
Neuro-Oncogenomics, German Cancer Consortium (DKTK) and German Cancer
Research Center (DKFZ), Moorenstraße
5, 40225 Düsseldorf, Germany
| | - Manfred Jung
- Institut
für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Holger Gohlke
- Institut
für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Matthias U. Kassack
- Institut
für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Thomas Kurz
- Institut
für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| |
Collapse
|
15
|
Design of nucleotide-mimetic and non-nucleotide inhibitors of the translation initiation factor eIF4E: Synthesis, structural and functional characterisation. Eur J Med Chem 2016; 124:200-217. [PMID: 27592390 PMCID: PMC5111791 DOI: 10.1016/j.ejmech.2016.08.047] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 08/03/2016] [Accepted: 08/21/2016] [Indexed: 12/02/2022]
Abstract
Eukaryotic translation initiation factor 4E (eIF4E) is considered as the corner stone in the cap-dependent translation initiation machinery. Its role is to recruit mRNA to the ribosome through recognition of the 5′-terminal mRNA cap structure (m7GpppN, where G is guanosine, N is any nucleotide). eIF4E is implicated in cell transformation, tumourigenesis, and angiogenesis by facilitating translation of oncogenic mRNAs; it is thus regarded as an attractive anticancer drug target. We have used two approaches to design cap-binding inhibitors of eIF4E by modifying the N7-substituent of m7GMP and replacing the phosphate group with isosteres such as squaramides, sulfonamides, and tetrazoles, as well as by structure-based virtual screening aimed at identifying non-nucleotide cap-binding antagonists. Phosphomimetic nucleotide derivatives and highly ranking virtual hits were evaluated in a series of in vitro and cell-based assays to identify the first non-nucleotide eIF4E cap-binding inhibitor with activities in cell-based assays, N-[(5,6-dihydro-6-oxo-1,3-dioxolo[4,5-g]quinolin-7-yl)methyl]-N′-(2-methyl-propyl)-N-(phenyl-methyl)thiourea (14), including down-regulation of oncogenic proteins and suppression of RNA incorporation into polysomes. Although we did not observe cellular activity with any of our modified m7GMP phosphate isostere compounds, we obtained X-ray crystallography structures of three such compounds in complex with eIF4E, 5′-deoxy-5′-(1,2-dioxo-3-hydroxycyclobut-3-en-4-yl)amino-N7-methyl-guanosine (4a), N7-3-chlorobenzyl-5′-deoxy-5′-(1,2-dioxo-3-hydroxy-cyclobut-3-en-4-yl)amino-guanosine (4f), and N7-benzyl-5′-deoxy-5′-(trifluoromethyl-sulfamoyl)guanosine (7a). Collectively, the data we present on structure-based design of eIF4E cap-binding inhibitors should facilitate the optimisation of such compounds as potential anticancer agents.
Collapse
|
16
|
Cobb RE, Bae B, Li Z, DeSieno MA, Nair SK, Zhao H. Structure-guided design and biosynthesis of a novel FR-900098 analogue as a potent Plasmodium falciparum 1-deoxy-D-xylulose-5-phosphate reductoisomerase (Dxr) inhibitor. Chem Commun (Camb) 2015; 51:2526-8. [PMID: 25567100 DOI: 10.1039/c4cc09181g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report here the enzymatic biosynthesis of FR-900098 analogues and establish an in vivo platform for the biosynthesis of an N-propionyl derivative FR-900098P. FR-900098P is found to be a significantly more potent inhibitor of Plasmodium falciparum 1-deoxy-D-xylulose 5-phosphate reductoisomerase (PfDxr) than the parent compound, and thus a more promising antimalarial drug candidate.
Collapse
Affiliation(s)
- Ryan E Cobb
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL 61801, USA
| | | | | | | | | | | |
Collapse
|
17
|
Chofor R, Sooriyaarachchi S, Risseeuw MDP, Bergfors T, Pouyez J, Johny C, Haymond A, Everaert A, Dowd CS, Maes L, Coenye T, Alex A, Couch RD, Jones TA, Wouters J, Mowbray SL, Van Calenbergh S. Synthesis and Bioactivity of β-Substituted Fosmidomycin Analogues Targeting 1-Deoxy-d-xylulose-5-phosphate Reductoisomerase. J Med Chem 2015; 58:2988-3001. [DOI: 10.1021/jm5014264] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- René Chofor
- Laboratory
for Medicinal Chemistry (FFW), Universiteit Gent, Ottergemsesteenweg
460, B-9000 Gent, Belgium
| | - Sanjeewani Sooriyaarachchi
- Department
of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Biomedical
Center, Box 596, SE-751 24 Uppsala, Sweden
| | - Martijn D. P. Risseeuw
- Laboratory
for Medicinal Chemistry (FFW), Universiteit Gent, Ottergemsesteenweg
460, B-9000 Gent, Belgium
| | - Terese Bergfors
- Department
of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Biomedical
Center, Box 596, SE-751 24 Uppsala, Sweden
| | - Jenny Pouyez
- Department
of Chemistry, University of Namur, Rue de Bruxelles 61, B-5000 Namur, Belgium
| | - Chinchu Johny
- Department
of Chemistry and Biochemistry, George Mason University, Manassas, Virginia 20110, United States
| | - Amanda Haymond
- Department
of Chemistry and Biochemistry, George Mason University, Manassas, Virginia 20110, United States
| | - Annelien Everaert
- Laboratory
of Pharmaceutical Microbiology, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Cynthia S. Dowd
- Department
of Chemistry, George Washington University, Washington, D.C. 20052, United States
| | - Louis Maes
- Laboratory
for Microbiology, Parasitology and Hygiene (LMPH), Faculty of Pharmaceutical,
Biomedical and Veterinary Sciences, University of Antwerp, Universiteitsplein
1, B-2610 Antwerp, Belgium
| | - Tom Coenye
- Laboratory
of Pharmaceutical Microbiology, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Alexander Alex
- Evenor Consulting Ltd., The
New Barn, Mill Lane, Eastry, Kent CT13 0JW, United Kingdom
| | - Robin D. Couch
- Department
of Chemistry and Biochemistry, George Mason University, Manassas, Virginia 20110, United States
| | - T. Alwyn Jones
- Department
of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Biomedical
Center, Box 596, SE-751 24 Uppsala, Sweden
| | - Johan Wouters
- Department
of Chemistry, University of Namur, Rue de Bruxelles 61, B-5000 Namur, Belgium
| | - Sherry L. Mowbray
- Department
of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Biomedical
Center, Box 596, SE-751 24 Uppsala, Sweden
| | - Serge Van Calenbergh
- Laboratory
for Medicinal Chemistry (FFW), Universiteit Gent, Ottergemsesteenweg
460, B-9000 Gent, Belgium
| |
Collapse
|
18
|
Tritsch D, Zinglé C, Rohmer M, Grosdemange-Billiard C. Flavonoids: true or promiscuous inhibitors of enzyme? The case of deoxyxylulose phosphate reductoisomerase. Bioorg Chem 2015; 59:140-4. [PMID: 25800132 DOI: 10.1016/j.bioorg.2015.02.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 02/11/2015] [Accepted: 02/23/2015] [Indexed: 10/23/2022]
Abstract
Flavonoids, due to their physical and chemical properties (among them hydrophobicity and metal chelation abilities), are potential inhibitors of the 1-deoxyxylulose 5-phosphate reductoisomerase and most of the tested flavonoids effectively inhibited its activity with encouraging IC50 values in the micromolar range. The addition of 0.01% Triton X100 in the assays led however, to a dramatic decrease of the inhibition revealing that a non-specific inhibition probably takes place. Our study highlights the possibility of erroneous conclusions regarding the inhibition of enzymes by flavonoids that are able to produce aggregates in micromolar range. Therefore, the addition of a detergent in the assays prevents possible false positive hits in high throughput screenings.
Collapse
Affiliation(s)
- Denis Tritsch
- Université de Strasbourg/CNRS, Strasbourg, UMR 7177, Institut Le Bel, 4 rue Blaise Pascal, 67081 Strasbourg, France.
| | - Catherine Zinglé
- Université de Strasbourg/CNRS, Strasbourg, UMR 7177, Institut Le Bel, 4 rue Blaise Pascal, 67081 Strasbourg, France
| | - Michel Rohmer
- Université de Strasbourg/CNRS, Strasbourg, UMR 7177, Institut Le Bel, 4 rue Blaise Pascal, 67081 Strasbourg, France
| | | |
Collapse
|
19
|
Brücher K, Gräwert T, Konzuch S, Held J, Lienau C, Behrendt C, Illarionov B, Maes L, Bacher A, Wittlin S, Mordmüller B, Fischer M, Kurz T. Prodrugs of reverse fosmidomycin analogues. J Med Chem 2015; 58:2025-35. [PMID: 25633870 DOI: 10.1021/jm5019719] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fosmidomycin inhibits IspC (Dxr, 1-deoxy-d-xylulose 5-phosphate reductoisomerase), a key enzyme in nonmevalonate isoprenoid biosynthesis that is essential in Plasmodium falciparum. The drug has been used successfully to treat malaria patients in clinical studies, thus validating IspC as an antimalarial target. However, improvement of the drug's pharmacodynamics and pharmacokinetics is desirable. Here, we show that the conversion of the phosphonate moiety into acyloxymethyl and alkoxycarbonyloxymethyl groups can increase the in vitro activity against asexual blood stages of P. falciparum by more than 1 order of magnitude. We also synthesized double prodrugs by additional esterification of the hydroxamate moiety. Prodrugs with modified hydroxamate moieties are subject to bioactivation in vitro. All prodrugs demonstrated improved antiplasmodial in vitro activity. Selected prodrugs and parent compounds were also tested for their cytotoxicity toward HeLa cells and in vivo in a Plasmodium berghei malaria model as well as in the SCID mouse P. falciparum model.
Collapse
Affiliation(s)
- Karin Brücher
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich Heine Universität , Universitätsstr. 1, 40225 Düsseldorf, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Inhibition of the Non-Mevalonate Isoprenoid Pathway by Reverse Hydroxamate Analogues of Fosmidomycin. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.proche.2015.03.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
21
|
Mechanism and inhibition of 1-deoxy-d-xylulose-5-phosphate reductoisomerase. Bioorg Chem 2014; 57:171-185. [DOI: 10.1016/j.bioorg.2014.06.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 06/06/2014] [Accepted: 06/09/2014] [Indexed: 12/23/2022]
|
22
|
Masini T, Hirsch AKH. Development of Inhibitors of the 2C-Methyl-d-erythritol 4-Phosphate (MEP) Pathway Enzymes as Potential Anti-Infective Agents. J Med Chem 2014; 57:9740-63. [DOI: 10.1021/jm5010978] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Tiziana Masini
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh
7, NL-9747
AG Groningen, The Netherlands
| | - Anna K. H. Hirsch
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh
7, NL-9747
AG Groningen, The Netherlands
| |
Collapse
|
23
|
Zinglé C, Tritsch D, Grosdemange-Billiard C, Rohmer M. Catechol–rhodanine derivatives: Specific and promiscuous inhibitors of Escherichia coli deoxyxylulose phosphate reductoisomerase (DXR). Bioorg Med Chem 2014; 22:3713-9. [DOI: 10.1016/j.bmc.2014.05.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 04/29/2014] [Accepted: 05/05/2014] [Indexed: 11/27/2022]
|
24
|
Jansson AM, Więckowska A, Björkelid C, Yahiaoui S, Sooriyaarachchi S, Lindh M, Bergfors T, Dharavath S, Desroses M, Suresh S, Andaloussi M, Nikhil R, Sreevalli S, Srinivasa BR, Larhed M, Jones TA, Karlén A, Mowbray SL. DXR Inhibition by Potent Mono- and Disubstituted Fosmidomycin Analogues. J Med Chem 2013; 56:6190-9. [DOI: 10.1021/jm4006498] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anna M. Jansson
- Department of Cell and Molecular
Biology, Uppsala University, Biomedical
Center, Box 596, SE-751 24 Uppsala, Sweden
| | - Anna Więckowska
- Department of Medicinal Chemistry, Uppsala University, Biomedical Center, Box 574, SE-751
23 Uppsala, Sweden
| | - Christofer Björkelid
- Department of Cell and Molecular
Biology, Uppsala University, Biomedical
Center, Box 596, SE-751 24 Uppsala, Sweden
| | - Samir Yahiaoui
- Department of Medicinal Chemistry, Uppsala University, Biomedical Center, Box 574, SE-751
23 Uppsala, Sweden
| | - Sanjeewani Sooriyaarachchi
- Department of Cell and Molecular
Biology, Uppsala University, Biomedical
Center, Box 596, SE-751 24 Uppsala, Sweden
| | - Martin Lindh
- Department of Medicinal Chemistry, Uppsala University, Biomedical Center, Box 574, SE-751
23 Uppsala, Sweden
| | - Terese Bergfors
- Department of Cell and Molecular
Biology, Uppsala University, Biomedical
Center, Box 596, SE-751 24 Uppsala, Sweden
| | - Shyamraj Dharavath
- Department of Medicinal Chemistry, Uppsala University, Biomedical Center, Box 574, SE-751
23 Uppsala, Sweden
| | - Matthieu Desroses
- Department of Medicinal Chemistry, Uppsala University, Biomedical Center, Box 574, SE-751
23 Uppsala, Sweden
| | - Surisetti Suresh
- Department of Medicinal Chemistry, Uppsala University, Biomedical Center, Box 574, SE-751
23 Uppsala, Sweden
| | - Mounir Andaloussi
- Department of Medicinal Chemistry, Uppsala University, Biomedical Center, Box 574, SE-751
23 Uppsala, Sweden
| | - Rautela Nikhil
- AstraZeneca India Private Limited, Bellary Road, Hebbal, Bangalore 560024,
India
| | - Sharma Sreevalli
- AstraZeneca India Private Limited, Bellary Road, Hebbal, Bangalore 560024,
India
| | | | - Mats Larhed
- Department of Medicinal Chemistry, Uppsala University, Biomedical Center, Box 574, SE-751
23 Uppsala, Sweden
| | - T. Alwyn Jones
- Department of Cell and Molecular
Biology, Uppsala University, Biomedical
Center, Box 596, SE-751 24 Uppsala, Sweden
| | - Anders Karlén
- Department of Medicinal Chemistry, Uppsala University, Biomedical Center, Box 574, SE-751
23 Uppsala, Sweden
| | - Sherry L. Mowbray
- Department of Cell and Molecular
Biology, Uppsala University, Biomedical
Center, Box 596, SE-751 24 Uppsala, Sweden
| |
Collapse
|
25
|
Kholodar SA, Murkin AS. DXP reductoisomerase: reaction of the substrate in pieces reveals a catalytic role for the nonreacting phosphodianion group. Biochemistry 2013; 52:2302-8. [PMID: 23473304 DOI: 10.1021/bi400092n] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The role of the nonreacting phosphodianion group of 1-deoxy-d-xylulose-5-phosphate (DXP) in catalysis by DXP reductoisomerase (DXR) was investigated for the reaction of the "substrate in pieces". The truncated substrate 1-deoxy-l-erythrulose is converted by DXR to 2-C-methylglycerol with a kcat/Km that is 10(6)-fold lower than that for DXP. Phosphite dianion was found to be a nonessential activator, providing 3.2 kcal/mol of transition state stabilization for the truncated substrate. These results implicate a phosphate-driven conformational change involving loop closure over the DXR active site to generate an environment poised for catalysis.
Collapse
Affiliation(s)
- Svetlana A Kholodar
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA
| | | |
Collapse
|
26
|
Nguyen-Trung AT, Tritsch D, Grosdemange-Billiard C, Rohmer M. Synthesis of tetrazole analogues of phosphonohydroxamic acids: an attempt to improve the inhibitory activity against the DXR. Bioorg Med Chem Lett 2013; 23:1643-7. [PMID: 23414808 DOI: 10.1016/j.bmcl.2013.01.080] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 01/15/2013] [Accepted: 01/17/2013] [Indexed: 11/19/2022]
Abstract
This work is focused on the design of new antimicrobial drugs and on the development of lipophilic inhibitors of the DXR, the second enzyme of the MEP pathway for the biosynthesis of isoprene units in most bacteria, by replacing the phosphonate group of fosmidomycin derivatives by a tetrazoyl moiety capable of multiple hydrogen bonding. The N- and C-substituted tetrazole analogues of phosphonohydroxamate inhibitors were synthesized and tested on the DXR of Escherichia coli. This work points out the hypothesis that the phosphonate/phosphate recognition site might be too rigid to accommodate other functional groups.
Collapse
Affiliation(s)
- Anh Thu Nguyen-Trung
- Université de Strasbourg, CNRS, Strasbourg, UMR 7177, Institut Le Bel, 4 rue Blaise Pascal, 67081 Strasbourg, France
| | | | | | | |
Collapse
|
27
|
Tanaka N, Umeda T, Kusakabe Y, Nakanishi M, Kitade Y, T. Nakamura K. Structural Biology for Developing Antimalarial Compounds. YAKUGAKU ZASSHI 2013; 133:527-37. [DOI: 10.1248/yakushi.13-00001-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
28
|
San Jose G, Jackson ER, Uh E, Johny C, Haymond A, Lundberg L, Pinkham C, Kehn-Hall K, Boshoff HI, Couch RD, Dowd CS. Design of Potential Bisubstrate Inhibitors against Mycobacterium tuberculosis (Mtb) 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase (Dxr)-Evidence of a Novel Binding Mode. MEDCHEMCOMM 2013; 4:1099-1104. [PMID: 23914289 DOI: 10.1039/c3md00085k] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In most bacteria, the nonmevalonate pathway is used to synthesize isoprene units. Dxr, the second step in the pathway, catalyzes the NADPH-dependent reductive isomerization of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol-4-phosphate (MEP). Dxr is inhibited by natural products fosmidomycin and FR900098, which bind in the DXP binding site. These compounds, while potent inhibitors of Dxr, lack whole cell activity against Mycobacterium tuberculosis (Mtb) due to their polarity. Our goal was to use the Mtb Dxr-fosmidomycin co-crystal structure to design bisubstrate ligands to bind to both the DXP and NADPH sites. Such compounds would be expected to demonstrate improved whole cell activity due to increased lipophilicity. Two series of compounds were designed and synthesized. Compounds from both series inhibited Mtb Dxr. The most potent compound (8) has an IC50 of 17.8 µM. Analysis shows 8 binds to Mtb Dxr via a novel, non-bisubstrate mechanism. Further, the diethyl ester of 8 inhibits Mtb growth making this class of compounds interesting lead molecules in the search for new antitubercular agents.
Collapse
Affiliation(s)
- Géraldine San Jose
- Department of Chemistry, George Washington University, Washington DC 20052, USA. ; Tel: 01 202 994 8405
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Zinglé C, Kuntz L, Tritsch D, Grosdemange-Billiard C, Rohmer M. Modifications around the hydroxamic acid chelating group of fosmidomycin, an inhibitor of the metalloenzyme 1-deoxyxylulose 5-phosphate reductoisomerase (DXR). Bioorg Med Chem Lett 2012; 22:6563-7. [DOI: 10.1016/j.bmcl.2012.09.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Revised: 09/04/2012] [Accepted: 09/06/2012] [Indexed: 11/30/2022]
|
30
|
McKenney ES, Sargent M, Khan H, Uh E, Jackson ER, Jose GS, Couch RD, Dowd CS, van Hoek ML. Lipophilic prodrugs of FR900098 are antimicrobial against Francisella novicida in vivo and in vitro and show GlpT independent efficacy. PLoS One 2012; 7:e38167. [PMID: 23077474 PMCID: PMC3471904 DOI: 10.1371/journal.pone.0038167] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Accepted: 05/04/2012] [Indexed: 01/01/2023] Open
Abstract
Bacteria, plants, and algae produce isoprenoids through the methylerythritol phosphate (MEP) pathway, an attractive pathway for antimicrobial drug development as it is present in prokaryotes and some lower eukaryotes but absent from human cells. The first committed step of the MEP pathway is catalyzed by 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR/MEP synthase). MEP pathway genes have been identified in many biothreat agents, including Francisella, Brucella, Bacillus, Burkholderia, and Yersinia. The importance of the MEP pathway to Francisella is demonstrated by the fact that MEP pathway mutations are lethal. We have previously established that fosmidomycin inhibits purified MEP synthase (DXR) from F. tularensis LVS. FR900098, the acetyl derivative of fosmidomycin, was found to inhibit the activity of purified DXR from F. tularensis LVS (IC50 = 230 nM). Fosmidomycin and FR900098 are effective against purified DXR from Mycobacterium tuberculosis as well, but have no effect on whole cells because the compounds are too polar to penetrate the thick cell wall. Fosmidomycin requires the GlpT transporter to enter cells, and this is absent in some pathogens, including M. tuberculosis. In this study, we have identified the GlpT homologs in F. novicida and tested transposon insertion mutants of glpT. We showed that FR900098 also requires GlpT for full activity against F. novicida. Thus, we synthesized several FR900098 prodrugs that have lipophilic groups to facilitate their passage through the bacterial cell wall and bypass the requirement for the GlpT transporter. One compound, that we termed “compound 1,” was found to have GlpT-independent antimicrobial activity. We tested the ability of this best performing prodrug to inhibit F. novicida intracellular infection of eukaryotic cell lines and the caterpillar Galleria mellonella as an in vivo infection model. As a lipophilic GlpT-independent DXR inhibitor, compound 1 has the potential to be a broad-spectrum antibiotic, and should be effective against most MEP-dependent organisms.
Collapse
Affiliation(s)
- Elizabeth S. McKenney
- School of Systems Biology, George Mason University, Manassas, Virginia, United States of America
| | - Michelle Sargent
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, United States of America
| | - Hameed Khan
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, United States of America
| | - Eugene Uh
- Department of Chemistry, George Washington University, Washington, D.C., United States of America
| | - Emily R. Jackson
- Department of Chemistry, George Washington University, Washington, D.C., United States of America
| | - Géraldine San Jose
- Department of Chemistry, George Washington University, Washington, D.C., United States of America
| | - Robin D. Couch
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, United States of America
- National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, Virginia, United States of America
| | - Cynthia S. Dowd
- Department of Chemistry, George Washington University, Washington, D.C., United States of America
| | - Monique L. van Hoek
- School of Systems Biology, George Mason University, Manassas, Virginia, United States of America
- National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, Virginia, United States of America
- * E-mail:
| |
Collapse
|
31
|
Schütz AP, Osawa S, Mathis J, Hirsch AKH, Bernet B, Illarionov B, Fischer M, Bacher A, Diederich F. Exploring the Ribose Sub-Pocket of the Substrate-Binding Site in Escherichia coli IspE: Structure-Based Design, Synthesis, and Biological Evaluation of Cytosines and Cytosine Analogues. European J Org Chem 2012. [DOI: 10.1002/ejoc.201200296] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
32
|
Ponaire S, Zinglé C, Tritsch D, Grosdemange-Billiard C, Rohmer M. Growth inhibition of Mycobacterium smegmatis by prodrugs of deoxyxylulose phosphate reducto-isomerase inhibitors, promising anti-mycobacterial agents. Eur J Med Chem 2012; 51:277-85. [DOI: 10.1016/j.ejmech.2012.02.031] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 02/15/2012] [Accepted: 02/16/2012] [Indexed: 10/28/2022]
|
33
|
Queffélec C, Petit M, Janvier P, Knight DA, Bujoli B. Surface modification using phosphonic acids and esters. Chem Rev 2012; 112:3777-807. [PMID: 22530923 DOI: 10.1021/cr2004212] [Citation(s) in RCA: 551] [Impact Index Per Article: 45.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Clémence Queffélec
- LUNAM Université, CNRS, UMR, Chimie Et Interdisciplinarité: Synthèse Analyse Modélisation, UFR Sciences et Techniques, Nantes, France
| | | | | | | | | |
Collapse
|
34
|
Pérez-Gil J, Calisto BM, Behrendt C, Kurz T, Fita I, Rodríguez-Concepción M. Crystal structure of Brucella abortus deoxyxylulose-5-phosphate reductoisomerase-like (DRL) enzyme involved in isoprenoid biosynthesis. J Biol Chem 2012; 287:15803-9. [PMID: 22442144 DOI: 10.1074/jbc.m112.354811] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Most bacteria use the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway for the synthesis of their essential isoprenoid precursors. The absence of the MEP pathway in humans makes it a promising new target for the development of much needed new and safe antimicrobial drugs. However, bacteria show a remarkable metabolic plasticity for isoprenoid production. For example, the NADPH-dependent production of MEP from 1-deoxy-D-xylulose 5-phosphate in the first committed step of the MEP pathway is catalyzed by 1-deoxy-D-xylulose-5-phosphate reductoisomerase (DXR) in most bacteria, whereas an unrelated DXR-like (DRL) protein was recently found to catalyze the same reaction in some organisms, including the emerging human and animal pathogens Bartonella and Brucella. Here, we report the x-ray crystal structures of the Brucella abortus DRL enzyme in its apo form and in complex with the broad-spectrum antibiotic fosmidomycin solved to 1.5 and 1.8 Å resolution, respectively. DRL is a dimer, with each polypeptide folding into three distinct domains starting with the NADPH-binding domain, in resemblance to the structure of bacterial DXR enzymes. Other than that, DRL and DXR show a low structural relationship, with a different disposition of the domains and a topologically unrelated C-terminal domain. In particular, the active site of DRL presents a unique arrangement, suggesting that the design of drugs that would selectively inhibit DRL-harboring pathogens without affecting beneficial or innocuous bacteria harboring DXR should be feasible. As a proof of concept, we identified two strong DXR inhibitors that have virtually no effect on DRL activity.
Collapse
Affiliation(s)
- Jordi Pérez-Gil
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG), Consejo Superior de Investigaciones Científicas (CSIC)-Institut de Recerca i Tecnologia Agroalimentàries (IRTA)-Universitat Autònoma de Barcelona (UAB), 08193 Barcelona, Spain
| | | | | | | | | | | |
Collapse
|
35
|
Björkelid C, Bergfors T, Unge T, Mowbray SL, Jones TA. Structural studies on Mycobacterium tuberculosis DXR in complex with the antibiotic FR-900098. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:134-43. [PMID: 22281742 DOI: 10.1107/s0907444911052231] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Accepted: 12/03/2011] [Indexed: 11/10/2022]
Abstract
A number of pathogens, including the causative agents of tuberculosis and malaria, synthesize the essential isoprenoid precursor isopentenyl diphosphate via the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway rather than the classical mevalonate pathway that is found in humans. As part of a structure-based drug-discovery program against tuberculosis, DXR, the enzyme that carries out the second step in the MEP pathway, has been investigated. This enzyme is the target for the antibiotic fosmidomycin and its active acetyl derivative FR-900098. The structure of DXR from Mycobacterium tuberculosis in complex with FR-900098, manganese and the NADPH cofactor has been solved and refined. This is a new crystal form that diffracts to a higher resolution than any other DXR complex reported to date. Comparisons with other ternary complexes show that the conformation is that of the enzyme in an active state: the active-site flap is well defined and the cofactor-binding domain has a conformation that brings the NADPH into the active site in a manner suitable for catalysis. The substrate-binding site is highly conserved in a number of pathogens that use this pathway, so any new inhibitor that is designed for the M. tuberculosis enzyme is likely to exhibit broad-spectrum activity.
Collapse
Affiliation(s)
- Christofer Björkelid
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
| | | | | | | | | |
Collapse
|
36
|
Gräwert T, Groll M, Rohdich F, Bacher A, Eisenreich W. Biochemistry of the non-mevalonate isoprenoid pathway. Cell Mol Life Sci 2011; 68:3797-814. [PMID: 21744068 PMCID: PMC11114746 DOI: 10.1007/s00018-011-0753-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Revised: 05/26/2011] [Accepted: 06/14/2011] [Indexed: 02/08/2023]
Abstract
The non-mevalonate pathway of isoprenoid (terpenoid) biosynthesis is essential in many eubacteria including the major human pathogen, Mycobacterium tuberculosis, in apicomplexan protozoa including the Plasmodium spp. causing malaria, and in the plastids of plants. The metabolic route is absent in humans and is therefore qualified as a promising target for new anti-infective drugs and herbicides. Biochemical and structural knowledge about all enzymes involved in the pathway established the basis for discovery and development of inhibitors by high-throughput screening of compound libraries and/or structure-based rational design.
Collapse
Affiliation(s)
- Tobias Gräwert
- Department Chemie, Lehrstuhl für Biochemie, Center for Integrated Protein Science München, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Michael Groll
- Department Chemie, Lehrstuhl für Biochemie, Center for Integrated Protein Science München, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | | | - Adelbert Bacher
- Department Chemie, Lehrstuhl für Biochemie, Center for Integrated Protein Science München, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Wolfgang Eisenreich
- Department Chemie, Lehrstuhl für Biochemie, Center for Integrated Protein Science München, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| |
Collapse
|
37
|
Nordqvist A, Björkelid C, Andaloussi M, Jansson AM, Mowbray SL, Karlén A, Larhed M. Synthesis of functionalized cinnamaldehyde derivatives by an oxidative Heck reaction and their use as starting materials for preparation of Mycobacterium tuberculosis 1-deoxy-D-xylulose-5-phosphate reductoisomerase inhibitors. J Org Chem 2011; 76:8986-98. [PMID: 21936546 PMCID: PMC3203620 DOI: 10.1021/jo201715x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
![]()
Cinnamaldehyde derivatives were synthesized in good to excellent yields in one step by a mild and selective, base-free palladium(II)-catalyzed oxidative Heck reaction starting from acrolein and various arylboronic acids. Prepared α,β-unsaturated aldehydes were used for synthesis of novel α-aryl substituted fosmidomycin analogues, which were evaluated for their inhibition of Mycobacterium tuberculosis 1-deoxy-d-xylulose 5-phosphate reductoisomerase. IC50 values between 0.8 and 27.3 μM were measured. The best compound showed activity comparable to that of the most potent previously reported α-aryl substituted fosmidomycin-class inhibitor.
Collapse
Affiliation(s)
- Anneli Nordqvist
- Division of Organic Pharmaceutical Chemistry, Department of Medicinal Chemistry, Uppsala University, Biomedical Center, Box 574, SE-751 23 Uppsala, Sweden
| | | | | | | | | | | | | |
Collapse
|
38
|
Behrendt CT, Kunfermann A, Illarionova V, Matheeussen A, Pein MK, Gräwert T, Kaiser J, Bacher A, Eisenreich W, Illarionov B, Fischer M, Maes L, Groll M, Kurz T. Reverse Fosmidomycin Derivatives against the Antimalarial Drug Target IspC (Dxr). J Med Chem 2011; 54:6796-802. [DOI: 10.1021/jm200694q] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Christoph T. Behrendt
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich Heine Universität, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Andrea Kunfermann
- Center for Integrated Protein Science München, Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Victoria Illarionova
- Institut für Lebensmittelchemie, Universität Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - An Matheeussen
- Laboratory for Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Groenenborgerlaan 171, 2020 Wilrijk, Belgium
| | - Miriam K. Pein
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich Heine Universität, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Tobias Gräwert
- Center for Integrated Protein Science München, Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Johannes Kaiser
- Center for Integrated Protein Science München, Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Adelbert Bacher
- Center for Integrated Protein Science München, Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Wolfgang Eisenreich
- Center for Integrated Protein Science München, Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Boris Illarionov
- Institut für Lebensmittelchemie, Universität Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Markus Fischer
- Institut für Lebensmittelchemie, Universität Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Louis Maes
- Laboratory for Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Groenenborgerlaan 171, 2020 Wilrijk, Belgium
| | - Michael Groll
- Center for Integrated Protein Science München, Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Thomas Kurz
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich Heine Universität, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| |
Collapse
|
39
|
Andaloussi M, Lindh M, Björkelid C, Suresh S, Wieckowska A, Iyer H, Karlén A, Larhed M. Substitution of the phosphonic acid and hydroxamic acid functionalities of the DXR inhibitor FR900098: An attempt to improve the activity against Mycobacterium tuberculosis. Bioorg Med Chem Lett 2011; 21:5403-7. [DOI: 10.1016/j.bmcl.2011.07.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2011] [Revised: 06/30/2011] [Accepted: 07/03/2011] [Indexed: 10/17/2022]
|
40
|
Andaloussi M, Henriksson LM, Wiȩckowska A, Lindh M, Björkelid C, Larsson AM, Suresh S, Iyer H, Srinivasa BR, Bergfors T, Unge T, Mowbray SL, Larhed M, Jones TA, Karlén A. Design, Synthesis, and X-ray Crystallographic Studies of α-Aryl Substituted Fosmidomycin Analogues as Inhibitors ofMycobacterium tuberculosis1-Deoxy-d-xylulose 5-Phosphate Reductoisomerase. J Med Chem 2011; 54:4964-76. [DOI: 10.1021/jm2000085] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
41
|
de Ruyck J, Wouters J, Poulter CD. Inhibition Studies on Enzymes Involved in Isoprenoid Biosynthesis: Focus on Two Potential Drug Targets: DXR and IDI-2 Enzymes. ACTA ACUST UNITED AC 2011; 7. [PMID: 24339799 DOI: 10.2174/157340811796575317] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Isoprenoid compounds constitute an immensely diverse group of acyclic, monocyclic and polycyclic compounds that play important roles in all living organisms. Despite the diversity of their structures, this plethora of natural products arises from only two 5-carbon precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). This review will discuss the enzymes in the mevalonate (MVA) and methylerythritol phosphate (MEP) biosynthetic pathways leading to IPP and DMAPP with a particular focus on MEP synthase (DXR) and IPP isomerase (IDI), which are potential targets for the development of antibiotic compounds. DXR is the second enzyme in the MEP pathway and the only one for which inhibitors with antimicrobial activity at pharmaceutically relevant concentrations are known. All of the published DXR inhibitors are fosmidomycin analogues, except for a few bisphosphonates with moderate inhibitory activity. These far, there are no other candidates that target DXR. IDI was first identified and characterised over 40 years ago (IDI-1) and a second convergently evolved isoform (IDI-2) was discovered in 2001. IDI-1 is a metalloprotein found in Eukarya and many species of Bacteria. Its mechanism has been extensively studied. In contrast, IDI-2 requires reduced flavin mononucleotide as a cofactor. The mechanism of action for IDI-2 is less well defined. This review will describe how lead inhibitors are being improved by structure-based drug design and enzymatic assays against DXR to lead to new drug families and how mechanistic probes are being used to address questions about the mechanisms of the isomerases.
Collapse
Affiliation(s)
- Jérôme de Ruyck
- Department of Chemistry, University of Utah, 315 South 1400 East RM 2020, Salt Lake City, UT 84112, USA
| | | | | |
Collapse
|
42
|
Umeda T, Tanaka N, Kusakabe Y, Nakanishi M, Kitade Y, Nakamura KT. Molecular basis of fosmidomycin's action on the human malaria parasite Plasmodium falciparum. Sci Rep 2011; 1:9. [PMID: 22355528 PMCID: PMC3216497 DOI: 10.1038/srep00009] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Revised: 04/05/2011] [Accepted: 04/05/2011] [Indexed: 11/30/2022] Open
Abstract
The human malaria parasite Plasmodium falciparum is responsible for the deaths of more than a million people each year. Fosmidomycin has been proven to be efficient in the treatment of P. falciparum malaria by inhibiting 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR), an enzyme of the non-mevalonate pathway, which is absent in humans. However, the structural details of DXR inhibition by fosmidomycin in P. falciparum are unknown. Here, we report the crystal structures of fosmidomycin-bound complete quaternary complexes of PfDXR. Our study revealed that (i) an intrinsic flexibility of the PfDXR molecule accounts for an induced-fit movement to accommodate the bound inhibitor in the active site and (ii) a cis arrangement of the oxygen atoms of the hydroxamate group of the bound inhibitor is essential for tight binding of the inhibitor to the active site metal. We expect the present structures to be useful guides for the design of more effective antimalarial compounds.
Collapse
Affiliation(s)
- Tomonobu Umeda
- School of Pharmacy, Showa University, Tokyo 142-8555, Japan
| | | | | | | | | | | |
Collapse
|
43
|
Behrendt CT, Kunfermann A, Illarionova V, Matheeussen A, Gräwert T, Groll M, Rohdich F, Bacher A, Eisenreich W, Fischer M, Maes L, Kurz T. Synthesis and Antiplasmodial Activity of Highly Active Reverse Analogues of the Antimalarial Drug Candidate Fosmidomycin. ChemMedChem 2010; 5:1673-6. [DOI: 10.1002/cmdc.201000276] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
44
|
Verbrugghen T, Cos P, Maes L, Van Calenbergh S. Synthesis and Evaluation of α-Halogenated Analogues of 3-(Acetylhydroxyamino)propylphosphonic Acid (FR900098) as Antimalarials. J Med Chem 2010; 53:5342-6. [DOI: 10.1021/jm100211e] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Thomas Verbrugghen
- Laboratory for Medicinal Chemistry (FFW), Ghent University, Harelbekestraat 72, B-9000 Gent, Belgium
| | - Paul Cos
- Laboratory for Microbiology, Parasitology, and Hygiene, Faculty of Pharmaceutical, Biomedical, and Veterinary Sciences, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
| | - Louis Maes
- Laboratory for Microbiology, Parasitology, and Hygiene, Faculty of Pharmaceutical, Biomedical, and Veterinary Sciences, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
| | - Serge Van Calenbergh
- Laboratory for Medicinal Chemistry (FFW), Ghent University, Harelbekestraat 72, B-9000 Gent, Belgium
| |
Collapse
|