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Kesharwani S, Eeba, Tandi M, Agarwal N, Sundriyal S. Design and synthesis of non-hydroxamate lipophilic inhibitors of 1-deoxy-d-xylulose 5-phosphate reductoisomerase (DXR): in silico, in vitro and antibacterial studies. RSC Adv 2024; 14:27530-27554. [PMID: 39221132 PMCID: PMC11362829 DOI: 10.1039/d4ra05083e] [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: 07/14/2024] [Accepted: 08/13/2024] [Indexed: 09/04/2024] Open
Abstract
1-Deoxy-d-xylulose 5-phosphate reductoisomerase (DXR) is a key enzyme of the 2-C-methyl-d-erythritol 4-phosphate (MEP) pathway operating in several pathogens, including Mycobacterium and Plasmodium. Since a DXR homologue is not present in humans, it is an important antimicrobial target. Fosmidomycin (FSM) and its analogues inhibit DXR function by chelating the divalent metal (Mn2+ or Mg2+) in its active site via a hydroxamate metal binding group (MBG). The latter, however, enhances the polarity of molecules and is known to display metabolic instability and toxicity issues. While attempts have been made to increase the lipophilicity of FSM by substituting the linker chain and prodrug approach, very few efforts have been made to replace the hydroxamate group with other lipophilic MBGs. We report a systematic in silico and experimental investigation to identify novel MBGs for designing non-hydroxamate lipophilic DXR inhibitors. The SAR studies with selected MBG fragments identified novel inhibitors of E. Coli DXR with IC50 values ranging from 0.29 to 106 μM. The promising inhibitors were also screened against ESKAPE pathogens and M. tuberculosis.
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Affiliation(s)
- Sharyu Kesharwani
- Department of Pharmacy, Birla Institute of Technology and Science-Pilani (BITS) Pilani Campus, Vidya Vihar, Pilani Rajasthan 333 031 India
| | - Eeba
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster 3rd Mile Stone, Gurugram-Faridabad Expressway Faridabad 121001 Haryana India
| | - Mukesh Tandi
- Department of Pharmacy, Birla Institute of Technology and Science-Pilani (BITS) Pilani Campus, Vidya Vihar, Pilani Rajasthan 333 031 India
| | - Nisheeth Agarwal
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster 3rd Mile Stone, Gurugram-Faridabad Expressway Faridabad 121001 Haryana India
| | - Sandeep Sundriyal
- Department of Pharmacy, Birla Institute of Technology and Science-Pilani (BITS) Pilani Campus, Vidya Vihar, Pilani Rajasthan 333 031 India
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Jamil SNH, Ali AH, Feroz SR, Lam SD, Agustar HK, Mohd Abd Razak MR, Latip J. Curcumin and Its Derivatives as Potential Antimalarial and Anti-Inflammatory Agents: A Review on Structure-Activity Relationship and Mechanism of Action. Pharmaceuticals (Basel) 2023; 16:ph16040609. [PMID: 37111366 PMCID: PMC10146798 DOI: 10.3390/ph16040609] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/31/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
Curcumin, one of the major ingredients of turmeric (Curcuma longa), has been widely reported for its diverse bioactivities, including against malaria and inflammatory-related diseases. However, curcumin's low bioavailability limits its potential as an antimalarial and anti-inflammatory agent. Therefore, research on the design and synthesis of novel curcumin derivatives is being actively pursued to improve the pharmacokinetic profile and efficacy of curcumin. This review discusses the antimalarial and anti-inflammatory activities and the structure-activity relationship (SAR), as well as the mechanisms of action of curcumin and its derivatives in malarial treatment. This review provides information on the identification of the methoxy phenyl group responsible for the antimalarial activity and the potential sites and functional groups of curcumin for structural modification to improve its antimalarial and anti-inflammatory actions, as well as potential molecular targets of curcumin derivatives in the context of malaria and inflammation.
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Affiliation(s)
- Siti Nur Hidayah Jamil
- Department of Chemical Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia
| | - Amatul Hamizah Ali
- Department of Chemical Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia
| | - Shevin Rizal Feroz
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia
| | - Su Datt Lam
- Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia
| | - Hani Kartini Agustar
- Department of Earth Sciences and Environment, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia
| | - Mohd Ridzuan Mohd Abd Razak
- Herbal Medicine Research Centre, Institute for Medical Research, National Institute of Health (NIH) Complex, Ministry of Health Malaysia, Shah Alam 40170, Selangor, Malaysia
| | - Jalifah Latip
- Department of Chemical Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia
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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.
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Tukulula M, Olasupo IA, Mugumbate GC, Lobb KA, Klein R, Sayed Y, Tshiwawa T, Kaye PT. Synthesis, stereochemistry and in vitro STD NMR and in silico HIV-1 PR enzyme-binding potential of MBH-derived inhibitors. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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5
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Mutorwa MK, Lobb KA, Klein R, Blatch GL, Kaye PT. Synthesis of 2,3-dihydroxy-3-(N-substituted carbamoyl)propylphosphonic acid derivatives as hybrid DOXP-fosmidomycin analogues. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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6
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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.
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Adeyemi CM, Conibear AC, Mutorwa MK, Nokalipa IC, Isaacs M, Mnkandhla D, Hoppe HC, Lobb KA, Klein R, Kaye PT. Synthesis and anti-parasitic activity of achiral N-benzylated phosphoramidic acid derivatives. Bioorg Chem 2020; 101:103947. [PMID: 32559578 DOI: 10.1016/j.bioorg.2020.103947] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 05/11/2020] [Accepted: 05/14/2020] [Indexed: 10/24/2022]
Abstract
Synthetic pathways have been developed to access a series of N-benzylated phosphoramidic acid derivatives as novel, achiral analogues of the established Plasmodium falciparum 1-deoxy-d-xylulose-5-phosphate reductase (PfDXR) enzyme inhibitor, FR900098. Bioassays of the targeted compounds and their synthetic precursors have revealed minimal antimalarial activity but encouraging anti-trypanosomal activity - in one case with an IC50 value of 5.4 µM against Trypanosoma brucei, the parasite responsible for Nagana (African cattle sleeping sickness). The results of relevant in silico modelling and docking studies undertaken in the design and evaluation of these compounds are discussed.
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Affiliation(s)
| | - Anne C Conibear
- Department of Chemistry, Rhodes University, Grahamstown 6140, South Africa
| | - Marius K Mutorwa
- Department of Chemistry, Rhodes University, Grahamstown 6140, South Africa
| | - Iviwe C Nokalipa
- Department of Chemistry, Rhodes University, Grahamstown 6140, South Africa
| | - Michelle Isaacs
- Centre for Chemico- and Biomedicinal Research, Rhodes University, Grahamstown 6140, South Africa
| | - Dumisani Mnkandhla
- Centre for Chemico- and Biomedicinal Research, 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
| | - Kevin A Lobb
- Department of Chemistry, 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; Centre for Chemico- and Biomedicinal Research, Rhodes University, Grahamstown 6140, South Africa
| | - Perry T Kaye
- Department of Chemistry, Rhodes University, Grahamstown 6140, South Africa; Centre for Chemico- and Biomedicinal Research, Rhodes University, Grahamstown 6140, South Africa.
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8
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Adeyemi CM, Isaacs M, Mnkandhla D, Klein R, Hoppe HC, Krause RW, Lobb KA, Kaye PT. Synthesis and anti-parasitic activity of C -benzylated ( N -arylcarbamoyl)alkylphosphonate esters. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.01.045] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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9
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Adeyemi CM, Faridoon, Isaacs M, Mnkandhla D, Hoppe HC, Krause RW, Kaye PT. Synthesis and antimalarial activity of N-benzylated (N-arylcarbamoyl)alkylphosphonic acid derivatives. Bioorg Med Chem 2016; 24:6131-6138. [DOI: 10.1016/j.bmc.2016.04.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/31/2016] [Accepted: 04/09/2016] [Indexed: 01/22/2023]
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10
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Omrani R, Efrit ML, Akacha AB. Reactivity of Phosphonothioamidates with Acid Chlorides and Primary Amines: Synthesis and Conformational Study of N-Acylated Phosphonothioamidates and Phosphonoamidines. PHOSPHORUS SULFUR 2015. [DOI: 10.1080/10426507.2015.1071372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- R. Omrani
- Laboratory of Heterocyclic and Organic Synthesis, Department of Chemistry, Faculty of Science, University El Manar, Tunis-Tunisia
| | - M. L. Efrit
- Laboratory of Heterocyclic and Organic Synthesis, Department of Chemistry, Faculty of Science, University El Manar, Tunis-Tunisia
| | - A. Ben Akacha
- Laboratory of Heterocyclic and Organic Synthesis, Department of Chemistry, Faculty of Science, University El Manar, Tunis-Tunisia
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11
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Abou-Seri SM, Eldehna WM, Ali MM, Abou El Ella DA. 1-Piperazinylphthalazines as potential VEGFR-2 inhibitors and anticancer agents: Synthesis and in vitro biological evaluation. Eur J Med Chem 2015; 107:165-79. [PMID: 26590508 DOI: 10.1016/j.ejmech.2015.10.053] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 10/28/2015] [Accepted: 10/29/2015] [Indexed: 01/07/2023]
Abstract
In our endeavor towards the development of effective VEGFR-2 inhibitors, three novel series of phthalazine derivatives based on 1-piperazinyl-4-arylphthalazine scaffold were synthesized. All the newly prepared phthalazines 16a-k, 18a-e and 21a-g were evaluated in vitro for their inhibitory activity against VEGFR-2. In particular, compounds 16k and 21d potently inhibited VEGFR-2 at sub-micromolar IC50 values 0.35 ± 0.03 and 0.40 ± 0.04 μM, respectively. Moreover, seventeen selected compounds 16c-e, 16g, 16h, 16j, 16k, 18c-e and 21a-g were evaluated for their in vitro anticancer activity according to US-NCI protocol, where compounds 16k and 21d proved to be the most potent anticancer agents. While, compound 16k exhibited potent broad spectrum anticancer activity with full panel GI50 (MG-MID) value of 3.62 μM, compound 21d showed high selectivity toward leukemia and prostate cancer subpanels [subpanel GI50 (MG-MID) 3.51 and 5.15 μM, respectively]. Molecular docking of compounds16k and 21d into VEGFR-2 active site was performed to explore their potential binding mode.
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Affiliation(s)
- Sahar M Abou-Seri
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo, P.O. Box 11562, Egypt
| | - Wagdy M Eldehna
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Egyptian Russian University, Badr City, Cairo, P.O. Box 11829, Egypt.
| | - Mamdouh M Ali
- Biochemistry Department, Division of Genetic Engineering and Biotechnology, National Research Centre, Dokki, 12622, Giza, Egypt
| | - Dalal A Abou El Ella
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ain Shams University, Cairo, Abbassia, P.O. Box 11566, Egypt.
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Rehman R, Hanif MA, Mushtaq Z, Al-Sadi AM. Biosynthesis of essential oils in aromatic plants: A review. FOOD REVIEWS INTERNATIONAL 2015. [DOI: 10.1080/87559129.2015.1057841] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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13
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Chofor R, Risseeuw MDP, Pouyez J, Johny C, Wouters J, Dowd CS, Couch RD, Van Calenbergh S. Synthetic Fosmidomycin analogues with altered chelating moieties do not inhibit 1-deoxy-d-xylulose 5-phosphate Reductoisomerase or Plasmodium falciparum growth in vitro. Molecules 2014; 19:2571-87. [PMID: 24566322 PMCID: PMC6271069 DOI: 10.3390/molecules19022571] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 02/18/2014] [Accepted: 02/19/2014] [Indexed: 11/17/2022] Open
Abstract
Fourteen new fosmidomycin analogues with altered metal chelating groups were prepared and evaluated for inhibition of E. coli Dxr, M. tuberculosis Dxr and the growth of P. falciparum K1 in human erythrocytes. None of the synthesized compounds showed activity against either enzyme or the Plasmodia. This study further underlines the importance of the hydroxamate functionality and illustrates that identifying effective alternative bidentate ligands for this target enzyme is challenging.
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Affiliation(s)
- René Chofor
- Laboratory for Medicinal Chemistry, Ghent University, Harelbekestraat 72, Ghent B-9000, Belgium.
| | - Martijn D P Risseeuw
- Laboratory for Medicinal Chemistry, Ghent University, Harelbekestraat 72, Ghent B-9000, Belgium.
| | - Jenny Pouyez
- Department of Chemistry, University of Namur, UNamur, Rue de Bruxelles 61, Namur B-5000, Belgium.
| | - Chinchu Johny
- Department of Chemistry and Biochemistry, George Mason University, Manassas, VA 20110, USA.
| | - Johan Wouters
- Department of Chemistry, University of Namur, UNamur, Rue de Bruxelles 61, Namur B-5000, Belgium.
| | - Cynthia S Dowd
- Department of Chemistry, George Washington University, Washington, DC 20052, USA.
| | - Robin D Couch
- Department of Chemistry and Biochemistry, George Mason University, Manassas, VA 20110, USA.
| | - Serge Van Calenbergh
- Laboratory for Medicinal Chemistry, Ghent University, Harelbekestraat 72, Ghent B-9000, Belgium.
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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
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15
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Bodill T, Conibear AC, Mutorwa MK, Goble JL, Blatch GL, Lobb KA, Klein R, Kaye PT. Exploring DOXP-reductoisomerase binding limits using phosphonated N-aryl and N-heteroarylcarboxamides as DXR inhibitors. Bioorg Med Chem 2013; 21:4332-41. [DOI: 10.1016/j.bmc.2013.04.076] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 04/22/2013] [Accepted: 04/23/2013] [Indexed: 10/26/2022]
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16
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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.
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Affiliation(s)
- Géraldine San Jose
- Department of Chemistry, George Washington University, Washington DC 20052, USA. ; Tel: 01 202 994 8405
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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]
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18
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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.
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Affiliation(s)
- Christofer Björkelid
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
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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.
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Affiliation(s)
- Jérôme de Ruyck
- Department of Chemistry, University of Utah, 315 South 1400 East RM 2020, Salt Lake City, UT 84112, USA
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