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Chen X, Zhao H, Wang C, Hamed M, Shang Q, Yang Y, Diao X, Sun X, Hu W, Jiang X, Zhang Y, Hirsch AKH, Wu D, Zhuang J. Two natural compounds as potential inhibitors against the Helicobacter pylori and Acinetobacter baumannii IspD enzymes. Int J Antimicrob Agents 2024; 63:107160. [PMID: 38537721 DOI: 10.1016/j.ijantimicag.2024.107160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 02/27/2024] [Accepted: 03/21/2024] [Indexed: 04/21/2024]
Abstract
In a vast majority of bacteria, protozoa and plants, the methylerythritol phosphate (MEP) pathway is utilized for the synthesis of isopentenyl diphosphate (IDP) and dimethylallyl diphosphate (DMADP), which are precursors for isoprenoids. Isoprenoids, such as cholesterol and coenzyme Q, play a variety of crucial roles in physiological activities, including cell-membrane formation, protein degradation, cell apoptosis, and transcription regulation. In contrast, humans employ the mevalonate (MVA) pathway for the production of IDP and DMADP, rendering proteins in the MEP pathway appealing targets for antimicrobial agents. This pathway consists of seven consecutive enzymatic reactions, of which 4-diphosphocytidyl-2C-methyl-D-erythritol synthase (IspD) and 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF) catalyze the third and fifth steps, respectively. In this study, we characterized the enzymatic activities and protein structures of Helicobacter pylori IspDF and Acinetobacter baumannii IspD. Then, using the direct interaction-based thermal shift assay, we conducted a compound screening of an approved drug library and identified 27 hit compounds potentially binding to AbIspD. Among them, two natural products, rosmarinic acid and tanshinone IIA sodium sulfonate, exhibited inhibitory activities against HpIspDF and AbIspD, by competing with one of the substrates, MEP. Moreover, tanshinone IIA sodium sulfonate also demonstrated certain antibacterial effects against H. pylori. In summary, we identified two IspD inhibitors from approved ingredients, broadening the scope for antibiotic discovery targeting the MEP pathway.
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Affiliation(s)
- Xiaoyu Chen
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Huilin Zhao
- Department of Pathogenic Biology, College of Basic Medicine, Binzhou Medical University, Yantai, China
| | - Chuandong Wang
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Mostafa Hamed
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI), Saarbrücken, Germany
| | - Qinghong Shang
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yating Yang
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xiaotong Diao
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xiangnan Sun
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Wei Hu
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xukai Jiang
- National Glycoengineering Research Center, Shandong University, Qingdao, China
| | - Youming Zhang
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI), Saarbrücken, Germany; Department of Pharmacy, Saarland University, Saarbrücken, Germany
| | - Dalei Wu
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.
| | - Jingjing Zhuang
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China; Marine College, Shandong University, Weihai, China.
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Simonet B, Herrscher V, Witjaksono C, Chaignon P, Massicot F, Vasse JL, Seemann M, Behr JB. Carbohydrate-Templated Syntheses of Trifluoromethyl-Substituted MEP Analogues for the Study of the Methylerythritol Phosphate Pathway. J Org Chem 2023; 88:15832-15843. [PMID: 37917513 DOI: 10.1021/acs.joc.3c01910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
Trifluoromethyl analogues of methylerythritol phosphate (MEP) and 2-C-methyl-erythritol 2,4-cyclodiphosphate (MEcPP), natural substrates of key enzymes from the MEP pathway, were prepared starting from d-glucose as the chiral template to secure absolute configurations. The obligate trifluoromethyl group was inserted with complete diastereoselectivity using the Ruppert-Prakash nucleophile. Target compounds were assayed against the corresponding enzymes showing that trifluoro-MEP did not disrupt IspD activity, whereas trifluoro-MEcPP induced 40% inhibition of IspG at 1 mM.
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Affiliation(s)
- Basile Simonet
- Institut de Chimie moléculaire de Reims, CNRS UMR 7312, Université de Reims Champagne-Ardenne, 51687 Reims, Cedex 2, France
| | - Vivien Herrscher
- Institut de Chimie moléculaire de Reims, CNRS UMR 7312, Université de Reims Champagne-Ardenne, 51687 Reims, Cedex 2, France
| | - Clea Witjaksono
- Equipe Chimie Biologique et Applications Thérapeutiques, Institut de Chimie de Strasbourg UMR 7177, Université de Strasbourg/CNRS, 4, Rue Blaise Pascal, 67070 Strasbourg, France
| | - Philippe Chaignon
- Equipe Chimie Biologique et Applications Thérapeutiques, Institut de Chimie de Strasbourg UMR 7177, Université de Strasbourg/CNRS, 4, Rue Blaise Pascal, 67070 Strasbourg, France
| | - Fabien Massicot
- Institut de Chimie moléculaire de Reims, CNRS UMR 7312, Université de Reims Champagne-Ardenne, 51687 Reims, Cedex 2, France
| | - Jean-Luc Vasse
- Institut de Chimie moléculaire de Reims, CNRS UMR 7312, Université de Reims Champagne-Ardenne, 51687 Reims, Cedex 2, France
| | - Myriam Seemann
- Equipe Chimie Biologique et Applications Thérapeutiques, Institut de Chimie de Strasbourg UMR 7177, Université de Strasbourg/CNRS, 4, Rue Blaise Pascal, 67070 Strasbourg, France
| | - Jean-Bernard Behr
- Institut de Chimie moléculaire de Reims, CNRS UMR 7312, Université de Reims Champagne-Ardenne, 51687 Reims, Cedex 2, France
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Bilska-Markowska M, Kaźmierczak M. Horner-Wadsworth-Emmons reaction as an excellent tool in the synthesis of fluoro-containing biologically important compounds. Org Biomol Chem 2023; 21:1095-1120. [PMID: 36632995 DOI: 10.1039/d2ob01969h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Selective introduction of a double bond motif into a multifunctional organic compound is always a big challenge. The Horner-Wadsworth-Emmons reaction is one of the most reliable, simple, and stereoselective olefination methods, widely used in organic chemistry. To the best of our knowledge, no review article on the application of HWE reaction in the synthesis of fluoroorganic compounds with direct biological interest has been published in recent years. The importance of the HWE reaction should be emphasised due to its simplicity and stereoselectivity. Under mild conditions and in one step, valuable compounds can be obtained. The HWE reaction is primarily a great tool in the synthesis of fluoroolefins that are, among others, peptide bond mimetics. Therefore, it can serve as an indispensable approach to access peptide bioisosteres and, consequently, analogues of numerous enzyme inhibitors. The protocol may be utilized to obtain florinated vinylphosphonate, vinylsulfone or sulfonate derivatives, which exhibit biological activity. In this review article, we would like to summarize the HWE reaction output of the last 12 years (since 2010).
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Affiliation(s)
- Monika Bilska-Markowska
- Faculty of Chemistry, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 8, 61-614 Poznań, Poland.
| | - Marcin Kaźmierczak
- Faculty of Chemistry, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 8, 61-614 Poznań, Poland. .,Centre for Advanced Technologies, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 10, 61-614 Poznań, Poland
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The Multifaceted MEP Pathway: Towards New Therapeutic Perspectives. Molecules 2023; 28:molecules28031403. [PMID: 36771066 PMCID: PMC9919496 DOI: 10.3390/molecules28031403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 01/27/2023] [Accepted: 01/28/2023] [Indexed: 02/05/2023] Open
Abstract
Isoprenoids, a diverse class of natural products, are present in all living organisms. Their two universal building blocks are synthesized via two independent pathways: the mevalonate pathway and the 2-C-methyl-ᴅ-erythritol 4-phosphate (MEP) pathway. The presence of the latter in pathogenic bacteria and its absence in humans make all its enzymes suitable targets for the development of novel antibacterial drugs. (E)-4-Hydroxy-3-methyl-but-2-enyl diphosphate (HMBPP), the last intermediate of this pathway, is a natural ligand for the human Vγ9Vδ2 T cells and the most potent natural phosphoantigen known to date. Moreover, 5-hydroxypentane-2,3-dione, a metabolite produced by Escherichia coli 1-deoxy-ᴅ-xylulose 5-phosphate synthase (DXS), the first enzyme of the MEP pathway, structurally resembles (S)-4,5-dihydroxy-2,3-pentanedione, a signal molecule implied in bacterial cell communication. In this review, we shed light on the diversity of potential uses of the MEP pathway in antibacterial therapies, starting with an overview of the antibacterials developed for each of its enzymes. Then, we provide insight into HMBPP, its synthetic analogs, and their prodrugs. Finally, we discuss the potential contribution of the MEP pathway to quorum sensing mechanisms. The MEP pathway, providing simultaneously antibacterial drug targets and potent immunostimulants, coupled with its potential role in bacterial cell-cell communication, opens new therapeutic perspectives.
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Elahi R, Prigge ST. New insights into apicoplast metabolism in blood-stage malaria parasites. Curr Opin Microbiol 2023; 71:102255. [PMID: 36563485 PMCID: PMC9852000 DOI: 10.1016/j.mib.2022.102255] [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: 10/03/2022] [Revised: 11/21/2022] [Accepted: 11/23/2022] [Indexed: 12/24/2022]
Abstract
The apicoplast of Plasmodium falciparum is the only source of essential isoprenoid precursors and Coenzyme A (CoA) in the parasite. Isoprenoid precursor synthesis relies on the iron-sulfur cluster (FeS) cofactors produced within the apicoplast, rendering FeS synthesis an essential function of this organelle. Recent reports provide important insights into the roles of FeS cofactors and the use of isoprenoid precursors and CoA both inside and outside the apicoplast. Here, we review the recent insights into the roles of these metabolites in blood-stage malaria parasites and discuss new questions that have been raised in light of these discoveries.
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Affiliation(s)
- Rubayet Elahi
- Department of Molecular Microbiology and Immunology, Johns Hopkins University, Baltimore, MD, USA; The Johns Hopkins Malaria Research Institute, Baltimore, MD, USA
| | - Sean T Prigge
- Department of Molecular Microbiology and Immunology, Johns Hopkins University, Baltimore, MD, USA; The Johns Hopkins Malaria Research Institute, Baltimore, MD, USA.
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6
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Allylic substitution reactions with fluorinated nucleophiles. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2022.214455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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7
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Rajasekhar S, Das S, Balamurali MM, Chanda K. Therapeutic Inhibitory Activities of
N
‐Hydroxy Derived Cytidines: A Patent Overview. ChemistrySelect 2021. [DOI: 10.1002/slct.202102856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Sreerama Rajasekhar
- Department of Chemistry School of Advanced Sciences Vellore Institute of Technology Vellore 632014 India
| | - Soumyadip Das
- Department of Chemistry School of Advanced Sciences Vellore Institute of Technology Vellore 632014 India
| | - M. M. Balamurali
- Division of Chemistry School of Advanced Sciences Vellore Institute of Technology, Chennai campus Vandalur-Kelambakkam Road Chennai 600 127 Tamil Nadu India
| | - Kaushik Chanda
- Department of Chemistry School of Advanced Sciences Vellore Institute of Technology Vellore 632014 India
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8
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Shevchuk M, Wang Q, Pajkert R, Xu J, Mei H, Röschenthaler G, Han J. Recent Advances in Synthesis of Difluoromethylene Phosphonates for Biological Applications. Adv Synth Catal 2021. [DOI: 10.1002/adsc.202001464] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Michael Shevchuk
- Department of Life Sciences and Chemistry Jacobs University Bremen gGmbH Campus Ring 1 28759 Bremen Germany
| | - Qian Wang
- Jiangsu Co–Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering Nanjing Forestry University Nanjing 210037 People's Republic of China
| | - Romana Pajkert
- Department of Life Sciences and Chemistry Jacobs University Bremen gGmbH Campus Ring 1 28759 Bremen Germany
| | - Jingcheng Xu
- Jiangsu Co–Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering Nanjing Forestry University Nanjing 210037 People's Republic of China
| | - Haibo Mei
- Jiangsu Co–Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering Nanjing Forestry University Nanjing 210037 People's Republic of China
| | - Gerd‐Volker Röschenthaler
- Department of Life Sciences and Chemistry Jacobs University Bremen gGmbH Campus Ring 1 28759 Bremen Germany
| | - Jianlin Han
- Jiangsu Co–Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering Nanjing Forestry University Nanjing 210037 People's Republic of China
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Panigrahi K, Fei X, Kitamura M, Berkowitz DB. Rapid Entry into Biologically Relevant α,α-Difluoroalkylphosphonates Bearing Allyl Protection-Deblocking under Ru(II)/(IV)-Catalysis. Org Lett 2019; 21:9846-9851. [PMID: 31789041 DOI: 10.1021/acs.orglett.9b03707] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A convenient synthetic route to α,α-difluoroalkylphosphonates is described. Structurally diverse aldehydes are condensed with LiF2CP(O)(OCH2CH═CH2)2. The resultant alcohols are captured as the pentafluorophenyl thionocarbonates and efficiently deoxygenated with HSnBu3, BEt3, and O2, and then smoothly deblocked with CpRu(IV)(π-allyl)quinoline-2-carboxylate (1-2 mol %) in methanol as an allyl cation scavenger. These mild deprotection conditions provide access to free α,α-difluoroalkylphosphonates in nearly quantitative yield. This methodology is used to rapidly construct new bis-α,α-difluoroalkyl phosphonate inhibitors of PTPIB (protein phosphotyrosine phosphatase-1B).
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Affiliation(s)
- Kaushik Panigrahi
- Department of Chemistry , University of Nebraska , Lincoln , Nebraska 68588-0304 , United States
| | - Xiang Fei
- Department of Chemistry , University of Nebraska , Lincoln , Nebraska 68588-0304 , United States
| | - Masato Kitamura
- Graduate School of Pharmaceutical Sciences , Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8602 , Japan
| | - David B Berkowitz
- Department of Chemistry , University of Nebraska , Lincoln , Nebraska 68588-0304 , United States
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10
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The Photoinduced Metal-Free Hydrotrifluoromethylation of Vinyl Phosphonates or Phosphine Oxides. European J Org Chem 2019. [DOI: 10.1002/ejoc.201901366] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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11
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Synthesis and Kinetic evaluation of an azido analogue of methylerythritol phosphate: a Novel Inhibitor of E. coli YgbP/IspD. Sci Rep 2018; 8:17892. [PMID: 30559447 PMCID: PMC6297244 DOI: 10.1038/s41598-018-35586-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 11/05/2018] [Indexed: 12/04/2022] Open
Abstract
As multidrug resistant pathogenic microorganisms are a serious health menace, it is crucial to continuously develop novel medicines in order to overcome the emerging resistance. The methylerythritol phosphate pathway (MEP) is an ideal target for antimicrobial development as it is absent in humans but present in most bacteria and in the parasite Plasmodium falciparum. Here, we report the synthesis and the steady-state kinetics of a novel potent inhibitor (MEPN3) of Escherichia coli YgbP/IspD, the third enzyme of the MEP pathway. MEPN3 inhibits E. coli YgbP/IspD in mixed type mode regarding both substrates. Interestingly, MEPN3 shows the highest inhibitory activity when compared to known inhibitors of E. coli YgbP/IspD. The mechanism of this enzyme was also studied by steady-state kinetic analysis and it was found that the substrates add to the enzyme in sequential manner.
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12
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Chellapandi P, Prathiviraj R, Prisilla A. Molecular evolution and functional divergence of IspD homologs in malarial parasites. INFECTION GENETICS AND EVOLUTION 2018; 65:340-349. [DOI: 10.1016/j.meegid.2018.08.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 08/10/2018] [Accepted: 08/14/2018] [Indexed: 01/19/2023]
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