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Astle S, Guggiari S, Frost JR, Hepburn HB, Klauber DJ, Christensen KE, Burton JW. Enantioselective Synthesis of Sealutomicin C. J Am Chem Soc 2024; 146:17757-17764. [PMID: 38885121 PMCID: PMC11228992 DOI: 10.1021/jacs.4c02969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 05/03/2024] [Accepted: 05/07/2024] [Indexed: 06/20/2024]
Abstract
The sealutomicins are a family of anthraquinone antibiotics featuring an enediyne (sealutomicin A) or Bergman-cyclized aromatic ring (sealutomicins B-D). Herein we report the development of an enantioselective organocatalytic method for the synthesis of dihydroquinolines and the use of the developed method in the total synthesis of sealutomicin C which features a transannular cyclization of an aryllithium onto a γ-lactone as a second key step.
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Affiliation(s)
- Stuart
M. Astle
- Chemistry
Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Sean Guggiari
- Chemistry
Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - James R. Frost
- UCB
Pharma, 216 Bath Road, Slough, Berkshire SL1 3WE, U.K.
| | - Hamish B. Hepburn
- Vertex
Pharmaceuticals, 86-88
Jubilee Avenue Milton Park, Abingdon OX14 4RW, U.K.
| | - David J. Klauber
- Chemical
Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield SK10 2NA, U.K.
| | - Kirsten E. Christensen
- Chemistry
Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Jonathan W. Burton
- Chemistry
Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
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2
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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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3
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Huang S, Xue Y, Ma Y, Zhou C. Microbial (E)-4-hydroxy-3-methylbut-2-enyl pyrophosphate reductase (IspH) and its biotechnological potential: A mini review. Front Bioeng Biotechnol 2022; 10:1057938. [DOI: 10.3389/fbioe.2022.1057938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/10/2022] [Indexed: 11/30/2022] Open
Abstract
(E)-4-hydroxy-3-methylbut-2-enyl pyrophosphate (HMBPP) reductase (IspH) is a [4Fe-4S] cluster-containing enzyme, involved in isoprenoid biosynthesis as the final enzyme of the methylerythritol phosphate (MEP) pathway found in many bacteria and malaria parasites. In recent years, many studies have revealed that isoprenoid compounds are an alternative to petroleum-derived fuels. Thus, ecofriendly methods harnessing the methylerythritol phosphate pathway in microbes to synthesize isoprenoid compounds and IspH itself have received notable attention from researchers. In addition to its applications in the field of biosynthesis, IspH is considered to be an attractive drug target for infectious diseases such as malaria and tuberculosis due to its survivability in most pathogenic bacterium and its absence in humans. In this mini-review, we summarize previous reports that have systematically illuminated the fundamental and structural properties, substrate binding and catalysis, proposed catalytic mechanism, and novel catalytic activities of IspH. Potential bioengineering and biotechnological applications of IspH are also discussed.
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4
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Herrscher V, Witjaksono C, Buchotte M, Ferret C, Massicot F, Vasse J, Borel F, Behr J, Seemann M. Irreversible Inhibition of IspG, a Target for the Development of New Antimicrobials, by a 2‐Vinyl Analogue of its MEcPP Substrate. Chemistry 2022; 28:e202200241. [DOI: 10.1002/chem.202200241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Vivien Herrscher
- Univ. Reims Champagne-Ardenne ICMR, CNRS UMR 7312 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
| | - Marie Buchotte
- Univ. Reims Champagne-Ardenne ICMR, CNRS UMR 7312 51687 Reims Cedex 2 France
| | - Claire Ferret
- 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
- Univ. Reims Champagne-Ardenne ICMR, CNRS UMR 7312 51687 Reims Cedex 2 France
| | - Jean‐Luc Vasse
- Univ. Reims Champagne-Ardenne ICMR, CNRS UMR 7312 51687 Reims Cedex 2 France
| | - Franck Borel
- Univ. Grenoble Alpes, CEA, CNRS, IBS 38000 Grenoble France
| | - Jean‐Bernard Behr
- Univ. Reims Champagne-Ardenne ICMR, CNRS UMR 7312 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
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5
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Jobelius H, Bianchino GI, Borel F, Chaignon P, Seemann M. The Reductive Dehydroxylation Catalyzed by IspH, a Source of Inspiration for the Development of Novel Anti-Infectives. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27030708. [PMID: 35163971 PMCID: PMC8837944 DOI: 10.3390/molecules27030708] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 01/11/2022] [Accepted: 01/18/2022] [Indexed: 11/16/2022]
Abstract
The non-mevalonate or also called MEP pathway is an essential route for the biosynthesis of isoprenoid precursors in most bacteria and in microorganisms belonging to the Apicomplexa phylum, such as the parasite responsible for malaria. The absence of this pathway in mammalians makes it an interesting target for the discovery of novel anti-infectives. As last enzyme of this pathway, IspH is an oxygen sensitive [4Fe-4S] metalloenzyme that catalyzes 2H+/2e− reductions and a water elimination by involving non-conventional bioinorganic and bioorganometallic intermediates. After a detailed description of the discovery of the [4Fe-4S] cluster of IspH, this review focuses on the IspH mechanism discussing the results that have been obtained in the last decades using an approach combining chemistry, enzymology, crystallography, spectroscopies, and docking calculations. Considering the interesting druggability of this enzyme, a section about the inhibitors of IspH discovered up to now is reported as well. The presented results constitute a useful and rational help to inaugurate the design and development of new potential chemotherapeutics against pathogenic organisms.
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Affiliation(s)
- Hannah Jobelius
- Equipe Chimie Biologique et Applications Thérapeutiques, Institut de Chimie de Strasbourg UMR 7177, Université de Strasbourg/CNRS, 4, rue Blaise Pascal, 67070 Strasbourg, France; (H.J.); (G.I.B.); (P.C.)
| | - Gabriella Ines Bianchino
- Equipe Chimie Biologique et Applications Thérapeutiques, Institut de Chimie de Strasbourg UMR 7177, Université de Strasbourg/CNRS, 4, rue Blaise Pascal, 67070 Strasbourg, France; (H.J.); (G.I.B.); (P.C.)
| | - Franck Borel
- Institut de Biologie Structurale, Université Grenoble Alpes/CEA/CNRS, 38000 Grenoble, 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; (H.J.); (G.I.B.); (P.C.)
| | - 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; (H.J.); (G.I.B.); (P.C.)
- Correspondence:
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6
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7
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Khan HPA, Chakraborty TK. Application of Cp 2TiCl-Promoted Radical-Induced Cyclization: An Expeditious Access to [ a]-Annelated Indoles. J Org Chem 2020; 85:8000-8012. [PMID: 32469214 DOI: 10.1021/acs.joc.0c00817] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
An efficient and novel route for assembling pyrrolo/piperido[1,2-a]indoles is portrayed involving a radical-mediated reductive epoxide opening reaction of N-tethered epoxy-indoles that trigger facile intramolecular cyclization followed by an oxidative quenching step. Capitalizing on the operational simplicity of the method involving just two steps and use of an efficient C-C bond-forming reaction, this radical-based protocol enables the modular assembly of an important class of N-fused indole derivatives with versatile functional and structural diversity.
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Affiliation(s)
- Hina P A Khan
- Department of Organic Chemistry, Indian Institute of Science, Bengaluru 560012, India
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8
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Chaignon P, Petit BE, Vincent B, Allouche L, Seemann M. Methylerythritol Phosphate Pathway: Enzymatic Evidence for a Rotation in the LytB/IspH-Catalyzed Reaction. Chemistry 2020; 26:1032-1036. [PMID: 31756006 DOI: 10.1002/chem.201904676] [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: 10/11/2019] [Indexed: 11/10/2022]
Abstract
IspH/LytB, an oxygen-sensitive [4Fe-4S] enzyme, catalyzes the last step of the methylerythritol phosphate (MEP) pathway, a target for the development of new antimicrobial agents. This metalloenzyme converts (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate (HMBPP) into the two isoprenoid precursors: isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Here, the synthesis of (S)-[4-2 H1 ]HMBPP and (R)-[4-2 H1 ]HMBPP is reported together with a detailed NMR analysis of the products formed after their respective incubation with E. coli IspH/LytB in the presence of the biological reduction system used by E. coli to reduce the [4Fe-4S] center. (S)-[4-2 H1 ]HMBPP was converted into [4-2 H1 ]DMAPP and (E)-[4-2 H1 ]IPP, whereas (R)-[4-2 H1 ]HMBPP yielded [4-2 H1 ]DMAPP and (Z)-[4-2 H1 ]IPP, hence providing the direct enzymatic evidence that the mechanism catalyzed by IspH/LytB involves a rotation of the CH2 OH group of the substrate to display it away from the [4Fe-4S].
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Affiliation(s)
- Philippe Chaignon
- Equipe Chimie Biologique et Applications Thérapeutiques, Institut de Chimie UMR 7177, Université de Strasbourg, CNRS, 4, rue Blaise Pascal, 67070, Strasbourg, France
| | - Benoît Eric Petit
- Equipe Chimie Biologique et Applications Thérapeutiques, Institut de Chimie UMR 7177, Université de Strasbourg, CNRS, 4, rue Blaise Pascal, 67070, Strasbourg, France
| | - Bruno Vincent
- Service de R.M.N., Fédération de Chimie Le Bel FR2010, Université de Strasbourg, CNRS, 1, rue Blaise Pascal, 67008, Strasbourg, France
| | - Lionel Allouche
- Service de R.M.N., Fédération de Chimie Le Bel FR2010, Université de Strasbourg, CNRS, 1, rue Blaise Pascal, 67008, Strasbourg, France
| | - Myriam Seemann
- Equipe Chimie Biologique et Applications Thérapeutiques, Institut de Chimie UMR 7177, Université de Strasbourg, CNRS, 4, rue Blaise Pascal, 67070, Strasbourg, France
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9
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Lentini NA, Hsiao CHC, Crull GB, Wiemer AJ, Wiemer DF. Synthesis and Bioactivity of the Alanyl Phosphonamidate Stereoisomers Derived from a Butyrophilin Ligand. ACS Med Chem Lett 2019; 10:1284-1289. [PMID: 31531198 DOI: 10.1021/acsmedchemlett.9b00153] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 08/06/2019] [Indexed: 02/07/2023] Open
Abstract
Aryloxy phosphonamidate derivatives of a butyrophilin 3A1 ligand are stimulants of Vγ9 Vδ2 T cells. However, when bonded to an aryl ester and an amine, the phosphorus is stereogenic, and past compounds were studied as racemates. To determine the impact of stereochemistry on the activity, we now have prepared phosphonate derivatives of l- and d-alanine ethyl ester, separated the diastereomers, and evaluated their biological activity as single stereoisomers. The results demonstrate that phosphonamidates substituted with l-alanine stimulate Vγ9 Vδ2 T cells at lower concentrations than the racemic glycine counterpart, while those derived from d-alanine require higher concentrations. All four diastereomers are more active than charged phosphoantigens such as HMBPP. Surprisingly, only a 2-fold difference was observed between the l-alanine phosphorus isomers, with the R P isomer more potent. This suggests that the small phosphoantigen scaffold reduces but does not eliminate dependence upon phosphorus stereochemistry for cellular activity.
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Affiliation(s)
- Nicholas A. Lentini
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242-1294, United States
| | - Chia-Hung Christine Hsiao
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269-3092, United States
| | - George B. Crull
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242-1294, United States
| | - Andrew J. Wiemer
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269-3092, United States
- Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut 06269-3092, United States
| | - David F. Wiemer
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242-1294, United States
- Department of Pharmacology, University of Iowa, Iowa City, Iowa 52242-1109, United States
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10
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Hanuš J, Nisler J, Strnad M. A Novel Method for Synthesis of cis-Zeatin and Its Valuable Precursor (Z)-4-Chloro-2-methyl-but-2-en-1-ol. ORG PREP PROCED INT 2019. [DOI: 10.1080/00304948.2019.1609817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Jan Hanuš
- Isotope Laboratory, Institute of Experimental Botany, Academy of Sciences of the Czech Republic (AS CR), Vídeňská 1083, 142 20 Prague 4, Czech Republic
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Medicinal Research, Institute of Experimental Botany AS CR & Palacky University, Slechtitelu 11, Olomouc 783 71, Czech Republic
| | - Jaroslav Nisler
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Medicinal Research, Institute of Experimental Botany AS CR & Palacky University, Slechtitelu 11, Olomouc 783 71, Czech Republic
| | - Miroslav Strnad
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Medicinal Research, Institute of Experimental Botany AS CR & Palacky University, Slechtitelu 11, Olomouc 783 71, Czech Republic
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11
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Bhuyan R, Seal A. Exploration and validation of diphosphate-based Plasmodium
LytB inhibitors using computational approaches. J Mol Recognit 2018; 32:e2762. [PMID: 30191613 DOI: 10.1002/jmr.2762] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 07/27/2018] [Accepted: 07/30/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Rajabrata Bhuyan
- BIF Centre, Department of Biochemistry & Biophysics; University of Kalyani; Kalyani West Bengal India
| | - Alpana Seal
- BIF Centre, Department of Biochemistry & Biophysics; University of Kalyani; Kalyani West Bengal India
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12
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Borel F, Barbier E, Krasutsky S, Janthawornpong K, Chaignon P, Poulter CD, Ferrer JL, Seemann M. Further Insight into Crystal Structures of Escherichia coli IspH/LytB in Complex with Two Potent Inhibitors of the MEP Pathway: A Starting Point for Rational Design of New Antimicrobials. Chembiochem 2017; 18:2137-2144. [PMID: 28862365 DOI: 10.1002/cbic.201700363] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Indexed: 01/12/2023]
Abstract
IspH, also called LytB, a protein involved in the biosynthesis of isoprenoids through the methylerythritol phosphate pathway, is an attractive target for the development of new antimicrobial drugs. Here, we report crystal structures of Escherichia coli IspH in complex with the two most potent inhibitors: (E)-4-mercapto-3-methylbut-2-en-1-yl diphosphate (TMBPP) and (E)-4-amino-3-methylbut-2-en-1-yl diphosphate (AMBPP) at 1.95 and 1.7 Å resolution, respectively. The structure of the E. coli IspH:TMBPP complex exhibited two conformers of the inhibitor. This unexpected feature was exploited to design and evolve new antimicrobial candidates in silico.
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Affiliation(s)
- Franck Borel
- Institut de Biologie Structurale IBS, Université Grenoble Alpes, CEA, CNRS, 38044, Grenoble, France
| | - Elodie Barbier
- Institut de Biologie Structurale IBS, Université Grenoble Alpes, CEA, CNRS, 38044, Grenoble, France
| | - Sergiy Krasutsky
- Department of Chemistry, University of Utah, 315 South 1400 East RM 2020, Salt Lake City, UT, 84112, USA
| | - Karnjapan Janthawornpong
- Université de Strasbourg, CNRS, Institut de Chimie UMR 7177, Chim Biol&Appl Therap, 4, rue Blaise Pascal, 67070, Strasbourg, France
| | - Philippe Chaignon
- Université de Strasbourg, CNRS, Institut de Chimie UMR 7177, Chim Biol&Appl Therap, 4, rue Blaise Pascal, 67070, Strasbourg, France
| | - C Dale Poulter
- Department of Chemistry, University of Utah, 315 South 1400 East RM 2020, Salt Lake City, UT, 84112, USA
| | - Jean-Luc Ferrer
- Institut de Biologie Structurale IBS, Université Grenoble Alpes, CEA, CNRS, 38044, Grenoble, France
| | - Myriam Seemann
- Université de Strasbourg, CNRS, Institut de Chimie UMR 7177, Chim Biol&Appl Therap, 4, rue Blaise Pascal, 67070, Strasbourg, France
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13
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Foust BJ, Poe MM, Lentini NA, Hsiao CHC, Wiemer AJ, Wiemer DF. Mixed Aryl Phosphonate Prodrugs of a Butyrophilin Ligand. ACS Med Chem Lett 2017; 8:914-918. [PMID: 28947936 DOI: 10.1021/acsmedchemlett.7b00245] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 08/09/2017] [Indexed: 02/08/2023] Open
Abstract
Studies of aryl phosphonate derivatives of a butyrophilin 3A1 ligand have resulted in identification of a potent stimulant of Vγ9 Vδ2 T cells. This compound, a mixed ester bearing one pivaloyloxymethyl substituent and one 1-naphthyl ester displayed an EC50 of 0.79 nM as a stimulant of T cell proliferation, and a 9.0 nM EC50 in an assay designed to measure interferon gamma production. In both assays, this is the most potent butyrophilin ligand prodrug yet reported, and thus it should be a valuable tool for studies of T cell function. Furthermore, mixed aryl/acyloxyalkyl esters may represent a new class of phosphonate prodrugs with high efficacy.
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Affiliation(s)
- Benjamin J. Foust
- Department
of Chemistry, University of Iowa, Iowa City, Iowa 52242-1294, United States
| | - Michael M. Poe
- Department
of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269-3092 United States
| | - Nicholas A. Lentini
- Department
of Chemistry, University of Iowa, Iowa City, Iowa 52242-1294, United States
| | - Chia-Hung Christine Hsiao
- Department
of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269-3092 United States
| | - Andrew J. Wiemer
- Department
of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269-3092 United States
- Institute
for Systems Genomics, University of Connecticut, Storrs, Connecticut 06269-3092, United States
| | - David F. Wiemer
- Department
of Chemistry, University of Iowa, Iowa City, Iowa 52242-1294, United States
- Department
of Pharmacology, University of Iowa, Iowa City, Iowa 52242-1109, United States
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14
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O'Dowd B, Williams S, Wang H, No JH, Rao G, Wang W, McCammon JA, Cramer SP, Oldfield E. Spectroscopic and Computational Investigations of Ligand Binding to IspH: Discovery of Non-diphosphate Inhibitors. Chembiochem 2017; 18:914-920. [PMID: 28253432 PMCID: PMC5445010 DOI: 10.1002/cbic.201700052] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Indexed: 11/11/2022]
Abstract
Isoprenoid biosynthesis is an important area for anti-infective drug development. One isoprenoid target is (E)-1-hydroxy-2-methyl-but-2-enyl 4-diphosphate (HMBPP) reductase (IspH), which forms isopentenyl diphosphate and dimethylallyl diphosphate from HMBPP in a 2H+ /2e- reduction. IspH contains a 4 Fe-4 S cluster, and in this work, we first investigated how small molecules bound to the cluster by using HYSCORE and NRVS spectroscopies. The results of these, as well as other structural and spectroscopic investigations, led to the conclusion that, in most cases, ligands bound to IspH 4 Fe-4 S clusters by η1 coordination, forming tetrahedral geometries at the unique fourth Fe, ligand side chains preventing further ligand (e.g., H2 O, O2 ) binding. Based on these ideas, we used in silico methods to find drug-like inhibitors that might occupy the HMBPP substrate binding pocket and bind to Fe, leading to the discovery of a barbituric acid analogue with a Ki value of ≈500 nm against Pseudomonas aeruginosa IspH.
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Affiliation(s)
- Bing O'Dowd
- Department of Chemistry, University of Illinois, 600 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Sarah Williams
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA, 92093, USA
| | - Hongxin Wang
- Department of Chemistry, University of California, 1 Shields Avenue, Davis, CA, 95616, USA
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Joo Hwan No
- Center for Biophysics and Computational Biology, 607 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Guodong Rao
- Department of Chemistry, University of Illinois, 600 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Weixue Wang
- Center for Biophysics and Computational Biology, 607 South Mathews Avenue, Urbana, IL, 61801, USA
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA, 92093, USA
- Howard Hughes Medical Institute, University of California at San Diego, La Jolla, CA, 92093, USA
- National Biomedical Computation Resource, University of California at San Diego, La Jolla, CA, 92093, USA
| | - Stephen P Cramer
- Department of Chemistry, University of California, 1 Shields Avenue, Davis, CA, 95616, USA
- Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Eric Oldfield
- Department of Chemistry, University of Illinois, 600 South Mathews Avenue, Urbana, IL, 61801, USA
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15
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Affiliation(s)
- Annika Frank
- Center for Integrated Protein
Science Munich (CIPSM) at the Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Michael Groll
- Center for Integrated Protein
Science Munich (CIPSM) at the Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany
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16
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Ferreri C, Golding BT, Jahn U, Ravanat JL. COST Action CM1201 "Biomimetic Radical Chemistry": free radical chemistry successfully meets many disciplines. Free Radic Res 2016; 50:S112-S128. [PMID: 27750460 DOI: 10.1080/10715762.2016.1248961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The COST Action CM1201 "Biomimetic Radical Chemistry" has been active since December 2012 for 4 years, developing research topics organized into four working groups: WG1 - Radical Enzymes, WG2 - Models of DNA damage and consequences, WG3 - Membrane stress, signalling and defenses, and WG4 - Bio-inspired synthetic strategies. International collaborations have been established among the participating 80 research groups with brilliant interdisciplinary achievements. Free radical research with a biomimetic approach has been realized in the COST Action and are summarized in this overview by the four WG leaders.
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Affiliation(s)
- Carla Ferreri
- a ISOF, Consiglio Nazionale delle Ricerche, BioFreeRadicals Group , Bologna , Italy
| | - Bernard T Golding
- b School of Chemistry, Bedson Building, Newcastle University , Newcastle-upon-Tyne , UK
| | - Ullrich Jahn
- c Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Prague , Czech Republic
| | - Jean-Luc Ravanat
- d INAC-SCIB & CEA, INAC-SyMMES Laboratoire des Lésions des Acides Nucléiques , Université Grenoble Alpes , Grenoble , France
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17
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Saggu GS, Pala ZR, Garg S, Saxena V. New Insight into Isoprenoids Biosynthesis Process and Future Prospects for Drug Designing in Plasmodium. Front Microbiol 2016; 7:1421. [PMID: 27679614 PMCID: PMC5020098 DOI: 10.3389/fmicb.2016.01421] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 08/26/2016] [Indexed: 12/20/2022] Open
Abstract
The MEP (Methyl Erythritol Phosphate) isoprenoids biosynthesis pathway is an attractive drug target to combat malaria, due to its uniqueness and indispensability for the parasite. It is functional in the apicoplast of Plasmodium and its products get transported to the cytoplasm, where they participate in glycoprotein synthesis, electron transport chain, tRNA modification and several other biological processes. Several compounds have been tested against the enzymes involved in this pathway and amongst them Fosmidomycin, targeted against IspC (DXP reductoisomerase) enzyme and MMV008138 targeted against IspD enzyme have shown good anti-malarial activity in parasite cultures. Fosmidomycin is now-a-days prescribed clinically, however, less absorption, shorter half-life, and toxicity at higher doses, limits its use as an anti-malarial. The potential of other enzymes of the pathway as candidate drug targets has also been determined. This review details the various drug molecules tested against these targets with special emphasis to Plasmodium. We corroborate that MEP pathway functional within the apicoplast of Plasmodium is a major drug target, especially during erythrocytic stages. However, the major bottlenecks, bioavailability and toxicity of the new molecules needs to be addressed, before considering any new molecule as a potent antimalarial.
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Affiliation(s)
- Gagandeep S Saggu
- Molecular Parasitology and Systems Biology Laboratory, Department of Biological Sciences, Birla Institute of Technology and Science Pilani, India
| | - Zarna R Pala
- Molecular Parasitology and Systems Biology Laboratory, Department of Biological Sciences, Birla Institute of Technology and Science Pilani, India
| | - Shilpi Garg
- Molecular Parasitology and Systems Biology Laboratory, Department of Biological Sciences, Birla Institute of Technology and Science Pilani, India
| | - Vishal Saxena
- Molecular Parasitology and Systems Biology Laboratory, Department of Biological Sciences, Birla Institute of Technology and Science Pilani, India
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18
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Abstract
IspH, (E)-1-hydroxy-2-methyl-but-2-enyl 4-diphosphate reductase, is an essential enzyme in isoprenoid biosynthesis and an important drug/herbicide target. Using X-ray crystallographic, bioinformatics, mutagenesis/kinetics/stability, and electron paramagnetic resonance (EPR) results, we show that organisms from different environments ultilize one of four main IspH classes. The classes are based on the arrangement of the aromatic residues near the 4Fe-4S cluster and the presence or absence of N- and C-terminal extensions. Class A enzymes are found primarily in anaerobic and microaerophilic bacteria. Class B enzymes are found in aerobic bacteria. Class C enzymes are found in cyanobacteria and plants. Class D enzymes are found in apicomplexan parasites. Using mutagenesis, we show that the cluster-associated aromatic groups in class A and class B IspHs enhance cluster oxidative stability. Y198A, F302A, and a C-terminal truncation mutant of the class B (Escherichia coli) IspH have catalytic activity lower than that of the wild-type protein when using methyl viologen as the electron donor, but higher activity with dithionite as the electron donor, due to ready access of the small reductant to the cluster, consistent with their increased oxygen and H2O2 sensitivity. F302A has the largest effect on the reaction rates, and EPR studies indicate this residue affects Fe-S cluster structure. Similar effects on cluster stability are seen with class A (F14A and Y98A) mutants; however, effects on ET rates are smaller, and there are no differences between the EPR spectra of mutant and wild-type proteins. Overall, the results are of general interest because they show, for the first time, that there are multiple IspH classes that have evolved to allow organisms to survive in diverse oxidative-stress environments.
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Affiliation(s)
- Guodong Rao
- Department of Chemistry, University of Illinois , Urbana, Illinois 61801, United States
| | - Eric Oldfield
- Department of Chemistry, University of Illinois , Urbana, Illinois 61801, United States
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19
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Faus I, Reinhard A, Rackwitz S, Wolny JA, Schlage K, Wille HC, Chumakov A, Krasutsky S, Chaignon P, Poulter CD, Seemann M, Schünemann V. Isoprenoidbiosynthese in pathogenen Bakterien: Nukleare inelastische Streuung ermöglicht Einblicke in den ungewöhnlichen [4Fe-4S]-Cluster vom E.- coli-Protein LytB/IspH. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502494] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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20
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Faus I, Reinhard A, Rackwitz S, Wolny JA, Schlage K, Wille HC, Chumakov A, Krasutsky S, Chaignon P, Poulter CD, Seemann M, Schünemann V. Isoprenoid Biosynthesis in Pathogenic Bacteria: Nuclear Resonance Vibrational Spectroscopy Provides Insight into the Unusual [4Fe-4S] Cluster of the E. coli LytB/IspH Protein. Angew Chem Int Ed Engl 2015; 54:12584-7. [PMID: 26118554 DOI: 10.1002/anie.201502494] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Indexed: 11/10/2022]
Abstract
The LytB/IspH protein catalyzes the last step of the methylerythritol phosphate (MEP) pathway which is used for the biosynthesis of essential terpenoids in most pathogenic bacteria. Therefore, the MEP pathway is a target for the development of new antimicrobial agents as it is essential for microorganisms, yet absent in humans. Substrate-free LytB has a special [4Fe-4S](2+) cluster with a yet unsolved structure. This motivated us to use synchrotron-based nuclear resonance vibrational spectroscopy (NRVS) in combination with quantum chemical-molecular mechanical (QM/MM) calculations to gain more insight into the structure of substrate-free LytB. The apical iron atom of the [4Fe-4S](2+) is clearly linked to three water molecules. We additionally present NRVS data of LytB bound to its natural substrate, (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate (HMBPP) and to the inhibitors (E)-4-amino-3-methylbut-2-en-1-yl diphosphate and (E)-4-mercapto-3-methylbut-2-en-1-yl diphosphate.
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Affiliation(s)
- Isabelle Faus
- Fachbereich Physik, TU Kaiserslautern, Erwin-Schrödinger-Strasse 46, 67653 Kaiserslautern (Germany)
| | - Annegret Reinhard
- Fachbereich Physik, TU Kaiserslautern, Erwin-Schrödinger-Strasse 46, 67653 Kaiserslautern (Germany)
| | - Sergej Rackwitz
- Fachbereich Physik, TU Kaiserslautern, Erwin-Schrödinger-Strasse 46, 67653 Kaiserslautern (Germany)
| | - Juliusz A Wolny
- Fachbereich Physik, TU Kaiserslautern, Erwin-Schrödinger-Strasse 46, 67653 Kaiserslautern (Germany)
| | - Kai Schlage
- P01, Petra III, DESY, Notkestrasse 85, D-22607 Hamburg (Germany)
| | | | - Aleksandr Chumakov
- ESRF - The European Synchrotron, CS40220, 38043 Grenoble Cedex 9 (France)
| | - Sergiy Krasutsky
- Department of Chemistry, University of Utah, 315 South 1400 East RM 2020, Salt Lake City, UT 84112 (USA)
| | - Philippe Chaignon
- Université de Strasbourg, UMR 7177 CNRS, Institut Le Bel, 4 rue Blaise Pascal, CS 90032, 67081 Strasbourg Cedex (France)
| | - C Dale Poulter
- Department of Chemistry, University of Utah, 315 South 1400 East RM 2020, Salt Lake City, UT 84112 (USA)
| | - Myriam Seemann
- Université de Strasbourg, UMR 7177 CNRS, Institut Le Bel, 4 rue Blaise Pascal, CS 90032, 67081 Strasbourg Cedex (France).
| | - Volker Schünemann
- Fachbereich Physik, TU Kaiserslautern, Erwin-Schrödinger-Strasse 46, 67653 Kaiserslautern (Germany).
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21
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Abdel-Azeim S, Jedidi A, Eppinger J, Cavallo L. Mechanistic insights into the reductive dehydroxylation pathway for the biosynthesis of isoprenoids promoted by the IspH enzyme. Chem Sci 2015; 6:5643-5651. [PMID: 28757951 PMCID: PMC5511988 DOI: 10.1039/c5sc01693b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 06/22/2015] [Indexed: 11/21/2022] Open
Abstract
Here, we report an integrated quantum mechanics/molecular mechanics (QM/MM) study of the bio-organometallic reaction pathway of the 2H+/2e- reduction of (E)-4-hydroxy-3-methylbut-2-enyl pyrophosphate (HMBPP) into the so called universal terpenoid precursors isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP), promoted by the IspH enzyme. Our results support the viability of the bio-organometallic pathway through rotation of the OH group of HMBPP away from the [Fe4S4] cluster at the core of the catalytic site, to become engaged in a H-bond with Glu126. This rotation is synchronous with π-coordination of the C2 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 C3 double bond of HMBPP to the apical Fe atom of the [Fe4S4] cluster. Dehydroxylation of HMBPP is triggered by a proton transfer from Glu126 to the OH group of HMBPP. The reaction pathway is completed by competitive proton transfer from the terminal phosphate group to the C2 or C4 atom of HMBPP.
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Affiliation(s)
- Safwat Abdel-Azeim
- King Abdullah University of Science and Technology , KAUST Catalysis Research Center , Physical Sciences and Engineering Division , Thuwal 23955-6900 , Saudi Arabia .
| | - Abdesslem Jedidi
- King Abdullah University of Science and Technology , KAUST Catalysis Research Center , Physical Sciences and Engineering Division , Thuwal 23955-6900 , Saudi Arabia .
| | - Jorg Eppinger
- King Abdullah University of Science and Technology , KAUST Catalysis Research Center , Physical Sciences and Engineering Division , Thuwal 23955-6900 , Saudi Arabia .
| | - Luigi Cavallo
- King Abdullah University of Science and Technology , KAUST Catalysis Research Center , Physical Sciences and Engineering Division , Thuwal 23955-6900 , Saudi Arabia .
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22
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Blachly PG, Sandala GM, Giammona DA, Bashford D, McCammon JA, Noodleman L. Broken-Symmetry DFT Computations for the Reaction Pathway of IspH, an Iron-Sulfur Enzyme in Pathogenic Bacteria. Inorg Chem 2015; 54:6439-61. [PMID: 26098647 PMCID: PMC4568833 DOI: 10.1021/acs.inorgchem.5b00751] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The recently discovered methylerythritol phosphate (MEP) pathway provides new targets for the development of antibacterial and antimalarial drugs. In the final step of the MEP pathway, the [4Fe-4S] IspH protein catalyzes the 2e(-)/2H(+) reductive dehydroxylation of (E)-4-hydroxy-3-methyl-but-2-enyl diphosphate (HMBPP) to afford the isoprenoid precursors isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP). Recent experiments have attempted to elucidate the IspH catalytic mechanism to drive inhibitor development. Two competing mechanisms have recently emerged, differentiated by their proposed HMBPP binding modes upon 1e(-) reduction of the [4Fe-4S] cluster: (1) a Birch reduction mechanism, in which HMBPP remains bound to the [4Fe-4S] cluster through its terminal C4-OH group (ROH-bound) until the -OH is cleaved as water; and (2) an organometallic mechanism, in which the C4-OH group rotates away from the [4Fe-4S] cluster, allowing the HMBPP olefin group to form a metallacycle complex with the apical iron (η(2)-bound). We perform broken-symmetry density functional theory computations to assess the energies and reduction potentials associated with the ROH- and η(2)-bound states implicated by these competing mechanisms. Reduction potentials obtained for ROH-bound states are more negative (-1.4 to -1.0 V) than what is typically expected of [4Fe-4S] ferredoxin proteins. Instead, we find that η(2)-bound states are lower in energy than ROH-bound states when the [4Fe-4S] cluster is 1e(-) reduced. Furthermore, η(2)-bound states can already be generated in the oxidized state, yielding reduction potentials of ca. -700 mV when electron addition occurs after rotation of the HMBPP C4-OH group. We demonstrate that such η(2)-bound states are kinetically accessible both when the IspH [4Fe-4S] cluster is oxidized and 1e(-) reduced. The energetically preferred pathway gives 1e(-) reduction of the cluster after substrate conformational change, generating the 1e(-) reduced intermediate proposed in the organometallic mechanism.
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Affiliation(s)
| | - Gregory M Sandala
- ‡Department of Chemistry and Biochemistry, Mount Allison University, 63C York Street, Sackville, New Brunswick E4L 1G8, Canada
| | - Debra Ann Giammona
- §Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Donald Bashford
- §Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | | | - Louis Noodleman
- #Department of Integrative Structural and Computational Biology, CB213, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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23
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Krasutsky S, Urbansky M, Davis CE, Lherbet C, Coates RM, Poulter CD. Synthesis of methylerythritol phosphate analogues and their evaluation as alternate substrates for IspDF and IspE from Agrobacterium tumefaciens. J Org Chem 2014; 79:9170-8. [PMID: 25184438 PMCID: PMC4184463 DOI: 10.1021/jo501529k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Indexed: 11/29/2022]
Abstract
The methylerythritol phosphate biosynthetic pathway, found in most Bacteria, some parasitic protists, and plant chloroplasts, converts D-glyceraldehyde phosphate and pyruvate to isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), where it intersects with the mevalonate pathway found in some Bacteria, Archaea, and Eukarya, including the cytosol of plants. D-3-Methylerythritol-4-phosphate (MEP), the first pathway-specific intermediate in the pathway, is converted to IPP and DMAPP by the consecutive action of the IspD-H proteins. We synthesized five D-MEP analogues-D-erythritol-4-phosphate (EP), D-3-methylthrietol-4-phosphate (MTP), D-3-ethylerythritol-4-phosphate (EEP), D-1-amino-3-methylerythritol-4-phosphate (NMEP), and D-3-methylerythritol-4-thiolophosphate (MESP)-and studied their ability to function as alternative substrates for the reactions catalyzed by the IspDF fusion and IspE proteins from Agrobacterium tumefaciens, which covert MEP to the corresponding eight-membered cyclic diphosphate. All of the analogues, except MTP, and their products were substrates for the three consecutive enzymes.
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Affiliation(s)
- Sergiy
G. Krasutsky
- Department
of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Marek Urbansky
- Department
of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Chad E. Davis
- Department
of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Christian Lherbet
- Department
of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Robert M. Coates
- Department
of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - C. Dale Poulter
- Department
of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
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24
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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
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25
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Wang Q, Qiao X, Liu CF, Ji S, Feng LM, Qian Y, Guo DA, Ye M. Metabolites identification of glycycoumarin, a major bioactive coumarin from licorice in rats. J Pharm Biomed Anal 2014; 98:287-95. [DOI: 10.1016/j.jpba.2014.06.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 05/06/2014] [Accepted: 06/02/2014] [Indexed: 11/15/2022]
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26
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Haymond A, Johny C, Dowdy T, Schweibenz B, Villarroel K, Young R, Mantooth CJ, Patel T, Bases J, Jose GS, Jackson ER, Dowd CS, Couch RD. Kinetic characterization and allosteric inhibition of the Yersinia pestis 1-deoxy-D-xylulose 5-phosphate reductoisomerase (MEP synthase). PLoS One 2014; 9:e106243. [PMID: 25171339 PMCID: PMC4149570 DOI: 10.1371/journal.pone.0106243] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 07/29/2014] [Indexed: 11/19/2022] Open
Abstract
The methylerythritol phosphate (MEP) pathway found in many bacteria governs the synthesis of isoprenoids, which are crucial lipid precursors for vital cell components such as ubiquinone. Because mammals synthesize isoprenoids via an alternate pathway, the bacterial MEP pathway is an attractive target for novel antibiotic development, necessitated by emerging antibiotic resistance as well as biodefense concerns. The first committed step in the MEP pathway is the reduction and isomerization of 1-deoxy-D-xylulose-5-phosphate (DXP) to methylerythritol phosphate (MEP), catalyzed by MEP synthase. To facilitate drug development, we cloned, expressed, purified, and characterized MEP synthase from Yersinia pestis. Enzyme assays indicate apparent kinetic constants of KMDXP = 252 µM and KMNADPH = 13 µM, IC50 values for fosmidomycin and FR900098 of 710 nM and 231 nM respectively, and Ki values for fosmidomycin and FR900098 of 251 nM and 101 nM respectively. To ascertain if the Y. pestis MEP synthase was amenable to a high-throughput screening campaign, the Z-factor was determined (0.9) then the purified enzyme was screened against a pilot scale library containing rationally designed fosmidomycin analogs and natural product extracts. Several hit molecules were obtained, most notably a natural product allosteric affector of MEP synthase and a rationally designed bisubstrate derivative of FR900098 (able to associate with both the NADPH and DXP binding sites in MEP synthase). It is particularly noteworthy that allosteric regulation of MEP synthase has not been described previously. Thus, our discovery implicates an alternative site (and new chemical space) for rational drug development.
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Affiliation(s)
- Amanda Haymond
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, United States of America
| | - Chinchu Johny
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, United States of America
| | - Tyrone Dowdy
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, United States of America
| | - Brandon Schweibenz
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, United States of America
| | - Karen Villarroel
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, United States of America
| | - Richard Young
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, United States of America
| | - Clark J. Mantooth
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, United States of America
| | - Trishal Patel
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, United States of America
| | - Jessica Bases
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, United States of America
| | - Geraldine San Jose
- Department of Chemistry, George Washington University, Washington DC, United States of America
| | - Emily R. Jackson
- Department of Chemistry, George Washington University, Washington DC, United States of America
| | - Cynthia S. Dowd
- Department of Chemistry, George Washington University, Washington DC, United States of America
| | - Robin D. Couch
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, United States of America
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27
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Span I, Wang K, Eisenreich W, Bacher A, Zhang Y, Oldfield E, Groll M. Insights into the binding of pyridines to the iron-sulfur enzyme IspH. J Am Chem Soc 2014; 136:7926-32. [PMID: 24813236 PMCID: PMC4063180 DOI: 10.1021/ja501127j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Indexed: 11/29/2022]
Abstract
(E)-1-Hydroxy-2-methylbut-2-enyl 4-diphosphate reductase (IspH) is a [Fe4S4] cluster-containing enzyme involved in isoprenoid biosynthesis in many bacteria as well as in malaria parasites and is an important drug target. Several inhibitors including amino and thiol substrate analogues, as well as acetylene and pyridine diphosphates, have been reported. Here, we investigate the mode of binding of four pyridine diphosphates to Escherichia coli IspH by using X-ray crystallography. In three cases, one of the iron atoms in the cluster is absent, but in the structure with (pyridin-3-yl)methyl diphosphate, the most potent pyridine-analogue inhibitor reported previously, the fourth iron of the [Fe4S4] cluster is present and interacts with the pyridine ring of the ligand. Based on the results of quantum chemical calculations together with the crystallographic results we propose a side-on η(2) coordination of the nitrogen and the carbon in the 2-position of the pyridine ring to the unique fourth iron in the cluster, which is in the reduced state. The X-ray structure enables excellent predictions using density functional theory of the (14)N hyperfine coupling and quadrupole coupling constants reported previously using HYSCORE spectroscopy, as well as providing a further example of the ability of such [Fe4S4]-containing proteins to form organometallic complexes.
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Affiliation(s)
- Ingrid Span
- Center
for Integrated Protein Science Munich, Chemistry Department, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Ke Wang
- Department
of Chemistry, 600 South
Mathews Avenue, University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Wolfgang Eisenreich
- Center
for Integrated Protein Science Munich, Chemistry Department, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Adelbert Bacher
- Center
for Integrated Protein Science Munich, Chemistry Department, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Yong Zhang
- Department
of Chemistry, Chemical Biology, and Biomedical Engineering, Stevens Institute of Technology, Castle Point on Hudson, Hoboken, New Jersey 07030, United States
| | - Eric Oldfield
- Department
of Chemistry, 600 South
Mathews Avenue, University
of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Michael Groll
- Center
for Integrated Protein Science Munich, Chemistry Department, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
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28
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Wang W, Oldfield E. Biometallorganische Chemie mit IspG und IspH: Struktur, Funktion und Hemmung der an der Isoprenoid-Biosynthese beteiligten [Fe 4S 4]-Proteine. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201306712] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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29
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Wang W, Oldfield E. Bioorganometallic chemistry with IspG and IspH: structure, function, and inhibition of the [Fe(4)S(4)] proteins involved in isoprenoid biosynthesis. Angew Chem Int Ed Engl 2014; 53:4294-310. [PMID: 24481599 DOI: 10.1002/anie.201306712] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Indexed: 11/12/2022]
Abstract
Enzymes of the methylerythritol phosphate pathway of isoprenoid biosynthesis are attractive anti-infective drug targets. The last two enzymes of this pathway, IspG and IspH, are [Fe4 S4 ] proteins that are not produced by humans and catalyze 2 H(+) / 2 e(-) reductions with novel mechanisms. In this Review, we summarize recent advances in structural, mechanistic, and inhibitory studies of these two enzymes. In particular, mechanistic proposals involving bioorganometallic intermediates are presented, and compared with other mechanistic possibilities. In addition, inhibitors based on substrate analogues as well as developed by rational design and compound-library screening, are discussed. The results presented support bioorganometallic catalytic mechanisms for IspG and IspH, and open up new routes to anti-infective drug design targeting [Fe4 S4 ] clusters in proteins.
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Affiliation(s)
- Weixue Wang
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 (USA)
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30
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Affiliation(s)
| | - Salim Al-Babili
- BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Eleanore T. Wurtzel
- The Graduate School and University Center, The City University of New York, New York, New York, USA
- Department of Biological Sciences, Lehman College, The City University of New York, Bronx, New York, USA
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Utilizing a dynamical description of IspH to aid in the development of novel antimicrobial drugs. PLoS Comput Biol 2013; 9:e1003395. [PMID: 24367248 PMCID: PMC3868525 DOI: 10.1371/journal.pcbi.1003395] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 10/30/2013] [Indexed: 02/05/2023] Open
Abstract
The nonmevalonate pathway is responsible for isoprenoid production in microbes, including H. pylori, M. tuberculosis and P. falciparum, but is nonexistent in humans, thus providing a desirable route for antibacterial and antimalarial drug discovery. We coordinate a structural study of IspH, a [4Fe-4S] protein responsible for converting HMBPP to IPP and DMAPP in the ultimate step in the nonmevalonate pathway. By performing accelerated molecular dynamics simulations on both substrate-free and HMBPP-bound [Fe4S4]2+ IspH, we elucidate how substrate binding alters the dynamics of the protein. Using principal component analysis, we note that while substrate-free IspH samples various open and closed conformations, the closed conformation observed experimentally for HMBPP-bound IspH is inaccessible in the absence of HMBPP. In contrast, simulations with HMBPP bound are restricted from accessing the open states sampled by the substrate-free simulations. Further investigation of the substrate-free simulations reveals large fluctuations in the HMBPP binding pocket, as well as allosteric pocket openings – both of which are achieved through the hinge motions of the individual domains in IspH. Coupling these findings with solvent mapping and various structural analyses reveals alternative druggable sites that may be exploited in future drug design efforts. Drug resistance has recently entered into media conversations through the lens of MRSA (methicillin-resistant Staphylococcus aureus) infections, but conventional therapies are also failing to address resistance in cases of malaria and other bacterial infections, such as tuberculosis. To address these problems, we must develop new antibacterial and antimalarial medications. Our research focuses on understanding the structure and dynamics of IspH, an enzyme whose function is necessary for the survival of most bacteria and malaria-causing protozoans. Using computer simulations, we track how the structure of IspH changes in the presence and absence of its natural substrate. By inspecting the pockets that form in the normal motions of IspH, we propose a couple new routes by which new molecules may be developed to disrupt the function of IspH. It is our hope that these structural studies may be precursors to the development of novel therapies that may add to our current arsenal against bacterial and malarial infections.
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Masini T, Kroezen BS, Hirsch AK. Druggability of the enzymes of the non-mevalonate-pathway. Drug Discov Today 2013; 18:1256-62. [DOI: 10.1016/j.drudis.2013.07.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Revised: 06/27/2013] [Accepted: 07/04/2013] [Indexed: 12/13/2022]
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Zhao L, Chang WC, Xiao Y, Liu HW, Liu P. Methylerythritol phosphate pathway of isoprenoid biosynthesis. Annu Rev Biochem 2013; 82:497-530. [PMID: 23746261 DOI: 10.1146/annurev-biochem-052010-100934] [Citation(s) in RCA: 162] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Isoprenoids are a class of natural products with more than 55,000 members. All isoprenoids are constructed from two precursors, isopentenyl diphosphate and its isomer dimethylallyl diphosphate. Two of the most important discoveries in isoprenoid biosynthetic studies in recent years are the elucidation of a second isoprenoid biosynthetic pathway [the methylerythritol phosphate (MEP) pathway] and a modified mevalonic acid (MVA) pathway. In this review, we summarize mechanistic insights on the MEP pathway enzymes. Because many isoprenoids have important biological activities, the need to produce them in sufficient quantities for downstream research efforts or commercial application is apparent. Recent advances in both MVA and MEP pathway-based synthetic biology are also illustrated by reviewing the landmark work of artemisinic acid and taxadien-5α-ol production through microbial fermentations.
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Affiliation(s)
- Lishan Zhao
- Amyris, Inc., Emeryville, California 94608, USA.
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