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Specific chemical modification of bacterial type I dehydroquinase – opportunities for drug discovery. Future Med Chem 2015; 7:2371-83. [DOI: 10.4155/fmc.15.145] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Type I dehydroquinase (DHQ1) is a class I aldolase enzyme that catalyzes the reversible dehydration of 3-dehydroquinic acid to form 3-dehydroshikimic acid by multistep mechanism that involves the formation of Schiff-base species. DHQ1 is present in plants and several bacterial sources but it does not have any counterpart in human cells. It has been suggested that DHQ1 may act as a virulence factor in vivo and therefore a promising target in the search for new antivirulence agents to combat widespread antibiotic resistance. This review covers recent progress in the structure-based design and chemical modifications caused by selective irreversible inhibitors. Computational studies aimed at understanding the experimentally obtained covalent modifications and inhibitory potencies of these inhibitors are also described.
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2
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Tizón L, Maneiro M, Peón A, Otero JM, Lence E, Poza S, van Raaij MJ, Thompson P, Hawkins AR, González-Bello C. Irreversible covalent modification of type I dehydroquinase with a stable Schiff base. Org Biomol Chem 2015; 13:706-16. [DOI: 10.1039/c4ob01782j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Structural and computational studies carried out with two epoxides provide insight into the irreversible inhibition of type I dehydroquinase.
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Affiliation(s)
- Lorena Tizón
- Centro Singular de Investigación en Química Biológica y Materiales Moleculares (CIQUS)
- Universidad de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - María Maneiro
- Centro Singular de Investigación en Química Biológica y Materiales Moleculares (CIQUS)
- Universidad de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - Antonio Peón
- Centro Singular de Investigación en Química Biológica y Materiales Moleculares (CIQUS)
- Universidad de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - José M. Otero
- Departamento de Bioquímica y Biología Molecular and CIQUS
- Universidad de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - Emilio Lence
- Centro Singular de Investigación en Química Biológica y Materiales Moleculares (CIQUS)
- Universidad de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - Sergio Poza
- Centro Singular de Investigación en Química Biológica y Materiales Moleculares (CIQUS)
- Universidad de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - Mark J. van Raaij
- Departamento de Estructura de Macromoléculas
- Centro Nacional de Biotecnología (CSIC)
- 28049 Madrid
- Spain
| | - Paul Thompson
- Institute of Cell and Molecular Biosciences
- Medical School
- University of Newcastle upon Tyne
- Newcastle upon Tyne NE2 4HH
- UK
| | - Alastair R. Hawkins
- Institute of Cell and Molecular Biosciences
- Medical School
- University of Newcastle upon Tyne
- Newcastle upon Tyne NE2 4HH
- UK
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biológica y Materiales Moleculares (CIQUS)
- Universidad de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
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3
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Insights into substrate binding and catalysis in bacterial type I dehydroquinase. Biochem J 2014; 462:415-24. [DOI: 10.1042/bj20140614] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The crystal structure of S. typhi type I dehydroquinase in complex with (2R)-3-methyl-3-dehydroquinic acid is described. A previously unknown key role of several conserved residues and a detailed knowledge of the substrate binding process is detailed.
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4
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Cheung VWN, Xue B, Hernandez-Valladares M, Go MK, Tung A, Aguda AH, Robinson RC, Yew WS. Identification of polyketide inhibitors targeting 3-dehydroquinate dehydratase in the shikimate pathway of Enterococcus faecalis. PLoS One 2014; 9:e103598. [PMID: 25072253 PMCID: PMC4114755 DOI: 10.1371/journal.pone.0103598] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 07/04/2014] [Indexed: 12/28/2022] Open
Abstract
Due to the emergence of resistance toward current antibiotics, there is a pressing need to develop the next generation of antibiotics as therapeutics against infectious and opportunistic diseases of microbial origins. The shikimate pathway is exclusive to microbes, plants and fungi, and hence is an attractive and logical target for development of antimicrobial therapeutics. The Gram-positive commensal microbe, Enterococcus faecalis, is a major human pathogen associated with nosocomial infections and resistance to vancomycin, the “drug of last resort”. Here, we report the identification of several polyketide-based inhibitors against the E. faecalis shikimate pathway enzyme, 3-dehydroquinate dehydratase (DHQase). In particular, marein, a flavonoid polyketide, both inhibited DHQase and retarded the growth of Enterococcus faecalis. The purification, crystallization and structural resolution of recombinant DHQase from E. faecalis (at 2.2 Å resolution) are also reported. This study provides a route in the development of polyketide-based antimicrobial inhibitors targeting the shikimate pathway of the human pathogen E. faecalis.
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Affiliation(s)
- Vivian Wing Ngar Cheung
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Bo Xue
- Institute of Molecular and Cell Biology, Singapore, Singapore
| | | | - Maybelle Kho Go
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Alvin Tung
- Institute of Molecular and Cell Biology, Singapore, Singapore
| | | | - Robert C. Robinson
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Institute of Molecular and Cell Biology, Singapore, Singapore
- * E-mail: (RCR); (WSY)
| | - Wen Shan Yew
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Synthetic Biology Research Consortium, National University of Singapore, Singapore, Singapore
- * E-mail: (RCR); (WSY)
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5
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Ratia K, Light SH, Antanasijevic A, Anderson WF, Caffrey M, Lavie A. Discovery of selective inhibitors of the Clostridium difficile dehydroquinate dehydratase. PLoS One 2014; 9:e89356. [PMID: 24586713 PMCID: PMC3931744 DOI: 10.1371/journal.pone.0089356] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 01/18/2014] [Indexed: 12/18/2022] Open
Abstract
A vibrant and healthy gut flora is essential for preventing the proliferation of Clostridium difficile, a pathogenic bacterium that causes severe gastrointestinal symptoms. In fact, most C. difficile infections (CDIs) occur after broad-spectrum antibiotic treatment, which, by eradicating the commensal gut bacteria, allows its spores to proliferate. Hence, a C. difficile specific antibiotic that spares the gut flora would be highly beneficial in treating CDI. Towards this goal, we set out to discover small molecule inhibitors of the C. difficile enzyme dehydroquinate dehydratase (DHQD). DHQD is the 3(rd) of seven enzymes that compose the shikimate pathway, a metabolic pathway absent in humans, and is present in bacteria as two phylogenetically and mechanistically distinct types. Using a high-throughput screen we identified three compounds that inhibited the type I C. difficile DHQD but not the type II DHQD from Bacteroides thetaiotaomicron, a highly represented commensal gut bacterial species. Kinetic analysis revealed that the compounds inhibit the C. difficile enzyme with Ki values ranging from 10 to 20 µM. Unexpectedly, kinetic and biophysical studies demonstrate that inhibitors also exhibit selectivity between type I DHQDs, inhibiting the C. difficile but not the highly homologous Salmonella enterica DHQD. Therefore, the three identified compounds seem to be promising lead compounds for the development of C. difficile specific antibiotics.
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Affiliation(s)
- Kiira Ratia
- Research Resources Center, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Samuel H. Light
- Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
- Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Aleksandar Antanasijevic
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Wayne F. Anderson
- Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
- Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Michael Caffrey
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Arnon Lavie
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, United States of America
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6
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Light SH, Minasov G, Duban ME, Anderson WF. Adherence to Bürgi-Dunitz stereochemical principles requires significant structural rearrangements in Schiff-base formation: insights from transaldolase complexes. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:544-52. [PMID: 24531488 PMCID: PMC3940192 DOI: 10.1107/s1399004713030666] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 11/08/2013] [Indexed: 11/10/2022]
Abstract
The Bürgi-Dunitz angle (αBD) describes the trajectory of approach of a nucleophile to an electrophile. The adoption of a stereoelectronically favorable αBD can necessitate significant reactive-group repositioning over the course of bond formation. In the context of enzyme catalysis, interactions with the protein constrain substrate rotation, which could necessitate structural transformations during bond formation. To probe this theoretical framework vis-à-vis biocatalysis, Schiff-base formation was analysed in Francisella tularensis transaldolase (TAL). Crystal structures of wild-type and Lys→Met mutant TAL in covalent and noncovalent complexes with fructose 6-phosphate and sedoheptulose 7-phosphate clarify the mechanism of catalysis and reveal that substrate keto moieties undergo significant conformational changes during Schiff-base formation. Structural changes compelled by the trajectory considerations discussed here bear relevance to bond formation in a variety of constrained enzymic/engineered systems and can inform the design of covalent therapeutics.
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Affiliation(s)
- Samuel H. Light
- Center for Structural Genomics of Infectious Diseases, USA
- Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - George Minasov
- Center for Structural Genomics of Infectious Diseases, USA
- Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Mark-Eugene Duban
- Center for Structural Genomics of Infectious Diseases, USA
- Department of Chemistry and Center for Molecular Innovation and Drug Discovery, Northwestern University, Evanston, IL 60201, USA
| | - Wayne F. Anderson
- Center for Structural Genomics of Infectious Diseases, USA
- Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
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7
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Light SH, Antanasijevic A, Krishna SN, Caffrey M, Anderson WF, Lavie A. Crystal structures of type I dehydroquinate dehydratase in complex with quinate and shikimate suggest a novel mechanism of Schiff base formation. Biochemistry 2014; 53:872-80. [PMID: 24437575 PMCID: PMC3985847 DOI: 10.1021/bi4015506] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
A component of the shikimate biosynthetic
pathway, dehydroquinate
dehydratase (DHQD) catalyzes the dehydration of 3-dehydroquniate (DHQ)
to 3-dehydroshikimate. In the type I DHQD reaction mechanism a lysine
forms a Schiff base intermediate with DHQ. The Schiff base acts as
an electron sink to facilitate the catalytic dehydration. To address
the mechanism of Schiff base formation, we determined structures of
the Salmonella enterica wild-type DHQD in complex
with the substrate analogue quinate and the product analogue shikimate.
In addition, we determined the structure of the K170M mutant (Lys170
being the Schiff base forming residue) in complex with quinate. Combined
with nuclear magnetic resonance and isothermal titration calorimetry
data that revealed altered binding of the analogue to the K170M mutant,
these structures suggest a model of Schiff base formation characterized
by the dynamic interplay of opposing forces acting on either side
of the substrate. On the side distant from the substrate 3-carbonyl
group, closure of the enzyme’s β8−α8 loop
is proposed to guide DHQ into the proximity of the Schiff base-forming
Lys170. On the 3-carbonyl side of the substrate, Lys170 sterically
alters the position of DHQ’s reactive ketone, aligning it at
an angle conducive for nucleophilic attack. This study of a type I
DHQD reveals the interplay between the enzyme and substrate required
for the correct orientation of a functional group constrained within
a cyclic substrate.
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Affiliation(s)
- Samuel H Light
- Center for Structural Genomics of Infectious Diseases and Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University , Chicago, Illinois 60611, United States
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Crystal structure of a type II dehydroquinate dehydratase-like protein from Bifidobacterium longum. ACTA ACUST UNITED AC 2013; 14:25-30. [PMID: 23539270 DOI: 10.1007/s10969-013-9149-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 03/14/2013] [Indexed: 10/27/2022]
Abstract
Dehydroquinate dehydratase (DHQD) catalyzes the third step in the biosynthetic shikimate pathway. Here we identify a Bifidobacterium longum protein with high sequence homology to type II DHQDs but no detectable DHQD activity under standard assay conditions. A crystal structure reveals that the B. longum protein adopts a DHQD-like tertiary structure but a distinct quaternary state. Apparently forming a dimer, the B. longum protein lacks the active site aspartic acid contributed from a neighboring protomer in the type II DHQD dodecamer. Relating to the absence of protein-protein interactions established in the type II DHQD dodecameric assembly, substantial conformational changes distinguish the would-be active site of the B. longum protein. As B. longum possess no other genes with homology to known DHQDs, these findings imply a unique DHQD activity within B. longum.
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Light SH, Anderson WF, Lavie A. Reassessing the type I dehydroquinate dehydratase catalytic triad: kinetic and structural studies of Glu86 mutants. Protein Sci 2013; 22:418-24. [PMID: 23341204 DOI: 10.1002/pro.2218] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Revised: 01/07/2013] [Accepted: 01/09/2013] [Indexed: 11/10/2022]
Abstract
Dehydroquinate dehydratase (DHQD) catalyzes the third reaction in the biosynthetic shikimate pathway. Type I DHQDs are members of the greater aldolase superfamily, a group of enzymes that contain an active site lysine that forms a Schiff base intermediate. Three residues (Glu86, His143, and Lys170 in the Salmonella enterica DHQD) have previously been proposed to form a triad vital for catalysis. While the roles of Lys170 and His143 are well defined-Lys170 forms the Schiff base with the substrate and His143 shuttles protons in multiple steps in the reaction-the role of Glu86 remains poorly characterized. To probe Glu86's role, Glu86 mutants were generated and subjected to biochemical and structural study. The studies presented here demonstrate that mutant enzymes retain catalytic proficiency, calling into question the previously attributed role of Glu86 in catalysis and suggesting that His143 and Lys170 function as a catalytic dyad. Structures of the Glu86Ala (E86A) mutant in complex with covalently bound reaction intermediate reveal a conformational change of the His143 side chain. This indicates a predominant steric role for Glu86, to maintain the His143 side chain in position consistent with catalysis. The structures also explain why the E86A mutant is optimally active at more acidic conditions than the wild-type enzyme. In addition, a complex with the reaction product reveals a novel, likely nonproductive, binding mode that suggests a mechanism of competitive product inhibition and a potential strategy for the design of therapeutics.
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Affiliation(s)
- Samuel H Light
- Center for Structural Genomics of Infectious Diseases and Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
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10
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Crystal structure of type I 3-dehydroquinate dehydratase of Aquifex aeolicus suggests closing of active site flap is not essential for enzyme action. Biochem Biophys Res Commun 2013; 432:350-4. [PMID: 23396056 DOI: 10.1016/j.bbrc.2013.01.099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 01/28/2013] [Indexed: 11/22/2022]
Abstract
Structural analyses of enzymes involved in biosynthetic pathways that are present in micro-organisms, but absent from mammals (for example Shikimate pathway) are important in developing anti-microbial drugs. Crystal structure of the Shikimate pathway enzyme, type I 3-dehydroquinate dehydratase (3-DHQase) from the hyperthermophilic bacterium Aquifex aeolicus was solved both as an apo form and in complex with a ligand. The complex structure revealed an interesting structural difference when compared to other ligand-bound type I 3-DHQases suggesting that closure of the active site loop is not essential for catalysis. This provides new insights into the catalytic mechanism of type I 3-DHQases.
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