1
|
Frlan R. An Evolutionary Conservation and Druggability Analysis of Enzymes Belonging to the Bacterial Shikimate Pathway. Antibiotics (Basel) 2022; 11:antibiotics11050675. [PMID: 35625318 PMCID: PMC9137983 DOI: 10.3390/antibiotics11050675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/11/2022] [Accepted: 05/13/2022] [Indexed: 11/25/2022] Open
Abstract
Enzymes belonging to the shikimate pathway have long been considered promising targets for antibacterial drugs because they have no counterpart in mammals and are essential for bacterial growth and virulence. However, despite decades of research, there are currently no clinically relevant antibacterial drugs targeting any of these enzymes, and there are legitimate concerns about whether they are sufficiently druggable, i.e., whether they can be adequately modulated by small and potent drug-like molecules. In the present work, in silico analyses combining evolutionary conservation and druggability are performed to determine whether these enzymes are candidates for broad-spectrum antibacterial therapy. The results presented here indicate that the substrate-binding sites of most enzymes in this pathway are suitable drug targets because of their reasonable conservation and druggability scores. An exception was the substrate-binding site of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase, which was found to be undruggable because of its high content of charged residues and extremely high overall polarity. Although the presented study was designed from the perspective of broad-spectrum antibacterial drug development, this workflow can be readily applied to any antimicrobial target analysis, whether narrow- or broad-spectrum. Moreover, this research also contributes to a deeper understanding of these enzymes and provides valuable insights into their properties.
Collapse
Affiliation(s)
- Rok Frlan
- The Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia
| |
Collapse
|
2
|
Mycobacterium tuberculosis Shikimate Pathway Enzymes as Targets for the Rational Design of Anti-Tuberculosis Drugs. Molecules 2020; 25:molecules25061259. [PMID: 32168746 PMCID: PMC7144000 DOI: 10.3390/molecules25061259] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/06/2020] [Accepted: 02/10/2020] [Indexed: 12/17/2022] Open
Abstract
Roughly a third of the world’s population is estimated to have latent Mycobacterium tuberculosis infection, being at risk of developing active tuberculosis (TB) during their lifetime. Given the inefficacy of prophylactic measures and the increase of drug-resistant M. tuberculosis strains, there is a clear and urgent need for the development of new and more efficient chemotherapeutic agents, with selective toxicity, to be implemented on patient treatment. The component enzymes of the shikimate pathway, which is essential in mycobacteria and absent in humans, stand as attractive and potential targets for the development of new drugs to treat TB. This review gives an update on published work on the enzymes of the shikimate pathway and some insight on what can be potentially explored towards selective drug development.
Collapse
|
3
|
Lence E, van der Kamp MW, González-Bello C, Mulholland AJ. QM/MM simulations identify the determinants of catalytic activity differences between type II dehydroquinase enzymes. Org Biomol Chem 2018; 16:4443-4455. [PMID: 29767194 PMCID: PMC6011038 DOI: 10.1039/c8ob00066b] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 04/18/2018] [Indexed: 11/29/2022]
Abstract
Type II dehydroquinase enzymes (DHQ2), recognized targets for antibiotic drug discovery, show significantly different activities dependent on the species: DHQ2 from Mycobacterium tuberculosis (MtDHQ2) and Helicobacter pylori (HpDHQ2) show a 50-fold difference in catalytic efficiency. Revealing the determinants of this activity difference is important for our understanding of biological catalysis and further offers the potential to contribute to tailoring specificity in drug design. Molecular dynamics simulations using a quantum mechanics/molecular mechanics potential, with correlated ab initio single point corrections, identify and quantify the subtle determinants of the experimentally observed difference in efficiency. The rate-determining step involves the formation of an enolate intermediate: more efficient stabilization of the enolate and transition state of the key step in MtDHQ2, mainly by the essential residues Tyr24 and Arg19, makes it more efficient than HpDHQ2. Further, a water molecule, which is absent in MtDHQ2 but involved in generation of the catalytic Tyr22 tyrosinate in HpDHQ2, was found to destabilize both the transition state and the enolate intermediate. The quantification of the contribution of key residues and water molecules in the rate-determining step of the mechanism also leads to improved understanding of higher potencies and specificity of known inhibitors, which should aid ongoing inhibitor design.
Collapse
Affiliation(s)
- Emilio Lence
- Centre for Computational Chemistry
, School of Chemistry
, University of Bristol
,
Cantock's Close
, BS8 1TS Bristol
, UK
.
; Tel: +44 (0)117 9289097
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS)
, Departamento de Química Orgánica
, Universidade de Santiago de Compostela
,
Jenaro de la Fuente s/n
, 15782 Santiago de Compostela
, Spain
.
; Tel: +34 881 815726
| | - Marc W. van der Kamp
- Centre for Computational Chemistry
, School of Chemistry
, University of Bristol
,
Cantock's Close
, BS8 1TS Bristol
, UK
.
; Tel: +44 (0)117 9289097
- School of Biochemistry
, University of Bristol
, University Walk
,
BS8 1TD Bristol
, UK
.
; Tel: +44 (0)117 3312147
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS)
, Departamento de Química Orgánica
, Universidade de Santiago de Compostela
,
Jenaro de la Fuente s/n
, 15782 Santiago de Compostela
, Spain
.
; Tel: +34 881 815726
| | - Adrian J. Mulholland
- Centre for Computational Chemistry
, School of Chemistry
, University of Bristol
,
Cantock's Close
, BS8 1TS Bristol
, UK
.
; Tel: +44 (0)117 9289097
| |
Collapse
|
4
|
Ávila MB, Azevedo WF. Development of machine learning models to predict inhibition of 3‐dehydroquinate dehydratase. Chem Biol Drug Des 2018; 92:1468-1474. [DOI: 10.1111/cbdd.13312] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 02/27/2018] [Accepted: 03/18/2018] [Indexed: 12/24/2022]
Affiliation(s)
- Maurício Boff Ávila
- Laboratory of Computational Systems BiologySchool of SciencesPontifical Catholic University of Rio Grande do Sul (PUCRS) Porto Alegre RS Brazil
- Graduate Program in Cellular and Molecular BiologyPontifical Catholic University of Rio Grande do Sul (PUCRS) Porto Alegre RS Brazil
| | - Walter Filgueira Azevedo
- Laboratory of Computational Systems BiologySchool of SciencesPontifical Catholic University of Rio Grande do Sul (PUCRS) Porto Alegre RS Brazil
- Graduate Program in Cellular and Molecular BiologyPontifical Catholic University of Rio Grande do Sul (PUCRS) Porto Alegre RS Brazil
| |
Collapse
|
5
|
Peón A, Robles A, Blanco B, Convertino M, Thompson P, Hawkins AR, Caflisch A, González-Bello C. Reducing the Flexibility of Type II Dehydroquinase for Inhibition: A Fragment-Based Approach and Molecular Dynamics Study. ChemMedChem 2017; 12:1512-1524. [DOI: 10.1002/cmdc.201700396] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 08/01/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Antonio Peón
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares, CIQUS, and Departamento de Química Orgánica; Universidade de Santiago de Compostela; calle Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
| | - Adrián Robles
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares, CIQUS, and Departamento de Química Orgánica; Universidade de Santiago de Compostela; calle Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
| | - Beatriz Blanco
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares, CIQUS, and Departamento de Química Orgánica; Universidade de Santiago de Compostela; calle Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
| | - Marino Convertino
- Department of Biochemistry; University of Zurich; 8057 Zurich Switzerland
- Current address: Department of Biochemistry and Biophysics; University of North Carolina, School of Medicine; Chapel Hill NC 27599 USA
| | - Paul Thompson
- Institute of Cell and Molecular Biosciences, Medical School; University of Newcastle upon Tyne; Catherine Cookson Building, Framlington Place Newcastle upon Tyne NE2 4HH UK
| | - Alastair R. Hawkins
- Institute of Cell and Molecular Biosciences, Medical School; University of Newcastle upon Tyne; Catherine Cookson Building, Framlington Place Newcastle upon Tyne NE2 4HH UK
| | - Amedeo Caflisch
- Department of Biochemistry; University of Zurich; 8057 Zurich Switzerland
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares, CIQUS, and Departamento de Química Orgánica; Universidade de Santiago de Compostela; calle Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
| |
Collapse
|
6
|
Lone MY, Athar M, Gupta VK, Jha PC. Prioritization of natural compounds against mycobacterium tuberculosis 3-dehydroquinate dehydratase: A combined in-silico and in-vitro study. Biochem Biophys Res Commun 2017; 491:1105-1111. [DOI: 10.1016/j.bbrc.2017.08.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 08/04/2017] [Indexed: 12/18/2022]
|
7
|
Blomberg LM, Mangold M, Mitchell JBO, Blumberger J. Theoretical Study of the Reaction Mechanism of Streptomyces coelicolor Type II Dehydroquinase. J Chem Theory Comput 2015; 5:1284-94. [PMID: 26609719 DOI: 10.1021/ct800480d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The reaction mechanism of a type II dehydroquinase (DHQase) from Streptomyces coelicolor was investigated using molecular dynamics simulation and density functional theory (DFT) calculations. DHQase catalyzes the elimination of a water molecule from dehydroquinate (DHQ), a key step in the biosynthesis of aromatic amino acids in bacteria, fungi, and plants. In the DFT calculations, 10 models, containing up to 230 atoms, were used to investigate different proposals for the reaction mechanism, suggested on the basis of crystal structures and kinetic data. Probing the flexibility of the active site, molecular dynamics simulation reveals that deprotonated Tyr28 can act as the base that catalyzes the first reaction step, the proton abstraction of the pro-S proton at C2 of DHQ, and formation of the enolate intermediate. The computed barrier for the first transition state (TS1), 13-15 kcal/mol, is only slightly affected by the active site model used and is in good agreement with the corresponding experimental barrier of 13.4 kcal/mol for the rate-determining step. The previously proposed enol form of the intermediate is found to be significantly higher in energy than the enolate form and is thus thermodynamically not competitive. In the second and final reaction step, protonation of the hydroxyl group at C1 by His106 followed by water elimination, there is a substantial buildup of dipole moment due to the net transfer of a proton from His106 to Tyr28. A barrier for the second transition state (TS2) that fits well with the corresponding experimental barrier could only be found if the buildup of dipole moment is at least partly compensated during the second reaction step. We speculate that this could be facilitated by regeneration of the Tyr28 anion or by proton transfer to the vicinity of His106 before TS2 is reached. A revised mechanism for type II DHQase is discussed in light of the results of the present calculations.
Collapse
Affiliation(s)
- L Mattias Blomberg
- Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - Martina Mangold
- Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - John B O Mitchell
- Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - Jochen Blumberger
- Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
| |
Collapse
|
8
|
González-Bello C, Tizón L, Lence E, Otero JM, van Raaij MJ, Martinez-Guitian M, Beceiro A, Thompson P, Hawkins AR. Chemical Modification of a Dehydratase Enzyme Involved in Bacterial Virulence by an Ammonium Derivative: Evidence of its Active Site Covalent Adduct. J Am Chem Soc 2015; 137:9333-43. [DOI: 10.1021/jacs.5b04080] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | | | - Mark J. van Raaij
- Departamento
de Estructura de Macromoléculas, Centro Nacional de Biotecnología (CSIC), Campus Cantoblanco, 28049 Madrid, Spain
| | - Marta Martinez-Guitian
- Servicio
de Microbiología-INIBIC, Complejo Hospitalario Universitario A Coruña (CHUAC), 15006 A Coruña, Spain
| | - Alejandro Beceiro
- Servicio
de Microbiología-INIBIC, Complejo Hospitalario Universitario A Coruña (CHUAC), 15006 A Coruña, Spain
| | - Paul Thompson
- Institute
of Cell and Molecular Biosciences, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Alastair R. Hawkins
- Institute
of Cell and Molecular Biosciences, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, United Kingdom
| |
Collapse
|
9
|
Liu C, Liu YM, Sun QL, Jiang CY, Liu SJ. Unraveling the kinetic diversity of microbial 3-dehydroquinate dehydratases of shikimate pathway. AMB Express 2015; 5:7. [PMID: 25852984 PMCID: PMC4314829 DOI: 10.1186/s13568-014-0087-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Accepted: 12/17/2014] [Indexed: 11/10/2022] Open
Abstract
3-Dehydroquinate dehydratase (DHQase) catalyzes the conversion of 3-dehydroquinic acid to 3-dehydroshikimic acid of the shikimate pathway. In this study, 3180 prokaryotic genomes were examined and 459 DHQase sequences were retrieved. Based on sequence analysis and their original hosts, 38 DHQase genes were selected for chemical synthesis. The selected DHQases were translated into new DNA sequences according to the genetic codon usage bias by both Escherichia coli and Corynebacterium glutamicum. The new DNA sequences were customized for synthetic biological applications by adding Biobrick adapters at both ends and by removal of any related restriction endonuclease sites. The customized DHQase genes were successfully expressed in E. coli, and functional DHQases were obtained. Kinetic parameters of Km, kcat, and Vmax of DHQases were determined with a newly established high-throughput method for DHQase activity assay. Results showed that DHQases possessed broad strength of substrate affinities and catalytic capacities. In addition to the DHQase kinetic diversities, this study generated a DHQase library with known catalytic constants that could be applied to design artificial modules of shikimate pathway for metabolic engineering and synthetic biology.
Collapse
|
10
|
Howard NI, Dias MVB, Peyrot F, Chen L, Schmidt MF, Blundell TL, Abell C. Design and Structural Analysis of Aromatic Inhibitors of Type II Dehydroquinase fromMycobacterium tuberculosis. ChemMedChem 2014; 10:116-33. [DOI: 10.1002/cmdc.201402298] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Indexed: 11/09/2022]
|
11
|
Blanco B, Sedes A, Peón A, Otero JM, van Raaij MJ, Thompson P, Hawkins AR, González-Bello C. Exploring the Water-Binding Pocket of the Type II Dehydroquinase Enzyme in the Structure-Based Design of Inhibitors. J Med Chem 2014; 57:3494-510. [DOI: 10.1021/jm500175z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Beatriz Blanco
- Centro
Singular de Investigación en Química Biológica
y Materiales Moleculares (CIQUS), Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Antía Sedes
- 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, 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), Campus Cantoblanco, 28049 Madrid, Spain
| | - Paul Thompson
- Institute
of Cell and Molecular Biosciences, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, U.K
| | - Alastair R. Hawkins
- Institute
of Cell and Molecular Biosciences, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, U.K
| | - Concepción González-Bello
- Centro
Singular de Investigación en Química Biológica
y Materiales Moleculares (CIQUS), Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| |
Collapse
|
12
|
Mechanistic insight into the reaction catalysed by bacterial type II dehydroquinases1. Biochem J 2014; 458:547-57. [DOI: 10.1042/bj20131103] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The present study identified the residue that deprotonates the essential tyrosine that triggers the catalytic process and provides details of the required motions for the catalytic turnover. A previously unknown key role for the essential arginine and two conserved arginines is also reported.
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
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.
Collapse
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
| | | | | | | | | | | |
Collapse
|
15
|
Mir R, Jallu S, Singh TP. The shikimate pathway: Review of amino acid sequence, function and three-dimensional structures of the enzymes. Crit Rev Microbiol 2013; 41:172-89. [DOI: 10.3109/1040841x.2013.813901] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
16
|
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.
Collapse
|
17
|
Lence E, Tizón L, Otero JM, Peón A, Prazeres VFV, Llamas-Saiz AL, Fox GC, van Raaij MJ, Lamb H, Hawkins AR, González-Bello C. Mechanistic basis of the inhibition of type II dehydroquinase by (2S)- and (2R)-2-benzyl-3-dehydroquinic acids. ACS Chem Biol 2013. [PMID: 23198883 DOI: 10.1021/cb300493s] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The structural changes caused by the substitution of the aromatic moiety in (2S)-2-benzyl-3-dehydroquinic acids and its epimers in C2 by electron-withdrawing or electron-donating groups in type II dehydroquinase enzyme from M. tuberculosis and H. pylori has been investigated by structural and computational studies. Both compounds are reversible competitive inhibitors of this enzyme, which is essential in these pathogenic bacteria. The crystal structures of M. tuberculosis and H. pylori in complex with (2S)-2-(4-methoxy)benzyl- and (2S)-2-perfluorobenzyl-3-dehydroquinic acids have been solved at 2.0, 2.3, 2.0, and 1.9 Å, respectively. The crystal structure of M. tuberculosis in complex with (2R)-2-(benzothiophen-5-yl)methyl-3-dehydroquinic acid is also reported at 1.55 Å. These crystal structures reveal key differences in the conformation of the flexible loop of the two enzymes, a difference that depends on the presence of electron-withdrawing or electron-donating groups in the aromatic moiety of the inhibitors. This loop closes over the active site after substrate binding, and its flexibility is essential for the function of the enzyme. These differences have also been investigated by molecular dynamics simulations in an effort to understand the significant inhibition potency differences observed between some of these compounds and also to obtain more information about the possible movements of the loop. These computational studies have also allowed us to identify key structural factors of the H. pylori loop that could explain its reduced flexibility in comparison to the M. tuberculosis loop, specifically by the formation of a key salt bridge between the side chains of residues Asp18 and Arg20.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Gavin C. Fox
- Proxima 2, Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin, F-91192
Gif-sur-Yvette, France
| | - Mark J. van Raaij
- Departamento de Estructura de
Macromoléculas, Centro Nacional de Biotecnología (CSIC), Campus Cantoblanco, 28049 Madrid, Spain
| | - Heather Lamb
- Institute of Cell and Molecular
Biosciences, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, U.K
| | - Alastair R. Hawkins
- Institute of Cell and Molecular
Biosciences, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, U.K
| | | |
Collapse
|
18
|
Peón A, Coderch C, Gago F, González-Bello C. Comparative binding energy COMBINE analysis for understanding the binding determinants of type II dehydroquinase inhibitors. ChemMedChem 2013; 8:740-7. [PMID: 23450741 DOI: 10.1002/cmdc.201300013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Indexed: 11/08/2022]
Abstract
Herein we report comparative binding energy (COMBINE) analyses to derive quantitative structure-activity relationship (QSAR) models that help rationalize the determinants of binding affinity for inhibitors of type II dehydroquinase (DHQ2), the third enzyme of the shikimic acid pathway. Independent COMBINE models were derived for Helicobacter pylori and Mycobacterium tuberculosis DHQ2, which is an essential enzyme in both these pathogenic bacteria that has no counterpart in human cells. These studies quantify the importance of the hydrogen bonding interactions between the ligands and the water molecule involved in the DHQ2 reaction mechanism. They also highlight important differences in the ligand interactions with the interface pocket close to the active site that could provide guides for future inhibitor design.
Collapse
Affiliation(s)
- Antonio Peón
- Centro Singular de Investigación en Química Biológica y Materiales, Moleculares CIQUS, Universidad de Santiago de Compostela calle Jenaro de la Fuente s/n, 15782 Santiago de Compostela Spain
| | | | | | | |
Collapse
|
19
|
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.
Collapse
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
| | | | | |
Collapse
|
20
|
Chu WT, Zheng QC, Wu YJ, Zhang JL, Liang CY, Chen L, Xue Q, Zhang HX. Molecular dynamics (MD) simulations and binding free energy calculation studies between inhibitors and type II dehydroquinase (DHQ2). MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2012.708416] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
21
|
Jiang M, Xiong B, Shen YM, Yang C. Design, synthesis, and preliminary biological evaluation of novel ketone derivatives of shikimic acid. RSC Adv 2013. [DOI: 10.1039/c3ra43755h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
22
|
Theoretical study of the reaction mechanism of Mycobacterium tuberculosis type II dehydroquinate dehydratase. COMPUT THEOR CHEM 2012. [DOI: 10.1016/j.comptc.2012.10.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
23
|
Blanco B, Sedes A, Peón A, Lamb H, Hawkins AR, Castedo L, González-Bello C. Synthesis of 3-alkyl enol mimics inhibitors of type II dehydroquinase: factors influencing their inhibition potency. Org Biomol Chem 2012; 10:3662-76. [DOI: 10.1039/c2ob07081b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
24
|
Yao Y, Li ZS. New insights into the mechanism of the Schiff base hydrolysis catalyzed by type I dehydroquinate dehydratase from S. enterica: a theoretical study. Org Biomol Chem 2012; 10:7037-44. [DOI: 10.1039/c2ob25605c] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
25
|
Light SH, Minasov G, Shuvalova L, Peterson SN, Caffrey M, Anderson WF, Lavie A. A conserved surface loop in type I dehydroquinate dehydratases positions an active site arginine and functions in substrate binding. Biochemistry 2011; 50:2357-63. [PMID: 21291284 DOI: 10.1021/bi102020s] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Dehydroquinate dehydratase (DHQD) catalyzes the third step in the biosynthetic shikimate pathway. We present three crystal structures of the Salmonella enterica type I DHQD that address the functionality of a surface loop that is observed to close over the active site following substrate binding. Two wild-type structures with differing loop conformations and kinetic and structural studies of a mutant provide evidence of both direct and indirect mechanisms of involvement of the loop in substrate binding. In addition to allowing amino acid side chains to establish a direct interaction with the substrate, closure of the loop necessitates a conformational change of a key active site arginine, which in turn positions the substrate productively. The absence of DHQD in humans and its essentiality in many pathogenic bacteria make the enzyme a target for the development of nontoxic antimicrobials. The structures and ligand binding insights presented here may inform the design of novel type I DHQD inhibiting molecules.
Collapse
Affiliation(s)
- Samuel H Light
- Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, United States
| | | | | | | | | | | | | |
Collapse
|
26
|
Paz S, Tizón L, Otero JM, Llamas-Saiz AL, Fox GC, van Raaij MJ, Lamb H, Hawkins AR, Lapthorn AJ, Castedo L, González-Bello C. Tetrahydrobenzothiophene derivatives: conformationally restricted inhibitors of type II dehydroquinase. ChemMedChem 2010; 6:266-72. [PMID: 21275050 DOI: 10.1002/cmdc.201000343] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Revised: 10/12/2010] [Indexed: 11/10/2022]
Affiliation(s)
- Sonia Paz
- Departamento de Química Orgánica y Centro Singular de Investigación en Química Biológica y Materiales Moleculares, Universidad de Santiago de Compostela calle Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Peón A, Otero JM, Tizón L, Prazeres VFV, Llamas-Saiz AL, Fox GC, van Raaij MJ, Lamb H, Hawkins AR, Gago F, Castedo L, González-Bello C. Understanding the Key Factors that Control the Inhibition of Type II Dehydroquinase by (2R)-2-Benzyl-3-dehydroquinic Acids. ChemMedChem 2010; 5:1726-33. [DOI: 10.1002/cmdc.201000281] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
28
|
Prazeres VFV, Castedo L, Lamb H, Hawkins AR, González-Bello C. 2-substituted-3-dehydroquinic acids as potent competitive inhibitors of type II dehydroquinase. ChemMedChem 2010; 4:1980-4. [PMID: 19856378 DOI: 10.1002/cmdc.200900319] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Verónica F V Prazeres
- Laboratorio de Química Orgánica (CSIC) y Departamento de Química Orgánica, Facultad de Química, Universidad de Santiago de Compostela, Avenida de las Ciencias s/n, 15782 Santiago de Compostela, Spain
| | | | | | | | | |
Collapse
|
29
|
Tran AT, Cergol KM, Britton WJ, Imran Bokhari SA, Ibrahim M, Lapthorn AJ, Payne RJ. Rapid assembly of potent type II dehydroquinase inhibitorsvia “Click” chemistry. MEDCHEMCOMM 2010. [DOI: 10.1039/c0md00097c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The rapid synthesis of a library of potent type II dehydroquinase inhibitors is described. Inhibitors were prepared via a key quinate-derived ene-yne intermediate using Cu(i)-catalysed azide-alkyne cycloaddition (CuAAC) chemistry with a variety of aryl- and heteroaryl-azides.
Collapse
Affiliation(s)
- Anh Thu Tran
- School of Chemistry
- The University of Sydney
- Sydney
- Australia
| | | | - Warwick J. Britton
- Faculty of Medicine, Blackburn Building
- The University of Sydney
- NSW 2006
- Australia and Mycobacterial Research Program
- Centenary Institute
| | - Syed Ali Imran Bokhari
- Department of Chemistry and Division of Biochemistry and Life Science
- University of Glasgow
- UK
| | - Musadiq Ibrahim
- Department of Chemistry and Division of Biochemistry and Life Science
- University of Glasgow
- UK
| | - Adrian J. Lapthorn
- Department of Chemistry and Division of Biochemistry and Life Science
- University of Glasgow
- UK
| | | |
Collapse
|
30
|
Prazeres VFV, Tizón L, Otero JM, Guardado-Calvo P, Llamas-Saiz AL, van Raaij MJ, Castedo L, Lamb H, Hawkins AR, González-Bello C. Synthesis and Biological Evaluation of New Nanomolar Competitive Inhibitors of Helicobacter pylori Type II Dehydroquinase. Structural Details of the Role of the Aromatic Moieties with Essential Residues. J Med Chem 2009; 53:191-200. [DOI: 10.1021/jm9010466] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Verónica F. V. Prazeres
- Laboratorio de Química Orgánica (CSIC) y Departamento de Química Orgánica, Facultad de Química, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Lorena Tizón
- Laboratorio de Química Orgánica (CSIC) y Departamento de Química Orgánica, Facultad de Química, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - José M. Otero
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Pablo Guardado-Calvo
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Antonio L. Llamas-Saiz
- Unidad de Rayos X, Edificio CACTUS, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Mark J. van Raaij
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
- Instituto de Biología Molecular de Barcelona, Consejo Superior de Investigaciones Científicas (IBMB-CSIC), Parc Científic de Barcelona, Baldiri Reixach 10-12, E-08028 Barcelona, Spain
| | - Luis Castedo
- Laboratorio de Química Orgánica (CSIC) y Departamento de Química Orgánica, Facultad de Química, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Heather Lamb
- Institute of Cell and Molecular Biosciences, Medical School, University, Newcastle upon Tyne, Catherine Cookson Building, Framlington Place, Newcastle upon Tyne NE2 4HH, U.K
| | - Alastair R. Hawkins
- Institute of Cell and Molecular Biosciences, Medical School, University, Newcastle upon Tyne, Catherine Cookson Building, Framlington Place, Newcastle upon Tyne NE2 4HH, U.K
| | - Concepción González-Bello
- Laboratorio de Química Orgánica (CSIC) y Departamento de Química Orgánica, Facultad de Química, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| |
Collapse
|
31
|
Kumar A, Imran Siddiqi M, Miertus S. New molecular scaffolds for the design of Mycobacterium tuberculosis type II dehydroquinase inhibitors identified using ligand and receptor based virtual screening. J Mol Model 2009; 16:693-712. [DOI: 10.1007/s00894-009-0595-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2009] [Accepted: 09/14/2009] [Indexed: 10/20/2022]
|
32
|
Sánchez-Sixto C, Prazeres VF, Castedo L, Suh S, Lamb H, Hawkins A, Cañada F, Jiménez-Barbero J, González-Bello C. Competitive Inhibitors ofHelicobacter pylori Type II Dehydroquinase: Synthesis, Biological Evaluation, and NMR Studies. ChemMedChem 2008; 3:756-70. [DOI: 10.1002/cmdc.200700307] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|
33
|
Payne RJ, Peyrot F, Kerbarh O, Abell AD, Abell C. Rational Design, Synthesis, and Evaluation of Nanomolar Type II Dehydroquinase Inhibitors. ChemMedChem 2007; 2:1015-29. [PMID: 17487900 DOI: 10.1002/cmdc.200700032] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The in silico design, synthesis, and biological evaluation of ten potent type II dehydroquinase inhibitors are described. These compounds contain an anhydroquinate core, incorporated as a mimic of the enolate reaction intermediate. This substructure is attached by a variety of linking units to a terminal phenyl group that binds in an adjacent pocket. Inhibitors were synthesised from (-)-quinic acid using palladium-catalysed Stille and carboamidation chemistry. Several inhibitors exhibited nanomolar inhibition constants against type II dehydroquinases from Streptomyces coelicolor and Mycobacterium tuberculosis. These are among the most potent inhibitors of these enzymes reported to date.
Collapse
Affiliation(s)
- Richard J Payne
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK
| | | | | | | | | |
Collapse
|
34
|
Toscano MD, Payne RJ, Chiba A, Kerbarh O, Abell C. Nanomolar Inhibition of Type II Dehydroquinase Based on the Enolate Reaction Mechanism. ChemMedChem 2007; 2:101-12. [PMID: 17068841 DOI: 10.1002/cmdc.200600194] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We describe the rational design of a novel, highly potent inhibitor of type II dehydroquinase, the dicarboxylate 6. The incorporation of a carboxylate at the 3-position mimics the putative enolate intermediate in the reaction mechanism, and allows a potential electrostatic binding interaction with the arginine on the active site flap. This results in a 1000-fold increase in potency, making the dicarboxylate 6 the most potent inhibitor of type II dehydroquinase reported to date, with a high ligand efficiency of -0.68 kcal mol(-1) per nonhydrogen atom. The systematic dissection of 6 in compounds 7-12, all of which show a drop in potency, confirm the synergistic importance of the two carboxylates, the C3 and C4 hydroxyl groups, and the anhydroquinate ring structure for the potency of 6.
Collapse
Affiliation(s)
- Miguel D Toscano
- Department of Chemistry, University of Cambridge, University Chemical Laboratory, Lensfield Road, Cambridge, CB2 1EW, UK
| | | | | | | | | |
Collapse
|
35
|
González-Bello C, Castedo L. Progress in type II dehydroquinase inhibitors: From concept to practice. Med Res Rev 2007; 27:177-208. [PMID: 17004270 DOI: 10.1002/med.20076] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Scientists are concerned by an ever-increasing rise in bacterial resistance to antibiotics, particularly in diseases such as malaria, toxoplasmosis, tuberculosis, and pneumonia, where the currently used therapies become progressively less efficient. It is therefore necessary to develop new, safe, and more efficient antibiotics. Recently, the existence of the shikimic acid pathway has been demonstrated in certain parasites such as the malaria parasite. These types of parasites cause more than a million casualties per year, and their effects are particularly strong in people with a compromised immune system such as HIV patients. In such cases it is possible that inhibitors of this pathway could be active against a large variety of microorganisms responsible for the more opportunistic infections in HIV patients. Interest in this pathway has resulted in the development of a wide variety of inhibitors for the enzymes involved. This review covers recent progress made in the development of inhibitors of the third enzyme of this pathway, i.e., the type II dehydroquinase. The X-ray crystal structures of several dehydroquinases (Streptomyces coelicolor, Mycobacterium tuberculosis, etc.) with an inhibitor bound in the active site have recently been solved. These complexes identified a number of key interactions involved in inhibitor binding and have shed light on several aspects of the catalytic mechanism. These crystal structures have also proven to be a useful tool for the design of potent and selective enzyme inhibitors, a feature that will also be discussed.
Collapse
Affiliation(s)
- Concepción González-Bello
- Departamento de Química Orgánica, Facultad de Química, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
| | | |
Collapse
|
36
|
Prazeres VFV, Sánchez-Sixto C, Castedo L, Canales A, Cañada FJ, Jiménez-Barbero J, Lamb H, Hawkins AR, González-Bello C. Determination of the Bound Conformation of a Competitive Nanomolar Inhibitor ofMycobacterium tuberculosis Type II Dehydroquinase by NMR Spectroscopy. ChemMedChem 2006; 1:990-6. [PMID: 16952136 DOI: 10.1002/cmdc.200600100] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The synergy between tuberculosis and the AIDS epidemic, along with the surge of multidrug-resistant isolates of M. tuberculosis, has reaffirmed tuberculosis as a primary public health threat. It is therefore necessary to discover new, safe, and more efficient antibiotics against this disease. On the other hand, mapping the dynamic interactions of inhibitors of a target protein can provide information for the development of more potent inhibitors and consequently, more potent potential drugs. In this context, the conformational binding of our previously reported nanomolar inhibitor of M. tuberculosis type II dehydroquinase, the 3-nitrophenyl derivative 1, was studied using saturation transfer difference (STD) and transferred NOESY experiments. These studies have shown that in the bound state, one conformation of those present in solution of the competitive nanomolar inhibitor 3-nitrophenyl derivative 1 is selected. In the bound conformation, the aromatic ring is slightly shifted from coplanarity, with the double bond and the nitro group of 1 oriented towards the double bond side.
Collapse
Affiliation(s)
- Verónica F V Prazeres
- Laboratorio de Química Orgánica, CSIC and Departamento de Química Orgánica, Facultad de Química, Universidad de Santiago de Compostela, Avenida de las Ciencias s/n, 15782 Santiago de Compostela, Spain
| | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Robinson DA, Stewart KA, Price NC, Chalk PA, Coggins JR, Lapthorn AJ. Crystal Structures of Helicobacter pylori Type II Dehydroquinase Inhibitor Complexes: New Directions for Inhibitor Design. J Med Chem 2006; 49:1282-90. [PMID: 16480265 DOI: 10.1021/jm0505361] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The crystal structures of the type II dehydroquinase (DHQase) from Helicobacter pylori in complex with three competitive inhibitors have been determined. The inhibitors are the substrate analogue 2,3-anhydroquinate (FA1), citrate, and an oxoxanthene sulfonamide derivative (AH9095). Despite the very different chemical nature of the inhibitors, in each case the primary point of interaction with the enzyme is via the residues that bind the C1 functionalities of the substrate, 3-dehydroquinate, i.e., N76, H102, I103, and H104. The DHQase/AH9095 complex crystal structure shows that sulfonamides can form a scaffold for nonsubstrate-like inhibitors and identifies a large conserved hydrophobic patch at the entrance to the active site as a locus that can be exploited in the development of new ligands.
Collapse
Affiliation(s)
- David A Robinson
- Division of Biochemistry and Molecular Biology, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland, UK
| | | | | | | | | | | |
Collapse
|
38
|
Toscano MD, Stewart KA, Coggins JR, Lapthorn AJ, Abell C. Rational design of new bifunctional inhibitors of type II dehydroquinase. Org Biomol Chem 2005; 3:3102-4. [PMID: 16106291 DOI: 10.1039/b507156a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Selective inhibitors of type II dehydroquinase were rationally designed to explore a second binding-pocket in the active-site. The molecular modelling, synthesis, inhibition studies and crystal structure determination are described.
Collapse
Affiliation(s)
- Miguel D Toscano
- University Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW, UK
| | | | | | | | | |
Collapse
|
39
|
Sánchez-Sixto C, Prazeres VFV, Castedo L, Lamb H, Hawkins AR, González-Bello C. Structure-Based Design, Synthesis, and Biological Evaluation of Inhibitors ofMycobacteriumtuberculosisType II Dehydroquinase. J Med Chem 2005; 48:4871-81. [PMID: 16033267 DOI: 10.1021/jm0501836] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The syntheses by Suzuki cross-coupling of 12 5-aryl analogues of the known inhibitor (1R,3R,4R)-1,3,4-trihydroxycyclohex-5-en-1-carboxylic acid are reported. These compounds were found to be reversible competitive inhibitors against Mycobacterium tuberculosis type II dehydroquinase, the third enzyme of the shikimic acid pathway. The most potent inhibitor, the 3-nitrophenyl derivative, has a K(i) of 54 nM, over 180 times more potent than the reported inhibitor (1R,3R,4R)-5-fluoro-1,3,4-trihydroxycyclohex-5-en-1-carboxylic acid and more than 700 times lower than the K(M) of the substrate, making it the most potent known inhibitor against any type II dehydroquinase. Docking studies using GOLD (version 2.2) indicated a key electrostatic binding interaction between the aromatic rings and Arg19, a residue that has been identified as essential for enzyme activity.
Collapse
Affiliation(s)
- Cristina Sánchez-Sixto
- Departamento de Química Orgánica y Unidad Asociada al C.S.I.C., Facultad de Química, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | | | | | | | | | | |
Collapse
|
40
|
Nichols CE, Lockyer M, Hawkins AR, Stammers DK. Crystal structures of Staphylococcus aureus type I dehydroquinase from enzyme turnover experiments. Proteins 2004; 56:625-8. [PMID: 15229896 DOI: 10.1002/prot.20165] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- C E Nichols
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | | | | | | |
Collapse
|
41
|
González-Bello C, Lence E, Toscano MD, Castedo L, Coggins JR, Abell C. Parallel Solid-Phase Synthesis and Evaluation of Inhibitors of Streptomyces coelicolor Type II Dehydroquinase. J Med Chem 2003; 46:5735-44. [PMID: 14667226 DOI: 10.1021/jm030987q] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A series of 1-substituted and 4-substituted benzyl analogues of the known inhibitor (1S,3R,4R)-1,3,4-trihydroxy-5-cyclohexene-1-carboxylic acid has been synthesized and tested as inhibitors of Streptomyces coelicolor type II dehydroquinase. The solid-phase syntheses of 18 new analogues are reported. The most potent inhibitor, 2-nitrobenzyloxy analogue 5i, has K(i) of 8 microM, more than 30 times lower than the K(M) of the substrate and approximately 4 times more potent than the original inhibitor. The binding modes of the synthesized analogues in the active site were studied by molecular docking with GOLD 2.0.
Collapse
Affiliation(s)
- Concepción González-Bello
- Departamento de Química Orgánica y Unidad Asociada al C.S.I.C., Facultad de Química, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
| | | | | | | | | | | |
Collapse
|
42
|
Toscano MD, Frederickson M, Evans DP, Coggins JR, Abell C, González-Bello C. Design, synthesis and evaluation of bifunctional inhibitors of type II dehydroquinase. Org Biomol Chem 2003; 1:2075-83. [PMID: 12945898 DOI: 10.1039/b301731a] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Inhibitors of type II dehydroquinase were designed to straddle the two distinct binding sites identified for the inhibitor (1S,3R,4R)-1,3,4-trihydroxy-5-cyclohexene-1-carboxylic acid and a glycerol molecule in a crystallographic study of the Streptomyces coelicolor enzyme. A number of compounds were designed to incorporate characteristics of both ligands. These analogues were synthesized from quinic acid, and were assayed against type I (Salmonella typhi) and type II (S. coelicolor) dehydroquinases. None of the analogues showed inhibition for type I dehydroquinase. Six of the analogues were shown to have inhibition constants in the micromolar to low millimolar range against the S. coelicolor type II dehydroquinase, while two showed no inhibition. The binding modes of the analogues in the active site of the S. coelicolor enzyme were studied by molecular docking with GOLD1.2. These studies suggest a binding mode where the ring is in a similar position to (1S,3R,4R)-1,3,4-trihydroxy-5-cyclohexene-1-carboxylic acid in the crystal structure and the side-chain occupies part of the glycerol binding-pocket.
Collapse
Affiliation(s)
- Miguel D Toscano
- University Chemical Laboratory, Lensfield Road, Cambridge, UK CB2 1EW
| | | | | | | | | | | |
Collapse
|
43
|
Evans LDB, Roszak AW, Noble LJ, Robinson DA, Chalk PA, Matthews JL, Coggins JR, Price NC, Lapthorn AJ. Specificity of substrate recognition by type II dehydroquinases as revealed by binding of polyanions. FEBS Lett 2002; 530:24-30. [PMID: 12387860 DOI: 10.1016/s0014-5793(02)03346-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The interactions between the polyanionic ligands phosphate and sulphate and the type II dehydroquinases from Streptomyces coelicolor and Mycobacterium tuberculosis have been characterised using a combination of structural and kinetic methods. From both approaches, it is clear that interactions are more complex in the case of the latter enzyme. The data provide new insights into the differences between the two enzymes in terms of substrate recognition and catalytic efficiency and may also explain the relative potencies of rationally designed inhibitors. An improved route to the synthesis of the substrate 3-dehydroquinic acid (dehydroquinate) is described.
Collapse
Affiliation(s)
- Lewis D B Evans
- Division of Biochemistry and Molecular Biology, Institute of Biomedical and Life Sciences, University of Glasgow, UK
| | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Roszak AW, Robinson DA, Krell T, Hunter IS, Fredrickson M, Abell C, Coggins JR, Lapthorn AJ. The structure and mechanism of the type II dehydroquinase from Streptomyces coelicolor. Structure 2002; 10:493-503. [PMID: 11937054 DOI: 10.1016/s0969-2126(02)00747-5] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The structure of the type II DHQase from Streptomyces coelicolor has been solved and refined to high resolution in complexes with a number of ligands, including dehydroshikimate and a rationally designed transition state analogue, 2,3-anhydro-quinic acid. These structures define the active site of the enzyme and the role of key amino acid residues and provide snap shots of the catalytic cycle. The resolution of the flexible lid domain (residues 21-31) shows that the invariant residues Arg23 and Tyr28 close over the active site cleft. The tyrosine acts as the base in the initial proton abstraction, and evidence is provided that the reaction proceeds via an enol intermediate. The active site of the structure of DHQase in complex with the transition state analog also includes molecules of tartrate and glycerol, which provide a basis for further inhibitor design.
Collapse
Affiliation(s)
- Aleksander W Roszak
- Department of Chemistry, Institute of Biomedical and Life Sciences, University of Glasgow, Scotland, United Kingdom
| | | | | | | | | | | | | | | |
Collapse
|
45
|
Larsen NA, Heine A, Crane L, Cravatt BF, Lerner RA, Wilson IA. Structural basis for a disfavored elimination reaction in catalytic antibody 1D4. J Mol Biol 2001; 314:93-102. [PMID: 11724535 DOI: 10.1006/jmbi.2001.5112] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Murine antibody 1D4 selectively catalyzes a highly disfavored beta-elimination reaction. Crystal structures of unliganded 1D4 and 1D4 in complex with a transition-state analog (TSA) have elucidated a possible general base mode of catalysis. The structures of the unliganded and liganded Fabs were determined to 1.80 and 1.85 A resolution, respectively. The structure of the complex reveals a binding pocket with high shape complementarity to the TSA, which is recruited to coerce the substrate into the sterically demanding, eclipsed conformation that is required for catalysis. A histidine residue and two water molecules are likely involved in the catalysis. The structure supports either a concerted E2 or stepwise E1cB-like mechanism for elimination. Finally, the liganded 1D4 structure shows minor conformational rearrangements in CDR H2, indicative of induced-fit binding of the hapten. 1D4 has pushed the boundaries of antibody-mediated catalysis into the realm of disfavored reactions and, hence, represents an important milestone in the development of this technology.
Collapse
Affiliation(s)
- N A Larsen
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Rd., La Jolla, CA 92037, USA
| | | | | | | | | | | |
Collapse
|
46
|
Mahmud T, Xu J, Choi YU. Synthesis of 5-epi-[6-(2)H(2)]valiolone and stereospecifically monodeuterated 5-epi-valiolones: exploring the steric course of 5-epi-valiolone dehydratase in validamycin A biosynthesis. J Org Chem 2001; 66:5066-73. [PMID: 11463258 DOI: 10.1021/jo0101003] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In validamycin A biosynthesis, as well as that of acarbose, the valienamine and validamine moieties are ultimately derived from a C(7) sugar, sedoheptulose 7-phosphate, which is cyclized to 2-epi-5-epi-valiolone by a cyclase that operates via a dehydroquinate (DHQ) synthase-like mechanism. 2-epi-5-epi-Valiolone is first epimerized at C-2 to give 5-epi-valiolone and then dehydrated between C-5 and C-6 to yield valienone. To probe the dehydration mechanism of 5-epi-valiolone to valienone, stereospecifically 6alpha- and 6beta-monodeuterated 5-epi-valiolones were synthesized. The key step in the synthesis was desulfurization of the tetrabenzyl-6,6-bis(methylthio)-5-epi-valiolone and introduction of the deuterium utilizing Zn, NiCl(2), ND(4)Cl/D(2)O, and THF. Extensive studies using various combinations of protio- and deuteroreagents and solvents probed the mechanism of the reductive desulfurization, which is crucial for the preparation of stereospecifically monodeuterated 5-epi-valiolones. Incorporation experiments with the labeled precursors in the validamycin A producer strain, Streptomyces hygroscopicus var. limoneus, revealed that the dehydration of 5-epi-valiolone to valienone occurs by a syn elimination of water.
Collapse
Affiliation(s)
- T Mahmud
- Department of Chemistry, Box 351700, University of Washington, Seattle, Washington 98195-1700, USA.
| | | | | |
Collapse
|
47
|
Bornemann S, Theoclitou ME, Brune M, Webb MR, Thorneley RN, Abell C. A Secondary beta Deuterium Kinetic Isotope Effect in the Chorismate Synthase Reaction. Bioorg Chem 2000; 28:191-204. [PMID: 11034781 DOI: 10.1006/bioo.2000.1174] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Chorismate synthase (EC 4.6.1.4) is the shikimate pathway enzyme that catalyzes the conversion of 5-enolpyruvylshikimate 3-phosphate (EPSP) to chorismate. The enzyme reaction is unusual because it involves a trans-1,4 elimination of the C-3 phosphate and the C-6 proR hydrogen and it has an absolute requirement for reduced flavin. Several mechanisms have been proposed to account for the cofactor requirement and stereochemistry of the reaction, including a radical mechanism. This paper describes the synthesis of [4-(2)H]EPSP and the observation of kinetic isotope effects using this substrate with both Neurospora crassa and Escherichia coli chorismate synthases. The magnitude of the effects were (D)(V) = 1.08 +/- 0.01 for the N. crassa enzyme and 1.10 +/- 0.02 on phosphate release under single-turnover conditions for the E. coli enzyme. The effects are best rationalised as substantial secondary beta isotope effects. It is most likely that the C(3)-O bond is cleaved first in a nonconcerted E1 or radical reaction mechanism. Although this study alone cannot rule out a concerted E2-type mechanism, the C(3)-O bond would have to be substantially more broken than the proR C(6)-H bond in a transition state of such a mechanism. Importantly, although the E. coli and N. crassa enzymes have different rate limiting steps, their catalytic mechanisms are most likely to be chemically identical. Copyright 2000 Academic Press.
Collapse
Affiliation(s)
- S Bornemann
- Biological Chemistry Department, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, United Kingdom
| | | | | | | | | | | |
Collapse
|
48
|
Bello CG, Harris JM, Manthey MK, Coggins JR, Abell C. Irreversible inhibition of type I dehydroquinase by substrates for type II dehydroquinase. Bioorg Med Chem Lett 2000; 10:407-9. [PMID: 10743936 DOI: 10.1016/s0960-894x(00)00057-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Mechanistic differences between type I and type II dehydroquinases have been exploited in the design of type specific inhibitors. (2R)-2-Bromo-3-dehydroquinic acid (3), (2R)-2-fluoro-3-dehydroquinic acid (5) and 2-bromo-3-dehydroshikimic acid (4), all excellent substrates for type II dehydroquinase, are shown to be irreversible inhibitors of type I dehydroquinase.
Collapse
Affiliation(s)
- C G Bello
- Cambridge Centre for Molecular Recognition, University Chemical Laboratory, UK
| | | | | | | | | |
Collapse
|
49
|
Parker EJ, González Bello C, Coggins JR, Hawkins AR, Abell C. Mechanistic studies on type I and type II dehydroquinase with (6R)- and (6S)-6-fluoro-3-dehydroquinic acids. Bioorg Med Chem Lett 2000; 10:231-4. [PMID: 10698442 DOI: 10.1016/s0960-894x(99)00660-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
(6R)- and (6S)-6-Fluoro-3-dehydroquinic acids are shown to be substrates for type I and type II dehydroquinases. Their differential reactivity provides insight into details of the reaction mechanism and enables a novel enzyme-substrate imine to be trapped on the type I enzyme.
Collapse
Affiliation(s)
- E J Parker
- University Chemical Laboratory, Cambridge, UK
| | | | | | | | | |
Collapse
|
50
|
Frederickson M, Parker EJ, Hawkins AR, Coggins JR, Abell C. Selective Inhibition of Type II Dehydroquinases. J Org Chem 1999; 64:2612-2613. [PMID: 11674325 DOI: 10.1021/jo990004q] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Martyn Frederickson
- University Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW, England, Department of Biochemistry and Genetics, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, England, and Department of Biochemistry and Molecular Biology, University of Glasgow, Glasgow G12 8QQ, Scotland
| | | | | | | | | |
Collapse
|