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Pawar A, Konwar C, Jha P, Kant R, Chopra M, Chaudhry U, Saluja D. Bactericidal activity of esculetin is associated with impaired cell wall synthesis by targeting glutamate racemase of Neisseria gonorrhoeae. Mol Divers 2024; 28:3181-3198. [PMID: 37880544 DOI: 10.1007/s11030-023-10745-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 10/08/2023] [Indexed: 10/27/2023]
Abstract
Neisseria gonorrhoeae (NG), the causative organism of gonorrhea, has been classified by the World Health Organization as 'Priority' two organism owing to its increased resistance to antibiotics and even failure of recommended dual therapy with ceftriaxone and azithromycin. As a result, the general and reproductive health of infected individuals is severely compromised. The imminent public health catastrophe of antimicrobial-resistant gonococci cannot be understated, as t he of severe complications and sequelae of infection are not only increasing but their treatment has also become more expensive. Tenacious attempts are underway to discover novel drug targets as well as new drugs to fight against NG. Therefore, a considerable number of phytochemicals have been tested for their remedial intercession via targeting bacterial proteins. The MurI gene encodes for an enzyme called glutamate racemase (MurI) that is primarily involved in peptidoglycan (PG) biosynthesis and is specific to the bacterial kingdom and hence can be exploited as a potential drug target for the treatment of bacterial diseases. Accordingly, diverse families of phytochemicals were screened in silico for their binding affinity with N. Gonorrhoeae MurI (NG-MurI) protein. Esculetin, one of the shortlisted compounds, was evaluated for its functional, structural, and anti-bacterial activity. Treatment with esculetin resulted in growth inhibition, cell wall damage, and altered permeability as revealed by fluorescence and electron microscopy. Furthermore, esculetin inhibited the racemization activity of recombinant, purified NG-MurI protein, one of the enzymes required for peptidoglycan biosynthesis. Our results suggest that esculetin could be further explored as a lead compound for developing new drug molecules against multidrug-resistant strains.
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Affiliation(s)
- Alka Pawar
- Dr. B. R. Ambedkar Center for Biomedical Research, Delhi School of Public Health, IoE, University of Delhi, Delhi, 110007, India
| | - Chandrika Konwar
- Dr. B. R. Ambedkar Center for Biomedical Research, Delhi School of Public Health, IoE, University of Delhi, Delhi, 110007, India
| | - Prakash Jha
- Dr. B. R. Ambedkar Center for Biomedical Research, Delhi School of Public Health, IoE, University of Delhi, Delhi, 110007, India
| | - Ravi Kant
- Dr. B. R. Ambedkar Center for Biomedical Research, Delhi School of Public Health, IoE, University of Delhi, Delhi, 110007, India
| | - Madhu Chopra
- Dr. B. R. Ambedkar Center for Biomedical Research, Delhi School of Public Health, IoE, University of Delhi, Delhi, 110007, India
| | - Uma Chaudhry
- Bhaskaracharya College of Applied Sciences, University of Delhi, Delhi, 110075, India
| | - Daman Saluja
- Dr. B. R. Ambedkar Center for Biomedical Research, Delhi School of Public Health, IoE, University of Delhi, Delhi, 110007, India.
- Delhi School of Public Health, IoE, University of Delhi, Delhi, 110007, India.
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2
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Ruan S, Tu CH, Bourne CR. Friend or Foe: Protein Inhibitors of DNA Gyrase. BIOLOGY 2024; 13:84. [PMID: 38392303 PMCID: PMC10886550 DOI: 10.3390/biology13020084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/20/2024] [Accepted: 01/26/2024] [Indexed: 02/24/2024]
Abstract
DNA gyrase is essential for the successful replication of circular chromosomes, such as those found in most bacterial species, by relieving topological stressors associated with unwinding the double-stranded genetic material. This critical central role makes gyrase a valued target for antibacterial approaches, as exemplified by the highly successful fluoroquinolone class of antibiotics. It is reasonable that the activity of gyrase could be intrinsically regulated within cells, thereby helping to coordinate DNA replication with doubling times. Numerous proteins have been identified to exert inhibitory effects on DNA gyrase, although at lower doses, it can appear readily reversible and therefore may have regulatory value. Some of these, such as the small protein toxins found in plasmid-borne addiction modules, can promote cell death by inducing damage to DNA, resulting in an analogous outcome as quinolone antibiotics. Others, however, appear to transiently impact gyrase in a readily reversible and non-damaging mechanism, such as the plasmid-derived Qnr family of DNA-mimetic proteins. The current review examines the origins and known activities of protein inhibitors of gyrase and highlights opportunities to further exert control over bacterial growth by targeting this validated antibacterial target with novel molecular mechanisms. Furthermore, we are gaining new insights into fundamental regulatory strategies of gyrase that may prove important for understanding diverse growth strategies among different bacteria.
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Affiliation(s)
- Shengfeng Ruan
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Chih-Han Tu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Christina R Bourne
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
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3
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Kant R, Jha P, Saluja D, Chopra M. Identification of novel inhibitors of Neisseria gonorrhoeae MurI using homology modeling, structure-based pharmacophore, molecular docking, and molecular dynamics simulation-based approach. J Biomol Struct Dyn 2023; 41:7433-7446. [PMID: 36106953 DOI: 10.1080/07391102.2022.2121943] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 09/01/2022] [Indexed: 10/14/2022]
Abstract
MurI is one of the most significant role players in the biosynthesis of the peptidoglycan layer in Neisseria gonorrhoeae (Ng). We attempted to highlight the structural and functional relationship between Ng-MurI and D-glutamate to design novel molecules targeting this interaction. The three-dimensional (3D) model of the protein was constructed by homology modeling and the quality and consistency of generated model were assessed. The binding site of the protein was identified by molecular docking studies and a pharmacophore was identified using the interactions of the control ligand. The structure-based pharmacophore model was validated and employed for high-throughput virtual screening and molecular docking to identify novel Ng-MurI inhibitors. Finally, the model was optimized by molecular dynamics (MD) simulations and the optimized model complex with the substrate glutamate and novel molecules facilitated us to confirm the stability of the protein-ligand docked complexes. The 100 ns MD simulations of the potential lead compounds with protein confirmed that the modeled complexes were stable. This study identifies novel potential compounds with good fitness and docking scores, which made the interactions of biological significance within the protein active site. Hence, the identified compounds may act as new leads to design and develop Ng-MurI inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ravi Kant
- Medical Biotechnology Laboratory, Dr. B. R. Ambedkar Center for Biomedical Research & Delhi School of Public Health, IoE, University of Delhi, Delhi, India
| | - Prakash Jha
- Laboratory of Molecular Modeling and Drug Development, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - Daman Saluja
- Medical Biotechnology Laboratory, Dr. B. R. Ambedkar Center for Biomedical Research & Delhi School of Public Health, IoE, University of Delhi, Delhi, India
| | - Madhu Chopra
- Laboratory of Molecular Modeling and Drug Development, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
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4
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Iida S, Nakamura HK, Mashimo T, Fukunishi Y. Structural Fluctuations of Aromatic Residues in an Apo-Form Reveal Cryptic Binding Sites: Implications for Fragment-Based Drug Design. J Phys Chem B 2020; 124:9977-9986. [PMID: 33140952 DOI: 10.1021/acs.jpcb.0c04963] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Cryptic sites are binding pockets that are transiently formed in an apo form or that are induced by ligand binding. The investigation of cryptic sites is crucial for drug discovery, since these sites are ubiquitous in disease-related human proteins, and targeting them expands the number of drug targets greatly. However, although many computational studies have attempted to identify cryptic sites, the detection remains challenging. Here, we aimed to characterize and detect cryptic sites in terms of structural fluctuations in an apo form, investigating proteins each of which possesses a cryptic site. From their X-ray structures, we saw that aromatic residues tended to be found in cryptic sites. To examine structural fluctuations of the apo forms, we performed molecular dynamics (MD) simulations, producing probability distributions of the solvent-accessible surface area per aromatic residue. To detect aromatic residues in cryptic sites, we have proposed a "cryptic-site index" based on the distribution, demonstrating the performance via several measures, such as recall and specificity. Besides, we found that high-ranking aromatic residues were likely to probe concaves in a cryptic site. This implies that such fluctuations provide a profile of scaffolds of compounds with the potential to bind to a particular cryptic site.
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Affiliation(s)
- Shinji Iida
- Technology Research Association for Next-Generation Natural Products Chemistry, 2-3-26, Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Hironori K Nakamura
- Biomodeling Research Co., Ltd., 1-704-2, Uedanishi, Tenpaku-ku, Nagoya, Aichi 468-0058, Japan
| | - Tadaaki Mashimo
- Technology Research Association for Next-Generation Natural Products Chemistry, 2-3-26, Aomi, Koto-ku, Tokyo 135-0064, Japan.,IMSBIO Co., Ltd., 4-21-1, Higashiikebukuro, Toshima-ku, Tokyo 170-0013, Japan
| | - Yoshifumi Fukunishi
- Cellular and Molecular Biotechnology Research Institute, AIST Tokyo Waterfront, 2-3-26 Aomi, Koto-ku, Tokyo 135-0064, Japan
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5
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Fischer C, Ahn YC, Vederas JC. Catalytic mechanism and properties of pyridoxal 5'-phosphate independent racemases: how enzymes alter mismatched acidity and basicity. Nat Prod Rep 2020; 36:1687-1705. [PMID: 30994146 DOI: 10.1039/c9np00017h] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Covering: up to March 2019 Amino acid racemases and epimerases are key enzymes that invert the configuration of common amino acids and supply many corresponding d-isomers in living organisms. Some d-amino acids are inherently bioactive, whereas others are building blocks for important biomolecules, for example lipid II, the bacterial cell wall precursor. Peptides containing them have enhanced proteolytic stability and can act as important recognition elements in mammalian systems. Selective inhibition of certain amino acid racemases (e.g. glutamate racemase) is believed to offer a promising target for new antibacterial drugs effective against pathogens resistant to current antibiotics. Many amino acid racemases employ imine formation with pyridoxal phosphate (PLP) as a cofactor to accelerate the abstraction of the alpha proton. However, the group reviewed herein achieves racemization of free amino acids without the use of cofactors or metals, and uses a thiol/thiolate pair for deprotonation and reprotonation. All bacteria and higher plants contain such enzymes, for example diaminopimelate epimerase, which is required for lysine biosynthesis in these organisms. This process cannot be accomplished without an enzyme catalyst as the acidities of a thiol and the substrate α-hydrogen are inherently mismatched by at least 10 orders of magnitude. This review describes the structural and mechanistic studies on PLP-independent racemases and the evolving view of key enzymatic machinery that accomplishes these remarkable transformations.
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Affiliation(s)
- Conrad Fischer
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, Alberta, Canada T6G 2G2.
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Singh H, Das S, Yadav J, Srivastava VK, Jyoti A, Kaushik S. In search of novel protein drug targets for treatment of Enterococcus faecalis infections. Chem Biol Drug Des 2019; 94:1721-1739. [PMID: 31260188 DOI: 10.1111/cbdd.13582] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 06/08/2019] [Accepted: 06/17/2019] [Indexed: 12/27/2022]
Abstract
Enterococcus faecalis (Ef) is one of the major pathogens involved in hospital-acquired infections. It can cause nosocomial bacteremia, surgical wound infection, and urinary tract infection. It is important to mention here that Ef is developing resistance against many commonly occurring antibiotics. The occurrence of multidrug resistance (MDR) and extensive-drug resistance (XDR) is now posing a major challenge to the medical community. In this regard, to combat the infections caused by Ef, we have to look for an alternative. Rational structure-based drug design exploits the three-dimensional structure of the target protein, which can be unraveled by various techniques such as X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. In this review, we have discussed the complete picture of Ef infections, the possible treatment available at present, and the alternative treatment options to be explored. This study will help in better understanding of novel biological targets against Ef and the compounds, which are likely to bind with these targets. Using these detailed structural informations, rational structure-based drug design is achievable and tight inhibitors against Ef can be prepared.
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Affiliation(s)
- Harpreet Singh
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Satyajeet Das
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Jyoti Yadav
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | | | - Anupam Jyoti
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Sanket Kaushik
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
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Mackie J, Kumar H, Bearne SL. Changes in quaternary structure cause a kinetic asymmetry of glutamate racemase-catalyzed homocysteic acid racemization. FEBS Lett 2018; 592:3399-3413. [PMID: 30194685 DOI: 10.1002/1873-3468.13248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 07/30/2018] [Accepted: 08/24/2018] [Indexed: 11/07/2022]
Abstract
Glutamate racemases (GR) catalyze the racemization of d- and l-glutamate and are targets for the development of antibiotics. We demonstrate that GR from the periodontal pathogen Fusobacterium nucleatum (FnGR) catalyzes the racemization of d-homocysteic acid (d-HCA), while l-HCA is a poor substrate. This enantioselectivity arises because l-HCA perturbs FnGR's monomer-dimer equilibrium toward inactive monomer. The inhibitory effect of l-HCA may be overcome by increasing the total FnGR concentration or by adding glutamate, but not by blocking access to the active site through site-directed mutagenesis, suggesting that l-HCA binds at an allosteric site. This phenomenon is also exhibited by GR from Bacillus subtilis, suggesting that enantiospecific, "substrate"-induced dissociation of oligomers to form inactive monomers may furnish a new inhibition strategy.
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Affiliation(s)
- Joanna Mackie
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Canada
| | - Himank Kumar
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Canada
| | - Stephen L Bearne
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Canada.,Department of Chemistry, Dalhousie University, Halifax, Canada
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8
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Alcolombri U, Lei L, Meltzer D, Vardi A, Tawfik DS. Assigning the Algal Source of Dimethylsulfide Using a Selective Lyase Inhibitor. ACS Chem Biol 2017; 12:41-46. [PMID: 28103686 DOI: 10.1021/acschembio.6b00844] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Atmospheric dimethylsulfide (DMS) is massively produced in the oceans by bacteria, algae, and corals. To enable identification of DMS sources, we developed a potent mechanism-based inhibitor of the algal Alma dimethylsulfoniopropionate lyase family that does not inhibit known bacterial lyases. Its application to coral holobiont indicates that DMS originates from Alma lyase(s). This biochemical profiling may complement meta-genomics and transcriptomics to provide better understanding of the marine sulfur cycle.
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Affiliation(s)
- Uria Alcolombri
- Department
of Biomolecular Sciences and ‡Department of Plant and Environmental
Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Lei Lei
- Department
of Biomolecular Sciences and ‡Department of Plant and Environmental
Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Diana Meltzer
- Department
of Biomolecular Sciences and ‡Department of Plant and Environmental
Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Assaf Vardi
- Department
of Biomolecular Sciences and ‡Department of Plant and Environmental
Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Dan S. Tawfik
- Department
of Biomolecular Sciences and ‡Department of Plant and Environmental
Sciences, Weizmann Institute of Science, Rehovot, Israel
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9
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Biochemical Characterization of Glutamate Racemase-A New Candidate Drug Target against Burkholderia cenocepacia Infections. PLoS One 2016; 11:e0167350. [PMID: 27898711 PMCID: PMC5127577 DOI: 10.1371/journal.pone.0167350] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 11/12/2016] [Indexed: 11/19/2022] Open
Abstract
The greatest obstacle for the treatment of cystic fibrosis patients infected with the Burkholderia species is their intrinsic antibiotic resistance. For this reason, there is a need to develop new effective compounds. Glutamate racemase, an essential enzyme for the biosynthesis of the bacterial cell wall, is an excellent candidate target for the design of new antibacterial drugs. To this aim, we recombinantly produced and characterized glutamate racemase from Burkholderia cenocepacia J2315. From the screening of an in-house library of compounds, two Zn (II) and Mn (III) 1,3,5-triazapentadienate complexes were found to efficiently inhibit the glutamate racemase activity with IC50 values of 35.3 and 10.0 μM, respectively. Using multiple biochemical approaches, the metal complexes have been shown to affect the enzyme activity by binding to the enzyme-substrate complex and promoting the formation of an inhibited dimeric form of the enzyme. Our results corroborate the value of glutamate racemase as a good target for the development of novel inhibitors against Burkholderia.
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Exploring the structure of glutamate racemase from Mycobacterium tuberculosis as a template for anti-mycobacterial drug discovery. Biochem J 2016; 473:1267-80. [PMID: 26964898 DOI: 10.1042/bcj20160186] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 03/09/2016] [Indexed: 11/17/2022]
Abstract
Glutamate racemase (MurI) is responsible for providing D-glutamate for peptidoglycan biosynthesis in bacteria and has been a favoured target in pharmaceutical drug design efforts. It has recently been proven to be essential in Mycobacterium tuberculosis, the causative organism of tuberculosis, a disease for which new medications are urgently needed. In the present study, we have determined the protein crystal structures of MurI from both M. tuberculosis and Mycobacterium smegmatis in complex with D-glutamate to 2.3 Å and 1.8 Å resolution respectively. These structures are conserved, but reveal differences in their active site architecture compared with that of other MurI structures. Furthermore, compounds designed to target other glutamate racemases have been screened but do not inhibit mycobacterial MurI, suggesting that a new drug design effort will be needed to develop inhibitors. A new type of MurI dimer arrangement has been observed in both structures, and this arrangement becomes the third biological dimer geometry for MurI found to date. The mycobacterial MurI dimer is tightly associated, with a KD in the nanomolar range. The enzyme binds D- and L-glutamate specifically, but is inactive in solution unless the dimer interface is mutated. We created triple mutants of this interface in the M. smegmatis glutamate racemase (D26R/R105A/G194R or E) that have appreciable activity (kcat=0.056-0.160 min(-1) and KM=0.26-0.51 mM) and can be utilized to screen proposed antimicrobial candidates for inhibition.
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11
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Whalen KL, Spies MA. Flooding enzymes: quantifying the contributions of interstitial water and cavity shape to ligand binding using extended linear response free energy calculations. J Chem Inf Model 2013; 53:2349-59. [PMID: 24111836 PMCID: PMC3782002 DOI: 10.1021/ci400244x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Glutamate
racemase (GR) is a cofactor independent amino acid racemase that has
recently garnered increasing attention as an antimicrobial drug target.
There are numerous high resolution crystal structures of GR, yet these
are invariably bound to either d-glutamate or very weakly
bound oxygen-based salts. Recent in silico screens have identified
a number of new competitive inhibitor scaffolds, which are not based
on d-Glu, but exploit many of the same hydrogen bond donor
positions. In silico studies on 1-H-benzimidazole-2-sulfonic
acid (BISA) show that the sulfonic acid points to the back of the
GR active site, in the most buried region, analogous to the C2-carboxylate
binding position in the GR-d-glutamate complex. Furthermore,
BISA has been shown to be the strongest nonamino acid competitive
inhibitor. Previously published computational studies have suggested
that a portion of this binding strength is derived from complexation
with a more closed active site, relative to weaker ligands, and in
which the internal water network is more isolated from the bulk solvent.
In order to validate key contacts between the buried sulfonate moiety
of BISA and moieties in the back of the enzyme active site, as well
as to probe the energetic importance of the potentially large number
of interstitial waters contacted by the BISA scaffold, we have designed
several mutants of Asn75. GR-N75A removes a key hydrogen bond donor
to the sulfonate of BISA, but also serves to introduce an additional
interstitial water, due to the newly created space of the mutation.
GR- N75L should also show the loss of a hydrogen bond donor to the
sulfonate of BISA, but does not (a priori) seem to permit an additional
interstitial water contact. In order to investigate the dynamics,
structure, and energies of this water-mediated complexation, we have
employed the extended linear response (ELR) approach for the calculation
of binding free energies to GR, using the YASARA2 knowledge based
force field on a set of ten GR complexes, and yielding an R-squared
value of 0.85 and a RMSE of 2.0 kJ/mol. Surprisingly, the inhibitor
set produces a uniformly large interstitial water contribution to
the electrostatic interaction energy (⟨Vel⟩), ranging from 30 to >50%, except for the natural
substrate (d-glutamate), which has only a 7% contribution
of ⟨Vel⟩ from water. The
broader implications for predicting and exploiting significant interstitial
water contacts in ligand–enzyme complexation are discussed.
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Affiliation(s)
- Katie L Whalen
- College of Pharmacy, Division of Medicinal and Natural Products Chemistry, and ‡Carver College of Medicine, Department of Biochemistry, The University of Iowa , Iowa City, Iowa 52242, United States
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Tamay-Cach F, Correa-Basurto J, Villa-Tanaca L, Mancilla-Percino T, Juárez-Montiel M, Trujillo-Ferrara JG. Evaluation of new antimicrobial agents on Bacillus spp. strains: docking affinity and in vitro inhibition of glutamate-racemase. J Enzyme Inhib Med Chem 2012; 28:1026-33. [DOI: 10.3109/14756366.2012.705837] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Feliciano Tamay-Cach
- Departamento de Bioquímica y Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón,
Casco de Santo Tomas, México, México
| | - José Correa-Basurto
- Departamento de Bioquímica y Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón,
Casco de Santo Tomas, México, México
- Laboratorio de Modelado Molecular y Bioinformática de la Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional,
Plan de San Luis y Díaz Mirón, México
| | - Lourdes Villa-Tanaca
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación Carpio y Plan de Ayala,
Casco de Santo Tomas, México, México
| | - Teresa Mancilla-Percino
- Departamento de Química, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional,
México, D.F., México
| | - Margarita Juárez-Montiel
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación Carpio y Plan de Ayala,
Casco de Santo Tomas, México, México
| | - José G. Trujillo-Ferrara
- Departamento de Bioquímica y Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón,
Casco de Santo Tomas, México, México
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Selwood T, Jaffe EK. Dynamic dissociating homo-oligomers and the control of protein function. Arch Biochem Biophys 2012; 519:131-43. [PMID: 22182754 PMCID: PMC3298769 DOI: 10.1016/j.abb.2011.11.020] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Revised: 11/16/2011] [Accepted: 11/28/2011] [Indexed: 11/20/2022]
Abstract
Homo-oligomeric protein assemblies are known to participate in dynamic association/disassociation equilibria under native conditions, thus creating an equilibrium of assembly states. Such quaternary structure equilibria may be influenced in a physiologically significant manner either by covalent modification or by the non-covalent binding of ligands. This review follows the evolution of ideas about homo-oligomeric equilibria through the 20th and into the 21st centuries and the relationship of these equilibria to allosteric regulation by the non-covalent binding of ligands. A dynamic quaternary structure equilibria is described where the dissociated state can have alternate conformations that cannot reassociate to the original multimer; the alternate conformations dictate assembly to functionally distinct alternate multimers of finite stoichiometry. The functional distinction between different assemblies provides a mechanism for allostery. The requirement for dissociation distinguishes this morpheein model of allosteric regulation from the classical MWC concerted and KNF sequential models. These models are described alongside earlier dissociating allosteric models. The identification of proteins that exist as an equilibrium of diverse native quaternary structure assemblies has the potential to define new targets for allosteric modulation with significant consequences for further understanding and/or controlling protein structure and function. Thus, a rationale for identifying proteins that may use the morpheein model of allostery is presented and a selection of proteins for which published data suggests this mechanism may be operative are listed.
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Affiliation(s)
- Trevor Selwood
- Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111
| | - Eileen K. Jaffe
- Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111
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14
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Kinetic characterization and quaternary structure of glutamate racemase from the periodontal anaerobe Fusobacterium nucleatum. Arch Biochem Biophys 2009; 491:16-24. [DOI: 10.1016/j.abb.2009.09.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2009] [Revised: 09/11/2009] [Accepted: 09/15/2009] [Indexed: 11/17/2022]
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Crystal Structure of Diaminopimelate Epimerase from Arabidopsis thaliana, an Amino Acid Racemase Critical for l-Lysine Biosynthesis. J Mol Biol 2009; 385:580-94. [DOI: 10.1016/j.jmb.2008.10.072] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2008] [Revised: 09/16/2008] [Accepted: 10/28/2008] [Indexed: 11/23/2022]
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16
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Fisher SL. Glutamate racemase as a target for drug discovery. Microb Biotechnol 2008; 1:345-60. [PMID: 21261855 PMCID: PMC3815242 DOI: 10.1111/j.1751-7915.2008.00031.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2007] [Revised: 01/11/2008] [Accepted: 02/15/2008] [Indexed: 11/28/2022] Open
Abstract
The bacterial cell wall is a highly cross-linked polymeric structure consisting of repeating peptidoglycan units, each of which contains a novel pentapeptide substitution which is cross-linked through transpeptidation. The incorporation of D-glutamate as the second residue is strictly conserved across the bacterial kingdom. Glutamate racemase, a member of the cofactor-independent, two-thiol-based family of amino acid racemases, has been implicated in the production and maintenance of sufficient d-glutamate pool levels required for growth. The subject of over four decades of research, it is now evident that the enzyme is conserved and essential for growth across the bacterial kingdom and has a conserved overall topology and active site architecture; however, several different mechanisms of regulation have been observed. These traits have recently been targeted in the discovery of both narrow and broad spectrum inhibitors. This review outlines the biological history of this enzyme, the recent biochemical and structural characterization of isozymes from a wide range of species and developments in the identification of inhibitors that target the enzyme as possible therapeutic agents.
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Affiliation(s)
- Stewart L Fisher
- Infection Discovery, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA.
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Lin YM, Chou IC, Wang JF, Ho FI, Chu YJ, Huang PC, Lu DK, Shen HL, Elbaz M, Huang SM, Cheng CP. Transposon mutagenesis reveals differential pathogenesis of Ralstonia solanacearum on tomato and Arabidopsis. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2008; 21:1261-1270. [PMID: 18700830 DOI: 10.1094/mpmi-21-9-1261] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Ralstonia solanacearum causes a deadly wilting disease on a wide range of crops. To elucidate pathogenesis of this bacterium in different host plants, we set out to identify R. solanacearum genes involved in pathogenesis by screening random transposon insertion mutants of a highly virulent strain, Pss190, on tomato and Arabidopsis thaliana. Mutants exhibiting various decreased virulence levels on these two hosts were identified. Sequence analysis showed that most, but not all, of the identified pathogenesis genes are conserved among distinct R. solanacearum strains. A few of the disrupted loci were not reported previously as being involved in R. solanacearum pathogenesis. Notably, a group of mutants exhibited differential pathogenesis on tomato and Arabidopsis. These results were confirmed by characterizing allelic mutants in one other R. solanacearum strain of the same phylotype. The significantly decreased mutants' colonization in Arabidopsis was found to be correlated with differential pathogenesis on these two plants. Differential requirement of virulence genes suggests adaptation of this bacterium in different host environments. Together, this study reveals commonalities and differences of R. solanacearum pathogenesis on single solanaceous and nonsolanaceous hosts, and provides important new insights into interactions between R. solanacearum and different host plants.
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Affiliation(s)
- Yu-Mei Lin
- Graduate Institute of Plant Biology, Department of Life Science, National Taiwan University, Taipei, Taiwan. Republic of China
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Barreteau H, Kovac A, Boniface A, Sova M, Gobec S, Blanot D. Cytoplasmic steps of peptidoglycan biosynthesis. FEMS Microbiol Rev 2008; 32:168-207. [PMID: 18266853 DOI: 10.1111/j.1574-6976.2008.00104.x] [Citation(s) in RCA: 482] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The biosynthesis of bacterial cell wall peptidoglycan is a complex process that involves enzyme reactions that take place in the cytoplasm (synthesis of the nucleotide precursors) and on the inner side (synthesis of lipid-linked intermediates) and outer side (polymerization reactions) of the cytoplasmic membrane. This review deals with the cytoplasmic steps of peptidoglycan biosynthesis, which can be divided into four sets of reactions that lead to the syntheses of (1) UDP-N-acetylglucosamine from fructose 6-phosphate, (2) UDP-N-acetylmuramic acid from UDP-N-acetylglucosamine, (3) UDP-N-acetylmuramyl-pentapeptide from UDP-N-acetylmuramic acid and (4) D-glutamic acid and dipeptide D-alanyl-D-alanine. Recent data concerning the different enzymes involved are presented. Moreover, special attention is given to (1) the chemical and enzymatic synthesis of the nucleotide precursor substrates that are not commercially available and (2) the search for specific inhibitors that could act as antibacterial compounds.
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Affiliation(s)
- Hélène Barreteau
- Laboratoire des Enveloppes Bactériennes et Antibiotiques, Institut de Biochimie et Biophysique Moléculaire et Cellulaire, Univ Paris-Sud, Orsay, France
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