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Sunder Raj D, Kesavan DK, Kottaisamy CPD, Kumar VP, Hopper W, Sankaran U. Atomic level and structural understanding of natural ligands inhibiting Helicobacter pylori peptide deformylase through ligand and receptor based screening, SIFT, molecular dynamics and DFT - a structural computational approach. J Biomol Struct Dyn 2022; 41:3440-3461. [PMID: 35293845 DOI: 10.1080/07391102.2022.2050946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Helicobacter pylori is a Gram-negative microaerophilic gastric pathogen, responsible for the cause of peptic ulcer around half of the global population. Although several antibiotics and combination therapies have been employed for H. pylori-related gastric ulcer and cancer regiments, identifying potent inhibitors for specific targets of this bacterium will help assessing better treatment periodicity and methods to eradicate H. pylori. Herein, 1,000,000 natural compounds were virtually screened against Helicobacter pylori Peptide deformylase (HpPDF). Pharmacophore hypotheses were created using ligand and receptor-based pharmacophore modeling of GLIDE. Stringent HTVS and IFD docking protocol of GLIDE predicted leads with stable intermolecular bonds and scores. Molecular dynamics simulation of HpPDF was carried out for 100 ns using GROMACS. Hits ZINC00225109 and ZINC44896875 came up with a glide score of -9.967 kcal/mol and -12.114 kcal/mol whereas; reference compound actinonin produced a glide score of -9.730 kcal/mol. Binding energy values of these hits revealed the involvement of significant Van der Waals and Coulomb forces and the deduction of lipophilic forces that portray the deep hydrophobic residues in the S1pocket of H. pylori. The DFT analysis established the electron density-based features of the molecules and observed that the results correlate with intermolecular docking interactions. Analysis of the MD trajectories revealed the crucial residues involved in HpPDF - ligand binding and the conformational changes in the receptor. We have identified and deciphered the crucial features necessary for the potent ligand binding at catalytic site of HpPDF. The resulting ZINC natural compound hits from the study could be further employed for potent drug development.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Divya Sunder Raj
- Department of Biotechnology, Manonmaniam Sundaranar University, Tirunelveli, India
| | | | | | - V Prasanth Kumar
- Department of Biotechnology, Manonmaniam Sundaranar University, Tirunelveli, India
| | - Waheetha Hopper
- Department of Biotechnology, School of Bioengineering, Faculty of Engineering & Technology, SRM University, Kattankulathur Campus, Chennai, India
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Metal utilization in genome-reduced bacteria: Do human mycoplasmas rely on iron? Comput Struct Biotechnol J 2021; 19:5752-5761. [PMID: 34765092 PMCID: PMC8566771 DOI: 10.1016/j.csbj.2021.10.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/08/2021] [Accepted: 10/12/2021] [Indexed: 12/04/2022] Open
Abstract
Mycoplasmas are parasitic bacteria with streamlined genomes and complex nutritional requirements. Although iron is vital for almost all organisms, its utilization by mycoplasmas is controversial. Despite its minimalist nature, mycoplasmas can survive and persist within the host, where iron availability is rigorously restricted through nutritional immunity. In this review, we describe the putative iron-enzymes, transporters, and metalloregulators of four relevant human mycoplasmas. This work brings in light critical differences in the mycoplasma-iron interplay. Mycoplasma penetrans, the species with the largest genome (1.36 Mb), shows a more classic repertoire of iron-related proteins, including different enzymes using iron-sulfur clusters as well as iron storage and transport systems. In contrast, the iron requirement is less apparent in the three species with markedly reduced genomes, Mycoplasma genitalium (0.58 Mb), Mycoplasma hominis (0.67 Mb) and Mycoplasma pneumoniae (0.82 Mb), as they exhibit only a few proteins possibly involved in iron homeostasis. The multiple facets of iron metabolism in mycoplasmas illustrate the remarkable evolutive potential of these minimal organisms when facing nutritional immunity and question the dependence of several human-infecting species for iron. Collectively, our data contribute to better understand the unique biology and infective strategies of these successful pathogens.
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Key Words
- ABC, ATP-binding cassette
- ECF transporter
- ECF, energy-coupling factor
- Fur, ferric uptake regulator
- Hrl, histidine-rich lipoprotein
- Iron homeostasis
- Metal acquisition
- Metalloenzyme
- Mge, Mycoplasma genitalium
- Mho, Mycoplasma hominis
- Mollicutes
- Mpe, Mycoplasma penetrans
- Mpn, Mycoplasma pneumonia
- Mycoplasmas
- PDB, protein data bank
- RNR, ribonucleotide reductase
- XRF, X-ray fluorescence
- ZIP, zinc-iron permease
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Abdel-Naby AS, Nabil S, Aldulaijan S, Ababutain IM, Alghamdi AI, Almubayedh S, Khalil KD. Synthesis, Characterization of Chitosan-Aluminum Oxide Nanocomposite for Green Synthesis of Annulated Imidazopyrazol Thione Derivatives. Polymers (Basel) 2021; 13:polym13071160. [PMID: 33916381 PMCID: PMC8038599 DOI: 10.3390/polym13071160] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 03/28/2021] [Accepted: 03/31/2021] [Indexed: 11/16/2022] Open
Abstract
Chitosan-aluminum oxide nanocomposite was synthesized, characterized, and used as a green heterogeneous catalyst to synthesize novel imidazopyrazolylthione derivatives. Nanocomposite polymeric material was characterized by EDS-SEM and XRD. The powerful catalytic activity, and its base character of the nanocomposite, was used to synthesize imidazopyrazolylthione (1) in a good yield compared to traditional cyclocondensation synthesis. Using the nanocomposite catalyst, substitution of the thiol group (1) afforded the corresponding thiourea (2) and the corresponding ester (3). The efficiency of the nanocomposite over the traditional base organic catalyst, Et3N and NaOH, makes it an effective, economic, and reproducible nontoxic catalyst. Moreover, the heterogeneous nanocomposite polymeric film was easily isolated from the reaction medium, and recycled up to four times, without a significant loss of its catalytic activity. The newly synthesized derivatives were screened as antibacterial agents and showed high potency. Molecular docking was also performed for a more in-depth investigation. The results of the docking studies have demonstrated that the docked compounds have strong interaction energies with both Gram-positive and Gram-negative bacteria.
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Affiliation(s)
- Abir S. Abdel-Naby
- Department of Chemistry, College of Science, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia; (S.N.); (S.A.)
- Water Treatment Unit, Basic & Applied Scientific Research Center (BASRC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia; (I.M.A.); (A.I.A.); (S.A.)
- Correspondence:
| | - Sara Nabil
- Department of Chemistry, College of Science, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia; (S.N.); (S.A.)
- Water Treatment Unit, Basic & Applied Scientific Research Center (BASRC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia; (I.M.A.); (A.I.A.); (S.A.)
| | - Sarah Aldulaijan
- Department of Chemistry, College of Science, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia; (S.N.); (S.A.)
- Water Treatment Unit, Basic & Applied Scientific Research Center (BASRC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia; (I.M.A.); (A.I.A.); (S.A.)
| | - Ibtisam M. Ababutain
- Water Treatment Unit, Basic & Applied Scientific Research Center (BASRC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia; (I.M.A.); (A.I.A.); (S.A.)
- Department of Biology, College of Science, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia
| | - Azzah I. Alghamdi
- Water Treatment Unit, Basic & Applied Scientific Research Center (BASRC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia; (I.M.A.); (A.I.A.); (S.A.)
- Department of Biology, College of Science, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia
| | - Somaiah Almubayedh
- Water Treatment Unit, Basic & Applied Scientific Research Center (BASRC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia; (I.M.A.); (A.I.A.); (S.A.)
| | - Khaled D. Khalil
- Department of Chemistry, Faculty of Science, Cairo University, Giza 12613, Egypt;
- Department of Chemistry, Faculty of Science, Taibah University, Al-Madinah Almunawrah, Yanbu 46423, Saudi Arabia
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Imlay JA, Sethu R, Rohaun SK. Evolutionary adaptations that enable enzymes to tolerate oxidative stress. Free Radic Biol Med 2019; 140:4-13. [PMID: 30735836 PMCID: PMC6684875 DOI: 10.1016/j.freeradbiomed.2019.01.048] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 01/31/2019] [Indexed: 10/27/2022]
Abstract
Biochemical mechanisms emerged and were integrated into the metabolic plan of cellular life long before molecular oxygen accumulated in the biosphere. When oxygen levels finaly rose, they threatened specific types of enzymes: those that use organic radicals as catalysts, and those that depend upon iron centers. Nature has found ways to ensure that such enzymes are still used by contemporary organisms. In some cases they are restricted to microbes that reside in anoxic habitats, but in others they manage to function inside aerobic cells. In the latter case, it is frequently true that the ancestral enzyme has been modified to fend off poisoning. In this review we survey a range of protein adaptations that permit radical-based and low-potential iron chemistry to succeed in oxic environments. In many cases, accessory domains shield the vulnerable radical or metal center from oxygen. In others, the structures of iron cofactors evolved to less oxidizable forms, or alternative metals replaced iron altogether. The overarching view is that some classes of biochemical mechanism are intrinsically incompatible with the presence of oxygen. The structural modification of target enzymes is an under-recognized response to this problem.
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Affiliation(s)
- James A Imlay
- Department of Microbiology, University of Illinois, 601 S. Goodwin Ave, Urbana, IL, 61801, USA.
| | - Ramakrishnan Sethu
- Department of Microbiology, University of Illinois, 601 S. Goodwin Ave, Urbana, IL, 61801, USA
| | - Sanjay Kumar Rohaun
- Department of Microbiology, University of Illinois, 601 S. Goodwin Ave, Urbana, IL, 61801, USA
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Emergence of metal selectivity and promiscuity in metalloenzymes. J Biol Inorg Chem 2019; 24:517-531. [DOI: 10.1007/s00775-019-01667-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 05/13/2019] [Indexed: 01/27/2023]
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Frank AT, Law SM, Ahlstrom LS, Brooks CL. Predicting protein backbone chemical shifts from Cα coordinates: extracting high resolution experimental observables from low resolution models. J Chem Theory Comput 2016; 11:325-31. [PMID: 25620895 PMCID: PMC4295808 DOI: 10.1021/ct5009125] [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: 10/14/2014] [Indexed: 12/18/2022]
Abstract
![]()
Given
the demonstrated utility of coarse-grained modeling and simulations
approaches in studying protein structure and dynamics, developing
methods that allow experimental observables to be directly recovered from coarse-grained models is of great importance. In
this work, we develop one such method that enables protein backbone
chemical shifts (1HN, 1Hα, 13Cα, 13C, 13Cβ, and 15N) to be predicted from Cα coordinates. We show that our Cα-based
method, LARMORCα, predicts backbone chemical shifts
with comparable accuracy to some all-atom approaches. More importantly,
we demonstrate that LARMORCα predicted chemical shifts
are able to resolve native structure from decoy pools that contain
both native and non-native models, and so it is sensitive to protein
structure. As an application, we use LARMORCα to
characterize the transient state of the fast-folding protein gpW using
recently published NMR relaxation dispersion derived backbone chemical
shifts. The model we obtain is consistent with the previously proposed
model based on independent analysis of the chemical shift dispersion
pattern of the transient state. We anticipate that LARMORCα will find utility as a tool that enables important protein conformational
substates to be identified by “parsing” trajectories
and ensembles generated using coarse-grained modeling and simulations.
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Affiliation(s)
- Aaron T Frank
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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Manhas A, Kumar SP, Jha PC. Molecular modeling of Plasmodium falciparum peptide deformylase and structure-based pharmacophore screening for inhibitors. RSC Adv 2016. [DOI: 10.1039/c6ra01071g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The role of metal coordination geometry and actinonin (inhibitor) binding was examined to develop pharmacophore-based inhibitor design strategy forPlasmodium falciparumpeptide deformylase.
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Affiliation(s)
- Anu Manhas
- School of Chemical Sciences
- Central University of Gujarat
- Gandhinagar-382030
- India
| | | | - Prakash Chandra Jha
- School of Chemical Sciences
- Central University of Gujarat
- Gandhinagar-382030
- India
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8
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Identification of crucial amino acids of bacterial Peptide deformylases affecting enzymatic activity in response to oxidative stress. J Bacteriol 2013; 196:90-9. [PMID: 24142250 DOI: 10.1128/jb.00916-13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Peptide deformylase (PDF) is an essential bacterial metalloprotease involved in deformylation of N-formyl group from nascent polypeptide chains during protein synthesis. Iron-containing variants of this enzyme from Salmonella enterica serovar Typhimurium (sPDF) and Mycobacterium tuberculosis (mPDF), although inhibited by oxidizing agents like H2O2, exhibited strikingly different 50% inhibitory concentrations (IC50s) that ranged from nanomolar (sPDF) to millimolar (mPDF) levels. Furthermore, the metal dissociation rate was higher in sPDF than mPDF. We hypothesized that a restriction in entry of environmental oxygen or oxidizing agents into the active site of mPDF might be the cause for such discrepancies between two enzymes. Since the active-site residues of the two proteins are similar, we evaluated the role of the oxidation-prone noncatalytic residue(s) in the process. Amino acid sequence analysis revealed that Cys-130 of sPDF corresponds to Met-145 of mPDF and that they are away from the active sites. Swapping methionine with cysteine in mPDF, the M145C protein displayed a drastic decrease in the IC50 for H2O2 and an increased metal dissociation rate compared to the wild type. Matrix-assisted laser desorption ionization (MALDI) analysis of a trypsin-digested fragment containing Cys-145 of the M145C protein also indicated its increased susceptibility to oxidation. To incorporate residues identical to those of mPDF, we created a double mutant of sPDF (C130M-V63C) that showed increased IC50 for H2O2 compared to the wild type. Interestingly, the oxidation state of cysteines in C130M-V63C was unaffected during H2O2 treatment. Taken together, our results unambiguously established the critical role of noncatalytic cysteine/methionine for enzymatic sensitivity to H2O2 and, thus, for conferring behavioral distinction of bacterial PDFs under oxidative stress conditions.
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Abstract
New antimicrobial agents are always needed to counteract the resistant pathogens that continue to be selected by current therapeutic regimens. This review provides a survey of known antimicrobial agents that were currently in clinical development in the fall of 2012 and spring of 2013. Data were collected from published literature primarily from 2010 to 2012, meeting abstracts (2011 to 2012), government websites, and company websites when appropriate. Compared to what was reported in previous surveys, a surprising number of new agents are currently in company pipelines, particularly in phase 3 clinical development. Familiar antibacterial classes of the quinolones, tetracyclines, oxazolidinones, glycopeptides, and cephalosporins are represented by entities with enhanced antimicrobial or pharmacological properties. More importantly, compounds of novel chemical structures targeting bacterial pathways not previously exploited are under development. Some of the most promising compounds include novel β-lactamase inhibitor combinations that target many multidrug-resistant Gram-negative bacteria, a critical medical need. Although new antimicrobial agents will continue to be needed to address increasing antibiotic resistance, there are novel agents in development to tackle at least some of the more worrisome pathogens in the current nosocomial setting.
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Affiliation(s)
| | - Karen Bush
- Indiana University, Bloomington, Indiana, USA
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10
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Lee SJ, Lee SJ, Lee SK, Yoon HJ, Lee HH, Kim KK, Lee BJ, Lee BI, Suh SW. Structures of Staphylococcus aureus peptide deformylase in complex with two classes of new inhibitors. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:784-93. [PMID: 22751663 DOI: 10.1107/s0907444912011912] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Accepted: 03/19/2012] [Indexed: 01/02/2023]
Abstract
Peptide deformylase (PDF) catalyzes the removal of the formyl group from the N-terminal methionine residue in newly synthesized polypeptides, which is an essential process in bacteria. Four new inhibitors of PDF that belong to two different classes, hydroxamate/pseudopeptide compounds [PMT387 (7a) and PMT497] and reverse-hydroxamate/nonpeptide compounds [PMT1039 (15e) and PMT1067], have been developed. These compounds inhibited the growth of several pathogens involved in respiratory-tract infections, such as Streptococcus pneumoniae, Moraxella catarrhalis and Haemophilus influenzae, and leading nosocomial pathogens such as Staphylococcus aureus and Klebsiella pneumoniae with a minimum inhibitory concentration (MIC) in the range 0.1-0.8 mg ml(-1). Interestingly, the reverse-hydroxamate/nonpeptide compounds showed a 250-fold higher antimicrobial activity towards S. aureus, although the four compounds showed similar K(i) values against S. aureus PDF enzymes, with K(i) values in the 11-85 nM range. To provide a structural basis for the discovery of additional PDF inhibitors, the crystal structures of S. aureus PDF in complex with the four inhibitors were determined at resolutions of 1.90-2.30 Å. The inhibitor-bound structures displayed distinct deviations depending on the inhibitor class. The distance between the Zn(2+) ion and the carbonyl O atom of the hydroxamate inhibitors (or the hydroxyl O atom of the reverse-hydroxamate inhibitors) appears to be correlated to S. aureus inhibition activity. The structural information reported in this study should aid in the discovery of new PDF inhibitors that can be used as novel antibacterial drugs.
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Affiliation(s)
- Sang Jae Lee
- Biomolecular Function Research Branch, Division of Convergence Technology, Research Institute, National Cancer Center, Goyang, Gyeonggi 410-749, Republic of Korea
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Oey CB, Bao X, Lewis C, Kerrigan JE, Fan H. High tolerance to mutations in a Chlamydia trachomatis peptide deformylase loop. World J Biol Chem 2011; 2:90-7. [PMID: 21666811 PMCID: PMC3110899 DOI: 10.4331/wjbc.v2.i5.90] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2011] [Revised: 04/27/2011] [Accepted: 05/04/2011] [Indexed: 02/05/2023] Open
Abstract
AIM: To determine if and how a loop region in the peptide deformylase (PDF) of Chlamydia trachomatis regulates enzyme function.
METHODS: Molecular dynamics simulation was used to study a structural model of the chlamydial PDF (cPDF) and predict the temperature factor per residue for the protein backbone atoms. Site-directed mutagenesis was performed to construct cPDF variants. Catalytic properties of the resulting variants were determined by an enzyme assay using formyl-Met-Ala-Ser as a substrate.
RESULTS: In silico analysis predicted a significant increase in atomic motion in the DGELV sequence (residues 68-72) of a loop region in a cPDF mutant, which is resistant to PDF inhibitors due to two amino acid substitutions near the active site, as compared to wild-type cPDF. The D68R and D68R/E70R cPDF variants demonstrated significantly increased catalytic efficiency. The E70R mutant showed only slightly decreased efficiency. Although deletion of residues 68-72 resulted in a nearly threefold loss in substrate binding, this deficiency was compensated for by increased catalytic efficiency.
CONCLUSION: Movement of the DGELV loop region is involved in a rate-limiting conformational change of the enzyme during catalysis. However, there is no stringent sequence requirement for this region for cPDF enzyme activity.
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Affiliation(s)
- Christopher B Oey
- Christopher B Oey, Xiaofeng Bao, Christal Lewis, Huizhou Fan, Department of Physiology and Biophysics, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, NJ 08854, United States
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Sharma A, Khuller GK, Sharma S. Peptide deformylase--a promising therapeutic target for tuberculosis and antibacterial drug discovery. Expert Opin Ther Targets 2009; 13:753-65. [PMID: 19530983 DOI: 10.1517/14728220903005590] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
BACKGROUND Tuberculosis (TB) remains the most important infectious disease causing morbidity and death, due to the human pathogen Mycobacterium tuberculosis. The emergence of multi-drug-resistant and extensively-drug-resistant forms of TB have resulted in an increase in the number of TB cases. Thus, there is an urgent need to identify new drugs with novel targets to ensure future therapeutic success. Studies have indicated that peptide deformylase is an interesting potential candidate for discovering antimicrobial agents. OBJECTIVE To explore the role of peptide deformylase, a highly conserved metalloprotease and an essential enzyme in bacterial life cycle, as a target for antibacterial as well as antimycobacterial drug development. METHODS This review is based on recent published literature and online resources related to peptide deformylase inhibitors and their antibacterial potential. RESULTS/CONCLUSION Peptide deformylase is an emerging therapeutic target for the treatment of tuberculosis and peptide deformylase inhibitors can act as potential future antibacterial agents.
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Affiliation(s)
- Anshika Sharma
- University of Notre Dame, Department of Biological Sciences, Notre Dame, IN-46556, USA
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Andreini C, Bertini I, Cavallaro G, Najmanovich RJ, Thornton JM. Structural analysis of metal sites in proteins: non-heme iron sites as a case study. J Mol Biol 2009; 388:356-80. [PMID: 19265704 DOI: 10.1016/j.jmb.2009.02.052] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2008] [Revised: 02/19/2009] [Accepted: 02/19/2009] [Indexed: 11/24/2022]
Abstract
In metalloproteins, the protein environment modulates metal properties to achieve the required goal, which can be protein stabilization or function. The analysis of metal sites at the atomic level of detail provided by protein structures can thus be of benefit in functional and evolutionary studies of proteins. In this work, we propose a structural bioinformatics approach to the study of metalloproteins based on structural templates of metal sites that include the PDB coordinates of protein residues forming the first and the second coordination sphere of the metal. We have applied this approach to non-heme iron sites, which have been analyzed at various levels. Templates of sites located in different protein domains have been compared, showing that similar sites can be found in unrelated proteins as the result of convergent evolution. Templates of sites located in proteins of a large superfamily have been compared, showing possible mechanisms of divergent evolution of proteins to achieve different functions. Furthermore, template comparisons have been used to predict the function of uncharacterized proteins, showing that similarity searches focused on metal sites can be advantageously combined with typical whole-domain comparisons. Structural templates of metal sites, finally, may constitute the basis for a systematic classification of metalloproteins in databases.
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Affiliation(s)
- Claudia Andreini
- Magnetic Resonance Center (CERM)-University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
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Escobar-Alvarez S, Goldgur Y, Yang G, Ouerfelli O, Li Y, Scheinberg DA. Structure and activity of human mitochondrial peptide deformylase, a novel cancer target. J Mol Biol 2009; 387:1211-28. [PMID: 19236878 DOI: 10.1016/j.jmb.2009.02.032] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Revised: 02/05/2009] [Accepted: 02/07/2009] [Indexed: 11/25/2022]
Abstract
Peptide deformylase proteins (PDFs) participate in the N-terminal methionine excision pathway of newly synthesized peptides. We show that the human PDF (HsPDF) can deformylate its putative substrates derived from mitochondrial DNA-encoded proteins. The first structural model of a mammalian PDF (1.7 A), HsPDF, shows a dimer with conserved topology of the catalytic residues and fold as non-mammalian PDFs. The HsPDF C-terminus topology and the presence of a helical loop (H2 and H3), however, shape a characteristic active site entrance. The structure of HsPDF bound to the peptidomimetic inhibitor actinonin (1.7 A) identified the substrate-binding site. A defined S1' pocket, but no S2' or S3' substrate-binding pockets, exists. A conservation of PDF-actinonin interaction across PDFs was observed. Despite the lack of true S2' and S3' binding pockets, confirmed through peptide binding modeling, enzyme kinetics suggest a combined contribution from P2'and P3' positions of a formylated peptide substrate to turnover.
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Affiliation(s)
- Sindy Escobar-Alvarez
- Molecular Pharmacology and Chemistry Program, Sloan-Kettering Institute, 415 E. 68th Street Zuckerman Z1941, New York, NY 10065, USA
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15
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Pichota A, Duraiswamy J, Yin Z, Keller TH, Alam J, Liung S, Lee G, Ding M, Wang G, Chan WL, Schreiber M, Ma I, Beer D, Ngew X, Mukherjee K, Nanjundappa M, Teo JWP, Thayalan P, Yap A, Dick T, Meng W, Xu M, Koehn J, Pan SH, Clark K, Xie X, Shoen C, Cynamon M. Peptide deformylase inhibitors of Mycobacterium tuberculosis: synthesis, structural investigations, and biological results. Bioorg Med Chem Lett 2008; 18:6568-72. [PMID: 19008098 DOI: 10.1016/j.bmcl.2008.10.040] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2008] [Revised: 09/24/2008] [Accepted: 10/01/2008] [Indexed: 11/19/2022]
Abstract
Bacterial peptide deformylase (PDF) belongs to a subfamily of metalloproteases catalyzing the removal of the N-terminal formyl group from newly synthesized proteins. We report the synthesis and biological activity of highly potent inhibitors of Mycobacterium tuberculosis (Mtb) PDF enzyme as well as the first X-ray crystal structure of Mtb PDF. Structure-activity relationship and crystallographic data clarified the structural requirements for high enzyme potency and cell based potency. Activities against single and multi-drug-resistant Mtb strains are also reported.
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Affiliation(s)
- Arkadius Pichota
- Novartis Institute for Tropical Diseases, 10 Biopolis Road, #05-01 Chromos, Singapore 138670, Singapore.
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16
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Saxena R, Kanudia P, Datt M, Dar HH, Karthikeyan S, Singh B, Chakraborti PK. Three consecutive arginines are important for the mycobacterial peptide deformylase enzyme activity. J Biol Chem 2008; 283:23754-64. [PMID: 18574247 DOI: 10.1074/jbc.m709672200] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Genes encoding the peptide deformylase enzyme (def) are present in all eubacteria and are involved in the deformylation of the N-formyl group of newly synthesized polypeptides during protein synthesis. We compared the amino acid sequences of this enzyme in different mycobacterial species and found that they are highly conserved (76% homology with 62% identity); however, when this comparison was extended to other eubacterial homologs, it emerged that the mycobacterial proteins have an insertion region containing three consecutive arginine residues (residues 77-79 in Mycobacterium tuberculosis peptide deformylase (mPDF)). Here, we demonstrate that these three arginines are important for the activity of mPDF. Circular dichroism studies of wild-type mPDF and of mPDF containing individual conservative substitutions (R77K, R78K, or R79K) or combined substitutions incorporated into a triple mutant (R77K/R78K/R79K) indicate that such mutations cause mPDF to undergo structural alterations. Molecular modeling of mPDF suggests that the three arginines are distal to the active site. Molecular dynamics simulations of wild-type and mutant mPDF structures indicate that the arginines may be involved in the stabilization of substrate binding pocket residues for their proper interaction with peptide(s). Treatment with 5'-phosphothiorate-modified antisense oligodeoxyribonucleotides directed against different regions of def from M. tuberculosis inhibits growth of Mycobacterium smegmatis in culture. Taken together, these results hold out the possibility of future design of novel mycobacteria-specific PDF inhibitors.
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Affiliation(s)
- Rahul Saxena
- Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
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17
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Abstract
Peptide deformylase (PDF) is a metalloenzyme that removes the N-terminal formyl groups from newly synthesized proteins. It is essential for bacterial survival, and is therefore-considered as a potential target for antimicrobial chemotherapy. However, some bacteria including medically relevant pathogens possess two or more def-like genes. Here we have examined two PDFs from Bacillus cereus. The two share only 32% sequence identity and the crystal structures show overall similarity with PDF2 having a longer C-terminus. However, there are differences at the two active sites, and these differences appear to contribute to the activity difference seen between the two. BcPDF2 is found as a dimer in the crystal form with two additional actinonin bound at that interface.
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Affiliation(s)
- Joon Kyu Park
- Life Sciences Division, Korea Institute of Science and Technology, 39-1 Hawolkok-dong, Sungbuk-gu, Seoul 136-791, Korea
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18
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Balakrishnan A, Wang L, Li X, Ohman-Strickland P, Malatesta P, Fan H. Inhibition of chlamydial infection in the genital tract of female mice by topical application of a peptide deformylase inhibitor. Microbiol Res 2007; 164:338-46. [PMID: 17936604 DOI: 10.1016/j.micres.2007.05.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2006] [Revised: 03/28/2007] [Accepted: 05/08/2007] [Indexed: 11/15/2022]
Abstract
Chlamydia trachomatis is an obligate intracellular bacterium responsible for a number of health problems, including sexually transmitted infection in humans. We recently discovered that C. trachomatis infection in cell culture is highly susceptible to inhibitors of peptide deformylase, an enzyme that removes the N-formyl group from newly synthesized polypeptides. In this study, one of the deformylase inhibitors, GM6001, was tested for potential antichlamydial activity using a murine genital C. muridarum infection model. Topical application of GM6001 significantly reduced C. muridarum loading in BALB/c mice that were vaginally infected with the pathogen. In striking contrast, growth of the probiotic Lactobacillus plantarum is strongly resistant to the PDF inhibitor. GM6001 demonstrated no detectable toxicity against host cells. On the basis of these data and our previous observations, we conclude that further evaluation of PDF inhibitors for prevention and treatment of sexually transmitted chlamydial infection is warranted.
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Affiliation(s)
- Amit Balakrishnan
- University of Medicine and Dentistry of New Jersey Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
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19
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Nguyen KT, Wu JC, Boylan JA, Gherardini FC, Pei D. Zinc is the metal cofactor of Borrelia burgdorferi peptide deformylase. Arch Biochem Biophys 2007; 468:217-25. [PMID: 17977509 DOI: 10.1016/j.abb.2007.09.023] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2007] [Revised: 09/21/2007] [Accepted: 09/22/2007] [Indexed: 11/26/2022]
Abstract
Peptide deformylase (PDF, E.C. 3.5.1.88) catalyzes the removal of N-terminal formyl groups from nascent ribosome-synthesized polypeptides. PDF contains a catalytically essential divalent metal ion, which is tetrahedrally coordinated by three protein ligands (His, His, and Cys) and a water molecule. Previous studies revealed that the metal cofactor is a Fe2+ ion in Escherichia coli and many other bacterial PDFs. In this work, we found that PDFs from two iron-deficient bacteria, Borrelia burgdorferi and Lactobacillus plantarum, are stable and highly active under aerobic conditions. The native B. burgdorferi PDF (BbPDF) was purified 1200-fold and metal analysis revealed that it contains approximately 1.1 Zn2+ ion/polypeptide but no iron. Our studies suggest that PDF utilizes different metal ions in different organisms. These data have important implications in designing PDF inhibitors and should help address some of the unresolved issues regarding PDF structure and catalytic function.
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Affiliation(s)
- Kiet T Nguyen
- Department of Chemistry and Ohio State Biochemistry Program, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA
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20
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Dean CR, Narayan S, Richards J, Daigle DM, Esterow S, Leeds JA, Kamp H, Puyang X, Wiedmann B, Mueller D, Voshol H, van Oostrum J, Wall D, Koehn J, Dzink-Fox J, Ryder NS. Reduced susceptibility of Haemophilus influenzae to the peptide deformylase inhibitor LBM415 can result from target protein overexpression due to amplified chromosomal def gene copy number. Antimicrob Agents Chemother 2007; 51:1004-10. [PMID: 17220413 PMCID: PMC1803149 DOI: 10.1128/aac.01103-06] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Previous genetic analysis of Haemophilus influenzae revealed two mechanisms associated with decreased susceptibility to the novel peptide deformylase inhibitor LBM415: AcrAB-TolC-mediated efflux and Fmt bypass, resulting from mutations in the pump repressor gene acrR and in the fmt gene, respectively. We have isolated an additional mutant, CDS23 (LBM415 MIC, 64 microg/ml versus 4 microg/ml against the parent strain NB65044) that lacks mutations in the acrR or fmt structural genes or in the gene encoding Def, the intracellular target of LBM415. Western immunoblot analysis, two-dimensional gel electrophoresis, and tryptic digestion combined with mass spectrometric identification showed that the Def protein was highly overexpressed in the mutant strain. Consistent with this, real-time reverse transcription-PCR revealed a significant increase in def transcript titer. No mutations were found in the region upstream of def that might account for altered expression; however, pulsed-field gel electrophoresis suggested that a genetic rearrangement of the region containing def had occurred. Using a combination of PCR, sequencing, and Southern blot analyses, it was determined that the def gene had undergone copy number amplification, explaining the high level of target protein expression. Inactivation of the AcrAB-TolC efflux pump in this mutant increased susceptibility 16-fold, highlighting the role of efflux in exacerbating the overall reduced susceptibility resulting from target overexpression.
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Affiliation(s)
- Charles R Dean
- Infectious Diseases, Novartis Institutes for BioMedical Research, 500 Technology Square, Cambridge, MA 02139, USA.
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21
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Affiliation(s)
- Kelly Aubart
- Microbial, Musculoskeletal, and Proliferative Diseases CEDD, GlaxoSmithKline Pharmaceuticals, Collegeville, PA 19426, USA
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22
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Saxena R, Chakraborti PK. Identification of regions involved in enzymatic stability of peptide deformylase of Mycobacterium tuberculosis. J Bacteriol 2005; 187:8216-20. [PMID: 16291698 PMCID: PMC1291256 DOI: 10.1128/jb.187.23.8216-8220.2005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sequence analysis of peptide deformylase of Mycobacterium tuberculosis revealed the presence of insertions (residues 74 to 85) and an unusually long carboxy-terminal end (residues 182 to 197). Our results with deletion mutants indicated the contribution of these regions in maintaining enzymatic stability. Furthermore, we showed that the region spanning the insertions was responsible for maintaining resistance to oxidizing agents, like H(2)O(2).
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Affiliation(s)
- Rahul Saxena
- Institute of Microbial Technology, Chandigarh, India
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23
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Zhou Z, Song X, Gong W. Novel conformational states of peptide deformylase from pathogenic bacterium Leptospira interrogans: implications for population shift. J Biol Chem 2005; 280:42391-6. [PMID: 16239225 DOI: 10.1074/jbc.m506370200] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Peptide deformylase is an attractive target for developing novel antibiotics. Previous studies at pH 3.0 showed peptide deformylase from Leptospira interrogans (LiPDF) exists as a dimer in which one monomer is in a closed form and the other is in an open form, with different conformations of the CD-loop controlling the entrance to the active pocket. Here we present structures of LiPDF at its active pH range. LiPDF forms a similar dimer at pH values 6.5-8.0 as it does at pH 3.0. Interestingly, both of the monomers are almost in the same closed form as that observed at pH 3.0. However, when the enzyme is complexed with the natural inhibitor actinotin, the conformation of the CD-loop is half-open. Two pairs of Arg109-mediated cation-pi interactions, as well as hydrogen bonds, have been identified to stabilize the different CD-loop conformations. These results indicate that LiPDF may be found in different structural states, a feature that has never before been observed in the peptide deformylase family. Based on our results, a novel substrate binding model, featured by an equilibrium between the closed and the open forms, is proposed. Our results present crystallographic evidence supporting population shift theory, which is distinguished from the conventional lock-and-key or induced-fit models. These results not only facilitate the development of peptide deformylase-targeted drugs but also provide structural insights into the mechanism of an unusual type of protein binding event.
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Affiliation(s)
- Zhaocai Zhou
- National Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
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24
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Molteni V, Kreusch A. Peptide deformylase inhibitors: a survey of the patent literature. Expert Opin Ther Pat 2005. [DOI: 10.1517/13543776.15.10.1423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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25
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Saxena R, Chakraborti PK. The carboxy-terminal end of the peptide deformylase from Mycobacterium tuberculosis is indispensable for its enzymatic activity. Biochem Biophys Res Commun 2005; 332:418-25. [PMID: 15896710 DOI: 10.1016/j.bbrc.2005.04.142] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2005] [Accepted: 04/19/2005] [Indexed: 10/25/2022]
Abstract
The peptide deformylase in bacteria is involved in removal of N-formyl group from newly synthesized proteins. The gene encoding this enzyme from Mycobacterium tuberculosis was cloned and expressed in Escherichia coli. The enzyme activity of the recombinant protein (mPDF) was insensitive to modulation by common monovalent/divalent cations. Kinetic analysis, using N-formylmethionine-alanine as the substrate, yielded K(cat)/K(m) of approximately 1220 M(-1)s(-1). Actinonin, a naturally occurring antibiotic, and 1,10-ortho-phenanthroline strongly inhibited the enzyme activity. The mPDF was very stable at 30 degrees C with a half-life of approximately 4h and exhibited resistance to oxidizing agents, like H(2)O(2). Thus, the mPDF achieved distinction in its behavior among any reported iron-containing peptide deformylases. Furthermore, amino acid sequence analysis of mPDF revealed the presence of an unusually long carboxy-terminal end (residues 182-197), which is atypical for any gram-positive bacteria. Our results, through deletion analysis, for the first time established the role of this region in mPDF enzyme activity.
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Affiliation(s)
- Rahul Saxena
- Institute of Microbial Technology, Sector 39A, Chandigarh 160 036, India
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26
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Moon JH, Park JK, Kim EE. Structure analysis of peptide deformylase from Bacillus cereus. Proteins 2005; 61:217-20. [PMID: 16049914 DOI: 10.1002/prot.20526] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jin Ho Moon
- Biomedical Research Center, Life Sciences Division, Korea Institute of Science and Technology, Seoul, Korea
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27
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Vido K, Diemer H, Van Dorsselaer A, Leize E, Juillard V, Gruss A, Gaudu P. Roles of thioredoxin reductase during the aerobic life of Lactococcus lactis. J Bacteriol 2005; 187:601-10. [PMID: 15629931 PMCID: PMC543548 DOI: 10.1128/jb.187.2.601-610.2005] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Thiol-disulfide bond balance is generally maintained in bacteria by thioredoxin reductase-thioredoxin and/or glutathione-glutaredoxin systems. Some gram-positive bacteria, including Lactococcus lactis, do not produce glutathione, and the thioredoxin system is presumed to be essential. We constructed an L. lactis trxB1 mutant. The mutant was obtained under anaerobic conditions in the presence of dithiothreitol (DTT). Unexpectedly, the trxB1 mutant was viable without DTT and under aerated static conditions, thus disproving the essentiality of this system. Aerobic growth of the trxB1 mutant did not require glutathione, also ruling out the need for this redox maintenance system. Proteomic analyses showed that known oxidative stress defense proteins are induced in the trxB1 mutant. Two additional effects of trxB1 were not previously reported in other bacteria: (i) induction of proteins involved in fatty acid or menaquinone biosynthesis, indicating that membrane synthesis is part of the cellular response to a redox imbalance, and (ii) alteration of the isoforms of the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GapB). We determined that the two GapB isoforms in L. lactis differed by the oxidation state of catalytic-site cysteine C152. Unexpectedly, a decrease specific to the oxidized, inactive form was observed in the trxB1 mutant, possibly because of proteolysis of oxidized GapB. This study showed that thioredoxin reductase is not essential in L. lactis and that its inactivation triggers induction of several mechanisms acting at the membrane and metabolic levels. The existence of a novel redox function that compensates for trxB1 deficiency is suggested.
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Affiliation(s)
- Karin Vido
- Unité de Recherches Laitières et Génétique Appliquée, INRA, Domaine de Vilvert, 78352 Jouy en Josas, France
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28
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Park JK, Moon JH, Kim JH, Kim EE. Crystallization and preliminary X-ray crystallographic analysis of peptide deformylase (PDF) from Bacillus cereus in ligand-free and actinonin-bound forms. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61:150-2. [PMID: 16508119 PMCID: PMC1952381 DOI: 10.1107/s1744309104032440] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2004] [Accepted: 12/08/2004] [Indexed: 11/10/2022]
Abstract
In bacteria, protein expression initiates with an N-formyl group and this needs to be removed in order to ensure proper bacterial growth. These formylation and deformylation processes are unique to eubacteria; therefore, inhibition of these would provide a novel antibacterial therapy. Deformylation is carried out by peptide deformylase (PDF). PDF from Bacillus cereus, one of the major pathogenic bacteria, was cloned into expression plasmid pET-28a (Novagen), overexpressed in Escherichia coli BL21 (DE3) and purified to high quality. Crystals have been obtained of both ligand-free PDF and PDF to which actinonin, a highly potent naturally occurring inhibitor, is bound. Both crystals belong to space group P2(1)2(1)2(1), with unit-cell parameters a = 42.72, b = 44.04, c = 85.19 A and a = 41.31, b = 44.56, c = 84.47 A, respectively. Diffraction data were collected to 1.7 A resolution for the inhibitor-free crystals and to 2.0 A resolution for the actinonin-bound crystals.
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Affiliation(s)
- Joon Kyu Park
- Life Sciences Division, Korea Institute of Science and Technology, Seoul 130-650, South Korea
- School of Life Sciences and Biotechnology, Korea University, Seoul 136-701, South Korea
| | - Jin Ho Moon
- Life Sciences Division, Korea Institute of Science and Technology, Seoul 130-650, South Korea
| | - Jae-Hong Kim
- School of Life Sciences and Biotechnology, Korea University, Seoul 136-701, South Korea
| | - Eunice EunKyeong Kim
- Life Sciences Division, Korea Institute of Science and Technology, Seoul 130-650, South Korea
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29
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Calí P, Naerum L, Mukhija S, Hjelmencrantz A. Isoxazole-3-hydroxamic acid derivatives as peptide deformylase inhibitors and potential antibacterial agents. Bioorg Med Chem Lett 2004; 14:5997-6000. [PMID: 15546716 DOI: 10.1016/j.bmcl.2004.09.087] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2004] [Revised: 08/29/2004] [Accepted: 09/30/2004] [Indexed: 11/24/2022]
Abstract
A series of isoxazole-3-hydroxamic acid derivatives has been identified as a new class of small, nonpeptidic inhibitors of peptide deformylase (PDF). The synthesis, enzyme inhibition and preliminary investigation of the binding mode of this potential antibacterial compounds are reported.
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Affiliation(s)
- Patrizia Calí
- Combio A/S, Vesterbrogade 188, DK-1800 Frederiksberg C, Denmark.
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30
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Yoon HJ, Kim HL, Lee SK, Kim HW, Kim HW, Lee JY, Mikami B, Suh SW. Crystal structure of peptide deformylase from Staphylococcus aureus in complex with actinonin, a naturally occurring antibacterial agent. Proteins 2004; 57:639-42. [PMID: 15382235 DOI: 10.1002/prot.20231] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Hye-Jin Yoon
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, Korea
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31
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Sonke T, Kaptein B, Wagner A, Quaedflieg PJ, Schultz S, Ernste S, Schepers A, Mommers JH, Broxterman QB. Peptide deformylase as biocatalyst for the synthesis of enantiomerically pure amino acid derivatives. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/j.molcatb.2004.02.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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