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Chen AY, Adamek RN, Dick BL, Credille CV, Morrison CN, Cohen SM. Targeting Metalloenzymes for Therapeutic Intervention. Chem Rev 2019; 119:1323-1455. [PMID: 30192523 PMCID: PMC6405328 DOI: 10.1021/acs.chemrev.8b00201] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metalloenzymes are central to a wide range of essential biological activities, including nucleic acid modification, protein degradation, and many others. The role of metalloenzymes in these processes also makes them central for the progression of many diseases and, as such, makes metalloenzymes attractive targets for therapeutic intervention. Increasing awareness of the role metalloenzymes play in disease and their importance as a class of targets has amplified interest in the development of new strategies to develop inhibitors and ultimately useful drugs. In this Review, we provide a broad overview of several drug discovery efforts focused on metalloenzymes and attempt to map out the current landscape of high-value metalloenzyme targets.
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Affiliation(s)
- Allie Y Chen
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Rebecca N Adamek
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Benjamin L Dick
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Cy V Credille
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Christine N Morrison
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Seth M Cohen
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
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2
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A unique peptide deformylase platform to rationally design and challenge novel active compounds. Sci Rep 2016; 6:35429. [PMID: 27762275 PMCID: PMC5071857 DOI: 10.1038/srep35429] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 09/29/2016] [Indexed: 11/25/2022] Open
Abstract
Peptide deformylase (PDF) is considered an excellent target to develop antibiotics. We have performed an extensive characterization of a new PDF from the pathogen Streptococcus agalactiae, showing properties similar to other known PDFs. S. agalactiae PDF could be used as PDF prototype as it allowed to get complete sets of 3-dimensional, biophysical and kinetic data with virtually any inhibitor compound. Structure-activity relationship analysis with this single reference system allowed us to reveal distinct binding modes for different PDF inhibitors and the key role of a hydrogen bond in potentiating the interaction between ligand and target. We propose this protein as an irreplaceable tool, allowing easy and relevant fine comparisons between series, to design, challenge and validate novel series of inhibitors. As proof-of-concept, we report here the design and synthesis of effective specific bacterial PDF inhibitors of an oxadiazole series with potent antimicrobial activity against a multidrug resistant clinical isolate.
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Ngo HPT, Ho TH, Lee I, Tran HT, Sur B, Kim S, Kim JG, Ahn YJ, Cha SS, Kang LW. Crystal Structures of Peptide Deformylase from Rice Pathogen Xanthomonas oryzae pv. oryzae in Complex with Substrate Peptides, Actinonin, and Fragment Chemical Compounds. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:7307-7314. [PMID: 27616570 DOI: 10.1021/acs.jafc.6b02976] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial blight on rice; this species is one of the most destructive pathogenic bacteria in rice cultivation worldwide. Peptide deformylase (PDF) catalyzes the removal of the N-formyl group from the N-terminus of newly synthesized polypeptides in bacterial cells and is an important target to develop antibacterial agents. We determined crystal structures of Xoo PDF (XoPDF) at up to 1.9 Å resolution, which include apo, two substrate-bound (methionine-alanine or methionine-alanine-serine), an inhibitor-bound (actinonin), and six fragment chemical-bound structures. Six fragment chemical compounds were bound in the substrate-binding pocket. The fragment chemical-bound structures were compared to the natural PDF inhibitor actinonin-bound structure. The fragment chemical molecules will be useful to design an inhibitor specific to XoPDF and a potential pesticide against Xoo.
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Affiliation(s)
- Ho-Phuong-Thuy Ngo
- Department of Biological Sciences, Konkuk University , Hwayang-dong, Gwangjin-gu, Seoul 05029, Korea
| | - Thien-Hoang Ho
- Department of Biological Sciences, Konkuk University , Hwayang-dong, Gwangjin-gu, Seoul 05029, Korea
| | - Inho Lee
- Department of Biological Sciences, Konkuk University , Hwayang-dong, Gwangjin-gu, Seoul 05029, Korea
| | - Huyen-Thi Tran
- Department of Biological Sciences, Konkuk University , Hwayang-dong, Gwangjin-gu, Seoul 05029, Korea
| | - Bookyo Sur
- Department of Biological Sciences, Konkuk University , Hwayang-dong, Gwangjin-gu, Seoul 05029, Korea
| | - Seunghwan Kim
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA) , Jeonju 54874, Korea
| | - Jeong-Gu Kim
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration (RDA) , Jeonju 54874, Korea
| | - Yeh-Jin Ahn
- Department of Life Science, Sangmyung University , 7 Hongji-dong, Jongno-gu, Seoul 03016, Korea
| | - Sun-Shin Cha
- Department of Chemistry & Nano Science, Ewha Womans University , 52, Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, Korea
| | - Lin-Woo Kang
- Department of Biological Sciences, Konkuk University , Hwayang-dong, Gwangjin-gu, Seoul 05029, Korea
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Synthesis, antibacterial activity, and biological evaluation of formyl hydroxyamino derivatives as novel potent peptide deformylase inhibitors against drug-resistant bacteria. Eur J Med Chem 2014; 86:133-52. [PMID: 25151577 DOI: 10.1016/j.ejmech.2014.07.106] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 07/22/2014] [Accepted: 07/29/2014] [Indexed: 12/29/2022]
Abstract
Peptide deformylase (PDF) has been identified as a promising target for novel antibacterial agents. In this study, a series of novel formyl hydroxyamino derivatives were designed and synthesized as PDF inhibitors and their antibacterial activities were evaluated. Among the potent PDF inhibitors (1o, 1q, 1o', 1q', and 1x), in vivo studies showed that compound 1q possesses mild toxicity, a good pharmacokinetic profile and protective effects. The good in vivo efficacy and low toxicity suggest that this class of compounds has potential for development and use in future antibacterial drugs.
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Liang H, Xing Y, Chen J, Zhang D, Guo S, Wang C. Antimicrobial activities of endophytic fungi isolated from Ophiopogon japonicus (Liliaceae). BMC COMPLEMENTARY AND ALTERNATIVE MEDICINE 2012. [PMID: 23190550 PMCID: PMC3534486 DOI: 10.1186/1472-6882-12-238] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Background Drug resistance in bacteria has become a global concern and the search for new antibacterial agents is urgent and ongoing. Endophytes provide an abundant reservoir of bioactive metabolites for medicinal exploitation, and an increasing number of novel compounds are being isolated from endophytic fungi. Ophiopogon japonicus, containing compounds with antibacterial activity, is a traditional Chinese medicinal plant used for eliminating phlegm, relieving coughs, latent heat in the lungs, and alleviating diabetes mellitus. We investigated the antimicrobial activities of 30 strains of O. japonicus. Methods Fungal endophytes were isolated from roots and stems of O. japonicus collected from Chongqing City, southwestern China. Mycelial extracts (MC) and fermentation broth (FB) were tested for antimicrobial activity using peptide deformylase (PDF) inhibition fluorescence assays and MTT cell proliferation assays. Results A total of 30 endophytic strains were isolated from O. japonicus; 22 from roots and eight from stems. 53.33% of the mycelial extracts (MC) and 33.33% of the fermentation broths (FB) displayed potent inhibition of PDF. 80% of MC and 33.33% of FB significantly inhibited Staphylococcus aureus. 70% of MC and 36.67% of FB showed strong activities against Cryptococcus neoformans. None showed influence on Escherichia coli. Conclusion The secondary metabolites of endophytic fungi from O. japonicus are potential antimicrobial agents.
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Kakkar D, Tiwari AK, Singh H, Mishra AK. Past and Present Scenario of Imaging Infection and Inflammation: A Nuclear Medicine Perspective. Mol Imaging 2012. [DOI: 10.2310/7290.2011.00051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Nuclear medicine techniques provide potential non-invasive tools for imaging infections and inflammations in the body in a precise way. These techniques are further exploited by the use of radiopharmaceuticals in conjunction with imaging tests such as scintigraphy and positron emission tomography. Improved agents for targeting infection exploit the specific accumulation of radiolabeled compounds to understand the pathophysiologic changes involved in the inflammatory process and correlate them with other chronic illnesses. In the recent past, a wide variety of radiopharmaceuticals have been developed, broadly classified as specific radiopharmaceuticals and nonspecific radiopharmaceuticals. New developments in positron emission (leveraging 18F and 18fluorodeoxyglucose) and heterocyclic/peptide chemistry and radiochemistry are resulting in unique agents with high specific activity. Various approaches to visualizing infection and inflammation are presented in this review, in an integral manner, that give a clear view of the existing radiopharmaceuticals in clinical practice and those under development.
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Affiliation(s)
- Dipti Kakkar
- From the Division of Cyclotron and Radiopharmaceutical Sciences, Institute of Nuclear Medicine and Allied Sciences, and the Centre for Biomedical Engineering, Indian Institute of Technology, Hauz Khas, New Delhi, India
| | - Anjani K. Tiwari
- From the Division of Cyclotron and Radiopharmaceutical Sciences, Institute of Nuclear Medicine and Allied Sciences, and the Centre for Biomedical Engineering, Indian Institute of Technology, Hauz Khas, New Delhi, India
| | - Harpal Singh
- From the Division of Cyclotron and Radiopharmaceutical Sciences, Institute of Nuclear Medicine and Allied Sciences, and the Centre for Biomedical Engineering, Indian Institute of Technology, Hauz Khas, New Delhi, India
| | - Anil K. Mishra
- From the Division of Cyclotron and Radiopharmaceutical Sciences, Institute of Nuclear Medicine and Allied Sciences, and the Centre for Biomedical Engineering, Indian Institute of Technology, Hauz Khas, New Delhi, India
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WANG QIANG, WANG JIANWU, CAI ZHENGTING, XU WEIREN. COMPUTATIONAL STUDY OF THE DYNAMICS OF PEPTIDE DEFORMYLASE COMPLEX FROM LEPTOSPIRA INTERROGANS: EXPLORING THE CONFORMATIONAL CHANGES OF THE SUBSTRATE POCKET. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633608004301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The peptide deformylase from Leptospira interrogans (LiPDF) shows many unusual characteristics. The substrate pocket of formate-bound complex adopts an open conformation. However, in the actinonin-bound LiPDF complex, a slightly open substrate pocket is observed. The opening is not large enough for the inhibitor, because the CD-loop restricts the access to the active site. To explore the conformational changes of the substrate pocket, we perform a 16,000 ps molecular dynamics simulation separately on the ligand-free LiPDF and actinonin-bound LiPDF. During the molecular dynamics simulations, extensive conformational changes have taken place. The comparison of the two MD results shows that the CD-loop, hydrophilic inhibitor, and hydrophobic cluster are necessary for the reopening of the substrate pocket. In addition, Tyr71 plays an important role in mediating the movements of CD-loop, and the transition of the substrate pocket from open to semi-open only occurs in the presence of an inhibitor, which are consistent with the experiment very well.
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Affiliation(s)
- QIANG WANG
- Institute of Theoretical Chemistry, Shandong University, Jinan 250100, China
| | - JIANWU WANG
- Institute of Organic Chemistry, Shandong University, Jinan 250100, China
| | - ZHENGTING CAI
- Institute of Theoretical Chemistry, Shandong University, Jinan 250100, China
| | - WEIREN XU
- Tianjin Institute of the Pharmaceutical Research, Tianjin 300193, China
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8
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East SP, Ayscough A, Toogood-Johnson I, Taylor S, Thomas W. Peptidomimetic inhibitors of bacterial peptide deformylase. Bioorg Med Chem Lett 2011; 21:4032-5. [PMID: 21621999 DOI: 10.1016/j.bmcl.2011.04.132] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Revised: 04/26/2011] [Accepted: 04/27/2011] [Indexed: 10/18/2022]
Abstract
A series of N-formyl hydroxylamine peptide deformylase inhibitors containing a cyclic azaamino acid moiety between the P1' and P3' substituents are presented. Selected compounds display antibacterial activity against pathogens associated with respiratory tract infections with representative compounds showing excellent MICs against Haemophilus influenzae.
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Affiliation(s)
- Stephen P East
- Vernalis (R&D) Ltd., Granta Park, Great Abington, Cambridge CB21 6GB, United Kingdom.
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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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10
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Wang Q, Wang J, Cai Z, Xu W. Prediction of the binding modes between BB-83698 and peptide deformylase from Bacillus stearothermophilus by docking and molecular dynamics simulation. Biophys Chem 2008; 134:178-84. [DOI: 10.1016/j.bpc.2008.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2007] [Revised: 02/10/2008] [Accepted: 02/11/2008] [Indexed: 11/30/2022]
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11
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Nguyen KT, Pei D. High-Throughput Screening of Peptide Deformylase Inhibitors. METHODS IN MOLECULAR MEDICINE™ 2008; 142:117-30. [DOI: 10.1007/978-1-59745-246-5_10] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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12
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Lee JY, Doddareddy MR, Cho YS, Choo H, Koh HY, Kang JH, No KT, Pae AN. Comparative QSAR studies on peptide deformylase inhibitors. J Mol Model 2007; 13:543-58. [PMID: 17333308 DOI: 10.1007/s00894-007-0175-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2006] [Accepted: 01/18/2007] [Indexed: 11/25/2022]
Abstract
Comparative quantitative structure-activity relationship (QSAR) analyses of peptide deformylase (PDF) inhibitors were performed with a series of previously published (British Biotech Pharmaceuticals, Oxford, UK) reverse hydroxamate derivatives having antibacterial activity against Escherichia coli PDF, using 2D and 3D QSAR methods, comparative molecular field analysis (CoMFA), comparative molecular similarity indices analysis (CoMSIA), and hologram QSAR (HQSAR). Statistically reliable models with good predictive power were generated from all three methods (CoMFA r (2) = 0.957, q (2) = 0.569; CoMSIA r (2) = 0.924, q (2) = 0.520; HQSAR r (2) = 0.860, q (2) = 0.578). The predictive capability of these models was validated by a set of compounds that were not included in the training set. The models based on CoMFA and CoMSIA gave satisfactory predictive r (2) values of 0.687 and 0.505, respectively. The model derived from the HQSAR method showed a low predictability of 0.178 for the test set. In this study, 3D prediction models showed better predictive power than 2D models for the test set. This might be because 3D information is more important in the case of datasets containing compounds with similar skeletons. Superimposition of CoMFA contour maps in the active site of the PDF crystal structure showed a meaningful correlation between receptor-ligand binding and biological activity. The final QSAR models, along with information gathered from 3D contour and 2D contribution maps, could be useful for the design of novel active inhibitors of PDF.
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Affiliation(s)
- Ji Young Lee
- Biochemicals Research Center, Korea Institute of Science and Technology, Cheongryang, Seoul, South Korea
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Wang Q, Zhang D, Wang J, Cai Z, Xu W. Docking studies of Nickel-Peptide deformylase (PDF) inhibitors: Exploring the new binding pockets. Biophys Chem 2006; 122:43-9. [PMID: 16545516 DOI: 10.1016/j.bpc.2006.02.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2005] [Revised: 02/13/2006] [Accepted: 02/16/2006] [Indexed: 11/30/2022]
Abstract
The binding modes of a series of known activity inhibitors docking to Peptide deformylase (PDF) have been studied using molecular docking software AutoDock3.0.5. In this study, good correlation (R(2)=0.894) between calculated binding energies and experimental inhibitory activities is obtained. We find that some shallow pockets near the known active pocket are very important which can accommodate the side-chains of the inhibitor. Moreover, a new binding pocket is also explored. All these may provide something useful for designing the potent inhibitors.
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Affiliation(s)
- Qiang Wang
- Institute of Theoretical Chemistry, Shandong University, Jinan 250100, China
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14
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Fieulaine S, Juillan-Binard C, Serero A, Dardel F, Giglione C, Meinnel T, Ferrer JL. The crystal structure of mitochondrial (Type 1A) peptide deformylase provides clear guidelines for the design of inhibitors specific for the bacterial forms. J Biol Chem 2005; 280:42315-24. [PMID: 16192279 DOI: 10.1074/jbc.m507155200] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Peptide deformylase (PDF) inhibitors have a strong potential to be used as a new class of antibiotics. However, recent studies have shown that the mitochondria of most eukaryotes, including humans, contain an essential PDF, PDF1A. The crystal structure of the Arabidopsis thaliana PDF1A (AtPDF1A), considered representative of PDF1As in general, has been determined. This structure displays several similarities to that of known bacterial PDFs. AtPDF1A behaves as a dimer, with the C-terminal residues responsible for linking the two subunits. This arrangement is similar to that of Leptospira interrogans PDF, the only other dimeric PDF identified to date. AtPDF1A is the first PDF for which zinc has been identified as the catalytic ion. However, the zinc binding pocket does not differ from the binding pockets of PDFs with iron rather than zinc. The crystal structure of AtPDF1A in complex with a substrate analog revealed that the substrate binding pocket of PDF1A displays strong modifications. The S1' binding pocket is significantly narrower, due to the creation of a floor from residues present in all PDF1As but not in bacterial PDFs. A true S3' pocket is created by the residues of a helical CD-loop, which is very long in PDF1As. Finally, these modified substrate binding pockets modify the position of the substrate in the active site. These differences provide guidelines for the design of bacterial PDF inhibitors that will not target mitochondrial PDFs.
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Affiliation(s)
- Sonia Fieulaine
- Institut de Biologie Structurale J-P. Ebel CEA-CNRS-UJF, UMR5075, Laboratoire de Cristallographie et Cristallogenèse des Protéines (LCCP/GSY), 41 Rue Jules Horowitz, F-38027 Grenoble Cedex 1, France
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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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16
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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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17
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Molteni V, He X, Nabakka J, Yang K, Kreusch A, Gordon P, Bursulaya B, Warner I, Shin T, Biorac T, Ryder NS, Goldberg R, Doughty J, He Y. Identification of novel potent bicyclic peptide deformylase inhibitors. Bioorg Med Chem Lett 2004; 14:1477-81. [PMID: 15006385 DOI: 10.1016/j.bmcl.2004.01.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2003] [Revised: 12/23/2003] [Accepted: 01/10/2004] [Indexed: 10/26/2022]
Abstract
Screening of our compound collection using Staphylococcus aureus Ni-Peptide deformylase (PDF) afforded a very potent PDF inhibitor with an IC(50) in the low nanomolar range but with poor antibacterial activity (MIC). Three-dimensional structural information obtained from Pseudomonas aeruginosa Ni-PDF complexed with the inhibitor suggested the synthesis of a variety of analogues that would maintain high binding affinity while attempting to improve antibacterial activity. Many of the compounds synthesized proved to be excellent PDF-Ni inhibitors and some showed increased antibacterial activity in selected strains.
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Affiliation(s)
- Valentina Molteni
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA.
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18
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Nguyen KT, Hu X, Pei D. Slow-binding inhibition of peptide deformylase by cyclic peptidomimetics as revealed by a new spectrophotometric assay. Bioorg Chem 2004; 32:178-91. [PMID: 15110195 DOI: 10.1016/j.bioorg.2004.01.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2003] [Indexed: 10/26/2022]
Abstract
A new spectrophotometric/fluorimetric assay for peptide deformylase (PDF) has been developed by coupling the PDF reaction with that of dipeptidyl peptidase I (DPPI) and using N-formyl-Met-Lys-AMC as substrate. Removal of the N-terminal formyl group by PDF renders the dipeptide an efficient substrate of DPPI, which subsequently removes the dipeptidyl units to release 7-amino-4-methylcoumarin as the chromophore/fluorophore. The PDF reaction is conveniently monitored on a UV-Vis spectrophotometer or a fluorimeter in a continuous fashion. The utility of the assay was demonstrated by determining the catalytic activity of PDF and the inhibition constants of PDF inhibitors. These studies revealed the slow-binding behavior of a previously reported macrocyclic PDF inhibitor. This method offers several advantages over the existing PDF assays and should be particularly useful for screening PDF inhibitors in the continuous fashion.
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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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East SP, Beckett RP, Brookings DC, Clements JM, Doel S, Keavey K, Pain G, Smith HK, Thomas W, Thompson AJ, Todd RS, Whittaker M. Peptide deformylase inhibitors with activity against respiratory tract pathogens. Bioorg Med Chem Lett 2004; 14:59-62. [PMID: 14684298 DOI: 10.1016/j.bmcl.2003.10.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
A series of analogues of the peptide deformylase (PDF) inhibitor BB-3497 where the P3' amide bond was replaced with a ketone functionality is described. The in vitro antibacterial profiling of these compounds revealed that they demonstrate activity against pathogens associated with respiratory tract infections.
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Affiliation(s)
- Stephen P East
- British Biotech Pharmaceuticals Limited, Watlington Road, Oxford OX4 6LY, UK.
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20
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Takayama W, Shirasaki Y, Sakai Y, Nakajima E, Fujita S, Sakamoto-Mizutani K, Inoue J. Synthesis and PDF inhibitory activities of novel benzothiazolylidenehydroxamic acid derivatives. Bioorg Med Chem Lett 2003; 13:3273-6. [PMID: 12951107 DOI: 10.1016/s0960-894x(03)00675-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
A novel series of benzothiazolylidenehydroxamic acid derivatives has been designed and synthesized as PDF inhibitors. Some of this novel class of PDF inhibitors exhibited micromolar order enzyme inhibitory activity and antibacterial activity.
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Affiliation(s)
- Wataru Takayama
- Research Laboratories, Senju Pharmaceutical Co., Ltd., 1-5-4 Murotani, Nishi-Ku, Kobe, Hyogo 651-2241, Japan.
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21
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Davies SJ, Ayscough AP, Beckett RP, Bragg RA, Clements JM, Doel S, Grew C, Launchbury SB, Perkins GM, Pratt LM, Smith HK, Spavold ZM, Thomas SW, Todd RS, Whittaker M. Structure-activity relationships of the peptide deformylase inhibitor BB-3497: modification of the methylene spacer and the P1' side chain. Bioorg Med Chem Lett 2003; 13:2709-13. [PMID: 12873499 DOI: 10.1016/s0960-894x(03)00532-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Structural modifications to the peptide deformylase inhibitor BB-3497 are described. In this paper, we describe the initial SAR around this lead for modifications to the methylene spacer and the P1' side chain. Enzyme inhibition and antibacterial activity data revealed that the optimum distance between the N-formyl hydroxylamine metal binding group and the P1' side chain is one unsubstituted methylene unit. Additionally, lipophilic P1' side chains that closely mimic the methionine residue in the substrate provided compounds with the best microbiological profile.
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Affiliation(s)
- Stephen J Davies
- British Biotech Pharmaceuticals Limited, Watlington Road, Oxford OX4 6LY, UK.
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22
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Davies SJ, Ayscough AP, Beckett RP, Clements JM, Doel S, Pratt LM, Spavold ZM, Thomas SW, Whittaker M. Structure--activity relationships of the peptide deformylase inhibitor BB-3497: modification of the P2' and P3' side chains. Bioorg Med Chem Lett 2003; 13:2715-8. [PMID: 12873500 DOI: 10.1016/s0960-894x(03)00533-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Structural modifications to the peptide deformylase inhibitor BB-3497 are described. In this paper, we describe the initial SAR around this lead for modifications to both the P2' and P3' side chains. Enzyme inhibition and antibacterial activity data revealed that a variety of substituents are tolerated at the P2' and P3' positions of the inhibitor backbone. The data from this study highlights the potential for modification at the P2' and P3' positions to optimise the physicochemical properties.
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Affiliation(s)
- Stephen J Davies
- British Biotech Pharmaceuticals Limited, Watlington Road, Oxford OX4 6LY, UK.
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23
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Smith KJ, Petit CM, Aubart K, Smyth M, McManus E, Jones J, Fosberry A, Lewis C, Lonetto M, Christensen SB. Structural variation and inhibitor binding in polypeptide deformylase from four different bacterial species. Protein Sci 2003; 12:349-60. [PMID: 12538898 PMCID: PMC2312423 DOI: 10.1110/ps.0229303] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Polypeptide deformylase (PDF) catalyzes the deformylation of polypeptide chains in bacteria. It is essential for bacterial cell viability and is a potential antibacterial drug target. Here, we report the crystal structures of polypeptide deformylase from four different species of bacteria: Streptococcus pneumoniae, Staphylococcus aureus, Haemophilus influenzae, and Escherichia coli. Comparison of these four structures reveals significant overall differences between the two Gram-negative species (E. coli and H. influenzae) and the two Gram-positive species (S. pneumoniae and S. aureus). Despite these differences and low overall sequence identity, the S1' pocket of PDF is well conserved among the four enzymes studied. We also describe the binding of nonpeptidic inhibitor molecules SB-485345, SB-543668, and SB-505684 to both S. pneumoniae and E. coli PDF. Comparison of these structures shows similar binding interactions with both Gram-negative and Gram-positive species. Understanding the similarities and subtle differences in active site structure between species will help to design broad-spectrum polypeptide deformylase inhibitor molecules.
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24
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Abstract
Bacteria have proved themselves able to develop resistance to every antibiotic used clinically. Traditional agents used for treatment of serious infections caused by Gram-positive species have recently been supplemented with the introduction of linezolid, quinupristin-dalfopristin, several new quinolones and telithromycin. However, resistance to many of these agents has already been reported and, although each currently retains activity against the vast majority of clinical isolates of its target species, their long-term efficacy is uncertain. We must look to develop other compounds to replace and hopefully improve upon existing anti-Gram-positive agents. Daptomycin (a lipopeptide), oritavancin and dalbavancin (both second-generation glycopeptides) and ramoplanin (a glycolipodepsipeptide) are among the agents in advanced stages of development and, at present, many seem likely to proceed to licensing. In addition, it is encouraging that many agents active against novel bacterial targets have been discovered and are in earlier stages of development. In the next two decades, we should be optimistic that a regular flow of new anti-Gram-positive agents will enable us to offset the constant spectre of bacterial resistance.
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Affiliation(s)
- Neil Woodford
- Antibiotic Resistance Monitoring and Reference Laboratory, 61 Colindale Avenue, London NW9 5HT, UK.
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25
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Smith HK, Beckett RP, Clements JM, Doel S, East SP, Launchbury SB, Pratt LM, Spavold ZM, Thomas W, Todd RS, Whittaker M. Structure-activity relationships of the peptide deformylase inhibitor BB-3497: modification of the metal binding group. Bioorg Med Chem Lett 2002; 12:3595-9. [PMID: 12443784 DOI: 10.1016/s0960-894x(02)00790-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
A series of analogues of the potent peptide deformylase (PDF) inhibitor BB-3497 containing alternative metal binding groups was synthesised. Enzyme inhibition and antibacterial activity data for these compounds revealed that the bidentate hydroxamic acid and N-formyl hydroxylamine structural motifs represent the optimum chelating groups on the pseudopeptidic BB-3497 backbone.
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Affiliation(s)
- Helen K Smith
- British Biotech Pharmaceuticals Limited, Watlington Road, Oxford OX4 6LY, UK
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26
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Baldwin ET, Harris MS, Yem AW, Wolfe CL, Vosters AF, Curry KA, Murray RW, Bock JH, Marshall VP, Cialdella JI, Merchant MH, Choi G, Deibel MR. Crystal structure of type II peptide deformylase from Staphylococcus aureus. J Biol Chem 2002; 277:31163-71. [PMID: 12048187 DOI: 10.1074/jbc.m202750200] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The first crystal structure of Class II peptide deformylase has been determined. The enzyme from Staphylococcus aureus has been overexpressed and purified in Escherichia coli and the structure determined by x-ray crystallography to 1.9 A resolution. The purified iron-enriched form of S. aureus peptide deformylase enzyme retained high activity over many months. In contrast, the iron-enriched form of the E. coli enzyme is very labile. Comparison of the two structures details many differences; however, there is no structural explanation for the dramatic activity differences we observed. The protein structure of the S. aureus enzyme reveals a fold similar, but not identical to, the well characterized E. coli enzyme. The most striking deviation of the S. aureus from the E. coli structure is the unique conformation of the C-terminal amino acids. The distinctive C-terminal helix of the latter is replaced by a strand in S. aureus which wraps around the enzyme, terminating near the active site. Although there are no differences at the amino acid level near the active site metal ion, significant changes are noted in the peptide binding cleft which may play a role in the design of general peptide deformylase inhibitors.
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Affiliation(s)
- Eric T Baldwin
- Department of Structural Analytical and Medicinal Chemistry, Pharmacia, 301 Henrietta Street, Kalamazoo, MI 49007, USA.
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27
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Guilloteau JP, Mathieu M, Giglione C, Blanc V, Dupuy A, Chevrier M, Gil P, Famechon A, Meinnel T, Mikol V. The crystal structures of four peptide deformylases bound to the antibiotic actinonin reveal two distinct types: a platform for the structure-based design of antibacterial agents. J Mol Biol 2002; 320:951-62. [PMID: 12126617 DOI: 10.1016/s0022-2836(02)00549-1] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Bacterial peptide deformylase (PDF) belongs to a sub-family of metalloproteases that catalyse the removal of the N-terminal formyl group from newly synthesised proteins. PDF is essential in prokaryotes and conserved throughout the eubacteria. It is therefore considered an attractive target for developing new antibacterial agents. Here, we report the crystal structures of four bacterial deformylases, free or bound to the naturally occurring antibiotic actinonin, including two from the major bacterial pathogens Pseudomonas aeruginosa and Staphylococcus aureus. The overall tertiary structure is essentially conserved but shows significant differences, namely at the C terminus, which are directly related to the deformylase type (i.e. I or II) they belong to. The geometry around the catalytic metal ion exhibits a high level of similarity within the different enzymes, as does the binding mode of actinonin to the various deformylases. However, some significant structural differences are found in the vicinity of the active site, highlighting the structural and molecular requirements for the design of a deformylase inhibitor active against a broad spectrum of bacterial strains.
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Affiliation(s)
- Jean-Pierre Guilloteau
- Drug Innovation & Approval, Aventis Pharma, 13 Quai Jules Guesde, BP.14, F-94403, Vitry-sur-Seine, France
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28
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Kumar A, Nguyen KT, Srivathsan S, Ornstein B, Turley S, Hirsh I, Pei D, Hol WGJ. Crystals of peptide deformylase from Plasmodium falciparum reveal critical characteristics of the active site for drug design. Structure 2002; 10:357-67. [PMID: 12005434 DOI: 10.1016/s0969-2126(02)00719-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Peptide deformylase catalyzes the deformylation reaction of the amino terminal fMet residue of newly synthesized proteins in bacteria, and most likely in Plasmodium falciparum, and has therefore been identified as a potential antibacterial and antimalarial drug target. The structure of P. falciparum peptide deformylase, determined at 2.8 A resolution with ten subunits per asymmetric unit, is similar to the bacterial enzyme with the residues involved in catalysis, the position of the bound metal ion, and a catalytically important water structurally conserved between the two enzymes. However, critical differences in the substrate binding region explain the poor affinity of E. coli deformylase inhibitors and substrates toward the Plasmodium enzyme. The Plasmodium structure serves as a guide for designing novel antimalarials.
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Affiliation(s)
- Abhinav Kumar
- Howard Hughes Medical Institute, University of Washington, Seattle 98195, USA
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29
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Bracchi-Ricard V, Nguyen KT, Zhou Y, Rajagopalan PT, Chakrabarti D, Pei D. Characterization of an eukaryotic peptide deformylase from Plasmodium falciparum. Arch Biochem Biophys 2001; 396:162-70. [PMID: 11747293 DOI: 10.1006/abbi.2001.2631] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Ribosomal protein synthesis in eubacteria and eukaryotic organelles initiates with an N-formylmethionyl-tRNA(i), resulting in N-terminal formylation of all nascent polypeptides. Peptide deformylase (PDF) catalyzes the subsequent removal of the N-terminal formyl group from the majority of bacterial proteins. Until recently, PDF has been thought as an enzyme unique to the bacterial kingdom. Searches of the genomic DNA databases identified several genes that encode proteins of high sequence homology to bacterial PDF from eukaryotic organisms. The cDNA encoding Plasmodium falciparum PDF (PfPDF) has been cloned and overexpressed in Escherichia coli. The recombinant protein is catalytically active in deformylating N-formylated peptides, shares many of the properties of bacterial PDF, and is inhibited by specific PDF inhibitors. Western blot analysis indicated expression of mature PfPDF in trophozoite, schizont, and segmenter stages of intraerythrocytic development. These results provide strong evidence that a functional PDF is present in P. falciparum. In addition, PDF inhibitors inhibited the growth of P. falciparum in the intraerythrocytic culture.
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Affiliation(s)
- V Bracchi-Ricard
- Department of Molecular Biology & Microbiology, University of Central Florida, Orlando, FL 32816, USA
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30
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Wang P, Snavley DF, Freitas MA, Pei D. Screening combinatorial libraries for optimal enzyme substrates by mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2001; 15:1166-1171. [PMID: 11445898 DOI: 10.1002/rcm.360] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A method has been developed for the rapid identification of optimal enzyme substrates from combinatorial libraries. This methodology was validated by screening a 361-member N-terminally formylated tripeptide library, f-XXR (X = 19 different amino acids), for optimal substrates of Escherichia coli peptide deformylase (PDF). The library was synthesized on a solid phase via the split-pool synthesis method. The N-terminal formyl group was added by treating the resin with a 1:1 (mol/mol) mixture of HCO(2)H and DCO(2)D in the presence of dicyclohexylcarbodiimide. In a mass spectrum, each member of the library produced a doublet peak (separated by 1.0063 Da). Limited treatment of this library with E. coli PDF resulted in the deformylation of those peptides that are the most efficient substrates of the enzyme. The deformylated products, due to loss of the mass-degenerate formyl group, each generated a singlet peak in the mass spectrum. Thus, the PDF product peaks were readily identified and sequenced via tandem mass spectrometry. The results showed that PDF strongly prefers a norleucine and, to a lesser extent, a phenylalanine as the N-terminal residue, whereas it has little selectivity at the penultimate position. This result is in excellent agreement with the literature data and therefore demonstrates the methodology as an effective approach to the identification of optimal enzyme substrates. This method should be generally applicable to other enzymes as well as synthetic catalysts.
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Affiliation(s)
- P Wang
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA
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