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Naithani K, Das A, Ushare M, Nath S, Biswas R, Kundu A, Ahmed KT, Mohan U, Bhowmik S. Design, synthesis, and evaluation of 1,4-benzothiazine-3-one containing bisamide derivatives as dual inhibitors of Staphylococcus aureus with plausible application in a urinary catheter. Front Chem 2024; 12:1420593. [PMID: 38988728 PMCID: PMC11233542 DOI: 10.3389/fchem.2024.1420593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Accepted: 06/03/2024] [Indexed: 07/12/2024] Open
Abstract
In this study, 1,4-benzothiazine-based bisamide derivatives, a new class of antibacterial agents targeting bacterial peptide deformylase (PDF), were designed and synthesized to combat Staphylococcus aureus infection. Molecular modeling of the designed molecules showed better docking scores compared to the natural product actinonin. Bioactivity assessment identified two derivatives with promising antibacterial activity in vitro. The stability of the most active molecule, 8bE, was assessed using molecular dynamics (MD) simulation. Significantly, compound 8bE could also inhibit the S. aureus biofilm at low concentrations. Furthermore, the capability of the synthesized molecule to inhibit S. aureus biofilm formation on medical devices like urinary catheters is also demonstrated.
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Affiliation(s)
- Kaushal Naithani
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Kolkata, West Bengal, India
| | - Arka Das
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Kolkata, West Bengal, India
| | - Mamta Ushare
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Kolkata, West Bengal, India
| | - Subham Nath
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Kolkata, West Bengal, India
- Microbiology Division, Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Kolkata, West Bengal, India
| | - Rashmita Biswas
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Kolkata, West Bengal, India
- Microbiology Division, Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Kolkata, West Bengal, India
| | - Anirban Kundu
- Department of Natural Product, National Institute of Pharmaceutical Education and Research, Kolkata, West Bengal, India
| | - Kazi Tawsif Ahmed
- Department of Botany, Visva Bharati University, Santiniketan, West Bengal, India
| | - Utpal Mohan
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Kolkata, West Bengal, India
- Microbiology Division, Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Kolkata, West Bengal, India
| | - Subhendu Bhowmik
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Kolkata, West Bengal, India
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Cyclization Reactions Involving 2-Aminoarenetellurols and Derivatives of α,β-Unsaturated Carboxylic Acids. HETEROATOM CHEMISTRY 2021. [DOI: 10.1155/2021/7140222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The reductive cyclization of arenetellurols carrying α,β-unsaturated amide functionalities in the ortho position was investigated. Conceptually, such compounds can form 1,3-tellurazoles without the involvement of the unsaturation in the ring closure, they can form 1,4-tellurazinone derivatives, or they can undergo ring closure to 1,5-tellurazepinones. Amides derived from acrylic and methacrylic acid generated 1,5-tellurazepinones while 2-cinnamylamidobenzenetellurol cyclized to a 1,3-tellurazole derivative. In contrast, the reaction of acetylenedicarboxylic acid and its derivatives with 2-aminoarenetellurols generated 1,4-tellurazepinones, including a derivative of novel tricyclic naphtho [1, 4]tellurazinone. A comparison with analogous reactions of sulfur congeners indicates that their chemistry is a good predictor for the products obtained from 2-aminoarenetellurols. Selected compounds were characterized by X-ray crystallography. The present work offers access to previously unexplored organotellurium heterocycles.
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3
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Zaghouani M, Bögeholz LAK, Mercier E, Wintermeyer W, Roche SP. Total synthesis of (±)-fumimycin and analogues for biological evaluation as peptide deformylase inhibitors. Tetrahedron 2019; 75:3216-3230. [PMID: 31555018 PMCID: PMC6759494 DOI: 10.1016/j.tet.2019.03.037] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A concise 7-step total synthesis of (±)-fumimycin in 11.6 % overall yield is reported. An acid-catalyzed intramolecular aza-Friedel-Crafts cyclization was developed to construct the benzofuranone skeleton of the natural product bearing an α,α-disubstituted amino acid moiety in a single step. Regioselective chlorination followed by a Suzuki-Miyaura cross-coupling rapidly enabled the preparation of a library of analogues which were evaluated against peptide deformylase for antibacterial activity.
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Affiliation(s)
- Mehdi Zaghouani
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, USA
| | - Lena A. K. Bögeholz
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Evan Mercier
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Wolfgang Wintermeyer
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Stéphane P. Roche
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, USA
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Merzoug A, Chikhi A, Bensegueni A, Boucherit H, Okay S. Virtual Screening Approach of Bacterial Peptide Deformylase Inhibitors Results in New Antibiotics. Mol Inform 2017; 37. [PMID: 28991412 DOI: 10.1002/minf.201700087] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Accepted: 09/27/2017] [Indexed: 11/07/2022]
Abstract
The increasing resistance of bacteria to antibacterial therapy poses an enormous health problem, it renders the development of new antibacterial agents with novel mechanism of action an urgent need. Peptide deformylase, a metalloenzyme which catalytically removes N-formyl group from N-terminal methionine of newly synthesized polypeptides, is an important target in antibacterial drug discovery. In this study, we report the structure-based virtual screening of ZINC database in order to discover potential hits as bacterial peptide deformylase enzyme inhibitors with more affinity as compared to GSK1322322, previously known inhibitor. After virtual screening, fifteen compounds of the top hits predicted were purchased and evaluated in vitro for their antibacterial activities against one Gram positive (Staphylococcus aureus) and three Gram negative (Escherichia coli, Pseudomonas aeruginosa and Klebsiella. pneumoniae) bacteria in different concentrations by disc diffusion method. Out of these, three compounds, ZINC00039650, ZINC03872971 and ZINC00126407, exhibited significant zone of inhibition. The results obtained were confirmed using the dilution method. Thus, these proposed compounds may aid the development of more efficient antibacterial agents.
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Affiliation(s)
- Amina Merzoug
- Laboratory of Applied Biochemistry, Department of Biochemistry and Cellular and Molecular Biology, Faculty of Natural and Life Sciences, Mentouri Brothers University, Constantine 1 -, Algeria.,Abdelhafid.Boussouf University Center, Mila, Algeria
| | - Abdelouahab Chikhi
- Laboratory of Applied Biochemistry, Department of Biochemistry and Cellular and Molecular Biology, Faculty of Natural and Life Sciences, Mentouri Brothers University, Constantine 1 -, Algeria
| | - Abderrahmane Bensegueni
- Laboratory of Applied Biochemistry, Department of Biochemistry and Cellular and Molecular Biology, Faculty of Natural and Life Sciences, Mentouri Brothers University, Constantine 1 -, Algeria
| | - Hanane Boucherit
- Laboratory of Applied Biochemistry, Department of Biochemistry and Cellular and Molecular Biology, Faculty of Natural and Life Sciences, Mentouri Brothers University, Constantine 1 -, Algeria.,Abdelhafid.Boussouf University Center, Mila, Algeria
| | - Sezer Okay
- Department of Biology, Faculty of Sciences, Cankiri Karatekin University, Turk
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Snow Setzer M, Sharifi-Rad J, Setzer WN. The Search for Herbal Antibiotics: An In-Silico Investigation of Antibacterial Phytochemicals. Antibiotics (Basel) 2016; 5:E30. [PMID: 27626453 PMCID: PMC5039526 DOI: 10.3390/antibiotics5030030] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 08/14/2016] [Accepted: 08/26/2016] [Indexed: 01/12/2023] Open
Abstract
Recently, the emergence and spread of pathogenic bacterial resistance to many antibiotics (multidrug-resistant strains) have been increasing throughout the world. This phenomenon is of great concern and there is a need to find alternative chemotherapeutic agents to combat these antibiotic-resistant microorganisms. Higher plants may serve as a resource for new antimicrobials to replace or augment current therapeutic options. In this work, we have carried out a molecular docking study of a total of 561 antibacterial phytochemicals listed in the Dictionary of Natural Products, including 77 alkaloids (17 indole alkaloids, 27 isoquinoline alkaloids, 4 steroidal alkaloids, and 28 miscellaneous alkaloids), 99 terpenoids (5 monoterpenoids, 31 sesquiterpenoids, 52 diterpenoids, and 11 triterpenoids), 309 polyphenolics (87 flavonoids, 25 chalcones, 41 isoflavonoids, 5 neoflavonoids, 12 pterocarpans, 10 chromones, 7 condensed tannins, 11 coumarins, 30 stilbenoids, 2 lignans, 5 phenylpropanoids, 13 xanthones, 5 hydrolyzable tannins, and 56 miscellaneous phenolics), 30 quinones, and 46 miscellaneous phytochemicals, with six bacterial protein targets (peptide deformylase, DNA gyrase/topoisomerase IV, UDP-galactose mutase, protein tyrosine phosphatase, cytochrome P450 CYP121, and NAD⁺-dependent DNA ligase). In addition, 35 known inhibitors were docked with their respective targets for comparison purposes. Prenylated polyphenolics showed the best docking profiles, while terpenoids had the poorest. The most susceptible protein targets were peptide deformylases and NAD⁺-dependent DNA ligases.
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Affiliation(s)
- Mary Snow Setzer
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA.
| | - Javad Sharifi-Rad
- Zabol Medicinal Plants Research Center, Zabol University of Medical Sciences, Zabol 61615-585, Iran.
- Department of Pharmacognosy, Zabol University of Medical Sciences, Zabol 61615-585, Iran.
| | - William N Setzer
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA.
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Sharifi A, Ansari M, Darabi HR, Abaee MS. Synergistic promoting effect of ball milling and KF–alumina support as a green tool for solvent-free synthesis of 2-arylidene-benzothiazinones. J Sulphur Chem 2016. [DOI: 10.1080/17415993.2016.1163699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Ali Sharifi
- Department of Organic Chemistry and Natural Products, Chemistry and Chemical Engineering Research Center of Iran, Tehran, Iran
| | - Mohammad Ansari
- Department of Organic Chemistry and Natural Products, Chemistry and Chemical Engineering Research Center of Iran, Tehran, Iran
| | - Hossein Reza Darabi
- Department of Organic Chemistry and Natural Products, Chemistry and Chemical Engineering Research Center of Iran, Tehran, Iran
| | - M. Saeed Abaee
- Department of Organic Chemistry and Natural Products, Chemistry and Chemical Engineering Research Center of Iran, Tehran, Iran
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Papadopoulos GN, Kokotos CG. Photoorganocatalytic One-Pot Synthesis of Hydroxamic Acids from Aldehydes. Chemistry 2016; 22:6964-7. [PMID: 27038037 DOI: 10.1002/chem.201600333] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Indexed: 12/27/2022]
Abstract
An efficient one-pot synthesis of hydroxamic acids from aldehydes and hydroxylamine is described. A fast, visible-light-mediated metal-free hydroacylation of dialkyl azodicarboxylates was used to develop the subsequent addition of hydroxylamine hydrochloride. A range of aliphatic and aromatic aldehydes were employed in this reaction to give hydroxamic acids in high to excellent yields. Application of the current methodology was demonstrated in the synthesis of the anticancer medicine vorinostat.
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Affiliation(s)
- Giorgos N Papadopoulos
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodestrian University of Athens, Panepistimiopolis, 15771, Athens, Greece
| | - Christoforos G Kokotos
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodestrian University of Athens, Panepistimiopolis, 15771, Athens, Greece.
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8
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Sharifi A, Ansari M, Darabi HR, Abaee MS. Synergistic promoting effect of ball milling and KF–alumina support for the green synthesis of benzothiazinones. Tetrahedron Lett 2016. [DOI: 10.1016/j.tetlet.2015.12.078] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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9
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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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Nagaraju A, Shukla G, Srivastava A, Ramulu BJ, Verma GK, Raghuvanshi K, Singh MS. Easy access to α-hydroxyimino-β-oxodithioesters and application towards the synthesis of diverse 1,4-thiazine-3-ones via reduction/annulation cascade. Tetrahedron 2014. [DOI: 10.1016/j.tet.2014.03.097] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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11
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Goodman CD, McFadden GI. Ycf93 (Orf105), a small apicoplast-encoded membrane protein in the relict plastid of the malaria parasite Plasmodium falciparum that is conserved in Apicomplexa. PLoS One 2014; 9:e91178. [PMID: 24705170 PMCID: PMC3976246 DOI: 10.1371/journal.pone.0091178] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 02/10/2014] [Indexed: 11/27/2022] Open
Abstract
Malaria parasites retain a relict plastid (apicoplast) from a photosynthetic ancestor shared with dinoflagellate algae. The apicoplast is a useful drug target; blocking housekeeping pathways such as genome replication and translation in the organelle kills parasites and protects against malaria. The apicoplast of Plasmodium falciparum encodes 30 proteins and a suite of rRNAs and tRNAs that facilitate their expression. orf105 is a hypothetical apicoplast gene that would encode a small protein (PfOrf105) with a predicted C-terminal transmembrane domain. We produced antisera to a predicted peptide within PfOrf105. Western blot analysis confirmed expression of orf105 and immunofluorescence localised the gene product to the apicoplast. Pforf105 encodes a membrane protein that has an apparent mass of 17.5 kDa and undergoes substantial turnover during the 48-hour asexual life cycle of the parasite in blood stages. The effect of actinonin, an antimalarial with a putative impact on post-translational modification of apicoplast proteins like PfOrf105, was examined. Unlike other drugs perturbing apicoplast housekeeping that induce delayed death, actinonin kills parasites immediately and has an identical drug exposure phenotype to the isopentenyl diphosphate synthesis blocker fosmidomycin. Open reading frames of similar size to PfOrf105, which also have predicted C-terminal trans membrane domains, occur in syntenic positions in all sequenced apicoplast genomes from Phylum Apicomplexa. We therefore propose to name these genes ycf93 (hypothetical chloroplast reading frame 93) according to plastid gene nomenclature convention for conserved proteins of unknown function.
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Affiliation(s)
| | - Geoffrey I. McFadden
- School of Botany, University of Melbourne, Parkville, Victoria, Australia
- * E-mail:
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12
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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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Gao J, Cheng Y, Cui W, Chen Q, Zhang F, Du Y, Ji M. 3D-QSAR and molecular docking studies of hydroxamic acids as peptide deformylase inhibitors. Med Chem Res 2011. [DOI: 10.1007/s00044-011-9672-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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Design, synthesis and antibacterial activity of 3-methylenepyrrolidine formyl hydroxyamino derivatives as novel peptide deformylase inhibitors. Bioorg Med Chem Lett 2011; 21:1060-3. [DOI: 10.1016/j.bmcl.2010.11.102] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2010] [Accepted: 11/22/2010] [Indexed: 02/03/2023]
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15
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Souizi A, Ghailane T, Saadouni M, Boukhris S, Habbadi N, Hassikou A, Kerbal A, Garrigues B. Regio-Controlled Synthesis of 1,4-Benzothiazinones. HETEROCYCLES 2011. [DOI: 10.3987/com-10-12096] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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16
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Abstract
The discovery of novel small-molecule antibacterial drugs has been stalled for many years. The purpose of this review is to underscore and illustrate those scientific problems unique to the discovery and optimization of novel antibacterial agents that have adversely affected the output of the effort. The major challenges fall into two areas: (i) proper target selection, particularly the necessity of pursuing molecular targets that are not prone to rapid resistance development, and (ii) improvement of chemical libraries to overcome limitations of diversity, especially that which is necessary to overcome barriers to bacterial entry and proclivity to be effluxed, especially in Gram-negative organisms. Failure to address these problems has led to a great deal of misdirected effort.
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Affiliation(s)
- Lynn L Silver
- LL Silver Consulting, LLC, 955 S. Springfield Ave., Unit C403, Springfield, NJ 07081, USA.
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17
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Petit S, Duroc Y, Larue V, Giglione C, Léon C, Soulama C, Denis A, Dardel F, Meinnel T, Artaud I. Structure-Activity Relationship Analysis of the Peptide Deformylase Inhibitor 5-Bromo-1H-indole-3-acetohydroxamic Acid. ChemMedChem 2009; 4:261-75. [DOI: 10.1002/cmdc.200800251] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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18
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Villain-Guillot P, Gualtieri M, Bastide L, Roquet F, Martinez J, Amblard M, Pugniere M, Leonetti JP. Structure−Activity Relationships of Phenyl-Furanyl-Rhodanines as Inhibitors of RNA Polymerase with Antibacterial Activity on Biofilms. J Med Chem 2007; 50:4195-204. [PMID: 17665895 DOI: 10.1021/jm0703183] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The dramatic rise of antibiotic-resistant bacteria over the past two decades has stressed the need for completely novel classes of antibacterial agents. Accordingly, recent advances in the study of prokaryotic transcription open new opportunities for such molecules. This paper reports the structure-activity relationships of a series of phenyl-furanyl-rhodanines (PFRs) as antibacterial inhibitors of RNA polymerase (RNAP). The molecules have been evaluated for their ability to inhibit transcription and affect growth of bacteria living in suspension or in a biofilm and for their propensity to interact with serum albumin, a critical parameter for antibacterial drug discovery. The most active of these molecules inhibit Escherichia coli RNAP transcription at concentrations of </=10 microM and have promising activities against various Gram-positive pathogens including Staphylococcus epidermidis biofilms, a major cause of nosocomial infection.
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Affiliation(s)
- Philippe Villain-Guillot
- CNRS UMR 5236, Centre d'études d'agents Pathogènes et Biotechnologie pour la Santé, and CNRS UMR 5247, Institut des Biomolécules Max Mousseron, Faculté de Pharmacie, 15 avenue Flahault, 34093 Montpellier cedex 5, France
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Wu XH, Quan JM, Wu YD. Theoretical Study of the Catalytic Mechanism and Metal-Ion Dependence of Peptide Deformylase. J Phys Chem B 2007; 111:6236-44. [PMID: 17497768 DOI: 10.1021/jp068611m] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The reaction pathway of deformylation catalyzed by E. coli peptide deformylase (PDF) has been investigated by the density functional theory method of PBE1PBE on a small model and by a two-layer ONIOM method on a realistic protein model. The deformylation proceeds in sequential steps involving nucleophilic addition of metal-coordinated water/hydroxide to the carbonyl carbon of the formyl group, proton transfer, and cleavage of the C-N bond. The first step is rate-determining for the deformylation, which occurs through a pentacoordinated metal center. The estimated activation energies with the ONIOM method are about 23.0, 15.0, and 14.9 kcal/mol for Zn-, Ni-, and Fe-PDFs, respectively. These calculated barriers are in close agreement with experimental observations. Our results demonstrate that the preference for metal coordination geometry exerts a significant influence on the catalytic activity of PDFs by affecting the activation of the carbonyl group of the substrate, the deprotonation of the metal-coordinated water, and the stabilization of the transition state. This preference for coordination geometry is mainly determined by the ligand environment and the intrinsic electronic structures of the metal center in the active site of the PDFs.
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Affiliation(s)
- Xian-Hui Wu
- Laboratory of Chemical Genomics, Shenzhen Graduate School of Peking University, Shenzhen, China
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M. El-Abadelah M, H. Al-Huniti M, A. Zahra J, M. El-Abadelah M. Heterocycles [h]Fused on 4-Oxoquinoline-3-carboxylic Acid, II. A Facile Synthesis of Some 2,7-Dioxo[1,4]thiazin[2,3-h]quinoline-8-carboxylic Acids. HETEROCYCLES 2007. [DOI: 10.3987/com-06-10930] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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21
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Bourque JR, Burley RKM, Bearne SL. Intermediate analogue inhibitors of mandelate racemase: N-Hydroxyformanilide and cupferron. Bioorg Med Chem Lett 2007; 17:105-8. [PMID: 17055725 DOI: 10.1016/j.bmcl.2006.09.079] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2006] [Revised: 09/26/2006] [Accepted: 09/27/2006] [Indexed: 11/24/2022]
Abstract
Mandelate racemase (MR) catalyzes the 1,1-proton transfer that interconverts the enantiomers of mandelate. The transition state/intermediate analogues N-hydroxyformanilide (K(i)=2.79+/-0.19 microM) and cupferron (K(i)=2.67+/-0.09 microM) are identified as potent competitive inhibitors of MR. The pH-pK(i) profile indicates that MR can bind either the protonated or deprotonated forms of N-hydroxyformanilide, with a 10-fold greater affinity for the latter form.
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Affiliation(s)
- Jennifer R Bourque
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
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22
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Boularot A, Giglione C, Petit S, Duroc Y, Alves de Sousa R, Larue V, Cresteil T, Dardel F, Artaud I, Meinnel T. Discovery and Refinement of a New Structural Class of Potent Peptide Deformylase Inhibitors. J Med Chem 2006; 50:10-20. [PMID: 17201406 DOI: 10.1021/jm060910c] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
New classes of antibiotics are urgently needed to counter increasing levels of pathogen resistance. Peptide deformylase (PDF) was originally selected as a specific bacterial target, but a human homologue, the inhibition of which causes cell death, was recently discovered. We developed a dual-screening strategy for selecting highly effective compounds with low inhibition effect against human PDF. We selected a new scaffold in vitro that discriminated between human and bacterial PDFs. Analyses of structure-activity relationships identified potent antibiotics such as 2-(5-bromo-1H-indol-3-yl)-N-hydroxyacetamide (6b) with the same mode of action in vivo as previously identified PDF inhibitors but without the apoptotic effects of these inhibitors in human cells.
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Affiliation(s)
- Adrien Boularot
- UPR2355, Centre National de la Recherche Scientifique, Bâtiment 23, 1 Avenue de la Terrasse, F-91198 Gif-Sur-Yvette Cedex, France
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Porcheddu A, Giacomelli G. Angeli−Rimini's Reaction on Solid Support: A New Approach to Hydroxamic Acids. J Org Chem 2006; 71:7057-9. [PMID: 16930063 DOI: 10.1021/jo061018g] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Angeli-Rimini's reaction has been performed for the first time on solid phase. A convenient one-step procedure for the synthesis of hydroxamic acids starting from aldehydes and solid-supported N-hydroxybenzenesulfonamide is reported. The hydroxamates are isolated in good to high yields and purities by simple evaporation of the volatile solvents, after treatment of the crude reaction mixture with sequestering agents.
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Affiliation(s)
- Andrea Porcheddu
- Dipartimento di Chimica, Università degli Studi di Sassari, Via Vienna 2, I-07100 Sassari, Italy.
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Ham J, Cho SJ, Ko J, Chin J, Kang H. A Facile One-Pot Preparation of Alkyl Aminoaryl Sulfides for the Synthesis of GW7647 as an Agonist of Peroxisome Proliferator-Activated Receptor α. J Org Chem 2006; 71:5781-4. [PMID: 16839165 DOI: 10.1021/jo060361i] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have developed two simple and high yielding one-pot syntheses of alkyl aminoaryl sulfides containing a series of four-steps: in situ protection of the free amine by reaction with a Grignard reagent, halogen-lithium exchange, sulfur insertion, and a substitution reaction with various electrophiles. Through this protocol, we have successfully synthesized tert-butyl-2-[4-(2-aminoethyl)phenylsulfanyl]-2-methylpropanoate, a key intermediate for the synthesis of GW7647 and GW9578 (ureido-TiBAs), in 92% yield. Furthermore, we were able to improve the overall yield of GW7647 to 66%, 3 times the yield previously reported.
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Affiliation(s)
- Jungyeob Ham
- Center for Marine Natural Products and Drug Discovery, School of Earth and Environmental Sciences, Seoul National University, NS-80, Seoul 151-747, Korea
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25
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Barker JJ. Antibacterial drug discovery and structure-based design. Drug Discov Today 2006; 11:391-404. [PMID: 16635801 DOI: 10.1016/j.drudis.2006.03.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2005] [Revised: 12/06/2005] [Accepted: 03/14/2006] [Indexed: 10/24/2022]
Abstract
Bacterial resistance continues to develop and pose a significant threat, both in hospitals and, more recently, in the community. A focus on other therapeutic areas by the larger pharmaceutical companies has left a shortfall in the pipeline of novel antibacterials. Recently, many new structures have been studied by structure-genomics initiatives, delivering a wealth of targets to consider. Using the tools of structure-based design, antibacterial discovery must exploit these targets to accelerate the process of drug discovery.
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Affiliation(s)
- John J Barker
- Evotec UK, 111 Milton Park, Abingdon, Oxfordshire, OX14 4RZ, UK.
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Affiliation(s)
- Kelly Aubart
- Microbial, Musculoskeletal, and Proliferative Diseases CEDD, GlaxoSmithKline Pharmaceuticals, Collegeville, PA 19426, USA
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27
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Chapter 15 Structure-Based Design of New Antibacterial Agents. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/s1574-1400(06)02015-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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28
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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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29
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Price S, Osbourn SE. Solid-Phase Synthesis of N-Formylhydroxylamines (Reverse/Retro-Hydroxamates). Org Lett 2005; 7:3761-3. [PMID: 16092869 DOI: 10.1021/ol0513995] [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] [Indexed: 11/29/2022]
Abstract
N-Formylhydroxylamines, also known as reverse- or retro-hydroxamates, have become of significant interest in the recent past as inhibitors of metalloenzymes. Although solution-phase synthetic routes to such compounds have been reported, these are often lengthy and involve purification at each stage. Herein, novel three-step solid-phase synthetic approaches are described that enable libraries of such compounds to be produced in a convergent and efficient manner using commercially available starting materials. [reaction: see text]
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Affiliation(s)
- Steve Price
- Argenta Discovery Ltd., 8/9 Spire Green Centre, Flex Meadow, Harlow, Essex, CM19 5TR, UK
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