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Qandeel BM, Mowafy S, Abouzid K, Farag NA. Lead generation of UPPS inhibitors targeting MRSA: Using 3D-QSAR pharmacophore modeling, virtual screening, molecular docking, and molecular dynamic simulations. BMC Chem 2024; 18:14. [PMID: 38245752 PMCID: PMC10800075 DOI: 10.1186/s13065-023-01110-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 12/21/2023] [Indexed: 01/22/2024] Open
Abstract
Undecaprenyl Pyrophosphate Synthase (UPPS) is a vital target enzyme in the early stages of bacterial cell wall biosynthesis. UPPS inhibitors have antibacterial activity against resistant strains such as MRSA and VRE. In this study, we used several consecutive computer-based protocols to identify novel UPPS inhibitors. The 3D QSAR pharmacophore model generation (HypoGen algorithm) protocol was used to generate a valid predictive pharmacophore model using a set of UPPS inhibitors with known reported activity. The developed model consists of four pharmacophoric features: one hydrogen bond acceptor, two hydrophobic, and one aromatic ring. It had a correlation coefficient of 0.86 and a null cost difference of 191.39, reflecting its high predictive power. Hypo1 was proven to be statistically significant using Fischer's randomization at a 95% confidence level. The validated pharmacophore model was used for the virtual screening of several databases. The resulting hits were filtered using SMART and Lipinski filters. The hits were docked into the binding site of the UPPS protein, affording 70 hits with higher docking affinities than the reference compound (6TC, - 21.17 kcal/mol). The top five hits were selected through extensive docking analysis and visual inspection based on docking affinities, fit values, and key residue interactions with the UPPS receptor. Moreover, molecular dynamic simulations of the top hits were performed to confirm the stability of the protein-ligand complexes, yielding five promising novel UPPS inhibitors.
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Affiliation(s)
- Basma M Qandeel
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Misr International University, Km28 Cairo-Ismailia Road, Ahmed Orabi District, Cairo, Egypt.
| | - Samar Mowafy
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Misr International University, Km28 Cairo-Ismailia Road, Ahmed Orabi District, Cairo, Egypt
| | - Khaled Abouzid
- Department of Pharmaceutical Chemistry, College of Pharmacy, Ain-Shams University, Abbasia, 11566, Egypt
| | - Nahla A Farag
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Misr International University, Km28 Cairo-Ismailia Road, Ahmed Orabi District, Cairo, Egypt.
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2
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Akiyama DY, Rocha MC, Costa JH, Teles CB, da Silva Zuccoli G, Malavazi I, Fill TP. The Penicillium brasilianum Histone Deacetylase Clr3 Regulates Secondary Metabolite Production and Tolerance to Oxidative Stress. J Fungi (Basel) 2022; 8:jof8050514. [PMID: 35628769 PMCID: PMC9146837 DOI: 10.3390/jof8050514] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/10/2022] [Accepted: 05/13/2022] [Indexed: 02/01/2023] Open
Abstract
Most of the biosynthetic gene clusters (BGCs) found in microbes are silent under standard laboratory cultivation conditions due to the lack of expression triggering stimuli, representing a considerable drawback in drug discovery. To access the full biosynthetic potential, studies towards the activation of cryptic BGCs are essential. Histone acetylation status is an important regulator of chromatin structure, which impacts cell physiology and the expression of BGCs. In this study, clr3, a gene encoding a histone deacetylase in Penicillium brasilianum LaBioMMi 136, is deleted and associated phenotypic and metabolic changes are evaluated. The results indicate reduced growth under oxidative stress conditions in the ∆clr3 strain, higher intracellular reactive oxygen species (ROS) levels, and a different transcriptional profile of 13 ROS-related genes of both strains under basal and ROS-induced conditions. Moreover, the production of 14 secondary metabolites, including austin-related meroterpenoids, brasiliamides, verruculogen, penicillic acid, and cyclodepsipeptides was evaluated in the ∆clr3 strain, most of them being reduced. Accordingly, the addition of epigenetic modulators responsible for HDAC inhibition into P. brasilianum’s growth media also culminated in the reduction in secondary metabolite production. The results suggest that Clr3 plays an essential role in secondary metabolite biosynthesis in P. brasilianum, thus offering new strategies for the regulation of natural product synthesis by assessing chromatin modification.
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Affiliation(s)
- Daniel Yuri Akiyama
- Department of Organic Chemistry, Institute of Chemistry, State University of Campinas, Campinas 13083-970, SP, Brazil; (D.Y.A.); (J.H.C.)
| | - Marina Campos Rocha
- Department of Genetic and Evolution, Federal University of São Carlos, São Carlos 13565-905, SP, Brazil;
| | - Jonas Henrique Costa
- Department of Organic Chemistry, Institute of Chemistry, State University of Campinas, Campinas 13083-970, SP, Brazil; (D.Y.A.); (J.H.C.)
| | - Caroline Brandão Teles
- Department of Biochemistry and Tissue Biology, Institute of Biology, State University of Campinas, Campinas 13083-970, SP, Brazil; (C.B.T.); (G.d.S.Z.)
| | - Giuliana da Silva Zuccoli
- Department of Biochemistry and Tissue Biology, Institute of Biology, State University of Campinas, Campinas 13083-970, SP, Brazil; (C.B.T.); (G.d.S.Z.)
| | - Iran Malavazi
- Department of Genetic and Evolution, Federal University of São Carlos, São Carlos 13565-905, SP, Brazil;
- Correspondence: (I.M.); (T.P.F.)
| | - Taicia Pacheco Fill
- Department of Organic Chemistry, Institute of Chemistry, State University of Campinas, Campinas 13083-970, SP, Brazil; (D.Y.A.); (J.H.C.)
- Correspondence: (I.M.); (T.P.F.)
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3
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Baire B, Yadav B. TfOH catalysed domino-double annulation of arenes with propargylic alcohols: a unified approach to indene polycyclic systems. Chem Commun (Camb) 2021; 57:12796-12799. [PMID: 34782905 DOI: 10.1039/d1cc05253e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The design and development of a TfOH catalysed domino strategy for the double annulation of arenes with propargylic alcohols for the rapid generation of indene based polycyclic systems is reported. The dehydration, intramolecular 6-endo-dig hydroarylation, and cationic cyclization were consecutively promoted by TfOH. The key features of this strategy are the formation of two C-C bonds, unified access to indene polycyclic systems, excellent yields (up to 95%), high atom economy (>90%), an operationally simple procedure, and water being the only byproduct. By extending this strategy, a two-step synthesis of the pentacyclic systems of hypoxylonol A (43% overall yield from α-tetralone), daldinone A (63% overall yield from β-tetralone) and spiro-tetracyclic framework of incarviatone A has also been achieved.
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Affiliation(s)
- Beeraiah Baire
- Department of Chemistry, Indian Institute of Technology Madras, Chennai-600036, Tamilnadu, India.
| | - Bhavna Yadav
- Department of Chemistry, Indian Institute of Technology Madras, Chennai-600036, Tamilnadu, India.
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4
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An Z, Liu Y, Sun Y, Yan R. TFA-Catalyzed [3+2] Spiroannulation of Cyclobutanols: A Route to Spiro[cyclobuta[a]indene-7,1'-cyclobutane] Skeletons. Chem Asian J 2020; 15:3812-3815. [PMID: 32997399 DOI: 10.1002/asia.202001048] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 09/27/2020] [Indexed: 12/15/2022]
Abstract
A straightforward method for the synthesis of spiro[cyclobuta[a]indene-7,1'-cyclobutane] derivatives from cyclobutanols has been developed via one-pot [3+2] spiroannulation. A series of new spiro[cyclobuta[a]indene-7,1'-cyclobutane] derivatives are facilely synthesized in good yields under mild reaction conditions.
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Affiliation(s)
- Zhenyu An
- State Key Laboratory of Applied Organic Chemistry, Key laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, P. R. China
| | - Yafeng Liu
- Chemical Science and Engineering College, North Minzu University, Yinchuan, 750000, P. R. China
| | - Yanwei Sun
- Research Institute of Exploration & Development, Tuha Oilfield Company, Xinjiang, 830000, P. R. China
| | - Rulong Yan
- State Key Laboratory of Applied Organic Chemistry, Key laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, P. R. China
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5
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Li W, Li L, Zhang C, Cai Y, Gao Q, Wang F, Cao Y, Lin J, Li J, Shang Z, Lin W. Investigations into the Antibacterial Mechanism of Action of Viridicatumtoxins. ACS Infect Dis 2020; 6:1759-1769. [PMID: 32437130 DOI: 10.1021/acsinfecdis.0c00031] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Viridicatumtoxins are a rare class of tetracycline-like antibiotics that strongly inhibit drug-resistant Gram-positive bacteria. Although reported to exhibit in vitro inhibition activity to undecaprenyl pyrophosphate synthase (UPPS), an essential enzyme in bacterial cell wall synthesis, the biological targets and mechanism of action of viridicatumtoxins, especially the drug-target interactions, remain largely unknown. In this study, the structure of Enterococcus faecalis UPPS (EfaUPPS) was first determined, uncovering that EfaUPPS can form not only a typical functional dimer but also an unexpected atypical dimer. We then observed that viridicatumtoxins A (VirA) and B (VirB) are able to bind to UPPSs of E. faecalis, S. aureus, and E. coli in a direct and high-affinity manner as evidenced by in vitro enzyme inhibition assay, surface plasmon resonance (SPR) binding analysis, and in vivo growth inhibition assay, demonstrating that viridicatumtoxins exert antibacterial effects through UPPS binding. The key amino acid residues involved in the interactions with VirA and VirB in EfaUPPS binding pocket were revealed by molecular docking studies, and further validated by site-directed mutagenesis. A single mutation of EfaUPPS at D29A, N31A, and R42A can obviously increase their affinities to VirA, while a single mutation at W228A conferred significant resistance to VirA. Moreover, translation inhibition assay showed that VirA and VirB can weakly inhibit E. coli 70S ribosome. The weak inhibition of ribosome was proposed to be attributed to steric hindrance between viridicatumtoxin ring F and 70S ribosome helix 34 by molecular docking study. Our structural, biochemical, and computational investigations on the interactions of viridicatumtoxins with UPPS and 70S ribosome not only disclosed the potential biological targets of viridicatumtoxins, but also provided a theoretical basis for structural optimization to make new viridicatumtoxin derivatives with improved antimicrobial activities.
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Affiliation(s)
- Weijia Li
- Department of Microbiology and Immunology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China
| | - Li Li
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Chao Zhang
- Department of Pharmacology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China
| | - Yuanheng Cai
- Biochemistry and Cell Biology Department, Stony Brook University, Stony Brook, New York 11794, United States
| | - Qiyu Gao
- Department of Microbiology and Immunology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China
| | - Fulin Wang
- Department of Microbiology and Immunology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China
| | - Yu Cao
- Department of Microbiology and Immunology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China
| | - Jinzhong Lin
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Jie Li
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Zhuo Shang
- Department of Microbiology and Immunology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Wei Lin
- Department of Microbiology and Immunology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu 211198, China
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Houbraken J, Kocsubé S, Visagie C, Yilmaz N, Wang XC, Meijer M, Kraak B, Hubka V, Bensch K, Samson R, Frisvad J. Classification of Aspergillus, Penicillium, Talaromyces and related genera ( Eurotiales): An overview of families, genera, subgenera, sections, series and species. Stud Mycol 2020; 95:5-169. [PMID: 32855739 PMCID: PMC7426331 DOI: 10.1016/j.simyco.2020.05.002] [Citation(s) in RCA: 264] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The Eurotiales is a relatively large order of Ascomycetes with members frequently having positive and negative impact on human activities. Species within this order gain attention from various research fields such as food, indoor and medical mycology and biotechnology. In this article we give an overview of families and genera present in the Eurotiales and introduce an updated subgeneric, sectional and series classification for Aspergillus and Penicillium. Finally, a comprehensive list of accepted species in the Eurotiales is given. The classification of the Eurotiales at family and genus level is traditionally based on phenotypic characters, and this classification has since been challenged using sequence-based approaches. Here, we re-evaluated the relationships between families and genera of the Eurotiales using a nine-gene sequence dataset. Based on this analysis, the new family Penicillaginaceae is introduced and four known families are accepted: Aspergillaceae, Elaphomycetaceae, Thermoascaceae and Trichocomaceae. The Eurotiales includes 28 genera: 15 genera are accommodated in the Aspergillaceae (Aspergillago, Aspergillus, Evansstolkia, Hamigera, Leiothecium, Monascus, Penicilliopsis, Penicillium, Phialomyces, Pseudohamigera, Pseudopenicillium, Sclerocleista, Warcupiella, Xerochrysium and Xeromyces), eight in the Trichocomaceae (Acidotalaromyces, Ascospirella, Dendrosphaera, Rasamsonia, Sagenomella, Talaromyces, Thermomyces, Trichocoma), two in the Thermoascaceae (Paecilomyces, Thermoascus) and one in the Penicillaginaceae (Penicillago). The classification of the Elaphomycetaceae was not part of this study, but according to literature two genera are present in this family (Elaphomyces and Pseudotulostoma). The use of an infrageneric classification system has a long tradition in Aspergillus and Penicillium. Most recent taxonomic studies focused on the sectional level, resulting in a well-established sectional classification in these genera. In contrast, a series classification in Aspergillus and Penicillium is often outdated or lacking, but is still relevant, e.g., the allocation of a species to a series can be highly predictive in what functional characters the species might have and might be useful when using a phenotype-based identification. The majority of the series in Aspergillus and Penicillium are invalidly described and here we introduce a new series classification. Using a phylogenetic approach, often supported by phenotypic, physiologic and/or extrolite data, Aspergillus is subdivided in six subgenera, 27 sections (five new) and 75 series (73 new, one new combination), and Penicillium in two subgenera, 32 sections (seven new) and 89 series (57 new, six new combinations). Correct identification of species belonging to the Eurotiales is difficult, but crucial, as the species name is the linking pin to information. Lists of accepted species are a helpful aid for researchers to obtain a correct identification using the current taxonomic schemes. In the most recent list from 2014, 339 Aspergillus, 354 Penicillium and 88 Talaromyces species were accepted. These numbers increased significantly, and the current list includes 446 Aspergillus (32 % increase), 483 Penicillium (36 % increase) and 171 Talaromyces (94 % increase) species, showing the large diversity and high interest in these genera. We expanded this list with all genera and species belonging to the Eurotiales (except those belonging to Elaphomycetaceae). The list includes 1 187 species, distributed over 27 genera, and contains MycoBank numbers, collection numbers of type and ex-type cultures, subgenus, section and series classification data, information on the mode of reproduction, and GenBank accession numbers of ITS, beta-tubulin (BenA), calmodulin (CaM) and RNA polymerase II second largest subunit (RPB2) gene sequences.
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Key Words
- Acidotalaromyces Houbraken, Frisvad & Samson
- Acidotalaromyces lignorum (Stolk) Houbraken, Frisvad & Samson
- Ascospirella Houbraken, Frisvad & Samson
- Ascospirella lutea (Zukal) Houbraken, Frisvad & Samson
- Aspergillus chaetosartoryae Hubka, Kocsubé & Houbraken
- Classification
- Evansstolkia Houbraken, Frisvad & Samson
- Evansstolkia leycettana (H.C. Evans & Stolk) Houbraken, Frisvad & Samson
- Hamigera brevicompacta (H.Z. Kong) Houbraken, Frisvad & Samson
- Infrageneric classification
- New combinations, series
- New combinations, species
- New genera
- New names
- New sections
- New series
- New taxa
- Nomenclature
- Paecilomyces lagunculariae (C. Ram) Houbraken, Frisvad & Samson
- Penicillaginaceae Houbraken, Frisvad & Samson
- Penicillago kabunica (Baghd.) Houbraken, Frisvad & Samson
- Penicillago mirabilis (Beliakova & Milko) Houbraken, Frisvad & Samson
- Penicillago moldavica (Milko & Beliakova) Houbraken, Frisvad & Samson
- Phialomyces arenicola (Chalab.) Houbraken, Frisvad & Samson
- Phialomyces humicoloides (Bills & Heredia) Houbraken, Frisvad & Samson
- Phylogeny
- Polythetic classes
- Pseudohamigera Houbraken, Frisvad & Samson
- Pseudohamigera striata (Raper & Fennell) Houbraken, Frisvad & Samson
- Talaromyces resinae (Z.T. Qi & H.Z. Kong) Houbraken & X.C. Wang
- Talaromyces striatoconidius Houbraken, Frisvad & Samson
- Taxonomic novelties: New family
- Thermoascus verrucosus (Samson & Tansey) Houbraken, Frisvad & Samson
- Thermoascus yaguchii Houbraken, Frisvad & Samson
- in Aspergillus: sect. Bispori S.W. Peterson, Varga, Frisvad, Samson ex Houbraken
- in Aspergillus: ser. Acidohumorum Houbraken & Frisvad
- in Aspergillus: ser. Inflati (Stolk & Samson) Houbraken & Frisvad
- in Penicillium: sect. Alfrediorum Houbraken & Frisvad
- in Penicillium: ser. Adametziorum Houbraken & Frisvad
- in Penicillium: ser. Alutacea (Pitt) Houbraken & Frisvad
- sect. Crypta Houbraken & Frisvad
- sect. Eremophila Houbraken & Frisvad
- sect. Formosana Houbraken & Frisvad
- sect. Griseola Houbraken & Frisvad
- sect. Inusitata Houbraken & Frisvad
- sect. Lasseniorum Houbraken & Frisvad
- sect. Polypaecilum Houbraken & Frisvad
- sect. Raperorum S.W. Peterson, Varga, Frisvad, Samson ex Houbraken
- sect. Silvatici S.W. Peterson, Varga, Frisvad, Samson ex Houbraken
- sect. Vargarum Houbraken & Frisvad
- ser. Alliacei Houbraken & Frisvad
- ser. Ambigui Houbraken & Frisvad
- ser. Angustiporcata Houbraken & Frisvad
- ser. Arxiorum Houbraken & Frisvad
- ser. Atramentosa Houbraken & Frisvad
- ser. Aurantiobrunnei Houbraken & Frisvad
- ser. Avenacei Houbraken & Frisvad
- ser. Bertholletiarum Houbraken & Frisvad
- ser. Biplani Houbraken & Frisvad
- ser. Brevicompacta Houbraken & Frisvad
- ser. Brevipedes Houbraken & Frisvad
- ser. Brunneouniseriati Houbraken & Frisvad
- ser. Buchwaldiorum Houbraken & Frisvad
- ser. Calidousti Houbraken & Frisvad
- ser. Canini Houbraken & Frisvad
- ser. Carbonarii Houbraken & Frisvad
- ser. Cavernicolarum Houbraken & Frisvad
- ser. Cervini Houbraken & Frisvad
- ser. Chevalierorum Houbraken & Frisvad
- ser. Cinnamopurpurea Houbraken & Frisvad
- ser. Circumdati Houbraken & Frisvad
- ser. Clavigera Houbraken & Frisvad
- ser. Conjuncti Houbraken & Frisvad
- ser. Copticolarum Houbraken & Frisvad
- ser. Coremiiformes Houbraken & Frisvad
- ser. Corylophila Houbraken & Frisvad
- ser. Costaricensia Houbraken & Frisvad
- ser. Cremei Houbraken & Frisvad
- ser. Crustacea (Pitt) Houbraken & Frisvad
- ser. Dalearum Houbraken & Frisvad
- ser. Deflecti Houbraken & Frisvad
- ser. Egyptiaci Houbraken & Frisvad
- ser. Erubescentia (Pitt) Houbraken & Frisvad
- ser. Estinogena Houbraken & Frisvad
- ser. Euglauca Houbraken & Frisvad
- ser. Fennelliarum Houbraken & Frisvad
- ser. Flavi Houbraken & Frisvad
- ser. Flavipedes Houbraken & Frisvad
- ser. Fortuita Houbraken & Frisvad
- ser. Fumigati Houbraken & Frisvad
- ser. Funiculosi Houbraken & Frisvad
- ser. Gallaica Houbraken & Frisvad
- ser. Georgiensia Houbraken & Frisvad
- ser. Goetziorum Houbraken & Frisvad
- ser. Gracilenta Houbraken & Frisvad
- ser. Halophilici Houbraken & Frisvad
- ser. Herqueorum Houbraken & Frisvad
- ser. Heteromorphi Houbraken & Frisvad
- ser. Hoeksiorum Houbraken & Frisvad
- ser. Homomorphi Houbraken & Frisvad
- ser. Idahoensia Houbraken & Frisvad
- ser. Implicati Houbraken & Frisvad
- ser. Improvisa Houbraken & Frisvad
- ser. Indica Houbraken & Frisvad
- ser. Japonici Houbraken & Frisvad
- ser. Jiangxiensia Houbraken & Frisvad
- ser. Kalimarum Houbraken & Frisvad
- ser. Kiamaensia Houbraken & Frisvad
- ser. Kitamyces Houbraken & Frisvad
- ser. Lapidosa (Pitt) Houbraken & Frisvad
- ser. Leporum Houbraken & Frisvad
- ser. Leucocarpi Houbraken & Frisvad
- ser. Livida Houbraken & Frisvad
- ser. Longicatenata Houbraken & Frisvad
- ser. Macrosclerotiorum Houbraken & Frisvad
- ser. Monodiorum Houbraken & Frisvad
- ser. Multicolores Houbraken & Frisvad
- ser. Neoglabri Houbraken & Frisvad
- ser. Neonivei Houbraken & Frisvad
- ser. Nidulantes Houbraken & Frisvad
- ser. Nigri Houbraken & Frisvad
- ser. Nivei Houbraken & Frisvad
- ser. Nodula Houbraken & Frisvad
- ser. Nomiarum Houbraken & Frisvad
- ser. Noonimiarum Houbraken & Frisvad
- ser. Ochraceorosei Houbraken & Frisvad
- ser. Olivimuriarum Houbraken & Frisvad
- ser. Osmophila Houbraken & Frisvad
- ser. Paradoxa Houbraken & Frisvad
- ser. Paxillorum Houbraken & Frisvad
- ser. Penicillioides Houbraken & Frisvad
- ser. Phoenicea Houbraken & Frisvad
- ser. Pinetorum (Pitt) Houbraken & Frisvad
- ser. Polypaecilum Houbraken & Frisvad
- ser. Pulvini Houbraken & Frisvad
- ser. Quercetorum Houbraken & Frisvad
- ser. Raistrickiorum Houbraken & Frisvad
- ser. Ramigena Houbraken & Frisvad
- ser. Restricti Houbraken & Frisvad
- ser. Robsamsonia Houbraken & Frisvad
- ser. Rolfsiorum Houbraken & Frisvad
- ser. Roseopurpurea Houbraken & Frisvad
- ser. Rubri Houbraken & Frisvad
- ser. Salinarum Houbraken & Frisvad
- ser. Samsoniorum Houbraken & Frisvad
- ser. Saturniformia Houbraken & Frisvad
- ser. Scabrosa Houbraken & Frisvad
- ser. Sclerotigena Houbraken & Frisvad
- ser. Sclerotiorum Houbraken & Frisvad
- ser. Sheariorum Houbraken & Frisvad
- ser. Simplicissima Houbraken & Frisvad
- ser. Soppiorum Houbraken & Frisvad
- ser. Sparsi Houbraken & Frisvad
- ser. Spathulati Houbraken & Frisvad
- ser. Spelaei Houbraken & Frisvad
- ser. Speluncei Houbraken & Frisvad
- ser. Spinulosa Houbraken & Frisvad
- ser. Stellati Houbraken & Frisvad
- ser. Steyniorum Houbraken & Frisvad
- ser. Sublectatica Houbraken & Frisvad
- ser. Sumatraensia Houbraken & Frisvad
- ser. Tamarindosolorum Houbraken & Frisvad
- ser. Teporium Houbraken & Frisvad
- ser. Terrei Houbraken & Frisvad
- ser. Thermomutati Houbraken & Frisvad
- ser. Thiersiorum Houbraken & Frisvad
- ser. Thomiorum Houbraken & Frisvad
- ser. Unguium Houbraken & Frisvad
- ser. Unilaterales Houbraken & Frisvad
- ser. Usti Houbraken & Frisvad
- ser. Verhageniorum Houbraken & Frisvad
- ser. Versicolores Houbraken & Frisvad
- ser. Virgata Houbraken & Frisvad
- ser. Viridinutantes Houbraken & Frisvad
- ser. Vitricolarum Houbraken & Frisvad
- ser. Wentiorum Houbraken & Frisvad
- ser. Westlingiorum Houbraken & Frisvad
- ser. Whitfieldiorum Houbraken & Frisvad
- ser. Xerophili Houbraken & Frisvad
- series Tularensia (Pitt) Houbraken & Frisvad
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Affiliation(s)
- J. Houbraken
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - S. Kocsubé
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - C.M. Visagie
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Hatfield, Pretoria, 0028, South Africa
| | - N. Yilmaz
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Hatfield, Pretoria, 0028, South Africa
| | - X.-C. Wang
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No. 3, 1st Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - M. Meijer
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - B. Kraak
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - V. Hubka
- Department of Botany, Charles University in Prague, Prague, Czech Republic
| | - K. Bensch
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - R.A. Samson
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - J.C. Frisvad
- Department of Biotechnology and Biomedicine Technical University of Denmark, Søltofts Plads, B. 221, Kongens Lyngby, DK 2800, Denmark
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7
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Zuo Z, Wang J, Liu J, Wang Y, Luan X. Palladium‐Catalyzed [2+2+1] Spiroannulation via Alkyne‐Directed Remote C−H Arylation and Subsequent Arene Dearomatization. Angew Chem Int Ed Engl 2020; 59:653-657. [DOI: 10.1002/anie.201909557] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/23/2019] [Indexed: 11/09/2022]
Affiliation(s)
- Zhijun Zuo
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of EducationCollege of Chemistry & Materials ScienceNorthwest University Xi'an 710127 China
| | - Jing Wang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of EducationCollege of Chemistry & Materials ScienceNorthwest University Xi'an 710127 China
| | - Jingjing Liu
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of EducationCollege of Chemistry & Materials ScienceNorthwest University Xi'an 710127 China
| | - Yaoyu Wang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of EducationCollege of Chemistry & Materials ScienceNorthwest University Xi'an 710127 China
| | - Xinjun Luan
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of EducationCollege of Chemistry & Materials ScienceNorthwest University Xi'an 710127 China
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8
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Capon RJ. Extracting value: mechanistic insights into the formation of natural product artifacts – case studies in marine natural products. Nat Prod Rep 2020; 37:55-79. [DOI: 10.1039/c9np00013e] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
This review highlights the importance of valuing natural product handling artifacts, to open a new window into, and provide a unique perspective of, bioactive chemical space.
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Affiliation(s)
- Robert J. Capon
- Division of Chemistry and Structural Biology
- Institute for Molecular Bioscience
- The University of Queensland
- St Lucia
- Australia
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9
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Zuo Z, Wang J, Liu J, Wang Y, Luan X. Palladium‐Catalyzed [2+2+1] Spiroannulation via Alkyne‐Directed Remote C−H Arylation and Subsequent Arene Dearomatization. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201909557] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Zhijun Zuo
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of EducationCollege of Chemistry & Materials ScienceNorthwest University Xi'an 710127 China
| | - Jing Wang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of EducationCollege of Chemistry & Materials ScienceNorthwest University Xi'an 710127 China
| | - Jingjing Liu
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of EducationCollege of Chemistry & Materials ScienceNorthwest University Xi'an 710127 China
| | - Yaoyu Wang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of EducationCollege of Chemistry & Materials ScienceNorthwest University Xi'an 710127 China
| | - Xinjun Luan
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of EducationCollege of Chemistry & Materials ScienceNorthwest University Xi'an 710127 China
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10
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Helal AM, Sayed AM, Omara M, Elsebaei MM, Mayhoub AS. Peptidoglycan pathways: there are still more! RSC Adv 2019; 9:28171-28185. [PMID: 35530449 PMCID: PMC9071014 DOI: 10.1039/c9ra04518j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 08/22/2019] [Indexed: 11/21/2022] Open
Abstract
The discovery of 3rd and 4th generations of currently existing classes of antibiotics has not hindered bacterial resistance, which is escalating at an alarming global level. This review follows WHO recommendations through implementing new criteria for newly discovered antibiotics. These recommendations focus on abandoning old scaffolds and hitting new targets. In light of these recommendations, this review discusses seven bacterial proteins that no commercial antibiotics have targeted yet, alongside their reported chemical scaffolds.
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Affiliation(s)
- Ahmed M Helal
- Department of Pharmaceutical Organic Chemistry, College of Pharmacy, Al-Azhar University Cairo 11884 Egypt
| | - Ahmed M Sayed
- Department of Pharmaceutical Organic Chemistry, College of Pharmacy, Al-Azhar University Cairo 11884 Egypt
| | - Mariam Omara
- Department of Pharmaceutical Organic Chemistry, College of Pharmacy, Al-Azhar University Cairo 11884 Egypt
| | - Mohamed M Elsebaei
- Department of Pharmaceutical Organic Chemistry, College of Pharmacy, Al-Azhar University Cairo 11884 Egypt
| | - Abdelrahman S Mayhoub
- Department of Pharmaceutical Organic Chemistry, College of Pharmacy, Al-Azhar University Cairo 11884 Egypt
- University of Science and Technology, Zewail City of Science and Technology Giza Egypt
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11
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Magnin A, Hoornaert L, Pollet E, Laurichesse S, Phalip V, Avérous L. Isolation and characterization of different promising fungi for biological waste management of polyurethanes. Microb Biotechnol 2019; 12:544-555. [PMID: 30592151 PMCID: PMC6465239 DOI: 10.1111/1751-7915.13346] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 10/10/2018] [Accepted: 11/10/2018] [Indexed: 12/24/2022] Open
Abstract
As a highly resistant polymer family, polyurethanes (PU) are responsible for increasing environmental issues. Then, PU biodegradation is a challenging way to develop sustainable waste management processes based on biological recycling. Since the metabolic diversity of fungi is a major asset for polymer degradation, nearly thirty strains were isolated from sampling on six different PU wastes-containing environments. A screening of the fungi on four thermoplastic PU (TPU) with different macromolecular architectures led to the selection of three strains able to use two polyester PU as sole carbon source: Alternaria sp., Penicillium section Lanata-Divaricata and Aspergillus section flavi. Weight loss, FT-IR, Scanning Electron Microscopy and Size Exclusion Chromatography analyses revealed that these three fungi degrade slightly and similarly a fatty acid dimer-based TPU while variability of degradation was noticed on a polycaprolactone-based TPU. On this last TPU, robust analysis of the degraded polymers showed that the Penicillium strain was the best degrading microorganism. Membrane enzymes seemed to be involved in this degradation. It is the first time that a strain of Penicillium of the section Lanata-Divaricata displaying PU biodegradation ability is isolated. These newly discovered fungi are promising for the development of polyester PU waste management process.
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Affiliation(s)
- Audrey Magnin
- BioTeam/ICPEES‐ECPMUMR CNRS 7515Université de Strasbourg25 rue Becquerel67087Strasbourg Cedex 2France
| | - Lucie Hoornaert
- BioTeam/ICPEES‐ECPMUMR CNRS 7515Université de Strasbourg25 rue Becquerel67087Strasbourg Cedex 2France
| | - Eric Pollet
- BioTeam/ICPEES‐ECPMUMR CNRS 7515Université de Strasbourg25 rue Becquerel67087Strasbourg Cedex 2France
| | | | - Vincent Phalip
- Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'OpaleEA 7394 – ICV – Institut Charles Viollette59000LilleFrance
| | - Luc Avérous
- BioTeam/ICPEES‐ECPMUMR CNRS 7515Université de Strasbourg25 rue Becquerel67087Strasbourg Cedex 2France
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12
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Nan J, Yuan Y, Bai L, Liu J, Luan X. Highly Chemoselective Construction of Spiro[4,5]decane-Embedded Polycyclic Scaffolds by a Palladium/Norbornene-Catalyzed C–H Activation/Arene Dearomatization Reaction. Org Lett 2018; 20:7731-7734. [DOI: 10.1021/acs.orglett.8b03518] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Jiang Nan
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi’an 710069, China
| | - Yini Yuan
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi’an 710069, China
| | - Lu Bai
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi’an 710069, China
| | - Jingjing Liu
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi’an 710069, China
| | - Xinjun Luan
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi’an 710069, China
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13
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Draft Genome Sequence of the Fungus Penicillium brasilianum (Strain LaBioMMi 136), a Plant Endophyte from Melia azedarach. Microbiol Resour Announc 2018; 7:MRA01235-18. [PMID: 30533840 PMCID: PMC6284728 DOI: 10.1128/mra.01235-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 11/03/2018] [Indexed: 11/20/2022] Open
Abstract
Penicillium brasilianum (strain LaBioMMi 136) has been reported to be a great producer of secondary metabolites and a source of enzymes of biotechnological interest. Here, we report the draft genome sequence of P. brasilianum (strain LaBioMMi 136), isolated as an endophyte from the plant Melia azedarach (family Meliaceae). Penicillium brasilianum (strain LaBioMMi 136) has been reported to be a great producer of secondary metabolites and a source of enzymes of biotechnological interest. Here, we report the draft genome sequence of P. brasilianum (strain LaBioMMi 136), isolated as an endophyte from the plant Melia azedarach (family Meliaceae).
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14
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Abstract
Natural products have served as powerful therapeutics against pathogenic bacteria since the golden age of antibiotics of the mid-20th century. However, the increasing frequency of antibiotic-resistant infections clearly demonstrates that new antibiotics are critical for modern medicine. Because combinatorial approaches have not yielded effective drugs, we propose that the development of new antibiotics around proven natural scaffolds is the best short-term solution to the rising crisis of antibiotic resistance. We analyze herein synthetic approaches aiming to reengineer natural products into potent antibiotics. Furthermore, we discuss approaches in modulating quorum sensing and biofilm formation as a nonlethal method, as well as narrow-spectrum pathogen-specific antibiotics, which are of interest given new insights into the implications of disrupting the microbiome.
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Affiliation(s)
- Sean E. Rossiter
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Madison H. Fletcher
- Department of Chemistry, Temple University, 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - William M. Wuest
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
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15
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A brief history of antibiotics and select advances in their synthesis. J Antibiot (Tokyo) 2017; 71:153-184. [DOI: 10.1038/ja.2017.62] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 04/17/2017] [Accepted: 04/23/2017] [Indexed: 12/20/2022]
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16
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Abstract
Over the past few years Penicillium brasilianum has been isolated from many different environmental sources as soil isolates, plant endophytes and onion pathogen. All investigated strains share a great ability to produce bioactive secondary metabolites. Different authors have investigated this great capability and here we summarize the metabolic potential and the biological activities related to P. brasilianum’s metabolites with diverse structures. They include secondary metabolites of an alkaloid nature, i.e., 2,5-diketopiperazines, cyclodepsipeptides, meroterpenoids and polyketides. Penicillium brasilianum is also described as a great source of enzymes with biotechnological application potential, which is also highlighted in this review. Additionally, this review will focus on several aspects of Penicillium brasilianum and interesting genomic insights.
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17
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Liu ZG, Bao L, Liu HW, Ren JW, Wang WZ, Wang L, Li W, Yin WB. Chemical diversity from the Tibetan Plateau fungi Penicillium kongii and P. brasilianum. Mycology 2017; 9:10-19. [PMID: 30123656 PMCID: PMC6059045 DOI: 10.1080/21501203.2017.1331937] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 05/14/2017] [Indexed: 02/06/2023] Open
Abstract
Two new secondary metabolites, kongiilines A and B (1, 7), and two asperphenamate derivatives, asperphenamates B and C (5–6), together with 16 known compounds (2–4, 8–20), were isolated from Tibetan Plateau fungi Penicillium kongii and Penicillium brasilianum. This is the first report on asperphenamates B and C as naturally occurring compounds, and that aspterric acid is isolated from P. brasilianum for the first time. Their structures were elucidated by different spectroscopic techniques including high-resolution electrospray ionisation mass spectrum, 1D nuclear magnetic resonance (NMR), and 2D NMR as well as electronic circular dichroism. Compounds 4, 5, and 10 exhibited cytotoxicity activities against human colon carcinoma HCT116 cell line with IC50 values of 88.16, 77.68, and 36.92 μM, respectively. Fungi from Tibetan Plateau represent important and rich resources for the investigation of new chemicals.
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Affiliation(s)
- Zhi-Guo Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Li Bao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Hong-Wei Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jin-Wei Ren
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Wen-Zhao Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Long Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Wei Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wen-Bing Yin
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
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18
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Nicolaou KC, Liu G, Beabout K, McCurry MD, Shamoo Y. Asymmetric Alkylation of Anthrones, Enantioselective Total Synthesis of (-)- and (+)-Viridicatumtoxins B and Analogues Thereof: Absolute Configuration and Potent Antibacterial Agents. J Am Chem Soc 2017; 139:3736-3746. [PMID: 28256128 DOI: 10.1021/jacs.6b12654] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A phase transfer catalyzed asymmetric alkylation of anthrones with cyclic allylic bromides using quinidine- or quinine-derived catalysts is described. Utilizing mild basic conditions and as low as 0.5 mol % catalyst loading, and achieving up to >99:1 dr selectivity, this asymmetric reaction was successfully applied to produce enantioselectively (-)- and (+)-viridicatumtoxins B, and thus allowed assignment of the absolute configuration of this naturally occurring antibiotic. While the developed asymmetric synthesis of C10 substituted anthrones is anticipated to find wider applications in organic synthesis, its immediate application to the construction of a variety of designed enantiopure analogues of viridicatumtoxin B led to the discovery of highly potent, yet simpler analogues of the molecule. These studies are expected to facilitate drug discovery and development efforts toward new antibacterial agents.
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Affiliation(s)
- K C Nicolaou
- Department of Chemistry, BioScience Research Collaborative and ‡Department of Biochemistry and Cell Biology, Rice University , 6100 Main Street, Houston, Texas 77005, United States
| | - Guodu Liu
- Department of Chemistry, BioScience Research Collaborative and ‡Department of Biochemistry and Cell Biology, Rice University , 6100 Main Street, Houston, Texas 77005, United States
| | - Kathryn Beabout
- Department of Chemistry, BioScience Research Collaborative and ‡Department of Biochemistry and Cell Biology, Rice University , 6100 Main Street, Houston, Texas 77005, United States
| | - Megan D McCurry
- Department of Chemistry, BioScience Research Collaborative and ‡Department of Biochemistry and Cell Biology, Rice University , 6100 Main Street, Houston, Texas 77005, United States
| | - Yousif Shamoo
- Department of Chemistry, BioScience Research Collaborative and ‡Department of Biochemistry and Cell Biology, Rice University , 6100 Main Street, Houston, Texas 77005, United States
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19
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New antibiotics from Nature’s chemical inventory. Bioorg Med Chem 2016; 24:6227-6252. [DOI: 10.1016/j.bmc.2016.09.014] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/07/2016] [Indexed: 01/07/2023]
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20
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Inokoshi J, Nakamura Y, Komada S, Komatsu K, Umeyama H, Tomoda H. Inhibition of bacterial undecaprenyl pyrophosphate synthase by small fungal molecules. J Antibiot (Tokyo) 2016; 69:798-805. [PMID: 27049441 DOI: 10.1038/ja.2016.35] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 02/09/2016] [Accepted: 02/17/2016] [Indexed: 11/09/2022]
Abstract
Viridicatumtoxin and spirohexaline, small fungal molecules with a tetracyclic scaffold and an additional spirobicyclic ring in common, were found to inhibit bacterial undecaprenyl pyrophosphate (UPP) synthase with IC50 values of 4 and 9 μm, respectively. These molecules showed weak inhibitory activity against catalytically related enzymes such as bacterial octaprenyl pyrophosphate synthase and yeast dehydrodolichyl pyrophosphate synthase, indicating that the compounds preferentially inhibit UPP synthase. They showed antimicrobial activity, particularly against Gram-positive bacteria including methicillin-resistant Staphylococcus aureus (MRSA). Furthermore, molecular modeling strongly suggested that the hydrophobic spirobicyclic ring of viridicatumtoxin interacts with three hydrophobic clefts of the active site in MRSA UPP synthase.
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Affiliation(s)
- Junji Inokoshi
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
| | - Yuichiro Nakamura
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
| | - Saori Komada
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
| | - Katsuichiro Komatsu
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
| | - Hideaki Umeyama
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
| | - Hiroshi Tomoda
- Graduate School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan
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21
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Affiliation(s)
- Hiroshi Tomoda
- Graduate School of Pharmaceutical Sciences, Kitasato University
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22
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El-Hashash MA, Rizk SA, Atta-Allah SR. Synthesis and Regioselective Reaction of Some Unsymmetrical Heterocyclic Chalcone Derivatives and Spiro Heterocyclic Compounds as Antibacterial Agents. Molecules 2015; 20:22069-83. [PMID: 26690393 PMCID: PMC6332078 DOI: 10.3390/molecules201219827] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 11/26/2015] [Accepted: 12/03/2015] [Indexed: 02/08/2023] Open
Abstract
A number of novel heterocyclic chalcone derivatives can be synthesized by thermal and microwave tools. Treatment of 4-(4-Acetylamino- and/or 4-bromo-phenyl)-4-oxobut-2-enoic acids with hydrogen peroxide in alkaline medium were afforded oxirane derivatives 2. Reaction of the epoxide 2 with 2-amino-5-aryl-1,3,4-thiadiazole derivatives yielded chalcone of imidazo[2,1-b]thiadiazole derivative 4 via two thermal routes. In one pot reaction of 4-bromoacetophenone, diethyloxalate, and 2-amino-5-aryl-1,3,4-thiadiazole derivatives in MW irradiation (W 250 and T 150 °C) under eco-friendly conditions afforded an unsuitable yield of the desired chalcone 4d. The chalcone derivatives 4 were used as a key starting material to synthesize some new spiroheterocyclic compounds via Michael and aza-Michael adducts. The chalcone 4f was similar to the aryl-oxo-vinylamide derivatives for the inhibition of tyrosine kinase and cancer cell growth. The electron-withdrawing substituents, such as halogens, and 2-amino-1,3,4-thiadiazole moeity decreasing the electron density, thereby decreasing the energy of HOMO, and the presence of imidazothiadiazole moiety should improve the antibacterial activity. Thus, the newly synthesized compounds were evaluated for their anti-bacterial activity against (ATCC 25923), (ATCC 10987), (ATCC 274,) and (SM514). The structure of the newly synthesized compounds was confirmed by elemental analysis and spectroscopic data.
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Affiliation(s)
- Maher A El-Hashash
- Chemistry Department, Science Faculty, Ain-Shams University, Abassia, Cairo 11566, Egypt.
| | - Sameh A Rizk
- Chemistry Department, Science Faculty, Ain-Shams University, Abassia, Cairo 11566, Egypt.
| | - Saad R Atta-Allah
- Chemistry Department, Science Faculty, Ain-Shams University, Abassia, Cairo 11566, Egypt.
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23
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Shang Z, Salim AA, Khalil Z, Quezada M, Bernhardt PV, Capon RJ. Viridicatumtoxins: Expanding on a Rare Tetracycline Antibiotic Scaffold. J Org Chem 2015; 80:12501-8. [PMID: 26605854 DOI: 10.1021/acs.joc.5b02367] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Viridicatumtoxins, which belong to a rare class of fungal tetracycline-like mycotoxins, were subjected to comprehensive spectroscopic and chemical analysis, leading to reassignment/assignment of absolute configurations and characterization of a remarkably acid-stable antibiotic scaffold. Structure activity relationship studies revealed exceptional growth inhibitory activity against vancomycin-resistant Enterococci (IC50 40 nM), >270-fold more potent than the commercial antibiotic oxytetracycline.
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Affiliation(s)
- Zhuo Shang
- Institute for Molecular Bioscience and ‡School of Chemistry and Molecular Biosciences, The University of Queensland , St. Lucia, Queensland 4072, Australia
| | - Angela A Salim
- Institute for Molecular Bioscience and ‡School of Chemistry and Molecular Biosciences, The University of Queensland , St. Lucia, Queensland 4072, Australia
| | - Zeinab Khalil
- Institute for Molecular Bioscience and ‡School of Chemistry and Molecular Biosciences, The University of Queensland , St. Lucia, Queensland 4072, Australia
| | - Michelle Quezada
- Institute for Molecular Bioscience and ‡School of Chemistry and Molecular Biosciences, The University of Queensland , St. Lucia, Queensland 4072, Australia
| | - Paul V Bernhardt
- Institute for Molecular Bioscience and ‡School of Chemistry and Molecular Biosciences, The University of Queensland , St. Lucia, Queensland 4072, Australia
| | - Robert J Capon
- Institute for Molecular Bioscience and ‡School of Chemistry and Molecular Biosciences, The University of Queensland , St. Lucia, Queensland 4072, Australia
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24
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Li G, Kusari S, Lamshöft M, Schüffler A, Laatsch H, Spiteller M. Antibacterial secondary metabolites from an endophytic fungus, Eupenicillium sp. LG41. JOURNAL OF NATURAL PRODUCTS 2014; 77:2335-41. [PMID: 25356913 DOI: 10.1021/np500111w] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Two new compounds containing the decalin moiety, eupenicinicols A and B (1 and 2), two new sirenin derivatives, eupenicisirenins A and B (3 and 4), and four known compounds, (2S)-butylitaconic acid (5), (2S)-hexylitaconic acid (6), xanthomegnin (7), and viridicatumtoxin (8), were isolated from an endophytic fungus, Eupenicillium sp. LG41, harbored in the roots of the Chinese medicinal plant Xanthium sibiricum. Their structures were confirmed through combined spectroscopic analysis (NMR and HRMS(n)), and their absolute configurations were deduced by ECD calculations or optical rotation data. Since the endophytic fungus was isolated from the roots, the antibacterial efficacies of the compounds 1-6 were investigated against Bacillus subtilis and Acinetobacter sp. BD4, which typically inhabit soil, as well as the clinically important Staphylococcus aureus and Escherichia coli. (2S)-Butylitaconic acid (5) and (2S)-hexylitaconic acid (6) exhibited pronounced efficacy against Acinetobacter sp., corroborating the notion that root-endophytes provide chemical defense to the host plants. Compound 2 was highly active against the clinically relevant S. aureus. By comparing 1 with 2, it was revealed that altering the substitution at C-11 could drastically increase the antibacterial efficacy of 1. Our study reveals plausible ecological roles of the endophyte and its potential pharmaceutical use as a source of antibacterial compounds.
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Affiliation(s)
- Gang Li
- Institute of Environmental Research (INFU), Department of Chemistry and Chemical Biology, Chair of Environmental Chemistry and Analytical Chemistry, TU Dortmund , Otto-Hahn-Straße 6, D-44221 Dortmund, Germany
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25
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Danley DE, Baima ET, Mansour M, Fennell KF, Chrunyk BA, Mueller JP, Liu S, Qiu X. Discovery and structural characterization of an allosteric inhibitor of bacterial cis-prenyltransferase. Protein Sci 2014; 24:20-6. [PMID: 25287857 DOI: 10.1002/pro.2579] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 10/03/2014] [Indexed: 11/06/2022]
Abstract
Undecaprenyl pyrophosphate synthase (UPPs) is an essential enzyme in a key bacterial cell wall synthesis pathway. It catalyzes the consecutive condensations of isopentenyl pyrophosphate (IPP) groups on to a trans-farnesyl pyrophosphate (FPP) to produce a C55 isoprenoid, undecaprenyl pyrophosphate (UPP). Here we report the discovery and co-crystal structures of a drug-like UPPs inhibitor in complex with Streptococcus pneumoniae UPPs, with and without substrate FPP, at resolutions of 2.2 and 2.1 Å, respectively. The UPPs inhibitor has a low molecular weight (355 Da), but displays potent inhibition of UPP synthesis in vitro (IC50 50 nM) that translates into excellent whole cell antimicrobial activity against pathogenic strains of Streptococcal species (MIC90 0.4 µg mL(-1) ). Interestingly, the inhibitor does not compete with the substrates but rather binds at a site adjacent to the FPP binding site and interacts with the tail of the substrate. Based on the structures, an allosteric inhibition mechanism of UPPs is proposed for this inhibitor. This inhibition mechanism is supported by biochemical and biophysical experiments, and provides a basis for the development of novel antibiotics targeting Streptococcus pneumoniae.
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Affiliation(s)
- Dennis E Danley
- Worldwide Research and Development, Pfizer Inc, Groton, Connecticut, 06340
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Nicolaou KC, Hale CR, Nilewski C, Ioannidou HA, ElMarrouni A, Nilewski LG, Beabout K, Wang TT, Shamoo Y. Total synthesis of viridicatumtoxin B and analogues thereof: strategy evolution, structural revision, and biological evaluation. J Am Chem Soc 2014; 136:12137-60. [PMID: 25317739 PMCID: PMC4210137 DOI: 10.1021/ja506472u] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Indexed: 11/29/2022]
Abstract
The details of the total synthesis of viridicatumtoxin B (1) are described. Initial synthetic strategies toward this intriguing tetracycline antibiotic resulted in the development of key alkylation and Lewis acid-mediated spirocyclization reactions to form the hindered EF spirojunction, as well as Michael-Dieckmann reactions to set the A and C rings. The use of an aromatic A-ring substrate, however, was found to be unsuitable for the introduction of the requisite hydroxyl groups at carbons 4a and 12a. Applying these previous tactics, we developed stepwise approaches to oxidize carbons 12a and 4a based on enol- and enolate-based oxidations, respectively, the latter of which was accomplished after systematic investigations that revealed critical reactivity patterns. The herein described synthetic strategy resulted in the total synthesis of viridicatumtoxin B (1), which, in turn, formed the basis for the revision of its originally assigned structure. The developed chemistry facilitated the synthesis of a series of viridicatumtoxin analogues, which were evaluated against Gram-positive and Gram-negative bacterial strains, including drug-resistant pathogens, revealing the first structure-activity relationships within this structural type.
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Affiliation(s)
- K. C. Nicolaou
- Department of Chemistry, Department of Biochemistry
and Cell Biology, and Department of
Ecology and Evolutionary Biology, Rice University, 6100 Main Street, Houston, Texas 77005, United States
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Christopher R.
H. Hale
- Department of Chemistry, Department of Biochemistry
and Cell Biology, and Department of
Ecology and Evolutionary Biology, Rice University, 6100 Main Street, Houston, Texas 77005, United States
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Christian Nilewski
- Department of Chemistry, Department of Biochemistry
and Cell Biology, and Department of
Ecology and Evolutionary Biology, Rice University, 6100 Main Street, Houston, Texas 77005, United States
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Heraklidia A. Ioannidou
- Department of Chemistry, Department of Biochemistry
and Cell Biology, and Department of
Ecology and Evolutionary Biology, Rice University, 6100 Main Street, Houston, Texas 77005, United States
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Abdelatif ElMarrouni
- Department of Chemistry, Department of Biochemistry
and Cell Biology, and Department of
Ecology and Evolutionary Biology, Rice University, 6100 Main Street, Houston, Texas 77005, United States
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Lizanne G. Nilewski
- Department of Chemistry, Department of Biochemistry
and Cell Biology, and Department of
Ecology and Evolutionary Biology, Rice University, 6100 Main Street, Houston, Texas 77005, United States
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Kathryn Beabout
- Department of Chemistry, Department of Biochemistry
and Cell Biology, and Department of
Ecology and Evolutionary Biology, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Tim T. Wang
- Department of Chemistry, Department of Biochemistry
and Cell Biology, and Department of
Ecology and Evolutionary Biology, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Yousif Shamoo
- Department of Chemistry, Department of Biochemistry
and Cell Biology, and Department of
Ecology and Evolutionary Biology, Rice University, 6100 Main Street, Houston, Texas 77005, United States
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Chooi YH, Hong YJ, Cacho RA, Tantillo DJ, Tang Y. A cytochrome P450 serves as an unexpected terpene cyclase during fungal meroterpenoid biosynthesis. J Am Chem Soc 2013; 135:16805-8. [PMID: 24161266 DOI: 10.1021/ja408966t] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Viridicatumtoxin (1) is a tetracycline-like fungal meroterpenoid with a unique, fused spirobicyclic ring system. Puzzlingly, no dedicated terpene cyclase is found in the gene cluster identified in Penicillium aethiopicum. Cytochrome P450 enzymes VrtE and VrtK in the vrt gene cluster were shown to catalyze C5-hydroxylation and spirobicyclic ring formation, respectively. Feeding acyclic previridicatumtoxin to Saccharomyces cerevisiae expressing VrtK confirmed that VrtK is the sole enzyme required for cyclizing the geranyl moiety. Thus, VrtK is the first example of a P450 that can catalyze terpene cyclization, most likely via initial oxidation of C17 to an allylic carbocation. Quantum chemical modeling revealed a possible new tertiary carbocation intermediate E that forms after allylic carbocation formation. Intermediate E can readily undergo concerted 1,2-alkyl shift/1,3-hydride shift, either spontaneously or further aided by VrtK, followed by C7 Friedel-Crafts alkylation to afford 1. The most likely stereochemical course of the reaction was proposed on the basis of the results of our computations.
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Affiliation(s)
- Yit-Heng Chooi
- Department of Chemical and Biomolecular Engineering and ‡Department of Chemistry and Biochemistry, University of California , Los Angeles, California 90095, United States
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Nicolaou KC, Nilewski C, Hale CRH, Ioannidou HA, ElMarrouni A, Koch LG. Totalsynthese und Revidierung der Struktur von Viridicatumtoxin B. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201304691] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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Nicolaou KC, Nilewski C, Hale CRH, Ioannidou HA, ElMarrouni A, Koch LG. Total synthesis and structural revision of viridicatumtoxin B. Angew Chem Int Ed Engl 2013; 52:8736-41. [PMID: 23893651 DOI: 10.1002/anie.201304691] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Indexed: 01/31/2023]
Affiliation(s)
- K C Nicolaou
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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Reducing the Level of Undecaprenyl Pyrophosphate Synthase Has Complex Effects on Susceptibility to Cell Wall Antibiotics. Antimicrob Agents Chemother 2013; 57:4267-4275. [PMID: 23796923 DOI: 10.1128/aac.00794-13] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 06/14/2013] [Indexed: 01/09/2023] Open
Abstract
Undecaprenyl pyrophosphate synthase (UppS) catalyzes the formation of the C55 lipid carrier (UPP) that is essential for bacterial peptidoglycan biosynthesis. We selected here a vancomycin (VAN)-resistant derivative of Bacillus subtilis W168 that contains a single-point mutation in the ribosome-binding site of the uppS gene designated uppS1 Genetic reconstruction experiments demonstrate that the uppS1 allele is sufficient to confer low-level VAN resistance and causes reduced UppS translation. The decreased level of UppS renders B. subtilis slightly more susceptible to many late-acting cell wall antibiotics, including β-lactams, but significantly more resistant to fosfomycin and d-cycloserine, antibiotics that interfere with the very early steps of cell wall synthesis. We further show that the uppS1 allele leads to slightly elevated expression of the σM regulon, possibly helping to compensate for the stress caused by a decrease in UPP levels. Notably, the uppS1 mutation increases resistance to VAN, fosfomycin, and d-cycloserine in wild-type cells, but this effect is greatly reduced or eliminated in a sigM mutant background. Our findings suggest that, although UppS is an attractive antibacterial target, incomplete inhibition of UppS function may lead to increased resistance to some cell wall-active antibiotics.
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Epi-trichosetin, a new undecaprenyl pyrophosphate synthase inhibitor, produced by Fusarium oxysporum FKI-4553. J Antibiot (Tokyo) 2013; 66:549-54. [PMID: 23715038 DOI: 10.1038/ja.2013.44] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 04/04/2013] [Accepted: 04/12/2013] [Indexed: 11/08/2022]
Abstract
A new compound, designated epi-trichosetin (1), was isolated along with the known compound trichosetin (2) from the culture broth of Fusarium oxysporum FKI-4553 by solvent extraction, silica gel column chromatography and reversed-phase HPLC. The structure of 1 was elucidated by comparing various spectral data with those of 2, revealing that 1 was a stereoisomer of 2. Compounds 1 and 2 inhibited the undecaprenyl pyrophosphate synthase activity of Staphylococcus aureus with IC50 values of 83 and 30 μM, respectively, and showed antimicrobial activity, particularly against Gram-positive bacteria, including methicillin-sensitive and -resistant S. aureus.
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Anti-infectious agents against MRSA. Molecules 2012; 18:204-24. [PMID: 23262449 PMCID: PMC6269750 DOI: 10.3390/molecules18010204] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 12/03/2012] [Accepted: 12/14/2012] [Indexed: 11/17/2022] Open
Abstract
Clinically useful antibiotics, β-lactams and vancomycin, are known to inhibit bacterial cell wall peptidoglycan synthesis. Methicillin-resistant Staphylococcus aureus (MRSA) has a unique cell wall structure consisting of peptidoglycan and wall teichoic acid. In recent years, new anti-infectious agents (spirohexaline, tripropeptin C, DMPI, CDFI, cyslabdan, 1835F03, and BPH-652) targeting MRSA cell wall biosynthesis have been discovered using unique screening methods. These agents were found to inhibit important enzymes involved in cell wall biosynthesis such as undecaprenyl pyrophosphate (UPP) synthase, FemA, flippase, or UPP phosphatase. In this review, the discovery, the mechanism of action, and the future of these anti-infectious agents are described.
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