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Eshboev F, Mamadalieva N, Nazarov PA, Hussain H, Katanaev V, Egamberdieva D, Azimova S. Antimicrobial Action Mechanisms of Natural Compounds Isolated from Endophytic Microorganisms. Antibiotics (Basel) 2024; 13:271. [PMID: 38534706 DOI: 10.3390/antibiotics13030271] [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: 02/27/2024] [Revised: 03/12/2024] [Accepted: 03/15/2024] [Indexed: 03/28/2024] Open
Abstract
Infectious diseases are a significant challenge to global healthcare, especially in the face of increasing antibiotic resistance. This urgent issue requires the continuous exploration and development of new antimicrobial drugs. In this regard, the secondary metabolites derived from endophytic microorganisms stand out as promising sources for finding antimicrobials. Endophytic microorganisms, residing within the internal tissues of plants, have demonstrated the capacity to produce diverse bioactive compounds with substantial pharmacological potential. Therefore, numerous new antimicrobial compounds have been isolated from endophytes, particularly from endophytic fungi and actinomycetes. However, only a limited number of these compounds have been subjected to comprehensive studies regarding their mechanisms of action against bacterial cells. Furthermore, the investigation of their effects on antibiotic-resistant bacteria and the identification of biosynthetic gene clusters responsible for synthesizing these secondary metabolites have been conducted for only a subset of these promising compounds. Through a comprehensive analysis of current research findings, this review describes the mechanisms of action of antimicrobial drugs and secondary metabolites isolated from endophytes, antibacterial activities of the natural compounds derived from endophytes against antibiotic-resistant bacteria, and biosynthetic gene clusters of endophytic fungi responsible for the synthesis of bioactive secondary metabolites.
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Affiliation(s)
- Farkhod Eshboev
- S. Yu. Yunusov Institute of the Chemistry of Plant Substances, Academy of Sciences of Uzbekistan, Mirzo Ulugbek Str. 77, Tashkent 100170, Uzbekistan
- School of Chemical Engineering, New Uzbekistan University, Movarounnahr Street 1, Mirzo Ulugbek District, Tashkent 100000, Uzbekistan
- Institute of Fundamental and Applied Research, National Research University TIIAME, 39 Kori Niyoziy Str., Tashkent 100000, Uzbekistan
- Faculty of Biology, National University of Uzbekistan, Tashkent 100174, Uzbekistan
| | - Nilufar Mamadalieva
- S. Yu. Yunusov Institute of the Chemistry of Plant Substances, Academy of Sciences of Uzbekistan, Mirzo Ulugbek Str. 77, Tashkent 100170, Uzbekistan
- School of Chemical Engineering, New Uzbekistan University, Movarounnahr Street 1, Mirzo Ulugbek District, Tashkent 100000, Uzbekistan
- Institute of Fundamental and Applied Research, National Research University TIIAME, 39 Kori Niyoziy Str., Tashkent 100000, Uzbekistan
| | - Pavel A Nazarov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 1/40 Leninskie Gory, Moscow 119991, Russia
| | - Hidayat Hussain
- Leibniz Institute of Plant Biochemistry, Department of Bioorganic Chemistry, Weinberg 3, D-06120 Halle, Germany
| | - Vladimir Katanaev
- Translational Research Center in Oncohaematology, Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
- School of Medicine and Life Sciences, Far Eastern Federal University, Vladivostok 690090, Russia
| | - Dilfuza Egamberdieva
- Institute of Fundamental and Applied Research, National Research University TIIAME, 39 Kori Niyoziy Str., Tashkent 100000, Uzbekistan
- Faculty of Biology, National University of Uzbekistan, Tashkent 100174, Uzbekistan
| | - Shakhnoz Azimova
- S. Yu. Yunusov Institute of the Chemistry of Plant Substances, Academy of Sciences of Uzbekistan, Mirzo Ulugbek Str. 77, Tashkent 100170, Uzbekistan
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Marina VI, Bidzhieva M, Tereshchenkov AG, Orekhov D, Sagitova VE, Sumbatyan NV, Tashlitsky VN, Ferberg AS, Maviza TP, Kasatsky P, Tolicheva O, Paleskava A, Polshakov VI, Osterman IA, Dontsova OA, Konevega AL, Sergiev PV. An easy tool to monitor the elemental steps of in vitro translation via gel electrophoresis of fluorescently labeled small peptides. RNA (NEW YORK, N.Y.) 2024; 30:298-307. [PMID: 38164606 PMCID: PMC10870375 DOI: 10.1261/rna.079766.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 11/22/2023] [Indexed: 01/03/2024]
Abstract
Several methods are available to visualize and assess the kinetics and efficiency of elemental steps of protein biosynthesis. However, each of these methods has its own limitations. Here, we present a novel, simple and convenient tool for monitoring stepwise in vitro translation initiated by BODIPY-Met-tRNA. Synthesis and release of very short, 1-7 amino acids, BODIPY-labeled peptides, can be monitored using urea-polyacrylamide gel electrophoresis. Very short BODIPY-labeled oligopeptides might be resolved this way, in contrast to widely used Tris-tricine gel electrophoresis, which is suitable to separate peptides larger than 1 kDa. The method described in this manuscript allows one to monitor the steps of translation initiation, peptide transfer, translocation, and termination as well as their inhibition at an unprecedented single amino acid resolution.
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Affiliation(s)
- Valeriya I Marina
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Skolkovo 121205, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Medina Bidzhieva
- Molecular and Radiation Biophysics Division, Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC "Kurchatov Institute," Gatchina 188300, Russia
- Institute of Biomedical Systems and Biotechnologies, Peter the Great St. Petersburg Polytechnic University, Saint Petersburg 195251, Russia
| | - Andrey G Tereshchenkov
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Dmitry Orekhov
- R&D Department, VIC Animal Health, Severny, Belgorod Region 308519, Russia
| | | | - Nataliya V Sumbatyan
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Vadim N Tashlitsky
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Artem S Ferberg
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Tinashe P Maviza
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Skolkovo 121205, Russia
| | - Pavel Kasatsky
- Molecular and Radiation Biophysics Division, Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC "Kurchatov Institute," Gatchina 188300, Russia
| | - Olga Tolicheva
- Molecular and Radiation Biophysics Division, Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC "Kurchatov Institute," Gatchina 188300, Russia
| | - Alena Paleskava
- Molecular and Radiation Biophysics Division, Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC "Kurchatov Institute," Gatchina 188300, Russia
- Institute of Biomedical Systems and Biotechnologies, Peter the Great St. Petersburg Polytechnic University, Saint Petersburg 195251, Russia
| | - Vladimir I Polshakov
- Faculty of Fundamental Medicine, Lomonosov Moscow State University Moscow, Moscow 119991, Russia
| | - Ilya A Osterman
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Skolkovo 121205, Russia
| | - Olga A Dontsova
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Skolkovo 121205, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia
- Department of Functioning of Living Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Andrey L Konevega
- Molecular and Radiation Biophysics Division, Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC "Kurchatov Institute," Gatchina 188300, Russia
- Institute of Biomedical Systems and Biotechnologies, Peter the Great St. Petersburg Polytechnic University, Saint Petersburg 195251, Russia
| | - Petr V Sergiev
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Skolkovo 121205, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia
- Institute of Functional Genomics, Lomonosov Moscow State University, Moscow 119991, Russia
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Rütten A, Kirchner T, Musiol-Kroll EM. Overview on Strategies and Assays for Antibiotic Discovery. Pharmaceuticals (Basel) 2022; 15:1302. [PMID: 36297414 PMCID: PMC9607151 DOI: 10.3390/ph15101302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/12/2022] [Accepted: 10/14/2022] [Indexed: 11/23/2022] Open
Abstract
The increase in antibiotic resistance poses a major threat to global health. Actinomycetes, the Gram-positive bacteria of the order Actinomycetales, are fertile producers of bioactive secondary metabolites, including antibiotics. Nearly two-thirds of antibiotics that are used for the treatment of bacterial infections were originally isolated from actinomycetes strains belonging to the genus Streptomyces. This emphasizes the importance of actinomycetes in antibiotic discovery. However, the identification of a new antimicrobial compound and the exploration of its mode of action are very challenging tasks. Therefore, different approaches that enable the "detection" of an antibiotic and the characterization of the mechanisms leading to the biological activity are indispensable. Beyond bioinformatics tools facilitating the identification of biosynthetic gene clusters (BGCs), whole cell-screenings-in which cells are exposed to actinomycete-derived compounds-are a common strategy applied at the very early stage in antibiotic drug development. More recently, target-based approaches have been established. In this case, the drug candidates were tested for interactions with usually validated targets. This review focuses on the bioactivity-based screening methods and provides the readers with an overview on the most relevant assays for the identification of antibiotic activity and investigation of mechanisms of action. Moreover, the article includes examples of the successful application of these methods and suggestions for improvement.
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Affiliation(s)
- Anika Rütten
- Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
- Cluster of Excellence ‘Controlling Microbes to Fight Infections’ (CMFI), University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Teresa Kirchner
- Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
- Cluster of Excellence ‘Controlling Microbes to Fight Infections’ (CMFI), University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Ewa Maria Musiol-Kroll
- Interfaculty Institute of Microbiology and Infection Medicine (IMIT), Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
- Cluster of Excellence ‘Controlling Microbes to Fight Infections’ (CMFI), University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
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Thépaut M, Campos-Silva R, Renard E, Barloy-Hubler F, Ennifar E, Boujard D, Gillet R. Safe and easy in vitro evaluation of tmRNA-SmpB-mediated trans-translation from ESKAPE pathogenic bacteria. RNA (NEW YORK, N.Y.) 2021; 27:1390-1399. [PMID: 34353925 PMCID: PMC8522692 DOI: 10.1261/rna.078773.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
In bacteria, trans-translation is the major quality control system for rescuing stalled ribosomes. It is mediated by tmRNA, a hybrid RNA with properties of both a tRNA and a mRNA, and the small protein SmpB. Because trans-translation is absent in eukaryotes but necessary for bacterial fitness or survival, it is a promising target for the development of novel antibiotics. To facilitate screening of chemical libraries, various reliable in vitro and in vivo systems have been created for assessing trans-translational activity. However, the aim of the current work was to permit the safe and easy in vitro evaluation of trans-translation from pathogenic bacteria, which are obviously the ones we should be targeting. Based on green fluorescent protein (GFP) reassembly during active trans-translation, we have created a cell-free assay adapted to the rapid evaluation of trans-translation in ESKAPE bacteria, with 24 different possible combinations. It can be used for easy high-throughput screening of chemical compounds as well as for exploring the mechanism of trans-translation in these pathogens.
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Affiliation(s)
- Marion Thépaut
- Université Rennes, CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR 6290, 35043 Rennes, France
- SATT Ouest-Valorisation, 35750 Rennes, France
| | - Rodrigo Campos-Silva
- Université Rennes, CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR 6290, 35043 Rennes, France
- Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre 90610-000, Brazil
| | - Eva Renard
- Architecture et Réactivité de l'ARN-CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 67084 Strasbourg, France
| | - Frédérique Barloy-Hubler
- Université Rennes, CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR 6290, 35043 Rennes, France
| | - Eric Ennifar
- Architecture et Réactivité de l'ARN-CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 67084 Strasbourg, France
| | - Daniel Boujard
- Université Rennes, CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR 6290, 35043 Rennes, France
| | - Reynald Gillet
- Université Rennes, CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR 6290, 35043 Rennes, France
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Dmitriev SE, Vladimirov DO, Lashkevich KA. A Quick Guide to Small-Molecule Inhibitors of Eukaryotic Protein Synthesis. BIOCHEMISTRY (MOSCOW) 2021; 85:1389-1421. [PMID: 33280581 PMCID: PMC7689648 DOI: 10.1134/s0006297920110097] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Eukaryotic ribosome and cap-dependent translation are attractive targets in the antitumor, antiviral, anti-inflammatory, and antiparasitic therapies. Currently, a broad array of small-molecule drugs is known that specifically inhibit protein synthesis in eukaryotic cells. Many of them are well-studied ribosome-targeting antibiotics that block translocation, the peptidyl transferase center or the polypeptide exit tunnel, modulate the binding of translation machinery components to the ribosome, and induce miscoding, premature termination or stop codon readthrough. Such inhibitors are widely used as anticancer, anthelmintic and antifungal agents in medicine, as well as fungicides in agriculture. Chemicals that affect the accuracy of stop codon recognition are promising drugs for the nonsense suppression therapy of hereditary diseases and restoration of tumor suppressor function in cancer cells. Other compounds inhibit aminoacyl-tRNA synthetases, translation factors, and components of translation-associated signaling pathways, including mTOR kinase. Some of them have antidepressant, immunosuppressive and geroprotective properties. Translation inhibitors are also used in research for gene expression analysis by ribosome profiling, as well as in cell culture techniques. In this article, we review well-studied and less known inhibitors of eukaryotic protein synthesis (with the exception of mitochondrial and plastid translation) classified by their targets and briefly describe the action mechanisms of these compounds. We also present a continuously updated database (http://eupsic.belozersky.msu.ru/) that currently contains information on 370 inhibitors of eukaryotic protein synthesis.
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Affiliation(s)
- S E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia. .,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia.,Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - D O Vladimirov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - K A Lashkevich
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
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