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Kim MS, Jeong DE, Jang JP, Jang JH, Choi SK. Mining biosynthetic gene clusters in Paenibacillus genomes to discover novel antibiotics. BMC Microbiol 2024; 24:226. [PMID: 38937695 PMCID: PMC11210098 DOI: 10.1186/s12866-024-03375-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 06/17/2024] [Indexed: 06/29/2024] Open
Abstract
BACKGROUND Bacterial antimicrobial resistance poses a severe threat to humanity, necessitating the urgent development of new antibiotics. Recent advances in genome sequencing offer new avenues for antibiotic discovery. Paenibacillus genomes encompass a considerable array of antibiotic biosynthetic gene clusters (BGCs), rendering these species as good candidates for genome-driven novel antibiotic exploration. Nevertheless, BGCs within Paenibacillus genomes have not been extensively studied. RESULTS We conducted an analysis of 554 Paenibacillus genome sequences, sourced from the National Center for Biotechnology Information database, with a focused investigation involving 89 of these genomes via antiSMASH. Our analysis unearthed a total of 848 BGCs, of which 716 (84.4%) were classified as unknown. From the initial pool of 554 Paenibacillus strains, we selected 26 available in culture collections for an in-depth evaluation. Genomic scrutiny of these selected strains unveiled 255 BGCs, encoding non-ribosomal peptide synthetases, polyketide synthases, and bacteriocins, with 221 (86.7%) classified as unknown. Among these strains, 20 exhibited antimicrobial activity against the gram-positive bacterium Micrococcus luteus, yet only six strains displayed activity against the gram-negative bacterium Escherichia coli. We proceeded to focus on Paenibacillus brasilensis, which featured five new BGCs for further investigation. To facilitate detailed characterization, we constructed a mutant in which a single BGC encoding a novel antibiotic was activated while simultaneously inactivating multiple BGCs using a cytosine base editor (CBE). The novel antibiotic was found to be localized to the cell wall and demonstrated activity against both gram-positive bacteria and fungi. The chemical structure of the new antibiotic was elucidated on the basis of ESIMS, 1D and 2D NMR spectroscopic data. The novel compound, with a molecular weight of 926, was named bracidin. CONCLUSIONS This study outcome highlights the potential of Paenibacillus species as valuable sources for novel antibiotics. In addition, CBE-mediated dereplication of antibiotics proved to be a rapid and efficient method for characterizing novel antibiotics from Paenibacillus species, suggesting that it will greatly accelerate the genome-based development of new antibiotics.
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Grants
- NRF-2018M3A9F3079565 National Research Foundation of Korea
- NRF-2018M3A9F3079565 National Research Foundation of Korea
- NRF-2018M3A9F3079565 National Research Foundation of Korea
- KGM9942421, KGM5292423, and KGM1222413 Korea Research Institute of Bioscience and Biotechnology
- KGM9942421, KGM5292423, and KGM1222413 Korea Research Institute of Bioscience and Biotechnology
- KGM9942421, KGM5292423, and KGM1222413 Korea Research Institute of Bioscience and Biotechnology
- KGM9942421, KGM5292423, and KGM1222413 Korea Research Institute of Bioscience and Biotechnology
- KGM9942421, KGM5292423, and KGM1222413 Korea Research Institute of Bioscience and Biotechnology
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Affiliation(s)
- Man Su Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Da-Eun Jeong
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Jun-Pil Jang
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea
| | - Jae-Hyuk Jang
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea.
- Department of Applied Biological Engineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, Republic of Korea.
| | - Soo-Keun Choi
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, Republic of Korea.
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Silva NBS, Menezes RP, Gonçalves DS, Santiago MB, Conejo NC, Souza SL, Santos ALO, da Silva RS, Ramos SB, Ferro EAV, Martins CHG. Exploring the antifungal, antibiofilm and antienzymatic potential of Rottlerin in an in vitro and in vivo approach. Sci Rep 2024; 14:11132. [PMID: 38750088 PMCID: PMC11096346 DOI: 10.1038/s41598-024-61179-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 05/02/2024] [Indexed: 05/18/2024] Open
Abstract
Candida species have been responsible for a high number of invasive infections worldwide. In this sense, Rottlerin has demonstrated a wide range of pharmacological activities. Therefore, this study aimed to evaluate the antifungal, antibiofilm and antivirulence activity of Rottlerin in vitro against Candida spp. and its toxicity and antifungal activity in vivo. Rottlerin showed antifungal activity against all yeasts evaluated, presenting Minimum Inhibitory and Fungicidal Concentration (MIC and MFC) values of 7.81 to > 1000 µg/mL. Futhermore, it was able to significantly inhibit biofilm production, presenting Biofilm Inhibitory Concentration (MICB50) values that ranged from 15.62 to 250 µg/mL and inhibition of the cell viability of the biofilm by 50% (IC50) from 2.24 to 12.76 µg/mL. There was a considerable reduction in all hydrolytic enzymes evaluated, with emphasis on hemolysin where Rottlerin showed a reduction of up to 20%. In the scanning electron microscopy (SEM) analysis, Rottlerin was able to completely inhibit filamentation by C. albicans. Regarding in vivo tests, Rottlerin did not demonstrate toxicity at the therapeutic concentrations demonstrated here and was able to increase the survival of C. elegans larvae infected. The results herein presented are innovative and pioneering in terms of Rottlerin's multipotentiality against these fungal infections.
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Affiliation(s)
- Nagela Bernadelli Sousa Silva
- Laboratory of Antimicrobial Testing, Institute of Biomedical Sciences (ICBIM), Federal University of Uberlândia (UFU), Av. Pará, 1720 - Umuarama, Uberlândia, 38405-320, Brazil
| | - Ralciane Paula Menezes
- Technical School of Health (ESTES), Federal University of Uberlândia (UFU), Uberlândia, Brazil
| | - Daniela Silva Gonçalves
- Laboratory of Antimicrobial Testing, Institute of Biomedical Sciences (ICBIM), Federal University of Uberlândia (UFU), Av. Pará, 1720 - Umuarama, Uberlândia, 38405-320, Brazil
| | - Mariana Brentini Santiago
- Laboratory of Antimicrobial Testing, Institute of Biomedical Sciences (ICBIM), Federal University of Uberlândia (UFU), Av. Pará, 1720 - Umuarama, Uberlândia, 38405-320, Brazil
| | - Noemi Chagas Conejo
- Laboratory of Antimicrobial Testing, Institute of Biomedical Sciences (ICBIM), Federal University of Uberlândia (UFU), Av. Pará, 1720 - Umuarama, Uberlândia, 38405-320, Brazil
| | - Sara Lemes Souza
- Laboratory of Antimicrobial Testing, Institute of Biomedical Sciences (ICBIM), Federal University of Uberlândia (UFU), Av. Pará, 1720 - Umuarama, Uberlândia, 38405-320, Brazil
| | - Anna Lívia Oliveira Santos
- Laboratory of Antimicrobial Testing, Institute of Biomedical Sciences (ICBIM), Federal University of Uberlândia (UFU), Av. Pará, 1720 - Umuarama, Uberlândia, 38405-320, Brazil
| | - Robinson Sabino da Silva
- Innovation Center in Salivary Diagnostic and Nanotheranostics, Institute of Biomedical Sciences (ICBIM), Federal University of Uberlandia (UFU), Uberlândia, Brazil
| | - Salvador Boccaletti Ramos
- Department of Engineering and Exact Sciences, Faculty of Agricultural and Veterinary Sciences - Jaboticabal (FCAV), São Paulo State University (UNESP), Jaboticabal, Brazil
| | - Eloisa Amália Vieira Ferro
- Laboratory of Immunophysiology of Reproduction, Institute of Biomedical Sciences (ICBIM), Federal University of Uberlandia, Uberlândia, Brazil
| | - Carlos Henrique Gomes Martins
- Laboratory of Antimicrobial Testing, Institute of Biomedical Sciences (ICBIM), Federal University of Uberlândia (UFU), Av. Pará, 1720 - Umuarama, Uberlândia, 38405-320, Brazil.
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3
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Hofer W, Deschner F, Jézéquel G, Pessanha de Carvalho L, Abdel-Wadood N, Pätzold L, Bernecker S, Morgenstern B, Kany AM, Große M, Stadler M, Bischoff M, Hirsch AKH, Held J, Herrmann J, Müller R. Functionalization of Chlorotonils: Dehalogenil as Promising Lead Compound for In Vivo Application. Angew Chem Int Ed Engl 2024; 63:e202319765. [PMID: 38502093 DOI: 10.1002/anie.202319765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/15/2024] [Accepted: 02/22/2024] [Indexed: 03/20/2024]
Abstract
The natural product chlorotonil displays high potency against multidrug-resistant Gram-positive bacteria and Plasmodium falciparum. Yet, its scaffold is characterized by low solubility and oral bioavailability, but progress was recently made to enhance these properties. Applying late-stage functionalization, we aimed to further optimize the molecule. Previously unknown reactions including a sulfur-mediated dehalogenation were revealed. Dehalogenil, the product of this reaction, was identified as the most promising compound so far, as this new derivative displayed improved solubility and in vivo efficacy while retaining excellent antimicrobial activity. We confirmed superb activity against multidrug-resistant clinical isolates of Staphylococcus aureus and Enterococcus spp. and mature transmission stages of Plasmodium falciparum. We also demonstrated favorable in vivo toxicity, pharmacokinetics and efficacy in infection models with S. aureus. Taken together, these results identify dehalogenil as an advanced lead molecule.
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Affiliation(s)
- Walter Hofer
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy at Saarland University Campus Building E8.1, 66123, Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124, Germany
| | - Felix Deschner
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy at Saarland University Campus Building E8.1, 66123, Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124, Germany
| | - Gwenaëlle Jézéquel
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy at Saarland University Campus Building E8.1, 66123, Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124, Germany
| | - Laìs Pessanha de Carvalho
- German Centre for Infection Research (DZIF), Braunschweig, 38124, Germany
- Institute of Tropical Medicine, Eberhard Karls University Tübingen, Wilhelmstraße 27, 72074, Tübingen, Germany
| | - Noran Abdel-Wadood
- Institute for Medical Microbiology and Hygiene, Saarland University, 66421, Homburg, Germany
- Institute of Anatomy and Cell Biology /, Saarland University, 66421, Homburg, Germany
| | - Linda Pätzold
- Institute for Medical Microbiology and Hygiene, Saarland University, 66421, Homburg, Germany
| | - Steffen Bernecker
- Microbial Drugs, Helmholtz Centre for Infection Research (HZI), Inhoffenstraße 7, 38124, Braunschweig, Germany
| | - Bernd Morgenstern
- Inorganic Solid State Chemistry, Saarland University Campus, 66123, Saarbrücken, Germany
| | - Andreas M Kany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy at Saarland University Campus Building E8.1, 66123, Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124, Germany
| | - Miriam Große
- German Centre for Infection Research (DZIF), Braunschweig, 38124, Germany
- Microbial Drugs, Helmholtz Centre for Infection Research (HZI), Inhoffenstraße 7, 38124, Braunschweig, Germany
| | - Marc Stadler
- German Centre for Infection Research (DZIF), Braunschweig, 38124, Germany
- Microbial Drugs, Helmholtz Centre for Infection Research (HZI), Inhoffenstraße 7, 38124, Braunschweig, Germany
| | - Markus Bischoff
- Institute for Medical Microbiology and Hygiene, Saarland University, 66421, Homburg, Germany
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy at Saarland University Campus Building E8.1, 66123, Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124, Germany
- Helmholtz International Lab for Anti-Infectives, Saarbrücken, 66123, Germany
| | - Jana Held
- German Centre for Infection Research (DZIF), Braunschweig, 38124, Germany
- Institute of Tropical Medicine, Eberhard Karls University Tübingen, Wilhelmstraße 27, 72074, Tübingen, Germany
- Centre de Recherches Médicales de Lambaréné, Lambaréné, BP 242, BP 242, Gabon
| | - Jennifer Herrmann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy at Saarland University Campus Building E8.1, 66123, Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy at Saarland University Campus Building E8.1, 66123, Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Braunschweig, 38124, Germany
- Helmholtz International Lab for Anti-Infectives, Saarbrücken, 66123, Germany
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MacNair CR, Rutherford ST, Tan MW. Alternative therapeutic strategies to treat antibiotic-resistant pathogens. Nat Rev Microbiol 2024; 22:262-275. [PMID: 38082064 DOI: 10.1038/s41579-023-00993-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2023] [Indexed: 04/19/2024]
Abstract
Resistance threatens to render antibiotics - which are essential for modern medicine - ineffective, thus posing a threat to human health. The discovery of novel classes of antibiotics able to overcome resistance has been stalled for decades, with the developmental pipeline relying almost entirely on variations of existing chemical scaffolds. Unfortunately, this approach has been unable to keep pace with resistance evolution, necessitating new therapeutic strategies. In this Review, we highlight recent efforts to discover non-traditional antimicrobials, specifically describing the advantages and limitations of antimicrobial peptides and macrocycles, antibodies, bacteriophages and antisense oligonucleotides. These approaches have the potential to stem the tide of resistance by expanding the physicochemical property space and target spectrum occupied by currently approved antibiotics.
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Affiliation(s)
- Craig R MacNair
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Steven T Rutherford
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Man-Wah Tan
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA.
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5
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Matias LLR, Damasceno KSFDSC, Pereira AS, Passos TS, Morais AHDA. Innovative Biomedical and Technological Strategies for the Control of Bacterial Growth and Infections. Biomedicines 2024; 12:176. [PMID: 38255281 PMCID: PMC10813423 DOI: 10.3390/biomedicines12010176] [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: 11/28/2023] [Revised: 01/05/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
Antibiotics comprise one of the most successful groups of pharmaceutical products. Still, they have been associated with developing bacterial resistance, which has become one of the most severe problems threatening human health today. This context has prompted the development of new antibiotics or co-treatments using innovative tools to reverse the resistance context, combat infections, and offer promising antibacterial therapy. For the development of new alternatives, strategies, and/or antibiotics for controlling bacterial growth, it is necessary to know the target bacteria, their classification, morphological characteristics, the antibiotics currently used for therapies, and their respective mechanisms of action. In this regard, genomics, through the sequencing of bacterial genomes, has generated information on diverse genetic resources, aiding in the discovery of new molecules or antibiotic compounds. Nanotechnology has been applied to propose new antimicrobials, revitalize existing drug options, and use strategic encapsulating agents with their biochemical characteristics, making them more effective against various bacteria. Advanced knowledge in bacterial sequencing contributes to the construction of databases, resulting in advances in bioinformatics and the development of new antimicrobials. Moreover, it enables in silico antimicrobial susceptibility testing without the need to cultivate the pathogen, reducing costs and time. This review presents new antibiotics and biomedical and technological innovations studied in recent years to develop or improve natural or synthetic antimicrobial agents to reduce bacterial growth, promote well-being, and benefit users.
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Affiliation(s)
- Lídia Leonize Rodrigues Matias
- Biochemistry and Molecular Biology Postgraduate Program, Biosciences Center, Federal University of Rio Grande do Norte, Natal 59078-970, RN, Brazil;
| | | | - Annemberg Salvino Pereira
- Nutrition Course, Center for Health Sciences, Federal University of Rio Grande do Norte, Natal 59078-970, RN, Brazil;
| | - Thaís Souza Passos
- Nutrition Postgraduate Program, Center for Health Sciences, Federal University of Rio Grande do Norte, Natal 59078-970, RN, Brazil; (K.S.F.d.S.C.D.); (T.S.P.)
| | - Ana Heloneida de Araujo Morais
- Biochemistry and Molecular Biology Postgraduate Program, Biosciences Center, Federal University of Rio Grande do Norte, Natal 59078-970, RN, Brazil;
- Nutrition Postgraduate Program, Center for Health Sciences, Federal University of Rio Grande do Norte, Natal 59078-970, RN, Brazil; (K.S.F.d.S.C.D.); (T.S.P.)
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Zhong M, Kang H, Liu W, Ma L, Liu D. Alkaloid diversity expansion of a talent fungus Penicillium raistrichii through OSMAC-based cultivation. Front Microbiol 2023; 14:1279140. [PMID: 38029208 PMCID: PMC10665910 DOI: 10.3389/fmicb.2023.1279140] [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: 08/17/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Alkaloidal natural products are attractive for their broad spectrum of pharmaceutical bioactivities. In the present work, the highly productive saline soil derived fungus, Penicillium raistrichii, was subjected to the strategy of OSMAC (one strain many compounds) with changes of cultivation status. Then, the work-flow led to the expansion of the alkaloid chemical diversity and subsequently induced the accumulation of four undescribed alkaloids, named raistrimides A-D (1-4), including three β-carbolines (1-3), one 2-quinolinone (4), and one new natural product, 2-quinolinone (5), along with five known alkaloid chemicals (6-10). Methods A set of NMR techniques including 1H, 13C, HSQC and HMBC, along with other spectroscopic data of UV-Vis, IR and HRESIMS, were introduced to assign the plain structures of compounds 1-10. The absolute configuration of 1-3 were elucidated by means of X-ray crystallography or spectroscopic analyses on optical rotation values and experimental electronic circular dichroism (ECD) data. In addition, it was the first report on the confirmation of structures of 6, 7 and 9 by X-ray crystallography data. The micro-broth dilution method was applied to evaluate antimicrobial effect of all compounds towards Staphylococcus aureus, Escherichia coli, and Candida albicans. Results and discussion The results indicated compounds 1, 3 and 4 to be bioactive, which may be potential for further development of anti-antimicrobial agents. The finding in this work implied that OSMAC strategy was a powerful and effective tool for promotion of new chemical entities from P. raistrichii.
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Affiliation(s)
| | | | | | - Liying Ma
- Laboratory of Natural Drug Discovery and Research, College of Pharmacy, Binzhou Medical University, Yantai, China
| | - Desheng Liu
- Laboratory of Natural Drug Discovery and Research, College of Pharmacy, Binzhou Medical University, Yantai, China
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Martínez JL, Baquero F. What are the missing pieces needed to stop antibiotic resistance? Microb Biotechnol 2023; 16:1900-1923. [PMID: 37417823 PMCID: PMC10527211 DOI: 10.1111/1751-7915.14310] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/21/2023] [Accepted: 06/25/2023] [Indexed: 07/08/2023] Open
Abstract
As recognized by several international agencies, antibiotic resistance is nowadays one of the most relevant problems for human health. While this problem was alleviated with the introduction of new antibiotics into the market in the golden age of antimicrobial discovery, nowadays few antibiotics are in the pipeline. Under these circumstances, a deep understanding on the mechanisms of emergence, evolution and transmission of antibiotic resistance, as well as on the consequences for the bacterial physiology of acquiring resistance is needed to implement novel strategies, beyond the development of new antibiotics or the restriction in the use of current ones, to more efficiently treat infections. There are still several aspects in the field of antibiotic resistance that are not fully understood. In the current article, we make a non-exhaustive critical review of some of them that we consider of special relevance, in the aim of presenting a snapshot of the studies that still need to be done to tackle antibiotic resistance.
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Affiliation(s)
| | - Fernando Baquero
- Ramón y Cajal Institute for Health Research (IRYCIS), Department of MicrobiologyRamón y Cajal University Hospital, CIBER en Epidemiología y Salud Pública (CIBERESP)MadridSpain
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Lei HM, Wang JT, Hu QY, Li CQ, Mo MH, Zhang KQ, Li GH, Zhao PJ. 2-Furoic acid associated with the infection of nematodes by Dactylellina haptotyla and its biocontrol potential on plant root-knot nematodes. Microbiol Spectr 2023; 11:e0189623. [PMID: 37754836 PMCID: PMC10580851 DOI: 10.1128/spectrum.01896-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 08/05/2023] [Indexed: 09/28/2023] Open
Abstract
Dactylellina haptotyla is a typical nematode-trapping fungus that has garnered the attention of many scholars for its highly effective lethal potential for nematodes. Secondary metabolites play an important role in D. haptotyla-nematode interactions, but which metabolites perform which function remains unclear. We report the metabolic functions based on high-quality, chromosome-level genome assembly of wild D. haptotyla YMF1.03409. The results indicate that a large variety of secondary metabolites and their biosynthetic genes were significantly upregulated during the nematode-trapping stage. In parallel, we identified that 2-furoic acid was specifically produced during nematode trapping by D. haptotyla YMF1.03409 and isolated it from fermentation production. 2-Furoic acid demonstrated strong nematicidal activity with an LD50 value of 55.05 µg/mL against Meloidogyne incognita at 48 h. Furthermore, the pot experiment showed that the number of galls of tomato root was significantly reduced in the experimental group treated with 2-furoic acid. The considerable increase in the 2-furoic acid content during the infection process and its virulent nematicidal activity revealed an essential synergistic effect during the process of nematode-trapping fungal infection. IMPORTANCE Dactylellina haptotyla have significant application potential in nematode biocontrol. In this study, we determined the chromosome-level genome sequence of D. haptotyla YMF1.03409 by long-read sequencing technology. Comparative genomic analysis identified a series of pathogenesis-related genes and revealed significant gene family contraction events during the evolution of D. haptotyla YMF1.03409. Combining transcriptomic and metabolomic data as well as in vitro activity test results, a compound with important application potential in nematode biocontrol, 2-furoic acid, was identified. Our result expanded the genetic resource of D. haptotyla and identified a previously unreported nematicidal small molecule, which provides new options for the development of plant biocontrol agents.
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Affiliation(s)
- Hong-Mei Lei
- State key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Jun-Tao Wang
- State key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Qian-Yi Hu
- State key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Chun-Qiang Li
- State key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Ming-He Mo
- State key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Ke-Qin Zhang
- State key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Guo-Hong Li
- State key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Pei-Ji Zhao
- State key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
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Labes A. Marine Resources Offer New Compounds and Strategies for the Treatment of Skin and Soft Tissue Infections. Mar Drugs 2023; 21:387. [PMID: 37504918 PMCID: PMC10381745 DOI: 10.3390/md21070387] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 06/26/2023] [Accepted: 06/28/2023] [Indexed: 07/29/2023] Open
Abstract
Bioprospecting of the marine environment for drug development has gained much attention in recent years owing to its massive chemical and biological diversity. Drugs for the treatment of skin and soft tissue infections have become part of the search, mainly with respect to enlarging the number of available antibiotics, with a special focus on multidrug-resistant Gram-positive bacteria, being the major causative agents in this field. Marine resources offer novel natural products with distinct biological activities of pharmaceutical importance, having the chance to provide new chemical scaffolds and new modes of action. New studies advance the field by proposing new strategies derived from an ecosystemic understanding for preventive activities against biofilms and new compounds suitable as disinfectants, which sustain the natural flora of the skin. Still, the development of new compounds is often stuck at the discovery level, as marine biotechnology also needs to overcome technological bottlenecks in drug development. This review summarizes its potential and shows these bottlenecks and new approaches.
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Affiliation(s)
- Antje Labes
- Department of Energy and Biotechnology, Flensburg University of Applied Sciences ZAiT, Kanzleistraße 91-93, D-24943 Flensburg, Germany
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10
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High-Resolution Bacterial Cytological Profiling Reveals Intrapopulation Morphological Variations upon Antibiotic Exposure. Antimicrob Agents Chemother 2023; 67:e0130722. [PMID: 36625642 PMCID: PMC9933734 DOI: 10.1128/aac.01307-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Phenotypic heterogeneity is crucial to bacterial survival and could provide insights into the mechanism of action (MOA) of antibiotics, especially those with polypharmacological actions. Although phenotypic changes among individual cells could be detected by existing profiling methods, due to the data complexity, only population average data were commonly used, thereby overlooking the heterogeneity. In this study, we developed a high-resolution bacterial cytological profiling method that can capture morphological variations of bacteria upon antibiotic treatment. With an unprecedented single-cell resolution, this method classifies morphological changes of individual cells into known MOAs with an overall accuracy above 90%. We next showed that combinations of two antibiotics induce altered cell morphologies that are either unique or similar to that of an antibiotic in the combinations. With these combinatorial profiles, this method successfully revealed multiple cytological changes caused by a natural product-derived compound that, by itself, is inactive against Acinetobacter baumannii but synergistically exerts its multiple antibacterial activities in the presence of colistin. The findings have paved the way for future single-cell profiling in bacteria and have highlighted previously underappreciated intrapopulation variations caused by antibiotic perturbation.
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de Medeiros LS, de Araújo Júnior MB, Peres EG, da Silva JCI, Bassicheto MC, Di Gioia G, Veiga TAM, Koolen HHF. Discovering New Natural Products Using Metabolomics-Based Approaches. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1439:185-224. [PMID: 37843810 DOI: 10.1007/978-3-031-41741-2_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
The incessant search for new natural molecules with biological activities has forced researchers in the field of chemistry of natural products to seek different approaches for their prospection studies. In particular, researchers around the world are turning to approaches in metabolomics to avoid high rates of re-isolation of certain compounds, something recurrent in this branch of science. Thanks to the development of new technologies in the analytical instrumentation of spectroscopic and spectrometric techniques, as well as the advance in the computational processing modes of the results, metabolomics has been gaining more and more space in studies that involve the prospection of natural products. Thus, this chapter summarizes the precepts and good practices in the metabolomics of microbial natural products using mass spectrometry and nuclear magnetic resonance spectroscopy, and also summarizes several examples where this approach has been applied in the discovery of bioactive molecules.
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Affiliation(s)
- Lívia Soman de Medeiros
- Grupo de Pesquisas LaBiORG - Laboratório de Química Bio-orgânica Otto Richard Gottlieb, Universidade Federal de São Paulo, Diadema, Brazil.
| | - Moysés B de Araújo Júnior
- Grupo de Pesquisa em Metabolômica e Espectrometria de Massas, Universidade do Estado do Amazonas, Manaus, Brazil
| | - Eldrinei G Peres
- Grupo de Pesquisa em Metabolômica e Espectrometria de Massas, Universidade do Estado do Amazonas, Manaus, Brazil
| | | | - Milena Costa Bassicheto
- Grupo de Pesquisas LaBiORG - Laboratório de Química Bio-orgânica Otto Richard Gottlieb, Universidade Federal de São Paulo, Diadema, Brazil
| | - Giordanno Di Gioia
- Grupo de Pesquisas LaBiORG - Laboratório de Química Bio-orgânica Otto Richard Gottlieb, Universidade Federal de São Paulo, Diadema, Brazil
| | - Thiago André Moura Veiga
- Grupo de Pesquisas LaBiORG - Laboratório de Química Bio-orgânica Otto Richard Gottlieb, Universidade Federal de São Paulo, Diadema, Brazil
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12
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Exploring Micromonospora as Phocoenamicins Producers. Mar Drugs 2022; 20:md20120769. [PMID: 36547916 PMCID: PMC9782249 DOI: 10.3390/md20120769] [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: 10/21/2022] [Revised: 12/01/2022] [Accepted: 12/03/2022] [Indexed: 12/13/2022] Open
Abstract
Over the past few years, new technological and scientific advances have reinforced the field of natural product discovery. The spirotetronate class of natural products has recently grown with the discovery of phocoenamicins, natural actinomycete derived compounds that possess different antibiotic activities. Exploring the MEDINA's strain collection, 27 actinomycete strains, including three marine-derived and 24 terrestrial strains, were identified as possible phocoenamicins producers and their taxonomic identification by 16S rDNA sequencing showed that they all belong to the Micromonospora genus. Using an OSMAC approach, all the strains were cultivated in 10 different media each, resulting in 270 fermentations, whose extracts were analyzed by LC-HRMS and subjected to High-throughput screening (HTS) against methicillin-resistant Staphylococcus aureus (MRSA), Mycobacterium tuberculosis H37Ra and Mycobacterium bovis. The combination of LC-UV-HRMS analyses, metabolomics analysis and molecular networking (GNPS) revealed that they produce several related spirotetronates not disclosed before. Variations in the culture media were identified as the most determining factor for phocoenamicin production and the best producer strains and media were established. Herein, we reported the chemically diverse production and metabolic profiling of Micromonospora sp. strains, including the known phocoenamicins and maklamicin, reported for the first time as being related to this family of compounds, as well as the bioactivity of their crude extracts. Although our findings do not confirm previous statements about phocoenamicins production only in unique marine environments, they have identified marine-derived Micromonospora species as the best producers of phocoenamicins in terms of both the abundance in their extracts of some major members of the structural class and the variety of molecular structures produced.
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13
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Cai D, Yang Y, Lu J, Yuan Z, Zhang Y, Yang X, Huang X, Li T, Tian X, Xu B, Wang P, Lei H. Injectable Carrier-Free Hydrogel Dressing with Anti-Multidrug-Resistant Staphylococcus aureus and Anti-Inflammatory Capabilities for Accelerated Wound Healing. ACS APPLIED MATERIALS & INTERFACES 2022; 14:43035-43049. [PMID: 36124878 DOI: 10.1021/acsami.2c15463] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Antibacterial hydrogels have gradually become a powerful weapon to treat bacterially infected wounds and accelerate healing. In this paper, we designed a small-molecule self-healing antibacterial hydrogel containing 100% drug-loaded benzyl 3β-amino-11-oxo-olean-12-en-30-oate (GN-Bn), which was governed by π-π stacking, hydrogen bonding, and van der Waals forces. Due to the carrier-free design concept, the problems of interbatch variability during sample preparation and carrier-related toxicity can be effectively avoided. Moreover, the GN-Bn hydrogel exhibited promising antibacterial activities against multidrug-resistant Staphylococcus aureus (MRSA). The minimum inhibitory concentration (MIC) of the GN-Bn hydrogel was 1.5625 nmol/mL, which was lower than those against clinical agents such as norfloxacin, penicillin, and tetracycline. This is attributed to its unique antibacterial mechanism that aims at killing bacteria or preventing their growth by regulating arginine biosynthesis and metabolism through both transcriptomic (RNA-seq) analysis and quantitative polymerase chain reaction (qPCR) analysis. In addition, the GN-Bn hydrogel can also inhibit proinflammatory cytokines (TNF-α, IL-1β, and IL-6) to promote wound healing. Collectively, the GN-Bn hydrogel elicited dual therapeutic effects on an MRSA-infected full-thickness skin wound model through its antibacterial and anti-inflammatory activities, which is attributed to the fact that the GN-Bn hydrogel has multiple advantages including sufficient mechanical stability, biocompatibility, and unique antibacterial mechanisms, making it significantly accelerate MRSA-infected full-thickness skin wound healing as a wound dressing. In a word, the GN-Bn antibacterial hydrogel dressing with an anti-inflammatory and antibacterial bifunctional material holds great potential in clinical application.
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Affiliation(s)
- Desheng Cai
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, P. R. China
| | - Yuqin Yang
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, P. R. China
| | - Jihui Lu
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, P. R. China
| | - Zhihua Yuan
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, P. R. China
| | - Yaozhi Zhang
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, P. R. China
| | - Xiaoyun Yang
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, P. R. China
| | - Xuemei Huang
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, P. R. China
| | - Tong Li
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, P. R. China
| | - Xuehao Tian
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, P. R. China
| | - Bing Xu
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, P. R. China
| | - Penglong Wang
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, P. R. China
| | - Haimin Lei
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, P. R. China
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14
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Zhao S, Xia Y, Liu H, Cui T, Fu P, Zhu W. A Cyclohexapeptide and Its Rare Glycosides from Marine Sponge-Derived Streptomyces sp. OUCMDZ-4539. Org Lett 2022; 24:6750-6754. [PMID: 36073973 DOI: 10.1021/acs.orglett.2c02520] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pyridapeptide A (1), a cyclohexapeptide containing hexahydropyridazine-3-carboxylic acid (HPDA), 5-hydroxytetrahydropyridazine-3-carboxylic acid (γ-OH-TPDA), and (2S,3R,4E,6E)-2-amino-3-hydroxy-8-methylnona-4,6-dienoic acid residues, and its four glycopeptides, pyridapeptides B-E (2-5, respectively), were isolated from the fermentation broth of the marine sponge-derived Streptomyces sp. OUCMDZ-4539. Their structures were determined on the basis of spectroscopic analysis and chemical methods. Pyridapeptides B-E have one or more 2,3,6-trideoxyhexose sugar units glycosylated at the γ-OH-TPDA residue. The biosynthetic pathways were proposed on the basis of gene cluster analysis. Compounds 4 and 5, containing four sugar groups, displayed significant antiproliferative activity against five human cancer cell lines (PC9, MKN45, HepG2, HCT-116, and K562).
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Affiliation(s)
- Shuige Zhao
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Yuwei Xia
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Haishan Liu
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China.,School of Biological Science and Technology, University of Jinan, Jinan 250022, China
| | - Tongxu Cui
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Peng Fu
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
| | - Weiming Zhu
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
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15
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Masota NE, Ohlsen K, Schollmayer C, Meinel L, Holzgrabe U. Isolation and Characterization of Galloylglucoses Effective against Multidrug-Resistant Strains of Escherichia coli and Klebsiella pneumoniae. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27155045. [PMID: 35956993 PMCID: PMC9370434 DOI: 10.3390/molecules27155045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/04/2022] [Accepted: 08/05/2022] [Indexed: 11/28/2022]
Abstract
The search for new antibiotics against multidrug-resistant (MDR), Gram-negative bacteria is crucial with respect to filling the antibiotics development pipeline, which is subject to a critical shortage of novel molecules. Screening of natural products is a promising approach for identifying antimicrobial compounds hosting a higher degree of novelty. Here, we report the isolation and characterization of four galloylglucoses active against different MDR strains of Escherichia coli and Klebsiella pneumoniae. A crude acetone extract was prepared from Paeonia officinalis Linnaeus leaves, and bioautography-guided isolation of active compounds from the extract was performed by liquid–liquid extraction, as well as open column, flash, and preparative chromatographic methods. Isolated active compounds were characterized and elucidated by a combination of spectroscopic and spectrometric techniques. In vitro antimicrobial susceptibility testing was carried out on E. coli and K. pneumoniae using 2 reference strains and 13 strains hosting a wide range of MDR phenotypes. Furthermore, in vivo antibacterial activities were assessed using Galleria mellonella larvae, and compounds 1,2,3,4,6-penta-O-galloyl-β-d-glucose, 3-O-digalloyl-1,2,4,6-tetra-O-galloyl-β-d-glucose, 6-O-digalloyl-1,2,3,4-tetra-O-galloyl-β-d-glucose, and 3,6-bis-O-digalloyl-1,2,4-tri-O-galloyl-β-d-glucose were isolated and characterized. They showed minimum inhibitory concentration (MIC) values in the range of 2–256 µg/mL across tested bacterial strains. These findings have added to the number of known galloylglucoses from P. officinalis and highlight their potential against MDR Gram-negative bacteria.
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Affiliation(s)
- Nelson E. Masota
- Institute of Pharmacy and Food Chemistry, University of Wuerzburg, Sandering 2, 97074 Wuerzburg, Germany
- School of Pharmacy, Muhimbili University of Health and Allied Sciences, Upanga West, Dar es Salaam P.O. Box 65013, Tanzania
| | - Knut Ohlsen
- Institute for Molecular Infection Biology, University of Wuerzburg, Josef-Schneider-Strasse 2, 97080 Wuerzburg, Germany
| | - Curd Schollmayer
- Institute of Pharmacy and Food Chemistry, University of Wuerzburg, Sandering 2, 97074 Wuerzburg, Germany
| | - Lorenz Meinel
- Institute of Pharmacy and Food Chemistry, University of Wuerzburg, Sandering 2, 97074 Wuerzburg, Germany
| | - Ulrike Holzgrabe
- Institute of Pharmacy and Food Chemistry, University of Wuerzburg, Sandering 2, 97074 Wuerzburg, Germany
- Correspondence: ; Tel.: +49-931-3185461
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16
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Hofer W, Oueis E, Fayad AA, Deschner F, Andreas A, de Carvalho LP, Hüttel S, Bernecker S, Pätzold L, Morgenstern B, Zaburannyi N, Bischoff M, Stadler M, Held J, Herrmann J, Müller R. Regio‐ and Stereoselective Epoxidation and Acidic Epoxide Opening of Antibacterial and Antiplasmodial Chlorotonils Yield Highly Potent Derivatives. Angew Chem Int Ed Engl 2022; 61:e202202816. [PMID: 35485800 PMCID: PMC9400904 DOI: 10.1002/anie.202202816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Indexed: 11/12/2022]
Abstract
The rise of antimicrobial resistance poses a severe threat to public health. The natural product chlorotonil was identified as a new antibiotic targeting multidrug resistant Gram‐positive pathogens and Plasmodium falciparum. Although chlorotonil shows promising activities, the scaffold is highly lipophilic and displays potential biological instabilities. Therefore, we strived towards improving its pharmaceutical properties by semisynthesis. We demonstrated stereoselective epoxidation of chlorotonils and epoxide ring opening in moderate to good yields providing derivatives with significantly enhanced solubility. Furthermore, in vivo stability of the derivatives was improved while retaining their nanomolar activity against critical human pathogens (e.g. methicillin‐resistant Staphylococcus aureus and P. falciparum). Intriguingly, we showed further superb activity for the frontrunner molecule in a mouse model of S. aureus infection.
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Affiliation(s)
- Walter Hofer
- Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy at Saarland University Campus Building E8.1 66123 Saarbrücken Germany
- German Centre for Infection Research (DZIF) Braunschweig Germany
| | - Emilia Oueis
- Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy at Saarland University Campus Building E8.1 66123 Saarbrücken Germany
- Department of Chemistry Khalifa University of Science and Technology 127788 Abu Dhabi United Arab Emirates
- American University of Beirut Faculty of Medicine DTS Bldg, Second Floor, Room 215-B Beirut Lebanon
| | - Antoine Abou Fayad
- Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy at Saarland University Campus Building E8.1 66123 Saarbrücken Germany
- Department of Experimental Pathology Immunology and Microbiology Center for Infectious Disease Research (CIDR) WHO Collaborating Center for Reference and Research on Bacterial Pathogens American University of Beirut Faculty of Medicine DTS Bldg, Second Floor, Room 215-B Beirut Lebanon
| | - Felix Deschner
- Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy at Saarland University Campus Building E8.1 66123 Saarbrücken Germany
- German Centre for Infection Research (DZIF) Braunschweig Germany
| | - Anastasia Andreas
- Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy at Saarland University Campus Building E8.1 66123 Saarbrücken Germany
- German Centre for Infection Research (DZIF) Braunschweig Germany
| | - Laìs Pessanha de Carvalho
- German Centre for Infection Research (DZIF) Braunschweig Germany
- Institute of Tropical Medicine Eberhard Karls University Tübingen Wilhelmstraße 27 72074 Tübingen Germany
| | - Stephan Hüttel
- German Centre for Infection Research (DZIF) Braunschweig Germany
- Microbial Drugs Helmholtz Centre for Infection Research (HZI) Inhoffenstraße 7 38124 Braunschweig Germany
| | - Steffen Bernecker
- Microbial Drugs Helmholtz Centre for Infection Research (HZI) Inhoffenstraße 7 38124 Braunschweig Germany
| | - Linda Pätzold
- Institute for Medical Microbiology and Hygiene Saarland University 66421 Homburg Germany
| | - Bernd Morgenstern
- Inorganic Solid State Chemistry Saarland University Campus 66123 Saarbrücken Germany
| | - Nestor Zaburannyi
- Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy at Saarland University Campus Building E8.1 66123 Saarbrücken Germany
| | - Markus Bischoff
- Institute for Medical Microbiology and Hygiene Saarland University 66421 Homburg Germany
| | - Marc Stadler
- German Centre for Infection Research (DZIF) Braunschweig Germany
- Microbial Drugs Helmholtz Centre for Infection Research (HZI) Inhoffenstraße 7 38124 Braunschweig Germany
| | - Jana Held
- German Centre for Infection Research (DZIF) Braunschweig Germany
- Institute of Tropical Medicine Eberhard Karls University Tübingen Wilhelmstraße 27 72074 Tübingen Germany
- Centre de Recherches Médicales de Lambaréné Lambaréné Gabon
| | - Jennifer Herrmann
- Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy at Saarland University Campus Building E8.1 66123 Saarbrücken Germany
- German Centre for Infection Research (DZIF) Braunschweig Germany
| | - Rolf Müller
- Microbial Natural Products Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy at Saarland University Campus Building E8.1 66123 Saarbrücken Germany
- German Centre for Infection Research (DZIF) Braunschweig Germany
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17
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Curcumin Displays Enhanced Solubility and Antibacterial Activities When Complexed with the Cell Penetrating Peptide pVEC. Int J Pept Res Ther 2022. [DOI: 10.1007/s10989-022-10415-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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18
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Müller R, Hofer W, Oueis E, Abou Fayad A, Deschner F, Andreas A, de Carvalho LP, Hüttel S, Bernecker S, Pätzold L, Morgenstern B, Zaburannyi N, Bischoff M, Stadler M, Held J, Herrmann J. Regio‐ and Stereoselective Epoxidation and Acidic Epoxide Opening of Antibacterial and Antiplasmodial Chlorotonils Yield Highly Potent Derivatives. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202202816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Rolf Müller
- Helmholtz-Institute for Pharmaceutical Research Saarland Microbial Natural Products Campus Building E8.1 66123 Saarbrücken GERMANY
| | - Walter Hofer
- Helmholtz-Institut fur Pharmazeutische Forschung Saarland Microbial Natural Products Campus Building E8.1 66123 Saarbrücken GERMANY
| | - Emilia Oueis
- Khalifa University of Science and Technology Department of Chemistry 127788 Abu Dhabi UNITED ARAB EMIRATES
| | - Antoine Abou Fayad
- American University of Beirut Department of Experimental Pathology, Immunology and Microbiology Beirut LEBANON
| | - Felix Deschner
- Helmholtz-Institut fur Pharmazeutische Forschung Saarland Microbial Natural Products Campus Building E8.1 66123 Saarbrücken GERMANY
| | - Anastasia Andreas
- Helmholtz-Institut fur Pharmazeutische Forschung Saarland Microbial Natural Products Campus Building E8.1 66123 Saarbrücken GERMANY
| | - Laìs Pessanha de Carvalho
- University of Tübingen: Eberhard Karls Universitat Tubingen Institute of Tropical Medicine Wilhelmstraße 27 72074 Tübingen GERMANY
| | - Stephan Hüttel
- Helmholtz Centre for Infection Research: Helmholtz-Zentrum fur Infektionsforschung GmbH Microbial Drugs Inhoffenstraße 7 38124 Braunschweig GERMANY
| | - Steffen Bernecker
- HZI: Helmholtz-Zentrum fur Infektionsforschung GmbH Microbial Drugs Inhoffenstraße 7 38124 Braunschweig GERMANY
| | - Linda Pätzold
- Universität des Saarlandes: Universitat des Saarlandes Institute for Medical Microbiology and Hygiene 66421 Homburg GERMANY
| | - Bernd Morgenstern
- Universität des Saarlandes: Universitat des Saarlandes Inorganic Solid State Chemistry 66123 Saarbrücken GERMANY
| | - Nestor Zaburannyi
- Helmholtz-Institut fur Pharmazeutische Forschung Saarland Microbial Natural Products 66123 Saarbrücken GERMANY
| | - Markus Bischoff
- Universität des Saarlandes: Universitat des Saarlandes Institute for Medical Microbiology and Hygiene 66421 Homburg GERMANY
| | - Marc Stadler
- HZI: Helmholtz-Zentrum fur Infektionsforschung GmbH Microbial Drugs Inhoffenstraße 7 38124 Braunschweig GERMANY
| | - Jana Held
- Eberhard Karls Universität Tübingen: Eberhard Karls Universitat Tubingen Institute of Tropical Medicine Wilhelmstraße 27 72074 Tübingen GERMANY
| | - Jennifer Herrmann
- Helmholtz-Institut fur Pharmazeutische Forschung Saarland Microbial Natural Products Campus Building E8.1 66123 Saarbrücken GERMANY
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19
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Pereira VV, Pereira NR, Pereira RCG, Duarte LP, Takahashi JA, Silva RR. Synthesis and Antimicrobial Activity of Ursolic Acid Ester Derivatives. Chem Biodivers 2022; 19:e202100566. [PMID: 34793623 DOI: 10.1002/cbdv.202100566] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 11/18/2021] [Indexed: 12/25/2022]
Abstract
Infections caused by microorganisms are a major cause of morbidity and mortality worldwide, and natural products continue to be important sources for the discovery of new antimicrobial agents. Ursolic acid is a triterpene with known antibacterial action, being naturally found in plants, such as Jaracanda oxyphylla and Jacaranda caroba (Bignoniaceae). Ursolic acid derivative esters have revealed potential biological activities, such as antitumor, antiviral, and antibacterial activity. In this study, sixteen esters (1-16) were synthesized from ursolic acid using DIC/DMAP and characterized by infrared (IR), nuclear magnetic resonance (1 H- and 13 C-NMR) and mass spectrometry. All ursolic acid esters were evaluated against Bacillus cereus, Staphylococcus aureus, Escherichia coli, Salmonella typhimurium, and the yeast Candida albicans. Six compounds are herein described for the first time (3, 9, 11, 13, 14 and 16) with yields up to 91.6 %. Compounds 11 (3β-(3,4-dimethoxybenzoyl)ursolic acid) and 15 (3β-nicotinoylursolic acid) displayed promising antifungal activity, with inhibition of C. albicans growth of 93.1 and 95.9 %, respectively.
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Affiliation(s)
- Vinicius Viana Pereira
- Faculty of Pharmacy, Universidade Federal de Minas Gerais, 31270-901, Belo Horizonte-MG, Brazil
| | - Nara Rúbia Pereira
- Chemistry Department, Universidade Federal dos Vales do Jequitinhonha e Mucuri, 39100-000, Diamantina-MG, Brazil
| | | | - Lucienir Pains Duarte
- Chemistry Department, Universidade Federal de Minas Gerais, 31270-901, Belo Horizonte-MG, Brazil
| | | | - Roqueline Rodrigues Silva
- Chemistry Department, Universidade Federal dos Vales do Jequitinhonha e Mucuri, 39100-000, Diamantina-MG, Brazil
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20
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Kaur R, Rani P, Atanasov AG, Alzahrani Q, Gupta R, Kapoor B, Gulati M, Chawla P. Discovery and Development of Antibacterial Agents: Fortuitous and Designed. Mini Rev Med Chem 2021; 22:984-1029. [PMID: 34939541 DOI: 10.2174/1570193x19666211221150119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 10/18/2021] [Accepted: 10/25/2021] [Indexed: 11/22/2022]
Abstract
Today, antibacterial drug resistance has turned into a significant public health issue. Repeated intake, suboptimal and/or unnecessary use of antibiotics, and, additionally, the transfer of resistance genes are the critical elements that make microorganisms resistant to conventional antibiotics. A substantial number of antibacterials that were successfully utilized earlier for prophylaxis and therapeutic purposes have been rendered inadequate due to this phenomenon. Therefore, the exploration of new molecules has become a continuous endeavour. Many such molecules are at various stages of investigation. A surprisingly high number of new molecules are currently in the stage of phase 3 clinical trials. A few new agents have been commercialized in the last decade. These include solithromycin, plazomicin, lefamulin, omadacycline, eravacycline, delafloxacin, zabofloxacin, finafloxacin, nemonoxacin, gepotidacin, zoliflodacin, cefiderocol, BAL30072, avycaz, zerbaxa, vabomere, relebactam, tedizolid, cadazolid, sutezolid, triclosan and afabiacin. This article aims to review the investigational and recently approved antibacterials with a focus on their structure, mechanisms of action/resistance, and spectrum of activity. Delving deep, their success or otherwise in various phases of clinical trials is also discussed while attributing the same to various causal factors.
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Affiliation(s)
- Ravleen Kaur
- Department of Health Sciences, Cape Breton University, Sydney, Nova Scotia. Canada
| | - Pooja Rani
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara. India
| | - Atanas G Atanasov
- Ludwig Boltzmann Institute of Digital Health and Patient Safety, Medical University of Vienna, Vienna. Austria
| | - Qushmua Alzahrani
- Department of Pharmacy/Nursing/Medicine Health and Environment, University of the Region of Joinville (UNIVILLE) volunteer researcher, Joinville. Brazil
| | - Reena Gupta
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara . India
| | - Bhupinder Kapoor
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara . India
| | - Monica Gulati
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara . India
| | - Pooja Chawla
- Department of Pharmaceutical Chemistry and Analysis, ISF College of Pharmacy, Ghal Kalan Moga, Punjab 142001. India
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21
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Caesar LK, Montaser R, Keller NP, Kelleher NL. Metabolomics and genomics in natural products research: complementary tools for targeting new chemical entities. Nat Prod Rep 2021; 38:2041-2065. [PMID: 34787623 PMCID: PMC8691422 DOI: 10.1039/d1np00036e] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Covering: 2010 to 2021Organisms in nature have evolved into proficient synthetic chemists, utilizing specialized enzymatic machinery to biosynthesize an inspiring diversity of secondary metabolites. Often serving to boost competitive advantage for their producers, these secondary metabolites have widespread human impacts as antibiotics, anti-inflammatories, and antifungal drugs. The natural products discovery field has begun a shift away from traditional activity-guided approaches and is beginning to take advantage of increasingly available metabolomics and genomics datasets to explore undiscovered chemical space. Major strides have been made and now enable -omics-informed prioritization of chemical structures for discovery, including the prospect of confidently linking metabolites to their biosynthetic pathways. Over the last decade, more integrated strategies now provide researchers with pipelines for simultaneous identification of expressed secondary metabolites and their biosynthetic machinery. However, continuous collaboration by the natural products community will be required to optimize strategies for effective evaluation of natural product biosynthetic gene clusters to accelerate discovery efforts. Here, we provide an evaluative guide to scientific literature as it relates to studying natural product biosynthesis using genomics, metabolomics, and their integrated datasets. Particular emphasis is placed on the unique insights that can be gained from large-scale integrated strategies, and we provide source organism-specific considerations to evaluate the gaps in our current knowledge.
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Affiliation(s)
- Lindsay K Caesar
- Department of Chemistry, Northwestern University, Evanston, IL, USA.
| | - Rana Montaser
- Department of Chemistry, Northwestern University, Evanston, IL, USA.
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology and Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Neil L Kelleher
- Department of Chemistry, Northwestern University, Evanston, IL, USA.
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
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22
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Valença CAS, Barbosa AAT, Souto EB, Caramão EB, Jain S. Volatile Nitrogenous Compounds from Bacteria: Source of Novel Bioactive Compounds. Chem Biodivers 2021; 18:e2100549. [PMID: 34643327 DOI: 10.1002/cbdv.202100549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 09/27/2021] [Indexed: 11/08/2022]
Abstract
Bacteria can produce nitrogenous compounds via both primary and secondary metabolic processes. Many bacterial volatile nitrogenous compounds produced during the secondary metabolism have been identified and reported for their antioxidant, antibacterial, antifungal, algicidal and antitumor activities. The production of these nitrogenous compounds depends on several factors, including the composition of culture media, growth conditions, and even the organic solvent used for their extraction, thus requiring their identification in specific conditions. In this review, we describe the volatile nitrogenous compounds produced by bacteria especially focusing on their antimicrobial activity. We concentrate on azo-compounds mainly pyrazines and pyrrolo-pyridines reported for their activity against several microorganisms. Whenever significant, extraction and identification methods of these compounds are also mentioned and discussed. To the best of our knowledge, this is first review describing volatile nitrogenous compounds from bacteria focusing on their biological activity.
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Affiliation(s)
- Camilla A S Valença
- Programa de Pós-Graduação em Biotecnologia Industrial, Universidade Tiradentes, Aracaju, Sergipe, Brazil
| | - Ana A T Barbosa
- Department of Morphology, Universidade Federal de Sergipe, São Cristóvão, Sergipe, Brazil
| | - Eliana B Souto
- CEB - Center of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Elina B Caramão
- Programa de Pós-Graduação em Biotecnologia Industrial, Universidade Tiradentes, Aracaju, Sergipe, Brazil.,Instituto Nacional de Ciência e Tecnologia - Energia e Ambiente, Universidade Federal da Bahia, Salvador, Bahia, Brazil
| | - Sona Jain
- Programa de Pós-Graduação em Biotecnologia Industrial, Universidade Tiradentes, Aracaju, Sergipe, Brazil
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23
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Marine dissolved organic matter: a vast and unexplored molecular space. Appl Microbiol Biotechnol 2021; 105:7225-7239. [PMID: 34536106 PMCID: PMC8494709 DOI: 10.1007/s00253-021-11489-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 07/29/2021] [Accepted: 07/31/2021] [Indexed: 01/02/2023]
Abstract
Abstract Marine dissolved organic matter (DOM) comprises a vast and unexplored molecular space. Most of it resided in the oceans for thousands of years. It is among the most diverse molecular mixtures known, consisting of millions of individual compounds. More than 1 Eg of this material exists on the planet. As such, it comprises a formidable source of natural products promising significant potential for new biotechnological purposes. Great emphasis has been placed on understanding the role of DOM in biogeochemical cycles and climate attenuation, its lifespan, interaction with microorganisms, as well as its molecular composition. Yet, probing DOM bioactivities is in its infancy, largely because it is technically challenging due to the chemical complexity of the material. It is of considerable interest to develop technologies capable to better discern DOM bioactivities. Modern screening technologies are opening new avenues allowing accelerated identification of bioactivities for small molecules from natural products. These methods diminish a priori the need for laborious chemical fractionation. We examine here the application of untargeted metabolomics and multiplexed high-throughput molecular-phenotypic screening techniques that are providing first insights on previously undetectable DOM bioactivities. Key points • Marine DOM is a vast, unexplored biotechnological resource. • Untargeted bioscreening approaches are emerging for natural product screening. • Perspectives for developing bioscreening platforms for marine DOM are discussed.
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24
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Masota NE, Vogg G, Ohlsen K, Holzgrabe U. Reproducibility challenges in the search for antibacterial compounds from nature. PLoS One 2021; 16:e0255437. [PMID: 34324599 PMCID: PMC8321225 DOI: 10.1371/journal.pone.0255437] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 07/14/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Reproducibility of reported antibacterial activities of plant extracts has long remained questionable. Although plant-related factors should be well considered in serious pharmacognostic research, they are often not addressed in many research papers. Here we highlight the challenges in reproducing antibacterial activities of plant extracts. METHODS Plants with reported antibacterial activities of interest were obtained from a literature review. Antibacterial activities against Escherichia coli and Klebsiella pneumoniae were tested using extracts' solutions in 10% DMSO and acetone. Compositions of working solutions from both solvents were established using LC-MS analysis. Moreover, the availability of details likely to affect reproducibility was evaluated in articles which reported antibacterial activities of studied plants. RESULTS Inhibition of bacterial growth at MIC of 256-1024 μg/mL was observed in only 15.4% of identical plant species. These values were 4-16-fold higher than those reported earlier. Further, 18.2% of related plant species had MICs of 128-256 μg/mL. Besides, 29.2% and 95.8% of the extracts were soluble to sparingly soluble in 10% DMSO and acetone, respectively. Extracts' solutions in both solvents showed similar qualitative compositions, with differing quantities of corresponding phytochemicals. Details regarding seasons and growth state at collection were missing in 65% and 95% of evaluated articles, respectively. Likewise, solvents used to dissolve the extracts were lacking in 30% of the articles, whereas 40% of them used unidentified bacterial isolates. CONCLUSION Reproducibility of previously reported activities from plants' extracts is a multi-factorial aspect. Thus, collective approaches are necessary in addressing the highlighted challenges.
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Affiliation(s)
- Nelson E. Masota
- Institute of Pharmacy and Food Chemistry, University of Wuerzburg, Wuerzburg, Germany
- School of Pharmacy, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Gerd Vogg
- Botanical Garden of The University of Wuerzburg, Wuerzburg, Germany
| | - Knut Ohlsen
- Institute for Molecular Infection Biology, University of Wuerzburg, Wuerzburg, Germany
| | - Ulrike Holzgrabe
- Institute of Pharmacy and Food Chemistry, University of Wuerzburg, Wuerzburg, Germany
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25
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Siupka P, Hansen FT, Schier A, Rocco S, Sørensen T, Piotrowska-Seget Z. Antifungal Activity and Biosynthetic Potential of New Streptomyces sp. MW-W600-10 Strain Isolated from Coal Mine Water. Int J Mol Sci 2021; 22:ijms22147441. [PMID: 34299061 PMCID: PMC8303363 DOI: 10.3390/ijms22147441] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/30/2021] [Accepted: 07/08/2021] [Indexed: 12/20/2022] Open
Abstract
Crop infections by fungi lead to severe losses in food production and pose risks for human health. The increasing resistance of pathogens to fungicides has led to the higher usage of these chemicals, which burdens the environment and highlights the need to find novel natural biocontrol agents. Members of the genus Streptomyces are known to produce a plethora of bioactive compounds. Recently, researchers have turned to extreme and previously unexplored niches in the search for new strains with antimicrobial activities. One such niche are underground coal mine environments. We isolated the new Streptomyces sp. MW-W600-10 strain from coal mine water samples collected at 665 m below ground level. We examined the antifungal activity of the strain against plant pathogens Fusarium culmorum DSM62188 and Nigrospora oryzae roseF7. Furthermore, we analyzed the strain’s biosynthetic potential with the antiSMASH tool. The strain showed inhibitory activity against both fungi strains. Genome mining revealed that it has 39 BGCs, among which 13 did not show similarity to those in databases. Additionally, we examined the activity of the Streptomyces sp. S-2 strain isolated from black soot against F. culmorum DSM62188. These results show that coal-related strains could be a source of novel bioactive compounds. Future studies will elucidate their full biotechnological potential.
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Affiliation(s)
- Piotr Siupka
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40032 Katowice, Poland; (A.S.); (S.R.); (Z.P.-S.)
- Correspondence:
| | - Frederik Teilfeldt Hansen
- Faculty of Engineering and Science, Department of Chemistry and Biosciences, University of Aalborg, 9220 Aalborg, Denmark; (F.T.H.); (T.S.)
| | - Aleksandra Schier
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40032 Katowice, Poland; (A.S.); (S.R.); (Z.P.-S.)
| | - Simone Rocco
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40032 Katowice, Poland; (A.S.); (S.R.); (Z.P.-S.)
| | - Trine Sørensen
- Faculty of Engineering and Science, Department of Chemistry and Biosciences, University of Aalborg, 9220 Aalborg, Denmark; (F.T.H.); (T.S.)
| | - Zofia Piotrowska-Seget
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40032 Katowice, Poland; (A.S.); (S.R.); (Z.P.-S.)
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26
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A User Guide for the Identification of New RiPP Biosynthetic Gene Clusters Using a RiPPER-Based Workflow. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2296:227-247. [PMID: 33977452 DOI: 10.1007/978-1-0716-1358-0_14] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
In recent years, genome mining has become a powerful strategy for the discovery of new specialized metabolites from microorganisms. However, the discovery of new groups of ribosomally synthesized and post-translationally modified peptides (RiPPs) by employing the currently available genome mining tools has proven challenging due to their inherent biases towards previously known RiPP families. In this chapter we provide detailed guidelines on using RiPPER, a recently developed RiPP-oriented genome mining tool conceived for the exploration of genomic database diversity in a flexible manner, thus allowing the discovery of truly new RiPP chemistry. In addition, using TfuA proteins of Alphaproteobacteria as an example, we present a complete workflow which integrates the functionalities of RiPPER with existing bioinformatic tools into a complete genome mining strategy. This includes some key updates to RiPPER (updated to version 1.1), which substantially simplify implementing this workflow.
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27
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Kim MS, Kim HR, Jeong DE, Choi SK. Cytosine Base Editor-Mediated Multiplex Genome Editing to Accelerate Discovery of Novel Antibiotics in Bacillus subtilis and Paenibacillus polymyxa. Front Microbiol 2021; 12:691839. [PMID: 34122396 PMCID: PMC8193733 DOI: 10.3389/fmicb.2021.691839] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 04/30/2021] [Indexed: 12/30/2022] Open
Abstract
Genome-based identification of new antibiotics is emerging as an alternative to traditional methods. However, uncovering hidden antibiotics under the background of known antibiotics remains a challenge. To over this problem using a quick and effective genetic approach, we developed a multiplex genome editing system using a cytosine base editor (CBE). The CBE system achieved simultaneous double, triple, quadruple, and quintuple gene editing with efficiencies of 100, 100, 83, and 75%, respectively, as well as the 100% editing efficiency of single targets in Bacillus subtilis. Whole-genome sequencing of the edited strains showed that they had an average of 8.5 off-target single-nucleotide variants at gRNA-independent positions. The CBE system was used to simultaneously knockout five known antibiotic biosynthetic gene clusters to leave only an uncharacterized polyketide biosynthetic gene cluster in Paenibacillus polymyxa E681. The polyketide showed antimicrobial activities against gram-positive bacteria, but not gram-negative bacteria and fungi. Therefore, our findings suggested that the CBE system might serve as a powerful tool for multiplex genome editing and greatly accelerating the unraveling of hidden antibiotics in Bacillus and Paenibacillus species.
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Affiliation(s)
- Man Su Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, South Korea
| | - Ha-Rim Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | - Da-Eun Jeong
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | - Soo-Keun Choi
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, South Korea
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28
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Breitling R, Avbelj M, Bilyk O, Carratore F, Filisetti A, Hanko EKR, Iorio M, Redondo RP, Reyes F, Rudden M, Severi E, Slemc L, Schmidt K, Whittall DR, Donadio S, García AR, Genilloud O, Kosec G, De Lucrezia D, Petković H, Thomas G, Takano E. Synthetic biology approaches to actinomycete strain improvement. FEMS Microbiol Lett 2021; 368:6289918. [PMID: 34057181 PMCID: PMC8195692 DOI: 10.1093/femsle/fnab060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/28/2021] [Indexed: 12/17/2022] Open
Abstract
Their biochemical versatility and biotechnological importance make actinomycete bacteria attractive targets for ambitious genetic engineering using the toolkit of synthetic biology. But their complex biology also poses unique challenges. This mini review discusses some of the recent advances in synthetic biology approaches from an actinomycete perspective and presents examples of their application to the rational improvement of industrially relevant strains.
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Affiliation(s)
- Rainer Breitling
- Department of Chemistry, Manchester Institute of Biotechnology, Manchester Synthetic Biology Research Centre SYNBIOCHEM, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Martina Avbelj
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Oksana Bilyk
- Department of Chemistry, Manchester Institute of Biotechnology, Manchester Synthetic Biology Research Centre SYNBIOCHEM, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Francesco Del Carratore
- Department of Chemistry, Manchester Institute of Biotechnology, Manchester Synthetic Biology Research Centre SYNBIOCHEM, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | | | - Erik K R Hanko
- Department of Chemistry, Manchester Institute of Biotechnology, Manchester Synthetic Biology Research Centre SYNBIOCHEM, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | | | | | - Fernando Reyes
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnologico de Ciencias de la Salud, 18016 Armilla, Granada, Spain
| | - Michelle Rudden
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | | | - Lucija Slemc
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Kamila Schmidt
- Department of Chemistry, Manchester Institute of Biotechnology, Manchester Synthetic Biology Research Centre SYNBIOCHEM, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Dominic R Whittall
- Department of Chemistry, Manchester Institute of Biotechnology, Manchester Synthetic Biology Research Centre SYNBIOCHEM, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | | | | | - Olga Genilloud
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnologico de Ciencias de la Salud, 18016 Armilla, Granada, Spain
| | - Gregor Kosec
- Acies Bio d.o.o., Tehnološki Park 21, 1000, Ljubljana, Slovenia
| | - Davide De Lucrezia
- Explora Biotech Srl, Doulix business unit, Via Torino 107, 30133 Venice, Italy
| | - Hrvoje Petković
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Gavin Thomas
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Eriko Takano
- Corresponding author: Department of Chemistry, Manchester Institute of Biotechnology, Manchester Synthetic Biology Research Centre SYNBIOCHEM, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK. E-mail:
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29
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Xu R, Song Y, Li J, Ju J, Li Q. Chemical Synthesis and Structure-Activity Relationship Study Yield Desotamide a Analogues with Improved Antibacterial Activity. Mar Drugs 2021; 19:md19060303. [PMID: 34073984 PMCID: PMC8225045 DOI: 10.3390/md19060303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 11/18/2022] Open
Abstract
Desotamides A, a cyclohexapeptide produced by the deep-sea-derived Streptomyces scopuliridis SCSIO ZJ46, displays notable antibacterial activities against strains of Streptococcus pnuemoniae, Staphylococcus aureus, and methicillin-resistant Staphylococcus epidermidis (MRSE). In this study, to further explore its antibacterial potential and reveal the antibacterial structure-activity relationship of desotamides, 13 cyclopeptides including 10 new synthetic desotamide A analogues and wollamides B/B1/B2 were synthesized and evaluated for their antibacterial activities against a panel of Gram-positive and -negative pathogens. The bioactivity data reveal that residues at position II and VI greatly impact antibacterial activity. The most potent antibacterial analogues are desotamide A4 (13) and A6 (15) where l-allo-Ile at position II was substituted with l-Ile and Gly at position VI was simultaneously replaced by d-Lys or d-Arg; desotamides A4 (13) and A6 (15) showed a 2–4-fold increase of antibacterial activities against a series of Gram-positive pathogens including the prevalent clinical drug-resistant pathogen methicillin-resistant Staphylococcus aureus (MRSA) with MIC values of 8–32 μg/mL compared to the original desotamide A. The enhanced antibacterial activity, broad antibacterial spectrum of desotamides A4 and A6 highlighted their potential as new antibiotic leads for further development.
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Affiliation(s)
- Run Xu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China; (R.X.); (Y.S.); (J.L.); (J.J.)
- School of Pharmacy, Zunyi Medical University, 201 Dalian Road, Zunyi 563000, China
| | - Yongxiang Song
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China; (R.X.); (Y.S.); (J.L.); (J.J.)
| | - Jun Li
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China; (R.X.); (Y.S.); (J.L.); (J.J.)
| | - Jianhua Ju
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China; (R.X.); (Y.S.); (J.L.); (J.J.)
- College of Oceanology, University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Qinglian Li
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China; (R.X.); (Y.S.); (J.L.); (J.J.)
- Correspondence: ; Tel./Fax: +86-20-3406-6449
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30
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Zhou LF, Wu J, Li S, Li Q, Jin LP, Yin CP, Zhang YL. Antibacterial Potential of Termite-Associated Streptomyces spp. ACS OMEGA 2021; 6:4329-4334. [PMID: 33623843 PMCID: PMC7893633 DOI: 10.1021/acsomega.0c05580] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/04/2021] [Indexed: 06/12/2023]
Abstract
Twenty-one strains of termite-associated actinomycetes were tested for their activities against three bacteria. The results showed that nine strains showed bacteriostatic activities against at least one tested bacterium, and the actinomycete YH01, which was isolated from the body surface of the queen of Odontotermes formosanus, had potent antibacterial activity. The YH01 was further identified as Streptomyces davaonensis. Two metabolites roseoflavin (1) and 8-methylamino-8-demethyl-d-riboflavin (2) were isolated and purified from S. davaonensis YH01. Their structures were determined by NMR, MS, and the related literature. The metabolite 1 showed strong inhibition activities against Bacillus subtilis (MIC = 1.56 μg/mL) and Staphylococcus aureus (MIC = 3.125 μg/mL), which were comparable to referenced gentamycin sulfate, with MIC values of 1.56 and 1.56 μg/mL, respectively. Furthermore, the anti-MRSA potential of compound 1 was determined against nine kinds of MRSA strains, with inhibition zones in the ranges of 12.7-19.7 mm under a concentration of 15 μg/6 mm discs and 18.3-22.7 mm under a concentration of 30 μg/6 mm discs. However, metabolite 1 had no inhibitory effect on Gram-negative bacteria. These results suggested that roseoflavin produced by YH01 holds promise for use against Gram-positive bacteria, especially to MRSA.
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Affiliation(s)
- Ling-Feng Zhou
- College
of Life Sciences, Anhui Agricultural University, Hefei 230036, People’s Republic of China
| | - Jun Wu
- College
of Life Sciences, Anhui Agricultural University, Hefei 230036, People’s Republic of China
| | - Shuai Li
- College
of Chemistry and Life Sciences, Zhejiang
Normal University, Jinhua 321004, People’s Republic
of China
| | - Qi Li
- Zhejiang
Jinhua Guangfu Hospital, Jinhua 321004, People’s Republic
of China
| | - Li-Ping Jin
- College
of Chemistry and Life Sciences, Zhejiang
Normal University, Jinhua 321004, People’s Republic
of China
| | - Cai-Ping Yin
- College
of Life Sciences, Anhui Agricultural University, Hefei 230036, People’s Republic of China
| | - Ying-Lao Zhang
- College
of Life Sciences, Anhui Agricultural University, Hefei 230036, People’s Republic of China
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31
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Devine R, McDonald HP, Qin Z, Arnold CJ, Noble K, Chandra G, Wilkinson B, Hutchings MI. Re-wiring the regulation of the formicamycin biosynthetic gene cluster to enable the development of promising antibacterial compounds. Cell Chem Biol 2021; 28:515-523.e5. [PMID: 33440167 PMCID: PMC8062789 DOI: 10.1016/j.chembiol.2020.12.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/12/2020] [Accepted: 12/17/2020] [Indexed: 12/17/2022]
Abstract
The formicamycins are promising antibiotics first identified in Streptomyces formicae KY5, which produces the compounds at low levels. Here, we show that by understanding the regulation of the for biosynthetic gene cluster (BGC), we can rewire the BGC to increase production levels. The for BGC consists of 24 genes expressed on nine transcripts. The MarR regulator ForJ represses expression of seven transcripts encoding the major biosynthetic genes as well as the ForGF two-component system that initiates biosynthesis. We show that overexpression of forGF in a ΔforJ background increases formicamycin production 10-fold compared with the wild-type. De-repression, by deleting forJ, also switches on biosynthesis in liquid culture and induces the production of additional, previously unreported formicamycin congeners. Furthermore, combining de-repression with mutations in biosynthetic genes leads to biosynthesis of additional bioactive precursors. Formicamycin biosynthesis requires 24 genes expressed on nine transcripts Deleting the MarR regulator ForJ increases formicamycin biosynthesis De-repressing formicamycin biosynthesis induces production in liquid culture Re-wiring regulation and biosynthesis results in the production of new congeners
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Affiliation(s)
- Rebecca Devine
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
| | - Hannah P McDonald
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Zhiwei Qin
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Corinne J Arnold
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Katie Noble
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Barrie Wilkinson
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
| | - Matthew I Hutchings
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
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32
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Curuțiu C, Dițu LM, Grumezescu AM, Holban AM. Polyphenols of Honeybee Origin with Applications in Dental Medicine. Antibiotics (Basel) 2020; 9:E856. [PMID: 33266173 PMCID: PMC7761219 DOI: 10.3390/antibiotics9120856] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/22/2020] [Accepted: 11/27/2020] [Indexed: 12/30/2022] Open
Abstract
Honeybee products are a great source of polyphenols with recognized applications in dental medicine. Although their biological mechanisms in oral diseases are not fully understood, numerous in vitro, in vivo and clinical studies have reported promising results in the prevention and treatment of oral diseases. Bioactivities, such as antibacterial, antiviral, antiparasite, anticancer, anti-inflammatory and anti-oxidant properties, recommend their future study in order to develop efficient alternatives in the management of widespread oral conditions, such as dental caries and periodontitis. The most investigated mechanisms of polyphenols in oral health rely on their ability to strengthen the dental enamel, decrease the development of dental plaque formation, inhibit the progression of dental caries and development of dental pathogens and show anti-inflammatory properties. These features recommend them as useful honeybee candidates in the management of emerging oral diseases.
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Affiliation(s)
- Carmen Curuțiu
- Department of Microbiology and Immunology, Faculty of Biology, University of Bucharest, 030018 Bucharest, Romania; (C.C.); (L.M.D.); (A.M.H.)
| | - Lia Mara Dițu
- Department of Microbiology and Immunology, Faculty of Biology, University of Bucharest, 030018 Bucharest, Romania; (C.C.); (L.M.D.); (A.M.H.)
| | - Alexandru Mihai Grumezescu
- Department of Science and Engineering of Oxide Materials and Nanomaterials, Faculty of Applied Chemistry and Materials Science, University Politehnica of Bucharest, 1-7 Polizu Street, 011061 Bucharest, Romania
- Research Institute of the University of Bucharest—ICUB, University of Bucharest, 90-92 Panduri Road, 050657 Bucharest, Romania
| | - Alina Maria Holban
- Department of Microbiology and Immunology, Faculty of Biology, University of Bucharest, 030018 Bucharest, Romania; (C.C.); (L.M.D.); (A.M.H.)
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Isochlorogenic acid (ICGA): natural medicine with potentials in pharmaceutical developments. Chin J Nat Med 2020; 18:860-871. [DOI: 10.1016/s1875-5364(20)60029-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Indexed: 01/11/2023]
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Garzón V, Bustos RH, G. Pinacho D. Personalized Medicine for Antibiotics: The Role of Nanobiosensors in Therapeutic Drug Monitoring. J Pers Med 2020; 10:E147. [PMID: 32993004 PMCID: PMC7712907 DOI: 10.3390/jpm10040147] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/05/2020] [Accepted: 09/07/2020] [Indexed: 01/01/2023] Open
Abstract
Due to the high bacterial resistance to antibiotics (AB), it has become necessary to adjust the dose aimed at personalized medicine by means of therapeutic drug monitoring (TDM). TDM is a fundamental tool for measuring the concentration of drugs that have a limited or highly toxic dose in different body fluids, such as blood, plasma, serum, and urine, among others. Using different techniques that allow for the pharmacokinetic (PK) and pharmacodynamic (PD) analysis of the drug, TDM can reduce the risks inherent in treatment. Among these techniques, nanotechnology focused on biosensors, which are relevant due to their versatility, sensitivity, specificity, and low cost. They provide results in real time, using an element for biological recognition coupled to a signal transducer. This review describes recent advances in the quantification of AB using biosensors with a focus on TDM as a fundamental aspect of personalized medicine.
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Affiliation(s)
- Vivian Garzón
- PhD Biosciences Program, Universidad de La Sabana, Chía 140013, Colombia;
| | - Rosa-Helena Bustos
- Therapeutical Evidence Group, Clinical Pharmacology, Universidad de La Sabana, Chía 140013, Colombia;
| | - Daniel G. Pinacho
- Therapeutical Evidence Group, Clinical Pharmacology, Universidad de La Sabana, Chía 140013, Colombia;
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Favero LM, Chideroli RT, Ferrari NA, Azevedo VADC, Tiwari S, Lopera-Barrero NM, Pereira UDP. In silico Prediction of New Drug Candidates Against the Multidrug-Resistant and Potentially Zoonotic Fish Pathogen Serotype III Streptococcus agalactiae. Front Genet 2020; 11:1024. [PMID: 33005185 PMCID: PMC7484375 DOI: 10.3389/fgene.2020.01024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 08/11/2020] [Indexed: 12/02/2022] Open
Abstract
Streptococcus agalactiae is an invasive multi-host pathogen that causes invasive diseases mainly in newborns, elderly, and individuals with underlying health complications. In fish, S. agalactiae causes streptococcosis, which is characterized by septicemia and neurological signs, and leads to great economic losses to the fish farming industry worldwide. These bacteria can be classified into different serotypes based on capsular antigens, and into different sequence types (ST) based on multilocus sequence typing (MLST). In 2015, serotype III ST283 was identified to be associated with a foodborne invasive disease in non-pregnant immunocompetent humans in Singapore, and the infection was related to raw fish consumption. In addition, a serotype III strain isolated from tilapia in Brazil has been reported to be resistant to five antibiotic classes. This specific serotype can serve as a reservoir of resistance genes and pose a serious threat to public health. Thus, new approaches for the control and treatment of S. agalactiae infections are needed. In the present study, 24 S. agalactiae serotype III complete genomes, isolated from human and fish hosts, were compared. The core genome was identified, and, using bioinformatics tools and subtractive criteria, five proteins were identified as potential drug targets. Furthermore, 5,008 drug-like natural compounds were virtually screened against the identified targets. The ligands with the best binding properties are suggested for further in vitro and in vivo analysis.
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Affiliation(s)
- Leonardo Mantovani Favero
- Laboratory of Fish Bacteriology, Department of Preventive Veterinary Medicine, State University of Londrina, Londrina, Brazil
| | - Roberta Torres Chideroli
- Laboratory of Fish Bacteriology, Department of Preventive Veterinary Medicine, State University of Londrina, Londrina, Brazil
| | - Natália Amoroso Ferrari
- Laboratory of Fish Bacteriology, Department of Preventive Veterinary Medicine, State University of Londrina, Londrina, Brazil
| | - Vasco Ariston De Carvalho Azevedo
- Institute of Biological Sciences, Department of Genetic, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Sandeep Tiwari
- Institute of Biological Sciences, Department of Genetic, Ecology, and Evolution, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | | | - Ulisses de Pádua Pereira
- Laboratory of Fish Bacteriology, Department of Preventive Veterinary Medicine, State University of Londrina, Londrina, Brazil
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Mohammadipanah F, Kermani F, Salimi F. Awakening the Secondary Metabolite Pathways of Promicromonospora kermanensis Using Physicochemical and Biological Elicitors. Appl Biochem Biotechnol 2020; 192:1224-1237. [PMID: 32715413 DOI: 10.1007/s12010-020-03361-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 06/22/2020] [Indexed: 12/20/2022]
Abstract
The drug discovery rate is dramatically decreasing due to the rediscovery of known compounds. Genome mining approaches have revealed that a large portion of the actinobacterial genome that encodes bioactive metabolites is cryptic and not expressed under standard lab conditions. In the present study, we aimed to induce antibiotic encoding biosynthetic genes in a member of Micrococcales as a new species of Promicromonospora, Promicromonospora kermanensis, by chemical and biological elicitors as it was considered to produce numerous valuable bioactive metabolites based on the whole genome results. Induction has been done via chemical (antibiotics, histone deacetylase inhibitors (HDAIs), rare earth elements (REEs), fatty acid synthesis inhibitors, and extreme pH changes) and biological elicitors (live and dead Gram-positive and negative bacteria). The results showed that valproic acid (as HDAIs), DMSO, lanthanum chloride (as REE), triclosan (as fatty acid synthesis inhibitors), alkaline pH, and supernatant of Pseudomonas aeruginosa UTMC 1404 culture could act as stimuli to provoke antibacterial synthetic pathways in Promicromonospora kermanensis DSM 45485. Moreover, it was revealed that eliciting agents in cell filtrated of P. aeruginosa culture is resistant to detergent, acidic, and basic condition and have amphipathic nature. The inducing effect of alkaline pH on metabolite induction of Actinobacteria was first reported in this study. In the follow-up studies, the induced antibacterial producing clusters can be subjected to the characterization, and the implemented approach in this study can be used for metabolites induction in other selected species.
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Affiliation(s)
- Fatemeh Mohammadipanah
- Pharmaceutical Biotechnology Lab, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, 14155-6455, Iran.
| | - Fatemeh Kermani
- Pharmaceutical Biotechnology Lab, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, 14155-6455, Iran
| | - Fatemeh Salimi
- Department of Cellular and Molecular Biology, School of Biology, Damghan University, Damghan, Iran
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Melior H, Maaß S, Li S, Förstner KU, Azarderakhsh S, Varadarajan AR, Stötzel M, Elhossary M, Barth-Weber S, Ahrens CH, Becher D, Evguenieva-Hackenberg E. The Leader Peptide peTrpL Forms Antibiotic-Containing Ribonucleoprotein Complexes for Posttranscriptional Regulation of Multiresistance Genes. mBio 2020; 11:e01027-20. [PMID: 32546623 PMCID: PMC7298713 DOI: 10.1128/mbio.01027-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 05/07/2020] [Indexed: 11/20/2022] Open
Abstract
Bacterial ribosome-dependent attenuators are widespread posttranscriptional regulators. They harbor small upstream open reading frames (uORFs) encoding leader peptides, for which no functions in trans are known yet. In the plant symbiont Sinorhizobium meliloti, the tryptophan biosynthesis gene trpE(G) is preceded by the uORF trpL and is regulated by transcription attenuation according to tryptophan availability. However, trpLE(G) transcription is initiated independently of the tryptophan level in S. meliloti, thereby ensuring a largely tryptophan-independent production of the leader peptide peTrpL. Here, we provide evidence for a tryptophan-independent role of peTrpL in trans We found that peTrpL increases the resistance toward tetracycline, erythromycin, chloramphenicol, and the flavonoid genistein, which are substrates of the major multidrug efflux pump SmeAB. Coimmunoprecipitation with a FLAG-peTrpL suggested smeR mRNA, which encodes the transcription repressor of smeABR, as a peptide target. Indeed, upon antibiotic exposure, smeR mRNA was destabilized and smeA stabilized in a peTrpL-dependent manner, showing that peTrpL acts in the differential regulation of smeABR Furthermore, smeR mRNA was coimmunoprecipitated with peTrpL in antibiotic-dependent ribonucleoprotein (ARNP) complexes, which, in addition, contained an antibiotic-induced antisense RNA complementary to smeRIn vitro ARNP reconstitution revealed that the above-mentioned antibiotics and genistein directly support complex formation. A specific region of the antisense RNA was identified as a seed region for ARNP assembly in vitro Altogether, our data show that peTrpL is involved in a mechanism for direct utilization of antimicrobial compounds in posttranscriptional regulation of multiresistance genes. Importantly, this role of peTrpL in resistance is conserved in other AlphaproteobacteriaIMPORTANCE Leader peptides encoded by transcription attenuators are widespread small proteins that are considered nonfunctional in trans We found that the leader peptide peTrpL of the soil-dwelling plant symbiont Sinorhizobium meliloti is required for differential, posttranscriptional regulation of a multidrug resistance operon upon antibiotic exposure. Multiresistance achieved by efflux of different antimicrobial compounds ensures survival and competitiveness in nature and is important from both evolutionary and medical points of view. We show that the leader peptide forms antibiotic- and flavonoid-dependent ribonucleoprotein complexes (ARNPs) for destabilization of smeR mRNA encoding the transcription repressor of the major multidrug resistance operon. The seed region for ARNP assembly was localized in an antisense RNA, whose transcription is induced by antimicrobial compounds. The discovery of ARNP complexes as new players in multiresistance regulation opens new perspectives in understanding bacterial physiology and evolution and potentially provides new targets for antibacterial control.
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Affiliation(s)
- Hendrik Melior
- Institute of Microbiology and Molecular Biology, University of Giessen, Giessen, Germany
| | - Sandra Maaß
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Siqi Li
- Institute of Microbiology and Molecular Biology, University of Giessen, Giessen, Germany
| | - Konrad U Förstner
- ZB MED-Information Centre for Life Sciences, University of Cologne, Cologne, Germany
| | - Saina Azarderakhsh
- Institute of Microbiology and Molecular Biology, University of Giessen, Giessen, Germany
| | | | - Maximilian Stötzel
- Institute of Microbiology and Molecular Biology, University of Giessen, Giessen, Germany
| | - Muhammad Elhossary
- ZB MED-Information Centre for Life Sciences, University of Cologne, Cologne, Germany
| | - Susanne Barth-Weber
- Institute of Microbiology and Molecular Biology, University of Giessen, Giessen, Germany
| | - Christian H Ahrens
- Agroscope & SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Dörte Becher
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
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Cushnie TPT, Cushnie B, Echeverría J, Fowsantear W, Thammawat S, Dodgson JLA, Law S, Clow SM. Bioprospecting for Antibacterial Drugs: a Multidisciplinary Perspective on Natural Product Source Material, Bioassay Selection and Avoidable Pitfalls. Pharm Res 2020; 37:125. [PMID: 32529587 DOI: 10.1007/s11095-020-02849-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 05/30/2020] [Indexed: 12/12/2022]
Abstract
Bioprospecting is the exploration, extraction and screening of biological material and sometimes indigenous knowledge to discover and develop new drugs and other products. Most antibiotics in current clinical use (eg. β-lactams, aminoglycosides, tetracyclines, macrolides) were discovered using this approach, and there are strong arguments to reprioritize bioprospecting over other strategies in the search for new antibacterial drugs. Academic institutions should be well positioned to lead the early stages of these efforts given their many thousands of locations globally and because they are not constrained by the same commercial considerations as industry. University groups can lack the full complement of knowledge and skills needed though (eg. how to tailor screening strategy to biological source material). In this article, we review three key aspects of the bioprospecting literature (source material and in vitro antibacterial and toxicity testing) and present an integrated multidisciplinary perspective on (a) source material selection, (b) legal, taxonomic and other issues related to source material, (c) cultivation methods, (d) bioassay selection, (e) technical standards available, (f) extract/compound dissolution, (g) use of minimum inhibitory concentration and selectivity index values to identify progressible extracts and compounds, and (h) avoidable pitfalls. The review closes with recommendations for future study design and information on subsequent steps in the bioprospecting process.
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Affiliation(s)
- T P Tim Cushnie
- Faculty of Medicine, Mahasarakham University, 269 Nakornsawan Road, Mahasarakham, 44000, Thailand.
| | - Benjamart Cushnie
- Faculty of Pharmacy, Mahasarakham University, Kantarawichai, Thailand
| | - Javier Echeverría
- Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Winita Fowsantear
- Faculty of Medicine, Mahasarakham University, 269 Nakornsawan Road, Mahasarakham, 44000, Thailand
| | - Sutthiwan Thammawat
- Faculty of Medicine, Mahasarakham University, 269 Nakornsawan Road, Mahasarakham, 44000, Thailand
| | | | - Samantha Law
- National Collection of Industrial, Food and Marine Bacteria (NCIMB) Ltd, Aberdeen, UK
| | - Simon M Clow
- PMI BioPharma Solutions LLC, Nashville, Tennessee, USA
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Núñez-Montero K, Quezada-Solís D, Khalil ZG, Capon RJ, Andreote FD, Barrientos L. Genomic and Metabolomic Analysis of Antarctic Bacteria Revealed Culture and Elicitation Conditions for the Production of Antimicrobial Compounds. Biomolecules 2020; 10:E673. [PMID: 32349314 PMCID: PMC7277857 DOI: 10.3390/biom10050673] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/15/2020] [Accepted: 04/21/2020] [Indexed: 01/08/2023] Open
Abstract
Concern about finding new antibiotics against drug-resistant pathogens is increasing every year. Antarctic bacteria have been proposed as an unexplored source of bioactive metabolites; however, most biosynthetic gene clusters (BGCs) producing secondary metabolites remain silent under common culture conditions. Our work aimed to characterize elicitation conditions for the production of antibacterial secondary metabolites from 34 Antarctic bacterial strains based on MS/MS metabolomics and genome mining approaches. Bacterial strains were cultivated under different nutrient and elicitation conditions, including the addition of lipopolysaccharide (LPS), sodium nitroprusside (SNP), and coculture. Metabolomes were obtained by HPLC-QTOF-MS/MS and analyzed through molecular networking. Antibacterial activity was determined, and seven strains were selected for genome sequencing and analysis. Biosynthesis pathways were activated by all the elicitation treatments, which varies among strains and dependents of culture media. Increased antibacterial activity was observed for a few strains and addition of LPS was related with inhibition of Gram-negative pathogens. Antibiotic BGCs were found for all selected strains and the expressions of putative actinomycin, carotenoids, and bacillibactin were characterized by comparison of genomic and metabolomic data. This work established the use of promising new elicitors for bioprospection of Antarctic bacteria and highlights the importance of new "-omics" comparative approaches for drug discovery.
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Affiliation(s)
- Kattia Núñez-Montero
- Laboratory of Molecular Applied Biology, Center of Excellence in Translational Medicine, Universidad de La Frontera, Avenida Alemania 0458, Temuco 4810296, Chile; (K.N.-M.); (D.Q.-S.)
- Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco 4811230, Chile
- Biotechnology Investigation Center, Department of Biology, Instituto Tecnológico de Costa Rica, Cartago 159-7050, Costa Rica
| | - Damián Quezada-Solís
- Laboratory of Molecular Applied Biology, Center of Excellence in Translational Medicine, Universidad de La Frontera, Avenida Alemania 0458, Temuco 4810296, Chile; (K.N.-M.); (D.Q.-S.)
| | - Zeinab G. Khalil
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia; (Z.G.K.); (R.J.C.)
| | - Robert J. Capon
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia; (Z.G.K.); (R.J.C.)
| | - Fernando D. Andreote
- Department of Soil Science, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, SP 13418-900, Brazil;
| | - Leticia Barrientos
- Laboratory of Molecular Applied Biology, Center of Excellence in Translational Medicine, Universidad de La Frontera, Avenida Alemania 0458, Temuco 4810296, Chile; (K.N.-M.); (D.Q.-S.)
- Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco 4811230, Chile
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Identification and Heterologous Expression of the Biosynthetic Gene Cluster Encoding the Lasso Peptide Humidimycin, a Caspofungin Activity Potentiator. Antibiotics (Basel) 2020; 9:antibiotics9020067. [PMID: 32046042 PMCID: PMC7168211 DOI: 10.3390/antibiotics9020067] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/03/2020] [Accepted: 02/05/2020] [Indexed: 12/19/2022] Open
Abstract
Humidimycin (MDN-0010) is a ribosomally synthesized and post-translationally modified peptide (RiPP) belonging to class I lasso peptides, and is structurally related to siamycins, which have been shown to have strong antimicrobial activities against Gram-positive bacteria and to possess anti-HIV activity. Humidimycin was isolated from the strain Streptomyces humidus CA-100629, and was shown to synergize the activity of the fungal cell wall inhibitor caspofungin. In this work, the biosynthetic gene cluster of humidimycin was identified by genome mining of S. humidus CA-100629, cloned by Gibson assembly, and heterologously expressed.
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