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Buijs NP, Vlaming HC, Kotsogianni I, Arts M, Willemse J, Duan Y, Alexander FM, Cochrane SA, Schneider T, Martin NI. A classic antibiotic reimagined: Rationally designed bacitracin variants exhibit potent activity against vancomycin-resistant pathogens. Proc Natl Acad Sci U S A 2024; 121:e2315310121. [PMID: 38990944 PMCID: PMC11260088 DOI: 10.1073/pnas.2315310121] [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: 09/08/2023] [Accepted: 06/13/2024] [Indexed: 07/13/2024] Open
Abstract
Bacitracin is a macrocyclic peptide antibiotic that is widely used as a topical treatment for infections caused by gram-positive bacteria. Mechanistically, bacitracin targets bacteria by specifically binding to the phospholipid undecaprenyl pyrophosphate (C55PP), which plays a key role in the bacterial lipid II cycle. Recent crystallographic studies have shown that when bound to C55PP, bacitracin adopts a highly ordered amphipathic conformation. In doing so, all hydrophobic side chains align on one face of the bacitracin-C55PP complex, presumably interacting with the bacterial cell membrane. These insights led us to undertake structure-activity investigations into the individual contribution of the nonpolar amino acids found in bacitracin. To achieve this we designed, synthesized, and evaluated a series of bacitracin analogues, a number of which were found to exhibit significantly enhanced antibacterial activity against clinically relevant, drug-resistant pathogens. As for the natural product, these next-generation bacitracins were found to form stable complexes with C55PP. The structure-activity insights thus obtained serve to inform the design of C55PP-targeting antibiotics, a key and underexploited antibacterial strategy.
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Affiliation(s)
- Ned P. Buijs
- Biological Chemistry Group, Institute of Biology, Leiden University, Leiden2333 BE, The Netherlands
| | - Halana C. Vlaming
- Biological Chemistry Group, Institute of Biology, Leiden University, Leiden2333 BE, The Netherlands
| | - Ioli Kotsogianni
- Biological Chemistry Group, Institute of Biology, Leiden University, Leiden2333 BE, The Netherlands
| | - Melina Arts
- Institute for Pharmaceutical Microbiology, University of Bonn, Bonn53115, Germany
| | - Joost Willemse
- Biological Chemistry Group, Institute of Biology, Leiden University, Leiden2333 BE, The Netherlands
| | - Yunhao Duan
- Biological Chemistry Group, Institute of Biology, Leiden University, Leiden2333 BE, The Netherlands
| | - Francesca M. Alexander
- School of Chemistry and Chemical Engineering, Queen’s University, BelfastBT9 5AG, United Kingdom
| | - Stephen A. Cochrane
- School of Chemistry and Chemical Engineering, Queen’s University, BelfastBT9 5AG, United Kingdom
| | - Tanja Schneider
- Institute for Pharmaceutical Microbiology, University of Bonn, Bonn53115, Germany
| | - Nathaniel I. Martin
- Biological Chemistry Group, Institute of Biology, Leiden University, Leiden2333 BE, The Netherlands
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da Silva Oliveira W, Teixeira CRV, Mantovani HC, Dolabella SS, Jain S, Barbosa AAT. Nisin variants: What makes them different and unique? Peptides 2024; 177:171220. [PMID: 38636811 DOI: 10.1016/j.peptides.2024.171220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 04/05/2024] [Accepted: 04/11/2024] [Indexed: 04/20/2024]
Abstract
Nisin A is a lantibiotic bacteriocin typically produced by strains of Lactococcus lactis. This bacteriocin has been approved as a natural food preservative since the late 1980 s and shows antimicrobial activity against a range of food-borne spoilage and pathogenic microorganisms. The therapeutic potential of nisin A has also been explored increasingly both in human and veterinary medicine. Nisin has been shown to be effective in treating bovine mastitis, dental caries, cancer, and skin infections. Recently, it was demonstrated that nisin has an affinity for the same receptor used by SARS-CoV-2 to enter human cells and was proposed as a blocker of the viral infection. Several nisin variants produced by distinct bacterial strains or modified by bioengineering have been described since the discovery of nisin A. These variants present modifications in the peptide structure, biosynthesis, mode of action, and spectrum of activity. Given the importance of nisin for industrial and therapeutic applications, the objective of this study was to describe the characteristics of the nisin variants, highlighting the main differences between these molecules and their potential applications. This review will be useful to researchers interested in studying the specifics of nisin A and its variants.
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Affiliation(s)
| | | | | | - Silvio Santana Dolabella
- Universidade Federal de Sergipe, São Cristóvão, SE, Brazil; Programa de Pós-Graduação em Biologia Parasitária, Universidade Federal de Sergipe, São Cristóvão, SE, Brazil
| | - Sona Jain
- Universidade Federal de Sergipe, São Cristóvão, SE, Brazil
| | - Ana Andréa Teixeira Barbosa
- Universidade Federal de Sergipe, São Cristóvão, SE, Brazil; Programa de Pós-Graduação em Biologia Parasitária, Universidade Federal de Sergipe, São Cristóvão, SE, Brazil.
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3
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Faure A, Manuse S, Gonin M, Grangeasse C, Jault JM, Orelle C. Daptomycin avoids drug resistance mediated by the BceAB transporter in Streptococcus pneumoniae. Microbiol Spectr 2024; 12:e0363823. [PMID: 38214521 PMCID: PMC10846014 DOI: 10.1128/spectrum.03638-23] [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: 10/12/2023] [Accepted: 12/19/2023] [Indexed: 01/13/2024] Open
Abstract
Drug-resistant bacteria are a serious threat to human health as antibiotics are gradually losing their clinical efficacy. Comprehending the mechanism of action of antimicrobials and their resistance mechanisms plays a key role in developing new agents to fight antimicrobial resistance. The lipopeptide daptomycin is an antibiotic that selectively disrupts Gram-positive bacterial membranes, thereby showing slower resistance development than many classical drugs. Consequently, it is often used as a last resort antibiotic to preserve its use as one of the least potent antibiotics at our disposal. The mode of action of daptomycin has been debated but was recently found to involve the formation of a tripartite complex between undecaprenyl precursors of cell wall biosynthesis and the anionic phospholipid phosphatidylglycerol. BceAB-type ABC transporters are known to confer resistance to antimicrobial peptides that sequester some precursors of the peptidoglycan, such as the undecaprenyl pyrophosphate or lipid II. The expression of these transporters is upregulated by dedicated two-component regulatory systems in the presence of antimicrobial peptides that are recognized by the system. Here, we investigated whether daptomycin evades resistance mediated by the BceAB transporter from the bacterial pathogen Streptococcus pneumoniae. Although daptomycin can bind to the transporter, our data showed that the BceAB transporter does not mediate resistance to the drug and its expression is not induced in its presence. These findings show that the pioneering membrane-active daptomycin has the potential to escape the resistance mechanism mediated by BceAB-type transporters and confirm that the development of this class of compounds has promising clinical applications.IMPORTANCEAntibiotic resistance is rising in all parts of the world. New resistance mechanisms are emerging and dangerously spreading, threatening our ability to treat common infectious diseases. Daptomycin is an antimicrobial peptide that is one of the last antibiotics approved for clinical use. Understanding the resistance mechanisms toward last-resort antibiotics such as daptomycin is critical for the success of future antimicrobial therapies. BceAB-type ABC transporters confer resistance to antimicrobial peptides that target precursors of cell-wall synthesis. In this study, we showed that the BceAB transporter from the human pathogen Streptococcus pneumoniae does not confer resistance to daptomycin, suggesting that this drug and other calcium-dependent lipopeptide antibiotics have the potential to evade the action of this type of ABC transporters in other bacterial pathogens.
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Affiliation(s)
- Agathe Faure
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Sylvie Manuse
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Mathilde Gonin
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Christophe Grangeasse
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Jean-Michel Jault
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Cédric Orelle
- Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
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4
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A review of potential antibacterial activities of nisin against Listeria monocytogenes: the combined use of nisin shows more advantages than single use. Food Res Int 2023; 164:112363. [PMID: 36737951 DOI: 10.1016/j.foodres.2022.112363] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 12/10/2022] [Accepted: 12/24/2022] [Indexed: 12/29/2022]
Abstract
Listeria monocytogenes is a foodborne pathogen causing serious public health problems. Nisin is a natural antimicrobial agent produced by Lactococcus lactis and widely used in the food industry. However, the anti-L. monocytogenes efficiency of nisin might be decreased due to natural or acquired resistance of L. monocytogenes to nisin, or complexity of the food environment. The limitation of nisin as a bacteriostatic agent in food could be improved using a combination of methods. In this review, the physiochemical characteristics, species, bioengineered mutants, and antimicrobial mechanism of nisin are reviewed. Strategies of nisin combined with other antibacterial methods, including physical, chemical, and natural substances, and nanotechnology to enhance antibacterial effect are highlighted and discussed. Additionally, the antibacterial efficiency of nisin applied in real meat, dairy, and aquatic products is evaluated and analyzed. Among the various binding treatments, the combination with natural substances is more effective than the combination with physical and chemical methods. However, the combination of nisin and nanotechnology has more potential in terms of the impact on food quality.
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Panina IS, Balandin SV, Tsarev AV, Chugunov AO, Tagaev AA, Finkina EI, Antoshina DV, Sheremeteva EV, Paramonov AS, Rickmeyer J, Bierbaum G, Efremov RG, Shenkarev ZO, Ovchinnikova TV. Specific Binding of the α-Component of the Lantibiotic Lichenicidin to the Peptidoglycan Precursor Lipid II Predetermines Its Antimicrobial Activity. Int J Mol Sci 2023; 24:ijms24021332. [PMID: 36674846 PMCID: PMC9863751 DOI: 10.3390/ijms24021332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/21/2022] [Accepted: 01/06/2023] [Indexed: 01/12/2023] Open
Abstract
To date, a number of lantibiotics have been shown to use lipid II-a highly conserved peptidoglycan precursor in the cytoplasmic membrane of bacteria-as their molecular target. The α-component (Lchα) of the two-component lantibiotic lichenicidin, previously isolated from the Bacillus licheniformis VK21 strain, seems to contain two putative lipid II binding sites in its N-terminal and C-terminal domains. Using NMR spectroscopy in DPC micelles, we obtained convincing evidence that the C-terminal mersacidin-like site is involved in the interaction with lipid II. These data were confirmed by the MD simulations. The contact area of lipid II includes pyrophosphate and disaccharide residues along with the first isoprene units of bactoprenol. MD also showed the potential for the formation of a stable N-terminal nisin-like complex; however, the conditions necessary for its implementation in vitro remain unknown. Overall, our results clarify the picture of two component lantibiotics mechanism of antimicrobial action.
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Affiliation(s)
- Irina S. Panina
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Sergey V. Balandin
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Correspondence: ; Tel.: +7-495-335-0900
| | - Andrey V. Tsarev
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Anton O. Chugunov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Andrey A. Tagaev
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Ekaterina I. Finkina
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Daria V. Antoshina
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Elvira V. Sheremeteva
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Alexander S. Paramonov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Jasmin Rickmeyer
- Institute of Medical Microbiology, Immunology and Parasitology, Medical Faculty, University of Bonn, 53117 Bonn, Germany
| | - Gabriele Bierbaum
- Institute of Medical Microbiology, Immunology and Parasitology, Medical Faculty, University of Bonn, 53117 Bonn, Germany
| | - Roman G. Efremov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
- Department of Applied Mathematics, National Research University Higher School of Economics, 101000 Moscow, Russia
| | - Zakhar O. Shenkarev
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Tatiana V. Ovchinnikova
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
- Department of Bioorganic Chemistry, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
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6
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Guo E, Fu L, Fang X, Xie W, Li K, Zhang Z, Hong Z, Si T. Robotic Construction and Screening of Lanthipeptide Variant Libraries in Escherichia coli. ACS Synth Biol 2022; 11:3900-3911. [PMID: 36379012 DOI: 10.1021/acssynbio.2c00344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Lanthipeptides are a major class of ribosomally synthesized and post-translationally modified peptides (RiPPs) characterized by thioether cross-links called lanthionine (Lan) and methyllanthionine (MeLan). Previously, we developed a method to produce mature lanthipeptides in recombinant Escherichia coli, but manual steps hinder large-scale analogue screening. Here we devised an automated workflow for creating and screening variant libraries of haloduracin, a two-component class II lanthipeptide. An integrated work cell of a synthetic biology foundry was programmed to robotically execute DNA library construction, host transformation, peptide production, mass spectrometry analysis, and activity screening by agar diffusion assay. For recombinantly produced Halα peptides, the sequence-activity relationship of 380 single-residue variants and >1300 triple-residue combinatorial variants were rapidly analyzed in microplates within weeks. The peptide expression levels in E. coli were also visualized via robotic creation and analysis of GFP-lanthipeptide fusions for select peptide mutants. Following shake-flask fermentation and purification, one Halα mutant was confirmed with enhanced specific antimicrobial activity relative to the wild-type peptide. Overall, this approach may be generally applicable for the high-throughput characterization and engineering of RiPP natural products.
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Affiliation(s)
- Erpeng Guo
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,BGI-Shenzhen, Shenzhen 518083, China
| | - Lihao Fu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoting Fang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Wenhao Xie
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Keyi Li
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Zhiyu Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Zhilai Hong
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,BGI-Shenzhen, Shenzhen 518083, China
| | - Tong Si
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,BGI-Shenzhen, Shenzhen 518083, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Shenzhen 518055, China
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7
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Ongpipattanakul C, Desormeaux EK, DiCaprio A, van der Donk WA, Mitchell DA, Nair SK. Mechanism of Action of Ribosomally Synthesized and Post-Translationally Modified Peptides. Chem Rev 2022; 122:14722-14814. [PMID: 36049139 PMCID: PMC9897510 DOI: 10.1021/acs.chemrev.2c00210] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a natural product class that has undergone significant expansion due to the rapid growth in genome sequencing data and recognition that they are made by biosynthetic pathways that share many characteristic features. Their mode of actions cover a wide range of biological processes and include binding to membranes, receptors, enzymes, lipids, RNA, and metals as well as use as cofactors and signaling molecules. This review covers the currently known modes of action (MOA) of RiPPs. In turn, the mechanisms by which these molecules interact with their natural targets provide a rich set of molecular paradigms that can be used for the design or evolution of new or improved activities given the relative ease of engineering RiPPs. In this review, coverage is limited to RiPPs originating from bacteria.
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Affiliation(s)
- Chayanid Ongpipattanakul
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Emily K. Desormeaux
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Adam DiCaprio
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
| | - Wilfred A. van der Donk
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Department of Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Departments of Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA.,Corresponding authors Wilfred A. van der Donk, , 217-244-5360, Douglas A. Mitchell, , 217-333-1345, Satish K. Nair, , 217-333-0641
| | - Douglas A. Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Department of Microbiology, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Departments of Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA.,Corresponding authors Wilfred A. van der Donk, , 217-244-5360, Douglas A. Mitchell, , 217-333-1345, Satish K. Nair, , 217-333-0641
| | - Satish K. Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA.,Departments of Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, USA.,Corresponding authors Wilfred A. van der Donk, , 217-244-5360, Douglas A. Mitchell, , 217-333-1345, Satish K. Nair, , 217-333-0641
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Rosenbergová Z, Oftedal TF, Ovchinnikov KV, Thiyagarajah T, Rebroš M, Diep DB. Identification of a Novel Two-Peptide Lantibiotic from Vagococcus fluvialis. Microbiol Spectr 2022; 10:e0095422. [PMID: 35730941 PMCID: PMC9431498 DOI: 10.1128/spectrum.00954-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 05/24/2022] [Indexed: 11/20/2022] Open
Abstract
Infections caused by multiresistant pathogens have become a major problem in both human and veterinary medicine. Due to the declining efficacy of many antibiotics, new antimicrobials are needed. Promising alternatives or additions to antibiotics are bacteriocins, antimicrobial peptides of bacterial origin with activity against many pathogens, including antibiotic-resistant strains. From a sample of fermented maize, we isolated a Vagococcus fluvialis strain producing a bacteriocin with antimicrobial activity against multiresistant Enterococcus faecium. Whole-genome sequencing revealed the genes for a novel two-peptide lantibiotic. The production of the lantibiotic by the isolate was confirmed by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry, which revealed distinct peaks at 4,009.4 m/z and 3,181.7 m/z in separate fractions from reversed-phase chromatography. The combination of the two peptides resulted in a 1,200-fold increase in potency, confirming the two-peptide nature of the bacteriocin, named vagococcin T. The bacteriocin was demonstrated to kill sensitive cells by the formation of pores in the cell membrane, and its inhibition spectrum covers most Gram-positive bacteria, including multiresistant pathogens. To our knowledge, this is the first bacteriocin characterized from Vagococcus. IMPORTANCE Enterococci are common commensals in the intestines of humans and animals, but in recent years, they have been identified as one of the major causes of hospital-acquired infections due to their ability to quickly acquire virulence and antibiotic resistance determinants. Many hospital isolates are multiresistant, thereby making current therapeutic options critically limited. Novel antimicrobials or alternative therapeutic approaches are needed to overcome this global problem. Bacteriocins, natural ribosomally synthesized peptides produced by bacteria to eliminate other bacterial species living in a competitive environment, provide such an alternative. In this work, we purified and characterized a novel two-peptide lantibiotic produced by Vagococcus fluvialis LMGT 4216 isolated from fermented maize. The novel lantibiotic showed a broad spectrum of inhibition of Gram-positive strains, including vancomycin-resistant Enterococcus faecium, demonstrating its therapeutic potential.
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Affiliation(s)
- Zuzana Rosenbergová
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
- Institute of Biotechnology, Faculty of Chemical and Food Technology, Slovak University of Technology, Bratislava, Slovakia
| | - Thomas F. Oftedal
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Kirill V. Ovchinnikov
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Thasanth Thiyagarajah
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Martin Rebroš
- Institute of Biotechnology, Faculty of Chemical and Food Technology, Slovak University of Technology, Bratislava, Slovakia
| | - Dzung B. Diep
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
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9
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Mavalizadeh A, Fazlara A, PourMahdi M, Bavarsad N. The effect of separate and combined treatments of nisin, Rosmarinus officinalis essential oil (nanoemulsion and free form) and chitosan coating on the shelf life of refrigerated chicken fillets. JOURNAL OF FOOD MEASUREMENT AND CHARACTERIZATION 2022. [DOI: 10.1007/s11694-022-01541-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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10
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Ouali R, Vieira LR, Salmon D, Bousbata S. Rhodnius prolixus Hemolymph Immuno-Physiology: Deciphering the Systemic Immune Response Triggered by Trypanosoma cruzi Establishment in the Vector Using Quantitative Proteomics. Cells 2022; 11:1449. [PMID: 35563760 PMCID: PMC9104911 DOI: 10.3390/cells11091449] [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: 03/26/2022] [Revised: 04/20/2022] [Accepted: 04/22/2022] [Indexed: 12/10/2022] Open
Abstract
Understanding the development of Trypanosoma cruzi within the triatomine vector at the molecular level should provide novel targets for interrupting parasitic life cycle and affect vectorial competence. The aim of the current study is to provide new insights into triatomines immunology through the characterization of the hemolymph proteome of Rhodnius prolixus, a major Chagas disease vector, in order to gain an overview of its immune physiology. Surprisingly, proteomics investigation of the immunomodulation of T. cruzi-infected blood reveals that the parasite triggers an early systemic response in the hemolymph. The analysis of the expression profiles of hemolymph proteins from 6 h to 24 h allowed the identification of a broad range of immune proteins expressed already in the early hours post-blood-feeding regardless of the presence of the parasite, ready to mount a rapid response exemplified by the significant phenol oxidase activation. Nevertheless, we have also observed a remarkable induction of the immune response triggered by an rpPGRP-LC and the overexpression of defensins 6 h post-T. cruzi infection. Moreover, we have identified novel proteins with immune properties such as the putative c1q-like protein and the immunoglobulin I-set domain-containing protein, which have never been described in triatomines and could play a role in T. cruzi recognition. Twelve proteins with unknown function are modulated by the presence of T. cruzi in the hemolymph. Determining the function of these parasite-induced proteins represents an exciting challenge for increasing our knowledge about the diversity of the immune response from the universal one studied in holometabolous insects. This will provide us with clear answers for misunderstood mechanisms in host-parasite interaction, leading to the development of new generation strategies to control vector populations and pathogen transmission.
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Affiliation(s)
- Radouane Ouali
- Proteomic Plateform, Laboratory of Microbiology, Department of Molecular Biology, Université Libre de Bruxelles, 6041 Gosselies, Belgium
| | - Larissa Rezende Vieira
- Institute of Medical Biochemistry Leopoldo de Meis, Centro de Ciências e da Saúde, Federal University of Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (L.R.V.); (D.S.)
| | - Didier Salmon
- Institute of Medical Biochemistry Leopoldo de Meis, Centro de Ciências e da Saúde, Federal University of Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (L.R.V.); (D.S.)
| | - Sabrina Bousbata
- Proteomic Plateform, Laboratory of Microbiology, Department of Molecular Biology, Université Libre de Bruxelles, 6041 Gosselies, Belgium
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11
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Escobar‐Salom M, Torrens G, Jordana‐Lluch E, Oliver A, Juan C. Mammals' humoral immune proteins and peptides targeting the bacterial envelope: from natural protection to therapeutic applications against multidrug‐resistant
Gram
‐negatives. Biol Rev Camb Philos Soc 2022; 97:1005-1037. [PMID: 35043558 PMCID: PMC9304279 DOI: 10.1111/brv.12830] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 12/12/2021] [Accepted: 12/15/2021] [Indexed: 12/11/2022]
Abstract
Mammalian innate immunity employs several humoral ‘weapons’ that target the bacterial envelope. The threats posed by the multidrug‐resistant ‘ESKAPE’ Gram‐negative pathogens (Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) are forcing researchers to explore new therapeutic options, including the use of these immune elements. Here we review bacterial envelope‐targeting (peptidoglycan and/or membrane‐targeting) proteins/peptides of the mammalian immune system that are most likely to have therapeutic applications. Firstly we discuss their general features and protective activity against ESKAPE Gram‐negatives in the host. We then gather, integrate, and discuss recent research on experimental therapeutics harnessing their bactericidal power, based on their exogenous administration and also on the discovery of bacterial and/or host targets that improve the performance of this endogenous immunity, as a novel therapeutic concept. We identify weak points and knowledge gaps in current research in this field and suggest areas for future work to obtain successful envelope‐targeting therapeutic options to tackle the challenge of antimicrobial resistance.
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Affiliation(s)
- María Escobar‐Salom
- Department of Microbiology University Hospital Son Espases‐Health Research Institute of the Balearic Islands (IdISBa) Carretera de Valldemossa 79 Palma Balearic Islands 07010 Spain
| | - Gabriel Torrens
- Department of Microbiology University Hospital Son Espases‐Health Research Institute of the Balearic Islands (IdISBa) Carretera de Valldemossa 79 Palma Balearic Islands 07010 Spain
| | - Elena Jordana‐Lluch
- Department of Microbiology University Hospital Son Espases‐Health Research Institute of the Balearic Islands (IdISBa) Carretera de Valldemossa 79 Palma Balearic Islands 07010 Spain
| | - Antonio Oliver
- Department of Microbiology University Hospital Son Espases‐Health Research Institute of the Balearic Islands (IdISBa) Carretera de Valldemossa 79 Palma Balearic Islands 07010 Spain
| | - Carlos Juan
- Department of Microbiology University Hospital Son Espases‐Health Research Institute of the Balearic Islands (IdISBa) Carretera de Valldemossa 79 Palma Balearic Islands 07010 Spain
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Multidrug resistance crisis during COVID-19 pandemic: Role of anti-microbial peptides as next-generation therapeutics. Colloids Surf B Biointerfaces 2021; 211:112303. [PMID: 34952285 PMCID: PMC8685351 DOI: 10.1016/j.colsurfb.2021.112303] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 12/03/2021] [Accepted: 12/16/2021] [Indexed: 02/07/2023]
Abstract
The decreasing effectiveness of conventional drugs due to multidrug-resistance is a major challenge for the scientific community, necessitating development of novel antimicrobial agents. In the present era of coronavirus 2 (COVID-19) pandemic, patients are being widely exposed to antimicrobial drugs and hence the problem of multidrug-resistance shall be aggravated in the days to come. Consequently, revisiting the phenomena of multidrug resistance leading to formulation of effective antimicrobial agents is the need of the hour. As a result, this review sheds light on the looming crisis of multidrug resistance in wake of the COVID-19 pandemic. It highlights the problem, significance and approaches for tackling microbial resistance with special emphasis on anti-microbial peptides as next-generation therapeutics against multidrug resistance associated diseases. Antimicrobial peptides exhibit exceptional mechanism of action enabling rapid killing of microbes at low concentration, antibiofilm activity, immunomodulatory properties along with a low tendency for resistance development providing them an edge over conventional antibiotics. The review is unique as it discusses the mode of action, pharmacodynamic properties and application of antimicrobial peptides in areas ranging from therapeutics to agriculture.
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13
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Zhu S, Gao B, Umetsu Y, Peigneur S, Li P, Ohki S, Tytgat J. Adaptively evolved human oral actinomyces-sourced defensins show therapeutic potential. EMBO Mol Med 2021; 14:e14499. [PMID: 34927385 PMCID: PMC8819291 DOI: 10.15252/emmm.202114499] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 11/29/2021] [Accepted: 12/03/2021] [Indexed: 12/12/2022] Open
Abstract
The development of eukaryote‐derived antimicrobial peptides as systemically administered drugs has proven a challenging task. Here, we report the first human oral actinomyces‐sourced defensin—actinomycesin—that shows promise for systemic therapy. Actinomycesin and its homologs are only present in actinobacteria and myxobacteria, and share similarity with a group of ancient invertebrate‐type defensins reported in fungi and invertebrates. Signatures of natural selection were detected in defensins from the actinomyces colonized in human oral cavity and ruminant rumen and dental plaque, highlighting their role in adaptation to complex multispecies bacterial communities. Consistently, actinomycesin exhibited potent antibacterial activity against oral bacteria and clinical isolates of Staphylococcus and synergized with two classes of human salivary antibacterial factors. Actinomycesin specifically inhibited bacterial peptidoglycan synthesis and displayed weak immunomodulatory activity and low toxicity on human and mammalian cells and ion channels in the heart and central nervous system. Actinomycesin was highly efficient in mice infected with Streptococcus pneumoniae and mice with MRSA‐induced experimental peritoneal infection. This work identifies human oral bacteria as a new source of systemic anti‐infective drugs.
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Affiliation(s)
- Shunyi Zhu
- Group of Peptide Biology and Evolution, State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Bin Gao
- Group of Peptide Biology and Evolution, State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yoshitaka Umetsu
- Center for Nano Materials and Technology (CNMT), Japan Advanced Institute of Science and Technology (JAIST), Nomi, Japan
| | - Steve Peigneur
- Toxicology and Pharmacology, University of Leuven, Leuven, Belgium
| | - Ping Li
- Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety (Chinese Academy of Sciences), National Center for Nanoscience and Technology, Beijing, China
| | - Shinya Ohki
- Center for Nano Materials and Technology (CNMT), Japan Advanced Institute of Science and Technology (JAIST), Nomi, Japan
| | - Jan Tytgat
- Toxicology and Pharmacology, University of Leuven, Leuven, Belgium
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Pokhrel R, Bhattarai N, Baral P, Gerstman BS, Park JH, Handfield M, Chapagain PP. Lipid II Binding and Transmembrane Properties of Various Antimicrobial Lanthipeptides. J Chem Theory Comput 2021; 18:516-525. [PMID: 34874159 DOI: 10.1021/acs.jctc.1c00666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
There has been an alarming rise in antibacterial resistant infections in recent years due to the widespread use of antibiotics, and there is a dire need for the development of new antibiotics utilizing novel modes of action. Lantibiotics are promising candidates to engage in the fight against resistant strains of bacteria due to their unique modes of action, including interference with cell wall synthesis by binding to lipid II and creating pores in bacterial membranes. In this study, we use atomic-scale molecular dynamics computational studies to compare both the lipid II binding ability and the membrane interactions of five lanthipeptides that are commonly used in antimicrobial research: nisin, Mutacin 1140 (MU1140), gallidermin, NVB302, and NAI107. Among the five peptides investigated, nisin is found to be the most efficient at forming water channels through a membrane, whereas gallidermin and MU1140 are found to be better at binding the lipid II molecules. Nisin's effectiveness in facilitating water transport across the membrane is due to the creation of several different water trajectories along with no significant water delay points along the paths. The shorter peptide deoxyactagardine B (NVB302) was found to not form a water channel. These detailed observations provide insights into the dual mechanisms of the action of lantibiotic peptides and can facilitate the design and development of novel lanthipeptides by strategic placement of different residues.
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Affiliation(s)
| | | | | | | | - Jae H Park
- Oragenics Inc., Alachua, Florida 32615, United States
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15
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Molecular Dynamics Insight into the Lipid II Recognition by Type A Lantibiotics: Nisin, Epidermin, and Gallidermin. MICROMACHINES 2021; 12:mi12101169. [PMID: 34683220 PMCID: PMC8538299 DOI: 10.3390/mi12101169] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/24/2021] [Accepted: 09/25/2021] [Indexed: 01/21/2023]
Abstract
Lanthionine-containing peptides (lantibiotics) have been considered as pharmaceutical candidates for decades, although their clinical application has been restricted. Most lantibiotics kill bacteria via targeting and segregating of the cell wall precursor—membrane-inserted lipid II molecule—in some cases accompanied by pores formation. Nisin-like lantibiotics specifically bind to pyrophosphate (PPi) moiety of lipid II with their structurally similar N-terminal thioether rings A and B. Although possessing higher pore-forming capability, nisin, in some cases, is 10-fold less efficient in vivo as compared to related epidermin and gallidermin peptides, differing just in a few amino acid residues within their target-binding regions. Here, using molecular dynamics simulations, we investigated atomistic details of intermolecular interactions between the truncated analogues of these peptides (residues 1–12) and lipid II mimic (dimethyl pyrophosphate, DMPPi). The peptides adopt similar conformation upon DMPPi binding with backbone amide protons orienting into a single center capturing PPi moiety via simultaneous formation of up to seven hydrogen bonds. Epidermin and gallidermin adopt the complex-forming conformation twice as frequent as nisin does, enhancing the binding by the lysine 4 side chain. Introduction of the similar residue to nisin in silico improves the binding, providing ideas for further design of prototypic antibiotics.
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16
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Gao B, Zhu S. A Fungal Defensin Targets the SARS-CoV-2 Spike Receptor-Binding Domain. J Fungi (Basel) 2021; 7:553. [PMID: 34356932 PMCID: PMC8304516 DOI: 10.3390/jof7070553] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/07/2021] [Accepted: 07/09/2021] [Indexed: 02/07/2023] Open
Abstract
Coronavirus Disease 2019 (COVID-19) elicited by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is calling for novel targeted drugs. Since the viral entry into host cells depends on specific interactions between the receptor-binding domain (RBD) of the viral Spike protein and the membrane-bound monocarboxypeptidase angiotensin converting enzyme 2 (ACE2), the development of high affinity RBD binders to compete with human ACE2 represents a promising strategy for the design of therapeutics to prevent viral entry. Here, we report the discovery of such a binder and its improvement via a combination of computational and experimental approaches. The binder micasin, a known fungal defensin from the dermatophytic fungus Microsporum canis with antibacterial activity, can dock to the crevice formed by the receptor-binding motif (RBM) of RBD via an extensive shape complementarity interface (855.9 Å2 in area) with numerous hydrophobic and hydrogen-bonding interactions. Using microscale thermophoresis (MST) technique, we confirmed that micasin and its C-terminal γ-core derivative with multiple predicted interacting residues exhibited a low micromolar affinity to RBD. Expanding the interface area of micasin through a single point mutation to 970.5 Å2 accompanying an enhanced hydrogen bond network significantly improved its binding affinity by six-fold. Our work highlights the naturally occurring fungal defensins as an emerging resource that may be suitable for the development into antiviral agents for COVID-19.
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Affiliation(s)
| | - Shunyi Zhu
- Group of Peptide Biology and Evolution, State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101, China;
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17
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Abstract
Lanthipeptides are a class of ribosomally synthesized and posttranslationally modified peptide (RiPP) natural products characterized by the presence of lanthionine and methyllanthionine. During the maturation of select lanthipeptides, five different alterations have been observed to the chemical structure of the peptide backbone. First, dehydratases generate dehydroalanine and dehydrobutyrine from Ser or Thr residues, respectively. A second example of introduction of unsaturation is the oxidative decarboxylation of C-terminal Cys residues catalyzed by the decarboxylase LanD. Both modifications result in loss of chirality at the α-carbon of the amino acid residues. Attack of a cysteine thiol onto a dehydrated amino acid results in thioether crosslink formation with either inversion or retention of the l-stereochemical configuration at the α-carbon of former Ser and Thr residues. A fourth modification of the protein backbone is the hydrogenation of dehydroamino acids to afford d-amino acids catalyzed by NAD(P)H-dependent reductases. A fifth modification is the conversion of Asp to isoAsp. Herein, the methods used to produce and characterize the lanthipeptide bicereucin will be described in detail along with a brief overview of other lanthipeptides.
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Affiliation(s)
- Richard S Ayikpoe
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Wilfred A van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL, United States.
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18
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Wang Y, Zhang J, Sun Y, Sun L. A Crustin from Hydrothermal Vent Shrimp: Antimicrobial Activity and Mechanism. Mar Drugs 2021; 19:176. [PMID: 33807037 PMCID: PMC8005205 DOI: 10.3390/md19030176] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 12/15/2022] Open
Abstract
Crustin is a type of antimicrobial peptide and plays an important role in the innate immunity of arthropods. We report here the identification and characterization of a crustin (named Crus1) from the shrimp Rimicaris sp. inhabiting the deep-sea hydrothermal vent in Manus Basin (Papua New Guinea). Crus1 shares the highest identity (51.76%) with a Type I crustin of Penaeus vannamei and possesses a whey acidic protein (WAP) domain, which contains eight cysteine residues that form the conserved 'four-disulfide core' structure. Recombinant Crus1 (rCrus1) bound to peptidoglycan and lipoteichoic acid, and effectively killed Gram-positive bacteria in a manner that was dependent on pH, temperature, and disulfide linkage. rCrus1 induced membrane leakage and structure damage in the target bacteria, but had no effect on bacterial protoplasts. Serine substitution of each of the 8 Cys residues in the WAP domain did not affect the bacterial binding capacity but completely abolished the bactericidal activity of rCrus1. These results provide new insights into the characteristic and mechanism of the antimicrobial activity of deep sea crustins.
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Affiliation(s)
- Yujian Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; (Y.W.); (J.Z.); (Y.S.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; (Y.W.); (J.Z.); (Y.S.)
- School of Ocean, Yantai University, Yantai 264005, China
| | - Yuanyuan Sun
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; (Y.W.); (J.Z.); (Y.S.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
| | - Li Sun
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; (Y.W.); (J.Z.); (Y.S.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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Reiners J, Lagedroste M, Gottstein J, Adeniyi ET, Kalscheuer R, Poschmann G, Stühler K, Smits SHJ, Schmitt L. Insights in the Antimicrobial Potential of the Natural Nisin Variant Nisin H. Front Microbiol 2020; 11:573614. [PMID: 33193179 PMCID: PMC7606277 DOI: 10.3389/fmicb.2020.573614] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 09/25/2020] [Indexed: 11/17/2022] Open
Abstract
Lantibiotics are a growing class of antimicrobial peptides, which possess antimicrobial activity against mainly Gram-positive bacteria including the highly resistant strains such as methicillin-resistant Staphylococcus aureus or vancomycin-resistant enterococci. In the last decades numerous lantibiotics were discovered in natural habitats or designed with bioengineering tools. In this study, we present an insight in the antimicrobial potential of the natural occurring lantibiotic nisin H from Streptococcus hyointestinalis as well as the variant nisin H F1I. We determined the yield of the heterologously expressed peptide and quantified the cleavage efficiency employing the nisin protease NisP. Furthermore, we analyzed the effect on the modification via mass spectrometry analysis. With standardized growth inhibition assays we benchmarked the activity of pure nisin H and the variant nisin H F1I, and their influence on the activity of the nisin immunity proteins NisI and NisFEG from Lactococcus lactis and the nisin resistance proteins SaNSR and SaNsrFP from Streptococcus agalactiae COH1. We further checked the antibacterial activity against clinical isolates of Staphylococcus aureus, Enterococcus faecium and Enterococcus faecalis via microdilution method. In summary, nisin H and the nisin H F1I variant possessed better antimicrobial potency than the natural nisin A.
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Affiliation(s)
- Jens Reiners
- Institute of Biochemistry, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany.,Center for Structural Studies, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Marcel Lagedroste
- Institute of Biochemistry, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Julia Gottstein
- Institute of Biochemistry, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Emmanuel T Adeniyi
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Rainer Kalscheuer
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Gereon Poschmann
- Institute for Molecular Medicine, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Kai Stühler
- Institute for Molecular Medicine, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany.,Molecular Proteomics Laboratory, BMFZ, Heinrich-Heine-University-Düsseldorf, Düsseldorf, Germany
| | - Sander H J Smits
- Institute of Biochemistry, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany.,Center for Structural Studies, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
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20
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Revilla-Guarinos A, Zhang Q, Loderer C, Alcántara C, Müller A, Rahnamaeian M, Vilcinskas A, Gebhard S, Zúñiga M, Mascher T. ABC Transporter DerAB of Lactobacillus casei Mediates Resistance against Insect-Derived Defensins. Appl Environ Microbiol 2020; 86:e00818-20. [PMID: 32414796 PMCID: PMC7357469 DOI: 10.1128/aem.00818-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 05/09/2020] [Indexed: 01/28/2023] Open
Abstract
Bce-like systems mediate resistance against antimicrobial peptides in Firmicutes bacteria. Lactobacillus casei BL23 encodes an "orphan" ABC transporter that, based on homology to BceAB-like systems, was proposed to contribute to antimicrobial peptide resistance. A mutant lacking the permease subunit was tested for sensitivity against a collection of peptides derived from bacteria, fungi, insects, and humans. Our results show that the transporter specifically conferred resistance against insect-derived cysteine-stabilized αβ defensins, and it was therefore renamed DerAB for defensin resistance ABC transporter. Surprisingly, cells lacking DerAB showed a marked increase in resistance against the lantibiotic nisin. This could be explained by significantly increased expression of the antimicrobial peptide resistance determinants regulated by the Bce-like systems PsdRSAB (formerly module 09) and ApsRSAB (formerly module 12). Bacterial two-hybrid studies in Escherichia coli showed that DerB could interact with proteins of the sensory complex in the Psd resistance system. We therefore propose that interaction of DerAB with this complex in the cell creates signaling interference and reduces the cell's potential to mount an effective nisin resistance response. In the absence of DerB, this negative interference is relieved, leading to the observed hyperactivation of the Psd module and thus increased resistance to nisin. Our results unravel the function of a previously uncharacterized Bce-like orphan resistance transporter with pleiotropic biological effects on the cell.IMPORTANCE Antimicrobial peptides (AMPs) play an important role in suppressing the growth of microorganisms. They can be produced by bacteria themselves-to inhibit competitors-but are also widely distributed in higher eukaryotes, including insects and mammals, where they form an important component of innate immunity. In low-GC-content Gram-positive bacteria, BceAB-like transporters play a crucial role in AMP resistance but have so far been primarily associated with interbacterial competition. Here, we show that the orphan transporter DerAB from the lactic acid bacterium Lactobacillus casei is crucial for high-level resistance against insect-derived AMPs. It therefore represents an important mechanism for interkingdom defense. Furthermore, our results support a signaling interference from DerAB on the PsdRSAB module that might prevent the activation of a full nisin response. The Bce modules from L. casei BL23 illustrate a biological paradox in which the intrinsic nisin detoxification potential only arises in the absence of a defensin-specific ABC transporter.
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Affiliation(s)
| | - Qian Zhang
- Institut für Mikrobiologie, Technische Universität Dresden, Dresden, Germany
| | - Christoph Loderer
- Institut für Mikrobiologie, Technische Universität Dresden, Dresden, Germany
| | - Cristina Alcántara
- Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Valencia, Spain
| | - Ariane Müller
- Institut für Zoologie, Technische Universität Dresden, Dresden, Germany
| | - Mohammad Rahnamaeian
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Department of Bioresources, Giessen, Germany
| | - Andreas Vilcinskas
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Department of Bioresources, Giessen, Germany
- Institute for Insect Biotechnology, Justus Liebig University Giessen, Giessen, Germany
| | - Susanne Gebhard
- Department of Biology and Biochemistry, Milner Centre for Evolution, University of Bath, United Kingdom
| | - Manuel Zúñiga
- Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Valencia, Spain
| | - Thorsten Mascher
- Institut für Mikrobiologie, Technische Universität Dresden, Dresden, Germany
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Sui X, Huang G, Ezzat N, Yuan Y. A concise and scalable synthesis of a novel l-allo-enduracididine derivative. Tetrahedron Lett 2020. [DOI: 10.1016/j.tetlet.2020.152148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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22
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The Killing Mechanism of Teixobactin against Methicillin-Resistant Staphylococcus aureus: an Untargeted Metabolomics Study. mSystems 2020; 5:5/3/e00077-20. [PMID: 32457238 PMCID: PMC7253363 DOI: 10.1128/msystems.00077-20] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Antimicrobial resistance is one of the greatest threats to the global health system. It is imperative that new anti-infective therapeutics be developed against problematic “superbugs.” The cyclic depsipeptide teixobactin holds much promise as a new class of antibiotics for highly resistant Gram-positive pathogens (e.g., methicillin-resistant Staphylococcus aureus [MRSA]). Understanding its molecular mechanism(s) of action could lead to the design of new compounds with a broader activity spectrum. Here, we describe the first metabolomics study to investigate the killing mechanism(s) of teixobactin against MRSA. Our findings revealed that teixobactin significantly disorganized the bacterial cell envelope, as reflected by a profound perturbation in the bacterial membrane lipids and cell wall biosynthesis (peptidoglycan and teichoic acid). Importantly, teixobactin significantly suppressed the main intermediate d-alanyl-d-lactate involved in the mechanism of vancomycin resistance in S. aureus. These novel results help explain the unique mechanism of action of teixobactin and its lack of cross-resistance with vancomycin. Antibiotics have served humankind through their use in modern medicine as effective treatments for otherwise fatal bacterial infections. Teixobactin is a first member of newly discovered natural antibiotics that was recently identified from a hitherto-unculturable soil bacterium, Eleftheria terrae, and recognized as a potent antibacterial agent against various Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci. The most distinctive characteristic of teixobactin as an effective antibiotic is that teixobactin resistance could not be evolved in a laboratory setting. It is purported that teixobactin’s “resistance-resistant” mechanism of action includes binding to the essential bacterial cell wall synthesis building blocks lipid II and lipid III. In the present study, metabolomics was used to investigate the potential metabolic pathways involved in the mechanisms of antibacterial activity of the synthetic teixobactin analogue Leu10-teixobactin against a MRSA strain, S. aureus ATCC 700699. The metabolomes of S. aureus ATCC 700699 cells 1, 3, and 6 h following treatment with Leu10-teixobactin (0.5 μg/ml, i.e., 0.5× MIC) were compared to those of the untreated controls. Leu10-teixobactin significantly perturbed bacterial membrane lipids (glycerophospholipids and fatty acids), peptidoglycan (lipid I and II) metabolism, and cell wall teichoic acid (lipid III) biosynthesis as early as after 1 h of treatment, reflecting an initial activity on the cell envelope. Concordant with its time-dependent antibacterial killing action, Leu10-teixobactin caused more perturbations in the levels of key intermediates in pathways of amino-sugar and nucleotide-sugar metabolism and their downstream peptidoglycan and teichoic acid biosynthesis at 3 and 6 h. Significant perturbations in arginine metabolism and the interrelated tricarboxylic acid cycle, histidine metabolism, pantothenate, and coenzyme A biosynthesis were also observed at 3 and 6 h. To conclude, this is the first study to provide novel metabolomics mechanistic information, which lends support to the development of teixobactin as an antibacterial drug for the treatment of multidrug-resistant Gram-positive infections. IMPORTANCE Antimicrobial resistance is one of the greatest threats to the global health system. It is imperative that new anti-infective therapeutics be developed against problematic “superbugs.” The cyclic depsipeptide teixobactin holds much promise as a new class of antibiotics for highly resistant Gram-positive pathogens (e.g., methicillin-resistant Staphylococcus aureus [MRSA]). Understanding its molecular mechanism(s) of action could lead to the design of new compounds with a broader activity spectrum. Here, we describe the first metabolomics study to investigate the killing mechanism(s) of teixobactin against MRSA. Our findings revealed that teixobactin significantly disorganized the bacterial cell envelope, as reflected by a profound perturbation in the bacterial membrane lipids and cell wall biosynthesis (peptidoglycan and teichoic acid). Importantly, teixobactin significantly suppressed the main intermediate d-alanyl-d-lactate involved in the mechanism of vancomycin resistance in S. aureus. These novel results help explain the unique mechanism of action of teixobactin and its lack of cross-resistance with vancomycin.
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23
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Cancelarich NL, Wilke N, Fanani MAL, Moreira DC, Pérez LO, Alves Barbosa E, Plácido A, Socodato R, Portugal CC, Relvas JB, de la Torre BG, Albericio F, Basso NG, Leite JR, Marani MM. Somuncurins: Bioactive Peptides from the Skin of the Endangered Endemic Patagonian Frog Pleurodema somuncurense. JOURNAL OF NATURAL PRODUCTS 2020; 83:972-984. [PMID: 32134261 DOI: 10.1021/acs.jnatprod.9b00906] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The skin glands of amphibian species hold a major component of their innate immunity, namely a unique set of antimicrobial peptides (AMPs). Although most of them have common characteristics, differences in AMP sequences allow a huge repertoire of biological activity with varying degrees of efficacy. We present the first study of the AMPs from Pleurodema somuncurence (Anura: Leptodactylidae: Leiuperinae). Among the 11 identified mature peptides, three presented antimicrobial activity. Somuncurin-1 (FIIWPLRYRK), somuncurin-2 (FILKRSYPQYY), and thaulin-3 (NLVGSLLGGILKK) inhibited Escherichia coli growth. Somuncurin-1 also showed antimicrobial activity against Staphylococcus aureus. Biophysical membrane model studies revealed that this peptide had a greater permeation effect in prokaryotic-like membranes and capacity to restructure liposomes, suggesting fusogenic activity, which could lead to cell aggregation and disruption of cell morphology. This study contributes to the characterization of peptides with new sequences to enrich the databases for the design of therapeutic agents. Furthermore, it highlights the importance of investing in nature conservation and the power of genetic description as a strategy to identify new compounds.
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Affiliation(s)
- Natalia L Cancelarich
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales, Consejo Nacional de Investigaciones Cientı́ficas y Técnicas (IPEEC-CONICET), Bv. Almirante Brown 2915, Puerto Madryn U9120ACD, Argentina
| | - Natalia Wilke
- Departamento de Quı́mica Biológica Ranwel Caputto, Facultad de Ciencias Quı́micas, Universidad Nacional de Córdoba, Córdoba 5016, Argentina
- Centro de Investigaciones en Quı́mica Biológica de Córdoba, CONICET, Ciudad Universitaria, Haya de la Torre y Medina Allende, Córdoba X5000HUA, Argentina
| | - Marı A L Fanani
- Departamento de Quı́mica Biológica Ranwel Caputto, Facultad de Ciencias Quı́micas, Universidad Nacional de Córdoba, Córdoba 5016, Argentina
- Centro de Investigaciones en Quı́mica Biológica de Córdoba, CONICET, Ciudad Universitaria, Haya de la Torre y Medina Allende, Córdoba X5000HUA, Argentina
| | - Daniel C Moreira
- Área de Morfologia, Faculdade de Medicina, Universidade de Brası́lia, Brası́lia 70910-900, Brazil
| | - Luis O Pérez
- Instituto Patagónico de Ciencias Sociales y Humanas, Consejo Nacional de Investigaciones Cientı́ficas y Técnicas (IPCSH-CONICET), Bv. Almirante Brown 2915, Puerto Madryn U9120ACD, Argentina
| | - Eder Alves Barbosa
- Laboratório de Espectrometria de Massa, EMBRAPA Recursos Genéticos e Biotecnologia, Brası́lia 70770-917, Brazil
- Laboratório de Sı́ntese e Análise de Biomoléculas, Instituto de Quı́mica, Universidade de Brası́lia, Brası́lia 70910-900, Brazil
| | - Alexandra Plácido
- LAQV/REQUIMTE, Departamento de Quı́mica e Bioquı́mica, Faculdade de Ciéncias da Universidade do Porto, 4169-007 Porto, Portugal
- Instituto de Investigação e Inovação em Saúde and Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen, 208 4200-135 Porto, Portugal
| | - Renato Socodato
- Instituto de Investigação e Inovação em Saúde and Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen, 208 4200-135 Porto, Portugal
| | - Camila C Portugal
- Instituto de Investigação e Inovação em Saúde and Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen, 208 4200-135 Porto, Portugal
| | - João B Relvas
- Instituto de Investigação e Inovação em Saúde and Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen, 208 4200-135 Porto, Portugal
| | - Beatriz G de la Torre
- KwaZulu-Natal Research Innovation and Sequencing Platform, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Fernando Albericio
- KwaZulu-Natal Research Innovation and Sequencing Platform, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
- CIBER-BBN (Networking Centre on Bioengineering, Biomaterials and Nanomedicine) and Department of Organic Chemistry, University of Barcelona, 08028 Barcelona, Spain
| | - Néstor G Basso
- Instituto de Diversidad y Evolución Austral, Consejo Nacional de Investigaciones Cientı́ficas y Técnicas (IDEAus-CONICET), Bv. Almirante Brown 2915, Puerto Madryn U9120ACD, Argentina
| | - José R Leite
- Área de Morfologia, Faculdade de Medicina, Universidade de Brası́lia, Brası́lia 70910-900, Brazil
| | - Mariela M Marani
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales, Consejo Nacional de Investigaciones Cientı́ficas y Técnicas (IPEEC-CONICET), Bv. Almirante Brown 2915, Puerto Madryn U9120ACD, Argentina
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24
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Fluorescence anisotropy assays for high throughput screening of compounds binding to lipid II, PBP1b, FtsW and MurJ. Sci Rep 2020; 10:6280. [PMID: 32286439 PMCID: PMC7156629 DOI: 10.1038/s41598-020-63380-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 03/30/2020] [Indexed: 12/03/2022] Open
Abstract
Lipid II precursor and its processing by a flippase and peptidoglycan polymerases are considered key hot spot targets for antibiotics. We have developed a fluorescent anisotropy (FA) assay using a unique and versatile probe (fluorescent lipid II) and monitored direct binding between lipid II and interacting proteins (PBP1b, FtsW and MurJ), as well as between lipid II and interacting antibiotics (vancomycin, nisin, ramoplanin and a small molecule). Competition experiments performed using unlabelled lipid II, four lipid II-binding antibiotics and moenomycin demonstrate that the assay can detect compounds interacting with lipid II or the proteins. These results provide a proof-of-concept for the use of this assay in a high-throughput screening of compounds against all these targets. In addition, the assay constitutes a powerful tool in the study of the mode of action of compounds that interfere with these processes. Interestingly, FA assay with lipid II probe has the advantage over moenomycin based probe to potentially identify compounds that interfere with both donor and acceptor sites of the aPBPs GTase as well as compounds that bind to lipid II. In addition, this assay would allow the screening of compounds against SEDS proteins and MurJ which do not interact with moenomycin.
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25
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Barbour A, Wescombe P, Smith L. Evolution of Lantibiotic Salivaricins: New Weapons to Fight Infectious Diseases. Trends Microbiol 2020; 28:578-593. [PMID: 32544444 DOI: 10.1016/j.tim.2020.03.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 01/20/2020] [Accepted: 03/09/2020] [Indexed: 02/06/2023]
Abstract
Lantibiotic salivaricins are polycyclic peptides containing lanthionine and/or β-methyllanthionine residues produced by certain strains of Streptococcus salivarius, which almost exclusively reside in the human oral cavity. The importance of these molecules stems from their antimicrobial activity towards relevant oral pathogens which has so far been applied through the development of salivaricin-producing probiotic strains. However, salivaricins may also prove to be of great value in the development of new and novel antibacterial therapies in this era of emerging antibiotic resistance. In this review, we describe the biosynthesis, antimicrobial activity, structure, and mode of action of the lantibiotic salivaricins characterized to date. Moreover, we also provide an expert opinion and suggestions for future development of this important field of microbiology.
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Affiliation(s)
| | - Philip Wescombe
- Yili Innovation Center Oceania, Lincoln University, Christchurch, New Zealand
| | - Leif Smith
- Department of Biology, College of Science, Texas A&M University, College Station, TX, USA
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26
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Ajingi YS, Ruengvisesh S, Khunrae P, Rattanarojpong T, Jongruja N. The combined effect of formic acid and Nisin on potato spoilage. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2020. [DOI: 10.1016/j.bcab.2020.101523] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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27
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Kietzman C, Tuomanen E. Acute Bacterial Meningitis: Challenges to Better Antibiotic Therapy. ACS Infect Dis 2019; 5:1987-1995. [PMID: 31268283 DOI: 10.1021/acsinfecdis.9b00122] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Bacterial meningitis is a medical emergency requiring highly bactericidal antibiotics to achieve cure. Many challenges exist to achieving optimal patient outcome. First, antibiotics must pass the blood brain barrier. Once in the subarachnoid space, achieving bactericidal therapy involves circumventing antibiotic resistance and, more commonly, antibiotic tolerance arising from the slow growth of bacteria in the nutrient poor cerebrospinal fluid. Finally, bactericidal therapy is most often bacteriolytic, and debris from lysis is highly inflammatory. Controlling damage from lytic products may require adjunctive therapy to prevent neuronal death. These challenges are an extreme example of the different requirements for treating infections in different body sites.
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Affiliation(s)
- Colin Kietzman
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Elaine Tuomanen
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
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28
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A small-molecule inhibitor of BamA impervious to efflux and the outer membrane permeability barrier. Proc Natl Acad Sci U S A 2019; 116:21748-21757. [PMID: 31591200 DOI: 10.1073/pnas.1912345116] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The development of new antimicrobial drugs is a priority to combat the increasing spread of multidrug-resistant bacteria. This development is especially problematic in gram-negative bacteria due to the outer membrane (OM) permeability barrier and multidrug efflux pumps. Therefore, we screened for compounds that target essential, nonredundant, surface-exposed processes in gram-negative bacteria. We identified a compound, MRL-494, that inhibits assembly of OM proteins (OMPs) by the β-barrel assembly machine (BAM complex). The BAM complex contains one essential surface-exposed protein, BamA. We constructed a bamA mutagenesis library, screened for resistance to MRL-494, and identified the mutation bamA E470K BamAE470K restores OMP biogenesis in the presence of MRL-494. The mutant protein has both altered conformation and activity, suggesting it could either inhibit MRL-494 binding or allow BamA to function in the presence of MRL-494. By cellular thermal shift assay (CETSA), we determined that MRL-494 stabilizes BamA and BamAE470K from thermally induced aggregation, indicating direct or proximal binding to both BamA and BamAE470K Thus, it is the altered activity of BamAE470K responsible for resistance to MRL-494. Strikingly, MRL-494 possesses a second mechanism of action that kills gram-positive organisms. In microbes lacking an OM, MRL-494 lethally disrupts the cytoplasmic membrane. We suggest that the compound cannot disrupt the cytoplasmic membrane of gram-negative bacteria because it cannot penetrate the OM. Instead, MRL-494 inhibits OMP biogenesis from outside the OM by targeting BamA. The identification of a small molecule that inhibits OMP biogenesis at the cell surface represents a distinct class of antibacterial agents.
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29
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Small-molecule inhibitors of nisin resistance protein NSR from the human pathogen Streptococcus agalactiae. Bioorg Med Chem 2019; 27:115079. [DOI: 10.1016/j.bmc.2019.115079] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 07/31/2019] [Accepted: 08/25/2019] [Indexed: 11/19/2022]
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30
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Dickman R, Mitchell SA, Figueiredo AM, Hansen DF, Tabor AB. Molecular Recognition of Lipid II by Lantibiotics: Synthesis and Conformational Studies of Analogues of Nisin and Mutacin Rings A and B. J Org Chem 2019; 84:11493-11512. [PMID: 31464129 PMCID: PMC6759747 DOI: 10.1021/acs.joc.9b01253] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Indexed: 12/12/2022]
Abstract
In response to the growing threat posed by antibiotic-resistant bacterial strains, extensive research is currently focused on developing antimicrobial agents that target lipid II, a vital precursor in the biosynthesis of bacterial cell walls. The lantibiotic nisin and related peptides display unique and highly selective binding to lipid II. A key feature of the nisin-lipid II interaction is the formation of a cage-like complex between the pyrophosphate moiety of lipid II and the two thioether-bridged rings, rings A and B, at the N-terminus of nisin. To understand the important structural factors underlying this highly selective molecular recognition, we have used solid-phase peptide synthesis to prepare individual ring A and B structures from nisin, the related lantibiotic mutacin, and synthetic analogues. Through NMR studies of these rings, we have demonstrated that ring A is preorganized to adopt the correct conformation for binding lipid II in solution and that individual amino acid substitutions in ring A have little effect on the conformation. We have also analyzed the turn structures adopted by these thioether-bridged peptides and show that they do not adopt the tight α-turn or β-turn structures typically found in proteins.
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Affiliation(s)
- Rachael Dickman
- Department
of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K.
| | - Serena A. Mitchell
- Department
of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K.
| | - Angelo M. Figueiredo
- Institute
of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, U.K.
| | - D. Flemming Hansen
- Institute
of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, U.K.
| | - Alethea B. Tabor
- Department
of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K.
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31
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Malin JJ, de Leeuw E. Therapeutic compounds targeting Lipid II for antibacterial purposes. Infect Drug Resist 2019; 12:2613-2625. [PMID: 31692545 PMCID: PMC6711568 DOI: 10.2147/idr.s215070] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 07/29/2019] [Indexed: 12/18/2022] Open
Abstract
Resistance against commonly used antibiotics has emerged in all bacterial pathogens. In fact, there is no antibiotic currently in clinical use against which resistance has not been reported. In particular, rapidly increasing urbanization in developing nations are sites of major concern. Additionally, the widespread practice by physicians to prescribe antibiotics in cases of viral infections puts selective pressure on antibiotics that still remain effective and it will only be a matter of time before resistance develops on a large scale. The biosynthesis pathway of the bacterial cell wall is well studied and a validated target for the development of antibacterial agents. Cell wall biosynthesis involves two major processes; 1) the biosynthesis of cell wall teichoic acids and 2) the biosynthesis of peptidoglycan. Key molecules in these pathways, including enzymes and precursor molecules are attractive targets for the development of novel antibacterial agents. In this review, we will focus on the major class of natural antibacterial compounds that target the peptidoglycan precursor molecule Lipid II; namely the glycopeptides, including the novel generation of lipoglycopeptides. We will discuss their mechanism-of-action and clinical applications. Further, we will briefly discuss additional peptides that target Lipid II such as the lantibiotic nisin and defensins. We will highlight recent developments and future perspectives.
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Affiliation(s)
- Jakob J Malin
- University of Cologne, Department I of Internal Medicine, Division of Infectious Diseases, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Erik de Leeuw
- Institute of Human Virology and Department of Molecular Biology & Biochemistry of the University of Maryland, Baltimore School of Medicine, Baltimore, MD 21201, USA
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32
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Medeiros‐Silva J, Jekhmane S, Breukink E, Weingarth M. Towards the Native Binding Modes of Antibiotics that Target Lipid II. Chembiochem 2019; 20:1731-1738. [PMID: 30725496 PMCID: PMC6767406 DOI: 10.1002/cbic.201800796] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Indexed: 12/22/2022]
Abstract
The alarming rise of antimicrobial resistance (AMR) imposes severe burdens on healthcare systems and the economy worldwide, urgently calling for the development of new antibiotics. Antimicrobial peptides could be ideal templates for next-generation antibiotics, due to their low propensity to cause resistance. An especially promising branch of antimicrobial peptides target lipid II, the precursor of the bacterial peptidoglycan network. To develop these peptides into clinically applicable compounds, detailed information on their pharmacologically relevant modes of action is of critical importance. Here we review the binding modes of a selection of peptides that target lipid II and highlight shortcomings in our molecular understanding that, at least partly, relate to the widespread use of artificial membrane mimics for structural studies of membrane-active antibiotics. In particular, with the example of the antimicrobial peptide nisin, we showcase how the native cellular membrane environment can be critical for understanding of the physiologically relevant binding mode.
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Affiliation(s)
- João Medeiros‐Silva
- NMR SpectroscopyBijvoet Center for Biomolecular ResearchDepartment of ChemistryFaculty of ScienceUtrecht UniversityPadualaan 83584 CHUtrechtThe Netherlands
| | - Shehrazade Jekhmane
- NMR SpectroscopyBijvoet Center for Biomolecular ResearchDepartment of ChemistryFaculty of ScienceUtrecht UniversityPadualaan 83584 CHUtrechtThe Netherlands
| | - Eefjan Breukink
- Membrane Biochemistry and BiophysicsBijvoet Center for Biomolecular ResearchDepartment of ChemistryFaculty of ScienceUtrecht UniversityPadualaan 83584 CHUtrechtThe Netherlands
| | - Markus Weingarth
- NMR SpectroscopyBijvoet Center for Biomolecular ResearchDepartment of ChemistryFaculty of ScienceUtrecht UniversityPadualaan 83584 CHUtrechtThe Netherlands
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33
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Minimal exposure of lipid II cycle intermediates triggers cell wall antibiotic resistance. Nat Commun 2019; 10:2733. [PMID: 31227716 PMCID: PMC6588590 DOI: 10.1038/s41467-019-10673-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 05/23/2019] [Indexed: 01/08/2023] Open
Abstract
Cell wall antibiotics are crucial for combatting the emerging wave of resistant bacteria. Yet, our understanding of antibiotic action is limited, as many strains devoid of all resistance determinants display far higher antibiotic tolerance in vivo than suggested by the antibiotic-target binding affinity in vitro. To resolve this conflict, here we develop a comprehensive theory for the bacterial cell wall biosynthetic pathway and study its perturbation by antibiotics. We find that the closed-loop architecture of the lipid II cycle of wall biosynthesis features a highly asymmetric distribution of pathway intermediates, and show that antibiotic tolerance scales inversely with the abundance of the targeted pathway intermediate. We formalize this principle of minimal target exposure as intrinsic resistance mechanism and predict how cooperative drug-target interactions can mitigate resistance. The theory accurately predicts the in vivo efficacy for various cell wall antibiotics in different Gram-positive bacteria and contributes to a systems-level understanding of antibiotic action.
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34
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Enkavi G, Javanainen M, Kulig W, Róg T, Vattulainen I. Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance. Chem Rev 2019; 119:5607-5774. [PMID: 30859819 PMCID: PMC6727218 DOI: 10.1021/acs.chemrev.8b00538] [Citation(s) in RCA: 173] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Indexed: 12/23/2022]
Abstract
Biological membranes are tricky to investigate. They are complex in terms of molecular composition and structure, functional over a wide range of time scales, and characterized by nonequilibrium conditions. Because of all of these features, simulations are a great technique to study biomembrane behavior. A significant part of the functional processes in biological membranes takes place at the molecular level; thus computer simulations are the method of choice to explore how their properties emerge from specific molecular features and how the interplay among the numerous molecules gives rise to function over spatial and time scales larger than the molecular ones. In this review, we focus on this broad theme. We discuss the current state-of-the-art of biomembrane simulations that, until now, have largely focused on a rather narrow picture of the complexity of the membranes. Given this, we also discuss the challenges that we should unravel in the foreseeable future. Numerous features such as the actin-cytoskeleton network, the glycocalyx network, and nonequilibrium transport under ATP-driven conditions have so far received very little attention; however, the potential of simulations to solve them would be exceptionally high. A major milestone for this research would be that one day we could say that computer simulations genuinely research biological membranes, not just lipid bilayers.
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Affiliation(s)
- Giray Enkavi
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Matti Javanainen
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy
of Sciences, Flemingovo naḿesti 542/2, 16610 Prague, Czech Republic
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Waldemar Kulig
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Tomasz Róg
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Ilpo Vattulainen
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
- MEMPHYS-Center
for Biomembrane Physics
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35
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Panina IS, Chugunov AO, Efremov RG. Lipid II as a Target for Novel Antibiotics: Structural and Molecular Dynamics Studies. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2019. [DOI: 10.1134/s1068162019010126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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36
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Lagedroste M, Reiners J, Smits SHJ, Schmitt L. Systematic characterization of position one variants within the lantibiotic nisin. Sci Rep 2019; 9:935. [PMID: 30700815 PMCID: PMC6353901 DOI: 10.1038/s41598-018-37532-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/04/2018] [Indexed: 11/09/2022] Open
Abstract
Lantibiotics are a growing class of natural compounds, which possess antimicrobial activity against a broad range of Gram-positive bacteria. Their high potency against human pathogenic strains such as MRSA and VRE makes them excellent candidates as substitutes for classic antibiotics in times of increasing multidrug resistance of bacterial strains. New lantibiotics are detected in genomes and can be heterologously expressed. The functionality of these novel lantibiotics requires a systematic purification and characterization to benchmark them against for example the well-known lantibiotic nisin. Here, we used a standardized workflow to characterize lantibiotics consisting of six individual steps. The expression and secretion of the lantibiotic was performed employing the promiscuous nisin modification machinery. We mutated the first amino acid of nisin into all proteinaceous amino acids and compared their bactericidal potency against sensitive strains as well as strains expressing nisin resistance proteins. Interestingly, we can highlight four distinct groups based on the residual activity of nisin against sensitive as well as resistant L. lactis strains.
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Affiliation(s)
- Marcel Lagedroste
- Institute of Biochemistry, Heinrich-Heine-University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany
| | - Jens Reiners
- Institute of Biochemistry, Heinrich-Heine-University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany
| | - Sander H J Smits
- Institute of Biochemistry, Heinrich-Heine-University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany.
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich-Heine-University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany.
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37
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Liu Y, Ding S, Shen J, Zhu K. Nonribosomal antibacterial peptides that target multidrug-resistant bacteria. Nat Prod Rep 2019; 36:573-592. [DOI: 10.1039/c8np00031j] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This review summarizes the development of nonribosomal antibacterial peptides from untapped sources that target multidrug-resistant bacteria.
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Affiliation(s)
- Yuan Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health
- College of Veterinary Medicine
- China Agricultural University
- Beijing 100193
- China
| | - Shuangyang Ding
- National Center for Veterinary Drug Safety Evaluation
- College of Veterinary Medicine
- China Agricultural University
- China
| | - Jianzhong Shen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health
- College of Veterinary Medicine
- China Agricultural University
- Beijing 100193
- China
| | - Kui Zhu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health
- College of Veterinary Medicine
- China Agricultural University
- Beijing 100193
- China
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38
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Affiliation(s)
- Matthew W McCarthy
- a Weill Cornell Medical College, Division of General Internal Medicine , New York-Presbyterian Hospital , New York , NY , USA
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39
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De Leon Rodriguez LM, Williams ET, Brimble MA. Chemical Synthesis of Bioactive Naturally Derived Cyclic Peptides Containing Ene‐Like Rigidifying Motifs. Chemistry 2018; 24:17869-17880. [DOI: 10.1002/chem.201802533] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Indexed: 12/12/2022]
Affiliation(s)
| | - Elyse T. Williams
- School of Chemical SciencesThe University of Auckland 23 Symonds St. Auckland 1142 New Zealand
| | - Margaret A. Brimble
- School of Biological SciencesThe University of Auckland 3 Symonds St. Auckland 1142 New Zealand
- School of Chemical SciencesThe University of Auckland 23 Symonds St. Auckland 1142 New Zealand
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40
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Egan K, Field D, Ross RP, Cotter PD, Hill C. In silico Prediction and Exploration of Potential Bacteriocin Gene Clusters Within the Bacterial Genus Geobacillus. Front Microbiol 2018; 9:2116. [PMID: 30298056 PMCID: PMC6160750 DOI: 10.3389/fmicb.2018.02116] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 08/20/2018] [Indexed: 11/30/2022] Open
Abstract
The thermophilic, endospore-forming genus of Geobacillus has historically been associated with spoilage of canned food. However, in recent years it has become the subject of much attention due its biotechnological potential in areas such as enzyme and biofuel applications. One aspect of this genus that has not been fully explored or realized is its use as a source of novel forms of the ribosomally synthesized antimicrobial peptides known as bacteriocins. To date only two bacteriocins have been fully characterized within this genus, i.e., Geobacillin I and II, with only a small number of others partially characterized. Here we bioinformatically investigate the potential of this genus as a source of novel bacteriocins through the use of the in silico screening software BAGEL3, which scans publically available genomes for potential bacteriocin gene clusters. In this study we examined the association of bacteriocin gene presence with niche and phylogenetic position within the genus. We also identified a number of candidates from multiple bacteriocin classes which may be promising antimicrobial candidates when investigated in vitro in future studies.
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Affiliation(s)
- Kevin Egan
- School of Microbiology, University College, Cork, Ireland
| | - Des Field
- School of Microbiology, University College, Cork, Ireland.,APC Microbiome Institute, Cork, Cork, Ireland
| | - R Paul Ross
- School of Microbiology, University College, Cork, Ireland.,APC Microbiome Institute, Cork, Cork, Ireland
| | - Paul D Cotter
- APC Microbiome Institute, Cork, Cork, Ireland.,Teagasc Food Research Centre, Moorepark, Fermoy, Co., Cork, Ireland
| | - Colin Hill
- School of Microbiology, University College, Cork, Ireland.,APC Microbiome Institute, Cork, Cork, Ireland
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41
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Bakhtiary A, Cochrane SA, Mercier P, McKay RT, Miskolzie M, Sit CS, Vederas JC. Insights into the Mechanism of Action of the Two-Peptide Lantibiotic Lacticin 3147. J Am Chem Soc 2017; 139:17803-17810. [PMID: 29164875 DOI: 10.1021/jacs.7b04728] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lacticin 3147 is a two peptide lantibiotc (LtnA1 and LtnA2) that displays nanomolar activity against many Gram-positive bacteria. Lacticin 3147 may exert its antimicrobial effect by several mechanisms. Isothermal titration calorimetry experiments show that only LtnA1 binds to the peptidoglycan precursor lipid II, which could inhibit peptidoglycan biosynthesis. An experimentally supported model of the resulting complex suggests that the key binding partners are the C-terminus of LtnA1 and pyrophosphate of lipid II. A combination of in vivo and in vitro assays indicates that LtnA1 and LtnA2 can induce rapid membrane lysis without the need for lipid II binding. However, the presence of lipid II substantially increases the activity of lacticin 3147. Furthermore, studies with synthetic LtnA2 analogues containing either desmethyl- or oxa-lanthionine rings confirm that the precise geometry of these rings is essential for this synergistic activity.
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Affiliation(s)
- Alireza Bakhtiary
- Department of Chemistry, University of Alberta , Edmonton, Alberta T6G 2G2, Canada
| | - Stephen A Cochrane
- School of Chemistry and Chemical Engineering, Queens University Belfast , Belfast BT9 5AG, United Kingdom
| | - Pascal Mercier
- National High Field NMR Centre, University of Alberta , Edmonton, Alberta T6G 2E1, Canada
| | - Ryan T McKay
- Department of Chemistry, University of Alberta , Edmonton, Alberta T6G 2G2, Canada
| | - Mark Miskolzie
- Department of Chemistry, University of Alberta , Edmonton, Alberta T6G 2G2, Canada
| | - Clarissa S Sit
- Department of Chemistry, Saint Mary's University , Halifax, Nova Scotia B3H 3C3, Canada
| | - John C Vederas
- Department of Chemistry, University of Alberta , Edmonton, Alberta T6G 2G2, Canada
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42
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't Hart P, Wood TM, Tehrani KHME, van Harten RM, Śleszyńska M, Rentero Rebollo I, Hendrickx APA, Willems RJL, Breukink E, Martin NI. De novo identification of lipid II binding lipopeptides with antibacterial activity against vancomycin-resistant bacteria. Chem Sci 2017; 8:7991-7997. [PMID: 29568446 PMCID: PMC5853558 DOI: 10.1039/c7sc03413j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 09/29/2017] [Indexed: 12/20/2022] Open
Abstract
Lipid II binding lipopeptides discovered via bicyclic peptide phage display exhibit promising antibacterial activity.
Creative strategies for identifying new antibiotics are essential to addressing the looming threat of a post-antibiotic era. We here report the use of a targeted peptide phage display screen as a means of generating novel antimicrobial lipopeptides. Specifically, a library of phage displayed bicyclic peptides was screened against a biomolecular target based on the bacterial cell wall precursor lipid II. In doing so we identified unique lipid II binding peptides that upon lipidation were found to be active against a range of Gram-positive bacteria including clinically relevant strains of vancomycin resistant bacteria. Optimization of the peptide sequence led to variants with enhanced antibacterial activity and reduced hemolytic activity. Biochemical experiments further confirm a lipid II mediated mode of action for these new-to-nature antibacterial lipopeptides.
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Affiliation(s)
- Peter 't Hart
- Department of Chemical Biology & Drug Discovery , Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Universiteitsweg 99 , 3584 CG Utrecht , The Netherlands .
| | - Thomas M Wood
- Department of Chemical Biology & Drug Discovery , Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Universiteitsweg 99 , 3584 CG Utrecht , The Netherlands .
| | - Kamaleddin Haj Mohammad Ebrahim Tehrani
- Department of Chemical Biology & Drug Discovery , Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Universiteitsweg 99 , 3584 CG Utrecht , The Netherlands .
| | - Roel M van Harten
- Department of Chemical Biology & Drug Discovery , Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Universiteitsweg 99 , 3584 CG Utrecht , The Netherlands .
| | - Małgorzata Śleszyńska
- Department of Chemical Biology & Drug Discovery , Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Universiteitsweg 99 , 3584 CG Utrecht , The Netherlands .
| | - Inmaculada Rentero Rebollo
- Institute of Chemical Sciences and Engineering , Ecole Polytechnique Fédérale de Lausanne , Lausanne , Switzerland
| | - Antoni P A Hendrickx
- Department of Medical Microbiology , University Medical Center , Utrecht , The Netherlands
| | - Rob J L Willems
- Department of Medical Microbiology , University Medical Center , Utrecht , The Netherlands
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics Group , Department of Chemistry , Utrecht University , The Netherlands
| | - Nathaniel I Martin
- Department of Chemical Biology & Drug Discovery , Utrecht Institute for Pharmaceutical Sciences , Utrecht University , Universiteitsweg 99 , 3584 CG Utrecht , The Netherlands .
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43
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Abdel Monaim SAH, Jad YE, El-Faham A, de la Torre BG, Albericio F. Teixobactin as a scaffold for unlimited new antimicrobial peptides: SAR study. Bioorg Med Chem 2017; 26:2788-2796. [PMID: 29029900 DOI: 10.1016/j.bmc.2017.09.040] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 09/22/2017] [Accepted: 09/29/2017] [Indexed: 11/26/2022]
Abstract
It looks that a new era of antimicrobial peptides (AMPs) started with the discovery of teixobactin, which is a "head to side-chain" cyclodepsipeptide. It was isolated from a soil gram-negative b-proteobacteria by means of a revolutionary technique. Since there, several groups have developed synthetic strategies for efficient synthesis of this peptide and its analogues as well. Herein, all chemistries reported as well as the biological activity of the analogues are analyzed. Finally, some inputs regarding new trends for the next generation of analogues are discussed.
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Affiliation(s)
- Shimaa A H Abdel Monaim
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Yahya E Jad
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Ayman El-Faham
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; Chemistry Department, Faculty of Science, Alexandria University, P.O. Box 426, Ibrahimia, Alexandria 12321, Egypt
| | - Beatriz G de la Torre
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa; KRISP, College of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa.
| | - Fernando Albericio
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa; Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; School of Chemistry and Physics, University of KwaZulu-Natal, Durban 4001, South Africa; Department of Organic Chemistry, University of Barcelona, Barcelona 08028, Spain; CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona Science Park, Barcelona 08028, Spain.
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44
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Henninot A, Collins JC, Nuss JM. The Current State of Peptide Drug Discovery: Back to the Future? J Med Chem 2017; 61:1382-1414. [PMID: 28737935 DOI: 10.1021/acs.jmedchem.7b00318] [Citation(s) in RCA: 643] [Impact Index Per Article: 91.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Over the past decade, peptide drug discovery has experienced a revival of interest and scientific momentum, as the pharmaceutical industry has come to appreciate the role that peptide therapeutics can play in addressing unmet medical needs and how this class of compounds can be an excellent complement or even preferable alternative to small molecule and biological therapeutics. In this Perspective, we give a concise description of the recent progress in peptide drug discovery in a holistic manner, highlighting enabling technological advances affecting nearly every aspect of this field: from lead discovery, to synthesis and optimization, to peptide drug delivery. An emphasis is placed on describing research efforts to overcome the inherent weaknesses of peptide drugs, in particular their poor pharmacokinetic properties, and how these efforts have been critical to the discovery, design, and subsequent development of novel therapeutics.
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Affiliation(s)
- Antoine Henninot
- Ferring Research Institute , 4245 Sorrento Valley Boulevard, San Diego, California 92121, United States
| | - James C Collins
- Ferring Research Institute , 4245 Sorrento Valley Boulevard, San Diego, California 92121, United States
| | - John M Nuss
- Ferring Research Institute , 4245 Sorrento Valley Boulevard, San Diego, California 92121, United States
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45
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Müller A, Klöckner A, Schneider T. Targeting a cell wall biosynthesis hot spot. Nat Prod Rep 2017; 34:909-932. [PMID: 28675405 DOI: 10.1039/c7np00012j] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Covering: up to 2017History points to the bacterial cell wall biosynthetic network as a very effective target for antibiotic intervention, and numerous natural product inhibitors have been discovered. In addition to the inhibition of enzymes involved in the multistep synthesis of the macromolecular layer, in particular, interference with membrane-bound substrates and intermediates essential for the biosynthetic reactions has proven a valuable antibacterial strategy. A prominent target within the peptidoglycan biosynthetic pathway is lipid II, which represents a particular "Achilles' heel" for antibiotic attack, as it is readily accessible on the outside of the cytoplasmic membrane. Lipid II is a unique non-protein target that is one of the structurally most conserved molecules in bacterial cells. Notably, lipid II is more than just a target molecule, since sequestration of the cell wall precursor may be combined with additional antibiotic activities, such as the disruption of membrane integrity or disintegration of membrane-bound multi-enzyme machineries. Within the membrane bilayer lipid II is likely organized in specific anionic phospholipid patches that form a particular "landing platform" for antibiotics. Nature has invented a variety of different "lipid II binders" of at least 5 chemical classes, and their antibiotic activities can vary substantially depending on the compounds' physicochemical properties, such as amphiphilicity and charge, and thus trigger diverse cellular effects that are decisive for antibiotic activity.
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Affiliation(s)
- Anna Müller
- Institute of Pharmaceutical Microbiology, University of Bonn, Bonn, Germany.
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46
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Whitney JC, Peterson SB, Kim J, Pazos M, Verster AJ, Radey MC, Kulasekara HD, Ching MQ, Bullen NP, Bryant D, Goo YA, Surette MG, Borenstein E, Vollmer W, Mougous JD. A broadly distributed toxin family mediates contact-dependent antagonism between gram-positive bacteria. eLife 2017; 6. [PMID: 28696203 PMCID: PMC5555719 DOI: 10.7554/elife.26938] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 07/10/2017] [Indexed: 12/24/2022] Open
Abstract
The Firmicutes are a phylum of bacteria that dominate numerous polymicrobial habitats of importance to human health and industry. Although these communities are often densely colonized, a broadly distributed contact-dependent mechanism of interbacterial antagonism utilized by Firmicutes has not been elucidated. Here we show that proteins belonging to the LXG polymorphic toxin family present in Streptococcus intermedius mediate cell contact- and Esx secretion pathway-dependent growth inhibition of diverse Firmicute species. The structure of one such toxin revealed a previously unobserved protein fold that we demonstrate directs the degradation of a uniquely bacterial molecule required for cell wall biosynthesis, lipid II. Consistent with our functional data linking LXG toxins to interbacterial interactions in S. intermedius, we show that LXG genes are prevalent in the human gut microbiome, a polymicrobial community dominated by Firmicutes. We speculate that interbacterial antagonism mediated by LXG toxins plays a critical role in shaping Firmicute-rich bacterial communities. DOI:http://dx.doi.org/10.7554/eLife.26938.001 Most bacteria live in densely colonized environments, such as the human gut, in which they must constantly compete with other microbes for space and nutrients. As a result, bacteria have evolved a wide array of strategies to directly fight their neighbors. For example, some bacteria release antimicrobial compounds into their surroundings, while others ‘inject’ protein toxins directly into adjacent cells. Bacteria can be classified into two groups known as Gram-positive and Gram-negative. Previous studies found that Gram-negative bacteria inject toxins into neighboring cells, but no comparable toxins in Gram-positive bacteria had been identified. Before a bacterium can inject molecules into an adjacent cell, it needs to move the toxins from its interior to the cell surface. It had been suggested that a transport system in Gram-positive bacteria called the Esx pathway may export toxins known as LXG proteins. However, it was not clear whether these proteins help Gram-positive bacteria to compete against other bacteria. Whitney et al. studied the LXG proteins in Gram-positive bacteria known as Firmicutes. The experiments reveal that Firmicutes found in the human gut possess LXG genes. A Firmicute known as Streptococcus intermedius produces three LXG proteins that are all toxic to bacteria. To avoid being harmed by its own LXG proteins, S. intermedius also produces matching antidote proteins. Further experiments show that LXG proteins are exported out of S. intermedius cells and into adjacent competitor bacteria by the Esx pathway. Examining one of these LXG proteins in more detail showed that it can degrade a molecule that bacteria need to make their cell wall. Together, these findings suggest that LXG proteins may influence the species living in many important microbial communities, including the human gut. Changes in the communities of gut microbes have been linked with many diseases. Therefore, understanding more about how the LXG proteins work may help us to develop ways to manipulate these communities to improve human health. DOI:http://dx.doi.org/10.7554/eLife.26938.002
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Affiliation(s)
- John C Whitney
- Department of Microbiology, University of Washington School of Medicine, Seattle, United States
| | - S Brook Peterson
- Department of Microbiology, University of Washington School of Medicine, Seattle, United States
| | - Jungyun Kim
- Department of Microbiology, University of Washington School of Medicine, Seattle, United States
| | - Manuel Pazos
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle, United Kingdom
| | - Adrian J Verster
- Department of Genome Sciences, University of Washington, Seattle, United States
| | - Matthew C Radey
- Department of Microbiology, University of Washington School of Medicine, Seattle, United States
| | - Hemantha D Kulasekara
- Department of Microbiology, University of Washington School of Medicine, Seattle, United States
| | - Mary Q Ching
- Department of Microbiology, University of Washington School of Medicine, Seattle, United States
| | - Nathan P Bullen
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Diane Bryant
- Experimental Systems Group, Advanced Light Source, Berkeley, United States
| | - Young Ah Goo
- Northwestern Proteomics Core Facility, Northwestern University, Chicago, United States
| | - Michael G Surette
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada.,Department of Medicine, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Canada
| | - Elhanan Borenstein
- Department of Genome Sciences, University of Washington, Seattle, United States.,Department of Computer Science and Engineering, University of Washington, Seattle, United States.,Santa Fe Institute, Santa Fe, United States
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle, United Kingdom
| | - Joseph D Mougous
- Department of Microbiology, University of Washington School of Medicine, Seattle, United States.,Howard Hughes Medical Institute, University of Washington School of Medicine, Seattle, United States
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47
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Baxter RHG, Contet A, Krueger K. Arthropod Innate Immune Systems and Vector-Borne Diseases. Biochemistry 2017; 56:907-918. [PMID: 28072517 DOI: 10.1021/acs.biochem.6b00870] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Arthropods, especially ticks and mosquitoes, are the vectors for a number of parasitic and viral human diseases, including malaria, sleeping sickness, Dengue, and Zika, yet arthropods show tremendous individual variation in their capacity to transmit disease. A key factor in this capacity is the group of genetically encoded immune factors that counteract infection by the pathogen. Arthropod-specific pattern recognition receptors and protease cascades detect and respond to infection. Proteins such as antimicrobial peptides, thioester-containing proteins, and transglutaminases effect responses such as lysis, phagocytosis, melanization, and agglutination. Effector responses are initiated by damage signals such as reactive oxygen species signaling from epithelial cells and recognized by cell surface receptors on hemocytes. Antiviral immunity is primarily mediated by siRNA pathways but coupled with interferon-like signaling, antimicrobial peptides, and thioester-containing proteins. Molecular mechanisms of immunity are closely linked to related traits of longevity and fertility, and arthropods have the capacity for innate immunological memory. Advances in understanding vector immunity can be leveraged to develop novel control strategies for reducing the rate of transmission of both ancient and emerging threats to global health.
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Affiliation(s)
- Richard H G Baxter
- Department of Chemistry and Molecular Biophysics & Biochemistry, Yale University , New Haven, Connecticut 06511, United States
| | - Alicia Contet
- Department of Chemistry and Molecular Biophysics & Biochemistry, Yale University , New Haven, Connecticut 06511, United States
| | - Kathryn Krueger
- Department of Chemistry and Molecular Biophysics & Biochemistry, Yale University , New Haven, Connecticut 06511, United States
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48
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Positive selection in cathelicidin host defense peptides: adaptation to exogenous pathogens or endogenous receptors? Heredity (Edinb) 2016; 118:453-465. [PMID: 27925615 PMCID: PMC5564380 DOI: 10.1038/hdy.2016.117] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 09/28/2016] [Accepted: 10/03/2016] [Indexed: 11/24/2022] Open
Abstract
The cause of adaptive protein evolution includes internal (for example, co-evolution of ligand-receptor pairs) and external (for example, adaptation to different ecological niches) mechanisms. Host defense peptides (HDPs) are a class of vertebrate-specific cationic antimicrobial peptides evolving under positive selection. Besides their antibiotic activity, HDPs also exert an effect on multiple host immune cells, thus providing an ideal model to study selective agents driving their evolution. On the basis of a combination of computational and experimental approaches, we studied the evolution of LL-37-type HDPs in mammals, the mature peptide of cathelicidin CAP18 (herein termed CAP18-MP) and investigated the driving force behind the evolution. Using codon-substitution maximum likelihood models, we analyzed CAP18-MPs in 40 species belonging to nine mammalian Orders and identified four positively selected sites (PSSs) that all are located on two terminal unordered regions of CAP18-MPs. Grafting the two positively selected regions of human or whale CAP18-MP to the α-helical scaffold of a rabbit homolog (substituting its corresponding parts) led to no alterations in antibacterial activity, spectrum and action mode. Likewise, further deletion of the two terminal regions did not alter its functional features. Evolutionary conservation analysis of mammalian FPR2, a receptor known to interact with the C-terminal positively selected region of LL-37, revealed high evolutionary variability in its ligand-binding extracellular loop domains, matching sequence diversity of the unordered regions in CAP18-MPs. This is the first report describing that the signature of positive selection of cathelicidins is not associated with their direct bactericidal activity, but rather with the evolutionary variability of their endogenous receptors.
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49
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Atkinson DJ, Naysmith BJ, Furkert DP, Brimble MA. Enduracididine, a rare amino acid component of peptide antibiotics: Natural products and synthesis. Beilstein J Org Chem 2016; 12:2325-2342. [PMID: 28144300 PMCID: PMC5238550 DOI: 10.3762/bjoc.12.226] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 10/20/2016] [Indexed: 11/23/2022] Open
Abstract
Rising resistance to current clinical antibacterial agents is an imminent threat to global public health and highlights the demand for new lead compounds for drug discovery. One such potential lead compound, the peptide antibiotic teixobactin, was recently isolated from an uncultured bacterial source, and demonstrates remarkably high potency against a wide range of resistant pathogens without apparent development of resistance. A rare amino acid residue component of teixobactin, enduracididine, is only known to occur in a small number of natural products that also possess promising antibiotic activity. This review highlights the presence of enduracididine in natural products, its biosynthesis together with a review of analogues of enduracididine. Reported synthetic approaches to the cyclic guanidine structure of enduracididine are discussed, illustrating the challenges encountered to date in the development of efficient synthetic routes to facilitate drug discovery efforts inspired by the discovery of teixobactin.
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Affiliation(s)
- Darcy J Atkinson
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3 Symonds Street, Auckland, New Zealand
| | - Briar J Naysmith
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3 Symonds Street, Auckland, New Zealand
| | - Daniel P Furkert
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3 Symonds Street, Auckland, New Zealand
| | - Margaret A Brimble
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3 Symonds Street, Auckland, New Zealand
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50
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Chauhan J, Cardinale S, Fang L, Huang J, Kwasny SM, Pennington MR, Basi K, diTargiani R, Capacio BR, MacKerell AD, Opperman TJ, Fletcher S, de Leeuw EPH. Towards Development of Small Molecule Lipid II Inhibitors as Novel Antibiotics. PLoS One 2016; 11:e0164515. [PMID: 27776124 PMCID: PMC5077133 DOI: 10.1371/journal.pone.0164515] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 09/25/2016] [Indexed: 12/28/2022] Open
Abstract
Recently we described a novel di-benzene-pyrylium-indolene (BAS00127538) inhibitor of Lipid II. BAS00127538 (1-Methyl-2,4-diphenyl-6-((1E,3E)-3-(1,3,3-trimethylindolin-2-ylidene)prop-1-en-1-yl)pyryl-1-ium) tetrafluoroborate is the first small molecule Lipid II inhibitor and is structurally distinct from natural agents that bind Lipid II, such as vancomycin. Here, we describe the synthesis and biological evaluation of 50 new analogs of BAS00127538 designed to explore the structure-activity relationships of the scaffold. The results of this study indicate an activity map of the scaffold, identifying regions that are critical to cytotoxicity, Lipid II binding and range of anti-bacterial action. One compound, 6jc48-1, showed significantly enhanced drug-like properties compared to BAS00127538. 6jc48-1 has reduced cytotoxicity, while retaining specific Lipid II binding and activity against Enterococcus spp. in vitro and in vivo. Further, this compound showed a markedly improved pharmacokinetic profile with a half-life of over 13 hours upon intravenous and oral administration and was stable in plasma. These results suggest that scaffolds like that of 6jc48-1 can be developed into small molecule antibiotic drugs that target Lipid II.
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Affiliation(s)
- Jamal Chauhan
- Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, Baltimore, Maryland, United States of America
- Center for Biomolecular Therapeutics, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Steven Cardinale
- Microbiotix, Inc., One Innovation Drive, Worcester, Massachusetts, United States of America
| | - Lei Fang
- Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, Baltimore, Maryland, United States of America
- Computer-Aided Drug Design Center, University of Maryland, School of Pharmacy, Baltimore, Maryland, United States of America
- Center for Biomolecular Therapeutics, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Jing Huang
- Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, Baltimore, Maryland, United States of America
- Computer-Aided Drug Design Center, University of Maryland, School of Pharmacy, Baltimore, Maryland, United States of America
| | - Steven M. Kwasny
- Microbiotix, Inc., One Innovation Drive, Worcester, Massachusetts, United States of America
| | - M. Ross Pennington
- U.S. Army Medical Research Institute of Chemical Defense, Aberdeen Proving Ground, Maryland, United States of America
| | - Kelly Basi
- U.S. Army Medical Research Institute of Chemical Defense, Aberdeen Proving Ground, Maryland, United States of America
| | - Robert diTargiani
- U.S. Army Medical Research Institute of Chemical Defense, Aberdeen Proving Ground, Maryland, United States of America
| | - Benedict R. Capacio
- U.S. Army Medical Research Institute of Chemical Defense, Aberdeen Proving Ground, Maryland, United States of America
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, Baltimore, Maryland, United States of America
- Computer-Aided Drug Design Center, University of Maryland, School of Pharmacy, Baltimore, Maryland, United States of America
| | - Timothy J. Opperman
- Microbiotix, Inc., One Innovation Drive, Worcester, Massachusetts, United States of America
| | - Steven Fletcher
- Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, Baltimore, Maryland, United States of America
| | - Erik P. H. de Leeuw
- Institute of Human Virology & Department of Biochemistry and Molecular Biology of the University of Maryland Baltimore School of Medicine, Baltimore, Maryland, United States of America
- * E-mail:
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