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Sarkar T, Vignesh SR, Sehgal T, Ronima KR, Thummer RP, Satpati P, Chatterjee S. Development of protease resistant and non-cytotoxic Jelleine analogs with enhanced broad spectrum antimicrobial efficacy. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184336. [PMID: 38763273 DOI: 10.1016/j.bbamem.2024.184336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/29/2024] [Accepted: 05/12/2024] [Indexed: 05/21/2024]
Abstract
Short systemic half- life of Antimicrobial Peptides (AMP) is one of the major bottlenecks that limits their successful commercialization as therapeutics. In this work, we have designed analogs of the natural AMP Jelleine, obtained from royal jelly of apis mellifera. Among the designed peptides, J3 and J4 were the most potent with broad spectrum activities against a varied class of ESKAPE pathogens and fungus C. albicans. All the developed peptides were more effective against Gram-negative bacteria in comparison to the Gram-positive pathogens, and were especially effective against P. aeruginosa and C. albicans.J3 and J4 were completely trypsin resistant and serum stable, while retaining the non-cytotoxicity of the parent Jelleine, Jc. The designed peptides were membranolytic in their mode of action. CD and MD simulations in the presence of bilayers, established that J3 and J4 were non-structured even upon membrane binding and suggested that biological properties of the AMPs were innocent of any specific secondary structural requirements. Enhancement of charge to increase the antimicrobial potency, controlling the hydrophobic-hydrophilic balance to maintain non-cytotoxicity and induction of unnatural amino acid residues to impart protease resistance, remains some of the fundamental principles in the design of more effective antimicrobial therapeutics of the future, which may help combat the quickly rising menace of antimicrobial resistance in the microbes.
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Affiliation(s)
- Tanumoy Sarkar
- Department of Chemistry, Indian Institute of Technology, Guwahati, Guwahati, India
| | - S R Vignesh
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Guwahati, Guwahati, India
| | - Tanya Sehgal
- Department of Chemistry, Indian Institute of Technology, Guwahati, Guwahati, India
| | - K R Ronima
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Guwahati, Guwahati, India
| | - Rajkumar P Thummer
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Guwahati, Guwahati, India
| | - Priyadarshi Satpati
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Guwahati, Guwahati, India.
| | - Sunanda Chatterjee
- Department of Chemistry, Indian Institute of Technology, Guwahati, Guwahati, India.
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2
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Parkhill SL, Johnson EO. Integrating bacterial molecular genetics with chemical biology for renewed antibacterial drug discovery. Biochem J 2024; 481:839-864. [PMID: 38958473 DOI: 10.1042/bcj20220062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/20/2024] [Accepted: 06/24/2024] [Indexed: 07/04/2024]
Abstract
The application of dyes to understanding the aetiology of infection inspired antimicrobial chemotherapy and the first wave of antibacterial drugs. The second wave of antibacterial drug discovery was driven by rapid discovery of natural products, now making up 69% of current antibacterial drugs. But now with the most prevalent natural products already discovered, ∼107 new soil-dwelling bacterial species must be screened to discover one new class of natural product. Therefore, instead of a third wave of antibacterial drug discovery, there is now a discovery bottleneck. Unlike natural products which are curated by billions of years of microbial antagonism, the vast synthetic chemical space still requires artificial curation through the therapeutics science of antibacterial drugs - a systematic understanding of how small molecules interact with bacterial physiology, effect desired phenotypes, and benefit the host. Bacterial molecular genetics can elucidate pathogen biology relevant to therapeutics development, but it can also be applied directly to understanding mechanisms and liabilities of new chemical agents with new mechanisms of action. Therefore, the next phase of antibacterial drug discovery could be enabled by integrating chemical expertise with systematic dissection of bacterial infection biology. Facing the ambitious endeavour to find new molecules from nature or new-to-nature which cure bacterial infections, the capabilities furnished by modern chemical biology and molecular genetics can be applied to prospecting for chemical modulators of new targets which circumvent prevalent resistance mechanisms.
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Affiliation(s)
- Susannah L Parkhill
- Systems Chemical Biology of Infection and Resistance Laboratory, The Francis Crick Institute, London, U.K
- Faculty of Life Sciences, University College London, London, U.K
| | - Eachan O Johnson
- Systems Chemical Biology of Infection and Resistance Laboratory, The Francis Crick Institute, London, U.K
- Faculty of Life Sciences, University College London, London, U.K
- Department of Chemistry, Imperial College, London, U.K
- Department of Chemistry, King's College London, London, U.K
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3
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Antunes B, Zanchi C, Johnston PR, Maron B, Witzany C, Regoes RR, Hayouka Z, Rolff J. The evolution of antimicrobial peptide resistance in Pseudomonas aeruginosa is severely constrained by random peptide mixtures. PLoS Biol 2024; 22:e3002692. [PMID: 38954678 DOI: 10.1371/journal.pbio.3002692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 05/28/2024] [Indexed: 07/04/2024] Open
Abstract
The prevalence of antibiotic-resistant pathogens has become a major threat to public health, requiring swift initiatives for discovering new strategies to control bacterial infections. Hence, antibiotic stewardship and rapid diagnostics, but also the development, and prudent use, of novel effective antimicrobial agents are paramount. Ideally, these agents should be less likely to select for resistance in pathogens than currently available conventional antimicrobials. The usage of antimicrobial peptides (AMPs), key components of the innate immune response, and combination therapies, have been proposed as strategies to diminish the emergence of resistance. Herein, we investigated whether newly developed random antimicrobial peptide mixtures (RPMs) can significantly reduce the risk of resistance evolution in vitro to that of single sequence AMPs, using the ESKAPE pathogen Pseudomonas aeruginosa (P. aeruginosa) as a model gram-negative bacterium. Infections of this pathogen are difficult to treat due the inherent resistance to many drug classes, enhanced by the capacity to form biofilms. P. aeruginosa was experimentally evolved in the presence of AMPs or RPMs, subsequentially assessing the extent of resistance evolution and cross-resistance/collateral sensitivity between treatments. Furthermore, the fitness costs of resistance on bacterial growth were studied and whole-genome sequencing used to investigate which mutations could be candidates for causing resistant phenotypes. Lastly, changes in the pharmacodynamics of the evolved bacterial strains were examined. Our findings suggest that using RPMs bears a much lower risk of resistance evolution compared to AMPs and mostly prevents cross-resistance development to other treatments, while maintaining (or even improving) drug sensitivity. This strengthens the case for using random cocktails of AMPs in favour of single AMPs, against which resistance evolved in vitro, providing an alternative to classic antibiotics worth pursuing.
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Affiliation(s)
- Bernardo Antunes
- Freie Universität Berlin, Evolutionary Biology, Berlin, Germany
- Institute of Biochemistry, Food Science and Nutrition, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Caroline Zanchi
- Freie Universität Berlin, Evolutionary Biology, Berlin, Germany
| | - Paul R Johnston
- Freie Universität Berlin, Evolutionary Biology, Berlin, Germany
- Berlin Centre for Genomics in Biodiversity Research, Berlin, Germany
- University of St. Andrews, School of Medicine, North Haugh, St Andrews, Fife, United Kingdom
| | - Bar Maron
- Institute of Biochemistry, Food Science and Nutrition, The Hebrew University of Jerusalem, Rehovot, Israel
| | | | - Roland R Regoes
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Zvi Hayouka
- Institute of Biochemistry, Food Science and Nutrition, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Jens Rolff
- Freie Universität Berlin, Evolutionary Biology, Berlin, Germany
- Berlin Centre for Genomics in Biodiversity Research, Berlin, Germany
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4
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Zeng P, Wang H, Zhang P, Leung SSY. Unearthing naturally-occurring cyclic antibacterial peptides and their structural optimization strategies. Biotechnol Adv 2024; 73:108371. [PMID: 38704105 DOI: 10.1016/j.biotechadv.2024.108371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 03/08/2024] [Accepted: 04/29/2024] [Indexed: 05/06/2024]
Abstract
Natural products with antibacterial activity are highly desired globally to combat against multidrug-resistant (MDR) bacteria. Antibacterial peptide (ABP), especially cyclic ABP (CABP), is one of the abundant classes. Most of them were isolated from microbes, demonstrating excellent bactericidal effects. With the improved proteolytic stability, CABPs are normally considered to have better druggability than linear peptides. However, most clinically-used CABP-based antibiotics, such as colistin, also face the challenges of drug resistance soon after they reached the market, urgently requiring the development of next-generation succedaneums. We present here a detail review on the novel naturally-occurring CABPs discovered in the past decade and some of them are under clinical trials, exhibiting anticipated application potential. According to their chemical structures, they were broadly classified into five groups, including (i) lactam/lactone-based CABPs, (ii) cyclic lipopeptides, (iii) glycopeptides, (iv) cyclic sulfur-rich peptides and (v) multiple-modified CABPs. Their chemical structures, antibacterial spectrums and proposed mechanisms are discussed. Moreover, engineered analogs of these novel CABPs are also summarized to preliminarily analyze their structure-activity relationship. This review aims to provide a global perspective on research and development of novel CABPs to highlight the effectiveness of derivatives design in identifying promising antibacterial agents. Further research efforts in this area are believed to play important roles in fighting against the multidrug-resistance crisis.
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Affiliation(s)
- Ping Zeng
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Honglan Wang
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Pengfei Zhang
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Sharon Shui Yee Leung
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong.
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5
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Banerjee U, Borbora SM, Guha M, Yadav V, Sanjay V, Singh A, Balaji KN, Chandra N. Inhibition of leukotriene-B4 signalling-mediated host response to tuberculosis is a potential mode of adjunctive host-directed therapy. Immunology 2024; 172:392-407. [PMID: 38504502 DOI: 10.1111/imm.13781] [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: 08/14/2023] [Accepted: 03/04/2024] [Indexed: 03/21/2024] Open
Abstract
Treatment of tuberculosis (TB) is faced with several challenges including the long treatment duration, drug toxicity and tissue pathology. Host-directed therapy provides promising avenues to find compounds for adjunctively assisting antimycobacterials in the TB treatment regimen, by promoting pathogen eradication or limiting tissue destruction. Eicosanoids are a class of lipid molecules that are potent mediators of inflammation and have been implicated in aspects of the host response against TB. Here, we have explored the blood transcriptome of pulmonary TB patients to understand the activity of leukotriene B4, a pro-inflammatory eicosanoid. Our study shows a significant upregulation in the leukotriene B4 signalling pathway in active TB patients, which is reversed with TB treatment. We have further utilized our in-house network analysis algorithm, ResponseNet, to identify potential downstream signal effectors of leukotriene B4 in TB patients including STAT1/2 and NADPH oxidase at a systemic as well as local level, followed by experimental validation of the same. Finally, we show the potential of inhibiting leukotriene B4 signalling as a mode of adjunctive host-directed therapy against TB. This study provides a new mode of TB treatment along with mechanistic insights which can be further explored in pre-clinical trials.
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Affiliation(s)
- Ushashi Banerjee
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | - Salik Miskat Borbora
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
| | - Madhura Guha
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
- Center for Infectious Disease Research, Indian Institute of Science, Bengaluru, India
| | - Vikas Yadav
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
- Center for Infectious Disease Research, Indian Institute of Science, Bengaluru, India
| | - V Sanjay
- Center for Infectious Disease Research, Indian Institute of Science, Bengaluru, India
| | - Amit Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
- Center for Infectious Disease Research, Indian Institute of Science, Bengaluru, India
| | | | - Nagasuma Chandra
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
- Center for Biosystems Science and Engineering, Indian Institute of Science, Bengaluru, India
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6
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Kim MS, Jeong DE, Jang JP, Jang JH, Choi SK. Mining biosynthetic gene clusters in Paenibacillus genomes to discover novel antibiotics. BMC Microbiol 2024; 24:226. [PMID: 38937695 PMCID: PMC11210098 DOI: 10.1186/s12866-024-03375-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 06/17/2024] [Indexed: 06/29/2024] Open
Abstract
BACKGROUND Bacterial antimicrobial resistance poses a severe threat to humanity, necessitating the urgent development of new antibiotics. Recent advances in genome sequencing offer new avenues for antibiotic discovery. Paenibacillus genomes encompass a considerable array of antibiotic biosynthetic gene clusters (BGCs), rendering these species as good candidates for genome-driven novel antibiotic exploration. Nevertheless, BGCs within Paenibacillus genomes have not been extensively studied. RESULTS We conducted an analysis of 554 Paenibacillus genome sequences, sourced from the National Center for Biotechnology Information database, with a focused investigation involving 89 of these genomes via antiSMASH. Our analysis unearthed a total of 848 BGCs, of which 716 (84.4%) were classified as unknown. From the initial pool of 554 Paenibacillus strains, we selected 26 available in culture collections for an in-depth evaluation. Genomic scrutiny of these selected strains unveiled 255 BGCs, encoding non-ribosomal peptide synthetases, polyketide synthases, and bacteriocins, with 221 (86.7%) classified as unknown. Among these strains, 20 exhibited antimicrobial activity against the gram-positive bacterium Micrococcus luteus, yet only six strains displayed activity against the gram-negative bacterium Escherichia coli. We proceeded to focus on Paenibacillus brasilensis, which featured five new BGCs for further investigation. To facilitate detailed characterization, we constructed a mutant in which a single BGC encoding a novel antibiotic was activated while simultaneously inactivating multiple BGCs using a cytosine base editor (CBE). The novel antibiotic was found to be localized to the cell wall and demonstrated activity against both gram-positive bacteria and fungi. The chemical structure of the new antibiotic was elucidated on the basis of ESIMS, 1D and 2D NMR spectroscopic data. The novel compound, with a molecular weight of 926, was named bracidin. CONCLUSIONS This study outcome highlights the potential of Paenibacillus species as valuable sources for novel antibiotics. In addition, CBE-mediated dereplication of antibiotics proved to be a rapid and efficient method for characterizing novel antibiotics from Paenibacillus species, suggesting that it will greatly accelerate the genome-based development of new antibiotics.
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Grants
- NRF-2018M3A9F3079565 National Research Foundation of Korea
- NRF-2018M3A9F3079565 National Research Foundation of Korea
- NRF-2018M3A9F3079565 National Research Foundation of Korea
- KGM9942421, KGM5292423, and KGM1222413 Korea Research Institute of Bioscience and Biotechnology
- KGM9942421, KGM5292423, and KGM1222413 Korea Research Institute of Bioscience and Biotechnology
- KGM9942421, KGM5292423, and KGM1222413 Korea Research Institute of Bioscience and Biotechnology
- KGM9942421, KGM5292423, and KGM1222413 Korea Research Institute of Bioscience and Biotechnology
- KGM9942421, KGM5292423, and KGM1222413 Korea Research Institute of Bioscience and Biotechnology
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Affiliation(s)
- Man Su Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Da-Eun Jeong
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Jun-Pil Jang
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea
| | - Jae-Hyuk Jang
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea.
- Department of Applied Biological Engineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, Republic of Korea.
| | - Soo-Keun Choi
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, Republic of Korea.
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7
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Crombie A, Kalaitzis JA, Chen R, Vuong D, Lacey AE, Lacey E, Shivas RG, Tan YP, Sbaraini N, Chooi YH, Piggott AM. Geministatins: new depside antibiotics from the fungus Austroacremonium gemini. J Antibiot (Tokyo) 2024:10.1038/s41429-024-00755-x. [PMID: 38926492 DOI: 10.1038/s41429-024-00755-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/22/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024]
Abstract
Two new depside antibiotics, geministatins A (1) and B (2), were isolated from the fungus Austroacremonium gemini MST-FP2131 (Sordariomycetes, Ascomycota), which was recovered from rotting wood in the wet tropics of northern Australia. The structures of the geministatins were elucidated by detailed spectroscopic analysis, chemical degradation and comparison with literature values. Chemical degradation of 1 and 2 yielded three new analogues, geministatins C-E (3-5), as well as a previously reported compound dehydromerulinic acid A (6). Compounds 1, 2 and 6 exhibited antibacterial activity against the Gram-positive bacteria Bacillus subtilis (MIC 0.2-1.6 µg mL-1) and Staphylococcus aureus (MIC 0.78-6.3 µg mL-1), including methicillin-resistant S. aureus (MRSA), while 4 exhibited antifungal activity against the yeast Saccharomyces cerevisiae (MIC 13 µg mL-1).
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Affiliation(s)
- Andrew Crombie
- Microbial Screening Technologies, Smithfield, NSW, 2164, Australia
| | - John A Kalaitzis
- School of Natural Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Rachel Chen
- Microbial Screening Technologies, Smithfield, NSW, 2164, Australia
| | - Daniel Vuong
- Microbial Screening Technologies, Smithfield, NSW, 2164, Australia
| | - Alastair E Lacey
- Microbial Screening Technologies, Smithfield, NSW, 2164, Australia
| | - Ernest Lacey
- Microbial Screening Technologies, Smithfield, NSW, 2164, Australia
- School of Natural Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Roger G Shivas
- Department of Agriculture and Fisheries, Plant Pathology Herbarium, Dutton Park, QLD, 4102, Australia
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, 4350, Australia
| | - Yu Pei Tan
- Department of Agriculture and Fisheries, Plant Pathology Herbarium, Dutton Park, QLD, 4102, Australia
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, 4350, Australia
| | - Nicolau Sbaraini
- School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | - Yit-Heng Chooi
- School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | - Andrew M Piggott
- School of Natural Sciences, Macquarie University, Sydney, NSW, 2109, Australia.
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Espinoza JL, Phillips A, Prentice MB, Tan GS, Kamath PL, Lloyd KG, Dupont CL. Unveiling the microbial realm with VEBA 2.0: a modular bioinformatics suite for end-to-end genome-resolved prokaryotic, (micro)eukaryotic and viral multi-omics from either short- or long-read sequencing. Nucleic Acids Res 2024:gkae528. [PMID: 38909293 DOI: 10.1093/nar/gkae528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 05/21/2024] [Accepted: 06/10/2024] [Indexed: 06/24/2024] Open
Abstract
The microbiome is a complex community of microorganisms, encompassing prokaryotic (bacterial and archaeal), eukaryotic, and viral entities. This microbial ensemble plays a pivotal role in influencing the health and productivity of diverse ecosystems while shaping the web of life. However, many software suites developed to study microbiomes analyze only the prokaryotic community and provide limited to no support for viruses and microeukaryotes. Previously, we introduced the Viral Eukaryotic Bacterial Archaeal (VEBA) open-source software suite to address this critical gap in microbiome research by extending genome-resolved analysis beyond prokaryotes to encompass the understudied realms of eukaryotes and viruses. Here we present VEBA 2.0 with key updates including a comprehensive clustered microeukaryotic protein database, rapid genome/protein-level clustering, bioprospecting, non-coding/organelle gene modeling, genome-resolved taxonomic/pathway profiling, long-read support, and containerization. We demonstrate VEBA's versatile application through the analysis of diverse case studies including marine water, Siberian permafrost, and white-tailed deer lung tissues with the latter showcasing how to identify integrated viruses. VEBA represents a crucial advancement in microbiome research, offering a powerful and accessible software suite that bridges the gap between genomics and biotechnological solutions.
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Affiliation(s)
- Josh L Espinoza
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA 92037, USA
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Allan Phillips
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA 92037, USA
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Melanie B Prentice
- School of Food and Agriculture, University of Maine, Orono, ME 04469, USA
| | - Gene S Tan
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Pauline L Kamath
- School of Food and Agriculture, University of Maine, Orono, ME 04469, USA
- Maine Center for Genetics in the Environment, University of Maine, Orono, ME 04469, USA
| | - Karen G Lloyd
- Microbiology Department, University of Tennessee, Knoxville, TN 37917, USA
| | - Chris L Dupont
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA 92037, USA
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
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9
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Zhao X, Zhong X, Yang S, Deng J, Deng K, Huang Z, Li Y, Yin Z, Liu Y, Viel JH, Wan H. Guiding antibiotics towards their target using bacteriophage proteins. Nat Commun 2024; 15:5287. [PMID: 38902231 PMCID: PMC11190222 DOI: 10.1038/s41467-024-49603-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 06/11/2024] [Indexed: 06/22/2024] Open
Abstract
Novel therapeutic strategies against difficult-to-treat bacterial infections are desperately needed, and the faster and cheaper way to get them might be by repurposing existing antibiotics. Nanodelivery systems enhance the efficacy of antibiotics by guiding them to their targets, increasing the local concentration at the site of infection. While recently described nanodelivery systems are promising, they are generally not easy to adapt to different targets, and lack biocompatibility or specificity. Here, nanodelivery systems are created that source their targeting proteins from bacteriophages. Bacteriophage receptor-binding proteins and cell-wall binding domains are conjugated to nanoparticles, for the targeted delivery of rifampicin, imipenem, and ampicillin against bacterial pathogens. They show excellent specificity against their targets, and accumulate at the site of infection to deliver their antibiotic payload. Moreover, the nanodelivery systems suppress pathogen infections more effectively than 16 to 32-fold higher doses of free antibiotics. This study demonstrates that bacteriophage sourced targeting proteins are promising candidates to guide nanodelivery systems. Their specificity, availability, and biocompatibility make them great options to guide the antibiotic nanodelivery systems that are desperately needed to combat difficult-to-treat infections.
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Affiliation(s)
- Xinghong Zhao
- Center for Sustainable Antimicrobials, Department of Pharmacy, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China.
- Center for Infectious Diseases Control (CIDC), College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Xinyi Zhong
- Center for Sustainable Antimicrobials, Department of Pharmacy, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
- Center for Infectious Diseases Control (CIDC), College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shinong Yang
- Center for Sustainable Antimicrobials, Department of Pharmacy, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
- Center for Infectious Diseases Control (CIDC), College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiarong Deng
- Center for Sustainable Antimicrobials, Department of Pharmacy, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
- Center for Infectious Diseases Control (CIDC), College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
| | - Kai Deng
- Center for Sustainable Antimicrobials, Department of Pharmacy, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
- Center for Infectious Diseases Control (CIDC), College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhengqun Huang
- Center for Sustainable Antimicrobials, Department of Pharmacy, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
- Center for Infectious Diseases Control (CIDC), College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuanfeng Li
- Translational Medicine Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Zhongqiong Yin
- Center for Sustainable Antimicrobials, Department of Pharmacy, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Yong Liu
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325001, China.
| | - Jakob H Viel
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG, Groningen, Netherlands
| | - Hongping Wan
- Center for Sustainable Antimicrobials, Department of Pharmacy, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China.
- Center for Infectious Diseases Control (CIDC), College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China.
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10
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Bakker AT, Kotsogianni I, Avalos M, Punt JM, Liu B, Piermarini D, Gagestein B, Slingerland CJ, Zhang L, Willemse JJ, Ghimire LB, van den Berg RJHBN, Janssen APA, Ottenhoff THM, van Boeckel CAA, van Wezel GP, Ghilarov D, Martin NI, van der Stelt M. Discovery of isoquinoline sulfonamides as allosteric gyrase inhibitors with activity against fluoroquinolone-resistant bacteria. Nat Chem 2024:10.1038/s41557-024-01516-x. [PMID: 38898213 DOI: 10.1038/s41557-024-01516-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 03/22/2024] [Indexed: 06/21/2024]
Abstract
Bacteria have evolved resistance to nearly all known antibacterials, emphasizing the need to identify antibiotics that operate via novel mechanisms. Here we report a class of allosteric inhibitors of DNA gyrase with antibacterial activity against fluoroquinolone-resistant clinical isolates of Escherichia coli. Screening of a small-molecule library revealed an initial isoquinoline sulfonamide hit, which was optimized via medicinal chemistry efforts to afford the more potent antibacterial LEI-800. Target identification studies, including whole-genome sequencing of in vitro selected mutants with resistance to isoquinoline sulfonamides, unanimously pointed to the DNA gyrase complex, an essential bacterial topoisomerase and an established antibacterial target. Using single-particle cryogenic electron microscopy, we determined the structure of the gyrase-LEI-800-DNA complex. The compound occupies an allosteric, hydrophobic pocket in the GyrA subunit and has a mode of action that is distinct from the clinically used fluoroquinolones or any other gyrase inhibitor reported to date. LEI-800 provides a chemotype suitable for development to counter the increasingly widespread bacterial resistance to fluoroquinolones.
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Affiliation(s)
- Alexander T Bakker
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Ioli Kotsogianni
- Biological Chemistry Group, Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Mariana Avalos
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Jeroen M Punt
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Bing Liu
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Diana Piermarini
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Berend Gagestein
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Cornelis J Slingerland
- Biological Chemistry Group, Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Le Zhang
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Joost J Willemse
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Leela B Ghimire
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK
| | | | - Antonius P A Janssen
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Tom H M Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Constant A A van Boeckel
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Gilles P van Wezel
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Dmitry Ghilarov
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK.
| | - Nathaniel I Martin
- Biological Chemistry Group, Institute of Biology, Leiden University, Leiden, the Netherlands.
| | - Mario van der Stelt
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands.
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11
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Perez AJ, Lamanna MM, Bruce KE, Touraev MA, Page JE, Shaw SL, Tsui HCT, Winkler ME. Elongasome core proteins and class A PBP1a display zonal, processive movement at the midcell of Streptococcus pneumoniae. Proc Natl Acad Sci U S A 2024; 121:e2401831121. [PMID: 38875147 PMCID: PMC11194595 DOI: 10.1073/pnas.2401831121] [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: 02/07/2024] [Accepted: 05/02/2024] [Indexed: 06/16/2024] Open
Abstract
Ovoid-shaped bacteria, such as Streptococcus pneumoniae (pneumococcus), have two spatially separated peptidoglycan (PG) synthase nanomachines that locate zonally to the midcell of dividing cells. The septal PG synthase bPBP2x:FtsW closes the septum of dividing pneumococcal cells, whereas the elongasome located on the outer edge of the septal annulus synthesizes peripheral PG outward. We showed previously by sm-TIRFm that the septal PG synthase moves circumferentially at midcell, driven by PG synthesis and not by FtsZ treadmilling. The pneumococcal elongasome consists of the PG synthase bPBP2b:RodA, regulators MreC, MreD, and RodZ, but not MreB, and genetically associated proteins Class A aPBP1a and muramidase MpgA. Given its zonal location separate from FtsZ, it was of considerable interest to determine the dynamics of proteins in the pneumococcal elongasome. We found that bPBP2b, RodA, and MreC move circumferentially with the same velocities and durations at midcell, driven by PG synthesis. However, outside of the midcell zone, the majority of these elongasome proteins move diffusively over the entire surface of cells. Depletion of MreC resulted in loss of circumferential movement of bPBP2b, and bPBP2b and RodA require each other for localization and circumferential movement. Notably, a fraction of aPBP1a molecules also moved circumferentially at midcell with velocities similar to those of components of the core elongasome, but for shorter durations. Other aPBP1a molecules were static at midcell or diffusing over cell bodies. Last, MpgA displayed nonprocessive, subdiffusive motion that was largely confined to the midcell region and less frequently detected over the cell body.
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Affiliation(s)
- Amilcar J. Perez
- Department of Biology, Indiana University Bloomington, Bloomington, IN47405
| | - Melissa M. Lamanna
- Department of Biology, Indiana University Bloomington, Bloomington, IN47405
| | - Kevin E. Bruce
- Department of Biology, Indiana University Bloomington, Bloomington, IN47405
| | - Marc A. Touraev
- Department of Biology, Indiana University Bloomington, Bloomington, IN47405
| | - Julia E. Page
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Sidney L. Shaw
- Department of Biology, Indiana University Bloomington, Bloomington, IN47405
| | | | - Malcolm E. Winkler
- Department of Biology, Indiana University Bloomington, Bloomington, IN47405
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12
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Amábile-Cuevas CF, Lund-Zaina S. Non-Canonical Aspects of Antibiotics and Antibiotic Resistance. Antibiotics (Basel) 2024; 13:565. [PMID: 38927231 PMCID: PMC11200725 DOI: 10.3390/antibiotics13060565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/09/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
The understanding of antibiotic resistance, one of the major health threats of our time, is mostly based on dated and incomplete notions, especially in clinical contexts. The "canonical" mechanisms of action and pharmacodynamics of antibiotics, as well as the methods used to assess their activity upon bacteria, have not changed in decades; the same applies to the definition, acquisition, selective pressures, and drivers of resistance. As a consequence, the strategies to improve antibiotic usage and overcome resistance have ultimately failed. This review gathers most of the "non-canonical" notions on antibiotics and resistance: from the alternative mechanisms of action of antibiotics and the limitations of susceptibility testing to the wide variety of selective pressures, lateral gene transfer mechanisms, ubiquity, and societal factors maintaining resistance. Only by having a "big picture" view of the problem can adequate strategies to harness resistance be devised. These strategies must be global, addressing the many aspects that drive the increasing prevalence of resistant bacteria aside from the clinical use of antibiotics.
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Affiliation(s)
| | - Sofia Lund-Zaina
- Department of Public Health, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
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13
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Qiu M, Xu Z. Berberine hydrochloride reduces staphyloxanthin synthesis by inhibiting fni genes in methicillin-resistant Staphylococcus aureus. Mol Biol Rep 2024; 51:761. [PMID: 38874884 DOI: 10.1007/s11033-024-09698-w] [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: 04/01/2024] [Accepted: 06/03/2024] [Indexed: 06/15/2024]
Abstract
BACKGROUND Methicillin-resistant Staphylococcus aureus (MRSA) poses a great health threat to humans. Looking for compounds that could reduce the resistance of S. aureus towards methicillin is an effective way to alleviate the antimicrobial resistance crisis. METHODS AND RESULTS Minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC), Time-killing growth curve, staphyloxanthin and penicillin-binding protein 2a (PBP2a) were detected. A quantitative polymerase chain reaction was used to measure the effect of BBH on the gene transcription profiles of MRSA. The MIC of MRSA-ST59-t437 towards oxacillin was 8 µg/ml, and MBC was 128 µg/ml. After adding a sub-inhibitory concentration of BBH, the MIC and MBC of MRSA-ST59-t478 towards oxacillin went down to 0.125 and 32 µg/ml respectively. The amount of PBP2a and staphyloxanthin were reduced after treatment with BBH. Moreover, the transcription levels of sarA, mecA and fni genes were downregulated. CONCLUSIONS It is for the first time reported that BBH could inhibit staphyloxanthin synthesis by inhibiting fni gene. Moreover, fni might be the target gene of sarA, and there might be another regulatory pathway to inhibit staphyloxanthin biosynthesis. BBH could effectively reduce the methicillin resistance of MRSA-ST59-t437 by downregulating fni, sarA and mecA genes.
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Affiliation(s)
- Mengyue Qiu
- Department of Sanitary Toxicology and Chemistry, Tianjin Medical University, Tianjin, 300070, China
- Tianjin Key Laboratory of Environment Nutrition and Public Health, Tianjin Medical University, Tianjin, 300070, China
- Center for International Collaborative Research on Environment Nutrition and Public Health, Tianjin Medical University, Tianjin, 300070, China
| | - Zhen Xu
- Department of Sanitary Toxicology and Chemistry, Tianjin Medical University, Tianjin, 300070, China.
- Tianjin Key Laboratory of Environment Nutrition and Public Health, Tianjin Medical University, Tianjin, 300070, China.
- Center for International Collaborative Research on Environment Nutrition and Public Health, Tianjin Medical University, Tianjin, 300070, China.
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14
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Adeniyi ET, Kruppa M, De Benedetti S, Ludwig KC, Krisilia V, Wassenberg TR, Both M, Schneider T, Müller TJJ, Kalscheuer R. Synthesis of Bisindole Alkaloids and Their Mode of Action against Methicillin-Resistant Staphylococcus Aureus. ACS Infect Dis 2024; 10:1958-1969. [PMID: 38841740 DOI: 10.1021/acsinfecdis.3c00657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
About 100,000 deaths are attributed annually to infections with methicillin-resistant Staphylococcus aureus (MRSA) despite concerted efforts toward vaccine development and clinical trials involving several preclinically efficacious drug candidates. This necessitates the development of alternative therapeutic options against this drug-resistant bacterial pathogen. Using the Masuda borylation-Suzuki coupling (MBSC) sequence, we previously synthesized and modified naturally occurring bisindole alkaloids, alocasin A, hyrtinadine A and scalaradine A, resulting in derivatives showing potent in vitro and in vivo antibacterial efficacy. Here, we report on a modified one-pot MBSC protocol for the synthesis of previously reported and several undescribed N-tosyl-protected bisindoles with anti-MRSA activities and moderate cytotoxicity against human monocytic and kidney cell lines. In continuation of the mode of action investigation of the previously synthesized membrane-permeabilizing hit compounds, mechanistic studies reveal that bisindoles impact the cytoplasmic membrane of Gram-positive bacteria by promiscuously interacting with lipid II and membrane phospholipids while rapidly dissipating membrane potential. The bactericidal and lipid II-interacting lead compounds 5c and 5f might be interesting starting points for drug development in the fight against MRSA.
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Affiliation(s)
- Emmanuel T Adeniyi
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Pharmaceutical Biology and Biotechnology, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Marco Kruppa
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Stefania De Benedetti
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn, 53115 Bonn, Germany
| | - Kevin C Ludwig
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn, 53115 Bonn, Germany
| | - Violetta Krisilia
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Pharmaceutical Biology and Biotechnology, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Tobias R Wassenberg
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Melissa Both
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Tanja Schneider
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn, 53115 Bonn, Germany
| | - Thomas J J Müller
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Rainer Kalscheuer
- Heinrich Heine University Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Pharmaceutical Biology and Biotechnology, Universitätsstraße 1, 40225 Düsseldorf, Germany
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15
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Ross CL, Lawer A, Sircombe KJ, Pletzer D, Gamble AB, Hook S. Site-Specific Antimicrobial Activity of a Dual-Responsive Ciprofloxacin Prodrug. J Med Chem 2024; 67:9599-9612. [PMID: 38780408 DOI: 10.1021/acs.jmedchem.4c00724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Bacterial infections create distinctive microenvironments with a unique mix of metabolites and enzymes compared with healthy tissues that can be used to trigger the activation of antibiotic prodrugs. Here, a single and dual prodrug masking the C3 carboxylate and C7 piperazine of the fluoroquinolone, ciprofloxacin, responsive to nitroreductase (NTR) and/or hydrogen sulfide (H2S), was developed. Masking both functional groups reduced the activity of the prodrug against Staphylococcus aureus and Escherichia coli, increasing its minimum inhibitory concentration (MIC) by ∼512-fold (S. aureus) and ∼8000-fold (E. coli strains), while masking a single group only increased the MIC by ∼128-fold. Bacteria subjected to prolonged prodrug exposure did not show any increase in resistance. Triggering assays demonstrated the conversion of prodrugs to ciprofloxacin, and in a murine infection model, responsive prodrugs showed antibacterial activity comparable to that of ciprofloxacin, suggesting in vivo activation of prodrugs. Thus, the potential for site-specific antibiotic treatment with reduced threat of resistance is demonstrated.
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Affiliation(s)
- Catherine L Ross
- School of Pharmacy, University of Otago, Dunedin 9054, New Zealand
- Department of Microbiology and Immunology, University of Otago, Dunedin 9054, New Zealand
| | - Aggie Lawer
- School of Pharmacy, University of Otago, Dunedin 9054, New Zealand
| | - Kathleen J Sircombe
- School of Pharmacy, University of Otago, Dunedin 9054, New Zealand
- Department of Microbiology and Immunology, University of Otago, Dunedin 9054, New Zealand
| | - Daniel Pletzer
- Department of Microbiology and Immunology, University of Otago, Dunedin 9054, New Zealand
| | - Allan B Gamble
- School of Pharmacy, University of Otago, Dunedin 9054, New Zealand
| | - Sarah Hook
- School of Pharmacy, University of Otago, Dunedin 9054, New Zealand
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16
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George NL, Bennett EC, Orlando BJ. Guarding the walls: the multifaceted roles of Bce modules in cell envelope stress sensing and antimicrobial resistance. J Bacteriol 2024:e0012324. [PMID: 38869304 DOI: 10.1128/jb.00123-24] [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: 06/14/2024] Open
Abstract
Bacteria have developed diverse strategies for defending their cell envelopes from external threats. In Firmicutes, one widespread strategy is to use Bce modules-membrane protein complexes that unite a peptide-detoxifying ABC transporter with a stress response coordinating two-component system. These modules provide specific, front-line defense for a wide variety of antimicrobial peptides and small molecule antibiotics as well as coordinate responses for heat, acid, and oxidative stress. Because of these abilities, Bce modules play important roles in virulence and the development of antibiotic resistance in a variety of pathogens, including Staphylococcus, Streptococcus, and Enterococcus species. Despite their importance, Bce modules are still poorly understood, with scattered functional data in only a small number of species. In this review, we will discuss Bce module structure in light of recent cryo-electron microscopy structures of the B. subtilis BceABRS module and explore the common threads and variations-on-a-theme in Bce module mechanisms across species. We also highlight the many remaining questions about Bce module function. Understanding these multifunctional membrane complexes will enhance our understanding of bacterial stress sensing and may point toward new therapeutic targets for highly resistant pathogens.
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Affiliation(s)
- Natasha L George
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
- Department of Microbiology, Genetics, and Immunology, Michigan State University, East Lansing, Michigan, USA
| | - Ellen C Bennett
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
- Department of Microbiology, Genetics, and Immunology, Michigan State University, East Lansing, Michigan, USA
| | - Benjamin J Orlando
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
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17
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Yang Y, Xie S, He F, Xu Y, Wang Z, Ihsan A, Wang X. Recent development and fighting strategies for lincosamide antibiotic resistance. Clin Microbiol Rev 2024; 37:e0016123. [PMID: 38634634 DOI: 10.1128/cmr.00161-23] [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] [Indexed: 04/19/2024] Open
Abstract
SUMMARYLincosamides constitute an important class of antibiotics used against a wide range of pathogens, including methicillin-resistant Staphylococcus aureus. However, due to the misuse of lincosamide and co-selection pressure, the resistance to lincosamide has become a serious concern. It is urgently needed to carefully understand the phenomenon and mechanism of lincosamide resistance to effectively prevent and control lincosamide resistance. To date, six mobile lincosamide resistance classes, including lnu, cfr, erm, vga, lsa, and sal, have been identified. These lincosamide resistance genes are frequently found on mobile genetic elements (MGEs), such as plasmids, transposons, integrative and conjugative elements, genomic islands, and prophages. Additionally, MGEs harbor the genes that confer resistance not only to antimicrobial agents of other classes but also to metals and biocides. The ultimate purpose of discovering and summarizing bacterial resistance is to prevent, control, and combat resistance effectively. This review highlights four promising strategies, including chemical modification of antibiotics, the development of antimicrobial peptides, the initiation of bacterial self-destruct program, and antimicrobial stewardship, to fight against resistance and safeguard global health.
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Affiliation(s)
- Yingying Yang
- National Reference Laboratory of Veterinary Drug Residues (HZAU), Huazhong Agricultural University, Wuhan, Hubei, China
- MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Shiyu Xie
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Fangjing He
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yindi Xu
- Institute of Animal Husbandry Research, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Zhifang Wang
- Institute of Animal Husbandry Research, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Awais Ihsan
- Department of Biosciences, COMSATS University Islamabad, Sahiwal campus, Islamabad, Pakistan
| | - Xu Wang
- National Reference Laboratory of Veterinary Drug Residues (HZAU), Huazhong Agricultural University, Wuhan, Hubei, China
- MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
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18
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Kennedy SJ, Atkinson CGF, Tubbs TJ, Baker BJ, Shaw LN. Culture-dependent identification of rare marine sediment bacteria from the Gulf of Mexico and Antarctica. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.11.598530. [PMID: 38915660 PMCID: PMC11195218 DOI: 10.1101/2024.06.11.598530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Laboratory-viable cultivars of previously uncultured bacteria further taxonomic understanding. Despite many years of modern microbiological investigations, the vast majority of bacterial taxonomy remains uncharacterized. While many attempts have been made to decrease this knowledge gap, culture-based approaches parse away at the unknown and are critical for improvement of both culturing techniques and computational prediction efficacy. To this end of providing culture-based approaches, we present a multi-faceted approach to recovering marine environmental bacteria. We employ combinations of nutritional availability, inoculation techniques, and incubation parameters in our recovery of marine sediment-associated bacteria from the Gulf of Mexico and Antarctica. The recovered biodiversity spans several taxa, with 16S-ITS-23S rRNA gene-based identification of multiple isolates belonging to rarer genera increasingly undergoing phylogenetic rearrangements. Our modifications to traditional culturing techniques have not only recovered rarer taxa, but also resulted in the recovery of biotechnologically promising bacteria. Together, we propose our stepwise combinations of recovery parameters as a viable approach to decreasing the bacterial knowledge gap.
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Affiliation(s)
- Sarah J. Kennedy
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, 4202 E. Fowler Avenue, ISA2015, Tampa, Florida 33620, United States
| | - Celine Grace F. Atkinson
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, 4202 E. Fowler Avenue, ISA2015, Tampa, Florida 33620, United States
| | - Tristan J. Tubbs
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, 4202 E. Fowler Avenue, ISA2015, Tampa, Florida 33620, United States
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, CHE205, Tampa, Florida 33620, United States
| | - Bill J. Baker
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, CHE205, Tampa, Florida 33620, United States
| | - Lindsey N. Shaw
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, 4202 E. Fowler Avenue, ISA2015, Tampa, Florida 33620, United States
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19
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Wan F, Torres MDT, Peng J, de la Fuente-Nunez C. Deep-learning-enabled antibiotic discovery through molecular de-extinction. Nat Biomed Eng 2024:10.1038/s41551-024-01201-x. [PMID: 38862735 DOI: 10.1038/s41551-024-01201-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 03/25/2024] [Indexed: 06/13/2024]
Abstract
Molecular de-extinction aims at resurrecting molecules to solve antibiotic resistance and other present-day biological and biomedical problems. Here we show that deep learning can be used to mine the proteomes of all available extinct organisms for the discovery of antibiotic peptides. We trained ensembles of deep-learning models consisting of a peptide-sequence encoder coupled with neural networks for the prediction of antimicrobial activity and used it to mine 10,311,899 peptides. The models predicted 37,176 sequences with broad-spectrum antimicrobial activity, 11,035 of which were not found in extant organisms. We synthesized 69 peptides and experimentally confirmed their activity against bacterial pathogens. Most peptides killed bacteria by depolarizing their cytoplasmic membrane, contrary to known antimicrobial peptides, which tend to target the outer membrane. Notably, lead compounds (including mammuthusin-2 from the woolly mammoth, elephasin-2 from the straight-tusked elephant, hydrodamin-1 from the ancient sea cow, mylodonin-2 from the giant sloth and megalocerin-1 from the extinct giant elk) showed anti-infective activity in mice with skin abscess or thigh infections. Molecular de-extinction aided by deep learning may accelerate the discovery of therapeutic molecules.
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Affiliation(s)
- Fangping Wan
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Marcelo D T Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Jacqueline Peng
- Graduate Group in Genomics and Computational Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA.
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, USA.
- Graduate Group in Genomics and Computational Biology, University of Pennsylvania, Philadelphia, PA, USA.
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20
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Li S, Liu J, Zhang T, Lu J, Li M, Zhang M, Chen H. Chemical modification, structure elucidation and antifungal mechanism studies of a peptide extracted from garlic (Allium sativum L.). JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024. [PMID: 38855916 DOI: 10.1002/jsfa.13633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 04/02/2024] [Accepted: 05/12/2024] [Indexed: 06/11/2024]
Abstract
BACKGROUND Garlic is a promising source of antimicrobial peptide separation, and chemical modification is an effective method for activity improvement. The present study aimed to improve the antifungal activity of a peptide extracted from garlic. Chemical modifications were conducted, and the structure-activity relationship and antifungal mechanism were investigated. RESULTS The results indicated that the cationic charge induced by Lys residue at the N-terminal was important for the antimicrobial activity, and the modified sequence exhibited significant antifungal activity with low mammalian toxicity and a low tendency of drug resistance (p < 0.05). The structure-activity relationship analysis revealed that the modified active peptide had a predominant α-helical structure and an inner cyclic correlation. Transcriptomic analysis showed that peptide KMLKKLFR (Lys-Met-Leu-Lys-Lyse-Leu-Phe-Arg) affected the rRNA processing and carbon metabolism process of Candida albicans. In addition, the membrane potential study indicated a non-membrane destruction mechanism, and molecular docking analysis and a DNA interaction assay suggested promising inner targets. CONCLUSION The results of the present study indicate that chemical modification by amino acid substitution was effective for antimicrobial activity improvement. The present study would benefit future antimicrobial peptide development and suggests that garlic is a great source of antibacterial peptides and peptide template separations for coping with antibiotic resistance. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Shuqin Li
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin, China
| | - Junyu Liu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin, China
| | - Tingting Zhang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin, China
| | - Jingyang Lu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin, China
| | - Mingyue Li
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin, China
| | - Min Zhang
- College of Food Science and Bioengineering, Tianjin Agricultural University, Tianjin, China
- State Key Laboratory of Nutrition and Safety, Tianjin University of Science & Technology, Tianjin, China
| | - Haixia Chen
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin, China
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21
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Zeng T, Liu S, Zou P, Yao X, Chen Q, Wei L, Wang Q, Zhang C, Zheng Y, Yu R. Create artilysins from a recombinant library to serve as bactericidal and antibiofilm agents targeting Pseudomonas aeruginosa. Int J Biol Macromol 2024; 273:132990. [PMID: 38857719 DOI: 10.1016/j.ijbiomac.2024.132990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 05/11/2024] [Accepted: 06/05/2024] [Indexed: 06/12/2024]
Abstract
Pseudomonas aeruginosa is a critical pathogen and novel treatments are urgently needed. The out membrane of P. aeruginosa facilitates biofilm formation and antibiotic resistance, and hinders the exogenous application against Gram-negative bacteria of endolysins. Engineered endolysins are investigated for enhancing antimicrobial activity, exemplified by artilysins. Nevertheless, existing research predominantly relies on laborious and time-consuming approaches of individually artilysin identification. This study proposes a novel strategy for expedited artilysin discovery using a recombinant artilysin library comprising proteins derived from 38 antimicrobial peptides and 8 endolysins. In this library, 19 colonies exhibited growth inhibition against P. aeruginosa exceeding 50 %, and three colonies were designated as dutarlysin-1, dutarlysin-2 and dutarlysin-3. Remarkably, dutarlysin-1, dutarlysin-2 and dutarlysin-3 demonstrated rapid and enhanced antibacterial activity, even minimum inhibitory concentration of them killed approximately 4.93 lg units, 6.75 lg units and 5.36 lg units P. aeruginosa, respectively. Dutarlysins were highly refractory to P. aeruginosa resistance development. Furthermore, 2 μmol/L dutarlysin-1 and dutarlysin-3 effectively eradicated over 76 % of the mature biofilm. These dutarlysins exhibited potential broad-spectrum activity against hospital susceptible Gram-negative bacteria. These results supported the effectiveness of this artilysins discovery strategy and suggested dutarlysin-1 and dutarlysin-3 could be promising antimicrobial agents for combating P. aeruginosa.
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Affiliation(s)
- Ting Zeng
- Department of Biopharmaceutics, West China School of Pharmacy, Sichuan University, Chengdu 610041, PR China; Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, PR China
| | - Shuang Liu
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, PR China
| | - Peixuan Zou
- Department of Biopharmaceutics, West China School of Pharmacy, Sichuan University, Chengdu 610041, PR China; Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, PR China
| | - Xin Yao
- Department of Biopharmaceutics, West China School of Pharmacy, Sichuan University, Chengdu 610041, PR China; Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, PR China
| | - Qiexin Chen
- Department of Biopharmaceutics, West China School of Pharmacy, Sichuan University, Chengdu 610041, PR China; Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, PR China
| | - Long Wei
- Department of Biopharmaceutics, West China School of Pharmacy, Sichuan University, Chengdu 610041, PR China; Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, PR China
| | - Qiantao Wang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, PR China
| | - Chun Zhang
- Department of Biopharmaceutics, West China School of Pharmacy, Sichuan University, Chengdu 610041, PR China; Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, PR China
| | - Yongxiang Zheng
- Department of Biopharmaceutics, West China School of Pharmacy, Sichuan University, Chengdu 610041, PR China; Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, PR China.
| | - Rong Yu
- Department of Biopharmaceutics, West China School of Pharmacy, Sichuan University, Chengdu 610041, PR China; Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, PR China.
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22
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Cheng Z, He BB, Lei K, Gao Y, Shi Y, Zhong Z, Liu H, Liu R, Zhang H, Wu S, Zhang W, Tang X, Li YX. Rule-based omics mining reveals antimicrobial macrocyclic peptides against drug-resistant clinical isolates. Nat Commun 2024; 15:4901. [PMID: 38851779 PMCID: PMC11162475 DOI: 10.1038/s41467-024-49215-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 05/28/2024] [Indexed: 06/10/2024] Open
Abstract
Antimicrobial resistance remains a significant global threat, driving up mortality rates worldwide. Ribosomally synthesized and post-translationally modified peptides have emerged as a promising source of novel peptide antibiotics due to their diverse chemical structures. Here, we report the discovery of new aminovinyl-(methyl)cysteine (Avi(Me)Cys)-containing peptide antibiotics through a synergistic approach combining biosynthetic rule-based omics mining and heterologous expression. We first bioinformatically identify 1172 RiPP biosynthetic gene clusters (BGCs) responsible for Avi(Me)Cys-containing peptides formation from a vast pool of over 50,000 bacterial genomes. Subsequently, we successfully establish the connection between three identified BGCs and the biosynthesis of five peptide antibiotics via biosynthetic rule-guided metabolic analysis. Notably, we discover a class V lanthipeptide, massatide A, which displays excellent activity against gram-positive pathogens, including drug-resistant clinical isolates like linezolid-resistant S. aureus and methicillin-resistant S. aureus, with a minimum inhibitory concentration of 0.25 μg/mL. The remarkable performance of massatide A in an animal infection model, coupled with a relatively low risk of resistance and favorable safety profile, positions it as a promising candidate for antibiotic development. Our study highlights the potential of Avi(Me)Cys-containing peptides in expanding the arsenal of antibiotics against multi-drug-resistant bacteria, offering promising drug leads in the ongoing battle against infectious diseases.
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Affiliation(s)
- Zhuo Cheng
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, 515832, China
| | - Bei-Bei He
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Kangfan Lei
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Ying Gao
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yuqi Shi
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Zheng Zhong
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Hongyan Liu
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Runze Liu
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Haili Zhang
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, 515832, China
| | - Song Wu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Wenxuan Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
| | - Xiaoyu Tang
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, 515832, China.
| | - Yong-Xin Li
- Department of Chemistry and The Swire Institute of Marine Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
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23
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Mundra S, Kabra A. Unveiling the Druggable Landscape of Bacterial Peptidyl tRNA Hydrolase: Insights into Structure, Function, and Therapeutic Potential. Biomolecules 2024; 14:668. [PMID: 38927071 PMCID: PMC11202043 DOI: 10.3390/biom14060668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/02/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
Bacterial peptidyl tRNA hydrolase (Pth) or Pth1 emerges as a pivotal enzyme involved in the maintenance of cellular homeostasis by catalyzing the release of peptidyl moieties from peptidyl-tRNA molecules and the maintenance of a free pool of specific tRNAs. This enzyme is vital for bacterial cells and an emerging drug target for various bacterial infections. Understanding the enzymatic mechanisms and structural intricacies of bacterial Pth is pivotal in designing novel therapeutics to combat antibiotic resistance. This review provides a comprehensive analysis of the multifaceted roles of Pth in bacterial physiology, shedding light on its significance as a potential drug target. This article delves into the diverse functions of Pth, encompassing its involvement in ribosome rescue, the maintenance of a free tRNA pool in bacterial systems, the regulation of translation fidelity, and stress response pathways within bacterial systems. Moreover, it also explores the druggability of bacterial Pth, emphasizing its promise as a target for antibacterial agents and highlighting the challenges associated with developing specific inhibitors against this enzyme. Structural elucidation represents a cornerstone in unraveling the catalytic mechanisms and substrate recognition of Pth. This review encapsulates the current structural insights of Pth garnered through various biophysical techniques, such as X-ray crystallography and NMR spectroscopy, providing a detailed understanding of the enzyme's architecture and conformational dynamics. Additionally, biophysical aspects, including its interaction with ligands, inhibitors, and substrates, are discussed, elucidating the molecular basis of bacterial Pth's function and its potential use in drug design strategies. Through this review article, we aim to put together all the available information on bacterial Pth and emphasize its potential in advancing innovative therapeutic interventions and combating bacterial infections.
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Affiliation(s)
- Surbhi Mundra
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
| | - Ashish Kabra
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, USA
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24
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Bennett ID, Burns JR, Ryadnov MG, Howorka S, Pyne ALB. Lipidated DNA Nanostructures Target and Rupture Bacterial Membranes. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2207585. [PMID: 38840451 DOI: 10.1002/smll.202207585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 03/01/2024] [Indexed: 06/07/2024]
Abstract
Chemistry has the power to endow supramolecular nanostructures with new biomedically relevant functions. Here it is reported that DNA nanostructures modified with cholesterol tags disrupt bacterial membranes to cause microbial cell death. The lipidated DNA nanostructures bind more readily to cholesterol-free bacterial membranes than to cholesterol-rich, eukaryotic membranes. These highly negatively charged, lipidated DNA nanostructures cause bacterial cell death by rupturing membranes. Strikingly, killing is mediated by clusters of barrel-shaped nanostructures that adhere to the membrane without the involvement of expected bilayer-puncturing barrels. These DNA nanomaterials may inspire the development of polymeric or small-molecule antibacterial agents that mimic the principles of selective binding and rupturing to help combat antimicrobial resistance.
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Affiliation(s)
- Isabel D Bennett
- London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London, WC1H 0AH, United Kingdom
- Division of Medicine, University College London, Cruciform Building, Gower Street, London, WC1E 6BT, United Kingdom
| | - Jonathan R Burns
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London, WC1H 0AJ, United Kingdom
| | - Maxim G Ryadnov
- National Physical Laboratory, Teddington, TW11 0LW, United Kingdom
- Department of Physics, King's College London, Strand Lane, London, WC2R 2LS, United Kingdom
| | - Stefan Howorka
- Department of Chemistry, Institute of Structural Molecular Biology, University College London, London, WC1H 0AJ, United Kingdom
| | - Alice L B Pyne
- London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London, WC1H 0AH, United Kingdom
- Department of Materials Science and Engineering, University of Sheffield, Sir Robert Hadfield Building, Sheffield, S1 3JD, United Kingdom
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25
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De Meester L, Vázquez-Domínguez E, Kassen R, Forest F, Bellon MR, Koskella B, Scherson RA, Colli L, Hendry AP, Crandall KA, Faith DP, Starger CJ, Geeta R, Araki H, Dulloo EM, Souffreau C, Schroer S, Johnson MTJ. A link between evolution and society fostering the UN sustainable development goals. Evol Appl 2024; 17:e13728. [PMID: 38884021 PMCID: PMC11178947 DOI: 10.1111/eva.13728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 06/18/2024] Open
Abstract
Given the multitude of challenges Earth is facing, sustainability science is of key importance to our continued existence. Evolution is the fundamental biological process underlying the origin of all biodiversity. This phylogenetic diversity fosters the resilience of ecosystems to environmental change, and provides numerous resources to society, and options for the future. Genetic diversity within species is also key to the ability of populations to evolve and adapt to environmental change. Yet, the value of evolutionary processes and the consequences of their impairment have not generally been considered in sustainability research. We argue that biological evolution is important for sustainability and that the concepts, theory, data, and methodological approaches used in evolutionary biology can, in crucial ways, contribute to achieving the UN Sustainable Development Goals (SDGs). We discuss how evolutionary principles are relevant to understanding, maintaining, and improving Nature Contributions to People (NCP) and how they contribute to the SDGs. We highlight specific applications of evolution, evolutionary theory, and evolutionary biology's diverse toolbox, grouped into four major routes through which evolution and evolutionary insights can impact sustainability. We argue that information on both within-species evolutionary potential and among-species phylogenetic diversity is necessary to predict population, community, and ecosystem responses to global change and to make informed decisions on sustainable production, health, and well-being. We provide examples of how evolutionary insights and the tools developed by evolutionary biology can not only inspire and enhance progress on the trajectory to sustainability, but also highlight some obstacles that hitherto seem to have impeded an efficient uptake of evolutionary insights in sustainability research and actions to sustain SDGs. We call for enhanced collaboration between sustainability science and evolutionary biology to understand how integrating these disciplines can help achieve the sustainable future envisioned by the UN SDGs.
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Affiliation(s)
- Luc De Meester
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB) Berlin Germany
- Laboratory of Aquatic Ecology, Evolution and Conservation KU Leuven Leuven Belgium
- Institute of Biology Freie University Berlin Berlin Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - Ella Vázquez-Domínguez
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México Ciudad Universitaria Ciudad de México Mexico
- Conservation and Evolutionary Genetics Group Estación Biológica de Doñana (EBD-CSIC) Sevilla Spain
| | - Rees Kassen
- Department of Biology McGill University Montreal Quebec Canada
| | | | - Mauricio R Bellon
- Comisión Nacional Para el Conocimiento y Uso de la Biodiversidad (CONABIO) México City Mexico
- Swette Center for Sustainable Food Systems Arizona State University Tempe Arizona USA
| | - Britt Koskella
- Department of Integrative Biology University of California Berkeley California USA
| | - Rosa A Scherson
- Laboratorio Evolución y Sistemática, Departamento de Silvicultura y Conservación de la Naturaleza Universidad de Chile Santiago Chile
| | - Licia Colli
- Dipartimento di Scienze Animali, Della Nutrizione e Degli Alimenti, BioDNA Centro di Ricerca Sulla Biodiversità e Sul DNA Antico, Facoltà di Scienze Agrarie, Alimentari e Ambientali Università Cattolica del Sacro Cuore Piacenza Italy
| | - Andrew P Hendry
- Redpath Museum & Department of Biology McGill University Montreal Quebec Canada
| | - Keith A Crandall
- Department of Biostatistics and Bioinformatics George Washington University Washington DC USA
- Department of Invertebrate Zoology, US National Museum of Natural History Smithsonian Institution Washington DC USA
| | | | - Craig J Starger
- School of Global Environmental Sustainability Colorado State University Fort Collins Colorado USA
| | - R Geeta
- Department of Botany University of Delhi New Delhi India
| | - Hitoshi Araki
- Research Faculty of Agriculture Hokkaido University Sapporo Japan
| | - Ehsan M Dulloo
- Effective Genetic Resources Conservation and Use Alliance of Bioversity International and CIAT Rome Italy
| | - Caroline Souffreau
- Laboratory of Aquatic Ecology, Evolution and Conservation KU Leuven Leuven Belgium
| | - Sibylle Schroer
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB) Berlin Germany
| | - Marc T J Johnson
- Department of Biology & Centre for Urban Environments University of Toronto Mississauga Mississauga Ontario Canada
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26
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Gopikrishnan M, Haryini S, C GPD. Emerging strategies and therapeutic innovations for combating drug resistance in Staphylococcus aureus strains: A comprehensive review. J Basic Microbiol 2024; 64:e2300579. [PMID: 38308076 DOI: 10.1002/jobm.202300579] [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: 10/03/2023] [Revised: 01/03/2024] [Accepted: 01/04/2024] [Indexed: 02/04/2024]
Abstract
In recent years, antibiotic therapy has encountered significant challenges due to the rapid emergence of multidrug resistance among bacteria responsible for life-threatening illnesses, creating uncertainty about the future management of infectious diseases. The escalation of antimicrobial resistance in the post-COVID era compared to the pre-COVID era has raised global concern. The prevalence of nosocomial-related infections, especially outbreaks of drug-resistant strains of Staphylococcus aureus, have been reported worldwide, with India being a notable hotspot for such occurrences. Various virulence factors and mutations characterize nosocomial infections involving S. aureus. The lack of proper alternative treatments leading to increased drug resistance emphasizes the need to investigate and examine recent research to combat future pandemics. In the current genomics era, the application of advanced technologies such as next-generation sequencing (NGS), machine learning (ML), and quantum computing (QC) for genomic analysis and resistance prediction has significantly increased the pace of diagnosing drug-resistant pathogens and insights into genetic intricacies. Despite prompt diagnosis, the elimination of drug-resistant infections remains unattainable in the absence of effective alternative therapies. Researchers are exploring various alternative therapeutic approaches, including phage therapy, antimicrobial peptides, photodynamic therapy, vaccines, host-directed therapies, and more. The proposed review mainly focuses on the resistance journey of S. aureus over the past decade, detailing its resistance mechanisms, prevalence in the subcontinent, innovations in rapid diagnosis of the drug-resistant strains, including the applicants of NGS and ML application along with QC, it helps to design alternative novel therapeutics approaches against S. aureus infection.
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Affiliation(s)
- Mohanraj Gopikrishnan
- Department of Integrative Biology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - Sree Haryini
- Department of Biomedical Sciences, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - George Priya Doss C
- Department of Integrative Biology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
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27
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Janzing NBM, Senges CHR, Dietze P, Haltli B, Marchbank DH, Kerr RG, Bandow JE. Mechanism of action of pseudopteroxazole and pseudopterosin G: Diterpenes from marine origin. Proteomics 2024; 24:e2300390. [PMID: 38158717 DOI: 10.1002/pmic.202300390] [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: 10/11/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 01/03/2024]
Abstract
Pseudopteroxazole (Ptx) and the pseudopterosins are marine natural products with promising antibacterial potential. While Ptx has attracted interest for its antimycobacterial activity, pseudopterosins are active against several clinically relevant pathogens. Both compound classes exhibit low cytotoxicity and accessibility to targeted synthesis, yet their antibacterial mechanisms remain elusive. In this study, we investigated the modes of action of Ptx and pseudopterosin G (PsG) in Bacillus subtilis employing an unbiased approach that combines gel-based proteomics with a mathematical similarity analysis of response profiles. Proteomic responses to sublethal concentrations of Ptx and PsG were compared to a library of antibiotic stress response profiles revealing that both induce a stress response characteristic for agents targeting the bacterial cell envelope by interfering with membrane-bound steps of cell wall biosynthesis. Microscopy-based assays confirmed that both compounds compromise the integrity of the bacterial cell wall without disrupting the membrane potential. Furthermore, LC-MSE analysis showed that the greater potency of PsG against B. subtilis, reflected in a lower MIC and a more pronounced proteomic response, may be rooted in a more effective association with and penetration of B. subtilis cells. We conclude that Ptx and PsG target the integrity of the gram-positive cell wall.
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Affiliation(s)
- Niklas B M Janzing
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Christoph H R Senges
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Pascal Dietze
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Bradley Haltli
- University of Prince Edward Island, Charlottetown, PE, Canada
- Nautilus Biosciences Croda, Charlottetown, Canada
| | - Douglas H Marchbank
- University of Prince Edward Island, Charlottetown, PE, Canada
- Nautilus Biosciences Croda, Charlottetown, Canada
| | - Russell G Kerr
- University of Prince Edward Island, Charlottetown, PE, Canada
| | - Julia E Bandow
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
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28
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Thompson TP, Gilmore BF. Exploring halophilic environments as a source of new antibiotics. Crit Rev Microbiol 2024; 50:341-370. [PMID: 37079280 DOI: 10.1080/1040841x.2023.2197491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 03/25/2023] [Indexed: 04/21/2023]
Abstract
Microbial natural products from microbes in extreme environments, including haloarchaea, and halophilic bacteria, possess a huge capacity to produce novel antibiotics. Additionally, enhanced isolation techniques and improved tools for genomic mining have expanded the efficiencies in the antibiotic discovery process. This review article provides a detailed overview of known antimicrobial compounds produced by halophiles from all three domains of life. We summarize that while halophilic bacteria, in particular actinomycetes, contribute the vast majority of these compounds the importance of understudied halophiles from other domains of life requires additional consideration. Finally, we conclude by discussing upcoming technologies- enhanced isolation and metagenomic screening, as tools that will be required to overcome the barriers to antimicrobial drug discovery. This review highlights the potential of these microbes from extreme environments, and their importance to the wider scientific community, with the hope of provoking discussion and collaborations within halophile biodiscovery. Importantly, we emphasize the importance of bioprospecting from communities of lesser-studied halophilic and halotolerant microorganisms as sources of novel therapeutically relevant chemical diversity to combat the high rediscovery rates. The complexity of halophiles will necessitate a multitude of scientific disciplines to unravel their potential and therefore this review reflects these research communities.
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Affiliation(s)
- Thomas P Thompson
- Biofilm Research Group, School of Pharmacy, Queen's University Belfast, Belfast, UK
| | - Brendan F Gilmore
- Biofilm Research Group, School of Pharmacy, Queen's University Belfast, Belfast, UK
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29
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Perez AJ, Lamanna MM, Bruce KE, Touraev MA, Page JE, Shaw SL, Tsui HCT, Winkler ME. Elongasome core proteins and class A PBP1a display zonal, processive movement at the midcell of Streptococcus pneumoniae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.10.575112. [PMID: 38328058 PMCID: PMC10849506 DOI: 10.1101/2024.01.10.575112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Ovoid-shaped bacteria, such as Streptococcus pneumoniae (pneumococcus), have two spatially separated peptidoglycan (PG) synthase nanomachines that locate zonally to the midcell of dividing cells. The septal PG synthase bPBP2x:FtsW closes the septum of dividing pneumococcal cells, whereas the elongasome located on the outer edge of the septal annulus synthesizes peripheral PG outward. We showed previously by sm-TIRFm that the septal PG synthase moves circumferentially at midcell, driven by PG synthesis and not by FtsZ treadmilling. The pneumococcal elongasome consists of the PG synthase bPBP2b:RodA, regulators MreC, MreD, and RodZ, but not MreB, and genetically associated proteins Class A aPBP1a and muramidase MpgA. Given its zonal location separate from FtsZ, it was of considerable interest to determine the dynamics of proteins in the pneumococcal elongasome. We found that bPBP2b, RodA, and MreC move circumferentially with the same velocities and durations at midcell, driven by PG synthesis. However, outside of the midcell zone, the majority of these elongasome proteins move diffusively over the entire surface of cells. Depletion of MreC resulted in loss of circumferential movement of bPBP2b, and bPBP2b and RodA require each other for localization and circumferential movement. Notably, a fraction of aPBP1a molecules also moved circumferentially at midcell with velocities similar to those of components of the core elongasome, but for shorter durations. Other aPBP1a molecules were static at midcell or diffusing over cell bodies. Last, MpgA displayed non-processive, subdiffusive motion that was largely confined to the midcell region and less frequently detected over the cell body.
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30
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Chen J, Wang W, Hu X, Yue Y, Lu X, Wang C, Wei B, Zhang H, Wang H. Medium-sized peptides from microbial sources with potential for antibacterial drug development. Nat Prod Rep 2024. [PMID: 38651516 DOI: 10.1039/d4np00002a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Covering: 1993 to the end of 2022As the rapid development of antibiotic resistance shrinks the number of clinically available antibiotics, there is an urgent need for novel options to fill the existing antibiotic pipeline. In recent years, antimicrobial peptides have attracted increased interest due to their impressive broad-spectrum antimicrobial activity and low probability of antibiotic resistance. However, macromolecular antimicrobial peptides of plant and animal origin face obstacles in antibiotic development because of their extremely short elimination half-life and poor chemical stability. Herein, we focus on medium-sized antibacterial peptides (MAPs) of microbial origin with molecular weights below 2000 Da. The low molecular weight is not sufficient to form complex protein conformations and is also associated to a better chemical stability and easier modifications. Microbially-produced peptides are often composed of a variety of non-protein amino acids and terminal modifications, which contribute to improving the elimination half-life of compounds. Therefore, MAPs have great potential for drug discovery and are likely to become key players in the development of next-generation antibiotics. In this review, we provide a detailed exploration of the modes of action demonstrated by 45 MAPs and offer a concise summary of the structure-activity relationships observed in these MAPs.
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Affiliation(s)
- Jianwei Chen
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Wei Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xubin Hu
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Yujie Yue
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xingyue Lu
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Chenjie Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Bin Wei
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Huawei Zhang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
| | - Hong Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China
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31
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Tan L, Ma R, Reeves T, Katz AJ, Levi N. Repurposing Farnesol for Combating Drug-Resistant and Persistent Single and Polymicrobial Biofilms. Antibiotics (Basel) 2024; 13:350. [PMID: 38667026 PMCID: PMC11047559 DOI: 10.3390/antibiotics13040350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/05/2024] [Accepted: 04/09/2024] [Indexed: 04/29/2024] Open
Abstract
Biofilm-associated infections caused by drug-resistant and persistent bacteria remain a significant clinical challenge. Here we report that farnesol, commercially available as a cosmetic and flavoring agent, shows significant anti-biofilm properties when dissolved in ethanol using a proprietary formulation emulsion technique. Farnesol in the new formulation inhibits biofilm formation and disrupts established biofilms for Gram-positive Staphylococcus aureus and Gram-negative Pseudomonas aeruginosa, including their polymicrobial biofilms, and, moreover, kills S. aureus persister cells that have developed tolerance to antibiotics. No resistance to farnesol was observed for S. aureus after twenty continuous passages. Farnesol combats biofilms by direct killing, while also facilitating biofilm detachment. Furthermore, farnesol was safe and effective for preventing and treating biofilm-associated infections of both types of bacteria in an ex vivo burned human skin model. These data suggest that farnesol in the new formulation is an effective broad-spectrum anti-biofilm agent with promising clinical potential. Due to its established safety, low-cost, versatility, and excellent efficacy-including ability to reduce persistent and resistant microbial populations-farnesol in the proprietary formulation represents a compelling transformative, translational, and commercial platform for addressing many unsolved clinical challenges.
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Affiliation(s)
- Li Tan
- Department of Plastic and Reconstructive Surgery, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA; (L.T.); (A.J.K.)
| | - Rong Ma
- Department of Plastic and Reconstructive Surgery, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA; (L.T.); (A.J.K.)
| | - Tony Reeves
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Adam J. Katz
- Department of Plastic and Reconstructive Surgery, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA; (L.T.); (A.J.K.)
| | - Nicole Levi
- Department of Plastic and Reconstructive Surgery, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA; (L.T.); (A.J.K.)
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32
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Xu Y, Yang T, Miao Y, Zhang Q, Yang M, Mao C. Injectable Phage-Loaded Microparticles Effectively Release Phages to Kill Methicillin-Resistant Staphylococcus aureus. ACS APPLIED MATERIALS & INTERFACES 2024; 16:17232-17241. [PMID: 38554078 PMCID: PMC11009905 DOI: 10.1021/acsami.3c19443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 01/30/2024] [Indexed: 04/01/2024]
Abstract
The increasing prevalence of bacterial multidrug antibiotic resistance has led to a serious threat to public health, emphasizing the urgent need for alternative antibacterial therapeutics. Lytic phages, a class of viruses that selectively infect and kill bacteria, offer promising potential as alternatives to antibiotics. However, injectable carriers with a desired release profile remain to be developed to deliver them to infection sites. To address this challenge, phage-loaded microparticles (Phage-MPs) have been developed to deliver phages to the infection site and release phages for an optimal therapeutic effect. The Phage-MPs are synthesized by allowing phages to be electrostatically attached onto the porous polyethylenimine-modified silk fibroin microparticles (SF-MPs). The high specific surface area of SF-MPs allows them to efficiently load phages, reaching about 1.25 × 1010 pfu per mg of microparticles. The Phage-MPs could release phages in a controlled manner to achieve potent antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA). Unlike the diffuse biodistribution of free phages post-intraperitoneal injection, Phage-MPs could continuously release phages to effectively boost the local phage concentration at the bacterial infection site after they are intraperitoneally injected into an abdominal MRSA-infected mouse model. In a mouse abdominal MRSA infection model, Phage-MPs significantly reduce the bacterial load in major organs, achieving an efficient therapeutic effect. Furthermore, Phage-MPs demonstrate outstanding biocompatibility both in vitro and in vivo. Overall, our research lays the foundation for a new generation of phage-based therapies to combat antibiotic-resistant bacterial infections.
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Affiliation(s)
- Yajing Xu
- School
of Materials Science and Engineering, Zhejiang
University, Hangzhou 310058, Zhejiang, China
| | - Tao Yang
- School
of Materials Science and Engineering, Zhejiang
University, Hangzhou 310058, Zhejiang, China
| | - Yao Miao
- School
of Materials Science and Engineering, Zhejiang
University, Hangzhou 310058, Zhejiang, China
| | - Qinglei Zhang
- Institute
of Applied Bioresource Research, College of Animal Science, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, Zhejiang, China
| | - Mingying Yang
- Institute
of Applied Bioresource Research, College of Animal Science, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058, Zhejiang, China
| | - Chuanbin Mao
- Department
of Biomedical Engineering, The Chinese University
of Hong Kong, Shatin 999077, Hong Kong SAR, China
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33
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Torres MDT, Cesaro A, de la Fuente-Nunez C. Peptides from non-immune proteins target infections through antimicrobial and immunomodulatory properties. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.25.586636. [PMID: 38585860 PMCID: PMC10996515 DOI: 10.1101/2024.03.25.586636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Encrypted peptides have been recently described as a new class of antimicrobial molecules. They have been proposed to play a role in host immunity and as alternatives to conventional antibiotics. Intriguingly, many of these peptides are found embedded in proteins unrelated to the immune system, suggesting that immunological responses may extend beyond traditional host immunity proteins. To test this idea, here we synthesized and tested representative peptides derived from non-immune proteins for their ability to exert antimicrobial and immunomodulatory properties. Our experiments revealed that most of the tested peptides from non-immune proteins, derived from structural proteins as well as proteins from the nervous and visual systems, displayed potent in vitro antimicrobial activity. These molecules killed bacterial pathogens by targeting their membrane, and those originating from the same region of the body exhibited synergistic effects when combined. Beyond their antimicrobial properties, nearly 90% of the peptides tested exhibited immunomodulatory effects, modulating inflammatory mediators such as IL-6, TNF-α, and MCP-1. Moreover, eight of the peptides identified, collagenin 3 and 4, zipperin-1 and 2, and immunosin-2, 3, 12, and 13, displayed anti-infective efficacy in two different preclinical mouse models, reducing bacterial infections by up to four orders of magnitude. Altogether, our results support the hypothesis that peptides from non-immune proteins may play a role in host immunity. These results potentially expand our notion of the immune system to include previously unrecognized proteins and peptides that may be activated upon infection to confer protection to the host.
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Yang H, Kreutzer AG, Nowick JS. Supramolecular Interactions of Teixobactin Analogues in the Crystal State. J Org Chem 2024; 89:5104-5108. [PMID: 38506062 PMCID: PMC11002827 DOI: 10.1021/acs.joc.3c02617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 03/01/2024] [Accepted: 03/07/2024] [Indexed: 03/21/2024]
Abstract
This Note presents the X-ray crystallographic structure of the N-methylated teixobactin analogue N-Me-d-Gln4,Lys10-teixobactin (1). Eight peptide molecules comprise the asymmetric unit, with each peptide molecule binding a chloride anion through hydrogen bonding with the amide NH group of residues 7, 8, 10, and 11. The peptide molecules form hydrogen-bonded antiparallel β-sheet dimers in the crystal lattice, with residues 1-3 comprising the dimerization interface. The dimers further assemble end-to-end in the crystal lattice.
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Affiliation(s)
- Hyunjun Yang
- Department
of Chemistry, University of California Irvine, Irvine, California 92697, United States
| | - Adam G. Kreutzer
- Department
of Chemistry, University of California Irvine, Irvine, California 92697, United States
| | - James S. Nowick
- Department
of Chemistry, University of California Irvine, Irvine, California 92697, United States
- Department
of Pharmaceutical Sciences, University of
California Irvine, Irvine, California 92697, United States
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35
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Mahey N, Tambat R, Kalia R, Ingavale R, Kodesia A, Chandal N, Kapoor S, Verma DK, Thakur KG, Jachak S, Nandanwar H. Pyrrole-based inhibitors of RND-type efflux pumps reverse antibiotic resistance and display anti-virulence potential. PLoS Pathog 2024; 20:e1012121. [PMID: 38593161 PMCID: PMC11003683 DOI: 10.1371/journal.ppat.1012121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 03/13/2024] [Indexed: 04/11/2024] Open
Abstract
Efflux pumps of the resistance-nodulation-cell division (RND) superfamily, particularly the AcrAB-TolC, and MexAB-OprM, besides mediating intrinsic and acquired resistance, also intervene in bacterial pathogenicity. Inhibitors of such pumps could restore the activities of antibiotics and curb bacterial virulence. Here, we identify pyrrole-based compounds that boost antibiotic activity in Escherichia coli and Pseudomonas aeruginosa by inhibiting their archetype RND transporters. Molecular docking and biophysical studies revealed that the EPIs bind to AcrB. The identified efflux pump inhibitors (EPIs) inhibit the efflux of fluorescent probes, attenuate persister formation, extend post-antibiotic effect, and diminish resistant mutant development. The bacterial membranes remained intact upon exposure to the EPIs. EPIs also possess an anti-pathogenic potential and attenuate P. aeruginosa virulence in vivo. The intracellular invasion of E. coli and P. aeruginosa inside the macrophages was hampered upon treatment with the lead EPI. The excellent efficacy of the EPI-antibiotic combination was evidenced in animal lung infection and sepsis protection models. These findings indicate that EPIs discovered herein with negligible toxicity are potential antibiotic adjuvants to address life-threatening Gram-negative bacterial infections.
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Affiliation(s)
- Nisha Mahey
- Clinical Microbiology & Antimicrobial Research Laboratory, CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Rushikesh Tambat
- Clinical Microbiology & Antimicrobial Research Laboratory, CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh, India
| | - Ritu Kalia
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Mohali, India
| | - Rajnita Ingavale
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Mohali, India
| | - Akriti Kodesia
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
- Structural Biology Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Nishtha Chandal
- Clinical Microbiology & Antimicrobial Research Laboratory, CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Srajan Kapoor
- Structural Biology Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Dipesh Kumar Verma
- Structural Biology Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Krishan Gopal Thakur
- Structural Biology Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Sanjay Jachak
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Mohali, India
| | - Hemraj Nandanwar
- Clinical Microbiology & Antimicrobial Research Laboratory, CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
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36
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Dwivedi GR, Pathak N, Tiwari N, Negi AS, Kumar A, Pal A, Sharma A, Darokar MP. Synergistic Antibacterial Activity of Gallic Acid Based Chalcone Indl 2 by Inhibiting Efflux Pump Transporters. Chem Biodivers 2024; 21:e202301820. [PMID: 38372508 DOI: 10.1002/cbdv.202301820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 02/16/2024] [Accepted: 02/17/2024] [Indexed: 02/20/2024]
Abstract
As a part of novel discovery of drugs from natural resources, present study was undertaken to explore the antibacterial potential of chalcone Indl-2 in combination with different group of antibiotics. MIC of antibiotics was reduced up to eight folds against the different cultures of E. coli by both chalcones. Among the two compounds, the i. e. 1-(3', 4,'5'-trimethoxyphenyl)-3-(3-Indyl)-prop-2-enone (6, Indl-2), a chalcone derivative of gallic acid (Indl-2) was better along with tetracycline (TET) worked synergistically and was found to inhibit efflux transporters as obvious by ethidium bromide efflux confirmed by ATPase assays and docking studies. In combination, Indl-2 kills the MDREC-KG4 cells, post-antibiotic effect (PAE) of TET was prolonged and mutant prevention concentration (MPC) of TET was also decreased. In-vivo studies revealed that Indl-2 reduces the concentration of TNF-α. In acute oral toxicity study, Indl-2 was non-toxic and well tolerated up-to dose of 2000 mg/kg. Perhaps, the study is going to report gallic acid derived chalcone as synergistic agent acting via inhibiting the primary efflux pumps.
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Affiliation(s)
- Gaurav Raj Dwivedi
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Near Kukrail Picnic Spot, P.O. CIMAP, Lucknow, 226015, India
- Microbiology Department, ICMR-Regional Medical Research Centre, Gorakhpur, 273013, U.P., India
| | - Nandini Pathak
- Phytochemistry Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Near Kukrail Picnic Spot, P.O. CIMAP, Lucknow, 226015, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, U.P. - 201002, India
| | - Nimisha Tiwari
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Near Kukrail Picnic Spot, P.O. CIMAP, Lucknow, 226015, India
| | - Arvind Singh Negi
- Phytochemistry Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Near Kukrail Picnic Spot, P.O. CIMAP, Lucknow, 226015, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, U.P. - 201002, India
| | - Akhil Kumar
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Near Kukrail Picnic Spot, P.O. CIMAP, Lucknow, 226015, India
| | - Anirban Pal
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Near Kukrail Picnic Spot, P.O. CIMAP, Lucknow, 226015, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, U.P. - 201002, India
| | - Ashok Sharma
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Near Kukrail Picnic Spot, P.O. CIMAP, Lucknow, 226015, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, U.P. - 201002, India
| | - Mahendra P Darokar
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Near Kukrail Picnic Spot, P.O. CIMAP, Lucknow, 226015, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, U.P. - 201002, India
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37
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Chen Z, Wu Y, Dolfing J, Zhuang S, Wang B, Li D, Huang S, Rittmann BE. Complex ammonium oxidation demands visualized resolution. Sci Bull (Beijing) 2024:S2095-9273(24)00210-X. [PMID: 38604937 DOI: 10.1016/j.scib.2024.03.054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Affiliation(s)
- Zhihao Chen
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resources of the People's Republic of China, Yichang 443605, China; University of Chinese Academy of Sciences, Beijing 100049, China; College of Nanjing, University of Chinese Academy of Sciences, Nanjing 211135, China
| | - Yonghong Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; Zigui Three Gorges Reservoir Ecosystem, Observation and Research Station of Ministry of Water Resources of the People's Republic of China, Yichang 443605, China; College of Nanjing, University of Chinese Academy of Sciences, Nanjing 211135, China.
| | - Jan Dolfing
- Faculty of Energy and Environment, Northumbria University, Newcastle-upon-Tyne NE1 8QH, UK
| | - Shunyao Zhuang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; College of Nanjing, University of Chinese Academy of Sciences, Nanjing 211135, China
| | - Baozhan Wang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Dan Li
- College of Urban Construction, Nanjing Tech University, Nanjing 211816, China
| | - Shan Huang
- Department of Civil and Environmental Engineering, Princeton University, Princeton NJ 08540, USA
| | - Bruce E Rittmann
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe AZ 85287-5701, USA
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38
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Kastrat E, Cheng HP. Escherichia coli has an undiscovered ability to inhibit the growth of both Gram-negative and Gram-positive bacteria. Sci Rep 2024; 14:7420. [PMID: 38548840 PMCID: PMC10978900 DOI: 10.1038/s41598-024-57996-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/25/2024] [Indexed: 04/01/2024] Open
Abstract
The ability for bacteria to form boundaries between neighboring colonies as the result of intra-species inhibition has been described for a limited number of species. Here, we report that intra-species inhibition is more common than previously recognized. We demonstrated that swimming colonies of four Escherichia coli strains and six other bacteria form inhibitory zones between colonies, which is not caused by nutrient depletion. This phenomenon was similarly observed with non-flagellated bacteria. We developed a square-streaking pattern assay which revealed that Escherichia coli BW25113 inhibits the growth of other E. coli, and surprisingly, other Gram-positive and negative bacteria, including multi-drug resistant clinical isolates. Altogether, our findings demonstrate intra-species inhibition is common and might be used by E. coli to inhibit other bacteria. Our findings raise the possibility for a common mechanism shared across bacteria for intra-species inhibition. This can be further explored for a potential new class of antibiotics.
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Affiliation(s)
- Ertan Kastrat
- Department of Biological Sciences, Lehman College, City University of New York, Bronx, NY, 10468, USA
- The Graduate Center, City University of New York, New York, NY, 10016, USA
| | - Hai-Ping Cheng
- Department of Biological Sciences, Lehman College, City University of New York, Bronx, NY, 10468, USA.
- The Graduate Center, City University of New York, New York, NY, 10016, USA.
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39
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Pelton JM, Hochuli JE, Sadecki PW, Katoh T, Suga H, Hicks LM, Muratov EN, Tropsha A, Bowers AA. Cheminformatics-Guided Cell-Free Exploration of Peptide Natural Products. J Am Chem Soc 2024; 146:8016-8030. [PMID: 38470819 PMCID: PMC11151186 DOI: 10.1021/jacs.3c11306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
There have been significant advances in the flexibility and power of in vitro cell-free translation systems. The increasing ability to incorporate noncanonical amino acids and complement translation with recombinant enzymes has enabled cell-free production of peptide-based natural products (NPs) and NP-like molecules. We anticipate that many more such compounds and analogs might be accessed in this way. To assess the peptide NP space that is directly accessible to current cell-free technologies, we developed a peptide parsing algorithm that breaks down peptide NPs into building blocks based on ribosomal translation logic. Using the resultant data set, we broadly analyze the biophysical properties of these privileged compounds and perform a retrobiosynthetic analysis to predict which peptide NPs could be directly synthesized in augmented cell-free translation reactions. We then tested these predictions by preparing a library of highly modified peptide NPs. Two macrocyclases, PatG and PCY1, were used to effect the head-to-tail macrocyclization of candidate NPs. This retrobiosynthetic analysis identified a collection of high-priority building blocks that are enriched throughout peptide NPs, yet they had not previously been tested in cell-free translation. To expand the cell-free toolbox into this space, we established, optimized, and characterized the flexizyme-enabled ribosomal incorporation of piperazic acids. Overall, these results demonstrate the feasibility of cell-free translation for peptide NP total synthesis while expanding the limits of the technology. This work provides a novel computational tool for exploration of peptide NP chemical space, that could be expanded in the future to allow design of ribosomal biosynthetic pathways for NPs and NP-like molecules.
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Affiliation(s)
- Jarrett M Pelton
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Joshua E Hochuli
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Patric W Sadecki
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Takayuki Katoh
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Leslie M Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Eugene N Muratov
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Alexander Tropsha
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Albert A Bowers
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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40
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Hughes D, Lawrence W, Peel J, Rosan DW, Ling L, Niiti N, Aaron P, Shukla R, MacGillavry H, Heine H, Martha H, Elbert W, Weingarth M, Lewis K. A Resistance-Evading Antibiotic for Treating Anthrax. RESEARCH SQUARE 2024:rs.3.rs-3991430. [PMID: 38585816 PMCID: PMC10996807 DOI: 10.21203/rs.3.rs-3991430/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
The antimicrobial resistance crisis (AMR) is associated with millions of deaths and undermines the franchise of medicine. Of particular concern is the threat of bioweapons, exemplified by anthrax. Introduction of novel antibiotics helps mitigate AMR, but does not address the threat of bioweapons with engineered resistance. We reasoned that teixobactin, an antibiotic with no detectable resistance, is uniquely suited to address the challenge of weaponized anthrax. Teixobactinbinds to immutable targets, precursors of cell wall polymers. Here we show that teixobactinis highly efficacious in a rabbit model of inhalation anthrax. Inhaling spores of Bacillus anthracis causes overwhelming morbidity and mortality. Treating rabbits with teixobactinafter the onset of disease rapidly eliminates the pathogen from blood and tissues, normalizes body temperature, and prevents tissue damage. Teixobactinassembles into an irreversible supramolecular structure of the surface of B. anthracis membrane, likely contributing to its unusually high potency against anthrax. Antibiotics evading resistance provide a rational solution to both AMR and engineered bioweapons.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Kim Lewis
- Antimicrobial Discovery Center, Department of Biology, Northeastern University
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41
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Wei X, Xue B, Ruan S, Guo J, Huang Y, Geng X, Wang D, Zhou C, Zheng J, Yuan Z. Supercharged precision killers: Genetically engineered biomimetic drugs of screened metalloantibiotics against Acinetobacter baumanni. SCIENCE ADVANCES 2024; 10:eadk6331. [PMID: 38517956 PMCID: PMC10959408 DOI: 10.1126/sciadv.adk6331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 02/16/2024] [Indexed: 03/24/2024]
Abstract
To eliminate multidrug-resistant bacteria of Acinetobacter baumannii, we screened 1100 Food and Drug Administration-approved small molecule drugs and accessed the broxyquinoline (Bq) efficacy in combination with various metal ions. Antibacterial tests demonstrated that the prepared Zn(Bq)2 complex showed ultralow minimum inhibitory concentration of ~0.21 micrograms per milliliter with no resistance after 30 passages. We then constructed the nano zeolitic imidazolate framework-8 (ZIF-8) as a drug carrier of Zn(Bq)2 and also incorporated the photosensitizer chlorin e6 (Ce6) to trace and boost the antibacterial effect. To further ensure the stable and targeted delivery, we genetically engineered outer membrane vesicles (OMVs) with the ability to selectively target A. baumannii. By coating the ZnBq/Ce6@ZIF-8 core with these OMV, the resulted drug (ZnBq/Ce6@ZIF-8@OMV) exhibited exceptional killing efficacy (>99.9999999%) of A. baumannii. In addition, in vitro and in vivo tests were also respectively carried out to inspect the remarkable efficacy of this previously unknown nanodrug in eradicating A. baumannii infections, including biofilms and meningitis.
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Affiliation(s)
- Xianyuan Wei
- Centre for Cognitive and brain Sciences and Ministry of Education Frontiers Science Center for Precision Oncology, University of Macau, Macau SAR, China
| | - Bin Xue
- Centre for Cognitive and brain Sciences and Ministry of Education Frontiers Science Center for Precision Oncology, University of Macau, Macau SAR, China
- Shenzhen Key Laboratory of Ultraintense Laser and Advanced Material Technology, Center for Intense Laser Application Technology and College of Engineering Physics, Shenzhen Technology University, Shenzhen 518118, China
| | - Shuangchen Ruan
- Shenzhen Key Laboratory of Ultraintense Laser and Advanced Material Technology, Center for Intense Laser Application Technology and College of Engineering Physics, Shenzhen Technology University, Shenzhen 518118, China
| | - Jintong Guo
- Centre for Cognitive and brain Sciences and Ministry of Education Frontiers Science Center for Precision Oncology, University of Macau, Macau SAR, China
| | - Yujing Huang
- Centre for Cognitive and brain Sciences and Ministry of Education Frontiers Science Center for Precision Oncology, University of Macau, Macau SAR, China
| | - Xiaorui Geng
- Centre for Cognitive and brain Sciences and Ministry of Education Frontiers Science Center for Precision Oncology, University of Macau, Macau SAR, China
| | - Dan Wang
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen 518000, China
| | - Cangtao Zhou
- Shenzhen Key Laboratory of Ultraintense Laser and Advanced Material Technology, Center for Intense Laser Application Technology and College of Engineering Physics, Shenzhen Technology University, Shenzhen 518118, China
| | - Jun Zheng
- Centre for Cognitive and brain Sciences and Ministry of Education Frontiers Science Center for Precision Oncology, University of Macau, Macau SAR, China
| | - Zhen Yuan
- Centre for Cognitive and brain Sciences and Ministry of Education Frontiers Science Center for Precision Oncology, University of Macau, Macau SAR, China
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42
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Oluwole A, Hernández-Rocamora VM, Cao Y, Li X, Vollmer W, Robinson CV, Bolla JR. Real-Time Biosynthetic Reaction Monitoring Informs the Mechanism of Action of Antibiotics. J Am Chem Soc 2024; 146:7007-7017. [PMID: 38428018 PMCID: PMC10941186 DOI: 10.1021/jacs.4c00081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 03/03/2024]
Abstract
The rapid spread of drug-resistant pathogens and the declining discovery of new antibiotics have created a global health crisis and heightened interest in the search for novel antibiotics. Beyond their discovery, elucidating mechanisms of action has necessitated new approaches, especially for antibiotics that interact with lipidic substrates and membrane proteins. Here, we develop a methodology for real-time reaction monitoring of the activities of two bacterial membrane phosphatases, UppP and PgpB. We then show how we can inhibit their activities using existing and newly discovered antibiotics such as bacitracin and teixobactin. Additionally, we found that the UppP dimer is stabilized by phosphatidylethanolamine, which, unexpectedly, enhanced the speed of substrate processing. Overall, our results demonstrate the potential of native mass spectrometry for real-time biosynthetic reaction monitoring of membrane enzymes, as well as their in situ inhibition and cofactor binding, to inform the mode of action of emerging antibiotics.
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Affiliation(s)
- Abraham
O. Oluwole
- Department
of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K.
- The
Kavli Institute for Nanoscience Discovery, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
| | - Víctor M. Hernández-Rocamora
- Centre
for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, U.K.
| | - Yihui Cao
- Department
of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR 999077, China
| | - Xuechen Li
- Department
of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong SAR 999077, China
| | - Waldemar Vollmer
- Centre
for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, U.K.
- Institute
for Molecular Bioscience, University of
Queensland, Carmody Road, Brisbane, Queensland 4072, Australia
| | - Carol V. Robinson
- Department
of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K.
- The
Kavli Institute for Nanoscience Discovery, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
| | - Jani R. Bolla
- The
Kavli Institute for Nanoscience Discovery, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
- Department
of Biology, University of Oxford, South Parks Road, Oxford OX1 3RB, U.K.
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43
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Espinoza JL, Phillips A, Prentice MB, Tan GS, Kamath PL, Lloyd KG, Dupont CL. Unveiling the Microbial Realm with VEBA 2.0: A modular bioinformatics suite for end-to-end genome-resolved prokaryotic, (micro)eukaryotic, and viral multi-omics from either short- or long-read sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.08.583560. [PMID: 38559265 PMCID: PMC10979853 DOI: 10.1101/2024.03.08.583560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The microbiome is a complex community of microorganisms, encompassing prokaryotic (bacterial and archaeal), eukaryotic, and viral entities. This microbial ensemble plays a pivotal role in influencing the health and productivity of diverse ecosystems while shaping the web of life. However, many software suites developed to study microbiomes analyze only the prokaryotic community and provide limited to no support for viruses and microeukaryotes. Previously, we introduced the Viral Eukaryotic Bacterial Archaeal (VEBA) open-source software suite to address this critical gap in microbiome research by extending genome-resolved analysis beyond prokaryotes to encompass the understudied realms of eukaryotes and viruses. Here we present VEBA 2.0 with key updates including a comprehensive clustered microeukaryotic protein database, rapid genome/protein-level clustering, bioprospecting, non-coding/organelle gene modeling, genome-resolved taxonomic/pathway profiling, long-read support, and containerization. We demonstrate VEBA's versatile application through the analysis of diverse case studies including marine water, Siberian permafrost, and white-tailed deer lung tissues with the latter showcasing how to identify integrated viruses. VEBA represents a crucial advancement in microbiome research, offering a powerful and accessible platform that bridges the gap between genomics and biotechnological solutions.
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Affiliation(s)
- Josh L. Espinoza
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA 92037, USA
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Allan Phillips
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA 92037, USA
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | | | - Gene S. Tan
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Pauline L. Kamath
- School of Food and Agriculture, University of Maine, Orono, ME 04469, USA
| | - Karen G. Lloyd
- Microbiology Department, University of Tennessee, Knoxville, TN 37917, USA
| | - Chris L. Dupont
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA 92037, USA
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
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44
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Megaw J, Skvortsov T, Gori G, Dabai AI, Gilmore BF, Allen CCR. A novel bioinformatic method for the identification of antimicrobial peptides in metagenomes. J Appl Microbiol 2024; 135:lxae045. [PMID: 38383848 DOI: 10.1093/jambio/lxae045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/16/2024] [Accepted: 02/20/2024] [Indexed: 02/23/2024]
Abstract
AIMS This study aimed to develop a new bioinformatic approach for the identification of novel antimicrobial peptides (AMPs), which did not depend on sequence similarity to known AMPs held within databases, but on structural mimicry of another antimicrobial compound, in this case an ultrashort, synthetic, cationic lipopeptide (C12-OOWW-NH2). METHODS AND RESULTS When applied to a collection of metagenomic datasets, our outlined bioinformatic method successfully identified several short (8-10aa) functional AMPs, the activity of which was verified via disk diffusion and minimum inhibitory concentration assays against a panel of 12 bacterial strains. Some peptides had activity comparable to, or in some cases, greater than, those from published studies that identified AMPs using more conventional methods. We also explored the effects of modifications, including extension of the peptides, observing an activity peak at 9-12aa. Additionally, the inclusion of a C-terminal amide enhanced activity in most cases. Our most promising candidate (named PB2-10aa-NH2) was thermally stable, lipid-soluble, and possessed synergistic activity with ethanol but not with a conventional antibiotic (streptomycin). CONCLUSIONS While several bioinformatic methods exist to predict AMPs, the approach outlined here is much simpler and can be used to quickly scan huge datasets. Searching for peptide sequences bearing structural similarity to other antimicrobial compounds may present a further opportunity to identify novel AMPs with clinical relevance, and provide a meaningful contribution to the pressing global issue of AMR.
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Affiliation(s)
- Julianne Megaw
- School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL, United Kingdom
| | - Timofey Skvortsov
- School of Pharmacy, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast BT9 7BL, United Kingdom
| | - Giulia Gori
- Department of Molecular and Developmental Medicine, University of Siena, 53100 Siena, Italy
| | - Aliyu I Dabai
- School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL, United Kingdom
| | - Brendan F Gilmore
- School of Pharmacy, Queen's University Belfast, Medical Biology Centre, 97 Lisburn Road, Belfast BT9 7BL, United Kingdom
| | - Christopher C R Allen
- School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast BT9 5DL, United Kingdom
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45
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Cain BN, Hergenrother PJ. Using permeation guidelines to design new antibiotics-A PASsagE into Pseudomonas aeruginosa. Clin Transl Med 2024; 14:e1600. [PMID: 38426413 PMCID: PMC10905542 DOI: 10.1002/ctm2.1600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 02/07/2024] [Indexed: 03/02/2024] Open
Affiliation(s)
- Brett N. Cain
- Department of Chemistry and Carl R. Woese Institute for Genomic BiologyUniversity of IllinoisUrbanaIllinoisUSA
| | - Paul J. Hergenrother
- Department of Chemistry and Carl R. Woese Institute for Genomic BiologyUniversity of IllinoisUrbanaIllinoisUSA
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46
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Zhao X, Wang W, Zeng X, Xu R, Yuan B, Yu W, Wang M, Jia R, Chen S, Zhu D, Liu M, Yang Q, Wu Y, Zhang S, Huang J, Ou X, Sun D, Cheng A. Klebicin E, a pore-forming bacteriocin of Klebsiella pneumoniae, exploits the porin OmpC and the Ton system for translocation. J Biol Chem 2024; 300:105694. [PMID: 38301890 PMCID: PMC10906532 DOI: 10.1016/j.jbc.2024.105694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 01/09/2024] [Accepted: 01/15/2024] [Indexed: 02/03/2024] Open
Abstract
Bacteriocins, which have narrow-spectrum activity and limited adverse effects, are promising alternatives to antibiotics. In this study, we identified klebicin E (KlebE), a small bacteriocin derived from Klebsiella pneumoniae. KlebE exhibited strong efficacy against multidrug-resistant K. pneumoniae isolates and conferred a significant growth advantage to the producing strain during intraspecies competition. A giant unilamellar vesicle leakage assay demonstrated the unique membrane permeabilization effect of KlebE, suggesting that it is a pore-forming toxin. In addition to a C-terminal toxic domain, KlebE also has a disordered N-terminal domain and a globular central domain. Pulldown assays and soft agar overlay experiments revealed the essential role of the outer membrane porin OmpC and the Ton system in KlebE recognition and cytotoxicity. Strong binding between KlebE and both OmpC and TonB was observed. The TonB-box, a crucial component of the toxin-TonB interaction, was identified as the 7-amino acid sequence (E3ETLTVV9) located in the N-terminal region. Further studies showed that a region near the bottom of the central domain of KlebE plays a primary role in recognizing OmpC, with eight residues surrounding this region identified as essential for KlebE toxicity. Finally, based on the discrepancies in OmpC sequences between the KlebE-resistant and sensitive strains, it was found that the 91st residue of OmpC, an aspartic acid residue, is a key determinant of KlebE toxicity. The identification and characterization of this toxin will facilitate the development of bacteriocin-based therapies targeting multidrug-resistant K. pneumoniae infections.
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Affiliation(s)
- Xinxin Zhao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Wenyu Wang
- Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiaoli Zeng
- Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Rong Xu
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, China
| | - Bing Yuan
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, China
| | - Wenyao Yu
- Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mingshu Wang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Renyong Jia
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Shun Chen
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Dekang Zhu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Mafeng Liu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Qiao Yang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Ying Wu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Shaqiu Zhang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Juan Huang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Xumin Ou
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Di Sun
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China
| | - Anchun Cheng
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China; Institute of Veterinary Medicine and Immunology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China; Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People's Republic of China, Chengdu, Sichuan, China.
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47
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Cui Y, Lanne A, Peng X, Browne E, Bhatt A, Coltman NJ, Craven P, Cox LR, Cundy NJ, Dale K, Feula A, Frampton J, Fung M, Morton M, Goff A, Salih M, Lang X, Li X, Moon C, Pascoe J, Portman V, Press C, Schulz-Utermoehl T, Lee S, Tortorella MD, Tu Z, Underwood ZE, Wang C, Yoshizawa A, Zhang T, Waddell SJ, Bacon J, Alderwick L, Fossey JS, Neagoie C. Azetidines Kill Multidrug-Resistant Mycobacterium tuberculosis without Detectable Resistance by Blocking Mycolate Assembly. J Med Chem 2024; 67:2529-2548. [PMID: 38331432 PMCID: PMC10895678 DOI: 10.1021/acs.jmedchem.3c01643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/19/2023] [Accepted: 01/23/2024] [Indexed: 02/10/2024]
Abstract
Tuberculosis (TB) is the leading cause of global morbidity and mortality resulting from infectious disease, with over 10.6 million new cases and 1.4 million deaths in 2021. This global emergency is exacerbated by the emergence of multidrug-resistant MDR-TB and extensively drug-resistant XDR-TB; therefore, new drugs and new drug targets are urgently required. From a whole cell phenotypic screen, a series of azetidines derivatives termed BGAz, which elicit potent bactericidal activity with MIC99 values <10 μM against drug-sensitive Mycobacterium tuberculosis and MDR-TB, were identified. These compounds demonstrate no detectable drug resistance. The mode of action and target deconvolution studies suggest that these compounds inhibit mycobacterial growth by interfering with cell envelope biogenesis, specifically late-stage mycolic acid biosynthesis. Transcriptomic analysis demonstrates that the BGAz compounds tested display a mode of action distinct from the existing mycobacterial cell wall inhibitors. In addition, the compounds tested exhibit toxicological and PK/PD profiles that pave the way for their development as antitubercular chemotherapies.
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Affiliation(s)
- Yixin Cui
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, U.K.
| | - Alice Lanne
- Institute
of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, West
Midlands B15 2TT, U.K.
| | - Xudan Peng
- State
Key Laboratory of Respiratory Disease, China-New Zealand Joint Laboratory
on Biomedicine and Health, Guangzhou Institutes of Biomedicine and
Health, Chinese Academy of Science, 190 Kai Yuan Avenue, Science Park, Guangzhou 510530, China
| | - Edward Browne
- Sygnature
Discovery, The Discovery Building, BioCity, Pennyfoot Street, Nottingham NG1 1GR, U.K.
| | - Apoorva Bhatt
- Institute
of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, West
Midlands B15 2TT, U.K.
| | - Nicholas J. Coltman
- School
of Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, U.K.
| | - Philip Craven
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, U.K.
| | - Liam R. Cox
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, U.K.
| | - Nicholas J. Cundy
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, U.K.
| | - Katie Dale
- Institute
of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, West
Midlands B15 2TT, U.K.
| | - Antonio Feula
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, U.K.
| | - Jon Frampton
- College of
Medical and Dental Sciences, University
of Birmingham, Edgbaston, Birmingham, West
Midlands B15 2TT, U.K.
| | - Martin Fung
- Centre
for Regenerative Medicine and Health, Hong Kong Institute of Science
& Innovation, Chinese Academy of Sciences, 15 Science Park West Avenue NT, Hong Kong SAR
| | - Michael Morton
- ApconiX
Ltd, BIOHUB at Alderly Park, Nether Alderly, Cheshire SK10 4TG, U.K.
| | - Aaron Goff
- Department
of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Falmer BN1 9PX, U.K.
| | - Mariwan Salih
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, U.K.
| | - Xingfen Lang
- State
Key Laboratory of Respiratory Disease, China-New Zealand Joint Laboratory
on Biomedicine and Health, Guangzhou Institutes of Biomedicine and
Health, Chinese Academy of Science, 190 Kai Yuan Avenue, Science Park, Guangzhou 510530, China
| | - Xingjian Li
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, U.K.
- State
Key Laboratory of Respiratory Disease, China-New Zealand Joint Laboratory
on Biomedicine and Health, Guangzhou Institutes of Biomedicine and
Health, Chinese Academy of Science, 190 Kai Yuan Avenue, Science Park, Guangzhou 510530, China
| | - Chris Moon
- TB
Research Group, National Infection Service, Public Health England (UKHSA), Manor Farm Road, Porton, Salisbury SP4 0JG, U.K.
| | - Jordan Pascoe
- TB
Research Group, National Infection Service, Public Health England (UKHSA), Manor Farm Road, Porton, Salisbury SP4 0JG, U.K.
| | - Vanessa Portman
- Sygnature
Discovery, The Discovery Building, BioCity, Pennyfoot Street, Nottingham NG1 1GR, U.K.
| | - Cara Press
- Institute
of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, West
Midlands B15 2TT, U.K.
| | - Timothy Schulz-Utermoehl
- Sygnature
Discovery, The Discovery Building, BioCity, Pennyfoot Street, Nottingham NG1 1GR, U.K.
| | - Suki Lee
- Centre
for Regenerative Medicine and Health, Hong Kong Institute of Science
& Innovation, Chinese Academy of Sciences, 15 Science Park West Avenue NT, Hong Kong SAR
| | - Micky D. Tortorella
- State
Key Laboratory of Respiratory Disease, China-New Zealand Joint Laboratory
on Biomedicine and Health, Guangzhou Institutes of Biomedicine and
Health, Chinese Academy of Science, 190 Kai Yuan Avenue, Science Park, Guangzhou 510530, China
- Centre
for Regenerative Medicine and Health, Hong Kong Institute of Science
& Innovation, Chinese Academy of Sciences, 15 Science Park West Avenue NT, Hong Kong SAR
| | - Zhengchao Tu
- State
Key Laboratory of Respiratory Disease, China-New Zealand Joint Laboratory
on Biomedicine and Health, Guangzhou Institutes of Biomedicine and
Health, Chinese Academy of Science, 190 Kai Yuan Avenue, Science Park, Guangzhou 510530, China
| | - Zoe E. Underwood
- TB
Research Group, National Infection Service, Public Health England (UKHSA), Manor Farm Road, Porton, Salisbury SP4 0JG, U.K.
| | - Changwei Wang
- State
Key Laboratory of Respiratory Disease, China-New Zealand Joint Laboratory
on Biomedicine and Health, Guangzhou Institutes of Biomedicine and
Health, Chinese Academy of Science, 190 Kai Yuan Avenue, Science Park, Guangzhou 510530, China
| | - Akina Yoshizawa
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, U.K.
| | - Tianyu Zhang
- State
Key Laboratory of Respiratory Disease, China-New Zealand Joint Laboratory
on Biomedicine and Health, Guangzhou Institutes of Biomedicine and
Health, Chinese Academy of Science, 190 Kai Yuan Avenue, Science Park, Guangzhou 510530, China
| | - Simon J. Waddell
- Department
of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Falmer BN1 9PX, U.K.
| | - Joanna Bacon
- TB
Research Group, National Infection Service, Public Health England (UKHSA), Manor Farm Road, Porton, Salisbury SP4 0JG, U.K.
| | - Luke Alderwick
- Institute
of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, West
Midlands B15 2TT, U.K.
- Discovery
Sciences, Charles River Laboratories, Chesterford Research Park, Saffron Walden CB10 1XL, U.K.
| | - John S. Fossey
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, U.K.
| | - Cleopatra Neagoie
- State
Key Laboratory of Respiratory Disease, China-New Zealand Joint Laboratory
on Biomedicine and Health, Guangzhou Institutes of Biomedicine and
Health, Chinese Academy of Science, 190 Kai Yuan Avenue, Science Park, Guangzhou 510530, China
- Centre
for Regenerative Medicine and Health, Hong Kong Institute of Science
& Innovation, Chinese Academy of Sciences, 15 Science Park West Avenue NT, Hong Kong SAR
- Visiting
Scientist, School of Chemistry, University
of Birmingham, Edgbaston, Birmingham, West
Midlands B15 2TT, U.K.
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48
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Iqbal S, Begum F, Ullah I, Jalal N, Shaw P. Peeling off the layers from microbial dark matter (MDM): recent advances, future challenges, and opportunities. Crit Rev Microbiol 2024:1-21. [PMID: 38385313 DOI: 10.1080/1040841x.2024.2319669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 02/10/2024] [Indexed: 02/23/2024]
Abstract
Microbes represent the most common organisms on Earth; however, less than 2% of microbial species in the environment can undergo cultivation for study under laboratory conditions, and the rest of the enigmatic, microbial world remains mysterious, constituting a kind of "microbial dark matter" (MDM). In the last two decades, remarkable progress has been made in culture-dependent and culture-independent techniques. More recently, studies of MDM have relied on culture-independent techniques to recover genetic material through either unicellular genomics or shotgun metagenomics to construct single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs), respectively, which provide information about evolution and metabolism. Despite the remarkable progress made in the past decades, the functional diversity of MDM still remains uncharacterized. This review comprehensively summarizes the recently developed culture-dependent and culture-independent techniques for characterizing MDM, discussing major challenges, opportunities, and potential applications. These activities contribute to expanding our knowledge of the microbial world and have implications for various fields including Biotechnology, Bioprospecting, Functional genomics, Medicine, Evolutionary and Planetary biology. Overall, this review aims to peel off the layers from MDM, shed light on recent advancements, identify future challenges, and illuminate the exciting opportunities that lie ahead in unraveling the secrets of this intriguing microbial realm.
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Affiliation(s)
- Sajid Iqbal
- Oujiang Lab (Zhejiang Laboratory for Regenerative Medicine, Vision, and Brain Health), Wenzhou, China
- School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, China
| | - Farida Begum
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Ihsan Ullah
- College of Chemical Engineering, Fuzhou University, Fuzhou, China
| | - Nasir Jalal
- Oujiang Lab (Zhejiang Laboratory for Regenerative Medicine, Vision, and Brain Health), Wenzhou, China
| | - Peter Shaw
- Oujiang Lab (Zhejiang Laboratory for Regenerative Medicine, Vision, and Brain Health), Wenzhou, China
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49
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Lafuente I, Sevillano E, Peña N, Cuartero A, Hernández PE, Cintas LM, Muñoz-Atienza E, Borrero J. Production of Pumilarin and a Novel Circular Bacteriocin, Altitudin A, by Bacillus altitudinis ECC22, a Soil-Derived Bacteriocin Producer. Int J Mol Sci 2024; 25:2020. [PMID: 38396696 PMCID: PMC10888436 DOI: 10.3390/ijms25042020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/01/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
The rise of antimicrobial resistance poses a significant global health threat, necessitating urgent efforts to identify novel antimicrobial agents. In this study, we undertook a thorough screening of soil-derived bacterial isolates to identify candidates showing antimicrobial activity against Gram-positive bacteria. A highly active antagonistic isolate was initially identified as Bacillus altitudinis ECC22, being further subjected to whole genome sequencing. A bioinformatic analysis of the B. altitudinis ECC22 genome revealed the presence of two gene clusters responsible for synthesizing two circular bacteriocins: pumilarin and a novel circular bacteriocin named altitudin A, alongside a closticin 574-like bacteriocin (CLB) structural gene. The synthesis and antimicrobial activity of the bacteriocins, pumilarin and altitudin A, were evaluated and validated using an in vitro cell-free protein synthesis (IV-CFPS) protocol coupled to a split-intein-mediated ligation procedure, as well as through their in vivo production by recombinant E. coli cells. However, the IV-CFPS of CLB showed no antimicrobial activity against the bacterial indicators tested. The purification of the bacteriocins produced by B. altitudinis ECC22, and their evaluation by MALDI-TOF MS analysis and LC-MS/MS-derived targeted proteomics identification combined with massive peptide analysis, confirmed the production and circular conformation of pumilarin and altitudin A. Both bacteriocins exhibited a spectrum of activity primarily directed against other Bacillus spp. strains. Structural three-dimensional predictions revealed that pumilarin and altitudin A may adopt a circular conformation with five- and four-α-helices, respectively.
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Affiliation(s)
- Irene Lafuente
- Departamento de Nutrición y Ciencia de los Alimentos (NUTRYCIAL), Sección Departamental de Nutrición y Ciencia de los Alimentos (SD-NUTRYCIAL), Facultad de Veterinaria, Universidad Complutense de Madrid (UCM), Avenida Puerta de Hierro, s/n, 28040 Madrid, Madrid, Spain; (I.L.); (E.S.); (N.P.); (P.E.H.); (L.M.C.)
| | - Ester Sevillano
- Departamento de Nutrición y Ciencia de los Alimentos (NUTRYCIAL), Sección Departamental de Nutrición y Ciencia de los Alimentos (SD-NUTRYCIAL), Facultad de Veterinaria, Universidad Complutense de Madrid (UCM), Avenida Puerta de Hierro, s/n, 28040 Madrid, Madrid, Spain; (I.L.); (E.S.); (N.P.); (P.E.H.); (L.M.C.)
| | - Nuria Peña
- Departamento de Nutrición y Ciencia de los Alimentos (NUTRYCIAL), Sección Departamental de Nutrición y Ciencia de los Alimentos (SD-NUTRYCIAL), Facultad de Veterinaria, Universidad Complutense de Madrid (UCM), Avenida Puerta de Hierro, s/n, 28040 Madrid, Madrid, Spain; (I.L.); (E.S.); (N.P.); (P.E.H.); (L.M.C.)
| | - Alicia Cuartero
- Centro de Educación Infantil, Primaria y Secundaria Obligatoria (CEIPSO) El Cantizal, Avenida Atenas s/n, 28232 Las Rozas, Madrid, Spain;
| | - Pablo E. Hernández
- Departamento de Nutrición y Ciencia de los Alimentos (NUTRYCIAL), Sección Departamental de Nutrición y Ciencia de los Alimentos (SD-NUTRYCIAL), Facultad de Veterinaria, Universidad Complutense de Madrid (UCM), Avenida Puerta de Hierro, s/n, 28040 Madrid, Madrid, Spain; (I.L.); (E.S.); (N.P.); (P.E.H.); (L.M.C.)
| | - Luis M. Cintas
- Departamento de Nutrición y Ciencia de los Alimentos (NUTRYCIAL), Sección Departamental de Nutrición y Ciencia de los Alimentos (SD-NUTRYCIAL), Facultad de Veterinaria, Universidad Complutense de Madrid (UCM), Avenida Puerta de Hierro, s/n, 28040 Madrid, Madrid, Spain; (I.L.); (E.S.); (N.P.); (P.E.H.); (L.M.C.)
| | - Estefanía Muñoz-Atienza
- Departamento de Nutrición y Ciencia de los Alimentos (NUTRYCIAL), Sección Departamental de Nutrición y Ciencia de los Alimentos (SD-NUTRYCIAL), Facultad de Veterinaria, Universidad Complutense de Madrid (UCM), Avenida Puerta de Hierro, s/n, 28040 Madrid, Madrid, Spain; (I.L.); (E.S.); (N.P.); (P.E.H.); (L.M.C.)
| | - Juan Borrero
- Departamento de Nutrición y Ciencia de los Alimentos (NUTRYCIAL), Sección Departamental de Nutrición y Ciencia de los Alimentos (SD-NUTRYCIAL), Facultad de Veterinaria, Universidad Complutense de Madrid (UCM), Avenida Puerta de Hierro, s/n, 28040 Madrid, Madrid, Spain; (I.L.); (E.S.); (N.P.); (P.E.H.); (L.M.C.)
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50
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Peng Z, Wang D, He Y, Wei Z, Xie M, Xiong T. Gut Distribution, Impact Factor, and Action Mechanism of Bacteriocin-Producing Beneficial Microbes as Promising Antimicrobial Agents in Gastrointestinal Infection. Probiotics Antimicrob Proteins 2024:10.1007/s12602-024-10222-6. [PMID: 38319538 DOI: 10.1007/s12602-024-10222-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2024] [Indexed: 02/07/2024]
Abstract
Gastrointestinal (GI) infection by intestinal pathogens poses great threats to human health, and the therapeutic use of antibiotics has reached a bottleneck due to drug resistance. The developments of antimicrobial peptides produced by beneficial bacteria have drawn attention by virtue of effective, safe, and not prone to developing resistance. Though bacteriocin as antimicrobial agent in gut infection has been intensively investigated and reviewed, reviews on that of bacteriocin-producing beneficial microbes are very rare. It is important to explicitly state the prospect of bacteriocin-producing microbes in prevention of gastrointestinal infection towards their application in host. This review discusses the potential of gut as an appropriate resource for mining targeted bacteriocin-producing microbes. Then, host-related factors affecting the bacteriocin production and activity of bacteriocin-producing microbes in the gut are summarized. Accordingly, the multiple mechanisms (direct inhibition and indirect inhibition) behind the preventive effects of bacteriocin-producing microbes on gut infection are discussed. Finally, we propose several targeted strategies for the manipulation of bacteriocin-producing beneficial microbes to improve their performance in antimicrobial outcomes. We anticipate an upcoming emergence of developments and applications of bacteriocin-producing beneficial microbes as antimicrobial agent in gut infection induced by pathogenic bacteria.
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Affiliation(s)
- Zhen Peng
- School of Food Science and Technology, Nanchang University, Nanchang, China
- International Institute of Food Innovation Co., Ltd., Nanchang University, Nanchang, Jiangxi, China
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, China
| | - Donglin Wang
- School of Food Science and Technology, Nanchang University, Nanchang, China
| | - Yuyan He
- School of Food Science and Technology, Nanchang University, Nanchang, China
| | - Ziqi Wei
- School of Food Science and Technology, Nanchang University, Nanchang, China
| | - Mingyong Xie
- School of Food Science and Technology, Nanchang University, Nanchang, China
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, China
| | - Tao Xiong
- School of Food Science and Technology, Nanchang University, Nanchang, China.
- International Institute of Food Innovation Co., Ltd., Nanchang University, Nanchang, Jiangxi, China.
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, China.
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