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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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2
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Ancajas CMF, Oyedele AS, Butt CM, Walker AS. Advances, opportunities, and challenges in methods for interrogating the structure activity relationships of natural products. Nat Prod Rep 2024. [PMID: 38912779 DOI: 10.1039/d4np00009a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Time span in literature: 1985-early 2024Natural products play a key role in drug discovery, both as a direct source of drugs and as a starting point for the development of synthetic compounds. Most natural products are not suitable to be used as drugs without further modification due to insufficient activity or poor pharmacokinetic properties. Choosing what modifications to make requires an understanding of the compound's structure-activity relationships. Use of structure-activity relationships is commonplace and essential in medicinal chemistry campaigns applied to human-designed synthetic compounds. Structure-activity relationships have also been used to improve the properties of natural products, but several challenges still limit these efforts. Here, we review methods for studying the structure-activity relationships of natural products and their limitations. Specifically, we will discuss how synthesis, including total synthesis, late-stage derivatization, chemoenzymatic synthetic pathways, and engineering and genome mining of biosynthetic pathways can be used to produce natural product analogs and discuss the challenges of each of these approaches. Finally, we will discuss computational methods including machine learning methods for analyzing the relationship between biosynthetic genes and product activity, computer aided drug design techniques, and interpretable artificial intelligence approaches towards elucidating structure-activity relationships from models trained to predict bioactivity from chemical structure. Our focus will be on these latter topics as their applications for natural products have not been extensively reviewed. We suggest that these methods are all complementary to each other, and that only collaborative efforts using a combination of these techniques will result in a full understanding of the structure-activity relationships of natural products.
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Affiliation(s)
| | | | - Caitlin M Butt
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
| | - Allison S Walker
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
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3
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Kim J, Kim J, Yun H, Ganbaatar B, Tahmasebi A, Seo SI, Kim PI, Lee CW. New strain Brevibacillus laterosporus TSA31-5 produces both brevicidine and brevibacillin, exhibiting distinct antibacterial modes of action against Gram-negative and Gram-positive bacteria. PLoS One 2024; 19:e0294474. [PMID: 38558002 PMCID: PMC10984550 DOI: 10.1371/journal.pone.0294474] [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: 08/15/2023] [Accepted: 11/01/2023] [Indexed: 04/04/2024] Open
Abstract
The growing prevalence of antibiotic resistance has made it imperative to search for new antimicrobial compounds derived from natural products. In the present study, Brevibacillus laterosporus TSA31-5, isolated from red clay soil, was chosen as the subject for conducting additional antibacterial investigations. The fractions exhibiting the highest antibacterial activity (30% acetonitrile eluent from solid phase extraction) were purified through RP-HPLC. Notably, two compounds (A and B) displayed the most potent antibacterial activity against both Escherichia coli and Staphylococcus aureus. ESI-MS/MS spectroscopy and NMR analysis confirmed that compound A corresponds to brevicidine and compound B to brevibacillin. Particularly, brevicidine displayed notable antibacterial activity against Gram-negative bacteria, with a minimum inhibitory concentration (MIC) range of 1-8 μg/mL. On the other hand, brevibacillin exhibited robust antimicrobial effectiveness against both Gram-positive bacterial strains (MIC range of 2-4 μg/mL) and Gram-negative bacteria (MIC range of 4-64 μg/mL). Scanning electron microscopy analysis and fluorescence assays uncovered distinctive morphological alterations in bacterial cell membranes induced by brevicidine and brevibacillin. These observations imply distinct mechanisms of antibacterial activity exhibited by the peptides. Brevicidine exhibited no hemolysis or cytotoxicity up to 512 μg/mL, comparable to the negative control. This suggests its promising therapeutic potential in treating infectious diseases. Conversely, brevibacillin demonstrated elevated cytotoxicity in in vitro assays. Nonetheless, owing to its noteworthy antimicrobial activity against pathogenic bacteria, brevibacillin could still be explored as a promising antimicrobial agent.
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Affiliation(s)
- Jeongeun Kim
- Department of Chemistry, Chonnam National University, Gwangju, Republic of Korea
| | - Jueun Kim
- Department of Chemistry, Chonnam National University, Gwangju, Republic of Korea
- Research Center, DAESANG InnoPark, Gangseo-gu, Seoul, Republic of Korea
| | - Hyosuk Yun
- Department of Chemistry, Chonnam National University, Gwangju, Republic of Korea
| | | | - Aminallah Tahmasebi
- Department of Chemistry, Chonnam National University, Gwangju, Republic of Korea
- Department of Agriculture, Minab Higher Education Center, University of Hormozgan, Bandar Abbas, Iran
| | - Sun Il Seo
- Center for Industrialization of Agricultural and Livestock Microorganism, Jeongeup-si, Jeollabuk-do, Republic of Korea
| | - Pyoung Il Kim
- Center for Industrialization of Agricultural and Livestock Microorganism, Jeongeup-si, Jeollabuk-do, Republic of Korea
| | - Chul Won Lee
- Department of Chemistry, Chonnam National University, Gwangju, Republic of Korea
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4
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Palpal-Latoc D, Horsfall AJ, Cameron AJ, Campbell G, Ferguson SA, Cook GM, Sander V, Davidson AJ, Harris PWR, Brimble MA. Synthesis, Structure-Activity Relationship Study, Bioactivity, and Nephrotoxicity Evaluation of the Proposed Structure of the Cyclic Lipodepsipeptide Brevicidine B. JOURNAL OF NATURAL PRODUCTS 2024. [PMID: 38423998 DOI: 10.1021/acs.jnatprod.3c00876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
The brevicidines represent a novel class of nonribosomal antimicrobial peptides that possess remarkable potency and selectivity toward highly problematic and resistant Gram-negative pathogenic bacteria. A recently discovered member of the brevicidine family, coined brevicidine B (2), comprises a single amino acid substitution (from d-Tyr2 to d-Phe2) in the amino acid sequence of the linear moiety of brevicidine (1) and was reported to exhibit broader antimicrobial activity against both Gram-negative (MIC = 2-4 μgmL-1) and Gram-positive (MIC = 2-8 μgmL-1) pathogens. Encouraged by this, we herein report the first total synthesis of the proposed structure of brevicidine B (2), building on our previously reported synthetic strategy to access brevicidine (1). In agreement with the original isolation paper, pleasingly, synthetic 2 demonstrated antimicrobial activity toward Escherichia coli, Pseudomonas aeruginosa, and Klebsiella pneumoniae (MIC = 4-8 μgmL-1). Interestingly, however, synthetic 2 was inactive toward all of the tested Gram-positive pathogens, including methicillin-resistant Staphylococcus aureus strains. Substitution of d-Phe2 with its enantiomer, and other hydrophobic residues, yields analogues that were either inactive or only exhibited activity toward Gram-negative strains. The striking difference in the biological activity of our synthetic 2 compared to the reported natural compound warrants the re-evaluation of the original natural product for purity or possible differences in relative configuration. Finally, the evaluation of synthetic 1 and 2 in a human kidney organoid model of nephrotoxicity revealed substantial toxicity of both compounds, although 1 was less toxic than 2 and polymyxin B. These results indicate that modification to position 2 may afford a strategy to mitigate the nephrotoxicity of brevicidine.
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Affiliation(s)
- Dennise Palpal-Latoc
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland 1010, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3 Symonds Street, Auckland 1010, New Zealand
- School of Biological Sciences, The University of Auckland, 3A Symonds Street, Auckland 1010, New Zealand
| | - Aimee J Horsfall
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland 1010, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3 Symonds Street, Auckland 1010, New Zealand
- School of Biological Sciences, The University of Auckland, 3A Symonds Street, Auckland 1010, New Zealand
| | - Alan J Cameron
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland 1010, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3 Symonds Street, Auckland 1010, New Zealand
- School of Biological Sciences, The University of Auckland, 3A Symonds Street, Auckland 1010, New Zealand
| | - Georgia Campbell
- Department of Microbiology and Immunology, School of Medical Sciences, The University of Otago, 720 Cumberland Street, Dunedin 9054, New Zealand
| | - Scott A Ferguson
- Department of Microbiology and Immunology, School of Medical Sciences, The University of Otago, 720 Cumberland Street, Dunedin 9054, New Zealand
| | - Gregory M Cook
- Department of Microbiology and Immunology, School of Medical Sciences, The University of Otago, 720 Cumberland Street, Dunedin 9054, New Zealand
| | - Veronika Sander
- Faculty of Medical and Health Sciences, The University of Auckland 85 Park Road, Grafton, Auckland 1023, New Zealand
| | - Alan J Davidson
- Faculty of Medical and Health Sciences, The University of Auckland 85 Park Road, Grafton, Auckland 1023, New Zealand
| | - Paul W R Harris
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland 1010, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3 Symonds Street, Auckland 1010, New Zealand
- School of Biological Sciences, The University of Auckland, 3A Symonds Street, Auckland 1010, New Zealand
| | - Margaret A Brimble
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland 1010, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3 Symonds Street, Auckland 1010, New Zealand
- School of Biological Sciences, The University of Auckland, 3A Symonds Street, Auckland 1010, New Zealand
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5
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Zhong X, Deng K, Yang X, Song X, Zou Y, Zhou X, Tang H, Li L, Fu Y, Yin Z, Wan H, Zhao X. Brevicidine acts as an effective sensitizer of outer membrane-impermeable conventional antibiotics for Acinetobacter baumannii treatment. Front Microbiol 2023; 14:1304198. [PMID: 38173680 PMCID: PMC10762313 DOI: 10.3389/fmicb.2023.1304198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 11/27/2023] [Indexed: 01/05/2024] Open
Abstract
The antibiotic resistance of Acinetobacter baumannii poses a significant threat to global public health, especially those strains that are resistant to carbapenems. Therefore, novel strategies are desperately needed for the treatment of infections caused by antibiotic-resistant A. baumannii. In this study, we report that brevicidine, a bacterial non-ribosomally produced cyclic lipopeptide, shows synergistic effects with multiple outer membrane-impermeable conventional antibiotics against A. baumannii. In particular, brevicidine, at a concentration of 1 μM, lowered the minimum inhibitory concentration of erythromycin, azithromycin, and rifampicin against A. baumannii strains by 32-128-fold. Furthermore, mechanistic studies were performed by employing erythromycin as an example of an outer membrane-impermeable conventional antibiotic, which showed the best synergistic effects with brevicidine against the tested A. baumannii strains in the present study. The results demonstrate that brevicidine disrupted the outer membrane of A. baumannii at a concentration range of 0.125-4 μM in a dose-dependent manner. This capacity of brevicidine could help the tested outer membrane-impermeable antibiotics enter A. baumannii cells and thereafter exert their antimicrobial activity. In addition, the results show that brevicidine-erythromycin combination exerted strong A. baumannii killing capacity by the enhanced inhibition of adenosine triphosphate biosynthesis and accumulation of reactive oxygen species, which are the main mechanisms causing the death of bacteria. Interestingly, brevicidine and erythromycin combination showed good therapeutic effects on A. baumannii-induced mouse peritonitis-sepsis models. These findings demonstrate that brevicidine is a promising sensitizer candidate of outer membrane-impermeable conventional antibiotics for treating A. baumannii infections in the post-antibiotic age.
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Affiliation(s)
- Xinyi Zhong
- Center for Sustainable Antimicrobials, Department of Pharmacy, Sichuan Agricultural University, Chengdu, China
- Center for Infectious Diseases Control (CIDC), Sichuan Agricultural University, Chengdu, China
| | - Kai Deng
- Center for Infectious Diseases Control (CIDC), Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xiuhan Yang
- Center for Sustainable Antimicrobials, Department of Pharmacy, Sichuan Agricultural University, Chengdu, China
- Center for Infectious Diseases Control (CIDC), Sichuan Agricultural University, Chengdu, China
| | - Xu Song
- Center for Sustainable Antimicrobials, Department of Pharmacy, Sichuan Agricultural University, Chengdu, China
- Center for Infectious Diseases Control (CIDC), Sichuan Agricultural University, Chengdu, China
| | - Yuanfeng Zou
- Center for Sustainable Antimicrobials, Department of Pharmacy, Sichuan Agricultural University, Chengdu, China
- Center for Infectious Diseases Control (CIDC), Sichuan Agricultural University, Chengdu, China
| | - Xun Zhou
- Center for Sustainable Antimicrobials, Department of Pharmacy, Sichuan Agricultural University, Chengdu, China
- Center for Infectious Diseases Control (CIDC), Sichuan Agricultural University, Chengdu, China
| | - Huaqiao Tang
- Center for Sustainable Antimicrobials, Department of Pharmacy, Sichuan Agricultural University, Chengdu, China
- Center for Infectious Diseases Control (CIDC), Sichuan Agricultural University, Chengdu, China
| | - Lixia Li
- Center for Sustainable Antimicrobials, Department of Pharmacy, Sichuan Agricultural University, Chengdu, China
- Center for Infectious Diseases Control (CIDC), Sichuan Agricultural University, Chengdu, China
| | - Yuping Fu
- Center for Sustainable Antimicrobials, Department of Pharmacy, Sichuan Agricultural University, Chengdu, China
- Center for Infectious Diseases Control (CIDC), Sichuan Agricultural University, Chengdu, China
| | - Zhongqiong Yin
- Center for Sustainable Antimicrobials, Department of Pharmacy, Sichuan Agricultural University, Chengdu, China
- Center for Infectious Diseases Control (CIDC), Sichuan Agricultural University, Chengdu, China
| | - Hongping Wan
- Center for Infectious Diseases Control (CIDC), Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xinghong Zhao
- Center for Sustainable Antimicrobials, Department of Pharmacy, Sichuan Agricultural University, Chengdu, China
- Center for Infectious Diseases Control (CIDC), Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
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6
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Abdelsalam NA, Elhadidy M, Saif NA, Elsayed SW, Mouftah SF, Sayed AA, Ziko L. Biosynthetic gene cluster signature profiles of pathogenic Gram-negative bacteria isolated from Egyptian clinical settings. Microbiol Spectr 2023; 11:e0134423. [PMID: 37707241 PMCID: PMC10580877 DOI: 10.1128/spectrum.01344-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 07/03/2023] [Indexed: 09/15/2023] Open
Abstract
Biosynthetic gene clusters (BGCs) are a subset of consecutive genes present within a variety of organisms to produce specialized metabolites (SMs). These SMs are becoming a cornerstone to produce multiple medications including antibacterial and anticancer agents. Natural products (NPs) also play a pivotal role in enhancing the virulence of ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.), which represent a global health threat. We aimed to sequence and computationally analyze the BGCs present in 66 strains pertaining to three different ESKAPE pathogenic species: 21 A. baumannii, 28 K. pneumoniae, and 17 P. aeruginosa strains recovered from clinical settings in Egypt. DNA was extracted using QIAamp DNA Mini kit and Illumina NextSeq 550 was used for whole-genome sequencing. The sequences were quality-filtered by fastp and assembled by Unicycler. BGCs were detected by antiSMASH, BAGEL, GECCO, and PRISM, and aligned using Clinker. The highest abundance of BGCs was detected in P. aeruginosa (590), then K. pneumoniae (146) and the least in A. baumannii strains (133). P. aeruginosa isolates shared mostly the non-ribosomal peptide synthase (NRPS) type, K. pneumoniae isolates shared the ribosomally synthesized and post-translationally modified peptide-like (RiPP-like) type, while A. baumannii isolates shared the siderophore type. Most of the isolates harbored non-ribosomal peptide (NRP) BGCs with few K. pneumoniae isolates encoding polyketide BGCs. Sactipeptides and bottromycin BGCs were the most frequently detected RiPP clusters. We hypothesize that each species' BGC signature confers its virulence. Future experiments will link the detected clusters with their species and determine whether the encoded SMs are produced and cause their virulence. IMPORTANCE Our study analyzes the biosynthetic gene clusters (BGCs) present in 66 assemblies from clinical ESKAPE pathogen isolates pertaining to Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa strains. We report their sequencing and assembly followed by the analysis of their BGCs using several bioinformatics tools. We then focused on the most abundant BGC type in each species and we discussed their potential roles in the virulence of each species. This study is pivotal to further build on its experimental work that deciphers the role in virulence, possible antibacterial effects, and characterization of the encoded specialized metabolites (SMs). The study highlights the importance of studying the "harmful" BGCs and understanding the pathogenicity and virulence of those species, as well as possible benefits if the SMs were used as antibacterial agents. This could be the first study of its kind from Egypt and would shed light on BGCs from ESKAPE pathogens from Egypt.
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Affiliation(s)
- Nehal Adel Abdelsalam
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Mohamed Elhadidy
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
| | - Nehal A. Saif
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
| | - Salma W. Elsayed
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Shaimaa F. Mouftah
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt
| | - Ahmed A. Sayed
- Genomic research program, Basic research department, Children’s Cancer Hospital Egypt, Cairo, Egypt
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Laila Ziko
- School of Life and Medical Sciences, University of Hertfordshire, Hosted by Global Academic Foundation, Cairo, Egypt
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7
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Abraham Versloot R, Arias-Orozco P, Tadema MJ, Rudolfus Lucas FL, Zhao X, Marrink SJ, Kuipers OP, Maglia G. Seeing the Invisibles: Detection of Peptide Enantiomers, Diastereomers, and Isobaric Ring Formation in Lanthipeptides Using Nanopores. J Am Chem Soc 2023; 145:18355-18365. [PMID: 37579582 PMCID: PMC10450680 DOI: 10.1021/jacs.3c04076] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Indexed: 08/16/2023]
Abstract
Mass spectrometry (MS) is widely used in proteomic analysis but cannot differentiate between molecules with the same mass-to-charge ratio. Nanopore technology might provide an alternative method for the rapid and cost-effective analysis and sequencing of proteins. In this study, we demonstrate that nanopore currents can distinguish between diastereomeric and enantiomeric differences in l- and d-peptides, not observed by conventional MS analysis, down to individual d-amino acids in small opioid peptides. Molecular dynamics simulations suggest that similar to chiral chromatography the resolution likely arises from multiple chiral interactions during peptide transport across the nanopore. Additionally, we used nanopore recordings to rapidly assess 4- and 11-amino acid ring formation in lanthipeptides, a process used in the synthesis of pharmaceutical peptides. The cyclization step requires distinguishing between constitutional isomers, which have identical MS signals and typically involve numerous tedious experiments to confirm. Hence, nanopore technology offers new possibilities for the rapid and cost-effective analysis of peptides, including those that cannot be easily differentiated by mass spectrometry.
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Affiliation(s)
| | - Patricia Arias-Orozco
- Groningen Biomolecular Sciences and
Biotechnology Institute, University of Groningen, 9747AG Groningen, Netherlands
| | - Matthijs Jonathan Tadema
- Groningen Biomolecular Sciences and
Biotechnology Institute, University of Groningen, 9747AG Groningen, Netherlands
| | | | - Xinghong Zhao
- Groningen Biomolecular Sciences and
Biotechnology Institute, University of Groningen, 9747AG Groningen, Netherlands
| | - Siewert J. Marrink
- Groningen Biomolecular Sciences and
Biotechnology Institute, University of Groningen, 9747AG Groningen, Netherlands
| | - Oscar Paul Kuipers
- Groningen Biomolecular Sciences and
Biotechnology Institute, University of Groningen, 9747AG Groningen, Netherlands
| | - Giovanni Maglia
- Groningen Biomolecular Sciences and
Biotechnology Institute, University of Groningen, 9747AG Groningen, Netherlands
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8
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Gordon CH, Hendrix E, He Y, Walker MC. AlphaFold Accurately Predicts the Structure of Ribosomally Synthesized and Post-Translationally Modified Peptide Biosynthetic Enzymes. Biomolecules 2023; 13:1243. [PMID: 37627309 PMCID: PMC10452190 DOI: 10.3390/biom13081243] [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: 07/21/2023] [Revised: 08/08/2023] [Accepted: 08/10/2023] [Indexed: 08/27/2023] Open
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a growing class of natural products biosynthesized from a genetically encoded precursor peptide. The enzymes that install the post-translational modifications on these peptides have the potential to be useful catalysts in the production of natural-product-like compounds and can install non-proteogenic amino acids in peptides and proteins. However, engineering these enzymes has been somewhat limited, due in part to limited structural information on enzymes in the same families that nonetheless exhibit different substrate selectivities. Despite AlphaFold2's superior performance in single-chain protein structure prediction, its multimer version lacks accuracy and requires high-end GPUs, which are not typically available to most research groups. Additionally, the default parameters of AlphaFold2 may not be optimal for predicting complex structures like RiPP biosynthetic enzymes, due to their dynamic binding and substrate-modifying mechanisms. This study assessed the efficacy of the structure prediction program ColabFold (a variant of AlphaFold2) in modeling RiPP biosynthetic enzymes in both monomeric and dimeric forms. After extensive benchmarking, it was found that there were no statistically significant differences in the accuracy of the predicted structures, regardless of the various possible prediction parameters that were examined, and that with the default parameters, ColabFold was able to produce accurate models. We then generated additional structural predictions for select RiPP biosynthetic enzymes from multiple protein families and biosynthetic pathways. Our findings can serve as a reference for future enzyme engineering complemented by AlphaFold-related tools.
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Affiliation(s)
| | | | | | - Mark C. Walker
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131, USA
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9
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Guo L, Wang C, Broos J, Kuipers OP. Lipidated variants of the antimicrobial peptide nisin produced via incorporation of methionine analogs for click chemistry show improved bioactivity. J Biol Chem 2023; 299:104845. [PMID: 37209826 PMCID: PMC10404616 DOI: 10.1016/j.jbc.2023.104845] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/10/2023] [Accepted: 05/14/2023] [Indexed: 05/22/2023] Open
Abstract
The increase in antibiotic resistance calls for accelerated molecular engineering strategies to diversify natural products for drug discovery. The incorporation of non-canonical amino acids (ncAAs) is an elegant strategy for this purpose, offering a diverse pool of building blocks to introduce desired properties into antimicrobial lanthipeptides. We here report an expression system using Lactococcus lactis as a host for non-canonical amino acid incorporation with high efficiency and yield. We show that incorporating the more hydrophobic analog ethionine (instead of methionine) into nisin improves its bioactivity against several Gram-positive strains we tested. New-to-nature variants were further created by click chemistry. By azidohomoalanine (Aha) incorporation and subsequent click chemistry, we obtained lipidated variants at different positions in nisin or in truncated nisin variants. Some of them show improved bioactivity and specificity against several pathogenic bacterial strains. These results highlight the ability of this methodology for lanthipeptide multi-site lipidation, to create new-to-nature antimicrobial products with diverse features, and extend the toolbox for (lanthi)peptide drug improvement and discovery.
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Affiliation(s)
- Longcheng Guo
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Chenhui Wang
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Jaap Broos
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.
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10
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Zhao X, Zhong X, Yang S, Deng K, Liu L, Song X, Zou Y, Li L, Zhou X, Jia R, Lin J, Tang H, Ye G, Yang J, Zhao S, Lang Y, Wan H, Yin Z, Kuipers OP. Elucidating the Mechanism of Action of the Gram-Negative-Pathogen-Selective Cyclic Antimicrobial Lipopeptide Brevicidine. Antimicrob Agents Chemother 2023; 67:e0001023. [PMID: 36912655 PMCID: PMC10190627 DOI: 10.1128/aac.00010-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 02/13/2023] [Indexed: 03/14/2023] Open
Abstract
Due to the accelerated appearance of antimicrobial-resistant (AMR) pathogens in clinical infections, new first-in-class antibiotics, operating via novel modes of action, are desperately needed. Brevicidine, a bacterial nonribosomally produced cyclic lipopeptide, has shown potent and selective antimicrobial activity against Gram-negative pathogens. However, before our investigations, little was known about how brevicidine exerts its potent bactericidal effect against Gram-negative pathogens. In this study, we find that brevicidine has potent antimicrobial activity against AMR Enterobacteriaceae pathogens, with MIC values ranging between 0.5 μM (0.8 mg/L) and 2 μM (3.0 mg/L). In addition, brevicidine showed potent antibiofilm activity against the Enterobacteriaceae pathogens, with the same 100% inhibition and 100% eradication concentration of 4 μM (6.1 mg/L). Further mechanistic studies showed that brevicidine exerts its potent bactericidal activity by interacting with lipopolysaccharide in the outer membrane, targeting phosphatidylglycerol and cardiolipin in the inner membrane, and dissipating the proton motive force of bacteria. This results in metabolic perturbation, including the inhibition of ATP synthesis; the inhibition of the dehydrogenation of NADH; the accumulation of reactive oxygen species in bacteria; and the inhibition of protein synthesis. Finally, brevicidine showed a good therapeutic effect in a mouse peritonitis-sepsis model. Our findings pave the way for further research on the clinical applications of brevicidine to combat prevalent infections caused by AMR Gram-negative pathogens worldwide.
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Affiliation(s)
- Xinghong Zhao
- Lab for Sustainable Antimicrobials, Department of Pharmacy, Sichuan Agricultural University, Chengdu, China
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xinyi Zhong
- Lab for Sustainable Antimicrobials, Department of Pharmacy, Sichuan Agricultural University, Chengdu, China
| | - Shinong Yang
- Lab for Sustainable Antimicrobials, Department of Pharmacy, Sichuan Agricultural University, Chengdu, China
| | - Kai Deng
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Lu Liu
- Lab for Sustainable Antimicrobials, Department of Pharmacy, Sichuan Agricultural University, Chengdu, China
| | - Xu Song
- Lab for Sustainable Antimicrobials, Department of Pharmacy, Sichuan Agricultural University, Chengdu, China
| | - Yuanfeng Zou
- Lab for Sustainable Antimicrobials, Department of Pharmacy, Sichuan Agricultural University, Chengdu, China
| | - Lixia Li
- Lab for Sustainable Antimicrobials, Department of Pharmacy, Sichuan Agricultural University, Chengdu, China
| | - Xun Zhou
- Lab for Sustainable Antimicrobials, Department of Pharmacy, Sichuan Agricultural University, Chengdu, China
| | - Renyong Jia
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Juchun Lin
- Lab for Sustainable Antimicrobials, Department of Pharmacy, Sichuan Agricultural University, Chengdu, China
| | - Huaqiao Tang
- Lab for Sustainable Antimicrobials, Department of Pharmacy, Sichuan Agricultural University, Chengdu, China
| | - Gang Ye
- Lab for Sustainable Antimicrobials, Department of Pharmacy, Sichuan Agricultural University, Chengdu, China
| | - Jianqing Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Wenjiang, Chengdu, Sichuan, China
| | - Shan Zhao
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yifei Lang
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Hongping Wan
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Zhongqiong Yin
- Lab for Sustainable Antimicrobials, Department of Pharmacy, Sichuan Agricultural University, Chengdu, China
| | - Oscar P. Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
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11
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Vagstad AL. Engineering ribosomally synthesized and posttranslationally modified peptides as new antibiotics. Curr Opin Biotechnol 2023; 80:102891. [PMID: 36702077 DOI: 10.1016/j.copbio.2023.102891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 11/22/2022] [Accepted: 12/19/2022] [Indexed: 01/25/2023]
Abstract
The rise of antimicrobial resistance is an urgent public health threat demanding the invention of new drugs to combat infections. Naturally sourced nonribosomal peptides (NRPs) have a long history as antimicrobial drugs. Through recent advances in genome mining and engineering technologies, their ribosomally synthesized and posttranslationally modified peptide (RiPP) counterparts are poised to further contribute to the arsenal of anti-infectives. As natural products from diverse organisms involved in interspecies competition, many RiPPs already possess antimicrobial activities that can be further optimized as drug candidates. Owing to the mutability of precursor protein genes that encode their core structures and the availability of diverse posttranslational modification (PTM) enzymes with broad substrate tolerances, RiPP systems are well suited to engineer complex peptides with desired functions.
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Affiliation(s)
- Anna L Vagstad
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland.
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12
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Mordhorst S, Ruijne F, Vagstad AL, Kuipers OP, Piel J. Emulating nonribosomal peptides with ribosomal biosynthetic strategies. RSC Chem Biol 2023; 4:7-36. [PMID: 36685251 PMCID: PMC9811515 DOI: 10.1039/d2cb00169a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
Peptide natural products are important lead structures for human drugs and many nonribosomal peptides possess antibiotic activity. This makes them interesting targets for engineering approaches to generate peptide analogues with, for example, increased bioactivities. Nonribosomal peptides are produced by huge mega-enzyme complexes in an assembly-line like manner, and hence, these biosynthetic pathways are challenging to engineer. In the past decade, more and more structural features thought to be unique to nonribosomal peptides were found in ribosomally synthesised and posttranslationally modified peptides as well. These streamlined ribosomal pathways with modifying enzymes that are often promiscuous and with gene-encoded precursor proteins that can be modified easily, offer several advantages to produce designer peptides. This review aims to provide an overview of recent progress in this emerging research area by comparing structural features common to both nonribosomal and ribosomally synthesised and posttranslationally modified peptides in the first part and highlighting synthetic biology strategies for emulating nonribosomal peptides by ribosomal pathway engineering in the second part.
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Affiliation(s)
- Silja Mordhorst
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4 8093 Zürich Switzerland
| | - Fleur Ruijne
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen Nijenborgh 7, 9747 AG Groningen The Netherlands
| | - Anna L Vagstad
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4 8093 Zürich Switzerland
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen Nijenborgh 7, 9747 AG Groningen The Netherlands
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4 8093 Zürich Switzerland
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13
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Arias-Orozco P, Yi Y, Ruijne F, Cebrián R, Kuipers OP. Investigating the Specificity of the Dehydration and Cyclization Reactions in Engineered Lanthipeptides by Synechococcal SyncM. ACS Synth Biol 2022; 12:164-177. [PMID: 36520855 PMCID: PMC9872173 DOI: 10.1021/acssynbio.2c00455] [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] [Indexed: 12/23/2022]
Abstract
ProcM-like enzymes are class II promiscuous lanthipeptide synthetases that are an attractive tool in synthetic biology for producing lanthipeptides with biotechnological or clinically desired properties. SyncM is a recently described modification enzyme from this family used to develop a versatile expression platform for engineering lanthipeptides. Most remarkably, SyncM can modify up to 79 SyncA substrates in a single strain. Six SyncAs were previously characterized from this pool of substrates. They showed particular characteristics, such as the presence of one or two lanthionine rings, different flanking residues influencing ring formation, and different ring directions, demonstrating the relaxed specificity of SyncM toward its precursor peptides. To gain a deeper understanding of the potential of SyncM as a biosynthetic tool, we further explored the enzyme's capabilities and limits in dehydration and ring formation. We used different SyncA scaffolds for peptide engineering, including changes in the ring's directionality (relative position of Ser/Thr to Cys in the peptide) and size. We further aimed to rationally design mimetics of cyclic antimicrobials and introduce macrocycles in prochlorosin-related and nonrelated substrates. This study highlights the largest lanthionine ring with 15 amino acids (ring-forming residues included) described to date. Taking advantage of the amino acid substrate tolerance of SyncM, we designed the first single-SyncA-based antimicrobial. The insights gained from this work will aid future bioengineering studies. Additionally, it broadens SyncM's application scope for introducing macrocycles in other bioactive molecules.
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Affiliation(s)
- Patricia Arias-Orozco
- Department
of Molecular Genetics, University of Groningen, Nijenborg 7, 9747 AG Groningen, The Netherlands
| | - Yunhai Yi
- Department
of Molecular Genetics, University of Groningen, Nijenborg 7, 9747 AG Groningen, The Netherlands
| | - Fleur Ruijne
- Department
of Molecular Genetics, University of Groningen, Nijenborg 7, 9747 AG Groningen, The Netherlands
| | - Rubén Cebrián
- Department
of Molecular Genetics, University of Groningen, Nijenborg 7, 9747 AG Groningen, The Netherlands,Department
of Clinical Microbiology, Instituto de Investigación Biosanitaria,
ibs. GRANADA, San Cecilio University Hospital, Av. De la Innovación s/n, 18016 Granada, Spain
| | - Oscar P. Kuipers
- Department
of Molecular Genetics, University of Groningen, Nijenborg 7, 9747 AG Groningen, The Netherlands,
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14
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Wenski SL, Thiengmag S, Helfrich EJ. Complex peptide natural products: Biosynthetic principles, challenges and opportunities for pathway engineering. Synth Syst Biotechnol 2022; 7:631-647. [PMID: 35224231 PMCID: PMC8842026 DOI: 10.1016/j.synbio.2022.01.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 01/03/2023] Open
Abstract
Complex peptide natural products exhibit diverse biological functions and a wide range of physico-chemical properties. As a result, many peptides have entered the clinics for various applications. Two main routes for the biosynthesis of complex peptides have evolved in nature: ribosomally synthesized and post-translationally modified peptide (RiPP) biosynthetic pathways and non-ribosomal peptide synthetases (NRPSs). Insights into both bioorthogonal peptide biosynthetic strategies led to the establishment of universal principles for each of the two routes. These universal rules can be leveraged for the targeted identification of novel peptide biosynthetic blueprints in genome sequences and used for the rational engineering of biosynthetic pathways to produce non-natural peptides. In this review, we contrast the key principles of both biosynthetic routes and compare the different biochemical strategies to install the most frequently encountered peptide modifications. In addition, the influence of the fundamentally different biosynthetic principles on past, current and future engineering approaches is illustrated. Despite the different biosynthetic principles of both peptide biosynthetic routes, the arsenal of characterized peptide modifications encountered in RiPP and NRPS systems is largely overlapping. The continuous expansion of the biocatalytic toolbox of peptide modifying enzymes for both routes paves the way towards the production of complex tailor-made peptides and opens up the possibility to produce NRPS-derived peptides using the ribosomal route and vice versa.
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15
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Arias-Orozco P, Inklaar M, Lanooij J, Cebrián R, Kuipers OP. Functional Expression and Characterization of the Highly Promiscuous Lanthipeptide Synthetase SyncM, Enabling the Production of Lanthipeptides with a Broad Range of Ring Topologies. ACS Synth Biol 2021; 10:2579-2591. [PMID: 34554737 PMCID: PMC8524650 DOI: 10.1021/acssynbio.1c00224] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
Lanthipeptides are
ribosomally synthesized and post-translationally
modified peptides characterized by the presence of lanthionine rings
that provide stability and functionality. Genome mining techniques
have shown their huge diversity and potential for the discovery of
novel active molecules. However, in many cases, they are not easily
produced under laboratory conditions. The heterologous expression
of these molecules using well-characterized lanthipeptide biosynthetic
enzymes is rising as an alternative system for the design and production
of new lanthipeptides with biotechnological or clinical properties.
Nevertheless, the substrate-enzyme specificity limits the complete
modification of the desired peptides and hence, their full stability
and/or biological activity. New low substrate-selective biosynthetic
enzymes are therefore necessary for the heterologous production of
new-to-nature peptides. Here, we have identified, cloned, and heterologously
expressed in Lactococcus lactis the
most promiscuous lanthipeptide synthetase described to date, i.e.,
SyncM from the marine cyanobacteria Synechococcus MITS9509. We have characterized the functionality of SyncM by the
successful expression of 15 out of 18 different SyncA substrates,
subsequently determining the dehydration and cyclization processes
in six representatives of them. This characterization highlights the
very relaxed substrate specificity of SyncM toward its precursors
and the ability to catalyze the formation of exceptionally large rings
in a variety of topologies. Our results suggest that SyncM could be
an attractive enzyme to design and produce a wide variety of new-to-nature
lanthipeptides with a broad range of ring topologies.
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Affiliation(s)
- Patricia Arias-Orozco
- Department of Molecular Genetics, University of Groningen, Groningen 9747AG, The Netherlands
| | - Maartje Inklaar
- Department of Molecular Genetics, University of Groningen, Groningen 9747AG, The Netherlands
| | - Judith Lanooij
- Department of Molecular Genetics, University of Groningen, Groningen 9747AG, The Netherlands
| | - Rubén Cebrián
- Department of Molecular Genetics, University of Groningen, Groningen 9747AG, The Netherlands
| | - Oscar P. Kuipers
- Department of Molecular Genetics, University of Groningen, Groningen 9747AG, The Netherlands
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16
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Hermant Y, Palpal-Latoc D, Kovalenko N, Cameron AJ, Brimble MA, Harris PWR. The Total Chemical Synthesis and Biological Evaluation of the Cationic Antimicrobial Peptides, Laterocidine and Brevicidine. JOURNAL OF NATURAL PRODUCTS 2021; 84:2165-2174. [PMID: 34338512 DOI: 10.1021/acs.jnatprod.1c00222] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Antimicrobial resistance is a significant threat to public health systems worldwide, prompting immediate attention to develop new therapeutic agents with novel mechanisms of action. Recently, two new cationic non-ribosomal peptides (CNRPs), laterocidine and brevicidine, were discovered from Brevibacillus laterosporus through a global genome-mining approach. Both laterocidine and brevicidine exhibit potent antimicrobial activity toward Gram-negative bacteria, including difficult-to-treat Pseudonomas aeruginosa and colistin-resistant Escherichia coli, and a low risk of resistance development. Herein, we report the first total syntheses of laterocidine and brevicidine via an efficient and high-yielding combination of solid-phase synthesis and solution-phase macrolactamization. The crucial depsipeptide bond of the macrolactone rings of laterocidine and brevicidine was established on-resin between the side-chain hydroxy group of Thr9 with Alloc-Gly-OH or Alloc-Ser(tBu)-OH, respectively. A conserved glycine residue within the lactone macrocycle is exploited for the initial immobilization onto the hyper acid-labile 2-chlorotrityl chloride resin, subsequently enabling an efficient solution-phase macrocyclization to yield laterocidine and brevicidine in 36% and 10% overall yields, respectively (with respect to resin loading). A biological evaluation against both Gram-positive and Gram-negative bacteria demonstrated that synthetic laterocidine and brevicidine possessed a potent and selective antimicrobial activity toward Gram-negative bacteria, in accordance with the isolated compounds.
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Affiliation(s)
- Yann Hermant
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street and 3b Symonds Street, Auckland 1142, New Zealand
- School of Biological Sciences, The University of Auckland, 3b Symonds Street, Auckland 1142, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3b Symonds Street, Auckland 1142, New Zealand
| | - Dennise Palpal-Latoc
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street and 3b Symonds Street, Auckland 1142, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3b Symonds Street, Auckland 1142, New Zealand
| | - Nadiia Kovalenko
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street and 3b Symonds Street, Auckland 1142, New Zealand
- School of Biological Sciences, The University of Auckland, 3b Symonds Street, Auckland 1142, New Zealand
| | - Alan J Cameron
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street and 3b Symonds Street, Auckland 1142, New Zealand
- School of Biological Sciences, The University of Auckland, 3b Symonds Street, Auckland 1142, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3b Symonds Street, Auckland 1142, New Zealand
| | - Margaret A Brimble
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street and 3b Symonds Street, Auckland 1142, New Zealand
- School of Biological Sciences, The University of Auckland, 3b Symonds Street, Auckland 1142, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3b Symonds Street, Auckland 1142, New Zealand
| | - Paul W R Harris
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street and 3b Symonds Street, Auckland 1142, New Zealand
- School of Biological Sciences, The University of Auckland, 3b Symonds Street, Auckland 1142, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3b Symonds Street, Auckland 1142, New Zealand
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17
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Zhao X, Xu Y, Viel JH, Kuipers OP. Semisynthetic Macrocyclic Lipo-lanthipeptides Display Antimicrobial Activity Against Bacterial Pathogens. ACS Synth Biol 2021; 10:1980-1991. [PMID: 34347446 PMCID: PMC8383303 DOI: 10.1021/acssynbio.1c00161] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A large number of antimicrobial peptides depend on intramolecular disulfide bonds for their biological activity. However, the relative instability of disulfide bonds has limited the potential of some of these peptides to be developed into therapeutics. Conversely, peptides containing intramolecular (methyl)lanthionine-based bonds, lanthipeptides, are highly stable under a broader range of biological and physical conditions. Here, the class-II lanthipeptide synthetase CinM, from the cinnamycin gene cluster, was employed to create methyllanthionine stabilized analogues of disulfide-bond-containing antimicrobial peptides. The resulting analogues were subsequently modified in vitro by adding lipid tails of variable lengths through chemical addition. Finally, the created compounds were characterized by MIC tests against several relevant pathogens, killing assays, membrane permeability assays, and hemolysis assays. It was found that CinM could successfully install methyllanthionine bonds at the intended positions of the analogues and that the lipidated macrocyclic core peptides have bactericidal activity against tested Gram-positive and Gram-negative pathogenic bacteria. Additionally, fluorescence microscopy assays revealed that the lipidated compounds disrupt the bacterial membrane and lyse bacterial cells, hinting toward a potential mode of action. Notably, the semisynthesized macrocyclic lipo-lanthipeptides show low hemolytic activity. These results show that the methods developed here extend the toolbox for novel antimicrobial development and might enable the further development of novel compounds with killing activity against relevant pathogenic bacteria.
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Affiliation(s)
- Xinghong Zhao
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Yanli Xu
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Jakob H. Viel
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Oscar P. Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
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18
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Zhao X, Kuipers OP. Nisin- and Ripcin-Derived Hybrid Lanthipeptides Display Selective Antimicrobial Activity against Staphylococcus aureus. ACS Synth Biol 2021; 10:1703-1714. [PMID: 34156232 PMCID: PMC8291769 DOI: 10.1021/acssynbio.1c00080] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Lanthipeptides are
(methyl)lanthionine ring-containing ribosomally
synthesized and post-translationally modified peptides (RiPPs). Many
lanthipeptides show strong antimicrobial activity against bacterial
pathogens, including antibiotic-resistant bacterial pathogens. The
group of disulfide-bond-containing antimicrobial peptides (AMPs) is
well-known in nature and forms a rich source of templates for the
production of novel peptides with corresponding (methyl)lanthionine
analogues instead of disulfides. Here, we show that novel macrocyclic
lanthipeptides (termed thanacin and ripcin) can be synthesized using
the known antimicrobials thanatin and rip-thanatin as templates. Notably,
the synthesized nisin(1–20)–ripcin hybrid lanthipeptides
(ripcin B–G) showed selective antimicrobial activity against S. aureus, including an antibiotic-resistant MRSA
strain. Interestingly, ripcin B–G, which are hybrid peptides
of nisin(1–20) and ripcin that are each inactive against Gram-negative
pathogens, showed substantial antimicrobial activity against the tested
Gram-negative pathogens. Moreover, ripcin B–G was highly resistant
against the nisin resistance protein (NSR; a peptidase that removes
the C-terminal 6 amino acids of nisin and strongly reduces its antimicrobial
activity), opposed to nisin itself. This study provides an example
of converting disulfide-bond-based AMPs into (methyl)lanthionine-based
macrocyclic hybrid lanthipeptides and can yield antimicrobial peptides
with selective antimicrobial activity against S. aureus.
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Affiliation(s)
- Xinghong Zhao
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, 9747 AG, The Netherlands
| | - Oscar P. Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, 9747 AG, The Netherlands
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19
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Zhao X, Wang X, Shukla R, Kumar R, Weingarth M, Breukink E, Kuipers OP. Brevibacillin 2V Exerts Its Bactericidal Activity via Binding to Lipid II and Permeabilizing Cellular Membranes. Front Microbiol 2021; 12:694847. [PMID: 34335524 PMCID: PMC8322648 DOI: 10.3389/fmicb.2021.694847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/28/2021] [Indexed: 11/14/2022] Open
Abstract
Lipo-tridecapeptides, a class of bacterial non-ribosomally produced peptides, show strong antimicrobial activity against Gram-positive pathogens, including antibiotic-resistant Staphylococcus aureus and Enterococcus spp. However, many of these lipo-tridecapeptides have shown high hemolytic activity and cytotoxicity, which has limited their potential to be developed into antibiotics. Recently, we reported a novel antimicrobial lipo-tridecapeptide, brevibacillin 2V, which showed no hemolytic activity against human red blood cells at a high concentration of 128 mg/L, opposite to other brevibacillins and lipo-tridecapeptides. In addition, brevibacillin 2V showed much lower cytotoxicity than the other members of the brevibacillin family. In this study, we set out to elucidate the antimicrobial mode of action of brevibacillin 2V. The results show that brevibacillin 2V acts as bactericidal antimicrobial agent against S. aureus (MRSA). Further studies show that brevibacillin 2V exerts its bactericidal activity by binding to the bacterial cell wall synthesis precursor Lipid II and permeabilizing the bacterial membrane. Combined solid-state NMR, circular dichroism, and isothermal titration calorimetry assays indicate that brevibacillin 2V binds to the GlcNAc-MurNAc moiety and/or the pentapeptide of Lipid II. This study provides an insight into the antimicrobial mode of action of brevibacillin 2V. As brevibacillin 2V is a novel and promising antibiotic candidate with low hemolytic activity and cytotoxicity, the here-elucidated mode of action will help further studies to develop it as an alternative antimicrobial agent.
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Affiliation(s)
- Xinghong Zhao
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Xiaoqi Wang
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Rhythm Shukla
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands.,NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Raj Kumar
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Markus Weingarth
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
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20
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Zhao X, Wang X, Shukla R, Kumar R, Weingarth M, Breukink E, Kuipers OP. Brevibacillin 2V, a Novel Antimicrobial Lipopeptide With an Exceptionally Low Hemolytic Activity. Front Microbiol 2021; 12:693725. [PMID: 34220785 PMCID: PMC8245773 DOI: 10.3389/fmicb.2021.693725] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 05/17/2021] [Indexed: 12/26/2022] Open
Abstract
Bacterial non-ribosomally produced peptides (NRPs) form a rich source of antibiotics, including more than 20 of these antibiotics that are used in the clinic, such as penicillin G, colistin, vancomycin, and chloramphenicol. Here we report the identification, purification, and characterization of a novel NRP, i.e., brevibacillin 2V (lipo-tridecapeptide), from Brevibacillus laterosporus DSM 25. Brevibacillin 2V has a strong antimicrobial activity against Gram-positive bacterial pathogens (minimum inhibitory concentration = 2 mg/L), including difficult-to-treat antibiotic-resistant Enterococcus faecium, Enterococcus faecalis, and Staphylococcus aureus. Notably, brevibacillin 2V has a much lower hemolytic activity (HC50 > 128 mg/L) and cytotoxicity (CC50 = 45.49 ± 0.24 mg/L) to eukaryotic cells than previously reported NRPs of the lipo-tridecapeptide family, including other brevibacillins, which makes it a promising candidate for antibiotic development. In addition, our results demonstrate that brevibacillins display a synergistic action with established antibiotics against Gram-negative bacterial pathogens. Probably due to the presence of non-canonical amino acids and D-amino acids, brevibacillin 2V showed good stability in human plasma. Thus, we identified and characterized a novel and promising antimicrobial candidate (brevibacillin 2V) with low hemolytic activity and cytotoxicity, which can be used either on its own or as a template for further total synthesis and modification.
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Affiliation(s)
- Xinghong Zhao
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Xiaoqi Wang
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Rhythm Shukla
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands.,NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Raj Kumar
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Markus Weingarth
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
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21
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Zhao X, Kuipers OP. BrevicidineB, a New Member of the Brevicidine Family, Displays an Extended Target Specificity. Front Microbiol 2021; 12:693117. [PMID: 34177875 PMCID: PMC8219939 DOI: 10.3389/fmicb.2021.693117] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 05/14/2021] [Indexed: 12/18/2022] Open
Abstract
The group of bacterial non-ribosomally produced peptides (NRPs) has formed a rich source for drug development. Brevicidine, a bacterial non-ribosomally produced cyclic lipo-dodecapeptide, displays selective antimicrobial activity against Gram-negative pathogens. Here, we show that brevicidineB, which contains a single substitution (Tyr2 to Phe2) in the amino acid sequence of the linear part of brevicidine, has a broadened antimicrobial spectrum, showing bactericidal activity against both Gram-negative (with a MIC value of 2 to 4 mg/L) and Gram-positive (with a MIC value of 2 to 8 mg/L) pathogens. Compared with an earlier reported member of the brevicidine family, the broadened antimicrobial spectrum of brevicidineB is caused by its increased membrane disruptive capacity on Gram-positive pathogens, which was evidenced by fluorescence microscopy assays. In addition, DiSC3(5) and resazurin assays show that brevicidine and brevicidineB exert their antimicrobial activity against Gram-negative bacteria via disrupting the proton motive force of cells. Notably, as a brevicidine family member, brevicidineB also showed neither hemolytic activity nor cytotoxicity at a high concentration of 64 mg/L. This study provides a promising antibiotic candidate (brevicidineB) with a broad antimicrobial spectrum, and provides novel insights into the antimicrobial mode of action of brevicidines.
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Affiliation(s)
- Xinghong Zhao
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
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22
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Combinatorial biosynthesis for the generation of new-to-nature peptide antimicrobials. Biochem Soc Trans 2021; 49:203-215. [PMID: 33439248 DOI: 10.1042/bst20200425] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/25/2020] [Accepted: 11/27/2020] [Indexed: 12/12/2022]
Abstract
Natural peptide products are a valuable source of important therapeutic agents, including antibiotics, antivirals and crop protection agents. Aided by an increased understanding of structure-activity relationships of these complex molecules and the biosynthetic machineries that produce them, it has become possible to re-engineer complete machineries and biosynthetic pathways to create novel products with improved pharmacological properties or modified structures to combat antimicrobial resistance. In this review, we will address the progress that has been made using non-ribosomally produced peptides and ribosomally synthesized and post-translationally modified peptides as scaffolds for designed biosynthetic pathways or combinatorial synthesis for the creation of novel peptide antimicrobials.
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