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Ostrówka M, Duda-Madej A, Pietluch F, Mackiewicz P, Gagat P. Testing Antimicrobial Properties of Human Lactoferrin-Derived Fragments. Int J Mol Sci 2023; 24:10529. [PMID: 37445717 DOI: 10.3390/ijms241310529] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
Lactoferrin, an iron-binding glycoprotein, plays a significant role in the innate immune system, with antibacterial, antivirial, antifungal, anticancer, antioxidant and immunomodulatory functions reported. It is worth emphasizing that not only the whole protein but also its derived fragments possess antimicrobial peptide (AMP) activity. Using AmpGram, a top-performing AMP classifier, we generated three novel human lactoferrin (hLF) fragments: hLF 397-412, hLF 448-464 and hLF 668-683, predicted with high probability as AMPs. For comparative studies, we included hLF 1-11, previously confirmed to kill some bacteria. With the four peptides, we treated three Gram-negative and three Gram-positive bacterial strains. Our results indicate that none of the three new lactoferrin fragments have antimicrobial properties for the bacteria tested, but hLF 1-11 was lethal against Pseudomonas aeruginosa. The addition of serine protease inhibitors with the hLF fragments did not enhance their activity, except for hLF 1-11 against P. aeruginosa, which MIC dropped from 128 to 64 µg/mL. Furthermore, we investigated the impact of EDTA with/without serine protease inhibitors and the hLF peptides on selected bacteria. We stress the importance of reporting non-AMP sequences for the development of next-generation AMP prediction models, which suffer from the lack of experimentally validated negative dataset for training and benchmarking.
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Affiliation(s)
- Michał Ostrówka
- Faculty of Biotechnology, University of Wrocław, Fryderyka Joliot-Curie 14a, 50-137 Wrocław, Poland
| | - Anna Duda-Madej
- Department of Microbiology, Faculty of Medicine, Wrocław Medical University, Chałubińskiego 4, 50-368 Wrocław, Poland
| | - Filip Pietluch
- Faculty of Biotechnology, University of Wrocław, Fryderyka Joliot-Curie 14a, 50-137 Wrocław, Poland
| | - Paweł Mackiewicz
- Faculty of Biotechnology, University of Wrocław, Fryderyka Joliot-Curie 14a, 50-137 Wrocław, Poland
| | - Przemysław Gagat
- Faculty of Biotechnology, University of Wrocław, Fryderyka Joliot-Curie 14a, 50-137 Wrocław, Poland
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2
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Design and Evaluation of Short Bovine Lactoferrin-Derived Antimicrobial Peptides against Multidrug-Resistant Enterococcus faecium. Antibiotics (Basel) 2022; 11:antibiotics11081085. [PMID: 36009954 PMCID: PMC9404989 DOI: 10.3390/antibiotics11081085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/05/2022] [Accepted: 08/06/2022] [Indexed: 11/17/2022] Open
Abstract
Enterococcus faecium has become an important drug-resistant nosocomial pathogen because of widespread antibiotic abuse. We developed short and chemically simple antimicrobial peptides (AMPs) with a selective amino acid composition, fixed charge, and hydrophobicity ratio based on the core antimicrobial motif of bovine lactoferrin (LfcinB6). Among these peptides, 5L and 6L (both 12 residues long) demonstrated a narrow spectrum and high antibacterial activity against drug-resistant E. faecium isolates with a minimal inhibitory concentration (MIC) that ranged from 4–16 µg/mL. At 32 µg/mL, peptides 5L and 6L inhibited E. faecium strain C68 biofilm formation by 90% and disrupted established biofilms by 75%. At 40 µg/mL, 5L reduced 1 × 107E. faecium persister cells by 3 logs within 120 min of exposure, whereas 6L eliminated all persister cells within 60 min. At 0.5× MIC, 5L and 6L significantly downregulated the expression of a crucial biofilm gene ace by 8 folds (p = 0.02) and 4 folds (p = 0.01), respectively. At 32 µg/mL, peptides 5L and 6L both depolarized the E. faecium membrane, increased fluidity, and eventually ruptured the membrane. Physiologically, 5L (at 8 µg/mL) altered the tricarboxylic acid cycle, glutathione, and purine metabolism. Interestingly, in an ex vivo model of porcine skin infection, compared to no treatment, 5L (at 10× MIC) effectively eliminated all 1 × 106 exponential (p = 0.0045) and persister E. faecium cells (p = 0.0002). In conclusion, the study outlines a roadmap for developing narrow-spectrum selective AMPs and presents peptide 5L as a potential therapeutic candidate to be explored against E. faecium.
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3
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Lopes BS, Hanafiah A, Nachimuthu R, Muthupandian S, Md Nesran ZN, Patil S. The Role of Antimicrobial Peptides as Antimicrobial and Antibiofilm Agents in Tackling the Silent Pandemic of Antimicrobial Resistance. Molecules 2022; 27:molecules27092995. [PMID: 35566343 PMCID: PMC9105241 DOI: 10.3390/molecules27092995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 01/11/2023] Open
Abstract
Just over a million people died globally in 2019 due to antibiotic resistance caused by ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species). The World Health Organization (WHO) also lists antibiotic-resistant Campylobacter and Helicobacter as bacteria that pose the greatest threat to human health. As it is becoming increasingly difficult to discover new antibiotics, new alternatives are needed to solve the crisis of antimicrobial resistance (AMR). Bacteria commonly found in complex communities enclosed within self-produced matrices called biofilms are difficult to eradicate and develop increased stress and antimicrobial tolerance. This review summarises the role of antimicrobial peptides (AMPs) in combating the silent pandemic of AMR and their application in clinical medicine, focusing on both the advantages and disadvantages of AMPs as antibiofilm agents. It is known that many AMPs display broad-spectrum antimicrobial activities, but in a variety of organisms AMPs are not stable (short half-life) or have some toxic side effects. Hence, it is also important to develop new AMP analogues for their potential use as drug candidates. The use of one health approach along with developing novel therapies using phages and breakthroughs in novel antimicrobial peptide synthesis can help us in tackling the problem of AMR.
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Affiliation(s)
- Bruno S. Lopes
- Department of Medical Microbiology, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB25 2ZD, UK
- Correspondence: (B.S.L.); (A.H.)
| | - Alfizah Hanafiah
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia;
- Correspondence: (B.S.L.); (A.H.)
| | - Ramesh Nachimuthu
- Antibiotic Resistance and Phage Therapy Laboratory, Department of Biomedical Sciences, Vellore Institute of Technology, School of Bioscience and Technology, Vellore 632014, India;
| | - Saravanan Muthupandian
- AMR and Nanotherapeutics Laboratory, Department of Pharmacology, Saveetha Institute of Medical and Technical Sciences, Saveetha Dental College, Chennai 600077, India;
| | - Zarith Nameyrra Md Nesran
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia;
| | - Sandip Patil
- Department of Hematology and Oncology, Shenzhen Children’s Hospital, Shenzhen 518038, China;
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4
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Luong HX, Ngan HD, Thi Phuong HB, Quoc TN, Tung TT. Multiple roles of ribosomal antimicrobial peptides in tackling global antimicrobial resistance. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211583. [PMID: 35116161 PMCID: PMC8790363 DOI: 10.1098/rsos.211583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 12/20/2021] [Indexed: 05/03/2023]
Abstract
In the last century, conventional antibiotics have played a significant role in global healthcare. Antibiotics support the body in controlling bacterial infection and simultaneously increase the tendency of drug resistance. Consequently, there is a severe concern regarding the regression of the antibiotic era. Despite the use of antibiotics, host defence systems are vital in fighting infectious diseases. In fact, the expression of ribosomal antimicrobial peptides (AMPs) has been crucial in the evolution of innate host defences and has been irreplaceable to date. Therefore, this valuable source is considered to have great potential in tackling the antimicrobial resistance (AMR) crisis. Furthermore, the possibility of bacterial resistance to AMPs has been intensively investigated. Here, we summarize all aspects related to the multiple applications of ribosomal AMPs and their derivatives in combating AMR.
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Affiliation(s)
- Huy Xuan Luong
- Faculty of Pharmacy, PHENIKAA University, Hanoi 12116, Vietnam
- PHENIKAA Institute for Advanced Study (PIAS), PHENIKAA University, Hanoi 12116, Vietnam
| | | | | | - Thang Nguyen Quoc
- Nuclear Medicine Unit, Vinmec Healthcare System, Hanoi 10000, Vietnam
| | - Truong Thanh Tung
- Faculty of Pharmacy, PHENIKAA University, Hanoi 12116, Vietnam
- PHENIKAA Institute for Advanced Study (PIAS), PHENIKAA University, Hanoi 12116, Vietnam
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Fungicidal Activity of Recombinant Javanicin against Cryptococcus neoformans Is Associated with Intracellular Target(s) Involved in Carbohydrate and Energy Metabolic Processes. Molecules 2021; 26:molecules26227011. [PMID: 34834105 PMCID: PMC8618071 DOI: 10.3390/molecules26227011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 11/12/2021] [Accepted: 11/18/2021] [Indexed: 01/06/2023] Open
Abstract
The occurrence of Cryptococcus neoformans, the human fungal pathogen that primarily infects immunocompromised individuals, has been progressing at an alarming rate. The increased incidence of infection of C. neoformans with antifungal drugs resistance has become a global concern. Potential antifungal agents with extremely low toxicity are urgently needed. Herein, the biological activities of recombinant javanicin (r-javanicin) against C. neoformans were evaluated. A time-killing assay was performed and both concentration- and time-dependent antifungal activity of r-javanicin were indicated. The inhibitory effect of the peptide was initially observed at 4 h post-treatment and ultimately eradicated within 36 to 48 h. Fungal outer surface alteration was characterized by the scanning electron microscope (SEM) whereas a negligible change with slight shrinkage of external morphology was observed in r-javanicin treated cells. Confocal laser scanning microscopic analysis implied that the target(s) of r-javanicin is conceivably resided in the cell thereby allowing the peptide to penetrate across the membrane and accumulate throughout the fungal body. Finally, cryptococcal cells coped with r-javanicin were preliminarily investigated using label-free mass spectrometry-based proteomics. Combined with microscopic and proteomics analysis, it was clearly elucidated the peptide localized in the intracellular compartment where carbohydrate metabolism and energy production associated with glycolysis pathway and mitochondrial respiration, respectively, were principally interfered. Overall, r-javanicin would be an alternative candidate for further development of antifungal agents.
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Shah P, Chen CS. Systematical Screening of Intracellular Protein Targets of Polyphemusin-I Using Escherichia coli Proteome Microarrays. Int J Mol Sci 2021; 22:ijms22179158. [PMID: 34502067 PMCID: PMC8431070 DOI: 10.3390/ijms22179158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/11/2021] [Accepted: 08/19/2021] [Indexed: 11/16/2022] Open
Abstract
With their wide repertoire of mechanisms, antimicrobial peptides (AMPs) are promising alternatives to fight against varied pathogenic microorganisms (bacteria, fungi, viruses, parasites, etc.). AMPs, novel components of the innate immune defense system, are secreted by all organisms. The aquatic environment represents a huge population and an enormous source of varied AMPs. Polyphemusin-I, a marine AMP isolated from hemocytes of an American horseshoe crab, possesses high antimicrobial activities. Studies on polyphemusin-I have verified the intracellular mechanisms of action, however, its intracellular targets are not yet explored. In this study, we employed Escherichia coli proteome microarrays to systematically screen the entire intracellular protein targets of polyphemusin-I. A total of 97 protein targets of polyphemusin-I were statistically analyzed from the quadruplicate Escherichia coli proteome microarrays assays. Among these identified protein targets, 56 proteins had cellular location inside the cell (i.e., cytoplasm), one in the plasma membrane, one in the periplasm and the rest 39 proteins had no specified cellular location. The bioinformatics analysis of these identified protein targets of polyphemusin-I in gene ontology (GO) enrichment category of molecular function revealed significant enrichment in nucleic acid related GO terms i.e., “RNA binding”, “nucleotide binding”, “nuclease activities”, “uracil DNA N-glycosylase activities” and others. Moreover, enrichment in GO category of biological process also depicted enrichment in nucleic acid related GO terms, such as “nucleic acid phosphodiester bond hydrolysis”, “deoxyribonucleotide metabolism”, and others. In accordance to GO enrichment analysis, protein families (PFAM) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enrichment analysis also showed significant enrichment in nucleic acid terms. These enrichment results suggest that polyphemusin-I targets nucleic acid-associated proteins. Furthermore, to provide a comprehensive study, we compared the identified protein targets of polyphemusin-I with previously identified protein targets of four AMPs (P-Der, Lfcin B, PR-39, and Bac 7) using Escherichia coli proteome microarrays. The comparison study of five AMPs (polyhemusin-I, P-Der, Lfcin B, PR-39, and Bac 7) showed only nine common protein targets in all the five AMPs, whereas a total of 39 and 43 common protein targets were identified among the two marine AMPs (polyphemusin-I and P-Der) and three terrestrial AMPs (Lfcin B, PR-39 and Bac7), respectively. To further reveal the target pattern of marine and terrestrial AMPs, the enrichment results obtained from common protein targets of marine AMPs with terrestrial AMPs were compared. The comparison result indicated that AMPs have unique mechanism of action among marine or terrestrial AMPs. Hence, in this study, we have not only identified the intracellular protein targets of polyphemusin-I, but also revealed the protein target differences between marine AMPs and terrestrial AMPs.
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Affiliation(s)
- Pramod Shah
- Institute of Systems Biology and Bioinformatics, Department of Biomedical Sciences and Engineering, College of Health Sciences and Technology, National Central University, Jhongli 300, Taiwan;
- Department of Nutritional Science, Fu Jen Catholic University, New Taipei City 242, Taiwan
| | - Chien-Sheng Chen
- Institute of Systems Biology and Bioinformatics, Department of Biomedical Sciences and Engineering, College of Health Sciences and Technology, National Central University, Jhongli 300, Taiwan;
- Department of Food Safety/Hygiene and Risk Management, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
- Correspondence: ; Tel.: +886-6-235-3535 (ext. 5964); Fax: +886-6-275-2484
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de Oliveira Costa B, Franco OL. Cryptic Host Defense Peptides: Multifaceted Activity and Prospects for Medicinal Chemistry. Curr Top Med Chem 2021; 20:1274-1290. [PMID: 32209042 DOI: 10.2174/1568026620666200325112425] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 02/03/2020] [Accepted: 02/24/2020] [Indexed: 01/22/2023]
Abstract
Host defense peptides (HDPs) comprise a heterogeneous group of evolutionarily conserved and biologically active small molecules that are produced by different organisms. HDPs are widely researched because they often have multiple biological activities, for example antimicrobial, immunomodulatory and anticancer activity. In this context, in this review we focus on cryptic HDPs, molecules derived specifically from proteolytic processing of endogenous precursor proteins. Here, we explore the biological activity of such molecules and we further discuss the development of optimized sequences based on these natural cryptic HDPs. In addition, we present clinical-phase studies of cryptic HDPs (natural or optimized), and point out the possible applicability of these molecules in medicinal chemistry.
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Affiliation(s)
- Bruna de Oliveira Costa
- S-inova Biotech, Graduate Program in Biotechnology, Universidade Catolica Dom Bosco, Campo Grande, MS, Brazil
| | - Octávio Luiz Franco
- S-inova Biotech, Graduate Program in Biotechnology, Universidade Catolica Dom Bosco, Campo Grande, MS, Brazil.,Department of Genomic Sciences and Biotechnology, Center for Analysis of Proteomics and Biochemistry, Catholic University of Brasília, Brasília, DF, Brazil.,Department of Molecular Pathology, Faculty of Medicine, University of Brasília, Brasília-DF, Brazil
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8
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Systematic Identification of Protein Targets of Sub5 Using Saccharomyces cerevisiae Proteome Microarrays. Int J Mol Sci 2021; 22:ijms22020760. [PMID: 33451135 PMCID: PMC7828587 DOI: 10.3390/ijms22020760] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/08/2020] [Accepted: 12/09/2020] [Indexed: 11/17/2022] Open
Abstract
Antimicrobial peptides (AMPs) are intensively studied in terms of alternative drugs. Sub5 is a synthetic 12-mer AMP with substitutions of five amino acids of bactenecin 2A (Bac2A), a linear-ized bactenecin variant of bovine. Sub5 is highly effective against fungi with an ability to trans-locate cell membrane, but its targets are unknown. Systematic analysis of Sub5 targets will facil-itate our understanding on its mechanism of action. In this study, we used high-throughput Saccharomyces cerevisiae proteome microarrays to explore the potential protein targets of Sub5. The screening results showed 128 potential protein targets of Sub5. Bioinformatics analysis of protein targets of Sub5 revealed significant gene ontology (GO) enrichment in actin related pro-cess of “actin filament-based process”, “actin filament organization”, “actin cortical patch or-ganization”, regulation of “actin filament bundle assembly”. Moreover, the other enriched cat-egories in GO enrichment mostly contained actin associate proteins. In total, 11 actin-associated proteins were identified in the protein targets of Sub5. Protein family (PFAM) enrichment anal-ysis shows protein domain enriched in actin binding, i.e., “Cytoskeletal-regulatory complex EF hand (helix E-loop-helix F motif)”. Being consistent with GO analysis, Search Tool for the Re-trieval of Interacting Genes/Proteins (STRING) analysis of the protein targets of Sub5 showed ac-tin network with involvement of 15 protein targets. Along with actin-network, STRING analysis showed protein–protein interaction network in ribonucleoprotein, transcription and translation, chromosome, histone, and ubiquitin related, DNA repair, and chaperone. Multiple Expression motifs for Motif Elicitation (MEME) suite provided a consensus binding motif of [ED][ED]EEE[ED][ED][ED][ED][ED], in total of 75 protein targets of Sub5. This motif was present in 9 out of 15 actin-related proteins identified among protein targets of Sub5.
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Mercer DK, Torres MDT, Duay SS, Lovie E, Simpson L, von Köckritz-Blickwede M, de la Fuente-Nunez C, O'Neil DA, Angeles-Boza AM. Antimicrobial Susceptibility Testing of Antimicrobial Peptides to Better Predict Efficacy. Front Cell Infect Microbiol 2020; 10:326. [PMID: 32733816 PMCID: PMC7358464 DOI: 10.3389/fcimb.2020.00326] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/29/2020] [Indexed: 12/11/2022] Open
Abstract
During the development of antimicrobial peptides (AMP) as potential therapeutics, antimicrobial susceptibility testing (AST) stands as an essential part of the process in identification and optimisation of candidate AMP. Standard methods for AST, developed almost 60 years ago for testing conventional antibiotics, are not necessarily fit for purpose when it comes to determining the susceptibility of microorganisms to AMP. Without careful consideration of the parameters comprising AST there is a risk of failing to identify novel antimicrobials at a time when antimicrobial resistance (AMR) is leading the planet toward a post-antibiotic era. More physiologically/clinically relevant AST will allow better determination of the preclinical activity of drug candidates and allow the identification of lead compounds. An important consideration is the efficacy of AMP in biological matrices replicating sites of infection, e.g., blood/plasma/serum, lung bronchiolar lavage fluid/sputum, urine, biofilms, etc., as this will likely be more predictive of clinical efficacy. Additionally, specific AST for different target microorganisms may help to better predict efficacy of AMP in specific infections. In this manuscript, we describe what we believe are the key considerations for AST of AMP and hope that this information can better guide the preclinical development of AMP toward becoming a new generation of urgently needed antimicrobials.
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Affiliation(s)
| | - 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, Penn Institute for Computational Science, and Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, United States
| | - Searle S. Duay
- Department of Chemistry, Institute of Materials Science, University of Connecticut, Storrs, CT, United States
| | - Emma Lovie
- NovaBiotics Ltd, Aberdeen, United Kingdom
| | | | | | - 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, Penn Institute for Computational Science, and Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, United States
| | | | - Alfredo M. Angeles-Boza
- Department of Chemistry, Institute of Materials Science, University of Connecticut, Storrs, CT, United States
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Ardila-Chantré N, Hernández-Cardona AK, Pineda-Castañeda HM, Estupiñan-Torres SM, Leal-Castro AL, Fierro-Medina R, Rivera-Monroy ZJ, García-Castañeda JE. Short peptides conjugated to non-peptidic motifs exhibit antibacterial activity. RSC Adv 2020; 10:29580-29586. [PMID: 35521126 PMCID: PMC9055962 DOI: 10.1039/d0ra05937d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 07/30/2020] [Indexed: 11/21/2022] Open
Abstract
Short peptides derived from buforin and lactoferricin B were conjugated with other antimicrobial molecules of different chemical natures.
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11
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Shah P, Wu WS, Chen CS. Systematical Analysis of the Protein Targets of Lactoferricin B and Histatin-5 Using Yeast Proteome Microarrays. Int J Mol Sci 2019; 20:ijms20174218. [PMID: 31466342 PMCID: PMC6747642 DOI: 10.3390/ijms20174218] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 08/23/2019] [Accepted: 08/23/2019] [Indexed: 12/12/2022] Open
Abstract
Antimicrobial peptides (AMPs) have potential antifungal activities; however, their intracellular protein targets are poorly reported. Proteome microarray is an effective tool with high-throughput and rapid platform that systematically identifies the protein targets. In this study, we have used yeast proteome microarrays for systematical identification of the yeast protein targets of Lactoferricin B (Lfcin B) and Histatin-5. A total of 140 and 137 protein targets were identified from the triplicate yeast proteome microarray assays for Lfcin B and Histatin-5, respectively. The Gene Ontology (GO) enrichment analysis showed that Lfcin B targeted more enrichment categories than Histatin-5 did in all GO biological processes, molecular functions, and cellular components. This might be one of the reasons that Lfcin B has a lower minimum inhibitory concentration (MIC) than Histatin-5. Moreover, pairwise essential proteins that have lethal effects on yeast were analyzed through synthetic lethality. A total of 11 synthetic lethal pairs were identified within the protein targets of Lfcin B. However, only three synthetic lethal pairs were identified within the protein targets of Histatin-5. The higher number of synthetic lethal pairs identified within the protein targets of Lfcin B might also be the reason for Lfcin B to have lower MIC than Histatin-5. Furthermore, two synthetic lethal pairs were identified between the unique protein targets of Lfcin B and Histatin-5. Both the identified synthetic lethal pairs proteins are part of the Spt-Ada-Gcn5 acetyltransferase (SAGA) protein complex that regulates gene expression via histone modification. Identification of synthetic lethal pairs between Lfcin B and Histatin-5 and their involvement in the same protein complex indicated synergistic combination between Lfcin B and Histatin-5. This hypothesis was experimentally confirmed by growth inhibition assay.
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Affiliation(s)
- Pramod Shah
- Graduate Institute of Systems Biology and Bioinformatics, National Central University, Jhongli 32001, Taiwan
- Department of Biomedical Science and Engineering, National Central University, Jhongli 32001, Taiwan
| | - Wei-Sheng Wu
- Department of Electrical Engineering, National Cheng Kung University, Tainan City 701, Taiwan
| | - Chien-Sheng Chen
- Graduate Institute of Systems Biology and Bioinformatics, National Central University, Jhongli 32001, Taiwan.
- Department of Biomedical Science and Engineering, National Central University, Jhongli 32001, Taiwan.
- Department of Food Safety/Hygiene and Risk Management, College of Medicine, National Cheng Kung University, Tainan City 701, Taiwan.
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12
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Maestri E, Pavlicevic M, Montorsi M, Marmiroli N. Meta-Analysis for Correlating Structure of Bioactive Peptides in Foods of Animal Origin with Regard to Effect and Stability. Compr Rev Food Sci Food Saf 2018; 18:3-30. [PMID: 33337011 DOI: 10.1111/1541-4337.12402] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 09/28/2018] [Accepted: 09/29/2018] [Indexed: 01/09/2023]
Abstract
Amino acid (AA) sequences of 807 bioactive peptides from foods of animal origin were examined in order to correlate peptide structure with activity (antihypertensive, antioxidative, immunomodulatory, antimicrobial, hypolipidemic, antithrombotic, and opioid) and stability in vivo. Food sources, such as milk, meat, eggs, and marine products, show different frequencies of bioactive peptides exhibiting specific effects. There is a correlation of peptide structure and effect, depending on type and position of AA. Opioid peptides contain a high percentage of aromatic AA residues, while antimicrobial peptides show an excess of positively charged AAs. AA residue position is significant, with those in the first and penultimate positions having the biggest effects on peptide activity. Peptides that have activity in vivo contain a high percentage (67%) of proline residues, but the positions of proline in the sequence depend on the length of the peptide. We also discuss the influence of processing on activity of these peptides, as well as methods for predicting release from the source protein and activity of peptides.
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Affiliation(s)
- Elena Maestri
- Dept. of Chemistry, Life Sciences and Environmental Sustainability, Univ. of Parma, Parco Area delle Scienze 11/A, 43124, Parma, Italy.,Interdepartmental Centre for Food Safety, Technologies and Innovation for Agri-food (SITEIA.PARMA), Univ. of Parma, Parco Area delle Scienze, 43124, Parma, Italy
| | - Milica Pavlicevic
- Inst. for Food Technology and Biochemistry, Faculty of Agriculture, Univ. of Belgrade, Belgrade, Serbia
| | - Michela Montorsi
- Dept. of Human Sciences and Promotion of the Quality of Life, San Raffaele Roma Open Univ., Via F. Daverio 7, 20122, Milan, Italy.,Consorzio Italbiotec, Via Fantoli, 16/15, 20138, Milano, Italy.,Inst. of Bioimaging and Molecular Physiology, National Council of Research (CNR), Via Fratelli Cervi 93, 20090, Segrate, Italy
| | - Nelson Marmiroli
- Dept. of Chemistry, Life Sciences and Environmental Sustainability, Univ. of Parma, Parco Area delle Scienze 11/A, 43124, Parma, Italy.,Interdepartmental Centre for Food Safety, Technologies and Innovation for Agri-food (SITEIA.PARMA), Univ. of Parma, Parco Area delle Scienze, 43124, Parma, Italy.,Consorzio Italbiotec, Via Fantoli, 16/15, 20138, Milano, Italy
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13
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Antimicrobial peptides: biochemical determinants of activity and biophysical techniques of elucidating their functionality. World J Microbiol Biotechnol 2018; 34:62. [PMID: 29651655 DOI: 10.1007/s11274-018-2444-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 04/05/2018] [Indexed: 10/17/2022]
Abstract
Antimicrobial peptides (AMPs) have been established over millennia as powerful components of the innate immune system of many organisms. Due to their broad spectrum of activity and the development of host resistance against them being unlikely, AMPs are strong candidates for controlling drug-resistant pathogenic microbial pathogens. AMPs cause cell death through several independent or cooperative mechanisms involving membrane lysis, non-lytic activity, and/or intracellular mechanisms. Biochemical determinants such as peptide length, primary sequence, charge, secondary structure, hydrophobicity, amphipathicity and host cell membrane composition together influence the biological activities of peptides. A number of biophysical techniques have been used in recent years to study the mechanisms of action of AMPs. This work appraises the molecular parameters that determine the biocidal activity of AMPs and overviews their mechanisms of actions and the diverse biochemical, biophysical and microscopy techniques utilised to elucidate these.
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14
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Abstract
INTRODUCTION High-content protein microarrays in principle enable the functional interrogation of the human proteome in a broad range of applications, including biomarker discovery, profiling of immune responses, identification of enzyme substrates, and quantifying protein-small molecule, protein-protein and protein-DNA/RNA interactions. As with other microarrays, the underlying proteomic platforms are under active technological development and a range of different protein microarrays are now commercially available. However, deciphering the differences between these platforms to identify the most suitable protein microarray for the specific research question is not always straightforward. Areas covered: This review provides an overview of the technological basis, applications and limitations of some of the most commonly used full-length, recombinant protein and protein fragment microarray platforms, including ProtoArray Human Protein Microarrays, HuProt Human Proteome Microarrays, Human Protein Atlas Protein Fragment Arrays, Nucleic Acid Programmable Arrays and Immunome Protein Arrays. Expert commentary: The choice of appropriate protein microarray platform depends on the specific biological application in hand, with both more focused, lower density and higher density arrays having distinct advantages. Full-length protein arrays offer advantages in biomarker discovery profiling applications, although care is required in ensuring that the protein production and array fabrication methodology is compatible with the required downstream functionality.
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Affiliation(s)
- Jessica G Duarte
- a Cancer Immunobiology Laboratory, Olivia Newton-John Cancer Research Institute/School of Cancer Medicine , La Trobe University , Heidelberg , Australia
| | - Jonathan M Blackburn
- b Institute of Infectious Disease and Molecular Medicine & Department of Integrative Biomedical Sciences, Faculty of Health Sciences , University of Cape Town , Observatory, South Africa
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15
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Gagarinova A, Phanse S, Cygler M, Babu M. Insights from protein-protein interaction studies on bacterial pathogenesis. Expert Rev Proteomics 2017; 14:779-797. [DOI: 10.1080/14789450.2017.1365603] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Alla Gagarinova
- Department of Biochemistry, University of Saskatchewan, Saskatoon, SK, Canada
| | - Sadhna Phanse
- Department of Biochemistry, University of Regina, Regina, SK, Canada
| | - Miroslaw Cygler
- Department of Biochemistry, University of Saskatchewan, Saskatoon, SK, Canada
| | - Mohan Babu
- Department of Biochemistry, University of Regina, Regina, SK, Canada
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Huertas NDJ, Monroy ZJR, Medina RF, Castañeda JEG. Antimicrobial Activity of Truncated and Polyvalent Peptides Derived from the FKCRRQWQWRMKKGLA Sequence against Escherichia coli ATCC 25922 and Staphylococcus aureus ATCC 25923. Molecules 2017; 22:molecules22060987. [PMID: 28613262 PMCID: PMC6152618 DOI: 10.3390/molecules22060987] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 06/08/2017] [Accepted: 06/12/2017] [Indexed: 12/29/2022] Open
Abstract
Peptides derived from LfcinB were designed and synthesized, and their antibacterial activity was tested against Escherichia coli ATCC 25922 and Staphylococcus aureus ATCC 25923. Specifically, a peptide library was constructed by systemically removing the flanking residues (N or C-terminal) of Lfcin 17–31 (17FKCRRWQWRMKKLGA31), maintaining in all peptides the 20RRWQWR25 sequence that corresponds to the minimal antimicrobial motif. For this research, also included were (i) a peptide containing an Ala instead of Cys ([Ala19]-LfcinB 17–31) and (ii) polyvalent peptides containing the RRWQWR sequence and a non-natural amino acid (aminocaproic acid). We established that the lineal peptides LfcinB 17–25 and LfcinB 17–26 exhibited the greatest activity against E. coli ATCC 25922 and S. aureus ATCC 25923, respectively. On the other hand, polyvalent peptides, a dimer and a tetramer, exhibited the greatest antibacterial activity, indicating that multiple copies of the sequence increase the activity. Our results suggest that the dimeric and tetrameric sequence forms potentiate the antibacterial activity of lineal sequences that have exhibited moderate antibacterial activity.
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Affiliation(s)
- Nataly de Jesús Huertas
- Chemistry Department, Universidad Nacional de Colombia, Bogotá Carrera 45 No. 26-85, Building 451, Office 409, Laboratory 334, Bogotá 11321, Colombia.
| | - Zuly Jenny Rivera Monroy
- Chemistry Department, Universidad Nacional de Colombia, Bogotá Carrera 45 No. 26-85, Building 451, Office 409, Laboratory 334, Bogotá 11321, Colombia.
| | - Ricardo Fierro Medina
- Chemistry Department, Universidad Nacional de Colombia, Bogotá Carrera 45 No. 26-85, Building 451, Office 409, Laboratory 334, Bogotá 11321, Colombia.
| | - Javier Eduardo García Castañeda
- Pharmacy Department, Universidad Nacional de Colombia, Bogotá Carrera 45 No. 26-85, Building 450, office 203, Bogotá 11321, Colombia.
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Heulot M, Jacquier N, Aeby S, Le Roy D, Roger T, Trofimenko E, Barras D, Greub G, Widmann C. The Anticancer Peptide TAT-RasGAP 317-326 Exerts Broad Antimicrobial Activity. Front Microbiol 2017. [PMID: 28638371 PMCID: PMC5461357 DOI: 10.3389/fmicb.2017.00994] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Antibiotic resistance has become a major health issue. Nosocomial infections and the prevalence of resistant pathogenic bacterial strains are rising steadily. Therefore, there is an urgent need to develop new classes of antibiotics effective on multi-resistant nosocomial pathogenic bacteria. We have previously shown that a cell-permeable peptide derived from the p120 Ras GTPase-activating protein (RasGAP), called TAT-RasGAP317-326, induces cancer cell death, inhibits metastatic progression, and sensitizes tumor cells to various anti-cancer treatments in vitro and in vivo. We here report that TAT-RasGAP317-326 also possesses antimicrobial activity. In vitro, TAT-RasGAP317-326, but not mutated or truncated forms of the peptide, efficiently killed a series of bacteria including Escherichia coli, Acinetobacter baumannii, Staphylococcus aureus, and Pseudomonas aeruginosa. In vivo experiments revealed that TAT-RasGAP317-326 protects mice from lethal E. coli-induced peritonitis if administrated locally at the onset of infection. However, the protective effect was lost when treatment was delayed, likely due to rapid clearance and inadequate biodistribution of the peptide. Peptide modifications might overcome these shortcomings to increase the in vivo efficacy of the compound in the context of the currently limited antimicrobial options.
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Affiliation(s)
- Mathieu Heulot
- Department of Physiology, University of LausanneLausanne, Switzerland
| | - Nicolas Jacquier
- Department of Laboratories, Institute of Microbiology, Lausanne University Hospital and University of LausanneLausanne, Switzerland
| | - Sébastien Aeby
- Department of Laboratories, Institute of Microbiology, Lausanne University Hospital and University of LausanneLausanne, Switzerland
| | - Didier Le Roy
- Infectious Diseases Service, Lausanne University HospitalEpalinges, Switzerland
| | - Thierry Roger
- Infectious Diseases Service, Lausanne University HospitalEpalinges, Switzerland
| | | | - David Barras
- Bioinformatics Core Facility, Swiss Institute of BioinformaticsLausanne, Switzerland
| | - Gilbert Greub
- Department of Laboratories, Institute of Microbiology, Lausanne University Hospital and University of LausanneLausanne, Switzerland
| | - Christian Widmann
- Department of Physiology, University of LausanneLausanne, Switzerland
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Abstract
Antimicrobial peptides (AMPs) are expressed in various living organisms as first-line host defenses against potential harmful encounters in their surroundings. AMPs are short polycationic peptides exhibiting various antimicrobial activities. The principal antibacterial activity is attributed to the membrane-lytic mechanism which directly interferes with the integrity of the bacterial cell membrane and cell wall. In addition, a number of AMPs form a transmembrane channel in the membrane by self-aggregation or polymerization, leading to cytoplasm leakage and cell death. However, an increasing body of evidence has demonstrated that AMPs are able to exert intracellular inhibitory activities as the primary or supportive mechanisms to achieve efficient killing. In this review, we focus on the major intracellular targeting activities reported in AMPs, which include nucleic acids and protein biosynthesis and protein-folding, protease, cell division, cell wall biosynthesis, and lipopolysaccharide inhibition. These multifunctional AMPs could serve as the potential lead peptides for the future development of novel antibacterial agents with improved therapeutic profiles.
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Huertas Méndez NDJ, Vargas Casanova Y, Gómez Chimbi AK, Hernández E, Leal Castro AL, Melo Diaz JM, Rivera Monroy ZJ, García Castañeda JE. Synthetic Peptides Derived from Bovine Lactoferricin Exhibit Antimicrobial Activity against E. coli ATCC 11775, S. maltophilia ATCC 13636 and S. enteritidis ATCC 13076. Molecules 2017; 22:molecules22030452. [PMID: 28287494 PMCID: PMC6155255 DOI: 10.3390/molecules22030452] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/01/2017] [Accepted: 03/08/2017] [Indexed: 12/14/2022] Open
Abstract
Linear, dimeric, tetrameric, and cyclic peptides derived from lactoferricin B–containing non-natural amino acids and the RWQWR motif were synthesized, purified, and characterized using RP-HPLC, MALDI-TOF mass spectrometry, and circular dichroism. The antibacterial activity of peptides against Escherichia coli ATCC 11775, Stenotrophomonas maltophilia ATCC 13636, and Salmonella enteritidis ATCC 13076 was evaluated. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) were determined. The synthetic bovine lactoferricin exhibited antibacterial activity against E. coli ATCC 11775 and S. enteritidis ATCC 13076. The dimeric peptide (RRWQWR)2K-Ahx exhibited the highest antibacterial activity against the tested bacterial strain. The monomeric, cyclic, tetrameric, and palindromic peptides containing the RWQWR motif exhibited high and specific activity against E. coli ATCC 11775. The results suggest that short peptides derived from lactoferricin B could be considered as potential candidates for the development of antibacterial agents against infections caused by E. coli.
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Affiliation(s)
- Nataly De Jesús Huertas Méndez
- Chemistry Department, Universidad Nacional de Colombia, Bogotá Carrera 45 No 26-85, Building 451, office 409, Bogotá 11321, Colombia.
| | - Yerly Vargas Casanova
- Bacteriology Department, Universidad Colegio Mayor de Cundinamarca, Bogotá Calle 28 No. 5B-02, Bogotá 110311; Colombia.
| | | | - Edith Hernández
- Bacteriology Department, Universidad Colegio Mayor de Cundinamarca, Bogotá Calle 28 No. 5B-02, Bogotá 110311; Colombia.
| | - Aura Lucia Leal Castro
- Medicine Faculty, Universidad Nacional de Colombia, Bogotá Carrera 45 No 26-85, Building 471, Bogotá 11321, Colombia.
| | - Javier Mauricio Melo Diaz
- Chemistry Department, Universidad Nacional de Colombia, Bogotá Carrera 45 No 26-85, Building 451, office 409, Bogotá 11321, Colombia.
| | - Zuly Jenny Rivera Monroy
- Chemistry Department, Universidad Nacional de Colombia, Bogotá Carrera 45 No 26-85, Building 451, office 409, Bogotá 11321, Colombia.
| | - Javier Eduardo García Castañeda
- Pharmacy Department, Universidad Nacional de Colombia, Bogotá Carrera 45 No 26-85, Building 450, office 203, Bogotá 11321, Colombia.
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20
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Revealing the sequence of interactions of PuroA peptide with Candida albicans cells by live-cell imaging. Sci Rep 2017; 7:43542. [PMID: 28252014 PMCID: PMC5333355 DOI: 10.1038/srep43542] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 01/27/2017] [Indexed: 01/09/2023] Open
Abstract
To determine the mechanism(s) of action of antimicrobial peptides (AMPs) it is desirable to provide details of their interaction kinetics with cellular, sub-cellular and molecular targets. The synthetic peptide, PuroA, displays potent antimicrobial activities which have been attributed to peptide-induced membrane destabilization, or intracellular mechanisms of action (DNA-binding) or both. We used time-lapse fluorescence microscopy and fluorescence lifetime imaging microscopy (FLIM) to directly monitor the localization and interaction kinetics of a FITC- PuroA peptide on single Candida albicans cells in real time. Our results reveal the sequence of events leading to cell death. Within 1 minute, FITC-PuroA was observed to interact with SYTO-labelled nucleic acids, resulting in a noticeable quenching in the fluorescence lifetime of the peptide label at the nucleus of yeast cells, and cell-cycle arrest. A propidium iodide (PI) influx assay confirmed that peptide translocation itself did not disrupt the cell membrane integrity; however, PI entry occurred 25–45 minutes later, which correlated with an increase in fractional fluorescence of pores and an overall loss of cell size. Our results clarify that membrane disruption appears to be the mechanism by which the C. albicans cells are killed and this occurs after FITC-PuroA translocation and binding to intracellular targets.
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21
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Bruni N, Capucchio MT, Biasibetti E, Pessione E, Cirrincione S, Giraudo L, Corona A, Dosio F. Antimicrobial Activity of Lactoferrin-Related Peptides and Applications in Human and Veterinary Medicine. Molecules 2016; 21:E752. [PMID: 27294909 PMCID: PMC6273662 DOI: 10.3390/molecules21060752] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 06/03/2016] [Accepted: 06/06/2016] [Indexed: 01/15/2023] Open
Abstract
Antimicrobial peptides (AMPs) represent a vast array of molecules produced by virtually all living organisms as natural barriers against infection. Among AMP sources, an interesting class regards the food-derived bioactive agents. The whey protein lactoferrin (Lf) is an iron-binding glycoprotein that plays a significant role in the innate immune system, and is considered as an important host defense molecule. In search for novel antimicrobial agents, Lf offers a new source with potential pharmaceutical applications. The Lf-derived peptides Lf(1-11), lactoferricin (Lfcin) and lactoferrampin exhibit interesting and more potent antimicrobial actions than intact protein. Particularly, Lfcin has demonstrated strong antibacterial, anti-fungal and antiparasitic activity with promising applications both in human and veterinary diseases (from ocular infections to osteo-articular, gastrointestinal and dermatological diseases).
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Affiliation(s)
- Natascia Bruni
- Istituto Farmaceutico Candioli, Beinasco (To) 10092, Italy.
| | | | - Elena Biasibetti
- Department of Veterinary Sciences, University of Torino, Torino 10095, Italy.
| | - Enrica Pessione
- Department of Life Sciences and Systems Biology, University of Torino, Torino 10123, Italy.
| | - Simona Cirrincione
- Department of Life Sciences and Systems Biology, University of Torino, Torino 10123, Italy.
| | | | | | - Franco Dosio
- Department of Drug Science and Technology, University of Torino, Torino 10125, Italy.
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22
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Ishida Y, Inouye M. Suppression of the toxicity of Bac7 (1-35), a bovine peptide antibiotic, and its production in E. coli. AMB Express 2016; 6:19. [PMID: 26936849 PMCID: PMC4775720 DOI: 10.1186/s13568-016-0190-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 02/23/2016] [Indexed: 11/10/2022] Open
Abstract
Bac7 (1-35) is an Arg- and Pro-rich peptide antibiotic, produced in bovine cells to protect them from microbial infection. It has been demonstrated to inhibit the protein synthesis in E. coli, leading to cell death. Because of its toxicity, no cost effective methods have been developed for Bac7 production in Escherichia coli for its potential clinical use. Here, we found a method to suppress Bac7 (1-35) toxicity in E. coli to establish its high expression system, in which Bac7 (1-35) was fused to the C-terminal end of protein S, a major spore-coat protein from Myxococcus xanthus, using a linker containing a Factor Xa cleavage site. The resulting His6-PrS2-Bac7 (1-35) (PrS2 is consisted of two N-terminal half domains of protein S connected in tandem) was well expressed using the Single-Protein Production (SPP) system at low temperature and subsequently purified in a single step by using a Ni column. The combination of protein S fusion and its expression in the SPP system at low temperature appeared to suppress Bac7 (1-35) toxicity. Both the purified His6-PrS2-Bac7 (1-35) and His6-PrS2-Bac7 (1-35) treated by Factor Xa were proven to be a potent inhibitor for cell-free protein synthesis.
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23
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Ho YH, Shah P, Chen YW, Chen CS. Systematic Analysis of Intracellular-targeting Antimicrobial Peptides, Bactenecin 7, Hybrid of Pleurocidin and Dermaseptin, Proline-Arginine-rich Peptide, and Lactoferricin B, by Using Escherichia coli Proteome Microarrays. Mol Cell Proteomics 2016; 15:1837-47. [PMID: 26902206 DOI: 10.1074/mcp.m115.054999] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Indexed: 01/12/2023] Open
Abstract
Antimicrobial peptides (AMPs) act either through membrane lysis or by attacking intracellular targets. Intracellular targeting AMPs are a resource for antimicrobial agent development. Several AMPs have been identified as intracellular targeting peptides; however, the intracellular targets of many of these peptides remain unknown. In the present study, we used an Escherichia coli proteome microarray to systematically identify the protein targets of three intracellular targeting AMPs: bactenecin 7 (Bac7), a hybrid of pleurocidin and dermaseptin (P-Der), and proline-arginine-rich peptide (PR-39). In addition, we also included the data of lactoferricin B (LfcinB) from our previous study for a more comprehensive analysis. We analyzed the unique protein hits of each AMP in the Kyoto Encyclopedia of Genes and Genomes. The results indicated that Bac7 targets purine metabolism and histidine kinase, LfcinB attacks the transcription-related activities and several cellular carbohydrate biosynthetic processes, P-Der affects several catabolic processes of small molecules, and PR-39 preferentially recognizes proteins involved in RNA- and folate-metabolism-related cellular processes. Moreover, both Bac7 and LfcinB target purine metabolism, whereas LfcinB and PR-39 target lipopolysaccharide biosynthesis. This suggested that LfcinB and Bac7 as well as LfcinB and PR-39 have a synergistic effect on antimicrobial activity, which was validated through antimicrobial assays. Furthermore, common hits of all four AMPs indicated that all of them target arginine decarboxylase, which is a crucial enzyme for Escherichia coli survival in extremely acidic environments. Thus, these AMPs may display greater inhibition to bacterial growth in extremely acidic environments. We have also confirmed this finding in bacterial growth inhibition assays. In conclusion, this comprehensive identification and systematic analysis of intracellular targeting AMPs reveals crucial insights into the intracellular mechanisms of the action of AMPs.
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Affiliation(s)
- Yu-Hsuan Ho
- From the ‡Graduate Institute of Systems Biology and Bioinformatics, National Central University, Jhongli 32001, Taiwan; §Department of Biomedical Science and Engineering, National Central University, Jhongli 32001, Taiwan
| | - Pramod Shah
- From the ‡Graduate Institute of Systems Biology and Bioinformatics, National Central University, Jhongli 32001, Taiwan; §Department of Biomedical Science and Engineering, National Central University, Jhongli 32001, Taiwan
| | - Yi-Wen Chen
- From the ‡Graduate Institute of Systems Biology and Bioinformatics, National Central University, Jhongli 32001, Taiwan; §Department of Biomedical Science and Engineering, National Central University, Jhongli 32001, Taiwan
| | - Chien-Sheng Chen
- From the ‡Graduate Institute of Systems Biology and Bioinformatics, National Central University, Jhongli 32001, Taiwan; §Department of Biomedical Science and Engineering, National Central University, Jhongli 32001, Taiwan
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24
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Shah P, Hsiao FSH, Ho YH, Chen CS. The proteome targets of intracellular targeting antimicrobial peptides. Proteomics 2016; 16:1225-37. [PMID: 26648572 DOI: 10.1002/pmic.201500380] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 10/30/2015] [Accepted: 12/03/2015] [Indexed: 01/28/2023]
Abstract
Antimicrobial peptides have been considered well-deserving candidates to fight the battle against microorganisms due to their broad-spectrum antimicrobial activities. Several studies have suggested that membrane disruption is the basic mechanism of AMPs that leads to killing or inhibiting microorganisms. Also, AMPs have been reported to interact with macromolecules inside the microbial cells such as nucleic acids (DNA/RNA), protein synthesis, essential enzymes, membrane septum formation and cell wall synthesis. Proteins are associated with many intracellular mechanisms of cells, thus protein targets may be specifically involved in mechanisms of action of AMPs. AMPs like pyrrhocoricin, drosocin, apidecin and Bac 7 are documented to have protein targets, DnaK and GroEL. Moreover, the intracellular targeting AMPs are reported to influence more than one protein targets inside the cell, suggesting for the multiple modes of actions. This complex mechanism of intracellular targeting AMPs makes them more difficult for the development of resistance. Herein, we have summarized the current status of AMPs in terms of their mode of actions, entry to cytoplasm and inhibition of macromolecules. To reveal the mechanism of action, we have focused on AMPs with intracellular protein targets. We have also included the use of high-throughput proteome microarray to determine the unidentified AMP protein targets in this review.
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Affiliation(s)
- Pramod Shah
- Graduate Institute of Systems Biology and Bioinformatics, National Central University, Jhongli, Taiwan.,Department of Biomedical Science and Engineering, National Central University, Jhongli, Taiwan
| | - Felix Shih-Hsiang Hsiao
- Graduate Institute of Systems Biology and Bioinformatics, National Central University, Jhongli, Taiwan.,Department of Biomedical Science and Engineering, National Central University, Jhongli, Taiwan
| | - Yu-Hsuan Ho
- Graduate Institute of Systems Biology and Bioinformatics, National Central University, Jhongli, Taiwan.,Department of Biomedical Science and Engineering, National Central University, Jhongli, Taiwan
| | - Chien-Sheng Chen
- Graduate Institute of Systems Biology and Bioinformatics, National Central University, Jhongli, Taiwan.,Department of Biomedical Science and Engineering, National Central University, Jhongli, Taiwan
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Shagaghi N, Palombo EA, Clayton AHA, Bhave M. Archetypal tryptophan-rich antimicrobial peptides: properties and applications. World J Microbiol Biotechnol 2016; 32:31. [PMID: 26748808 DOI: 10.1007/s11274-015-1986-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Accepted: 11/25/2015] [Indexed: 12/17/2022]
Abstract
Drug-resistant microorganisms ('superbugs') present a serious challenge to the success of antimicrobial treatments. Subsequently, there is a crucial need for novel bio-control agents. Many antimicrobial peptides (AMPs) show a broad-spectrum activity against bacteria, fungi or viruses and are strong candidates to complement or substitute current antimicrobial agents. Some AMPs are also effective against protozoa or cancer cells. The tryptophan (Trp)-rich peptides (TRPs) are a subset of AMPs that display potent antimicrobial activity, credited to the unique biochemical properties of tryptophan that allow it to insert into biological membranes. Further, many Trp-rich AMPs cross bacterial membranes without compromising their integrity and act intracellularly, suggesting interactions with nucleic acids and enzymes. In this work, we overview some archetypal TRPs derived from natural sources, i.e., indolicidin, tritrpticin and lactoferricin, summarising their biochemical properties, structures, antimicrobial activities, mechanistic studies and potential applications.
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Affiliation(s)
- Nadin Shagaghi
- Faculty of Science, Engineering and Technology, Swinburne University of Technology, PO Box 218, Hawthorn, VIC, 3122, Australia
| | - Enzo A Palombo
- Faculty of Science, Engineering and Technology, Swinburne University of Technology, PO Box 218, Hawthorn, VIC, 3122, Australia
| | - Andrew H A Clayton
- Faculty of Science, Engineering and Technology, Swinburne University of Technology, PO Box 218, Hawthorn, VIC, 3122, Australia
| | - Mrinal Bhave
- Faculty of Science, Engineering and Technology, Swinburne University of Technology, PO Box 218, Hawthorn, VIC, 3122, Australia.
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26
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Taniguchi M, Ochiai A, Kondo H, Fukuda S, Ishiyama Y, Saitoh E, Kato T, Tanaka T. Pyrrhocoricin, a proline-rich antimicrobial peptide derived from insect, inhibits the translation process in the cell-free Escherichia coli protein synthesis system. J Biosci Bioeng 2015; 121:591-8. [PMID: 26472128 DOI: 10.1016/j.jbiosc.2015.09.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 09/07/2015] [Accepted: 09/07/2015] [Indexed: 01/28/2023]
Abstract
Previous studies have shown that pyrrhocoricin, a proline-rich antimicrobial peptide (PrAMP), killed sensitive species in a dose-dependent manner by specifically binding to DnaK. Here, on the basis of the finding that DnaK-deficient Escherichia coli strains are susceptible to PrAMPs, we used pyrrhocoricin to investigate internal targets other than DnaK. Using conventional antibiotics (bleomycin, streptomycin, and fosfomycin) that have known modes of action, first, we validated the availability of an assay using a cell-free rapid translation system (RTS), which is an in vitro protein synthesis system based on E. coli lysate, for evaluating inhibition of protein synthesis. We found that, similarly to bleomycin and streptomycin, pyrrhocoricin inhibited GFP synthesis in RTS in a concentration-dependent manner. In addition, blockage of transcription and translation steps in RTS was individually estimated using RT-PCR after gene expression to determine mRNA products and using sodium dodecyl sulfate-polyacrylamide gel electrophoresis to determine the amounts of GFP expressed from purified mRNA, respectively. The results demonstrated that this inhibition of GFP synthesis by pyrrhocoricin did not occur at the transcription step but rather at the translation step, in a manner similar to that of GFP synthesis by streptomycin, an inhibitor of the translation step by causing misreading of tRNA. These results suggest that RTS is a powerful assay system for determining if antimicrobial peptides inhibit protein synthesis and its transcription and/or translation steps. This is the first study to have shown that pyrrhocoricin inhibited protein synthesis by specifically repressing the translation step.
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Affiliation(s)
- Masayuki Taniguchi
- Department of Materials Science and Technology, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan; Center for Transdisciplinary Research, Niigata University, Niigata 950-2181, Japan.
| | - Akihito Ochiai
- Department of Materials Science and Technology, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan
| | - Hiroshi Kondo
- Department of Materials Science and Technology, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan
| | - Shun Fukuda
- Department of Materials Science and Technology, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan
| | - Yohei Ishiyama
- Center for Fostering Innovative Leadership, Niigata University, Niigata 950-2181, Japan
| | - Eiichi Saitoh
- Graduate School of Technology, Niigata Institute of Technology, Niigata 945-1195, Japan
| | - Tetsuo Kato
- Department of Chemistry, Tokyo Dental College, Tokyo 101-0062, Japan
| | - Takaaki Tanaka
- Department of Materials Science and Technology, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan
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27
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Basu A, Mishra B, Leong SSJ. Global transcriptome analysis reveals distinct bacterial response towards soluble and surface-immobilized antimicrobial peptide (Lasioglossin-III). RSC Adv 2015. [DOI: 10.1039/c5ra14862f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Bacterial response towards soluble and immobilized AMP molecules revealed through global transcriptome analysis.
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Affiliation(s)
- Anindya Basu
- School of Chemical and Biomedical Engineering
- Nanyang Technological University
- Singapore 637459
| | - Biswajit Mishra
- School of Chemical and Biomedical Engineering
- Nanyang Technological University
- Singapore 637459
| | - Susanna Su Jan Leong
- Singapore Institute of Technology
- Singapore 138683
- Department of Biochemistry
- Yong Loo Lin School of Medicine
- National University of Singapore
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Théolier J, Fliss I, Jean J, Hammami R. Antimicrobial Peptides of Dairy Proteins: From Fundamental to Applications. FOOD REVIEWS INTERNATIONAL 2014. [DOI: 10.1080/87559129.2014.896017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Haney EF, Petersen AP, Lau CK, Jing W, Storey DG, Vogel HJ. Mechanism of action of puroindoline derived tryptophan-rich antimicrobial peptides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:1802-13. [DOI: 10.1016/j.bbamem.2013.03.023] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 03/24/2013] [Accepted: 03/25/2013] [Indexed: 02/06/2023]
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Abstract
Protein microarray technology is an emerging field that provides a versatile platform for the characterization of hundreds of thousands of proteins in a highly parallel and high-throughput manner. Protein microarrays are composed of two major classes: analytical and functional. In addition, tissue or cell lysates can also be fractionated and spotted on a slide to form a reverse-phase protein microarray. Applications of protein microarrays, especially functional protein microarrays, have flourished over the past decade as the fabrication technology has matured. In this unit, advances in protein microarray technologies are reviewed, and then a series of examples are presented to illustrate the applications of analytical and functional protein microarrays in both basic and clinical research. Relevant areas of research include the detection of various binding properties of proteins, the study of protein post-translational modifications, the analysis of host-microbe interactions, profiling antibody specificity, and the identification of biomarkers in autoimmune diseases.
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Affiliation(s)
- F X Reymond Sutandy
- Graduate Institute of Systems Biology and Bioinformatics, National Central University, Jhongli, Taiwan
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