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Zhen B, Geng C, Yang Y, Liang H, Jiang Y, Li X, Ye G. Systematic alanine and stapling mutational analysis of antimicrobial peptide Chem-KVL. Bioorg Med Chem Lett 2024; 107:129794. [PMID: 38735344 DOI: 10.1016/j.bmcl.2024.129794] [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: 03/24/2024] [Revised: 05/07/2024] [Accepted: 05/09/2024] [Indexed: 05/14/2024]
Abstract
Chem-KVL is a tandem repeating peptide, with 14 amino acids that was modified based on a short peptide from a fragment of the human host defense protein chemerin. Chem-KVL increases cationicity and hydrophobicity and shows broad-spectrum antibacterial activity. To determine the molecular determinants of Chem-KVL and whether staple-modified Chem-KVL would improve antibacterial activity and protease stability or decrease cytotoxicity, we combined alanine and stapling scanning, and designed a series of alanine and staple-derived Chem-KVL peptides, termed Chem-A1 to Chem-A14 and SCL-1 to SCL-7. We next examined their antibacterial activity against several gram-positive and gram-negative bacteria, their proteolytic stability, and their cytotoxicity. Ala scanning of Chem-KVL suggested that both the positively charged residues (Lys and Arg) and the hydrophobic residues (Lue and Val) were critical for the antibacterial activities of Chem-KVL peptide. Of note, Chem-A4 was able to remarkably inhibit the growth of gram-positive and gram-negative bacteria when compared to the original peptide. And the antibacterial activities of stapled SCL-4 and SCL-7 were several times higher than those of the linear peptide against gram-positive and gram-negative bacteria. Stapling modification of peptides resulted in increased helicity and protein stability when compared with the linear peptide. These stapled peptides, especially SCL-4 and SCL-7, may serve as the leading compounds for further optimization and antimicrobial therapy.
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Affiliation(s)
- Borui Zhen
- School of Pharmacy, Dali University, Dali 671000, China; School of Pharmacy, Naval Medical University, Shanghai 200433, China
| | - Chenchen Geng
- School of Pharmacy, Naval Medical University, Shanghai 200433, China
| | - Yi Yang
- School of Pharmacy, Naval Medical University, Shanghai 200433, China
| | - Haiyan Liang
- School of Pharmacy, Naval Medical University, Shanghai 200433, China
| | | | - Xiang Li
- School of Pharmacy, Naval Medical University, Shanghai 200433, China.
| | - Guangming Ye
- Wuxi Branch of Ruijin Hospital Shanghai Jiao Tong University School of Medicine, Wuxi 214000, China.
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2
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Wan F, Torres MDT, Peng J, de la Fuente-Nunez C. Deep-learning-enabled antibiotic discovery through molecular de-extinction. Nat Biomed Eng 2024:10.1038/s41551-024-01201-x. [PMID: 38862735 DOI: 10.1038/s41551-024-01201-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 03/25/2024] [Indexed: 06/13/2024]
Abstract
Molecular de-extinction aims at resurrecting molecules to solve antibiotic resistance and other present-day biological and biomedical problems. Here we show that deep learning can be used to mine the proteomes of all available extinct organisms for the discovery of antibiotic peptides. We trained ensembles of deep-learning models consisting of a peptide-sequence encoder coupled with neural networks for the prediction of antimicrobial activity and used it to mine 10,311,899 peptides. The models predicted 37,176 sequences with broad-spectrum antimicrobial activity, 11,035 of which were not found in extant organisms. We synthesized 69 peptides and experimentally confirmed their activity against bacterial pathogens. Most peptides killed bacteria by depolarizing their cytoplasmic membrane, contrary to known antimicrobial peptides, which tend to target the outer membrane. Notably, lead compounds (including mammuthusin-2 from the woolly mammoth, elephasin-2 from the straight-tusked elephant, hydrodamin-1 from the ancient sea cow, mylodonin-2 from the giant sloth and megalocerin-1 from the extinct giant elk) showed anti-infective activity in mice with skin abscess or thigh infections. Molecular de-extinction aided by deep learning may accelerate the discovery of therapeutic molecules.
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Affiliation(s)
- Fangping Wan
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Marcelo D T Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Jacqueline Peng
- Graduate Group in Genomics and Computational Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA.
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, USA.
- Graduate Group in Genomics and Computational Biology, University of Pennsylvania, Philadelphia, PA, USA.
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3
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Cui M, Wang M, Sun H, Yu L, Su Z, Zhang X, Zheng Y, Xia M, Shen Y, Wang M. Identifying and characterization of novel broad-spectrum bacteriocins from the Shanxi aged vinegar microbiome: Machine learning, molecular simulation, and activity validation. Int J Biol Macromol 2024; 270:132272. [PMID: 38734334 DOI: 10.1016/j.ijbiomac.2024.132272] [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: 02/29/2024] [Revised: 04/24/2024] [Accepted: 05/08/2024] [Indexed: 05/13/2024]
Abstract
Shanxi aged vinegar microbiome encodes a wide variety of bacteriocins. The aim of this study was to mine, screen and characterize novel broad-spectrum bacteriocins from the large-scale microbiome data of Shanxi aged vinegar through machine learning, molecular simulation and activity validation. A total of 158 potential bacteriocins were innovatively mined from 117,552 representative genes based on metatranscriptomic information from the Shanxi aged vinegar microbiome using machine learning techniques and 12 microorganisms were identified to secrete bacteriocins at the genus level. Subsequently, employing AlphaFold2 structure prediction and molecular dynamics simulations, eight bacteriocins with high stability were further screened, and all of them were confirmed to have bacteriostatic activity by the Escherichia coli BL21 expression system. Then, gene_386319 (named LAB-3) and gene_403047 (named LAB-4) with the strongest antibacterial activities were purified by two-step methods and analyzed by mass spectrometry. The two bacteriocins have broad-spectrum antimicrobial activity with minimum inhibitory concentration values of 6.79 μg/mL-15.31 μg/mL against Staphylococcus aureus and Escherichia coli. Furthermore, molecular docking analysis indicated that LAB-3 and LAB-4 could interact with dihydrofolate reductase through hydrogen bonds, salt-bridge forces and hydrophobic forces. These findings suggested that the two bacteriocins could be considered as promising broad-spectrum antimicrobial agents.
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Affiliation(s)
- Meili Cui
- State Key Laboratory of Food Nutrition and Safety, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control. College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Mengyue Wang
- State Key Laboratory of Food Nutrition and Safety, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control. College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Haoyan Sun
- State Key Laboratory of Food Nutrition and Safety, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control. College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Lu Yu
- State Key Laboratory of Food Nutrition and Safety, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control. College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Zhenhua Su
- State Key Laboratory of Food Nutrition and Safety, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control. College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Xiaofeng Zhang
- State Key Laboratory of Food Nutrition and Safety, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control. College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yu Zheng
- State Key Laboratory of Food Nutrition and Safety, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control. College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Menglei Xia
- State Key Laboratory of Food Nutrition and Safety, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control. College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yanbing Shen
- State Key Laboratory of Food Nutrition and Safety, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control. College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China.
| | - Min Wang
- State Key Laboratory of Food Nutrition and Safety, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control. College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China.
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Ma X, Aminov R, Franco OL, de la Fuente-Nunez C, Wang G, Wang J. Editorial: Antimicrobial peptides and their druggability, bio-safety, stability, and resistance. Front Microbiol 2024; 15:1425952. [PMID: 38846567 PMCID: PMC11154904 DOI: 10.3389/fmicb.2024.1425952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 05/14/2024] [Indexed: 06/09/2024] Open
Affiliation(s)
- Xuanxuan Ma
- Innovative Team of Antimicrobial Peptides and Alternatives to Antibiotics, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Rustam Aminov
- The School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, United Kingdom
| | - Octavio Luiz Franco
- S-Inova Biotech, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil
- Centro de Análises Proteômicas e Bioquímicas Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Perelman School of Medicine, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, United States
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, United States
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, United States
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, United States
| | - Guangshun Wang
- Department of Pathology, Microbiology, and Immunology, University of Nebraska Medical Center, Omaha, NE, United States
| | - Jianhua Wang
- Innovative Team of Antimicrobial Peptides and Alternatives to Antibiotics, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing, China
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Cashman-Kadri S, Lagüe P, Subirade M, Fliss I, Beaulieu L. Insights into Molecular Interactions between a GAPDH-Related Fish Antimicrobial Peptide, Analogs Thereof, and Bacterial Membranes. Biochemistry 2024; 63:1257-1269. [PMID: 38683758 PMCID: PMC11112741 DOI: 10.1021/acs.biochem.4c00049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 05/02/2024]
Abstract
Interactions between SJGAP (skipjack tuna GAPDH-related antimicrobial peptide) and four analogs thereof with model bacterial membranes were studied using Fourier-transform infrared spectroscopy (FTIR) and molecular dynamics (MD) simulations. MD trajectory analyses showed that the N-terminal segment of the peptide analogs has many contacts with the polar heads of membrane phospholipids, while the central α helix interacts strongly with the hydrophobic core of the membranes. The peptides also had a marked influence on the wave numbers associated with the phase transition of phospholipids organized as liposomes in both the interface and aliphatic chain regions of the infrared spectra, supporting the interactions observed in the MD trajectories. In addition, interesting links were found between peptide interactions with the aliphatic chains of membrane phospholipids, as determined by FTIR and from the MD trajectories, and the membrane permeabilization capacity of these peptide analogs, as previously demonstrated. To summarize, the combined experimental and computational efforts have provided insights into crucial aspects of the interactions between the investigated peptides and bacterial membranes. This work thus makes an original contribution to our understanding of the molecular interactions underlying the antimicrobial activity of these GAPDH-related antimicrobial peptides from Scombridae.
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Affiliation(s)
- Samuel Cashman-Kadri
- Institute
of Nutrition and Functional Foods (INAF), Université Laval, Québec, Québec G1V 0A6, Canada
- Department
of Food Science, Faculty of Agricultural and Food Sciences, Université Laval, Québec, Québec G1V 0A6, Canada
- Québec-Océan, Université Laval, Québec, Québec G1V 0A6, Canada
| | - Patrick Lagüe
- Department
of Biochemistry, Microbiology and Bioinformatics, Faculty of Sciences
and Engineering, Université Laval, Quebec, Québec G1V 0A6, Canada
- Institute
for Integrative Systems Biology, Pavillon Charles-Eugene-Marchand, Université Laval, 1030 Avenue de la Medecine, Québec, Québec G1V 0A6, Canada
- The
Quebec Network for Research on Protein Function, Engineering, and
Applications (PROTEO), Québec, Québec G1V 0A6, Canada
| | - Muriel Subirade
- Institute
of Nutrition and Functional Foods (INAF), Université Laval, Québec, Québec G1V 0A6, Canada
- Department
of Food Science, Faculty of Agricultural and Food Sciences, Université Laval, Québec, Québec G1V 0A6, Canada
| | - Ismail Fliss
- Institute
of Nutrition and Functional Foods (INAF), Université Laval, Québec, Québec G1V 0A6, Canada
- Department
of Food Science, Faculty of Agricultural and Food Sciences, Université Laval, Québec, Québec G1V 0A6, Canada
| | - Lucie Beaulieu
- Institute
of Nutrition and Functional Foods (INAF), Université Laval, Québec, Québec G1V 0A6, Canada
- Department
of Food Science, Faculty of Agricultural and Food Sciences, Université Laval, Québec, Québec G1V 0A6, Canada
- Québec-Océan, Université Laval, Québec, Québec G1V 0A6, Canada
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6
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Zheng Y, Yu Q, Han L, Chen X. Molecular Characterization of Resistance and Virulence Factors of Trueperella pyogenes Isolated from Clinical Bovine Mastitis Cases in China. Infect Drug Resist 2024; 17:1979-1986. [PMID: 38800580 PMCID: PMC11122176 DOI: 10.2147/idr.s433578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 04/11/2024] [Indexed: 05/29/2024] Open
Abstract
Purpose The present study was designed to investigate the resistance determinants and virulence factors of 45 Trueperella pyogenes isolates from clinical bovine mastitis in Hexi Corridor of Gansu, China. Methods Minimum inhibitory concentrations (MICs) was tested by E-test method. Gene of antimicrobial resistance, virulence integrase and integron gene cassettes were determined by PCR and DNA sequencing. Results The T. pyogenes isolates exhibited high resistance to streptomycin (88.9%) and tetracycline (64.4%), followed by erythromycin (15.6%) and gentamicin (13.3%). Resistance to streptomycin was most commonly encoded by aadA9 (88.9%); and to tetracycline, by tetW (64.4%). Importantly, all streptomycin-resistant isolates carried aadA9 alone or in combination with aadA1, aadA11 and strA-strB. Similarly, all tetracycline-resistant isolates harbored tetW alone or in combination with tetA33. Meanwhile, ermX was detected in 13.3% isolates, only one erythromycin-resistant isolate was not identified for this gene. Moreover, all T. pyogenes isolates carried class 1 integrons, and 17.8% of them contained gene cassettes, including arrays aadA1-aadB (4.4%), aad A24-dfrA1-ORF1 (2.2%) and aadA1 (2.2%). Furthermore, all tested isolates harbored virulent genes plo and fimA, followed by fimC (88.9%), fimE (86.6%) nanP (75.6%), nanH (40.0%), cbpA (35.6%) and fimG (6.7%). Conclusion To our knowledge, this is the first report of integron gene cassettes of T. pyogenes isolates from bovine mastitis cases in China. These findings are useful for developing the prevention and the virulence factors of T. pyogenes could be promising candidates for vaccine antigens for bovine mastitis caused by T. pyogenes in China.
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Affiliation(s)
- Ya Zheng
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, Gansu, 730070, People’s Republic of China
| | - Qunli Yu
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, Gansu, 730070, People’s Republic of China
| | - Ling Han
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, Gansu, 730070, People’s Republic of China
| | - Xinyi Chen
- School of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People’s Republic of China
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7
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Wongchai M, Wongkaewkhiaw S, Kanthawong S, Roytrakul S, Aunpad R. Dual-function antimicrobial-antibiofilm peptide hybrid to tackle biofilm-forming Staphylococcus epidermidis. Ann Clin Microbiol Antimicrob 2024; 23:44. [PMID: 38755634 PMCID: PMC11100219 DOI: 10.1186/s12941-024-00701-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 04/28/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND Due to their resistance and difficulty in treatment, biofilm-associated infections are problematic among hospitalized patients globally and account for 60% of all bacterial infections in humans. Antibiofilm peptides have recently emerged as an alternative treatment since they can be effectively designed and exert a different mode of biofilm inhibition and eradication. METHODS A novel antibiofilm peptide, BiF, was designed from the conserved sequence of 18 α-helical antibiofilm peptides by template-assisted technique and its activity was improved by hybridization with a lipid binding motif (KILRR). Novel antibiofilm peptide derivatives were modified by substituting hydrophobic amino acids at positions 5 or 7, and both, with positively charged lysines (L5K, L7K). These peptide derivatives were tested for antibiofilm and antimicrobial activities against biofilm-forming Staphylococcus epidermidis and multiple other microbes using crystal violet and broth microdilution assays, respectively. To assess their impact on mammalian cells, the toxicity of peptides was determined through hemolysis and cytotoxicity assays. The stability of candidate peptide, BiF2_5K7K, was assessed in human serum and its secondary structure in bacterial membrane-like environments was analyzed using circular dichroism. The action of BiF2_5K7K on planktonic S. epidermidis and its effect on biofilm cell viability were assessed via viable counting assays. Its biofilm inhibition mechanism was investigated through confocal laser scanning microscopy and transcription analysis. Additionally, its ability to eradicate mature biofilms was examined using colony counting. Finally, a preliminary evaluation involved coating a catheter with BiF2_5K7K to assess its preventive efficacy against S. epidermidis biofilm formation on the catheter and its surrounding area. RESULTS BiF2_5K7K, the modified antibiofilm peptide, exhibited dose-dependent antibiofilm activity against S. epidermidis. It inhibited biofilm formation at subinhibitory concentrations by altering S. epidermidis extracellular polysaccharide production and quorum-sensing gene expression. Additionally, it exhibited broad-spectrum antimicrobial activity and no significant hemolysis or toxicity against mammalian cell lines was observed. Its activity is retained when exposed to human serum. In bacterial membrane-like environments, this peptide formed an α-helix amphipathic structure. Within 4 h, a reduction in the number of S. epidermidis colonies was observed, demonstrating the fast action of this peptide. As a preliminary test, a BiF2_5K7K-coated catheter was able to prevent the development of S. epidermidis biofilm both on the catheter surface and in its surrounding area. CONCLUSIONS Due to the safety and effectiveness of BiF2_5K7K, we suggest that this peptide be further developed to combat biofilm infections, particularly those of biofilm-forming S. epidermidis.
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Affiliation(s)
- Mathira Wongchai
- Graduate Program in Biomedical Sciences, Faculty of Allied Health Sciences, Thammasat University, Pathum Thani, Thailand
| | - Saharut Wongkaewkhiaw
- School of Dentistry, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand
| | - Sakawrat Kanthawong
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Sittiruk Roytrakul
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Ratchaneewan Aunpad
- Graduate Program in Biomedical Sciences, Faculty of Allied Health Sciences, Thammasat University, Pathum Thani, Thailand.
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8
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Hao S, Shi W, Chen L, Kong T, Wang B, Chen S, Guo X. CATH-2-derived antimicrobial peptide inhibits multidrug-resistant Escherichia coli infection in chickens. Front Cell Infect Microbiol 2024; 14:1390934. [PMID: 38812753 PMCID: PMC11133627 DOI: 10.3389/fcimb.2024.1390934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 04/18/2024] [Indexed: 05/31/2024] Open
Abstract
Avian colibacillosis (AC), caused by infection with Escherichia coli (E. coli), is a major threat to poultry health, food safety and public health, and results in high mortality and significant economic losses. Currently, new drugs are urgently needed to replace antibiotics due to the continuous emergence and increasing resistance of multidrug-resistant (MDR) strains of E. coli caused by the irrational use of antibiotics in agriculture and animal husbandry. In recent years, antimicrobial peptides (AMPs), which uniquely evolved to protect the host, have emerged as a leading alternative to antibiotics in clinical settings. CATH-2, a member of the antimicrobial cathelicidin peptide family, has been reported to have antibacterial activity. To enhance the antimicrobial potency and reduce the adverse effects on animals, we designed five novel AMPs, named C2-1, C2-2, C2-3, C2-4 and C2-5, based on chicken CATH-2, the secondary structures of these AMPs were consistently α-helical and had an altered net charge and hydrophobicity compared to those of the CATH-2 (1-15) sequences. Subsequently, the antimicrobial activities of CATH-2 (1-15) and five designed peptides against MDR E. coli were evaluated in vitro. Specifically, C2-2 showed excellent antimicrobial activity against either the ATCC standard strain or veterinary clinical isolates of MDR E. coli, with concentrations ranging from 2-8 μg/mL. Furthermore, C2-2 maintained its strong antibacterial efficacy under high temperature and saline conditions, demonstrating significant stability. Similarly, C2-2 retained a high level of safety with no significant hemolytic activity on chicken mature red blood cells or cytotoxicity on chicken kidney cells over the concentration range of 0-64 μg/mL. Moreover, the administration of C2-2 improved the survival rate and reduced the bacterial load in the heart, liver and spleen during MDR E. coli infection in chickens. Additionally, pathological damage to the heart, liver and intestine was prevented when MDR E. coli infected chickens were treated with C2-2. Together, our study showed that C2-2 may be a promising novel therapeutic agent for the treatment of MDR E. coli infections and AC.
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Affiliation(s)
- Shihao Hao
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, China
| | - Wenhui Shi
- Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Liujun Chen
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, China
| | - Tianyou Kong
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, China
| | - Bin Wang
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, China
| | - Shuming Chen
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, China
| | - Xiaomin Guo
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, China
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9
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MacNair CR, Rutherford ST, Tan MW. Alternative therapeutic strategies to treat antibiotic-resistant pathogens. Nat Rev Microbiol 2024; 22:262-275. [PMID: 38082064 DOI: 10.1038/s41579-023-00993-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2023] [Indexed: 04/19/2024]
Abstract
Resistance threatens to render antibiotics - which are essential for modern medicine - ineffective, thus posing a threat to human health. The discovery of novel classes of antibiotics able to overcome resistance has been stalled for decades, with the developmental pipeline relying almost entirely on variations of existing chemical scaffolds. Unfortunately, this approach has been unable to keep pace with resistance evolution, necessitating new therapeutic strategies. In this Review, we highlight recent efforts to discover non-traditional antimicrobials, specifically describing the advantages and limitations of antimicrobial peptides and macrocycles, antibodies, bacteriophages and antisense oligonucleotides. These approaches have the potential to stem the tide of resistance by expanding the physicochemical property space and target spectrum occupied by currently approved antibiotics.
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Affiliation(s)
- Craig R MacNair
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Steven T Rutherford
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Man-Wah Tan
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA.
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10
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Yang H, Wang J, Wang X, Wang S, Xu J, Shan Q, Wang J, Ma X, Zhu Y. Nanofiber Peptides for Bacterial Trapping: A Novel Approach to Antibiotic Alternatives in Wound Infections. Adv Healthc Mater 2024:e2304657. [PMID: 38607802 DOI: 10.1002/adhm.202304657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 04/09/2024] [Indexed: 04/14/2024]
Abstract
The pervasive employment of antibiotics has engendered the advent of drug-resistant bacteria, imperiling the well-being and health of both humans and animals. Infections precipitated by such multi-resistant bacteria, especially those induced by methicillin-resistant Staphylococcus aureus (MRSA), pervade hospital settings, constituting a grave menace to patient vitality. Antimicrobial peptides (AMPs) have garnered considerable attention as a potent countermeasure against multidrug resistant bacteria. In preceding research endeavors, an insect-derived antimicrobial peptide is identified that, while possessing antimicrobial attributes, manifested suboptimal efficacy against drug-resistant Gram-positive bacteria. To ameliorate this issue, this work enhances the antimicrobial capabilities of the initial β-hairpin AMPs by substituting the structural sequence of the original AMPs with variant lengths of hydrophobic amino acid-hydrophilic amino acid repeat units. Throughout this endeavor, this work has identified a number of peptides that possess highly effective antibacterial characteristics against a wide range of bacteria. Additionally, some of these peptides have the ability to self-assemble into nanofibers, which then build networks in a distinctive manner to capture bacteria. Consequently, they represent prospective antibiotic alternatives for addressing wound infections engendered by drug-resistant bacteria.
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Affiliation(s)
- Hao Yang
- College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Jiufeng Wang
- College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
- College of Veterinary Medicine, Sanya Institute of China Agricultural University, Sanya, 572025, China
| | - Xue Wang
- College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Siyu Wang
- College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Jieru Xu
- College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Qiang Shan
- College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Jingyi Wang
- College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Xi Ma
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yaohong Zhu
- College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
- College of Veterinary Medicine, Sanya Institute of China Agricultural University, Sanya, 572025, China
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11
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Torres MDT, Cesaro A, de la Fuente-Nunez C. Peptides from non-immune proteins target infections through antimicrobial and immunomodulatory properties. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.25.586636. [PMID: 38585860 PMCID: PMC10996515 DOI: 10.1101/2024.03.25.586636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Encrypted peptides have been recently described as a new class of antimicrobial molecules. They have been proposed to play a role in host immunity and as alternatives to conventional antibiotics. Intriguingly, many of these peptides are found embedded in proteins unrelated to the immune system, suggesting that immunological responses may extend beyond traditional host immunity proteins. To test this idea, here we synthesized and tested representative peptides derived from non-immune proteins for their ability to exert antimicrobial and immunomodulatory properties. Our experiments revealed that most of the tested peptides from non-immune proteins, derived from structural proteins as well as proteins from the nervous and visual systems, displayed potent in vitro antimicrobial activity. These molecules killed bacterial pathogens by targeting their membrane, and those originating from the same region of the body exhibited synergistic effects when combined. Beyond their antimicrobial properties, nearly 90% of the peptides tested exhibited immunomodulatory effects, modulating inflammatory mediators such as IL-6, TNF-α, and MCP-1. Moreover, eight of the peptides identified, collagenin 3 and 4, zipperin-1 and 2, and immunosin-2, 3, 12, and 13, displayed anti-infective efficacy in two different preclinical mouse models, reducing bacterial infections by up to four orders of magnitude. Altogether, our results support the hypothesis that peptides from non-immune proteins may play a role in host immunity. These results potentially expand our notion of the immune system to include previously unrecognized proteins and peptides that may be activated upon infection to confer protection to the host.
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12
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Lucas DR, Damica FZ, Toledo EB, Cogo AJD, Okorokova-Façanha AL, Gomes VM, de Oliveira Carvalho A. Bioinspired peptides induce different cell death mechanisms against opportunistic yeasts. Probiotics Antimicrob Proteins 2024; 16:649-672. [PMID: 37076595 PMCID: PMC10115610 DOI: 10.1007/s12602-023-10064-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/10/2023] [Indexed: 04/21/2023]
Abstract
The management of fungal diseases imposes an urgent need for the development of effective antifungal drugs. Among new drug candidates are the antimicrobial peptides, and especially their derivatives. Here, we investigated the molecular mechanism of action of three bioinspired peptides against the opportunistic yeasts Candida tropicalis and Candida albicans. We assessed morphological changes, mitochondrial functionality, chromatin condensation, ROS production, activation of metacaspases, and the occurrence of cell death. Our results indicated that the peptides induced sharply contrasting death kinetics, of 6 h for RR and 3 h for D-RR to C. tropicalis and 1 h for WR to C. albicans. Both peptide-treated yeasts exhibited increased ROS levels, mitochondrial hyperpolarization, cell size reduction, and chromatin condensation. RR and WR induced necrosis in C. tropicalis and C. albicans, but not D-RR in C. tropicalis. The antioxidant ascorbic acid reverted the toxic effect of RR and D-RR, but not WR, suggesting that instead of ROS there is a second signal triggered that leads to yeast death. Our data suggest that RR induced a regulated accidental cell death in C. tropicalis, D-RR induced a programmed cell death metacaspase-independent in C. tropicalis, while WR induced an accidental cell death in C. albicans. Our results were obtained with the LD100 and within the time that the peptides induce the yeast death. Within this temporal frame, our results allow us to gain clarity on the events triggered by the peptide-cell interaction and their temporal order, providing a better understanding of the death process induced by them.
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Affiliation(s)
- Douglas Ribeiro Lucas
- Laboratório de Fisiologia e Bioquímica de Microrganismos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Av. Alberto Lamego, nº 2000, Campos dos Goytacazes-RJ, 28013-602, Brazil
| | - Filipe Zaniratti Damica
- Laboratório de Fisiologia e Bioquímica de Microrganismos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Av. Alberto Lamego, nº 2000, Campos dos Goytacazes-RJ, 28013-602, Brazil
| | - Estefany Braz Toledo
- Laboratório de Fisiologia e Bioquímica de Microrganismos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Av. Alberto Lamego, nº 2000, Campos dos Goytacazes-RJ, 28013-602, Brazil
| | - Antônio Jesus Dorighetto Cogo
- Laboratório de Fisiologia e Bioquímica de Microrganismos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Av. Alberto Lamego, nº 2000, Campos dos Goytacazes-RJ, 28013-602, Brazil
| | - Anna Lvovna Okorokova-Façanha
- Laboratório de Fisiologia e Bioquímica de Microrganismos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Av. Alberto Lamego, nº 2000, Campos dos Goytacazes-RJ, 28013-602, Brazil
| | - Valdirene Moreira Gomes
- Laboratório de Fisiologia e Bioquímica de Microrganismos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Av. Alberto Lamego, nº 2000, Campos dos Goytacazes-RJ, 28013-602, Brazil
| | - André de Oliveira Carvalho
- Laboratório de Fisiologia e Bioquímica de Microrganismos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Av. Alberto Lamego, nº 2000, Campos dos Goytacazes-RJ, 28013-602, Brazil.
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13
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Xu J, Xu X, Jiang Y, Fu Y, Shen C. Waste to resource: Mining antimicrobial peptides in sludge from metagenomes using machine learning. ENVIRONMENT INTERNATIONAL 2024; 186:108574. [PMID: 38507933 DOI: 10.1016/j.envint.2024.108574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/26/2024] [Accepted: 03/09/2024] [Indexed: 03/22/2024]
Abstract
The emergence of antibiotic-resistant bacteria poses a huge threat to the treatment of infections. Antimicrobial peptides are a class of short peptides that widely exist in organisms and are considered as potential substitutes for traditional antibiotics. Here, we use metagenomics combined with machine learning to find antimicrobial peptides from environmental metagenomes and successfully obtained 16,044,909 predicted AMPs. We compared the abundance of potential antimicrobial peptides in natural environments and engineered environments, and found that engineered environments also have great potential. Further, we chose sludge as a typical engineered environmental sample, and tried to mine antimicrobial peptides from it. Through metaproteome analysis and correlation analysis, we mined 27 candidate AMPs from sludge. We successfully synthesized 25 peptides by chemical synthesis, and experimentally verified that 21 peptides had antibacterial activity against the 4 strains tested. Our work highlights the potential for mining new antimicrobial peptides from engineered environments and demonstrates the effectiveness of mining antimicrobial peptides from sludge.
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Affiliation(s)
- Jiaqi Xu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China; Zhejiang Provincial Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China
| | - Xin Xu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China; Zhejiang Provincial Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China
| | - Yunhan Jiang
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China; Zhejiang Provincial Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China
| | - Yulong Fu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China; Innovation Center of Yangtze River Delta, Zhejiang University, China
| | - Chaofeng Shen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China; Innovation Center of Yangtze River Delta, Zhejiang University, China.
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14
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Fandiño-Devia E, Santa-González GA, Klaiss-Luna MC, Manrique-Moreno M. Study of the Membrane Activity of the Synthetic Peptide ∆M3 Against Extended-Spectrum β-lactamase Escherichia coli Isolates. J Membr Biol 2024; 257:51-61. [PMID: 38315239 PMCID: PMC11006780 DOI: 10.1007/s00232-024-00306-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 01/03/2024] [Indexed: 02/07/2024]
Abstract
Escherichia coli is the most common microorganism causing nosocomial or community-acquired bacteremia, and extended-spectrum β-lactamase-producing Escherichia coli isolates are identified worldwide with increasing frequency. For this reason, it is necessary to evaluate potential new molecules like antimicrobial peptides. They are recognized for their biological potential which makes them promising candidates in the fight against infections. The goal of this research was to evaluate the potential of the synthetic peptide ΔM3 on several extended-spectrum β-lactamase producing E. coli isolates. The antimicrobial and cytotoxic activity of the peptide was spectrophotometrically determined. Additionally, the capacity of the peptide to interact with the bacterial membrane was monitored by fluorescence microscopy and infrared spectroscopy. The results demonstrated that the synthetic peptide is active against Escherichia coli isolates at concentrations similar to Meropenem. On the other hand, no cytotoxic effect was observed in HaCaT keratinocyte cells even at 10 times the minimal inhibitory concentration. Microscopy results showed a permeabilizing effect of the peptide on the bacteria. The infrared results showed that ΔM3 showed affinity for the lipids of the microorganism's membrane. The results suggest that the ∆M3 interacts with the negatively charged lipids from the E. coli by a disturbing effect on membrane. Finally, the secondary structure experiments of the peptide showed a random structure in solution that did not change during the interaction with the membranes.
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Affiliation(s)
- Estefanía Fandiño-Devia
- Chemistry Institute, Faculty of Exact and Natural Sciences, University of Antioquia, A.A. 1226, Medellin, 050010, Colombia
| | - Gloria A Santa-González
- Grupo de Investigación e Innovación Biomédica, Facultad de Ciencias Exactas y Aplicadas, Instituto Tecnológico Metropolitano, A.A. 54959, Medellín, 050010, Colombia
| | - Maria C Klaiss-Luna
- Chemistry Institute, Faculty of Exact and Natural Sciences, University of Antioquia, A.A. 1226, Medellin, 050010, Colombia
| | - Marcela Manrique-Moreno
- Chemistry Institute, Faculty of Exact and Natural Sciences, University of Antioquia, A.A. 1226, Medellin, 050010, Colombia.
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15
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Chen Z, Wang L, He D, Liu Q, Han Q, Zhang J, Zhang AM, Song Y. Exploration of the Antibacterial and Anti-Inflammatory Activity of a Novel Antimicrobial Peptide Brevinin-1BW. Molecules 2024; 29:1534. [PMID: 38611812 PMCID: PMC11013252 DOI: 10.3390/molecules29071534] [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: 02/20/2024] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
Antibiotic resistance has emerged as a grave threat to global public health, leading to an increasing number of treatment failures. Antimicrobial peptides (AMPs) are widely regarded as potential substitutes for traditional antibiotics since they are less likely to induce resistance when used. A novel AMP named Brevinin-1BW (FLPLLAGLAASFLPTIFCKISRKC) was obtained by the Research Center of Molecular Medicine of Yunnan Province from the skin of the Pelophylax nigromaculatus. Brevinia-1BW had effective inhibitory effects on Gram-positive bacteria, with a minimum inhibitory concentration (MIC) of 3.125 μg/mL against Enterococcus faecalis (ATCC 29212) and 6.25 μg/mL against both Staphylococcus aureus (ATCC 25923) and multidrug-resistant Staphylococcus aureus (ATCC 29213) but had weaker inhibitory effects on Gram-negative bacteria, with a MIC of ≥100 μg/mL. Studies using scanning electron microscopy (SEM) and flow cytometry have revealed that it exerts its antibacterial activity by disrupting bacterial membranes. Additionally, it possesses strong biofilm inhibitory and eradication activities as well as significant lipopolysaccharide (LPS)-binding activity. Furthermore, Brevinin-1BW has shown a significant anti-inflammatory effect in LPS-treated RAW264.7 cells. In conclusion, Brevinin-1BW is anticipated to be a promising clinical agent with potent anti-Gram-positive bacterial and anti-inflammatory properties.
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Affiliation(s)
- Zhizhi Chen
- Research Center of Molecular Medicine of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650504, China; (Z.C.); (L.W.); (D.H.); (Q.L.); (Q.H.); (J.Z.); (A.-M.Z.)
| | - Lei Wang
- Research Center of Molecular Medicine of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650504, China; (Z.C.); (L.W.); (D.H.); (Q.L.); (Q.H.); (J.Z.); (A.-M.Z.)
| | - Dongxia He
- Research Center of Molecular Medicine of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650504, China; (Z.C.); (L.W.); (D.H.); (Q.L.); (Q.H.); (J.Z.); (A.-M.Z.)
| | - Qi Liu
- Research Center of Molecular Medicine of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650504, China; (Z.C.); (L.W.); (D.H.); (Q.L.); (Q.H.); (J.Z.); (A.-M.Z.)
| | - Qinqin Han
- Research Center of Molecular Medicine of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650504, China; (Z.C.); (L.W.); (D.H.); (Q.L.); (Q.H.); (J.Z.); (A.-M.Z.)
| | - Jinyang Zhang
- Research Center of Molecular Medicine of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650504, China; (Z.C.); (L.W.); (D.H.); (Q.L.); (Q.H.); (J.Z.); (A.-M.Z.)
| | - A-Mei Zhang
- Research Center of Molecular Medicine of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650504, China; (Z.C.); (L.W.); (D.H.); (Q.L.); (Q.H.); (J.Z.); (A.-M.Z.)
| | - Yuzhu Song
- Research Center of Molecular Medicine of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650504, China; (Z.C.); (L.W.); (D.H.); (Q.L.); (Q.H.); (J.Z.); (A.-M.Z.)
- School of Medicine, Kunming University of Science and Technology, Kunming 650504, China
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16
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Nazarian-Firouzabadi F, Torres MDT, de la Fuente-Nunez C. Recombinant production of antimicrobial peptides in plants. Biotechnol Adv 2024; 71:108296. [PMID: 38042311 DOI: 10.1016/j.biotechadv.2023.108296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/10/2023] [Accepted: 11/26/2023] [Indexed: 12/04/2023]
Abstract
Classical plant breeding methods are limited in their ability to confer disease resistance on plants. However, in recent years, advancements in molecular breeding and biotechnological have provided new approaches to overcome these limitations and protect plants from disease. Antimicrobial peptides (AMPs) constitute promising agents that may be able to protect against infectious agents. Recently, peptides have been recombinantly produced in plants at scale and low cost. Because AMPs are less likely than conventional antimicrobials to elicit resistance of pathogenic bacteria, they open up exciting new avenues for agricultural applications. Here, we review recent advances in the design and production of bioactive recombinant AMPs that can effectively protect crop plants from diseases.
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Affiliation(s)
- Farhad Nazarian-Firouzabadi
- Production Engineering and Plant Genetics Department, Faculty of Agriculture, Lorestan University, P.O. Box, 465, Khorramabad, Iran.
| | - Marcelo Der Torossian Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America; Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, United States of America; Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America; Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, United States of America; Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, United States of America.
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17
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Almeida CV, de Oliveira CFR, Almeida LHDO, Ramalho SR, Gutierrez CDO, Sardi JDCO, Franco OL, Cardoso MH, Macedo MLR. Computer-made peptide RQ18 acts as a dual antifungal and antibiofilm peptide though membrane-associated mechanisms of action. Arch Biochem Biophys 2024; 753:109884. [PMID: 38218361 DOI: 10.1016/j.abb.2024.109884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/16/2023] [Accepted: 01/08/2024] [Indexed: 01/15/2024]
Abstract
The spread of fungi resistant to conventional drugs has become a threatening problem. In this context, antimicrobial peptides (AMPs) have been considered as one of the main alternatives for controlling fungal infections. Here, we report the antifungal and antibiofilm activity and some clues about peptide RQ18's mechanism of action against Candida and Cryptococcus. This peptide inhibited yeast growth from 2.5 μM and killed all Candida tropicalis cells within 2 h incubation. Moreover, it showed a synergistic effect with antifungal agent the amphotericin b. RQ18 reduced biofilm formation and promoted C. tropicalis mature biofilms eradication. RQ18's mechanism of action involves fungal cell membrane damage, which was confirmed by the results of RQ18 in the presence of free ergosterol in the medium and fluorescence microscopy by Sytox green. No toxic effects were observed in murine macrophage cell lines and Galleria mellonella larvae, suggesting fungal target selectivity. Therefore, peptide RQ18 represents a promising strategy as a dual antifungal and antibiofilm agent that contributes to infection control without damaging mammalian cells.
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Affiliation(s)
- Claudiane Vilharroel Almeida
- Laboratório de Purificação de Proteínas e suas Funções Biológicas, FACFAN, Universidade Federal de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Caio Fernando Ramalho de Oliveira
- Laboratório de Purificação de Proteínas e suas Funções Biológicas, FACFAN, Universidade Federal de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Luís Henrique de Oliveira Almeida
- Laboratório de Purificação de Proteínas e suas Funções Biológicas, FACFAN, Universidade Federal de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Suellen Rodrigues Ramalho
- Laboratório de Purificação de Proteínas e suas Funções Biológicas, FACFAN, Universidade Federal de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Camila de Oliveira Gutierrez
- Laboratório de Purificação de Proteínas e suas Funções Biológicas, FACFAN, Universidade Federal de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Janaina de Cassia Orlandi Sardi
- Laboratório de Purificação de Proteínas e suas Funções Biológicas, FACFAN, Universidade Federal de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Octávio Luiz Franco
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Mato Grosso do Sul, Brazil; Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
| | - Marlon Henrique Cardoso
- Laboratório de Purificação de Proteínas e suas Funções Biológicas, FACFAN, Universidade Federal de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil; S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Mato Grosso do Sul, Brazil; Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Distrito Federal, Brazil
| | - Maria Ligia Rodrigues Macedo
- Laboratório de Purificação de Proteínas e suas Funções Biológicas, FACFAN, Universidade Federal de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil.
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18
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Oshiro KGN, Freitas CDP, Rezende SB, Orozco RMQ, Chan LY, Lawrence N, Lião LM, Macedo MLR, Craik DJ, Cardoso MH, Franco OL. Deciphering the structure and mechanism of action of computer-designed mastoparan peptides. FEBS J 2024; 291:865-883. [PMID: 37997610 DOI: 10.1111/febs.17010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 10/05/2023] [Accepted: 11/08/2023] [Indexed: 11/25/2023]
Abstract
Mastoparans are cationic peptides with multifunctional pharmacological properties. Mastoparan-R1 and mastoparan-R4 were computationally designed based on native mastoparan-L from wasps and have improved therapeutic potential for the control of bacterial infections. Here, we evaluated whether these peptides maintain their activity against Escherichia coli strains under a range of salt concentrations. We found that mastoparan-R1 and mastoparan-R4 preserved their activity under the conditions tested, including having antibacterial activities at physiological salt concentrations. The overall structure of the peptides was investigated using circular dichroism spectroscopy in a range of solvents. No significant changes in secondary structure were observed (random coil in aqueous solutions and α-helix in hydrophobic and anionic environments). The three-dimensional structures of mastoparan-R1 and mastoparan-R4 were elucidated through nuclear magnetic resonance spectroscopy, revealing amphipathic α-helical segments for Leu3-Ile13 (mastoparan-R1) and Leu3-Ile14 (mastoparan-R4). Possible membrane-association mechanisms for mastoparan-R1 and mastoparan-R4 were investigated through surface plasmon resonance and leakage studies with synthetic POPC and POPC/POPG (4:1) lipid bilayers. Mastoparan-L had the highest affinity for both membrane systems, whereas the two analogs had weaker association, but improved selectivity for lysing anionic membranes. This finding was also supported by molecular dynamics simulations, in which mastoparan-R1 and mastoparan-R4 were found to have greater interactions with bacteria-like membranes compared with model mammalian membranes. Despite having a few differences in their functional and structural profiles, the mastoparan-R1 analog stood out with the highest activity, greater bacteriostatic potential, and selectivity for lysing anionic membranes. This study reinforces the potential of mastoparan-R1 as a drug candidate.
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Affiliation(s)
- Karen G N Oshiro
- Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brazil
- S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
- Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brazil
| | - Carlos D P Freitas
- Laboratório de RMN, Instituto de Química, Universidade Federal de Goiás, Goiânia, Brazil
| | - Samilla B Rezende
- S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
- Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brazil
| | - Raquel M Q Orozco
- S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
- Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brazil
| | - Lai Y Chan
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Nicole Lawrence
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Luciano M Lião
- Laboratório de RMN, Instituto de Química, Universidade Federal de Goiás, Goiânia, Brazil
| | - Maria L R Macedo
- Laboratório de Purificação de Proteínas e suas Funções Biológicas, Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Marlon H Cardoso
- Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brazil
- S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
- Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brazil
- Laboratório de Purificação de Proteínas e suas Funções Biológicas, Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil
| | - Octávio L Franco
- Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brazil
- S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Brazil
- Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brazil
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19
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Abdullah SJ, Yan BTS, Palanivelu N, Dhanabal VB, Bifani JP, Bhattacharjya S. Outer-Membrane Permeabilization, LPS Transport Inhibition: Activity, Interactions, and Structures of Thanatin Derived Antimicrobial Peptides. Int J Mol Sci 2024; 25:2122. [PMID: 38396798 PMCID: PMC10888688 DOI: 10.3390/ijms25042122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 01/30/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Currently, viable antibiotics available to mitigate infections caused by drug-resistant Gram-negative bacteria are highly limited. Thanatin, a 21-residue-long insect-derived antimicrobial peptide (AMP), is a promising lead molecule for the potential development of novel antibiotics. Thanatin is extremely potent, particularly against the Enterobacter group of Gram-negative pathogens, e.g., E. coli and K. pneumoniae. As a mode of action, cationic thanatin efficiently permeabilizes the LPS-outer membrane and binds to the periplasmic protein LptAm to inhibit outer membrane biogenesis. Here, we have utilized N-terminal truncated 16- and 14-residue peptide fragments of thanatin and investigated structure, activity, and selectivity with correlating modes of action. A designed 16-residue peptide containing D-Lys (dk) named VF16 (V1PIIYCNRRT-dk-KCQRF16) demonstrated killing activity in Gram-negative bacteria. The VF16 peptide did not show any detectable toxicity to the HEK 293T cell line and kidney cell line Hep G2. As a mode of action, VF16 interacted with LPS, permeabilizing the outer membrane and binding to LptAm with high affinity. Atomic-resolution structures of VF16 in complex with LPS revealed cationic and aromatic surfaces involved in outer membrane interactions and permeabilization. Further, analyses of an inactive 14-residue native thanatin peptide (IM14: IIYCNRRTGKCQRM) delineated the requirement of the β-sheet structure in activity and target interactions. Taken together, this work would pave the way for the designing of short analogs of thanatin-based antimicrobials.
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Affiliation(s)
- Swaleeha Jaan Abdullah
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore; (S.J.A.); (N.P.)
| | - Bernice Tan Siu Yan
- A*Star Infectious Diseases Labs, 8A Biomedical Grove, Immunos, Singapore 138648, Singapore
| | - Nithya Palanivelu
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore; (S.J.A.); (N.P.)
| | - Vidhya Bharathi Dhanabal
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore; (S.J.A.); (N.P.)
| | - Juan Pablo Bifani
- A*Star Infectious Diseases Labs, 8A Biomedical Grove, Immunos, Singapore 138648, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
| | - Surajit Bhattacharjya
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore; (S.J.A.); (N.P.)
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20
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Behera LM, Ghosh M, Gupta PK, Rana S. A rationally engineered small antimicrobial peptide with potent antibacterial activity. J Cell Biochem 2024; 125:e30503. [PMID: 37992185 DOI: 10.1002/jcb.30503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/01/2023] [Accepted: 11/06/2023] [Indexed: 11/24/2023]
Abstract
Antimicrobial resistance (AMR) is a silent pandemic declared by the WHO that requires urgent attention in the post-COVID world. AMR is a critical public health concern worldwide, potentially affecting people at different stages of life, including the veterinary and agriculture industries. Notably, very few new-age antimicrobial agents are in the current developmental pipeline. Thus, the design, discovery, and development of new antimicrobial agents are required to address the menace of AMR. Antimicrobial peptides (AMPs) are an important class of antimicrobial agents for combating AMR due to their broad-spectrum activity and ability to evade AMR through a multimodal mechanism of action. However, molecular size, aggregability, proteolytic degradation, cytotoxicity, and hemolysis activity significantly limit the clinical application of natural AMPs. The de novo design and engineering of a short synthetic amphipathic AMP (≤16 aa, Mol. Wt. ≤ 2 kDa) with an unusual architecture comprised of coded and noncoded amino acids (NCAAs) is presented here, which demonstrates potent antibacterial activity against a few selected bacterial strains mentioned in the WHO priority list. The designer AMP is conformationally ordered in solution and effectively permeabilizes the outer and inner membranes, leading to bacterial growth inhibition and death. Additionally, the peptide is resistant to proteolysis and has negligible cytotoxicity and hemolysis activity up to 150 μM toward cultured human cell lines and erythrocytes. The designer AMP is unique and appears to be a potent therapeutic candidate, which can be subsequently subjected to preclinical studies to explicitly understand and address the menace of AMR.
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Affiliation(s)
- Lalita Mohan Behera
- Chemical Biology Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Odisha, India
| | - Manaswini Ghosh
- Chemical Biology Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Odisha, India
| | - Pulkit Kr Gupta
- Chemical Biology Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Odisha, India
| | - Soumendra Rana
- Chemical Biology Laboratory, School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Odisha, India
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21
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Haddad H, Mejri R, de Araujo AR, Zaïri A. Evaluation of the Antibacterial Activity of New Dermaseptin Derivatives against Acinetobacter baumannii. Pharmaceuticals (Basel) 2024; 17:171. [PMID: 38399385 PMCID: PMC10892451 DOI: 10.3390/ph17020171] [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: 12/26/2023] [Revised: 01/06/2024] [Accepted: 01/17/2024] [Indexed: 02/25/2024] Open
Abstract
Nosocomial infections represent one of the biggest health problems nowadays. Acinetobacter baumannii is known as an opportunistic pathogen in humans, affecting people with compromised immune systems, and is becoming increasingly important as a hospital-derived infection. It is known that in recent years, more and more bacteria have become multidrug-resistant (MDR) and, for this reason, the development of new drugs is a priority. However, these products must not affect the human body, and therefore, cytotoxicity studies are mandatory. In this context, antimicrobial peptides with potential antibacterial proprieties could be an alternative. In this research, we describe the synthesis and the bioactivity of dermaseptins and their derivatives against Acinetobacter baumannii. The cytotoxicity of these compounds was investigated on the HEp-2 cell line by MTT cell viability assay. Thereafter, we studied the morphological alterations caused by the action of one of the active peptides on the bacterial membrane using atomic force microscopy (AFM). The cytotoxicity of dermaseptins was concentration-dependent at microgram concentrations. It was observed that all tested analogs exhibited antibacterial activity with Minimum Inhibitory Concentrations (MICs) ranging from 3.125 to 12.5 μg/mL and Minimum Bactericidal Concentrations (MBCs) ranging from 6.25 to 25 μg/mL. Microscopic images obtained by AFM revealed morphological changes on the surface of the treated bacteria caused by K4S4(1-16), as well as significant surface alterations. Overall, these findings demonstrate that dermaseptins might constitute new lead structures for the development of potent antibacterial agents against Acinetobacter baumannii infections.
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Affiliation(s)
- Houda Haddad
- BIOLIVAL Laboratory, LR14ES06, The Higher Institute of Biotechnology of Monastir ISBM, University of Monastir, Monastir 5000, Tunisia;
- Biochemistry Department, LR18ES47, Faculty of Medicine, University of Sousse, Sousse 4002, Tunisia;
| | - Radhia Mejri
- Biochemistry Department, LR18ES47, Faculty of Medicine, University of Sousse, Sousse 4002, Tunisia;
| | - Alyne Rodrigues de Araujo
- Biodiversity and Biotechnology Research Center, BIOTEC, Federal University of Piauí, Parnaíba 64202-020, PI, Brazil;
| | - Amira Zaïri
- Biochemistry Department, LR18ES47, Faculty of Medicine, University of Sousse, Sousse 4002, Tunisia;
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22
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Yue L, Song L, Zhu S, Fu X, Li X, He C, Li J. Machine learning assisted rational design of antimicrobial peptides based on human endogenous proteins and their applications for cosmetic preservative system optimization. Sci Rep 2024; 14:947. [PMID: 38200054 PMCID: PMC10781772 DOI: 10.1038/s41598-023-50832-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 12/26/2023] [Indexed: 01/12/2024] Open
Abstract
Preservatives are essential components in cosmetic products, but their safety issues have attracted widespread attention. There is an urgent need for safe and effective alternatives. Antimicrobial peptides (AMPs) are part of the innate immune system and have potent antimicrobial properties. Using machine learning-assisted rational design, we obtained a novel antibacterial peptide, IK-16-1, with significant antibacterial activity and maintaining safety based on β-defensins. IK-16-1 has broad-spectrum antimicrobial properties against Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, and Candida albicans, and has no haemolytic activity. The use of IK-16-1 holds promise in the cosmetics industry, since it can serve as a preservative synergist to reduce the amount of other preservatives in cosmetics. This study verified the feasibility of combining computational design with artificial intelligence prediction to design AMPs, achieving rapid screening and reducing development costs.
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Affiliation(s)
- Lizhi Yue
- Key Laboratory of Cosmetic of China National Light Industry, School of Light Industry Science and Engineering, Beijing Technology and Business University, Beijing, China
- School of Chemistry and Chemical Engineering, Qilu Normal University, Shandong, China
| | - Liya Song
- Key Laboratory of Cosmetic of China National Light Industry, School of Light Industry Science and Engineering, Beijing Technology and Business University, Beijing, China
| | - Siyu Zhu
- AGECODE R&D Center, Yangtze Delta Region Institute of Tsinghua University, Zhejiang, China
- Harvest Biotech (Zhejiang) Co., Ltd., Zhejiang, China
| | - Xiaolei Fu
- AGECODE R&D Center, Yangtze Delta Region Institute of Tsinghua University, Zhejiang, China
- Harvest Biotech (Zhejiang) Co., Ltd., Zhejiang, China
| | - Xuhui Li
- AGECODE R&D Center, Yangtze Delta Region Institute of Tsinghua University, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Applied Enzymology, Yangtze Delta Region Institute of Tsinghua University, Zhejiang, China
| | - Congfen He
- Key Laboratory of Cosmetic of China National Light Industry, School of Light Industry Science and Engineering, Beijing Technology and Business University, Beijing, China.
| | - Junxiang Li
- AGECODE R&D Center, Yangtze Delta Region Institute of Tsinghua University, Zhejiang, China.
- Harvest Biotech (Zhejiang) Co., Ltd., Zhejiang, China.
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23
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Mildenberger V, Alpízar-Pedraza D, Martell-Huguet EM, Krämer M, Bolotnikov G, Otero-Gonzalez AJ, Weil T, Rodriguez-Alfonso A, Preising N, Ständker L, Vogel V, Spellerberg B, Kissmann AK, Rosenau F. The Designed Pore-Forming Antimicrobial Peptide C14R Combines Excellent Activity against the Major Opportunistic Human Pathogen Pseudomonas aeruginosa with Low Cytotoxicity. Pharmaceuticals (Basel) 2024; 17:83. [PMID: 38256916 PMCID: PMC10820675 DOI: 10.3390/ph17010083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/21/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
The diminishing portfolio of mankind's available antibiotics urges science to develop novel potent drugs. Here, we present a peptide fitting the typical blueprint of amphipathic and membrane-active antimicrobial peptides, denominated C14R. This 2 kDa peptide consists of 16 amino acid residues, with seven being either hydrophobic, aromatic, or non-polar, and nine being polar or positively charged, strictly separated on opposite sides of the predicted α-helix. The affinity of the peptide C14R to P. aeruginosa membranes and its intrinsic tendency to productively insert into membranes of such composition were analyzed by dynamic simulations. Its biological impact on the viability of two different P. aeruginosa reference strains was demonstrated by determining the minimal inhibitory concentrations (MICs), which were found to be in the range of 10-15 µg/mL. C14R's pore-forming capability was verified in a permeabilization assay based on the peptide-triggered uptake of fluorescent dyes into the bacterial cells. Finally, the peptide was used in radial diffusion assays, which are commonly used for susceptibility testing of antimicrobial peptides in clinical microbiology. In comparison to reference strains, six clinical P. aeruginosa isolates were clearly affected, thereby paving the way for further in-depth analyses of C14R as a promising new AMP drug in the future.
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Affiliation(s)
- Vanessa Mildenberger
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (V.M.); (M.K.); (G.B.)
| | - Daniel Alpízar-Pedraza
- Center for Pharmaceutical Research and Development (CIDEM), 26th Avenue, No. 1605, Nuevo Vedado, La Habana 10400, Cuba;
| | - Ernesto M. Martell-Huguet
- Center for Protein Studies, Faculty of Biology, University of Havana, 25 and I, La Habana 10400, Cuba; (E.M.M.-H.); (A.J.O.-G.)
| | - Markus Krämer
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (V.M.); (M.K.); (G.B.)
| | - Grigory Bolotnikov
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (V.M.); (M.K.); (G.B.)
| | - Anselmo J. Otero-Gonzalez
- Center for Protein Studies, Faculty of Biology, University of Havana, 25 and I, La Habana 10400, Cuba; (E.M.M.-H.); (A.J.O.-G.)
| | - Tanja Weil
- Max Planck Institute for Polymer Research Mainz, Ackermannweg 10, 55128 Mainz, Germany;
| | - Armando Rodriguez-Alfonso
- Core Facility for Functional Peptidomics (CFP), Faculty of Medicine, Ulm University, 89081 Ulm, Germany; (A.R.-A.); (N.P.); (L.S.)
- Core Unit of Mass Spectrometry and Proteomics, Faculty of Medicine, Ulm University, 89081 Ulm, Germany
| | - Nico Preising
- Core Facility for Functional Peptidomics (CFP), Faculty of Medicine, Ulm University, 89081 Ulm, Germany; (A.R.-A.); (N.P.); (L.S.)
| | - Ludger Ständker
- Core Facility for Functional Peptidomics (CFP), Faculty of Medicine, Ulm University, 89081 Ulm, Germany; (A.R.-A.); (N.P.); (L.S.)
| | - Verena Vogel
- Institute of Medical Microbiology and Hygiene, University Clinic of Ulm, TBC1 Forschung, Albert-Einstein-Allee 11, 89081 Ulm, Germany (B.S.)
| | - Barbara Spellerberg
- Institute of Medical Microbiology and Hygiene, University Clinic of Ulm, TBC1 Forschung, Albert-Einstein-Allee 11, 89081 Ulm, Germany (B.S.)
| | - Ann-Kathrin Kissmann
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (V.M.); (M.K.); (G.B.)
- Max Planck Institute for Polymer Research Mainz, Ackermannweg 10, 55128 Mainz, Germany;
| | - Frank Rosenau
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (V.M.); (M.K.); (G.B.)
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24
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Zhang G, Wang Y, Qiu H, Lu L. Facile one-pot synthesis of flower-like ellagic acid microparticles incorporating anti-microbial peptides for enhanced wound healing. J Mater Chem B 2024; 12:500-507. [PMID: 38099474 DOI: 10.1039/d3tb02016a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Anti-microbial peptides (AMPs) have gained significant attention as potential antimicrobial agents due to their cytocompatibility and reduced drug resistance. However, AMPs often suffer from low stability due to their vulnerable molecular structure. This study presents a one-pot synthesis method for ellagic acid (EA)-based, flower-like AMPs@EAMP particles, combining the antibacterial properties of EA with AMPs. The resulting particles exhibit an enlarged surface area for the adsorption or embedding of AMPs, enhancing their antibacterial efficacy. Furthermore, in vitro evaluations demonstrate excellent biocompatibility and broad-spectrum activity against bacterial strains including both Gram-positive S. epidermidis and Gram-negative E. coli. In vivo studies indicate AMPs@EAMPs' potential to reconstruct the immune barrier, inhibit pathogens, and reduce inflammation, promoting orderly tissue repair. This innovative synthesis strategy provides a straightforward and effective approach for large-scale production of flower-like AMPs@EAMP particles with remarkable antibacterial properties, addressing the challenges associated with MDR infections.
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Affiliation(s)
- Guo Zhang
- School & Hospital of Stomatology, Wenzhou Medical University, Wenzhou, 325035, China.
- Key Lab. of Advanced Technology for Materials of Education Ministry, School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Yu Wang
- Sichuan Engineering Research Center for Biomimetic Synthesis of Natural Drugs, School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
| | - Hua Qiu
- Stomatologic Hospital and College, Key Laboratory of Oral Diseases Research of Anhui Province, Anhui Medical University, Hefei, Anhui 230032, China.
| | - Lei Lu
- School & Hospital of Stomatology, Wenzhou Medical University, Wenzhou, 325035, China.
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25
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Stefanik O, Majerova P, Kovac A, Mikus P, Piestansky J. Capillary electrophoresis in the analysis of therapeutic peptides-A review. Electrophoresis 2024; 45:120-164. [PMID: 37705480 DOI: 10.1002/elps.202300141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/10/2023] [Accepted: 08/14/2023] [Indexed: 09/15/2023]
Abstract
Therapeutic peptides are a growing class of innovative drugs with high efficiency and a low risk of adverse effects. These biomolecules fall within the molecular mass range between that of small molecules and proteins. However, their inherent instability and potential for degradation underscore the importance of reliable and effective analytical methods for pharmaceutical quality control, therapeutic drug monitoring, and compliance testing. Liquid chromatography-mass spectrometry (LC-MS) has long time been the "gold standard" conventional method for peptide analysis, but capillary electrophoresis (CE) is increasingly being recognized as a complementary and, in some cases, superior, highly efficient, green, and cost-effective alternative technique. CE can separate peptides composed of different amino acids owing to differences in their net charge and size, determining their migration behavior in an electric field. This review provides a comprehensive overview of therapeutic peptides that have been used in the clinical environment for the last 25 years. It describes the properties, classification, current trends in development, and clinical use of therapeutic peptides. From the analytical point of view, it discusses the challenges associated with the analysis of therapeutic peptides in pharmaceutical and biological matrices, as well as the evaluation of CE as a whole and the comparison with LC methods. The article also highlights the use of microchip electrophoresis, nonaqueous CE, and nonconventional hydrodynamically closed CE systems and their applications. Overall, the article emphasizes the importance of developing new CE-based analytical methods to ensure the high quality, safety, and efficacy of therapeutic peptides in clinical practice.
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Affiliation(s)
- Ondrej Stefanik
- Department of Pharmaceutical Analysis and Nuclear Pharmacy, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava, Slovak Republic
- Toxicological and Antidoping Center, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava, Slovak Republic
| | - Petra Majerova
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Andrej Kovac
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Peter Mikus
- Department of Pharmaceutical Analysis and Nuclear Pharmacy, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava, Slovak Republic
- Toxicological and Antidoping Center, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava, Slovak Republic
| | - Juraj Piestansky
- Toxicological and Antidoping Center, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava, Slovak Republic
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovak Republic
- Department of Galenic Pharmacy, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava, Slovak Republic
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26
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Lin H, Song L, Zhou S, Fan C, Zhang M, Huang R, Zhou R, Qiu J, Ma S, He J. A Hybrid Antimicrobial Peptide Targeting Staphylococcus aureus with a Dual Function of Inhibiting Quorum Sensing Signaling and an Antibacterial Effect. J Med Chem 2023; 66:17105-17117. [PMID: 38099725 DOI: 10.1021/acs.jmedchem.3c02027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Community-associated methicillin-resistant Staphylococcus aureus (MRSA) is now a major cause of bacterial infection. Antivirulence therapy does not stimulate evolution of a pathogen toward a resistant phenotype, providing a novel method to treat infectious diseases. Here, we used a cyclic peptide of CP7, an AIP-III variant that specifically inhibited the virulence and biofilm formation of Staphylococcus aureus (S. aureus) in a nonbiocidal manner, to conjugate with a broad-spectrum antimicrobial peptide (AMP) via two N-termini to obtain a hybrid AMP called CP7-FP13-2. This peptide not only specifically inhibited the production of virulence of S. aureus at low micromolar concentrations but also killed S. aureus, including MRSA, by disrupting the integrity of the bacterial cell membrane. In addition, CP7-FP13-2 inhibited the formation of the S. aureus biofilm and showed good antimicrobial efficacy against the S. aureus-infected Kunming mice model. Therefore, this study provides a promising strategy against the resistance and virulence of S. aureus.
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Affiliation(s)
- Haixing Lin
- Group of peptides and natural products Research, School of Pharmaceutical Sciences, Southern Medical University, 1838 Guangzhou Avenue North, Guangzhou 510515, P. R. China
- Department of Urology, Tongren Municipal People's Hospital, 120 Taoyuan Avenue, Tongren, Guizhou 554300, P. R. China
| | - Li Song
- Group of peptides and natural products Research, School of Pharmaceutical Sciences, Southern Medical University, 1838 Guangzhou Avenue North, Guangzhou 510515, P. R. China
| | - Shaofen Zhou
- Group of peptides and natural products Research, School of Pharmaceutical Sciences, Southern Medical University, 1838 Guangzhou Avenue North, Guangzhou 510515, P. R. China
| | - Cuiqiong Fan
- Group of peptides and natural products Research, School of Pharmaceutical Sciences, Southern Medical University, 1838 Guangzhou Avenue North, Guangzhou 510515, P. R. China
| | - Minna Zhang
- Department of Nephrology, Tongren Municipal People's Hospital, 120 Taoyuan Avenue, Tongren, Guizhou 554300, P. R. China
| | - Ruifeng Huang
- Group of peptides and natural products Research, School of Pharmaceutical Sciences, Southern Medical University, 1838 Guangzhou Avenue North, Guangzhou 510515, P. R. China
| | - Runhong Zhou
- Group of peptides and natural products Research, School of Pharmaceutical Sciences, Southern Medical University, 1838 Guangzhou Avenue North, Guangzhou 510515, P. R. China
| | - Jingnan Qiu
- Group of peptides and natural products Research, School of Pharmaceutical Sciences, Southern Medical University, 1838 Guangzhou Avenue North, Guangzhou 510515, P. R. China
| | - Shuaiqi Ma
- Group of peptides and natural products Research, School of Pharmaceutical Sciences, Southern Medical University, 1838 Guangzhou Avenue North, Guangzhou 510515, P. R. China
| | - Jian He
- Group of peptides and natural products Research, School of Pharmaceutical Sciences, Southern Medical University, 1838 Guangzhou Avenue North, Guangzhou 510515, P. R. China
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27
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Pimchan T, Tian F, Thumanu K, Rodtong S, Yongsawatdigul J. Anti-Salmonella Activity of a Novel Peptide, KGGDLGLFEPTL, Derived from Egg Yolk Hydrolysate. Antibiotics (Basel) 2023; 13:19. [PMID: 38247578 PMCID: PMC10812675 DOI: 10.3390/antibiotics13010019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/16/2023] [Accepted: 12/21/2023] [Indexed: 01/23/2024] Open
Abstract
The present study aimed to characterize the mode of action of a novel antimicrobial peptide isolated from egg yolk hydrolysate. The EYHp6, KGGDLGLFEPTL, exhibited inhibition against Salmonella enterica serovar Typhimurium TISTR 292 and S. enterica serovar Enteritidis DMST 15679 with a MIC value of 2 mM. In contrast, S. enterica serovar Newport ATCC 6962 and other strains of Typhimurium and Enteritidis were inhibited at 4 mM. EYHp6 increased the cell membrane permeability of S. Typhimurium TISTR 292, leading to DNA leakage. Membrane integrity determined by propidium iodide and SYTO9 staining visualized by confocal microscopy demonstrated that EYHp6 at 1 × MIC induced disruption of cell membranes. Electron microscopy revealed that treatment of S. Typhimurium with EYHp6 led to damage to the cell membrane, causing the leakage of intracellular contents. Synchrotron-based Fourier-transform infrared spectroscopy indicated that EYHp6 killed S. Typhimurium by targeting fatty acids and nucleic acids in the cell membrane. The peptide did not show hemolytic activity up to 4 mM. These findings suggest that EYHp6 could be a promising antibacterial agent for controlling the growth of S. enterica.
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Affiliation(s)
- Thippawan Pimchan
- School of Food Technology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand;
| | - Fu Tian
- College of Food and Pharmaceutical Engineering, Guizhou Institute of Technology, Guiyang 550003, China;
| | - Kanjana Thumanu
- Synchrotron Light Research Institute (Public Organization), Nakhon Ratchasima 30000, Thailand;
| | - Sureelak Rodtong
- School of Preclinical Sciences, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand;
| | - Jirawat Yongsawatdigul
- School of Food Technology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand;
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28
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Garvey M. Medical Device-Associated Healthcare Infections: Sterilization and the Potential of Novel Biological Approaches to Ensure Patient Safety. Int J Mol Sci 2023; 25:201. [PMID: 38203372 PMCID: PMC10778788 DOI: 10.3390/ijms25010201] [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: 11/29/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
Healthcare-associated infections caused by multi-drug-resistant pathogens are increasing globally, and current antimicrobial options have limited efficacy against these robust species. The WHO details the critically important bacterial and fungal species that are often associated with medical device HAIs. The effective sterilization of medical devices plays a key role in preventing infectious disease morbidity and mortality. A lack of adherence to protocol and limitations associated with each sterilization modality, however, allows for the incidence of disease. Furthermore, issues relating to carcinogenic emissions from ethylene oxide gas (EtO) have motivated the EPA to propose limiting EtO use or seeking alternative sterilization methods for medical devices. The Food and Drug Administration supports the sterilization of healthcare products using low-temperature VH2O2 as an alternative to EtO. With advances in biomaterial and medical devices and the increasing use of combination products, current sterilization modalities are becoming limited. Novel approaches to disinfection and sterilization of medical devices, biomaterials, and therapeutics are warranted to safeguard public health. Bacteriophages, endolysins, and antimicrobial peptides are considered promising options for the prophylactic and meta-phylactic control of infectious diseases. This timely review discusses the application of these biologics as antimicrobial agents against critically important WHO pathogens, including ESKAPE bacterial species.
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Affiliation(s)
- Mary Garvey
- Department of Life Science, Atlantic Technological University, F91 YW50 Sligo, Ireland;
- Centre for Precision Engineering, Materials and Manufacturing Research (PEM), Atlantic Technological University, F91 YW50 Sligo, Ireland
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29
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Savinov A, Swanson S, Keating AE, Li GW. High-throughput computational discovery of inhibitory protein fragments with AlphaFold. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.19.572389. [PMID: 38187731 PMCID: PMC10769210 DOI: 10.1101/2023.12.19.572389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Peptides can bind to specific sites on larger proteins and thereby function as inhibitors and regulatory elements. Peptide fragments of larger proteins are particularly attractive for achieving these functions due to their inherent potential to form native-like binding interactions. Recently developed experimental approaches allow for high-throughput measurement of protein fragment inhibitory activity in living cells. However, it has thus far not been possible to predict de novo which of the many possible protein fragments bind their protein targets, let alone act as inhibitors. We have developed a computational method, FragFold, that employs AlphaFold to predict protein fragment binding to full-length protein targets in a high-throughput manner. Applying FragFold to thousands of fragments tiling across diverse proteins revealed peaks of predicted binding along each protein sequence. These predictions were compared with experimentally measured peaks of inhibitory activity in E. coli. We establish that our approach is a sensitive predictor of protein fragment function: Evaluating inhibitory fragments derived from known protein-protein interaction interfaces, we found 87% were predicted by FragFold to bind in a native-like mode. Across full protein sequences, 68% of FragFold-predicted binding peaks match experimentally measured inhibitory peaks. This is true even when the underlying inhibitory mechanism is unclear from existing structural data, and we find FragFold is able to predict novel binding modes for inhibitory fragments of unknown structure, explaining previous genetic and biochemical data for these fragments. The success rate of FragFold demonstrates that this computational approach should be broadly applicable for discovering inhibitory protein fragments across proteomes.
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Affiliation(s)
- Andrew Savinov
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sebastian Swanson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Amy E. Keating
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Center for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Gene-Wei Li
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
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30
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Xu K, Zhao X, Tan Y, Wu J, Cai Y, Zhou J, Wang X. A systematical review on antimicrobial peptides and their food applications. BIOMATERIALS ADVANCES 2023; 155:213684. [PMID: 37976831 DOI: 10.1016/j.bioadv.2023.213684] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 10/29/2023] [Accepted: 11/02/2023] [Indexed: 11/19/2023]
Abstract
Food safety issues are a major concern in food processing and packaging industries. Food spoilage is caused by microbial contamination, where antimicrobial peptides (APs) provide solutions by eliminating microorganisms. APs such as nisin have been successfully and commonly used in food processing and preservation. Here, we discuss all aspects of the functionalization of APs in food applications. We briefly review the natural sources of APs and their native functions. Recombinant expression of APs in microorganisms and their yields are described. The molecular mechanisms of AP antibacterial action are explained, and this knowledge can further benefit the design of functional APs. We highlight current utilities and challenges for the application of APs in the food industry, and address rational methods for AP design that may overcome current limitations.
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Affiliation(s)
- Kangjie Xu
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - XinYi Zhao
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Yameng Tan
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Junheng Wu
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Yiqing Cai
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China..
| | - Xinglong Wang
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
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31
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R PA, Anbarasu A. Antimicrobial Peptides as Immunomodulators and Antimycobacterial Agents to Combat Mycobacterium tuberculosis: a Critical Review. Probiotics Antimicrob Proteins 2023; 15:1539-1566. [PMID: 36576687 DOI: 10.1007/s12602-022-10018-6] [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] [Accepted: 11/22/2022] [Indexed: 12/29/2022]
Abstract
Tuberculosis (TB) is a devastating disease foisting a significantly high morbidity, prepotent in low- and middle-income developing countries. Evolution of drug resistance among Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, has made the TB treatment more complicated. The protracted nature of present TB treatment, persistent and tolerant Mtb populations, interaction with antiretroviral therapy and existing toxicity concerned with conventional anti-TB drugs are the four major challenges inflicted with emergence of drug-resistant mycobacterial strains, and the standard medications are unable to combat these strains. These factors emphasize an exigency to develop new drugs to overcome these barriers in current TB therapy. With this regard, antimycobacterial peptides derived from various sources such as human cells, bacterial sources, mycobacteriophages, fungal, plant and animal sources could be considered as antituberculosis leads as most of these peptides are associated with dual advantages of having both bactericidal activity towards Mtb as well as immuno-regulatory property. Some of the peptides possess the additional advantage of interacting synergistically with antituberculosis medications too, thereby increasing their efficiency, underscoring the vigour of antimicrobial peptides (AMPs) as best possible alternative therapeutic candidates or adjuvants in TB treatment. Albeit the beneficiary features of these peptides, few obstacles allied with them like cytotoxicity and proteolytic degradation are matter of concerns too. In this review, we have focused on structural hallmarks, targeting mechanisms and specific structural aspects contributing to antimycobacterial activity and discovered natural and synthetic antimycobacterial peptides along with their sources, anti-TB, immuno-regulatory properties, merits and demerits and possible delivery methods of AMPs.
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Affiliation(s)
- Preethi A R
- Medical & Biological Computing Laboratory, School of Bio-Sciences & Technology, Vellore Institute of Technology, Vellore-632014, India
- Department of Biotechnology, SBST, VIT, Vellore-632014, Tamil Nadu, India
| | - Anand Anbarasu
- Medical & Biological Computing Laboratory, School of Bio-Sciences & Technology, Vellore Institute of Technology, Vellore-632014, India.
- Department of Biotechnology, SBST, VIT, Vellore-632014, Tamil Nadu, India.
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32
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Kong J, Wang Y, Han Y, Zhou H, Huang Z, Zhang X, Zhou C, Cao J, Zhou T. Octominin: An antimicrobial peptide with antibacterial and anti-inflammatory activity against carbapenem-resistant Escherichia coli both in vitro and in vivo. J Glob Antimicrob Resist 2023; 35:172-180. [PMID: 37716532 DOI: 10.1016/j.jgar.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 08/26/2023] [Accepted: 09/07/2023] [Indexed: 09/18/2023] Open
Abstract
OBJECTIVES The emergence of carbapenem-resistant Escherichia coli (CREC) is a global concern as its prevalence restricts treatment options and poses a considerable threat to public health. In this study, in vitro and in vivo activity of the antimicrobial peptide Octominin against CREC was investigated to reveal possible mechanisms of action. Furthermore, its safety and factors influencing its antibacterial effect were assessed. Additionally, the anti-inflammatory effects of Octominin were examined. METHODS The antimicrobial activity of Octominin against 11 strains of CREC was determined using the broth microdilution method, growth curve, and time-kill assay. Its possible mechanism of action was unraveled using the propidium iodide and N-phenyl-1-naphthylamine fluorochrome and lipopolysaccharide-binding assays. To understand the safety and stability of Octominin, its cytotoxicity, hemolysis, and antibacterial activity under various conditions (i.e, temperature, ions) were estimated. Additionally, a Galleria mellonella infection model was utilized to evaluate the efficacy of Octominin in vivo, and qRT-PCR was performed to assess its effect on the expression of proinflammatory cytokines. RESULTS Octominin displayed a significant antibacterial effect, with MICs of 4-8 µg/mL and MBCs of 8-16 µg/mL. Octominin exerted its antibacterial effect by disrupting bacterial membranes. Cytotoxicity and hemolysis tests demonstrated the potential application of Octominin in vivo. The G. mellonella infection model asserted the in vivo efficacy of Octominin. Furthermore, Octominin inhibited the expression of proinflammatory cytokines. Although the temperature had little effect on its the activity, serum and ions reduced activity. CONCLUSION Octominin is a promising alternative agent with remarkable antibacterial and anti-inflammatory effects for treating infections caused by CREC.
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Affiliation(s)
- Jingchun Kong
- Department of Medical Lab Science, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, China; Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou, Zhejiang Province, China
| | - Yue Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou, Zhejiang Province, China
| | - Yijia Han
- Department of Medical Lab Science, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Huijing Zhou
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou, Zhejiang Province, China
| | - Zhenyun Huang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou, Zhejiang Province, China
| | - Xiaodong Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou, Zhejiang Province, China
| | - Cui Zhou
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou, Zhejiang Province, China
| | - Jianming Cao
- Department of Medical Lab Science, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Tieli Zhou
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou, Zhejiang Province, China.
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33
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Chiloeches A, Zágora J, Plachá D, Torres MDT, de la Fuente-Nunez C, López-Fabal F, Gil-Romero Y, Fernández-García R, Fernández-García M, Echeverría C, Muñoz-Bonilla A. Synergistic Combination of Antimicrobial Peptides and Cationic Polyitaconates in Multifunctional PLA Fibers. ACS APPLIED BIO MATERIALS 2023; 6:4805-4813. [PMID: 37862451 PMCID: PMC10852355 DOI: 10.1021/acsabm.3c00576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 10/05/2023] [Indexed: 10/22/2023]
Abstract
Combining different antimicrobial agents has emerged as a promising strategy to enhance efficacy and address resistance evolution. In this study, we investigated the synergistic antimicrobial effect of a cationic biobased polymer and the antimicrobial peptide (AMP) temporin L, with the goal of developing multifunctional electrospun fibers for potential biomedical applications, particularly in wound dressing. A clickable polymer with pendent alkyne groups was synthesized by using a biobased itaconic acid building block. Subsequently, the polymer was functionalized through click chemistry with thiazolium groups derived from vitamin B1 (PTTIQ), as well as a combination of thiazolium and AMP temporin L, resulting in a conjugate polymer-peptide (PTTIQ-AMP). The individual and combined effects of the cationic PTTIQ, Temporin L, and PTTIQ-AMP were evaluated against Gram-positive and Gram-negative bacteria as well as Candida species. The results demonstrated that most combinations exhibited an indifferent effect, whereas the covalently conjugated PTTIQ-AMP displayed an antagonistic effect, potentially attributed to the aggregation process. Both antimicrobial compounds, PTTIQ and temporin L, were incorporated into poly(lactic acid) electrospun fibers using the supercritical solvent impregnation method. This approach yielded fibers with improved antibacterial performance, as a result of the potent activity exerted by the AMP and the nonleaching nature of the cationic polymer, thereby enhancing long-term effectiveness.
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Affiliation(s)
- Alberto Chiloeches
- Instituto
de Ciencia y Tecnología de Polímeros (ICTP-CSIC), C/Juan de la Cierva 3, Madrid 28006, Spain
- Universidad
Nacional de Educación a Distancia (UNED), C/Bravo Murillo 38, Madrid 28015, Spain
| | - Jakub Zágora
- Nanotechnology
Centre, CEET, VSB—Technical University
of Ostrava, 17. Listopadu 2172/15, Ostrava-Poruba 708 00, Czech Republic
| | - Daniela Plachá
- Nanotechnology
Centre, CEET, VSB—Technical University
of Ostrava, 17. Listopadu 2172/15, Ostrava-Poruba 708 00, Czech Republic
| | - Marcelo D. T. Torres
- Machine
Biology Group, Departments of Psychiatry and Microbiology, Institute
for Biomedical Informatics, Institute for Translational Medicine and
Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Departments
of Bioengineering and Chemical and Biomolecular Engineering, School
of Engineering and Applied Science, University
of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Penn Institute
for Computational Science, University of
Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Cesar de la Fuente-Nunez
- Machine
Biology Group, Departments of Psychiatry and Microbiology, Institute
for Biomedical Informatics, Institute for Translational Medicine and
Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Departments
of Bioengineering and Chemical and Biomolecular Engineering, School
of Engineering and Applied Science, University
of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Penn Institute
for Computational Science, University of
Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Fátima López-Fabal
- Hospital
Universitario de Móstoles C/Dr. Luis Montes, s/n, Móstoles 28935, Madrid, Spain
- Facultad
de Ciencias Experimentales, Universidad
Francisco de Vitoria, Carretera Pozuelo a Majadahonda, Km 1.800, Madrid 28223, Spain
| | - Yolanda Gil-Romero
- Hospital
Universitario de Móstoles C/Dr. Luis Montes, s/n, Móstoles 28935, Madrid, Spain
| | | | - Marta Fernández-García
- Instituto
de Ciencia y Tecnología de Polímeros (ICTP-CSIC), C/Juan de la Cierva 3, Madrid 28006, Spain
| | - Coro Echeverría
- Instituto
de Ciencia y Tecnología de Polímeros (ICTP-CSIC), C/Juan de la Cierva 3, Madrid 28006, Spain
| | - Alexandra Muñoz-Bonilla
- Instituto
de Ciencia y Tecnología de Polímeros (ICTP-CSIC), C/Juan de la Cierva 3, Madrid 28006, Spain
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34
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Putri RA, Rohman MS, Swasono RT, Raharjo TJ. A novel synthetic peptide analog enhanced antibacterial activity of the frog-derived skin peptide wuchuanin-A1. J Biomol Struct Dyn 2023:1-11. [PMID: 37968993 DOI: 10.1080/07391102.2023.2281633] [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: 09/05/2023] [Accepted: 11/04/2023] [Indexed: 11/17/2023]
Abstract
In recent years, there has been a growing focus on the development of novel antibacterial compounds for clinical applications, such as antimicrobial peptide (AMP). Among the developed AMP, wuchuanin-A1, a coil-shaped bioactive peptide derived from Odorrana wuchuanensis frog skin, has been reported to exhibit antibacterial, antifungal, and antioxidant activity, but there are limited studies on its potential as an antibacterial agent. Therefore, this study aims to molecularly modify the sequence of wuchuanin-A1 to enhance its antibacterial properties. The interaction of both the native and analog peptide with bacterial inner membranes was initially assessed using computational methods. Specific amino acid substitutions were then used to enhance the modified peptide's antibacterial efficacy, followed by several preliminary tests to evaluate its activity. This study bridges the gap in exploring the potential of wuchuanin-A1 for antibacterial purposes, providing insights into the design of effective antimicrobial agents.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | | | - Tri Joko Raharjo
- Department of Chemistry, Universitas Gadjah Mada, Bulaksumur, Indonesia
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35
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Sneideris T, Erkamp NA, Ausserwöger H, Saar KL, Welsh TJ, Qian D, Katsuya-Gaviria K, Johncock MLLY, Krainer G, Borodavka A, Knowles TPJ. Targeting nucleic acid phase transitions as a mechanism of action for antimicrobial peptides. Nat Commun 2023; 14:7170. [PMID: 37935659 PMCID: PMC10630377 DOI: 10.1038/s41467-023-42374-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 10/10/2023] [Indexed: 11/09/2023] Open
Abstract
Antimicrobial peptides (AMPs), which combat bacterial infections by disrupting the bacterial cell membrane or interacting with intracellular targets, are naturally produced by a number of different organisms, and are increasingly also explored as therapeutics. However, the mechanisms by which AMPs act on intracellular targets are not well understood. Using machine learning-based sequence analysis, we identified a significant number of AMPs that have a strong tendency to form liquid-like condensates in the presence of nucleic acids through phase separation. We demonstrate that this phase separation propensity is linked to the effectiveness of the AMPs in inhibiting transcription and translation in vitro, as well as their ability to compact nucleic acids and form clusters with bacterial nucleic acids in bacterial cells. These results suggest that the AMP-driven compaction of nucleic acids and modulation of their phase transitions constitute a previously unrecognised mechanism by which AMPs exert their antibacterial effects. The development of antimicrobials that target nucleic acid phase transitions may become an attractive route to finding effective and long-lasting antibiotics.
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Affiliation(s)
- Tomas Sneideris
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK
| | - Nadia A Erkamp
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK
| | - Hannes Ausserwöger
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK
| | - Kadi L Saar
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK
| | - Timothy J Welsh
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK
| | - Daoyuan Qian
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK
| | - Kai Katsuya-Gaviria
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, UK
| | - Margaret L L Y Johncock
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK
| | - Georg Krainer
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK
| | - Alexander Borodavka
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, UK.
| | - Tuomas P J Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK.
- Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Ave, Cambridge, UK.
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36
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Jiang Z, Fu L, Wei C, Fu Q, Pan S. Antibacterial micro/nanomotors: advancing biofilm research to support medical applications. J Nanobiotechnology 2023; 21:388. [PMID: 37875896 PMCID: PMC10599038 DOI: 10.1186/s12951-023-02162-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 10/13/2023] [Indexed: 10/26/2023] Open
Abstract
Multi-drug resistant (MDR) bacterial infections are gradually increasing in the global scope, causing a serious burden to patients and society. The formation of bacterial biofilms, which is one of the key reasons for antibiotic resistance, blocks antibiotic penetration by forming a physical barrier. Nano/micro motors (MNMs) are micro-/nanoscale devices capable of performing complex tasks in the bacterial microenvironment by transforming various energy sources (including chemical fuels or external physical fields) into mechanical motion or actuation. This autonomous movement provides significant advantages in breaking through biological barriers and accelerating drug diffusion. In recent years, MNMs with high penetrating power have been used as carriers of antibiotics to overcome bacterial biofilms, enabling efficient drug delivery and improving the therapeutic effectiveness of MDR bacterial infections. Additionally, non-antibiotic antibacterial strategies based on nanomaterials, such as photothermal therapy and photodynamic therapy, are continuously being developed due to their non-invasive nature, high effectiveness, and non-induction of resistance. Therefore, multifunctional MNMs have broad prospects in the treatment of MDR bacterial infections. This review discusses the performance of MNMs in the breakthrough and elimination of bacterial biofilms, as well as their application in the field of anti-infection. Finally, the challenges and future development directions of antibacterial MNMs are introduced.
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Affiliation(s)
- Zeyu Jiang
- Department of Emergency Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266003, China
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, 266021, China
| | - Lejun Fu
- School of Chemistry and Materials Science, Anhui Normal University, Wuhu, 230022, China
| | - Chuang Wei
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, 266021, China
| | - Qinrui Fu
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, 266021, China.
| | - Shuhan Pan
- Department of Emergency Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266003, China.
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37
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Pedron CN, Torres MDT, Oliveira CS, Silva AF, Andrade GP, Wang Y, Pinhal MAS, Cerchiaro G, da Silva Junior PI, da Silva FD, Radhakrishnan R, de la Fuente-Nunez C, Oliveira Junior VX. Molecular hybridization strategy for tuning bioactive peptide function. Commun Biol 2023; 6:1067. [PMID: 37857855 PMCID: PMC10587126 DOI: 10.1038/s42003-023-05254-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/17/2023] [Indexed: 10/21/2023] Open
Abstract
The physicochemical and structural properties of antimicrobial peptides (AMPs) determine their mechanism of action and biological function. However, the development of AMPs as therapeutic drugs has been traditionally limited by their toxicity for human cells. Tuning the physicochemical properties of such molecules may abolish toxicity and yield synthetic molecules displaying optimal safety profiles and enhanced antimicrobial activity. Here, natural peptides were modified to improve their activity by the hybridization of sequences from two different active peptide sequences. Hybrid AMPs (hAMPs) were generated by combining the amphipathic faces of the highly toxic peptide VmCT1, derived from scorpion venom, with parts of four other naturally occurring peptides having high antimicrobial activity and low toxicity against human cells. This strategy led to the design of seven synthetic bioactive variants, all of which preserved their structure and presented increased antimicrobial activity (3.1-128 μmol L-1). Five of the peptides (three being hAMPs) presented high antiplasmodial at 0.8 μmol L-1, and virtually no undesired toxic effects against red blood cells. In sum, we demonstrate that peptide hybridization is an effective strategy for redirecting biological activity to generate novel bioactive molecules with desired properties.
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Affiliation(s)
- Cibele Nicolaski Pedron
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, 09210580, Brazil
- Departamento de Bioquímica, Universidade Federal de São Paulo, São Paulo, SP, 04044020, Brazil
| | - Marcelo Der Torossian Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Cyntia Silva Oliveira
- Departamento de Bioquímica, Universidade Federal de São Paulo, São Paulo, SP, 04044020, Brazil
| | - Adriana Farias Silva
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo, SP, 04044020, Brazil
| | - Gislaine Patricia Andrade
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, 09210580, Brazil
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo, SP, 04044020, Brazil
| | - Yiming Wang
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Giselle Cerchiaro
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, 09210580, Brazil
| | | | - Fernanda Dias da Silva
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, 09210580, Brazil
| | - Ravi Radhakrishnan
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA.
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, USA.
| | - Vani Xavier Oliveira Junior
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, 09210580, Brazil.
- Departamento de Bioquímica, Universidade Federal de São Paulo, São Paulo, SP, 04044020, Brazil.
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38
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Agrillo B, Porritiello A, Gratino L, Balestrieri M, Proroga YT, Mancusi A, Cozzi L, Vicenza T, Dardano P, Miranda B, Escribá PV, Gogliettino M, Palmieri G. Antimicrobial activity, membrane interaction and structural features of short arginine-rich antimicrobial peptides. Front Microbiol 2023; 14:1244325. [PMID: 37869668 PMCID: PMC10585156 DOI: 10.3389/fmicb.2023.1244325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 09/18/2023] [Indexed: 10/24/2023] Open
Abstract
Antimicrobial activity of many AMPs can be improved by lysine-to-arginine substitution due to a more favourable interaction of arginine guanidinium moiety with bacterial membranes. In a previous work, the structural and functional characterization of an amphipathic antimicrobial peptide named RiLK1, including lysine and arginine as the positively charged amino acids in its sequence, was reported. Specifically, RiLK1 retained its β-sheet structure under a wide range of environmental conditions (temperature, pH, and ionic strength), and exhibited bactericidal activity against Gram-positive and Gram-negative bacteria and fungal pathogens with no evidence of toxicity on mammalian cells. To further elucidate the influence of a lysine-to-arginine replacement on RiLK1 conformational properties, antimicrobial activity and peptide-liposome interaction, a new RiLK1-derivative, named RiLK3, in which the lysine is replaced with an arginine residue, was projected and characterised in comparison with its parental compound. The results evidenced that lysine-to-arginine mutation not only did not assure an improvement in the antimicrobial potency of RiLK1 in terms of bactericidal, virucidal and fungicidal activities, but rather it was completely abolished against the hepatitis A virus. Therefore, RiLK1 exhibited a wide range of antimicrobial activity like other cationic peptides, although the exact mechanisms of action are not completely understood. Moreover, tryptophan fluorescence measurements confirmed that RiLK3 bound to negatively charged lipid vesicles with an affinity lower than that of RiLK1, although no substantial differences from the structural and self-assembled point of view were evidenced. Therefore, our findings imply that antimicrobial efficacy and selectivity are affected by several complex and interrelated factors related to substitution of lysine with arginine, such as their relative proportion and position. In this context, this study could provide a better rationalisation for the optimization of antimicrobial peptide sequences, paving the way for the development of novel AMPs with broad applications.
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Affiliation(s)
| | - Alessandra Porritiello
- National Research Council (IBBR-CNR), Institute of Biosciences and Bioresources, Napoli, Italy
| | - Lorena Gratino
- National Research Council (IBBR-CNR), Institute of Biosciences and Bioresources, Napoli, Italy
| | - Marco Balestrieri
- National Research Council (IBBR-CNR), Institute of Biosciences and Bioresources, Napoli, Italy
| | - Yolande Therese Proroga
- Department of Food Microbiology, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - Andrea Mancusi
- Department of Food Microbiology, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - Loredana Cozzi
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Teresa Vicenza
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Principia Dardano
- National Research Council (ISASI-CNR), Institute of Applied Sciences and Intelligent Systems, Napoli, Italy
| | - Bruno Miranda
- National Research Council (ISASI-CNR), Institute of Applied Sciences and Intelligent Systems, Napoli, Italy
| | - Pablo V. Escribá
- Laboratory of Molecular Cell Biomedicine, University of the Balearic Islands, Palma, Spain
- Laminar Pharmaceuticals, Palma, Spain
| | - Marta Gogliettino
- National Research Council (IBBR-CNR), Institute of Biosciences and Bioresources, Napoli, Italy
| | - Gianna Palmieri
- National Research Council (IBBR-CNR), Institute of Biosciences and Bioresources, Napoli, Italy
- Materias S.R.L., Naples, Italy
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Santos-Júnior CD, Der Torossian Torres M, Duan Y, del Río ÁR, Schmidt TS, Chong H, Fullam A, Kuhn M, Zhu C, Houseman A, Somborski J, Vines A, Zhao XM, Bork P, Huerta-Cepas J, de la Fuente-Nunez C, Coelho LP. Computational exploration of the global microbiome for antibiotic discovery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.31.555663. [PMID: 37693522 PMCID: PMC10491242 DOI: 10.1101/2023.08.31.555663] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Novel antibiotics are urgently needed to combat the antibiotic-resistance crisis. We present a machine learning-based approach to predict prokaryotic antimicrobial peptides (AMPs) by leveraging a vast dataset of 63,410 metagenomes and 87,920 microbial genomes. This led to the creation of AMPSphere, a comprehensive catalog comprising 863,498 non-redundant peptides, the majority of which were previously unknown. We observed that AMP production varies by habitat, with animal-associated samples displaying the highest proportion of AMPs compared to other habitats. Furthermore, within different human-associated microbiota, strain-level differences were evident. To validate our predictions, we synthesized and experimentally tested 50 AMPs, demonstrating their efficacy against clinically relevant drug-resistant pathogens both in vitro and in vivo. These AMPs exhibited antibacterial activity by targeting the bacterial membrane. Additionally, AMPSphere provides valuable insights into the evolutionary origins of peptides. In conclusion, our approach identified AMP sequences within prokaryotic microbiomes, opening up new avenues for the discovery of antibiotics.
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Affiliation(s)
- Célio Dias Santos-Júnior
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai, China
| | - Marcelo Der Torossian Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania; Philadelphia, Pennsylvania, United States of America
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania; Philadelphia, Pennsylvania, United States of America
- Penn Institute for Computational Science, University of Pennsylvania; Philadelphia, Pennsylvania, United States of America
| | - Yiqian Duan
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai, China
| | - Álvaro Rodríguez del Río
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo-UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Thomas S.B. Schmidt
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Hui Chong
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai, China
| | - Anthony Fullam
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Michael Kuhn
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Chengkai Zhu
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai, China
| | - Amy Houseman
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai, China
| | - Jelena Somborski
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai, China
| | - Anna Vines
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai, China
| | - Xing-Ming Zhao
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai, China
- Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai, China
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Fudan University, Shanghai, China
- MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence
- MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
- International Human Phenome Institute, Shanghai, China
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, Berlin, Germany
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Jaime Huerta-Cepas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo-UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania; Philadelphia, Pennsylvania, United States of America
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania; Philadelphia, Pennsylvania, United States of America
- Penn Institute for Computational Science, University of Pennsylvania; Philadelphia, Pennsylvania, United States of America
| | - Luis Pedro Coelho
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai, China
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Cashman-Kadri S, Lagüe P, Fliss I, Beaulieu L. Assessing the Activity under Different Physico-Chemical Conditions, Digestibility, and Innocuity of a GAPDH-Related Fish Antimicrobial Peptide and Analogs Thereof. Antibiotics (Basel) 2023; 12:1410. [PMID: 37760707 PMCID: PMC10525732 DOI: 10.3390/antibiotics12091410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/30/2023] [Accepted: 09/01/2023] [Indexed: 09/29/2023] Open
Abstract
The antimicrobial activity of SJGAP (skipjack tuna GAPDH-related antimicrobial peptide) and four chemical analogs thereof was determined under different physicochemical conditions, including different pH values, the presence of monovalent and divalent cations, and after a heating treatment. The toxicity of these five peptides was also studied with hemolytic activity assays, while their stability under human gastrointestinal conditions was evaluated using a dynamic in vitro digestion model and chromatographic and mass spectrometric analyses. The antibacterial activity of all analogs was found to be inhibited by the presence of divalent cations, while monovalent cations had a much less pronounced impact, even promoting the activity of the native SJGAP. The peptides were also more active at acidic pH values, but they did not all show the same stability following a heat treatment. SJGAP and its analogs did not show significant hemolytic activity (except for one of the analogs at a concentration equivalent to 64 times that of its minimum inhibitory concentration), and the two analogs whose digestibility was studied degraded very rapidly once they entered the stomach compartment of the digestion model. This study highlights for the first time the characteristics of antimicrobial peptides from Scombridae or homologous to GAPDH that are directly related to their potential clinical or food applications.
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Affiliation(s)
- Samuel Cashman-Kadri
- Institute of Nutrition and Functional Foods (INAF), Université Laval, Québec, QC G1V 0A6, Canada; (S.C.-K.); (I.F.)
- Department of Food Science, Faculty of Agricultural and Food Sciences, Université Laval, Québec, QC G1V 0A6, Canada
- Québec-Océan, Université Laval, Québec, QC G1V 0A6, Canada
| | - Patrick Lagüe
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Quebec, QC G1V 0A6, Canada;
- Institute for Integrative Systems Biology, Department of Biochemistry, Microbiology and Bio-Informatics, Pavillon, Alexandre-Vachon, Université Laval, 1045 Avenue de la Medecine, Québec, QC G1V 0A6, Canada
- The Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), 1045 Avenue de la Medecine, Québec, QC G1V 0A6, Canada
| | - Ismail Fliss
- Institute of Nutrition and Functional Foods (INAF), Université Laval, Québec, QC G1V 0A6, Canada; (S.C.-K.); (I.F.)
- Department of Food Science, Faculty of Agricultural and Food Sciences, Université Laval, Québec, QC G1V 0A6, Canada
| | - Lucie Beaulieu
- Institute of Nutrition and Functional Foods (INAF), Université Laval, Québec, QC G1V 0A6, Canada; (S.C.-K.); (I.F.)
- Department of Food Science, Faculty of Agricultural and Food Sciences, Université Laval, Québec, QC G1V 0A6, Canada
- Québec-Océan, Université Laval, Québec, QC G1V 0A6, Canada
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Torres MDT, Brooks E, Cesaro A, Sberro H, Nicolaou C, Bhatt AS, de la Fuente-Nunez C. Human gut metagenomic mining reveals an untapped source of peptide antibiotics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.31.555711. [PMID: 37693399 PMCID: PMC10491270 DOI: 10.1101/2023.08.31.555711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Drug-resistant bacteria are outpacing traditional antibiotic discovery efforts. Here, we computationally mined 444,054 families of putative small proteins from 1,773 human gut metagenomes, identifying 323 peptide antibiotics encoded in small open reading frames (smORFs). To test our computational predictions, 78 peptides were synthesized and screened for antimicrobial activity in vitro, with 59% displaying activity against either pathogens or commensals. Since these peptides were unique compared to previously reported antimicrobial peptides, we termed them smORF-encoded peptides (SEPs). SEPs killed bacteria by targeting their membrane, synergized with each other, and modulated gut commensals, indicating that they may play a role in reconfiguring microbiome communities in addition to counteracting pathogens. The lead candidates were anti-infective in both murine skin abscess and deep thigh infection models. Notably, prevotellin-2 from Prevotella copri presented activity comparable to the commonly used antibiotic polymyxin B. We report the discovery of hundreds of peptide sequences in the human gut.
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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, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States of America
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States of America
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States of America
| | - Erin Brooks
- Department of Medicine (Hematology; Blood and Marrow Transplantation), Stanford University, Stanford, CA, United States of America
| | - Angela Cesaro
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States of America
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States of America
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States of America
| | - Hila Sberro
- Department of Medicine (Hematology; Blood and Marrow Transplantation), Stanford University, Stanford, CA, United States of America
| | - Cosmos Nicolaou
- Department of Medicine (Hematology; Blood and Marrow Transplantation), Stanford University, Stanford, CA, United States of America
| | - Ami S. Bhatt
- Department of Medicine (Hematology; Blood and Marrow Transplantation), Stanford University, Stanford, CA, United States of America
- Department of Genetics, Stanford University, Stanford, CA, United States of America
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States of America
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States of America
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States of America
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Abbasali Z, Pirestani M, Dalimi A, Badri M, Fasihi-Ramandi M. Anti-parasitic activity of a chimeric peptide Cecropin A (2-8)-Melittin (6-9) (CM11) against tachyzoites of Toxoplasma gondii and the BALB/c mouse model of acute toxoplasmosis. Mol Biochem Parasitol 2023; 255:111578. [PMID: 37348706 DOI: 10.1016/j.molbiopara.2023.111578] [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: 01/30/2023] [Revised: 06/18/2023] [Accepted: 06/18/2023] [Indexed: 06/24/2023]
Abstract
Toxoplasmosis is a zoonotic disease that infects most animals, including humans. Pyrimethamine/sulfadiazine is the standard treatment for toxoplasmosis. Although this treatment has been successful, it is often associated with side effects that cannot be tolerated. Therefore, various compounds have been proposed as alternative treatments for toxoplasmosis. Antimicrobial peptides (AMPs) act on various pathogens, from viruses to protozoa. The purpose of the present study was to evaluate the effects of CM11 on in vitro and in vivo Toxoplasma gondii infection. For in vitro experiments, VERO cells were treated with different concentrations of CM11 (1-128 μg/ml) compared to sulfadiazine (SDZ) (0.78-100 μg/ml). MTT and lactate dehydrogenase (LDH) assays evaluated the cell viability and plasma membrane integrity. Then, the inhibitory concentration (IC50) values were determined for treating tachyzoites of T. gondii before or on cells previously infected. Annexin V-FITC/propidium iodide (PI) staining was used to distinguish viable and apoptotic cells. The effect of CM11, SDZ, and a combination of CM11 and SDZ was evaluated in the BALB/c mouse model of acute toxoplasmosis. CM11 was effective on tachyzoites of T. gondii and had a time and dose-dependent manner. The results of the MTT assay showed that the CC50 values of CM11 and SDZ were estimated at 17.4 µg/ml and 62.3 µg/ml after 24-h, respectively. The inhibitory concentration (IC50) of CM11 and SDZ on infected cells was estimated at 1.9 µg/ml and 1.4 µg/ml after 24-h, respectively. The highest rate of apoptosis (early and late) in high concentrations of SDZ and CM11 was determined for tachyzoites (2.13 % and 13.88 %), non-infected VERO cells (6.1 % and 19.76 %), and infected VERO cells (7.45 % and 29.9 %), respectively. Treating infected mice with CM11 and a combination of CM11 and SDZ had increased survival time. Based on the mentioned results, it can be concluded that CM11 has a beneficial effect on tachyzoites of T. gondii in vitro. The result of the mouse model suggests that CM11, either alone or in combination with other chemotherapeutic agents, could be a potential therapeutic for toxoplasmosis. Hence, antimicrobial peptides could be applied as promising anti-toxoplasma agents for treating toxoplasmosis.
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Affiliation(s)
- Zahra Abbasali
- Department of Parasitology, Faculty of Medical Sciences, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Majid Pirestani
- Department of Parasitology, Faculty of Medical Sciences, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Abdolhossein Dalimi
- Department of Parasitology, Faculty of Medical Sciences, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Milad Badri
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Mahdi Fasihi-Ramandi
- Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
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Alsaab FM, Dean SN, Bobde S, Ascoli GG, van Hoek ML. Computationally Designed AMPs with Antibacterial and Antibiofilm Activity against MDR Acinetobacter baumannii. Antibiotics (Basel) 2023; 12:1396. [PMID: 37760693 PMCID: PMC10525135 DOI: 10.3390/antibiotics12091396] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 08/28/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
The discovery of new antimicrobials is necessary to combat multidrug-resistant (MDR) bacteria, especially those that infect wounds and form prodigious biofilms, such as Acinetobacter baumannii. Antimicrobial peptides (AMPs) are a promising class of new therapeutics against drug-resistant bacteria, including gram-negatives. Here, we utilized a computational AMP design strategy combining database filtering technology plus positional analysis to design a series of novel peptides, named HRZN, designed to be active against A. baumannii. All of the HRZN peptides we synthesized exhibited antimicrobial activity against three MDR A. baumannii strains with HRZN-15 being the most active (MIC 4 µg/mL). This peptide also inhibited and eradicated biofilm of A. baumannii strain AB5075 at 8 and 16 µg/mL, which is highly effective. HRZN-15 permeabilized and depolarized the membrane of AB5075 rapidly, as demonstrated by the killing kinetics. HRZN 13 and 14 peptides had little to no hemolysis activity against human red blood cells, whereas HRZN-15, -16, and -17 peptides demonstrated more significant hemolytic activity. HRZN-15 also demonstrated toxicity to waxworms. Further modification of HRZN-15 could result in a new peptide with an improved toxicity profile. Overall, we successfully designed a set of new AMPs that demonstrated activity against MDR A. baumannii using a computational approach.
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Affiliation(s)
- Fahad M. Alsaab
- School of Systems Biology, George Mason University, Manassas, VA 20110, USA (S.B.)
- College of Applied Medical Sciences, King Saud bin Abdulaziz University for Health Sciences, Al Ahsa 36428, Saudi Arabia
| | - Scott N. Dean
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Washington, DC 20375, USA
| | - Shravani Bobde
- School of Systems Biology, George Mason University, Manassas, VA 20110, USA (S.B.)
| | - Gabriel G. Ascoli
- Aspiring Scientist Summer Internship Program, George Mason University, Manassas, VA 20110, USA
| | - Monique L. van Hoek
- School of Systems Biology, George Mason University, Manassas, VA 20110, USA (S.B.)
- Center for Infectious Disease Research, George Mason University, Manassas, VA 20110, USA
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Wang C, Shao S, Li N, Zhang Z, Zhang H, Liu B. Advances in Alzheimer's Disease-Associated Aβ Therapy Based on Peptide. Int J Mol Sci 2023; 24:13110. [PMID: 37685916 PMCID: PMC10487952 DOI: 10.3390/ijms241713110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/11/2023] [Accepted: 08/19/2023] [Indexed: 09/10/2023] Open
Abstract
Alzheimer's disease (AD) urgently needs innovative treatments due to the increasing aging population and lack of effective drugs and therapies. The amyloid fibrosis of AD-associated β-amyloid (Aβ) that could induce a series of cascades, such as oxidative stress and inflammation, is a critical factor in the progression of AD. Recently, peptide-based therapies for AD are expected to be great potential strategies for the high specificity to the targets, low toxicity, fast blood clearance, rapid cell and tissue permeability, and superior biochemical characteristics. Specifically, various chiral amino acids or peptide-modified interfaces draw much attention as effective manners to inhibit Aβ fibrillation. On the other hand, peptide-based inhibitors could be obtained through affinity screening such as phage display or by rational design based on the core sequence of Aβ fibrosis or by computer aided drug design based on the structure of Aβ. These peptide-based therapies can inhibit Aβ fibrillation and reduce cytotoxicity induced by Aβ aggregation and some have been shown to relieve cognition in AD model mice and reduce Aβ plaques in mice brains. This review summarizes the design method and characteristics of peptide inhibitors and their effect on the amyloid fibrosis of Aβ. We further describe some analysis methods for evaluating the inhibitory effect and point out the challenges in these areas, and possible directions for the design of AD drugs based on peptides, which lay the foundation for the development of new effective drugs in the future.
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Affiliation(s)
- Cunli Wang
- School of Biomedical Engineering, Faculty of Medicine, Dalian University of Technology, Lingshui Road, Dalian 116024, China; (C.W.); (S.S.); (N.L.); (Z.Z.); (H.Z.)
| | - Shuai Shao
- School of Biomedical Engineering, Faculty of Medicine, Dalian University of Technology, Lingshui Road, Dalian 116024, China; (C.W.); (S.S.); (N.L.); (Z.Z.); (H.Z.)
- Liaoning Key Lab of Integrated Circuit and Biomedical Electronic System, Dalian University of Technology, Dalian 116024, China
| | - Na Li
- School of Biomedical Engineering, Faculty of Medicine, Dalian University of Technology, Lingshui Road, Dalian 116024, China; (C.W.); (S.S.); (N.L.); (Z.Z.); (H.Z.)
- Liaoning Key Lab of Integrated Circuit and Biomedical Electronic System, Dalian University of Technology, Dalian 116024, China
| | - Zhengyao Zhang
- School of Biomedical Engineering, Faculty of Medicine, Dalian University of Technology, Lingshui Road, Dalian 116024, China; (C.W.); (S.S.); (N.L.); (Z.Z.); (H.Z.)
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin 124221, China
| | - Hangyu Zhang
- School of Biomedical Engineering, Faculty of Medicine, Dalian University of Technology, Lingshui Road, Dalian 116024, China; (C.W.); (S.S.); (N.L.); (Z.Z.); (H.Z.)
- Liaoning Key Lab of Integrated Circuit and Biomedical Electronic System, Dalian University of Technology, Dalian 116024, China
| | - Bo Liu
- School of Biomedical Engineering, Faculty of Medicine, Dalian University of Technology, Lingshui Road, Dalian 116024, China; (C.W.); (S.S.); (N.L.); (Z.Z.); (H.Z.)
- Liaoning Key Lab of Integrated Circuit and Biomedical Electronic System, Dalian University of Technology, Dalian 116024, China
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Saini S, Rathore A, Sharma S, Saini A. Exploratory data analysis of physicochemical parameters of natural antimicrobial and anticancer peptides: Unraveling the patterns and trends for the rational design of novel peptides. BIOIMPACTS : BI 2023; 14:26438. [PMID: 38327633 PMCID: PMC10844588 DOI: 10.34172/bi.2023.26438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 11/04/2022] [Accepted: 12/04/2022] [Indexed: 02/09/2024]
Abstract
Introduction Peptide-based research has attained new avenues in the antibiotics and cancer drug resistance era. The basis of peptide design research lies in playing with or altering physicochemical parameters. Here in this work, we have done exploratory data analysis (EDA) of physicochemical parameters of antimicrobial peptides (AMPs) and anticancer peptides (ACPs), two promising therapeutics for microbial and cancer drug resistance to deduce patterns and trends. Methods Briefly, we have captured the natural AMPs and ACPs data from the APD3 database. After cleaning the data manually and by CD-HIT web server, further data analysis has been done using Python-based packages, modlAMP and Pandas. We have extracted the descriptive statistics of 10 physicochemical parameters of AMPs and ACPs to build a comprehensive dataset containing all major parameters. The global analysis of datasets has been done using modlAMP to find the initial patterns in global data. The subsets of AMPs and ACPs were curated based on the length of the peptides and were analyzed by Pandas package to deduce the graphical profile of AMPs and ACPs. Results EDA of AMPs and ACPs shows selectivity in the length and amino acid compositions. The distribution of physicochemical parameters in defined quartile ranges was observed in the descriptive statistical and graphical analysis. The preferred length range of AMPs and ACPs was found to be 21-30 amino acids, whereas few outliers in each parameter were evident after EDA analysis. Conclusion The derived patterns from natural AMPs and ACPs can be used for the rational design of novel peptides. The statistical and graphical data distribution findings will help in combining the different parameters for potent design of novel AMPs and ACPs.
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Affiliation(s)
- Sandeep Saini
- Department of Biophysics, Panjab University, Sector 25, Chandigarh 160014, India
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32-C, Chandigarh 160030, India
| | - Aayushi Rathore
- Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Bengaluru 560100, India
| | - Sheetal Sharma
- Department of Biophysics, Panjab University, Sector 25, Chandigarh 160014, India
| | - Avneet Saini
- Department of Biophysics, Panjab University, Sector 25, Chandigarh 160014, India
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Li S, Liu G, Kang J, Li Z, Cao Z. The inhibitory activity of a new scorpion venom-derived antimicrobial peptide Hp1470 against Gram-positive bacteria. Toxicon 2023; 231:107189. [PMID: 37295751 DOI: 10.1016/j.toxicon.2023.107189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 05/28/2023] [Accepted: 06/07/2023] [Indexed: 06/12/2023]
Abstract
Antimicrobial peptides (AMPs) are a new type of antibiotic and target a variety of microbes, including antibiotic-resistant strains; thus, AMPs have attracted widespread interest. Scorpion venoms contain many bioactive peptides, including AMPs, and have become an important natural resource of peptide-based drugs. Here, the antibacterial peptide gene Hp1470 from the venom of the scorpion Heterometrus petersii was characterized, and its antibacterial activity was determined. The cDNA sequence of Hp1470 is 300 nt in length and contains an open reading frame (ORF) of 207 nt. The ORF was shown to encode 68 amino acid residues, including a signal peptide (23 aa), a mature peptide (13 aa), a C-terminal posttranslational processing signal (3 aa), and a propeptide (29 aa). Multiple sequence alignment results indicated that Hp1470 is an antibacterial peptide. The mature peptide Hp1470, which has a molecular mass of 1564.09 Da, was further chemically synthesized with a purity of greater than 95%. Antimicrobial assays showed that the synthesized Hp1470 exerted an inhibitory effect on Gram-positive bacteria and clinical drug-resistant strains, including PRSA and MRSA, but not Gram-negative bacteria. Hp1470 was further found to protect mice from MRSA infection, suggesting its potential application as an in vivo antimicrobial agent. Interestingly, Hp1470 only inhibited bacterial growth but did not kill bacteria, which was consistent with scanning electron microscopy results showing that Hp1470 did not lyse the cell membrane of Staphylococcus aureus. Our work provides a new direction for developing antibacterial agents with different modes of action from natural scorpion venoms.
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Affiliation(s)
- Songryong Li
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China; Center for BioDrug Research, Wuhan University, Wuhan, 430072, China; Faculty of Life Science, Kim Hyong Jik University of Education, Pyongyang, Democratic People's Republic of Korea
| | - Gaomin Liu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jongguk Kang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zhongjie Li
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zhijian Cao
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China; Center for BioDrug Research, Wuhan University, Wuhan, 430072, China.
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Botelho Sampaio de Oliveira K, Lopes Leite M, Albuquerque Cunha V, Brito da Cunha N, Luiz Franco O. Challenges and advances in antimicrobial peptide development. Drug Discov Today 2023; 28:103629. [PMID: 37230283 DOI: 10.1016/j.drudis.2023.103629] [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: 12/09/2022] [Revised: 05/04/2023] [Accepted: 05/18/2023] [Indexed: 05/27/2023]
Abstract
Microbial resistance is a major concern for public health worldwide, mainly because of the inappropriate use of antimicrobials. In this scenario, antimicrobial peptides (AMPs) have emerged as a potential therapeutic alternative means by which to control infectious diseases, because of their broad spectrum of action. However, some challenges can make their clinical application problematic, including metabolic instability and toxicity. Here, we provide a clear description of AMPs as promising molecules for the development of unusual antimicrobial drugs. We also describe current strategies used to overcome the main difficulties related to AMP clinical application, including different peptide designs and nanoformulation.
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Affiliation(s)
- Kamila Botelho Sampaio de Oliveira
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brazil
| | - Michel Lopes Leite
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brazil; Departamento de Biologia Molecular, Instituto de Ciências Biológicas, Universidade de Brasília, Campus Darcy Ribeiro, Bloco K, 70.790-900, Brasília, Brazil
| | - Victor Albuquerque Cunha
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brazil
| | - Nicolau Brito da Cunha
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brazil; Universidade de Brasília, Faculdade de Agronomia e Medicina Veterinária, Campus Darcy Ribeiro, Brasilia, Brazil.
| | - Octávio Luiz Franco
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brazil; Pós-graduação em Patologia Molecular, Universidade de Brasília, Campus Darcy Ribeiro, Brasília, Brazil; S-Inova Biotech, Pós-graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, Mato Grosso do Sul, Brazil.
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48
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Liu X, Zhang P, Liu Y, Li J, Yang D, Liu Z, Jiang L. Anti- Toxoplasma gondii Effects of Lipopeptide Derivatives of Lycosin-I. Toxins (Basel) 2023; 15:477. [PMID: 37624234 PMCID: PMC10467082 DOI: 10.3390/toxins15080477] [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: 06/12/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/26/2023] Open
Abstract
Toxoplasmosis, caused by Toxoplasma gondii (T. gondii), is a serious zoonotic parasitic disease. We previously found that Lycosin-I exhibited anti-T. gondii activity, but its serum stability was not good enough. In this study, we aimed to improve the stability and activity of Lycosin-I through fatty acid chain modification, so as to find a better anti-T. gondii drug candidate. The α/ε-amino residues of different lysine residues of Lycosin-I were covalently coupled with lauric acid to obtain eight lipopeptides, namely L-C12, L-C12-1, L-C12-2, L-C12-3, L-C12-4, L-C12-5, L-C12-6, and L-C12-7. Among these eight lipopeptides, L-C12 showed the best activity against T. gondii in vitro in a trypan blue assay. We then conjugated a shorter length fatty chain, aminocaproic acid, at the same modification site of L-C12, namely L-an. The anti-T. gondii effects of Lycosin-I, L-C12 and L-an were evaluated via an invasion assay, proliferation assay and plaque assay in vitro. A mouse model acutely infected with T. gondii tachyzoites was established to evaluate their efficacy in vivo. The serum stability of L-C12 and L-an was improved, and they showed comparable or even better activity than Lycosin-I did in inhibiting the invasion and proliferation of tachyzoites. L-an effectively prolonged the survival time of mice acutely infected with T. gondii. These results suggest that appropriate fatty acid chain modification can improve serum stability and enhance anti-T. gondii effect of Lycosin-I. The lipopeptide derivatives of Lycosin-I have potential as a novel anti-T. gondii drug candidate.
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Affiliation(s)
- Xiaohua Liu
- Department of Parasitology, Xiangya School of Medicine, Central South University, Changsha 410013, China; (X.L.); (Y.L.); (J.L.); (D.Y.)
| | - Peng Zhang
- The National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China; (P.Z.); (Z.L.)
| | - Yuan Liu
- Department of Parasitology, Xiangya School of Medicine, Central South University, Changsha 410013, China; (X.L.); (Y.L.); (J.L.); (D.Y.)
| | - Jing Li
- Department of Parasitology, Xiangya School of Medicine, Central South University, Changsha 410013, China; (X.L.); (Y.L.); (J.L.); (D.Y.)
| | - Dongqian Yang
- Department of Parasitology, Xiangya School of Medicine, Central South University, Changsha 410013, China; (X.L.); (Y.L.); (J.L.); (D.Y.)
| | - Zhonghua Liu
- The National & Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China; (P.Z.); (Z.L.)
| | - Liping Jiang
- Department of Parasitology, Xiangya School of Medicine, Central South University, Changsha 410013, China; (X.L.); (Y.L.); (J.L.); (D.Y.)
- China-Africa Research Center of Infectious Diseases, Xiangya School of Medicine, Central South University, Changsha 410013, China
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Kalpana S, Lin WY, Wang YC, Fu Y, Wang HY. Alternate Antimicrobial Therapies and Their Companion Tests. Diagnostics (Basel) 2023; 13:2490. [PMID: 37568853 PMCID: PMC10417861 DOI: 10.3390/diagnostics13152490] [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: 06/30/2023] [Accepted: 07/14/2023] [Indexed: 08/13/2023] Open
Abstract
New antimicrobial approaches are essential to counter antimicrobial resistance. The drug development pipeline is exhausted with the emergence of resistance, resulting in unsuccessful trials. The lack of an effective drug developed from the conventional drug portfolio has mandated the introspection into the list of potentially effective unconventional alternate antimicrobial molecules. Alternate therapies with clinically explicable forms include monoclonal antibodies, antimicrobial peptides, aptamers, and phages. Clinical diagnostics optimize the drug delivery. In the era of diagnostic-based applications, it is logical to draw diagnostic-based treatment for infectious diseases. Selection criteria of alternate therapeutics in infectious diseases include detection, monitoring of response, and resistance mechanism identification. Integrating these diagnostic applications is disruptive to the traditional therapeutic development. The challenges and mitigation methods need to be noted. Applying the goals of clinical pharmacokinetics that include enhancing efficacy and decreasing toxicity of drug therapy, this review analyses the strong correlation of alternate antimicrobial therapeutics in infectious diseases. The relationship between drug concentration and the resulting effect defined by the pharmacodynamic parameters are also analyzed. This review analyzes the perspectives of aligning diagnostic initiatives with the use of alternate therapeutics, with a particular focus on companion diagnostic applications in infectious diseases.
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Affiliation(s)
- Sriram Kalpana
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan 333423, Taiwan;
| | - Wan-Ying Lin
- Department of Medicine, University of California San Diego, San Diego, CA 92093, USA;
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA;
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Yu-Chiang Wang
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA;
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Yiwen Fu
- Department of Medicine, Kaiser Permanente Santa Clara Medical Center, Santa Clara, CA 95051, USA;
| | - Hsin-Yao Wang
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan 333423, Taiwan;
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA;
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
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50
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Boaro A, Ageitos L, Torres MDT, Blasco EB, Oztekin S, de la Fuente-Nunez C. Structure-function-guided design of synthetic peptides with anti-infective activity derived from wasp venom. CELL REPORTS. PHYSICAL SCIENCE 2023; 4:101459. [PMID: 38239869 PMCID: PMC10795512 DOI: 10.1016/j.xcrp.2023.101459] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2024]
Abstract
Antimicrobial peptides (AMPs) derived from natural toxins and venoms offer a promising alternative source of antibiotics. Here, through structure-function-guided design, we convert two natural AMPs derived from the venom of the solitary eumenine wasp Eumenes micado into α-helical AMPs with reduced toxicity that kill Gram-negative bacteria in vitro and in a preclinical mouse model. To identify the sequence determinants conferring antimicrobial activity, an alanine scan screen and strategic single lysine substitutions are made to the amino acid sequence of these natural peptides. These efforts yield a total of 34 synthetic derivatives, including alanine substituted and lysine-substituted sequences with stabilized α-helical structures and increased net positive charge. The resulting lead synthetic peptides kill the Gram-negative pathogens Escherichia coli and Pseudomonas aeruginosa (PAO1 and PA14) by rapidly permeabilizing both their outer and cytoplasmic membranes, exhibit anti-infective efficacy in a mouse model by reducing bacterial loads by up to three orders of magnitude, and do not readily select for bacterial resistance.
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Affiliation(s)
- Andreia Boaro
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA 19104, USA
- Present address: Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, São Paulo 09210-580, Brazil
- These authors contributed equally
| | - Lucía Ageitos
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA 19104, USA
- Present address: CICA - Centro Interdisciplinar de Química e Bioloxía, Departamento de Química, Facultade de Ciencias, Universidade da Coruña, 15008 A Coruña, Spain
- These authors contributed equally
| | - Marcelo Der Torossian Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Esther Broset Blasco
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sebahat Oztekin
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA 19104, USA
- Present address: Faculty of Engineering, Department of Food Engineering, Bayburt University, Bayburt 69000, Turkey
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA 19104, USA
- Lead contact
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