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Wang J, Zhang M, Li C, Liu M, Qi Y, Xie X, Zhou C, Ma L. A novel cathelicidin TS-CATH derived from Thamnophis sirtalis combats drug-resistant gram-negative bacteria in vitro and in vivo. Comput Struct Biotechnol J 2024; 23:2388-2406. [PMID: 38882682 PMCID: PMC11176561 DOI: 10.1016/j.csbj.2024.05.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 05/08/2024] [Accepted: 05/13/2024] [Indexed: 06/18/2024] Open
Abstract
Antimicrobial peptides are promising therapeutic agents for treating drug-resistant bacterial disease due to their broad-spectrum antimicrobial activity and decreased susceptibility to evolutionary resistance. In this study, three novel cathelicidin antimicrobial peptides were identified from Thamnophis sirtalis, Balaenoptera musculus, and Lipotes vexillifer by protein database mining and sequence alignment and were subsequently named TS-CATH, BM-CATH, and LV-CATH, respectively. All three peptides exhibited satisfactory antibacterial activity and broad antibacterial spectra against clinically isolated E. coli, P. aeruginosa, K. pneumoniae, and A. baumannii in vitro. Among them, TS-CATH displayed the best antimicrobial/bactericidal activity, with a rapid elimination efficiency against the tested drug-resistant gram-negative bacteria within 20 min, and exhibited the lowest cytotoxicity toward mammalian cells. Furthermore, TS-CATH effectively enhanced the survival rate of mice with ceftazidime-resistant E. coli bacteremia and promoted wound healing in meropenem-resistant P. aeruginosa infection. These results were achieved through the eradication of bacterial growth in target organs and wounds, further inhibiting the systemic dissemination of bacteria and the inflammatory response. TS-CATH exhibited direct antimicrobial activity by damaging the inner and outer membranes, resulting in leakage of the bacterial contents at super-MICs. Moreover, TS-CATH disrupted the bacterial respiratory chain, which inhibited ATP synthesis and induced ROS formation, significantly contributing to its antibacterial efficacy at sub-MICs. Overall, TS-CATH has potential for use as an antibacterial agent.
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Affiliation(s)
- Jian Wang
- Institution of all authors: College of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu 211198, China
| | - Meina Zhang
- Institution of all authors: College of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu 211198, China
| | - Chao Li
- Institution of all authors: College of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu 211198, China
| | - Mengyuan Liu
- Institution of all authors: College of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu 211198, China
| | - Yixin Qi
- Institution of all authors: College of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu 211198, China
| | - Xiaolin Xie
- Institution of all authors: College of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu 211198, China
| | - Changlin Zhou
- Institution of all authors: College of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu 211198, China
| | - Lingman Ma
- Institution of all authors: College of Life Science and Technology, China Pharmaceutical University, Nanjing, Jiangsu 211198, China
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2
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Bhaumik KN, Spohn R, Dunai A, Daruka L, Olajos G, Zákány F, Hetényi A, Pál C, Martinek TA. Chemically diverse antimicrobial peptides induce hyperpolarization of the E. coli membrane. Commun Biol 2024; 7:1264. [PMID: 39367191 PMCID: PMC11452689 DOI: 10.1038/s42003-024-06946-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 09/24/2024] [Indexed: 10/06/2024] Open
Abstract
The negative membrane potential within bacterial cells is crucial in various essential cellular processes. Sustaining a hyperpolarised membrane could offer a novel strategy to combat antimicrobial resistance. However, it remains uncertain which molecules are responsible for inducing hyperpolarization and what the underlying molecular mechanisms are. Here, we demonstrate that chemically diverse antimicrobial peptides (AMPs) trigger hyperpolarization of the bacterial cytosolic membrane when applied at subinhibitory concentrations. Specifically, these AMPs adopt a membrane-induced amphipathic structure and, thereby, generate hyperpolarization in Escherichia coli without damaging the cell membrane. These AMPs act as selective ionophores for K+ (over Na+) or Cl- (over H2PO4- and NO3-) ions, generating diffusion potential across the membrane. At lower dosages of AMPs, a quasi-steady-state membrane polarisation value is achieved. Our findings highlight the potential of AMPs as a valuable tool for chemically hyperpolarising bacteria, with implications for antimicrobial research and bacterial electrophysiology.
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Affiliation(s)
- Kaushik Nath Bhaumik
- Department of Medical Chemistry, University of Szeged, Dóm tér 8, Szeged, Hungary
| | - Réka Spohn
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Hungarian Research Network (HUN-REN), Szeged, Hungary
| | - Anett Dunai
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Hungarian Research Network (HUN-REN), Szeged, Hungary
| | - Lejla Daruka
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Hungarian Research Network (HUN-REN), Szeged, Hungary
| | - Gábor Olajos
- Department of Medical Chemistry, University of Szeged, Dóm tér 8, Szeged, Hungary
| | - Florina Zákány
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Anasztázia Hetényi
- Department of Medical Chemistry, University of Szeged, Dóm tér 8, Szeged, Hungary.
| | - Csaba Pál
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, National Laboratory of Biotechnology, Hungarian Research Network (HUN-REN), Szeged, Hungary
| | - Tamás A Martinek
- Department of Medical Chemistry, University of Szeged, Dóm tér 8, Szeged, Hungary.
- HUN-REN-SZTE Biomimetic Systems Research Group, Dóm tér 8, Szeged, Hungary.
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3
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Yun S, Min J, Han S, Sim HS, Kim SK, Lee JB, Yoon JW, Yeom J, Park W. Experimental evolution under different nutritional conditions changes the genomic architecture and virulence of Acinetobacter baumannii. Commun Biol 2024; 7:1274. [PMID: 39369115 PMCID: PMC11455985 DOI: 10.1038/s42003-024-06978-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 09/27/2024] [Indexed: 10/07/2024] Open
Abstract
This study uncovers the molecular processes governing the adaptive evolution of multidrug-resistant (MDR) pathogens without antibiotic pressure. Genomic analysis of MDR Acinetobacter baumannii cells cultured for 8000 generations under starvation conditions (EAB1) or nutrient-rich conditions (EAB2) revealed significant genomic changes, primarily by insertion sequence (IS)-mediated insertions and deletions. Only two Acinetobacter-specific prophage-related deletions and translocations were observed in the EAB1 strain. Both evolved strains exhibited higher virulence in mouse infection studies, each with different modes of action. The EAB1 strain displayed a heightened ability to cross the epithelial barrier of human lung tissue, evade the immune system, and spread to lung tissues, ultimately resulting in cellular mortality. In contrast, the EAB2 strain strongly attached to epithelial cells, leading to increased synthesis of proinflammatory cytokines and chemokines. The genomic alterations and increased virulence observed in evolved strains during short-term evolution underscore the need for caution when handling these pathogens, as these risks persist even without antibiotic exposure.
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Affiliation(s)
- Sohyeon Yun
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, Republic of Korea
| | - Jihyeon Min
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, Republic of Korea
| | - Sunyong Han
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, Republic of Korea
| | - Ho Seok Sim
- Department of Microbiology and Immunology, Department of Biomedical Science, and Cancer Research Institute, College of Medicine, Seoul National University, Jongno-gu, Seoul, Republic of Korea
| | - Se Kye Kim
- College of Veterinary Medicine & Institute of Veterinary Science, Kangwon National University, Chuncheon, Gangwon, Republic of Korea
| | - Jun Bong Lee
- College of Veterinary Medicine & Institute of Veterinary Science, Kangwon National University, Chuncheon, Gangwon, Republic of Korea
| | - Jang Won Yoon
- College of Veterinary Medicine & Institute of Veterinary Science, Kangwon National University, Chuncheon, Gangwon, Republic of Korea
| | - Jinki Yeom
- Department of Microbiology and Immunology, Department of Biomedical Science, and Cancer Research Institute, College of Medicine, Seoul National University, Jongno-gu, Seoul, Republic of Korea.
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, Republic of Korea.
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4
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Jandl B, Dighe S, Gasche C, Makristathis A, Muttenthaler M. Intestinal biofilms: pathophysiological relevance, host defense, and therapeutic opportunities. Clin Microbiol Rev 2024; 37:e0013323. [PMID: 38995034 PMCID: PMC11391705 DOI: 10.1128/cmr.00133-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024] Open
Abstract
SUMMARYThe human intestinal tract harbors a profound variety of microorganisms that live in symbiosis with the host and each other. It is a complex and highly dynamic environment whose homeostasis directly relates to human health. Dysbiosis of the gut microbiota and polymicrobial biofilms have been associated with gastrointestinal diseases, including irritable bowel syndrome, inflammatory bowel diseases, and colorectal cancers. This review covers the molecular composition and organization of intestinal biofilms, mechanistic aspects of biofilm signaling networks for bacterial communication and behavior, and synergistic effects in polymicrobial biofilms. It further describes the clinical relevance and diseases associated with gut biofilms, the role of biofilms in antimicrobial resistance, and the intestinal host defense system and therapeutic strategies counteracting biofilms. Taken together, this review summarizes the latest knowledge and research on intestinal biofilms and their role in gut disorders and provides directions toward the development of biofilm-specific treatments.
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Affiliation(s)
- Bernhard Jandl
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna, Vienna, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Vienna, Austria
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Satish Dighe
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Christoph Gasche
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, Medical University of Vienna, Vienna, Austria
- Loha for Life, Center for Gastroenterology and Iron Deficiency, Vienna, Austria
| | - Athanasios Makristathis
- Department of Laboratory Medicine, Division of Clinical Microbiology, Medical University of Vienna, Vienna, Austria
| | - Markus Muttenthaler
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna, Vienna, Austria
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
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5
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Mesny F, Bauer M, Zhu J, Thomma BPHJ. Meddling with the microbiota: Fungal tricks to infect plant hosts. CURRENT OPINION IN PLANT BIOLOGY 2024; 82:102622. [PMID: 39241281 DOI: 10.1016/j.pbi.2024.102622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2024] [Revised: 07/31/2024] [Accepted: 08/11/2024] [Indexed: 09/09/2024]
Abstract
Plants associate with a wealth of microbes, collectively referred to as the plant microbiota, whose composition is determined by host plant genetics, immune responses, environmental factors and intermicrobial relations. Unsurprisingly, microbiota compositions change during disease development. Recent evidence revealed that some of these changes can be attributed to effector proteins with antimicrobial activities that are secreted by plant pathogens to manipulate host microbiota to their advantage. Intriguingly, many of these effectors have ancient origins, predating land plant emergence, and evolved over long evolutionary trajectories to acquire selective antimicrobial activities to target microbial antagonists in host plant microbiota. Thus, we argue that host-pathogen co-evolution likely involved arms races within the host-associated microbiota.
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Affiliation(s)
- Fantin Mesny
- University of Cologne, Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), 50674 Cologne, Germany
| | - Martha Bauer
- University of Cologne, Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), 50674 Cologne, Germany
| | - Jinyi Zhu
- University of Cologne, Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), 50674 Cologne, Germany
| | - Bart P H J Thomma
- University of Cologne, Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), 50674 Cologne, Germany.
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6
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Anurag Anand A, Amod A, Anwar S, Sahoo AK, Sethi G, Samanta SK. A comprehensive guide on screening and selection of a suitable AMP against biofilm-forming bacteria. Crit Rev Microbiol 2024; 50:859-878. [PMID: 38102871 DOI: 10.1080/1040841x.2023.2293019] [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: 10/04/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023]
Abstract
Lately, antimicrobial resistance (AMR) is increasing at an exponential rate making it important to search alternatives to antibiotics in order to combat multi-drug resistant (MDR) bacterial infections. Out of the several antibacterial and antibiofilm strategies being tested, antimicrobial peptides (AMPs) have shown to give better hopes in terms of a long-lasting solution to the problem. To select a desired AMP, it is important to make right use of available tools and databases that aid in identification, classification, and analysis of the physiochemical properties of AMPs. To identify the targets of these AMPs, it becomes crucial to understand their mode-of-action. AMPs can also be used in combination with other antibacterial and antibiofilm agents so as to achieve enhanced efficacy against bacteria and their biofilms. Due to concerns regarding toxicity, stability, and bioavailability, strategizing drug formulation at an early-stage becomes crucial. Although there are few concerns regarding development of bacterial resistance to AMPs, the evolution of resistance to AMPs occurs extremely slowly. This comprehensive review gives a deep insight into the selection of the right AMP, deciding the right target and combination strategy along with the type of formulation needed, and the possible resistance that bacteria can develop to these AMPs.
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Affiliation(s)
- Ananya Anurag Anand
- Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Prayagraj, India
| | - Ayush Amod
- Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Prayagraj, India
| | - Sarfraz Anwar
- Department of Bioinformatics, University of Allahabad, Prayagraj, India
| | - Amaresh Kumar Sahoo
- Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Prayagraj, India
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Sintu Kumar Samanta
- Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Prayagraj, India
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7
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Liang Y, Zhang Y, Huang Y, Xu C, Chen J, Zhang X, Huang B, Gan Z, Dong X, Huang S, Li C, Jia S, Zhang P, Yuan Y, Zhang H, Wang Y, Yuan B, Bao Y, Xiao S, Xiong M. Helicity-directed recognition of bacterial phospholipid via radially amphiphilic antimicrobial peptides. SCIENCE ADVANCES 2024; 10:eadn9435. [PMID: 39213359 PMCID: PMC11364095 DOI: 10.1126/sciadv.adn9435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 07/25/2024] [Indexed: 09/04/2024]
Abstract
The fundamental differences in phospholipids between bacterial and mammalian cell membranes present remarkable opportunities for antimicrobial design. However, it is challenging to distinguish bacterial anionic phospholipid phosphatidylglycerol (PG) from mammalian anionic phosphatidylserine (PS) with the same net charge. Here, we report a class of radially amphiphilic α helix antimicrobial peptides (RAPs) that can selectively discriminate PG from PS, relying on the helix structure. The representative RAP, L10-MMBen, can direct the rearrangement of PG vesicles into a lamellar structure with its helix axis parallel to the PG membrane surface. The helical structure imparts both the thermodynamic and kinetic advantages of L10-MMBen/PG assembly, and the hiding of hydrophobic regions in RAPs is crucial for PG recognition. L10-MMBen exhibits high selectivity against bacteria depending on PG recognition, showing low in vivo toxicity and significant treatment efficacy in mice infection models. Our study introduces a helicity-direct bacterial phospholipid recognition paradigm for designing highly selective antimicrobial peptides.
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Affiliation(s)
- Yangbin Liang
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou 511442, P. R. China
- National Engineering Research Centre for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou 510006, P. R. China
| | - Yuhao Zhang
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou 511442, P. R. China
- National Engineering Research Centre for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou 510006, P. R. China
| | - Yu Huang
- CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Cheng Xu
- Songshan Lake Materials Laboratory, Institute of Physics, Chinese Academy of Sciences, Dongguan, 523808, P. R. China
| | - Jingxian Chen
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou 511442, P. R. China
- National Engineering Research Centre for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou 510006, P. R. China
| | - Xinshuang Zhang
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou 511442, P. R. China
- National Engineering Research Centre for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou 510006, P. R. China
| | - Bingchuan Huang
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou 511442, P. R. China
- National Engineering Research Centre for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou 510006, P. R. China
| | - Zhanhui Gan
- South China Advanced Institute for Soft Matter Science and Technology, School of Emergent Soft Matter, South China University of Technology, Guangzhou 510640, China
| | - Xuehui Dong
- South China Advanced Institute for Soft Matter Science and Technology, School of Emergent Soft Matter, South China University of Technology, Guangzhou 510640, China
| | - Songyin Huang
- Biotherapy Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, P. R. China
| | - Chengrun Li
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou 511442, P. R. China
- National Engineering Research Centre for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou 510006, P. R. China
| | - Shuyi Jia
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou 511442, P. R. China
- National Engineering Research Centre for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou 510006, P. R. China
| | - Pengfei Zhang
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou 511442, P. R. China
| | - Yueling Yuan
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou 511442, P. R. China
- Key Laboratory of Biomedical Materials and Engineering of the Ministry of Education, South China University of Technology, Guangzhou, Guangdong 510006, P. R. China
| | - Houbing Zhang
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou 511442, P. R. China
| | - Yucai Wang
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, P. R. China
| | - Bing Yuan
- Songshan Lake Materials Laboratory, Institute of Physics, Chinese Academy of Sciences, Dongguan, 523808, P. R. China
| | - Yan Bao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, P. R. China
| | - Shiyan Xiao
- CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Menghua Xiong
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou 511442, P. R. China
- National Engineering Research Centre for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou 510006, P. R. China
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8
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Deb R, Torres MDT, Boudný M, Koběrská M, Cappiello F, Popper M, Dvořáková
Bendová K, Drabinová M, Hanáčková A, Jeannot K, Petřík M, Mangoni ML, Balíková Novotná G, Mráz M, de la Fuente-Nunez C, Vácha R. Computational Design of Pore-Forming Peptides with Potent Antimicrobial and Anticancer Activities. J Med Chem 2024; 67:14040-14061. [PMID: 39116273 PMCID: PMC11345766 DOI: 10.1021/acs.jmedchem.4c00912] [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: 04/17/2024] [Revised: 07/05/2024] [Accepted: 07/25/2024] [Indexed: 08/10/2024]
Abstract
Peptides that form transmembrane barrel-stave pores are potential alternative therapeutics for bacterial infections and cancer. However, their optimization for clinical translation is hampered by a lack of sequence-function understanding. Recently, we have de novo designed the first synthetic barrel-stave pore-forming antimicrobial peptide with an identified function of all residues. Here, we systematically mutate the peptide to improve pore-forming ability in anticipation of enhanced activity. Using computer simulations, supported by liposome leakage and atomic force microscopy experiments, we find that pore-forming ability, while critical, is not the limiting factor for improving activity in the submicromolar range. Affinity for bacterial and cancer cell membranes needs to be optimized simultaneously. Optimized peptides more effectively killed antibiotic-resistant ESKAPEE bacteria at submicromolar concentrations, showing low cytotoxicity to human cells and skin model. Peptides showed systemic anti-infective activity in a preclinical mouse model of Acinetobacter baumannii infection. We also demonstrate peptide optimization for pH-dependent antimicrobial and anticancer activity.
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Affiliation(s)
- Rahul Deb
- CEITEC
− Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic
- National
Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno 625 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
- Department
of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Miroslav Boudný
- CEITEC
− Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic
- Department
of Internal Medicine, Hematology and Oncology, University Hospital
Brno and Faculty of Medicine, Masaryk University, Brno 625 00, Czech Republic
| | - Markéta Koběrská
- Institute
of Microbiology, Czech Academy of Sciences,
BIOCEV, Vestec 252 50, Czech Republic
| | - Floriana Cappiello
- Department
of Biochemical Sciences, Laboratory Affiliated to Istituto Pasteur
Italia-Fondazione Cenci Bolognetti, Sapienza
University of Rome, Rome 00185, Italy
| | - Miroslav Popper
- Institute
of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University, Olomouc 779 00, Czech Republic
| | - Kateřina Dvořáková
Bendová
- Institute
of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University, Olomouc 779 00, Czech Republic
| | - Martina Drabinová
- CEITEC
− Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic
| | - Adelheid Hanáčková
- CEITEC
− Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic
| | - Katy Jeannot
- University
of Franche-Comté, CNRS, Chrono-environment, Besançon 25030, France
- National Reference Centre for Antibiotic
Resistance, Besançon 25030, France
| | - Miloš Petřík
- Institute
of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University, Olomouc 779 00, Czech Republic
- Czech
Advanced Technology and Research Institute, Palacký University, Olomouc 779 00, Czech Republic
| | - Maria Luisa Mangoni
- Department
of Biochemical Sciences, Laboratory Affiliated to Istituto Pasteur
Italia-Fondazione Cenci Bolognetti, Sapienza
University of Rome, Rome 00185, Italy
| | | | - Marek Mráz
- CEITEC
− Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic
- Department
of Internal Medicine, Hematology and Oncology, University Hospital
Brno and Faculty of Medicine, Masaryk University, Brno 625 00, Czech Republic
| | - 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
- Department
of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Robert Vácha
- CEITEC
− Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic
- National
Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
- Department
of Condensed Matter Physics, Faculty of Science, Masaryk University, Brno 611 37, Czech Republic
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9
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Moule MG, Benjamin AB, Burger ML, Herlan C, Lebedev M, Lin JS, Koster KJ, Wavare N, Adams LG, Bräse S, Munoz-Medina R, Cannon CL, Barron AE, Cirillo JD. Peptide-mimetic treatment of Pseudomonas aeruginosa in a mouse model of respiratory infection. Commun Biol 2024; 7:1033. [PMID: 39174819 PMCID: PMC11341572 DOI: 10.1038/s42003-024-06725-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 08/13/2024] [Indexed: 08/24/2024] Open
Abstract
The rise of drug resistance has become a global crisis, with >1 million deaths due to resistant bacterial infections each year. Pseudomonas aeruginosa, in particular, remains a serious problem with limited solutions due to complex resistance mechanisms that now lead to more than 32,000 multidrug-resistant (MDR) infections and over 2000 deaths in the U.S. annually. While the emergence of resistant bacteria has become ominously common, identification of useful new drug classes has been limited over the past over 40 years. We found that a potential novel therapeutic, the peptide-mimetic TM5, is effective at killing P. aeruginosa and displays sufficiently low toxicity in mammalian cells to allow for use in treatment of infections. Interestingly, TM5 kills P. aeruginosa more rapidly than traditional antibiotics, within 30-60 min in vitro, and is effective against a range of clinical isolates, including extensively drug resistant strains. In vivo, TM5 significantly reduced bacterial load in the lungs within 24 h compared to untreated mice and demonstrated few adverse effects. Taken together, these observations suggest that TM5 shows promise as an alternative therapy for MDR P. aeruginosa respiratory infections.
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Affiliation(s)
- Madeleine G Moule
- Department of Microbial Pathogenesis and Immunology, Texas A&M School of Medicine, Bryan, TX, USA
- Institute of Immunology & Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Aaron B Benjamin
- Department of Microbial Pathogenesis and Immunology, Texas A&M School of Medicine, Bryan, TX, USA
| | - Melanie L Burger
- Institute of Immunology & Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Claudine Herlan
- Institute of Biological and Chemical Systems - Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Maxim Lebedev
- Department of Microbial Pathogenesis and Immunology, Texas A&M School of Medicine, Bryan, TX, USA
| | - Jennifer S Lin
- Department of Bioengineering, Stanford University Schools of Medicine and of Engineering, Stanford, CA, USA
| | - Kent J Koster
- Department of Microbial Pathogenesis and Immunology, Texas A&M School of Medicine, Bryan, TX, USA
| | - Neha Wavare
- Department of Microbial Pathogenesis and Immunology, Texas A&M School of Medicine, Bryan, TX, USA
| | - Leslie G Adams
- Department of Veterinary Pathobiology, Texas A&M School of Veterinary Medicine & Biomedical Sciences, College Station, TX, USA
| | - Stefan Bräse
- Institute of Biological and Chemical Systems - Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Ricardo Munoz-Medina
- Department of Microbial Pathogenesis and Immunology, Texas A&M School of Medicine, Bryan, TX, USA
| | - Carolyn L Cannon
- Department of Microbial Pathogenesis and Immunology, Texas A&M School of Medicine, Bryan, TX, USA
| | - Annelise E Barron
- Department of Bioengineering, Stanford University Schools of Medicine and of Engineering, Stanford, CA, USA.
| | - Jeffrey D Cirillo
- Department of Microbial Pathogenesis and Immunology, Texas A&M School of Medicine, Bryan, TX, USA.
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10
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Dang TC, Fields L, Li L. MotifQuest: An Automated Pipeline for Motif Database Creation to Improve Peptidomics Database Searching Programs. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1902-1912. [PMID: 39058243 DOI: 10.1021/jasms.4c00192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/28/2024]
Abstract
Endogenous peptides are an abundant and versatile class of biomolecules with vital roles pertinent to the functionality of the nervous, endocrine, and immune systems and others. Mass spectrometry stands as a premier technique for identifying endogenous peptides, yet the field still faces challenges due to the lack of optimized computational resources for reliable raw mass spectra analysis and interpretation. Current database searching programs can exhibit discrepancies due to the unique properties of endogenous peptides, which typically require specialized search considerations. Herein, we present a high throughput, novel scoring algorithm for the extraction and ranking of conserved amino acid sequence motifs within any endogenous peptide database. Motifs are conserved patterns across organisms, representing sequence moieties crucial for biological functions, including maintenance of homeostasis. MotifQuest, our novel motif database generation algorithm, is designed to work in partnership with EndoGenius, a program optimized for database searching of endogenous peptides and that is powered by a motif database to capitalize on biological context to produce identifications. MotifQuest aims to quickly develop motif databases without any prior knowledge, a laborious task not possible with traditional sequence alignment resources. In this work we illustrate the utility of MotifQuest to expand EndoGenius' identification utility to other endogenous peptides by showcasing its ability to identify antimicrobial peptides. Additionally, we discuss the potential utility of MotifQuest to parse out motifs from a FASTA database file that can be further validated as new peptide drug candidates.
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Affiliation(s)
- Tina C Dang
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705, United States
| | - Lauren Fields
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, Wisconsin 53705, United States
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
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11
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Nyhoegen C, Bonhoeffer S, Uecker H. The many dimensions of combination therapy: How to combine antibiotics to limit resistance evolution. Evol Appl 2024; 17:e13764. [PMID: 39100751 PMCID: PMC11297101 DOI: 10.1111/eva.13764] [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: 11/19/2023] [Revised: 05/30/2024] [Accepted: 07/14/2024] [Indexed: 08/06/2024] Open
Abstract
In combination therapy, bacteria are challenged with two or more antibiotics simultaneously. Ideally, separate mutations are required to adapt to each of them, which is a priori expected to hinder the evolution of full resistance. Yet, the success of this strategy ultimately depends on how well the combination controls the growth of bacteria with and without resistance mutations. To design a combination treatment, we need to choose drugs and their doses and decide how many drugs get mixed. Which combinations are good? To answer this question, we set up a stochastic pharmacodynamic model and determine the probability to successfully eradicate a bacterial population. We consider bacteriostatic and two types of bactericidal drugs-those that kill independent of replication and those that kill during replication. To establish results for a null model, we consider non-interacting drugs and implement the two most common models for drug independence-Loewe additivity and Bliss independence. Our results show that combination therapy is almost always better in limiting the evolution of resistance than administering just one drug, even though we keep the total drug dose constant for a 'fair' comparison. Yet, exceptions exist for drugs with steep dose-response curves. Combining a bacteriostatic and a bactericidal drug which can kill non-replicating cells is particularly beneficial. Our results suggest that a 50:50 drug ratio-even if not always optimal-is usually a good and safe choice. Applying three or four drugs is beneficial for treatment of strains with large mutation rates but adding more drugs otherwise only provides a marginal benefit or even a disadvantage. By systematically addressing key elements of treatment design, our study provides a basis for future models which take further factors into account. It also highlights conceptual challenges with translating the traditional concepts of drug independence to the single-cell level.
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Affiliation(s)
- Christin Nyhoegen
- Research Group Stochastic Evolutionary Dynamics, Department of Theoretical BiologyMax Planck Institute for Evolutionary BiologyPlonGermany
| | - Sebastian Bonhoeffer
- Department of Environmental Systems Science, Institute of Integrative BiologyETH ZurichZurichSwitzerland
| | - Hildegard Uecker
- Research Group Stochastic Evolutionary Dynamics, Department of Theoretical BiologyMax Planck Institute for Evolutionary BiologyPlonGermany
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12
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Santos-Júnior CD, Torres MDT, Duan Y, Rodríguez Del Río Á, Schmidt TSB, 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. Discovery of antimicrobial peptides in the global microbiome with machine learning. Cell 2024; 187:3761-3778.e16. [PMID: 38843834 DOI: 10.1016/j.cell.2024.05.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 04/11/2024] [Accepted: 05/06/2024] [Indexed: 06/25/2024]
Abstract
Novel antibiotics are urgently needed to combat the antibiotic-resistance crisis. We present a machine-learning-based approach to predict antimicrobial peptides (AMPs) within the global microbiome and leverage a vast dataset of 63,410 metagenomes and 87,920 prokaryotic genomes from environmental and host-associated habitats to create the AMPSphere, a comprehensive catalog comprising 863,498 non-redundant peptides, few of which match existing databases. AMPSphere provides insights into the evolutionary origins of peptides, including by duplication or gene truncation of longer sequences, and we observed that AMP production varies by habitat. To validate our predictions, we synthesized and tested 100 AMPs against clinically relevant drug-resistant pathogens and human gut commensals both in vitro and in vivo. A total of 79 peptides were active, with 63 targeting pathogens. These active AMPs exhibited antibacterial activity by disrupting bacterial membranes. In conclusion, our approach identified nearly one million prokaryotic AMP sequences, an open-access resource for antibiotic discovery.
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Affiliation(s)
- Célio Dias Santos-Júnior
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai 200433, China; Laboratory of Microbial Processes & Biodiversity - LMPB, Department of Hydrobiology, Universidade Federal de São Carlos - UFSCar, São Carlos, São Paulo 13565-905, Brazil
| | - 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
| | - Yiqian Duan
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai 200433, 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, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Thomas S B Schmidt
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany; APC Microbiome & School of Medicine, University College Cork, Cork, Ireland
| | - Hui Chong
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai 200433, 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 200433, China
| | - Amy Houseman
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai 200433, China
| | - Jelena Somborski
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai 200433, China
| | - Anna Vines
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai 200433, China
| | - Xing-Ming Zhao
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai 200433, 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 and MOE Frontiers Center for Brain Science, Fudan University, 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, Pozuelo de Alarcón, 28223 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, 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.
| | - Luis Pedro Coelho
- Institute of Science and Technology for Brain-Inspired Intelligence - ISTBI, Fudan University, Shanghai 200433, China; Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology, Translational Research Institute, Woolloongabba, QLD, Australia.
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13
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Antunes B, Zanchi C, Johnston PR, Maron B, Witzany C, Regoes RR, Hayouka Z, Rolff J. The evolution of antimicrobial peptide resistance in Pseudomonas aeruginosa is severely constrained by random peptide mixtures. PLoS Biol 2024; 22:e3002692. [PMID: 38954678 PMCID: PMC11218975 DOI: 10.1371/journal.pbio.3002692] [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: 02/26/2024] [Accepted: 05/28/2024] [Indexed: 07/04/2024] Open
Abstract
The prevalence of antibiotic-resistant pathogens has become a major threat to public health, requiring swift initiatives for discovering new strategies to control bacterial infections. Hence, antibiotic stewardship and rapid diagnostics, but also the development, and prudent use, of novel effective antimicrobial agents are paramount. Ideally, these agents should be less likely to select for resistance in pathogens than currently available conventional antimicrobials. The usage of antimicrobial peptides (AMPs), key components of the innate immune response, and combination therapies, have been proposed as strategies to diminish the emergence of resistance. Herein, we investigated whether newly developed random antimicrobial peptide mixtures (RPMs) can significantly reduce the risk of resistance evolution in vitro to that of single sequence AMPs, using the ESKAPE pathogen Pseudomonas aeruginosa (P. aeruginosa) as a model gram-negative bacterium. Infections of this pathogen are difficult to treat due the inherent resistance to many drug classes, enhanced by the capacity to form biofilms. P. aeruginosa was experimentally evolved in the presence of AMPs or RPMs, subsequentially assessing the extent of resistance evolution and cross-resistance/collateral sensitivity between treatments. Furthermore, the fitness costs of resistance on bacterial growth were studied and whole-genome sequencing used to investigate which mutations could be candidates for causing resistant phenotypes. Lastly, changes in the pharmacodynamics of the evolved bacterial strains were examined. Our findings suggest that using RPMs bears a much lower risk of resistance evolution compared to AMPs and mostly prevents cross-resistance development to other treatments, while maintaining (or even improving) drug sensitivity. This strengthens the case for using random cocktails of AMPs in favour of single AMPs, against which resistance evolved in vitro, providing an alternative to classic antibiotics worth pursuing.
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Affiliation(s)
- Bernardo Antunes
- Freie Universität Berlin, Evolutionary Biology, Berlin, Germany
- Institute of Biochemistry, Food Science and Nutrition, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Caroline Zanchi
- Freie Universität Berlin, Evolutionary Biology, Berlin, Germany
| | - Paul R. Johnston
- Freie Universität Berlin, Evolutionary Biology, Berlin, Germany
- Berlin Centre for Genomics in Biodiversity Research, Berlin, Germany
- University of St. Andrews, School of Medicine, North Haugh, St Andrews, Fife, United Kingdom
| | - Bar Maron
- Institute of Biochemistry, Food Science and Nutrition, The Hebrew University of Jerusalem, Rehovot, Israel
| | | | - Roland R. Regoes
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Zvi Hayouka
- Institute of Biochemistry, Food Science and Nutrition, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Jens Rolff
- Freie Universität Berlin, Evolutionary Biology, Berlin, Germany
- Berlin Centre for Genomics in Biodiversity Research, Berlin, Germany
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14
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Recktenwald M, Kaur M, Benmassaoud MM, Copling A, Khanna T, Curry M, Cortes D, Fleischer G, Carabetta VJ, Vega SL. Antimicrobial Peptide Screening for Designing Custom Bactericidal Hydrogels. Pharmaceutics 2024; 16:860. [PMID: 39065557 PMCID: PMC11279943 DOI: 10.3390/pharmaceutics16070860] [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: 06/03/2024] [Revised: 06/21/2024] [Accepted: 06/25/2024] [Indexed: 07/28/2024] Open
Abstract
Staphylococcus aureus (S. aureus) is an opportunistic pathogen that lives on surfaces and skin and can cause serious infections inside the body. Antimicrobial peptides (AMPs) are part of the innate immune system and can eliminate pathogens, including bacteria and viruses, and are a promising alternative to antibiotics. Although studies have reported that AMP-functionalized hydrogels can prevent bacterial adhesion and biofilm formation, AMP dosing and the combined effects of multiple AMPs are not well understood. Here, three AMPs with different antibacterial properties were synthesized and the soluble minimum inhibitory concentrations (MICs) of each AMP against methicillin-susceptible S. aureus (MSSA) and methicillin-resistant S. aureus (MRSA) were determined. Hydrogels with immobilized AMPs at their MIC (DD13-RIP 27.5 µM; indolicidin 43.8 µM; P10 120 µM) were effective in preventing MRSA adhesion and biofilm formation. Checkerboard AMP screens identified synergy between indolicidin (3.1 µM) and P10 (12.5 µM) based on soluble fractional inhibitory concentration indices (FICIs) against MRSA, and hydrogels formed with these AMPs at half of their synergistic concentrations (total peptide concentration, 7.8 µM) were highly efficacious in killing MRSA. Mammalian cells cultured atop these hydrogels were highly viable, demonstrating that these AMP hydrogels are biocompatible and selectively eradicate bacteria, based on soluble checkerboard-screening data.
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Affiliation(s)
- Matthias Recktenwald
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA; (M.R.); (M.M.B.)
| | - Muskanjot Kaur
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ 08103, USA; (M.K.); (M.C.); (D.C.); (G.F.)
| | - Mohammed M. Benmassaoud
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA; (M.R.); (M.M.B.)
| | - Aryanna Copling
- Department of Translational Biomedical Sciences, Rowan University, Glassboro, NJ 08028, USA;
| | - Tulika Khanna
- Department of Biological Sciences, Rowan University, Glassboro, NJ 08028, USA;
| | - Michael Curry
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ 08103, USA; (M.K.); (M.C.); (D.C.); (G.F.)
| | - Dennise Cortes
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ 08103, USA; (M.K.); (M.C.); (D.C.); (G.F.)
| | - Gilbert Fleischer
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ 08103, USA; (M.K.); (M.C.); (D.C.); (G.F.)
| | - Valerie J. Carabetta
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ 08103, USA; (M.K.); (M.C.); (D.C.); (G.F.)
| | - Sebastián L. Vega
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA; (M.R.); (M.M.B.)
- Department of Orthopedic Surgery, Cooper Medical School of Rowan University, Camden, NJ 08103, USA
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15
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Tajer L, Paillart JC, Dib H, Sabatier JM, Fajloun Z, Abi Khattar Z. Molecular Mechanisms of Bacterial Resistance to Antimicrobial Peptides in the Modern Era: An Updated Review. Microorganisms 2024; 12:1259. [PMID: 39065030 PMCID: PMC11279074 DOI: 10.3390/microorganisms12071259] [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: 05/08/2024] [Revised: 06/10/2024] [Accepted: 06/18/2024] [Indexed: 07/28/2024] Open
Abstract
Antimicrobial resistance (AMR) poses a serious global health concern, resulting in a significant number of deaths annually due to infections that are resistant to treatment. Amidst this crisis, antimicrobial peptides (AMPs) have emerged as promising alternatives to conventional antibiotics (ATBs). These cationic peptides, naturally produced by all kingdoms of life, play a crucial role in the innate immune system of multicellular organisms and in bacterial interspecies competition by exhibiting broad-spectrum activity against bacteria, fungi, viruses, and parasites. AMPs target bacterial pathogens through multiple mechanisms, most importantly by disrupting their membranes, leading to cell lysis. However, bacterial resistance to host AMPs has emerged due to a slow co-evolutionary process between microorganisms and their hosts. Alarmingly, the development of resistance to last-resort AMPs in the treatment of MDR infections, such as colistin, is attributed to the misuse of this peptide and the high rate of horizontal genetic transfer of the corresponding resistance genes. AMP-resistant bacteria employ diverse mechanisms, including but not limited to proteolytic degradation, extracellular trapping and inactivation, active efflux, as well as complex modifications in bacterial cell wall and membrane structures. This review comprehensively examines all constitutive and inducible molecular resistance mechanisms to AMPs supported by experimental evidence described to date in bacterial pathogens. We also explore the specificity of these mechanisms toward structurally diverse AMPs to broaden and enhance their potential in developing and applying them as therapeutics for MDR bacteria. Additionally, we provide insights into the significance of AMP resistance within the context of host-pathogen interactions.
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Affiliation(s)
- Layla Tajer
- Laboratory of Applied Biotechnology (LBA3B), Azm Center for Research in Biotechnology and Its Applications, Department of Cell Culture, EDST, Lebanese University, Tripoli 1300, Lebanon; (L.T.); (Z.F.)
| | - Jean-Christophe Paillart
- CNRS, Architecture et Réactivité de l’ARN, UPR 9002, Université de Strasbourg, 2 Allée Konrad Roentgen, F-67000 Strasbourg, France;
| | - Hanna Dib
- College of Engineering and Technology, American University of the Middle East, Egaila 54200, Kuwait;
| | - Jean-Marc Sabatier
- CNRS, INP, Inst Neurophysiopathol, Aix-Marseille Université, 13385 Marseille, France
| | - Ziad Fajloun
- Laboratory of Applied Biotechnology (LBA3B), Azm Center for Research in Biotechnology and Its Applications, Department of Cell Culture, EDST, Lebanese University, Tripoli 1300, Lebanon; (L.T.); (Z.F.)
- Department of Biology, Faculty of Sciences 3, Lebanese University, Campus Michel Slayman Ras Maska, Tripoli 1352, Lebanon
| | - Ziad Abi Khattar
- Faculty of Medicine and Medical Sciences, University of Balamand, Kalhat, P.O. Box 100, Tripoli, Lebanon
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16
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Lachat J, Lextrait G, Jouan R, Boukherissa A, Yokota A, Jang S, Ishigami K, Futahashi R, Cossard R, Naquin D, Costache V, Augusto L, Tissières P, Biondi EG, Alunni B, Timchenko T, Ohbayashi T, Kikuchi Y, Mergaert P. Hundreds of antimicrobial peptides create a selective barrier for insect gut symbionts. Proc Natl Acad Sci U S A 2024; 121:e2401802121. [PMID: 38865264 PMCID: PMC11194567 DOI: 10.1073/pnas.2401802121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 05/08/2024] [Indexed: 06/14/2024] Open
Abstract
The spatial organization of gut microbiota is crucial for the functioning of the gut ecosystem, although the mechanisms that organize gut bacterial communities in microhabitats are only partially understood. The gut of the insect Riptortus pedestris has a characteristic microbiota biogeography with a multispecies community in the anterior midgut and a monospecific bacterial population in the posterior midgut. We show that the posterior midgut region produces massively hundreds of specific antimicrobial peptides (AMPs), the Crypt-specific Cysteine-Rich peptides (CCRs) that have membrane-damaging antimicrobial activity against diverse bacteria but posterior midgut symbionts have elevated resistance. We determined by transposon-sequencing the genetic repertoire in the symbiont Caballeronia insecticola to manage CCR stress, identifying different independent pathways, including AMP-resistance pathways unrelated to known membrane homeostasis functions as well as cell envelope functions. Mutants in the corresponding genes have reduced capacity to colonize the posterior midgut, demonstrating that CCRs create a selective barrier and resistance is crucial in gut symbionts. Moreover, once established in the gut, the bacteria differentiate into a CCR-sensitive state, suggesting a second function of the CCR peptide arsenal in protecting the gut epithelia or mediating metabolic exchanges between the host and the gut symbionts. Our study highlights the evolution of an extreme diverse AMP family that likely contributes to establish and control the gut microbiota.
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Affiliation(s)
- Joy Lachat
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, Gif-sur-Yvette91198, France
| | - Gaëlle Lextrait
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, Gif-sur-Yvette91198, France
| | - Romain Jouan
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, Gif-sur-Yvette91198, France
| | - Amira Boukherissa
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, Gif-sur-Yvette91198, France
| | - Aya Yokota
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, Gif-sur-Yvette91198, France
| | - Seonghan Jang
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Hokkaido Center, Sapporo062-8517, Japan
- Unit of Applied Biological Chemistry, Graduate School of Agriculture, Hokkaido University, 060-8589Sapporo, Japan
| | - Kota Ishigami
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Hokkaido Center, Sapporo062-8517, Japan
- Unit of Applied Biological Chemistry, Graduate School of Agriculture, Hokkaido University, 060-8589Sapporo, Japan
| | - Ryo Futahashi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba305-8566, Japan
| | - Raynald Cossard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, Gif-sur-Yvette91198, France
| | - Delphine Naquin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, Gif-sur-Yvette91198, France
| | - Vlad Costache
- MIMA2 Imaging Core Facility, Microscopie et Imagerie des Microorganismes, Animaux et Aliments (MIMA2), INRAe, Jouy-en-Josas78352, France
| | - Luis Augusto
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, Gif-sur-Yvette91198, France
| | - Pierre Tissières
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, Gif-sur-Yvette91198, France
| | - Emanuele G. Biondi
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, Gif-sur-Yvette91198, France
| | - Benoît Alunni
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, Gif-sur-Yvette91198, France
| | - Tatiana Timchenko
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, Gif-sur-Yvette91198, France
| | - Tsubasa Ohbayashi
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, Gif-sur-Yvette91198, France
| | - Yoshitomo Kikuchi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Hokkaido Center, Sapporo062-8517, Japan
- Unit of Applied Biological Chemistry, Graduate School of Agriculture, Hokkaido University, 060-8589Sapporo, Japan
| | - Peter Mergaert
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, Gif-sur-Yvette91198, France
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17
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Chen M, Hu Z, Shi J, Xie Z. Human β-defensins and their synthetic analogs: Natural defenders and prospective new drugs of oral health. Life Sci 2024; 346:122591. [PMID: 38548013 DOI: 10.1016/j.lfs.2024.122591] [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: 01/12/2024] [Revised: 03/08/2024] [Accepted: 03/24/2024] [Indexed: 04/14/2024]
Abstract
As a family of cationic host defense peptides, human β-defensins (HBDs) are ubiquitous in the oral cavity and are mainly synthesized primarily by epithelial cells, serving as the primary barrier and aiming to prevent microbial invasion, inflammation, and disease while maintaining physiological homeostasis. In recent decades, there has been great interest in their biological functions, structure-activity relationships, mechanisms of action, and therapeutic potential in oral diseases. Meanwhile, researchers are dedicated to improving the properties of HBDs for clinical application. In this review, we first describe the classification, structural characteristics, functions, and mechanisms of HBDs. Next, we cover the role of HBDs and their synthetic analogs in oral diseases, including dental caries and pulp infections, periodontitis, peri-implantitis, fungal/viral infections and oral mucosal diseases, and oral squamous cell carcinoma. Finally, we discuss the limitations and challenges of clinical translation of HBDs and their synthetic analogs, including, but not limited to, stability, bioavailability, antimicrobial activity, resistance, and toxicity. Above all, this review summarizes the biological functions, mechanisms of action, and therapeutic potential of both natural HBDs and their synthetic analogs in oral diseases, as well as the challenges associated with clinical translation, thus providing substantial insights into the laboratory development and clinical application of HBDs in oral diseases.
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Affiliation(s)
- Mumian Chen
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Engineering Research Center of Oral Biomaterials and Devices of Zhejiang Province, Hangzhou 310000, China.
| | - Zihe Hu
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Engineering Research Center of Oral Biomaterials and Devices of Zhejiang Province, Hangzhou 310000, China.
| | - Jue Shi
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Engineering Research Center of Oral Biomaterials and Devices of Zhejiang Province, Hangzhou 310000, China.
| | - Zhijian Xie
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Engineering Research Center of Oral Biomaterials and Devices of Zhejiang Province, Hangzhou 310000, China.
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18
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Wang Y, Zhang Y, Su R, Wang Y, Qi W. Antimicrobial therapy based on self-assembling peptides. J Mater Chem B 2024; 12:5061-5075. [PMID: 38726712 DOI: 10.1039/d4tb00260a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
The emergence of drug-resistant microorganisms has threatened global health, and microbial infections have severely limited the use of medical materials. For example, the attachment and colonization of pathogenic bacteria to medical implant materials can lead to wound infections, inflammation and complications, as well as implant failure, shortening their lifespan and even resulting in patient death. In the era of antibiotic resistance, antimicrobial drug discovery needs to prioritize unconventional therapies that act on new targets or adopt new mechanisms. In this regard, supramolecular antimicrobial peptides have emerged as attractive therapeutic platforms, both as bactericides for combination antibiotics and as delivery vehicles. By taking advantage of their programmable intermolecular and intramolecular interactions, peptides can be modified to form higher-order structures (including nanofibers and nanoparticles) with unique functionality. This paper begins with an analysis of the relationship between peptide self-assembly and antimicrobial activity, describes in detail the research and development of various self-assembled antimicrobial peptides in recent years, and finally explores different combinatorial strategies for self-assembling antimicrobial peptides.
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Affiliation(s)
- Yuqi Wang
- Chemical Engineering Research Center, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China.
| | - Yexi Zhang
- Chemical Engineering Research Center, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China.
| | - Rongxin Su
- Chemical Engineering Research Center, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China.
- State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300072, P. R. China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, P. R. China
- Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Yuefei Wang
- Chemical Engineering Research Center, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China.
- State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300072, P. R. China
- Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Wei Qi
- Chemical Engineering Research Center, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China.
- State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300072, P. R. China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, P. R. China
- Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin 300072, P. R. China
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19
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Chen C, Shi J, Wang D, Kong P, Wang Z, Liu Y. Antimicrobial peptides as promising antibiotic adjuvants to combat drug-resistant pathogens. Crit Rev Microbiol 2024; 50:267-284. [PMID: 36890767 DOI: 10.1080/1040841x.2023.2186215] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 07/19/2022] [Accepted: 10/26/2022] [Indexed: 03/10/2023]
Abstract
The widespread antimicrobial resistance (AMR) calls for the development of new antimicrobial strategies. Antibiotic adjuvant rescues antibiotic activity and increases the life span of the antibiotics, representing a more productive, timely, and cost-effective strategy in fighting drug-resistant pathogens. Antimicrobial peptides (AMPs) from synthetic and natural sources are considered new-generation antibacterial agents. Besides their direct antimicrobial activity, growing evidence shows that some AMPs effectively enhance the activity of conventional antibiotics. The combinations of AMPs and antibiotics display an improved therapeutic effect on antibiotic-resistant bacterial infections and minimize the emergence of resistance. In this review, we discuss the value of AMPs in the age of resistance, including modes of action, limiting evolutionary resistance, and their designing strategies. We summarise the recent advances in combining AMPs and antibiotics against antibiotic-resistant pathogens, as well as their synergistic mechanisms. Lastly, we highlight the challenges and opportunities associated with the use of AMPs as potential antibiotic adjuvants. This will shed new light on the deployment of synergistic combinations to address the AMR crisis.
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Affiliation(s)
- Chen Chen
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Jingru Shi
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Dejuan Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Pan Kong
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Zhiqiang Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Yuan Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education of China, Yangzhou University, Yangzhou, China
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20
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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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21
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Cresti L, Cappello G, Pini A. Antimicrobial Peptides towards Clinical Application-A Long History to Be Concluded. Int J Mol Sci 2024; 25:4870. [PMID: 38732089 PMCID: PMC11084544 DOI: 10.3390/ijms25094870] [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: 03/27/2024] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 05/13/2024] Open
Abstract
Antimicrobial peptides (AMPs) are molecules with an amphipathic structure that enables them to interact with bacterial membranes. This interaction can lead to membrane crossing and disruption with pore formation, culminating in cell death. They are produced naturally in various organisms, including humans, animals, plants and microorganisms. In higher animals, they are part of the innate immune system, where they counteract infection by bacteria, fungi, viruses and parasites. AMPs can also be designed de novo by bioinformatic approaches or selected from combinatorial libraries, and then produced by chemical or recombinant procedures. Since their discovery, AMPs have aroused interest as potential antibiotics, although few have reached the market due to stability limits or toxicity. Here, we describe the development phase and a number of clinical trials of antimicrobial peptides. We also provide an update on AMPs in the pharmaceutical industry and an overall view of their therapeutic market. Modifications to peptide structures to improve stability in vivo and bioavailability are also described.
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Affiliation(s)
- Laura Cresti
- Medical Biotechnology Department, University of Siena, Via A Moro 2, 53100 Siena, Italy; (G.C.); (A.P.)
| | - Giovanni Cappello
- Medical Biotechnology Department, University of Siena, Via A Moro 2, 53100 Siena, Italy; (G.C.); (A.P.)
| | - Alessandro Pini
- Medical Biotechnology Department, University of Siena, Via A Moro 2, 53100 Siena, Italy; (G.C.); (A.P.)
- SetLance srl, Via Fiorentina 1, 53100 Siena, Italy
- Laboratory of Clinical Pathology, Santa Maria alle Scotte University Hospital, 53100 Siena, Italy
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22
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Feng J, Sun M, Liu C, Zhang W, Xu C, Wang J, Wang G, Wan S. SAMP: Identifying Antimicrobial Peptides by an Ensemble Learning Model Based on Proportionalized Split Amino Acid Composition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.25.590553. [PMID: 38712184 PMCID: PMC11071531 DOI: 10.1101/2024.04.25.590553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
It is projected that 10 million deaths could be attributed to drug-resistant bacteria infections in 2050. To address this concern, identifying new-generation antibiotics is an effective way. Antimicrobial peptides (AMPs), a class of innate immune effectors, have received significant attention for their capacity to eliminate drug-resistant pathogens, including viruses, bacteria, and fungi. Recent years have witnessed widespread applications of computational methods especially machine learning (ML) and deep learning (DL) for discovering AMPs. However, existing methods only use features including compositional, physiochemical, and structural properties of peptides, which cannot fully capture sequence information from AMPs. Here, we present SAMP, an ensemble random projection (RP) based computational model that leverages a new type of features called Proportionalized Split Amino Acid Composition (PSAAC) in addition to conventional sequence-based features for AMP prediction. With this new feature set, SAMP captures the residue patterns like sorting signals at around both the N-terminus and the C-terminus, while also retaining the sequence order information from the middle peptide fragments. Benchmarking tests on different balanced and imbalanced datasets demonstrate that SAMP consistently outperforms existing state-of-the-art methods, such as iAMPpred and AMPScanner V2, in terms of accuracy, MCC, G-measure and F1-score. In addition, by leveraging an ensemble RP architecture, SAMP is scalable to processing large-scale AMP identification with further performance improvement, compared to those models without RP. To facilitate the use of SAMP, we have developed a Python package freely available at https://github.com/wan-mlab/SAMP .
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Gafar MA, Omolo CA, Elhassan E, Ibrahim UH, Govender T. Applications of peptides in nanosystems for diagnosing and managing bacterial sepsis. J Biomed Sci 2024; 31:40. [PMID: 38637839 PMCID: PMC11027418 DOI: 10.1186/s12929-024-01029-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Accepted: 04/10/2024] [Indexed: 04/20/2024] Open
Abstract
Sepsis represents a critical medical condition stemming from an imbalanced host immune response to infections, which is linked to a significant burden of disease. Despite substantial efforts in laboratory and clinical research, sepsis remains a prominent contributor to mortality worldwide. Nanotechnology presents innovative opportunities for the advancement of sepsis diagnosis and treatment. Due to their unique properties, including diversity, ease of synthesis, biocompatibility, high specificity, and excellent pharmacological efficacy, peptides hold great potential as part of nanotechnology approaches against sepsis. Herein, we present a comprehensive and up-to-date review of the applications of peptides in nanosystems for combating sepsis, with the potential to expedite diagnosis and enhance management outcomes. Firstly, sepsis pathophysiology, antisepsis drug targets, current modalities in management and diagnosis with their limitations, and the potential of peptides to advance the diagnosis and management of sepsis have been adequately addressed. The applications have been organized into diagnostic or managing applications, with the last one being further sub-organized into nano-delivered bioactive peptides with antimicrobial or anti-inflammatory activity, peptides as targeting moieties on the surface of nanosystems against sepsis, and peptides as nanocarriers for antisepsis agents. The studies have been grouped thematically and discussed, emphasizing the constructed nanosystem, physicochemical properties, and peptide-imparted enhancement in diagnostic and therapeutic efficacy. The strengths, limitations, and research gaps in each section have been elaborated. Finally, current challenges and potential future paths to enhance the use of peptides in nanosystems for combating sepsis have been deliberately spotlighted. This review reaffirms peptides' potential as promising biomaterials within nanotechnology strategies aimed at improving sepsis diagnosis and management.
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Affiliation(s)
- Mohammed A Gafar
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban, South Africa
- Department of Pharmaceutics, Faculty of Pharmacy, University of Khartoum, P.O. Box 1996, Khartoum, Sudan
| | - Calvin A Omolo
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban, South Africa.
- Department of Pharmaceutics and Pharmacy Practice, School of Pharmacy and Health Sciences, United States International University-Africa, P. O. Box 14634-00800, Nairobi, Kenya.
| | - Eman Elhassan
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban, South Africa
| | - Usri H Ibrahim
- Discipline of Human Physiology, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Thirumala Govender
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban, South Africa.
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Fang P, Yu S, Ma X, Hou L, Li T, Gao K, Wang Y, Sun Q, Shang L, Liu Q, Nie M, Yang J. Applications of tandem mass spectrometry (MS/MS) in antimicrobial peptides field: Current state and new applications. Heliyon 2024; 10:e28484. [PMID: 38601527 PMCID: PMC11004759 DOI: 10.1016/j.heliyon.2024.e28484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/12/2024] Open
Abstract
Antimicrobial peptides (AMPs) constitute a group of small molecular peptides that exhibit a wide range of antimicrobial activity. These peptides are abundantly present in the innate immune system of various organisms. Given the rise of multidrug-resistant bacteria, microbiological studies have identified AMPs as potential natural antibiotics. In the context of antimicrobial resistance across various human pathogens, AMPs hold considerable promise for clinical applications. However, numerous challenges exist in the detection of AMPs, particularly by immunological and molecular biological methods, especially when studying of newly discovered AMPs in proteomics. This review outlines the current status of AMPs research and the strategies employed in their development, considering resent discoveries and methodologies. Subsequently, we focus on the advanced techniques of mass spectrometry for the quantification of AMPs in diverse samples, and analyzes their application, advantages, and limitations. Additionally, we propose suggestions for the future development of tandem mass spectrometry for the detection of AMPs.
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Affiliation(s)
- Panpan Fang
- Zhengzhou Key Laboratory of Children's Infection and Immunity, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, PR China
| | - Songlin Yu
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, 100730, PR China
| | - Xiaoli Ma
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, 100730, PR China
| | - Lian Hou
- Department of Laboratory Medicine, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, 100730, PR China
| | - Tiewei Li
- Zhengzhou Key Laboratory of Children's Infection and Immunity, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, PR China
| | - Kaijie Gao
- Zhengzhou Key Laboratory of Children's Infection and Immunity, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, PR China
| | - Yingyuan Wang
- Department of Neonatal Intensive Care Unit, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, PR China
| | - Qianqian Sun
- Zhengzhou Key Laboratory of Children's Infection and Immunity, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, PR China
| | - Lujun Shang
- Department of Laboratory Medicine, Guizhou Provincial People's Hospital, Guiyang, 550004, PR China
| | - Qianqian Liu
- Zhengzhou Key Laboratory of Children's Infection and Immunity, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, PR China
| | - Manjie Nie
- Zhengzhou Key Laboratory of Children's Infection and Immunity, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, PR China
| | - Junmei Yang
- Zhengzhou Key Laboratory of Children's Infection and Immunity, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, PR China
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25
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Lim J, Myung H, Lim D, Song M. Antimicrobial peptide thanatin fused endolysin PA90 (Tha-PA90) for the control of Acinetobacter baumannii infection in mouse model. J Biomed Sci 2024; 31:36. [PMID: 38622637 PMCID: PMC11020296 DOI: 10.1186/s12929-024-01027-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 04/08/2024] [Indexed: 04/17/2024] Open
Abstract
BACKGROUND This study addresses the urgent need for infection control agents driven by the rise of drug-resistant pathogens such as Acinetobacter baumannii. Our primary aim was to develop and assess a novel endolysin, Tha-PA90, designed to combat these challenges. METHODS Tha-PA90 incorporates an antimicrobial peptide (AMP) called thanatin at its N-terminus, enhancing bacterial outer membrane permeability and reducing host immune responses. PA90 was selected as the endolysin component. The antibacterial activity of the purified Tha-PA90 was evaluated using an in vitro colony-forming unit (CFU) reduction assay and a membrane permeability test. A549 cells were utilized to measure the penetration into the cytosol and the cytotoxicity of Tha-PA90. Finally, infection control was monitored in A. baumannii infected mice following the intraperitoneal administration of Tha-PA90. RESULTS Tha-PA90 demonstrated remarkable in vitro efficacy, completely eradicating A. baumannii strains, even drug-resistant variants, at a low concentration of 0.5 μM. Notably, it outperformed thanatin, achieving only a < 3-log reduction at 4 μM. Tha-PA90 exhibited 2-3 times higher membrane permeability than a PA90 and thanatin mixture or PA90 alone. Tha-PA90 was found within A549 cells' cytosol with no discernible cytotoxic effects. Furthermore, Tha-PA90 administration extended the lifespan of A. baumannii-infected mice, reducing bacterial loads in major organs by up to 3 logs. Additionally, it decreased proinflammatory cytokine levels (TNF-α and IL-6), reducing the risk of sepsis from rapid bacterial lysis. Our findings indicate that Tha-PA90 is a promising solution for combating drug-resistant A. baumannii. Its enhanced efficacy, low cytotoxicity, and reduction of proinflammatory responses render it a potential candidate for infection control. CONCLUSIONS This study underscores the significance of engineered endolysins in addressing the pressing challenge of drug-resistant pathogens and offers insights into improved infection management strategies.
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Affiliation(s)
- Jeonghyun Lim
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Yongin, 17035, Republic of Korea
| | - Heejoon Myung
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Yongin, 17035, Republic of Korea
- LyseNTech Co., Ltd., Seongnam-Si, 13486, Republic of Korea
| | - Daejin Lim
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea.
| | - Miryoung Song
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Yongin, 17035, Republic of Korea.
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Vargiu M, Xu Y, Kuipers OP, Roelfes G. Selective Aza-Michael Addition to Dehydrated Amino Acids in Natural Antimicrobial Peptides. Chembiochem 2024; 25:e202400043. [PMID: 38334959 DOI: 10.1002/cbic.202400043] [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: 01/17/2024] [Revised: 02/07/2024] [Accepted: 02/09/2024] [Indexed: 02/10/2024]
Abstract
We report the efficient and site selective modification of non-canonical dehydroamino acids in ribosomally synthesized and post-transationally modified peptides (RiPPs) by β-amination. The singly modified thiopeptide Thiostrepton showed an up to 35-fold increase in water solubility, and minimum inhibitory concentration (MIC) assays showed that antimicrobial activity remained good, albeit lower than the unmodified peptide. Also the lanthipeptide nisin could be modified using this method.
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Affiliation(s)
- Michela Vargiu
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Yanli Xu
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands
| | - Gerard Roelfes
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands
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27
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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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28
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Zhao C, Yan S, Luo Y, Song Y, Xia X. Analyzing resistome in soil and Human gut: a study on the characterization and risk evaluation of antimicrobial peptide resistance. Front Microbiol 2024; 15:1352531. [PMID: 38591036 PMCID: PMC10999558 DOI: 10.3389/fmicb.2024.1352531] [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: 12/08/2023] [Accepted: 02/26/2024] [Indexed: 04/10/2024] Open
Abstract
Objective The limited existing knowledge regarding resistance to antimicrobial peptides (AMPs) is hindering their broad utilization. The aim of this study is to enhance the understanding of AMP resistance, a pivotal factor in the exploration of alternative drug development in response to the escalating challenge of antibiotic resistance. Methods We utilized metagenomic functional selection to analyze genes resistant to AMPs, with a specific focus on the microbiota in soil and the human gut. Through a combination of experimental methods and bioinformatics analyses, our investigation delved into the possibilities of the evolution of resistance to AMPs, as well as the transfer or interchange of resistance genes among the environment, the human body, and pathogens. Additionally, we examined the cross-resistance between AMPs and evaluated interactions among AMPs and conventional antibiotics. Results The presence of AMP resistance, including various resistance mechanisms, was observed in both soil and the human gut microbiota, as indicated by our findings. Significantly, the study underscored the facile evolution of AMP resistance and the potential for gene sharing or exchange among different environments. Notably, cross-resistance among AMPs was identified as a phenomenon, while cross-resistance between AMPs and antibiotics was found to be relatively infrequent. Conclusion The results of our study highlight the significance of taking a cautious stance when considering the extensive application of AMPs. It is imperative to thoroughly assess potential resistance risks, with a particular focus on the development of resistance to AMPs across diverse domains. A comprehensive grasp of these aspects is essential for making well-informed decisions and ensuring the responsible utilization of AMPs in the ongoing fight against antibiotic resistance.
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Affiliation(s)
| | | | | | - Yuzhu Song
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Xueshan Xia
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
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29
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Wang C, Ren YY, Han LM, Yi PC, Wang WX, Zhang CY, Chen XZ, Chi MZ, Wang A, Chen W, Hu CM. ApoE Mimetic Peptide COG1410 Kills Mycobacterium smegmatis via Directly Interfering ClpC's ATPase Activity. Antibiotics (Basel) 2024; 13:278. [PMID: 38534713 DOI: 10.3390/antibiotics13030278] [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: 02/05/2024] [Revised: 03/10/2024] [Accepted: 03/13/2024] [Indexed: 03/28/2024] Open
Abstract
Antimicrobial peptides (AMPs) hold promise as alternatives to combat bacterial infections, addressing the urgent global threat of antibiotic resistance. COG1410, a synthetic peptide derived from apolipoprotein E, has exhibited potent antimicrobial properties against various bacterial strains, including Mycobacterium smegmatis. However, our study reveals a previously unknown resistance mechanism developed by M. smegmatis against COG1410 involving ClpC. Upon subjecting M. smegmatis to serial passages in the presence of sub-MIC COG1410, resistance emerged. The comparative genomic analysis identified a point mutation in ClpC (S437P), situated within its middle domain, which led to high resistance to COG1410 without compromising bacterial fitness. Complementation of ClpC in mutant restored bacterial sensitivity. In-depth analyses, including transcriptomic profiling and in vitro assays, uncovered that COG1410 interferes with ClpC at both transcriptional and functional levels. COG1410 not only stimulated the ATPase activity of ClpC but also enhanced the proteolytic activity of Clp protease. SPR analysis confirmed that COG1410 directly binds with ClpC. Surprisingly, the identified S437P mutation did not impact their binding affinity. This study sheds light on a unique resistance mechanism against AMPs in mycobacteria, highlighting the pivotal role of ClpC in this process. Unraveling the interplay between COG1410 and ClpC enriches our understanding of AMP-bacterial interactions, offering potential insights for developing innovative strategies to combat antibiotic resistance.
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Affiliation(s)
- Chun Wang
- Department of Tuberculosis, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing 210003, China
| | - Yun-Yao Ren
- Clinical Research Center, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing 210003, China
| | - Li-Mei Han
- Department of Tuberculosis, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing 210003, China
| | - Peng-Cheng Yi
- Department of Tuberculosis, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing 210003, China
| | - Wei-Xiao Wang
- Clinical Research Center, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing 210003, China
| | - Cai-Yun Zhang
- Clinical Research Center, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing 210003, China
| | - Xiu-Zhen Chen
- Clinical Research Center, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing 210003, China
| | - Ming-Zhe Chi
- State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai 200433, China
| | - Apeng Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Wei Chen
- Clinical Research Center, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing 210003, China
| | - Chun-Mei Hu
- Department of Tuberculosis, The Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Nanjing 210003, China
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30
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Xu Y, Wang H, Ye S, Liang Z, Chen Z, Wang X, Zhou L, Yan B. Goethite adaptation prompts alterations in antibiotic susceptibility and suppresses development of antibiotic resistance in bacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 916:170248. [PMID: 38244632 DOI: 10.1016/j.scitotenv.2024.170248] [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: 10/23/2023] [Revised: 01/13/2024] [Accepted: 01/15/2024] [Indexed: 01/22/2024]
Abstract
Understanding the impact of environmental factors on antibiotic sensitivity and the emergence of antibiotic resistance in microorganism is crucial for antibiotics management and environmental risk assessment. Natural materials, like mineral particles, are prevalent in aquatic and terrestrial ecosystems. However, it remains unclear how microorganism adapt to the physical stress of mineral particles and whether this adaptation influences antibiotic sensitivity and the evolution of antibiotic resistance. In this study, the model bacterium Escherichia coli (E. coli) was exposed to the mineral particle goethite for 30 generations. Adaptive morphogenesis, including an increase in the fraction of spherical bacteria, variations in bacterial mobility, a slightly increased cell membrane thickness, and genome-wide changes in the transcriptomic profile, were observed in adapted E. coli samples to counteract the stress. Moreover, the goethite adapted E. coli showed increased susceptibility to antibiotics including amoxicillin and tetracycline, and decreased susceptibility to kanamycin compared to its ancestral counterparts. These alterations in antibiotic susceptibility in the adapted E. coli were not heritable, as evidenced by the gradual recovery of antibiotic tolerance in cells with the cessation of goethite exposure. Transcriptomic data and a series of experiments suggested that these changes may be associated with variations in cell membrane property and iron metabolism. In addition, the evolution of antibiotic resistance in adapted cells occurred at a slower rate compared to their ancestral counterparts. For instance, E. coli adapted to goethite at a concentration of 1 mg/mL did not acquire antibiotic resistance even after 13 generations, probably due to its poor biofilm-formation capacity. Our findings underscore the occurrence of microbial adaptation to goethite, which influenced antibiotic sensitivity and decelerated the development of resistance in microorganisms. This insight contributes to our comprehension of the natural dynamics surrounding the evolution of antibiotic resistance and opens new perspectives for addressing this issue through nanotechnology-based approaches.
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Affiliation(s)
- Yongtao Xu
- Institute of Environmental Research at Great Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, Guangdong 510006, PR China
| | - Haiqing Wang
- College of Biological and Environmental Engineering, Shandong University of Aeronautics, Binzhou, Shandong 256600, China
| | - Sheng Ye
- Institute of Environmental Research at Great Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, Guangdong 510006, PR China
| | - Zhenda Liang
- Institute of Environmental Research at Great Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, Guangdong 510006, PR China
| | - Zhiquan Chen
- Institute of Environmental Research at Great Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, Guangdong 510006, PR China
| | - Xiaohong Wang
- Institute of Environmental Research at Great Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, Guangdong 510006, PR China.
| | - Li Zhou
- Institute of Environmental Research at Great Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, Guangdong 510006, PR China.
| | - Bing Yan
- Institute of Environmental Research at Great Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, Guangdong 510006, PR China
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31
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Verma H, Mihooliya KN, Nandal J, Sahoo DK. Studies on a new antimicrobial peptide from Vibrio proteolyticus MT110. Prep Biochem Biotechnol 2024; 54:193-206. [PMID: 37184469 DOI: 10.1080/10826068.2023.2209892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The marine environment is known for its vast diversity of the microbial population; however, less explored for bioactive compounds. In this study, an AMP produced by a new marine isolate, Vibrio proteolyticus MT110, showed broad-spectrum antimicrobial activity against Gram-positive and Gram-negative bacteria. The AMP was purified to homogeneity using ethyl acetate extraction followed by RP-HPLC, and LC-MS analysis showed its molecular weight as 980 Da. The MIC of AMP (peptide-MT110) was obtained in the 7.81-31.25 µg/mL range against different indicator strains. Peptide-MT110 showed stability of its antimicrobial activity at 15-121 °C and pH 4-10 and in the presence of various hydrolytic enzymes. The peaks at 1536 cm-1 and 1712 cm-1 wavenumbers in FTIR spectra confirmed the peptidic nature of AMP, and its amino acid analysis confirmed the presence of tyrosine and isoleucine. The antibacterial activity of peptide-MT110 is confirmed by PI assay and TEM. The optimization of peptide-MT110 production using statistical methods resulted in a 2.64-fold higher production. The physicochemical properties and stability in wide pH and temperature ranges showed the potential of peptide-MT110 for its development as a drug candidate. This is believed to be the first report on an AMP from Vibrio proteolyticus.
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Affiliation(s)
- Himanshu Verma
- Biochemical Engineering Research and Process Development Centre, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Kanti N Mihooliya
- Biochemical Engineering Research and Process Development Centre, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Jitender Nandal
- Biochemical Engineering Research and Process Development Centre, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Debendra K Sahoo
- Biochemical Engineering Research and Process Development Centre, CSIR-Institute of Microbial Technology, Chandigarh, India
- Accademy of Scientific and Innovative Research, New Delhi, India
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32
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Li C, Zhou Z, Wang W, Zhao Y, Yin X, Meng Y, Zhao P, Wang M, Liu X, Wang X, Wang S, Ren B, Zhang L, Xia X. Development of Antibacterial Peptides with Membrane Disruption and Folate Pathway Inhibitory Activities against Methicillin-Resistant Staphylococcus aureus. J Med Chem 2024; 67:1044-1060. [PMID: 38173250 DOI: 10.1021/acs.jmedchem.3c01360] [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
Antimicrobial peptides (AMPs) offer an opportunity to overcome multidrug resistance. Here, novel peptides were designed based on AMP fragments derived from sea cucumber hemolytic lectin to enhance anti-methicillin-resistant Staphylococcus aureus (MRSA) activity with less side effects. Two designed peptides, CGS19 (LARVARRVIRFIRRAW-NH2) and CGS20 (RRRLARRLIFFIRRAW-NH2), exhibited strong antibacterial activities against clinically isolated MRSA with MICs of 3-6 μM, but no obvious cytotoxicity was observed. Consistently, CGS19 and CGS20 exerted rapid bactericidal activity and effectively induced 5.9 and 5.8 log reduction of MRSA counts in mouse subeschar, respectively. Further, CGS19 and CGS20 kill bacteria not only through disturbing membrane integrity but also by binding formate-tetrahydrofolate ligase, a key enzyme in the folate metabolism pathway, thereby inhibiting the folate pathway of MRSA. CGS19 and CGS20 are promising lead candidates for drug development against MRSA infection. The dual mechanisms on the identical peptide sequence or scaffold might be an underappreciated manner of treating life-threatening pathogens.
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Affiliation(s)
- Chunlei Li
- Shandong Provincial Key Laboratory for Bio-Manufacturing, Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250103, China
- Department of Pharmacy, Qilu Hospital, Cheloo College of Medicine, Shandong University, Jinan 250012, China
| | - Ziyi Zhou
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China School of Stomatology, Sichuan University, Chengdu 610041, China
| | - Weitao Wang
- Shandong Provincial Key Laboratory for Bio-Manufacturing, Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250103, China
| | - Yanqiu Zhao
- Shandong Provincial Key Laboratory for Bio-Manufacturing, Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250103, China
| | - Xin Yin
- Shandong Provincial Key Laboratory for Bio-Manufacturing, Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250103, China
| | - Yiwei Meng
- Shandong Provincial Key Laboratory for Bio-Manufacturing, Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250103, China
| | - Peipei Zhao
- Shandong Provincial Key Laboratory for Bio-Manufacturing, Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250103, China
| | - Mengmeng Wang
- Shandong Provincial Key Laboratory for Bio-Manufacturing, Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250103, China
| | - Xueting Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Xinye Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Shenlin Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Biao Ren
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China School of Stomatology, Sichuan University, Chengdu 610041, China
| | - Lixin Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Xuekui Xia
- Shandong Provincial Key Laboratory for Bio-Manufacturing, Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250103, China
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33
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He S, Deber CM. Interaction of designed cationic antimicrobial peptides with the outer membrane of gram-negative bacteria. Sci Rep 2024; 14:1894. [PMID: 38253659 PMCID: PMC10803810 DOI: 10.1038/s41598-024-51716-1] [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: 07/27/2023] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
The outer membrane (OM) is a hallmark feature of gram-negative bacteria that provides the species with heightened resistance against antibiotic threats while cationic antimicrobial peptides (CAPs) are natural antibiotics broadly recognized for their ability to disrupt bacterial membranes. It has been well-established that lipopolysaccharides present on the OM are among major targets of CAP activity against gram-negative species. Here we investigate how the relative distribution of charged residues along the primary peptide sequence, in conjunction with its overall hydrophobicity, affects such peptide-OM interactions in the natural CAP Ponericin W1. Using a designed peptide library derived from Ponericin W1, we determined that the consecutive placement of Lys residues at the peptide N- or C-terminus (ex. "PonN": KKKKKKWLGSALIGALLPSVVGLFQ) enhances peptide binding affinity to OM lipopolysaccharides compared to constructs where Lys residues are interspersed throughout the primary sequence (ex. "PonAmp": WLKKALKIGAKLLPSVVKLFKGSGQ). Antimicrobial activity against multidrug resistant strains of Pseudomonas aeruginosa was similarly found to be highest among Lys-clustered sequences. Our findings suggest that while native Ponericin W1 exerts its initial activity at the OM, Lys-clustering may be a promising means to enhance potency towards this interface, thereby augmenting peptide entry and activity at the IM, with apparent advantage against multidrug-resistant species.
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Affiliation(s)
- Shelley He
- Program in Molecular Medicine, Research Institute, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, M5S 1A8, Canada
| | - Charles M Deber
- Program in Molecular Medicine, Research Institute, Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.
- Department of Biochemistry, University of Toronto, Toronto, M5S 1A8, Canada.
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34
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Maeda T, Furusawa C. Laboratory Evolution of Antimicrobial Resistance in Bacteria to Develop Rational Treatment Strategies. Antibiotics (Basel) 2024; 13:94. [PMID: 38247653 PMCID: PMC10812413 DOI: 10.3390/antibiotics13010094] [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: 12/25/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 01/23/2024] Open
Abstract
Laboratory evolution studies, particularly with Escherichia coli, have yielded invaluable insights into the mechanisms of antimicrobial resistance (AMR). Recent investigations have illuminated that, with repetitive antibiotic exposures, bacterial populations will adapt and eventually become tolerant and resistant to the drugs. Through intensive analyses, these inquiries have unveiled instances of convergent evolution across diverse antibiotics, the pleiotropic effects of resistance mutations, and the role played by loss-of-function mutations in the evolutionary landscape. Moreover, a quantitative analysis of multidrug combinations has shed light on collateral sensitivity, revealing specific drug combinations capable of suppressing the acquisition of resistance. This review article introduces the methodologies employed in the laboratory evolution of AMR in bacteria and presents recent discoveries concerning AMR mechanisms derived from laboratory evolution. Additionally, the review outlines the application of laboratory evolution in endeavors to formulate rational treatment strategies.
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Affiliation(s)
- Tomoya Maeda
- Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan
- Center for Biosystems Dynamics Research, RIKEN, 6-2-3 Furuedai, Suita 565-0874, Japan;
| | - Chikara Furusawa
- Center for Biosystems Dynamics Research, RIKEN, 6-2-3 Furuedai, Suita 565-0874, Japan;
- Universal Biology Institute, The University of Tokyo, 7-3-1 Hongo, Tokyo 113-0033, Japan
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35
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Wichmann N, Gruseck R, Zumstein M. Hydrolysis of Antimicrobial Peptides by Extracellular Peptidases in Wastewater. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:717-726. [PMID: 38103013 PMCID: PMC10785756 DOI: 10.1021/acs.est.3c06506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 11/10/2023] [Accepted: 12/01/2023] [Indexed: 12/17/2023]
Abstract
Several antimicrobial peptides (AMPs) are emerging as promising novel antibiotics. When released into wastewater streams after use, AMPs might be hydrolyzed and inactivated by wastewater peptidases─resulting in a reduced release of active antimicrobials into wastewater-receiving environments. A key step towards a better understanding of the fate of AMPs in wastewater systems is to investigate the activity and specificity of wastewater peptidases. Here, we quantified peptidase activity in extracellular extracts from different stages throughout the wastewater treatment process. For all four tested municipal wastewater treatment plants, we detected highest activity in raw wastewater. Complementarily, we assessed the potential of enzymes in raw wastewater extracts to biotransform 10 selected AMPs. We found large variations in the susceptibility of AMPs to enzymatic transformation, indicating substantial substrate specificity of extracted enzymes. To obtain insights into peptidase specificities, we searched for hydrolysis products of rapidly biotransformed AMPs and quantified selected products using synthetic standards. We found that hydrolysis occurred at specific sites and that these sites were remarkably conserved across the four tested wastewaters. Together, these findings provide insights into the fate of AMPs in wastewater systems and can inform the selection and design of peptide-based antibiotics that are hydrolyzable by wastewater peptidases.
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Affiliation(s)
- Natalie Wichmann
- Division
of Environmental Geosciences, Centre for Microbiology and Environmental
Systems Science, University of Vienna, Josef-Holaubek-Platz 2, Vienna 1090, Austria
- Department
of Environmental Microbiology, Swiss Federal
Institute of Aquatic Science and Technology (Eawag), Überlandstrasse 133, Dübendorf 8600, Switzerland
| | - Richard Gruseck
- Division
of Environmental Geosciences, Centre for Microbiology and Environmental
Systems Science, University of Vienna, Josef-Holaubek-Platz 2, Vienna 1090, Austria
| | - Michael Zumstein
- Division
of Environmental Geosciences, Centre for Microbiology and Environmental
Systems Science, University of Vienna, Josef-Holaubek-Platz 2, Vienna 1090, Austria
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36
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Lei R, Yang C, Sun Y, Li D, Hao L, Li Y, Wu S, Li H, Lan C, Fang X. Turning cationic antimicrobial peptide KR-12 into self-assembled nanobiotics with potent bacterial killing and LPS neutralizing activities. NANOSCALE 2024; 16:887-902. [PMID: 38105768 DOI: 10.1039/d3nr05174a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Gram-negative sepsis has become a substantial and escalating global healthcare challenge due to the growing antibiotic resistance crisis and the sluggish development of new antibiotics. LL-37, a unique Cathelicidin species found in humans, exhibits a wide range of bioactive properties, including direct bactericidal effects, inflammation regulation, and LPS neutralization. KR-12, the smallest yet potent peptide fragment of LL-37, has been modified to create more effective antimicrobials. In this study, we designed two myristoylated derivatives of KR-12, referred to as Myr-KR-12N and Myr-KR-12C. These derivatives displayed remarkable ability to spontaneously assemble into nanoparticles when mixed with deionized water. Myristoylated KR-12 derivatives exhibited broad-spectrum and intensified bactericidal activity by disrupting bacterial cell membranes. In particular, Myr-KR-12N showed superior capability to rescue mice from lethal E. coli-induced sepsis in comparison with the conventional antibiotic meropenem. We also confirmed that the myristoylated KR-12 nanobiotic possesses significant LPS binding capacity and effectively reduces inflammation in vitro. In an in vivo context, Myr-KR-12N outperformed polymyxin B in rescuing mice from LPS-induced sepsis. Crucially, toxicological assessments revealed that neither Myr-KR-12N nor Myr-KR-12C nanobiotics induced meaningful hemolysis or caused damage to the liver and kidneys. Collectively, our study has yielded an innovative nanobiotic with dual capabilities of bactericidal action and LPS-neutralization, offering substantial promise for advancing the clinical translation of antimicrobial peptides and the development of novel antibiotics. This addresses the critical need for effective solutions to combat Gram-negative sepsis, a pressing global medical challenge.
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Affiliation(s)
- Ruyi Lei
- Department of Emergency Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China.
| | - Chujun Yang
- Department of Emergency Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China.
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450052, China
| | - Yaqi Sun
- China National Clinical Research Center for Child Health, Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310052, China
| | - Dejian Li
- Department of Emergency Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China.
| | - Liman Hao
- Department of Anesthesiology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China.
| | - Yang Li
- Department of Anesthesiology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China.
| | - Shuijing Wu
- Department of Anesthesiology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China.
| | - Hui Li
- Department of Anesthesiology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China.
| | - Chao Lan
- Department of Emergency Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China.
| | - Xiangming Fang
- Department of Anesthesiology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China.
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37
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Hirano M, Yokoo H, Ohoka N, Ito T, Misawa T, Oba M, Inoue T, Demizu Y. Rational Design of Amphipathic Antimicrobial Peptides with Alternating L-/D-Amino Acids That Form Helical Structures. Chem Pharm Bull (Tokyo) 2024; 72:149-154. [PMID: 38296556 DOI: 10.1248/cpb.c23-00465] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Antimicrobial peptides (AMPs) are promising therapeutic agents against bacteria. We have previously reported an amphipathic AMP Stripe composed of cationic L-Lys and hydrophobic L-Leu/L-Ala residues, and Stripe exhibited potent antimicrobial activity against Gram-positive and Gram-negative bacteria. Gramicidin A (GA), composed of repeating sequences of L- and D-amino acids, has a unique β6.3-helix structure and exhibits broad antimicrobial activity. Inspired by the structural properties and antimicrobial activities of LD-alternating peptides such as GA, in this study, we designed Stripe derivatives with LD-alternating sequences. We found that simply alternating L- and D-amino acids in the Stripe sequence to give StripeLD caused a reduction in antimicrobial activity. In contrast, AltStripeLD, with cationic and hydrophobic amino acids rearranged to yield an amphipathic distribution when the peptide adopts a β6.3-helix, displayed higher antimicrobial activity than AltStripe. These results suggest that alternating L-/D-cationic and L-/D-hydrophobic amino acids in accordance with the helical structure of an AMP may be a useful way to improve antimicrobial activity and develop new AMP drugs.
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Affiliation(s)
- Motoharu Hirano
- National Institute of Health Sciences
- Graduate School of Medical Life Science, Yokohama City University
| | - Hidetomo Yokoo
- National Institute of Health Sciences
- Medical Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine
| | | | - Takahito Ito
- National Institute of Health Sciences
- Graduate School of Medical Life Science, Yokohama City University
| | | | - Makoto Oba
- Medical Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine
| | | | - Yosuke Demizu
- National Institute of Health Sciences
- Graduate School of Medical Life Science, Yokohama City University
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38
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Dwivedi M, Parmar MD, Mukherjee D, Yadava A, Yadav H, Saini NP. Biochemistry, Mechanistic Intricacies, and Therapeutic Potential of Antimicrobial Peptides: An Alternative to Traditional Antibiotics. Curr Med Chem 2024; 31:6110-6139. [PMID: 37818561 DOI: 10.2174/0109298673268458230926105224] [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: 06/21/2023] [Revised: 08/03/2023] [Accepted: 08/24/2023] [Indexed: 10/12/2023]
Abstract
The emergence of drug-resistant strains of pathogens becomes a major obstacle to treating human diseases. Antibiotics and antivirals are in the application for a long time but now these drugs are not much effective anymore against disease-causing drugresistant microbes and gradually it is becoming a serious complication worldwide. The development of new antibiotics cannot be a stable solution to treat drug-resistant strains due to their evolving nature and escaping antibiotics. At this stage, antimicrobial peptides (AMPs) may provide us with novel therapeutic leads against drug-resistant pathogens. Structurally, antimicrobial peptides are mostly α-helical peptide molecules with amphiphilic properties that carry the positive charge (cationic) and belong to host defense peptides. These positively charged AMPs can interact with negatively charged bacterial cell membranes and may cause the alteration in electrochemical potential on bacterial cell membranes and consequently lead to the death of microbial cells. In the present study, we will elaborate on the implication of AMPs in the treatment of various diseases along with their specific structural and functional properties. This review will provide information which assists in the development of new synthetic peptide analogues to natural AMPs. These analogues will eliminate the limitations of natural AMPs like toxicity and severe hemolytic activities.
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Affiliation(s)
- Manish Dwivedi
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, 226028, India
| | - Meet Dineshbhai Parmar
- Department of Biological Sciences and Biotechnology, Institute of Advanced Research, Gandhinagar, Gujarat, India
| | | | - Anuradha Yadava
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, 226028, India
| | - Hitendra Yadav
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, 226028, India
| | - Nandini Pankaj Saini
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, 226028, India
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39
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Al-Rasheed AA, Garba B, Handool KO, Al-Jashamy KA, Odhah MNA, Dirie NI, Daud HM. An in-vivo experimental evaluation of the efficacy of fish-derived antimicrobial peptides against multidrug-resistant Pseudomonas aeruginosa. Pan Afr Med J 2023; 46:112. [PMID: 38465008 PMCID: PMC10924623 DOI: 10.11604/pamj.2023.46.112.38578] [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: 12/20/2022] [Accepted: 12/16/2023] [Indexed: 03/12/2024] Open
Abstract
Introduction due to the fact that antimicrobial peptides antimicrobial peptides (AMPs) from climbing perch have not been fully explored for their antimicrobial potency, this investigation was undertaken to explore that possibility. Methods antimicrobial peptides (AMPs) from the mucous secretion of climbing perch were obtained and an in-vivo analysis was conducted using mice. Results the results showed inhibitory effects on multidrug-resistant multidrug-resistant Pseudomonas aeruginosa with reduced mortality from 100% among the non-treated group to 25%. Similarly, the level of serum transaminase enzymes (AST and ALT), creatinine levels, and pro-inflammatory cytokines (TNF-α and IL-6) were all found to be higher in the non-treatment group compared to the AMP-treatment group. Also, extensive tissue damage in the lung, liver, and spleen of the non-treated control group mice was observed based on the histopathological lesions recorded. As expected, AMPs from climbing perch significantly alleviated multidrug-resistant P. aeruginosa infection in-vivo and produced enhanced therapeutic efficacy superior to the ciprofloxacin treatment. Conclusion this study provides insight into the potential antimicrobial activity of fish innate immune system-derived peptides that could serve as a candidate for the substitute of antibiotics.
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Affiliation(s)
- Agharid Ali Al-Rasheed
- Department of Microbiology, Faculty of Veterinary Medicine, Tikrit University, Tikrit, Iraq
- Department of Clinical Studies, Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Selangor Darul Ehsan, Malaysia
| | - Bashiru Garba
- Department of Veterinary Public Health and Preventive Medicine, Faculty of Veterinary Medicine, Usmanu Danfodiyo University, Sokoto, Nigeria
| | | | - Karim Alwan Al-Jashamy
- Department of Radiology and Sonar Technology, Bilad Alrafidain University College, Baghdad, Iraq
| | - Mohamed Naji Ahmed Odhah
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Thamar University, Dhamar, Yemen
| | - Najib Isse Dirie
- Department of Urology, Dr. Sumait Hospital, Faculty of Medicine and Health Sciences, SIMAD University, Mogadishu, Somalia
| | - Hassan Mohd Daud
- Department of Clinical Studies, Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Selangor Darul Ehsan, Malaysia
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Salinas-Restrepo C, Naranjo-Duran AM, Quintana J, Bueno J, Guzman F, Hoyos Palacio LM, Segura C. Short Antimicrobial Peptide Derived from the Venom Gland Transcriptome of Pamphobeteus verdolaga Increases Gentamicin Susceptibility of Multidrug-Resistant Klebsiella pneumoniae. Antibiotics (Basel) 2023; 13:6. [PMID: 38275316 PMCID: PMC10812672 DOI: 10.3390/antibiotics13010006] [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: 10/11/2023] [Revised: 11/07/2023] [Accepted: 11/17/2023] [Indexed: 01/27/2024] Open
Abstract
Infectious diseases account for nine percent of annual human deaths, and the widespread emergence of antimicrobial resistances threatens to significantly increase this number in the coming decades. The prospect of antimicrobial peptides (AMPs) derived from venomous animals presents an interesting alternative for developing novel active pharmaceutical ingredients (APIs). Small, cationic and amphiphilic peptides were predicted from the venom gland transcriptome of Pamphobeteus verdolaga using a custom database of the arthropod's AMPs. Ninety-four candidates were chemically synthesized and screened against ATCC® strains of Escherichia coli and Staphylococcus aureus. Among them, one AMP, named PvAMP66, showed broad-spectrum antimicrobial properties with selectivity towards Gram-negative bacteria. It also exhibited activity against Pseudomonas aeruginosa, as well as both an ATCC® and a clinically isolated multidrug-resistant (MDR) strain of K. pneumoniae. The scanning electron microscopy analysis revealed that PvAMP66 induced morphological changes of the MDR K. pneumoniae strain suggesting a potential "carpet model" mechanism of action. The isobologram analysis showed an additive interaction between PvAMP66 and gentamicin in inhibiting the growth of MDR K. pneumoniae, leading to a ten-fold reduction in gentamicin's effective concentration. A cytotoxicity against erythrocytes or peripheral blood mononuclear cells was observed at concentrations three to thirteen-fold higher than those exhibited against the evaluated bacterial strains. This evidence suggests that PvAMP66 can serve as a template for the development of AMPs with enhanced activity and deserves further pre-clinical studies as an API in combination therapy.
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Affiliation(s)
- Cristian Salinas-Restrepo
- Grupo Toxinología, Alternativas Terapéuticas y Alimentarias, Facultad de Ciencias Farmacéuticas y Alimentarias, Universidad de Antioquia, Medellín 050012, Colombia; (C.S.-R.); (A.M.N.-D.)
| | - Ana María Naranjo-Duran
- Grupo Toxinología, Alternativas Terapéuticas y Alimentarias, Facultad de Ciencias Farmacéuticas y Alimentarias, Universidad de Antioquia, Medellín 050012, Colombia; (C.S.-R.); (A.M.N.-D.)
| | - Juan Quintana
- Facultad de Medicina, Universidad Cooperativa de Colombia, Medellín 050012, Colombia;
| | - Julio Bueno
- Grupo Reproducción, Facultad de Medicina, Universidad de Antioquia, Medellín 050012, Colombia;
| | - Fanny Guzman
- Núcleo Biotecnología Curauma (NBC), Pontificia Universidad Católica de Valparaíso, Valparaíso 3100000, Chile;
| | - Lina M. Hoyos Palacio
- Escuela de Ciencias de la Salud, Grupo de Investigación Biología de Sistemas, Universidad Pontificia Bolivariana, Medellín 050031, Colombia;
| | - Cesar Segura
- Grupo Malaria, Facultad de Medicina, Universidad de Antioquia, Medellín 050012, Colombia
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Pipiya SO, Kudzhaev AM, Mirzoeva NZ, Mokrushina YA, Ziganshin RH, Komlev AS, Petrova PE, Smirnov IV, Gabibov AG, Shamova OV, Terekhov SS. Bioengineering the Antimicrobial Activity of Yeast by Recombinant Thanatin Production. Antibiotics (Basel) 2023; 12:1719. [PMID: 38136753 PMCID: PMC10741026 DOI: 10.3390/antibiotics12121719] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
The global spread of antibiotic resistance marks the end of the era of conventional antibiotics. Mankind desires new molecular tools to fight pathogenic bacteria. In this regard, the development of new antimicrobials based on antimicrobial peptides (AMPs) is again of particular interest. AMPs have various mechanisms of action on bacterial cells. Moreover, AMPs have been reported to be efficient in preclinical studies, demonstrating a low level of resistance formation. Thanatin is a small, beta-hairpin antimicrobial peptide with a bacterial-specific mode of action, predetermining its low cytotoxicity toward eukaryotic cells. This makes thanatin an exceptional candidate for new antibiotic development. Here, a microorganism was bioengineered to produce an antimicrobial agent, providing novel opportunities in antibiotic research through the directed creation of biocontrol agents. The constitutive heterologous production of recombinant thanatin (rThan) in the yeast Pichia pastoris endows the latter with antibacterial properties. Optimized expression and purification conditions enable a high production level, yielding up to 20 mg/L of rThan from the culture medium. rThan shows a wide spectrum of activity against pathogenic bacteria, similarly to its chemically synthesized analogue. The designed approach provides new avenues for AMP engineering and creating live biocontrol agents to fight antibiotic resistance.
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Affiliation(s)
- Sofiya O. Pipiya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (A.M.K.); (N.Z.M.); (Y.A.M.); (R.H.Z.); (I.V.S.); (A.G.G.)
| | - Arsen M. Kudzhaev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (A.M.K.); (N.Z.M.); (Y.A.M.); (R.H.Z.); (I.V.S.); (A.G.G.)
| | - Nisso Z. Mirzoeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (A.M.K.); (N.Z.M.); (Y.A.M.); (R.H.Z.); (I.V.S.); (A.G.G.)
| | - Yuliana A. Mokrushina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (A.M.K.); (N.Z.M.); (Y.A.M.); (R.H.Z.); (I.V.S.); (A.G.G.)
| | - Rustam H. Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (A.M.K.); (N.Z.M.); (Y.A.M.); (R.H.Z.); (I.V.S.); (A.G.G.)
| | - Alexey S. Komlev
- Institute of Experimental Medicine, WCRC “Center for Personalized Medicine”, Saint-Petersburg 197022, Russia; (A.S.K.); (P.E.P.); (O.V.S.)
| | - Polina E. Petrova
- Institute of Experimental Medicine, WCRC “Center for Personalized Medicine”, Saint-Petersburg 197022, Russia; (A.S.K.); (P.E.P.); (O.V.S.)
| | - Ivan V. Smirnov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (A.M.K.); (N.Z.M.); (Y.A.M.); (R.H.Z.); (I.V.S.); (A.G.G.)
- Department of Chemistry, Lomonosov Mscow State University, Moscow 119991, Russia
| | - Alexander G. Gabibov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (A.M.K.); (N.Z.M.); (Y.A.M.); (R.H.Z.); (I.V.S.); (A.G.G.)
- Department of Chemistry, Lomonosov Mscow State University, Moscow 119991, Russia
| | - Olga V. Shamova
- Institute of Experimental Medicine, WCRC “Center for Personalized Medicine”, Saint-Petersburg 197022, Russia; (A.S.K.); (P.E.P.); (O.V.S.)
- Department of Biochemistry, Saint Petersburg State University, Saint-Petersburg 199034, Russia
| | - Stanislav S. Terekhov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; (A.M.K.); (N.Z.M.); (Y.A.M.); (R.H.Z.); (I.V.S.); (A.G.G.)
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42
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Qi G, Tang Y, Shi L, Zhuang J, Liu X, Liu B. Capsule Shedding and Membrane Binding Enhanced Photodynamic Killing of Gram-Negative Bacteria by a Unimolecular Conjugated Polyelectrolyte. NANO LETTERS 2023; 23:10374-10382. [PMID: 37921703 DOI: 10.1021/acs.nanolett.3c02965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
The development of new antimicrobial agents to treat infections caused by Gram-negative bacteria is of paramount importance due to increased antibiotic resistance worldwide. Herein, we show that a water-soluble porphyrin-cored hyperbranched conjugated polyelectrolyte (PorHP) exhibits high photodynamic bactericidal activity against the Gram-negative bacteria tested, including a multidrug-resistant (MDR) pathogen, while demonstrating low cytotoxicity toward mammalian cells. Comprehensive analyses reveal that the antimicrobial activity of PorHP proceeds via a multimodal mechanism by effective bacterial capsule shedding, strong bacterial outer membrane binding, and singlet oxygen generation. Through this multimodal antimicrobial mechanism, PorHP displays significant performance for Gram-negative bacteria with >99.9% photodynamic killing efficacy. Overall, PorHP shows great potential as an antimicrobial agent in fighting the growing threat of Gram-negative bacteria.
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Affiliation(s)
- Guobin Qi
- Department of Chemical and Biomolecular Engineering, National University of Singapore (Singapore), 4 Engineering Drive 4, Singapore 117585
| | - Yufu Tang
- Department of Chemical and Biomolecular Engineering, National University of Singapore (Singapore), 4 Engineering Drive 4, Singapore 117585
| | - Leilei Shi
- Precision Research Center for Refractory Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201600, China
| | - Jiahao Zhuang
- Department of Chemical and Biomolecular Engineering, National University of Singapore (Singapore), 4 Engineering Drive 4, Singapore 117585
- Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University (Fuzhou, China), Binhai New City, Fuzhou 350207, China
| | - Xianglong Liu
- Department of Chemical and Biomolecular Engineering, National University of Singapore (Singapore), 4 Engineering Drive 4, Singapore 117585
- Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University (Fuzhou, China), Binhai New City, Fuzhou 350207, China
| | - Bin Liu
- Department of Chemical and Biomolecular Engineering, National University of Singapore (Singapore), 4 Engineering Drive 4, Singapore 117585
- Joint School of National University of Singapore and Tianjin University, International Campus of Tianjin University (Fuzhou, China), Binhai New City, Fuzhou 350207, China
- Institute for Functional Intelligent Materials, National University of Singapore (Singapore), Blk S9, Level 9, 4 Science Drive 2, Singapore 117544
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Wang Z, Teng D, Mao R, Hao Y, Yang N, Wang X, Wang J. A cleavable chimeric peptide with targeting and killing domains enhances LPS neutralization and antibacterial properties against multi-drug resistant E. coli. Commun Biol 2023; 6:1170. [PMID: 37973936 PMCID: PMC10654507 DOI: 10.1038/s42003-023-05528-0] [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: 02/19/2021] [Accepted: 10/31/2023] [Indexed: 11/19/2023] Open
Abstract
Pathogenic Escherichia coli is one of the most common causes of diarrhea diseases and its characteristic component of the outer membrane-lipopolysaccharide (LPS) is a major inducer of sepsis. Few drugs have been proven to kill bacteria and simultaneously neutralize LPS toxicity. Here, the chimeric peptides-R7, A7 and G7 were generated by connecting LBP14 (LPS-targeting domain) with L7 (killing domain) via different linkers to improve antibacterial and anti-inflammatory activities. Compared to parent LBP14-RKRR and L7, the antibacterial activity of R7 with a cleavable "RKRR" linker and the "LBP14-RKRR + L7" cocktail against Escherichia coli, Salmonella typhimurium and Staphylococcus aureus was increased by 2 ~ 4-fold. Both A7 and G7 with non-cleavable linkers almost lost antibacterial activity. The ability of R7 to neutralize LPS was markedly higher than that of LBP14-RKRR and L7. In vivo, R7 could be cleaved by furin in a time-dependent manner, and release L7 and LBP14-RKRR in serum. In vivo, R7 can enhance mouse survival more effectively than L7 and alleviate lung injuries by selective inhibition of the NF-κB signaling pathways and promoting higher IAP activity. It suggests that R7 may be promising dual-function candidates as antibacterial and anti-endotoxin agents.
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Affiliation(s)
- Zhenlong Wang
- Team of AMP & Alternatives to Antibiotics, Gene Engineering Laboratory, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
- Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing, 100081, People's Republic of China
| | - Da Teng
- Team of AMP & Alternatives to Antibiotics, Gene Engineering Laboratory, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
- Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing, 100081, People's Republic of China
| | - Ruoyu Mao
- Team of AMP & Alternatives to Antibiotics, Gene Engineering Laboratory, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
- Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing, 100081, People's Republic of China
| | - Ya Hao
- Team of AMP & Alternatives to Antibiotics, Gene Engineering Laboratory, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
- Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing, 100081, People's Republic of China
| | - Na Yang
- Team of AMP & Alternatives to Antibiotics, Gene Engineering Laboratory, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
- Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing, 100081, People's Republic of China
| | - Xiumin Wang
- Team of AMP & Alternatives to Antibiotics, Gene Engineering Laboratory, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China.
- Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing, 100081, People's Republic of China.
| | - Jianhua Wang
- Team of AMP & Alternatives to Antibiotics, Gene Engineering Laboratory, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China.
- Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing, 100081, People's Republic of China.
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Vogel J, de Lorenzo V. EAM highlights in FEMS 2023: from the Petri dish to planet Earth. MICROLIFE 2023; 4:uqad045. [PMID: 38107236 PMCID: PMC10723851 DOI: 10.1093/femsml/uqad045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 11/02/2023] [Indexed: 12/19/2023]
Abstract
On 9-13 July 2023, the 10th FEMS Congress took place in Hamburg, Germany. As part of this major event in European microbiology, the European Academy of Microbiology (EAM) organized two full sessions. One of these sessions aimed to highlight the research of four recently elected EAM fellows and saw presentations on bacterial group behaviours and development of resistance to antibiotics, as well as on new RNA viruses including bacteriophages and giant viruses of amoebae. The other session included five frontline environmental microbiologists who showcased real-world examples of how human activities have disrupted the balance in microbial ecosystems, not just to assess the current situation but also to explore fresh approaches for coping with external disturbances. Both sessions were very well attended, and no doubt helped to gain the EAM and its fellows more visibility.
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Affiliation(s)
- Jörg Vogel
- Helmholtz Center for Infection Research, Helmholtz Institute for RNA-based Infection Research and Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Victor de Lorenzo
- Systems Biology Department, National Center of Biotechnology CSIC, Madrid, Spain
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45
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Bui Thi Phuong H, Le Uyen C, Doan Ngan H, Luong Xuan H. Impact of chemical modifications on the antimicrobial and hemolytic activity of helical amphipathic peptide Lasioglossin LL-III. Amino Acids 2023; 55:1531-1544. [PMID: 37737904 DOI: 10.1007/s00726-023-03326-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 08/29/2023] [Indexed: 09/23/2023]
Abstract
Insect venom is abundant in potential antimicrobial peptides (AMPs), which can serve as novel alternatives to conventional antibiotics. Among them, Lasioglossin III LL-III) is a promising candidate with a broad spectrum against many fungi strains and both types of bacteria, whereas almost non-toxic to red blood cells. Many chemical approaches have been recently applied to improve its pharmacological properties and provide useful information regarding structure-activity relationships. Hence, this review focused on highlighting the lesson learned from each modification and supporting the future design of potent, selective, and metabolically stable AMPs.
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Affiliation(s)
| | - Chi Le Uyen
- Faculty of Pharmacy, Phenikaa University, Hanoi, 12116, Vietnam
| | - Hoa Doan Ngan
- Faculty of Medical Technology, Phenikaa University, Hanoi, 12116, Vietnam
| | - Huy Luong Xuan
- Faculty of Pharmacy, Phenikaa University, Hanoi, 12116, Vietnam.
- Phenikaa Institute for Advanced Study (PIAS), Phenikaa University, Hanoi, 12116, Vietnam.
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Concilio M, Garcia Maset R, Lemonche LP, Kontrimas V, Song JI, Rajendrakumar SK, Harrison F, Becer CR, Perrier S. Mechanism of Action of Oxazoline-Based Antimicrobial Polymers Against Staphylococcus aureus: In Vivo Antimicrobial Activity Evaluation. Adv Healthc Mater 2023; 12:e2301961. [PMID: 37522292 DOI: 10.1002/adhm.202301961] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Indexed: 08/01/2023]
Abstract
Antimicrobial-resistant pathogens have reached alarming levels, becoming one of the most pressing global health issues. Hence, new treatments are necessary for the fight against antimicrobial resistance. Synthetic nanoengineered antimicrobial polymers (SNAPs) have emerged as a promising alternative to antimicrobial peptides, overcoming some of their limitations while keeping their key features. Herein, a library of amphiphilic oxazoline-based SNAPs using cationic ring-opening polymerization (CROP) is designed. Amphipathic compounds with 70% cationic content exhibit the highest activity against clinically relevant Staphylococcus aureus isolates, maintaining good biocompatibility in vitro and in vivo. The mechanism of action of the lead compounds against S. aureus is assessed using various microscopy techniques, indicating cell membrane disruption, while the cell wall remains unaffected. Furthermore, a potential interaction of the compounds with bacterial DNA is shown, with possible implications on bacterial division. Finally, one of the compounds exhibits high efficacy in vivo in an insect infection model.
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Affiliation(s)
- Matilde Concilio
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - Ramón Garcia Maset
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | | | - Vito Kontrimas
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Ji-Inn Song
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | | | - Freya Harrison
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - C Remzi Becer
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - Sébastien Perrier
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
- Faculty of Pharmacy and Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
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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: 9] [Impact Index Per Article: 9.0] [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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Clarke M, Hind CK, Ferguson PM, Manzo G, Mistry B, Yue B, Romanopulos J, Clifford M, Bui TT, Drake AF, Lorenz CD, Sutton JM, Mason AJ. Synergy between Winter Flounder antimicrobial peptides. NPJ ANTIMICROBIALS AND RESISTANCE 2023; 1:8. [PMID: 38686212 PMCID: PMC11057203 DOI: 10.1038/s44259-023-00010-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/23/2023] [Indexed: 05/02/2024]
Abstract
Some antimicrobial peptides (AMPs) have potent bactericidal activity and are being considered as potential alternatives to classical antibiotics. In response to an infection, such AMPs are often produced in animals alongside other peptides with low or no perceivable antimicrobial activity, whose role is unclear. Here we show that six AMPs from the Winter Flounder (WF) act in synergy against a range of bacterial pathogens and provide mechanistic insights into how this increases the cooperativity of the dose-dependent bactericidal activity and potency that enable therapy. Only two WF AMPs have potent antimicrobial activity when used alone but we find a series of two-way combinations, involving peptides which otherwise have low or no activity, yield potent antimicrobial activity. Weakly active WF AMPs modulate the membrane interactions of the more potent WF AMPs and enable therapy in a model of Acinetobacter baumannii burn wound infection. The observed synergy and emergent behaviour may explain the evolutionary benefits of producing a family of related peptides and are attractive properties to consider when developing AMPs towards clinical applications.
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Affiliation(s)
- Maria Clarke
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH UK
| | - Charlotte K. Hind
- Technology Development Group, UK Health Security Agency, Research and Evaluation, Porton Down, Salisbury, SP4 0JG UK
| | - Philip M. Ferguson
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH UK
| | - Giorgia Manzo
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH UK
| | - Bhumil Mistry
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH UK
| | - Bingkun Yue
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH UK
| | - Janis Romanopulos
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH UK
| | - Melanie Clifford
- Technology Development Group, UK Health Security Agency, Research and Evaluation, Porton Down, Salisbury, SP4 0JG UK
| | - Tam T. Bui
- Centre for Biomolecular Spectroscopy and Randall Division of Cell and Molecular Biophysics, King’s College London, New Hunt’s House, London, SE1 1UL UK
| | - Alex F. Drake
- Centre for Biomolecular Spectroscopy and Randall Division of Cell and Molecular Biophysics, King’s College London, New Hunt’s House, London, SE1 1UL UK
| | | | - J. Mark Sutton
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH UK
- Technology Development Group, UK Health Security Agency, Research and Evaluation, Porton Down, Salisbury, SP4 0JG UK
| | - A. James Mason
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH UK
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Ioannou P, Baliou S, Kofteridis DP. Antimicrobial Peptides in Infectious Diseases and Beyond-A Narrative Review. Life (Basel) 2023; 13:1651. [PMID: 37629508 PMCID: PMC10455936 DOI: 10.3390/life13081651] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023] Open
Abstract
Despite recent medical research and clinical practice developments, the development of antimicrobial resistance (AMR) significantly limits therapeutics for infectious diseases. Thus, novel treatments for infectious diseases, especially in this era of increasing AMR, are urgently needed. There is ongoing research on non-classical therapies for infectious diseases utilizing alternative antimicrobial mechanisms to fight pathogens, such as bacteriophages or antimicrobial peptides (AMPs). AMPs are evolutionarily conserved molecules naturally produced by several organisms, such as plants, insects, marine organisms, and mammals, aiming to protect the host by fighting pathogenic microorganisms. There is ongoing research regarding developing AMPs for clinical use in infectious diseases. Moreover, AMPs have several other non-medical applications in the food industry, such as preservatives, animal husbandry, plant protection, and aquaculture. This review focuses on AMPs, their origins, biology, structure, mechanisms of action, non-medical applications, and clinical applications in infectious diseases.
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Affiliation(s)
- Petros Ioannou
- School of Medicine, University of Crete, 71003 Heraklion, Greece
- Internal Medicine, University Hospital of Heraklion, 71110 Heraklion, Greece
| | - Stella Baliou
- Internal Medicine, University Hospital of Heraklion, 71110 Heraklion, Greece
| | - Diamantis P. Kofteridis
- School of Medicine, University of Crete, 71003 Heraklion, Greece
- Internal Medicine, University Hospital of Heraklion, 71110 Heraklion, Greece
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Tang R, Tan H, Dai Y, Li L, Huang Y, Yao H, Cai Y, Yu G. Application of antimicrobial peptides in plant protection: making use of the overlooked merits. FRONTIERS IN PLANT SCIENCE 2023; 14:1139539. [PMID: 37538059 PMCID: PMC10394246 DOI: 10.3389/fpls.2023.1139539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 04/07/2023] [Indexed: 08/05/2023]
Abstract
Pathogen infection is one of the major causes of yield loss in the crop field. The rapid increase of antimicrobial resistance in plant pathogens has urged researchers to develop both new pesticides and management strategies for plant protection. The antimicrobial peptides (AMPs) showed potential on eliminating plant pathogenic fungi and bacteria. Here, we first summarize several overlooked advantages and merits of AMPs, which includes the steep dose-response relations, fast killing ability, broad synergism, slow resistance selection. We then discuss the possible application of AMPs for plant protection with above merits, and highlight how AMPs can be incorporated into a more efficient integrated management system that both increases the crop yield and reduce resistance evolution of pathogens.
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