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Ramos-Llorens M, Bello-Madruga R, Valle J, Andreu D, Torrent M. PyAMPA: a high-throughput prediction and optimization tool for antimicrobial peptides. mSystems 2024; 9:e0135823. [PMID: 38934543 PMCID: PMC11264690 DOI: 10.1128/msystems.01358-23] [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] [Received: 12/23/2023] [Accepted: 05/27/2024] [Indexed: 06/28/2024] Open
Abstract
The alarming rise of antibiotic-resistant bacterial infections is driving efforts to develop alternatives to conventional antibiotics. In this context, antimicrobial peptides (AMPs) have emerged as promising candidates for their ability to target a broad range of microorganisms. However, the development of AMPs with optimal potency, selectivity, and/or stability profiles remains a challenge. To address it, computational tools for predicting AMP properties and designing novel peptides have gained increasing attention. PyAMPA is a novel platform for AMP discovery. It consists of five modules, namely AMPScreen, AMPValidate, AMPSolve, AMPMutate, and AMPOptimize, that allow high-throughput proteome inspection, candidate screening, and optimization through point-mutation and genetic algorithms. The platform also offers additional tools for predicting and evaluating AMP properties, including antimicrobial and cytotoxic activity, and peptide half-life. By providing innovative and accessible inroads into AMP motifs in proteomes, PyAMPA will enable advances in AMP development and potential translation into clinically useful molecules. PyAMPA is available at: https://github.com/SysBioUAB/PyAMPA. IMPORTANCE This paper introduces PyAMPA, a new bioinformatics platform designed for the discovery and optimization of antimicrobial peptides (AMPs). It addresses the urgent need for new antimicrobials due to the rise of antibiotic-resistant infections. PyAMPA, with its five predictive modules -AMPScreen, AMPValidate, AMPSolve, AMPMutate and AMPOptimize, enables high-throughput screening of proteomes to identify potential AMP motifs and optimize them for clinical use. Its unique approach, combining prediction, design, and optimization tools, makes PyAMPA a robust solution for developing new AMP-based therapies, offering a significant advance in combatting antibiotic resistance.
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Affiliation(s)
- Marc Ramos-Llorens
- Systems Biology of Infection Lab, Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Roberto Bello-Madruga
- Systems Biology of Infection Lab, Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Javier Valle
- Barcelona Biomedical Research Park, Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - David Andreu
- Barcelona Biomedical Research Park, Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Marc Torrent
- Systems Biology of Infection Lab, Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Autònoma de Barcelona, Barcelona, Spain
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2
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Shanthappa PM, Suravajhala R, Kumar G, Melethadathil N. Computational exploration of novel antimicrobial modalities targeting fucose-binding lectins and ribosomes in Mycobacterium smegmatis using tRNA-encoded peptides. J Biomol Struct Dyn 2024:1-13. [PMID: 38676533 DOI: 10.1080/07391102.2024.2335555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 03/19/2024] [Indexed: 04/29/2024]
Abstract
tRNA-Encoded Peptides (tREPs), encoded by small open reading frames (smORFs) within tRNA genes, have recently emerged as a new class of functional peptides exhibiting antiparasitic activity. The discovery of tREPs has led to a re-evaluation of the role of tRNAs in biology and has expanded our understanding of the genetic code. This presents an immense, unexplored potential in the realm of tRNA-peptide interactions, paving the way for groundbreaking discoveries and innovative applications in various biological functions. This study explores the antimicrobial potential of tREPs against protein targets by employing a computational method that uses verified data sources and highly recognized predictive algorithms to provide a sorted list of likely antimicrobial peptides, which were then filtered for toxicity, cell permeability, allergenicity and half-life. These peptides were then docked with screened protein targets and computationally validated using molecular dynamics (MD) simulations for 150 ns and the binding free energy was estimated. The peptides Pep2 (VVLWRKPRVRKTG) and Pep6 (HRLRLRRRKPWW) exhibited good binding affinities of -110.5 +/- 2.5 and -129.0 +/- 3.9, respectively, with RMSD values of 0.4 and 0.25 nm against the fucose-binding lectin (7NEF) and the 30S ribosome of Mycobacterium smegmatis (5O5J) protein targets. The 7NEF-Pep2 and 5O5J-Pep6 complexes indicated higher negative binding free energies of -52.55 kcal/mol and -55.52 kcal/mol respectively, as calculated by Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA). Thus, the tREPs derived peptides designed as a part of this study, provide novel approaches for potential anti-bacterial therapeutic modalities.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Pallavi M Shanthappa
- Department of Computer Science, School of Computing, Amrita Vishwa Vidyapeetham, Mysuru, India
| | | | - Geetha Kumar
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, India
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3
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Bui Thi Phuong H, Doan Ngan H, Le Huy B, Vu Dinh H, Luong Xuan H. The amphipathic design in helical antimicrobial peptides. ChemMedChem 2024; 19:e202300480. [PMID: 38408263 DOI: 10.1002/cmdc.202300480] [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: 09/07/2023] [Revised: 12/18/2023] [Indexed: 02/28/2024]
Abstract
Amphipathicity is a critical characteristic of helical antimicrobial peptides (AMPs). The hydrophilic region, primarily composed of cationic residues, plays a pivotal role in the initial binding to negatively charged components on bacterial membranes through electrostatic interactions. Subsequently, the hydrophobic region interacts with hydrophobic components, inducing membrane perturbation, ultimately leading to cell death, or inhibiting intracellular function. Due to the extensive diversity of natural and synthetic AMPs with regard to the design of amphipathicity, it is complicated to study the structure-activity relationships. Therefore, this work aims to categorize the common amphipathic design and investigate their impact on the biological properties of AMPs. Besides, the connection between current structural modification approaches and amphipathic styles was also discussed.
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Affiliation(s)
| | - Hoa Doan Ngan
- Faculty of Medical Technology, PHENIKAA University, Hanoi, 12116, Vietnam
| | - Binh Le Huy
- Center for High Technology Development, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Hanoi, 11307, Vietnam
- School of Chemical Engineering -, Hanọi University of Science and Technology, 1 Dai Co Viet, Hai Ba Trung, Hanoi, 11615, Vietnam
| | - Hoang Vu Dinh
- School of Chemical Engineering -, Hanọi University of Science and Technology, 1 Dai Co Viet, Hai Ba Trung, Hanoi, 11615, Vietnam
| | - Huy Luong Xuan
- Faculty of Pharmacy, PHENIKAA University, Hanoi, 12116, Vietnam
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4
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Schüttel M, Will E, Sangouard G, Zarda A, Habeshian S, Nielsen AL, Heinis C. Solid-phase peptide synthesis in 384-well plates. J Pept Sci 2024; 30:e3555. [PMID: 38220145 DOI: 10.1002/psc.3555] [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: 07/06/2023] [Revised: 08/31/2023] [Accepted: 11/03/2023] [Indexed: 01/16/2024]
Abstract
Newer solid-phase peptide synthesis and release strategies enable the production of short peptides with high purity, allowing direct screening for desired bioactivity without prior chromatographic purification. However, the maximum number of peptides that can currently be synthesized per microplate reactor is 96, allowing the parallel synthesis of 384 peptides in modern devices that have space for 4 microplate reactors. To synthesize larger numbers of peptides, we modified a commercially available peptide synthesizer to enable the production of peptides in 384-well plates, which allows the synthesis of 1,536 peptides in one run (4 × 384 peptides). We report new hardware components and customized software that allowed for the synthesis of 1,536 short peptides in good quantity (average > 0.5 μmol), at high concentration (average > 10 mM), and decent purity without purification (average > 80%). The high-throughput peptide synthesis, which we developed with peptide drug development in mind, may be widely used for peptide library synthesis and screening, antibody epitope scanning, epitope mimetic development, or protease/kinase substrate screening.
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Affiliation(s)
- Mischa Schüttel
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Edward Will
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Gontran Sangouard
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Anne Zarda
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Sevan Habeshian
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Alexander L Nielsen
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Christian Heinis
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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5
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Hansson A, Karlsen EA, Stensen W, Svendsen JSM, Berglin M, Lundgren A. Preventing E. coli Biofilm Formation with Antimicrobial Peptide-Functionalized Surface Coatings: Recognizing the Dependence on the Bacterial Binding Mode Using Live-Cell Microscopy. ACS APPLIED MATERIALS & INTERFACES 2024; 16:6799-6812. [PMID: 38294883 PMCID: PMC10875647 DOI: 10.1021/acsami.3c16004] [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: 10/25/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 02/02/2024]
Abstract
Antimicrobial peptides (AMPs) can kill bacteria by destabilizing their membranes, yet translating these molecules' properties into a covalently attached antibacterial coating is challenging. Rational design efforts are obstructed by the fact that standard microbiology methods are ill-designed for the evaluation of coatings, disclosing few details about why grafted AMPs function or do not function. It is particularly difficult to distinguish the influence of the AMP's molecular structure from other factors controlling the total exposure, including which type of bonds are formed between bacteria and the coating and how persistent these contacts are. Here, we combine label-free live-cell microscopy, microfluidics, and automated image analysis to study the response of surface-bound Escherichia coli challenged by the same small AMP either in solution or grafted to the surface through click chemistry. Initially after binding, the grafted AMPs inhibited bacterial growth more efficiently than did AMPs in solution. Yet, after 1 h, E. coli on the coated surfaces increased their expression of type-1 fimbriae, leading to a change in their binding mode, which diminished the coating's impact. The wealth of information obtained from continuously monitoring the growth, shape, and movements of single bacterial cells allowed us to elucidate and quantify the different factors determining the antibacterial efficacy of the grafted AMPs. We expect this approach to aid the design of elaborate antibacterial material coatings working by specific and selective actions, not limited to contact-killing. This technology is needed to support health care and food production in the postantibiotic era.
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Affiliation(s)
- Adam Hansson
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Gothenburg 40530, Sweden
- Department
of Chemistry and Materials, RISE Research
Institutes of Sweden, Borås 50115, Sweden
| | - Eskil André Karlsen
- Amicoat
A/S, Sykehusvegen 23, Tromsø 9019, Norway
- Department
of Chemistry, UiT The Arctic University
of Norway, Tromsø 9037, Norway
| | - Wenche Stensen
- Department
of Chemistry, UiT The Arctic University
of Norway, Tromsø 9037, Norway
| | - John S. M. Svendsen
- Amicoat
A/S, Sykehusvegen 23, Tromsø 9019, Norway
- Department
of Chemistry, UiT The Arctic University
of Norway, Tromsø 9037, Norway
| | - Mattias Berglin
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Gothenburg 40530, Sweden
- Department
of Chemistry and Materials, RISE Research
Institutes of Sweden, Borås 50115, Sweden
| | - Anders Lundgren
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Gothenburg 40530, Sweden
- Centre
for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg 41346, Sweden
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6
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Czerczak-Kwiatkowska K, Kaminska M, Fraczyk J, Majsterek I, Kolesinska B. Searching for EGF Fragments Recreating the Outer Sphere of the Growth Factor Involved in Receptor Interactions. Int J Mol Sci 2024; 25:1470. [PMID: 38338748 PMCID: PMC10855902 DOI: 10.3390/ijms25031470] [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: 12/12/2023] [Revised: 01/21/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
The aims of this study were to determine whether it is possible to use peptide microarrays obtained using the SPOT technique (immobilized on cellulose) and specific polyclonal antibodies to select fragments that reconstruct the outer sphere of proteins and to ascertain whether the selected peptide fragments can be useful in the study of their protein-protein and/or peptide-protein interactions. Using this approach, epidermal growth factor (EGF) fragments responsible for the interaction with the EGF receptor were searched. A library of EGF fragments immobilized on cellulose was obtained using triazine condensing reagents. Experiments on the interactions with EGFR confirmed the high affinity of the selected peptide fragments. Biological tests on cells showed the lack of cytotoxicity of the EGF fragments. Selected EGF fragments can be used in various areas of medicine.
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Affiliation(s)
- Katarzyna Czerczak-Kwiatkowska
- Faculty of Chemistry, Institute of Organic Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland; (K.C.-K.); (J.F.)
| | - Marta Kaminska
- Division of Biophysics, Institute of Materials Science and Engineering, Lodz University of Technology, Stefanowskiego 1/15, 90-924 Lodz, Poland;
| | - Justyna Fraczyk
- Faculty of Chemistry, Institute of Organic Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland; (K.C.-K.); (J.F.)
| | - Ireneusz Majsterek
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, Narutowicza 60, 90-136 Lodz, Poland;
| | - Beata Kolesinska
- Faculty of Chemistry, Institute of Organic Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland; (K.C.-K.); (J.F.)
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7
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Scoffone VC, Barbieri G, Irudal S, Trespidi G, Buroni S. New Antimicrobial Strategies to Treat Multi-Drug Resistant Infections Caused by Gram-Negatives in Cystic Fibrosis. Antibiotics (Basel) 2024; 13:71. [PMID: 38247630 PMCID: PMC10812592 DOI: 10.3390/antibiotics13010071] [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: 12/20/2023] [Revised: 01/05/2024] [Accepted: 01/09/2024] [Indexed: 01/23/2024] Open
Abstract
People with cystic fibrosis (CF) suffer from recurrent bacterial infections which induce inflammation, lung tissue damage and failure of the respiratory system. Prolonged exposure to combinatorial antibiotic therapies triggers the appearance of multi-drug resistant (MDR) bacteria. The development of alternative antimicrobial strategies may provide a way to mitigate antimicrobial resistance. Here we discuss different alternative approaches to the use of classic antibiotics: anti-virulence and anti-biofilm compounds which exert a low selective pressure; phage therapies that represent an alternative strategy with a high therapeutic potential; new methods helping antibiotics activity such as adjuvants; and antimicrobial peptides and nanoparticle formulations. Their mechanisms and in vitro and in vivo efficacy are described, in order to figure out a complete landscape of new alternative approaches to fight MDR Gram-negative CF pathogens.
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Affiliation(s)
| | | | | | | | - Silvia Buroni
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy; (V.C.S.); (G.B.); (S.I.); (G.T.)
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8
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Mildenberger V, Alpízar-Pedraza D, Martell-Huguet EM, Krämer M, Bolotnikov G, Otero-Gonzalez AJ, Weil T, Rodriguez-Alfonso A, Preising N, Ständker L, Vogel V, Spellerberg B, Kissmann AK, Rosenau F. The Designed Pore-Forming Antimicrobial Peptide C14R Combines Excellent Activity against the Major Opportunistic Human Pathogen Pseudomonas aeruginosa with Low Cytotoxicity. Pharmaceuticals (Basel) 2024; 17:83. [PMID: 38256916 PMCID: PMC10820675 DOI: 10.3390/ph17010083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/21/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
The diminishing portfolio of mankind's available antibiotics urges science to develop novel potent drugs. Here, we present a peptide fitting the typical blueprint of amphipathic and membrane-active antimicrobial peptides, denominated C14R. This 2 kDa peptide consists of 16 amino acid residues, with seven being either hydrophobic, aromatic, or non-polar, and nine being polar or positively charged, strictly separated on opposite sides of the predicted α-helix. The affinity of the peptide C14R to P. aeruginosa membranes and its intrinsic tendency to productively insert into membranes of such composition were analyzed by dynamic simulations. Its biological impact on the viability of two different P. aeruginosa reference strains was demonstrated by determining the minimal inhibitory concentrations (MICs), which were found to be in the range of 10-15 µg/mL. C14R's pore-forming capability was verified in a permeabilization assay based on the peptide-triggered uptake of fluorescent dyes into the bacterial cells. Finally, the peptide was used in radial diffusion assays, which are commonly used for susceptibility testing of antimicrobial peptides in clinical microbiology. In comparison to reference strains, six clinical P. aeruginosa isolates were clearly affected, thereby paving the way for further in-depth analyses of C14R as a promising new AMP drug in the future.
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Affiliation(s)
- Vanessa Mildenberger
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (V.M.); (M.K.); (G.B.)
| | - Daniel Alpízar-Pedraza
- Center for Pharmaceutical Research and Development (CIDEM), 26th Avenue, No. 1605, Nuevo Vedado, La Habana 10400, Cuba;
| | - Ernesto M. Martell-Huguet
- Center for Protein Studies, Faculty of Biology, University of Havana, 25 and I, La Habana 10400, Cuba; (E.M.M.-H.); (A.J.O.-G.)
| | - Markus Krämer
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (V.M.); (M.K.); (G.B.)
| | - Grigory Bolotnikov
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (V.M.); (M.K.); (G.B.)
| | - Anselmo J. Otero-Gonzalez
- Center for Protein Studies, Faculty of Biology, University of Havana, 25 and I, La Habana 10400, Cuba; (E.M.M.-H.); (A.J.O.-G.)
| | - Tanja Weil
- Max Planck Institute for Polymer Research Mainz, Ackermannweg 10, 55128 Mainz, Germany;
| | - Armando Rodriguez-Alfonso
- Core Facility for Functional Peptidomics (CFP), Faculty of Medicine, Ulm University, 89081 Ulm, Germany; (A.R.-A.); (N.P.); (L.S.)
- Core Unit of Mass Spectrometry and Proteomics, Faculty of Medicine, Ulm University, 89081 Ulm, Germany
| | - Nico Preising
- Core Facility for Functional Peptidomics (CFP), Faculty of Medicine, Ulm University, 89081 Ulm, Germany; (A.R.-A.); (N.P.); (L.S.)
| | - Ludger Ständker
- Core Facility for Functional Peptidomics (CFP), Faculty of Medicine, Ulm University, 89081 Ulm, Germany; (A.R.-A.); (N.P.); (L.S.)
| | - Verena Vogel
- Institute of Medical Microbiology and Hygiene, University Clinic of Ulm, TBC1 Forschung, Albert-Einstein-Allee 11, 89081 Ulm, Germany (B.S.)
| | - Barbara Spellerberg
- Institute of Medical Microbiology and Hygiene, University Clinic of Ulm, TBC1 Forschung, Albert-Einstein-Allee 11, 89081 Ulm, Germany (B.S.)
| | - Ann-Kathrin Kissmann
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (V.M.); (M.K.); (G.B.)
- Max Planck Institute for Polymer Research Mainz, Ackermannweg 10, 55128 Mainz, Germany;
| | - Frank Rosenau
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (V.M.); (M.K.); (G.B.)
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9
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Hilpert K, Munshi T, López-Pérez PM, Sequeira-Garcia J, Hofmann S, Bull TJ. Discovery of Antimicrobial Peptides That Can Accelerate Culture Diagnostics of Slow-Growing Mycobacteria Including Mycobacterium tuberculosis. Microorganisms 2023; 11:2225. [PMID: 37764069 PMCID: PMC10536189 DOI: 10.3390/microorganisms11092225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/24/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
Antimicrobial peptides (AMPs) can directly kill Gram-positive bacteria, Gram-negative bacteria, mycobacteria, fungi, enveloped viruses, and parasites. At sublethal concentrations, some AMPs and also conventional antibiotics can stimulate bacterial response increasing their resilience, also called the hormetic response. This includes stimulation of growth, mobility, and biofilm production. Here, we describe the discovery of AMPs that stimulate the growth of certain mycobacteria. Peptide 14 showed a growth stimulating effect on Mycobacteria tuberculosis (MTB), M. bovis, M. avium subsp. paratuberculosis (MAP), M. marinum, M. avium-intracellulare, M. celatum, and M. abscessus. The effect was more pronounced at low bacterial inocula. The peptides induce a faster transition from the lag phase to the log phase and keep the bacteria longer in the log phase before entering stationary phase when compared to nontreated controls. In some cases, an increase in the division rate was observed. An initial screen using MAP and a collection of 75 peptides revealed 13 peptides with a hormetic effect. For MTB, a collection of 25 artificial peptides were screened and 13 were found to reduce the time to positivity (TTP) by at least 5%, improving growth. A screen of 43 naturally occurring peptides, 11 fragments of naturally occurring peptides and 5 designed peptides, all taken from the database APD3, identified a further 44 peptides that also lowered TTP by at least 5%. Lasioglossin LL-III (Bee) and Ranacyclin E (Frog) were the most active natural peptides, and the human cathelicidin LL37 fragment GF-17 and a porcine cathelicidin protegrin-1 fragment were the most active fragments of naturally occurring peptides. Peptide 14 showed growth-stimulating activity between 10 ng/mL and 10 µg/mL, whereas the stability-optimised Peptide 14D had a narrow activity range of 0.1-1 µg/mL. Peptides identified in this study are currently in commercial use to improve recovery and culture for the diagnostics of mycobacteria in humans and animals.
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Affiliation(s)
- Kai Hilpert
- Institute of Infection and Immunity, St George’s, University of London, Cranmer Terrace, London SW17 0RE, UK (T.J.B.)
| | - Tulika Munshi
- Institute of Infection and Immunity, St George’s, University of London, Cranmer Terrace, London SW17 0RE, UK (T.J.B.)
| | | | | | - Sven Hofmann
- Institute of Infection and Immunity, St George’s, University of London, Cranmer Terrace, London SW17 0RE, UK (T.J.B.)
| | - Tim J. Bull
- Institute of Infection and Immunity, St George’s, University of London, Cranmer Terrace, London SW17 0RE, UK (T.J.B.)
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10
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Hilpert K, Rumancev C, Gani J, Collis DWP, Lopez-Perez PM, Garamus VM, Mikut R, Rosenhahn A. Can BioSAXS detect ultrastructural changes of antifungal compounds in Candida albicans?-an exploratory study. Front Pharmacol 2023; 14:1141785. [PMID: 37533629 PMCID: PMC10393279 DOI: 10.3389/fphar.2023.1141785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 07/06/2023] [Indexed: 08/04/2023] Open
Abstract
The opportunistic yeast Candida albicans is the most common cause of candidiasis. With only four classes of antifungal drugs on the market, resistance is becoming a problem in the treatment of fungal infections, especially in immunocompromised patients. The development of novel antifungal drugs with different modes of action is urgent. In 2016, we developed a groundbreaking new medium-throughput method to distinguish the effects of antibacterial agents. Using small-angle X-ray scattering for biological samples (BioSAXS), it is now possible to screen hundreds of new antibacterial compounds and select those with the highest probability for a novel mode of action. However, yeast (eukaryotic) cells are highly structured compared to bacteria. The fundamental question to answer was if the ultrastructural changes induced by the action of an antifungal drug can be detected even when most structures in the cell stay unchanged. In this exploratory work, BioSAXS was used to measure the ultrastructural changes of C. albicans that were directly or indirectly induced by antifungal compounds. For this, the well-characterized antifungal drug Flucytosine was used. BioSAXS measurements were performed on the synchrotron P12 BioSAXS beamline, EMBL (DESY, Hamburg) on treated and untreated yeast C. albicans. BioSAXS curves were analysed using principal component analysis (PCA). The PCA showed that Flucytosine-treated and untreated yeast were separated. Based on that success further measurements were performed on five antifungal peptides {1. Cecropin A-melittin hybrid [CA (1-7) M (2-9)], KWKLFKKIGAVLKVL; 2. Lasioglossin LL-III, VNWKKILGKIIKVVK; 3. Mastoparan M, INLKAIAALAKKLL; 4. Bmkn2, FIGAIARLLSKIFGKR; and 5. optP7, KRRVRWIIW}. The ultrastructural changes of C. albicans indicate that the peptides may have different modes of action compared to Flucytosine as well as to each other, except for the Cecropin A-melittin hybrid [CA (1-7) M (2-9)] and optP7, showing very similar effects on C. albicans. This very first study demonstrates that BioSAXS shows promise to be used for antifungal drug development. However, this first study has limitations and further experiments are necessary to establish this application.
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Affiliation(s)
- Kai Hilpert
- Institute of Infection and Immunology, St. George’s, University of London (SGUL), London, United Kingdom
| | - Christoph Rumancev
- Laboratory Analytical Chemistry—Biointerfaces, Ruhr-University Bochum, Bochum, Germany
| | - Jurnorain Gani
- Institute of Infection and Immunology, St. George’s, University of London (SGUL), London, United Kingdom
| | | | | | | | - Ralf Mikut
- Institute for Automation and Applied Informatics (IAI), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Axel Rosenhahn
- Laboratory Analytical Chemistry—Biointerfaces, Ruhr-University Bochum, Bochum, Germany
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11
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Costa L, Sousa E, Fernandes C. Cyclic Peptides in Pipeline: What Future for These Great Molecules? Pharmaceuticals (Basel) 2023; 16:996. [PMID: 37513908 PMCID: PMC10386233 DOI: 10.3390/ph16070996] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/06/2023] [Accepted: 07/08/2023] [Indexed: 07/30/2023] Open
Abstract
Cyclic peptides are molecules that are already used as drugs in therapies approved for various pharmacological activities, for example, as antibiotics, antifungals, anticancer, and immunosuppressants. Interest in these molecules has been growing due to the improved pharmacokinetic and pharmacodynamic properties of the cyclic structure over linear peptides and by the evolution of chemical synthesis, computational, and in vitro methods. To date, 53 cyclic peptides have been approved by different regulatory authorities, and many others are in clinical trials for a wide diversity of conditions. In this review, the potential of cyclic peptides is presented, and general aspects of their synthesis and development are discussed. Furthermore, an overview of already approved cyclic peptides is also given, and the cyclic peptides in clinical trials are summarized.
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Affiliation(s)
- Lia Costa
- Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal;
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Edifício do Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4050-208 Matosinhos, Portugal
| | - Emília Sousa
- Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal;
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Edifício do Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4050-208 Matosinhos, Portugal
| | - Carla Fernandes
- Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal;
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Edifício do Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4050-208 Matosinhos, Portugal
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12
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Ayon NJ. High-Throughput Screening of Natural Product and Synthetic Molecule Libraries for Antibacterial Drug Discovery. Metabolites 2023; 13:625. [PMID: 37233666 PMCID: PMC10220967 DOI: 10.3390/metabo13050625] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 04/29/2023] [Accepted: 05/01/2023] [Indexed: 05/27/2023] Open
Abstract
Due to the continued emergence of resistance and a lack of new and promising antibiotics, bacterial infection has become a major public threat. High-throughput screening (HTS) allows rapid screening of a large collection of molecules for bioactivity testing and holds promise in antibacterial drug discovery. More than 50% of the antibiotics that are currently available on the market are derived from natural products. However, with the easily discoverable antibiotics being found, finding new antibiotics from natural sources has seen limited success. Finding new natural sources for antibacterial activity testing has also proven to be challenging. In addition to exploring new sources of natural products and synthetic biology, omics technology helped to study the biosynthetic machinery of existing natural sources enabling the construction of unnatural synthesizers of bioactive molecules and the identification of molecular targets of antibacterial agents. On the other hand, newer and smarter strategies have been continuously pursued to screen synthetic molecule libraries for new antibiotics and new druggable targets. Biomimetic conditions are explored to mimic the real infection model to better study the ligand-target interaction to enable the designing of more effective antibacterial drugs. This narrative review describes various traditional and contemporaneous approaches of high-throughput screening of natural products and synthetic molecule libraries for antibacterial drug discovery. It further discusses critical factors for HTS assay design, makes a general recommendation, and discusses possible alternatives to traditional HTS of natural products and synthetic molecule libraries for antibacterial drug discovery.
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Affiliation(s)
- Navid J Ayon
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
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13
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Wang J, Li J, Shen Z, Wang D, Tang BZ. Phospholipid-Mimetic Aggregation-Induced Emission Luminogens for Specific Elimination of Gram-Positive and Gram-Negative Bacteria. ACS NANO 2023; 17:4239-4249. [PMID: 36802498 DOI: 10.1021/acsnano.2c05821] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Precise elimination of both Gram-positive and Gram-negative bacteria greatly contributes to the fight against bacterial infection but remains challenging. Herein, we present a series of phospholipid-mimetic aggregation-induced emission luminogens (AIEgens) that selectively kill bacteria by capitalizing on both the different structure of two bacterial membrane and the regulated length of substituted alkyl chains of AIEgens. Because of the positive charges that they contain, these AIEgens are able to kill bacteria by anchoring onto the bacterial membrane. For AIEgens with short alkyl chains, they could combine with the membrane of Gram-positive bacteria other than Gram-negative bacteria, because of their complicated outer layers, thus exhibiting selective ablation to Gram-positive bacteria. On the other hand, AIEgens with long alkyl chains have strong hydrophobicity with bacterial membranes, as well as large sizes. This inhibits the combination with Gram-positive bacterial membrane but destroys the membranes of Gram-negative bacteria, resulting in selective ablation to Gram-negative bacteria. Moreover, the combined processes to two bacteria are clearly observed by fluorescent imaging, and in vitro and in vivo experiments show the extraordinary antibacterial selectivity toward a Gram-positive and Gram-negative bacterium. This work could facilitate the development of species-specific antibacterial agents.
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Affiliation(s)
- Jianxing Wang
- Center for AIE Research, Shenzhen Key Laboratory of Polymer Science and Technology, Guangdong Research Center for Interfacial Engineering of Functional Materials, College of Materials Science and Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Jie Li
- Center for AIE Research, Shenzhen Key Laboratory of Polymer Science and Technology, Guangdong Research Center for Interfacial Engineering of Functional Materials, College of Materials Science and Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Zipeng Shen
- Center for AIE Research, Shenzhen Key Laboratory of Polymer Science and Technology, Guangdong Research Center for Interfacial Engineering of Functional Materials, College of Materials Science and Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Dong Wang
- Center for AIE Research, Shenzhen Key Laboratory of Polymer Science and Technology, Guangdong Research Center for Interfacial Engineering of Functional Materials, College of Materials Science and Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Ben Zhong Tang
- Center for AIE Research, Shenzhen Key Laboratory of Polymer Science and Technology, Guangdong Research Center for Interfacial Engineering of Functional Materials, College of Materials Science and Engineering, Shenzhen University, Shenzhen, 518060, China
- School of Science and Engineering, Shenzhen Key Laboratory of Functional Aggregate Materials, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China
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14
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Wang X, Yang X, Wang Q, Meng D. Unnatural amino acids: promising implications for the development of new antimicrobial peptides. Crit Rev Microbiol 2023; 49:231-255. [PMID: 35254957 DOI: 10.1080/1040841x.2022.2047008] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The increasing incidence and rapid spread of bacterial resistance to conventional antibiotics are a serious global threat to public health, highlighting the need to develop new antimicrobial alternatives. Antimicrobial peptides (AMPs) represent a class of promising natural antibiotic candidates due to their broad-spectrum activity and low tendency to induce resistance. However, the development of AMPs for medical use is hampered by several obstacles, such as moderate activity, lability to proteolytic degradation, and low bioavailability. To date, many researchers have focussed on the optimization or design of novel artificial AMPs with desired properties. Unnatural amino acids (UAAs) are valuable building blocks in the manufacture of a variety of pharmaceuticals, and have been used to develop artificial AMPs with specific structural and physicochemical properties. Rational incorporation of UAAs has become a very promising approach to endow AMPs with strong and long-lasting activity but no toxicity. This review aims to summarize key approaches that have been used to incorporate UAAs to develop novel AMPs with improved properties and better performance. It is anticipated that this review will guide future design considerations for UAA-based antimicrobial applications.
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Affiliation(s)
- Xiuhong Wang
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin, People's Republic of China
| | - Xiaomin Yang
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin, People's Republic of China
| | - Qiaoe Wang
- Key Laboratory of Cosmetic, China National Light Industry, Beijing Technology and Business University, Beijing, People's Republic of China
| | - Demei Meng
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin, People's Republic of China.,Tianjin Gasin-DH Preservation Technology Co., Ltd, Tianjin, People's Republic of China
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15
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Ouyang L, Chen B, Liu X, Wang D, Li Y, Liao Y, Yeung KW, Liu X. Puerarin@Chitosan composite for infected bone repair through mimicking the bio-functions of antimicrobial peptides. Bioact Mater 2023; 21:520-530. [PMID: 36185735 PMCID: PMC9508162 DOI: 10.1016/j.bioactmat.2022.09.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/01/2022] [Accepted: 09/12/2022] [Indexed: 11/30/2022] Open
Abstract
It is important to eliminate lipopolysaccharide (LPS) along with killing bacteria in periprosthetic joint infection (PJI) therapy for promoting bone repair due to its effect to regulate macrophages response. Although natural antimicrobial peptides (AMPs) offer a good solution, the unknown toxicity, high cost and exogenetic immune response hamper their applications in clinic. In this work, we fabricated a nanowire-like composite material, named P@C, by combining chitosan and puerarin via solid-phase reaction, which can finely mimic the bio-functions of AMPs. Chitosan, serving as the bacteria membrane puncture agent, and puerarin, serving as the LPS target agent, synergistically destroy the bacterial membrane structure and inhibit its recovery, thus endowing P@C with good antibacterial property. In addition, P@C possesses good osteoimmunomodulation due to its ability of LPS elimination and macrophage differentiation modulation. The in vivo results show that P@C can inhibit the LPS induced bone destruction in the Escherichia coli infected rat. P@C exhibits superior bone regeneration in Escherichia coli infected rat due to the comprehensive functions of its superior antibacterial property, and its ability of LPS elimination and immunomodulation. P@C can well mimic the functions of AMPs, which provides a novel and effective method for treating the PJI in clinic. P@C was fabricated through solid reaction with chitosan and puerarin. P@C punctures bacteria membrane and eliminates LPS, thus sterilizes bacteria. P@C improves bone formation of PEEK under infection via polarizing macrophage to M2.
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16
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Huang J, Xu Y, Xue Y, Huang Y, Li X, Chen X, Xu Y, Zhang D, Zhang P, Zhao J, Ji J. Identification of potent antimicrobial peptides via a machine-learning pipeline that mines the entire space of peptide sequences. Nat Biomed Eng 2023:10.1038/s41551-022-00991-2. [PMID: 36635418 DOI: 10.1038/s41551-022-00991-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 11/29/2022] [Indexed: 01/14/2023]
Abstract
Systematically identifying functional peptides is difficult owing to the vast combinatorial space of peptide sequences. Here we report a machine-learning pipeline that mines the hundreds of billions of sequences in the entire virtual library of peptides made of 6-9 amino acids to identify potent antimicrobial peptides. The pipeline consists of trainable machine-learning modules (for performing empirical selection, classification, ranking and regression tasks) assembled sequentially following a coarse-to-fine design principle to gradually narrow down the search space. The leading three antimicrobial hexapeptides identified by the pipeline showed strong activities against a wide range of clinical isolates of multidrug-resistant pathogens. In mice with bacterial pneumonia, aerosolized formulations of the identified peptides showed therapeutic efficacy comparable to penicillin, negligible toxicity and a low propensity to induce drug resistance. The machine-learning pipeline may accelerate the discovery of new functional peptides.
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Affiliation(s)
- Junjie Huang
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, China.,International Research Center for X Polymers, International Campus, Zhejiang University, Haining, China
| | - Yanchao Xu
- College of Computer Science and Technology, Zhejiang University, Hangzhou, China
| | - Yunfan Xue
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, China.,International Research Center for X Polymers, International Campus, Zhejiang University, Haining, China
| | - Yue Huang
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, China
| | - Xu Li
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, China
| | - Xiaohui Chen
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, China
| | - Yao Xu
- R&D Department of AtaGenix Laboratories Co., Ltd. (Wuhan), Wuhan, China
| | - Dongxiang Zhang
- College of Computer Science and Technology, Zhejiang University, Hangzhou, China
| | - Peng Zhang
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, China. .,International Research Center for X Polymers, International Campus, Zhejiang University, Haining, China.
| | - Junbo Zhao
- College of Computer Science and Technology, Zhejiang University, Hangzhou, China.
| | - Jian Ji
- MOE Key Laboratory of Macromolecule Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, China. .,International Research Center for X Polymers, International Campus, Zhejiang University, Haining, China.
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17
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Fan D, Liu X, Ren Y, Bai S, Li Y, Luo Z, Dong J, Chen F, Zeng W. Functional insights to the development of bioactive material for combating bacterial infections. Front Bioeng Biotechnol 2023; 11:1186637. [PMID: 37152653 PMCID: PMC10160456 DOI: 10.3389/fbioe.2023.1186637] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 04/13/2023] [Indexed: 05/09/2023] Open
Abstract
The emergence of antibiotic-resistant "superbugs" poses a serious threat to human health. Nanomaterials and cationic polymers have shown unprecedented advantages as effective antimicrobial therapies due to their flexibility and ability to interact with biological macromolecules. They can incorporate a variety of antimicrobial substances, achieving multifunctional effects without easily developing drug resistance. Herein, this article discusses recent advances in cationic polymers and nano-antibacterial materials, including material options, fabrication techniques, structural characteristics, and activity performance, with a focus on their fundamental active elements.
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Affiliation(s)
- Duoyang Fan
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Changsha, China
| | - Xiaohui Liu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Changsha, China
| | - Yueming Ren
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Changsha, China
| | - Shuaige Bai
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Changsha, China
| | - Yanbing Li
- Xiangya Hospital, Central South University, Changsha, China
| | - Ziheng Luo
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Changsha, China
| | - Jie Dong
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Changsha, China
| | - Fei Chen
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Changsha, China
- *Correspondence: Fei Chen, ; Wenbin Zeng,
| | - Wenbin Zeng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
- Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Changsha, China
- *Correspondence: Fei Chen, ; Wenbin Zeng,
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18
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Sharma L, Bisht GS. Short Antimicrobial Peptides: Therapeutic Potential and Recent Advancements. Curr Pharm Des 2023; 29:3005-3017. [PMID: 38018196 DOI: 10.2174/0113816128248959231102114334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 09/28/2023] [Accepted: 10/11/2023] [Indexed: 11/30/2023]
Abstract
There has been a lot of interest in antimicrobial peptides (AMPs) as potential next-generation antibiotics. They are components of the innate immune system. AMPs have broad-spectrum action and are less prone to resistance development. They show potential applications in various fields, including medicine, agriculture, and the food industry. However, despite the good activity and safety profiles, AMPs have had difficulty finding success in the clinic due to their various limitations, such as production cost, proteolytic susceptibility, and oral bioavailability. To overcome these flaws, a number of solutions have been devised, one of which is developing short antimicrobial peptides. Short antimicrobial peptides do have an advantage over longer peptides as they are more stable and do not collapse during absorption. They have generated a lot of interest because of their evolutionary success and advantageous properties, such as low molecular weight, selective targets, cell or organelles with minimal toxicity, and enormous therapeutic potential. This article provides an overview of the development of short antimicrobial peptides with an emphasis on those with ≤ 30 amino acid residues as a potential therapeutic agent to fight drug-resistant microorganisms. It also emphasizes their applications in many fields and discusses their current state in clinical trials.
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Affiliation(s)
- Lalita Sharma
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Himachal Pradesh, India
| | - Gopal Singh Bisht
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Himachal Pradesh, India
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19
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Evaluation of the antimicrobial attribute of bioactive peptides derived from colostrum whey fermented by Lactobacillus against diarrheagenic E. coli strains. JOURNAL OF FOOD SCIENCE AND TECHNOLOGY 2023; 60:211-221. [PMID: 36259044 PMCID: PMC9559551 DOI: 10.1007/s13197-022-05606-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Revised: 08/30/2022] [Accepted: 09/19/2022] [Indexed: 01/09/2023]
Abstract
Colostrum known as "liquid gold" contains approximately 60-80% of whey proteins that can be a great source of bioactive peptide production. Therefore, this study aimed to perform a comparative antimicrobial evaluation of the bioactive peptide generated from L. rhamnosus C25, L. rhamnosus C6, and L. casei NCDC17 fermented colostrum whey. Peptide fractions 10 kDa, 5 kDa, and 3 kDa were isolated using their respective molecular weight cut-off membranes and antimicrobial activity was evaluated against diarrheagenic E. coli strains. The higher inhibition was shown by < 10 kDa peptide fractions from L. rhamnosus C25 fermented colostrum whey and the zone of inhibition was 15 ± 0.06 (E. coli MTCC 723), 17 ± 0.04 (E. coli MTCC 724), 18 ± 0.05 (E. coli MTCC 725), and 17 ± 0.02 (E. coli ATCC 25922). In addition, ST-1 and LT-1 genes of E. coli strains were also confirmed using PCR which is responsible for the diarrheagenic property. Further, the interaction of potent peptides against E. coli strains was also observed by scanning electron microscope. Hence, the significance of the present study emphasized that these bioactive peptides generated from fermented colostrum whey can be used as ingredients in functional food against diarrhoea.
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20
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Application of a deep generative model produces novel and diverse functional peptides against microbial resistance. Comput Struct Biotechnol J 2022; 21:463-471. [PMID: 36618982 PMCID: PMC9804011 DOI: 10.1016/j.csbj.2022.12.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 12/13/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022] Open
Abstract
Antimicrobial resistance could threaten millions of lives in the immediate future. Antimicrobial peptides (AMPs) are an alternative to conventional antibiotics practice against infectious diseases. Despite the potential contribution of AMPs to the antibiotic's world, their development and optimization have encountered serious challenges. Cutting-edge methods with novel and improved selectivity toward resistant targets must be established to create AMPs-driven treatments. Here, we present AMPTrans-lstm, a deep generative network-based approach for the rational design of AMPs. The AMPTrans-lstm pipeline involves pre-training, transfer learning, and module identification. The AMPTrans-lstm model has two sub-models, namely, (long short-term memory) LSTM sampler and Transformer converter, which can be connected in series to make full use of the stability of LSTM and the novelty of Transformer model. These elements could generate AMPs candidates, which can then be tailored for specific applications. By analyzing the generated sequence and trained AMPs, we prove that AMPTrans-lstm can expand the design space of the trained AMPs and produce reasonable and brand-new AMPs sequences. AMPTrans-lstm can generate functional peptides for antimicrobial resistance with good novelty and diversity, so it is an efficient AMPs design tool.
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21
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Arias-Orozco P, Yi Y, Ruijne F, Cebrián R, Kuipers OP. Investigating the Specificity of the Dehydration and Cyclization Reactions in Engineered Lanthipeptides by Synechococcal SyncM. ACS Synth Biol 2022; 12:164-177. [PMID: 36520855 PMCID: PMC9872173 DOI: 10.1021/acssynbio.2c00455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
ProcM-like enzymes are class II promiscuous lanthipeptide synthetases that are an attractive tool in synthetic biology for producing lanthipeptides with biotechnological or clinically desired properties. SyncM is a recently described modification enzyme from this family used to develop a versatile expression platform for engineering lanthipeptides. Most remarkably, SyncM can modify up to 79 SyncA substrates in a single strain. Six SyncAs were previously characterized from this pool of substrates. They showed particular characteristics, such as the presence of one or two lanthionine rings, different flanking residues influencing ring formation, and different ring directions, demonstrating the relaxed specificity of SyncM toward its precursor peptides. To gain a deeper understanding of the potential of SyncM as a biosynthetic tool, we further explored the enzyme's capabilities and limits in dehydration and ring formation. We used different SyncA scaffolds for peptide engineering, including changes in the ring's directionality (relative position of Ser/Thr to Cys in the peptide) and size. We further aimed to rationally design mimetics of cyclic antimicrobials and introduce macrocycles in prochlorosin-related and nonrelated substrates. This study highlights the largest lanthionine ring with 15 amino acids (ring-forming residues included) described to date. Taking advantage of the amino acid substrate tolerance of SyncM, we designed the first single-SyncA-based antimicrobial. The insights gained from this work will aid future bioengineering studies. Additionally, it broadens SyncM's application scope for introducing macrocycles in other bioactive molecules.
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Affiliation(s)
- Patricia Arias-Orozco
- Department
of Molecular Genetics, University of Groningen, Nijenborg 7, 9747 AG Groningen, The Netherlands
| | - Yunhai Yi
- Department
of Molecular Genetics, University of Groningen, Nijenborg 7, 9747 AG Groningen, The Netherlands
| | - Fleur Ruijne
- Department
of Molecular Genetics, University of Groningen, Nijenborg 7, 9747 AG Groningen, The Netherlands
| | - Rubén Cebrián
- Department
of Molecular Genetics, University of Groningen, Nijenborg 7, 9747 AG Groningen, The Netherlands,Department
of Clinical Microbiology, Instituto de Investigación Biosanitaria,
ibs. GRANADA, San Cecilio University Hospital, Av. De la Innovación s/n, 18016 Granada, Spain
| | - Oscar P. Kuipers
- Department
of Molecular Genetics, University of Groningen, Nijenborg 7, 9747 AG Groningen, The Netherlands,
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22
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Greve JM, Cowan JA. Activity and Synergy of Cu-ATCUN Antimicrobial Peptides. Int J Mol Sci 2022; 23:ijms232214151. [PMID: 36430622 PMCID: PMC9692552 DOI: 10.3390/ijms232214151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/08/2022] [Accepted: 11/11/2022] [Indexed: 11/19/2022] Open
Abstract
Antibiotic resistance demands innovative strategies and therapies. The pairs of antimicrobial peptides tested in this work show broad-spectrum synergy and are capable of interacting with diverse bacterial membranes. In most cases, the ATCUN motif enhanced the activity of peptides tested in combination. Our studies also show CP10A to be a multifaceted peptide, displaying both cell membrane and intracellular activity and acting as a chameleon, improving the activity of other peptides as needed. The results of the synergy experiments demonstrate the importance of varied modes of action and how these changes can affect the ability to combat pathogens, while also illustrating the value of the metal-binding domain in enhancing the activity of antimicrobial peptides in combination.
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23
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Matching amino acids membrane preference profile to improve activity of antimicrobial peptides. Commun Biol 2022; 5:1199. [PMID: 36347951 PMCID: PMC9643456 DOI: 10.1038/s42003-022-04164-4] [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: 05/27/2022] [Accepted: 10/25/2022] [Indexed: 11/11/2022] Open
Abstract
Antimicrobial peptides (AMPs) are cationic antibiotics that can kill multidrug-resistant bacteria via membrane insertion. However, their weak activity limits their clinical use. Ironically, the cationic charge of AMPs is essential for membrane binding, but it obstructs membrane insertion. In this study, we postulate that this problem can be overcome by locating cationic amino acids at the energetically preferred membrane surface. All amino acids have an energetically preferred or less preferred membrane position profile, and this profile is strongly related to membrane insertion. However, most AMPs do not follow this profile. One exception is protegrin-1, a powerful but neglected AMP. In the present study, we found that a potent AMP, WCopW5, strongly resembles protegrin-1 and that the match between its sequence and the preferred position profile closely correlates with its antimicrobial activity. One of its derivatives, WCopW43, has antimicrobial activity comparable to that of the most effective AMPs in clinical use.
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24
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Luong AD, Buzid A, Luong JHT. Important Roles and Potential Uses of Natural and Synthetic Antimicrobial Peptides (AMPs) in Oral Diseases: Cavity, Periodontal Disease, and Thrush. J Funct Biomater 2022; 13:jfb13040175. [PMID: 36278644 PMCID: PMC9589978 DOI: 10.3390/jfb13040175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 01/10/2023] Open
Abstract
Numerous epithelial cells and sometimes leukocytes release AMPs as their first line of defense. AMPs encompass cationic histatins, defensins, and cathelicidin to encounter oral pathogens with minimal resistance. However, their concentrations are significantly below the effective levels and AMPs are unstable under physiological conditions due to proteolysis, acid hydrolysis, and salt effects. In parallel to a search for more effective AMPs from natural sources, considerable efforts have focused on synthetic stable and low-cytotoxicy AMPs with significant activities against microorganisms. Using natural AMP templates, various attempts have been used to synthesize sAMPs with different charges, hydrophobicity, chain length, amino acid sequence, and amphipathicity. Thus far, sAMPs have been designed to target Streptococcus mutans and other common oral pathogens. Apart from sAMPs with antifungal activities against Candida albicans, future endeavors should focus on sAMPs with capabilities to promote remineralization and antibacterial adhesion. Delivery systems using nanomaterials and biomolecules are promising to stabilize, reduce cytotoxicity, and improve the antimicrobial activities of AMPs against oral pathogens. Nanostructured AMPs will soon become a viable alternative to antibiotics due to their antimicrobial mechanisms, broad-spectrum antimicrobial activity, low drug residue, and ease of synthesis and modification.
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Affiliation(s)
- Albert Donald Luong
- Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, University of Buffalo, Buffalo, NY 14215, USA
| | - Alyah Buzid
- Department of Chemistry, College of Science, King Faisal University, P.O. Box 380, Al-Ahsa 31982, Saudi Arabia
| | - John H. T. Luong
- School of Chemistry and Analytical & Biological Chemistry Research Facility (ABCRF), University College Cork, College Road, T12 YN60 Cork, Ireland
- Correspondence: or
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Wesseling CJ, Martin NI. Synergy by Perturbing the Gram-Negative Outer Membrane: Opening the Door for Gram-Positive Specific Antibiotics. ACS Infect Dis 2022; 8:1731-1757. [PMID: 35946799 PMCID: PMC9469101 DOI: 10.1021/acsinfecdis.2c00193] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
New approaches to target antibacterial agents toward Gram-negative bacteria are key, given the rise of antibiotic resistance. Since the discovery of polymyxin B nonapeptide as a potent Gram-negative outer membrane (OM)-permeabilizing synergist in the early 1980s, a vast amount of literature on such synergists has been published. This Review addresses a range of peptide-based and small organic compounds that disrupt the OM to elicit a synergistic effect with antibiotics that are otherwise inactive toward Gram-negative bacteria, with synergy defined as a fractional inhibitory concentration index (FICI) of <0.5. Another requirement for the inclusion of the synergists here covered is their potentiation of a specific set of clinically used antibiotics: erythromycin, rifampicin, novobiocin, or vancomycin. In addition, we have focused on those synergists with reported activity against Gram-negative members of the ESKAPE family of pathogens namely, Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, and/or Acinetobacter baumannii. In cases where the FICI values were not directly reported in the primary literature but could be calculated from the published data, we have done so, allowing for more direct comparison of potency with other synergists. We also address the hemolytic activity of the various OM-disrupting synergists reported in the literature, an effect that is often downplayed but is of key importance in assessing the selectivity of such compounds for Gram-negative bacteria.
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26
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Juretić D. Designed Multifunctional Peptides for Intracellular Targets. Antibiotics (Basel) 2022; 11:antibiotics11091196. [PMID: 36139975 PMCID: PMC9495127 DOI: 10.3390/antibiotics11091196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/25/2022] [Accepted: 08/29/2022] [Indexed: 11/25/2022] Open
Abstract
Nature’s way for bioactive peptides is to provide them with several related functions and the ability to cooperate in performing their job. Natural cell-penetrating peptides (CPP), such as penetratins, inspired the design of multifunctional constructs with CPP ability. This review focuses on known and novel peptides that can easily reach intracellular targets with little or no toxicity to mammalian cells. All peptide candidates were evaluated and ranked according to the predictions of low toxicity to mammalian cells and broad-spectrum activity. The final set of the 20 best peptide candidates contains the peptides optimized for cell-penetrating, antimicrobial, anticancer, antiviral, antifungal, and anti-inflammatory activity. Their predicted features are intrinsic disorder and the ability to acquire an amphipathic structure upon contact with membranes or nucleic acids. In conclusion, the review argues for exploring wide-spectrum multifunctionality for novel nontoxic hybrids with cell-penetrating peptides.
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Affiliation(s)
- Davor Juretić
- Mediterranean Institute for Life Sciences, 21000 Split, Croatia;
- Faculty of Science, University of Split, 21000 Split, Croatia;
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27
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Tian S, Lu Y, He Z, Yue Q, Zhuang Z, Wang Y, Meng F, Luo L. Polydiacetylene-based poly-ion complex enabling aggregation-induced emission and photodynamic therapy dual turn-on for on-demand pathogenic bacteria elimination. Sci China Chem 2022. [DOI: 10.1007/s11426-022-1317-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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28
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Synthetic Antimicrobial Immunomodulatory Peptides: Ongoing Studies and Clinical Trials. Antibiotics (Basel) 2022; 11:antibiotics11081062. [PMID: 36009931 PMCID: PMC9405281 DOI: 10.3390/antibiotics11081062] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/30/2022] [Accepted: 08/03/2022] [Indexed: 11/25/2022] Open
Abstract
The increasingly widespread antimicrobial resistance forces the search for new antimicrobial substances capable of fighting infection. Antimicrobial peptides (AMPs) and their synthetic analogs form an extensive group of compounds of great structural diversity and multifunctionality, different modes of antimicrobial action, and considerable market potential. Some AMPs, in addition to their proven antibacterial, antifungal, and antiviral activity, also demonstrate anti-inflammatory and immunomodulatory capabilities; these are called innate defense regulator (IDR) peptides. IDR peptides stimulate or inhibit the body’s immune system, e.g., by stimulating leukocyte migration to the site of infection, driving macrophage differentiation and activation, providing chemotactic action for neutrophils, degranulation and activation of mast cells, altering chemokine and cytokine production, and even induction of angiogenesis and wound healing. Such multifunctional immunomodulatory peptide molecules are currently being investigated and developed. Exploring and utilizing IDR peptides as an indirect weapon against infectious diseases could represent a completely new strategy to cope with the issue of antimicrobial resistance.
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29
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Rational Discovery of Antimicrobial Peptides by Means of Artificial Intelligence. MEMBRANES 2022; 12:membranes12070708. [PMID: 35877911 PMCID: PMC9320227 DOI: 10.3390/membranes12070708] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 11/16/2022]
Abstract
Antibiotic resistance is a worldwide public health problem due to the costs and mortality rates it generates. However, the large pharmaceutical industries have stopped searching for new antibiotics because of their low profitability, given the rapid replacement rates imposed by the increasingly observed resistance acquired by microorganisms. Alternatively, antimicrobial peptides (AMPs) have emerged as potent molecules with a much lower rate of resistance generation. The discovery of these peptides is carried out through extensive in vitro screenings of either rational or non-rational libraries. These processes are tedious and expensive and generate only a few AMP candidates, most of which fail to show the required activity and physicochemical properties for practical applications. This work proposes implementing an artificial intelligence algorithm to reduce the required experimentation and increase the efficiency of high-activity AMP discovery. Our deep learning (DL) model, called AMPs-Net, outperforms the state-of-the-art method by 8.8% in average precision. Furthermore, it is highly accurate to predict the antibacterial and antiviral capacity of a large number of AMPs. Our search led to identifying two unreported antimicrobial motifs and two novel antimicrobial peptides related to them. Moreover, by coupling DL with molecular dynamics (MD) simulations, we were able to find a multifunctional peptide with promising therapeutic effects. Our work validates our previously proposed pipeline for a more efficient rational discovery of novel AMPs.
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30
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Antimicrobial peptides for tackling cystic fibrosis related bacterial infections: a review. Microbiol Res 2022; 263:127152. [DOI: 10.1016/j.micres.2022.127152] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 11/18/2022]
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31
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Barzan G, Kokalari I, Gariglio G, Ghibaudi E, Devocelle M, Monopoli MP, Sacco A, Greco A, Giovannozzi AM, Rossi AM, Fenoglio I. Molecular Aspects of the Interaction with Gram-Negative and Gram-Positive Bacteria of Hydrothermal Carbon Nanoparticles Associated with Bac8c 2,5Leu Antimicrobial Peptide. ACS OMEGA 2022; 7:16402-16413. [PMID: 35601297 PMCID: PMC9118266 DOI: 10.1021/acsomega.2c00305] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 04/18/2022] [Indexed: 06/15/2023]
Abstract
Antimicrobial peptides (AMPs) are widely studied as therapeutic agents due to their broad-spectrum efficacy against infections. However, their clinical use is hampered by the low in vivo bioavailability and systemic toxicity. Such limitations might be overcome by using appropriate drug delivery systems. Here, the preparation of a drug delivery system (DDS) by physical conjugation of an arginine-rich peptide and hydrothermal carbon nanoparticles (CNPs) has been explored, and its antimicrobial efficacy against Eschericia coli (E. coli) and Staphylococcus aureus investigated in comparison with the unloaded carrier and the free peptide. The mechanism of interaction between CNPs and the bacteria was investigated by scanning electron microscopy and a combined dielectrophoresis-Raman spectroscopy method for real-time analysis. In view of a possible systemic administration, the effect of proteins on the stability of the DDS was investigated by using albumin as a model protein. The peptide was bounded electrostatically to the CNPs surface, establishing an equilibrium modulated by pH and albumin. The DDS exhibited antimicrobial activity toward the two bacterial strains, albeit lower as compared to the free peptide. The decrease in effectiveness toward E. coli was likely due to the rapid formation of a particle-induced extracellular matrix. The present results are relevant for the future development of hydrothermal CNPs as drug delivery agents of AMPs.
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Affiliation(s)
- Giulia Barzan
- National
Institute of Metrological Research (INRiM), 10135 Torino, Italy
- Department
of Electronics and Telecommunications, Politecnico
di Torino, 10129 Torino, Italy
| | - Ida Kokalari
- Department
of Chemistry, University of Torino, 10125 Torino, Italy
| | - Giacomo Gariglio
- Department
of Chemistry, University of Torino, 10125 Torino, Italy
| | - Elena Ghibaudi
- Department
of Chemistry, University of Torino, 10125 Torino, Italy
| | - Marc Devocelle
- Department
of Chemistry, Royal College of Surgeons
in Ireland (RCSI), Dublin 2, Ireland
| | - Marco P. Monopoli
- Department
of Chemistry, Royal College of Surgeons
in Ireland (RCSI), Dublin 2, Ireland
| | - Alessio Sacco
- National
Institute of Metrological Research (INRiM), 10135 Torino, Italy
| | - Angelo Greco
- National
Institute of Metrological Research (INRiM), 10135 Torino, Italy
- Department
of Electronics and Telecommunications, Politecnico
di Torino, 10129 Torino, Italy
| | | | - Andrea M. Rossi
- National
Institute of Metrological Research (INRiM), 10135 Torino, Italy
| | - Ivana Fenoglio
- Department
of Chemistry, University of Torino, 10125 Torino, Italy
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32
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Chen CH, Bepler T, Pepper K, Fu D, Lu TK. Synthetic molecular evolution of antimicrobial peptides. Curr Opin Biotechnol 2022; 75:102718. [PMID: 35395425 DOI: 10.1016/j.copbio.2022.102718] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/14/2022] [Accepted: 03/01/2022] [Indexed: 01/18/2023]
Abstract
As we learn more about how peptide structure and activity are related, we anticipate that antimicrobial peptides will be engineered to have strong potency and distinct functions and that synthetic peptides will have new biomedical applications, such as treatments for emerging infectious diseases. As a result of the enormous number of possible amino acid sequences and the low-throughput nature of antimicrobial peptide assays, computational tools for peptide design and optimization are needed for direct experimentation toward obtaining functional sequences. Recent developments in computational tools have improved peptide design, saving labor, reagents, costs, and time. At the same time, improvements in peptide synthesis and experimental platforms continue to reduce the cost and increase the throughput of peptide-drug screening. In this review, we discuss the current methods of peptide design and engineering, including in silico methods and peptide synthesis and screening, and highlight areas of potential improvement.
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Affiliation(s)
- Charles H Chen
- Synthetic Biology Center, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Tristan Bepler
- Synthetic Biology Center, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Simons Machine Learning Center, New York Structural Biology Center, New York, NY 10027, USA
| | - Karen Pepper
- Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Debbie Fu
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Timothy K Lu
- Synthetic Biology Center, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02142, USA; Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02142, USA; Senti Biosciences, South San Francisco, CA 94080, USA.
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33
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Guo K, Zhang M, Cai J, Ma Z, Fang Z, Zhou H, Chen J, Gao M, Wang L. Peptide-Engineered AIE Nanofibers with Excellent and Precisely Adjustable Antibacterial Activity. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2108030. [PMID: 35307954 DOI: 10.1002/smll.202108030] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/27/2022] [Indexed: 06/14/2023]
Abstract
Photosensitizers with aggregation-induced emission properties (AIEgens) can produce reactive oxygen species (ROS) under irradiation, showing great potential in the antibacterial field. However, due to the limited molecular skeletons, the development of AIEgens with precisely adjustable antibacterial activity is still a daunting challenge. Herein, a series of AIE nanofibers (AIE-NFs) based on the AIEgen of DTPM as the inner core and rationally designed peptides as bacterial recognition ligands (e.g., antimicrobial peptide (AMP) HHC36, ditryptophan, polyarginine, and polylysine) is developed. These AIE-NFs show precisely adjustable antibacterial behaviors simply by changing the decorated peptides, which can regulate the aggregation and inhibition of different bacteria. By mechanistic analysis, it is demonstrated that this effect can be attributed to the synergistic antibacterial activities of the ROS and the peptides. It is noteworthy that the optimized AIE-NFs, NFs-K18, can efficiently aggregate bacteria to cluster and kill four types of clinical bacteria under irradiation in vitro, inhibit the infection of methicillin-resistant Staphylococcus aureus (MRSA) and promote wound healing in vivo. To the authors' knowledge, this is the first report of AIE-NFs with precisely adjustable antibacterial activity, providing new opportunities for photodynamic therapy (PDT) treatment of infection.
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Affiliation(s)
- Kunzhong Guo
- National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou, 510006, China
| | - Minjie Zhang
- School of Materials Science and Engineering, South China University of Technology, Guangzhou, 510641, China
| | - Junyi Cai
- National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou, 510006, China
| | - Zunwei Ma
- National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou, 510006, China
| | - Zhou Fang
- National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou, 510006, China
| | - Haiyan Zhou
- Key Laboratory of Biomedical Engineering of Guangdong Province, South China University of Technology, Guangzhou, 510641, China
| | - Junjian Chen
- Key Laboratory of Biomedical Engineering of Guangdong Province, South China University of Technology, Guangzhou, 510641, China
| | - Meng Gao
- School of Materials Science and Engineering, South China University of Technology, Guangzhou, 510641, China
| | - Lin Wang
- National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou, 510006, China
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Matthyssen T, Li W, Holden JA, Lenzo JC, Hadjigol S, O’Brien-Simpson NM. The Potential of Modified and Multimeric Antimicrobial Peptide Materials as Superbug Killers. Front Chem 2022; 9:795433. [PMID: 35083194 PMCID: PMC8785218 DOI: 10.3389/fchem.2021.795433] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 11/24/2021] [Indexed: 01/10/2023] Open
Abstract
Antimicrobial peptides (AMPs) are found in nearly all living organisms, show broad spectrum antibacterial activity, and can modulate the immune system. Furthermore, they have a very low level of resistance induction in bacteria, which makes them an ideal target for drug development and for targeting multi-drug resistant bacteria 'Superbugs'. Despite this promise, AMP therapeutic use is hampered as typically they are toxic to mammalian cells, less active under physiological conditions and are susceptible to proteolytic degradation. Research has focused on addressing these limitations by modifying natural AMP sequences by including e.g., d-amino acids and N-terminal and amino acid side chain modifications to alter structure, hydrophobicity, amphipathicity, and charge of the AMP to improve antimicrobial activity and specificity and at the same time reduce mammalian cell toxicity. Recently, multimerisation (dimers, oligomer conjugates, dendrimers, polymers and self-assembly) of natural and modified AMPs has further been used to address these limitations and has created compounds that have improved activity and biocompatibility compared to their linear counterparts. This review investigates how modifying and multimerising AMPs impacts their activity against bacteria in planktonic and biofilm states of growth.
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Affiliation(s)
- Tamara Matthyssen
- ACTV Research Group, The University of Melbourne, Melbourne Dental School, Centre for Oral Health Research, Royal Dental Hospital, Melbourne, VIC, Australia
| | - Wenyi Li
- ACTV Research Group, The University of Melbourne, Melbourne Dental School, Centre for Oral Health Research, Royal Dental Hospital, Melbourne, VIC, Australia
| | - James A. Holden
- Centre for Oral Health Research, The University of Melbourne, Melbourne Dental School, Royal Dental Hospital, Melbourne, VIC, Australia
| | - Jason C. Lenzo
- Centre for Oral Health Research, The University of Melbourne, Melbourne Dental School, Royal Dental Hospital, Melbourne, VIC, Australia
| | - Sara Hadjigol
- ACTV Research Group, The University of Melbourne, Melbourne Dental School, Centre for Oral Health Research, Royal Dental Hospital, Melbourne, VIC, Australia
| | - Neil M. O’Brien-Simpson
- ACTV Research Group, The University of Melbourne, Melbourne Dental School, Centre for Oral Health Research, Royal Dental Hospital, Melbourne, VIC, Australia
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Nicolas M, Beito B, Oliveira M, Tudela Martins M, Gallas B, Salmain M, Boujday S, Humblot V. Strategies for Antimicrobial Peptides Immobilization on Surfaces to Prevent Biofilm Growth on Biomedical Devices. Antibiotics (Basel) 2021; 11:13. [PMID: 35052891 PMCID: PMC8772980 DOI: 10.3390/antibiotics11010013] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/20/2021] [Accepted: 12/22/2021] [Indexed: 01/04/2023] Open
Abstract
Nosocomial and medical device-induced biofilm infections affect millions of lives and urgently require innovative preventive approaches. These pathologies have led to the development of numerous antimicrobial strategies, an emergent topic involving both natural and synthetic routes, among which some are currently under testing for clinical approval and use. Antimicrobial peptides (AMPs) are ideal candidates for this fight. Therefore, the strategies involving surface functionalization with AMPs to prevent bacterial attachment/biofilms formation have experienced a tremendous development over the last decade. In this review, we describe the different mechanisms of action by which AMPs prevent bacterial adhesion and/or biofilm formation to better address their potential as anti-infective agents. We additionally analyze AMP immobilization techniques on a variety of materials, with a focus on biomedical applications. Furthermore, we summarize the advances made to date regarding the immobilization strategies of AMPs on various surfaces and their ability to prevent the adhesion of various microorganisms. Progress toward the clinical approval of AMPs in antibiotherapy is also reviewed.
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Affiliation(s)
- Mathieu Nicolas
- Sorbonne Université, UMR 7197, Laboratoire de Réactivité de Surface, Centre National de la Recherche Scientifique (CNRS), 4 Place Jussieu, F-75005 Paris, France;
- Sorbonne Université, Institute of Nanosciences Paris (INSP), Centre National de la Recherche Scientifique (CNRS), 4 Place Jussieu, F-75005 Paris, France;
| | - Bruno Beito
- Sorbonne Université, Master de Chimie, Profil MatNanoBio, Faculté des Sciences et Ingénierie of Sorbonne Université, 4 Place Jussieu, F-75005 Paris, France; (B.B.); (M.O.); (M.T.M.)
| | - Marta Oliveira
- Sorbonne Université, Master de Chimie, Profil MatNanoBio, Faculté des Sciences et Ingénierie of Sorbonne Université, 4 Place Jussieu, F-75005 Paris, France; (B.B.); (M.O.); (M.T.M.)
| | - Maria Tudela Martins
- Sorbonne Université, Master de Chimie, Profil MatNanoBio, Faculté des Sciences et Ingénierie of Sorbonne Université, 4 Place Jussieu, F-75005 Paris, France; (B.B.); (M.O.); (M.T.M.)
| | - Bruno Gallas
- Sorbonne Université, Institute of Nanosciences Paris (INSP), Centre National de la Recherche Scientifique (CNRS), 4 Place Jussieu, F-75005 Paris, France;
| | - Michèle Salmain
- Sorbonne Université, Institut Parisien de Chimie Moléculaire (IPCM), Centre National de la Recherche Scientifique (CNRS), 4 Place Jussieu, F-75005 Paris, France;
| | - Souhir Boujday
- Sorbonne Université, UMR 7197, Laboratoire de Réactivité de Surface, Centre National de la Recherche Scientifique (CNRS), 4 Place Jussieu, F-75005 Paris, France;
| | - Vincent Humblot
- Sorbonne Université, UMR 7197, Laboratoire de Réactivité de Surface, Centre National de la Recherche Scientifique (CNRS), 4 Place Jussieu, F-75005 Paris, France;
- Franche-Comté Électronique Mécanique Thermique et Optique-Sciences et Technologies (FEMTO-ST) Institute, Centre National de la Recherche Scientifique (CNRS), UMR 6174, Université Bourgogne Franche-Comté, 15B Avenue des Montboucons, F-25030 Besançon, France
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36
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Kerr RV, Fairbairn JA, Merritt AT, Bugg TDH. Peptidomimetic analogues of an Arg-Trp-x-x-Trp motif responsible for interaction of translocase MraY with bacteriophage ϕX174 lysis protein E. Bioorg Med Chem 2021; 52:116502. [PMID: 34808406 DOI: 10.1016/j.bmc.2021.116502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/29/2021] [Accepted: 10/29/2021] [Indexed: 11/25/2022]
Abstract
Translocase MraY is the target for bacteriophage ϕX174 lysis protein E, which interacts via a protein-protein interaction mediated by Phe-288 and Glu-287 of E. coli MraY, and an Arg-Trp-x-x-Trp motif on protein E, also found in several cationic antimicrobial peptides. Analogues of Arg-Trp-octyl ester, found previously to show antimicrobial activity, were tested for antimicrobial activity, with Lys-Trp-oct (MIC50P. fluorescens 5 µg/mL) and Arg-Trp-decyl ester (MIC50P. fluorescens 3 µg/mL) showing enhanced antimicrobial activity. Synthesis and testing of α-helix peptidomimetic analogues for this motif revealed improved antibacterial activity (MIC50E. coli 4-7 µg/mL) for analogues containing two aromatic substituents, mimicking the Arg-Trp-x-x-Trp motif, and MraY inhibition (IC50 140 µM) by one such peptidomimetic. Investigation of mechanism of action using the Alamar Blue membrane permeabilisation assay revealed bacteriostatic and bacteriocidal mechanisms in different members of this set of compounds, raising the possibility of more than one biological target. The observed antimicrobial activity and MraY inhibition shown by peptidomimetic compounds confirms that this site could be targeted by drug-like molecules.
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Affiliation(s)
- Rachel V Kerr
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Julia A Fairbairn
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Andrew T Merritt
- LifeArc, SBC Open Innovation Campus, Stevenage, Herts SG1 2FX, UK
| | - Timothy D H Bugg
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK.
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37
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Oulas A, Zachariou M, Chasapis CT, Tomazou M, Ijaz UZ, Schmartz GP, Spyrou GM, Vlamis-Gardikas A. Putative Antimicrobial Peptides Within Bacterial Proteomes Affect Bacterial Predominance: A Network Analysis Perspective. Front Microbiol 2021; 12:752674. [PMID: 34867874 PMCID: PMC8636115 DOI: 10.3389/fmicb.2021.752674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/11/2021] [Indexed: 11/13/2022] Open
Abstract
The predominance of bacterial taxa in the gut, was examined in view of the putative antimicrobial peptide sequences (AMPs) within their proteomes. The working assumption was that compatible bacteria would share homology and thus immunity to their putative AMPs, while competing taxa would have dissimilarities in their proteome-hidden AMPs. A network-based method ("Bacterial Wars") was developed to handle sequence similarities of predicted AMPs among UniProt-derived protein sequences from different bacterial taxa, while a resulting parameter ("Die" score) suggested which taxa would prevail in a defined microbiome. T he working hypothesis was examined by correlating the calculated Die scores, to the abundance of bacterial taxa from gut microbiomes from different states of health and disease. Eleven publicly available 16S rRNA datasets and a dataset from a full shotgun metagenomics served for the analysis. The overall conclusion was that AMPs encrypted within bacterial proteomes affected the predominance of bacterial taxa in chemospheres.
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Affiliation(s)
- Anastasis Oulas
- Bioinformatics Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,The Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Margarita Zachariou
- Bioinformatics Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,The Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Christos T Chasapis
- NMR Center, Instrumental Analysis Laboratory, School of Natural Sciences, University of Patras, Patras, Greece
| | - Marios Tomazou
- Bioinformatics Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,The Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Umer Z Ijaz
- School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | | | - George M Spyrou
- Bioinformatics Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,The Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Alexios Vlamis-Gardikas
- Division of Organic Chemistry, Biochemistry and Natural Products, Department of Chemistry, University of Patras, Patras, Greece
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38
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Luna-Reyes I, Pérez-Hernández EG, Delgado-Coello B, Mas-Oliva J. Peptides as Therapeutic Molecules to Neutralize Gram-negative Bacterial Lipopolysaccharides in Sepsis and Septic Shock. Arch Med Res 2021; 52:798-807. [DOI: 10.1016/j.arcmed.2021.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 08/03/2021] [Indexed: 11/16/2022]
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39
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Yu K, Alzahrani A, Khoddami S, Cheng JTJ, Mei Y, Gill A, Luo HD, Haney EF, Hilpert K, Hancock REW, Lange D, Kizhakkedathu JN. Rapid Assembly of Infection-Resistant Coatings: Screening and Identification of Antimicrobial Peptides Works in Cooperation with an Antifouling Background. ACS APPLIED MATERIALS & INTERFACES 2021; 13:36784-36799. [PMID: 34328312 DOI: 10.1021/acsami.1c07515] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Bacterial adhesion and the succeeding biofilm formation onto surfaces are responsible for implant- and device-associated infections. Bifunctional coatings integrating both nonfouling components and antimicrobial peptides (AMPs) are a promising approach to develop potent antibiofilm coatings. However, the current approaches and chemistry for such coatings are time-consuming and dependent on substrates and involve a multistep process. Also, the information is limited on the influence of the coating structure or its components on the antibiofilm activity of such AMP-based coatings. Here, we report a new strategy to rapidly assemble a stable, potent, and substrate-independent AMP-based antibiofilm coating in a nonfouling background. The coating structure allowed for the screening of AMPs in a relevant nonfouling background to identify optimal peptide combinations that work in cooperation to generate potent antibiofilm activity. The structure of the coating was changed by altering the organization of the hydrophilic polymer chains within the coatings. The coatings were thoroughly characterized using various surface analytical techniques and correlated with the efficiency to prevent biofilm formation against diverse bacteria. The coating method that allowed the conjugation of AMPs without altering the steric protection ability of hydrophilic polymer structure results in a bifunctional surface coating with excellent antibiofilm activity. In contrast, the conjugation of AMPs directly to the hydrophilic polymer chains resulted in a surface with poor antibiofilm activity and increased adhesion of bacteria. Using this coating approach, we further established a new screening method and identified a set of potent surface-tethered AMPs with high activity. The success of this new peptide screening and coating method is demonstrated using a clinically relevant mouse infection model to prevent catheter-associated urinary tract infection (CAUTI).
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Affiliation(s)
- Kai Yu
- Centre for Blood Research and Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Amal Alzahrani
- The Stone Centre at VGH, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia V5Z 1M9, Canada
| | - Sara Khoddami
- The Stone Centre at VGH, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia V5Z 1M9, Canada
| | - John T J Cheng
- Department of Microbiology and Immunology and Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Yan Mei
- Centre for Blood Research and Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Arshdeep Gill
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Haiming D Luo
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Evan F Haney
- Department of Microbiology and Immunology and Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Kai Hilpert
- Institute of Infection and Immunology, St. George's University of London (SGUL), London SW17 0RE, United Kingdom
| | - Robert E W Hancock
- Department of Microbiology and Immunology and Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Dirk Lange
- The Stone Centre at VGH, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia V5Z 1M9, Canada
| | - Jayachandran N Kizhakkedathu
- Centre for Blood Research and Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
- The School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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40
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Gu J, Isozumi N, Yuan S, Jin L, Gao B, Ohki S, Zhu S. Evolution-Based Protein Engineering for Antifungal Peptide Improvement. Mol Biol Evol 2021; 38:5175-5189. [PMID: 34320203 PMCID: PMC8557468 DOI: 10.1093/molbev/msab224] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Antimicrobial peptides (AMPs) have been considered as the alternatives to antibiotics because of their less susceptibility to microbial resistance. However, compared with conventional antibiotics they show relatively low activity and the consequent high cost and nonspecific cytotoxicity, hindering their clinical application. What’s more, engineering of AMPs is a great challenge due to the inherent complexity in their sequence, structure, and function relationships. Here, we report an evolution-based strategy for improving the antifungal activity of a nematode-sourced defensin (Cremycin-5). This strategy utilizes a sequence-activity comparison between Cremycin-5 and its functionally diverged paralogs to identify sites associated with antifungal activity for screening of enhanceable activity-modulating sites for subsequent saturation mutagenesis. Using this strategy, we identified a site (Glu-15) whose mutations with nearly all other types of amino acids resulted in a universally enhanced activity against multiple fungal species, which is thereby defined as a Universally Enhanceable Activity-Modulating Site (UEAMS). Especially, Glu15Lys even exhibited >9-fold increased fungicidal potency against several clinical isolates of Candida albicans through inhibiting cytokinesis. This mutant showed high thermal and serum stability and quicker killing kinetics than clotrimazole without detectable hemolysis. Molecular dynamic simulations suggest that the mutations at the UEAMS likely limit the conformational flexibility of a distant functional residue via allostery, enabling a better peptide–fungus interaction. Further sequence, structural, and mutational analyses of the Cremycin-5 ortholog uncover an epistatic interaction between the UEAMS and another site that may constrain its evolution. Our work lights one new road to success of engineering AMP drug leads.
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Affiliation(s)
- Jing Gu
- Group of Peptide Biology and Evolution, State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Noriyoshi Isozumi
- Center for Nano Materials and Technology (CNMT), Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Shouli Yuan
- Group of Peptide Biology and Evolution, State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ling Jin
- Group of Peptide Biology and Evolution, State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bin Gao
- Group of Peptide Biology and Evolution, State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101, China
| | - Shinya Ohki
- Center for Nano Materials and Technology (CNMT), Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Shunyi Zhu
- Group of Peptide Biology and Evolution, State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101, China
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41
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Fennouri A, List J, Ducrey J, Dupasquier J, Sukyte V, Mayer SF, Vargas RD, Pascual Fernandez L, Bertani F, Rodriguez Gonzalo S, Yang J, Mayer M. Tuning the Diameter, Stability, and Membrane Affinity of Peptide Pores by DNA-Programmed Self-Assembly. ACS NANO 2021; 15:11263-11275. [PMID: 34128638 DOI: 10.1021/acsnano.0c10311] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Protein pores recently enabled a breakthrough in bioanalytics by making it possible to sequence individual DNA and RNA strands during their translocation through the lumen of the pore. Despite this success and the overall promise of nanopore-based single-molecule analytics, protein pores have not yet reached their full potential for the analysis and characterization of globular biomolecules such as natively folded proteins. One reason is that the diameters of available protein pores are too small for accommodating the translocation of most folded globular proteins through their lumen. The work presented here provides a step toward overcoming this limitation by programmed self-assembly of α-helical pore-forming peptides with covalently attached single-stranded DNA (ssDNA). Specifically, hybridization of the peptide ceratotoxin A (CtxA) with N-terminally attached ssDNA to a complementary DNA template strand with 4, 8, or 12 hybridization sites made it possible to trigger the assembly of pores with various diameters ranging from approximately 0.5 to 4 nm. Hybridization of additional DNA strands to these assemblies achieved extended functionality in a modular fashion without the need for modifying the amino acid sequence of the peptides. For instance, functionalization of these semisynthetic biological nanopores with DNA-cholesterol anchors increased their affinity to lipid membranes compared to pores formed by native CtxA, while charged transmembrane segments prolonged their open-state lifetime. Assembly of these hybrid DNA-peptides by a template increased their cytotoxic activity and made it possible to kill cancer cells at 20-fold lower total peptide concentrations than nontemplated CtxA.
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Affiliation(s)
- Aziz Fennouri
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, 1700 Fribourg, Switzerland
| | - Jonathan List
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, 1700 Fribourg, Switzerland
| | - Julie Ducrey
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, 1700 Fribourg, Switzerland
| | - Jessica Dupasquier
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, 1700 Fribourg, Switzerland
| | - Viktorija Sukyte
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, 1700 Fribourg, Switzerland
| | - Simon F Mayer
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, 1700 Fribourg, Switzerland
| | - Reyner D Vargas
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, 1700 Fribourg, Switzerland
| | - Laura Pascual Fernandez
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, 1700 Fribourg, Switzerland
| | - Frederick Bertani
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, 1700 Fribourg, Switzerland
| | - Sandra Rodriguez Gonzalo
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, 1700 Fribourg, Switzerland
| | - Jerry Yang
- Department of Chemistry and Biochemistry, University of California, San Diego, California 92093, United States
| | - Michael Mayer
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, 1700 Fribourg, Switzerland
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42
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Antibiofilm activity of host defence peptides: complexity provides opportunities. Nat Rev Microbiol 2021; 19:786-797. [PMID: 34183822 DOI: 10.1038/s41579-021-00585-w] [Citation(s) in RCA: 109] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2021] [Indexed: 12/21/2022]
Abstract
Host defence peptides (HDPs) are integral components of innate immunity across all living organisms. These peptides can exert direct antibacterial effects, targeting planktonic cells (referred to as antimicrobial peptides), and exhibit antibiofilm (referred to as antibiofilm peptides), antiviral, antifungal and host-directed immunomodulatory activities. In this Review, we discuss how the complex functional attributes of HDPs provide many opportunities for the development of antimicrobial therapeutics, focusing particularly on their emerging antibiofilm properties. The mechanisms of action of antibiofilm peptides are compared and contrasted with those of antimicrobial peptides. Furthermore, obstacles for the practical translation of candidate peptides into therapeutics and the potential solutions are discussed. Critically, HDPs have the value-added assets of complex functional attributes, particularly antibiofilm and anti-inflammatory activities and their synergy with conventional antibiotics.
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43
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Marzuoli I, Cruz CHB, Lorenz CD, Fraternali F. Nanocapsule designs for antimicrobial resistance. NANOSCALE 2021; 13:10342-10355. [PMID: 34137751 DOI: 10.1039/d0nr08146a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The pressing need of new antimicrobial products is growing stronger, particularly because of widespread antimicrobial resistance, endangering our ability to treat common infections. The recent coronavirus pandemic has dramatically highlighted the necessity of effective antibacterial and antiviral protection. This work explores at the molecular level the mechanism of action of antibacterial nanocapsules assembled in virus-like particles, their stability and their interaction with mammal and antimicrobial model membranes. We use Molecular Dynamics with force-fields of different granularity and protein design strategies to study the stability, self-assembly and membrane poration properties of these nanocapsules.
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Affiliation(s)
- Irene Marzuoli
- Randall Centre for Cell and Molecular Biology, King's College London, London, UK.
| | - Carlos H B Cruz
- Randall Centre for Cell and Molecular Biology, King's College London, London, UK.
| | | | - Franca Fraternali
- Randall Centre for Cell and Molecular Biology, King's College London, London, UK.
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44
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Pirtskhalava M, Vishnepolsky B, Grigolava M, Managadze G. Physicochemical Features and Peculiarities of Interaction of AMP with the Membrane. Pharmaceuticals (Basel) 2021; 14:471. [PMID: 34067510 PMCID: PMC8156082 DOI: 10.3390/ph14050471] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/25/2021] [Accepted: 04/29/2021] [Indexed: 02/06/2023] Open
Abstract
Antimicrobial peptides (AMPs) are anti-infectives that have the potential to be used as a novel and untapped class of biotherapeutics. Modes of action of antimicrobial peptides include interaction with the cell envelope (cell wall, outer- and inner-membrane). A comprehensive understanding of the peculiarities of interaction of antimicrobial peptides with the cell envelope is necessary to perform a rational design of new biotherapeutics, against which working out resistance is hard for microbes. In order to enable de novo design with low cost and high throughput, in silico predictive models have to be invoked. To develop an efficient predictive model, a comprehensive understanding of the sequence-to-function relationship is required. This knowledge will allow us to encode amino acid sequences expressively and to adequately choose the accurate AMP classifier. A shared protective layer of microbial cells is the inner, plasmatic membrane. The interaction of AMP with a biological membrane (native and/or artificial) has been comprehensively studied. We provide a review of mechanisms and results of interactions of AMP with the cell membrane, relying on the survey of physicochemical, aggregative, and structural features of AMPs. The potency and mechanism of AMP action are presented in terms of amino acid compositions and distributions of the polar and apolar residues along the chain, that is, in terms of the physicochemical features of peptides such as hydrophobicity, hydrophilicity, and amphiphilicity. The survey of current data highlights topics that should be taken into account to come up with a comprehensive explanation of the mechanisms of action of AMP and to uncover the physicochemical faces of peptides, essential to perform their function. Many different approaches have been used to classify AMPs, including machine learning. The survey of knowledge on sequences, structures, and modes of actions of AMP allows concluding that only possessing comprehensive information on physicochemical features of AMPs enables us to develop accurate classifiers and create effective methods of prediction. Consequently, this knowledge is necessary for the development of design tools for peptide-based antibiotics.
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Affiliation(s)
- Malak Pirtskhalava
- Ivane Beritashvili Center of Experimental Biomedicine, Tbilisi 0160, Georgia; (B.V.); (M.G.); (G.M.)
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45
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Thompson Z, Greve JM, Cowan JA. Enhanced Synergism and Mechanism of Action Studies of Synthetic Antimicrobial Metallopeptides. ChemMedChem 2021; 16:2112-2120. [PMID: 33825350 DOI: 10.1002/cmdc.202100063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Indexed: 11/08/2022]
Abstract
Antimicrobial peptides (AMPs) are found throughout most kingdoms of life, are an important part of host immunity, and have been shown to act synergistically in various organisms to ameliorate bacterial infections. Herein, we report the synergistic behavior observed between two AMPs, Sub5 and CP10A, against E. coli. In addition, enhanced synergistic activity against E. coli and MRSA 43300 for two derivatives of Sub5, extended with the amino-terminal copper and nickel (ATCUN) binding motif, is observed when dosed together with CP10A, while displaying little cytotoxicity towards human dermal fibroblasts. All three combinations of peptides co-localized within bacterial cells as evidenced by fluorescence confocal microscopy. Investigations into the mechanism of synergy shows that all peptides indirectly damage DNA within cells, while only the ATCUN derivatives can oxidize phospholipids. Combinations of peptides were also shown to upregulate the concentration of reactive oxygen species within both E. coli and MRSA 43300. These results suggest that the production of reactive oxygen species is an important aspect mechanistically and further highlights the potential of these metallopeptides to aid in the treatment of antibiotic-resistant infections.
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Affiliation(s)
- Zechariah Thompson
- Chemistry and Biochemistry, The Ohio State University, Evans Laboratory of Chemistry 100, West 18th Avenue, Columbus, Ohio, 43210, USA
| | - Jenna M Greve
- Chemistry and Biochemistry, The Ohio State University, Evans Laboratory of Chemistry 100, West 18th Avenue, Columbus, Ohio, 43210, USA
| | - James Allan Cowan
- Chemistry and Biochemistry, The Ohio State University, Evans Laboratory of Chemistry 100, West 18th Avenue, Columbus, Ohio, 43210, USA
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46
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Van Oort CM, Ferrell JB, Remington JM, Wshah S, Li J. AMPGAN v2: Machine Learning-Guided Design of Antimicrobial Peptides. J Chem Inf Model 2021; 61:2198-2207. [PMID: 33787250 DOI: 10.1021/acs.jcim.0c01441] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Antibiotic resistance is a critical public health problem. Each year ∼2.8 million resistant infections lead to more than 35 000 deaths in the U.S. alone. Antimicrobial peptides (AMPs) show promise in treating resistant infections. However, applications of known AMPs have encountered issues in development, production, and shelf-life. To drive the development of AMP-based treatments, it is necessary to create design approaches with higher precision and selectivity toward resistant targets. Previously, we developed AMPGAN and obtained proof-of-concept evidence for the generative approach to design AMPs with experimental validation. Building on the success of AMPGAN, we present AMPGAN v2, a bidirectional conditional generative adversarial network (BiCGAN)-based approach for rational AMP design. AMPGAN v2 uses generator-discriminator dynamics to learn data-driven priors and controls generation using conditioning variables. The bidirectional component, implemented using a learned encoder to map data samples into the latent space of the generator, aids iterative manipulation of candidate peptides. These elements allow AMPGAN v2 to generate candidates that are novel, diverse, and tailored for specific applications, making it an efficient AMP design tool.
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Affiliation(s)
- Colin M Van Oort
- Department of Computer Science, University of Vermont, Burlington, Vermont 05405, United States
| | - Jonathon B Ferrell
- Department of Chemistry, University of Vermont, Burlington, Vermont 05405, United States
| | - Jacob M Remington
- Department of Chemistry, University of Vermont, Burlington, Vermont 05405, United States
| | - Safwan Wshah
- Department of Computer Science, University of Vermont, Burlington, Vermont 05405, United States
| | - Jianing Li
- Department of Chemistry, University of Vermont, Burlington, Vermont 05405, United States
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47
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Blumenthal I, Davis LR, Berman CM, Griswold KE. Nonclassical antagonism between human lysozyme and AMPs against Pseudomonas aeruginosa. FEBS Open Bio 2021; 11:705-713. [PMID: 33480189 PMCID: PMC7931236 DOI: 10.1002/2211-5463.13094] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/25/2020] [Accepted: 01/14/2021] [Indexed: 12/28/2022] Open
Abstract
Combinations of human lysozyme (hLYS) and antimicrobial peptides (AMPs) are known to exhibit either additive or synergistic activity, and as a result, they have therapeutic potential for persistent and antibiotic‐resistant infections. We examined hLYS activity against Pseudomonas aeruginosa when combined with six different AMPs. In contrast to prior reports, we discovered that some therapeutically relevant AMPs manifest striking antagonistic interactions with hLYS across particular concentration ranges. We further found that the synthetic AMP Tet009 can inhibit hLYS‐mediated bacterial lysis. To the best of our knowledge, these results represent the first observations of antagonism between hLYS and AMPs, and they advise that future development of lytic enzyme and AMP combination therapies considers the potential for antagonistic interactions.
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Affiliation(s)
- Ian Blumenthal
- Thayer School of Engineering, Dartmouth, Hanover, NH, USA
| | - Lydia R Davis
- Thayer School of Engineering, Dartmouth, Hanover, NH, USA
| | - Chet M Berman
- Thayer School of Engineering, Dartmouth, Hanover, NH, USA
| | - Karl E Griswold
- Thayer School of Engineering, Dartmouth, Hanover, NH, USA.,Lyticon LLC, Lebanon, NH, USA
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48
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Zhang W, Lv Y, Lv A, Wei S, Zhang S, Li C, Hu Y. Sub3 inhibits Aspergillus flavus growth by disrupting mitochondrial energy metabolism, and has potential biocontrol during peanut storage. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2021; 101:486-496. [PMID: 32643802 DOI: 10.1002/jsfa.10657] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 06/16/2020] [Accepted: 07/09/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Aspergillus flavus, a saprophytic fungus, is regularly detected in oil-enriched seeds. During colonization, this organism releases aflatoxins that pose a serious risk to food safety and human health. Therefore, an eco-friendly biological approach to inhibit the pathogen is desirable. RESULTS Experimental results indicated that A. flavus spores could not germinate in potato dextrose broth culture medium, when the concentration of Sub3 exceeded 0.15 g L-1 . Morphological evaluation performed by flow cytometry and scanning electron microscopy indicated that spores were shrunken and pitted following Sub3 exposure. Physiological assessment using propidium iodide, 5,5',6,6'-tetrachloro-1,1',3,3'-tetraethylbenzimidazolocarbocyanine iodide, 2,7-dichlorodihydrofluorescein diacetate and 4',6-diamidino-2-phenylindole staining revealed damaged cell membranes, decreased mitochondrial membrane potential, increased intracellular reactive oxygen species levels, and elevated large nuclear condensation and DNA fragmentation. Moreover, mitochondrial dehydrogenase activity was reduced by 29.42% and 45.48% after treatment with 0.1 and 0.15 g L-1 Sub3, respectively. Additionally, colonization capacity in peanut was significantly decreased, and the number of spores on seeds treated with Sub3 was decreased by 26.86% (0.1 g L-1 ) and 77.74% (0.15 g L-1 ) compared with the control group. CONCLUSION Sub3 likely inhibits A. flavus by crossing the cell wall and targeting the cell membrane, disrupting mitochondrial energy metabolism, and inducing DNA damage, leading to spore death. Thus, Sub3 may provide a useful biocontrol strategy to control A. flavus growth in peanuts. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Wei Zhang
- College of Biological Engineering, Henan University of Technology, Zhengzhou, P. R. China
| | - Yangyong Lv
- College of Biological Engineering, Henan University of Technology, Zhengzhou, P. R. China
| | - Ang Lv
- College of Biological Engineering, Henan University of Technology, Zhengzhou, P. R. China
| | - Shan Wei
- College of Biological Engineering, Henan University of Technology, Zhengzhou, P. R. China
| | - Shuaibing Zhang
- College of Biological Engineering, Henan University of Technology, Zhengzhou, P. R. China
| | - Cuixiang Li
- College of Biological Engineering, Henan University of Technology, Zhengzhou, P. R. China
| | - Yuansen Hu
- College of Biological Engineering, Henan University of Technology, Zhengzhou, P. R. China
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49
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Wu BC, Haney EF, Akhoundsadegh N, Pletzer D, Trimble MJ, Adriaans AE, Nibbering PH, Hancock REW. Human organoid biofilm model for assessing antibiofilm activity of novel agents. NPJ Biofilms Microbiomes 2021; 7:8. [PMID: 33495449 PMCID: PMC7835231 DOI: 10.1038/s41522-020-00182-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 12/11/2020] [Indexed: 02/08/2023] Open
Abstract
Bacterial biofilms cause 65% of all human infections and are highly resistant to antibiotic therapy but lack specific treatments. To provide a human organoid model for studying host-microbe interplay and enabling screening for novel antibiofilm agents, a human epidermis organoid model with robust methicillin-resistant Staphylococcus aureus (MRSA) USA300 and Pseudomonas aeruginosa PAO1 biofilm was developed. Treatment of 1-day and 3-day MRSA and PAO1 biofilms with antibiofilm peptide DJK-5 significantly and substantially reduced the bacterial burden. This model enabled the screening of synthetic host defense peptides, revealing their superior antibiofilm activity against MRSA compared to the antibiotic mupirocin. The model was extended to evaluate thermally wounded skin infected with MRSA biofilms resulting in increased bacterial load, cytotoxicity, and pro-inflammatory cytokine levels that were all reduced upon treatment with DJK-5. Combination treatment of DJK-5 with an anti-inflammatory peptide, 1002, further reduced cytotoxicity and skin inflammation.
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Affiliation(s)
- Bing Catherine Wu
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Evan F Haney
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Noushin Akhoundsadegh
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Daniel Pletzer
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, University of Otago, Dunedin, Otago, New Zealand
| | - Michael J Trimble
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Alwin E Adriaans
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter H Nibbering
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Robert E W Hancock
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada.
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50
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Schulte C, Khayenko V, Nordblom NF, Tippel F, Peck V, Gupta AJ, Maric HM. High-throughput determination of protein affinities using unmodified peptide libraries in nanomolar scale. iScience 2021; 24:101898. [PMID: 33364586 PMCID: PMC7753147 DOI: 10.1016/j.isci.2020.101898] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/13/2020] [Accepted: 12/01/2020] [Indexed: 12/02/2022] Open
Abstract
Protein-protein interactions (PPIs) are of fundamental importance for our understanding of physiology and pathology. PPIs involving short, linear motifs play a major role in immunological recognition, signaling, and regulation and provide attractive starting points for pharmaceutical intervention. Yet, state-of-the-art protein-peptide affinity determination approaches exhibit limited throughput and sensitivity, often resulting from ligand immobilization, labeling, or synthesis. Here, we introduce a high-throughput method for in-solution analysis of protein-peptide interactions using a phenomenon called temperature related intensity change (TRIC). We use TRIC for the identification and fine-mapping of low- and high-affinity protein interaction sites and the definition of sequence binding requirements. Validation is achieved by microarray-based studies using wild-type and mutated recombinant protein and the native protein within tissue lysates. On-chip neutralization and strong correlation with structural data establish TRIC as a quasi-label-free method to determine binding affinities of unmodified peptide libraries with large dynamic range.
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Affiliation(s)
- Clemens Schulte
- Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, University of Wuerzburg, Josef-Schneider-Str. 2, 97080 Wuerzburg, Germany
| | - Vladimir Khayenko
- Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, University of Wuerzburg, Josef-Schneider-Str. 2, 97080 Wuerzburg, Germany
| | - Noah Frieder Nordblom
- Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, University of Wuerzburg, Josef-Schneider-Str. 2, 97080 Wuerzburg, Germany
| | - Franziska Tippel
- Nanotemper Technologies GmbH, Flößergasse 4, 81369 Munich, Germany
| | - Violetta Peck
- Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, University of Wuerzburg, Josef-Schneider-Str. 2, 97080 Wuerzburg, Germany
| | - Amit Jean Gupta
- Nanotemper Technologies GmbH, Flößergasse 4, 81369 Munich, Germany
| | - Hans Michael Maric
- Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, University of Wuerzburg, Josef-Schneider-Str. 2, 97080 Wuerzburg, Germany
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