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Tang Y, Zhang Y, Zhang D, Liu Y, Nussinov R, Zheng J. Exploring pathological link between antimicrobial and amyloid peptides. Chem Soc Rev 2024. [PMID: 39041297 DOI: 10.1039/d3cs00878a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Amyloid peptides (AMYs) and antimicrobial peptides (AMPs) are considered as the two distinct families of peptides, characterized by their unique sequences, structures, biological functions, and specific pathological targets. However, accumulating evidence has revealed intriguing pathological connections between these peptide families in the context of microbial infection and neurodegenerative diseases. Some AMYs and AMPs share certain structural and functional characteristics, including the ability to self-assemble, the presence of β-sheet-rich structures, and membrane-disrupting mechanisms. These shared features enable AMYs to possess antimicrobial activity and AMPs to acquire amyloidogenic properties. Despite limited studies on AMYs-AMPs systems, the cross-seeding phenomenon between AMYs and AMPs has emerged as a crucial factor in the bidirectional communication between the pathogenesis of neurodegenerative diseases and host defense against microbial infections. In this review, we examine recent developments in the potential interplay between AMYs and AMPs, as well as their pathological implications for both infectious and neurodegenerative diseases. By discussing the current progress and challenges in this emerging field, this account aims to inspire further research and investments to enhance our understanding of the intricate molecular crosstalk between AMYs and AMPs. This knowledge holds great promise for the development of innovative therapies to combat both microbial infections and neurodegenerative disorders.
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Affiliation(s)
- Yijing Tang
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Ohio 44325, USA.
| | - Yanxian Zhang
- Division of Endocrinology and Diabetes, Department of Pediatrics, School of Medicine, Stanford University, Palo Alto, CA 94304, USA
| | - Dong Zhang
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, USA
| | - Yonglan Liu
- Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
- Department of Human Molecular Genetics and Biochemistry Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Jie Zheng
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Ohio 44325, USA.
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2
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Prince A, Tiwari A, Mandal T, Koiri D, Meher G, Sinha DK, Saleem M. Lipid Specificity of the Fusion of Bacterial Extracellular Vesicles with the Host Membrane. J Phys Chem B 2024. [PMID: 38981091 DOI: 10.1021/acs.jpcb.4c02321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
Bacterial membrane vesicles (MVs) facilitate the long-distance delivery of virulence factors crucial for pathogenicity. The entry and trafficking mechanisms of virulence factors inside host cells are recently emerging; however, whether bacterial MVs can fuse and modulate the physicochemical properties of the host lipid membrane and membrane lipid parameter for fusion remains unknown. In this study, we reconstituted the interaction of bacterial MVs with host cell lipid membranes and quantitatively showed that bacterial MV interaction increases the fluidity, dipole potential, and compressibility of a biologically relevant multicomponent host membrane upon fusion. The presence of cylindrical lipids, such as phosphatidylcholine, and a moderate acyl chain length of C16 help the MV interaction. While significant binding of bacterial MVs to the raft-like lipid membranes with phase-separated regions of the membrane was observed, however, MVs prefer binding to the liquid-disordered regions of the membrane. Furthermore, the elevated levels of cholesterol tend to hinder the interaction of bacterial MVs, as evident from the favorable excess Gibbs free energy of mixing bacterial MVs with host lipid membranes. The findings provide new insights that might have implications for the regulation of host machinery by bacterial pathogens through manipulation of the host membrane properties.
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Affiliation(s)
- Ashutosh Prince
- Department of Life Sciences, National Institute of Technology, Rourkela 769008, India
| | - Anuj Tiwari
- Department of Life Sciences, National Institute of Technology, Rourkela 769008, India
| | - Titas Mandal
- Department of Physical Biochemistry, University of Potsdam, Potsdam 14476, Germany
| | - Debraj Koiri
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, India
- Homi Bhabha National Institute, Mumbai 400094, India
| | - Geetanjali Meher
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, India
- Homi Bhabha National Institute, Mumbai 400094, India
| | - Deepak Kumar Sinha
- Department of Biological Chemistry, Indian Association for the Cultivation of Sciences, Kolkata 700032, India
| | - Mohammed Saleem
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, India
- Homi Bhabha National Institute, Mumbai 400094, India
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3
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Tang Y, Zhang D, Zheng J. Repurposing Antimicrobial Protegrin-1 as a Dual-Function Amyloid Inhibitor via Cross-seeding. ACS Chem Neurosci 2023; 14:3143-3155. [PMID: 37589476 DOI: 10.1021/acschemneuro.3c00293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023] Open
Abstract
Amyloids and antimicrobial peptides have traditionally been recognized as distinct families with separate biological functions and targets. However, certain amyloids and antimicrobial peptides share structural and functional characteristics that contribute to the development of neurodegenerative diseases. Specifically, the aggregation of amyloid-β (Aβ) and microbial infections are interconnected pathological factors in Alzheimer's disease (AD). In this study, we propose and demonstrate a novel repurposing strategy for an antimicrobial peptide of protegrin-1 (PG-1), which exhibits the ability to simultaneously prevent Aβ aggregation and microbial infection both in vitro and in vivo. Through a comprehensive analysis using protein, cell, and worm assays, we uncover multiple functions of PG-1 against Aβ, including the following: (i) complete inhibition of Aβ aggregation at a low molar ratio of PG-1/Aβ = 0.25:1, (ii) disassembly of the preformed Aβ fibrils into amorphous aggregates, (iii) reduction of Aβ-induced cytotoxicity in SH-SY5Y cells and transgenic GMC101 nematodes, and (iv) preservation of original antimicrobial activity against P.A., E.coli., S.A., and S.E. strains in the presence of Aβ. Mechanistically, the dual anti-amyloid and anti-bacterial functions of PG-1 primarily arise from its strong binding to distinct Aβ seeds (KD = 1.24-1.90 μM) through conformationally similar β-sheet associations. This work introduces a promising strategy to repurpose antimicrobial peptides as amyloid inhibitors, effectively targeting multiple pathological pathways in AD.
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Affiliation(s)
- Yijing Tang
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Dong Zhang
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Jie Zheng
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Akron, Ohio 44325, United States
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4
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John T, Piantavigna S, Dealey TJA, Abel B, Risselada HJ, Martin LL. Lipid oxidation controls peptide self-assembly near membranes through a surface attraction mechanism. Chem Sci 2023; 14:3730-3741. [PMID: 37035708 PMCID: PMC10074436 DOI: 10.1039/d3sc00159h] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 02/17/2023] [Indexed: 03/06/2023] Open
Abstract
The self-assembly of peptides into supramolecular structures has been linked to neurodegenerative diseases but has also been observed in functional roles. Peptides are physiologically exposed to crowded environments of biomacromolecules, and particularly cellular membrane lipids. Previous research has shown that membranes can both accelerate and inhibit peptide self-assembly. Here, we studied the impact of membrane models that mimic cellular oxidative stress and compared this to mammalian and bacterial membranes. Using molecular dynamics simulations and experiments, we propose a model that explains how changes in peptide-membrane binding, electrostatics, and peptide secondary structure stabilization determine the nature of peptide self-assembly. We explored the influence of zwitterionic (POPC), anionic (POPG) and oxidized (PazePC) phospholipids, as well as cholesterol, and mixtures thereof, on the self-assembly kinetics of the amyloid β (1-40) peptide (Aβ40), linked to Alzheimer's disease, and the amyloid-forming antimicrobial peptide uperin 3.5 (U3.5). We show that the presence of an oxidized lipid had similar effects on peptide self-assembly as the bacterial mimetic membrane. While Aβ40 fibril formation was accelerated, U3.5 aggregation was inhibited by the same lipids at the same peptide-to-lipid ratio. We attribute these findings and peptide-specific effects to differences in peptide-membrane adsorption with U3.5 being more strongly bound to the membrane surface and stabilized in an α-helical conformation compared to Aβ40. Different peptide-to-lipid ratios resulted in different effects. We found that electrostatic interactions are a primary driving force for peptide-membrane interaction, enabling us to propose a model for predicting how cellular changes might impact peptide self-assembly in vivo.
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Affiliation(s)
- Torsten John
- School of Chemistry, Monash University Clayton VIC 3800 Australia
- Leibniz Institute of Surface Engineering (IOM) Permoserstraße 15 04318 Leipzig Germany
- Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry, Institute of Chemical Technology, Leipzig University Linnéstraße 3 04103 Leipzig Germany
| | | | - Tiara J A Dealey
- School of Chemistry, Monash University Clayton VIC 3800 Australia
| | - Bernd Abel
- Leibniz Institute of Surface Engineering (IOM) Permoserstraße 15 04318 Leipzig Germany
- Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry, Institute of Chemical Technology, Leipzig University Linnéstraße 3 04103 Leipzig Germany
| | - Herre Jelger Risselada
- Leibniz Institute of Surface Engineering (IOM) Permoserstraße 15 04318 Leipzig Germany
- Institute for Theoretical Physics, Georg-August-Universität Göttingen Friedrich-Hund-Platz 1 37077 Göttingen Germany
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5
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Robinson MJ, Newbury S, Singh K, Leonenko Z, Beazely MA. The Interplay Between Cholesterol and Amyloid-β on HT22 Cell Viability, Morphology, and Receptor Tyrosine Kinase Signaling. J Alzheimers Dis 2023; 96:1663-1683. [PMID: 38073391 DOI: 10.3233/jad-230753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
BACKGROUND There is a lack of understanding in the molecular and cellular mechanisms of Alzheimer's disease that has hindered progress on therapeutic development. The focus has been on targeting toxic amyloid-β (Aβ) pathology, but these therapeutics have generally failed in clinical trials. Aβ is an aggregation-prone protein that has been shown to disrupt cell membrane structure in molecular biophysics studies and interfere with membrane receptor signaling in cell and animal studies. Whether the lipid membrane or specific receptors are the primary target of attack has not been determined. OBJECTIVE This work elucidates some of the interplay between membrane cholesterol and Aβ42 on HT22 neuronal cell viability, morphology, and platelet-derived growth factor (PDGF) signaling pathways. METHODS The effects of cholesterol depletion by methyl-β-cyclodextrin followed by treatment with Aβ and/or PDGF-AA were assessed by MTT cell viability assays, western blot, optical and AFM microscopy. RESULTS Cell viability studies show that cholesterol depletion was mildly protective against Aβ toxicity. Together cholesterol reduction and Aβ42 treatment compounded the disruption of the PDGFα receptor activation. Phase contrast optical microscopy and live cell atomic force microscopy imaging revealed that cytotoxic levels of Aβ42 caused morphological changes including cell membrane damage, cytoskeletal disruption, and impaired cell adhesion; cell damage was ameliorated by cellular cholesterol depletion. CONCLUSIONS Cholesterol depletion impacted the effects of Aβ42 on HT22 cell viability, morphology, and receptor tyrosine kinase signaling.
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Affiliation(s)
- Morgan J Robinson
- School of Pharmacy, University of Waterloo, Waterloo, ON, Canada
- Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, Canada
| | - Sean Newbury
- School of Pharmacy, University of Waterloo, Waterloo, ON, Canada
| | - Kartar Singh
- School of Pharmacy, University of Waterloo, Waterloo, ON, Canada
| | - Zoya Leonenko
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
- Department of Physics and Astronomy, University of Waterloo, Waterloo, ON, Canada
- Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, Canada
| | - Michael A Beazely
- School of Pharmacy, University of Waterloo, Waterloo, ON, Canada
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
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6
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Baltutis V, O'Leary PD, Martin LL. Self-Assembly of Linear, Natural Antimicrobial Peptides: An Evolutionary Perspective. Chempluschem 2022; 87:e202200240. [PMID: 36198638 DOI: 10.1002/cplu.202200240] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 08/29/2022] [Indexed: 01/31/2023]
Abstract
Antimicrobial peptides are an ancient and innate system of host defence against a wide range of microbial assailants. Mechanistically, unstructured peptides undergo a secondary structure transition into amphipathic α-helices, upon contact with membrane surfaces. This leads to peptide binding and removal of the membrane components in a detergent-like manner or via self-organisation into trans-membrane pores (either barrel-stave or toroidal pore) thereby destroying the microbe. Self-assembly of antimicrobial peptides into oligomers and ultimately amyloid has been mostly examined in parallel, however recent findings link diseases, such as Alzheimer's disease as an aberrant activity of a protective neuropeptide with antimicrobial activity. These self-assembled oligomers can also interact with membranes. Here, we review those antimicrobial peptides reported to self-assemble into amyloid, where supported by structural evidence. We consider their membrane activities as antimicrobial peptides and present evidence of consistent self-assembly patterns across major evolutionary groups. Trends are apparent across these groups, supporting the mounting data that self-assembly of antimicrobial peptides into amyloid should be considered as synergistic to the antimicrobial peptide response.
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Affiliation(s)
- Verity Baltutis
- School of Chemistry, Monash University, 3800, Clayton, Vic, Australia
| | - Paul D O'Leary
- School of Chemistry, Monash University, 3800, Clayton, Vic, Australia
| | - Lisandra L Martin
- School of Chemistry, Monash University, 3800, Clayton, Vic, Australia
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7
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Alvarez AB, Caruso B, Petersen SB, Rodríguez PEA, Fidelio GD. Melittin-solid phospholipid mixed films trigger amyloid-like nano-fibril arrangements at air-water interface. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:184048. [PMID: 36115495 DOI: 10.1016/j.bbamem.2022.184048] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 08/22/2022] [Accepted: 09/06/2022] [Indexed: 06/15/2023]
Abstract
We used the Langmuir monolayers technique to study the surface properties of melittin toxin mixed with either liquid-condensed DSPC or liquid-expanded POPC phospholipids. Pure melittin peptide forms stable insoluble monolayers at the air-water interface without interacting with Thioflavin T (Th-T), a sensitive probe to detect protein amyloid formation. When melittin peptide is mixed with DSPC lipid at 50 % of peptide area proportion at the surface, we observed the formation of fibril-like structures detected by Brewster angle microscopy (BAM), but they were not observable with POPC. The nano-structures in the melittin-DSPC mixtures became Th-T positive labeling when the arrangement was observed with fluorescence microscopy. In this condition, Th-T undergoes an unexpected shift in the typical emission wavelength of this amyloid marker when a 2D fluorescence analysis is conducted. Even when reflectivity analysis of BAM imaging evidenced that these structures would correspond to the DSPC lipid component of the mixture, the interpretation of ATR-FTIR and Th-T data suggested that both components were involved in a new lipid-peptide rearrangement. These nano-fibril arrangements were also evidenced by scanning electron and atomic force microscopy when the films were transferred to a mica support. The fibril formation was not detected when melittin was mixed with the liquid-expanded POPC lipid. We postulated that DSPC lipids can dynamically trigger the process of amyloid-like nano-arrangement formation at the interface. This process is favored by the relative peptide content, the quality of the interfacial environment, and the physical state of the lipid at the surface.
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Affiliation(s)
- Alain Bolaño Alvarez
- Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Argentina; Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, CONICET, Universidad Nacional de Córdoba, Argentina
| | - Benjamín Caruso
- Cátedra de Química Biológica, Departamento de Química, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Argentina; Instituto de Investigaciones Biológicas y Tecnológicas (IIBYT), CONICET, Universidad Nacional de Córdoba. Córdoba, Argentina
| | | | | | - Gerardo D Fidelio
- Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Argentina; Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, CONICET, Universidad Nacional de Córdoba, Argentina.
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8
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Chen D, Liu X, Chen Y, Lin H. Amyloid peptides with antimicrobial and/or microbial agglutination activity. Appl Microbiol Biotechnol 2022; 106:7711-7720. [PMID: 36322251 PMCID: PMC9628408 DOI: 10.1007/s00253-022-12246-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 11/07/2022]
Abstract
Abstract Microbe (including bacteria, fungi, and virus) infection in brains is associated with amyloid fibril deposit and neurodegeneration. Increasing findings suggest that amyloid proteins, like Abeta (Aβ), are important innate immune effectors in preventing infections. In some previous studies, amyloid peptides have been linked to antimicrobial peptides due to their common mechanisms in membrane-disruption ability, while the other mechanisms of bactericidal protein aggregation and protein function knockdown are less discussed. Besides, another important function of amyloid peptides in pathogen agglutination is rarely illustrated. In this review, we summarized and divided the different roles and mechanisms of amyloid peptides against microbes in antimicrobial activity and microbe agglutination activity. Besides, the range of amyloids’ antimicrobial spectrum, the effectiveness of amyloid peptide states (monomers, oligomers, and fibrils), and cytotoxicity are discussed. The good properties of amyloid peptides against microbes might provide implications for the development of novel antimicrobial drug. Key points • Antimicrobial and/or microbial agglutination is a characteristic of amyloid peptides. • Various mechanisms of amyloid peptides against microbes are discovered recently. • Amyloid peptides might be developed into novel antimicrobial drugs. Supplementary information The online version contains supplementary material available at 10.1007/s00253-022-12246-w.
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Affiliation(s)
- Dongru Chen
- Department of Orthodontics, Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, Guangdong, China
| | - Xiangqi Liu
- Department of Oral and Maxillofacial Surgery, Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, Guangdong, China
| | - Yucong Chen
- Department of Preventive Dentistry, Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, Guangdong, China
| | - Huancai Lin
- Department of Preventive Dentistry, Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, Guangdong, China.
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9
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Design, characterization and structure-function analysis of novel antimicrobial peptides based on the N-terminal CATH-2 fragment. Sci Rep 2022; 12:12058. [PMID: 35835842 PMCID: PMC9283491 DOI: 10.1038/s41598-022-16303-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 07/07/2022] [Indexed: 11/28/2022] Open
Abstract
The emergence of multidrug resistance coupled with shrinking antibiotic pipelines has increased the demand of antimicrobials with novel mechanisms of action. Therefore, researchers across the globe are striving to develop new antimicrobial substances to alleviate the pressure on conventional antibiotic therapies. Host-Defence Peptides (HDPs) and their derivatives are emerging as effective therapeutic agents against microbial resistance. In this study, five analogs (DP1-5) of the N-terminal (N-15) fragment of CATH-2 were designed based on the delicate balance between various physicochemical properties such as charge, aliphatic character, amphipathicity and hydrophobicity. By means of in-silico and in-vitro studies a novel peptide (DP1) with the sequence “RFGRFLRKILRFLKK” was found to be more effective and less toxic than the N-terminal CATH-2 peptide. Circular dichroism spectroscopy and differential scanning calorimetry were applied for structural insights. Antimicrobial, haemolytic, and cytotoxic activities were also assessed. The resulting peptide was characterized by low cytotoxicity, low haemolytic activity, and efficient anti-microbial activity. Structurally, it displayed strong helical properties irrespective of the solvent environment and was stable in membrane-mimicking environments. Taken together, the data suggests that DP1 can be explored as a promising therapeutic agent with possible clinical applications.
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10
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Pohl C, Effantin G, Kandiah E, Meier S, Zeng G, Streicher W, Segura DR, Mygind PH, Sandvang D, Nielsen LA, Peters GHJ, Schoehn G, Mueller-Dieckmann C, Noergaard A, Harris P. pH- and concentration-dependent supramolecular assembly of a fungal defensin plectasin variant into helical non-amyloid fibrils. Nat Commun 2022; 13:3162. [PMID: 35672293 PMCID: PMC9174238 DOI: 10.1038/s41467-022-30462-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 04/28/2022] [Indexed: 02/04/2023] Open
Abstract
Self-assembly and fibril formation play important roles in protein behaviour. Amyloid fibril formation is well-studied due to its role in neurodegenerative diseases and characterized by refolding of the protein into predominantly β-sheet form. However, much less is known about the assembly of proteins into other types of supramolecular structures. Using cryo-electron microscopy at a resolution of 1.97 Å, we show that a triple-mutant of the anti-microbial peptide plectasin, PPI42, assembles into helical non-amyloid fibrils. The in vitro anti-microbial activity was determined and shown to be enhanced compared to the wildtype. Plectasin contains a cysteine-stabilised α-helix-β-sheet structure, which remains intact upon fibril formation. Two protofilaments form a right-handed protein fibril. The fibril formation is reversible and follows sigmoidal kinetics with a pH- and concentration dependent equilibrium between soluble monomer and protein fibril. This high-resolution structure reveals that α/β proteins can natively assemble into fibrils. Here the authors report the cryo-EM structure of a triple-mutant of the anti-microbial peptide plectasin, PPI42, assembling in a pH- and concentration dependent manner into helical non-amyloid fibrils. The fibrils formation is reversible, and follows a sigmoidal kinetics. The fibrils adopt a right-handed helical superstructure composed by two protofilaments, stabilized by an outer hydrophobic ring and an inner hydrophobic centre. These findings reveal that α/β proteins can natively assemble into fibrils.
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11
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Evolving and assembling to pierce through: Evolutionary and structural aspects of antimicrobial peptides. Comput Struct Biotechnol J 2022; 20:2247-2258. [PMID: 35615024 PMCID: PMC9117813 DOI: 10.1016/j.csbj.2022.05.002] [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: 02/16/2022] [Revised: 04/27/2022] [Accepted: 05/01/2022] [Indexed: 11/24/2022] Open
Abstract
The burgeoning menace of antimicrobial resistance across the globe has necessitated investigations into other chemotherapeutic strategies to combat infections. Antimicrobial peptides, or host defense peptides, are a set of promising therapeutic candidates in this regard. Most of them cause membrane permeabilization and are a key component of the innate immune response to pathogenic invasion. It has also been reported that peptide self-assembly is a driving factor governing the microbicidal activity of these peptide candidates. While efforts have been made to develop novel synthetic peptides against various microbes, many clinical trials of such peptides have failed due to toxicity and hemolytic activity to the host. A function-guided rational peptide engineering, based on evolutionary principles, physicochemical properties and activity determinants of AMP activity, is expected to help in targeting specific microbes. Furthermore, it is important to develop a unified understanding of the evolution of AMPs in order to fully appreciate their importance in host defense. This review seeks to explore the evolution of AMPs and the physicochemical determinants of AMP activity. The specific interactions driving AMP self-assembly have also been reviewed, emphasizing implications of this self-assembly on microbicidal and immunomodulatory activity.
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12
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Prasad AK, Tiwari C, Ray S, Holden S, Armstrong DA, Rosengren KJ, Rodger A, Panwar AS, Martin LL. Secondary Structure Transitions for a Family of Amyloidogenic, Antimicrobial Uperin 3 Peptides in Contact with Sodium Dodecyl Sulfate. Chempluschem 2022; 87:e202100408. [DOI: 10.1002/cplu.202100408] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 11/10/2021] [Indexed: 11/10/2022]
Affiliation(s)
- Anup K. Prasad
- IITB-Monash Research Academy Indian Institute of Technology Bombay Powai Mumbai 400076 India
- Department of Metallurgical Engineering and Materials Science Indian Institute of Technology Bombay Powai Mumbai 400076 India
| | - Chandni Tiwari
- IITB-Monash Research Academy Indian Institute of Technology Bombay Powai Mumbai 400076 India
- School of Chemistry Monash University Clayton VIC 3800 Australia
| | - Sourav Ray
- IITB-Monash Research Academy Indian Institute of Technology Bombay Powai Mumbai 400076 India
- Department of Metallurgical Engineering and Materials Science Indian Institute of Technology Bombay Powai Mumbai 400076 India
| | - Stephanie Holden
- School of Chemistry Monash University Clayton VIC 3800 Australia
| | - David A. Armstrong
- School of Biomedical Sciences The University of Queensland Brisbane QLD, 4072 Australia
| | - K. Johan Rosengren
- School of Biomedical Sciences The University of Queensland Brisbane QLD, 4072 Australia
| | - Alison Rodger
- Department of Molecular Sciences Macquarie University Macquarie Park NSW, 2109 Australia
| | - Ajay S. Panwar
- Department of Metallurgical Engineering and Materials Science Indian Institute of Technology Bombay Powai Mumbai 400076 India
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13
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Tang Y, Zhang D, Gong X, Zheng J. Repurposing of intestinal defensins as multi-target, dual-function amyloid inhibitors via cross-seeding. Chem Sci 2022; 13:7143-7156. [PMID: 35799805 PMCID: PMC9214849 DOI: 10.1039/d2sc01447e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/19/2022] [Indexed: 12/13/2022] Open
Abstract
Amyloid formation and microbial infection are the two common pathological causes of neurogenerative diseases, including Alzheimer's disease (AD), type II diabetes (T2D), and medullary thyroid carcinoma (MTC). While significant efforts have been made to develop different prevention strategies and preclinical hits for these diseases, conventional design strategies of amyloid inhibitors are mostly limited to either a single prevention mechanism (amyloid cascade vs. microbial infection) or a single amyloid protein (Aβ, hIAPP, or hCT), which has prevented the launch of any successful drug on the market. Here, we propose and demonstrate a new “anti-amyloid and anti-bacteria” strategy to repurpose two intestinal defensins, human α-defensin 6 (HD-6) and human β-defensin 1 (HBD-1), as multiple-target, dual-function, amyloid inhibitors. Both HD-6 and HBD-1 can cross-seed with three amyloid peptides, Aβ (associated with AD), hIAPP (associated with T2D), and hCT (associated with MTC), to prevent their aggregation towards amyloid fibrils from monomers and oligomers, rescue SH-SY5Y and RIN-m5F cells from amyloid-induced cytotoxicity, and retain their original antimicrobial activity against four common bacterial strains at sub-stoichiometric concentrations. Such sequence-independent anti-amyloid and anti-bacterial functions of intestinal defensins mainly stem from their cross-interactions with amyloid proteins through amyloid-like mimicry of β-sheet associations. In a broader view, this work provides a new out-of-the-box thinking to search and repurpose a huge source of antimicrobial peptides as amyloid inhibitors, allowing the blocking of the two interlinked pathological pathways and bidirectional communication between the central nervous system and intestines via the gut–brain axis associated with neurodegenerative diseases. Amyloid formation and microbial infection are the two common pathological causes of neurogenerative diseases. Here, we proposed a new “anti-amyloid and anti-bacteria” strategy to repurpose two intestinal defensins as multiple-target, dual-function amyloid inhibitors.![]()
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Affiliation(s)
- Yijing Tang
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Ohio, USA
| | - Dong Zhang
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Ohio, USA
| | - Xiong Gong
- School of Polymer Science and Polymer Engineering, The University of Akron, Ohio, USA
| | - Jie Zheng
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, Ohio, USA
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Ye Z, Aparicio C. Interactions of two enantiomers of a designer antimicrobial peptide with structural components of the bacterial cell envelope. J Pept Sci 2022; 28:e3299. [PMID: 33496073 PMCID: PMC8310526 DOI: 10.1002/psc.3299] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 01/13/2021] [Accepted: 01/15/2021] [Indexed: 01/03/2023]
Abstract
Antimicrobial peptides (AMPs) have great potential in treating multi-drug resistant bacterial infections. The antimicrobial activity of d-enantiomers is significantly higher than l-enantiomers and sometimes selectively enhanced against Gram-positive bacteria. Unlike phospholipids in the bacterial plasma membrane, the role of other bacterial cell envelop components is often overlooked in the mode of action of AMPs. In this work, we explored the structural interactions between the main different structural components in Gram-negative/Gram-positive bacteria and the two enantiomers of a designer AMP, GL13K. We observed that both l-GL13K and d-GL13K formed self-assembled amyloid-like nanofibrils when the peptides interacted with lipopolysaccharide and lipoteichoic acid, components of the outer membrane of Gram-negative bacteria and cell wall of Gram-positive bacteria, respectively. Another cell wall component, peptidoglycan, showed strong interactions exclusively with d-GL13K and formed distinct laminar structures. This specific interaction between peptidoglycans and d-GL13K might contribute to the enhanced activity of d-GL13K against Gram-positive bacteria as they have a much thicker peptidoglycan layer than Gram-negative bacteria. A better understanding of the specific role of bacterial cell envelop components in the AMPs mechanism of action can guide the design of more effective Gram-selective AMPs.
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15
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Tang Y, Zhang D, Gong X, Zheng J. A mechanistic survey of Alzheimer's disease. Biophys Chem 2021; 281:106735. [PMID: 34894476 DOI: 10.1016/j.bpc.2021.106735] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/26/2021] [Accepted: 11/26/2021] [Indexed: 02/06/2023]
Abstract
Alzheimer's disease (AD) is the most common, age-dependent neurodegenerative disorder. While AD has been intensively studied from different aspects, there is no effective cure for AD, largely due to a lack of a clear mechanistic understanding of AD. In this mini-review, we mainly focus on the discussion and summary of mechanistic causes of Alzheimer's disease (AD). While different AD mechanisms illustrate different molecular and cellular pathways in AD pathogenesis, they do not necessarily exclude each other. Instead, some of them could work together to initiate, trigger, and promote the onset and development of AD. In a broader viewpoint, some AD mechanisms (e.g., amyloid aggregation mechanism, microbial infection/neuroinflammation mechanism, and amyloid cross-seeding mechanism) could also be applicable to other amyloid diseases including type II diabetes, Parkinson's disease, and prion disease. Such common mechanisms for AD and other amyloid diseases explain not only the pathogenesis of individual amyloid diseases, but also the spreading of pathologies between these diseases, which will inspire new strategies for therapeutic intervention and prevention for AD.
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Affiliation(s)
- Yijing Tang
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, OH, United States of America
| | - Dong Zhang
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, OH, United States of America
| | - Xiong Gong
- Department of Polymer Engineering, The University of Akron, OH, United States of America
| | - Jie Zheng
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron, OH, United States of America.
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Zhang Y, Liu Y, Tang Y, Zhang D, He H, Wu J, Zheng J. Antimicrobial α-defensins as multi-target inhibitors against amyloid formation and microbial infection. Chem Sci 2021; 12:9124-9139. [PMID: 34276942 PMCID: PMC8261786 DOI: 10.1039/d1sc01133b] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 05/27/2021] [Indexed: 12/22/2022] Open
Abstract
Amyloid aggregation and microbial infection are considered as pathological risk factors for developing amyloid diseases, including Alzheimer's disease (AD), type II diabetes (T2D), Parkinson's disease (PD), and medullary thyroid carcinoma (MTC). Due to the multifactorial nature of amyloid diseases, single-target drugs and treatments have mostly failed to inhibit amyloid aggregation and microbial infection simultaneously, thus leading to marginal benefits for amyloid inhibition and medical treatments. Herein, we proposed and demonstrated a new "anti-amyloid and antimicrobial hypothesis" to discover two host-defense antimicrobial peptides of α-defensins containing β-rich structures (human neutrophil peptide of HNP-1 and rabbit neutrophil peptide of NP-3A), which have demonstrated multi-target, sequence-independent functions to (i) prevent the aggregation and misfolding of different amyloid proteins of amyloid-β (Aβ, associated with AD), human islet amyloid polypeptide (hIAPP, associated with T2D), and human calcitonin (hCT, associated with MTC) at sub-stoichiometric concentrations, (ii) reduce amyloid-induced cell toxicity, and (iii) retain their original antimicrobial activity upon the formation of complexes with amyloid peptides. Further structural analysis showed that the sequence-independent amyloid inhibition function of α-defensins mainly stems from their cross-interactions with amyloid proteins via β-structure interactions. The discovery of antimicrobial peptides containing β-structures to inhibit both microbial infection and amyloid aggregation greatly expands the new therapeutic potential of antimicrobial peptides as multi-target amyloid inhibitors for better understanding pathological causes and treatments of amyloid diseases.
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Affiliation(s)
- Yanxian Zhang
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron Ohio USA
| | - Yonglan Liu
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron Ohio USA
| | - Yijing Tang
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron Ohio USA
| | - Dong Zhang
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron Ohio USA
| | - Huacheng He
- College of Chemistry and Materials Engineering, Wenzhou University Zhejiang China
| | - Jiang Wu
- School of Pharmaceutical Sciences, Wenzhou Medical University Zhejiang China
| | - Jie Zheng
- Department of Chemical, Biomolecular, and Corrosion Engineering, The University of Akron Ohio USA
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The amphibian antimicrobial peptide uperin 3.5 is a cross-α/cross-β chameleon functional amyloid. Proc Natl Acad Sci U S A 2021; 118:2014442118. [PMID: 33431675 DOI: 10.1073/pnas.2014442118] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Antimicrobial activity is being increasingly linked to amyloid fibril formation, suggesting physiological roles for some human amyloids, which have historically been viewed as strictly pathological agents. This work reports on formation of functional cross-α amyloid fibrils of the amphibian antimicrobial peptide uperin 3.5 at atomic resolution, an architecture initially discovered in the bacterial PSMα3 cytotoxin. The fibrils of uperin 3.5 and PSMα3 comprised antiparallel and parallel helical sheets, respectively, recapitulating properties of β-sheets. Uperin 3.5 demonstrated chameleon properties of a secondary structure switch, forming mostly cross-β fibrils in the absence of lipids. Uperin 3.5 helical fibril formation was largely induced by, and formed on, bacterial cells or membrane mimetics, and led to membrane damage and cell death. These findings suggest a regulation mechanism, which includes storage of inactive peptides as well as environmentally induced activation of uperin 3.5, via chameleon cross-α/β amyloid fibrils.
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Matiiv AB, Trubitsina NP, Matveenko AG, Barbitoff YA, Zhouravleva GA, Bondarev SA. Amyloid and Amyloid-Like Aggregates: Diversity and the Term Crisis. BIOCHEMISTRY (MOSCOW) 2021; 85:1011-1034. [PMID: 33050849 DOI: 10.1134/s0006297920090035] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Active accumulation of the data on new amyloids continuing nowadays dissolves boundaries of the term "amyloid". Currently, it is most often used to designate aggregates with cross-β structure. At the same time, amyloids also exhibit a number of other unusual properties, such as: detergent and protease resistance, interaction with specific dyes, and ability to induce transition of some proteins from a soluble form to an aggregated one. The same features have been also demonstrated for the aggregates lacking cross-β structure, which are commonly called "amyloid-like" and combined into one group, although they are very diverse. We have collected and systematized information on the properties of more than two hundred known amyloids and amyloid-like proteins with emphasis on conflicting examples. In particular, a number of proteins in membraneless organelles form aggregates with cross-β structure that are morphologically indistinguishable from the other amyloids, but they can be dissolved in the presence of detergents, which is not typical for amyloids. Such paradoxes signify the need to clarify the existing definition of the term amyloid. On the other hand, the demonstrated structural diversity of the amyloid-like aggregates shows the necessity of their classification.
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Affiliation(s)
- A B Matiiv
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia
| | - N P Trubitsina
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia
| | - A G Matveenko
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia
| | - Y A Barbitoff
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia.,Bioinformatics Institute, St. Petersburg, 197342, Russia
| | - G A Zhouravleva
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia.,Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, 199034, Russia
| | - S A Bondarev
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia. .,Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, 199034, Russia
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19
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Juhl DW, Glattard E, Lointier M, Bampilis P, Bechinger B. The Reversible Non-covalent Aggregation Into Fibers of PGLa and Magainin 2 Preserves Their Antimicrobial Activity and Synergism. Front Cell Infect Microbiol 2020; 10:526459. [PMID: 33102247 PMCID: PMC7554302 DOI: 10.3389/fcimb.2020.526459] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 08/18/2020] [Indexed: 01/29/2023] Open
Abstract
Magainin 2 and PGLa are antimicrobial peptides found together in frog skin secretions. When added as a mixture they show an order of magnitude increase in antibacterial activity and in model membrane permeation assays. Here we demonstrate that both peptides can form fibers with beta-sheet/turn signature in ATR-FTIR- and CD-spectroscopic analyses, but with different morphologies in EM images. Whereas, fiber formation results in acute reduction of the antimicrobial activity of the individual peptides, the synergistic enhancement of activity remains for the equimolar mixture of PGLa and magainin 2 also after fibril formation. The biological significance and potential applications of such supramolecular aggregates are discussed.
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Affiliation(s)
- Dennis Wilkens Juhl
- University of Strasbourg/CNRS, UMR7177, Institut de Chimie de Strasbourg, Strasbourg, France
| | - Elise Glattard
- University of Strasbourg/CNRS, UMR7177, Institut de Chimie de Strasbourg, Strasbourg, France
| | - Morane Lointier
- University of Strasbourg/CNRS, UMR7177, Institut de Chimie de Strasbourg, Strasbourg, France
| | - Panos Bampilis
- University of Strasbourg/CNRS, UMR7177, Institut de Chimie de Strasbourg, Strasbourg, France
| | - Burkhard Bechinger
- University of Strasbourg/CNRS, UMR7177, Institut de Chimie de Strasbourg, Strasbourg, France
- Institut Universitaire de France (IUF), Paris, France
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20
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Lee EY, Srinivasan Y, de Anda J, Nicastro LK, Tükel Ç, Wong GCL. Functional Reciprocity of Amyloids and Antimicrobial Peptides: Rethinking the Role of Supramolecular Assembly in Host Defense, Immune Activation, and Inflammation. Front Immunol 2020; 11:1629. [PMID: 32849553 PMCID: PMC7412598 DOI: 10.3389/fimmu.2020.01629] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 06/17/2020] [Indexed: 12/15/2022] Open
Abstract
Pathological self-assembly is a concept that is classically associated with amyloids, such as amyloid-β (Aβ) in Alzheimer's disease and α-synuclein in Parkinson's disease. In prokaryotic organisms, amyloids are assembled extracellularly in a similar fashion to human amyloids. Pathogenicity of amyloids is attributed to their ability to transform into several distinct structural states that reflect their downstream biological consequences. While the oligomeric forms of amyloids are thought to be responsible for their cytotoxicity via membrane permeation, their fibrillar conformations are known to interact with the innate immune system to induce inflammation. Furthermore, both eukaryotic and prokaryotic amyloids can self-assemble into molecular chaperones to bind nucleic acids, enabling amplification of Toll-like receptor (TLR) signaling. Recent work has shown that antimicrobial peptides (AMPs) follow a strikingly similar paradigm. Previously, AMPs were thought of as peptides with the primary function of permeating microbial membranes. Consistent with this, many AMPs are facially amphiphilic and can facilitate membrane remodeling processes such as pore formation and fusion. We show that various AMPs and chemokines can also chaperone and organize immune ligands into amyloid-like ordered supramolecular structures that are geometrically optimized for binding to TLRs, thereby amplifying immune signaling. The ability of amphiphilic AMPs to self-assemble cooperatively into superhelical protofibrils that form structural scaffolds for the ordered presentation of immune ligands like DNA and dsRNA is central to inflammation. It is interesting to explore the notion that the assembly of AMP protofibrils may be analogous to that of amyloid aggregates. Coming full circle, recent work has suggested that Aβ and other amyloids also have AMP-like antimicrobial functions. The emerging perspective is one in which assembly affords a more finely calibrated system of recognition and response: the detection of single immune ligands, immune ligands bound to AMPs, and immune ligands spatially organized to varying degrees by AMPs, result in different immunologic outcomes. In this framework, not all ordered structures generated during multi-stepped AMP (or amyloid) assembly are pathological in origin. Supramolecular structures formed during this process serve as signatures to the innate immune system to orchestrate immune amplification in a proportional, situation-dependent manner.
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Affiliation(s)
- Ernest Y Lee
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, United States.,UCLA-Caltech Medical Scientist Training Program, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Yashes Srinivasan
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, United States
| | - Jaime de Anda
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, United States
| | - Lauren K Nicastro
- Department of Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
| | - Çagla Tükel
- Department of Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
| | - Gerard C L Wong
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, United States.,Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, United States.,California Nano Systems Institute, University of California, Los Angeles, Los Angeles, CA, United States
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21
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Mercer DK, Torres MDT, Duay SS, Lovie E, Simpson L, von Köckritz-Blickwede M, de la Fuente-Nunez C, O'Neil DA, Angeles-Boza AM. Antimicrobial Susceptibility Testing of Antimicrobial Peptides to Better Predict Efficacy. Front Cell Infect Microbiol 2020; 10:326. [PMID: 32733816 PMCID: PMC7358464 DOI: 10.3389/fcimb.2020.00326] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/29/2020] [Indexed: 12/11/2022] Open
Abstract
During the development of antimicrobial peptides (AMP) as potential therapeutics, antimicrobial susceptibility testing (AST) stands as an essential part of the process in identification and optimisation of candidate AMP. Standard methods for AST, developed almost 60 years ago for testing conventional antibiotics, are not necessarily fit for purpose when it comes to determining the susceptibility of microorganisms to AMP. Without careful consideration of the parameters comprising AST there is a risk of failing to identify novel antimicrobials at a time when antimicrobial resistance (AMR) is leading the planet toward a post-antibiotic era. More physiologically/clinically relevant AST will allow better determination of the preclinical activity of drug candidates and allow the identification of lead compounds. An important consideration is the efficacy of AMP in biological matrices replicating sites of infection, e.g., blood/plasma/serum, lung bronchiolar lavage fluid/sputum, urine, biofilms, etc., as this will likely be more predictive of clinical efficacy. Additionally, specific AST for different target microorganisms may help to better predict efficacy of AMP in specific infections. In this manuscript, we describe what we believe are the key considerations for AST of AMP and hope that this information can better guide the preclinical development of AMP toward becoming a new generation of urgently needed antimicrobials.
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Affiliation(s)
| | - Marcelo D. T. Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, Penn Institute for Computational Science, and Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, United States
| | - Searle S. Duay
- Department of Chemistry, Institute of Materials Science, University of Connecticut, Storrs, CT, United States
| | - Emma Lovie
- NovaBiotics Ltd, Aberdeen, United Kingdom
| | | | | | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, Penn Institute for Computational Science, and Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, United States
| | | | - Alfredo M. Angeles-Boza
- Department of Chemistry, Institute of Materials Science, University of Connecticut, Storrs, CT, United States
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Peptide Self-Assembly Is Linked to Antibacterial, but Not Antifungal, Activity of Histatin 5 Derivatives. mSphere 2020; 5:5/2/e00021-20. [PMID: 32238567 PMCID: PMC7113582 DOI: 10.1128/msphere.00021-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Antimicrobial peptides are important modulators of host defense against bacterial, fungal, and viral pathogens in humans and other multicellular organisms. Two converging paradigms point to a link between antimicrobial peptides that self-assemble into amyloid-like nanoassemblies and classical amyloidogenic peptides that often have potent broad-spectrum antimicrobial activity, suggesting that antimicrobial and amyloidogenic peptides may represent two sides of the same coin. Here, we asked if the ability of an antifungal peptide to self-assemble affects its antifungal or antibacterial activity. We found that modifications of classical antifungal peptide derivative allowed it to self-assemble and did not alter its antifungal activity, and yet self-assembly substantially increased the antibacterial activity of the peptide. These results support the idea that peptide self-assembly can enhance antibacterial activities and emphasize a distinction between the action of antifungal peptides and that of antibacterial peptides. Accordingly, we suggest that the possible generality of this distinction should be widely tested. The rise of multidrug-resistant pathogens has awakened interest in new drug candidates such as antimicrobial peptides and their derivatives. Recent work suggests that some antimicrobial peptides have the ability to self-assemble into ordered amyloid-like nanostructures which facilitate their antibacterial activity. Here, we evaluate a histatin-based antimicrobial peptide, and its self-assembling derivative, in the interplay between self-assembly, membrane interactions, and antibacterial and antifungal activities. We demonstrate substantial membrane targeting by both peptides, as well as mechanistic insights into this mode of action, which correlates to their antifungal activity and is not affected by their self-assembling state. The ability to self-assemble does, however, significantly affect peptide antibacterial activity against both Gram-negative and Gram-positive bacteria. These results are surprising and hint at important distinctions between antifungal and antibacterial peptide activities in prokaryotes and eukaryotic microbes. IMPORTANCE Antimicrobial peptides are important modulators of host defense against bacterial, fungal, and viral pathogens in humans and other multicellular organisms. Two converging paradigms point to a link between antimicrobial peptides that self-assemble into amyloid-like nanoassemblies and classical amyloidogenic peptides that often have potent broad-spectrum antimicrobial activity, suggesting that antimicrobial and amyloidogenic peptides may represent two sides of the same coin. Here, we asked if the ability of an antifungal peptide to self-assemble affects its antifungal or antibacterial activity. We found that modifications of classical antifungal peptide derivative allowed it to self-assemble and did not alter its antifungal activity, and yet self-assembly substantially increased the antibacterial activity of the peptide. These results support the idea that peptide self-assembly can enhance antibacterial activities and emphasize a distinction between the action of antifungal peptides and that of antibacterial peptides. Accordingly, we suggest that the possible generality of this distinction should be widely tested.
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Zhang L. Disulfide Bonds Affect the Binding Sites of Human β Defensin Type 3 on Negatively Charged Lipid Membranes. J Phys Chem B 2020; 124:2088-2100. [PMID: 32091905 DOI: 10.1021/acs.jpcb.9b10529] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Human β defensin type 3 (hBD-3) is a small natural antimicrobiotic. It is strongly cationic and has six cysteine residues which can form three pairs of intramolecular disulfide bonds under oxidized condition. Those disulfide bonds can break under reducing condition. However, the antibacterial activities of hBD-3 in its wild-type and analog forms are similar. In this project, the structure and dynamics of hBD-3 were investigated by running simulations on hBD-3 in its wild-type and analog forms in solvent, binding to negatively charged lipid bilayers, and self-assembly with POPG lipids. It was found that the RMSFs of hBD-3 in both its wild-type and analog forms are similar in solvent, while they are very diverse depending on the binding sites of hBD-3 with negatively charged bilayers. Calculating both the distance map and insertion depths for 18 hBD-3 molecules binding on the POPG bilayer, hBD-3 in its analog form binds stably with the POPG bilayer through the head and loop regions, while hBD-3 wild-type binds with the POPG bilayer on the two loop regions stably. hBD-3 analog caused membrane thinning and disrupted the POPG lipids more significantly than the wildtype. Based on the self-assembly simulations, hBD-3 monomer can bind with and embed inside the negatively charged POPG lipid membrane and have more contacts with the POPG lipid heads than with tails. The current work emphasized the structural diversity of hBD-3 interacting with negatively charged lipid membrane affected by the disulfide bonding states.
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Affiliation(s)
- Liqun Zhang
- Department of Chemical Engineering, Tennessee Technological University, Cookeville, Tennessee 38505, United States
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24
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Gour S, Kumar V, Rana M, Yadav JK. Pheromone peptide cOB1 from native Enterococcus faecalis forms amyloid-like structures: A new paradigm for peptide pheromones. J Pept Sci 2019; 25:e3178. [PMID: 31317612 DOI: 10.1002/psc.3178] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 04/29/2019] [Accepted: 05/04/2019] [Indexed: 12/19/2022]
Abstract
Pheromone peptides are an important component of bacterial quorum-sensing system. The pheromone peptide cOB1 (VAVLVLGA) of native commensal Enterococcus faecalis has also been identified as an antimicrobial peptide (AMP) and reported to kill the prototype clinical isolate strain of E. faecalis V583. In this study, the pheromone peptide cOB1 has shown to form amyloid-like structures, a characteristic which is never reported for a pheromone peptide so far. With in silico analysis, the peptide was predicted to be highly amyloidogenic. Further, under experimental conditions, cOB1 formed aggregates displaying characteristics of amyloid structures such as bathochromic shift in Congo red absorbance, enhancement in thioflavin T fluorescence, and fibrillar morphology under transmission electron microscopy. This novel property of pheromone peptide cOB1 may have some direct effects on the binding of the pheromone to the receptor cells and subsequent conjugative transfer, making this observation more important for the therapeutics, dealing with the generation of virulent and multidrug-resistant pathogenic strains.
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Affiliation(s)
- Shalini Gour
- Department of Biotechnology, Central University of Rajasthan, NH-8 Bandarsindri, Kishangarh Ajmer, 305817, Rajasthan, India
| | - Vijay Kumar
- Department of Biotechnology, Central University of Rajasthan, NH-8 Bandarsindri, Kishangarh Ajmer, 305817, Rajasthan, India
| | - Monika Rana
- Department of Chemistry, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh Ajmer, 305817, Rajasthan, India
| | - Jay Kant Yadav
- Department of Biotechnology, Central University of Rajasthan, NH-8 Bandarsindri, Kishangarh Ajmer, 305817, Rajasthan, India
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25
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Bartels EJH, Dekker D, Amiche M. Dermaseptins, Multifunctional Antimicrobial Peptides: A Review of Their Pharmacology, Effectivity, Mechanism of Action, and Possible Future Directions. Front Pharmacol 2019; 10:1421. [PMID: 31849670 PMCID: PMC6901996 DOI: 10.3389/fphar.2019.01421] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 11/07/2019] [Indexed: 12/13/2022] Open
Abstract
Dermaseptins are a group of α-helical shaped polycationic peptides isolated from the Hylid frogs, with antimicrobial effects against bacteria, parasites, protozoa, viruses in vitro. Besides, anti-tumor effects have been demonstrated. However, few animal experiments and no clinical trials have been conducted thus far. This review summarizes the current knowledge on the pharmacology, ethno pharmacology, effectivity against infectious pathogens and tumors cells and the mechanism of action of the Dermaseptins. Future research should focus on further clarification of the mechanisms of action, the effectivity of Dermaseptins against several cancer cell lines and their applicability in humans.
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Affiliation(s)
| | - Douwe Dekker
- Dutch Poisons Information Center, University Medical Center Utrecht, Utrecht, Netherlands
| | - Mohamed Amiche
- Mondor Institute of Biomedical Research, INSERM U955 Team 7, School of Medicine, University Paris Est Créteil, Créteil, France
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Gour S, Kumar V, Singh A, Gadhave K, Goyal P, Pandey J, Giri R, Yadav JK. Mammalian antimicrobial peptide protegrin‐4 self assembles and forms amyloid‐like aggregates: Assessment of its functional relevance. J Pept Sci 2019; 25:e3151. [DOI: 10.1002/psc.3151] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 12/18/2018] [Accepted: 01/13/2019] [Indexed: 01/06/2023]
Affiliation(s)
- Shalini Gour
- Department of BiotechnologyCentral University of Rajasthan Ajmer India
| | - Vijay Kumar
- Department of BiotechnologyCentral University of Rajasthan Ajmer India
| | - Ashutosh Singh
- School of Basic SciencesIndian Institute of Technology Mandi Kamand India
| | - Kundlik Gadhave
- School of Basic SciencesIndian Institute of Technology Mandi Kamand India
| | - Pankaj Goyal
- Department of BiotechnologyCentral University of Rajasthan Ajmer India
| | - Janmejay Pandey
- Department of BiotechnologyCentral University of Rajasthan Ajmer India
| | - Rajanish Giri
- School of Basic SciencesIndian Institute of Technology Mandi Kamand India
| | - Jay Kant Yadav
- Department of BiotechnologyCentral University of Rajasthan Ajmer India
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Malekkhaiat Häffner S, Malmsten M. Influence of self-assembly on the performance of antimicrobial peptides. Curr Opin Colloid Interface Sci 2018. [DOI: 10.1016/j.cocis.2018.09.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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28
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Hoffmann AR, Saravanan MS, Lequin O, Killian JA, Khemtemourian L. A single mutation on the human amyloid polypeptide modulates fibril growth and affects the mechanism of amyloid-induced membrane damage. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1783-1792. [DOI: 10.1016/j.bbamem.2018.02.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 02/19/2018] [Accepted: 02/20/2018] [Indexed: 12/30/2022]
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Unveiling the Multifaceted Mechanisms of Antibacterial Activity of Buforin II and Frenatin 2.3S Peptides from Skin Micro-Organs of the Orinoco Lime Treefrog ( Sphaenorhynchus lacteus). Int J Mol Sci 2018; 19:ijms19082170. [PMID: 30044391 PMCID: PMC6121439 DOI: 10.3390/ijms19082170] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 07/19/2018] [Indexed: 12/15/2022] Open
Abstract
Amphibian skin is a rich source of natural compounds with diverse antimicrobial and immune defense properties. Our previous studies showed that the frog skin secretions obtained by skin micro-organs from various species of Colombian anurans have antimicrobial activities against bacteria and viruses. We purified for the first time two antimicrobial peptides from the skin micro-organs of the Orinoco lime treefrog (Sphaenorhynchus lacteus) that correspond to Buforin II (BF2) and Frenatin 2.3S (F2.3S). Here, we have synthesized the two peptides and tested them against Gram-negative and Gram-positive bacteria, observing an effective bactericidal activity at micromolar concentrations. Evaluation of BF2 and F2.3S membrane destabilization activity on bacterial cell cultures and synthetic lipid bilayers reveals a distinct membrane interaction mechanism. BF2 agglutinates E. coli cells and synthetic vesicles, whereas F2.3S shows a high depolarization and membrane destabilization activities. Interestingly, we found that F2.3S is able to internalize within bacterial cells and can bind nucleic acids, as previously reported for BF2. Moreover, bacterial exposure to both peptides alters the expression profile of genes related to stress and resistance response. Overall, these results show the multifaceted mechanism of action of both antimicrobial peptides that can provide alternative tools in the fight against bacterial resistance.
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Martin LL, Kubeil C, Piantavigna S, Tikkoo T, Gray NP, John T, Calabrese AN, Liu Y, Hong Y, Hossain MA, Patil N, Abel B, Hoffmann R, Bowie JH, Carver JA. Amyloid aggregation and membrane activity of the antimicrobial peptide uperin 3.5. Pept Sci (Hoboken) 2018. [DOI: 10.1002/pep2.24052] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
| | - Clemens Kubeil
- School of Chemistry; Monash University; Clayton Victoria 3800 Australia
| | | | - Tarun Tikkoo
- School of Chemistry; Monash University; Clayton Victoria 3800 Australia
| | - Nicholas P. Gray
- School of Chemistry; Monash University; Clayton Victoria 3800 Australia
| | - Torsten John
- School of Chemistry; Monash University; Clayton Victoria 3800 Australia
- Leibniz Institute of Surface Engineering (IOM) and Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry; Leipzig University; Leipzig 04318 Germany
| | - Antonio N. Calabrese
- Department of Chemistry and School of Physical Sciences; The University of Adelaide; Adelaide South Australia 5005 Australia
| | - Yanqin Liu
- Department of Chemistry and School of Physical Sciences; The University of Adelaide; Adelaide South Australia 5005 Australia
| | - Yuning Hong
- Department of Chemistry and Physics; La Trobe Institute for Molecular Science, La Trobe University; Melbourne Victoria 3086 Australia
| | - Mohammed A. Hossain
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne; Parkville Victoria 3010 Australia
| | - Nitin Patil
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne; Parkville Victoria 3010 Australia
| | - Bernd Abel
- Leibniz Institute of Surface Engineering (IOM) and Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry; Leipzig University; Leipzig 04318 Germany
| | - Ralf Hoffmann
- Institute of Bioanalytical Chemistry, and Center for Biotechnology and Biomedicine (BBZ), Universität Leipzig; Leipzig 04103 Germany
| | - John H. Bowie
- Department of Chemistry and School of Physical Sciences; The University of Adelaide; Adelaide South Australia 5005 Australia
| | - John A. Carver
- Research School of Chemistry; The Australian National University; Acton Australian Capital Territory 2601 Australia
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Schnaider L, Brahmachari S, Schmidt NW, Mensa B, Shaham-Niv S, Bychenko D, Adler-Abramovich L, Shimon LJW, Kolusheva S, DeGrado WF, Gazit E. Self-assembling dipeptide antibacterial nanostructures with membrane disrupting activity. Nat Commun 2017; 8:1365. [PMID: 29118336 PMCID: PMC5678095 DOI: 10.1038/s41467-017-01447-x] [Citation(s) in RCA: 249] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 09/19/2017] [Indexed: 01/08/2023] Open
Abstract
Peptide-based supramolecular assemblies are a promising class of nanomaterials with important biomedical applications, specifically in drug delivery and tissue regeneration. However, the intrinsic antibacterial capabilities of these assemblies have been largely overlooked. The recent identification of common characteristics shared by antibacterial and self-assembling peptides provides a paradigm shift towards development of antibacterial agents. Here we present the antibacterial activity of self-assembled diphenylalanine, which emerges as the minimal model for antibacterial supramolecular polymers. The diphenylalanine nano-assemblies completely inhibit bacterial growth, trigger upregulation of stress-response regulons, induce substantial disruption to bacterial morphology, and cause membrane permeation and depolarization. We demonstrate the specificity of these membrane interactions and the development of antibacterial materials by integration of the peptide assemblies into tissue scaffolds. This study provides important insights into the significance of the interplay between self-assembly and antimicrobial activity and establishes innovative design principles toward the development of antimicrobial agents and materials. Peptide-based supramolecular assemblies are a promising class of nanomaterials with important biomedical applications, but their antibacterial properties can be overlooked. Here the authors show the antibacterial activity of self-assembled diphenylalanine, which emerges as the minimal model for antibacterial supramolecular polymers.
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Affiliation(s)
- Lee Schnaider
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Sayanti Brahmachari
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Nathan W Schmidt
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, CA, 94158, USA
| | - Bruk Mensa
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, CA, 94158, USA
| | - Shira Shaham-Niv
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Darya Bychenko
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Lihi Adler-Abramovich
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Linda J W Shimon
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Sofiya Kolusheva
- Ilse Katz Institute for Nanotechnology, Ben Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, CA, 94158, USA.
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel. .,Department of Materials Science and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv, 69978, Israel.
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Machine learning-enabled discovery and design of membrane-active peptides. Bioorg Med Chem 2017; 26:2708-2718. [PMID: 28728899 DOI: 10.1016/j.bmc.2017.07.012] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 06/29/2017] [Accepted: 07/06/2017] [Indexed: 11/23/2022]
Abstract
Antimicrobial peptides are a class of membrane-active peptides that form a critical component of innate host immunity and possess a diversity of sequence and structure. Machine learning approaches have been profitably employed to efficiently screen sequence space and guide experiment towards promising candidates with high putative activity. In this mini-review, we provide an introduction to antimicrobial peptides and summarize recent advances in machine learning-enabled antimicrobial peptide discovery and design with a focus on a recent work Lee et al. Proc. Natl. Acad. Sci. USA 2016;113(48):13588-13593. This study reports the development of a support vector machine classifier to aid in the design of membrane active peptides. We use this model to discover membrane activity as a multiplexed function in diverse peptide families and provide interpretable understanding of the physicochemical properties and mechanisms governing membrane activity. Experimental validation of the classifier reveals it to have learned membrane activity as a unifying signature of antimicrobial peptides with diverse modes of action. Some of the discriminating rules by which it performs classification are in line with existing "human learned" understanding, but it also unveils new previously unknown determinants and multidimensional couplings governing membrane activity. Integrating machine learning with targeted experimentation can guide both antimicrobial peptide discovery and design and new understanding of the properties and mechanisms underpinning their modes of action.
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Sayegh RSR, Batista IDFC, de Melo RL, Riske KA, Daffre S, Montich G, da Silva Junior PI. Longipin: An Amyloid Antimicrobial Peptide from the Harvestman Acutisoma longipes (Arachnida: Opiliones) with Preferential Affinity for Anionic Vesicles. PLoS One 2016; 11:e0167953. [PMID: 27997568 PMCID: PMC5172563 DOI: 10.1371/journal.pone.0167953] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 11/22/2016] [Indexed: 12/24/2022] Open
Abstract
In contrast to vertebrate immune systems, invertebrates lack an adaptive response and rely solely on innate immunity in which antimicrobial peptides (AMPs) play an essential role. Most of them are membrane active molecules that are typically unstructured in solution and adopt secondary/tertiary structures upon binding to phospholipid bilayers. This work presents the first characterization of a constitutive AMP from the hemolymph of an Opiliones order animal: the harvestman Acutisoma longipes. This peptide was named longipin. It presents 18 aminoacid residues (SGYLPGKEYVYKYKGKVF) and a positive net charge at neutral pH. No similarity with other AMPs was observed. However, high sequence similarity with heme-lipoproteins from ticks suggested that longipin might be a protein fragment. The synthetic peptide showed enhanced antifungal activity against Candida guilliermondii and C. tropicalis yeasts (MIC: 3.8–7.5 μM) and did not interfered with VERO cells line viability at all concentrations tested (200–0.1 μM). This selectivity against microbial cells is related to the highest affinity of longipin for anionic charged vesicles (POPG:POPC) compared to zwitterionic ones (POPC), once microbial plasma membrane are generally more negatively charged compared to mammalian cells membrane. Dye leakage from carboxyfluorescein-loaded POPG:POPC vesicles suggested that longipin is a membrane active antimicrobial peptide and FT-IR spectroscopy showed that the peptide chain is mainly unstructured in solution or in the presence of POPC vesicles. However, upon binding to POPG:POPC vesicles, the FT-IR spectrum showed bands related to β-sheet and amyloid-like fibril conformations in agreement with thioflavin-T binding assays, indicating that longipin is an amyloid antimicrobial peptide.
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Affiliation(s)
- Raphael Santa Rosa Sayegh
- Programa Interunidades em Biotecnologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
- Laboratório Especial de Toxinologia Aplicada, Instituto Butantan, São Paulo, Brazil
- * E-mail: (RSSS); (PISJ)
| | - Isabel de Fátima Correia Batista
- Unidade de Sequenciamento de Proteínas e Peptídeos, Instituto Butantan, São Paulo, Brazil
- Laboratório de Bioquímica e Biofísica, Instituto Butantan, São Paulo, Brazil
| | - Robson Lopes de Melo
- Laboratório Especial de Toxinologia Aplicada, Instituto Butantan, São Paulo, Brazil
| | - Karin A. Riske
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Sirlei Daffre
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Guillermo Montich
- Centro de Investigaciones en Quimica Biológica de Córdoba (CIQUIBIC, UNC-CONICET), Departamento de Química Biológica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Pedro Ismael da Silva Junior
- Programa Interunidades em Biotecnologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
- Laboratório Especial de Toxinologia Aplicada, Instituto Butantan, São Paulo, Brazil
- * E-mail: (RSSS); (PISJ)
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Mapping membrane activity in undiscovered peptide sequence space using machine learning. Proc Natl Acad Sci U S A 2016; 113:13588-13593. [PMID: 27849600 DOI: 10.1073/pnas.1609893113] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
There are some ∼1,100 known antimicrobial peptides (AMPs), which permeabilize microbial membranes but have diverse sequences. Here, we develop a support vector machine (SVM)-based classifier to investigate ⍺-helical AMPs and the interrelated nature of their functional commonality and sequence homology. SVM is used to search the undiscovered peptide sequence space and identify Pareto-optimal candidates that simultaneously maximize the distance σ from the SVM hyperplane (thus maximize its "antimicrobialness") and its ⍺-helicity, but minimize mutational distance to known AMPs. By calibrating SVM machine learning results with killing assays and small-angle X-ray scattering (SAXS), we find that the SVM metric σ correlates not with a peptide's minimum inhibitory concentration (MIC), but rather its ability to generate negative Gaussian membrane curvature. This surprising result provides a topological basis for membrane activity common to AMPs. Moreover, we highlight an important distinction between the maximal recognizability of a sequence to a trained AMP classifier (its ability to generate membrane curvature) and its maximal antimicrobial efficacy. As mutational distances are increased from known AMPs, we find AMP-like sequences that are increasingly difficult for nature to discover via simple mutation. Using the sequence map as a discovery tool, we find a unexpectedly diverse taxonomy of sequences that are just as membrane-active as known AMPs, but with a broad range of primary functions distinct from AMP functions, including endogenous neuropeptides, viral fusion proteins, topogenic peptides, and amyloids. The SVM classifier is useful as a general detector of membrane activity in peptide sequences.
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Rossi G, Monticelli L. Gold nanoparticles in model biological membranes: A computational perspective. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2380-2389. [PMID: 27060434 DOI: 10.1016/j.bbamem.2016.04.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 03/31/2016] [Accepted: 04/02/2016] [Indexed: 01/15/2023]
Abstract
The electronic, optical, catalytic, and magnetic properties of metal nanoparticles (NPs) make them extremely interesting for biomedical applications. In this rapidly moving field, monolayer-protected gold nanoparticles emerge both as a reference system and as promising candidates for drug and gene delivery, photothermal treatment, and imaging applications. Despite the technological relevance, there is still poor understanding of the molecular processes driving the interactions of metal nanoparticles with cells, and with cell membranes in particular. In this paper we review molecular-level computational studies of the interaction between monolayer-protected gold NPs and model lipid membranes. Our review comprises a brief description of the most relevant experimental results in this field and of the questions they raised, followed by a description of the computational achievements reported so far. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Giulia Rossi
- Department of Physics, University of Genoa, via Dodecaneso 33, 16146 Genoa, Italy.
| | - Luca Monticelli
- Molecular Microbiology and Structural Biochemistry (MMSB), CNRS UMR 5086, 7 Passage du Vercors, 69007 Lyon, France.
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NH125 kills methicillin-resistant Staphylococcus aureus persisters by lipid bilayer disruption. Future Med Chem 2016; 8:257-69. [PMID: 26910612 DOI: 10.4155/fmc.15.189] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND NH125, a known WalK inhibitor kills MRSA persisters. However, its precise mode of action is still unknown. METHODS & RESULTS The mode of action of NH125 was investigated by comparing its spectrum of antimicrobial activity and its effects on membrane permeability and giant unilamellar vesicles (GUVs) with walrycin B, a WalR inhibitor and benzyldimethylhexadecylammonium chloride (16-BAC), a cationic surfactant. NH125 killed persister cells of a variety of Staphylococcus aureus strains. Similar to 16-BAC, NH125 killed MRSA persisters by inducing rapid membrane permeabilization and caused the rupture of GUVs, whereas walrycin B did not kill MRSA persisters or induce membrane permeabilization and did not affect GUVs. CONCLUSION NH125 kills MRSA persisters by interacting with and disrupting membranes in a detergent-like manner.
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López-Abarrategui C, McBeth C, Mandal SM, Sun ZJ, Heffron G, Alba-Menéndez A, Migliolo L, Reyes-Acosta O, García-Villarino M, Nolasco DO, Falcão R, Cherobim MD, Dias SC, Brandt W, Wessjohann L, Starnbach M, Franco OL, Otero-González AJ. Cm-p5: an antifungal hydrophilic peptide derived from the coastal mollusk Cenchritis muricatus (Gastropoda: Littorinidae). FASEB J 2015; 29:3315-25. [PMID: 25921828 DOI: 10.1096/fj.14-269860] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 04/05/2015] [Indexed: 12/20/2022]
Abstract
Antimicrobial peptides form part of the first line of defense against pathogens for many organisms. Current treatments for fungal infections are limited by drug toxicity and pathogen resistance. Cm-p5 (SRSELIVHQRLF), a peptide derived from the marine mollusk Cenchritis muricatus peptide Cm-p1, has a significantly increased fungistatic activity against pathogenic Candida albicans (minimal inhibitory concentration, 10 µg/ml; EC50, 1.146 µg/ml) while exhibiting low toxic effects against a cultured mammalian cell line. Cm-p5 as characterized by circular dichroism and nuclear magnetic resonance revealed an α-helical structure in membrane-mimetic conditions and a tendency to random coil folding in aqueous solutions. Additional studies modeling Cm-p5 binding to a phosphatidylserine bilayer in silico and isothermal titration calorimetry using lipid monophases demonstrated that Cm-p5 has a high affinity for the phospholipids of fungal membranes (phosphatidylserine and phosphatidylethanolamine), only moderate interactions with a mammalian membrane phospholipid, low interaction with ergosterol, and no interaction with chitin. Adhesion of Cm-p5 to living C. albicans cells was confirmed by fluorescence microscopy with FITC-labeled peptide. In a systemic candidiasis model in mice, intraperitoneal administration of Cm-p5 was unable to control the fungal kidney burden, although its low amphiphaticity could be modified to generate new derivatives with improved fungicidal activity and stability.
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Affiliation(s)
- Carlos López-Abarrategui
- Center for Protein Studies, Faculty of Biology, Havana University, Branch of Parasitology, Institute of Tropical Medicine "Pedro Kourí," and Laboratory of Peptide Analysis and Synthesis, Center of Genetic Engineering and Biotechnology, Havana, Cuba
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Wang J, Li Y, Wang X, Chen W, Sun H, Wang J. Lipopolysaccharide induces amyloid formation of antimicrobial peptide HAL-2. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:2910-8. [PMID: 25109934 DOI: 10.1016/j.bbamem.2014.07.028] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Revised: 07/01/2014] [Accepted: 07/30/2014] [Indexed: 10/24/2022]
Abstract
Lipopolysaccharide (LPS), the important component of the outer membrane of Gram-negative bacteria, contributes to the integrity of the outer membrane and protects the cell against bactericidal agents, including antimicrobial peptides. However, the mechanisms of interaction between antimicrobial peptides and LPS are not clearly understood. Halictines-2 (HAL-2), one of the novel antimicrobial peptides, was isolated from the venom of the eusocial bee Halictus sexcinctus. HAL-2 has exhibited potent antimicrobial activity against Gram-positive and Gram-negative bacteria and even against cancer cells. Here, we studied the interactions between HAL-2 and LPS to elucidate the antibacterial mechanism of HAL-2 in vitro. Our results show that HAL-2 adopts a significant degree of β-strand structure in the presence of LPS. LPS is capable of inducing HAL-2 amyloid formation, which may play a vital role in its antimicrobial activity.
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Affiliation(s)
- Jiarong Wang
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei, Anhui 230031, PR China
| | - Yan Li
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei, Anhui 230031, PR China
| | - Xiaoming Wang
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei, Anhui 230031, PR China
| | - Wei Chen
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei, Anhui 230031, PR China
| | - Hongbin Sun
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei, Anhui 230031, PR China.
| | - Junfeng Wang
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei, Anhui 230031, PR China.
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Landreh M, Johansson J, Jörnvall H. Separate molecular determinants in amyloidogenic and antimicrobial peptides. J Mol Biol 2014; 426:2159-66. [PMID: 24650898 DOI: 10.1016/j.jmb.2014.03.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 02/17/2014] [Accepted: 03/06/2014] [Indexed: 10/25/2022]
Abstract
Several amyloid-forming and antimicrobial peptides (AMYs and AMPs) have the ability to bind to and damage cell membranes. In addition, some AMYs possess antimicrobial activity and some AMPs form amyloid-like fibrils, relating the two peptide types and their properties. However, a comparison of their sequence characteristics reveals important differences. The high β-strand and aggregation propensities typical of AMYs are largely absent in α-helix-forming AMPs, which are instead marked by a strong amphipathic moment not generally found in AMYs. Although a few peptides, for example, islet amyloid polypeptide and dermaseptin S9, combine some determinants of both groups, the structural distinctions suggest that antimicrobial activity and amyloid formation are separate features not generally associated.
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Affiliation(s)
- Michael Landreh
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden
| | - Jan Johansson
- KI Alzheimer's Disease Research Center, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, S-141 86 Stockholm, Sweden; Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, S-751 23 Uppsala, Sweden
| | - Hans Jörnvall
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden.
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