1
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Miura Y. The conformational properties of alamethicin in ethanol studied by NMR. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2024; 53:267-276. [PMID: 38849514 DOI: 10.1007/s00249-024-01711-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 04/02/2024] [Accepted: 05/10/2024] [Indexed: 06/09/2024]
Abstract
Alamethicin, a peptide consisted of 20 amino acid residues, has been known to function as an antibiotic. The peptides self-associate in biological membranes, form an ion channel, and then induce cell death by leaking intracellular contents through a transmembrane pore of an ion channel. We investigated conformation and its thermal stability of alamethicin-A6 and -U6 in ethanol using proton nuclear magnetic resonance (NMR) spectroscopy; alamethicin-A6 and -U6 have the amino acid sequences of UPUAUAQUVUGLUPVUUQQO and UPUAUUQUVUGLUPVUUQQO, respectively, where U and O represent α-aminoisobutyric acid and phenylalaninol, respectively. As indicated by the under bars in the sequences, only the residue 6 differs between the alamethicins. We show that the alamethicins in ethanol form helix conformation in the region of the residues 2-11 and a non-regular conformation in the regions of the N- and C-termini, and that the helices are maintained up to 66 °C at least. Conformations in the region of the residues 12-18 of the alamethicins, however, are not well identified due to the lack of NMR data. In addition, we demonstrate that the amide proton chemical shift temperature coefficients' method, which is known as an indicator for intramolecular hydrogen bonds in peptides and proteins in aqueous solutions, can be also applied to the alamethicins in ethanol. Further, we show that the conformation around the C-terminus of alamethicin-A6 is restrained by intramolecular hydrogen bonds, whereas that of alamethicin-U6 is either restrained or unrestrained by intramolecular hydrogen bonds; the alamethicin-U6 molecules having the restrained and unrestrained conformations coexist in ethanol. We discuss the two types of conformations using a model chain consisting of particles linked by rigid bonds called as the free jointed chain.
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Affiliation(s)
- Yoshinori Miura
- Center for Advanced Instrumental Analysis, Kyushu University, Kasuga, 816-8580, Japan.
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2
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Desai N, Rana D, Salave S, Benival D, Khunt D, Prajapati BG. Achieving Endo/Lysosomal Escape Using Smart Nanosystems for Efficient Cellular Delivery. Molecules 2024; 29:3131. [PMID: 38999083 PMCID: PMC11243486 DOI: 10.3390/molecules29133131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 06/27/2024] [Accepted: 06/28/2024] [Indexed: 07/14/2024] Open
Abstract
The delivery of therapeutic agents faces significant hurdles posed by the endo-lysosomal pathway, a bottleneck that hampers clinical effectiveness. This comprehensive review addresses the urgent need to enhance cellular delivery mechanisms to overcome these obstacles. It focuses on the potential of smart nanomaterials, delving into their unique characteristics and mechanisms in detail. Special attention is given to their ability to strategically evade endosomal entrapment, thereby enhancing therapeutic efficacy. The manuscript thoroughly examines assays crucial for understanding endosomal escape and cellular uptake dynamics. By analyzing various assessment methods, we offer nuanced insights into these investigative approaches' multifaceted aspects. We meticulously analyze the use of smart nanocarriers, exploring diverse mechanisms such as pore formation, proton sponge effects, membrane destabilization, photochemical disruption, and the strategic use of endosomal escape agents. Each mechanism's effectiveness and potential application in mitigating endosomal entrapment are scrutinized. This paper provides a critical overview of the current landscape, emphasizing the need for advanced delivery systems to navigate the complexities of cellular uptake. Importantly, it underscores the transformative role of smart nanomaterials in revolutionizing cellular delivery strategies, leading to a paradigm shift towards improved therapeutic outcomes.
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Affiliation(s)
- Nimeet Desai
- Indian Institute of Technology Hyderabad, Kandi 502285, Telangana, India;
| | - Dhwani Rana
- National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad 382355, Gujarat, India; (D.R.); (S.S.); (D.B.)
| | - Sagar Salave
- National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad 382355, Gujarat, India; (D.R.); (S.S.); (D.B.)
| | - Derajram Benival
- National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad 382355, Gujarat, India; (D.R.); (S.S.); (D.B.)
| | - Dignesh Khunt
- School of Pharmacy, Gujarat Technological University, Gandhinagar 382027, Gujarat, India
| | - Bhupendra G. Prajapati
- Shree S. K. Patel College of Pharmaceutical Education and Research, Ganpat University, Kherva 384012, Gujarat, India
- Faculty of Pharmacy, Silpakorn University, Nakhon Pathom 73000, Thailand
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3
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Peigneur S, Tibery D, Tytgat J. The Helix Ring Peptide U 11 from the Venom of the Ant, Tetramorium bicarinatum, Acts as a Putative Pore-Forming Toxin. MEMBRANES 2024; 14:114. [PMID: 38786948 PMCID: PMC11123039 DOI: 10.3390/membranes14050114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/26/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024]
Abstract
An insect neuroactive helix ring peptide called U11-MYRTX-Tb1a (abbreviated as U11) from the venom of the ant, Tetramorium bicarinatum. U11 is a 34-amino-acid peptide that is claimed to be one of the most paralytic peptides ever reported from ant venoms acting against blowflies and honeybees. The peptide features a compact triangular ring helix structure stabilized by a single disulfide bond, which is a unique three-dimensional scaffold among animal venoms. Pharmacological assays using Drosophila S2 cells have demonstrated that U11 is not cytotoxic but instead suggest that it may modulate potassium channels via the presence of a functional dyad. In our work described here, we have tested this hypothesis by investigating the action of synthetically made U11 on a wide array of voltage-gated K and Na channels since it is well known that these channels play a crucial role in the phenomenon of paralysis. Using the Xenopus laevis oocyte heterologous expression system and voltage clamp, our results have not shown any modulatory effect of 1 μM U11 on the activity of Kv1.1, Kv1.3, Kv1.4, Kv1.5, Shaker IR, Kv4.2, Kv7.1, Kv10.1, Kv11.1 and KQT1, nor on DmNav and BgNav. Instead, 10 μM U11 caused a quick and irreversible cytolytic effect, identical to the cytotoxic effect caused by Apis mellifera venom, which indicates that U11 can act as a pore-forming peptide. Interestingly, the paralytic dose (PD50) on blowflies and honeybees corresponds with the concentration at which U11 displays clear pore-forming activity. In conclusion, our results indicate that the insecticidal and paralytic effects caused by U11 may be explained by the putative pore formation of the peptide.
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Affiliation(s)
- Steve Peigneur
- Toxicology and Pharmacology, University of Leuven (KU Leuven), P.O. Box 922, Herestraat 49, 3000 Leuven, Belgium; (S.P.); (D.T.)
| | - Diogo Tibery
- Toxicology and Pharmacology, University of Leuven (KU Leuven), P.O. Box 922, Herestraat 49, 3000 Leuven, Belgium; (S.P.); (D.T.)
- Laboratory of Neuropharmacology, Department of Physiological Sciences, University of Brasília, Distrito Federal, Brasília 70910-900, Brazil
| | - Jan Tytgat
- Toxicology and Pharmacology, University of Leuven (KU Leuven), P.O. Box 922, Herestraat 49, 3000 Leuven, Belgium; (S.P.); (D.T.)
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4
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Meleleo D, Avato P, Conforti F, Argentieri MP, Messina G, Cibelli G, Mallamaci R. Interaction of Quercetin, Cyanidin, and Their O-Glucosides with Planar Lipid Models: Implications for Their Biological Effects. MEMBRANES 2023; 13:600. [PMID: 37367804 DOI: 10.3390/membranes13060600] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/10/2023] [Accepted: 06/13/2023] [Indexed: 06/28/2023]
Abstract
Flavonoids are specialized metabolites produced by plants, as free aglycones or as glycosylated derivatives, which are particularly endowed with a variety of beneficial health properties. The antioxidant, anti-inflammatory, antimicrobial, anticancer, antifungal, antiviral, anti-Alzheimer's, anti-obesity, antidiabetic, and antihypertensive effects of flavonoids are now known. These bioactive phytochemicals have been shown to act on different molecular targets in cells including the plasma membrane. Due to their polyhydroxylated structure, lipophilicity, and planar conformation, they can either bind at the bilayer interface or interact with the hydrophobic fatty acid tails of the membrane. The interaction of quercetin, cyanidin, and their O-glucosides with planar lipid membranes (PLMs) similar in composition to those of the intestine was monitored using an electrophysiological approach. The obtained results show that the tested flavonoids interact with PLM and form conductive units. The modality of interaction with the lipids of the bilayer and the alteration of the biophysical parameters of PLMs induced by the tested substances provided information on their location in the membrane, helping to elucidate the mechanism of action which underlies some pharmacological properties of flavonoids. To our knowledge, the interaction of quercetin, cyanidin, and their O-glucosides with PLM surrogates of the intestinal membrane has never been previously monitored.
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Affiliation(s)
- Daniela Meleleo
- Department of Science of Agriculture, Food, Natural Resources and Engineering, University of Foggia, 71122 Foggia, Italy
| | - Pinarosa Avato
- Department of Pharmacy-Drug Sciences, University of Bari "Aldo Moro", 70125 Bari, Italy
| | - Filomena Conforti
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy
| | - Maria Pia Argentieri
- Department of Pharmacy-Drug Sciences, University of Bari "Aldo Moro", 70125 Bari, Italy
| | - Giovanni Messina
- Department of Clinical and Experimental Medicine, University of Foggia, 71122 Foggia, Italy
| | - Giuseppe Cibelli
- Department of Clinical and Experimental Medicine, University of Foggia, 71122 Foggia, Italy
| | - Rosanna Mallamaci
- Department of Biosciences, Biotechnologies and Environment, University of Bari "Aldo Moro", 70125 Bari, Italy
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5
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Roy A, Sarangi NK, Ghosh S, Prabhakaran A, Keyes TE. Leaflet by Leaflet Synergistic Effects of Antimicrobial Peptides on Bacterial and Mammalian Membrane Models. J Phys Chem Lett 2023; 14:3920-3928. [PMID: 37075204 PMCID: PMC10150393 DOI: 10.1021/acs.jpclett.3c00119] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Antimicrobial peptides (AMPs) offer significant hope in the fight against antibiotic resistance. Operating via a mechanism different from that of antibiotics, they target the microbial membrane and ideally should damage it without impacting mammalian cells. Here, the interactions of two AMPs, magainin 2 and PGLa, and their synergistic effects on bacterial and mammalian membrane models were studied using electrochemical impedance spectroscopy, atomic force microscopy (AFM), and fluorescence correlation spectroscopy. Toroidal pore formation was observed by AFM when the two AMPs were combined, while individually AMP effects were confined to the exterior leaflet of the bacterial membrane analogue. Using microcavity-supported lipid bilayers, the diffusivity of each bilayer leaflet could be studied independently, and we observed that combined, the AMPs penetrate both leaflets of the bacterial model but individually each peptide had a limited impact on the proximal leaflet of the bacterial model. The impact of AMPs on a ternary, mammalian mimetic membrane was much weaker.
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Affiliation(s)
- Arpita Roy
- School of Chemical Sciences and National Centre for Sensor Research, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Nirod Kumar Sarangi
- School of Chemical Sciences and National Centre for Sensor Research, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Surajit Ghosh
- School of Chemical Sciences and National Centre for Sensor Research, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Amrutha Prabhakaran
- School of Chemical Sciences and National Centre for Sensor Research, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Tia E Keyes
- School of Chemical Sciences and National Centre for Sensor Research, Dublin City University, Glasnevin, Dublin 9, Ireland
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6
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Mondal N, Yadav KS, Dalal DC. Enhanced Drug Uptake on Application of Electroporation in a Single-Cell Model. J Membr Biol 2023; 256:243-255. [PMID: 36988647 DOI: 10.1007/s00232-023-00283-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 03/09/2023] [Indexed: 03/30/2023]
Abstract
Electroporation method is a useful tool for delivering drugs into various diseased tissues in the human body. As a result of an applied electric field, drug particles enter the intracellular compartment through the temporarily permeabilized cell membrane. Consequently, electroporation method allows better penetration of the drug into the diseased tissue and improves treatment clinically. In this study, a more generalized model of drug transport in a single cell is proposed. The model is able to capture non-homogeneous drug transport in the cell due to non-uniform cell membrane permeabilization. Several numerical experiments are conducted to understand the effects of electric field and drug permeability on drug uptake into the cell. Through investigation, the appropriate electric field and drug permeability are identified, which lead to sufficient drug uptake into the cell. This model can be used by experimentalists to get information prior to conduct any experiment, and it may help reduce the number of actual experiments that might be conducted otherwise.
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7
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Ascoët S, Touchard A, Téné N, Lefranc B, Leprince J, Paquet F, Jouvensal L, Barassé V, Treilhou M, Billet A, Bonnafé E. The mechanism underlying toxicity of a venom peptide against insects reveals how ants are master at disrupting membranes. iScience 2023; 26:106157. [PMID: 36879819 PMCID: PMC9985030 DOI: 10.1016/j.isci.2023.106157] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/17/2023] [Accepted: 02/02/2023] [Indexed: 02/10/2023] Open
Abstract
Hymenopterans represent one of the most abundant groups of venomous organisms but remain little explored due to the difficult access to their venom. The development of proteo-transcriptomic allowed us to explore diversity of their toxins offering interesting perspectives to identify new biological active peptides. This study focuses on U9 function, a linear, amphiphilic and polycationic peptide isolated from ant Tetramorium bicarinatum venom. It shares physicochemical properties with M-Tb1a, exhibiting cytotoxic effects through membrane permeabilization. In the present study, we conducted a comparative functional investigation of U9 and M-Tb1a and explored the mechanisms underlying their cytotoxicity against insect cells. After showing that both peptides induced the formation of pores in cell membrane, we demonstrated that U9 induced mitochondrial damage and, at high concentrations, localized into cells and induced caspase activation. This functional investigation highlighted an original mechanism of U9 questioning on potential valorization and endogen activity in T. bicarinatum venom.
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Affiliation(s)
- Steven Ascoët
- BTSB-UR 7417, Université de Toulouse, Institut National Universitaire Jean-François Champollion, Place de Verdun, 81000 Albi, France
| | - Axel Touchard
- CNRS, UMR Ecologie des Forêts de Guyane, AgroParisTech, CIRAD, INRA, Université de Guyane, Université des Antilles, Campus Agronomique, BP316 97310 Kourou, France
| | - Nathan Téné
- BTSB-UR 7417, Université de Toulouse, Institut National Universitaire Jean-François Champollion, Place de Verdun, 81000 Albi, France
| | - Benjamin Lefranc
- Inserm U1239, NorDiC, Laboratoire de Différenciation et Communication Neuroendocrine, Endocrine et Germinale, Université de Rouen-Normandie, 76000 Rouen, France
- Inserm US51, HeRacLeS, Université de Rouen-Normandie, 76000 Rouen, France
| | - Jérôme Leprince
- Inserm U1239, NorDiC, Laboratoire de Différenciation et Communication Neuroendocrine, Endocrine et Germinale, Université de Rouen-Normandie, 76000 Rouen, France
- Inserm US51, HeRacLeS, Université de Rouen-Normandie, 76000 Rouen, France
| | - Françoise Paquet
- Centre de Biophysique Moléculaire, CNRS UPR 4301, Rue Charles Sadron CS-80054, 45071 Orléans, France
| | - Laurence Jouvensal
- Centre de Biophysique Moléculaire, CNRS UPR 4301, Rue Charles Sadron CS-80054, 45071 Orléans, France
| | - Valentine Barassé
- BTSB-UR 7417, Université de Toulouse, Institut National Universitaire Jean-François Champollion, Place de Verdun, 81000 Albi, France
| | - Michel Treilhou
- BTSB-UR 7417, Université de Toulouse, Institut National Universitaire Jean-François Champollion, Place de Verdun, 81000 Albi, France
| | - Arnaud Billet
- BTSB-UR 7417, Université de Toulouse, Institut National Universitaire Jean-François Champollion, Place de Verdun, 81000 Albi, France
| | - Elsa Bonnafé
- BTSB-UR 7417, Université de Toulouse, Institut National Universitaire Jean-François Champollion, Place de Verdun, 81000 Albi, France
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8
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Duque HM, Rodrigues G, Santos LS, Franco OL. The biological role of charge distribution in linear antimicrobial peptides. Expert Opin Drug Discov 2023; 18:287-302. [PMID: 36720196 DOI: 10.1080/17460441.2023.2173736] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
INTRODUCTION Antimicrobial peptides (AMP) have received particular attention due to their capacity to kill bacteria. Although much is known about them, peptides are currently being further researched. A large number of AMPs have been discovered, but only a few have been approved for topical use, due to their promiscuity and other challenges, which need to be overcome. AREAS COVERED AMPs are diverse in structure. Consequently, they have varied action mechanisms when targeting microorganisms or eukaryotic cells. Herein, the authors focus on linear peptides, particularly those that are alpha-helical structured, and examine how their charge distribution and hydrophobic amino acids could modulate their biological activity. EXPERT OPINION The world currently needs urgent solutions to the infective problems caused by resistant pathogens. In order to start the race for antimicrobial development from the charge distribution viewpoint, bioinformatic tools will be necessary. Currently, there is no software available that allows to discriminate charge distribution in AMPs and predicts the biological effects of this event. Furthermore, there is no software available that predicts the side-chain length of residues and its role in biological functions. More specialized software is necessary.
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Affiliation(s)
- Harry Morales Duque
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, PC: (CEP) 70.790-160, Brasília-DF, Brazil
| | - Gisele Rodrigues
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, PC: (CEP) 70.790-160, Brasília-DF, Brazil
| | - Lucas Souza Santos
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, PC: (CEP) 70.790-160, Brasília-DF, Brazil
| | - Octávio Luiz Franco
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, PC: (CEP) 70.790-160, Brasília-DF, Brazil.,S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, PC: (CEP) 79117-010, Campo Grande-MS, Brazil
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9
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C-terminal modification of a de novo designed antimicrobial peptide via capping of macrolactam rings. Bioorg Chem 2022; 130:106251. [DOI: 10.1016/j.bioorg.2022.106251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 10/20/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022]
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10
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Implanted synthetic cells trigger tissue angiogenesis through de novo production of recombinant growth factors. Proc Natl Acad Sci U S A 2022; 119:e2207525119. [PMID: 36095208 PMCID: PMC9499519 DOI: 10.1073/pnas.2207525119] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Progress in bottom-up synthetic biology has stimulated the development of synthetic cells (SCs), autonomous protein-manufacturing particles, as dynamic biomimetics for replacing diseased natural cells and addressing medical needs. Here, we report that SCs genetically encoded to produce proangiogenic factors triggered the physiological process of neovascularization in mice. The SCs were constructed of giant lipid vesicles and were optimized to facilitate enhanced protein production. When introduced with the appropriate genetic code, the SCs synthesized a recombinant human basic fibroblast growth factor (bFGF), reaching expression levels of up to 9⋅106 protein copies per SC. In culture, the SCs induced endothelial cell proliferation, migration, tube formation, and angiogenesis-related intracellular signaling, confirming their proangiogenic activity. Integrating the SCs with bioengineered constructs bearing endothelial cells promoted the remodeling of mature vascular networks, supported by a collagen-IV basement membrane-like matrix. In vivo, prolonged local administration of the SCs in mice triggered the infiltration of blood vessels into implanted Matrigel plugs without recorded systemic immunogenicity. These findings emphasize the potential of SCs as therapeutic platforms for activating physiological processes by autonomously producing biological drugs inside the body.
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11
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Epremyan KK, Goleva TN, Rogov AG, Lavrushkina SV, Zinovkin RA, Zvyagilskaya RA. The First Yarrowia lipolytica Yeast Models Expressing Hepatitis B Virus X Protein: Changes in Mitochondrial Morphology and Functions. Microorganisms 2022; 10:microorganisms10091817. [PMID: 36144419 PMCID: PMC9501646 DOI: 10.3390/microorganisms10091817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 09/04/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022] Open
Abstract
Chronic hepatitis B virus infection is the dominant cause of hepatocellular carcinoma, the main cause of cancer death. HBx protein, a multifunctional protein, is essential for pathogenesis development; however, the underlying mechanisms are not fully understood. The complexity of the system itself, and the intricate interplay of many factors make it difficult to advance in understanding the mechanisms underlying these processes. The most obvious solution is to use simpler systems by reducing the number of interacting factors. Yeast cells are particularly suitable for studying the relationships between oxidative stress, mitochondrial dynamics (mitochondrial fusion and fragmentation), and mitochondrial dysfunction involved in HBx-mediated pathogenesis. For the first time, genetically modified yeast, Y. lipolytica, was created, expressing the hepatitis B virus core protein HBx, as well as a variant fused with eGFP at the C-end. It was found that cells expressing HBx experienced stronger oxidative stress than the control cells. Oxidative stress was alleviated by preincubation with the mitochondria-targeted antioxidant SkQThy. Consistent with these data, in contrast to the control cells (pZ-0) containing numerous mitochondrial forming a mitochondrial reticulum, in cells expressing HBx protein, mitochondria were fragmented, and preincubation with SkQThy partially restored the mitochondrial reticulum. Expression of HBx had a significant influence on the bioenergetic function of mitochondria, making them loosely coupled with decreased respiratory rate and reduced ATP formation. In sum, the first highly promising yeast model for studying the impact of HBx on bioenergy, redox-state, and dynamics of mitochondria in the cell and cross-talk between these parameters was offered. This fairly simple model can be used as a platform for rapid screening of potential therapeutic agents, mitigating the harmful effects of HBx.
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Affiliation(s)
- Khoren K. Epremyan
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33/2, 119071 Moscow, Russia
- Correspondence: (K.K.E.); (R.A.Z.); Tel.: +7-(917)-575-3560 (K.K.E.)
| | - Tatyana N. Goleva
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33/2, 119071 Moscow, Russia
| | - Anton G. Rogov
- National Research Center “Kurchatov Institute”, Akademika Kurchatova pl. 1, 123182 Moscow, Russia
| | - Svetlana V. Lavrushkina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskye Gory 1/40, 119992 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskye Gory 1/73, 119234 Moscow, Russia
| | - Roman A. Zinovkin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskye Gory 1/40, 119992 Moscow, Russia
| | - Renata A. Zvyagilskaya
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33/2, 119071 Moscow, Russia
- Correspondence: (K.K.E.); (R.A.Z.); Tel.: +7-(917)-575-3560 (K.K.E.)
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12
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Wang R, Shi MY, Ma BB, Sheng J. Mechanism of Leakage in Phosphatidylserine-Containing Membranes by Melittin. Mol Biol 2022. [DOI: 10.1134/s0026893322060206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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13
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Morales-Martínez A, Bertrand B, Hernández-Meza JM, Garduño-Juárez R, Silva-Sanchez J, Munoz-Garay C. Membrane fluidity, composition, and charge affect the activity and selectivity of the AMP ascaphin-8. Biophys J 2022; 121:3034-3048. [PMID: 35842753 PMCID: PMC9463648 DOI: 10.1016/j.bpj.2022.07.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 06/28/2022] [Accepted: 07/12/2022] [Indexed: 12/29/2022] Open
Abstract
Ascaphins are cationic antimicrobial peptides that have been shown to have potential in the treatment of infectious diseases caused by multidrug-resistant pathogens (MDR). However, to date, their principal molecular target and mechanism of action are unknown. Results from peptide prediction software and molecular dynamics simulations confirmed that ascaphin-8 is an alpha-helical peptide. For the first time, the peptide was described as membranotrophic using biophysical approaches including calcein liposome leakage, Laurdan general polarization, and dynamic light scattering. Ascaphin-8's activity and selectivity were modulated by rearranging the spatial distribution of lysine (Var-K5), aspartic acid (Var-D4) residues, or substitution of phenylalanine with tyrosine (Var-Y). The parental peptide and its variants presented high affinity toward the bacterial membrane model (≤2 μM), but lost activity in sterol-enriched membranes (mammal and fungal models, with cholesterol and ergosterol, respectively). The peptide-induced pore size was estimated to be >20 nm in the bacterial model, with no difference among peptides. The same pattern was observed in membrane fluidity (general polarization) assays, where all peptides reduced membrane fluidity of the bacterial model but not in the models containing sterols. The peptides also showed high activity toward MDR bacteria. Moreover, peptide sensitivity of the artificial membrane models compared with pathogenic bacterial isolates were in good agreement.
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Affiliation(s)
- Adriana Morales-Martínez
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México (ICF-UNAM), Cuernavaca, Morelos, México
| | - Brandt Bertrand
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México (ICF-UNAM), Cuernavaca, Morelos, México
| | - Juan M Hernández-Meza
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México (ICF-UNAM), Cuernavaca, Morelos, México
| | - Ramón Garduño-Juárez
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México (ICF-UNAM), Cuernavaca, Morelos, México
| | - Jesús Silva-Sanchez
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - Carlos Munoz-Garay
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México (ICF-UNAM), Cuernavaca, Morelos, México.
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14
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Greve JM, Cowan JA. Tackling antimicrobial stewardship through synergy and antimicrobial peptides. RSC Med Chem 2022; 13:511-521. [PMID: 35694695 PMCID: PMC9132191 DOI: 10.1039/d2md00048b] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 04/04/2022] [Indexed: 11/21/2022] Open
Abstract
The unrestricted use of antibiotics has led to rapid development of antibiotic resistance (AR) and renewed calls to address this serious problem. This review summarizes the most common mechanisms of antibiotic action, and in turn antibiotic resistance, as well as pathways to mitigate the harm. Focus is then turned to emerging antibiotic strategies, including antimicrobial peptides (AMPs), with a discussion of their modes of action, biochemical features, and potential challenges for their use as antibiotics. The role of synergy in antimicrobials is also examined, with a focus on the synergy of AMPs and other emerging interactions with synergistic potential.
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Affiliation(s)
- Jenna M Greve
- Department of Chemistry and Biochemistry, The Ohio State University 100 West 18th Avenue Columbus Ohio 43210 USA +1 614 292 2703
| | - James A Cowan
- Department of Chemistry and Biochemistry, The Ohio State University 100 West 18th Avenue Columbus Ohio 43210 USA +1 614 292 2703
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15
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Molecular Simulation Approaches to the Study of Thermotropic and Lyotropic Liquid Crystals. CRYSTALS 2022. [DOI: 10.3390/cryst12050685] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Over the last decade, the availability of computer time, together with new algorithms capable of exploiting parallel computer architectures, has opened up many possibilities in molecularly modelling liquid crystalline systems. This perspective article points to recent progress in modelling both thermotropic and lyotropic systems. For thermotropic nematics, the advent of improved molecular force fields can provide predictions for nematic clearing temperatures within a 10 K range. Such studies also provide valuable insights into the structure of more complex phases, where molecular organisation may be challenging to probe experimentally. Developments in coarse-grained models for thermotropics are discussed in the context of understanding the complex interplay of molecular packing, microphase separation and local interactions, and in developing methods for the calculation of material properties for thermotropics. We discuss progress towards the calculation of elastic constants, rotational viscosity coefficients, flexoelectric coefficients and helical twisting powers. The article also covers developments in modelling micelles, conventional lyotropic phases, lyotropic phase diagrams, and chromonic liquid crystals. For the latter, atomistic simulations have been particularly productive in clarifying the nature of the self-assembled aggregates in dilute solution. The development of effective coarse-grained models for chromonics is discussed in detail, including models that have demonstrated the formation of the chromonic N and M phases.
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16
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Priyadarshini D, Ivica J, Separovic F, de Planque MRR. Characterisation of cell membrane interaction mechanisms of antimicrobial peptides by electrical bilayer recording. Biophys Chem 2022; 281:106721. [PMID: 34808479 DOI: 10.1016/j.bpc.2021.106721] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/09/2021] [Accepted: 11/11/2021] [Indexed: 12/29/2022]
Abstract
Many antimicrobial peptides (AMPs) are cationic host defence peptides (HDPs) that interact with microbial membranes. This ability may lead to implementation of AMPs as therapeutics to overcome the wide-spread antibiotic resistance problem as the affected bacteria may not be able to recover from membrane lysis types of attack. AMP interactions with lipid bilayer membranes are typically explained through three mechanisms, i.e., barrel-stave pore, toroidal pore and carpet models. Electrical bilayer recording is a relatively simple and sensitive technique that is able to capture the nanoscale perturbations caused by the AMPs in the bilayer membranes. Molecular-level understanding of the behaviour of AMPs in relation to lipid bilayers mimicking bacterial and human cell membranes is essential for their development as novel therapeutic agents that are capable of targeted action against disease causing micro-organisms. The effects of four AMPs (aurein 1.2, caerin 1.1, citropin 1.1 and maculatin 1.1 from the skin secretions of Australian tree frogs) and the toxin melittin (found in the venom of honeybees) on two different phospholipid membranes were studied using the electrical bilayer recording technique. Bilayers composed of zwitterionic (DPhPC) and anionic (DPhPC/POPG) lipids were used to mimic the charge of eukaryotic and prokaryotic cell membranes, respectively, so as to determine the corresponding interaction mechanisms for different concentrations of the peptide. Analysis of the dataset corresponding to the four frog AMPs, as well as the resulting dataset corresponding to the bee toxin, confirms the proposed peptide-bilayer interaction models in existing publications and demonstrates the importance of using appropriate bilayer compositions and peptide concentrations for AMP studies.
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Affiliation(s)
- Diana Priyadarshini
- Electronics and Computer Science, Faculty of Physical & Applied Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Josip Ivica
- Electronics and Computer Science, Faculty of Physical & Applied Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Frances Separovic
- School of Chemistry, Bio21 Institute, University of Melbourne, Melbourne, VIC 3010, Australia.
| | - Maurits R R de Planque
- Electronics and Computer Science, Faculty of Physical & Applied Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom
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17
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Róg T, Girych M, Bunker A. Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design. Pharmaceuticals (Basel) 2021; 14:1062. [PMID: 34681286 PMCID: PMC8537670 DOI: 10.3390/ph14101062] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 11/17/2022] Open
Abstract
We review the use of molecular dynamics (MD) simulation as a drug design tool in the context of the role that the lipid membrane can play in drug action, i.e., the interaction between candidate drug molecules and lipid membranes. In the standard "lock and key" paradigm, only the interaction between the drug and a specific active site of a specific protein is considered; the environment in which the drug acts is, from a biophysical perspective, far more complex than this. The possible mechanisms though which a drug can be designed to tinker with physiological processes are significantly broader than merely fitting to a single active site of a single protein. In this paper, we focus on the role of the lipid membrane, arguably the most important element outside the proteins themselves, as a case study. We discuss work that has been carried out, using MD simulation, concerning the transfection of drugs through membranes that act as biological barriers in the path of the drugs, the behavior of drug molecules within membranes, how their collective behavior can affect the structure and properties of the membrane and, finally, the role lipid membranes, to which the vast majority of drug target proteins are associated, can play in mediating the interaction between drug and target protein. This review paper is the second in a two-part series covering MD simulation as a tool in pharmaceutical research; both are designed as pedagogical review papers aimed at both pharmaceutical scientists interested in exploring how the tool of MD simulation can be applied to their research and computational scientists interested in exploring the possibility of a pharmaceutical context for their research.
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Affiliation(s)
- Tomasz Róg
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Mykhailo Girych
- Department of Physics, University of Helsinki, 00014 Helsinki, Finland;
| | - Alex Bunker
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, 00014 Helsinki, Finland;
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18
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Internalization and membrane activity of the antimicrobial peptide CGA-N12. Biochem J 2021; 478:1907-1919. [PMID: 33955460 DOI: 10.1042/bcj20201006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 04/21/2021] [Accepted: 05/06/2021] [Indexed: 12/21/2022]
Abstract
Antimicrobial peptides (AMPs) are conventional antibiotic alternatives due to their broad-spectrum antimicrobial activities and special mechanisms of action against pathogens. The antifungal peptide CGA-N12 was originally derived from human chromogranin A (CGA) and consists of the 65th to 76th amino acids of the CGA N-terminal region. In the present study, we found that CGA-N12 had fungicidal activity and exhibited time-dependent inhibition activity against Candida tropicalis. CGA-N12 entered the cells to exert its antagonist activity. The internalization of CGA-N12 was energy-dependent and accompanied by actin cytoskeleton-, clathrin-, sulfate proteoglycan-, endosome-, and lipid-depleting agent-mediated endocytosis. Moreover, the CGA-N12 internalization pathway was related to the peptide concentration. The effects of CGA-N12 on the cell membrane were investigated. CGA-N12 at a low concentration less than 4 × MIC100 did not destroy the cell membrane. While with increasing concentration, the damage to the cell membrane caused by CGA-N12 became more serious. At concentrations greater than 4 × MIC100, CGA-N12 destroyed the cell membrane integrity. Therefore, the membrane activity of CGA-N12 is concentration dependant.
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