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Kim YE, Kim KY. A Bee Trp-Arg Dense Peptide with Antiproliferation Efficacy against the Prostate Cancer Cell Line DU145. Curr Issues Mol Biol 2024; 46:2251-2262. [PMID: 38534760 DOI: 10.3390/cimb46030144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/08/2024] [Accepted: 03/08/2024] [Indexed: 03/28/2024] Open
Abstract
Prostate cancer accounts for 14% of male cancer-related fatalities in the UK. Given the challenges associated with hormone-based therapies in the context of androgen-independent prostate cancer, there is an imperative need for research into anticancer drugs. N0821, a peptide belonging to the Trp-Arg dense region and derived from the homologous region of various bee species, shows substantial potential for an anticancer effect. Both MTT assays and 3D spheroid assays were conducted to substantiate its antiproliferation potential and strongly indicated the antiproliferation effect of N0820 (WWWWRWWRKI) and N0821 (YWWWWRWWRKI). Notably, the mechanism underlying this effect is related to the downregulation of CCNA2 and the upregulation of CCNE1. Cell cycle arrest results from the reduction of CCNA2 in the S/G2 phase, leading to the accumulation of CCNE1. Our peptides were predicted to make an α-helix structure. This can act as an ion channel in the cell membrane. Therefore, we analyzed genes implicated in the influx of calcium ions into the mitochondria. Trp-Arg dense-region peptides are known for their antibacterial properties in targeting cell membranes, making the development of resistance less likely. Hence, further research in this area is essential and promising.
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Affiliation(s)
- Ye-Eun Kim
- Graduate School of Biotechnology, Kyung Hee University, Seocheon, Giheung, Yongin 17104, Republic of Korea
| | - Ki-Young Kim
- Graduate School of Biotechnology, Kyung Hee University, Seocheon, Giheung, Yongin 17104, Republic of Korea
- Department of Genetics and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
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2
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Miao F, Tai Z, Wang Y, Zhu Q, Fang JKH, Hu M. Tachyplesin I Analogue Peptide as an Effective Antimicrobial Agent against Candida albicans- Staphylococcus aureus Poly-Biofilm Formation and Mixed Infection. ACS Infect Dis 2022; 8:1839-1850. [PMID: 35998684 DOI: 10.1021/acsinfecdis.2c00080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Microbial biofilms are difficult to tackle in many infectious diseases. Candida albicans and Staphylococcus aureus are prevalent symbiotic strains in polymicrobial biofilms, which showed enhanced antimicrobial resistance and made identifying effective treatment techniques more difficult. The antibiofilm abilities of tachplesin I analogue peptide (TP11A) and tachplesin I were investigated quantitatively in this study. Both inhibited C. albicans monomicrobial, S. aureus monomicrobial, and C. albicans-S. aureus polymicrobial biofilms quite well. TP11A suppressed the biofilm- and virulence-related genes of C. albicans (hwp 1) and S. aureus (ica A, fnb B, agr A, hla, nor A, and sig B) in the mixed biofilm, according to quantitative reverse transcription polymerase chain reaction analysis. We created an injectable thermosensitive in situ PLEL@TP11A gel system by simply adding TP11A into poly(d,l-lactide)-poly(ethylene glycol)-poly(d,l-lactide) (PLEL). Using C. albicans-S. aureus mixed infected wound models of mice, the in vivo therapeutic effect of TP11A and PLEL@TP11A in polymicrobial infections was investigated. The findings revealed that TP11A and PLEL@TP11A could efficiently reduce bacterial and fungal burden in wound infections, as well as accelerated wound healing. Based on above findings, TP11A might be an effective antimicrobial against C. albicans-S. aureus poly-biofilm formation and mixed infection.
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Affiliation(s)
- Fengze Miao
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai 201306, China.,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China
| | - Zongguang Tai
- Shanghai Skin Disease Hospital, Tongji University School of Medicine, Shanghai 200443, China.,Shanghai Engineering Research Center for Topical Chinese Medicine, Shanghai 200443, China
| | - Youji Wang
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai 201306, China.,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China
| | - Quangang Zhu
- Shanghai Skin Disease Hospital, Tongji University School of Medicine, Shanghai 200443, China.,Shanghai Engineering Research Center for Topical Chinese Medicine, Shanghai 200443, China
| | - James Kar-Hei Fang
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon 999077, China
| | - Menghong Hu
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai 201306, China.,Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai 201306, China
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3
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Müller AT, Posselt G, Gabernet G, Neuhaus C, Bachler S, Blatter M, Pfeiffer B, Hiss JA, Dittrich PS, Altmann KH, Wessler S, Schneider G. Morphing of Amphipathic Helices to Explore the Activity and Selectivity of Membranolytic Antimicrobial Peptides. Biochemistry 2020; 59:3772-3781. [PMID: 32936629 PMCID: PMC7547863 DOI: 10.1021/acs.biochem.0c00565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/07/2020] [Indexed: 01/17/2023]
Abstract
Naturally occurring membranolytic antimicrobial peptides (AMPs) are rarely cell-type selective and highly potent at the same time. Template-based peptide design can be used to generate AMPs with improved properties de novo. Following this approach, 18 linear peptides were obtained by computationally morphing the natural AMP Aurein 2.2d2 GLFDIVKKVVGALG into the synthetic model AMP KLLKLLKKLLKLLK. Eleven of the 18 chimeric designs inhibited the growth of Staphylococcus aureus, and six peptides were tested and found to be active against one resistant pathogenic strain or more. One of the peptides was broadly active against bacterial and fungal pathogens without exhibiting toxicity to certain human cell lines. Solution nuclear magnetic resonance and molecular dynamics simulation suggested an oblique-oriented membrane insertion mechanism of this helical de novo peptide. Temperature-resolved circular dichroism spectroscopy pointed to conformational flexibility as an essential feature of cell-type selective AMPs.
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Affiliation(s)
- Alex T. Müller
- Department
of Chemistry and Applied Biosciences, ETH
Zurich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Gernot Posselt
- Department
of Biosciences, Division of Microbiology, Paris Lodron University of Salzburg, Billrothstrasse 11, 5020 Salzburg, Austria
| | - Gisela Gabernet
- Department
of Chemistry and Applied Biosciences, ETH
Zurich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Claudia Neuhaus
- Department
of Chemistry and Applied Biosciences, ETH
Zurich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Simon Bachler
- Department
of Biosystems Science and Engineering, ETH
Zurich, Mattenstrasse
26, 4058 Basel, Switzerland
| | - Markus Blatter
- Novartis
Institutes for BioMedical Research, Novartis
Pharma AG, Novartis Campus, 4002 Basel, Switzerland
| | - Bernhard Pfeiffer
- Department
of Chemistry and Applied Biosciences, ETH
Zurich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Jan A. Hiss
- Department
of Chemistry and Applied Biosciences, ETH
Zurich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Petra S. Dittrich
- Department
of Biosystems Science and Engineering, ETH
Zurich, Mattenstrasse
26, 4058 Basel, Switzerland
| | - Karl-Heinz Altmann
- Department
of Chemistry and Applied Biosciences, ETH
Zurich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Silja Wessler
- Department
of Biosciences, Division of Microbiology, Paris Lodron University of Salzburg, Billrothstrasse 11, 5020 Salzburg, Austria
| | - Gisbert Schneider
- Department
of Chemistry and Applied Biosciences, ETH
Zurich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
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4
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Arg-substituted VmCT1 analogs reveals promising candidate for the development of new antichagasic agent. Parasitology 2020; 147:1810-1818. [PMID: 33004083 DOI: 10.1017/s0031182020001882] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
VmCT1 is an antimicrobial peptide (AMP) isolated from the venom of the scorpion Vaejovis mexicanus with antimicrobial, anticancer and antimalarial activities, which the rational design with Arg-substitution has yielded AMPs with higher antimicrobial activity than VmCT1. Chagas is a neglected tropical disease, becoming the development of new antichagasic agents is urgent. Thus, we aimed to evaluate the antichagasic effect of VmCT1 and three Arg-substituted analogues, as well their action mechanism. Peptides were tested against the epimastigote, trypomastigote, amastigote forms of Trypanossoma cruzi Y strain and against LLC-MK2 mammalian cells. The mechanism of action of these peptides was evaluated by means of flow cytometry and scanning electron microscopy. VmCT1 presented activity against all three forms of T. cruzi, with EC50 against trypomastigote forms of 1.37 μmol L-1 and selectivity index (SI) of 58. [Arg]3-VmCT1, [Arg]7-VmCT1 and [Arg]11-VmCT1 also showed trypanocidal effect, but [Arg]11-VmCT1 had the best effect, being able to decrease the EC50 against trypomastigote forms to 0.8 μmol L-1 and increase SI to 175. Necrosis was cell death pathway of VmCT1, as well [Arg]7-VmCT1 and [Arg]11-VmCT1, such as observed by membrane damage in flow cytometry analyses and scanning-electron-microscopy. In conclusion, [Arg]11-VmCT1 revealed promising as a candidate for new antichagasic therapeutics.
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5
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Kim S, Nam HY, Lee J, Seo J. Mitochondrion-Targeting Peptides and Peptidomimetics: Recent Progress and Design Principles. Biochemistry 2019; 59:270-284. [PMID: 31696703 DOI: 10.1021/acs.biochem.9b00857] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Mitochondria are multifunctional subcellular organelles whose operations encompass energy production, signal transduction, and metabolic regulation. Given their wide range of roles, they have been studied extensively as a potential therapeutic target for the treatment of various diseases, including cancer, diabetes, and neurodegenerative diseases. Mitochondrion-mediated pathways have been identified as promising targets in the context of these diseases. However, the delivery of specific probes and drugs to the mitochondria is one of the major problems that remains to be solved. Over the past decade, much effort has been devoted to developing mitochondrion-targeted delivery methods based on the membrane characteristics and the protein import machinery of mitochondria. While various methods utilizing small molecules to polymeric particles have been introduced, it is notable that many of these compounds share common structural elements and physicochemical properties for optimal selectivity and efficiency. In this Perspective, we will review the most recently developed mitochondrion-targeting peptides and peptidomimetics to outline the key aspects of structural requirements and design principles. We will also discuss successful and potential applications of mitochondrial delivery to assess opportunities and challenges in the targeting of mitochondria.
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Affiliation(s)
- Soyoung Kim
- Department of Chemistry, School of Physics and Chemistry , Gwangju Institute of Science and Technology , Gwangju 61005 , Republic of Korea
| | - Ho Yeon Nam
- Department of Chemistry, School of Physics and Chemistry , Gwangju Institute of Science and Technology , Gwangju 61005 , Republic of Korea
| | - Jiyoun Lee
- Department of Global Medical Science , Sungshin University , Seoul 01133 , Republic of Korea
| | - Jiwon Seo
- Department of Chemistry, School of Physics and Chemistry , Gwangju Institute of Science and Technology , Gwangju 61005 , Republic of Korea
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6
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Cuesta S, Gallegos F, Arias J, Pilaquinga F, Blasco-Zúñiga A, Proaño-Bolaños C, Rivera M, Meneses L. Molecular modeling of four Dermaseptin-related peptides of the gliding tree frog Agalychnis spurrelli. J Mol Model 2019; 25:260. [PMID: 31422479 DOI: 10.1007/s00894-019-4141-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 07/17/2019] [Indexed: 01/24/2023]
Abstract
In this research, we present a preliminary computational study of four Dermaseptin-related peptides from the skin exudate of the gliding tree frog Agalychnis spurrelli. Experimentally, the amino acid sequence of these peptides was elucidated through molecular cloning and tandem mass spectrometry and synthetic peptides were assayed against E. coli, S. aureus, and C. albicans to determine their antimicrobial properties. With the sequences on hand, a computational study of the structures was carried out, obtaining their physicochemical properties, secondary structure, and their similarity to other known peptides. A molecular docking study of these peptides was also performed against cell membrane and several enzymes are known to be vital for the organisms. Results showed that Dermaseptin-related peptides are α-helical cationic peptides with an isoelectric point above 9.70 and a positive charge of physiological pH. Introducing theses peptides in a database, it was determined that their identity compared with known peptides range from 36 to 82% meaning these four Dermaseptins are novel peptides. This preliminary study of molecular docking suggests the mechanism of action of this peptide is not given by the inhibition of essential enzymatic pathways, but by cell lysis. Graphical abstract.
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Affiliation(s)
- Sebastián Cuesta
- Laboratorios LIFE, Av. De la Prensa y Juan Galarza, Quito, Ecuador
| | - Felipe Gallegos
- Laboratorio de Química Computacional, Escuela de Ciencias Químicas, Pontificia Universidad Católica del Ecuador, Av. 12 de Octubre 1076 y Roca, Apartado 17-01-2184, Quito, Ecuador
| | - Josefa Arias
- Laboratorio de Química Computacional, Escuela de Ciencias Químicas, Pontificia Universidad Católica del Ecuador, Av. 12 de Octubre 1076 y Roca, Apartado 17-01-2184, Quito, Ecuador
| | - Fernanda Pilaquinga
- Laboratorio de Química Computacional, Escuela de Ciencias Químicas, Pontificia Universidad Católica del Ecuador, Av. 12 de Octubre 1076 y Roca, Apartado 17-01-2184, Quito, Ecuador
| | - Ailín Blasco-Zúñiga
- Laboratorio de Investigación en Citogenética y Biomoléculas de Anfibios-LICBA, Centro de Investigación para la Salud en América Latina-CISeAL, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Av. 12 de octubre 1076 y Roca, Apartado 17-01-2184, Quito, Ecuador
| | - Carolina Proaño-Bolaños
- Laboratorio de Biología Molecular y Bioquímica, Universidad Regional Amazónica Ikiam, Km 7 vía Muyuna, Tena, Ecuador
| | - Miryan Rivera
- Laboratorio de Investigación en Citogenética y Biomoléculas de Anfibios-LICBA, Centro de Investigación para la Salud en América Latina-CISeAL, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Av. 12 de octubre 1076 y Roca, Apartado 17-01-2184, Quito, Ecuador
| | - Lorena Meneses
- Laboratorio de Química Computacional, Escuela de Ciencias Químicas, Pontificia Universidad Católica del Ecuador, Av. 12 de Octubre 1076 y Roca, Apartado 17-01-2184, Quito, Ecuador.
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7
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Gabernet G, Gautschi D, Müller AT, Neuhaus CS, Armbrecht L, Dittrich PS, Hiss JA, Schneider G. In silico design and optimization of selective membranolytic anticancer peptides. Sci Rep 2019; 9:11282. [PMID: 31375699 PMCID: PMC6677754 DOI: 10.1038/s41598-019-47568-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 06/17/2019] [Indexed: 12/31/2022] Open
Abstract
Membranolytic anticancer peptides represent a potential strategy in the fight against cancer. However, our understanding of the underlying structure-activity relationships and the mechanisms driving their cell selectivity is still limited. We developed a computational approach as a step towards the rational design of potent and selective anticancer peptides. This machine learning model distinguishes between peptides with and without anticancer activity. This classifier was experimentally validated by synthesizing and testing a selection of 12 computationally generated peptides. In total, 83% of these predictions were correct. We then utilized an evolutionary molecular design algorithm to improve the peptide selectivity for cancer cells. This simulated molecular evolution process led to a five-fold selectivity increase with regard to human dermal microvascular endothelial cells and more than ten-fold improvement towards human erythrocytes. The results of the present study advocate for the applicability of machine learning models and evolutionary algorithms to design and optimize novel synthetic anticancer peptides with reduced hemolytic liability and increased cell-type selectivity.
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Affiliation(s)
- Gisela Gabernet
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Damian Gautschi
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Alex T Müller
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Claudia S Neuhaus
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Lucas Armbrecht
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Petra S Dittrich
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Jan A Hiss
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland.
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8
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The effect of lysine substitutions in the biological activities of the scorpion venom peptide VmCT1. Eur J Pharm Sci 2019; 136:104952. [DOI: 10.1016/j.ejps.2019.06.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 05/27/2019] [Accepted: 06/03/2019] [Indexed: 12/14/2022]
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9
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Juretić D, Simunić J. Design of α-helical antimicrobial peptides with a high selectivity index. Expert Opin Drug Discov 2019; 14:1053-1063. [DOI: 10.1080/17460441.2019.1642322] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Davor Juretić
- Mediterranean Institute for Life Sciences, Split, Croatia
- Department of Physics, Faculty of Science, University of Split, Split, Croatia
| | - Juraj Simunić
- Division of molecular biology, Ruđer Bošković Institute, Zagreb, Croatia
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10
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Avci FG, Akbulut BS, Ozkirimli E. Membrane Active Peptides and Their Biophysical Characterization. Biomolecules 2018; 8:biom8030077. [PMID: 30135402 PMCID: PMC6164437 DOI: 10.3390/biom8030077] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 08/08/2018] [Accepted: 08/13/2018] [Indexed: 12/12/2022] Open
Abstract
In the last 20 years, an increasing number of studies have been reported on membrane active peptides. These peptides exert their biological activity by interacting with the cell membrane, either to disrupt it and lead to cell lysis or to translocate through it to deliver cargos into the cell and reach their target. Membrane active peptides are attractive alternatives to currently used pharmaceuticals and the number of antimicrobial peptides (AMPs) and peptides designed for drug and gene delivery in the drug pipeline is increasing. Here, we focus on two most prominent classes of membrane active peptides; AMPs and cell-penetrating peptides (CPPs). Antimicrobial peptides are a group of membrane active peptides that disrupt the membrane integrity or inhibit the cellular functions of bacteria, virus, and fungi. Cell penetrating peptides are another group of membrane active peptides that mainly function as cargo-carriers even though they may also show antimicrobial activity. Biophysical techniques shed light on peptide–membrane interactions at higher resolution due to the advances in optics, image processing, and computational resources. Structural investigation of membrane active peptides in the presence of the membrane provides important clues on the effect of the membrane environment on peptide conformations. Live imaging techniques allow examination of peptide action at a single cell or single molecule level. In addition to these experimental biophysical techniques, molecular dynamics simulations provide clues on the peptide–lipid interactions and dynamics of the cell entry process at atomic detail. In this review, we summarize the recent advances in experimental and computational investigation of membrane active peptides with particular emphasis on two amphipathic membrane active peptides, the AMP melittin and the CPP pVEC.
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Affiliation(s)
- Fatma Gizem Avci
- Bioengineering Department, Marmara University, Kadikoy, 34722 Istanbul, Turkey.
| | | | - Elif Ozkirimli
- Chemical Engineering Department, Bogazici University, Bebek, 34342 Istanbul, Turkey.
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Sharma A, Vaghasiya K, Ray E, Verma RK. Nano-encapsulated HHC10 host defense peptide (HDP) reduces the growth of Escherichia coli via multimodal mechanisms. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2018; 46:S156-S165. [PMID: 30032649 DOI: 10.1080/21691401.2018.1489823] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The eradication of several pathogenic drug resistant "Superbug" such as Escherichia coli became difficult especially in chronic infections using existing antibiotics due to the emergence of antibiotic resistance. Owing to their unique antibacterial properties, host defense peptides (HDP) have gained significant attention to combat colonization of bacteria. This study aims designing delivery systems for HHC10 peptide to target bacteria inside the cells might be a promising approach by protecting from degradation, controlling the release, enhancing the susceptibility of target microbes and improving bioavailability. Nano-formulated HHC10 was evaluated for its efficacy (CFU assay) and possible mechanism of action (membrane interaction and apoptosis) against E. coli. Dose-dependent inhibition of E. coli growth is observed for nano-encapsulated and bare HHC10 and encapsulated form remain non-toxic to macrophage mouse cells (RAW264.6) up to 20 μM. Mechanistic analyses using transmission electron microscopy and flow cytometry techniques revealed that bactericidal activity of HHC10-NP progresses via a multimodal mechanism of bacterial cell death by cell-membrane lysis on direct interaction with bacteria while through induction of the apoptotic death pathway inside the host cells. These results offer an insight on future strategies for the development and application of antimicrobial peptides as antibacterial alternatives. Controlled delivery of HHC10 peptide from PLGA-NP kills bacteria by two different mechanism: (i) direct killing: HHC10 disintegrate the cell membrane of bacteria by electrostatic interactions and (ii) indirect killing: induction of apoptosis in bacteria infect cells.
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Affiliation(s)
- Ankur Sharma
- a Institute of Nano Science and Technology (INST) , Mohali , Punjab , India
| | - Kalpesh Vaghasiya
- a Institute of Nano Science and Technology (INST) , Mohali , Punjab , India
| | - Eupa Ray
- a Institute of Nano Science and Technology (INST) , Mohali , Punjab , India
| | - Rahul Kumar Verma
- a Institute of Nano Science and Technology (INST) , Mohali , Punjab , India
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12
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Müller AT, Hiss JA, Schneider G. Recurrent Neural Network Model for Constructive Peptide Design. J Chem Inf Model 2018; 58:472-479. [PMID: 29355319 DOI: 10.1021/acs.jcim.7b00414] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We present a generative long short-term memory (LSTM) recurrent neural network (RNN) for combinatorial de novo peptide design. RNN models capture patterns in sequential data and generate new data instances from the learned context. Amino acid sequences represent a suitable input for these machine-learning models. Generative models trained on peptide sequences could therefore facilitate the design of bespoke peptide libraries. We trained RNNs with LSTM units on pattern recognition of helical antimicrobial peptides and used the resulting model for de novo sequence generation. Of these sequences, 82% were predicted to be active antimicrobial peptides compared to 65% of randomly sampled sequences with the same amino acid distribution as the training set. The generated sequences also lie closer to the training data than manually designed amphipathic helices. The results of this study showcase the ability of LSTM RNNs to construct new amino acid sequences within the applicability domain of the model and motivate their prospective application to peptide and protein design without the need for the exhaustive enumeration of sequence libraries.
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Affiliation(s)
- Alex T Müller
- Swiss Federal Institute of Technology (ETH) , Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
| | - Jan A Hiss
- Swiss Federal Institute of Technology (ETH) , Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
| | - Gisbert Schneider
- Swiss Federal Institute of Technology (ETH) , Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
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