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Bolosov IA, Panteleev PV, Sychev SV, Khokhlova VA, Safronova VN, Toropygin IY, Kombarova TI, Korobova OV, Pereskokova ES, Borzilov AI, Ovchinnikova TV, Balandin SV. Design of Protegrin-1 Analogs with Improved Antibacterial Selectivity. Pharmaceutics 2023; 15:2047. [PMID: 37631261 PMCID: PMC10458893 DOI: 10.3390/pharmaceutics15082047] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 07/27/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023] Open
Abstract
Protegrin-1 (PG-1) is a cationic β-hairpin pore-forming antimicrobial peptide having a membranolytic mechanism of action. It possesses in vitro a potent antimicrobial activity against a panel of clinically relevant MDR ESKAPE pathogens. However, its extremely high hemolytic activity and cytotoxicity toward mammalian cells prevent the further development of the protegrin-based antibiotic for systemic administration. In this study, we rationally modulated the PG-1 charge and hydrophobicity by substituting selected residues in the central β-sheet region of PG-1 to design its analogs, which retain a high antimicrobial activity but have a reduced toxicity toward mammalian cells. In this work, eight PG-1 analogs with single amino acid substitutions and five analogs with double substitutions were obtained. These analogs were produced as thioredoxin fusions in Escherichia coli. It was shown that a significant reduction in hemolytic activity without any loss of antimicrobial activity could be achieved by a single amino acid substitution, V16R in the C-terminal β-strand, which is responsible for the PG-1 oligomerization. As the result, a selective analog with a ≥30-fold improved therapeutic index was obtained. FTIR spectroscopy analysis of analog, [V16R], revealed that the peptide is unable to form oligomeric structures in a membrane-mimicking environment, in contrast to wild-type PG-1. Analog [V16R] showed a reasonable efficacy in septicemia infection mice model as a systemic antibiotic and could be considered as a promising lead for further drug design.
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Affiliation(s)
- Ilia A. Bolosov
- M. M. Shemyakin & Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, 117997 Moscow, Russia; (I.A.B.); (P.V.P.); (T.V.O.)
| | - Pavel V. Panteleev
- M. M. Shemyakin & Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, 117997 Moscow, Russia; (I.A.B.); (P.V.P.); (T.V.O.)
| | - Sergei V. Sychev
- M. M. Shemyakin & Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, 117997 Moscow, Russia; (I.A.B.); (P.V.P.); (T.V.O.)
| | - Veronika A. Khokhlova
- M. M. Shemyakin & Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, 117997 Moscow, Russia; (I.A.B.); (P.V.P.); (T.V.O.)
| | - Victoria N. Safronova
- M. M. Shemyakin & Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, 117997 Moscow, Russia; (I.A.B.); (P.V.P.); (T.V.O.)
| | - Ilia Yu. Toropygin
- V. N. Orekhovich Research Institute of Biomedical Chemistry, 119121 Moscow, Russia
| | - Tatiana I. Kombarova
- State Research Center for Applied Microbiology & Biotechnology (SRCAMB), 142279 Obolensk, Russia
| | - Olga V. Korobova
- State Research Center for Applied Microbiology & Biotechnology (SRCAMB), 142279 Obolensk, Russia
| | - Eugenia S. Pereskokova
- State Research Center for Applied Microbiology & Biotechnology (SRCAMB), 142279 Obolensk, Russia
| | - Alexander I. Borzilov
- State Research Center for Applied Microbiology & Biotechnology (SRCAMB), 142279 Obolensk, Russia
| | - Tatiana V. Ovchinnikova
- M. M. Shemyakin & Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, 117997 Moscow, Russia; (I.A.B.); (P.V.P.); (T.V.O.)
- Department of Biotechnology, I. M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Sergey V. Balandin
- M. M. Shemyakin & Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, 117997 Moscow, Russia; (I.A.B.); (P.V.P.); (T.V.O.)
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2
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Zharkova MS, Komlev AS, Filatenkova TA, Sukhareva MS, Vladimirova EV, Trulioff AS, Orlov DS, Dmitriev AV, Afinogenova AG, Spiridonova AA, Shamova OV. Combined Use of Antimicrobial Peptides with Antiseptics against Multidrug-Resistant Bacteria: Pros and Cons. Pharmaceutics 2023; 15:291. [PMID: 36678918 PMCID: PMC9863607 DOI: 10.3390/pharmaceutics15010291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/09/2023] [Accepted: 01/12/2023] [Indexed: 01/18/2023] Open
Abstract
Antimicrobial peptides (AMPs) are acknowledged as a promising template for designing new antimicrobials. At the same time, existing toxicity issues and limitations in their pharmacokinetics make topical application one of the less complicated routes to put AMPs-based therapeutics into actual medical practice. Antiseptics are one of the common components for topical treatment potent against antibiotic-resistant pathogens but often with toxicity limitations of their own. Thus, the interaction of AMPs and antiseptics is an interesting topic that is also less explored than combined action of AMPs and antibiotics. Herein, we analyzed antibacterial, antibiofilm, and cytotoxic activity of combinations of both membranolytic and non-membranolytic AMPs with a number of antiseptic agents. Fractional concentration indices were used as a measure of possible effective concentration reduction achievable due to combined application. Cases of both synergistic and antagonistic interaction with certain antiseptics and surfactants were identified, and trends in the occurrence of these types of interaction were discussed. The data may be of use for AMP-based drug development and suggest that the topic requires further attention for successfully integrating AMPs-based products in the context of complex treatment. AMP/antiseptic combinations show promise for creating topical formulations with improved activity, lowered toxicity, and, presumably, decreased chances of inducing bacterial resistance. However, careful assessment is required to avoid AMP neutralization by certain antiseptic classes in either complex drug design or AMP application alongside other therapeutics/care products.
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Affiliation(s)
- Maria S. Zharkova
- Institute of Experimental Medicine, WCRC “Center for Personalized Medicine”, 12 Academic Pavlov Street, St. Petersburg 197022, Russia
| | - Aleksey S. Komlev
- Institute of Experimental Medicine, WCRC “Center for Personalized Medicine”, 12 Academic Pavlov Street, St. Petersburg 197022, Russia
| | - Tatiana A. Filatenkova
- Institute of Experimental Medicine, WCRC “Center for Personalized Medicine”, 12 Academic Pavlov Street, St. Petersburg 197022, Russia
| | - Maria S. Sukhareva
- Institute of Experimental Medicine, WCRC “Center for Personalized Medicine”, 12 Academic Pavlov Street, St. Petersburg 197022, Russia
| | - Elizaveta V. Vladimirova
- Institute of Experimental Medicine, WCRC “Center for Personalized Medicine”, 12 Academic Pavlov Street, St. Petersburg 197022, Russia
| | - Andrey S. Trulioff
- Institute of Experimental Medicine, WCRC “Center for Personalized Medicine”, 12 Academic Pavlov Street, St. Petersburg 197022, Russia
| | - Dmitriy S. Orlov
- Institute of Experimental Medicine, WCRC “Center for Personalized Medicine”, 12 Academic Pavlov Street, St. Petersburg 197022, Russia
| | - Alexander V. Dmitriev
- Institute of Experimental Medicine, WCRC “Center for Personalized Medicine”, 12 Academic Pavlov Street, St. Petersburg 197022, Russia
| | - Anna G. Afinogenova
- St. Petersburg Pasteur Institute, 14 Mira Street, St. Petersburg 197101, Russia
| | - Anna A. Spiridonova
- Department of Clinical Microbiology, Pavlov First Saint Petersburg State Medical University, 6/8 Lev Tolstoy Street, St. Petersburg 197022, Russia
| | - Olga V. Shamova
- Institute of Experimental Medicine, WCRC “Center for Personalized Medicine”, 12 Academic Pavlov Street, St. Petersburg 197022, Russia
- Department of Biochemistry, Saint Petersburg State University, 7/9 Universitetskaya Embankment, St. Petersburg 199034, Russia
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3
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Remington JM, Ferrell JB, Schneebeli ST, Li J. Concerted Rolling and Penetration of Peptides during Membrane Binding. J Chem Theory Comput 2022; 18:3921-3929. [PMID: 35507824 DOI: 10.1021/acs.jctc.2c00014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptide binding to membranes is common and fundamental in biochemistry and biophysics and critical for applications ranging from drug delivery to the treatment of bacterial infections. However, it is largely unclear, from a theoretical point of view, what peptides of different sequences and structures share in the membrane-binding and insertion process. In this work, we analyze three prototypical membrane-binding peptides (α-helical magainin, PGLa, and β-hairpin tachyplesin) during membrane binding, using molecular details provided by Markov state modeling and microsecond-long molecular dynamics simulations. By leveraging both geometric and data-driven collective variables that capture the essential physics of the amphiphilic and cationic peptide-membrane interactions, we reveal how the slowest kinetic process of membrane binding is the dynamic rolling of the peptide from an attached to a fully bound state. These results not only add fundamental knowledge of the theory of how peptides bind to biological membranes but also open new avenues to study general peptides in more complex environments for further applications.
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Affiliation(s)
- Jacob M Remington
- Department of Chemistry, The University of Vermont, Burlington, Vermont 05405, United States
| | - Jonathon B Ferrell
- Department of Chemistry, The University of Vermont, Burlington, Vermont 05405, United States
| | - Severin T Schneebeli
- Department of Chemistry, The University of Vermont, Burlington, Vermont 05405, United States
| | - Jianing Li
- Department of Chemistry, The University of Vermont, Burlington, Vermont 05405, United States
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4
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Isolation and Characterization of Antimicrobial Peptides Isolated from Fagonia bruguieri. Appl Biochem Biotechnol 2022; 194:4319-4332. [PMID: 35041129 DOI: 10.1007/s12010-022-03818-7] [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] [Accepted: 12/31/2021] [Indexed: 01/08/2023]
Abstract
The majority of pathogenic microorganisms have developed resistance to commercial antibiotics. It causes the risk of illness relapse with current antimicrobial therapy regimens; additional and/or different antibacterial drugs are needed to treat diseases caused by these pathogenic microorganisms. The applied analysis in the present study was purification and characterization of plant peptides isolated from the leaves of Fagonia bruguieri as well as their antibacterial activities against Gram-positive bacteria, Staphylococcus aureus, Bacillus subtilis, Micrococcus luteus, and methicillin-resistant Staphylococcus aureus, in addition to Gram-negative bacteria, Escherichia coli and Pseudomonas aeruginosa. The minimum inhibitory concentration for the isolated peptide ranges from 25 to 62.5 mg/mL. The methanolic solvent was used for the extraction followed by reversed-phase high-performance liquid chromatography for purification of peptides. Eventually, the peptide characterization and identification were also determined by MALDI-TOF/TOF and SEM analysis. This study paves a way to the effective antimicrobials from the plant resources.
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5
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Chen EHL, Weng CW, Li YM, Wu MC, Yang CC, Lee KT, Chen RPY, Cheng CP. De Novo Design of Antimicrobial Peptides With a Special Charge Pattern and Their Application in Combating Plant Pathogens. FRONTIERS IN PLANT SCIENCE 2021; 12:753217. [PMID: 34659322 PMCID: PMC8514817 DOI: 10.3389/fpls.2021.753217] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 09/06/2021] [Indexed: 06/13/2023]
Abstract
Plant diseases are important issues in agriculture, and the development of effective and environment-friendly means of disease control is crucial and highly desired. Antimicrobial peptides (AMPs) are known as potential alternatives to chemical pesticides because of their potent broad-spectrum antimicrobial activity and because they have no risk, or have only a low risk, of developing chemical-resistant pathogens. In this study, we designed a series of amphipathic helical peptides with different spatial distributions of positive charges and found that the peptides that had a special sequence pattern "BBHBBHHBBH" ("B" for basic residue and "H" for hydrophobic residue) displayed excellent bactericidal and fungicidal activities in a wide range of economically important plant pathogens. The peptides with higher helical propensity had lower antimicrobial activity. When we modified the peptides with a long acyl chain at their N-terminus, their plant protection effect improved. Our application of the fatty acyl-modified peptides on the leaves of tomato and Arabidopsis plants lessened the infection caused by Pectobacterium carotovorum subsp. carotovorum and Botrytis cinerea. Our study provides important insights on the development of more potent novel AMPs for plant protection.
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Affiliation(s)
- Eric H. -L. Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Cheng-Wei Weng
- Institute of Plant Biology, National Taiwan University, Taipei, Taiwan
| | - Yi-Min Li
- Institute of Plant Biology, National Taiwan University, Taipei, Taiwan
| | - Ming-Chin Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Chien-Chih Yang
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Kung-Ta Lee
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Rita P. -Y. Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Chiu-Ping Cheng
- Institute of Plant Biology, National Taiwan University, Taipei, Taiwan
- Department of Life Science, National Taiwan University, Taipei, Taiwan
- Global Agriculture Technology and Genomic Science Master Program, National Taiwan University, Taipei, Taiwan
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6
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In silico design of antimicrobial oligopeptides based on 3D-QSAR modeling and bioassay evaluation. Med Chem Res 2021. [DOI: 10.1007/s00044-021-02789-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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7
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He S, Stone TA, Deber CM. Uncoupling Amphipathicity and Hydrophobicity: Role of Charge Clustering in Membrane Interactions of Cationic Antimicrobial Peptides. Biochemistry 2021; 60:2586-2592. [PMID: 34423969 DOI: 10.1021/acs.biochem.1c00367] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptides with a combination of high positive charge and high hydrophobicity have high antimicrobial activity, as epitomized by peptide venoms, which are designed by nature as disruptors of host membranes yet also display significant efficacy against pathogens. To investigate this phenomenon systematically, here we focus on ponericin W1, a peptide venom isolated from Pachycondyla goeldii ants (WLGSALKIGAKLLPSVVGLFKKKKQ) to examine whether Lys positioning can be broadly applied to optimize the functional range of existing natural sequences. We prepared sets of ponericin W1 analogues, where Lys residues were either distributed in an amphipathic manner throughout the sequence (PonAmp), clustered at the N-terminus (PonN), or clustered at the C-terminus (PonC), along with their counterparts of reduced hydrophobicity through 2-4 Leu-to-Ala replacements. We found that wild-type ponericin W1 and all three variants displayed toxicity against human erythrocytes, but hemolysis was eliminated by the replacement of two or more Leu residues by Ala residues. As well, peptides containing up to 3 Leu-to-Ala replacements retained antimicrobial activity against E. coli bacteria. Biophysical analyses of peptide-membrane interaction patterns by circular dichroism spectroscopy revealed a novel mode of cluster-dependent peptide positioning vis-à-vis the water-membrane interface, where PonAmp and PonC peptides displayed full or partial helical structures, while PonN peptides were unstructured, likely due, in part, to dynamic interchange between aqueous and membrane surface environments. The overall findings suggest that the lower membrane penetration of N-terminal charge-clustered constructs coupled with moderate sequence hydrophobicity may be advantageous for conferring enhanced target selectivity for bacterial versus mammalian membranes.
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Affiliation(s)
- Shelley He
- Program in Molecular Medicine, Research Institute, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Tracy A Stone
- Program in Molecular Medicine, Research Institute, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Charles M Deber
- Program in Molecular Medicine, Research Institute, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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8
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Farrag HN, Metwally K, Ikeno S, Kato T. Design and Synthesis of a New Amphipathic Cyclic Decapeptide with Rapid, Stable, and Continuous Antibacterial Effects. PERTANIKA JOURNAL OF SCIENCE AND TECHNOLOGY 2020. [DOI: 10.47836/pjst.28.s2.15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Pathogens can acquire high resistance against even the most powerful antibiotics because of the long periods of treatment and high usage of antimicrobial agents. In addition, the severe side effects of commonly used antibiotics can initiate secondary diseases or may lead to death. Antimicrobial peptides (AMPs) have been reported to exhibit prokaryotic selectivity and low microbial resistance. Furthermore, AMPs show a good ability to penetrate the cell walls of microorganisms. In this study, a cyclic decapeptide and its linear counterpart were synthesized by a standard solid phase peptide synthesis method (SPPS) in a quantitative yield of the linear decapeptide (97%) and a good yield of the cyclic form (45%). Antibacterial studies were performed using Escherichia coli (a widespread Gram-negative pathogen) and Bacillus thuringiensis as a representative Gram-positive pathogen. The minimal inhibitory concentration (MIC) values were evaluated by the broth microdilution method. The cyclic peptide and its linear counterpart exhibited MIC values of 0.16 and 0.3 mg/mL, respectively, against Escherichia coli. Against Bacillus thuringiensis, the peptides had the same MIC value of 0.24 mg/mL. Time-kill studies were performed using E. coli, which indicated a fast killing effect of both peptides (≥ 99% of the bacterial cells) after 1 h of incubation using a concentration of two times the MIC value for each peptide. Moreover, bacterial cell viability studies against E. coli carried out using a high bacterial concentration showed that both peptides have a maximum killing effect of more than 80% of the tested bacterial cells.
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9
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Yurkova MS, Zenin VA, Sadykhov EG, Fedorov AN. Dimerization of Antimicrobial Peptide Polyphemusin I into One Polypeptide Chain: Theoretical and Practical Consequences. APPL BIOCHEM MICRO+ 2020. [DOI: 10.1134/s0003683820090100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Purification and characterization of antimicrobial peptide fractions of Junipers seravschanica. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2020. [DOI: 10.1016/j.bcab.2020.101554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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11
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Rodnin MV, Vasquez-Montes V, Nepal B, Ladokhin AS, Lazaridis T. Experimental and Computational Characterization of Oxidized and Reduced Protegrin Pores in Lipid Bilayers. J Membr Biol 2020; 253:287-298. [PMID: 32500172 DOI: 10.1007/s00232-020-00124-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 05/23/2020] [Indexed: 12/16/2022]
Abstract
Protegrin-1 (PG-1), an 18-residue β-hairpin stabilized by two disulfide bonds, is a member of a family of powerful antimicrobial peptides which are believed to act through membrane permeabilization. Here we used a combination of experimental and computational approaches to characterize possible structural arrangements of PG-1 in lipid bilayers mimicking bacterial membranes. We have measured the dose-response function of the PG-1-induced leakage of markers of various sizes from vesicles and found it to be consistent with the formation of pores of two different sizes. The first one allows the release of small dyes and occurs at peptide:lipid ratios < 0.006. Above this ratio, larger pores are observed through which the smallest of dextrans FD4 can be released. In parallel with pore formation, we observe a general large-scale destabilization of vesicles which is probably related to complete rupture of some vesicles. The population of vesicles that are completely ruptured depends linearly on PG-1:lipid ratio. Neither pore size, nor vesicle rupture are influenced by the formation of disulfide bonds. Previous computational work on oxidized protegrin is complemented here by all-atom MD simulations of PG-1 with reduced disulfide bonds both in solution (monomer) and in a bilayer (dimer and octamer). The simulations provide molecular insights into the influence of disulfide bonds on peptide conformation, aggregation, and oligomeric structure.
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Affiliation(s)
- Mykola V Rodnin
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Victor Vasquez-Montes
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Binod Nepal
- Department of Chemistry and Biochemistry, City College of New York, New York, NY, 10031, USA
| | - Alexey S Ladokhin
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS, 66160, USA.
| | - Themis Lazaridis
- Department of Chemistry and Biochemistry, City College of New York, New York, NY, 10031, USA. .,Graduate Programs in Chemistry, Biochemistry, and Physics, The Graduate Center, City University of New York, New York, NY, 10016, USA.
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12
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Cavaco M, Gaspar D, ARB Castanho M, Neves V. Antibodies for the Treatment of Brain Metastases, a Dream or a Reality? Pharmaceutics 2020; 12:E62. [PMID: 31940974 PMCID: PMC7023012 DOI: 10.3390/pharmaceutics12010062] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/13/2019] [Accepted: 12/28/2019] [Indexed: 12/25/2022] Open
Abstract
The incidence of brain metastases (BM) in cancer patients is increasing. After diagnosis, overall survival (OS) is poor, elicited by the lack of an effective treatment. Monoclonal antibody (mAb)-based therapy has achieved remarkable success in treating both hematologic and non-central-nervous system (CNS) tumors due to their inherent targeting specificity. However, the use of mAbs in the treatment of CNS tumors is restricted by the blood-brain barrier (BBB) that hinders the delivery of either small-molecules drugs (sMDs) or therapeutic proteins (TPs). To overcome this limitation, active research is focused on the development of strategies to deliver TPs and increase their concentration in the brain. Yet, their molecular weight and hydrophilic nature turn this task into a challenge. The use of BBB peptide shuttles is an elegant strategy. They explore either receptor-mediated transcytosis (RMT) or adsorptive-mediated transcytosis (AMT) to cross the BBB. The latter is preferable since it avoids enzymatic degradation, receptor saturation, and competition with natural receptor substrates, which reduces adverse events. Therefore, the combination of mAbs properties (e.g., selectivity and long half-life) with BBB peptide shuttles (e.g., BBB translocation and delivery into the brain) turns the therapeutic conjugate in a valid approach to safely overcome the BBB and efficiently eliminate metastatic brain cells.
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Affiliation(s)
| | | | - Miguel ARB Castanho
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal; (M.C.); (D.G.)
| | - Vera Neves
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal; (M.C.); (D.G.)
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13
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Deplazes E, Chin YKY, King GF, Mancera RL. The unusual conformation of cross-strand disulfide bonds is critical to the stability of β-hairpin peptides. Proteins 2019; 88:485-502. [PMID: 31589791 DOI: 10.1002/prot.25828] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 08/27/2019] [Accepted: 09/17/2019] [Indexed: 01/04/2023]
Abstract
The cross-strand disulfides (CSDs) found in β-hairpin antimicrobial peptides (β-AMPs) show a unique disulfide geometry that is characterized by unusual torsion angles and a short Cα-Cα distance. While the sequence and disulfide bond connectivity of disulfide-rich peptides is well studied, much less is known about the disulfide geometry found in CSDs and their role in the stability of β-AMPs. To address this, we solved the nuclear magnetic resonance (NMR) structure of the β-AMP gomesin (Gm) at 278, 298, and 310 K, examined the disulfide bond geometry of over 800 disulfide-rich peptides, and carried out extensive molecular dynamics (MD) simulation of the peptides Gm and protegrin. The NMR data suggests Cα-Cα distances characteristic for CSDs are independent of temperature. Analysis of disulfide-rich peptides from the Protein Data Bank revealed that right-handed and left-handed rotamers are equally likely in CSDs. The previously reported preference for right-handed rotamers was likely biased by restricting the analysis to peptides and proteins solved using X-ray crystallography. Furthermore, data from MD simulations showed that the short Cα-Cα distance is critical for the stability of these peptides. The unique disulfide geometry of CSDs poses a challenge to biomolecular force fields and to retain the stability of β-hairpin fold over long simulation times, restraints on the torsion angles might be required.
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Affiliation(s)
- Evelyne Deplazes
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and Curtin Institute for Computation, Curtin University, Perth, Western Australia, Australia
| | - Yanni K-Y Chin
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
| | - Glenn F King
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
| | - Ricardo L Mancera
- School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute and Curtin Institute for Computation, Curtin University, Perth, Western Australia, Australia
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14
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Zharkova MS, Orlov DS, Golubeva OY, Chakchir OB, Eliseev IE, Grinchuk TM, Shamova OV. Application of Antimicrobial Peptides of the Innate Immune System in Combination With Conventional Antibiotics-A Novel Way to Combat Antibiotic Resistance? Front Cell Infect Microbiol 2019; 9:128. [PMID: 31114762 PMCID: PMC6503114 DOI: 10.3389/fcimb.2019.00128] [Citation(s) in RCA: 156] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Accepted: 04/10/2019] [Indexed: 01/10/2023] Open
Abstract
Rapidly growing resistance of pathogenic bacteria to conventional antibiotics leads to inefficiency of traditional approaches of countering infections and determines the urgent need for a search of fundamentally new anti-infective drugs. Antimicrobial peptides (AMPs) of the innate immune system are promising candidates for a role of such novel antibiotics. However, some cytotoxicity of AMPs toward host cells limits their active implementation in medicine and forces attempts to design numerous structural analogs of the peptides with optimized properties. An alternative route for the successful AMPs introduction may be their usage in combination with conventional antibiotics. Synergistic antibacterial effects have been reported for a number of such combinations, however, the molecular mechanisms of the synergy remain poorly understood and little is known whether AMPs cytotoxicy for the host cells increases upon their application with antibiotics. Our study is directed to examination of a combined action of natural AMPs with different structure and mode of action (porcine protegrin 1, caprine bactenecin ChBac3.4, human alpha- and beta-defensins (HNP-1, HNP-4, hBD-2, hBD-3), human cathelicidin LL-37), and egg white lysozyme with varied antibiotic agents (gentamicin, ofloxacin, oxacillin, rifampicin, polymyxin B, silver nanoparticles) toward selected bacteria, including drug-sensitive and drug-resistant strains, as well as toward some mammalian cells (human erythrocytes, PBMC, neutrophils, murine peritoneal macrophages and Ehrlich ascites carcinoma cells). Using “checkerboard titrations” for fractional inhibitory concentration indexes evaluation, it was found that synergy in antibacterial action mainly occurs between highly membrane-active AMPs (e.g., protegrin 1, hBD-3) and antibiotics with intracellular targets (e.g., gentamicin, rifampcin), suggesting bioavailability increase as the main model of such interaction. In some combinations modulation of dynamics of AMP-bacterial membrane interaction in presence of the antibiotic was also shown. Cytotoxic effects of the same combinations toward normal eukaryotic cells were rarely synergistic. The obtained data approve that combined application of antimicrobial peptides with antibiotics or other antimicrobials is a promising strategy for further development of new approach for combating antibiotic-resistant bacteria by usage of AMP-based therapeutics. Revealing the conventional antibiotics that increase the activity of human endogenous AMPs against particular pathogens is also important for cure strategies elaboration.
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Affiliation(s)
- Maria S Zharkova
- Laboratory of Design and Synthesis of Biologically Active Peptides, Department of General Pathology and Pathophysiology, FSBSI Institute of Experimental Medicine, Saint Petersburg, Russia
| | - Dmitriy S Orlov
- Laboratory of Design and Synthesis of Biologically Active Peptides, Department of General Pathology and Pathophysiology, FSBSI Institute of Experimental Medicine, Saint Petersburg, Russia
| | - Olga Yu Golubeva
- Laboratory of Nanostructures Research, Institute of Silicate Chemistry of the Russian Academy of Sciences, Saint Petersburg, Russia
| | - Oleg B Chakchir
- Nanobiotechnology Laboratory, Saint Petersburg National Research Academic University of the Russian Academy of Science, Saint Petersburg, Russia
| | - Igor E Eliseev
- Nanobiotechnology Laboratory, Saint Petersburg National Research Academic University of the Russian Academy of Science, Saint Petersburg, Russia
| | - Tatyana M Grinchuk
- Laboratory of Intracellular Signaling, Institute of Cytology of the Russian Academy of Science, Saint Petersburg, Russia
| | - Olga V Shamova
- Laboratory of Design and Synthesis of Biologically Active Peptides, Department of General Pathology and Pathophysiology, FSBSI Institute of Experimental Medicine, Saint Petersburg, Russia
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15
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Ermakova E, Kurbanov R, Zuev Y. Coarse-grained molecular dynamics of membrane semitoroidal pore formation in model lipid-peptide systems. J Mol Graph Model 2019; 87:1-10. [DOI: 10.1016/j.jmgm.2018.11.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 11/06/2018] [Accepted: 11/06/2018] [Indexed: 12/31/2022]
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16
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17
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Boonpa K, Tantong S, Weerawanich K, Panpetch P, Pringsulaka O, Roytrakul S, Sirikantaramas S. In Silico Analyses of Rice Thionin Genes and the Antimicrobial Activity of OsTHION15 Against Phytopathogens. PHYTOPATHOLOGY 2019; 109:27-35. [PMID: 30028233 DOI: 10.1094/phyto-06-17-0217-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Thionins are a family of antimicrobial peptides. We performed in silico expression analyses of the 44 rice (Oryza sativa) thionins (OsTHIONs). Modulated expression levels of OsTHIONs under different treatments suggest their involvement in many processes, including biotic, abiotic, and nutritional stress responses, and in hormone signaling. OsTHION15 (LOC_Os06g32600) was selected for further characterization based on several in silico analyses. OsTHION15 in O. sativa subsp. indica 'KDML 105' was expressed in all of the tissues and organs examined, including germinating seed, leaves, and roots of seedlings and mature plants, and inflorescences. To investigate the antimicrobial activity of OsTHION15, we produced a recombinant peptide in Escherichia coli Rosetta-gami (DE3). The recombinant OsTHION15 exhibited inhibitory activities toward rice-pathogenic bacteria such as Xanthomonas oryzae pv. oryzae and Pectobacterium carotovorum pv. atroseptica, with minimum inhibitory concentrations of 112.6 and 14.1 µg ml-1, respectively. A significant hyphal growth inhibition was also observed toward Fusarium oxysporum f. sp. cubense and Helminthosporium oryzae. In addition, we demonstrated the in planta antibacterial activity of this peptide in Nicotiana benthamiana against X. campestris pv. glycines. These activities suggest the possible application of OsTHION15 in plant disease control.
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Affiliation(s)
- Krissana Boonpa
- First author: Biotechnology Program, and second, third, fourth, and seventh authors: Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; fifth author: Department of Microbiology, Faculty of Science, Srinakharinwirot University, Bangkok 10110, Thailand; sixth author: Genome Technology Research Unit, National Center for Genetic Engineering and Biotechnology, Klong Luang, Pathumthani, 12120, Thailand; and seventh author: Natural Product Biotechnology Research Unit, Chulalongkorn University
| | - Suparuk Tantong
- First author: Biotechnology Program, and second, third, fourth, and seventh authors: Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; fifth author: Department of Microbiology, Faculty of Science, Srinakharinwirot University, Bangkok 10110, Thailand; sixth author: Genome Technology Research Unit, National Center for Genetic Engineering and Biotechnology, Klong Luang, Pathumthani, 12120, Thailand; and seventh author: Natural Product Biotechnology Research Unit, Chulalongkorn University
| | - Kamonwan Weerawanich
- First author: Biotechnology Program, and second, third, fourth, and seventh authors: Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; fifth author: Department of Microbiology, Faculty of Science, Srinakharinwirot University, Bangkok 10110, Thailand; sixth author: Genome Technology Research Unit, National Center for Genetic Engineering and Biotechnology, Klong Luang, Pathumthani, 12120, Thailand; and seventh author: Natural Product Biotechnology Research Unit, Chulalongkorn University
| | - Pawinee Panpetch
- First author: Biotechnology Program, and second, third, fourth, and seventh authors: Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; fifth author: Department of Microbiology, Faculty of Science, Srinakharinwirot University, Bangkok 10110, Thailand; sixth author: Genome Technology Research Unit, National Center for Genetic Engineering and Biotechnology, Klong Luang, Pathumthani, 12120, Thailand; and seventh author: Natural Product Biotechnology Research Unit, Chulalongkorn University
| | - Onanong Pringsulaka
- First author: Biotechnology Program, and second, third, fourth, and seventh authors: Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; fifth author: Department of Microbiology, Faculty of Science, Srinakharinwirot University, Bangkok 10110, Thailand; sixth author: Genome Technology Research Unit, National Center for Genetic Engineering and Biotechnology, Klong Luang, Pathumthani, 12120, Thailand; and seventh author: Natural Product Biotechnology Research Unit, Chulalongkorn University
| | - Sittiruk Roytrakul
- First author: Biotechnology Program, and second, third, fourth, and seventh authors: Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; fifth author: Department of Microbiology, Faculty of Science, Srinakharinwirot University, Bangkok 10110, Thailand; sixth author: Genome Technology Research Unit, National Center for Genetic Engineering and Biotechnology, Klong Luang, Pathumthani, 12120, Thailand; and seventh author: Natural Product Biotechnology Research Unit, Chulalongkorn University
| | - Supaart Sirikantaramas
- First author: Biotechnology Program, and second, third, fourth, and seventh authors: Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; fifth author: Department of Microbiology, Faculty of Science, Srinakharinwirot University, Bangkok 10110, Thailand; sixth author: Genome Technology Research Unit, National Center for Genetic Engineering and Biotechnology, Klong Luang, Pathumthani, 12120, Thailand; and seventh author: Natural Product Biotechnology Research Unit, Chulalongkorn University
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18
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Shruti SR, Rajasekaran R. Identification of protegrin-1 as a stable and nontoxic scaffold among protegrin family - a computational approach. J Biomol Struct Dyn 2018; 37:2430-2439. [PMID: 30047844 DOI: 10.1080/07391102.2018.1491418] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Achieving both, nontoxicity and stability in antimicrobial peptides (AMP) is a challenge. This study predicts a structurally stable, nontoxic scaffold among the protegrin family, for future therapeutic peptide analogs. Protegrins (PG) are a class of pharmaceutically approved, in demand AMPs, which require further improvement in terms of nontoxicity and stability. Out of five protegrins viz., PG1, PG2, PG3, PG4 and PG5, PG1 has been predicted as best scaffold. Prediction was based upon sequential elimination of other protegrins, using computational methods to assess the extracellular bacterial membrane penetrability, nontoxicity and structural stability by geometric observables. Initially, PG2 and PG4 showing the lowest membrane penetrability and highest toxicity respectively, were screened out. Among the remaining three protegrins, PG1 displayed both lowest root mean square deviation and radius of gyration, with a considerable occupancy of seven H-bonds and established uniform secondary structure profile throughout its ensembles. Therefore, the authors claim the superiority of PG1 as a nontoxic stable scaffold among its family. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- S R Shruti
- a Department of Biotechnology, Bioinformatics lab, School of Biosciences and Technology , VIT (Deemed to be University) , Vellore , Tamil Nadu , India
| | - R Rajasekaran
- a Department of Biotechnology, Bioinformatics lab, School of Biosciences and Technology , VIT (Deemed to be University) , Vellore , Tamil Nadu , India
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19
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Reißer S, Strandberg E, Steinbrecher T, Elstner M, Ulrich AS. Best of Two Worlds? How MD Simulations of Amphiphilic Helical Peptides in Membranes Can Complement Data from Oriented Solid-State NMR. J Chem Theory Comput 2018; 14:6002-6014. [PMID: 30289704 DOI: 10.1021/acs.jctc.8b00283] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The membrane alignment of helical amphiphilic peptides in oriented phospholipid bilayers can be obtained as ensemble and time averages from solid state 2H NMR by fitting the quadrupolar splittings to ideal α-helices. At the same time, molecular dynamics (MD) simulations can provide atomistic insight into peptide-membrane systems. Here, we evaluate the potential of MD simulations to complement the experimental NMR data that is available on three exemplary systems: the natural antimicrobial peptide PGLa and the two designer-made peptides MSI-103 and KIA14, whose sequences were derived from PGLa. Each peptide was simulated for 1 μs in a DMPC lipid bilayer. We calculated from the MD simulations the local angles which define the side chain geometry with respect to the peptide helix. The peptide orientation was then calculated (i) directly from the simulation, (ii) from back-calculated MD-derived NMR splittings, and (iii) from experimental 2H NMR splittings. Our findings are that (1) the membrane orientation and secondary structure of the peptides found in the NMR analysis are generally well reproduced by the simulations; (2) the geometry of the side chains with respect to the helix backbone can deviate significantly from the ideal structure depending on the specific residue, but on average all side chains have the same orientation; and (3) for all of our peptides, the azimuthal rotation angle found from the MD-derived splittings is about 15° smaller than the experimental value.
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Affiliation(s)
- Sabine Reißer
- Institute of Organic Chemistry , Karlsruhe Institute of Technology (KIT) , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany
| | - Erik Strandberg
- Institute of Biological Interfaces (IBG-2), KIT , P.O. Box 3640, 76012 Karlsruhe , Germany
| | - Thomas Steinbrecher
- Institute of Physical Chemistry, KIT , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany
| | - Marcus Elstner
- Institute of Physical Chemistry, KIT , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany
| | - Anne S Ulrich
- Institute of Organic Chemistry , Karlsruhe Institute of Technology (KIT) , Fritz-Haber-Weg 6 , 76131 Karlsruhe , Germany.,Institute of Biological Interfaces (IBG-2), KIT , P.O. Box 3640, 76012 Karlsruhe , Germany
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20
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Castro VI, Craveiro R, Silva JM, Reis RL, Paiva A, C. Duarte AR. Natural deep eutectic systems as alternative nontoxic cryoprotective agents. Cryobiology 2018; 83:15-26. [DOI: 10.1016/j.cryobiol.2018.06.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 06/21/2018] [Accepted: 06/23/2018] [Indexed: 10/28/2022]
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21
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Lai PK, Kaznessis YN. Insights into Membrane Translocation of Protegrin Antimicrobial Peptides by Multistep Molecular Dynamics Simulations. ACS OMEGA 2018; 3:6056-6065. [PMID: 29978143 PMCID: PMC6026836 DOI: 10.1021/acsomega.8b00483] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 05/08/2018] [Indexed: 06/08/2023]
Abstract
Protegrin-1 (PG-1) is a cationic arginine-rich antimicrobial peptide. It is widely accepted that PG-1 induces membrane disruption by forming pores that lead to cell death. However, the insertion mechanism for these highly cationic peptides into the hydrophobic membrane environment is still poorly understood at the molecular scale. It has previously been determined that the association of arginine guanidinium and lipid phosphate groups results in strong bidentate bonds that stabilize peptide-lipid complexes. It has also been suggested that arginine residues are able to drag phosphate groups as they insert inside the membrane to form a toroidal pore. However, whether bidentate bonds play a significant role in inducing a pore formation remains unclear. To investigate the role of bidentate complexes in PG-1 translocation, we conducted molecular dynamics simulations. Two computational electroporation methods were implemented to examine the translocation process. We found that PG-1 could insert into the membrane, provided the external electric potential is large enough to first induce a water column or a pore within the lipid bilayer membrane. We also found that the highly charged PG-1 is capable in itself of inducing molecular electroporation. Substitution of arginines with charge-equivalent lysines showed a markedly reduced tendency for insertion. This indicates that the guanidinium group likely facilitates PG-1 translocation. Potential of mean force calculations suggests that peptide insertion inside the hydrophobic environment of the membrane core is not favored. We found that formation of a water column or a pore might be a prerequisite for PG-1 translocation. We also found that PG-1 can stabilize the pore after insertion. We suggest that PG-1 could be a pore inducer and stabilizer. This work sheds some light on PG-1 translocation mechanisms at the molecular level. Methods presented in this study may be extended to other arginine-rich antimicrobial and cell-penetrating peptides.
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22
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Conjugates and nano-delivery of antimicrobial peptides for enhancing therapeutic activity. J Drug Deliv Sci Technol 2018. [DOI: 10.1016/j.jddst.2017.12.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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23
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Lipkin R, Lazaridis T. Computational studies of peptide-induced membrane pore formation. Philos Trans R Soc Lond B Biol Sci 2018. [PMID: 28630158 DOI: 10.1098/rstb.2016.0219] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
A variety of peptides induce pores in biological membranes; the most common ones are naturally produced antimicrobial peptides (AMPs), which are small, usually cationic, and defend diverse organisms against biological threats. Because it is not possible to observe these pores directly on a molecular scale, the structure of AMP-induced pores and the exact sequence of steps leading to their formation remain uncertain. Hence, these questions have been investigated via molecular modelling. In this article, we review computational studies of AMP pore formation using all-atom, coarse-grained, and implicit solvent models; evaluate the results obtained and suggest future research directions to further elucidate the pore formation mechanism of AMPs.This article is part of the themed issue 'Membrane pores: from structure and assembly, to medicine and technology'.
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Affiliation(s)
- Richard Lipkin
- Department of Chemistry, City College of New York, 160 Convent Avenue, New York, NY 10031, USA.,Graduate Program in Chemistry, The Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - Themis Lazaridis
- Department of Chemistry, City College of New York, 160 Convent Avenue, New York, NY 10031, USA
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24
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Sun L, Mao J, Zhao Y, Quan C, Zhong M, Fan S. Coarse-grained molecular dynamics simulation of interactions between cyclic lipopeptide Bacillomycin D and cell membranes. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1384632] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Liang Sun
- College of Life Science, Dalian Minzu University, Dalian, China
| | - Jiashun Mao
- College of Mechanical and Electronic Engineering, Dalian Minzu University, Dalian, China
| | - Ying Zhao
- School of Physics and Materials Engineering, Key Laboratory of Photosensitive Material & Device of Liaoning Province, Key Laboratory of New Energy & Rare Earth Resource Utilization of State Ethnic Affairs Commission, Dalian Minzu University, Dalian, China
| | - Chunshan Quan
- College of Life Science, Dalian Minzu University, Dalian, China
| | - Meiling Zhong
- College of Life Science, Dalian Minzu University, Dalian, China
| | - Shengdi Fan
- College of Life Science, Dalian Minzu University, Dalian, China
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25
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Lipkin R, Pino-Angeles A, Lazaridis T. Transmembrane Pore Structures of β-Hairpin Antimicrobial Peptides by All-Atom Simulations. J Phys Chem B 2017; 121:9126-9140. [PMID: 28879767 DOI: 10.1021/acs.jpcb.7b06591] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Protegrin-1 is an 18-residue β-hairpin antimicrobial peptide (AMP) that has been suggested to form transmembrane β-barrels in biological membranes. However, alternative structures have also been proposed. Here, we performed multimicrosecond, all-atom molecular dynamics simulations of various protegrin-1 oligomers on the membrane surface and in transmembrane topologies. The membrane surface simulations indicated that protegrin dimers are stable, whereas trimers and tetramers break down. Tetrameric arcs remained stably inserted in lipid membranes, but the pore water was displaced by lipid molecules. Unsheared protegrin β-barrels opened into β-sheets that surrounded stable aqueous pores, whereas tilted barrels with sheared hydrogen bonding patterns were stable in most topologies. A third type of observed pore consisted of multiple small oligomers surrounding a small, partially lipidic pore. We also considered the β-hairpin AMP tachyplesin, which showed less tendency to oligomerize than protegrin: the octameric bundle resulted in small pores surrounded by six peptides as monomers and dimers, with some peptides returning to the membrane surface. The results imply that multiple configurations of protegrin oligomers may produce aqueous pores and illustrate the relationship between topology and putative steps in protegrin-1's pore formation. However, the long-term stability of these structures needs to be assessed further.
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Affiliation(s)
- Richard Lipkin
- Department of Chemistry, City College of New York , 160 Convent Avenue, New York, New York 10031, United States.,Graduate Program in Chemistry, The Graduate Center, City University of New York , 365 Fifth Avenue, New York, New York 10016, United States
| | - Almudena Pino-Angeles
- Department of Chemistry, City College of New York , 160 Convent Avenue, New York, New York 10031, United States
| | - Themis Lazaridis
- Department of Chemistry, City College of New York , 160 Convent Avenue, New York, New York 10031, United States
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26
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Kuzmin DV, Emelianova AA, Kalashnikova MB, Panteleev PV, Balandin SV, Serebrovskaya EO, Belogurova-Ovchinnikova OY, Ovchinnikova TV. Comparative in vitro study on cytotoxicity of recombinant β-hairpin peptides. Chem Biol Drug Des 2017; 91:294-303. [PMID: 28815904 DOI: 10.1111/cbdd.13081] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Revised: 07/19/2017] [Accepted: 07/27/2017] [Indexed: 02/06/2023]
Abstract
Natural antimicrobial peptides (AMPs) are important components of the innate immune system with a wide spectrum of biological activity. In this study, we investigated the cytotoxic effect of three recombinant β-hairpin cationic AMPs: arenicin-1 from the polychaeta Arenicola marina, tachyplesin I from the horseshoe crab Tachypleus tridentatus, and gomesin from the spider Acanthoscurria gomesiana. All the three β-hairpin AMPs were overexpressed in Escherichia coli. Different cell lines were incubated with various concentrations of the investigated AMPs in order to evaluate their cytotoxic activity. Double staining with subsequent flow cytometric analysis was used to determine the predominant way of cell death mediated by each AMP. Hemolytic activity of the peptides was tested against fresh human red blood cells. Our results indicated that all the three AMPs exhibited significant cytotoxic effect against cancer cells that varied depending on the cell line type and, in most cases, on the presence of serum components. Flow cytometric analysis implicitly indicated that tachyplesin I mostly promoted late apoptosis/necrosis, while arenicin-1 and gomesin induced early apoptosis under the same conditions. Tachyplesin I proved to be the most promising therapeutic candidate as it displayed the highest specific cytotoxicity against cancer cell lines, independent of the serum presence.
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Affiliation(s)
- Denis V Kuzmin
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Anna A Emelianova
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Mariana B Kalashnikova
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Pavel V Panteleev
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Sergey V Balandin
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina O Serebrovskaya
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | | | - Tatiana V Ovchinnikova
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
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27
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de Miguel A, Tapia-Rojo R, Utesch T, Mroginski MA. Structure, dynamics and kinetics of two-component Lantibiotic Lichenicidin. PLoS One 2017; 12:e0179962. [PMID: 28654661 PMCID: PMC5487065 DOI: 10.1371/journal.pone.0179962] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 06/07/2017] [Indexed: 11/19/2022] Open
Abstract
Two variants of the two-component Lantibiotic Lichenicidin, produced by the strains B. Licheniformis VK21 and I89 (Lchα/ Lchβ and Bliα/ Bliβ peptides, respectively) have been investigated by means of 2 μs-long all-atom molecular dynamics simulations combined with Markov State Models. This rigorous statistical analysis enabled to evaluate the dynamic and kinetic properties of the aforementioned systems which are not accessible via experimental techniques. The structural flexibility characteristic of these small peptides is understood by a delicate equilibrium between random coil, α-helices and β-sheet structures. The undergoing secondary structure transitions from an α-helix to a β-sheet observed for Lchα and Lchβ peptides, were not present in the Bliα component and provide new insights to understand their mechanism of action.
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Affiliation(s)
- Alejandra de Miguel
- Department of Biophysical Chemistry, Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Rafael Tapia-Rojo
- Departamento de Física de la Materia Condensada, Universidad de Zaragoza, Zaragoza, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, Zaragoza, Spain
| | - Tillmann Utesch
- Department of Biophysical Chemistry, Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Maria Andrea Mroginski
- Department of Biophysical Chemistry, Institut für Chemie, Technische Universität Berlin, Berlin, Germany
- * E-mail:
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28
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Lipkin R, Lazaridis T. Computational prediction of the optimal oligomeric state for membrane-inserted β-barrels of protegrin-1 and related mutants. J Pept Sci 2017; 23:334-345. [PMID: 28382709 DOI: 10.1002/psc.2992] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 02/17/2017] [Accepted: 02/18/2017] [Indexed: 11/07/2022]
Abstract
Protegrin-1 is a widely studied 18-residue β-hairpin antimicrobial peptide. Evidence suggests that it acts via a β-barrel pore formation mechanism, but the exact number of peptides comprising the pore state is unknown. In this study, we performed molecular dynamics simulations of β-barrels of protegrin and three related mutants (v14v16l, v14v16a, and r4n) in NCNC parallel topology in implicit membrane pores of varying radius and curvature for oligomeric numbers 6-14. We then identified the optimal pore radius and curvature values for all constructs and determined the total effective energy and the translational and rotational entropic losses. These, along with an estimate of membrane deformation free energy from experimental line tension values, provided an estimate of the overall energetics of formation of each pore state. The results indicated that oligomeric numbers 7-13 are generally stable, allowing the possibility of a heterogeneous pore state. The optimal oligomeric state for protegrin is the nonamer, shifting to higher numbers for the mutants. Protegrin, v14v16l, and r4n are stable as membrane-inserted β-barrels, but v14v16a seems much less so because of its decreased hydrophobicity. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.
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Affiliation(s)
- Richard Lipkin
- Department of Chemistry, City College of New York, 160 Convent Ave., New York, NY, 10031, USA.,Graduate Program in Chemistry, Graduate Center, City University of New York, 365 Fifth Ave, New York, NY, 10016, USA
| | - Themis Lazaridis
- Department of Chemistry, City College of New York, 160 Convent Ave., New York, NY, 10031, USA
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Qi Y, Cheng X, Lee J, Vermaas JV, Pogorelov TV, Tajkhorshid E, Park S, Klauda JB, Im W. CHARMM-GUI HMMM Builder for Membrane Simulations with the Highly Mobile Membrane-Mimetic Model. Biophys J 2016; 109:2012-22. [PMID: 26588561 DOI: 10.1016/j.bpj.2015.10.008] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 10/06/2015] [Accepted: 10/09/2015] [Indexed: 12/12/2022] Open
Abstract
Slow diffusion of the lipids in conventional all-atom simulations of membrane systems makes it difficult to sample large rearrangements of lipids and protein-lipid interactions. Recently, Tajkhorshid and co-workers developed the highly mobile membrane-mimetic (HMMM) model with accelerated lipid motion by replacing the lipid tails with small organic molecules. The HMMM model provides accelerated lipid diffusion by one to two orders of magnitude, and is particularly useful in studying membrane-protein associations. However, building an HMMM simulation system is not easy, as it requires sophisticated treatment of the lipid tails. In this study, we have developed CHARMM-GUI HMMM Builder (http://www.charmm-gui.org/input/hmmm) to provide users with ready-to-go input files for simulating HMMM membrane systems with/without proteins. Various lipid-only and protein-lipid systems are simulated to validate the qualities of the systems generated by HMMM Builder with focus on the basic properties and advantages of the HMMM model. HMMM Builder supports all lipid types available in CHARMM-GUI and also provides a module to convert back and forth between an HMMM membrane and a full-length membrane. We expect HMMM Builder to be a useful tool in studying membrane systems with enhanced lipid diffusion.
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Affiliation(s)
- Yifei Qi
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, Lawrence, Kansas
| | - Xi Cheng
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, Lawrence, Kansas
| | - Jumin Lee
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, Lawrence, Kansas
| | - Josh V Vermaas
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois; Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Taras V Pogorelov
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois; School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois; National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, Illinois; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Emad Tajkhorshid
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois; Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Soohyung Park
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, Lawrence, Kansas
| | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering and the Biophysics Program, The University of Maryland, College Park, Maryland
| | - Wonpil Im
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, Lawrence, Kansas.
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Oligomerization of the antimicrobial peptide Protegrin-5 in a membrane-mimicking environment. Structural studies by high-resolution NMR spectroscopy. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2016; 46:293-300. [PMID: 27589857 DOI: 10.1007/s00249-016-1167-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 08/23/2016] [Accepted: 08/26/2016] [Indexed: 10/21/2022]
Abstract
Protegrin pore formation is believed to occur in a stepwise fashion that begins with a nonspecific peptide interaction with the negatively charged bacterial cell walls via hydrophobic and positively charged amphipathic surfaces. There are five known nature protegrins (PG1-PG5), and early studies of PG-1 (PDB ID:1PG1) shown that it could form antiparallel dimer in membrane mimicking environment which could be a first step for further oligomeric membrane pore formation. Later, we solved PG-2 (PDB ID:2MUH) and PG-3 (PDB ID:2MZ6) structures in the same environment and for PG-3 observed a strong dαα NOE effects between residues R18 and F12, V14, and V16. These "inconsistent" with monomer structure NOEs appears due to formation of an additional antiparallel β-sheet between two monomers. It was also suggested that there is a possible association of protegrins dimers to form octameric or decameric β-barrels in an oligomer state. In order to investigate a more detailed oligomerization process of protegrins, in the present article we report the monomer (PDB ID: 2NC7) and octamer pore structures of the protegrin-5 (PG-5) in the presence of DPC micelles studied by solution NMR spectroscopy. In contrast to PG-1, PG-2, and PG-3 studies, for PG-5 we observed not only dimer NOEs but also several additional NOEs between side chains, which allows us to calculate an octamer pore structure of PG-5 that was in good agreement with previous AFM and PMF data.
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Rai M, Pandit R, Gaikwad S, Kövics G. Antimicrobial peptides as natural bio-preservative to enhance the shelf-life of food. JOURNAL OF FOOD SCIENCE AND TECHNOLOGY 2016; 53:3381-3394. [PMID: 27777445 PMCID: PMC5069246 DOI: 10.1007/s13197-016-2318-5] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 07/30/2016] [Accepted: 08/15/2016] [Indexed: 12/31/2022]
Abstract
Antimicrobial peptides (AMPs) are diverse group of natural proteins present in animals, plants, insects and bacteria. These peptides are responsible for defense of host from pathogenic organisms. Chemical, enzymatic and recombinant techniques are used for the synthesis of antimicrobial peptides. These peptides have been found to be an alternative to the chemical preservatives. Currently, nisin is the only antimicrobial peptide, which is widely utilized in the preservation of food. Antimicrobial peptides can be used alone or in combination with other antimicrobial, essential oils and polymeric nanoparticles to enhance the shelf-life of food. This review presents an overview on different types of antimicrobial peptides, purification techniques, mode of action and application in food preservation.
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Affiliation(s)
- Mahendra Rai
- Department of Biotechnology, S.G.B. Amravati University, Amravati, Maharashtra 444602 India
| | - Raksha Pandit
- Department of Biotechnology, S.G.B. Amravati University, Amravati, Maharashtra 444602 India
| | - Swapnil Gaikwad
- Department of Biotechnology, S.G.B. Amravati University, Amravati, Maharashtra 444602 India
- Department of Biotechnology, Engineering School of Lorena, University of Sao Paulo, Estrada Municipal do Campinho, sn, Lorena, SP 12602-810 Brazil
| | - György Kövics
- Institute of Plant Protection, Debrecen Agricultural University, P.O. Box 36, Debrecen, H-4015 Hungary
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Kyriakou PK, Ekblad B, Kristiansen PE, Kaznessis YN. Interactions of a class IIb bacteriocin with a model lipid bilayer, investigated through molecular dynamics simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:824-35. [PMID: 26774214 DOI: 10.1016/j.bbamem.2016.01.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 01/06/2016] [Accepted: 01/12/2016] [Indexed: 01/15/2023]
Abstract
The emergence of antibiotic resistant microorganisms poses an alarming threat to global health. Antimicrobial peptides (AMPs) are considered a possible effective alternative to conventional antibiotic therapies. An understanding of the mechanism of action of AMPs is needed in order to better control and optimize their bactericidal activity. Plantaricin EF is a heterodimeric AMP, consisting of two peptides Plantaricin E (PlnE) and Plantaricin F (PlnF). We studied the behavior of these peptides on the surface of a model lipid bilayer. We identified the residues that facilitate peptide-peptide interactions. We also identified residues that mediate interactions of the dimer with the membrane. PlnE interacts with the membrane through amino acids at both its termini, while only the N terminus of PlnF approaches the membrane. By comparing the activity of single-site mutants of the two-peptide bacteriocin and the simulations of the bacteriocin on the surface of a model lipid bilayer, structure activity relationships are proposed. These studies allow us to generate hypotheses that relate biophysical interactions observed in simulations with the experimentally measured activity. We find that single-site amino acid substitutions result in markedly stronger antimicrobial activity when they strengthen the interactions between the two peptides, while, concomitantly, they weaken peptide-membrane association. This effect is more pronounced in the case of the PlnE mutant (G20A), which interacts the strongest with PlnF and the weakest with the membrane while displaying the highest activity.
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Affiliation(s)
- Panagiota K Kyriakou
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, United States
| | - Bie Ekblad
- Department of Biosciences, University of Oslo, Post box 1041 Blindern, 0316 Oslo, Norway
| | - Per Eugen Kristiansen
- Department of Biosciences, University of Oslo, Post box 1041 Blindern, 0316 Oslo, Norway
| | - Yiannis N Kaznessis
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, United States.
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deRonde BM, Tew GN. Development of protein mimics for intracellular delivery. Biopolymers 2015; 104:265-80. [PMID: 25858701 PMCID: PMC4516575 DOI: 10.1002/bip.22658] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 03/24/2015] [Accepted: 03/30/2015] [Indexed: 12/19/2022]
Abstract
Designing delivery agents for therapeutics is an ongoing challenge. As treatments and desired cargoes become more complex, the need for improved delivery vehicles becomes critical. Excellent delivery vehicles must ensure the stability of the cargo, maintain the cargo's solubility, and promote efficient delivery and release. In order to address these issues, many research groups have looked to nature for design inspiration. Proteins, such as HIV-1 trans-activator of transcription (TAT) and Antennapedia homeodomain protein, are capable of crossing cellular membranes. However, due to the complexities of their structures, they are synthetically challenging to reproduce in the laboratory setting. Being able to incorporate the key features of these proteins that enable cell entry into simpler scaffolds opens up a wide range of opportunities for the development of new delivery reagents with improved performance. This review charts the development of protein mimics based on cell-penetrating peptides (CPPs) and how structure-activity relationships (SARs) with these molecules and their protein counterparts ultimately led to the use of polymeric scaffolds. These scaffolds deviate from the normal peptide backbone, allowing for simpler, synthetic procedures to make carriers and tune chemical compositions for application specific needs. Successful design of polymeric protein mimics would allow researchers to further understand the key features in proteins and peptides necessary for efficient delivery and to design the next generation of more efficient delivery reagents.
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Affiliation(s)
- Brittany M deRonde
- Department of Polymer Science and Engineering, University of Massachusetts Amherst, Amherst, MA, 01003
| | - Gregory N Tew
- Department of Polymer Science and Engineering, University of Massachusetts Amherst, Amherst, MA, 01003
- Department of Veterinary and Animal Sciences, University of Massachusetts Amherst, Amherst, MA, 01003
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA, 01003
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Zare-Zardini H, Fesahat F, Anbari F, Halvaei I, Ebrahimi L. Assessment of spermicidal activity of the antimicrobial peptide sarcotoxin Pd: A potent contraceptive agent. EUR J CONTRACEP REPR 2015; 21:15-21. [PMID: 26052043 DOI: 10.3109/13625187.2015.1052395] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
OBJECTIVES In searching for new spermicidal microbicides for use in the prevention of unplanned pregnancy and sexually transmitted infections (STIs) we investigated the spermicidal and cytotoxicity activities of the antimicrobial peptide sarcotoxin Pd. METHODS Washed sperm from 10 healthy, normal volunteers was treated with different concentrations of sarcotoxin Pd. Sperm motility and morphology were assessed at 0, 0.3, 5, 10 and 15 min. The cytotoxicity of sarcotoxin Pd in normal human cervical HeLa cells was measured. Percentage cell survival was expressed as the number of live cells in the test group. RESULTS The cytotoxic effect of sarcotoxin Pd was concentration-dependent. Significant cytotoxicity was observed at concentrations above 24 μg/ml. Sarcotoxin Pd immobilised 100% of spermatozoa at a dose of 90 and 80 μg/ml after 0.3 and 5 min, respectively, and immobilised 50% of spermatozoa after 15 min at lower doses. Sarcotoxin Pd inhibited sperm motility in a dose-dependent manner. The peptide immobilised sperm within 20 s at its maximal effective concentration of 90 μg/ml. CONCLUSIONS Sarcotoxin Pd appears to be a good candidate for a contraceptive agent in the prevention of unplanned pregnancy and STIs.
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Affiliation(s)
- Hadi Zare-Zardini
- a Young Researchers and Elite Club, Yazd Branch, Islamic Azad University , Yazd , Iran.,b Pediatric Hematology and Oncology Research Center, Shahid Sadoughi University of Medical Sciences and Health Services , Yazd , Iran
| | - Farzaneh Fesahat
- c Research and Clinical Center for Infertility, Shahid Sadoughi University of Medical Sciences , Yazd , Iran.,d Faculty of Medicine, Shahid Sadoughi University of Medical Sciences , Yazd , Iran
| | - Fatemeh Anbari
- c Research and Clinical Center for Infertility, Shahid Sadoughi University of Medical Sciences , Yazd , Iran
| | - Iman Halvaei
- c Research and Clinical Center for Infertility, Shahid Sadoughi University of Medical Sciences , Yazd , Iran
| | - Leila Ebrahimi
- e Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine , Tehran , Iran
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Esmaili E, Shahlaei M. Analysis of the flexibility and stability of the structure of magainin in a bilayer, and in aqueous and nonaqueous solutions using molecular dynamics simulations. J Mol Model 2015; 21:73. [PMID: 25750019 DOI: 10.1007/s00894-015-2622-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 02/15/2015] [Indexed: 11/25/2022]
Abstract
The precise mode of the antimicrobial activity of Magainin (Mag)-an antimicrobial peptide (AMP)-is still unclear. In this study, the conformation of Mag was characterized in water, and in a methanol and lipid bilayer [palmitoyl-oleoylphosphatidylcholine (POPC)] using a molecular dynamics (MD) simulation technique. To describe the role conformation plays in Mag function, the global conformational differences within three systems were studied. Through analysis of the resulting configuration ensembles, the differences in the three systems, such as overall flexibility and average secondary structure, were studied. It is suggested that these differences may be important enough to influence interactions with lipid biomembranes, thereby influencing key properties such as penetration into cell membrane and stability.
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Affiliation(s)
- Elham Esmaili
- Department of Biochemistry, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran
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Li C, Blencke HM, Haug T, Stensvåg K. Antimicrobial peptides in echinoderm host defense. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2015; 49:190-197. [PMID: 25445901 DOI: 10.1016/j.dci.2014.11.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 10/02/2014] [Accepted: 11/03/2014] [Indexed: 06/04/2023]
Abstract
Antimicrobial peptides (AMPs) are important effector molecules in innate immunity. Here we briefly summarize characteristic traits of AMPs and their mechanisms of antimicrobial activity. Echinoderms live in a microbe-rich marine environment and are known to express a wide range of AMPs. We address two novel AMP families from coelomocytes of sea urchins: cysteine-rich AMPs (strongylocins) and heterodimeric AMPs (centrocins). These peptide families have conserved preprosequences, are present in both adults and pluteus stage larvae, have potent antimicrobial properties, and therefore appear to be important innate immune effectors. Strongylocins have a unique cysteine pattern compared to other cysteine-rich peptides, which suggests a novel AMP folding pattern. Centrocins and SdStrongylocin 2 contain brominated tryptophan residues in their native form. This review also includes AMPs isolated from other echinoderms, such as holothuroidins, fragments of beta-thymosin, and fragments of lectin (CEL-III). Echinoderm AMPs are crucial molecules for the understanding of echinoderm immunity, and their potent antimicrobial activity makes them potential precursors of novel drug leads.
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Affiliation(s)
- Chun Li
- Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, Breivika, N-9037 Tromsø, Norway.
| | - Hans-Matti Blencke
- Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, Breivika, N-9037 Tromsø, Norway; Centre for Research-based Innovation on Marine Bioactives and Drug Discovery (MabCent-SFI), UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Tor Haug
- Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, Breivika, N-9037 Tromsø, Norway; Centre for Research-based Innovation on Marine Bioactives and Drug Discovery (MabCent-SFI), UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Klara Stensvåg
- Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, Breivika, N-9037 Tromsø, Norway; Centre for Research-based Innovation on Marine Bioactives and Drug Discovery (MabCent-SFI), UiT The Arctic University of Norway, N-9037 Tromsø, Norway.
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NIU MINGFU, CHAI SHUMAO, YOU XIAOYAN, WANG WENHUI, QIN CUILI, GONG QIANG, ZHANG TINGTING, WAN PENG. Expression of porcine protegrin-1 in Pichia pastoris and its anticancer activity in vitro.. Exp Ther Med 2015; 9:1075-1079. [PMID: 25667681 PMCID: PMC4316971 DOI: 10.3892/etm.2015.2202] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Accepted: 01/15/2015] [Indexed: 12/27/2022] Open
Abstract
Protegrin-1 (PG-1), a β-hairpin antimicrobial peptide (AMP), is amongst the shortest AMPs in sequence length while remaining active against a variety of microorganisms. The aim of this study was produce recombinant PG-1 and investigate its anticancer activity. A DNA sequence encoding the mature PG-1, fused with a 6His-tag, was cloned into the pPICZα-A vector and transformed into Pichia pastoris. Expression was induced following culture for ~96 h with 1% methanol at 28°C, and ~15.6 mg PG-1 was expressed in 100 ml culture medium. Following purification using a Ni-chelating Sepharose column, ~20 mg pure active PG-1 was obtained from 500 ml culture broth supernatant. The expressed PG-1/6His exhibited strong dose- and time-dependent anticancer activity against HepG2 cells in vitro.
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Affiliation(s)
- MINGFU NIU
- Correspondence to: Professor Mingfu Niu, Food and Bioengineering College, Henan University of Science and Technology, 263 Kaiyuan Avenue, Luoyang, Henan 471003, P.R. China, E-mail:
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Borkar MR, Pissurlenkar RRS, Coutinho EC. Mapping activity elements of protegrin antimicrobial peptides by HomoSAR. RSC Adv 2015. [DOI: 10.1039/c5ra14402g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
HomoSAR has been able to shed light on the relationship between sequences of protegrin peptides and their activity on six specific micro-organisms.
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Affiliation(s)
| | | | - Evans C. Coutinho
- Department of Pharmaceutical Chemistry
- Bombay College of Pharmacy
- Mumbai 400098
- India
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Baul U, Vemparala S. Membrane-Bound Conformations of Antimicrobial Agents and Their Modes of Action. ADVANCES IN PLANAR LIPID BILAYERS AND LIPOSOMES 2015. [DOI: 10.1016/bs.adplan.2015.06.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Abstract
The rapid spread of drug-resistant pathogenic microbial strains has created an urgent need for the development of new anti-infective molecules, having different mechanism of action in comparison to existing drugs. Natural antimicrobial peptides (AMPs) represent a novel class of molecules with a broad spectrum of activity and a low rate in inducing bacterial resistance. In particular, linear alpha-helical cationic antimicrobial peptides are among the most widespread membrane-disruptive AMPs in nature, representing a particularly successful structural arrangement of the innate defense against microbes. However, until now, many AMPs have failed in clinical trials because of several drawbacks that strongly limit their applicability such as degradation, cytotoxicity, and high production cost. Thus, to overcome the limitations of native peptides, a rational in silico approach to AMPs design becomes a promising strategy that drastically reduce production costs and the time required for evaluation of activity and toxicity. This chapter focuses on the strategies and methods for de novo design of potentially active AMPs. In particular, statistical-based design strategies and MD methods for modelling AMPs are elucidated.
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Affiliation(s)
- Giuseppe Maccari
- Center for Nanotechnology Innovation @NEST, Istituto Italiano di Tecnologia, Pisa, Italy
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Lipkin RB, Lazaridis T. Implicit Membrane Investigation of the Stability of Antimicrobial Peptide β-Barrels and Arcs. J Membr Biol 2014; 248:469-86. [PMID: 25430621 DOI: 10.1007/s00232-014-9759-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 11/18/2014] [Indexed: 12/31/2022]
Abstract
Previous simulations showed that the β-hairpin antimicrobial peptide (AMP) protegrin-1 can form stable octameric β-barrels and tetrameric arcs (half barrels) in both implicit and explicit membranes. Here, we extend this investigation to several AMPs of similar structure: tachyplesin, androctonin, polyphemusin, gomesin, and the retrocyclin θ-defensin. These peptides form short β-hairpins stabilized by 2-3 disulfide bonds. We also examine synthetic β-sheet peptides selected from a combinatorial library for their ability or inability to form pores in lipid membranes. When heptameric, octameric, and decameric β-barrels and tetrameric arcs of these peptides were embedded in pre-formed neutral or anionic lipid pores (i.e., pores in neutral or anionic membranes, respectively), a variety of behaviors and membrane binding energies were observed. Due to the cationic charge of the peptides, more favorable transfer energies and more stable binding were observed in anionic than neutral pores. The synthetic peptides bound very strongly and formed stable barrels and arcs in both neutral and anionic pores. The natural AMPs exhibited unfavorable or marginally favorable binding energy and kinetic stability in neutral pores, consistent with the lower hemolytic activity of some of them compared with protegrin-1. Binding to anionic pores was more favorable, but significant distortions of the barrel or arc structures were sometimes noted. These results are discussed in light of the available experimental data. The diversity of behaviors obtained makes it unlikely that the barrel and arc mechanisms are valid for the entire family of β-hairpin AMPs.
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Affiliation(s)
- Richard B Lipkin
- Department of Chemistry, City College of the City University of New York, 160 Convent Ave., New York, NY, 10031, USA
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42
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Protein arcs may form stable pores in lipid membranes. Biophys J 2014; 106:154-61. [PMID: 24411247 DOI: 10.1016/j.bpj.2013.11.4490] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2013] [Revised: 11/04/2013] [Accepted: 11/22/2013] [Indexed: 01/22/2023] Open
Abstract
Electron microscopy and atomic force microscopy images of cholesterol-dependent cytolysins and related proteins that form large pores in lipid membranes have revealed the presence of incomplete rings, or arcs. Some evidence indicates that these arcs are inserted into the membrane and induce membrane leakage, but other experiments seem to refute that. Could such pores, only partially lined by protein, be kinetically and thermodynamically stable? How would the lipids be structured in such a pore? Using the antimicrobial peptide protegrin-1 as a model, we test the stability of pores only partially lined by peptide using all-atom molecular dynamics simulations in POPC and POPE/POPG membranes. The data show that, whereas pure lipid pores close rapidly, pores partially lined by protegrin arcs are stable for at least 300 ns. Estimates of the thermodynamic stability of these arcs using line tension data and implicit solvent calculations show that these arcs can be marginally stable in both zwitterionic and anionic membranes. Arcs provide an explanation for the observed ion selectivity in protegrin electrophysiology experiments and could possibly be involved in other membrane permeabilization processes where lipids are thought to participate, such as those induced by antimicrobial peptides and colicins, as well as the Bax apoptotic pore.
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Horn JN, Cravens A, Grossfield A. Interactions between fengycin and model bilayers quantified by coarse-grained molecular dynamics. Biophys J 2014; 105:1612-23. [PMID: 24094402 DOI: 10.1016/j.bpj.2013.08.034] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 08/20/2013] [Accepted: 08/22/2013] [Indexed: 11/28/2022] Open
Abstract
Bacteria, particularly of the genus Bacillus, produce a wide variety of antifungal compounds. They act by affecting the lipid bilayers of fungal membranes, causing curvature-induced strain and eventual permeabilization. One class of these, known as fengycins, has been commercialized for treating agricultural infections and shows some promise as a possible antifungal pharmaceutical. Understanding the mechanism by which fengycins damage lipid bilayers could prove useful to the future development of related antifungal treatments. In this work, we present multi-microsecond-long simulations of fengycin interacting with different lipid bilayer systems. We see fengycin aggregation and uncover a clear aggregation pattern that is partially influenced by bilayer composition. We also quantify some local bilayer perturbations caused by fengycin binding, including curvature of the lipid bilayer and local electrostatic-driven reorganization.
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Affiliation(s)
- Joshua N Horn
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York
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Ruiz J, Calderon J, Rondón-Villarreal P, Torres R. Analysis of Structure and Hemolytic Activity Relationships of Antimicrobial Peptides (AMPs). ADVANCES IN INTELLIGENT SYSTEMS AND COMPUTING 2014. [DOI: 10.1007/978-3-319-01568-2_36] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
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Antimicrobial peptides. Pharmaceuticals (Basel) 2013; 6:1543-75. [PMID: 24287494 PMCID: PMC3873676 DOI: 10.3390/ph6121543] [Citation(s) in RCA: 847] [Impact Index Per Article: 77.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 11/21/2013] [Accepted: 11/25/2013] [Indexed: 12/20/2022] Open
Abstract
The rapid increase in drug-resistant infections has presented a serious challenge to antimicrobial therapies. The failure of the most potent antibiotics to kill “superbugs” emphasizes the urgent need to develop other control agents. Here we review the history and new development of antimicrobial peptides (AMPs), a growing class of natural and synthetic peptides with a wide spectrum of targets including viruses, bacteria, fungi, and parasites. We summarize the major types of AMPs, their modes of action, and the common mechanisms of AMP resistance. In addition, we discuss the principles for designing effective AMPs and the potential of using AMPs to control biofilms (multicellular structures of bacteria embedded in extracellular matrixes) and persister cells (dormant phenotypic variants of bacterial cells that are highly tolerant to antibiotics).
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Munyuki G, Jackson GE, Venter GA, Kövér KE, Szilágyi L, Rautenbach M, Spathelf BM, Bhattacharya B, van der Spoel D. β-Sheet Structures and Dimer Models of the Two Major Tyrocidines, Antimicrobial Peptides from Bacillus aneurinolyticus. Biochemistry 2013; 52:7798-806. [DOI: 10.1021/bi401363m] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gadzikano Munyuki
- Department
of Chemistry, University of Cape Town, P Bag X3, Rondebosch, Cape Town, South Africa 7701
- Uppsala
Center for Computational Chemistry, Science for Life Laboratory, Department
of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box
596, SE-751 24 Uppsala, Sweden
| | - Graham E. Jackson
- Department
of Chemistry, University of Cape Town, P Bag X3, Rondebosch, Cape Town, South Africa 7701
| | - Gerhard A. Venter
- Department
of Chemistry, University of Cape Town, P Bag X3, Rondebosch, Cape Town, South Africa 7701
| | - Katalin E. Kövér
- Department
of Chemistry, University of Debrecen, H-4010 Debrecen, Egyetem tér 1, Pf. 20, Hungary
| | - László Szilágyi
- Department
of Chemistry, University of Debrecen, H-4010 Debrecen, Egyetem tér 1, Pf. 20, Hungary
| | - Marina Rautenbach
- BIOPEP
Peptide group, Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa 7600
| | - Barbara M. Spathelf
- BIOPEP
Peptide group, Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa 7600
| | - Bhaswati Bhattacharya
- BIOPEP
Peptide group, Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa 7600
| | - David van der Spoel
- Uppsala
Center for Computational Chemistry, Science for Life Laboratory, Department
of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box
596, SE-751 24 Uppsala, Sweden
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47
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Zeitler B, Herrera Diaz A, Dangel A, Thellmann M, Meyer H, Sattler M, Lindermayr C. De-novo design of antimicrobial peptides for plant protection. PLoS One 2013; 8:e71687. [PMID: 23951222 PMCID: PMC3741113 DOI: 10.1371/journal.pone.0071687] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 07/08/2013] [Indexed: 12/17/2022] Open
Abstract
This work describes the de-novo design of peptides that inhibit a broad range of plant pathogens. Four structurally different groups of peptides were developed that differ in size and position of their charged and hydrophobic clusters and were assayed for their ability to inhibit bacterial growth and fungal spore germination. Several peptides are highly active at concentrations between 0,1 and 1 µg/ml against plant pathogenic bacteria, such as Pseudomonas syringae, Pectobacterium carotovorum, and Xanthomonas vesicatoria. Importantly, no hemolytic activity could be detected for these peptides at concentrations up to 200 µg/ml. Moreover, the peptides are also active after spraying on the plant surface demonstrating a possible way of application. In sum, our designed peptides represent new antimicrobial agents and with the increasing demand for antimicrobial compounds for production of “healthy” food, these peptides might serve as templates for novel antibacterial and antifungal agents.
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Affiliation(s)
- Benjamin Zeitler
- Department of Environmental Science, Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, München-Neuherberg, Germany.
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48
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Lazaridis T, He Y, Prieto L. Membrane interactions and pore formation by the antimicrobial peptide protegrin. Biophys J 2013; 104:633-42. [PMID: 23442914 DOI: 10.1016/j.bpj.2012.12.038] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2012] [Revised: 12/06/2012] [Accepted: 12/21/2012] [Indexed: 11/18/2022] Open
Abstract
Protegrin is an antimicrobial peptide with a β-hairpin structure stabilized by a pair of disulfide bonds. It has been extensively studied by solid-state NMR and computational methods. Here we use implicit membrane models to examine the binding of monomers on the surface and in the interior of the membrane, the energetics of dimerization, the binding to membrane pores, and the stability of different membrane barrel structures in pores. Our results challenge a number of conclusions based on previous experimental and theoretical work. The burial of monomers into the membrane interior is found to be unfavorable for any membrane thickness. Because of its imperfect amphipathicity, protegrin binds weakly, at most, on the surface of zwitterionic membranes. However, it binds more favorably onto toroidal pores. Anionic charge on the membrane facilitates the binding due to electrostatic interactions. Solid-state NMR results have suggested a parallel NCCN association of monomers in dimers and association of dimers to form octameric or decameric β-barrels. We find that this structure is not energetically plausible for binding to bilayers, because in this configuration the hydrophobic sides of two monomers point in opposite directions. In contrast, the antiparallel NCCN and especially the parallel NCNC octamers are stable and exhibit a favorable binding energy to the pore. The results of 100-ns simulations in explicit bilayers corroborate the higher stability of the parallel NCNC barrel compared with the parallel NCCN barrel. The ability to form pores in zwitterionic membranes provides a rationalization for the peptide's cytotoxicity. The discrepancies between our results and experiment are discussed, and new experiments are proposed to resolve them and to test the validity of the models.
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Affiliation(s)
- Themis Lazaridis
- Department of Chemistry, City College of New York/CUNY, New York, New York, USA.
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49
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Elmore DE. Insights into buforin II membrane translocation from molecular dynamics simulations. Peptides 2012; 38:357-62. [PMID: 23022591 PMCID: PMC3513657 DOI: 10.1016/j.peptides.2012.09.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Revised: 09/18/2012] [Accepted: 09/19/2012] [Indexed: 11/19/2022]
Abstract
Buforin II is a histone-derived antimicrobial peptide that readily translocates across lipid membranes without causing significant membrane permeabilization. Previous studies showed that mutating the sole proline of buforin II dramatically decreases its translocation. As well, researchers have proposed that the peptide crosses membranes in a cooperative manner by forming transient toroidal pores. This paper reports molecular dynamics simulations designed to investigate the structure of buforin II upon membrane entry and evaluate whether the peptide is able to form toroidal pore structures. These simulations showed a relationship between protein-lipid interactions and increased structural deformations of the buforin N-terminal region promoted by proline. Moreover, simulations with multiple peptides show how buforin II can embed deeply into membranes and potentially form toroidal pores. Together, these simulations provide structural insight into the translocation process for buforin II in addition to providing more general insight into the role proline can play in antimicrobial peptides.
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Affiliation(s)
- Donald E Elmore
- Department of Chemistry, Wellesley College, 106 Central St, Wellesley, MA 02481, United States.
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50
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Bolintineanu DS, Vivcharuk V, Kaznessis YN. Multiscale models of the antimicrobial peptide protegrin-1 on gram-negative bacteria membranes. Int J Mol Sci 2012; 13:11000-11011. [PMID: 23109834 PMCID: PMC3472726 DOI: 10.3390/ijms130911000] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 08/15/2012] [Accepted: 08/22/2012] [Indexed: 12/22/2022] Open
Abstract
Antimicrobial peptides (AMPs) are naturally-occurring molecules that exhibit strong antibiotic properties against numerous infectious bacterial strains. Because of their unique mechanism of action, they have been touted as a potential source for novel antibiotic drugs. We present a summary of computational investigations in our lab aimed at understanding this unique mechanism of action, in particular the development of models that provide a quantitative connection between molecular-level biophysical phenomena and relevant biological effects. Our work is focused on protegrins, a potent class of AMPs that attack bacteria by associating with the bacterial membrane and forming transmembrane pores that facilitate the unrestricted transport of ions. Using fully atomistic molecular dynamics simulations, we have computed the thermodynamics of peptide-membrane association and insertion, as well as peptide aggregation. We also present a multi-scale analysis of the ion transport properties of protegrin pores, ranging from atomistic molecular dynamics simulations to mesoscale continuum models of single-pore electrodiffusion to models of transient ion transport from bacterial cells. Overall, this work provides a quantitative mechanistic description of the mechanism of action of protegrin antimicrobial peptides across multiple length and time scales.
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Affiliation(s)
- Dan S. Bolintineanu
- Department of Chemical Engineering and Materials Science, University of Minnesota, 421 Washington Ave SE, Minneapolis, MN 55455, USA; E-Mails: (D.S.B.); (V.V.)
| | - Victor Vivcharuk
- Department of Chemical Engineering and Materials Science, University of Minnesota, 421 Washington Ave SE, Minneapolis, MN 55455, USA; E-Mails: (D.S.B.); (V.V.)
| | - Yiannis N. Kaznessis
- Department of Chemical Engineering and Materials Science, University of Minnesota, 421 Washington Ave SE, Minneapolis, MN 55455, USA; E-Mails: (D.S.B.); (V.V.)
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