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Duffy F, Maheshwari N, Buchete NV, Shields D. Computational Opportunities and Challenges in Finding Cyclic Peptide Modulators of Protein-Protein Interactions. Methods Mol Biol 2019; 2001:73-95. [PMID: 31134568 DOI: 10.1007/978-1-4939-9504-2_5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Peptide cyclization can improve stability, conformational constraint, and compactness. However, apart from beta-turn structures, which are well incorporated into cyclic peptides (CPs), many primary peptide structures and functions are markedly altered by cyclization. Accordingly, to mimic linear peptide interfaces with cyclic peptides, it can be beneficial to screen combinatorial cyclic peptide libraries. Computational methods have been developed to screen CPs, but face a number of challenges. Here, we review methods to develop in silico computational libraries, and the potential for screening naturally occurring libraries of CPs. The simplest and most rapid computational pharmacophore methods that estimate peptide three-dimensional structures to be screened versus targets are relatively easy to implement, and while the constraint on structure imposed by cyclization makes them more effective than the same approaches with linear peptides, there are a large number of limiting assumptions. In contrast, full molecular dynamics simulations of cyclic peptide structures not only are costly to implement, but also require careful attention to interpretation, so that not only is the computation time rate limiting, but the interpretation time is also rate limiting due to the analysis of the typically complex underlying conformational space of CPs. A challenge for the field of computational cyclic peptide screening is to bridge this gap effectively. Natural compound libraries of short cyclic peptides, and short cyclized regions of proteins, encoded in the genomes of many organisms present a potential treasure trove of novel functionality which may be screened via combined computational and experimental screening approaches.
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Affiliation(s)
- Fergal Duffy
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Nikunj Maheshwari
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | | | - Denis Shields
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland. .,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.
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52
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Thery T, Shwaiki LN, O'Callaghan YC, O'Brien NM, Arendt EK. Antifungal activity of a de novo synthetic peptide and derivatives against fungal food contaminants. J Pept Sci 2018; 25:e3137. [PMID: 30488526 DOI: 10.1002/psc.3137] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 10/26/2018] [Accepted: 11/02/2018] [Indexed: 12/13/2022]
Abstract
The development of novel solutions to fight microbial food contaminants rests upon two pillars, which are the development of resistant strains and consumers' desire for a reduced consumption of synthetic drugs. Natural antimicrobial peptides possess the qualities to overcome these issues. De novo synthesis of novel antifungal compounds is a major progress that has been facilitated by the identification of parameters involved in the antimicrobial activity. A 14-residue peptide named KK14, with the sequence KKFFRAWWAPRFLK-NH2 , was designed and inhibited conidial germination and fungal growth of food contaminants within the range 6.25 to 50 μg/ml and 6.25 to 100 μg/ml, respectively. The study of three analogues of the peptide highlighted the role of some residues in the structural conformation of the peptide and its antifungal activity. The substitution of a Pro residue with Arg increased the helical content of the peptide not only its antifungal activity but also its cytotoxicity. The insertion of an unnatural bulky residue β-diphenylalanine or a full d-enantiomerization overall increased the antifungal potency. The four peptides showed similar behaviour towards salt increase, heat treatment, and pH decrease. Interestingly, the denantiomer remained the most active at high pH and after proteolytic digestion. The four peptides did not present haemolytic activity up to 200 μg/ml but had different behaviours of cytotoxicity. These differences could be crucial for potential application as pharmaceutical or food preservatives.
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Affiliation(s)
- Thibaut Thery
- School of Food and Nutritional Sciences, University College Cork, Cork, Ireland
| | - Laila N Shwaiki
- School of Food and Nutritional Sciences, University College Cork, Cork, Ireland
| | | | - Nora M O'Brien
- School of Food and Nutritional Sciences, University College Cork, Cork, Ireland
| | - Elke K Arendt
- School of Food and Nutritional Sciences, University College Cork, Cork, Ireland.,APC Microbiome Institute, University College Cork, Cork, Ireland
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53
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Touti F, Lautrette G, Johnson KD, Delaney JC, Wollacott A, Tissire H, Viswanathan K, Shriver Z, Mong SK, Mijalis AJ, Plante OJ, Pentelute BL. Antibody-Bactericidal Macrocyclic Peptide Conjugates To Target Gram-Negative Bacteria. Chembiochem 2018; 19:2039-2044. [DOI: 10.1002/cbic.201800295] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Indexed: 12/24/2022]
Affiliation(s)
- Fayçal Touti
- Department of Chemistry; Massachusetts Institute of Technology; Cambridge MA 02139 USA
| | - Guillaume Lautrette
- Department of Chemistry; Massachusetts Institute of Technology; Cambridge MA 02139 USA
| | | | | | | | - Hamid Tissire
- Visterra, Inc.; 275 2nd Avenue 4th Floor Waltham MA 02451 USA
| | | | - Zachary Shriver
- Visterra, Inc.; 275 2nd Avenue 4th Floor Waltham MA 02451 USA
| | - Surin K. Mong
- Department of Chemistry; Massachusetts Institute of Technology; Cambridge MA 02139 USA
| | - Alexander J. Mijalis
- Department of Chemistry; Massachusetts Institute of Technology; Cambridge MA 02139 USA
| | | | - Bradley L. Pentelute
- Department of Chemistry; Massachusetts Institute of Technology; Cambridge MA 02139 USA
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54
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Farzanegan A, Roudbary M, Falahati M, Khoobi M, Gholibegloo E, Farahyar S, Karimi P, Khanmohammadi M. Synthesis, characterization and antifungal activity of a novel formulated nanocomposite containing Indolicidin and Graphene oxide against disseminated candidiasis. J Mycol Med 2018; 28:628-636. [PMID: 30126717 DOI: 10.1016/j.mycmed.2018.07.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 06/29/2018] [Accepted: 07/31/2018] [Indexed: 01/22/2023]
Abstract
OBJECTIVE Candidiasis is one of the most opportunistic fungal infections in immunocompromised patients. The emergence of multidrug-resistant Candida species necessitates the development of novel antifungal agents. Seeking to the discovery of natural antifungal agents, this study aimed to synthesize a novel formulated nanocomposite containing Indolicidin (IN), antimicrobial peptide, and Graphene oxide (GO), kind of nanomaterial, against Candida growth using in vitro and in vivo experiments for the first time. METHODS The formulated nanocomposite (GO-IN) synthetized and was characterized using scanning electron microscopy, X-ray power diffraction, and fourier transform infrared method analysis. The in vitro antifungal activity of fluconazole (FLU), GO, IN, and GO-IN was determined against Candida albicans (C. albicans) compared to control groups, cell cytotoxicity assay on human intestinal epithelial cells (IEP) and hemolytic activities were performed. Moreover, in vivo experiments of nanocomposite were assessed in BALB/c mice. RESULTS Our results showed that nanocomposite had the highest inhibitory effect against C. albicans (MIC 3.12μg/mL) compared with flu (MIC 4μg/mL), IN (MIC 12.5μg/mL), and GO (MIC 6.25μg/mL). Viability of human intestinal cell line at the MIC concentration (3.12μg/mL) of nanocomposite (GO-IN) was detected as 60% (P<0.05). The results of hemolytic activity showed that nanocomposite cause 2.73% of red blood cell membrane damage. For in vivo experiments, infected mice were successfully treated with GO-IN once a day within 7 days. GO-IN treated group eliminated the Candida infection in the spleen and liver of BALB/c mice (P=0.001) similar to fluconazole. There was no significant difference in histological manifestations between flu and GO-IN groups. CONCLUSION This study suggests that synergistic combination of GO and IN provide a new option, representing a potential therapeutic efficiency against disseminated candidiasis in an animal model as well as might be used as adjunct therapy in the management of candidiasis. However, further investigation is needed to evaluate the efficacy of the nanocomposite.
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Affiliation(s)
- A Farzanegan
- Department of Medical Mycology and Parasitology, School of Medicine, Iran University of Medical Sciences, 14496-14530 Tehran, Iran
| | - M Roudbary
- Department of Medical Mycology and Parasitology, School of Medicine, Iran University of Medical Sciences, 14496-14530 Tehran, Iran.
| | - M Falahati
- Department of Medical Mycology and Parasitology, School of Medicine, Iran University of Medical Sciences, 14496-14530 Tehran, Iran
| | - M Khoobi
- Nanobiomaterials group, Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences, 141761411 Tehran, Iran; Department of Organic Chemistry, University of Zanjan, Zanjan, Iran
| | - E Gholibegloo
- Department of Chemistry, Faculty of Sciences, University of Zanjan, Zanjan, Iran
| | - S Farahyar
- Department of Medical Mycology and Parasitology, School of Medicine, Iran University of Medical Sciences, 14496-14530 Tehran, Iran
| | - P Karimi
- Department of Medical Mycology and Parasitology, School of Medicine, Iran University of Medical Sciences, 14496-14530 Tehran, Iran
| | - M Khanmohammadi
- Department of Medical Mycology and Parasitology, School of Medicine, Iran University of Medical Sciences, 14496-14530 Tehran, Iran
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Jeanne Dit Fouque D, Lartia R, Maroto A, Memboeuf A. Quantification of intramolecular click chemistry modified synthetic peptide isomers in mixtures using tandem mass spectrometry and the survival yield technique. Anal Bioanal Chem 2018; 410:5765-5777. [DOI: 10.1007/s00216-018-1258-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 07/10/2018] [Indexed: 10/28/2022]
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56
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Vasilchenko AS, Vasilchenko AV, Pashkova TM, Smirnova MP, Kolodkin NI, Manukhov IV, Zavilgelsky GB, Sizova EA, Kartashova OL, Simbirtsev AS, Rogozhin EA, Duskaev GK, Sycheva MV. Antimicrobial activity of the indolicidin-derived novel synthetic peptide In-58. J Pept Sci 2018; 23:855-863. [PMID: 29193518 DOI: 10.1002/psc.3049] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 09/28/2017] [Accepted: 10/01/2017] [Indexed: 12/26/2022]
Abstract
Natural peptides with antimicrobial activity are extremely diverse, and peptide synthesis technologies make it possible to significantly improve their properties for specific tasks. Here, we investigate the biological properties of the natural peptide indolicidin and the indolicidin-derived novel synthetic peptide In-58. In-58 was generated by replacing all tryptophan residues on phenylalanine in D-configuration; the α-amino group in the main chain also was modified by unsaturated fatty acid. Compared with indolicidin, In-58 is more bactericidal, more resistant to proteinase K, and less toxic to mammalian cells. Using molecular physics approaches, we characterized the action of In-58 on bacterial cells at the cellular level. Also, we have found that studied peptides damage bacterial membranes. Using the Escherichia coli luminescent biosensor strain MG1655 (pcolD'::lux), we investigated the action of indolicidin and In-58 at the subcellular level. At subinhibitory concentrations, indolicidin and In-58 induced an SOS response. Our data suggest that indolicidin damages the DNA, but bacterial membrane perturbation is its principal mode of action. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.
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Affiliation(s)
- A S Vasilchenko
- Tyumen State University, ul. Volodarsky, 6, Tyumen, 625003, Russia
| | - A V Vasilchenko
- Tyumen State University, ul. Volodarsky, 6, Tyumen, 625003, Russia
| | - T M Pashkova
- Institute of Cellular and Intracellular Symbiosis, Russian Academy of Sciences, ul. Pionerskaya, Orenburg, 11, Russia
| | - M P Smirnova
- Research Institute of Highly Pure Biopreparations, Pudozhsakya str., St. Petersburg, 197110, Russia
| | - N I Kolodkin
- Research Institute of Highly Pure Biopreparations, Pudozhsakya str., St. Petersburg, 197110, Russia
| | - I V Manukhov
- State Research Institute of Genetics and Selection of Industrial Microorganisms, 1, 1st Dorozhny pr., Moscow, 113545, Russia.,Moscow Institute of Physics and Technology (State University), 9 Institutskiy per., Dolgoprudnyi, 141701, Russia
| | - G B Zavilgelsky
- State Research Institute of Genetics and Selection of Industrial Microorganisms, 1, 1st Dorozhny pr., Moscow, 113545, Russia
| | - E A Sizova
- All-Russia Research Institute of Beef Cattle Breeding, Russian Academy of Sciences, ul. Pionerskaya, Orenburg, 11, Russia.,Orenburg State University, Pobedy str., Orenburg, 13, Russia
| | - O L Kartashova
- Institute of Cellular and Intracellular Symbiosis, Russian Academy of Sciences, ul. Pionerskaya, Orenburg, 11, Russia
| | - A S Simbirtsev
- Research Institute of Highly Pure Biopreparations, Pudozhsakya str., St. Petersburg, 197110, Russia
| | - E A Rogozhin
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, ul. Miklukho-Maklaya, 16, Orenburg, /10, Russia.,Gause Institute of New Antibiotics, ul. Bolshaya Pirogovskaya, Moscow, 11, Russia
| | - G K Duskaev
- All-Russia Research Institute of Beef Cattle Breeding, Russian Academy of Sciences, ul. Pionerskaya, Orenburg, 11, Russia
| | - M V Sycheva
- Institute of Cellular and Intracellular Symbiosis, Russian Academy of Sciences, ul. Pionerskaya, Orenburg, 11, Russia.,Orenburg State Agrarian University, ul. Chelyuskintsev, Orenburg, 18, Russia
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57
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Kłodzińska SN, Molchanova N, Franzyk H, Hansen PR, Damborg P, Nielsen HM. Biopolymer nanogels improve antibacterial activity and safety profile of a novel lysine-based α-peptide/β-peptoid peptidomimetic. Eur J Pharm Biopharm 2018; 128:1-9. [DOI: 10.1016/j.ejpb.2018.03.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Revised: 03/23/2018] [Accepted: 03/28/2018] [Indexed: 12/25/2022]
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58
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Yang M, Zhang C, Zhang MZ, Zhang S. Beta-defensin derived cationic antimicrobial peptides with potent killing activity against gram negative and gram positive bacteria. BMC Microbiol 2018; 18:54. [PMID: 29871599 PMCID: PMC5989455 DOI: 10.1186/s12866-018-1190-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 05/18/2018] [Indexed: 11/23/2022] Open
Abstract
Background Avian β-defensins (AvBD) are cationic antimicrobial peptides (CAMP) with broad-spectrum antimicrobial activity, chemotactic property, and low host cytotoxicity. However, their bactericidal activity is greatly compromised under physiological salt concentrations which limits the use of these peptides as therapeutic agents. The length and the complex structure involving three conserved disulfide bridges are additional drawbacks associated with high production cost. In the present study, short linear CAMPs (11 to 25 a.a. residues) were developed based on the key functional components of AvBDs with additional modifications. Their biological functions were characterized. Results CAMP-t1 contained the CCR2 binding domain (N-terminal loop and adjacent α-helix) of AvBD-12 whereas CAMP-t2 comprised the key a.a. residues responsible for the concentrated positive surface charge and hydrophobicity of AvBD-6. Both CAMP-t1 and CAMP-t2 demonstrated strong antimicrobial activity against Pseudomonas aeruginosa, Staphylococcus aureus and Staphylococcus pseudintermedius. However, CAMP-t1 failed to show chemotactic activity and CAMP-t2, although superior in killing Staphylococcus spp., remained sensitive to salts. Using an integrated design approach, CAMP-t2 was further modified to yield CAMP-A and CAMP-B which possessed the following characteristics: α-helical structure with positively and negatively charged residues aligned on the opposite side of the helix, lack of protease cutting sites, C-terminal poly-Trp tail, N-terminal acetylation, and C-terminal amidation. Both CAMP-A and CAMP-B demonstrated strong antimicrobial activity against multidrug-resistant P. aeruginosa and methicillin-resistant S. pseudintermedius (MRSP) strains. These peptides were resistant to major proteases and fully active at physiological concentrations of NaCl and CaCl2. The peptides were minimally cytotoxic to avian and murine cells and their therapeutic index was moderate (≥ 4.5). Conclusions An integrated design approach can be used to develop short and potent antimicrobial peptides, such as CAMP-A and CAMP-B. The advantageous characteristics, including structural simplicity, resistance to salts and proteases, potent antimicrobial activity, rapid membrane attacking mode, and moderate therapeutic index, suggest that CAMP-A and CAMP-B are excellent candidates for development as therapeutic agents against multidrug-resistant P. aeruginosa and methicillin-resistant staphylococci.
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Affiliation(s)
- Ming Yang
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA
| | - Chunye Zhang
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA
| | - Michael Z Zhang
- Department of Biomedical Science, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA.,Veterinary Medical Diagnostic Laboratory, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA
| | - Shuping Zhang
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA. .,Veterinary Medical Diagnostic Laboratory, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA.
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59
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Optimisation of the antifungal potency of the amidated peptide H-Orn-Orn-Trp-Trp-NH2 against food contaminants. Int J Food Microbiol 2018; 265:40-48. [DOI: 10.1016/j.ijfoodmicro.2017.10.024] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 09/03/2017] [Accepted: 10/20/2017] [Indexed: 12/19/2022]
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60
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Baxter AA, Lay FT, Poon IKH, Kvansakul M, Hulett MD. Tumor cell membrane-targeting cationic antimicrobial peptides: novel insights into mechanisms of action and therapeutic prospects. Cell Mol Life Sci 2017; 74:3809-3825. [PMID: 28770291 PMCID: PMC11107634 DOI: 10.1007/s00018-017-2604-z] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 07/18/2017] [Accepted: 07/28/2017] [Indexed: 12/26/2022]
Abstract
There is an ongoing need for effective and targeted cancer treatments that can overcome the detrimental side effects presented by current treatment options. One class of novel anticancer molecules with therapeutic potential currently under investigation are cationic antimicrobial peptides (CAPs). CAPs are small innate immunity peptides found ubiquitously throughout nature that are typically membrane-active against a wide range of pathogenic microbes. A number of CAPs can also target mammalian cells and often display selective activity towards tumor cells, making them attractive candidates as novel anticancer agents warranting further investigation. This current and comprehensive review describes key examples of naturally occurring membrane-targeting CAPs and their modified derivatives that have demonstrated anticancer activity, across multiple species of origin and structural subfamilies. In addition, we address recent advances made in the field and the ongoing challenges faced in translating experimental findings into clinically relevant treatments.
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Affiliation(s)
- Amy A Baxter
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia.
| | - Fung T Lay
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Ivan K H Poon
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Marc Kvansakul
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Mark D Hulett
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
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Park OJ, Kim J, Ahn KB, Lee JY, Park YJ, Kum KY, Yun CH, Han SH. A 15-amino acid C-terminal peptide of beta-defensin-3 inhibits bone resorption by inhibiting the osteoclast differentiation and disrupting podosome belt formation. J Mol Med (Berl) 2017; 95:1315-1325. [DOI: 10.1007/s00109-017-1589-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 08/22/2017] [Accepted: 08/29/2017] [Indexed: 02/05/2023]
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62
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Valeur E, Guéret SM, Adihou H, Gopalakrishnan R, Lemurell M, Waldmann H, Grossmann TN, Plowright AT. New Modalities for Challenging Targets in Drug Discovery. Angew Chem Int Ed Engl 2017; 56:10294-10323. [PMID: 28186380 DOI: 10.1002/anie.201611914] [Citation(s) in RCA: 246] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 01/31/2017] [Indexed: 12/11/2022]
Abstract
Our ever-increasing understanding of biological systems is providing a range of exciting novel biological targets, whose modulation may enable novel therapeutic options for many diseases. These targets include protein-protein and protein-nucleic acid interactions, which are, however, often refractory to classical small-molecule approaches. Other types of molecules, or modalities, are therefore required to address these targets, which has led several academic research groups and pharmaceutical companies to increasingly use the concept of so-called "new modalities". This Review defines for the first time the scope of this term, which includes novel peptidic scaffolds, oligonucleotides, hybrids, molecular conjugates, as well as new uses of classical small molecules. We provide the most representative examples of these modalities to target large binding surface areas such as those found in protein-protein interactions and for biological processes at the center of cell regulation.
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Affiliation(s)
- Eric Valeur
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal, 431 83, Sweden
| | - Stéphanie M Guéret
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal, 431 83, Sweden.,AstraZeneca MPI Satellite Unit, Abteilung Chemische Biologie, Max Planck Institut für Molekulare Physiologie, Dortmund, Germany
| | - Hélène Adihou
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal, 431 83, Sweden.,AstraZeneca MPI Satellite Unit, Abteilung Chemische Biologie, Max Planck Institut für Molekulare Physiologie, Dortmund, Germany
| | - Ranganath Gopalakrishnan
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal, 431 83, Sweden.,AstraZeneca MPI Satellite Unit, Abteilung Chemische Biologie, Max Planck Institut für Molekulare Physiologie, Dortmund, Germany
| | - Malin Lemurell
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal, 431 83, Sweden
| | - Herbert Waldmann
- Abteilung Chemische Biologie, Max Planck Institut für Molekulare Physiologie, Dortmund, Germany.,Fakultät für Chemie und Chemische Biologie, Technische Universität Dortmund, Germany
| | - Tom N Grossmann
- Chemical Genomics Centre of the Max Planck Society, Dortmund, Germany.,Department of Chemistry & Pharmaceutical Sciences, VU University Amsterdam, The Netherlands
| | - Alleyn T Plowright
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, Mölndal, 431 83, Sweden
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63
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Valeur E, Guéret SM, Adihou H, Gopalakrishnan R, Lemurell M, Waldmann H, Grossmann TN, Plowright AT. Neue Modalitäten für schwierige Zielstrukturen in der Wirkstoffentwicklung. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611914] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Eric Valeur
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 431 83 Schweden
| | - Stéphanie M. Guéret
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 431 83 Schweden
- AstraZeneca MPI Satellite Unit; Abteilung Chemische Biologie; Max-Planck-Institut für Molekulare Physiologie; Dortmund Deutschland
| | - Hélène Adihou
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 431 83 Schweden
- AstraZeneca MPI Satellite Unit; Abteilung Chemische Biologie; Max-Planck-Institut für Molekulare Physiologie; Dortmund Deutschland
| | - Ranganath Gopalakrishnan
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 431 83 Schweden
- AstraZeneca MPI Satellite Unit; Abteilung Chemische Biologie; Max-Planck-Institut für Molekulare Physiologie; Dortmund Deutschland
| | - Malin Lemurell
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 431 83 Schweden
| | - Herbert Waldmann
- Abteilung Chemische Biologie; Max-Planck-Institut für Molekulare Physiologie; Dortmund Deutschland
- Fakultät für Chemie and Chemische Biologie; Technische Universität Dortmund; Deutschland
| | - Tom N. Grossmann
- Chemical Genomics Centre der Max-Planck-Gesellschaft; Dortmund Deutschland
- Department of Chemistry & Pharmaceutical Sciences; VU University Amsterdam; Niederlande
| | - Alleyn T. Plowright
- Cardiovascular and Metabolic Diseases; Innovative Medicines and Early Development Biotech Unit; AstraZeneca; Pepparedsleden 1 Mölndal 431 83 Schweden
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Koistinen H, Wallén E, Ylikangas H, Meinander K, Lahtela-Kakkonen M, Närvänen A, Stenman UH. Development of molecules stimulating the activity of KLK3 - an update. Biol Chem 2017; 397:1229-1235. [PMID: 27383882 DOI: 10.1515/hsz-2016-0189] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 06/30/2016] [Indexed: 01/03/2023]
Abstract
Kallikrein-related peptidase-3 (KLK3, known also as prostate-specific antigen, PSA) is highly expressed in the prostate. KLK3 possess antiangiogenic activity, which we have found to be related to its proteolytic activity. Thus, it may be possible to slow down the growth of prostatic tumors by enhancing this activity. We have developed peptides that enhance the proteolytic activity of KLK3. As these peptides are degraded in circulation and rapidly excreted, we have started to modify them and have succeeded in creating bioactive and more stable pseudopeptides. We have also identified small molecules stimulating the activity of KLK3, especially in synergy with peptides.
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Omar R, Yadav A. A mechanistic study of anti-HIV activities of antifungal peptides. CAN J CHEM 2017. [DOI: 10.1139/cjc-2017-0046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
HIV patients are constantly at risk of developing internal fungal infection and are thus regularly prescribed antifungal medications. Several classes of antifungal agents have been developed to combat ever increasing cases of resistant strains of fungi. Azoles, despite being the most popular clinical choice, are not devoid of side effects. Many antimicrobial peptides have also been tested in search of safe, nontoxic antifungals but none succeeded as a commercial alternative. Recent research attempts show continued interest in these compounds and the complexities associated. Some experimental observations indicate involvement of these antimicrobial peptides in enhancing the efficacy of anti-HIV agents. We present here an intertwined approach to deal with two fatal diseases, internal fungal infection and HIV infection. Several naturally occurring antimicrobial peptides have been studied for their possible interaction with the viral RNA primer binding site (template) through interactions other than the base pair – base pair type. Peptides have been prepared and docked into viral template utilizing extra precision, flexible ligand docking. Implicit solvent was added around the complex and MMGBSA interaction energies were computed. Druggability aspects were explored by calculating ADME-related properties. A peptidomimetic compound has been strategically designed to introduce some druggability features in the peptide maintaining its viral template inhibition capability. The designed peptidomimetic lead compound may help in obtaining nontoxic anti-HIV agents in the future. This is the first study to suggest a plausible explanation for the anti-HIV activity of antifungal peptides at the molecular level and corroborate experimental findings of synergistic effects of these peptides on anti-HIV agents.
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Affiliation(s)
- Ruchi Omar
- Department of Chemistry, University Institute of Engineering and Technology, Chhatrapati Shahuji Maharaj University, Kanpur 208024, India
- Department of Chemistry, University Institute of Engineering and Technology, Chhatrapati Shahuji Maharaj University, Kanpur 208024, India
| | - Arpita Yadav
- Department of Chemistry, University Institute of Engineering and Technology, Chhatrapati Shahuji Maharaj University, Kanpur 208024, India
- Department of Chemistry, University Institute of Engineering and Technology, Chhatrapati Shahuji Maharaj University, Kanpur 208024, India
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66
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Dias SA, Freire JM, Pérez-Peinado C, Domingues MM, Gaspar D, Vale N, Gomes P, Andreu D, Henriques ST, Castanho MARB, Veiga AS. New Potent Membrane-Targeting Antibacterial Peptides from Viral Capsid Proteins. Front Microbiol 2017; 8:775. [PMID: 28522994 PMCID: PMC5415599 DOI: 10.3389/fmicb.2017.00775] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 04/18/2017] [Indexed: 12/02/2022] Open
Abstract
The increasing prevalence of multidrug-resistant bacteria urges the development of new antibacterial agents. With a broad spectrum activity, antimicrobial peptides have been considered potential antibacterial drug leads. Using bioinformatic tools we have previously shown that viral structural proteins are a rich source for new bioactive peptide sequences, namely antimicrobial and cell-penetrating peptides. Here, we test the efficacy and mechanism of action of the most promising peptides among those previously identified against both Gram-positive and Gram-negative bacteria. Two cell-penetrating peptides, vCPP 0769 and vCPP 2319, have high antibacterial activity against Staphylococcus aureus, MRSA, Escherichia coli, and Pseudomonas aeruginosa, being thus multifunctional. The antibacterial mechanism of action of the two most active viral protein-derived peptides, vAMP 059 and vCPP 2319, was studied in detail. Both peptides act on both Gram-positive S. aureus and Gram-negative P. aeruginosa, with bacterial cell death occurring within minutes. Also, these peptides cause bacterial membrane permeabilization and damage of the bacterial envelope of P. aeruginosa cells. Overall, the results show that structural viral proteins are an abundant source for membrane-active peptides sequences with strong antibacterial properties.
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Affiliation(s)
- Susana A Dias
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de LisboaLisbon, Portugal
| | - João M Freire
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de LisboaLisbon, Portugal.,Department of Virology, Institut PasteurParis, France
| | - Clara Pérez-Peinado
- Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona Biomedical Research ParkBarcelona, Spain
| | - Marco M Domingues
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de LisboaLisbon, Portugal
| | - Diana Gaspar
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de LisboaLisbon, Portugal
| | - Nuno Vale
- UCIBIO-REQUIMTE, Faculdade de Farmácia, Universidade do PortoPorto, Portugal
| | - Paula Gomes
- LAQV-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do PortoPorto, Portugal
| | - David Andreu
- Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona Biomedical Research ParkBarcelona, Spain
| | - Sónia T Henriques
- Institute for Molecular Bioscience, The University of Queensland, BrisbaneQLD, Australia
| | - Miguel A R B Castanho
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de LisboaLisbon, Portugal
| | - Ana S Veiga
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de LisboaLisbon, Portugal
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Bacalum M, Janosi L, Zorila F, Tepes AM, Ionescu C, Bogdan E, Hadade N, Craciun L, Grosu I, Turcu I, Radu M. Modulating short tryptophan- and arginine-rich peptides activity by substitution with histidine. Biochim Biophys Acta Gen Subj 2017; 1861:1844-1854. [PMID: 28372989 DOI: 10.1016/j.bbagen.2017.03.024] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 03/06/2017] [Accepted: 03/31/2017] [Indexed: 12/21/2022]
Abstract
BACKGROUND High antimicrobial efficacy of short tryptophan-and arginine-rich peptides makes them good candidates in the fight against pathogens. Substitution of tryptophan and arginine by histidine could be used to modulate the peptides efficacy by optimizing their structures. METHODS The peptide (RRWWRWWRR), reported to showed good antimicrobial efficacy, was used as template, seven new analogs being designed substituting tryptophan or arginine with histidine. The peptides' efficacy was tested against E. coli, B. subtilis and S. aureus. The cytotoxicity and hemolytic effect were evaluated and the therapeutic index was inferred for each peptide. Atomic force microscopy and molecular simulation were used to analyze the effects of peptides on bacterial membrane. RESULTS The substitution of tryptophan by histidine proved to strongly modulate the antimicrobial activity, mainly by changing the peptide-to-membrane binding energy. The substitution of arginine has low effect on the antimicrobial efficacy. The presence of histidine residue reduced the cytotoxic and hemolytic activity of the peptides in some cases maintaining the same efficacy against bacteria. The peptides' antimicrobial activity was correlated to the 3D-hydrophobic moment and to a simple structure-based packing parameter. CONCLUSION The results show that some of these peptides have the potential to become good candidates to fight against bacteria. The substitution by histidine proved to fine tune the therapeutic index allowing the optimization of the peptide structure mainly by changing its binding energy and 3D-hydrophobic moment. GENERAL SIGNIFICANCE The short tryptophan reach peptides therapeutic index can be maximized using the histidine substitution to optimize their structure.
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Affiliation(s)
- Mihaela Bacalum
- Department of Life and Environmental Physics, Horia Hulubei National Institute for Physics and Nuclear Engineering, Reactorului 30, PO Box MG-6, Măgurele 077125, Romania
| | - Lorant Janosi
- Molecular and Biomolecular Physics Department, National Institute for Research and Development of Isotopic and Molecular Technologies, 65-103 Donath Street, 400293 Cluj-Napoca, Romania
| | - Florina Zorila
- Multipurpose Irradiation Facility Center, Horia Hulubei National Institute for Physics and Nuclear Engineering, Reactorului 30, PO Box MG-6, Măgurele 077125, Romania
| | - Ana-Maria Tepes
- Babeş-Bolyai University, Supramolecular Organic and Organometallic Chemistry Center (SOOMCC), Cluj-Napoca, 11 Arany Janos Street, 400028 Cluj-Napoca, Romania
| | - Cristina Ionescu
- Applied Nuclear Physics Department, Horia Hulubei National Institute for Physics and Nuclear Engineering, Reactorului 30, PO Box MG-6, Măgurele 077125, Romania
| | - Elena Bogdan
- Babeş-Bolyai University, Supramolecular Organic and Organometallic Chemistry Center (SOOMCC), Cluj-Napoca, 11 Arany Janos Street, 400028 Cluj-Napoca, Romania
| | - Niculina Hadade
- Babeş-Bolyai University, Supramolecular Organic and Organometallic Chemistry Center (SOOMCC), Cluj-Napoca, 11 Arany Janos Street, 400028 Cluj-Napoca, Romania
| | - Liviu Craciun
- Applied Nuclear Physics Department, Horia Hulubei National Institute for Physics and Nuclear Engineering, Reactorului 30, PO Box MG-6, Măgurele 077125, Romania
| | - Ion Grosu
- Babeş-Bolyai University, Supramolecular Organic and Organometallic Chemistry Center (SOOMCC), Cluj-Napoca, 11 Arany Janos Street, 400028 Cluj-Napoca, Romania
| | - Ioan Turcu
- Molecular and Biomolecular Physics Department, National Institute for Research and Development of Isotopic and Molecular Technologies, 65-103 Donath Street, 400293 Cluj-Napoca, Romania.
| | - Mihai Radu
- Department of Life and Environmental Physics, Horia Hulubei National Institute for Physics and Nuclear Engineering, Reactorului 30, PO Box MG-6, Măgurele 077125, Romania.
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Hacker DE, Hoinka J, Iqbal ES, Przytycka TM, Hartman MCT. Highly Constrained Bicyclic Scaffolds for the Discovery of Protease-Stable Peptides via mRNA Display. ACS Chem Biol 2017; 12:795-804. [PMID: 28146347 DOI: 10.1021/acschembio.6b01006] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Highly constrained peptides such as the knotted peptide natural products are promising medicinal agents because of their impressive biostability and potent activity. Yet, libraries of highly constrained peptides are challenging to prepare. Here, we present a method which utilizes two robust, orthogonal chemical steps to create highly constrained bicyclic peptide libraries. This technology was optimized to be compatible with in vitro selections by mRNA display. We performed side-by-side monocyclic and bicyclic selections against a model protein (streptavidin). Both selections resulted in peptides with mid-nanomolar affinity, and the bicyclic selection yielded a peptide with remarkable protease resistance.
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Affiliation(s)
- David E. Hacker
- Virginia Commonwealth University, Department of Chemistry, 1001 West Main Street, Richmond, Virginia 23284-2006, United States
- National Center for Biotechnology Information, 8600 Rockville Pike, Bethesda, Maryland 20894, United States
| | - Jan Hoinka
- Virginia Commonwealth University, Department of Chemistry, 1001 West Main Street, Richmond, Virginia 23284-2006, United States
- National Center for Biotechnology Information, 8600 Rockville Pike, Bethesda, Maryland 20894, United States
| | - Emil S. Iqbal
- Virginia Commonwealth University, Department of Chemistry, 1001 West Main Street, Richmond, Virginia 23284-2006, United States
- National Center for Biotechnology Information, 8600 Rockville Pike, Bethesda, Maryland 20894, United States
| | - Teresa M. Przytycka
- Virginia Commonwealth University, Department of Chemistry, 1001 West Main Street, Richmond, Virginia 23284-2006, United States
- National Center for Biotechnology Information, 8600 Rockville Pike, Bethesda, Maryland 20894, United States
| | - Matthew C. T. Hartman
- Virginia Commonwealth University, Department of Chemistry, 1001 West Main Street, Richmond, Virginia 23284-2006, United States
- National Center for Biotechnology Information, 8600 Rockville Pike, Bethesda, Maryland 20894, United States
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Cruz J, Flórez J, Torres R, Urquiza M, Gutiérrez JA, Guzmán F, Ortiz CC. Antimicrobial activity of a new synthetic peptide loaded in polylactic acid or poly(lactic-co-glycolic) acid nanoparticles against Pseudomonas aeruginosa, Escherichia coli O157:H7 and methicillin resistant Staphylococcus aureus (MRSA). NANOTECHNOLOGY 2017; 28:135102. [PMID: 28266350 DOI: 10.1088/1361-6528/aa5f63] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Nanocarrier systems are currently being developed for peptide, protein and gene delivery to protect them in the blood circulation and in the gastrointestinal tract. Polylactic acid (PLA) and poly(lactic-co-glycolic) acid (PLGA) nanoparticles loaded with a new antimicrobial GIBIM-P5S9K peptide were obtained by the double emulsion solvent extraction/evaporation method. PLA- and PLGA-NPs were spherical with sizes between 300 and 400 nm for PLA and 200 and 300 nm for PLGA and <0.3 polydispersity index as determined by dynamic light scattering and scanning electron microscopy), having the zeta potential of >20 mV. The peptide-loading efficiency of PLA-NP and PLGA-NPs was 75% and 55%, respectively. PLA- and PLGA-NPs released around 50% of this peptide over 8 h. In 10% human sera the size of peptide loaded PLA- and PLGA-NPs increased between 25.2% and 39.3%, the PDI changed from 3.2 to 5.1 and the surface charge from -7.15 to 14.6 mV. Both peptide loaded PLA- and PLGA-NPs at 0.5 μM peptide concentration inhibited the growth of Escherichia coli O157:H7 (E. coli O157:H7), methicillin-resistant Staphylococcus aureus (MRSA) and Pseudomonas. aeruginosa (P. aeruginosa). In contrast, free peptide inhibited at 10 μM but did not inhibit at 0.5 and 1 μM. These PLA- and PLGA-NPs presented <10% hemolysis indicating that they are hemocompatible and promising for delivery and protection system of GIBIM-P5S9K peptide.
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Affiliation(s)
- J Cruz
- Escuela de Química, Facultad de Ciencias, Universidad Industrial de Santander, Cra 27 # calle 9 (CP680002) Bucaramanga, Colombia. Departamento de Química, Universidad Nacional de Colombia, Cra 30 # 45-03, 111321 Bogotá, Colombia
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70
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Amano Y, Umezawa N, Sato S, Watanabe H, Umehara T, Higuchi T. Activation of lysine-specific demethylase 1 inhibitor peptide by redox-controlled cleavage of a traceless linker. Bioorg Med Chem 2017; 25:1227-1234. [DOI: 10.1016/j.bmc.2016.12.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 12/20/2016] [Accepted: 12/21/2016] [Indexed: 12/21/2022]
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71
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An efficient liquid chromatography-high resolution mass spectrometry approach for the optimization of the metabolic stability of therapeutic peptides. Anal Bioanal Chem 2017; 409:2685-2696. [DOI: 10.1007/s00216-017-0213-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 01/09/2017] [Accepted: 01/16/2017] [Indexed: 11/25/2022]
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72
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Massonnet P, Haler JRN, Upert G, Degueldre M, Morsa D, Smargiasso N, Mourier G, Gilles N, Quinton L, De Pauw E. Ion Mobility-Mass Spectrometry as a Tool for the Structural Characterization of Peptides Bearing Intramolecular Disulfide Bond(s). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1637-1646. [PMID: 27488317 DOI: 10.1007/s13361-016-1443-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 06/19/2016] [Accepted: 06/24/2016] [Indexed: 06/06/2023]
Abstract
Disulfide bonds are post-translationnal modifications that can be crucial for the stability and the biological activities of natural peptides. Considering the importance of these disulfide bond-containing peptides, the development of new techniques in order to characterize these modifications is of great interest. For this purpose, collision cross cections (CCS) of a large data set of 118 peptides (displaying various sequences) bearing zero, one, two, or three disulfide bond(s) have been measured in this study at different charge states using ion mobility-mass spectrometry. From an experimental point of view, CCS differences (ΔCCS) between peptides bearing various numbers of disulfide bonds and peptides having no disulfide bonds have been calculated. The ΔCCS calculations have also been applied to peptides bearing two disulfide bonds but different cysteine connectivities (Cys1-Cys2/Cys3-Cys4; Cys1-Cys3/Cys2-Cys4; Cys1-Cys4/Cys2-Cys3). The effect of the replacement of a proton by a potassium adduct on a peptidic structure has also been investigated. Graphical Abstract ᅟ.
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Affiliation(s)
- Philippe Massonnet
- Laboratory of Mass Spectrometry, University of Liege, Quartier Agora, Allée du six Aout 11, B-4000, Liege, Belgium
| | - Jean R N Haler
- Laboratory of Mass Spectrometry, University of Liege, Quartier Agora, Allée du six Aout 11, B-4000, Liege, Belgium
| | - Gregory Upert
- Commissariat à l'Energie Atomique, DRF/iBiTec-S/SIMOPRO, CE Saclay, 91191, Gif-sur-Yvette, France
| | - Michel Degueldre
- Laboratory of Mass Spectrometry, University of Liege, Quartier Agora, Allée du six Aout 11, B-4000, Liege, Belgium
| | - Denis Morsa
- Laboratory of Mass Spectrometry, University of Liege, Quartier Agora, Allée du six Aout 11, B-4000, Liege, Belgium
| | - Nicolas Smargiasso
- Laboratory of Mass Spectrometry, University of Liege, Quartier Agora, Allée du six Aout 11, B-4000, Liege, Belgium
| | - Gilles Mourier
- Commissariat à l'Energie Atomique, DRF/iBiTec-S/SIMOPRO, CE Saclay, 91191, Gif-sur-Yvette, France
| | - Nicolas Gilles
- Commissariat à l'Energie Atomique, DRF/iBiTec-S/SIMOPRO, CE Saclay, 91191, Gif-sur-Yvette, France
| | - Loïc Quinton
- Laboratory of Mass Spectrometry, University of Liege, Quartier Agora, Allée du six Aout 11, B-4000, Liege, Belgium
| | - Edwin De Pauw
- Laboratory of Mass Spectrometry, University of Liege, Quartier Agora, Allée du six Aout 11, B-4000, Liege, Belgium.
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Topical delivery of low-cost protein drug candidates made in chloroplasts for biofilm disruption and uptake by oral epithelial cells. Biomaterials 2016; 105:156-166. [PMID: 27521618 DOI: 10.1016/j.biomaterials.2016.07.042] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 07/27/2016] [Accepted: 07/31/2016] [Indexed: 11/20/2022]
Abstract
Protein drugs (PD) are minimally utilized in dental medicine due to high cost and invasive surgical delivery. There is limited clinical advancement in disrupting virulent oral biofilms, despite their high prevalence in causing dental caries. Poor efficacy of antimicrobials following topical treatments or to penetrate and disrupt formed biofilms is a major challenge. We report an exciting low-cost approach using plant-made antimicrobial peptides (PMAMPs) retrocyclin or protegrin with complex secondary structures (cyclic/hairpin) for topical use to control biofilms. The PMAMPs rapidly killed the pathogen Streptococcus mutans and impaired biofilm formation following a single topical application of tooth-mimetic surface. Furthermore, we developed a synergistic approach using PMAMPs combined with matrix-degrading enzymes to facilitate their access into biofilms and kill the embedded bacteria. In addition, we identified a novel role for PMAMPs in delivering drugs to periodontal and gingival cells, 13-48 folds more efficiently than any other tested cell penetrating peptides. Therefore, PDs fused with protegrin expressed in plant cells could potentially play a dual role in delivering therapeutic proteins to gum tissues while killing pathogenic bacteria when delivered as topical oral formulations or in chewing gums. Recent FDA approval of plant-produced PDs augurs well for clinical advancement of this novel concept.
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74
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Yang H, Li S, Li F, Xiang J. Structure and Bioactivity of a Modified Peptide Derived from the LPS-Binding Domain of an Anti-Lipopolysaccharide Factor (ALF) of Shrimp. Mar Drugs 2016; 14:md14050096. [PMID: 27213409 PMCID: PMC4882570 DOI: 10.3390/md14050096] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 05/09/2016] [Accepted: 05/10/2016] [Indexed: 01/29/2023] Open
Abstract
The lipopolysaccharide binding domain (LBD) in anti-lipopolysaccharide factor (ALF) is the main functional element of ALF, which exhibits antimicrobial activities. Our previous studies show that the peptide LBDv, synthesized based on the modified sequence of LBD (named LBD2) from FcALF2, exhibited an apparently enhanced antimicrobial activity. To learn the prospect of LBDv application, the characteristics of LBDv were analyzed in the present study. The LBDv peptide showed higher antimicrobial and bactericidal activities compared with LBD2. These activities of the LBDv peptide were stable after heat treatment. LBDv could also exhibit in vivo antimicrobial activity to Vibrio harveyi. The LBDv peptide was found to bind bacteria, quickly cause bacterial agglutination, and kill bacteria by damaging their membrane integrity. Structure analysis showed that both LBDv and LBD2 held the β-sheet structure, and the positive net charge and amphipathicity characteristic were speculated as two important components for their antimicrobial activity. The cytotoxicity of LBDv was evaluated in cultured Spodoptera frugiperda (Sf9) cells and Cherax quadricarinatus hemocytes. More than 80% cells could survive with the LBDv concentration up to 16 μM. Collectively, these findings highlighted the potential antimicrobial mechanism of LBD peptides, and provided important information for the commercial use of LBDv in the future.
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Affiliation(s)
- Hui Yang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Shihao Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
| | - Fuhua Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
| | - Jianhai Xiang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
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Gottschalk S, Ingmer H, Thomsen LE. The lysine-peptoid hybrid LP5 maintain activity under physiological conditions and affects virulence gene expression in Staphylococcus aureus. Peptides 2016; 78:24-9. [PMID: 26851701 DOI: 10.1016/j.peptides.2016.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 02/01/2016] [Accepted: 02/01/2016] [Indexed: 01/26/2023]
Abstract
The antimicrobial peptide, LP5, is a lysine-peptoid hybrid, with antimicrobial activity against clinically relevant bacteria. Here, we investigated how various environmental conditions affect the antimicrobial activity of LP5 against Staphylococcus aureus (S. aureus). We found that LP5 maintained activity under host physiological conditions of NaCl, MgCl2 and pH. However, when exposed to serum, LP5 lost activity. Furthermore, when increasing NaCl concentration and lowering pH, the peptide showed reduces activity. When investigating the tolerance mechanisms of S. aureus toward antimicrobial peptides, we found that LP5 was protease resistant. However, the dltA and vraF genes, involved in reducing the net anionic charge of the bacterial cell envelope and sensing of antimicrobial peptides, respectively, played a role in the tolerance of S. aureus against LP5. In addition, the exposure of S. aureus to sub-inhibitory concentrations of LP5 affected the expression of the major virulence factors of S. aureus, revealing a potential as anti-virulence compound. Thus, these results show how environmental factors affect the peptide efficiency and further add to the knowledge on how the peptide affects S. aureus, which is crucial information for designing new peptides for optimizing antimicrobial therapy.
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Affiliation(s)
- Sanne Gottschalk
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-1870 Frederiksberg, Denmark.
| | - Hanne Ingmer
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-1870 Frederiksberg, Denmark.
| | - Line E Thomsen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-1870 Frederiksberg, Denmark.
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76
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Ravensdale J, Wood F, O'Brien F, Gregg K. Investigations into methods to improve the antibacterial activity of Acticoat. J Med Microbiol 2016; 65:397-405. [PMID: 26944631 DOI: 10.1099/jmm.0.000246] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Multiple studies have shown that the antibacterial dressing Acticoat can inhibit growth of bacteria but is unable to completely clear a wound of infection, which could leave patients vulnerable to sepsis. Agar inoculated with four different Staphylococcus aureus strains and overlain with Acticoat showed growth inhibition beneath and within a 1 mm perimeter of the dressing after 24 h. When lifted from inoculated agar and briefly blotted onto fresh agar plates, Acticoat transferred viable bacteria. Scanning electron microscopy of the surface of Acticoat that overlaid meticillin-resistant S. aureus for 24, 48 and 72 h showed dense clusters of apparently undamaged bacteria distributed across the mesh. The number of bacteria growing on inoculated pig skin, underneath and on the surface of Acticoat, was lower than on controls for the first 8 h, but after 24 h the number of bacteria on the skin was 2.3-fold greater than the untreated controls. In contrast, after 24 h the number of bacteria surviving on the surface of the Acticoat was 11.9 % of controls. Acticoat moistened with 10 % glycerol plus antimicrobial peptides (AMPs) mel12-26 or bac8c (50 μg ml- 1) reduced the numbers of bacteria on the dressing and on the skin underneath to below 10 % and 0.01 % of the controls, respectively. When lysozyme (1 mg ml- 1) was added to Acticoat wetted with glycerol and the AMP bac8c, the dressing was able to prevent the survival of bacteria on densely inoculated pig skin and on the surface of Acticoat for up to 24 h. In effect, biocompatible solvents and AMPs significantly enhance the bactericidal efficacy of Acticoat.
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Affiliation(s)
- Joshua Ravensdale
- School of Biomedical Sciences, Curtin University, Perth,Western Australia,Australia
| | - Fiona Wood
- Fiona Wood Foundation, Fiona Stanley Hospital, Murdoch,Western Australia,Australia
| | - Francis O'Brien
- School of Biomedical Sciences, Curtin University, Perth,Western Australia,Australia
| | - Keith Gregg
- School of Biomedical Sciences, Curtin University, Perth,Western Australia,Australia
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Gour S, Kaushik V, Kumar V, Bhat P, Yadav SC, Yadav JK. Antimicrobial peptide (Cn-AMP2) from liquid endosperm ofCocos nuciferaforms amyloid-like fibrillar structure. J Pept Sci 2016; 22:201-7. [DOI: 10.1002/psc.2860] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 12/15/2015] [Accepted: 01/04/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Shalini Gour
- Department of Biotechnology; Central University of Rajasthan; Bandersindri NH-8 Jaipur-Ajmer Highway, Dist. Ajmer 305 801 Rajasthan India
| | - Vibha Kaushik
- Department of Biotechnology; Central University of Rajasthan; Bandersindri NH-8 Jaipur-Ajmer Highway, Dist. Ajmer 305 801 Rajasthan India
| | - Vijay Kumar
- Department of Biotechnology; Central University of Rajasthan; Bandersindri NH-8 Jaipur-Ajmer Highway, Dist. Ajmer 305 801 Rajasthan India
| | - Priyanka Bhat
- Department of Biotechnology; Central University of Rajasthan; Bandersindri NH-8 Jaipur-Ajmer Highway, Dist. Ajmer 305 801 Rajasthan India
| | - Subhash C. Yadav
- Department of Anatomy; All India Institute of Medical Sciences; New Delhi -110029 India
| | - Jay K. Yadav
- Department of Biotechnology; Central University of Rajasthan; Bandersindri NH-8 Jaipur-Ajmer Highway, Dist. Ajmer 305 801 Rajasthan India
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Nguyen LT, Chau JK, Zaat SAJ, Vogel HJ. Cyclic Tritrpticin Analogs with Distinct Biological Activities. Probiotics Antimicrob Proteins 2016; 3:132-43. [PMID: 26781579 DOI: 10.1007/s12602-011-9067-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Tritrpticin is a Trp-, Arg-, and Pro-rich cathelicidin peptide with promising antimicrobial activity. Cyclic analogs of tritrpticin were designed using two different approaches: circularization of the backbone by a head-to-tail peptide bond (TritrpCyc) or disulfide bridging between two Cys residues introduced at the termini of the peptide (TritrpDisu). Compared to the parent peptide, TritrpCyc has greatly improved therapeutic potential, showing stronger bactericidal activities and diminished hemolytic activity. Unexpectedly, the opposite effect was observed for TritrpDisu, which has lost its antimicrobial activity and is very hemolytic. In a membrane mimetic environment, NMR spectra show that TritrpDisu adopts an amphipathic turn-turn structure similar to linear tritrpticin. The structure of membrane-bound TritrpCyc has some similarity to that of TritrpDisu; however, the lipid interactions were not sufficient to restrain the structure of the former peptide in a single well-defined conformation. To help explain the distinct biological properties of the analogs, experiments investigating alternative antimicrobial targets were pursued: the membrane bilayer, lipopolysaccharides, and DNA. Although the hemolytic activity of TritrpDisu can be explained by the peptide's ability to induce higher leakage from the model mammalian membranes, TritrpCyc and TritrpDisu show no significant differences in these functional assays. Overall, our studies show that TritrpCyc holds great promise as a candidate for further development toward antimicrobial therapy.
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Affiliation(s)
- Leonard T Nguyen
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, Alberta, Canada
| | - Johnny K Chau
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, Alberta, Canada
| | - Sebastian A J Zaat
- Department of Medical Microbiology, Centre for Infection and Immunity Amsterdam, Academic Medical Center, Amsterdam, The Netherlands
| | - Hans J Vogel
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, Alberta, Canada.
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79
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Shagaghi N, Palombo EA, Clayton AHA, Bhave M. Archetypal tryptophan-rich antimicrobial peptides: properties and applications. World J Microbiol Biotechnol 2016; 32:31. [PMID: 26748808 DOI: 10.1007/s11274-015-1986-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Accepted: 11/25/2015] [Indexed: 12/17/2022]
Abstract
Drug-resistant microorganisms ('superbugs') present a serious challenge to the success of antimicrobial treatments. Subsequently, there is a crucial need for novel bio-control agents. Many antimicrobial peptides (AMPs) show a broad-spectrum activity against bacteria, fungi or viruses and are strong candidates to complement or substitute current antimicrobial agents. Some AMPs are also effective against protozoa or cancer cells. The tryptophan (Trp)-rich peptides (TRPs) are a subset of AMPs that display potent antimicrobial activity, credited to the unique biochemical properties of tryptophan that allow it to insert into biological membranes. Further, many Trp-rich AMPs cross bacterial membranes without compromising their integrity and act intracellularly, suggesting interactions with nucleic acids and enzymes. In this work, we overview some archetypal TRPs derived from natural sources, i.e., indolicidin, tritrpticin and lactoferricin, summarising their biochemical properties, structures, antimicrobial activities, mechanistic studies and potential applications.
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Affiliation(s)
- Nadin Shagaghi
- Faculty of Science, Engineering and Technology, Swinburne University of Technology, PO Box 218, Hawthorn, VIC, 3122, Australia
| | - Enzo A Palombo
- Faculty of Science, Engineering and Technology, Swinburne University of Technology, PO Box 218, Hawthorn, VIC, 3122, Australia
| | - Andrew H A Clayton
- Faculty of Science, Engineering and Technology, Swinburne University of Technology, PO Box 218, Hawthorn, VIC, 3122, Australia
| | - Mrinal Bhave
- Faculty of Science, Engineering and Technology, Swinburne University of Technology, PO Box 218, Hawthorn, VIC, 3122, Australia.
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80
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Gottschalk S, Gottlieb CT, Vestergaard M, Hansen PR, Gram L, Ingmer H, Thomsen LE. Amphibian antimicrobial peptide fallaxin analogue FL9 affects virulence gene expression and DNA replication in Staphylococcus aureus. J Med Microbiol 2015; 64:1504-1513. [DOI: 10.1099/jmm.0.000177] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Sanne Gottschalk
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-1870 Frederiksberg, Denmark
| | - Caroline T. Gottlieb
- National Institute of Aquatic Resources, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Martin Vestergaard
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-1870 Frederiksberg, Denmark
| | - Paul R. Hansen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Lone Gram
- Department of Systems Biology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Hanne Ingmer
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-1870 Frederiksberg, Denmark
| | - Line E. Thomsen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-1870 Frederiksberg, Denmark
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81
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Inhibitory Effects of Antimicrobial Peptides on Lipopolysaccharide-Induced Inflammation. Mediators Inflamm 2015; 2015:167572. [PMID: 26612970 PMCID: PMC4647054 DOI: 10.1155/2015/167572] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 08/17/2015] [Accepted: 08/25/2015] [Indexed: 01/08/2023] Open
Abstract
Antimicrobial peptides (AMPs) are usually small molecule peptides, which display broad-spectrum antimicrobial activity, high efficiency, and stability. For the multiple-antibiotic-resistant strains, AMPs play a significant role in the development of novel antibiotics because of their broad-spectrum antimicrobial activities and specific antimicrobial mechanism. Besides broad-spectrum antibacterial activity, AMPs also have anti-inflammatory activity. The neutralization of lipopolysaccharides (LPS) plays a key role in anti-inflammatory action of AMPs. On the one hand, AMPs can readily penetrate the cell wall barrier by neutralizing LPS to remove Gram-negative bacteria that can lead to infection. On the contrary, AMPs can also inhibit the production of biological inflammatory cytokines to reduce the inflammatory response through neutralizing circulating LPS. In addition, AMPs also modulate the host immune system by chemotaxis of leukocytes, to promote immune cell proliferation, epithelialization, and angiogenesis and thus play a protective role. This review summarizes some recent researches about anti-inflammatory AMPs, with a focus on the interaction of AMPs and LPS on the past decade.
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82
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Wang J, Liu HB, Tong Z, Ha CS. Fluorescent/luminescent detection of natural amino acids by organometallic systems. Coord Chem Rev 2015. [DOI: 10.1016/j.ccr.2015.05.008] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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83
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Van Hove AH, Benoit DSW. Depot-Based Delivery Systems for Pro-Angiogenic Peptides: A Review. Front Bioeng Biotechnol 2015; 3:102. [PMID: 26236708 PMCID: PMC4504170 DOI: 10.3389/fbioe.2015.00102] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Accepted: 06/29/2015] [Indexed: 01/13/2023] Open
Abstract
Insufficient vascularization currently limits the size and complexity for all tissue engineering approaches. Additionally, increasing or re-initiating blood flow is the first step toward restoration of ischemic tissue homeostasis. However, no FDA-approved pro-angiogenic treatments exist, despite the many pre-clinical approaches that have been developed. The relatively small size of peptides gives advantages over protein-based treatments, specifically with respect to synthesis and stability. While many pro-angiogenic peptides have been identified and shown promising results in vitro and in vivo, the majority of biomaterials developed for pro-angiogenic drug delivery focus on protein delivery. This narrow focus limits pro-angiogenic therapeutics as peptides, similar to proteins, suffer from poor pharmacokinetics in vivo, necessitating the development of controlled release systems. This review discusses pro-angiogenic peptides and the biomaterials delivery systems that have been developed, or that could easily be adapted for peptide delivery, with a particular focus on depot-based delivery systems.
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Affiliation(s)
- Amy H. Van Hove
- Department of Biomedical Engineering, University of Rochester, Rochester, NY, USA
| | - Danielle S. W. Benoit
- Department of Biomedical Engineering, University of Rochester, Rochester, NY, USA
- Department of Chemical Engineering, University of Rochester, Rochester, NY, USA
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY, USA
- Department of Orthopaedics, Center for Musculoskeletal Research, University of Rochester Medical Center, Rochester, NY, USA
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84
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Peptides and Peptidomimetics for Antimicrobial Drug Design. Pharmaceuticals (Basel) 2015; 8:366-415. [PMID: 26184232 PMCID: PMC4588174 DOI: 10.3390/ph8030366] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 05/27/2015] [Accepted: 06/17/2015] [Indexed: 12/21/2022] Open
Abstract
The purpose of this paper is to introduce and highlight a few classes of traditional antimicrobial peptides with a focus on structure-activity relationship studies. After first dissecting the important physiochemical properties that influence the antimicrobial and toxic properties of antimicrobial peptides, the contributions of individual amino acids with respect to the peptides antibacterial properties are presented. A brief discussion of the mechanisms of action of different antimicrobials as well as the development of bacterial resistance towards antimicrobial peptides follows. Finally, current efforts on novel design strategies and peptidomimetics are introduced to illustrate the importance of antimicrobial peptide research in the development of future antibiotics.
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85
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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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86
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Duffy FJ, Devocelle M, Shields DC. Computational approaches to developing short cyclic peptide modulators of protein-protein interactions. Methods Mol Biol 2015; 1268:241-71. [PMID: 25555728 DOI: 10.1007/978-1-4939-2285-7_11] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Cyclic peptides are a promising class of bioactive molecules potentially capable of modulating "difficult" targets, such as protein-protein interactions. Cyclic peptides have long been used as therapeutics derived from natural product derivatives, but remain an underexplored class of compounds from the perspective of rational drug design, possibly due to the known weaknesses of peptide drugs in general. While cyclic peptides are non"druglike" by the accepted empirical rules, their unique structure may lend itself to both membrane permeability and proteolytic resistance-the main barriers to oral delivery. The constrained shape of cyclic peptides also lends itself better to virtual screening approaches, and new tools and successes in this area have been recently noted. An increasing number of strategies are available, both to generate and screen cyclic peptide libraries, and best practises and current successes are described within. This chapter will describe various computational strategies for virtual screening cyclic peptides, along with known implementations and applications. We will explore the generation and screening of diverse combinatorial virtual libraries, incorporating a range of cyclization strategies and structural modifications. More advanced approaches covered include evolutionary algorithms designed to aid in screening large structural libraries, machine learning approaches, and harnessing bioinformatics resources to bias cyclic peptide virtual libraries towards known bioactive structures.
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Affiliation(s)
- Fergal J Duffy
- School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
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87
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Ong ZY, Wiradharma N, Yang YY. Strategies employed in the design and optimization of synthetic antimicrobial peptide amphiphiles with enhanced therapeutic potentials. Adv Drug Deliv Rev 2014; 78:28-45. [PMID: 25453271 DOI: 10.1016/j.addr.2014.10.013] [Citation(s) in RCA: 207] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Revised: 10/13/2014] [Accepted: 10/15/2014] [Indexed: 12/30/2022]
Abstract
Antimicrobial peptides (AMPs) which predominantly act via membrane active mechanisms have emerged as an exciting class of antimicrobial agents with tremendous potential to overcome the global epidemic of antibiotics-resistant infections. The first generation of AMPs derived from natural sources as diverse as plants, insects and humans has provided a wealth of compositional and structural information to design novel synthetic AMPs with enhanced antimicrobial potencies and selectivities, reduced cost of production due to shorter sequences and improved stabilities under physiological conditions. In this review, we will first discuss the common strategies employed in the design and optimization of synthetic AMPs, followed by highlighting the various approaches utilized to enhance the therapeutic potentials of designed AMPs under physiological conditions. Lastly, future perspectives on the development of improved AMPs for therapeutic applications will be presented.
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88
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Kang SJ, Park SJ, Mishig-Ochir T, Lee BJ. Antimicrobial peptides: therapeutic potentials. Expert Rev Anti Infect Ther 2014; 12:1477-86. [DOI: 10.1586/14787210.2014.976613] [Citation(s) in RCA: 135] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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89
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Singh A, Dirain ML, Wilczynski A, Chen C, Gosnell BA, Levine AS, Edison AS, Haskell-Luevano C. Synthesis, biophysical, and pharmacological evaluation of the melanocortin agonist AST3-88: modifications of peptide backbone at Trp 7 position lead to a potent, selective, and stable ligand of the melanocortin 4 receptor (MC4R). ACS Chem Neurosci 2014; 5:1020-31. [PMID: 25141170 PMCID: PMC4198065 DOI: 10.1021/cn5000953] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
![]()
The
melanocortin-3 (MC3R) and melanocortin-4 (MC4R) receptors are
expressed in the brain and are implicated in the regulation of food
intake and energy homeostasis. The endogenous agonist ligands for
these receptors (α-, β-, γ-MSH and ACTH) are linear
peptides with limited receptor subtype selectivity and metabolic stability,
thus minimizing their use as probes to characterize the overlapping
pharmacological and physiological functions of the melanocortin receptor
subtypes. In the present study, an engineered template, in which the
peptide backbone was modified by a heterocyclic reverse turn mimetic
at the Trp7 residue, was synthesized using solid phase
peptide synthesis and characterized by a β-galactosidase cAMP
based reporter gene assay. The functional assay identified a ∼5
nM mouse MC4R agonist (AST3-88) with more than 50-fold selectivity
over the mMC3R. Biophysical studies (2D 1H NMR spectroscopy
and molecular dynamics) of AST3-88 identified a type VIII β-turn
secondary structure spanning the pharmacophore domain stabilized by
the intramolecular interactions between the side chains of the His
and Trp residues. Enzymatic studies of AST3-88 revealed enhanced stability
of AST3-88 over the α-MSH endogenous peptide in rat serum. Upon
central administration of AST3-88 into rats, a decreased food intake
response was observed. This is the first study to probe the in vivo
physiological activity of this engineered peptide-heterocycle template.
These findings advance the present knowledge of pharmacophore design
for potent, selective, and metabolically stable melanocortin ligands.
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Affiliation(s)
- Anamika Singh
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | | | | | | | | | | | | | - Carrie Haskell-Luevano
- Department
of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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90
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Blum AP, Kammeyer JK, Yin J, Crystal DT, Rush AM, Gilson MK, Gianneschi NC. Peptides displayed as high density brush polymers resist proteolysis and retain bioactivity. J Am Chem Soc 2014; 136:15422-37. [PMID: 25314576 PMCID: PMC4227725 DOI: 10.1021/ja5088216] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We describe a strategy for rendering peptides resistant to proteolysis by formulating them as high-density brush polymers. The utility of this approach is demonstrated by polymerizing well-established cell-penetrating peptides (CPPs) and showing that the resulting polymers are not only resistant to proteolysis but also maintain their ability to enter cells. The scope of this design concept is explored by studying the proteolytic resistance of brush polymers composed of peptides that are substrates for either thrombin or a metalloprotease. Finally, we demonstrate that the proteolytic susceptibility of peptide brush polymers can be tuned by adjusting the density of the polymer brush and offer in silico models to rationalize this finding. We contend that this strategy offers a plausible method of preparing peptides for in vivo use, where rapid digestion by proteases has traditionally restricted their utility.
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Affiliation(s)
- Angela P Blum
- Department of Chemistry & Biochemistry, ‡Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego , La Jolla, California 92093, United States
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91
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Effect of a synthetic indolicidin analogue on lipid peroxidation in thermal burns. Bull Exp Biol Med 2014; 157:447-9. [PMID: 25110080 DOI: 10.1007/s10517-014-2587-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Indexed: 10/24/2022]
Abstract
Experimental simulation of burn was followed by accumulation of LPO products and suppression of antioxidant enzyme activity in the burn wound. Application of a synthetic analogue of indolicidin led to an increase in MDA and acylhydroperoxide concentrations in the burn wound on experimental day 1. Further application of the peptide in a dose of 100 mg/kg had no significant effect on the studied parameters, while the peptide in a dose of 500 mg/kg was followed by a decrease in the level of LPO products on days 10 and 14. Changes in antioxidant enzyme activities in rats treated with 500 mg/kg indolicidin analogue had a two-phase pattern: an increase on day 4 was followed by a decrease.
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92
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Antimicrobial peptides. Pharmaceuticals (Basel) 2013; 6:1543-75. [PMID: 24287494 PMCID: PMC3873676 DOI: 10.3390/ph6121543] [Citation(s) in RCA: 835] [Impact Index Per Article: 75.9] [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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93
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Murugan RN, Jacob B, Ahn M, Hwang E, Sohn H, Park HN, Lee E, Seo JH, Cheong C, Nam KY, Hyun JK, Jeong KW, Kim Y, Shin SY, Bang JK. De novo design and synthesis of ultra-short peptidomimetic antibiotics having dual antimicrobial and anti-inflammatory activities. PLoS One 2013; 8:e80025. [PMID: 24302996 PMCID: PMC3841161 DOI: 10.1371/journal.pone.0080025] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 09/27/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Much attention has been focused on the design and synthesis of potent, cationic antimicrobial peptides (AMPs) that possess both antimicrobial and anti-inflammatory activities. However, their development into therapeutic agents has been limited mainly due to their large size (12 to 50 residues in length) and poor protease stability. METHODOLOGY/PRINCIPAL FINDINGS In an attempt to overcome the issues described above, a set of ultra-short, His-derived antimicrobial peptides (HDAMPs) has been developed for the first time. Through systematic tuning of pendant hydrophobic alkyl tails at the N(π)- and N(τ)-positions on His, and the positive charge of Arg, much higher prokaryotic selectivity was achieved, compared to human AMP LL-37. Additionally, the most potent HDAMPs showed promising dual antimicrobial and anti-inflammatory activities, as well as anti-methicillin-resistant Staphylococcus aureus (MRSA) activity and proteolytic resistance. Our results from transmission electron microscopy, membrane depolarization, confocal laser-scanning microscopy, and calcein-dye leakage experiments propose that HDAMP-1 kills microbial cells via dissipation of the membrane potential by forming pore/ion channels on bacterial cell membranes. CONCLUSION/SIGNIFICANCE The combination of the ultra-short size, high-prokaryotic selectivity, potent anti-MRSA activity, anti-inflammatory activity, and proteolytic resistance of the designed HDAMP-1, -3, -5, and -6 makes these molecules promising candidates for future antimicrobial therapeutics.
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Affiliation(s)
- Ravichandran N. Murugan
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chung-Buk, Republic of Korea
| | - Binu Jacob
- Department of Bio-Materials, Graduate School and Department of Cellular & Molecular Medicine, School of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Mija Ahn
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chung-Buk, Republic of Korea
| | - Eunha Hwang
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chung-Buk, Republic of Korea
| | - Hoik Sohn
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas, United States of America
| | - Hyo-Nam Park
- Division of Electron Microscopic Research, Korea Basic Science Institute, Daejeon, Republic of Korea
| | - Eunjung Lee
- Department of Bioscience and Biotechnology, Institute of SMART Biotechnology, Konkuk University, Seoul, Republic of Korea
| | - Ji-Hyung Seo
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chung-Buk, Republic of Korea
| | - Chaejoon Cheong
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chung-Buk, Republic of Korea
| | - Ky-Youb Nam
- Bioinformatics and Molecular Design Research Center, Yonsei University Research Complex, Seoul, Republic of Korea
| | - Jae-Kyung Hyun
- Division of Electron Microscopic Research, Korea Basic Science Institute, Daejeon, Republic of Korea
| | - Ki-Woong Jeong
- Department of Bioscience and Biotechnology, Institute of SMART Biotechnology, Konkuk University, Seoul, Republic of Korea
| | - Yangmee Kim
- Department of Bioscience and Biotechnology, Institute of SMART Biotechnology, Konkuk University, Seoul, Republic of Korea
| | - Song Yub Shin
- Department of Bio-Materials, Graduate School and Department of Cellular & Molecular Medicine, School of Medicine, Chosun University, Gwangju, Republic of Korea
- * E-mail: (JKB); (SYS)
| | - Jeong Kyu Bang
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, Chung-Buk, Republic of Korea
- * E-mail: (JKB); (SYS)
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94
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Góngora-Benítez M, Tulla-Puche J, Albericio F. Multifaceted Roles of Disulfide Bonds. Peptides as Therapeutics. Chem Rev 2013; 114:901-26. [DOI: 10.1021/cr400031z] [Citation(s) in RCA: 388] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Miriam Góngora-Benítez
- Institute
for Research in Biomedicine (IRB Barcelona), Barcelona, 08028 Spain
- CIBER-BBN, Barcelona Science
Park, Barcelona, 08028 Spain
| | - Judit Tulla-Puche
- Institute
for Research in Biomedicine (IRB Barcelona), Barcelona, 08028 Spain
- CIBER-BBN, Barcelona Science
Park, Barcelona, 08028 Spain
| | - Fernando Albericio
- Institute
for Research in Biomedicine (IRB Barcelona), Barcelona, 08028 Spain
- CIBER-BBN, Barcelona Science
Park, Barcelona, 08028 Spain
- Department
of Organic Chemistry, University of Barcelona, Barcelona, 08028 Spain
- School of Chemistry & Physics, University of KwaZulu-Natal, 4001 Durban, South Africa
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95
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Template-constrained macrocyclic peptides prepared from native, unprotected precursors. Proc Natl Acad Sci U S A 2013; 110:E3753-60. [PMID: 24043790 DOI: 10.1073/pnas.1311706110] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Peptide-protein interactions are important mediators of cellular-signaling events. Consensus binding motifs (also known as short linear motifs) within these contacts underpin molecular recognition, yet have poor pharmacological properties as discrete species. Here, we present methods to transform intact peptides into stable, templated macrocycles. Two simple steps install the template. The key reaction is a palladium-catalyzed macrocyclization. The catalysis has broad scope and efficiently forms large rings by engaging native peptide functionality including phenols, imidazoles, amines, and carboxylic acids without the necessity of protecting groups. The tunable reactivity of the template gives the process special utility. Defined changes in reaction conditions markedly alter chemoselectivity. In all cases examined, cyclization occurs rapidly and in high yield at room temperature, regardless of peptide composition or chain length. We show that conformational restraints imparted by the template stabilize secondary structure and enhance proteolytic stability in vitro. Palladium-catalyzed internal cinnamylation is a strong complement to existing methods for peptide modification.
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96
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De novo generation of short antimicrobial peptides with enhanced stability and cell specificity. J Antimicrob Chemother 2013; 69:121-32. [DOI: 10.1093/jac/dkt322] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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97
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Antimicrobial peptides: versatile biological properties. INTERNATIONAL JOURNAL OF PEPTIDES 2013; 2013:675391. [PMID: 23935642 PMCID: PMC3710626 DOI: 10.1155/2013/675391] [Citation(s) in RCA: 144] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 06/04/2013] [Accepted: 06/09/2013] [Indexed: 01/08/2023]
Abstract
Antimicrobial peptides are diverse group of biologically active molecules with multidimensional properties. In recent past, a wide variety of AMPs with diverse structures have been reported from different sources such as plants, animals, mammals, and microorganisms. The presence of unusual amino acids and structural motifs in AMPs confers unique structural properties to the peptide that attribute for their specific mode of action. The ability of these active AMPs to act as multifunctional effector molecules such as signalling molecule, immune modulators, mitogen, antitumor, and contraceptive agent makes it an interesting candidate to study every aspect of their structural and biological properties for prophylactic and therapeutic applications. In addition, easy cloning and recombinant expression of AMPs in heterologous plant host systems provided a pipeline for production of disease resistant transgenic plants. Besides these properties, AMPs were also used as drug delivery vectors to deliver cell impermeable drugs to cell interior. The present review focuses on the diversity and broad spectrum antimicrobial activity of AMPs along with its multidimensional properties that could be exploited for the application of these bioactive peptides as a potential and promising drug candidate in pharmaceutical industries.
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98
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Tadokoro T, Kazama H, Koga Y, Takano K, Kanaya S. Investigating the Structural Dependence of Protein Stabilization by Amino Acid Substitution. Biochemistry 2013; 52:2839-47. [DOI: 10.1021/bi400076f] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Takashi Tadokoro
- Department of Material and Life
Science, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hirotaka Kazama
- Department of Material and Life
Science, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yuichi Koga
- Department of Material and Life
Science, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kazufumi Takano
- Department of Material and Life
Science, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- Department of Biomolecular Chemistry, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo,
Sakyo-ku, Kyoto 606-8522, Japan
| | - Shigenori Kanaya
- Department of Material and Life
Science, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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Xi D, Teng D, Wang X, Mao R, Yang Y, Xiang W, Wang J. Design, expression and characterization of the hybrid antimicrobial peptide LHP7, connected by a flexible linker, against Staphylococcus and Streptococcus. Process Biochem 2013. [DOI: 10.1016/j.procbio.2013.01.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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100
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Human cathelicidin LL-37 prevents bacterial biofilm formation. Future Med Chem 2012; 4:1587-99. [PMID: 22917247 DOI: 10.4155/fmc.12.97] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Human pathogens often colonize their host by the formation of biofilms. These surface-attached aggregates of bacteria are characterized by a self-produced extracellular matrix, which makes them highly resistant towards antibiotic treatment. Their abilities to adhere to abiotic surfaces (e.g., catheters and other medical devices) also makes bacterial biofilm formation a challenge in modern medicine. Antimicrobial peptides have lately been introduced as a potential class of drug molecules for combating severe hospital-acquired infections. One of these peptides, human cathelicidin LL-37, has recently been demonstrated to bridge innate and adaptive host defence, in addition to facilitating a robust antibiofilm effect at sub-inhibitory concentrations. In this review we will discuss the evidence, potential and challenges for LL-37 as a candidate molecule for therapeutic use.
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