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Special Issue "Cyclic Peptides"

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Bioorganic Chemistry".

Deadline for manuscript submissions: closed (31 July 2018)

Special Issue Editor

Guest Editor
Prof. Irene Izzo

Dipartimento di Chimica e Biologia "A. Zambelli", Università degli Studi,di Salerno, 84084 Fisciano (SA), Italy
Website | E-Mail
Interests: organic synthesis; asymmetric synthesis; marine natural products; peptido mimetics; peptides; cyclopeptoids

Special Issue Information

Dear Colleagues,

In recent decades, considerable efforts have been devoted to the isolation, characterization and synthesis of peptide macrocycles. Natural compounds and synthetic analogues have found applications that range from therapeutics to bionanomaterials. This is due to their functional and structural properties, good bioavailability and enzymatic stability, when compared to their linear counterparts. From a therapeutic point of view, though cyclopeptides show a wide range of biological activities (anti-cancer, cytotoxic, antimicrobial, anthelmintic, anti-HIV and anti-insecticidal), to date few mechanisms of action and molecular receptors are known. This explains the growing interest of academia and pharmaceutical companies for peptide-based macrocycles. Considering that isolation from natural sources is expensive and time consuming, synthetic organic chemistry plays a crucial role for the preparation of these macrocyclic targets. However, the presence of unusual amino acids, heterocyclic building blocks and ester linkages still represent a challenge for synthetic chemists (as much as the macrocyclization step itself). The present Special Issue is aimed at covering recent isolated cyclopeptides, new synthetic strategies, as well as novel applications in different areas of this intriguing class of compounds, being that the research on macrocycles is promising, exciting and still underexplored.

Prof. Irene  Izzo
Guest Editor

Manuscript Submission Information

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Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • natural products
  • peptides
  • depsipeptides
  • macrocyclization
  • therapeutic agents
  • bionanomaterials

Published Papers (7 papers)

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Research

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Open AccessArticle Effects of Different Cultivation Parameters on the Production of Surfactin Variants by a Bacillus subtilis Strain
Molecules 2018, 23(10), 2675; https://doi.org/10.3390/molecules23102675
Received: 11 September 2018 / Revised: 16 October 2018 / Accepted: 17 October 2018 / Published: 18 October 2018
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Abstract
Surfactins are lipopeptide-type biosurfactants produced mainly by Bacillus species, consisting of a peptide loop of seven amino acids and a hydrophobic fatty acid chain (C12–C16). These molecules have been proven to exhibit various biological activities; thus, their therapeutic and
[...] Read more.
Surfactins are lipopeptide-type biosurfactants produced mainly by Bacillus species, consisting of a peptide loop of seven amino acids and a hydrophobic fatty acid chain (C12–C16). These molecules have been proven to exhibit various biological activities; thus, their therapeutic and environmental applications are considered. Within the surfactin lipopeptide family, there is a wide spectrum of different homologues and isomers; to date, more than 30 variants have been described. Since the newest members of these lipopeptides were described recently, there is no information that is available on their characteristic features, e.g., the dependence of their production from different cultivation parameters. This study examined the effects of both the different carbon sources and various metal ions on the surfactin production of a selected B. subtilis strain. Among the applied carbon sources, fructose and xylose had the highest impacts on the ratio of the different variants, regarding both the peptide sequences and the lengths of the fatty acids. Furthermore, the application of metal ions Mn2+, Cu2+ and Ni2+ in the media completely changed the surfactin variant compositions of the fermenting broths leading to the appearance of methyl esterified surfactin forms, and resulted in the appearance of novel surfactin variants with fatty acid chains containing no more than 11 carbon atoms. Full article
(This article belongs to the Special Issue Cyclic Peptides)
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Open AccessArticle Application of HPCCC Combined with Polymeric Resins and HPLC for the Separation of Cyclic Lipopeptides Muscotoxins A–C and Their Antimicrobial Activity
Molecules 2018, 23(10), 2653; https://doi.org/10.3390/molecules23102653
Received: 20 July 2018 / Revised: 2 October 2018 / Accepted: 10 October 2018 / Published: 16 October 2018
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Abstract
Muscotoxins are cyanobacterial cyclic lipopeptides with potential applications in biomedicine and biotechnology. In this study, Desmonostoc muscorum CCALA125 strain extracts were enriched by polymeric resin treatment, and subjected to HPCCC affording three cyclic lipopeptides (13), which were further repurified
[...] Read more.
Muscotoxins are cyanobacterial cyclic lipopeptides with potential applications in biomedicine and biotechnology. In this study, Desmonostoc muscorum CCALA125 strain extracts were enriched by polymeric resin treatment, and subjected to HPCCC affording three cyclic lipopeptides (13), which were further repurified by semi-preparative HPLC, affording 1, 2, and 3, with a purity of 86%, 92%, and 90%, respectively. The chemical identities of 23 were determined as muscotoxins A and B, respectively, by comparison with previously reported ESI-HRMS/MS data, whereas 1 was determined as a novel muscotoxin variant (muscotoxin C) using NMR and ESI-HRMS/MS data. Owing to the high yield (50 mg), compound 2 was broadly screened for its antimicrobial potential exhibiting a strong antifungal activity against Alternaria alternata, Monographella cucumerina, and Aspergillus fumigatus, with minimum inhibitory concentration (MIC) values of 0.58, 2.34, and 2.34 µg/mL; respectively, and weak antibacterial activity against Bacillus subtilis with a MIC value of 37.5 µg/mL. Compounds 1 and 3 were tested only against the plant pathogenic fungus Sclerotinia sclerotiorum due to their low yield, displaying a moderate antifungal activity. The developed chromatographic method proved to be an efficient tool for obtaining muscotoxins with potent antifungal properties. Full article
(This article belongs to the Special Issue Cyclic Peptides)
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Open AccessArticle Phosphate-Catalyzed Succinimide Formation from an NGR-Containing Cyclic Peptide: A Novel Mechanism for Deammoniation of the Tetrahedral Intermediate
Molecules 2018, 23(9), 2217; https://doi.org/10.3390/molecules23092217
Received: 13 July 2018 / Revised: 15 August 2018 / Accepted: 30 August 2018 / Published: 31 August 2018
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Abstract
Spontaneous deamidation in the Asn-Gly-Arg (NGR) motif that yields an isoAsp-Gly-Arg (isoDGR) sequence has recently attracted considerable attention because of the possibility of application to dual tumor targeting. It is well known that Asn deamidation reactions in peptide chains occur
[...] Read more.
Spontaneous deamidation in the Asn-Gly-Arg (NGR) motif that yields an isoAsp-Gly-Arg (isoDGR) sequence has recently attracted considerable attention because of the possibility of application to dual tumor targeting. It is well known that Asn deamidation reactions in peptide chains occur via the five-membered ring succinimide intermediate. Recently, we computationally showed by the B3LYP density functional theory method, that inorganic phosphate and the Arg side chain can catalyze the NGR deamidation using a cyclic peptide, c[CH2CO–NGRC]–NH2. In this previous study, the tetrahedral intermediate of the succinimide formation was assumed to be readily protonated at the nitrogen originating from the Asn side chain by the solvent water before the release of an NH3 molecule. In the present study, we found a new mechanism for the decomposition of the tetrahedral intermediate that does not require the protonation by an external proton source. The computational method is the same as in the previous study. In the new mechanism, the release of an NH3 molecule occurs after a proton exchange between the peptide and the phosphate and conformational changes. The rate-determining step of the overall reaction course is the previously reported first step, i.e., the cyclization to form the tetrahedral intermediate. Full article
(This article belongs to the Special Issue Cyclic Peptides)
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Open AccessArticle Cyclic Octamer Peptoids: Simplified Isosters of Bioactive Fungal Cyclodepsipeptides
Molecules 2018, 23(7), 1779; https://doi.org/10.3390/molecules23071779
Received: 6 July 2018 / Revised: 13 July 2018 / Accepted: 14 July 2018 / Published: 19 July 2018
Cited by 1 | PDF Full-text (2952 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Cyclic peptoids have recently emerged as an important class of bioactive scaffolds with unique conformational properties and excellent metabolic stabilities. In this paper, we describe the design and synthesis of novel cyclic octamer peptoids as simplified isosters of mycotoxin depsipeptides bassianolide, verticilide A1,
[...] Read more.
Cyclic peptoids have recently emerged as an important class of bioactive scaffolds with unique conformational properties and excellent metabolic stabilities. In this paper, we describe the design and synthesis of novel cyclic octamer peptoids as simplified isosters of mycotoxin depsipeptides bassianolide, verticilide A1, PF1022A and PF1022B. We also examine their complexing abilities in the presence of sodium tetrakis[3,5-bis(trifluoromethyl)phenyl]borate (TFPB) salt and explore their general insecticidal activity. Finally, we discuss the possible relationship between structural features of free and Na+-complexed cyclic octamer peptoids and bioactivities in light of conformational isomerism, a crucial factor affecting cyclic peptoids’ biomimetic potentials. Full article
(This article belongs to the Special Issue Cyclic Peptides)
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Open AccessArticle Identification of Peptides in Flowers of Sambucus nigra with Antimicrobial Activity against Aquaculture Pathogens
Molecules 2018, 23(5), 1033; https://doi.org/10.3390/molecules23051033
Received: 27 March 2018 / Revised: 25 April 2018 / Accepted: 26 April 2018 / Published: 27 April 2018
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Abstract
The elder (Sambucus spp.) tree has a number of uses in traditional medicine. Previous studies have demonstrated the antimicrobial properties of elderberry liquid extract against human pathogenic bacteria and also influenza viruses. These properties have been mainly attributed to phenolic compounds. However,
[...] Read more.
The elder (Sambucus spp.) tree has a number of uses in traditional medicine. Previous studies have demonstrated the antimicrobial properties of elderberry liquid extract against human pathogenic bacteria and also influenza viruses. These properties have been mainly attributed to phenolic compounds. However, other plant defense molecules, such as antimicrobial peptides (AMPs), may be present. Here, we studied peptide extracts from flowers of Sambucus nigra L. The mass spectrometry analyses determined peptides of 3 to 3.6 kDa, among them, cysteine-rich peptides were identified with antimicrobial activity against various Gram-negative bacteria, including recurrent pathogens of Chilean aquaculture. In addition, membrane blebbing on the bacterial surface after exposure to the cyclotide was visualized by SEM microscopy and SYTOX Green permeabilization assay showed the ability to disrupt the bacterial membrane. We postulate that these peptides exert their action by destroying the bacterial membrane. Full article
(This article belongs to the Special Issue Cyclic Peptides)
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Open AccessFeature PaperArticle Chemical Synthesis and Functional Analysis of VarvA Cyclotide
Molecules 2018, 23(4), 952; https://doi.org/10.3390/molecules23040952
Received: 29 March 2018 / Revised: 14 April 2018 / Accepted: 17 April 2018 / Published: 19 April 2018
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Abstract
Cyclotides are circular peptides found in various plant families. A cyclized backbone, together with multiple disulfide bonds, confers the peptides’ exceptional stability against protease digestion and thermal denaturation. In addition, the features of these antimicrobial molecules make them suitable for use in animal
[...] Read more.
Cyclotides are circular peptides found in various plant families. A cyclized backbone, together with multiple disulfide bonds, confers the peptides’ exceptional stability against protease digestion and thermal denaturation. In addition, the features of these antimicrobial molecules make them suitable for use in animal farming, such as aquaculture. Fmoc solid phase peptide synthesis on 2-chlorotrityl chlorine (CTC) resin using the “tea-bag” approach was conducted to generate the VarvA cyclotide identified previously from Viola arvensis. MALDI-TOF mass spectrometry determined the correct peptide amino acid sequence and the cyclization sites-critical in this multicyclic compound. The cyclotide showed antimicrobial activity against various Gram-negative bacteria, including recurrent pathogens present in Chilean aquaculture. The highest antimicrobial activity was found to be against Flavobacterium psychrophilum. In addition, membrane blebbing on the bacterial surface after exposure to the cyclotide was visualized by SEM microscopy and the Sytox Green permeabilization assay showed the ability to disrupt the bacterial membrane. We postulate that this compound can be proposed for the control of fish farming infections. Full article
(This article belongs to the Special Issue Cyclic Peptides)
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Review

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Open AccessFeature PaperReview Natural Cyclic Peptides as an Attractive Modality for Therapeutics: A Mini Review
Molecules 2018, 23(8), 2080; https://doi.org/10.3390/molecules23082080
Received: 30 July 2018 / Revised: 14 August 2018 / Accepted: 19 August 2018 / Published: 20 August 2018
Cited by 1 | PDF Full-text (2117 KB) | HTML Full-text | XML Full-text
Abstract
Peptides are important biomolecules which facilitate the understanding of complex biological processes, which in turn could be serendipitous biological targets for future drugs. They are classified as a unique therapeutic niche and will play an important role as fascinating agents in the pharmaceutical
[...] Read more.
Peptides are important biomolecules which facilitate the understanding of complex biological processes, which in turn could be serendipitous biological targets for future drugs. They are classified as a unique therapeutic niche and will play an important role as fascinating agents in the pharmaceutical landscape. Until now, more than 40 cyclic peptide drugs are currently in the market, and approximately one new cyclopeptide drug enters the market annually on average. Interestingly, the majority of clinically approved cyclic peptides are derived from natural sources, such as peptide antibiotics and human peptide hormones. In this report, the importance of cyclic peptides is discussed, and their role in drug discovery as interesting therapeutic biomolecules will be highlighted. Recently isolated naturally occurring cyclic peptides from microorganisms, sponges, and other sources with a wide range of pharmacological properties are reviewed herein. Full article
(This article belongs to the Special Issue Cyclic Peptides)
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