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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) | Viewed by 37354

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Prof. Dr. Irene Izzo

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Dipartimento di Chimica e Biologia "A. Zambelli", Università degli Studi,di Salerno, 84084 Fisciano (SA), Italy
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

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Keywords

natural products
peptides
depsipeptides
macrocyclization
therapeutic agents
bionanomaterials

Published Papers (7 papers)

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Research

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14 pages, 2454 KiB

Open AccessArticle

Effects of Different Cultivation Parameters on the Production of Surfactin Variants by a Bacillus subtilis Strain

by Attila Bartal, Aruna Vigneshwari, Bettina Bóka, Mónika Vörös, István Takács, László Kredics, László Manczinger, Mónika Varga, Csaba Vágvölgyi and András Szekeres

Molecules 2018, 23(10), 2675; https://doi.org/10.3390/molecules23102675 - 18 Oct 2018

Cited by 27 | Viewed by 4953

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 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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17 pages, 1601 KiB

Open AccessArticle

Application of HPCCC Combined with Polymeric Resins and HPLC for the Separation of Cyclic Lipopeptides Muscotoxins A–C and Their Antimicrobial Activity

by José Cheel, Jan Hájek, Marek Kuzma, Kumar Saurav, Iva Smýkalová, Eliška Ondráčková, Petra Urajová, Dai Long Vu, Karine Faure, Jiří Kopecký and Pavel Hrouzek

Molecules 2018, 23(10), 2653; https://doi.org/10.3390/molecules23102653 - 16 Oct 2018

Cited by 13 | Viewed by 3302

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 (1–3), 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 2–3 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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17 pages, 5097 KiB

Open AccessArticle

Phosphate-Catalyzed Succinimide Formation from an NGR-Containing Cyclic Peptide: A Novel Mechanism for Deammoniation of the Tetrahedral Intermediate

by Ryota Kirikoshi, Noriyoshi Manabe and Ohgi Takahashi

Molecules 2018, 23(9), 2217; https://doi.org/10.3390/molecules23092217 - 31 Aug 2018

Cited by 5 | Viewed by 3619

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 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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16 pages, 2952 KiB

Open AccessArticle

Cyclic Octamer Peptoids: Simplified Isosters of Bioactive Fungal Cyclodepsipeptides

by Assunta D’Amato, Giorgio Della Sala, Irene Izzo, Chiara Costabile, Yuichi Masuda and Francesco De Riccardis

Molecules 2018, 23(7), 1779; https://doi.org/10.3390/molecules23071779 - 19 Jul 2018

Cited by 8 | Viewed by 3722

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, 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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11 pages, 1550 KiB

Open AccessArticle

Identification of Peptides in Flowers of Sambucus nigra with Antimicrobial Activity against Aquaculture Pathogens

by Claudio Andrés Álvarez, Andrés Barriga, Fernando Albericio, María Soledad Romero and Fanny Guzmán

Molecules 2018, 23(5), 1033; https://doi.org/10.3390/molecules23051033 - 27 Apr 2018

Cited by 20 | Viewed by 5605

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, 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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15 pages, 2415 KiB

Open AccessFeature PaperArticle

Chemical Synthesis and Functional Analysis of VarvA Cyclotide

by Claudio A. Álvarez, Paula A. Santana, Omar Luna, Constanza Cárdenas, Fernando Albericio, María S. Romero and Fanny Guzmán

Molecules 2018, 23(4), 952; https://doi.org/10.3390/molecules23040952 - 19 Apr 2018

Cited by 8 | Viewed by 4021

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 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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19 pages, 2117 KiB

Open AccessFeature PaperReview

Natural Cyclic Peptides as an Attractive Modality for Therapeutics: A Mini Review

by Muna Ali Abdalla and Lyndy J. McGaw

Molecules 2018, 23(8), 2080; https://doi.org/10.3390/molecules23082080 - 20 Aug 2018

Cited by 92 | Viewed by 11301

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 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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