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Design and Synthesis of Peptides: Impact on Current Biomedicine, Biotechnology, and Chemical Biology

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biology".

Deadline for manuscript submissions: closed (31 December 2021) | Viewed by 15910

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Special Issue Editors

Prof. Dr. Ernest Giralt

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Guest Editor

1. Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
2. Department of Organic Chemistry, University of Barcelona, 08028 Barcelona, Spain
Interests: peptide chemistry; protein chemistry; molecular recognition; brain delivery; conformational analysis; nuclear magnetic resonance

Dr. Macarena Sánchez-Navarro

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Guest Editor

Instituto de Parasitología y Biomedicina “López Neyra” IPBLN-CSIC, Granada, Spain
Interests: peptides; chemical modification of proteins; protein delivery; BBB-shuttle peptides

Special Issue Information

Dear Colleagues,

Peptide chemistry has remarkably evolved and matured, but despite the wide variety of synthetic methods available, there are still many challenges to overcome, such as the development of greener synthetic methodologies or cost-effective methods to produce large proteins.

Today, peptide chemistry allows the design and synthesis of a wide variety of peptides with high precision and efficacy, impacting many scientific and technical areas. In the current issue, we aim to present an updated overview of the main innovations in the design and synthesis of peptide molecules together with a wide variety of examples of peptide applications to answer questions or to solve problems related to the areas of biomedicine, biotechnology, or chemical biology, to name a few.

Prof. Dr. Ernest Giralt
Dr. Macarena Sánchez-Navarro
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

peptides
synthesis
solid-phase peptide synthesis
proteins
molecular recognition
protein–protein interactions
biomedicine
biotechnology
chemical biology

Published Papers (5 papers)

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Research

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12 pages, 1372 KiB

Open AccessArticle

Smaller, Stronger, More Stable: Peptide Variants of a SARS-CoV-2 Neutralizing Miniprotein

by Lucas Weißenborn, Elie Richel, Helena Hüseman, Julia Welzer, Silvan Beck, Simon Schäfer, Heinrich Sticht, Klaus Überla and Jutta Eichler

Int. J. Mol. Sci. 2022, 23(11), 6309; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23116309 - 04 Jun 2022

Cited by 9 | Viewed by 2643

Abstract

Based on the structure of a de novo designed miniprotein (LCB1) in complex with the receptor binding domain (RBD) of the SARS-CoV-2 spike protein, we have generated and characterized truncated peptide variants of LCB1, which present only two of the three LCB1 helices, and which fully retained the virus neutralizing potency against different SARS-CoV-2 variants of concern (VOC). This antiviral activity was even 10-fold stronger for a cyclic variant of the two-helix peptides, as compared to the full-length peptide. Furthermore, the proteolytic stability of the cyclic peptide was substantially improved, rendering it a better potential candidate for SARS-CoV-2 therapy. In a more mechanistic approach, the peptides also served as tools to dissect the role of individual mutations in the RBD for the susceptibility of the resulting virus variants to neutralization by the peptides. As the peptides reported here were generated through chemical synthesis, rather than recombinant protein expression, they are amenable to further chemical modification, including the incorporation of a wide range of non-proteinogenic amino acids, with the aim to further stabilize the peptides against proteolytic degradation, as well as to improve the strength, as well the breadth, of their virus neutralizing capacity. Full article

(This article belongs to the Special Issue Design and Synthesis of Peptides: Impact on Current Biomedicine, Biotechnology, and Chemical Biology)

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16 pages, 1056 KiB

Open AccessArticle

Peptides Bearing Multiple Post-Translational Modifications as Antigenic Targets for Severe Rheumatoid Arthritis Patients

by Cristina García-Moreno, María J. Gómara, Raúl Castellanos-Moreira, Raimon Sanmartí and Isabel Haro

Int. J. Mol. Sci. 2021, 22(24), 13290; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms222413290 - 10 Dec 2021

Cited by 4 | Viewed by 2561

Abstract

Rheumatoid arthritis (RA) is characterized by the presence of autoantibodies that are of paramount importance for the diagnosis and prognosis of the disease and have been implicated in its pathogenesis. Proteins resulting from post-translational modifications (PTMs) are capable of triggering autoimmune responses important for the development of RA. In this work, we investigate serum antibody reactivity in patients with an established RA against a panel of chimeric peptides derived from fibrin and filaggrin proteins and bearing from one to three PTMs (citrullination, carbamylation and acetylation) by home-designed ELISA tests (anti-AMPA autoantibodies). The role of anti-AMPAs as biomarkers linked to the presence of a more severe RA phenotype (erosive disease with radiological structural damage) and to the presence of interstitial lung disease (ILD), a severe extra-articular manifestation in RA patients entailing a high mortality, was also analyzed. In general, the association with the clinical phenotype of RA was confirmed with the different autoantibodies, and especially for IgA and IgM isotypes. The prevalence of severe joint damage was only statistically significant for the IgG isotype when working with the peptide bearing three PTMs. Furthermore, the median titers were significantly higher in patients with RA-ILD, a finding not observed for the IgG isotype when working with the single- and double-modified peptides. Full article

(This article belongs to the Special Issue Design and Synthesis of Peptides: Impact on Current Biomedicine, Biotechnology, and Chemical Biology)

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15 pages, 2280 KiB

Open AccessArticle

D-Amino Acid-Containing Lipopeptides Derived from the Lead Peptide BP100 with Activity against Plant Pathogens

by Àngel Oliveras, Luís Moll, Gerard Riesco-Llach, Arnau Tolosa-Canudas, Sergio Gil-Caballero, Esther Badosa, Anna Bonaterra, Emilio Montesinos, Marta Planas and Lidia Feliu

Int. J. Mol. Sci. 2021, 22(12), 6631; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22126631 - 21 Jun 2021

Cited by 10 | Viewed by 2511

Abstract

From a previous collection of lipopeptides derived from BP100, we selected 18 sequences in order to improve their biological profile. In particular, analogues containing a D-amino acid at position 4 were designed, prepared, and tested against plant pathogenic bacteria and fungi. The biological activity of these sequences was compared with that of the corresponding parent lipopeptides with all L-amino acids. In addition, the influence of the length of the hydrophobic chain on the biological activity was evaluated. Interestingly, the incorporation of a D-amino acid into lipopeptides bearing a butanoyl or a hexanoyl chain led to less hemolytic sequences and, in general, that were as active or more active than the corresponding all L-lipopeptides. The best lipopeptides were BP475 and BP485, both incorporating a D-Phe at position 4 and a butanoyl group, with MIC values between 0.8 and 6.2 µM, low hemolysis (0 and 24% at 250 µM, respectively), and low phytotoxicity. Characterization by NMR of the secondary structure of BP475 revealed that the D-Phe at position 4 disrupts the α-helix and that residues 6 to 10 are able to fold in an α-helix. This secondary structure would be responsible for the high antimicrobial activity and low hemolysis of this lipopeptide. Full article

(This article belongs to the Special Issue Design and Synthesis of Peptides: Impact on Current Biomedicine, Biotechnology, and Chemical Biology)

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Review

Jump to: Research

18 pages, 1802 KiB

Open AccessReview

The Importance of 6-Aminohexanoic Acid as a Hydrophobic, Flexible Structural Element

by Agnieszka Markowska, Adam Roman Markowski and Iwona Jarocka-Karpowicz

Int. J. Mol. Sci. 2021, 22(22), 12122; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms222212122 - 09 Nov 2021

Cited by 12 | Viewed by 3401

Abstract

6-aminohexanoic acid is an ω-amino acid with a hydrophobic, flexible structure. Although the ω-amino acid in question is mainly used clinically as an antifibrinolytic drug, other applications are also interesting and important. This synthetic lysine derivative, without an α-amino group, plays a significant role in chemical synthesis of modified peptides and in the polyamide synthetic fibers (nylon) industry. It is also often used as a linker in various biologically active structures. This review concentrates on the role of 6-aminohexanoic acid in the structure of various molecules. Full article

(This article belongs to the Special Issue Design and Synthesis of Peptides: Impact on Current Biomedicine, Biotechnology, and Chemical Biology)

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27 pages, 2183 KiB

Open AccessReview

Emerging Emulsifiers: Conceptual Basis for the Identification and Rational Design of Peptides with Surface Activity

by Fabian Ricardo, Diego Pradilla, Juan C. Cruz and Oscar Alvarez

Int. J. Mol. Sci. 2021, 22(9), 4615; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22094615 - 28 Apr 2021

Cited by 23 | Viewed by 3861

Abstract

Emulsifiers are gradually evolving from synthetic molecules of petrochemical origin to biomolecules mainly due to health and environmental concerns. Peptides represent a type of biomolecules whose molecular structure is composed of a sequence of amino acids that can be easily tailored to have specific properties. However, the lack of knowledge about emulsifier behavior, structure–performance relationships, and the implementation of different design routes have limited the application of these peptides. Some computational and experimental approaches have tried to close this knowledge gap, but restrictions in understanding the fundamental phenomena and the limited property data availability have made the performance prediction for emulsifier peptides an area of intensive research. This study provides the concepts necessary to understand the emulsifying behavior of peptides. Additionally, a straightforward description is given of how the molecular structure and conditions of the system directly impact the peptides’ ability to stabilize emulsion droplets. Moreover, the routes to design and discover novel peptides with interfacial and emulsifying activity are also discussed, along with the strategies to address some of their major pitfalls and challenges. Finally, this contribution reviews methodologies to build and use data sets containing standard properties of emulsifying peptides by looking at successful applications in different fields. Full article

(This article belongs to the Special Issue Design and Synthesis of Peptides: Impact on Current Biomedicine, Biotechnology, and Chemical Biology)

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