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New Strategies for the Synthesis and Modification of Peptides and Proteins

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

Deadline for manuscript submissions: closed (15 January 2022) | Viewed by 26404

Special Issue Editors

Istituto di Scienze e Tecnologie Chimiche “G. Natta”, CNR, Milan, Italy
Interests: bioorganic chemistry; peptide chemistry; peptide design; bioactive peptides; chemical ligation; protein chemical synthesis; bioconjugation
Special Issues, Collections and Topics in MDPI journals
Istituto di Biostrutture e Bioimmagini, CNR, Naples, Italy
Interests: protein and peptide synthesis; chemical ligation; protein bioconjugation; bioactive peptides

Special Issue Information

Dear Colleagues,

The ability to synthesize peptides and proteins and site-specifically decorate them with a multitude of chemical agents has revolutionized research in the life sciences, allowing the preparation of sophisticated molecular tools and paving the way to countless applications, especially in biomedicine. The research field highlighted in this Special Issue is fervent and in continuous development, leading—in a few decades—to an impressive expansion of the portfolio of chemistries available to synthesize and selectively modify peptides and proteins.

This Special Issue is intended to offer a showcase for presenting novel and straightforward chemical and enzymatic methods allowing protein and peptide synthesis and/or modification and showing the results of research studies performed using these synthetic or semi-synthetic biomolecules. Modifications of interest include, but are not limited to, post-translational modifications, dyes, imaging probes, drugs, polymers and unnatural amino acids. We are also interested in the discussion of innovative strategies for conjugating peptides/proteins to biomaterials and nanoparticles. As a consequence, the applications of interest are not limited to biomedicine but we are also expecting papers reporting exciting results in biomaterial and biosensor science, chemical biology and structural biology. All types of contributions, such as research or review articles, covering the topic area are welcome.

Dr. Luca D. D'Andrea
Dr. Lucia De Rosa
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. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 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

  • Peptide and protein bioconjugation
  • Chemo-selective reactions
  • Chemical ligation
  • Protein chemical synthesis and semi-synthesis
  • Peptide and protein site-specific labeling
  • Expressed protein ligation and intein chemistry
  • Enzyme-mediated peptide/protein modification
  • Mirror proteins and racemic crystallography
  • Synthesis of C-terminal activated peptides

Published Papers (7 papers)

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Research

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13 pages, 2482 KiB  
Article
The Inducible Intein-Mediated Self-Cleaving Tag (IIST) System: A Novel Purification and Amidation System for Peptides and Proteins
by A. Sesilja Aranko and Hideo Iwaï
Molecules 2021, 26(19), 5948; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26195948 - 30 Sep 2021
Cited by 4 | Viewed by 2858
Abstract
An efficient self-cleavable purification tag could be a powerful tool for purifying recombinant proteins and peptides without additional proteolytic processes using specific proteases. Thus, the intein-mediated self-cleavage tag was developed and has been commercially available as the IMPACT™ system. However, uncontrolled cleavages of [...] Read more.
An efficient self-cleavable purification tag could be a powerful tool for purifying recombinant proteins and peptides without additional proteolytic processes using specific proteases. Thus, the intein-mediated self-cleavage tag was developed and has been commercially available as the IMPACT™ system. However, uncontrolled cleavages of the purification tag by the inteins in the IMPACT™ system have been reported, thereby reducing final yields. Therefore, controlling the protein-splicing activity of inteins has become critical. Here we utilized conditional protein splicing by salt conditions. We developed the inducible intein-mediated self-cleaving tag (IIST) system based on salt-inducible protein splicing of the MCM2 intein from the extremely halophilic archaeon, Halorhabdus utahensis and applied it to small peptides. Moreover, we described a method for the amidation using the same IIST system and demonstrated 15N-labeling of the C-terminal amide group of a single domain antibody (VHH). Full article
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9 pages, 1044 KiB  
Article
Silylated Tag-Assisted Peptide Synthesis: Continuous One-Pot Elongation for the Production of Difficult Peptides under Environmentally Friendly Conditions
by Shinya Yano, Toshihiro Mori and Hideki Kubota
Molecules 2021, 26(12), 3497; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26123497 - 08 Jun 2021
Cited by 5 | Viewed by 3051
Abstract
Addition of the silylated tag (STag) enables peptides to be highly soluble in CPME, allowing them to be used at high concentrations in a coupling reaction to enhance reactivity and achieve effective synthesis of sterically hindered peptides. We described the development of a [...] Read more.
Addition of the silylated tag (STag) enables peptides to be highly soluble in CPME, allowing them to be used at high concentrations in a coupling reaction to enhance reactivity and achieve effective synthesis of sterically hindered peptides. We described the development of a continuous one-pot STag-assisted peptide synthesis platform as a method that provides near-stoichiometric, speedy, environmentally friendly, and scalable peptide synthesis. Full article
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14 pages, 2614 KiB  
Article
Site-Specific Conversion of Cysteine in a Protein to Dehydroalanine Using 2-Nitro-5-thiocyanatobenzoic Acid
by Yuchen Qiao, Ge Yu, Sunshine Z. Leeuwon and Wenshe Ray Liu
Molecules 2021, 26(9), 2619; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26092619 - 29 Apr 2021
Cited by 3 | Viewed by 3307
Abstract
Dehydroalanine exists natively in certain proteins and can also be chemically made from the protein cysteine. As a strong Michael acceptor, dehydroalanine in proteins has been explored to undergo reactions with different thiolate reagents for making close analogues of post-translational modifications (PTMs), including [...] Read more.
Dehydroalanine exists natively in certain proteins and can also be chemically made from the protein cysteine. As a strong Michael acceptor, dehydroalanine in proteins has been explored to undergo reactions with different thiolate reagents for making close analogues of post-translational modifications (PTMs), including a variety of lysine PTMs. The chemical reagent 2-nitro-5-thiocyanatobenzoic acid (NTCB) selectively modifies cysteine to form S-cyano-cysteine, in which the S–Cβ bond is highly polarized. We explored the labile nature of this bond for triggering E2 elimination to generate dehydroalanine. Our results indicated that when cysteine is at the flexible C-terminal end of a protein, the dehydroalanine formation is highly effective. We produced ubiquitin and ubiquitin-like proteins with a C-terminal dehydroalanine residue with high yields. When cysteine is located at an internal region of a protein, the efficiency of the reaction varies with mainly hydrolysis products observed. Dehydroalanine in proteins such as ubiquitin and ubiquitin-like proteins can serve as probes for studying pathways involving ubiquitin and ubiquitin-like proteins and it is also a starting point to generate proteins with many PTM analogues; therefore, we believe that this NTCB-triggered dehydroalanine formation method will find broad applications in studying ubiquitin and ubiquitin-like protein pathways and the functional annotation of many PTMs in proteins such as histones. Full article
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16 pages, 1667 KiB  
Article
Insights into the Mechanism and Catalysis of Peptide Thioester Synthesis by Alkylselenols Provide a New Tool for Chemical Protein Synthesis
by Florent Kerdraon, Gemma Bogard, Benoît Snella, Hervé Drobecq, Muriel Pichavant, Vangelis Agouridas and Oleg Melnyk
Molecules 2021, 26(5), 1386; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26051386 - 04 Mar 2021
Cited by 2 | Viewed by 2276
Abstract
While thiol-based catalysts are widely employed for chemical protein synthesis relying on peptide thioester chemistry, this is less true for selenol-based catalysts whose development is in its infancy. In this study, we compared different selenols derived from the selenocysteamine scaffold for their capacity [...] Read more.
While thiol-based catalysts are widely employed for chemical protein synthesis relying on peptide thioester chemistry, this is less true for selenol-based catalysts whose development is in its infancy. In this study, we compared different selenols derived from the selenocysteamine scaffold for their capacity to promote thiol–thioester exchanges in water at mildly acidic pH and the production of peptide thioesters from bis(2-sulfanylethyl)amido (SEA) peptides. The usefulness of a selected selenol compound is illustrated by the total synthesis of a biologically active human chemotactic protein, which plays an important role in innate and adaptive immunity. Full article
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27 pages, 13058 KiB  
Article
Aluminium Binding to Modified Amyloid-β Peptides: Implications for Alzheimer’s Disease
by Cosmin Stefan Mocanu, Monica Jureschi and Gabi Drochioiu
Molecules 2020, 25(19), 4536; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules25194536 - 03 Oct 2020
Cited by 17 | Viewed by 2886
Abstract
Aluminium (Al) is clearly neurotoxic and considerable evidence exists that Al may play a role in the aetiology or pathogenesis of Alzheimer’s disease (AD). Nevertheless, the link between AD pathology and Al is still open to debate. Therefore, we investigated here the interaction [...] Read more.
Aluminium (Al) is clearly neurotoxic and considerable evidence exists that Al may play a role in the aetiology or pathogenesis of Alzheimer’s disease (AD). Nevertheless, the link between AD pathology and Al is still open to debate. Therefore, we investigated here the interaction of aluminium ions with two Aβ peptide fragments and their analogues. First, we synthesised by the Fmoc/tBu solid-phase peptide synthesis (SPPS) strategy using an automated peptide synthesiser two new peptides starting from the Aβ(1–16) native peptide fragment. For this purpose, the three histidine residues (H6, H13, and H14) of the Aβ(1–16) peptide were replaced by three alanine and three serine residues to form the modified peptides Aβ(1–16)A36,13,14 and Aβ(1–16)S36,13,14 (primary structures: H-1DAEFRADSGYEVAAQK16-NH2 and H-1DAEFRSDSGYEVSSQK16-NH2). In addition, the Aβ(9–16) peptide fragment (H-9GYEVHHQK16-NH2) and its glycine analogues, namely Aβ(9–16)G110, (H-9GGEVHHQK16-NH2), Aβ(9–16)G213,14 (H-9GYEVGGQK16-NH2), and Aβ(9–16)G310,13,14 (H-9GGEVGGQK16-NH2), were manually synthesised in order to study Al binding to more specific amino acid residues. Both the peptides and the corresponding complexes with aluminium were comparatively investigated by mass spectrometry (MS), circular dichroism spectroscopy (CD), atomic force microscopy (AFM), scanning electron microscopy (SEM), and Fourier transform infrared spectroscopy (FT-IR). Al–peptide molecular ions and Al-fragment ions were unambiguously identified in the MS and MS/MS spectra. AFM images showed dramatic changes in the film morphology of peptides upon Al binding. Our findings from the investigation of N-terminal 1-16 and even 9-16 normal and modified sequences of Aβ peptides suggest that they have the capability to be involved in aluminium ion binding associated with AD. Full article
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Review

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45 pages, 8952 KiB  
Review
Synthesis, Characterization and Evaluation of Peptide Nanostructures for Biomedical Applications
by Fanny d’Orlyé, Laura Trapiella-Alfonso, Camille Lescot, Marie Pinvidic, Bich-Thuy Doan and Anne Varenne
Molecules 2021, 26(15), 4587; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26154587 - 29 Jul 2021
Cited by 17 | Viewed by 3611
Abstract
There is a challenging need for the development of new alternative nanostructures that can allow the coupling and/or encapsulation of therapeutic/diagnostic molecules while reducing their toxicity and improving their circulation and in-vivo targeting. Among the new materials using natural building blocks, peptides have [...] Read more.
There is a challenging need for the development of new alternative nanostructures that can allow the coupling and/or encapsulation of therapeutic/diagnostic molecules while reducing their toxicity and improving their circulation and in-vivo targeting. Among the new materials using natural building blocks, peptides have attracted significant interest because of their simple structure, relative chemical and physical stability, diversity of sequences and forms, their easy functionalization with (bio)molecules and the possibility of synthesizing them in large quantities. A number of them have the ability to self-assemble into nanotubes, -spheres, -vesicles or -rods under mild conditions, which opens up new applications in biology and nanomedicine due to their intrinsic biocompatibility and biodegradability as well as their surface chemical reactivity via amino- and carboxyl groups. In order to obtain nanostructures suitable for biomedical applications, the structure, size, shape and surface chemistry of these nanoplatforms must be optimized. These properties depend directly on the nature and sequence of the amino acids that constitute them. It is therefore essential to control the order in which the amino acids are introduced during the synthesis of short peptide chains and to evaluate their in-vitro and in-vivo physico-chemical properties before testing them for biomedical applications. This review therefore focuses on the synthesis, functionalization and characterization of peptide sequences that can self-assemble to form nanostructures. The synthesis in batch or with new continuous flow and microflow techniques will be described and compared in terms of amino acids sequence, purification processes, functionalization or encapsulation of targeting ligands, imaging probes as well as therapeutic molecules. Their chemical and biological characterization will be presented to evaluate their purity, toxicity, biocompatibility and biodistribution, and some therapeutic properties in vitro and in vivo. Finally, their main applications in the biomedical field will be presented so as to highlight their importance and advantages over classical nanostructures. Full article
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20 pages, 2505 KiB  
Review
Exploiting Protein N-Terminus for Site-Specific Bioconjugation
by Lucia De Rosa, Rossella Di Stasi, Alessandra Romanelli and Luca Domenico D’Andrea
Molecules 2021, 26(12), 3521; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26123521 - 09 Jun 2021
Cited by 17 | Viewed by 7303
Abstract
Although a plethora of chemistries have been developed to selectively decorate protein molecules, novel strategies continue to be reported with the final aim of improving selectivity and mildness of the reaction conditions, preserve protein integrity, and fulfill all the increasing requirements of the [...] Read more.
Although a plethora of chemistries have been developed to selectively decorate protein molecules, novel strategies continue to be reported with the final aim of improving selectivity and mildness of the reaction conditions, preserve protein integrity, and fulfill all the increasing requirements of the modern applications of protein conjugates. The targeting of the protein N-terminal alpha-amine group appears a convenient solution to the issue, emerging as a useful and unique reactive site universally present in each protein molecule. Herein, we provide an updated overview of the methodologies developed until today to afford the selective modification of proteins through the targeting of the N-terminal alpha-amine. Chemical and enzymatic strategies enabling the selective labeling of the protein N-terminal alpha-amine group are described. Full article
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