Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
7.4
4.2
Journals
Molecules
Special Issues
Peptide Science: From Synthesis to Application
molecules-logo
Submit to Molecules Review for Molecules Propose a Special Issue

Journal Menu

► Journal Menu

Journal Browser

► Journal Browser
share announcement

Peptide Science: From Synthesis to Application

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

Deadline for manuscript submissions: closed (30 November 2021) | Viewed by 17536

Special Issue Editors

Dr. Hiroyuki Konno

E-Mail Website
Guest Editor
Graduate School of Science and Engineering, Yamagata University, Yonezawa, Yamagata 992‐8510, Japan
Interests: total synthesis of peptidyl natural products; stereoselective synthesis of unusual amino acids; bioactive peptides; antimicrobials and antifungals
Special Issues, Collections and Topics in MDPI journals
Dr. Kenichi Akaji

E-Mail Website
Guest Editor
Department of Medicinal Chemistry, Kyoto Pharmaceutical University, Yamashina‐ku, Kyoto 607‐8412, Japan
Interests: medicinal chemistry; synthetic organic chemistry of unnatural amino acids; peptides; protein
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues, 

Peptide is one of the most important molecules in research fields such as pharmaceuticals, biomaterials, and advanced materials. Amino acids and the mimics are significant building blocks of a variety of peptides as well as natural products, drug candidates, and biomaterials. Thus, for the preparation of these amino acids, various stereospecific procedures using chiral auxiliaties, asymmetric catalysts or chiral pool methods have been developed. In parallel with those synthetic studies on amino acids, effective procedures for the synthesis of peptides by solid-phase procedures and/or specific ligation strategies have also been developed and shown to be highly effective. This Special Issue aims to illustrate the most recent developments on the multiple and innovative uses of amino acids, including unnatural amino acids and those mimics as well as peptides containing those amino acids and mimics. Each article in this Special Issue will clearly demonstrate the essential contribution of peptides and their related chemistry on a variety of research fields concerning bioorganic chemistry. 

Prof. Kenichi Akaji
Prof. Hiroyuki Konno
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

  • Preparation of unusual amino acids 
  • Solid-phase peptide synthesis 
  • Native chemical ligation 
  • Peptidyl natural product 
  • Protecting groups for the peptide synthesis 
  • Glycopeptide 
  • Antimicrobial peptides 
  • Chemical biology of peptides and their target proteins 
  • Peptides as the lead compound for drugs
  • Peptides in medicinal chemistry 
  • Cell-penetrative peptides 
  • Secondary structures of peptide mimetics 
  • Structural analysis of protein and peptide 
  • Cell adhesion factor 
  • Mass spectrum for protein and peptide

Published Papers (6 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

14 pages, 26202 KiB  
Article
Structural Requirement of hA5G18 Peptide (DDFVFYVGGYPS) from Laminin α5 Chain for Amyloid-like Fibril Formation and Cell Adhesion
by Guangrui Zhang, Yuji Yamada, Jun Kumai, Keisuke Hamada, Yamato Kikkawa and Motoyoshi Nomizu
Molecules 2022, 27(19), 6610; https://doi.org/10.3390/molecules27196610 - 5 Oct 2022
Viewed by 1194
Abstract
The hA5G18 peptide (DDFVFYVGGYPS) identified from the human laminin α5 chain G domain promotes cell attachment and spreading when directly coated on a plastic plate, but does not show activity when it is conjugated on a chitosan matrix. Here, we focused on the [...] Read more.
The hA5G18 peptide (DDFVFYVGGYPS) identified from the human laminin α5 chain G domain promotes cell attachment and spreading when directly coated on a plastic plate, but does not show activity when it is conjugated on a chitosan matrix. Here, we focused on the structural requirement of hA5G18 for activity. hA5G18 was stained with Congo red and formed amyloid-like fibrils. A deletion analysis of hA5G18 revealed that FVFYV was a minimum active sequence for the formation of amyloid-like fibrils, but FVFYV did not promote cell attachment. Next, we designed functional fibrils using FVFYV as a template for amyloid-like fibrils. When we conjugated an integrin binding sequence Arg-Gly-Asp (RGD) to the FVFYV peptide with Gly-Gly (GG) as a spacer, FVFYVGGRGD promoted cell attachment in a plate coat assay, but a negative control sequence RGE conjugated peptide, FVFYVGGRGE, also showed activity. However, when the peptides were conjugated to Sepharose beads, the FVFYVGGRGD beads showed cell attachment activity, but the FVFYVGGRGE beads did not. These results suggest that RGD and RGE similarly contribute to cell attachment activity in amyloid-like fibrils, but only RGD contributes the activity on the Sepharose beads. Further, we conjugated a basic amino acid (Arg, Lys, and His) to the FVFYV peptide. Arg or Lys-conjugated FVFYV peptides, FVFYVGGR and FVFYVGGK, showed cell attachment activity when they were coated on a plate, but a His-conjugated FVFYV peptide FVFYVGGH did not show activity. None of the basic amino acid-conjugated peptides showed cell attachment in a Sepharose bead assay. The cell attachment and spreading on FVFYVGGR and FVFYVGGK were inhibited by an anti-integrin β1 antibody. These results suggest that the Arg and Lys residues play critical roles in the interaction with integrins in amyloid-like fibrils. FVFYV is useful to use as a template for amyloid-like fibrils and to develop multi-functional biomaterials. Full article
(This article belongs to the Special Issue Peptide Science: From Synthesis to Application)
►▼ Show Figures

Figure 1

12 pages, 1712 KiB  
Article
The Effects of Side-Chain Configurations of a Retro–Inverso-Type Inhibitor on the Human T-Cell Leukemia Virus (HTLV)-1 Protease
by Chiyuki Awahara, Daiki Oku, Saki Furuta, Kazuya Kobayashi, Kenta Teruya, Kenichi Akaji and Yasunao Hattori
Molecules 2022, 27(5), 1646; https://doi.org/10.3390/molecules27051646 - 2 Mar 2022
Cited by 4 | Viewed by 2113
Abstract
In this study, the effects of side-chain configurations of D-Ile residues of a retro–inverso (RI)-type inhibitor on the human T-cell leukemia virus type 1 (HTLV-1) protease containing a hydroxyethylamine dipeptide isostere were clarified. Prior to evaluation using the RI-type inhibitor, the effects of [...] Read more.
In this study, the effects of side-chain configurations of D-Ile residues of a retro–inverso (RI)-type inhibitor on the human T-cell leukemia virus type 1 (HTLV-1) protease containing a hydroxyethylamine dipeptide isostere were clarified. Prior to evaluation using the RI-type inhibitor, the effects of side-chain configurations of Ile residues of the substrate peptide on the HTLV-1 protease were examined to estimate the influence of side-chain configurations on enzyme activity. Based on the estimation of the influence of side-chain configurations on protease affinity, the RI-type inhibitors containing a D-allo-Ile residue in the corresponding substrate sequence, instead of a D-Ile residue, were synthesized via 9-fluorenylmethoxycarbonyl-based solid-phase peptide synthesis. Refolded recombinant HTLV-1 protease (1-116, L40I) was used for the simple and short evaluation of the inhibitory activities of the synthesized RI-type inhibitors. The results clearly indicated that mimicking the whole topology, comprising both the main- and side-chain structures of the parent inhibitor, is effective for the design of potent RI-modified protease inhibitors. Full article
(This article belongs to the Special Issue Peptide Science: From Synthesis to Application)
►▼ Show Figures

Figure 1

14 pages, 747 KiB  
Article
The Hydrophobicity and Antifungal Potentiation of Burkholdine Analogues
by Hiroyuki Konno, Mio Sasaki, Hinata Sano, Keima Osawa, Kazuto Nosaka and Shigekazu Yano
Molecules 2022, 27(4), 1191; https://doi.org/10.3390/molecules27041191 - 10 Feb 2022
Cited by 2 | Viewed by 1656
Abstract
The burkholdines are a family of cyclic lipopeptides reported to exhibit antifungal activity. We synthesized a series of 18 burkholdine analogues in good yield by conventional Fmoc-SPPS followed by cyclization with DIPCI/HOBt in the solution phase. Although none of the synthesized peptides exhibited [...] Read more.
The burkholdines are a family of cyclic lipopeptides reported to exhibit antifungal activity. We synthesized a series of 18 burkholdine analogues in good yield by conventional Fmoc-SPPS followed by cyclization with DIPCI/HOBt in the solution phase. Although none of the synthesized peptides exhibited antifungal activity, several did potentiate the antibiotic effect of the antibiotic G418, including the Thr-bearing Bk analogue (4b) and the tartaramide-bearing Bk analogue (5b). This work exemplifies the potential of burkholdine analogues as potentiating agents. Full article
(This article belongs to the Special Issue Peptide Science: From Synthesis to Application)
►▼ Show Figures

Graphical abstract

10 pages, 4758 KiB  
Article
Ultrasonication Improves Solid Phase Synthesis of Peptides Specific for Fibroblast Growth Factor Receptor and for the Protein-Protein Interface RANK-TRAF6
by Rúben D. M. Silva, João Franco Machado, Kyle Gonçalves, Francisco M. Lucas, Salete Batista, Rita Melo, Tânia S. Morais and João D. G. Correia
Molecules 2021, 26(23), 7349; https://doi.org/10.3390/molecules26237349 - 3 Dec 2021
Cited by 3 | Viewed by 3063
Abstract
Considering our interest in the use of peptides as potential target-specific drugs or as delivery vectors of metallodrugs for various biomedical applications, it is crucial to explore improved synthetic methodologies to accomplish the highest peptide crude purity in the shortest time possible. Therefore, [...] Read more.
Considering our interest in the use of peptides as potential target-specific drugs or as delivery vectors of metallodrugs for various biomedical applications, it is crucial to explore improved synthetic methodologies to accomplish the highest peptide crude purity in the shortest time possible. Therefore, we compared “classical” fluorenylmethoxycarbonyl (Fmoc)-solid phase peptide synthesis (SPPS) with ultrasound(US)-assisted SPPS based on the preparation of three peptides, namely the fibroblast growth factor receptor 3(FGFR3)-specific peptide Pep1 (VSPPLTLGQLLS-NH2) and the novel peptides Pep2 (RQMATADEA-NH2) and Pep3 (AAVALLPAVLLALLAPRQMATADEA-NH2), which are being developed aimed at interfering with the intracellular protein-protein interaction(PPI) RANK-TRAF6. Our results demonstrated that US-assisted SPPS led to a 14-fold (Pep1) and 4-fold time reduction (Pep2) in peptide assembly compared to the “classical” method. Interestingly, US-assisted SPPS yielded Pep1 in higher purity (82%) than the “classical” SPPS (73%). The significant time reduction combined with high crude peptide purity attained prompted use to apply US-assisted SPPS to the large peptide Pep3, which displays a high number of hydrophobic amino acids and homooligo-sequences. Remarkably, the synthesis of this 25-mer peptide was attained during a “working day” (347 min) in moderate purity (approx. 49%). In conclusion, we have reinforced the importance of using US-SPPS towards facilitating the production of peptides in shorter time with increased efficacy in moderate to high crude purity. This is of special importance for long peptides such as the case of Pep3. Full article
(This article belongs to the Special Issue Peptide Science: From Synthesis to Application)
►▼ Show Figures

Graphical abstract

19 pages, 4889 KiB  
Article
Synthesis of New Modified with Rhodamine B Peptides for Antiviral Protection of Textile Materials
by Petar Todorov, Stela Georgieva, Desislava Staneva, Petia Peneva, Petar Grozdanov, Ivanka Nikolova and Ivo Grabchev
Molecules 2021, 26(21), 6608; https://doi.org/10.3390/molecules26216608 - 31 Oct 2021
Cited by 9 | Viewed by 2512
Abstract
Here we report on the synthesis and characterization of three new N-modified analogues of hemorphin-4 with rhodamine B. Modified with chloroacetyl, chloride cotton fabric has been dyed and color coordinates of the obtained textile materials were determined. Antiviral and virucidal activities of both [...] Read more.
Here we report on the synthesis and characterization of three new N-modified analogues of hemorphin-4 with rhodamine B. Modified with chloroacetyl, chloride cotton fabric has been dyed and color coordinates of the obtained textile materials were determined. Antiviral and virucidal activities of both the peptide-rhodamine B compounds and the dyed textile material were studied. Basic physicochemical properties (acid-base behavior, solvent influence, kinetics) related to the elucidation of structural activity of the new modified peptides based on their steric open/closed ring effect were studied. The obtained results lead to the conclusion that in protic solvent with change in pH of the environment, direct control over the dyeing of textiles can be achieved. Both the new hybrid peptide compounds and the modification of functionalized textile materials with these bioactive hemorphins showed virucidal activity against the human respiratory syncytial virus (HRSV-S2) and human adenovirus serotype 5 (HAdV-5) for different time intervals (30 and 60 min) and the most active compound was Rh-3. Full article
(This article belongs to the Special Issue Peptide Science: From Synthesis to Application)
►▼ Show Figures

Graphical abstract

12 pages, 1905 KiB  
Article
PepFun: Open Source Protocols for Peptide-Related Computational Analysis
by Rodrigo Ochoa and Pilar Cossio
Molecules 2021, 26(6), 1664; https://doi.org/10.3390/molecules26061664 - 16 Mar 2021
Cited by 12 | Viewed by 4313
Abstract
Peptide research has increased during the last years due to their applications as biomarkers, therapeutic alternatives or as antigenic sub-units in vaccines. The implementation of computational resources have facilitated the identification of novel sequences, the prediction of properties, and the modelling of structures. [...] Read more.
Peptide research has increased during the last years due to their applications as biomarkers, therapeutic alternatives or as antigenic sub-units in vaccines. The implementation of computational resources have facilitated the identification of novel sequences, the prediction of properties, and the modelling of structures. However, there is still a lack of open source protocols that enable their straightforward analysis. Here, we present PepFun, a compilation of bioinformatics and cheminformatics functionalities that are easy to implement and customize for studying peptides at different levels: sequence, structure and their interactions with proteins. PepFun enables calculating multiple characteristics for massive sets of peptide sequences, and obtaining different structural observables derived from protein-peptide complexes. In addition, random or guided library design of peptide sequences can be customized for screening campaigns. The package has been created under the python language based on built-in functions and methods available in the open source projects BioPython and RDKit. We present two tutorials where we tested peptide binders of the MHC class II and the Granzyme B protease. Full article
(This article belongs to the Special Issue Peptide Science: From Synthesis to Application)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-6
Back to TopTop