The Amazing World of Peptide Engineering

A special issue of Processes (ISSN 2227-9717). This special issue belongs to the section "Biological Processes and Systems".

Deadline for manuscript submissions: 30 August 2024 | Viewed by 12858

Special Issue Editors

Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Chuo-ku, Kobe 650-0047, Japan
Interests: design of peptides; self-assembly of peptides; mineralization using peptides; analytical systems using peptides; peptide engineering
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Guest Editor
Department of Materials Chemistry, Ryukoku University, Seta, Otsu 520-2194, Japan
Interests: drug delivery system; organic–inorganic hybrid materials; materials for regenerative medicine; noble metal recovery
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Following the success of the previous Special Issue on “Advances of Peptide Engineering”, it is our pleasure to announce the launch of a second Special Issue named “The Amazing World of Peptide Engineering”.

Peptides have been gaining increasing attention for their applications in various fields, such as the medical, biotechnological, and nanotechnological fields. Peptides are promising compounds for use in all-round engineering scenes because they confer several advantages: i) they can be designed to form secondary structures such as helices, strands, sheets, and turns by arranging amino acids to mimic naturally occurring functional small proteins; ii) they can be prepared in large quantities by well-established chemical synthetic procedures; iii) they are stable against oxidative degradation and dryness compared with proteins; iv) they can be site-selectively modified with functional groups such as unnatural amino acid residues and fluorophores via chemical treatments; and v) they can be produced to be multifunctional molecules by combining properties including membrane spanning, hormonal, inorganic compound precipitating, or self-assembling.

This Special Issue will collect high-quality research papers and mini reviews compiling methodology, know-how, and techniques from different research groups, as well as reviews pertaining to the current trends and developments in the fields of peptide engineering and addressing the solutions for biological/chemical/medical/industrial concerns encountered. Topics of interest include but are not necessarily limited to the following:

  • Peptide chemistry: synthetic methods, purification methods, methods for phage display, peptide library, self-assembly;
  • Pharmaceutics: drugs, prodrugs, drug delivery system, structure–activity relationships;
  • Materials/biomaterials/organic–inorganic composites: hydrogels, biomineralization, fibers, materials for regenerative medicine, antibacterial, cell adhesion;
  • Bioprocess: modifications of enzymes, artificial enzymes, catalytic mechanisms, fermentation, separation;
  • Engineering: diagnostic systems, chemical analytical systems, bioanalytical systems, molecular machine/robotics.

Dr. Kenji Usui
Prof. Dr. Kin-ya Tomizaki
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 papers will be 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. Processes is an international peer-reviewed open access monthly 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 2000 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
  • drug
  • materials
  • enzyme
  • analytical system
  • molecular machine
  • synthesis
  • phage display
  • self-assembly
  • pharmaceutics
  • engineering

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Published Papers (8 papers)

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Research

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14 pages, 2029 KiB  
Article
Pyrene-Modified Cyclic Peptides Detect Cu2+ Ions by Fluorescence in Water
by Yuhi Maekawa, Sora Sakura, Yuji Furutani, Rento Fujihara, Hisashi Sugime, Takashi Ohtsuki and Mizuki Kitamatsu
Processes 2024, 12(4), 746; https://doi.org/10.3390/pr12040746 - 7 Apr 2024
Viewed by 474
Abstract
The detection of metal ions is an option for maintaining water quality and diagnosing metal ion-related diseases. In this study, we successfully detected metal ions using fluorescent peptides in water. First, we prepared seven linear (L1L7) and seven cyclic [...] Read more.
The detection of metal ions is an option for maintaining water quality and diagnosing metal ion-related diseases. In this study, we successfully detected metal ions using fluorescent peptides in water. First, we prepared seven linear (L1L7) and seven cyclic (C1C7) peptides containing two pyrenyl (Pyr) units and assessed the response to various metal ions by fluorescence. The results indicated that C1, which contains a hexameric cyclic peptide moiety consisting of Pyr and Gly units, did not show a fluorescent response to metal ions, while the linear L1 corresponding to C1 showed a response to Cu2+, but its selectivity was found to be poor through a competition assay for each metal ion. We then assessed C2C7 and L2L7, in which Gly was replaced by His units at various positions in the same manner. The results showed that C2C7 responded to Cu2+ in a manner dependent on the His position. Additionally, superior selectivity was observed in C7 through a competition assay. These results demonstrate that the structural restriction of peptides and the sequence affect the selective detection of Cu2+ and reveal that peptides with an appropriate structure can accomplish the fluorescent detection of Cu2+ specifically. Full article
(This article belongs to the Special Issue The Amazing World of Peptide Engineering)
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9 pages, 1825 KiB  
Article
Reaction of Chloroacetyl-Modified Peptides with Mercaptoundecahydrododecaborate (BSH) Is Accelerated by Basic Amino Acid Residues in the Peptide
by Mizuki Kitamatsu, Ken Inoue, Naoki Yamagata and Hiroyuki Michiue
Processes 2022, 10(11), 2200; https://doi.org/10.3390/pr10112200 - 26 Oct 2022
Cited by 3 | Viewed by 1252
Abstract
We assessed a reactivity of chloroacetyl-modified tripeptides consisting of various amino acid residues (Cl-3X) and mercaptoundecahydrododecaborate (BSH) by converting Cl-3X to its reactant (BS-3X). We showed that the Cl-3X consisting of basic amino acid residues (e.g., Arg) reacted with BSH effectively and its [...] Read more.
We assessed a reactivity of chloroacetyl-modified tripeptides consisting of various amino acid residues (Cl-3X) and mercaptoundecahydrododecaborate (BSH) by converting Cl-3X to its reactant (BS-3X). We showed that the Cl-3X consisting of basic amino acid residues (e.g., Arg) reacted with BSH effectively and its conversion decreased as the number of Arg residues in the Cl-3X decreased. Furthermore, a reactivity of the peptides with introduction of an alkyl linker between the triarginine and the chloroacetyl group (Cl-Cn-3R) with BSH decreased with increasing alkyl linker length. These results indicate that an electrostatic attraction of positively charged amino acid residues in the tripeptides and negatively charged BSH causes BSH to gather in a vicinity of the chloroacetyl group, resulting in an accelerated reaction. This work should aid a development of new boron agents using BSH in boron neutron capture therapy. Full article
(This article belongs to the Special Issue The Amazing World of Peptide Engineering)
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12 pages, 2119 KiB  
Article
Cell Behavior on Peptide-Immobilized Substrate with Cell Aggregation Inducing Property
by Ikumi Amimoto, Rino Watanabe and Yoshiaki Hirano
Processes 2022, 10(9), 1779; https://doi.org/10.3390/pr10091779 - 5 Sep 2022
Cited by 1 | Viewed by 1295
Abstract
Cell aggregates have been applied in various fields such as regenerative medicine and drug toxicity testing. We have shown that H-(Lys-Pro)12-OH (KP24), a repeating sequence of lysine (Lys) and proline (Pro), induces uniformly sized cell aggregates simply by its presence in [...] Read more.
Cell aggregates have been applied in various fields such as regenerative medicine and drug toxicity testing. We have shown that H-(Lys-Pro)12-OH (KP24), a repeating sequence of lysine (Lys) and proline (Pro), induces uniformly sized cell aggregates simply by its presence in cell suspension. In this study, we considered that this peptide could be applied to a three-dimensional culture substrate that can induce uniform cell aggregates by immobilizing it on the substrate. Therefore, mouse fibroblasts (L929) were seeded on KP24-immobilized glass substrates and cell behavior was observed. We also seeded human-derived cells, namely, human mesenchymal stem cells (hMSC), on KP24-immobilized substrates and characterized their cell assemblies. Furthermore, KP24 was chemically immobilized on the substrate surface, which allowed us to trace the mechanism of KP24–cell interaction. As a mechanism analysis of the cell aggregation ability of KP24, we investigated whether KP24 interacts with the cell surface without being incorporated into the cell. Full article
(This article belongs to the Special Issue The Amazing World of Peptide Engineering)
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16 pages, 2503 KiB  
Article
Development of Antibody-like Proteins Targeting the Oncogenic Ser/Thr Protein Phosphatase PPM1D
by Megumi Ikeura, Hiroto Tashiro, Yuka Yamagata, Hikaru Saito, Tamaki Kobayashi, Masataka Mizunuma, Kazuki Yamazaki, Keisuke Baba, Kazuhiro Furukawa and Yoshiro Chuman
Processes 2022, 10(8), 1501; https://doi.org/10.3390/pr10081501 - 29 Jul 2022
Cited by 1 | Viewed by 1957
Abstract
PPM1D, a protein Ser/Thr phosphatase, is overexpressed in various cancers and functions as an oncogenic protein by inactivating the p53 pathway. Therefore, molecules that bind PPM1D are expected to be useful anti-cancer agents. In this study, we constructed a phage display library based [...] Read more.
PPM1D, a protein Ser/Thr phosphatase, is overexpressed in various cancers and functions as an oncogenic protein by inactivating the p53 pathway. Therefore, molecules that bind PPM1D are expected to be useful anti-cancer agents. In this study, we constructed a phage display library based on the antibody-like small molecule protein adnectin and screened for PPM1D-specific binding molecules. We identified two adnectins, PMDB-1 and PMD-24, that bind PPM1D specific B-loop and PPM1D430 as targets, respectively. Specificity analyses of these recombinant proteins using other Ser/Thr protein phosphatases showed that these molecules bind to only PPM1D. Expression of PMDB-1 in breast cancer-derived MCF-7 cells overexpressing endogenous PPM1D stabilized p53, indicating that PMDB-1 functions as an inhibitor of PPM1D. Furthermore, MTT assay exhibited that MCF-7 cells expressing PMDB-1 showed inhibition of cell proliferation. These data suggest that the adnectin PMDB-1 identified in this study can be used as a lead compound for anti-cancer drugs targeting intracellular PPM1D. Full article
(This article belongs to the Special Issue The Amazing World of Peptide Engineering)
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11 pages, 3307 KiB  
Article
Adjusting the Structure of a Peptide Nucleic Acid (PNA) Molecular Beacon and Promoting Its DNA Detection by a Hybrid with Quencher-Modified DNA
by Hajime Shigeto, Takamasa Kishi, Koki Ishii, Takashi Ohtsuki, Shohei Yamamura and Mizuki Kitamatsu
Processes 2022, 10(4), 722; https://doi.org/10.3390/pr10040722 - 8 Apr 2022
Cited by 1 | Viewed by 1963
Abstract
In this study, we performed an elaborate adjustment of the structure of peptide nucleic acid (PNA) molecular beacons as probes for detecting nucleic acids. We synthesized the PNA beacons with various numbers of Glu, Lys, and dabcyl (Dab) quenchers in them, and we [...] Read more.
In this study, we performed an elaborate adjustment of the structure of peptide nucleic acid (PNA) molecular beacons as probes for detecting nucleic acids. We synthesized the PNA beacons with various numbers of Glu, Lys, and dabcyl (Dab) quenchers in them, and we investigated their fluorescence changes (F1/1/F0) with and without full-match DNA. As the numbers of Glu/Lys or Dab increased, the F1/1/F0 tended to decrease. Among the different beacons, the PNA beacon with one Glu and one Lys (P1Q1) showed the largest F1/1/F0. On the other hand, a relatively large F1/1/F0 was obtained when the number of Glu/Lys and the number of Dab were the same, and the balance between the numbers of Glu/Lys and Dab seemed to affect the F1/1/F0. We also investigated the DNA detection by the prehybrid of P1Q1, which consists of the T790M base sequence, [P1Q1(T790M)], with quencher-modified DNA (Q-DNA). We examined the DNA detection with single-base mismatch by P1Q1(T790M), and we clarified that there was difficulty in detecting the sequence with P1Q1 alone, but that the sequence was successfully detected by the prehybrid of P1Q1 with the Q-DNA. Full article
(This article belongs to the Special Issue The Amazing World of Peptide Engineering)
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16 pages, 2335 KiB  
Article
Miniaturization of Anthracene-Containing Nonapeptides for Selective Precipitation/Recovery of Metallic Gold from Aqueous Solutions Containing Gold and Platinum Ions
by Kin-ya Tomizaki, Tatsuki Tonoda, Shungo Teramura, Haruka Okazaki, Takahito Imai and Masahiro Asano
Processes 2021, 9(11), 2010; https://doi.org/10.3390/pr9112010 - 10 Nov 2021
Cited by 1 | Viewed by 1408
Abstract
The separation and recovery of noble metals is increasingly of interest, in particular the recovery of gold nanocrystals, which have applications in medicine and industry. Typically, metal recovery is performed using liquid–liquid extraction or electrowinning. However, it is necessary to develop noble metal [...] Read more.
The separation and recovery of noble metals is increasingly of interest, in particular the recovery of gold nanocrystals, which have applications in medicine and industry. Typically, metal recovery is performed using liquid–liquid extraction or electrowinning. However, it is necessary to develop noble metal recovery systems providing high selectivity in conjunction with a one-pot setup, ready product recovery, and the use of dilute aqueous solutions. In prior work, our group developed a selective gold recovery process using peptides. This previous research showed that RU065, a nonapeptide containing an anthracene moiety (at a concentration of 2.0 × 10−4 M), is capable of selective reduction of HAuCl4 to recover gold from a solution of HAuCl4 and H2PtCl6, each at 5.0 × 10−5 M. However, peptide molecules are generally costly to synthesize, and therefore it is important to determine the minimum required structural features to design non-peptide anthracene derivatives that could reduce operational costs. In this study, we used RU065 together with 23 of its fragment peptides and investigated the selective precipitation/recovery of metallic gold. RU0654–8, a fragment peptide comprising five amino acid residues (having two lysine, one L-isoleusine, and one L-alanine residue (representing six amide groups) along with an L-2-anthrylalanine residue) provided an Au/Pt atomic ratio of approximately 8, which was comparable to that for the full-length original RU065. The structural features identified in this study are expected to contribute to the design of non-peptide anthracene derivatives for low-cost, one-pot selective gold recovery. Full article
(This article belongs to the Special Issue The Amazing World of Peptide Engineering)
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Review

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14 pages, 4658 KiB  
Review
Non-Classical Circularly Polarized Luminescence Control of Peptide Luminophore Based on Precise Chiral Space Control
by Yoshitane Imai and Mizuki Kitamatsu
Processes 2023, 11(9), 2778; https://doi.org/10.3390/pr11092778 - 17 Sep 2023
Viewed by 713
Abstract
Light that rotates in a circular spiral when viewed from the front is known as circularly polarized luminescence (CPL), and can be divided into two types, namely, left- and right-rotating light. To emit both left- and right-rotating CPLs, two types of optically active [...] Read more.
Light that rotates in a circular spiral when viewed from the front is known as circularly polarized luminescence (CPL), and can be divided into two types, namely, left- and right-rotating light. To emit both left- and right-rotating CPLs, two types of optically active luminophores, namely, enantiomer D- and L-bodies, are generally required. This mini-review mainly discusses our latest study on CPL properties via the control of the pyrene ring as the luminescent unit incorporated into chiral peptides. In this study, optically active peptide–pyrene organoluminescent materials that emit CPL were synthesized by combining a peptide as a frame and two pyrene rings as a luminescent unit. By adjusting the interpyrene distance, external conditions, and absolute chiral configuration (D- or L-configuration), the chiral spatial configuration of the luminescent pyrene ring was precisely controlled. Consequently, the direction of CPL rotation from pyrenylalanine-containing peptides with the same configuration was successfully controlled. Full article
(This article belongs to the Special Issue The Amazing World of Peptide Engineering)
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24 pages, 14658 KiB  
Review
Helical Foldamers and Stapled Peptides as New Modalities in Drug Discovery: Modulators of Protein-Protein Interactions
by Keisuke Tsuchiya, Takashi Kurohara, Kiyoshi Fukuhara, Takashi Misawa and Yosuke Demizu
Processes 2022, 10(5), 924; https://doi.org/10.3390/pr10050924 - 6 May 2022
Cited by 9 | Viewed by 2763
Abstract
A “foldamer” is an artificial oligomeric molecule with a regular secondary or tertiary structure consisting of various building blocks. A “stapled peptide” is a peptide with stabilized secondary structures, in particular, helical structures by intramolecular covalent side-chain cross-linking. Helical foldamers and stapled peptides [...] Read more.
A “foldamer” is an artificial oligomeric molecule with a regular secondary or tertiary structure consisting of various building blocks. A “stapled peptide” is a peptide with stabilized secondary structures, in particular, helical structures by intramolecular covalent side-chain cross-linking. Helical foldamers and stapled peptides are potential drug candidates that can target protein-protein interactions because they enable multipoint molecular recognition, which is difficult to achieve with low-molecular-weight compounds. This mini-review describes a variety of peptide-based foldamers and stapled peptides with a view to their applications in drug discovery, including our recent progress. Full article
(This article belongs to the Special Issue The Amazing World of Peptide Engineering)
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Title: Foldamers as new modalities in drug discovery
Authors: Keisuke Tsuchiya, Takashi Kurohara, Takashi Misawa, Yosuke Demizu(CA)
Affiliation: National Institute of Health Sciences, Japan
Abstract: "Foldamer" is an artificial oligomeric molecule with a regular secondary or tertiary structure consisting a low molecular unit. Foldamers have the potential to be drug candidates that target protein-protein interactions because they enable multipoint molecular recognition, which is difficult to achieve with low-molecular-weight compounds. This mini-review describes a variety of foldamers with a view to their application in drug discovery including our recent progress.

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