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Polymers
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Advances of Bio-Based Polymeric Materials
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Advances of Bio-Based Polymeric Materials

A special issue of Polymers (ISSN 2073-4360). This special issue belongs to the section "Biobased and Biodegradable Polymers".

Deadline for manuscript submissions: closed (20 February 2022) | Viewed by 5223

Special Issue Editor

Prof. Dr. Yeng-Tseng Wang

E-Mail Website
Guest Editor
School of Post-Baccalaureate Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 8070, Taiwan
Interests: bioinformatic; physical chemistry; computer-aided drug design; molecular dynamics; quantum mechanics; biochemistry; macromolecular
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Protein–Protein Interactions (PPIs) as drug targets commonly refer to the surface of two interacting intracellular proteins or a complex of proteins that can potentially be disrupted or stabilized by proteins/peptides/antibodies that penetrate the cell. This is in contrast to proteins/peptides/antibodies—target proteins, whose activity can be measured in a biophysical, biochemical, or theoretical assay. Due to the growing interest in this field, this Special Issue aims to publish high-quality original research papers on the experimental and theoretical applications of Protein–Protein Interactions.

Prof. Dr. Yeng-Tseng Wang
Guest Editor

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. Polymers 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

  • protein–protein interaction
  • peptide–protein interaction
  • antibody–protein interaction
  • theoretical simulations
  • experimental approach

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Published Papers (2 papers)

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17 pages, 5523 KiB  
Article
Cyclic Peptide Inhibitors of the Tsg101 UEV Protein Interactions Refined through Global Docking and Gaussian Accelerated Molecular Dynamics Simulations
by Wen-Wei Lin, Yu-Jen Wang, Cheng-Wen Ko, Tain-Lu Cheng and Yeng-Tseng Wang
Polymers 2020, 12(10), 2235; https://doi.org/10.3390/polym12102235 - 28 Sep 2020
Cited by 4 | Viewed by 2795
Abstract
Tsg101 UEV domain proteins are potential targets for virus infection therapy, especially for HIV and Ebola viruses. Peptides are key in curbing virus transmission, and cyclic peptides have a greater survival time than their linear peptides. To date, the accurate prediction of cyclic [...] Read more.
Tsg101 UEV domain proteins are potential targets for virus infection therapy, especially for HIV and Ebola viruses. Peptides are key in curbing virus transmission, and cyclic peptides have a greater survival time than their linear peptides. To date, the accurate prediction of cyclic peptide-protein receptors binding conformations still is challenging because of high peptide flexibility. Here, a useful approach combined the global peptide docking, Gaussian accelerated molecular dynamics (GaMD), two-dimensional (2D) potential of mean force (PMF), normal molecular dynamics (cMD), and solvated interaction energy (SIE) techniques. Then we used this approach to investigate the binding conformations of UEV domain proteins with three cyclic peptides inhibitors. We reported the possible cyclic peptide-UEV domain protein binding conformations via 2D PMF free energy profiles and SIE free energy calculations. The residues Trp145, Tyr147, and Trp148 of the native cyclic peptide (CP1) indeed play essential roles in the cyclic peptides-UEV domain proteins interactions. Our findings might increase the accuracy of cyclic peptide-protein conformational prediction, which may facilitate cyclic peptide inhibitor design. Our approach is expected to further aid in addressing the challenges in cyclic peptide inhibitor design. Full article
(This article belongs to the Special Issue Advances of Bio-Based Polymeric Materials)
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22 pages, 1759 KiB  
Review
Exploiting the Amazing Diversity of Natural Source-Derived Polysaccharides: Modern Procedures of Isolation, Engineering, and Optimization of Antiviral Activities
by Bimalendu Ray, Martin Schütz, Shuvam Mukherjee, Subrata Jana, Sayani Ray and Manfred Marschall
Polymers 2021, 13(1), 136; https://doi.org/10.3390/polym13010136 - 30 Dec 2020
Cited by 32 | Viewed by 4222
Abstract
Naturally occurring polysaccharide sulfates are highly diverse, owning variations in the backbone structure, linkage pattern and stereochemistry, branching diversity, sulfate content and positions of sulfate group(s). These structural characteristics bring about diverse sulfated polymers with dissimilar negative charge densities and structure–activity relationships. Herein, [...] Read more.
Naturally occurring polysaccharide sulfates are highly diverse, owning variations in the backbone structure, linkage pattern and stereochemistry, branching diversity, sulfate content and positions of sulfate group(s). These structural characteristics bring about diverse sulfated polymers with dissimilar negative charge densities and structure–activity relationships. Herein, we start with a short discussion of techniques needed for extraction, purification, chemical sulfation, and structural characterization of polysaccharides. Processes of isolation and sulfation of plant-derived polysaccharides are challenging and usually involve two steps. In this context, we describe an integrated extraction-sulfation procedure that produces polysaccharide sulfates from natural products in one step, thereby generating additional pharmacological activities. Finally, we provide examples of the spectrum of natural source-derived polysaccharides possessing specific features of bioactivity, in particular focusing on current aspects of antiviral drug development and drug–target interaction. Thus, the review presents a detailed view on chemically engineered polysaccharides, especially sulfated derivatives, and underlines their promising biomedical perspectives. Full article
(This article belongs to the Special Issue Advances of Bio-Based Polymeric Materials)
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