Co-and Post-translational Modifications of Therapeutic Proteins

A special issue of Pharmaceuticals (ISSN 1424-8247). This special issue belongs to the section "Biopharmaceuticals".

Deadline for manuscript submissions: closed (31 October 2022) | Viewed by 8312

Special Issue Editors


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Guest Editor
School of Biology & Basic Medical Sciences; Soochow University; No. 199, Renai Street, Industrial Park, Suzhou 215123, China
Interests: PTM; Structural bioinformatics; protein-structural-dynamics-function; drug design

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Guest Editor
Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada
Interests: machine learning; computational chemistry; software engineering; protein structure-function relationship

Special Issue Information

Post-translational modifications (PTMs) add a layer of complexity to the proteome through the addition of biochemical moieties to specific residues of proteins, with low evolutionary cost. With the rapid development of high-throughput mass spectrum in the discovery of PTM sites, functional studies have become the bottleneck in the coming era of functional omics. PTMs could alter protein associations, protein structural conformations, and cellular localizations, involved in various of biological processes and disease pathogenesis. With the deciphering of PTM functional landscape, PTMs can play crucial roles as biomarkers in precision medicine. On the other hand, concerning the limited biological space in drug design, the introduction of PTM functional groups would extremely enlarge the target space for drug design with high selectivity. In the research of PTM function, two layers would be considered. First is the molecular level, where, with the introduction of PTMs, the structural and dynamics effects on proteins should be considered. Second, PTMs act as the connector of protein–protein interactions, which could provide us with a systematic view for PTM functions. In our PTM issue, we shall focus on functional research for PTM sites and protein structural isoforms with PTMs, both computationally and experimentally, including but not limited to:

  1.      Biological functions of protein with PTMs (experimental studies and computational studies);
  2.      Structure–dynamics–function relationship of PTM structural isoforms;
  3.      Machine learning models for the prediction of PTM functions;
  4.      Machine learning models for the prediction of crosstalk of PTM pairs;
  5.      Research on PTM intermediated PPI networks in specific disease;
  6.      Chemical-biology-related studies of PTMs;
  7.      Drug discovery targeting PTMs and PTM structural isoforms.

Dr. Zhongjie Liang
Dr. Fanwang Meng
Guest Editors

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Keywords

  • PTM function
  • PTM isoform
  • machine learning
  • PTM intermediated PPI network
  • drug design

Published Papers (2 papers)

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Research

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16 pages, 2046 KiB  
Article
MPMABP: A CNN and Bi-LSTM-Based Method for Predicting Multi-Activities of Bioactive Peptides
by You Li, Xueyong Li, Yuewu Liu, Yuhua Yao and Guohua Huang
Pharmaceuticals 2022, 15(6), 707; https://doi.org/10.3390/ph15060707 - 3 Jun 2022
Cited by 8 | Viewed by 3603
Abstract
Bioactive peptides are typically small functional peptides with 2–20 amino acid residues and play versatile roles in metabolic and biological processes. Bioactive peptides are multi-functional, so it is vastly challenging to accurately detect all their functions simultaneously. We proposed a convolution neural network [...] Read more.
Bioactive peptides are typically small functional peptides with 2–20 amino acid residues and play versatile roles in metabolic and biological processes. Bioactive peptides are multi-functional, so it is vastly challenging to accurately detect all their functions simultaneously. We proposed a convolution neural network (CNN) and bi-directional long short-term memory (Bi-LSTM)-based deep learning method (called MPMABP) for recognizing multi-activities of bioactive peptides. The MPMABP stacked five CNNs at different scales, and used the residual network to preserve the information from loss. The empirical results showed that the MPMABP is superior to the state-of-the-art methods. Analysis on the distribution of amino acids indicated that the lysine preferred to appear in the anti-cancer peptide, the leucine in the anti-diabetic peptide, and the proline in the anti-hypertensive peptide. The method and analysis are beneficial to recognize multi-activities of bioactive peptides. Full article
(This article belongs to the Special Issue Co-and Post-translational Modifications of Therapeutic Proteins)
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Review

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17 pages, 1863 KiB  
Review
The Glycosylation of Immune Checkpoints and Their Applications in Oncology
by Linlin Zheng, Qi Yang, Feifei Li, Min Zhu, Haochi Yang, Tian Tan, Binghuo Wu, Mingxin Liu, Chuan Xu, Jun Yin and Chenhui Cao
Pharmaceuticals 2022, 15(12), 1451; https://doi.org/10.3390/ph15121451 - 23 Nov 2022
Cited by 4 | Viewed by 3905
Abstract
Tumor therapies have entered the immunotherapy era. Immune checkpoint inhibitors have achieved tremendous success, with some patients achieving long-term tumor control. Tumors, on the other hand, can still accomplish immune evasion, which is aided by immune checkpoints. The majority of immune checkpoints are [...] Read more.
Tumor therapies have entered the immunotherapy era. Immune checkpoint inhibitors have achieved tremendous success, with some patients achieving long-term tumor control. Tumors, on the other hand, can still accomplish immune evasion, which is aided by immune checkpoints. The majority of immune checkpoints are membrane glycoproteins, and abnormal tumor glycosylation may alter how the immune system perceives tumors, affecting the body’s anti-tumor immunity. Furthermore, RNA can also be glycosylated, and GlycoRNA is important to the immune system. Glycosylation has emerged as a new hallmark of tumors, with glycosylation being considered a potential therapeutic approach. The glycosylation modification of immune checkpoints and the most recent advances in glycosylation-targeted immunotherapy are discussed in this review. Full article
(This article belongs to the Special Issue Co-and Post-translational Modifications of Therapeutic Proteins)
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