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Biomolecules
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Experimental and Theoretical Approaches to Protein-Targeting Drug Discovery: 2nd Edition
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Experimental and Theoretical Approaches to Protein-Targeting Drug Discovery: 2nd Edition

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Chemical Biology".

Deadline for manuscript submissions: 10 May 2025 | Viewed by 7162

Special Issue Editors

Dr. Caterina Vicidomini

E-Mail Website
Guest Editor
Istituto di Biostrutture e Bioimmagini IBB-CNR, Via Tommaso De Amicis 95, 80145 Naples, Italy
Interests: pharmaceutical chemistry; neurodrugs; protein interactions; spectroscopy; computational chemistry; phytochemistry
Special Issues, Collections and Topics in MDPI journals
Dr. Giovanni N. Roviello

E-Mail Website
Guest Editor
Institute of Biostructures and Bioimaging, Italian National Council for Research (IBB-CNR), Via P. Castellino 111, 80131 Naples, Italy
Interests: spectroscopy; computational chemistry; biomolecular binding; bioactive compounds; drug discovery
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Following a very successful first run, we are pleased to announce the launch of a second edition of the Special Issue “Experimental and Theoretical Approaches to Protein-Targeting Drug Discovery”.

Protein-driven biological processes are of fundamental importance in biomedicine because they are related to pathologies of enormous social relevance, including cancer, neurodegeneration, and viral diseases, such as the recent COVID-19 pandemic. In this Special Issue, we wish to focus on the novel experimental and theoretical approaches for drug discovery, design, and development, with particular attention being paid to the mechanisms of drug interference with protein-driven biological pathways. Contributions on nucleic acid–protein interaction, aptamers, peptide aggregation, nucleopeptide chemistry, and antimicrobial polyamino acids are also welcome as they could improve our overall knowledge of the amino-acid-based biochemistry at the interface between drug design and therapy. Other themes of interest are inherent to computational chemistry, in particular, tp molecular docking and molecular dynamics, applied to protein and peptide science.

This Special Issue is open to the submission of both original articles and reviews that describe research and ideas on the themes outlined here for protein-based molecular strategies.

Dr. Caterina Vicidomini
Dr. Giovanni N. Roviello
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. Biomolecules 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 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

  • proteins
  • peptides
  • amyloid
  • aptamers
  • molecular docking
  • Alzheimer disease
  • Parkinson’s disease
  • neurodrugs
  • biotechnological enzymes
  • antiviral drugs
  • vaccines
  • biomolecular targets
  • COVID-19
  • SARS-CoV-2
  • spike protein
  • peptide aggregation
  • drug repurposing
  • natural products
  • synthetic antivirals
  • anticancer therapeutics

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Related Special Issue

Published Papers (5 papers)

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Research

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17 pages, 6429 KiB  
Article
Discovery and Characterization of Two Selective Inhibitors for a Mu-Class Glutathione S-Transferase of 25 kDa from Taenia solium Using Computational and Bioinformatics Tools
by César Sánchez-Juárez, Roberto Flores-López, Lluvia de Carolina Sánchez-Pérez, Ponciano García-Gutiérrez, Lucía Jiménez, Abraham Landa and Rafael A. Zubillaga
Biomolecules 2025, 15(1), 7; https://doi.org/10.3390/biom15010007 - 25 Dec 2024
Viewed by 1078
Abstract
Glutathione S-transferases (GSTs) are promising pharmacological targets for developing antiparasitic agents against helminths, as they play a key role in detoxifying cytotoxic xenobiotics and managing oxidative stress. Inhibiting GST activity can compromise parasite viability. This study reports the successful identification of two selective [...] Read more.
Glutathione S-transferases (GSTs) are promising pharmacological targets for developing antiparasitic agents against helminths, as they play a key role in detoxifying cytotoxic xenobiotics and managing oxidative stress. Inhibiting GST activity can compromise parasite viability. This study reports the successful identification of two selective inhibitors for the mu-class glutathione S-transferase of 25 kDa (Ts25GST) from Taenia solium, named i11 and i15, using a computationally guided approach. The workflow involved modeling and refining the 3D structure from the sequence using the AlphaFold algorithm and all-atom molecular dynamics simulations with an explicit solvent. Representative structures from these simulations and a putative binding site with low conservation relative to human GSTs, identified via the SILCS methodology, were employed for virtual screening through ensemble docking against a commercial compound library. The two compounds were found to reduce the enzyme’s activity by 50–70% under assay conditions, while showing a reduction of only 30–35% for human mu-class GSTM1, demonstrating selectivity for Ts25GST. Notable, i11 displayed competitive inhibition with CDNB, while i15 exhibited a non-competitive inhibition type. Full article
(This article belongs to the Special Issue Experimental and Theoretical Approaches to Protein-Targeting Drug Discovery: 2nd Edition)
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15 pages, 2221 KiB  
Article
α-Methylacyl-CoA Racemase from Mycobacterium tuberculosis—Detailed Kinetic and Structural Characterization of the Active Site
by Otsile O. Mojanaga, Timothy J. Woodman, Matthew D. Lloyd and K. Ravi Acharya
Biomolecules 2024, 14(3), 299; https://doi.org/10.3390/biom14030299 - 2 Mar 2024
Cited by 1 | Viewed by 2208
Abstract
α-Methylacyl-CoA racemase in M. tuberculosis (MCR) has an essential role in fatty acid metabolism and cholesterol utilization, contributing to the bacterium’s survival and persistence. Understanding the enzymatic activity and structural features of MCR provides insights into its physiological and pathological significance and potential [...] Read more.
α-Methylacyl-CoA racemase in M. tuberculosis (MCR) has an essential role in fatty acid metabolism and cholesterol utilization, contributing to the bacterium’s survival and persistence. Understanding the enzymatic activity and structural features of MCR provides insights into its physiological and pathological significance and potential as a therapeutic target. Here, we report high-resolution crystal structures for wild-type MCR in a new crystal form (at 1.65 Å resolution) and for three active-site mutants, H126A, D156A and E241A, at 2.45, 1.64 and 1.85 Å resolutions, respectively. Our analysis of the new wild-type structure revealed a similar dimeric arrangement of MCR molecules to that previously reported and details of the catalytic site. The determination of the structures of these H126A, D156A and E241A mutants, along with their detailed kinetic analysis, has now allowed for a rigorous assessment of their catalytic properties. No significant change outside the enzymatic active site was observed in the three mutants, establishing that the diminution of catalytic activity is mainly attributable to disruption of the catalytic apparatus involving key hydrogen bonding and water-mediated interactions. The wild-type structure, together with detailed mutational and biochemical data, provide a basis for understanding the catalytic properties of this enzyme, which is important for the design of future anti-tuberculosis drug molecules. Full article
(This article belongs to the Special Issue Experimental and Theoretical Approaches to Protein-Targeting Drug Discovery: 2nd Edition)
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Review

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26 pages, 2942 KiB  
Review
HPMA Copolymers: A Versatile Platform for Targeted Peptide Drug Delivery
by Ya Li, Liangda Xing, Mingliang Zhu, Xian Li, Fangfang Wei, Wenyan Sun and Yinnong Jia
Biomolecules 2025, 15(4), 596; https://doi.org/10.3390/biom15040596 - 17 Apr 2025
Viewed by 228
Abstract
Peptide drugs have been broadly applied in cancer treatment and diagnosis due to their ability to accurately identify biomarkers with good biocompatibility. However, their clinical application is limited by protease degradation, which induces short circulation half-life, low bioavailability, and high renal clearance. In [...] Read more.
Peptide drugs have been broadly applied in cancer treatment and diagnosis due to their ability to accurately identify biomarkers with good biocompatibility. However, their clinical application is limited by protease degradation, which induces short circulation half-life, low bioavailability, and high renal clearance. In recent years, delivery systems based on nanomaterial technology have become an important strategy to break through the bottleneck of peptide drug delivery. Among them, N-(2-hydroxypropyl) methacrylamide (HPMA) copolymers have attracted much attention due to their good biocompatibility, hydrophilicity, and low immunogenicity. The high molecular weight of HPMA copolymer–peptide can circumvent renal clearance, significantly prolong the circulation time in the body, and achieve drug accumulation and microenvironment-triggered release synergistically with EPR effects and active targeting. This review introduces the basic properties of HPMA copolymers, including solubility, biocompatibility, and tunable chemical structure. The important applications of HPMA copolymer–peptide in tumor diagnosis and treatment are discussed. This review deepens our understanding of the future development of HPMA copolymers and will provide more references for improving peptides by simple copolymers. Full article
(This article belongs to the Special Issue Experimental and Theoretical Approaches to Protein-Targeting Drug Discovery: 2nd Edition)
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45 pages, 9857 KiB  
Review
Plant-Based Inhibitors of Protein Aggregation
by Olha Zhytniakivska, Tanmay Chaturvedi and Mette Hedegaard Thomsen
Biomolecules 2025, 15(4), 481; https://doi.org/10.3390/biom15040481 - 25 Mar 2025
Viewed by 297
Abstract
The assembly of amyloidogenic proteins and peptides into toxic oligomeric and fibrillar aggregates is closely connected to the onset and progression of more than 50 protein diseases, such as Alzheimer’s disease, Parkinson’s disease, prion disease, and type 2 diabetes, to name only a [...] Read more.
The assembly of amyloidogenic proteins and peptides into toxic oligomeric and fibrillar aggregates is closely connected to the onset and progression of more than 50 protein diseases, such as Alzheimer’s disease, Parkinson’s disease, prion disease, and type 2 diabetes, to name only a few. Considerable research efforts at identifying the therapeutic strategies against these maladies are currently focused on preventing and inhibiting pathogenic protein aggregation by various agents. Plant-based extracts and compounds have emerged as promising sources of potential inhibitors due to their dual role as nutraceuticals as part of healthy diets and as specific pharmaceuticals when administered at higher concentrations. In recent decades, several plant extracts and plant-extracted compounds have shown potential to modulate protein aggregation. An ever-growing body of research on plant-based amyloid inhibitors requires a detail analysis of existing data to identify potential knowledge gaps. This review summarizes the recent progress in amyloid inhibition using 17 flavonoids, 11 polyphenolic non-flavonoid compounds, 23 non-phenolic inhibitors, and 59 plant extracts, with the main emphasis on directly modulating the fibrillation of four amyloid proteins, namely amyloid-β peptide, microtubule-associated protein tau, α-synuclein, and human islet amyloid polypeptide. Full article
(This article belongs to the Special Issue Experimental and Theoretical Approaches to Protein-Targeting Drug Discovery: 2nd Edition)
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26 pages, 1530 KiB  
Review
A Survey on Computational Methods in Drug Discovery for Neurodegenerative Diseases
by Caterina Vicidomini, Francesco Fontanella, Tiziana D’Alessandro and Giovanni N. Roviello
Biomolecules 2024, 14(10), 1330; https://doi.org/10.3390/biom14101330 - 19 Oct 2024
Cited by 5 | Viewed by 2492
Abstract
Currently, the age structure of the world population is changing due to declining birth rates and increasing life expectancy. As a result, physicians worldwide have to treat an increasing number of age-related diseases, of which neurological disorders represent a significant part. In this [...] Read more.
Currently, the age structure of the world population is changing due to declining birth rates and increasing life expectancy. As a result, physicians worldwide have to treat an increasing number of age-related diseases, of which neurological disorders represent a significant part. In this context, there is an urgent need to discover new therapeutic approaches to counteract the effects of neurodegeneration on human health, and computational science can be of pivotal importance for more effective neurodrug discovery. The knowledge of the molecular structure of the receptors and other biomolecules involved in neurological pathogenesis facilitates the design of new molecules as potential drugs to be used in the fight against diseases of high social relevance such as dementia, Alzheimer’s disease (AD) and Parkinson’s disease (PD), to cite only a few. However, the absence of comprehensive guidelines regarding the strengths and weaknesses of alternative approaches creates a fragmented and disconnected field, resulting in missed opportunities to enhance performance and achieve successful applications. This review aims to summarize some of the most innovative strategies based on computational methods used for neurodrug development. In particular, recent applications and the state-of-the-art of molecular docking and artificial intelligence for ligand- and target-based approaches in novel drug design were reviewed, highlighting the crucial role of in silico methods in the context of neurodrug discovery for neurodegenerative diseases. Full article
(This article belongs to the Special Issue Experimental and Theoretical Approaches to Protein-Targeting Drug Discovery: 2nd Edition)
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