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 4126

Special Issue Editors


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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
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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

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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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Published Papers (2 papers)

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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
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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
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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 2 | Viewed by 1584
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
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