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Antiviral Drug Targets: Structure, Function, and Drug Design—3rd Edition
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Antiviral Drug Targets: Structure, Function, and Drug Design—3rd Edition

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Pharmacology".

Deadline for manuscript submissions: 20 May 2026 | Viewed by 2903

Special Issue Editors

Dr. Mattia Mori

E-Mail Website
Guest Editor
Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
Interests: zinc-binding proteins; medicinal chemistry; molecular dynamics; virtual screening; natural products; antiviral agents; anticancer agents; chemoinformatics; computational structural biology; lead optimization
Special Issues, Collections and Topics in MDPI journals
Dr. Ilaria Vicenti

E-Mail Website
Guest Editor
Department of Medical Biotechnologies, University of Siena, Siena, Italy
Interests: flaviviruses; HIV-1; SARS-COV-2; antivirals; cell-based viral assays; drug resistance, live virus neutralization
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Today, viral infections present a serious health and social problem, as underlined by the recent coronavirus pandemic. Several other viruses (e.g., Ebola, Zika, West Nile, Dengue, and Chikungunya virus) which lack available drugs or vaccines also present a concrete risk of epidemic spread. Antiviral drug design adopts contributions from different disciplines—characterization of virus type, elucidation of structural features of macromolecular targets, and understanding of the mechanisms of viral replication in the host— to notably accelerate the identification of suitable drug targets. Antiviral agents are designed and optimized accordingly, through multiple techniques including computational, chemical, biochemical, biophysical, and biological studies, as well as through integrated combinations of these methods.

This Special Issue collates recent findings on antiviral drug targets, with a focus on structural and functional elucidations and drug design. Submissions of original research papers and reviews within this broad and relevant field are welcome.

Dr. Mattia Mori
Dr. Ilaria Vicenti
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 250 words) can be sent to the Editorial Office for assessment.

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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • viral infections
  • drug design
  • protein structures
  • functional studies
  • viruses
  • antiviral drugs

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Related Special Issues

Published Papers (3 papers)

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Research

18 pages, 17888 KB  
Article
Construction and Application of a Canine SLAM Receptor-Based System from Vero Cell Line to Virus Isolation and Parallel Antibody Screening
by Jianbo Xu, Xiangda Hu, Sizhuo Chen, Zhenhuan Zhao, Zhangchang Wang, Minghui Wang, Zhongchuan Tang, Mingqian Feng, Zhiyuan Zhao and Xin Chen
Int. J. Mol. Sci. 2026, 27(4), 1895; https://doi.org/10.3390/ijms27041895 - 16 Feb 2026
Viewed by 112
Abstract
Canine distemper virus (CDV) remains a highly contagious and lethal pathogen, posing a severe global threat to domestic dogs and wild carnivores. To address the urgent need for effective interventions, we utilized a proprietary Vero-SLAM cell platform to isolate a wild-type CDV strain [...] Read more.
Canine distemper virus (CDV) remains a highly contagious and lethal pathogen, posing a severe global threat to domestic dogs and wild carnivores. To address the urgent need for effective interventions, we utilized a proprietary Vero-SLAM cell platform to isolate a wild-type CDV strain and generate neutralizing polyclonal antibodies. Subsequently, phage display technology was employed to screen for single-chain variable fragments (scFvs) targeting the CDV hemagglutinin protein (CDV-H). This approach led to the identification of a specific scFv with virus-binding affinity comparable to commercial antibodies, which effectively blocks CDV infection in Vero-SLAM cells. Molecular docking and molecular dynamics simulations were conducted to elucidate the interaction mechanism, suggesting that this scFv binds to a novel and unique epitope on the CDV-H. These findings not only expand our understanding of the antigenic properties of the CDV H protein but also provide a theoretical foundation and a promising candidate molecule for the development of future CDV diagnostics and antiviral strategies. Full article
(This article belongs to the Special Issue Antiviral Drug Targets: Structure, Function, and Drug Design—3rd Edition)
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33 pages, 3225 KB  
Article
Discovery of N-Hydroxypyridinedione-Based Inhibitors of HBV RNase H: Design, Synthesis, and Extended SAR Studies
by Dea Chotzalli, Vasiliki Pardali, Holly M. Walden, Dimitrios Perivolaris, Dimitrios Moianos, Maria Makri, Antonios Drakopoulos, Erofili Giannakopoulou, Razia Tajwar, Molly E. Woodson, John E. Tavis and Grigoris Zoidis
Int. J. Mol. Sci. 2025, 26(20), 10239; https://doi.org/10.3390/ijms262010239 - 21 Oct 2025
Viewed by 1189
Abstract
Hepatitis B Virus (HBV) continues to pose a significant global health challenge, with over 254 million chronic infections and current therapies being non-curative, necessitating lifelong treatment. The HBV ribonuclease H (RNase H) is essential during HBV reverse transcription by cleaving the viral pregenomic [...] Read more.
Hepatitis B Virus (HBV) continues to pose a significant global health challenge, with over 254 million chronic infections and current therapies being non-curative, necessitating lifelong treatment. The HBV ribonuclease H (RNase H) is essential during HBV reverse transcription by cleaving the viral pregenomic RNA after it has been copied into the (−) polarity DNA strand, enabling the viral polymerase to synthesize the (+) DNA strand. Although RNase H inhibition terminates viral replication and thus viral infectiveness, its targeting as an HBV treatment is unexploited. Its catalytic site contains four carboxylates that bind to two Mg2+ ions essential for RNA hydrolysis. As part of our ongoing research on RNase H inhibitors, we developed 23 novel N-hydroxypyridinedione (HPD) analogues. Specifically, 17 HPD imines, 4 HPD oximes, 1 2,6-diamino-4-((substituted)oxy)pyrimidine 1-oxide derivative, and 1 barbituric acid analogue were designed, synthesized, and tested for their anti-HBV activity. The HPD derivatives could be docked in the RNase H active site to coordinate the two Mg2+ ions and effectively inhibited viral replication in cellular assays. The 50% effective concentration (EC50) values of these HPD compounds ranged from 0.5 to 73 μM, while the 50% cytotoxic concentration (CC50) values ranged from 15 to 100 μM, resulting in selectivity indexes (SIs) up to 112. Furthermore, the novel HPD derivatives exhibited favourable pharmacokinetic-relevant characteristics, including high cellular permeability, good aqueous solubility, and overall drug-like properties. These findings indicate that HPD imines and oximes possess substantial antiviral potency and selectivity against HBV, underscoring the potential of the HPD scaffold as a promising framework for the development of next-generation anti-HBV agents. Full article
(This article belongs to the Special Issue Antiviral Drug Targets: Structure, Function, and Drug Design—3rd Edition)
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13 pages, 645 KB  
Article
Influenza a Virus Inhibition: Evaluating Computationally Identified Cyproheptadine Through In Vitro Assessment
by Sanja Glisic, Kristina Stevanovic, Andrej Perdih, Natalya Bukreyeva, Junki Maruyama, Vladimir Perovic, Sergi López-Serrano, Ayub Darji, Draginja Radosevic, Milan Sencanski, Veljko Veljkovic, Bruno Botta, Mattia Mori and Slobodan Paessler
Int. J. Mol. Sci. 2025, 26(13), 5962; https://doi.org/10.3390/ijms26135962 - 21 Jun 2025
Viewed by 1209
Abstract
Influenza is still a chronic global health threat, inducing a sustained search for effective antiviral therapeutics. Computational methods have played a pivotal role in developing small molecule therapeutics. In this study, we applied a combined in silico and in vitro approach to explore [...] Read more.
Influenza is still a chronic global health threat, inducing a sustained search for effective antiviral therapeutics. Computational methods have played a pivotal role in developing small molecule therapeutics. In this study, we applied a combined in silico and in vitro approach to explore the potential anti-influenza activity of cyproheptadine, a clinically used histamine H1 receptor antagonist. Virtual screening based on the average quasivalence number (AQVN) and electron–ion interaction potential (EIIP) descriptors suggests similarities between cyproheptadine and several established anti-influenza agents. The subsequent ligand-based pharmacophore screening of a focused H1 antagonist library was aligned with the bioinformatics prediction, and further experimental in vitro evaluation of cyproheptadine demonstrated its anti-influenza activity. These findings provide proof of concept for cyproheptadine’s in silico-predicted antiviral potential and underscore the value of integrating computational predictions with experimental validation. The results of the current study provide a preliminary proof of concept for the predicted anti-influenza potential based on computational analysis and emphasize the utility of integrating in silico screening with experimental validation in the early stages of drug repurposing efforts. Full article
(This article belongs to the Special Issue Antiviral Drug Targets: Structure, Function, and Drug Design—3rd Edition)
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