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Novel Antiviral Agents: Synthesis, Molecular Modelling Studies and Biological Investigation,...
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Novel Antiviral Agents: Synthesis, Molecular Modelling Studies and Biological Investigation, 2nd Edition

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "Viral Immunology, Vaccines, and Antivirals".

Deadline for manuscript submissions: closed (31 December 2024) | Viewed by 8578

Special Issue Editor

Dr. Simone Brogi

E-Mail Website
Guest Editor
Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
Interests: in silico pharmacology; computational toxicology; computer-aided drug design; modelling and simulation; infectious diseases
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Infectious diseases continue to be one of the major causes of human and animal morbidity and mortality, accounting for ~20% of global deaths. Among them, viruses are responsible for about one-third of these deaths. During the last two decades, emerging and re-emerging viruses, such as the recent SARS-CoV-2 as well as related coronaviruses (SARS and MERS), avian influenza A (H5N1, H1N1, and H7N9) viruses, Zika virus, and enteroviruses, have posed significant global public health threats. Accordingly, the necessity to identify innovative antiviral agents, vaccines, novel therapeutic approaches based on drug repurposing, and novel strategies for early diagnosis and prevention are urgently needed, also considering the possibility of future outbreaks. In this scenario, computational procedures, including innovative machine learning approaches, could accelerate the discovery of effective antiviral agents and therapeutic strategies. To this end, we cordially invite researchers working in the antiviral drug discovery field, with a special focus on computer-aided drug discovery and molecular virology, to submit original research articles, short communications, and review articles related to the discovery of novel antiviral agents.

Dr. Simone Brogi
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. Viruses 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 2600 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

  • antiviral agents
  • in silico tools
  • emerging infectious diseases
  • viruses

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Related Special Issue

Published Papers (6 papers)

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Editorial

Jump to: Research, Review

7 pages, 4012 KiB  
Editorial
Novel Antiviral Agents: Synthesis, Molecular Modelling Studies and Biological Investigation, 2nd Edition
by Simone Brogi
Viruses 2025, 17(5), 601; https://doi.org/10.3390/v17050601 - 23 Apr 2025
Viewed by 155
Abstract
After the success of the Special Issue entitled “Novel Antiviral Agents: Synthesis, Molecular Modelling Studies and Biological Investigation” (https://www [...] Full article
(This article belongs to the Special Issue Novel Antiviral Agents: Synthesis, Molecular Modelling Studies and Biological Investigation, 2nd Edition)
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Research

Jump to: Editorial, Review

27 pages, 11687 KiB  
Article
Modeling and Molecular Dynamics Studies of Flavone―DENV E-3 Protein―SWCNT Interaction at the Flavonoid Binding Sites
by Cecilia Espíndola
Viruses 2025, 17(4), 525; https://doi.org/10.3390/v17040525 - 4 Apr 2025
Viewed by 307
Abstract
The DENV virus circulates freely in endemic regions and causes dengue disease. The vectors are Aedes aegypti and Aedes albopictus. The difficulties inherent in the nature of the DENV virus, its epidemiology, and its increasing incidence in recent years have led to [...] Read more.
The DENV virus circulates freely in endemic regions and causes dengue disease. The vectors are Aedes aegypti and Aedes albopictus. The difficulties inherent in the nature of the DENV virus, its epidemiology, and its increasing incidence in recent years have led to the development of viable alternatives in the search for effective solutions for the treatment of this severe disease. Flavones such as tropoflavin, baicalein, and luteolin have anti-DENV activity. Molecular docking studies were performed between the flavones tropoflavin, baicalein, and luteolin and the DENV E-3 protein. Flavone—DENV E-3 complex interactions were analyzed at the flavonoid binding sites domain I of the B chain and domain II of the A chain reported in the literature. H-bond, π-π stacking, and π-cation interactions between flavones and the DENV E-3 protein at different binding energies were evaluated. Molecular dynamics studies for these interactions were performed to determine the molecular stability of the Flavone—DENV E-3 complexes. I also present here the results of the molecular interactions of the Flavone—DENV E-3―SWCNT complex. Due to recent advances in nanotechnology and their physicochemical properties, the utilization of nanoparticles such as SWCNT has increased in antiviral drug delivery. Full article
(This article belongs to the Special Issue Novel Antiviral Agents: Synthesis, Molecular Modelling Studies and Biological Investigation, 2nd Edition)
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16 pages, 2775 KiB  
Article
Development of a Cell Culture Model for Inducible SARS-CoV-2 Replication
by Xiaoyan Wang, Yuanfei Zhu, Qiong Wu, Nan Jiang, Youhua Xie and Qiang Deng
Viruses 2024, 16(5), 708; https://doi.org/10.3390/v16050708 - 29 Apr 2024
Cited by 1 | Viewed by 1864
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) induces direct cytopathic effects, complicating the establishment of low-cytotoxicity cell culture models for studying its replication. We initially developed a DNA vector-based replicon system utilizing the CMV promoter to generate a recombinant viral genome bearing reporter [...] Read more.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) induces direct cytopathic effects, complicating the establishment of low-cytotoxicity cell culture models for studying its replication. We initially developed a DNA vector-based replicon system utilizing the CMV promoter to generate a recombinant viral genome bearing reporter genes. However, this system frequently resulted in drug resistance and cytotoxicity, impeding model establishment. Herein, we present a novel cell culture model with SARS-CoV-2 replication induced by Cre/LoxP-mediated DNA recombination. An engineered SARS-CoV-2 transcription unit was subcloned into a bacterial artificial chromosome (BAC) vector. To enhance biosafety, the viral spike protein gene was deleted, and the nucleocapsid gene was replaced with a reporter gene. An exogenous sequence was inserted within NSP1 as a modulatory cassette that is removable after Cre/LoxP-mediated DNA recombination and subsequent RNA splicing. Using the PiggyBac transposon strategy, the transcription unit was integrated into host cell chromatin, yielding a stable cell line capable of inducing recombinant SARS-CoV-2 RNA replication. The model exhibited sensitivity to the potential antivirals forsythoside A and verteporfin. An innovative inducible SARS-CoV-2 replicon cell model was introduced to further explore the replication and pathogenesis of the virus and facilitate screening and assessment of anti-SARS-CoV-2 therapeutics. Full article
(This article belongs to the Special Issue Novel Antiviral Agents: Synthesis, Molecular Modelling Studies and Biological Investigation, 2nd Edition)
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21 pages, 3915 KiB  
Article
Structure-Based High-Throughput Virtual Screening and Molecular Dynamics Simulation for the Discovery of Novel SARS-CoV-2 NSP3 Mac1 Domain Inhibitors
by Behnaz Yazdani, Hajar Sirous, Simone Brogi and Vincenzo Calderone
Viruses 2023, 15(12), 2291; https://doi.org/10.3390/v15122291 - 22 Nov 2023
Cited by 7 | Viewed by 2511
Abstract
Since the emergence of SARS-CoV-2, many genetic variations within its genome have been identified, but only a few mutations have been found in nonstructural proteins (NSPs). Among this class of viral proteins, NSP3 is a multidomain protein with 16 different domains, and its [...] Read more.
Since the emergence of SARS-CoV-2, many genetic variations within its genome have been identified, but only a few mutations have been found in nonstructural proteins (NSPs). Among this class of viral proteins, NSP3 is a multidomain protein with 16 different domains, and its largest domain is known as the macrodomain or Mac1 domain. In this study, we present a virtual screening campaign in which we computationally evaluated the NCI anticancer library against the NSP3 Mac1 domain, using Molegro Virtual Docker. The top hits with the best MolDock and Re-Rank scores were selected. The physicochemical analysis and drug-like potential of the top hits were analyzed using the SwissADME data server. The binding stability and affinity of the top NSC compounds against the NSP3 Mac1 domain were analyzed using molecular dynamics (MD) simulation, using Desmond software, and their interaction energies were analyzed using the MM/GBSA method. In particular, by applying subsequent computational filters, we identified 10 compounds as possible NSP3 Mac1 domain inhibitors. Among them, after the assessment of binding energies (ΔGbind) on the whole MD trajectories, we identified the four most interesting compounds that acted as strong binders of the NSP3 Mac1 domain (NSC-358078, NSC-287067, NSC-123472, and NSC-142843), and, remarkably, it could be further characterized for developing innovative antivirals against SARS-CoV-2. Full article
(This article belongs to the Special Issue Novel Antiviral Agents: Synthesis, Molecular Modelling Studies and Biological Investigation, 2nd Edition)
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15 pages, 4642 KiB  
Article
Lichen or Associated Micro-Organism Compounds Are Active against Human Coronaviruses
by Lowiese Desmarets, Marion Millot, Marylène Chollet-Krugler, Joël Boustie, Charline Camuzet, Nathan François, Yves Rouillé, Sandrine Belouzard, Sophie Tomasi, Lengo Mambu and Karin Séron
Viruses 2023, 15(9), 1859; https://doi.org/10.3390/v15091859 - 31 Aug 2023
Cited by 6 | Viewed by 1852
Abstract
(1) Background: Since the emergence of SARS-CoV-2, responsible for the COVID-19 pandemic, efforts have been made to identify antiviral compounds against human coronaviruses. With the aim of increasing the diversity of molecule scaffolds, 42 natural compounds, of which 28 were isolated from lichens [...] Read more.
(1) Background: Since the emergence of SARS-CoV-2, responsible for the COVID-19 pandemic, efforts have been made to identify antiviral compounds against human coronaviruses. With the aim of increasing the diversity of molecule scaffolds, 42 natural compounds, of which 28 were isolated from lichens and 14 from their associated microorganisms (bacteria and fungi), were screened against human coronavirus HCoV-229E. (2) Methods: Antiviral assays were performed using HCoV-229E in Huh-7 and Huh-7/TMPRSS2 cells and SARS-CoV-2 in a Vero-81-derived clone with a GFP reporter probe. (3) Results: Four lichen compounds, including chloroatranol, emodin, perlatolic acid and vulpinic acid, displayed high activities against HCoV-229E (IC50 = 68.86, 59.25, 16.42 and 14.58 μM, respectively) and no toxicity at active concentrations. Kinetics studies were performed to determine their mode of action. The four compounds were active when added at the replication step. Due to their significant activity, they were further tested on SARS-CoV-2. Perlatolic acid was shown to be active against SARS-CoV-2. (4) Conclusions: Taken together, these results show that lichens are a source of interesting antiviral agents against human coronaviruses. Moreover, perlatolic acid might be further studied for its pan-coronavirus antiviral activity. Full article
(This article belongs to the Special Issue Novel Antiviral Agents: Synthesis, Molecular Modelling Studies and Biological Investigation, 2nd Edition)
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Review

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33 pages, 8711 KiB  
Review
A Comparison of Conserved Features in the Human Coronavirus Family Shows That Studies of Viruses Less Pathogenic than SARS-CoV-2, Such as HCoV-OC43, Are Good Model Systems for Elucidating Basic Mechanisms of Infection and Replication in Standard Laboratories
by Audrey L. Heffner and Tracey A. Rouault
Viruses 2025, 17(2), 256; https://doi.org/10.3390/v17020256 - 13 Feb 2025
Viewed by 951
Abstract
In 2021, at the height of the COVID-19 pandemic, coronavirus research spiked, with over 83,000 original research articles related to the word “coronavirus” added to the online resource PubMed. Just 2 years later, in 2023, only 30,900 original research articles related to [...] Read more.
In 2021, at the height of the COVID-19 pandemic, coronavirus research spiked, with over 83,000 original research articles related to the word “coronavirus” added to the online resource PubMed. Just 2 years later, in 2023, only 30,900 original research articles related to the word “coronavirus” were added. While, irrefutably, the funding of coronavirus research drastically decreased, a possible explanation for the decrease in interest in coronavirus research is that projects on SARS-CoV-2, the causative agent of COVID-19, halted due to the challenge of establishing a good cellular or animal model system. Most laboratories do not have the capabilities to culture SARS-CoV-2 ‘in house’ as this requires a Biosafety Level (BSL) 3 laboratory. Until recently, BSL 2 laboratory research on endemic coronaviruses was arduous due to the low cytopathic effect in isolated cell culture infection models and the lack of means to quantify viral loads. The purpose of this review article is to compare the human coronaviruses and provide an assessment of the latest techniques that use the endemic coronaviruses—HCoV-229E, HCoV-OC43, HCoV-NL63, and HCoV-HKU1—as lower-biosafety-risk models for the more pathogenic coronaviruses—SARS-CoV-2, SARS-CoV, and MERS-CoV. Full article
(This article belongs to the Special Issue Novel Antiviral Agents: Synthesis, Molecular Modelling Studies and Biological Investigation, 2nd Edition)
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