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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

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Published Papers (2 papers)

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Research

21 pages, 3915 KiB

Open AccessArticle

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 1 | Viewed by 1261

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 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 (ΔG_bind) 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

Open AccessArticle

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 2 | Viewed by 987

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 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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