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Viruses
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De Novo Drug Design for Emerging and Reemerging Viruses
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De Novo Drug Design for Emerging and Reemerging Viruses

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 2022) | Viewed by 25449

Special Issue Editors

Prof. Dr. Ke Xu

E-Mail Website
Guest Editor
State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
Interests: viral-host interplay; SARS-CoV; influenza A virus; site-targeted antivirals
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Yu Chen

grade E-Mail Website
Guest Editor
State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
Interests: RNA virus infection; viral infection, replication; antiviral immunity; viral RNA processing; viral pathogenesis; anti-viral strategy

Special Issue Information

Dear Colleagues

For emerging and re-emerging viruses that are zoonotic in origin, de novo drug design targeting viral proteins and viral life cycles provides an efficient approach to inhibit virus replication and therefore cure the disease. A greater understanding of the basic virology of these viruses, including virus entry, cellular receptors, virus–cell fusion, viral RNA or DNA synthesis and duplication, and virus assembly and release, has resulted in many successful antiviral drugs in the last 20 years. Computer-based drug design or high-throughput drug screening against Influenza virus, Hepatitis C, and HIV have generated effective drugs that are available in many countries clinically. The development of drugs against highly pathogenic viruses such as the Ebola Virus and SARS-CoV-2 is yet ongoing and should be encouraged more because a considerable number of patients are still suffering from these viruses.

Additionally, drugs targeting cellular factors and regulating host immune response have been found to have great potential in antiviral applications. So-called “host-targeting antivirals (HTA)” are meant to be a novel strategy for broad-spectrum antivirals.

This Special Issue is designed to provide an up-to-date review of the latest progress and technologies in de novo drug design (such drugs can be small molecular, peptides, antibodies, etc.) for emerging and re-emerging viruses targeting viral or host proteins based on their protein structures or their unique functions in the viral life cycle.

Prof. Dr. Ke Xu
Prof. Dr. Yu Chen
Dr. Li Zhou
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. 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 drugs
  • de-novo drug design
  • emerging virus
  • SARS-CoV 2

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Published Papers (7 papers)

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Research

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19 pages, 4200 KiB  
Article
Design of Three Residues Peptides against SARS-CoV-2 Infection
by Carla Zannella, Annalisa Chianese, Giuseppe Greco, Biagio Santella, Giuseppe Squillaci, Alessandra Monti, Nunzianna Doti, Giuseppina Sanna, Aldo Manzin, Alessandra Morana, Anna De Filippis, Gianni D’Angelo, Francesco Palmieri, Gianluigi Franci and Massimiliano Galdiero
Viruses 2022, 14(10), 2103; https://doi.org/10.3390/v14102103 - 22 Sep 2022
Cited by 11 | Viewed by 2837
Abstract
The continuous and rapid spread of the COVID-19 pandemic has emphasized the need to seek new therapeutic and prophylactic treatments. Peptide inhibitors are a valid alternative approach for the treatment of emerging viral infections, mainly due to their low toxicity and high efficiency. [...] Read more.
The continuous and rapid spread of the COVID-19 pandemic has emphasized the need to seek new therapeutic and prophylactic treatments. Peptide inhibitors are a valid alternative approach for the treatment of emerging viral infections, mainly due to their low toxicity and high efficiency. Recently, two small nucleotide signatures were identified in the genome of some members of the Coronaviridae family and many other human pathogens. In this study, we investigated whether the corresponding amino acid sequences of such nucleotide sequences could have effects on the viral infection of two representative human coronaviruses: HCoV-OC43 and SARS-CoV-2. Our results showed that the synthetic peptides analyzed inhibit the infection of both coronaviruses in a dose-dependent manner by binding the RBD of the Spike protein, as suggested by molecular docking and validated by biochemical studies. The peptides tested do not provide toxicity on cultured cells or human erythrocytes and are resistant to human serum proteases, indicating that they may be very promising antiviral peptides. Full article
(This article belongs to the Special Issue De Novo Drug Design for Emerging and Reemerging Viruses)
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12 pages, 2445 KiB  
Article
High-Throughput Screening of FDA-Approved Drug Library Reveals Ixazomib Is a Broad-Spectrum Antiviral Agent against Arboviruses
by Cuiling Ding, Wanda Tang, Binghui Xia, Haoran Peng, Yan Liu, Jiaqi Wang, Xu Zheng, Yangang Liu, Lanjuan Zhao, Yanhua He, Zhongtian Qi, Hao Ren, Hailin Tang and Ping Zhao
Viruses 2022, 14(7), 1381; https://doi.org/10.3390/v14071381 - 24 Jun 2022
Cited by 7 | Viewed by 2274
Abstract
The emergence of significant arboviruses and their spillover transmission to humans represent a major threat to global public health. No approved drugs are available for the treatment of significant arboviruses in circulation today. The repurposing of clinically approved drugs is one of the [...] Read more.
The emergence of significant arboviruses and their spillover transmission to humans represent a major threat to global public health. No approved drugs are available for the treatment of significant arboviruses in circulation today. The repurposing of clinically approved drugs is one of the most rapid and promising strategies in the identification of effective treatments for diseases caused by arboviruses. Here, we screened small-molecule compounds with anti-tick-borne encephalitis virus, West Nile virus, yellow fever virus and chikungunya virus activity from 2580 FDA-approved drugs. In total, 60 compounds showed antiviral efficacy against all four of the arboviruses in Huh7 cells. Among these compounds, ixazomib and ixazomib citrate (inhibitors of 20S proteasome β5) exerted antiviral effects at a low-micromolar concentration. The time-of-drug-addition assay suggested that ixazomib and ixazomib citrate disturbed multiple processes in viruses’ life cycles. Furthermore, ixazomib and ixazomib citrate potently inhibited chikungunya virus replication and relieved virus-induced footpad swelling in a mouse model. These results offer critical information which supports the role of ixazomib as a broad-spectrum agent against arboviruses. Full article
(This article belongs to the Special Issue De Novo Drug Design for Emerging and Reemerging Viruses)
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13 pages, 2159 KiB  
Article
Azelnidipine Exhibits In Vitro and In Vivo Antiviral Effects against Flavivirus Infections by Targeting the Viral RdRp
by Zhuang Wang, Yunzheng Yan, Qingsong Dai, Yijie Xu, Jiye Yin, Wei Li, Yuexiang Li, Xiaotong Yang, Xiaojia Guo, Miaomiao Liu, Xingjuan Chen, Ruiyuan Cao and Wu Zhong
Viruses 2022, 14(6), 1228; https://doi.org/10.3390/v14061228 - 5 Jun 2022
Cited by 3 | Viewed by 2491
Abstract
Flaviviruses, represented by Zika and dengue virus (ZIKV and DENV), are widely present around the world and cause various diseases with serious consequences. However, no antiviral drugs have been clinically approved for use against them. Azelnidipine (ALP) is a dihydropyridine calcium channel blocker [...] Read more.
Flaviviruses, represented by Zika and dengue virus (ZIKV and DENV), are widely present around the world and cause various diseases with serious consequences. However, no antiviral drugs have been clinically approved for use against them. Azelnidipine (ALP) is a dihydropyridine calcium channel blocker and has been approved for use as an antihypertensive drug. In the present study, ALP was found to show potent anti-flavivirus activities in vitro and in vivo. ALP effectively prevented the cytopathic effect induced by ZIKV and DENV and inhibited the production of viral RNA and viral protein in a dose-dependent manner. Moreover, treatment with 0.3 mg/kg of ALP protected 88.89% of mice from lethal challenge. Furthermore, using the time-of-drug-addition assay, the enzymatic inhibition assay, the molecular docking, and the surface plasmon resonance assay, we revealed that ALP acted at the replication stage of the viral infection cycle by targeting the viral RNA-dependent RNA polymerase. These findings highlight the potential for the use of ALP as an antiviral agent to combat flavivirus infections. Full article
(This article belongs to the Special Issue De Novo Drug Design for Emerging and Reemerging Viruses)
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12 pages, 1639 KiB  
Article
Molnupiravir and Its Active Form, EIDD-1931, Show Potent Antiviral Activity against Enterovirus Infections In Vitro and In Vivo
by Yuexiang Li, Miaomiao Liu, Yunzheng Yan, Zhuang Wang, Qingsong Dai, Xiaotong Yang, Xiaojia Guo, Wei Li, Xingjuan Chen, Ruiyuan Cao and Wu Zhong
Viruses 2022, 14(6), 1142; https://doi.org/10.3390/v14061142 - 25 May 2022
Cited by 13 | Viewed by 3367
Abstract
Enterovirus infections can cause hand, foot, and mouth disease (HFDM), aseptic meningitis, encephalitis, myocarditis, and acute flaccid myelitis, leading to death of infants and young children. However, no specific antiviral drug is currently available for the treatment of this type of infection. The [...] Read more.
Enterovirus infections can cause hand, foot, and mouth disease (HFDM), aseptic meningitis, encephalitis, myocarditis, and acute flaccid myelitis, leading to death of infants and young children. However, no specific antiviral drug is currently available for the treatment of this type of infection. The Unites States and United Kingdom health authorities recently approved a new antiviral drug, molnupiravir, for the treatment of COVID-19. In this study, we reported that molnupiravir (EIDD-2801) and its active form, EIDD-1931, have broad-spectrum anti-enterovirus potential. Our data showed that EIDD-1931 could significantly reduce the production of EV-A71 progeny virus and the expression of EV-A71 viral protein at non-cytotoxic concentrations. The results of the time-of-addition assay suggest that EIDD-1931 acts at the post-entry step, which is in accordance with its antiviral mechanism. The intraperitoneal administration of EIDD-1931 and EIDD-2801 protected 1-day-old ICR suckling mice from lethal EV-A71 challenge by reducing the viral load in various tissues of the infected mice. The pharmacokinetics analysis indicated that the plasma drug concentration overwhelmed the EC50 for enteroviruses, suggesting the clinical potential of molnupiravir against enteroviruses. Thus, molnupiravir along with its active form, EIDD-1931, may be a promising drug candidate against enterovirus infections. Full article
(This article belongs to the Special Issue De Novo Drug Design for Emerging and Reemerging Viruses)
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Review

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15 pages, 1024 KiB  
Review
New Targets for Antiviral Therapy: Inhibitory Receptors and Immune Checkpoints on Myeloid Cells
by Yanni Liu, Paul Nicklin and Yuan He
Viruses 2022, 14(6), 1144; https://doi.org/10.3390/v14061144 - 25 May 2022
Viewed by 1981
Abstract
Immune homeostasis is achieved by balancing the activating and inhibitory signal transduction pathways mediated via cell surface receptors. Activation allows the host to mount an immune response to endogenous and exogenous antigens; suppressive modulation via inhibitory signaling protects the host from excessive inflammatory [...] Read more.
Immune homeostasis is achieved by balancing the activating and inhibitory signal transduction pathways mediated via cell surface receptors. Activation allows the host to mount an immune response to endogenous and exogenous antigens; suppressive modulation via inhibitory signaling protects the host from excessive inflammatory damage. The checkpoint regulation of myeloid cells during immune homeostasis raised their profile as important cellular targets for treating allergy, cancer and infectious disease. This review focuses on the structure and signaling of inhibitory receptors on myeloid cells, with particular attention placed on how the interplay between viruses and these receptors regulates antiviral immunity. The status of targeting inhibitory receptors on myeloid cells as a new therapeutic approach for antiviral treatment will be analyzed. Full article
(This article belongs to the Special Issue De Novo Drug Design for Emerging and Reemerging Viruses)
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17 pages, 4294 KiB  
Review
A Broad Antiviral Strategy: Inhibitors of Human DHODH Pave the Way for Host-Targeting Antivirals against Emerging and Re-Emerging Viruses
by Yucheng Zheng, Shiliang Li, Kun Song, Jiajie Ye, Wenkang Li, Yifan Zhong, Ziyan Feng, Simeng Liang, Zeng Cai and Ke Xu
Viruses 2022, 14(5), 928; https://doi.org/10.3390/v14050928 - 28 Apr 2022
Cited by 27 | Viewed by 5214
Abstract
New strategies to rapidly develop broad-spectrum antiviral therapies are urgently required for emerging and re-emerging viruses. Host-targeting antivirals (HTAs) that target the universal host factors necessary for viral replication are the most promising approach, with broad-spectrum, foresighted function, and low resistance. We and [...] Read more.
New strategies to rapidly develop broad-spectrum antiviral therapies are urgently required for emerging and re-emerging viruses. Host-targeting antivirals (HTAs) that target the universal host factors necessary for viral replication are the most promising approach, with broad-spectrum, foresighted function, and low resistance. We and others recently identified that host dihydroorotate dehydrogenase (DHODH) is one of the universal host factors essential for the replication of many acute-infectious viruses. DHODH is a rate-limiting enzyme catalyzing the fourth step in de novo pyrimidine synthesis. Therefore, it has also been developed as a therapeutic target for many diseases relying on cellular pyrimidine resources, such as cancers, autoimmune diseases, and viral or bacterial infections. Significantly, the successful use of DHODH inhibitors (DHODHi) against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection further supports the application prospects. This review focuses on the advantages of HTAs and the antiviral effects of DHODHi with clinical applications. The multiple functions of DHODHi in inhibiting viral replication, stimulating ISGs expression, and suppressing cytokine storms make DHODHi a potent strategy against viral infection. Full article
(This article belongs to the Special Issue De Novo Drug Design for Emerging and Reemerging Viruses)
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26 pages, 2047 KiB  
Review
Polysaccharides and Their Derivatives as Potential Antiviral Molecules
by Hadrien Claus-Desbonnet, Elsa Nikly, Vanya Nalbantova, Diana Karcheva-Bahchevanska, Stanislava Ivanova, Guillaume Pierre, Niko Benbassat, Plamen Katsarov, Philippe Michaud, Paolina Lukova and Cédric Delattre
Viruses 2022, 14(2), 426; https://doi.org/10.3390/v14020426 - 18 Feb 2022
Cited by 45 | Viewed by 6083
Abstract
In the current context of the COVID-19 pandemic, it appears that our scientific resources and the medical community are not sufficiently developed to combat rapid viral spread all over the world. A number of viruses causing epidemics have already disseminated across the world [...] Read more.
In the current context of the COVID-19 pandemic, it appears that our scientific resources and the medical community are not sufficiently developed to combat rapid viral spread all over the world. A number of viruses causing epidemics have already disseminated across the world in the last few years, such as the dengue or chinkungunya virus, the Ebola virus, and other coronavirus families such as Middle East respiratory syndrome (MERS-CoV) and severe acute respiratory syndrome (SARS-CoV). The outbreaks of these infectious diseases have demonstrated the difficulty of treating an epidemic before the creation of vaccine. Different antiviral drugs already exist. However, several of them cause side effects or have lost their efficiency because of virus mutations. It is essential to develop new antiviral strategies, but ones that rely on more natural compounds to decrease the secondary effects. Polysaccharides, which have come to be known in recent years for their medicinal properties, including antiviral activities, are an excellent alternative. They are essential for the metabolism of plants, microorganisms, and animals, and are directly extractible. Polysaccharides have attracted more and more attention due to their therapeutic properties, low toxicity, and availability, and seem to be attractive candidates as antiviral drugs of tomorrow. Full article
(This article belongs to the Special Issue De Novo Drug Design for Emerging and Reemerging Viruses)
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