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Microorganisms
Special Issues
Viral Proteases in Viral Infection and Drug Development
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Viral Proteases in Viral Infection and Drug Development

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Virology".

Deadline for manuscript submissions: 31 October 2025 | Viewed by 3457

Special Issue Editors

Dr. Ye Qiu

E-Mail Website
Guest Editor
Hunan Provincial Key Laboratory of Medical Virology, College of Biology, Hunan University, Changsha 410012, China
Interests: enterovirus; virus–host interaction; pathogenic mechanism; antiviral
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Xing-Yi Ge

E-Mail Website
Guest Editor
Hunan Provincial Key Laboratory of Medical Virology, College of Biology, Hunan University, Changsha 410012, China
Interests: virus discovery; viral diversity and evolution; coronavirus; emerging pathogens
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The frequent emergence of viral epidemics has become a severe threat to public health around the world. Proteases are commonly expressed by various viruses, and viral proteases were initially believed to be required for viral protein processes. Increasingly more studies have since revealed that most viral proteases also cleave host proteins, benefiting viral replication, modulating the immune response, and determining viral pathogenesis. For instance, the 2A protease of enteroviruses cleaves eukaryotic initiation factor 4G, causing it to release more translational machinery for viral translation. Meanwhile, NSP3, the papain-like protease expressed by SARS-CoV-2, cleaves IRF3, which dulls the antiviral immunity mediated by Type-I interferons. Currently, viral proteases are important targets for the development of therapies against viral diseases. However, there are few studies regarding their cleavage patterns and interactions with host proteins, especially for the proteases of newly identified viruses. Investigating the roles of viral proteases in viral infection and immunity will deepen our understanding of viral pathogenesis and promote the development of antiviral drugs.

This Special Issue will focused on the following four points: (1) mutation and evolutionary features of viral proteases expressed by viruses and their impact on viral pathogenesis and transmissibility; (2) novel molecular mechanisms of viral proteases expressed by pathogenic viruses affecting viral infection, immunity, and pathogenesis, especially for epidemic or pandemic viruses; (3) database and algorithm for the prediction of cleavage sites targeted by viral proteases and their interactive networks with host proteins; and (4) strategies for drug development targeting viral proteases.

Dr. Ye Qiu
Prof. Dr. Xing-Yi Ge
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. Microorganisms 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 2700 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

  • virus
  • protease
  • proteolysis
  • immunity
  • virus–host interaction
  • pathogenic mechanism
  • antiviral drug
  • protease inhibitor

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Published Papers (3 papers)

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Research

17 pages, 8320 KB  
Article
ROS-Mediated Necroptosis Promotes Coxsackievirus B3 Replication and Myocardial Injury
by Junbo Huang, Yanjun Di, Qing Song, Zhiyun Cheng, Hao Wu, Mei Wu, Minjian He, Genrui Zhang, Fucai Wang and Lei Tong
Microorganisms 2025, 13(10), 2389; https://doi.org/10.3390/microorganisms13102389 - 17 Oct 2025
Viewed by 307
Abstract
Coxsackievirus B3 (CVB3) is a primary causative agent of viral myocarditis (VMC), which can lead to both acute and chronic cardiac inflammation accompanied by progressive heart failure and arrhythmias. Although CVB3 has been implicated in various forms of programmed cell death, whether it [...] Read more.
Coxsackievirus B3 (CVB3) is a primary causative agent of viral myocarditis (VMC), which can lead to both acute and chronic cardiac inflammation accompanied by progressive heart failure and arrhythmias. Although CVB3 has been implicated in various forms of programmed cell death, whether it triggers necroptosis and the underlying mechanisms remains unclear. This study aimed to investigate the role and mechanism of CVB3-induced necroptosis and its effect on viral replication. Using both in vitro and in vivo models, we demonstrated that CVB3 infection significantly upregulates the expression of key necroptotic markers RIP1 and RIP3 in HeLa cells and mouse myocardial tissues. This upregulation was accompanied by elevated intracellular reactive oxygen species (ROS) levels and suppression of the Nrf2/HO-1 antioxidant pathway. Intervention with the necroptosis inhibitor Necrostatin-1 (Nec-1) or the ROS scavenger N-acetylcysteine (NAC) markedly attenuated cell death, suppressed viral replication, and ameliorated myocardial injury and inflammatory responses in infected mice. Mechanistically, CVB3 inhibits the Nrf2/HO-1 pathway, thereby inducing substantial ROS accumulation that promotes necroptosis. This effect can be reversed by NAC treatment. Our study reveals a novel mechanism through which CVB3 induces ROS-dependent necroptosis via the suppression of the Nrf2/HO-1 pathway, providing new insights into the pathogenesis of viral myocarditis and suggesting potential therapeutic strategies. Full article
(This article belongs to the Special Issue Viral Proteases in Viral Infection and Drug Development)
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18 pages, 5272 KB  
Article
Cyclodextrin Counteracts Coxsackievirus-Induced Cardiac Damage by Protecting Desmosome Integrity and Suppressing Proinflammatory Cytokine Expression
by Guangze Zhao, Huifang M. Zhang, Grace J. Zhang, Wenli Yang, Christoph Küper, Bruce M. McManus and Decheng Yang
Microorganisms 2025, 13(10), 2294; https://doi.org/10.3390/microorganisms13102294 - 2 Oct 2025
Viewed by 399
Abstract
Nuclear factor of activated T cells 5 (NFAT5), an osmosensitive transcription factor, has been shown to protect against coxsackievirus B3 (CVB3)-induced myocarditis but is susceptible to cleavage by viral proteases. Identifying agents that upregulate NFAT5 may offer a novel antiviral strategy. Cyclodextrins, cyclic [...] Read more.
Nuclear factor of activated T cells 5 (NFAT5), an osmosensitive transcription factor, has been shown to protect against coxsackievirus B3 (CVB3)-induced myocarditis but is susceptible to cleavage by viral proteases. Identifying agents that upregulate NFAT5 may offer a novel antiviral strategy. Cyclodextrins, cyclic oligosaccharides that influence cellular osmolality, are promising candidates. In this study, we demonstrate that NFAT5 is critical for maintaining desmosomal integrity in cardiomyocytes. Cardiac-specific Nfat5-knockout mice showed a significant reduction in desmosomes, as observed by transmission electron microscopy. Furthermore, we identified desmoplakin (DSP), a structural desmosomal protein, as a direct transcriptional target of NFAT5, with reduced expression in Nfat5-knockout mouse hearts and NFAT5-knockdown HeLa cells. Notably, treatment with 5 mM cyclodextrin significantly upregulated NFAT5 expression with minimal cytotoxicity, restored DSP expression, and suppressed CVB3 replication by inhibiting viral RNA transcription, protein synthesis, and virion production. Additionally, cyclodextrin reduced mRNA levels of proinflammatory cytokines interleukin-1 beta and interleukin-8, indicating its potential role as an alleviator of excessive cytokine production. These findings identify NFAT5 as a key regulator of desmoplakin expression and prove cyclodextrin as a dual-functioning agent in counteracting cardiac damage through NFAT5-DSP-mediated protection of desmosome integrity and suppressing proinflammatory cytokine expression in CVB3-induced myocarditis. Full article
(This article belongs to the Special Issue Viral Proteases in Viral Infection and Drug Development)
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20 pages, 5392 KB  
Article
Coxsackievirus B3-Induced m6A Modification of RNA Enhances Viral Replication via Suppression of YTHDF-Mediated Stress Granule Formation
by Guangze Zhao, Huifang M. Zhang, Yankuan T. Chen, Kerry Shi, Sana Aghakeshmiri, Fione Yip, Honglin Luo, Bruce McManus and Decheng Yang
Microorganisms 2024, 12(11), 2152; https://doi.org/10.3390/microorganisms12112152 - 26 Oct 2024
Cited by 2 | Viewed by 2221
Abstract
N6-methyladenosine (m6A) is the most prevalent internal RNA modification. Here, we demonstrate that coxsackievirus B3 (CVB3), a common causative agent of viral myocarditis, induces m6A modification primarily at the stop codon and 3′ untranslated regions of its genome. As [...] Read more.
N6-methyladenosine (m6A) is the most prevalent internal RNA modification. Here, we demonstrate that coxsackievirus B3 (CVB3), a common causative agent of viral myocarditis, induces m6A modification primarily at the stop codon and 3′ untranslated regions of its genome. As a positive-sense single-stranded RNA virus, CVB3 replicates exclusively in the cytoplasm through a cap-independent translation initiation mechanism. Our study shows that CVB3 modulates the expression and nucleo-cytoplasmic transport of the m6A machinery components—METTL3, ALKBH5 and YTHDFs—resulting in increased m6A modifications that enhance viral replication. Mechanistically, this enhancement is mediated through YTHDF-driven stress granule (SG) formation. We observed that YTHDF proteins co-localize with human antigen R (HuR), a protein facilitating cap-independent translation, in SGs during early infection. Later in infection, YTHDFs are cleaved, suppressing SG formation. Notably, for the first time, we identified that during early infection CVB3’s RNA-dependent RNA polymerase (3D) and double-stranded RNA (dsRNA) are stored in SGs, co-localizing with HuR. This early-stage sequestration likely protects viral components for use in late-phase replication, when SGs are disrupted due to YTHDF cleavage. In summary, our findings reveal that CVB3-induced m6A modifications enhance viral replication by regulating YTHDF-mediated SG dynamics. This study provides a potential therapeutic strategy for CVB3-induced myocarditis. Full article
(This article belongs to the Special Issue Viral Proteases in Viral Infection and Drug Development)
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