Antiviral Drug Targets of Single-Stranded RNA Viruses Causing Chronic Human Diseases

Liposome-Mediated Anti-Viral Drug Delivery Across Blood-Brain Barrier: Can Lipid Droplet Target Be Game Changers?

Lipid droplets (LDs) are subcellular organelles secreted from the endoplasmic reticulum (ER) that play a major role in lipid homeostasis. Recent research elucidates additional roles of LDs in cellular bioenergetics and innate immunity. LDs activate signaling cascades for interferon response and secretion of pro-inflammatory cytokines. Since balanced lipid homeostasis is critical for neuronal health, LDs play a crucial role in neurodegenerative diseases. RNA viruses enhance the secretion of LDs to support various phases of their life cycle in neurons which further leads to neurodegeneration. Targeting the excess LD formation in the brain could give us a new arsenal of antiviral therapeutics against neuroviruses. Liposomes are a suitable drug delivery system that could be used for drug delivery in the brain by crossing the Blood-Brain Barrier. Utilizing this, various pharmacological inhibitors and non-coding RNAs can be delivered that could inhibit the biogenesis of LDs or reduce their sizes, reversing the excess lipid-related imbalance in neurons. Liposome-Mediated Antiviral Drug Delivery Across Blood-Brain Barrier. Developing effective antiviral drug is challenging and it doubles against neuroviruses that needs delivery across the Blood-Brain Barrier (BBB). Lipid Droplets (LDs) are interesting targets for developing antivirals, hence targeting LD formation by drugs delivered using Liposomes can be game changers.

In silico screening of chalcones and flavonoids as potential inhibitors against yellow head virus 3C-like protease

Yellow head virus (YHV) is one of the most important pathogens in prawn cultivation. The outbreak of YHV could potentially result in collapses in aquaculture industries. Although a flurry of development has been made in searching for preventive and therapeutic approaches against YHV, there is still no effective therapy available in the market. Previously, computational screening has suggested a few cancer drugs to be used as YHV protease (3CL^pro) inhibitors. However, their toxic nature is still of concern. Here, we exploited various computational approaches, such as deep learning-based structural modeling, molecular docking, pharmacological prediction, and molecular dynamics simulation, to search for potential YHV 3CL^pro inhibitors. A total of 272 chalcones and flavonoids were in silico screened using molecular docking. The bioavailability, toxicity, and specifically drug-likeness of hits were predicted. Among the hits, molecular dynamics simulation and trajectory analysis were performed to scrutinize the compounds with high binding affinity. Herein, the four selected compounds including chalcones cpd26, cpd31 and cpd50, and a flavonoid DN071_f could be novel potent compounds to prevent YHV and GAV propagation in shrimp. The molecular mechanism at the atomistic level is also enclosed that can be used to further antiviral development.

Near-physiological-temperature serial crystallography reveals conformations of SARS-CoV-2 main protease active site for improved drug repurposing

The COVID-19 pandemic has resulted in 198 million reported infections and more than 4 million deaths as of July 2021 (covid19.who.int). Research to identify effective therapies for COVID-19 includes: (1) designing a vaccine as future protection; (2) de novo drug discovery; and (3) identifying existing drugs to repurpose them as effective and immediate treatments. To assist in drug repurposing and design, we determine two apo structures of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease at ambient temperature by serial femtosecond X-ray crystallography. We employ detailed molecular simulations of selected known main protease inhibitors with the structures and compare binding modes and energies. The combined structural and molecular modeling studies not only reveal the dynamics of small molecules targeting the main protease but also provide invaluable opportunities for drug repurposing and structure-based drug design strategies against SARS-CoV-2.

Specific antiviral effect of violaceoid E on bovine leukemia virus

Bovine leukemia virus (BLV) infection has spread worldwide causing significant economic losses in the livestock industry. In countries with a high prevalence of BLV, minimizing economic losses is challenging; thus, research into various countermeasures is important for improving BLV control. Because anti-BLV drugs have not been developed, the present study explored a promising chemical compound with anti-BLV activity. Initially, screening of a chemical compound library revealed that violaceoid E (vioE), which is isolated from fungus, showed antiviral activity. Further analysis demonstrated that the antiviral effect of vioE inhibited transcriptional activation of BLV. Cellular thermal shift assay and pulldown assays provided evidence for a direct interaction between vioE and the viral transactivator protein, Tax. These data indicate that interference with Tax-dependent transcription could be a novel target for development of anti-BLV drugs. Therefore, it is suggested that vioE is a novel antiviral compound against BLV.

A Mini Review on Emerging Targets and Approaches for the Synthesis of Anti-viral Compounds: In Perspective to COVID-19

The novel Coronavirus disease (COVID-19) is an epidemic disease that appeared at the end of the year 2019 with a sudden increase in number and came to be considered as a pandemic disease caused by a viral infection which has threatened most countries for an emergency search for new anti-SARS-COV drugs /vaccines. At present, the number of clinical trials is ongoing worldwide on different drugs i.e. Hydroxychloroquine, Remedisvir, Favipiravir that utilize various mechanisms of action. A few countries are currently processing clinical trials, which may result in a positive outcome. Favipiravir (FPV) represents one of the feasible treatment options for COVID-19, if the result of the trials turns out positive. Favipiravir will be one of the developed possibly authoritative drugs to warrant benefits to mankind with large-scale production to meet the demands of the current pandemic Covid-19 outbreak and future epidemic outbreaks. In this review, the authors tried to explore key molecules, which will be supportive for devising COVID-19 research.

Antiviral activity of bioactive phytocompounds against coronavirus: An update

Viral infections are one of the main cause of diseases worldwide due to the rising trends of migration, urbanization and global mobility of humans. The outbreak of corona virus diseases caused by SARS-CoV (year 2003), MERS-CoV (year 2012) and SARS-CoV-2 (year 2019) raised global health concerns. The side effects associated with the conventional drugs and increase in cases of anti-microbial resistance have led the researchers to switch to natural sources, especially plants, as they have immense potential to be used as antiviral agents. The aim of the article is to summarize the evidences of the bioactive phytocompounds from different plants as an effective alternative for the treatment of infections caused by coronaviruses. However, the use of most plant compounds succumbs to limitations due to lack of experimental evidences and safety studies. Therefore, further research and studies are required to validate their therapeutic uses for wide application of plant-based medicine, including anti-virals.

Addressing Non-linear System Dynamics of Single-Strand RNA Virus-Host Interaction

Positive single-strand ribonucleic acid [(+)ssRNA] viruses can cause multiple outbreaks, for which comprehensive tailored therapeutic strategies are still missing. Virus and host cell dynamics are tightly connected, generating a complex dynamics that conveys in virion assembly to ensure virus spread in the body. Starting from the knowledge of relevant processes in (+ss)RNA virus replication, transcription, translation, virions budding and shedding, and their respective energy costs, we built up a systems thinking (ST)-based diagram of the virus-host interaction, comprehensive of stocks, flows, and processes as well-described in literature. In ST approach, stocks and flows are expressed by a proxy of the energy embedded and transmitted, respectively, whereas processes are referred to the energy required for the system functioning. In this perspective, healthiness is just a particular configuration, in which stocks relevant for the system (equivalent but not limited to proteins, RNA, DNA, and all metabolites required for the survival) are constant, and the system behavior is stationary. At time of infection, the presence of additional stocks (e.g., viral protein and RNA and all metabolites required for virion assembly and spread) confers a complex network of feedbacks leading to new configurations, which can evolve to maximize the virions stock, thus changing the system structure, output, and purpose. The dynamic trajectories will evolve to achieve a new stationary status, a phenomenon described in microbiology as integration and symbiosis when the system is resilient enough to the changes, or the system may stop functioning and die. Application of external driving forces, acting on processes, can affect the dynamic trajectories adding a further degree of complexity, which can be captured by ST approach, used to address these new configurations. Investigation of system configurations in response to external driving forces acting is developed by computational analysis based on ST diagrams, with the aim at designing novel therapeutic approaches.

Antiviral activity of chlorpromazine, fluphenazine, perphenazine, prochlorperazine, and thioridazine towards RNA-viruses. A review

In 2020 the whole world focused on antivirus drugs towards SARS-CoV-2. Most of the researchers focused on drugs used in other viral infections or malaria. We have not seen such mobilization towards one topic in this century. The whole situation makes clear that progress needs to be made in antiviral drug development. The first step to do it is to characterize the potential antiviral activity of new or already existed drugs on the market. Phenothiazines are antipsychotic agents used previously as antiseptics, anthelminthics, and antimalarials. Up to date, they are tested for a number of other disorders including the broad spectrum of viruses. The goal of this paper was to summarize the current literature on activity toward RNA-viruses of such drugs like chlorpromazine, fluphenazine, perphenazine, prochlorperazine, and thioridazine. We identified 49 papers, where the use of the phenothiazines for 23 viruses from different families were tested. Chlorpromazine, fluphenazine, perphenazine, prochlorperazine, and thioridazine possess anti-viral activity towards different types of viruses. These drugs inhibit clathrin-dependent endocytosis, cell-cell fusion, infection, replication of the virus, decrease viral invasion as well as suppress entry into the host cells. Additionally, since the drugs display activity at nontoxic concentrations they have therapeutic potential for some viruses, still, further research on animal and human subjects are needed in this field to verify cell base research.

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Phenothiazines possess antiviral activity towards RNA viruses.

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An antiviral activity can be achieved below toxic serum concentration.

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Phenothiazines are characterized by multidirectional points of action.

Multiple Gene Expression Dataset Analysis Reveals Toll-Like Receptor Signaling Pathway is Strongly Associated With Chronic Obstructive Pulmonary Disease Pathogenesis

Chronic obstructive pulmonary disease is a complex pulmonary disease that causes airflow obstruction in humans. To identify the core genes in COPD pathogenesis, seven diverse microarray datasets (GSE475, GSE1122, GSE1650, GSE3212, GSE8823, GSE37768, and GSE22148) were downloaded from the gene expression omnibus database. All the datasets were analyzed independently with the R/Bioconductor package to screen the differentially expressed genes (DEGs). The gene ontology and pathway enrichment analysis were performed for the acquired DEGs using DAVID (Database for Annotation, Visualization, and Integrated Discovery). Further protein-protein interaction network was constructed for the DEGs and their potential hub genes and sub-networks were identified using Cytoscape software. From the selected seven datasets, 188 overlapped DEGs were perceived eventually based on considering the repetitive genes between at-least one dataset. Gene Ontology analysis reveals that most of the DEGs were significantly enriched in immune response, inflammatory response, extracellular region, lipid binding, cytokine, and chemokine activity. Moreover, genes from the sub-network analysis were again submitted to the DAVID server to validate the results which uncover the Toll-like receptor signaling pathway was significantly enriched and all the genes present in this pathway were likewise detected as hub genes from Cytoscape software. CXCL9, CXCL10, CXCL11, CCL4, TLR7, and SPP1 hub genes in the toll-like receptor signaling pathway were explored in this study as potential biomarker genes associated with COPD pathogenesis.

The emerging role and significance of circular RNAs in viral infections and antiviral immune responses: possible implication as theranostic agents

Circular RNAs (circRNAs) are ubiquitously expressed, covalently closed rings, produced by pre-mRNA splicing in a reversed order during post-transcriptional processing. Circularity endows 3'-5'-linked circRNAs with stability and resistance to exonucleolytic degradation which raises the question whether circRNAs may be relevant as potential therapeutic targets or agents. High stability in biological systems is the most remarkable property and a major criterion for why circRNAs could be exploited for a range of RNA-centred medical applications. Even though various biological roles and regulatory functions of circRNAs have been reported, their in-depth study is challenging because of their circular structure and sequence-overlap with linear mRNA counterparts. Moreover, little is known about their role in viral infections and in antiviral immune responses. We believe that an in-depth and detailed understanding of circRNA mediated viral protein regulations will increase our knowledge of the biology of these novel molecules. In this review, we aimed to provide a comprehensive basis and overview on the biogenesis, significance and regulatory roles of circRNAs in the context of antiviral immune responses and viral infections including hepatitis C virus infection, hepatitis B virus infection, hepatitis delta virus infection, influenza A virus infection, Epstein-Barr virus infection, kaposi's sarcoma herpesvirus infection, human cytomegalovirus infection, herpes simplex virus infection, human immunodeficiency virus infection, porcine epidemic diarrhoea virus infection, ORF virus infection, avian leukosis virus infection, simian vacuolating virus 40 infection, transmissible gastroenteritis coronavirus infection, and bovine viral diarrhoea virus infection. We have also discussed the critical regulatory role of circRNAs in provoking antiviral immunity, providing evidence for implications as therapeutic agents and as diagnostic markers.

High throughput virtual screening reveals SARS-CoV-2 multi-target binding natural compounds to lead instant therapy for COVID-19 treatment

The present-day world is severely suffering from the recently emerged SARS-CoV-2. The lack of prescribed drugs for the deadly virus has stressed the likely need to identify novel inhibitors to alleviate and stop the pandemic. In the present high throughput virtual screening study, we used in silico techniques like receptor-ligand docking, Molecular dynamic (MD), and ADME properties to screen natural compounds. It has been documented that many natural compounds display antiviral activities, including anti–SARS-CoV effect. The present study deals with compounds of Natural Product Activity and Species Source (NPASS) database with known biological activity that probably impedes the activity of six essential enzymes of the virus. Promising drug-like compounds were identified, demonstrating better docking score and binding energy for each druggable targets. After an extensive screening analysis, three novel multi-target natural compounds were predicted to subdue the activity of three/more major drug targets simultaneously. Concerning the utility of natural compounds in the formulation of many therapies, we propose these compounds as excellent lead candidates for the development of therapeutic drugs against SARS-CoV-2.