Antiviral Molecules Research Articles

Musashi1 inhibit the release of Newcastle disease viruses through preventing apoptosis of DF-1 cells

The efficient proliferation of Newcastle disease virus (NDV) depends on its inhibition of host cell innate immunity. V protein acts as a nonstructural protein which plays a significant role in virus replication, whereas its function remains to be further explored. In this study, Musashi RNA binding protein 1 (MSI1) was selected and its interaction with V protein was further verified by Co-immunoprecipitation (Co-IP) and Immuno-colocalization test. Through the transfection of pCMV-HA-MSI1 in DF-1 cells, the overexpression of MSI1 reduced virus particles in the cell supernatant but not reduced mRNA and virus protein in cells pellet, which suggests that MSI1may act as a new antiviral molecule by inhibiting viral release. Cell early apoptosis was detected by flow cytometry (FCM), the result shows that overexpression of MSI1 inhibit cell apoptosis, implying MSI1 Inhibit virus release may through this way. Taken together, MSI1 and NDV V protein has a detectable interaction, and may block apoptosis to inhibit the release of NDV. However, this is the first report about the interaction between MSI1 and V protein of NDV that can inhibit the NDV replicated.

Flavonoids as potential therapeutics against novel coronavirus disease-2019 (nCOVID-19)

Since time immemorial natural products have been a great source of medicine to mankind. The anti-viral activities from several ayurvedic herbal medicines (in the form of crude extract or fraction or isolated compounds) have been established but their effectiveness against coronavirus still needs to be explored. They can provide a rich resource of anti-SARS-CoV-2 drug candidates. In this paper, in-silico techniques have been used to identify the potential lead molecules against SARS-CoV-2. A list of flavonoids having anti-viral activity was prepared and evaluated against the selected target. Rhoifolin, 5,7-dimethoxyflavanone-4′-O-β-d-glucopyranoside, baicalin, astragalin, luteolin, and kaempferol showed good binding affinity and thus these could be promising compounds. In-silico screening such as ADMET prediction has been performed which predicted that the selected flavonoids have good pharmacokinetics and pharmacodynamics properties. Molecular dynamics simulation studies and MM-PBSA binding free energy calculations showed luteolin to be a more effective candidate against viral protein Mpro. The novelty of the approach mainly rests in the identification of potent anti-viral natural molecules from natural products flavonoid group of molecules to be effective against the latest coronavirus infection. Communicated by Ramaswamy H. Sarma

TLR7 Is Critical for Anti-Viral Humoral Immunity to EV71 Infection in the Spinal Cord

Enterovirus 71 (EV71) is a positive single-stranded RNA (ssRNA) virus from the enterovirus genus of Picornaviridae family and causes diseases ranged from the mild disease of hand, foot and mouth disease (HFMD) to the severe disease of neurological involvement in young children. TLR7 is an intracellular pattern recognition receptor (PRR) recognizing viral ssRNA. In this study, we investigated the role of TLR7 in EV71 infection in mouse pups (10-12 days old) and found that wild-type (WT) and TLR7 knock-out (TLR7KO) mice infected with EV71 showed similar limb paralysis at the onset and peak of the disease, comparable loss of motor neurons, and similar levels of antiviral molecules in the spinal cord. These results suggest that TLR7 is not the absolute PRR for EV71 in the spinal cord. Interestingly, TLR7KO mice infected with EV71 exhibited significantly delayed recovery from limb paralysis compared with WT mice. TLR7KO mice infected with EV71 showed significantly decreased levels of IgM and IgG2, important antibodies for antiviral humoral immunity. Furthermore, TLR7KO mice infected with EV71 showed a decrease of germinal center B cells in the spleen compared with WT mice. Altogether, our study suggests that TLR7 plays a critical role in anti-viral humoral immunity rather than in being a PRR in the spinal cord during EV71 infection in young mice.

Molecular docking, binding mode analysis, molecular dynamics, and prediction of ADMET/toxicity properties of selective potential antiviral agents against SARS-CoV-2 main protease: an effort toward drug repurposing to combat COVID-19.

The importance of the main protease (Mpro) enzyme of SARS-CoV-2 in the digestion of viral polyproteins introduces Mpro as an attractive drug target for antiviral drug design. This study aims to carry out the molecular docking, molecular dynamics studies, and prediction of ADMET properties of selected potential antiviral molecules. The study provides an insight into biomolecular interactions to understand the inhibitory mechanism and the spatial orientation of the tested ligands and further, identification of key amino acid residues within the substrate-binding pocket that can be applied for structure-based drug design. In this regard, we carried out molecular docking studies of chloroquine (CQ), hydroxychloroquine (HCQ), remdesivir (RDV), GS441524, arbidol (ARB), and natural product glycyrrhizin (GA) using AutoDock 4.2 tool. To study the drug-receptor complex's stability, selected docking possesses were further subjected to molecular dynamics studies with Schrodinger software. The prediction of ADMET/toxicity properties was carried out on ADMET Prediction™. The docking studies suggested a potential role played by CYS145, HIS163, and GLU166 in the interaction of molecules within the active site of COVID-19 Mpro. In the docking studies, RDV and GA exhibited superiority in binding with the crystal structure of Mpro over the other selected molecules in this study. Spatial orientations of the molecules at the active site of Mpro exposed the significance of S1–S4 subsites and surrounding amino acid residues. Among GA and RDV, RDV showed better and stable interactions with the protein, which is the reason for the lesser RMSD values for RDV. Overall, the present in silico study indicated the direction to combat COVID-19 using FDA-approved drugs as promising agents, which do not need much toxicity studies and could also serve as starting points for lead optimization in drug discovery.Graphic abstract

SARS-COV-2 and Ocular Surface: From Physiology to Pathology, a Route to Understand Transmission and Disease.

Coronaviruses gained public attention during the severe acute respiratory syndrome (SARS) outbreak in East Asia in 2003 and spread of Middle Eastern respiratory syndrome (MERS) in 2012. Direct human-to-human contact and droplet are the main methods of transmission. Viral stability in aerosols on different surfaces supports evidence on indirect viral acquisition from fomites through the mucous membranes of the mouth, nose, and eyes. Given the pandemic circumstances, the level of evidence in COVID-19 and ophthalmology regarding eye infection, conjunctival transmission, and viral shedding through tears is insufficient. Presently, conjunctival transmission of coronaviruses has not been confirmed and remains controversial. Considering the physiology of the lacrimal system and ocular surface, the eyes are considered an immunoprotective site, with several antiviral molecules and anti-inflammatory proteins. Nevertheless, they represent an interface with the exterior world and face daily putative aggressors. Understanding the host’s ocular surface immunological and protective environment is crucial to clarify the potential of the conjunctiva as an entry route for SARS-CoV-2 and as part of this viral infection. We will discuss hypothetical ocular surface transmission mechanisms and related counterarguments addressed to both angiotensin-converting enzyme 2 receptors found on the conjunctival and corneal epithelia and lactoferrin, lysozyme, lipocalin and secretory IgA levels in the tear film. Hopefully, we will promote better understanding of this organ in COVID-19 infection and the potential transmission route that can be helpful in setting recommendations on best practices and protective guidelines to mitigate the disease spread.

Ribavirin inhibits colorectal cancer growth by downregulating PRMT5 expression and H3R8me2s and H4R3me2s accumulation

Eukaryotic translation initiation factor 4E (eIF4E) and protein arginine methyltransferase 5 (PRMT5) are frequently overexpressed in colorectal cancer (CRC) tissues and associated with poor prognosis. Ribavirin, the only clinically approved drug known to target eIF4E, is an anti-viral molecule currently used in hepatitis C therapy. The potential of ribavirin to treat CRC remains largely unknown. Ribavirin treatment in CRC cell lines drastically inhibited cell proliferation and colony formation, induced S phase arrest and reduced cyclin D1, cyclin A/E and proliferating cell nuclear antigen (PCNA) levels in vitro, and suppressed tumorigenesis in mouse model of colitis-associated CRC. Mechanistically, ribavirin treatment significantly reduced PRMT5 and eIF4E protein levels and the accumulation of symmetric dimethylation of histone 3 at arginine 8 (H3R8me2s) and that of histone 4 at arginine 3 (H4R3me2s). Importantly, inhibition of PRMT5 by ribavirin resulted in promoted H3R8 methylation in eIF4E promoter region. Our results demonstrate the anti-cancer efficacy of ribavirin in CRC and suggest that the anti-cancer efficacy of ribavirin may be mediated by downregulating PRMT5 levels but not its enzymatic activity.

Promising Antiviral Molecules from Ayurvedic Herbs and Spices against COVID-19.

Promising Antiviral Molecules from Ayurvedic Herbs and Spices against COVID-19.

Screening, simulation, and optimization design of small molecule inhibitors of the SARS-CoV-2 spike glycoprotein.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak is a public health emergency of international concern. The spike glycoprotein (S protein) of SARS-CoV-2 is a key target of antiviral drugs. Focusing on the existing S protein structure, molecular docking was used in this study to calculate the binding energy and interaction sites between 14 antiviral molecules with different structures and the SARS-CoV-2 S protein, and the potential drug candidates targeting the SARS-CoV-2 S protein were analyzed. Tizoxanide, dolutegravir, bictegravir, and arbidol were found to have high binding energies, and they effectively bind key sites of the S1 and S2 subunits, inhibiting the virus by causing conformational changes in S1 and S2 during the fusion of the S protein with host cells. Based on the interactions among the drug molecules, the S protein and the amino acid environment around the binding sites, rational structure-based optimization was performed using the molecular connection method and bioisosterism strategy to obtain Ti-2, BD-2, and Ar-3, which have much stronger binding ability to the S protein than the original molecules. This study provides valuable clues for identifying S protein inhibitor binding sites and the mechanism of the anti-SARS-CoV-2 effect as well as useful inspiration and help for the discovery and optimization of small molecule S protein inhibitors.

Medicinal Plants and Their Bacterial Microbiota: A Review on Antimicrobial Compounds Production for Plant and Human Health.

Medicinal plants (MPs) have been used since antiquity in traditional and popular medicine, and they represent a very important source of bioactive molecules, including antibiotic, antiviral, and antifungal molecules. Such compounds are often of plant origin, but in some cases, an origin or a modification from plant microbiota has been shown. Actually, the research continues to report the production of bioactive molecules by plants, but the role of plant–endophytic interaction is emerging. Classic examples are mainly concerned with fungal endophytes; however, it has been recently shown that bacterial endophytes can also play an important role in influencing the plant metabolism related to the synthesis of bioactive compounds. In spite of this, a deep investigation on the power of MP bacterial endophytes is lacking. Here, an overview of the studies on MP bacterial microbiota and its role in the production of plant antimicrobial compounds contributing to prime host defense system and representing a huge resource for biotech and therapeutic applications is provided.

Measuring the subcellular compartmentalization of viral infections by protein complementation assay

The recent emergence and reemergence of viruses in the human population has highlighted the need to develop broader panels of therapeutic molecules. High-throughput screening assays opening access to untargeted steps of the viral replication cycle will provide powerful leverage to identify innovative antiviral molecules. We report here the development of an innovative protein complementation assay, termed αCentauri, to measure viral translocation between subcellular compartments. As a proof of concept, the Centauri fragment was either tethered to the nuclear pore complex or sequestered in the nucleus, while the complementary α fragment (<16 amino acids) was attached to the integrase proteins of infectious HIV-1. The translocation of viral ribonucleoproteins from the cytoplasm to the nuclear envelope or to the nucleoplasm efficiently reconstituted superfolder green fluorescent protein or NanoLuc αCentauri reporters. These fluorescence- or bioluminescence-based assays offer a robust readout of specific steps of viral infection in a multiwell format that is compatible for high-throughput screening and is validated by a short hairpin RNA-based prototype screen.

Screening and in vitro antiviral assessment of small molecules against fluorescent protein-expressing Bunyamwera virus in a cell-based assay using high-content imaging.

Many species of the order Bunyavirales contain potentially fatal viruses that lack effective medical countermeasures and are therefore collectively a major public health threat. Here, we describe a cell-based assay using Bunyamwera virus (BUNV)-mCherry to identify and characterize new antiviral molecules against bunyaviruses. BUNV is the type species for the genus Orthobunyavirus and has been reported to cause mild symptoms in humans, such as fever, joint pain, and rash. One major benefit of using our fluorescence-based assay over classical CPE-based assays is the fact that the antiviral effect of the tested compounds and their effect on the cell viability can be determined within the same assay well. For that reason, this type of assay could significantly advance our preclinical efforts towards finding new antiviral molecules against bunyaviruses.

The seven constitutive respiratory defense barriers against SARS-CoV-2 infection.

Before eliciting an adaptive immune response, SARS-CoV-2 must overcome seven constitutive respiratory defense barriers. The first is the mucus covering the respiratory tract’s luminal surface, which entraps inhaled particles, including infectious agents, and eliminates them by mucociliary clearance. The second barrier comprises various components present in the airway lining fluid, the surfactants. Besides providing low surface tension that allows efficient gas exchange at the alveoli, surfactants inhibit the invasion of epithelial cells by respiratory viruses, enhance pathogen uptake by phagocytes, and regulate immune cells’ functions. The respiratory tract microbiota constitutes the third defense barrier against SARS-CoV-2. It activates the innate and adaptive immune cells and elicits anti-infectious molecules such as secretory IgA antibodies, defensins, and interferons. The fourth defense barrier comprises the antimicrobial peptides defensins, and lactoferrin. They show direct antiviral activity, inhibit viral fusion, and modulate the innate and adaptive immune responses. Secretory IgA antibodies, the fifth defense barrier, besides protecting the local microbiota against noxious agents, also inhibit SARS-CoV-2 cell invasion. If the virus overcomes this barrier, it reaches its target, the respiratory epithelial cells. However, these cells also act as a defense barrier, the sixth one, since they hinder the virus’ access to receptors and produce antiviral and immunomodulatory molecules such as interferons, lactoferrin, and defensins. Finally, the sensing of the virus by the cells of innate immunity, the last constitutive defense barrier, elicits a cascade of signals that activate adaptive immune cells and may inhibit the development of productive infection. The subject of the present essay is discussing these mechanisms.

Investigation of Promising Antiviral Candidate Molecules based on Algal Phlorotannin for the Prevention of COVID-19 Pandemic by in silico Studies

Background: Coronavirus disease 19 (COVID-19) is a highly contagious and pathogenic viral infection. Research has been stepped up due to the lack of vaccine for this viral infection and no effective treatment against this new virus. In order to control the spread, the effectiveness of algal phlorotannin-derived natural molecules on COVID-19, which are easy to obtain, maintainable and have antiviral efficacy by focusing on the Spike (S) protein of the virus, was investigated by in silico methods. Materials and methods: In this study, molecular docking was performed to highlight the emerging role of the top three molecules amongst the selected 11 compounds against SARS CoV-2-RBD/ACE2 and SARS CoV-2-Spike/TMPRSS2. Results and Discussion: An in silico model of algal molecules interactivity on SARS CoV-2-RBD/ACE2 and SARS CoV-2-Spike/TMPRSS2 receptor was observed. Results suggested that based on in silico model, out of algal phlorotannin ligands, only a diecol showed good binding affinity toward SARS CoV-2-RBD/ACE2 interface, compared as remdesivir, chloroquine and hydroxychloroquine sulfate. Moreover within these potential molecules based phlorofucofuroeckol B can also be protector for only TMPRSS2. Conclusion: In future, these results may be aid to direction of the design and development of potent drugs for COVID-19 treatment based on the severity of infection.

Methods in Screening Antiviral Drugs Against Enterovirus 71.

Enteroviruses 71 (EV71) is a single-stranded, neurotrophic RNA virus responsible for the numerous outbreaks of hand, foot, and mouth disease (HFMD) in the Asia-Pacific regions. HFMD primarily affects children to cause range of infection, from mild symptoms to acute flaccid paralysis, and hemorrhage. Despite increased incidence of EV71 epidemics globally and research against EV71 becoming prioritized, no antiviral agent against EV71 has yet been licensed and approved worldwide. In this chapter, detailed EV71 antiviral screening techniques are described, including plaque assay which determines viral titers through the use of a semisolid overlay, carboxymethyl cellulose to allow even viral spread and infection across the host cellular monolayers as well as a crystal violet, a distinct counterstain to visualize circular regions of infectious zones-plaques. qRT-PCR is used to quantify the viral genomic RNA in the infected samples and MTS cell viability assay to quantify the cell viability after infection or toxicity of the compound on the cells. Furthermore, various antiviral inhibition assays including prophylactic, post infection, and virucidal assays are demonstrated for estimation of the antiviral activity of potential antiviral drugs against EV71. These methods can be effectively utilized in virology laboratories for effective high-throughput screening of antiviral molecules against EV71 that can assist in the future development of antiviral drugs.

Anti-Influenza Drug Discovery and Development: Targeting the Virus and Its Host by All Possible Means.

Infections by influenza virus constitute a major and recurrent threat for human health. Together with vaccines, antiviral drugs play a key role in the prevention and treatment of influenza virus infection and disease. Today, the number of antiviral molecules approved for the treatment of influenza is relatively limited, and their use is threatened by the emergence of viral strains with resistance mutations. There is therefore a real need to expand the prophylactic and therapeutic arsenal. This chapter summarizes the state of the art in drug discovery and development for the treatment of influenza virus infections, with a focus on both virus-targeting and host cell-targeting strategies. Novel antiviral strategies targeting other viral proteins or targeting the host cell, some of which are based on drug repurposing, may be used in combination to strengthen our therapeutic arsenal against this major pathogen.

Docking fundamentals for simulation in nanoscience

This work reviews the literature on the molecular docking process, presenting the simulation methodology, the construction parameters and how the results are interpreted. In this context, a study of molecular docking is carried out using the binding protein of the COVID-19 virus with the human cell, called spike, and an antiviral molecule called heparin. As a result, the parameters reached, distances, energies and three-dimensional positioning of the ligand-receptor system are shown. This type of work is currently done in the area of discovering new drugs, or drugs discovered with the aid of the computer. As a final discussion, it concludes the importance of computational knowledge as a way to support various chemical, physical and biological activities in the multidisciplinary field of nanoscience and nanotechnology.

Exosomes Transport Anti-Human Immunodeficiency Virus Factors from Human Cervical Epithelial Cells to Macrophages

The female reproductive tract (FRT) is a major site of HIV sexual transmission. As the outermost layer of cells in the FRT, the human cervical epithelial cells (HCEs) have direct contact with HIV or infected cells. Our early work showed that supernatant (SN) from TLR3-activated HCEs contain the antiviral factors that could potently inhibit HIV replication in macrophages. However, it remains to be determined how HCEs transport the anti-HIV factors to macrophages. This follow-up study examined the role of exosomes in HCE-mediated anti-HIV activity. We found that TLR3 activation of HCEs resulted in the release of exosomes that contained multiple IFN-stimulated genes (ISGs: ISG56, OAS1, MxA, and Mx2) and the HIV restriction microRNAs (miR-28, miR-29 family members, miR-125b, miR-150, miR-382, miR-223, miR-20a, and miR-198). The depletion of exosomes from SN of TLR3-activated HCEs diminished HCE-mediated anti-HIV activity in macrophages, indicating that HCE-derived exosomes are responsible for transporting the antiviral molecules to macrophages. These in vitro findings suggest a novel antiviral mechanism by which HCEs participate in the FRT innate immunity against HIV infection. Further in vivo studies are necessary in order to develop an exosome-based delivery system for prevention and treatment of HIV infection through sexual transmission.

Vaccine Design through Machine Learning and Nanotechnology to Terminate COVID-19 Pandemic

The COVID-19 vaccine development involves high-tech platforms such as viral vectors, antigen carriers, and delivery technology. Nanotechnology tools can play a pivotal role in advancing COVID-19 treatment and vaccine design. Information related to the structural morphology of the SARS-CoV-2 virus, its pathophysiology, and related immunological response is the most important factor at the nanotechnology point of view. In the absence of a specific antiviral against SARS- CoV-2, present therapeutics target the multifaceted molecular interactions involved in viral infections and major comprises repurposing already existing antiviral molecules used for other RNA viruses. Furthermore, various kinds of vaccine candidate’s structure could be screened by using ma- chine learning. Recently, it is equally important to look for a suitable Nano-carrier delivery technology to make these repurposed therapeutics as well as new vaccine development safer and more effective affordable methodologies so that nanotechnology can reach patients.

Molecular structure, NBO analysis of the hydrogen-bonded interactions, spectroscopic (FT–IR, FT–Raman), drug likeness and molecular docking of the novel anti COVID-2 molecule (2E)-N-methyl-2-[(4-oxo-4H-chromen-3-yl)methylidene]-hydrazinecarbothioamide (Dimer) - quantum chemical approach

Prospective antiviral molecule (2E)-N-methyl-2-[(4-oxo-4H-chromen-3-yl)methylidene]-hydrazinecarbothioamide has been probed using Fourier transform infrared (FTIR), FT-Raman and quantum chemical computations. The geometry equilibrium and natural bond orbital analysis have been carried out with density functional theory employing Becke, 3-parameter, Lee-Yang-Parr method with the 6-311G++(d,p) basis set. The vibrational assignments pertaining to different modes of vibrations have been augmented by normal coordinate analysis, force constant and potential energy distributions. Drug likeness and oral activity have been carried out based on Lipinski's rule of five. The inhibiting potency of 2(2E)-methyl-2-[(4-oxo-4H-chromen-3-yl)methylidene]-hydrazinecarbothioamide has been investigated by docking simulation against SARS-CoV-2 protein.The optimized geometry shows a planar structure between the chromone and the side chain. Differences in the geometries due to the substitution of the electronegative atom and intermolecular contacts due to the chromone and hydrazinecarbothioamide were analyzed. NBO analysis confirms the presence of two strong stable hydrogen bonded NH⋯O intermolecular interactions and two weak hydrogen bonded CH⋯O interactions. The red shift in NH stretching frequency exposed from IR substantiates the formation of NH⋯O intermolecular hydrogen bond and the blue shift in CH stretching frequency substantiates the formation of CH⋯O intermolecular hydrogen bond. Drug likeness, absorption, distribution, metabolism, excretion and toxicity property gives an idea about the pharmacokinetic properties of the title molecule. The binding energy of the nonbonding interaction with Histidine 41 and Cysteine 145, present a clear view that 2(2E)-methyl-2-[(4-oxo-4H-chromen-3-yl)methylidene]-hydrazinecarbothioamide can irreversibly interact with SARS-CoV-2 protease.

Drug Discovery of Small Molecules for the Treatment of COVID-19: A Review on Clinical Studies.

Recently, a sudden outbreak of novel coronavirus disease (COVID-19) was caused by a zoonotic virus known as severe acute respiratory syndrome coronavirus (SARS-CoV-2). It has caused pandemic situations around the globe affecting the lives of millions of people. So far, no drug has been approved for the treatment of SARS-CoV-2 infected patients. As of now, more than 1000 clinical trials are going on for repurposing of FDA-approved drugs and for evaluating the safety and efficiency of experimental antiviral molecules to combat COVID-19. Since the development of new drugs may require months to years to reach the market, this review focusses on the potential of existing small molecule FDA approved drugs and the molecules already in the clinical pipeline against viral infections like HIV, hepatitis B, Ebola virus, and other viruses of coronavirus family (SARS-CoV and MERS-CoV). The review also discusses the natural products and traditional medicines in clinical studies against COVID-19. Currently, 1978 studies are active, 143 completed and 4 posted results (as of June 13, 2020) on clinicaltrials.gov.