Antiviral Drug Discovery Research Articles

Open drug discovery of anti-virals critical for Canada’s pandemic strategy

In the event of the current COVID-19 pandemic and in preparation for future pandemics, open science can support mission-oriented research and development, as well as commercialization. Open science shares skills and resources across sectors; avoids duplication and provides the basis for rapid and effective validation due to full transparency. It is a strategy that can adjust quickly to reflect changing incentives and priorities, because it does not rely on any one actor or sector. While eschewing patents, it can ensure high-quality drugs, low pricing, and access through existing regulatory mechanisms. Open science practices and partnerships decrease transaction costs, increase diversity of actors, reduce overall costs, open new, higher-risk/higher-impact approaches to research, and provide entrepreneurs freedom to operate and freedom to innovate. We argue that it is time to re-open science, not only in its now restricted arena of fundamental research, but throughout clinical translation. Our model and attendant recommendations map onto a strategy to accelerate discovery of novel broad-spectrum anti-viral drugs and clinical trials of those drugs, from first-in-human safety-focused trials to late stage trials for efficacy. The goal is to ensure low-cost and rapid access, globally, and to ensure that Canadians do not pay a premium for drugs developed from Canadian science.

Development of hybrid model for improving the prediction of dengue-human protein interaction for anti-viral drug discovery

Dengue fever is the most common viral disease caused by mosquitoes. Due to the lack of curable drugs, there is an urgent need to develop anti-viral against dengue disease. Several innovative computational approaches were incorporated for the discovery of a new lead molecule that acts on the dengue virus target. The target can be a viral or host protein. Predicting the type of interaction between the virus and human protein will give better knowledge in developing therapeutics against the dengue disease. The main objective of this study is to propose a hybrid model which combines feed forward back propagation neural network (FFBPNN) with firefly algorithm to predict the dengue-human protein interaction. The novelty in this study is to focus on optimising the weights and bias of the artificial neural network to improve the efficiency of algorithm. While comparing with existing C4.5 and FFBPNN classification algorithms, the results show that the proposed hybrid method fitted the interaction data efficiently and predicts the interaction type which leads to the development of anti-viral drugs. The accuracy of the classification gained by C4.5 is 88%, FFBPNN is 97% and hybrid FFBPNN is 99%.

Development of hybrid model for improving the prediction of dengue-human protein interaction for anti-viral drug discovery

Development of hybrid model for improving the prediction of dengue-human protein interaction for anti-viral drug discovery

Nanobody-based sandwich reporter system for living cell sensing influenza A virus infection

The influenza epidemic is a huge burden to public health. Current influenza vaccines provide limited protection against new variants due to frequent mutation of the virus. The continual emergence of novel variants necessitates the method rapidly monitoring influenza virus infection in experimental systems. Although several replication-competent reporter viruses carrying fluorescent proteins or small luciferase have been generated in previous studies, visualizing influenza virus infection via such strategy requires reverse genetic modification for each viral strain which is usually time-consuming and inconvenient. Here, we created a novel influenza A nucleoprotein (NP) dependent reporter gene transcription activation module using NP-specific nanobodies. Our results demonstrated the modular design allowed reporter genes (mNeonGreen fluorescent protein and Gaussia luciferase) specifically expressing to detect intracellular NP protein, and therefore acts as a universal biosensor to monitor infection of various influenza A subtypes in living cells. The new system may provide a powerful tool to analyze influenza A infections at the cellular level to facilitate new antiviral drug discovery. Moreover, this approach may easily extend to develop live-cell biosensors for other viruses.

Flavivirus RNA-Dependent RNA Polymerase Interacts with Genome UTRs and Viral Proteins to Facilitate Flavivirus RNA Replication.

Flaviviruses, most of which are emerging and re-emerging human pathogens and significant public health concerns worldwide, are positive-sense RNA viruses. Flavivirus replication occurs on the ER and is regulated by many mechanisms and factors. NS5, which consists of a C-terminal RdRp domain and an N-terminal methyltransferase domain, plays a pivotal role in genome replication and capping. The C-terminal RdRp domain acts as the polymerase for RNA synthesis and cooperates with diverse viral proteins to facilitate productive RNA proliferation within the replication complex. Here, we provide an overview of the current knowledge of the functions and characteristics of the RdRp, including the subcellular localization of NS5, as well as the network of interactions formed between the RdRp and genome UTRs, NS3, and the methyltransferase domain. We posit that a detailed understanding of RdRp functions may provide a target for antiviral drug discovery and therapeutics.

Perspectives towards antiviral drug discovery against Ebola virus.

Ebola virus disease (EVD), caused by Ebola viruses, resulted in more than 11 500 deaths according to a recent 2018 WHO report. With mortality rates up to 90%, it is nowadays one of the most deadly infectious diseases. However, no Food and Drug Administration‐approved Ebola drugs or vaccines are available yet with the mainstay of therapy being supportive care. The high fatality rate and absence of effective treatment or vaccination make Ebola virus a category‐A biothreat pathogen. Fortunately, a series of investigational countermeasures have been developed to control and prevent this global threat. This review summarizes the recent therapeutic advances and ongoing research progress from research and development to clinical trials in the development of small‐molecule antiviral drugs, small‐interference RNA molecules, phosphorodiamidate morpholino oligomers, full‐length monoclonal antibodies, and vaccines. Moreover, difficulties are highlighted in the search for effective countermeasures against EVD with additional focus on the interplay between available in silico prediction methods and their evidenced potential in antiviral drug discovery.

A Graph-Based Approach for Finding the Dengue Infection Pathways in Humans Using Protein-Protein Interactions.

Dengue virus (DENV) is one of the deadly arboviruses, which is primarily transmitted by Aedes aegypti, and causes dengue infection to the humans. According to WHO, every year around 390 million humans are affected by DENV, of which around 50 million deaths are reported. Knowledge of the various diseases caused by the DENV would greatly encourage to understand the infection mechanism and help to design new antiviral drug discovery. We propose a quasi-clique and quasi-biclique algorithm to classify infection gateway proteins of the human body and possible pathways of DENV leading to various diseases. For this, we have examined three networks, dengue-human protein-protein interaction network, human protein interaction network, and human proteins-disease association network. The prediction result states that DENV may lead to various diseases in the human body, including cancer, asthma, ulcerative colitis, multiple sclerosis, premature birth, and so on. Some of the results have recently been validated experimentally. This study may endow with potential targets for more effective anti-dengue remedial contribution.

Fluorine-Containing Chrysin Derivatives

Chrysin, a flavonoid, has played a great role in the fields of anticancer, antibacterial, and antiviral drug discovery. A large number of chrysin derivatives have been synthesized recently. The fluorine atom represents an important substituent group for a great number of natural products and pharmaceuticals. Taking into account the importance of both chrysin and the fluorine atom in medicinal chemistry, the synthesis of fluorine-containing chrysin derivatives has gained great interest. Chemically, the synthetic methods for these new chrysin derivatives have also been developed rapidly. In recent years, research on their synthesis has been focused on speeding up the reaction process by changing the catalyst. Biologically, the purpose of introducing fluorine into chrysin was to improve its lipophilicity, but today it is mainly focused on the enhancement and improvement of either its anticancer or antimicrobial activities by incorporating the special properties of fluorine atoms. In this review, synthetic methods for the introduction of fluorine atoms into chrysin are summarized, and their anticancer, antibacterial, antiviral, and hypoglycemic effects are discussed.

Enhancing Hepatitis C virus pseudoparticles infectivity through p7NS2 cellular expression

Hepatitis C pseudoparticles (HCVpp) are used to evaluate HCV cell entry while screening for neutralizing antibodies induced upon vaccination or while screening for new antiviral drugs. In this work we explore the stable production of HCVpp aiming to reduce the variability associated with transient productions. The performance of stably produced HCVpp was assessed by evaluating the influence of Human Serum and the impact of CD81 cellular expression on the infectivity of HCVpp. After evaluating the performance of stably produced HCVpp we studied the effect of co-expressing p7NS2 openreading frame (ORF) on HCVpp infectivity. Our data clearly shows an enhanced infectivity of HCVppp7NS2. Even though the exact mechanism was not completely elucidated, the enhanced infectivity of HCVppp7NS2 is neither a result of an increase production of virus particles nor a result from increased envelope density. The inhibitory effect of p7 inhibitory molecules such as rimantadine suggests a direct contribution of p7 ion channel for the enhanced infectivity of HCVppp7NS2 which is coherent with a pH-dependent cell entry mechanism. In conclusion, we report the establishment of a stable production system of HCVpp with enhanced infectivity through the overexpression of p7NS2 ORF contributing to improve HCV entry assessment assays widely used in antiviral drug discovery and vaccine development.

ERADICATION OF HCV INFECTION IN PATIENTS WITH LIVER CIRRHOSIS: FACTOR OF CANCER PREVENTION OR CARCINOGENESIS?

Hepatocellular carcinoma (HCC) is one of the most common causes of death from cancer and is the final stage of chronic liver disease, usually occurring in patients with cirrhosis (CP). Chronic infection with hepatitis C virus (HCV) leads to progressive liver inflammation and cirrhosis because this virus specifically affects liver tissue. Previously used interferon therapy had a relatively low efficiency and very high risks of side effects. During the period of administration of interferon (IFN) schemes it was proved that elimination of the virus significantly reduced risk of liver cancer development. Discovery of direct-acting antiviral (DAA ) drugs have revolutionized HCV therapy with virus elimination rate of more than 95 % and an excellent safety profile. However, the risk of transformation of liver cirrhosis into hepatocellular carcinoma is still high even after complete eradication of the virus. Numerous studies have shown conflicting results on the possible relationship between the use of new antiviral drugs and the increase in the frequency of newly diagnosed or recurrent hepatocellular carcinoma. Thus, the long-term prognosis in terms of risk for HCC development among patients with sustained virological response (SVR) remains unclear.The purpose of the studywas to analyze the literature on the effect of antiviral therapy of chronic hepatitis C with interferon-containing regimens and drugs of direct antiviral action on the risk of developing or recurring hepatocellular carcinoma.Material and Methods. We analyzed publications available from PubMed, S copus, E-library, Web of S cience using the key words “hepatocellular carcinoma”, “chronic hepatitis C”, “direct-acting antiviral drugs”, “liver cirrhosis”, “interferons”, and “sustained virological response”. Of the 99 studies found, 21 were used to write a systematic review.Results.Eradication of the virus reduces the risks of HCC. Despite reports on high risk of occurrence or recurrence of hepatocellular carcinoma in patients with cirrhosis after treatment with DAA s compared with interferon-containing regimens, there is not enough data confirming the direct link between the use of DAA s and the development of hepatocellular carcinoma. No statistically significant difference in the frequency of HCC between patients treated with interferon or DAA s was detected.Conclusion.Eradication of the virus is the most significant factor in the prevention of HCC; therefore, treatment of CHC should not be delayed due to the risk of HCC. Patients with liver cirrhosis require a long period of follow-up, even after successful treatment of chronic hepatitis C with DAA drugs. Stratification of HCC risk requires further research.

A Hydrophobic Network: Intersubunit and Intercapsomer Interactions Stabilizing the Bacteriophage P22 Capsid.

Double-stranded DNA (dsDNA) tailed phages and herpesviruses assemble their capsids using coat proteins that have the ubiquitous HK97 fold. Though this fold is common, we do not have a thorough understanding of the different ways viruses adapt it to maintain stability in various environments. The HK97-fold E-loop, which connects adjacent subunits at the outer periphery of capsomers, has been implicated in capsid stability. Here, we show that in bacteriophage P22, residue W61 at the tip of the E-loop plays a role in stabilizing procapsids and in maturation. We hypothesize that a hydrophobic pocket is formed by residues I366 and W410 in the P domain of a neighboring subunit within a capsomer, into which W61 fits like a peg. In addition, W61 likely bridges to residues A91 and L401 in P-domain loops of an adjacent capsomer, thereby linking the entire capsid together with a network of hydrophobic interactions. There is conservation of this hydrophobic network in the distantly related P22-like phages, indicating that this structural feature is likely important for stabilizing this family of phages. Thus, our data shed light on one of the varied elegant mechanisms used in nature to consistently build stable viral genome containers through subtle adaptation of the HK97 fold.IMPORTANCE Similarities in assembly reactions and coat protein structures of the dsDNA tailed phages and herpesviruses make phages ideal models to understand capsid assembly and identify potential targets for antiviral drug discovery. The coat protein E-loops of these viruses are involved in both intra- and intercapsomer interactions. In phage P22, hydrophobic interactions peg the coat protein subunits together within a capsomer, where the E-loop hydrophobic residue W61 of one subunit packs into a pocket of hydrophobic residues I366 and W410 of the adjacent subunit. W61 also makes hydrophobic interactions with A91 and L401 of a subunit in an adjacent capsomer. We show these intra- and intercapsomer hydrophobic interactions form a network crucial to capsid stability and proper assembly.

Phylogenetically based establishment of a dengue virus panel, representing all available genotypes, as a tool in dengue drug discovery

Dengue fever is the most widespread of the human arbovirus diseases, with approximately one third of the world's population at risk of infection. Dengue viruses are members of the genus Flavivirus (family Flaviviridae) and, antigenically, they separate as four closely related serotypes (1–4) that share 60–75% amino acid homology. This genetic diversity complicates the process of antiviral drug discovery. Thus, currently no approved dengue-specific therapeutic treatments are available. With the aim of providing an efficient tool for dengue virus drug discovery, a collection of nineteen dengue viruses, representing the genotypic diversity within the four serotypes, was developed. After phylogenetic analysis of the full-length genomes, we selected relevant strains from the EVAg collection at Aix-Marseille University and completed the virus collection, using a reverse genetic system based on the infectious sub-genomic amplicons technique. Finally, we evaluated this dengue virus collection against three published dengue inhibitory compounds. NITD008, which targets the highly conserved active site of the viral NS5 polymerase enzyme, exhibited similar antiviral potencies against each of the different dengue genotypes in the panel. Compounds targeting less conserved protein subdomains, such as the capsid inhibitor ST-148, or SDM25N, a ∂ opioid receptor antagonist which indirectly targets NS4B, exhibited larger differences in potency against the various genotypes of dengue viruses. These results illustrate the importance of a phylogenetically based dengue virus reference panel for dengue antiviral research. The collection developed in this study, which includes such representative dengue viruses, has been made available to the scientific community through the European Virus Archive to evaluate novel DENV antiviral candidates.

Pharmacophore modeling, molecular docking and molecular dynamics simulation for screening and identifying anti-dengue phytocompounds

Dengue is a fast spreading mosquito borne viral disease that poses a serious threat to human health. Lack of therapeutic drugs and vaccines signify that more resources need to be explored. Accumulated evidence has suggested that plants offer a vast reservoir for antiviral drug discovery which are safe for human consumption. Plant-based drug discovery is a complex and time-consuming process as plants possess rich repository of chemically diverse compounds. Various in silico methods can make this process simple and economic. We, therefore, performed pharmacophore mapping, molecular docking, molecular dynamics (MD) simulations and ADME (absorption, distribution, metabolism, excretion) prediction to screen potential candidates against dengue. In particular, combined pharmacophore mapping and molecular docking were used to prioritize the potentially active ligands from a ligand library. Biological activities of plant based ligands were predicted using 3D-QSAR pharmacophore modeling. Interaction between proteins, namely, envelope G protein, NS2B/NS3 protease, NS5 methyltransferase, NS1, NS5 polymerase and active plant-based ligands (pIC50 > 5.1) were analyzed using molecular docking. Best docked complex, namely, envelope G protein–mulberroside C, NS2B-NS3 protease–curcumin, NS5 methyltransferase–chebulic acid, NS1–mulberroside A, NS5 methyltransferase–punigluconin and NS5 methyltransferase–chebulic acid were further subjected to MD simulations study to assess the fluctuation and conformational changes during protein–ligand interaction. ADME studies were performed to assess their drug-likeness properties. Collectively, these in silico results helped to identify the potential plant-based hits against the various receptors of dengue virus which can be further validated by bioactivity-based experiments.Communicated by Ramaswamy H. Sarma

Drug Repurposing in Antiviral Research: A Current Scenario

: Better understand the unexplored parts of the drugs you know than the drugs unidentified. Drug repurposing is a promising, fast and cost-effective method that can overcome traditional de novo drug discovery and development challenges of targeting various diseases and disorders. Drug repurposing, the process of identifying new uses for the existing or candidate drugs is an effective strategy for drug discovery in various diseases. Identifying new drugs and new target is significant in today’s world with a new disease emerging every day. With increase in number of the emerging viral infections day by day, the targeted therapies for those are not discovered in parallel. The drug repurposing approach has given many promising drug candidates for various viral infectious diseases like Ebola, ZIKA, dengue, influenza, HIV, HSV, CMV infections and various other infectious diseases. The emergence of resistance to existing antiviral drugs and re-emerging viral infections are the biggest challenges in the antiviral drug discovery. The drug repurposing approach is an assuring strategy in finding new potential antiviral agents within a short span of time to overcome the challenges in antiviral therapy. In this review, we describe the most promising results of the drug repurposing approach in the treatment of various infectious diseases.Key words: Antiviral, Drug resistance, Re-emerging viral infections, Repurposing.

Serum Exosomes from Newborn Piglets Restrict Porcine Epidemic Diarrhea Virus Infection.

Exosomes are vehicles in the body fluid that participate in many biological processes, especially immune responses. In this study, we employed comparative proteome analysis to investigate the roles of serum exosomes during viral infection in neonates using porcine epidemic diarrhea virus (PEDV), a devastating enteric virus in newborn piglets, as a model virus. Serum exosomes were first isolated from newborn piglets infected with PEDV or mock-infected newborn piglets, followed by label-free LC-MS/MS-based comparative quantitative proteomic analysis. Among the 441 detected proteins, 10 complement proteins were found in the serum exosomes, and significantly decreased expression levels of the C3, C6, and CFB complements were measured in PEDV-infected serum exosomes compared to those in mock-infected serum exosomes. After confirmation by Western blot, we then investigated the function of these exosomes in PEDV infection and discovered that exosomes from mock-infected newborn piglets restricted PEDV infection. However, this inhibition disappeared after the exosomes were heat-inactivated, suggesting that complements are key antiviral molecules. Our findings improve the understanding of antiviral responses mediated by exosomes in neonatal piglets and facilitate the discovery of novel antiviral drugs.

Development of a high-performance thin-layer chromatographic method for the simultaneous determination of newly co-formulated antiviral drugs sofosbuvir and velpatasvir in their pure forms and tablet dosage form

The discovery of new direct-acting antiviral drugs gave rise to a leap forward in the treatment of hepatitis C viral infections. For the first time since 1998, the Food and Drug Administration (FDA) approved interferon-free oral treatment paradigms. Among the new treatment regimens, the combinations of sofosbuvir/daclat-asvir and sofosbuvir/velpatasvir became ideal treatment regimens for being potent, highly tolerated, and used once daily. For that purpose, a new sensitive high-performance thin-layer chroma-tography (HPTLC) method was developed and validated for the simultaneous determination of sofosbuvir and velpatasvir. The proposed method used Merck HPTLC silica gel 60 F254 aluminum plates as the stationary phase. The mobile phase was a combinat ion of methylene chloride-methanolethyl acetate-ammonia (25%) at a ratio of 5:1:3:1 (v/v). The calibration curves were linear over a wide range of 100–2000 ng per spot for the studied drugs. The limits of detection were 30.02 and 27.60 ng per spot, and the limits of quantification were 90.06 and 82.80 ng per spot for sofosbuvir and velpatasvir, respectively. The suggested method was successfully applied for analysis of the studied drugs in their pharmaceutical dosage forms, and excellent recovery results were obtained. Being simple, fast, robust, and economic, this method is eligible for use in the routine work in pharmaceutical quality control laboratories.

Fragment-Based Discovery of a Qualified Hit Targeting the Latency-Associated Nuclear Antigen of the Oncogenic Kaposi's Sarcoma-Associated Herpesvirus/Human Herpesvirus 8.

The latency-associated nuclear antigen (LANA) is required for latent replication and persistence of Kaposi's sarcoma-associated herpesvirus/human herpesvirus 8. It acts via replicating and tethering the virus episome to the host chromatin and exerts other functions. We conceived a new approach for the discovery of antiviral drugs to inhibit the interaction between LANA and the viral genome. We applied a biophysical screening cascade and identified the first LANA binders from small, structurally diverse compound libraries. Starting from a fragment-sized scaffold, we generated optimized hits via fragment growing using a dedicated fluorescence-polarization-based assay as the structure-activity-relationship driver. We improved compound potency to the double-digit micromolar range. Importantly, we qualified the resulting hit through orthogonal methods employing EMSA, STD-NMR, and MST methodologies. This optimized hit provides an ideal starting point for subsequent hit-to-lead campaigns providing evident target-binding, suitable ligand efficiencies, and favorable physicochemical properties.

DESIGN, SYNTHESIS AND MOLECULAR MECHANISM OF FEW NEURAMINIDASE INHIBITORS IN TREATMENT OF H1N1 BY NMR TECHNIQUES

Considering the issue of resistance to anti-influenza drugs, there is a need for discovery of new antiviral drugs. In view of this, flavones and their synthetic precursors i.e. chalcones were designed as inhibitors of influenza virus - H1N1 neuraminidase enzyme using structure-based drug design. Based on the best docking scores, some chalcone and flavone derivatives were synthesized and characterized by IR and proton NMR. Few of them were selected for 31P NMR studies, in order to probe the molecular mechanism of their antiviral action. Reasonably good correlation between docking scores and 31P NMR results were observed. As antiviral drugs are known to show membrane stabilizing effect on host cell, 31P NMR data for methoxy chalcone showed stabilization effect on model membrane pointing towards good antiviral activity which remained unaffected even after its cyclization to flavone. These derivatives can be explored further to provide a future therapeutic option for the treatment and prophylaxis of H1N1 viral infections.

Antiviral Drug Discovery: Norovirus Proteases and Development of Inhibitors.

Proteases are a major enzyme group playing important roles in a wide variety of biological processes in life forms ranging from viruses to mammalians. The aberrant activity of proteases can lead to various diseases; consequently, host proteases have been the focus of intense investigation as potential therapeutic targets. A wide range of viruses encode proteases which play an essential role in viral replication and, therefore, constitute attractive targets for the development of antiviral therapeutics. There are numerous examples of successful drug development targeting cellular and viral proteases, including antivirals against human immunodeficiency virus and hepatitis C virus. Most FDA-approved antiviral agents are peptidomimetics and macrocyclic compounds that interact with the active site of a targeted protease. Norovirus proteases are cysteine proteases that contain a chymotrypsin-like fold in their 3D structures. This review focuses on our group’s efforts related to the development of norovirus protease inhibitors as potential anti-norovirus therapeutics. These protease inhibitors are rationally designed transition-state inhibitors encompassing dipeptidyl, tripeptidyl and macrocyclic compounds. Highly effective inhibitors validated in X-ray co-crystallization, enzyme and cell-based assays, as well as an animal model, were generated by launching an optimization campaign utilizing the initial hit compounds. A prodrug approach was also explored to improve the pharmacokinetics (PK) of the identified inhibitors.

Structural and functional similarities in bunyaviruses: Perspectives for pan-bunya antivirals.

SummaryThe order of Bunyavirales includes numerous (re)emerging viruses that collectively have a major impact on human and animal health worldwide. There are no vaccines for human use or antiviral drugs available to prevent or treat infections with any of these viruses. The development of efficacious and safe drugs and vaccines is a pressing matter. Ideally, such antivirals possess pan‐bunyavirus antiviral activity, allowing the containment of every bunya‐related threat. The fact that many bunyaviruses need to be handled in laboratories with biosafety level 3 or 4, the great variety of species and the frequent emergence of novel species complicate such efforts. We here examined the potential druggable targets of bunyaviruses, together with the level of conservation of their biological functions, structure, and genetic similarity by means of heatmap analysis. In the light of this, we revised the available models and tools currently available, pointing out directions for antiviral drug discovery.