Viral RNA Polymerase Inhibitors Research Articles

Dynamic diversity of SARS-CoV-2 genetic mutations in a lung transplantation patient with persistent COVID-19.

Numerous SARS-CoV-2 variant strains with altered characteristics have emerged since the onset of the COVID-19 pandemic. Remdesivir (RDV), a ribonucleotide analogue inhibitor of viral RNA polymerase, has become a valuable therapeutic agent. However, immunosuppressed hosts may respond inadequately to RDV and develop chronic persistent infections. A patient with respiratory failure caused by interstitial pneumonia, who had undergone transplantation of the left lung, developed COVID-19 caused by Omicron BA.5 strain with persistent chronic viral shedding, showing viral fusogenicity. Genome-wide sequencing analyses revealed the occurrence of several viral mutations after RDV treatment, followed by dynamic changes in the viral populations. The C799F mutation in nsp12 was found to play a pivotal role in conferring RDV resistance, preventing RDV-triphosphate from entering the active site of RNA-dependent RNA polymerase. The occurrence of diverse mutations is a characteristic of SARS-CoV-2, which mutates frequently. Herein, we describe the clinical case of an immunosuppressed host in whom inadequate treatment resulted in highly diverse SARS-CoV-2 mutations that threatened the patient's health due to the development of drug-resistant variants.

Personalized Assessment of Mortality Risk and Hospital Stay Duration in Hospitalized Patients with COVID-19 Treated with Remdesivir: A Machine Learning Approach.

Background: Despite advancements in vaccination, early treatments, and understanding of SARS-CoV-2, its impact remains significant worldwide. Many patients require intensive care due to severe COVID-19. Remdesivir, a key treatment option among viral RNA polymerase inhibitors, lacks comprehensive studies on factors associated with its effectiveness. Methods: We conducted a retrospective study in 2022, analyzing data from 252 hospitalized COVID-19 patients treated with remdesivir. Six machine learning algorithms were compared to predict factors influencing remdesivir's clinical benefits regarding mortality and hospital stay. Results: The extreme gradient boost (XGB) method showed the highest accuracy for both mortality (95.45%) and hospital stay (94.24%). Factors associated with worse outcomes in terms of mortality included limitations in life support, ventilatory support needs, lymphopenia, low albumin and hemoglobin levels, flu and/or coinfection, and cough. For hospital stay, factors included vaccine doses, lung density, pulmonary radiological status, comorbidities, oxygen therapy, troponin, lactate dehydrogenase levels, and asthenia. Conclusions: These findings underscore XGB's effectiveness in accurately categorizing COVID-19 patients undergoing remdesivir treatment.

Treatment with Remdesivir of Children with SARS-CoV-2 Infection: Experience from a Clinical Hospital in Romania.

The COVID-19 pandemic was characterized by mild-to-moderate disease in children and adolescents, with low incidences of severe cases and mortality. Most of the information on drug therapy in COVID-19-positive children was derived from research in adult patients. Remdesivir, an inhibitor of viral RNA polymerase, was shown to be effective in COVID-19 patients with moderate-to-severe disease. In this study, we present our experience of the use of remdesivir in pediatric patients hospitalized with COVID-19. This retrospective study was based on the early use of remdesivir in 14 children with mild, moderate, and severe clinical forms of COVID-19, who were hospitalized between 1 January 2022, and 30 September 2023. The patients included eight infants and six children older than 1 day (the age range was 2 months to 17 years). Most of them (92.85%) had documented pneumonia. Four patients had associated acute laryngitis, and another had bronchiolitis. Coinfections with Streptococcus pneumoniae were diagnosed in two patients. The clinical course was favorable in 12/14 (85.71%) children. Two patients were transferred to the pediatric intensive care unit because of aggravation of associated acute diseases (acute laryngitis and bronchiolitis, respectively). Mild increases in alanine aminotransferase levels occurred in two patients, with no increase in serum creatinine, during treatment with remdesivir. The appropriate use of remdesivir proved safe and efficient in our group of patients. However, further studies are required to support the efficiency, tolerability, and safety of remdesivir in children.

Neurological side effects and drug interactions of antiviral compounds against SARS-CoV-2.

The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), rapidly spread across the globe. Tremendous efforts have been mobilized to create effective antiviral treatment options to reduce the burden of the disease. This article summarizes the available knowledge about the antiviral drugs against SARS-CoV-2 from a neurologist's perspective. We summarize neurological aspects of antiviral compounds against SARS-CoV-2 with full, conditional, or previous marketing authorization by the European Medicines Agency (EMA). Nirmatrelvir/ritonavir targets the SARS-CoV-2 3c-like protease using combinatorial chemistry. Nirmatrelvir/ritonavir levels are affected by medications metabolized by or inducing CYP3A4, including those used in neurological diseases. Dysgeusia with a bitter or metallic taste is a common side effect of nirmatrelvir/ritonavir. Molnupiravir is a nucleotide analog developed to inhibit the replication of viruses. No clinically significant interactions with other drugs have been identified, and no specific considerations for people with neurological comorbidity are required. In the meantime, inconsistent results from clinical trials regarding efficacy have led to the withdrawal of marketing authorization by the EMA. Remdesivir is a viral RNA polymerase inhibitor and interferes with the production of viral RNA. The most common side effect in patients with COVID-19 is nausea. Remdesivir is a substrate for CYP3A4. Neurological side effects and drug interactions must be considered for antiviral compounds against SARS-CoV-2. Further studies are required to better evaluate their efficacy and adverse events in patients with concomitant neurological diseases. Moreover, evidence from real-world studies will complement the current knowledge.

Early 3‑day course of remdesivir for the prevention of the progression to severe COVID‑19 in the elderly: A single‑centre, real‑life cohort study.

Remdesivir, a viral RNA polymerase inhibitor, has constituted a key component of therapeutic regimens against the pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Originally approved for administration in hospitalized patients, remdesivir leads to improved outcomes in patients with moderate to severe coronavirus disease 2019 (COVID-19). After proving to be effective in hospitalized patients, its use gained approval in early-stage disease for symptomatic outpatients who are at a high risk of progression to severe disease. The present study is a real-life prospective cohort study involving 143 elderly non-hospitalized patients with SARS-CoV-2 (≥65 years of age) who attended the emergency department of the authors' hospital seeking care for COVID-19 symptoms appearing within the prior 7 days. Eligible patients received intravenous remdesivir at a dose of 200 mg on the first day and 100 mg on days 2 and 3. The efficacy endpoints were set as the need for COVID-19-related hospitalization and all-cause mortality in the following 28 days. A total of 143 patients participated in the study. Of these patients, 118 (82.5%) patients were vaccinated with at least two doses. All patients enrolled completed the 3-day course, with a total of 6 out of 143 patients (4.2%) having a COVID-19-related hospitalization by day 28, and 5 patients (3.5%) succumbing to the disease within the study period. In the univariate Cox regression analysis, the neutrophil-to-lymphocyte ratio and haematological malignancy were identified as predictors of progression to severe disease, and albumin levels, the C-reactive protein-to-albumin ratio (CAR) and haematological malignancy were identified as predictors of 28-day mortality. On the whole, the findings of the present study demonstrated that among the elderly outpatients, a 3-day course of intravenous remdesivir was associated with favourable outcomes.

Remdesivir saves lives. Were 3 years needed to learn that?

Remdesivir saves lives. Were 3 years needed to learn that?

Favipiravir (6‐Fluoro‐3‐hydroxy‐2‐pyrazinecarboxamide) a Broad Spectrum Inhibitor of Viral RNA Polymerase in COVID‐19 Treatment

AbstractA pandemic disease, COVID‐19, affecting over 253 million and 5.1 million deaths reported as on November 2021 from across the globe. The worst hit pandemic since a century. Scientists around the world are working towards the development of drugs for its treatment. Several existing antiviral medications have been tried for the same. Among these, Favipiravir, a broad‐spectrum antiviral drug originally developed to treat influenza, shows noted activity against an ample range of RNA viruses. It is an oral antiviral drug with good bioavailability found to be effective in the treatment of COVID‐19. This drug has acquired FDA manifestation for drug‐resistant Influenza as it has confirmed its safety profile. There has been growing evidence that it helps in early viral clearance and speedy symptomatic relief against COVID‐19. This review attempts to provide synthetic methods of favipiravir, mechanism of action and its importance in the treatment of COVID‐19 and other viruses.

Development and validation of a sensitive, fast and simple LC-MS / MS method for the quantitation of favipiravir in human serum

Favipiravir is a broad-spectrum inhibitor of viral RNA polymerase. It is currently used as a possible treatment for coronavirus disease 2019 (COVID-19). Pre-clinical or clinical trials of favipiravir require robust, sensitive, and accurate bioanalytical methods for quantitation of favipiravir levels. Recently, several studies have been reported about developing a validated liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for measuring favipiravir levels. However, these methods were validated predominantly for plasma samples, electrospray ionization was operated only in negative or positive mode, and clinical application of these methods has not been applied for patients with COVID-19. This study aimed was to develop a validated LC-MS/MS method for the measurement of favipiravir levels in positive and negative electrospray ionization mode and to perform a pilot study in patients with COVID-19 receiving favipiravir to demonstrate the applicability of this method in biological samples. Simple protein precipitation was used for the extraction of favipiravir from the desired matrix. Favipiravir levels were quantitated using MS / MS with an electrospray ionization source in positive and negative multiple reaction monitoring (MRM) mode. The chromatographic detection was performed on a reverse-phase Phenomenex C18 column (50 mm × 4.6 mm, 5 µm, 100 Å) with gradient elution using 0.1% formic acid in water and 0.1% formic acid in methanol as mobile phase. The method was linear over the concentration ranges of 0.048–50 µg/mL (in negative ionization mode) and 0.062–50 µg/mL (in positive ionization mode) with a correlation coefficient (r2) better than 0.998. The total run time was 3.5 min. The intra-assay and inter-assay %CV values were less than 7.2% and 8.0%, respectively. A simple, rapid and robust LC-MS / MS method was developed for the measurement of favipiravir and validation studies were performed. The validated method was successfully applied for drug level measurement in COVID-19 patients receiving favipiravir.

Drug synergy of combinatory treatment with remdesivir and the repurposed drugs fluoxetine and itraconazole effectively impairs SARS-CoV-2 infection in vitro.

Background and PurposeThe SARS‐COV‐2 pandemic and the global spread of coronavirus disease 2019 (COVID‐19) urgently call for efficient and safe antiviral treatment strategies. A straightforward approach to speed up drug development at lower costs is drug repurposing. Here, we investigated the therapeutic potential of targeting the interface of SARS CoV‐2 with the host via repurposing of clinically licensed drugs and evaluated their use in combinatory treatments with virus‐ and host‐directed drugs in vitro.Experimental ApproachWe tested the antiviral potential of the antifungal itraconazole and the antidepressant fluoxetine on the production of infectious SARS‐CoV‐2 particles in the polarized Calu‐3 cell culture model and evaluated the added benefit of a combinatory use of these host‐directed drugs with the direct acting antiviral remdesivir, an inhibitor of viral RNA polymerase.Key ResultsDrug treatments were well‐tolerated and potently impaired viral replication. Importantly, both itraconazole–remdesivir and fluoxetine–remdesivir combinations inhibited the production of infectious SARS‐CoV‐2 particles > 90% and displayed synergistic effects, as determined in commonly used reference models for drug interaction.Conclusion and ImplicationsItraconazole–remdesivir and fluoxetine–remdesivir combinations are promising starting points for therapeutic options to control SARS‐CoV‐2 infection and severe progression of COVID‐19.

Favipiravir, will it be the Answer for the Specific Management of COVID-19?: A Review

Background: The COVID-19 has created havoc all over the world as no specific treatment available tilldate. Total COVID-19 cases had crossed 11,125,245 including 528,204 deaths as per the WHO data till 5July 2020. Unfortunately, India secured third place in total tally of COVID-19 cases with 6,77,719 totalcases including 19693 deaths as of 5th July 2020. The antiviral drug, Favipiravir, previously known as T-705approved in Japan for treatment of Influenza. It is selective & potent inhibitor of viral RNA polymerase. Itis promising drug for treatment of wide range of RNA viruses including SARSCoV-2.Method: The systematic review of Articles was done with the help of search engines like Embase, Medline,PubMed & Google Scholar, clinicaltrials.gov. The Peer reviewed articles published through 6th of July 2020were included in the study. This review was done to establish clinical evidence for use of Favipiravir inCOVID-19.Conclusion: It was found that due to lack of conclusive evidence, Favipiravir cannot be included in mainarmamentarium for COVID-19.

Exploring Local Chemical Space in De Novo Molecular Generation Using Multi-Agent Deep Reinforcement Learning

Single-agent reinforcement learning (RL) is commonly used to learn how to play computer games, in which the agent makes one move before making the next in a sequential decision process. Recently single agent was also employed in the design of molecules and drugs. While a single agent is a good fit for computer games, it has limitations when used in molecule design. Its sequential learning makes it impossible to modify or improve the previous steps while working on the current step. In this paper, we proposed to apply the multi-agent RL approach to the research of molecules, which can optimize all sites of a molecule simultaneously. To elucidate the validity of our approach, we chose one chemical compound Favipiravir to explore its local chemical space. Favipiravir is a broad-spectrum inhibitor of viral RNA polymerase, and is one of the compounds that are currently being used in SARS-CoV-2 (COVID-19) clinical trials. Our experiments revealed the collaborative learning of a team of deep RL agents as well as the learning of its individual learning agent in the exploration of Favipiravir. In particular, our multi-agents not only discovered the molecules near Favipiravir in chemical space, but also the learnability of each site in the string representation of Favipiravir, critical information for us to understand the underline mechanism that supports machine learning of molecules.

Human soluble ACE2 improves the effect of remdesivir in SARS-CoV-2 infection.

There is a critical need for safe and effective drugs for COVID‐19. Only remdesivir has received authorization for COVID‐19 and has been shown to improve outcomes but not decrease mortality. However, the dose of remdesivir is limited by hepatic and kidney toxicity. ACE2 is the critical cell surface receptor for SARS‐CoV‐2. Here, we investigated additive effect of combination therapy using remdesivir with recombinant soluble ACE2 (high/low dose) on Vero E6 and kidney organoids, targeting two different modalities of SARS‐CoV‐2 life cycle: cell entry via its receptor ACE2 and intracellular viral RNA replication. This combination treatment markedly improved their therapeutic windows against SARS‐CoV‐2 in both models. By using single amino‐acid resolution screening in haploid ES cells, we report a singular critical pathway required for remdesivir toxicity, namely, Adenylate Kinase 2. The data provided here demonstrate that combining two therapeutic modalities with different targets, common strategy in HIV treatment, exhibit strong additive effects at sub‐toxic concentrations. Our data lay the groundwork for the study of combinatorial regimens in future COVID‐19 clinical trials.

The use of viral RNA polymerase inhibitors in combination with a fusion inhibitor in the treatment of patients with COVID-19: hypothesis

This review article considers the possibilities of combined antiviral therapy in the treatment of patients with COVID-19, based on the analysis of the mechanism of action of known antiviral drugs in the framework of the medical hypothesis. The potential effectiveness of the joint use of viral RNA polymerase inhibitors and a fusion inhibitor in this pathology is discussed. The review discusses the main representatives of these groups of drugs - ribavirin, riamilovir, umifenovir, favipiravir. The efficacy and safety profile of these drugs was analyzed, including the experience of their use in clinical trials conducted during the COVID-19 pandemic, as well as earlier work performed during the SARS and MERS epidemics.

Coronavirus infection: principles of ethyotropic chemotherapy

In the development of the infectious process caused by coronaviruses, two stages can be distinguished: early (ethiotropic) and late (pathogenetic). Therapeutic principles depend on these stages. At the first stage, when the virus accumulates, ethiotropic chemotherapeutic drugs suppressing virus reproduction are predominantly used. The article considers 7 major chemotherapeutic approaches aimed at specific targets in the replication of coronaviruses: viral RNA polymerase inhibitors, inhibitors of viral protease Mpro, inhibitors of proteolytic activation of viral protein S, which carries out the virus entry into the target cell, inhibitors of virus uncoating in the intracellular endosomes, exogenous interferon compounds, preparations of natural and recombinant virus neutralizing antibodies, as well as combinations of the above drugs. At the second stage, when the virus multiplication drops down and threatening pathological processes of excessive inflammation, acute respiratory distress syndrome, pulmonary edema, hypoxia and threatening sepsis develop, it is reasonable to realize antipathogenetic approaches, such as extracorporeal blood oxygenation, detoxication, anti-inflammatory and antibacterial therapeutic drugs and measures.

Promising and potential drugs for the treatment of COVID-19

Coronavirus disease 2019 (COVID-19) is characterized by respiratory alterations with varied symptoms ranging from mild manifestations to more severe conditions that can cause death. The objective of this narrative review of the literature is to synthesize in a concrete way the information available on potential drugs for the treatment of patients with COVID-19 and to serve as a support guide for health professionals. Taking into account previous experiences for the management of SARS-CoV and MERS-CoV in the past, some of these drugs have been used as a starting point to seek the elimination of SARS-CoV-2. This review presents the current state of research on promising drugs as potential treatments for COVID-19 worldwide and is developed in the text on four types of anti-SARS-Cov-2 agents: regulators of the immune response, intracellular medium modifiers, viral RNA polymerase inhibitors and protease inhibitors. To date all the drugs described in this review need clinical studies to validate their use. However, until the results of these trials are available, the best available evidence should be used for the prevention and treatment of COVID-19.

Molecular Targets in the Chemotherapy of Coronavirus Infection.

In the pathogenesis of the infectious process in the respiratory tract by SARS, MERS, and COVID-19 coronaviruses, two stages can be distinguished: early (etiotropic) and late (pathogenetic) ones. In the first stage, when the virus multiplication and accumulation are prevalent under insufficient host immune response, the use of chemotherapeutic agents blocking the reproduction of the virus is reasonable to suppress the development of the disease. This article considers six major chemotherapeutic classes aimed at certain viral targets: inhibitors of viral RNA polymerase, inhibitors of viral protease Mpro, inhibitors of proteolytic activation of viral protein S allowing virus entry into the target cell, inhibitors of virus uncoating in cellular endosomes, compounds of exogenous interferons, and compounds of natural and recombinant virus-neutralizing antibodies. In the second stage, when the multiplication of the virus decreases and threatening pathological processes of excessive inflammation, acute respiratory distress syndrome, pulmonary edema, hypoxia, and secondary bacterial pneumonia and sepsis events develop, a pathogenetic therapeutic approach including extracorporeal blood oxygenation, detoxification, and anti-inflammatory and anti-bacterial therapy seems to be the most effective way for the patient’s recovery.

SUN-519 Hypoparathyroidism after Harvoni Treatment for Hepatitis C

Background: Hepatitis C (Hep C) infection is one of the leading causes of end stage liver disease and hepatocellular carcinoma. Several advances have been made in the treatment of Hep C infection. Harvoni (ledipasvir and sofosbuvir) is one of the treatment options. There have been no case reports of hypocalcemia or hypoparathyroidism associated with Harvoni therapy. We report a case of hypocalcemia and permanent hypoparathyroidism that began after Harvoni therapy. Case Presentation: A 64-year old African American man presented with weight loss and was diagnosed to have Hep C. He was treated with 12 weeks course of Harvoni. He was first noted to have low calcium level at 8.4 (8.4 – 10.3 mg/dl), during the last week of Harvoni treatment. Several previous calcium levels were normal. Four months later, he presented to Emergency Department with numbness, palpitations, and muscle cramping. His calcium was then 6.6 mg/dl, albumin 4.3 (3.4 - 4.8 mg/dl), PTH 18 (15 - 65 pg/ml), 25-hydroxy vitamin D 11 (30 - 50 ng/ml), magnesium 2.2 (1.6 – 2.6 mg/dl), phosphorus 3.8 (2.3 - 4.7 mg/dl) and 24-hour urine calcium was less than 2. Oral calcitriol, ergocalciferol and calcium carbonate were initiated and his calcium normalized. His calcium remained normal on calcitriol and calcium carbonate, but twice he had to be treated in emergency department for symptomatic hypocalcemia after missing his medications. Recently, he began PTH (1-84) (NATPARA). He has been tolerating parathyroid hormone injections well. Discussion: Harvoni is a combination medication of Ledipasvir and Sofosbuvir. Ledipasvir is a NS5A inhibitor. NS5A is an RNA binding protein required for the activity of RNA polymerase of hepatitis C virus. Sofosbuvir is a viral RNA polymerase inhibitor. There have been no case reports of hypoparathyroidism occurring with Harvoni therapy in the literature. Hypoparathyroidism most commonly results after anterior neck surgery like thyroidectomy, parathyroidectomy, or anterior neck dissection. Other causes include neck irradiation, infections like HIV, infiltration of the glands by heavy metals such as iron or copper; genetic disorders of parathyroid gland development, parathyroid hormone synthesis and calcium sensing receptor mutations, and finally autoimmune etiologies. Our patient had none of the risk factors for developing hypoparathyroidism. Nevertheless, he developed permanent, symptomatic hypoparathyroidism towards the end of Harvoni treatment, making Harvoni as the most likely cause of his hypoparathyroidism. More long-term data on this drug is needed to assess the risk of hypoparathyroidism after Harvoni therapy. Conclusion: Hypoparathyroidism leading to hypocalcemia could be a potential complication of Harvoni treatment. Monitoring calcium and parathyroid hormone levels prior to initiation and periodically after completion of Harvoni treatment should be recommended for all patients.

Favipiravir inhibits in vitro Usutu virus replication and delays disease progression in an infection model in mice

Usutu virus (USUV) is an emerging flavivirus that causes Usutu disease mainly in birds, but infection of mammals such as rodents, bats and horses has also been demonstrated. In addition, human cases (both in immunocompromised and -competent individuals) were also reported. Large outbreaks with other flaviviruses, such as West Nile virus and Zika virus, indicate that one should be vigilant for yet other outbreaks. To allow the identification of inhibitors of USUV replication, we established in vitro antiviral assays, which were validated using a small selection of known flavivirus inhibitors, including the broad-spectrum viral RNA polymerase inhibitor favipiravir (T-705). Next, an USUV infection model in AG129 (IFN-α/β and IFN-γ receptor knockout) mice was established. AG129 mice proved highly susceptible to USUV; an inoculum as low as 102 PFU (1.3 × 105 TCID50) resulted in the development of symptoms as early as 3 days post infection with viral RNA being detectable in various tissues. Treatment of mice with favipiravir (150 mg/kg/dose, BID, oral gavage) significantly reduced viral load in blood and tissues and significantly delayed virus-induced disease. This USUV mouse model is thus amenable for assessing the potential in vivo efficacy of (novel) USUV/flavivirus inhibitors.

Vesicular stomatitis virus (VSV) as a paradigm for predicting antiviral activity against Ebola virus (EBOV)

There are at present no antivirals available which have been formally licensed for clinical use for the treatment of Ebola virus (EBOV) infections in humans. The most advanced to be approved for this purpose is favipiravir (T-705), a viral RNA polymerase inhibitor. Under consideration are BCX4430, also a viral RNA polymerase inhibitor, and 3-deazaneplanocin A and various other S-adenosylhomocysteine (SAH) hydrolase inhibitors. A number of compounds which have been approved for other purposes seem to interact with the cell entry of EBOV. Some compounds like pyrazofurin have been found to be exquisitely potent inhibitors of vesicular stomatitis virus (VSV). VSV belongs to the rhabdoviridae, a family closely related to the family of the filoviridae to which EBOV and Marburg virus belong. VSV, unlike EBOV and Marburg virus which require biosafety level 4, can be handled in conventional safety conditions. Key words: Ebola virus (EBOV); vesicular stomatitis virus (VSV); rhabdoviridae; filoviridae; favipiravir; BCX4430; pyrazofurin; SAH hydrolase

The Fight against the Influenza A Virus H1N1: Synthesis, Molecular Modeling, and Biological Evaluation of Benzofurazan Derivatives as Viral RNA Polymerase Inhibitors

The influenza RNA polymerase complex, which consists of the three subunits PA, PB1, and PB2, is a promising target for the development of new antiviral drugs. A large library of benzofurazan compounds was synthesized and assayed against influenza virus A/WSN/33 (H1N1). Most of the new derivatives were found to act by inhibiting the viral RNA polymerase complex through disruption of the complex formed between subunits PA and PB1. Docking studies were also performed to elucidate the binding mode of benzofurazans within the PB1 binding site in PA and to identify amino acids involved in their mechanism of action. The predicted binding pose is fully consistent with the biological data and lays the foundation for the rational development of more effective PA-PB1 inhibitors.