Virus NS5B Polymerase Research Articles

Regulation of NS5B Polymerase Activity of Hepatitis C Virus by Target Specific Phytotherapeutics: An In-Silico Molecular Dynamics Approach.

Chronic hepatitis caused by the hepatitis C virus (HCV) is closely linked with the advancement of liver disease. The research hypothesis suggests that the NS5B enzyme (non-structural 5B protein) of HCV plays a pivotal role in facilitating viral replication within host cells. Hence, the objective of the present investigation is to identify the binding interactions between the structurally diverse phytotherapeutics and those of the catalytic residue of the target NS5B polymerase protein. Results of our docking simulations reveal that compounds such as arjunolic acid, sesamin, arjungenin, astragalin, piperic acid, piperidine, piperine, acalyphin, adhatodine, amyrin, anisotine, apigenin, cuminaldehyde, and curcumin exhibit a maximum of three interactions with the catalytic residues (Asp 220, Asp 318, and Asp 319) present on the Hepatitis C virus NS5B polymerase of HCV. Molecular dynamic simulation, particularly focusing on the best binding lead compound, arjunolic acid (-8.78 kcal/mol), was further extensively analyzed using RMSD, RMSF, Rg, and SASA techniques. The results of the MD simulation confirm that the NS5B-arjunolic acid complex becomes increasingly stable from 20 to 100 ns. The orientation of both arjunolic acid and sofosbuvir triphosphate (standard) within the active site was investigated through DCCM, PCA, and FEL analysis, indicating highly stable interactions of the lead arjunolic acid with the catalytic region of the NS5B enzyme. The findings of our current investigation suggest that bioactive therapeutics like arjunolic acid could serve as promising candidates for limiting the NS5B polymerase activity of the hepatitis C virus, offering hope for the future of HCV treatment.

Computational insight to design new potential hepatitis C virus NS5B polymerase inhibitors with drug-likeness and pharmacokinetic ADMET parameters predictions

BackgroundHepatitis C virus (HCV) is considered a worldwide health problem since it affects over 3% of the population and causes 300,000 fatalities per year. Chronic infection causes high morbidity and mortality in patients, leading to liver cirrhosis, hepatocellular carcinoma, fibrosis, liver cancer, and other HCV-related illnesses. Finding novel and better HCV treatments is a top international health goal right now. As a result, the pressing need for new HCV antiviral drugs has fueled research into the structural requirements of NS5B polymerase inhibitors at a molecular basis.ResultsIn this study, an in silico technique was applied to study 79 compounds with HCV inhibitory bioactivity, with the best statistical results (R^{2}= 0.7051, Q^{2} = 0.6455, R_{{{text{pred}}}}^{2} = 0.6992, ^{{text{c}}} R_{{text{r}}}^{2} = 0.6570, SEE = 0.2694).ConclusionsThis QSAR investigation allowed the research team to evaluate the influence of straightforward descriptors, shedding insight into the critical elements that guide the design of innovative effective molecules. Most of the innovative effective molecules exhibited better binding affinity (− 195.6 kcal/mol) than dasabuvir the reference drug (− 171.0 kcal/mol) with the target receptor (hepatitis C virus NS5B RNA polymerase). ADMET prediction disclosed enhanced pharmacokinetic properties with lower MRTD (maximum tolerated dose) of some new derivatives.

Recent advances in the chromatographic determination of the most commonly used anti-hepatitis C drug sofosbuvir and its co-administered drugs in human plasma.

Sofosbuvir is a direct-acting antiviral drug that inhibits hepatitis C virus (HCV) NS5B polymerase, which in turn affects the virus replication inside biological systems. The clinical importance of sofosbuvir is based not only on its effect on HCV but also on other lethal viruses such as Zika and severe acute respiratory syndrome coronavirus disease 2019 (SARS-COVID-19). Accordingly, there is a continuous shedding of light on the development and validation of accurate and fast analytical methods for the determination of sofosbuvir in different environments. This work critically reviews the recent advances in chromatographic methods for the analysis of sofosbuvir and/or its metabolites in pure samples, pharmaceutical dosage forms, and in the presence of other co-administered drugs to highlight the current status and future perspectives to enhance its determination in different matrixes.

Medicinal chemistry of anthranilic acid derivatives: A mini review.

Anthranilic acid and its analogues present a privileged profile as pharmacophores for the rational development of pharmaceuticals deliberated for managing the pathophysiology and pathogenesis of various diseases. The substitution on anthranilic acid scaffold provides large compound libraries, which enable a comprehensive assessment of the structure activity relationship (SAR) analysis for the identification of hits and leads in a typical drug development paradigm. Besides, their widespread applications as anti-inflammatory fenamates, the amide and anilide derivatives of anthranilic acid analogues play a central role in the management of several metabolic disorders. In addition, these derivatives of anthranilic acid exhibit interesting antimicrobial, antiviral and insecticidal properties, whereas the derivatives based on anthranilic diamide scaffold present applications as P-glycoprotein inhibitors for managing the drug resistance in cancer cells. In addition, the anthranilic acid derivatives serve as the inducers of apoptosis, inhibitors of hedgehog signaling pathway, inhibitors of mitogen activated protein kinase pathway, and the inhibitors of aldo-keto reductase enzymes. The antiviral derivatives of anthranilic acid focus on the inhibition of hepatitis C virus NS5B polymerase to manifest considerable antiviral properties. The anthranilic acid derivatives reportedly present neuroprotective applications by downregulating the key pathways responsible for the manifestation of neuropathological features and neurodegeneration. Nevertheless, the transition metal complexes of anthranilic acid derivatives offer therapeutic applications in diabetes mellitus, and obesity by regulating the activity of α-glucosidase. The present review demonstrates a critical analysis of the therapeutic profile of the key derivatives of anthranilic acid and its analogues for the rational development of pharmaceuticals and therapeutic molecules.

Novel intramolecular aminohydroxylation toward the syntheses of 2′-amino-2′-ethynyl nucleosides

Syntheses of both 2′-amino-2′-ethynyl guanosine and uridine, using an intramolecular aminohydroxylation reaction as the key step, are described. The corresponding 5′-O-triphosphates of the aforementioned nucleosides were obtained and the inhibitory activity was subsequently evaluated against the hepatitis C virus NS5B polymerase.

Insight into the drug resistance mechanisms of GS-9669 caused by mutations of HCV NS5B polymerase via molecular simulation

GS-9669 is a non-nucleos(t)ide inhibitor (NNI) binding to the thumb site II of the Hepatitis C virus (HCV) NS5B polymerase and has advanced into phase II trials. To clarify the drug resistance mechanisms of GS-9669 caused by M423T/I/V, L419M, R422K, and I482L mutations of NS5B polymerase (GT1b) and the receptor-ligand interactions during the binding process, a series of molecular simulation methods including molecular dynamics (MD) simulations and adaptive steered molecular dynamics (ASMD) simulations were performed for the wild-type (WT) and six mutant NS5B/GS-9669 complexes. The calculated results indicate that the binding free energies of the mutant systems are less negative than that of the WT system, indicating that these mutations will indeed cause NS5B to produce different degrees of resistance to GS-9669. The mutation-induced drug resistances are mainly caused by the loss of binding affinities of Leu419 and Trp528 with GS-9669 or the formation of multiple solvent bridges. Moreover, the ASMD calculations show that GS-9669 binds to the thumb II sites of the seven NS5B polymerases in distinct pathways without any obvious energy barriers. Although the recognition methods and binding pathways are distinct, the binding processes of GS-9669 with the WT and mutant NS5B polymerases are basically controlled thermodynamically. This study clearly reveals the resistance mechanisms of GS-9669 caused by M423T/I/V, L419M, R422K, and I482L mutations of HCV NS5B polymerase and provides some valuable clues for further optimization and design of novel NS5B inhibitors.

Safety, pharmacokinetics and antiviral activity of AT-527, a novel purine nucleotide prodrug, in HCV-infected subjects with and without cirrhosis.

AT-527 is a novel modified guanosine nucleotide prodrug inhibitor of the hepatitis C virus (HCV) NS5B polymerase, with increased in vitro antiviral activity as compared to sofosbuvir and a highly differentiated favorable preclinical profile compared to other anti-HCV nucleoside/nucleotide analogs. This was a multiple part clinical study where multiple ascending doses of AT-527 up to 600 mg (expressed as AT-527 salt form; equivalent to 553 mg free base) once daily for seven days were evaluated in a randomized, double-blind, placebo-controlled study of treatment-naïve, non-cirrhotic, genotype 1b, HCV-infected subjects. The highest dose of AT-527 for the same duration was then evaluated in two open label cohorts of a) non-cirrhotic, genotype 3, HCV-infected subjects and b) HCV-infected subjects of any genotype with compensated (Child-Pugh A) cirrhosis. AT-527 was well tolerated for seven days in all cohorts. At the highest dose tested, mean HCV RNA reductions of up to 2.4 log10 IU/mL occurred within the first 24 hours of dosing. Mean maximum reductions observed with seven days of dosing were 4.4, 4.5 and 4.6 log10 IU/mL in non-cirrhotic subjects with HCV genotype 1b, non-cirrhotic subjects with HCV genotype 3, and subjects with compensated cirrhosis, respectively. The systemic half-life of AT-273, the nucleoside metabolite considered a surrogate of intracellular phosphates including the active triphosphate, exceeded 20 hours, supporting once daily dosing. In summary, AT-527 demonstrated rapid, potent, dose/exposure-related and pan-genotypic antiviral activity with similar responses between subjects with and without cirrhosis. Exposure-antiviral response analysis identified 550 mg (free base equivalent) as the optimal dose of AT-527. Safety and antiviral activity data from this study warrant continued clinical development of AT-527 dosed once daily.

Design and Construction of Aroyl-Hydrazone Derivatives: Synthesis, Crystal Structure, Molecular Docking and Their Biological Activities.

Here, we report the synthesis and characterization of four new aroyl-hydrazone derivatives L1 -L4 , and their structural as well as biological activities have been explored. In addition to docking with bovine serum albumin (BSA) and duplex DNA, the experimental results demonstrate the effective binding of L1 -L4 with BSA protein and calf thymus DNA (ct-DNA) which is in agreement with the docking results. Further biological activities of L1 -L4 have been examined through molecular docking with different proteins which are involved in the propagation of viral or cancer diseases. L1 shows best binding affinity with influenza A virus polymerase PB2 subunit (2VY7) with binding energy -11.42 kcal/mol and inhibition constant 4.23 nm, whereas L2 strongly bind with the hepatitis C virus NS5B polymerase (2WCX) with binding energy -10.47 kcal/mol and inhibition constant 21.06 nm. Ligand L3 binds strongly with TGF-beta receptor 1 (3FAA) and L4 with cancer-related EphA2 protein kinases (1MQB) with binding energy -10.61 kcal/mol, -10.02 kcal/mol and inhibition constant 16.67 nm and 45.41 nm, respectively. The binding energies of L1 -L4 are comparable with binding energies of their proven inhibitors. L1 , L3 and L4 can be considered as both 3FAA and 1MQB dual targeting anticancer agents, while L1 and L3 are both 2VY7 and 2WCX dual targeting antiviral agents. On the other side, L2 and L4 target only one virus related target (2WCX). Furthermore, the geometry optimizations of L1 -L4 were performed via density functional theory (DFT). Moreover, all four ligands (L1 -L4 ) were characterized by NMR, FT-IR, ESI-MS, elemental analysis and their molecular structures were validated by single crystal X-ray diffraction studies.

Synthesis and Anti-HCV Activities of 4'-Fluoro-2'-Substituted Uridine Triphosphates and Nucleotide Prodrugs: Discovery of 4'-Fluoro-2'- C-methyluridine 5'-Phosphoramidate Prodrug (AL-335) for the Treatment of Hepatitis C Infection.

We report the synthesis and biological evaluation of a series of 4'-fluoro-2'- C-substituted uridines. Triphosphates of the uridine analogues exhibited a potent inhibition of hepatitis C virus (HCV) NS5B polymerase with IC50 values as low as 27 nM. In an HCV subgenomic replicon assay, the phosphoramidate prodrugs of these uridine analogues demonstrated a very potent activity with EC50 values as low as 20 nM. A lead compound AL-335 (53) demonstrated high levels of the nucleoside triphosphate in vitro in primary human hepatocytes and Huh-7 cells as well as in dog liver following a single oral dose. Compound 53 was selected for the clinical development where it showed promising results in phase 1 and 2 trials.

Design and evaluation of novel tetracyclic benzofurans as palm site allosteric inhibitors of HCV NS5B polymerase.

Hepatitis C virus (HCV) NS5B polymerase is a prime target for the development of direct-acting antiviral drugs for the treatment of chronic HCV infection. Several novel and potent HCV NS5B non-nucleoside inhibitors with unique tetracyclic bezonfuran-based structures were prepared and evaluated. Similar to clinical developmental compound MK-8876, N-linked (compounds 1 and 2) and C-linked (compounds 3 and 4) tetracyclic structures maintained broad spectrum anti-replicon potency profiles and demonstrated moderate to excellent oral bioavailability and pharmacokinetic parameters across the three preclinical animal species. To better understand the importance of tetracyclic structures related to pan genotypic potency profiles especially against clinically relevant GT1a variants, the teracycles with different ring size were prepared and in vitro evaluations suggested compounds with six number ring have better overall potency profiles.

Quantification of Sofosbuvir in Human Plasma: RP-HPLC Method Development and Validation

Sofosbuvir, a potential inhibitor of the nucleotide analog of hepatitis C virus (HCV) NS5B polymerase, is used to treat hepatitis C and marketed under brand name Sovaldi. This study was aimed to develop and validate a simple, sensitive and precise RP-HPLC method for the estimation of sofosbuvir in human blood plasma using quinine sulfate as internal standard (ISTD). Separation was achieved using Shimadzu-HPLC system equipped with Gracesmart RP-C 18 (250 mm � 4.6 mm, 5 �m) column eluted at a flow rate of 0.5 mL/min and detected at 260 nm. The mobile-phase composition was optimized to be ammonium formate (pH 3.0; 10 mM) and acetonitrile (67 : 33, % v/v). The retention times of sofosbuvir and quinine sulfate were found to be 13.60 and 8.39 min, respectively. The proposed method was linear over a range from 20 to 1200 ng/mL. Liquid–liquid extraction technique was applied for the extraction of drug and ISTD from human plasma using TBME – DCM (80 : 20, % v/v) mixture. The proposed method was validated as per bioanalytical method validation guidelines for industry.

Efficacy and safety of sofosbuvir-containing regimens in chronic hepatitis C patients with genotype 2 and 3: a comprehensive analysis of 18 randomized controlled trials.

Sofosbuvir is a hepatitis C virus (HCV) NS5B polymerase inhibitor. The objective of this study was to explore the efficacy and safety of sofosbuvir for HCV genotype (GT) 2 and 3 infected patients. We searched randomized controlled trials (RCTs) which analyzed the efficacy and safety of sofosbuvir-containing regimens for HCV GT 2/3 infected patients and collected data. The endpoints were sustained virological response 12- and 24-weeks after the cessation of therapy (SVR12 and SVR24), the adverse events (AEs) and the severe adverse events (SAEs). Eighteen trials comprising 2,975 HCV GT 2/3 infected patients were included. The pooled estimate SVR12, SVR24, AEs and SAEs rates were 84.6% (95% CI: 83.2-86.0), 83.7% (95% CI: 82.0-85.2), 83.8 (95% CI: 82.3-85.3) and 3.9 (95% CI: 3.2-4.8). The SVR12 rate of sofosbuvir-containing regimens for HCV GT 2 infection was higher than that for HCV GT 3 infection (95.7% vs. 80.8%). The sofosbuvir combined with velpatasvir (with or without ribavirin) regimen presented a higher SVR12 rate and lower AEs rate than the sofosbuvir combined with ribavirin (with or without peg-IFN) regimen (94.9% vs. 80.7% for SVR12 rate; 69.3% vs. 87.7% for AEs rate). The sofosbuvir-containing regimens in patients with HCV GT 2 infection have better efficacy than in patients with HCV GT 3 infection.

Design, synthesis, and structure-activity relationships of novel imidazo[4,5-c]pyridine derivatives as potent non-nucleoside inhibitors of hepatitis C virus NS5B

The hepatitis C virus (HCV) NS5B polymerase is an attractive target for the development of novel and selective inhibitors of HCV replication. In this paper, the design, synthesis, and preliminary SAR studies of novel inhibitors of HCV NS5B polymerase based on the structure of tegobuvir have been described. The efforts to optimize the antiviral potency and reduce the treatment side effects with respect to genotype 1b resulted in the discovery of compound 3, which exhibited an EC50 of 1.163 nM and a CC50 >200 nM in a cell-based HCV replicon system assay. Additionally, testing for inhibition of the hERG channel showed a marked improvement over tegobuvir and the pharmacokinetic properties of compound 3 indicated that it was worthy of further investigation as a non-nucleoside inhibitor of HCV NS5B polymerase.

Quality-by-design approach to selective stability indicating RP- HPLC meth-od development and validation for estimation of Sofosbuvir in bulk drug

By utilizing Quality by design approach a simple, robust and selective Reverse phase liquid chromatography (RP-HPLC) method was developed for the estimation of Sofosbuvir in API. Sofosbuvir is a nucleotide Hepatitis C Virus (HCV) NS5B polymerase inhibitor that has antiviral activity. Analyte target profile of Sofosbuvir was constructed and CAA’s were identified. LC analysis was performed on Agilent LC 1200 equipped with a photodiode array detector (PDA) at 261 nm. Initial method was developed on an Inersil ODS (250 mm x 4.6, 5 micron) 65: 35 Methanol and Water at 261nm witha flow rate of 1 mL/min. The degradation studies of Sofosbuvir were carried out under the stress conditions of hydrolysis (acid, base and neutral), oxidation, photolytic and thermal as per ICH guidelines. The alkali hydrolysis shows more critical impurities which were well resolved from pure drug with the application of DoE. Three method variables were selected and their interaction were studied through central composite design and two method responses like retention time of drug and resolution between degradants and active drug were studied. Based on DoE, the optimized method was developed using 60:40 of Methanol and Water, at pH 4 with a flow rate of 1.2 mL/min which produce satisfactory retention time and resolution. This method has been validated and shown to be linear, accurate, robust, precise and specific. Keywords: Stability indicating assay, RP-HPLC, Sofosbuvir, QbD, Validation

Sofosbuvir/Velpatasvir/Voxilaprevir: A Review in Chronic Hepatitis C.

A fixed-dose combination of the hepatitis C virus (HCV) NS5B polymerase inhibitor sofosbuvir, the HCV NS5A inhibitor velpatasvir and the HCV NS3/4A protease inhibitor voxilaprevir (sofosbuvir/velpatasvir/voxilaprevir; Vosevi®) is approved in the EU for the treatment of chronic HCV genotype 1, 2, 3, 4, 5 or 6 infection in adults. In the phase III POLARIS trials, in patients who had HCV genotype 1-6 infection with or without compensated cirrhosis, overall rates of sustained virological response at 12weeks post-treatment (SVR12) with sofosbuvir/velpatasvir/voxilaprevir were high after 8weeks of treatment in direct-acting antiviral (DAA)-naïve patients and 12weeks of treatment in DAA-experienced patients. However, 8weeks of sofosbuvir/velpatasvir/voxilaprevir was inferior to 12weeks of sofosbuvir/velpatasvir in cirrhotic or non-cirrhotic DAA-naïve patients with HCV genotype 1, 2, 4, 5 or 6 infection and non-cirrhotic DAA-naïve patients with HCV genotype 3 infection, mostly due to an insufficient treatment period. Sofosbuvir/velpatasvir/voxilaprevir was generally well tolerated, with most adverse events being of mild or moderate intensity. The most common adverse events included headache, fatigue, nausea and diarrhoea. In conclusion, sofosbuvir/velpatasvir/voxilaprevir is an important and effective option for the treatment of HCV genotype 1-6 infection in adults, especially those who have previously failed a DAA therapy with or without an HCV NS5A inhibitor.

Characterization of interactions between hepatitis C virus NS5B polymerase, annexin A2 and RNA \u2013 effects on NS5B catalysis and allosteric inhibition

BackgroundDirect acting antivirals (DAAs) provide efficient hepatitis C virus (HCV) therapy and clearance for a majority of patients, but are not available or effective for all patients. They risk developing HCV-induced hepatocellular carcinoma (HCC), for which the mechanism remains obscure and therapy is missing. Annexin A2 (AnxA2) has been reported to co-precipitate with the non-structural (NS) HCV proteins NS5B and NS3/NS4A, indicating a role in HCC tumorigenesis and effect on DAA therapy.MethodsSurface plasmon resonance biosensor technology was used to characterize direct interactions between AnxA2 and HCV NS5B, NS3/NS4 and RNA, and the subsequent effects on catalysis and inhibition.ResultsNo direct interaction between AnxA2 and NS3/NS4A was detected, while AnxA2 formed a slowly dissociating, high affinity (KD = 30 nM), complex with NS5B, decreasing its catalytic activity and affinity for the allosteric inhibitor filibuvir. The RNA binding of the two proteins was independent and AnxA2 and NS5B interacted with different RNAs in ternary complexes of AnxA2:NS5B:RNA, indicating specific preferences.ConclusionsThe complex interplay revealed between NS5B, AnxA2, RNA and filibuvir, suggests that AnxA2 may have an important role for the progression and treatment of HCV infections and the development of HCC, which should be considered also when designing new allosteric inhibitors.

Improving Metabolic Stability with Deuterium: The Discovery of BMT-052, a Pan-genotypic HCV NS5B Polymerase Inhibitor.

Iterative structure-activity analyses in a class of highly functionalized furo[2,3-b]pyridines led to the identification of the second generation pan-genotypic hepatitis C virus NS5B polymerase primer grip inhibitor BMT-052 (14), a potential clinical candidate. The key challenge of poor metabolic stability was overcome by strategic incorporation of deuterium at potential metabolic soft spots. The preclinical profile and status of BMT-052 (14) is described.

Synthesis, biological evaluation and molecular modeling of 2-Hydroxyisoquinoline-1,3-dione analogues as inhibitors of HIV reverse transcriptase associated ribonuclease H and polymerase

Human immunodeficiency virus (HIV) reverse transcriptase (RT) associated ribonuclease H (RNase H) remains the only virally encoded enzymatic function not clinically validated as an antiviral target. 2-Hydroxyisoquinoline-1,3-dione (HID) is known to confer active site directed inhibition of divalent metal-dependent enzymatic functions, such as HIV RNase H, integrase (IN) and hepatitis C virus (HCV) NS5B polymerase. We report herein the synthesis and biochemical evaluation of a few C-5, C-6 or C-7 substituted HID subtypes as HIV RNase H inhibitors. Our data indicate that while some of these subtypes inhibited both the RNase H and polymerase (pol) functions of RT, potent and selective RNase H inhibition was achieved with subtypes 8–9 as exemplified with compounds 8c and 9c.

HQSAR study and molecular design of benzimidazole 5-carboxylic derivatives of hepatitis C virus NS5B polymerase

HQSAR study and molecular design of benzimidazole 5-carboxylic derivatives of hepatitis C virus NS5B polymerase

Discovery of Novel Allosteric HCV NS5B Inhibitors. 2. Lactam-Containing Thiophene Carboxylates.

Lomibuvir (1) is a non-nucleoside, allosteric inhibitor of the hepatitis C virus NS5B polymerase with demonstrated clinical efficacy. Further development efforts within this class of inhibitor focused on improving the antiviral activity and physicochemical and pharmacokinetic properties. Recently, we reported the development of this series, leading to compound 2, a molecule with comparable potency and an improved physicochemical profile relative to 1. Further exploration of the amino amide-derived side chain led to a series of lactam derivatives, inspired by the X-ray crystal structure of related thiophene carboxylate inhibitors. This series, exemplified by 12f, provided 3-5-fold improvement in potency against HCV replication, as measured by replicon assays. The synthesis, structure-activity relationships, in vitro ADME characterization, and in vivo evaluation of this novel series are discussed.