Severe hepatocellular injury with apoptosis induced by a hepatitis C polymerase inhibitor

Applications of Quantitative Systems Pharmacology (QSP) in Drug Development for NAFLD and NASH and Its Regulatory Application

Nonalcoholic steatohepatitis (NASH) is a widely prevalent disease, but approved pharmaceutical treatments are not available. As such, there is great activity within the pharmaceutical industry to accelerate drug development in this area and improve the quality of life and reduce mortality for NASH patients. The use of quantitative systems pharmacology (QSP) can help make this overall process more efficient. This mechanism-based mathematical modeling approach describes both the pathophysiology of a disease and how pharmacological interventions can modify pathophysiologic mechanisms. Multiple capabilities are provided by QSP modeling, including the use of model predictions to optimize clinical studies. The use of this approach has grown over the last 20 years, motivating discussions between modelers and regulators to agree upon methodologic standards. These include model transparency, documentation, and inclusion of clinical pharmacodynamic biomarkers. Several QSP models have been developed that describe NASH pathophysiology to varying extents. One specific application of NAFLDsym, a QSP model of NASH, is described in this manuscript. Simulations were performed to help understand if patient behaviors could help explain the relatively high rate of fibrosis stage reductions in placebo cohorts. Simulated food intake and body weight fluctuated periodically over time. The relatively slow turnover of liver collagen allowed persistent reductions in predicted fibrosis stage despite return to baseline for liver fat, plasma ALT, and the NAFLD activity score. Mechanistic insights such as this that have been derived from QSP models can help expedite the development of safe and effective treatments for NASH patients.

Small molecule NS5B RdRp non-nucleoside inhibitors for the treatment of HCV infection: A medicinal chemistry perspective

Hepatitis C virus (HCV) infection has become a global health problem with enormous risks. Nonstructural protein 5B (NS5B) RNA-dependent RNA polymerase (RdRp) is a component of HCV, which can promote the formation of the viral RNA replication complex and is also an essential part of the replication complex itself. It plays a vital role in the synthesis of the positive and negative strands of HCV RNA. Therefore, the development of small-molecule inhibitors targeting NS5B RdRp is of great value for treating HCV infection-related diseases. Compared with NS5B RdRp nucleoside inhibitors, non-nucleoside inhibitors have more flexible structures, simpler mechanisms of action, and more predictable efficacy and safety of drugs in humans. Technological advances over the past decade have led to remarkable achievements in developing NS5B RdRp inhibitors. This review will summarize the non-nucleoside inhibitors targeting NS5B RdRp developed in the past decade and describe their structure optimization process and structure-activity relationship.

RNA-dependent RNA polymerase (RdRp) inhibitors: The current landscape and repurposing for the COVID-19 pandemic

The widespread nature of several viruses is greatly credited to their rapidly altering RNA genomes that enable the infection to persist despite challenges presented by host cells. Within the RNA genome of infections is RNA-dependent RNA polymerase (RdRp), which is an essential enzyme that helps in RNA synthesis by catalysing the RNA template-dependent development of phosphodiester bonds. Therefore, RdRp is an important therapeutic target in RNA virus-caused diseases, including SARS-CoV-2. In this review, we describe the promising RdRp inhibitors that have been launched or are currently in clinical studies for the treatment of RNA virus infections. Structurally, nucleoside inhibitors (NIs) bind to the RdRp protein at the enzyme active site, and nonnucleoside inhibitors (NNIs) bind to the RdRp protein at allosteric sites. By reviewing these inhibitors, more precise guidelines for the development of more promising anti-RNA virus drugs should be set, and due to the current health emergency, they will eventually be used for COVID-19 treatment.

Design of N-Benzoxaborole Benzofuran GSK8175-Optimization of Human Pharmacokinetics Inspired by Metabolites of a Failed Clinical HCV Inhibitor

We previously described the discovery of GSK5852 (1), a non-nucleoside polymerase (NS5B) inhibitor of hepatitis C virus (HCV), in which an N-benzyl boronic acid was essential for potent antiviral activity. Unfortunately, facile benzylic oxidation resulted in a short plasma half-life (5 h) in human volunteers, and a backup program was initiated to remove metabolic liabilities associated with 1. Herein, we describe second-generation NS5B inhibitors including GSK8175 (49), a sulfonamide-N-benzoxaborole analog with low in vivo clearance across preclinical species and broad-spectrum activity against HCV replicons. An X-ray structure of NS5B protein cocrystallized with 49 revealed unique protein-inhibitor interactions mediated by an extensive network of ordered water molecules and the first evidence of boronate complex formation within the binding pocket. In clinical studies, 49 displayed a 60–63 h half-life and a robust decrease in viral RNA levels in HCV-infected patients, thereby validating our hypothesis that reducing benzylic oxidation would improve human pharmacokinetics and lower efficacious doses relative to 1.

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.

Discovery of novel potent HCV NS5B polymerase non-nucleoside inhibitors bearing a fused benzofuran scaffold

This letter describes the discovery of a fused benzofuran scaffold viable for preparing a series of novel potent HCV NS5B polymerase non-nucleoside inhibitors. Designed on the basis of the functionalized benzofuran derivative nesbuvir (HCV-796), these compounds presumably bind similarly to the allosteric binding site in the "palm" domain of HCV NS5B protein. SAR of each potential hydrogen-bonding interaction site of this novel scaffold is discussed along with some preliminary genotypic profile and PK data of several advanced compounds.

The discovery of a pan-genotypic, primer grip inhibitor of HCV NS5B polymerase

The development of a series of novel 7-azabenzofurans exhibiting pan-genotype inhibition of HCV NS5B polymerase via binding to the primer grip site is presented. Many challenges, including poor oral bioavailability, high clearance, bioactivation, high human serum shift, and metabolic stability were encountered and overcome through SAR studies. This work culminated in the selection of BMS-986139 (43) as a preclinical candidate.

Cytokeratins in hepatitis

Experimental and clinical evidence suggests that cytokeratins (CK), among other physiological functions, are expressed in hepatocytes and can be released in the bloodstream after acute or chronic inflammatory liver injury. Interest in CK in viral and nonviral hepatitis has been rapidly increasing during the last years, especially as they have been proposed as circulating biomarkers of hepatocyte necrosis and apoptosis. In the present review, we sought to summarize and discuss the alterations in circulating CK levels in different form viral and nonviral hepatitis, as well as their potential relation with liver histology. Understanding the mechanisms of hepatitis impact on CK and vice versa is a promising area of research that will positively enhance our understanding of the complexity of acute and chronic inflammatory liver injury.

The cytoskeleton in nonalcoholic steatohepatitis: 100 years old but still youthful

The hepatocellular cytoskeleton consists of three filamentous systems: microfilaments, microtubules and keratins (Ks). While the alterations in microfilaments and microtubules during nonalcoholic steatohepatitis (NASH) are largely unexplored, K8/K18 reorganization into Mallory-Denk bodies (MDBs) represents a NASH hallmark, and serological K18 fragments constitute an established tool to monitor NASH severity. To commemorate the 100th anniversary of the first description of MDBs, this article summarizes the composition and function of the hepatocellular cytoskeleton, as well as the importance of cytoskeletal alterations in NASH. The significance of MDBs in clinical routine is illustrated, as are the findings from MDB mouse models, which shape our current view of MDB pathogenesis. Even after 100 years, the cytoskeleton represents a fascinating but greatly understudied area of NASH biology.

Serum markers of hepatocyte death and apoptosis are non invasive biomarkers of severe fibrosis in patients with alcoholic liver disease

Background

Quantification of hepatotocyte death is useful to evaluate the progression of alcoholic liver diseases. Our aims were to quantify and correlate the circulating levels of Cytokeratin 18 (CK18) and its caspases-generated fragment to disease severity in heavy alcoholics.

Methodology/Principal Findings

CK18 and CK18-fragment were evaluated in the serum of 143 heavy alcoholics. Serum levels of markers of hepatocyte death (CK18), apoptosis (CK18 fragment) and necrosis (CK18 -CK18 fragment) increased in patients with severe fibrosis compared to patients with mild fibrosis. These markers strongly correlated with Mallory-Denk bodies, hepatocyte ballooning, fibrosis and with hepatic TNFα and TGFβ assessed in the liver of 24 patients. Elevated levels of serum hepatocyte death and apoptotic markers were independent risk factors in predicting severe fibrosis in a model combining alkaline phosphatase, bilirubin, prothrombin index, hyaluronate, hepatocyte death and apoptotic markers. The level of markers of hepatocyte death and apoptosis had an area under the receiving operator curve that predicted severe fibrosis of 0.84 and 0.76, respectively.

Conclusion/Significance

Death of hepatocytes can be easily evaluated with serum markers and correlated with severe fibrosis in heavy alcohol drinkers. These biomarkers could be useful to rapidly evaluate liver injuries and the efficacy of therapies.

Ligand-induced changes in hepatitis C virus NS5B polymerase structure

Hepatitis C virus (HCV) RNA-dependent RNA polymerase (NS5B) is required for viral replication. Crystal structures of the NS5B apoprotein show that the finger and thumb domains interact to encircle the active site, and that inhibitors defined by P495 resistance that bind to the thumb-finger interface displace the Δ1 finger loop and disrupt this structure. Since crystal structures may not reveal all of the conformations of a protein in solution we have developed an alternative method, using limited trypsin protease digestion, to investigate the impact of inhibitors as well as substrates on the movement of the Δ1 loop. This assay can be used to study NS5B under conditions that support enzymatic activity. In the absence of inhibitors, no specific region of NS5B was hypersensitive to trypsin, and no specific intermediate cleavage products were formed. Binding of P495-site inhibitors to NS5B induced specific trypsin hypersensitivity at lysine residues 50 and 51. Previously characterized inhibitors and mutant polymerases were used to link this specific trypsin hypersensitivity to movement of the Δ1 loop. Trypsin hypersensitivity identical to the inhibitor pattern was also induced by the binding of the RNA template. The addition of primer to the NS5B-template complex eliminated the hypersensitivity. The data are consistent with displacement of the Δ1 finger loop from the thumb by the binding of template, and reversal by the addition of primer or NTP. Our results complement inhibitor-enzyme co-crystal studies, and the assay provides a rapid and sensitive method to study dynamic changes in HCV NS5B polymerase conformation under conditions that support functional activity.

Development of novel antiviral therapies for hepatitis C virus

Over 170 million people worldwide are infected with hepatitis C virus (HCV), a major cause of liver diseases. Current interferon-based therapy is of limited efficacy and has significant side effects and more effective and better tolerated therapies are urgently needed. HCV is a positive, single-stranded RNA virus with a 9.6 kb genome that encodes ten viral proteins. Among them, the NS3 protease and the NS5B polymerase are essential for viral replication and have been the main focus of drug discovery efforts. Aided by structure-based drug design, potent and specific inhibitors of NS3 and NS5B have been identified, some of which are in late stage clinical trials and may significantly improve current HCV treatment. Inhibitors of other viral targets such as NS5A are also being pursued. However, HCV is an RNA virus characterized by high replication and mutation rates and consequently, resistance emerges quickly in patients treated with specific antivirals as monotherapy. A complementary approach is to target host factors such as cyclophilins that are also essential for viral replication and may present a higher genetic barrier to resistance. Combinations of these inhibitors of different mechanism are likely to become the essential components of future HCV therapies in order to maximize antiviral efficacy and prevent the emergence of resistance.

Non-nucleoside inhibitors of hepatitis C virus polymerase: current progress and future challenges

The current standard of care for hepatitis C virus (HCV) infection is a combination of PEGylated interferon and ribavirin, which offer limited efficacy and significant side effects. Novel HCV-specific inhibitors, including those directed at the viral polymerase, have become the focus of HCV drug-discovery efforts in the past decade. In addition to the active site targeted by traditional nucleoside inhibitors, at least four different allosteric-binding sites have been reported for the HCV polymerase, which offer ample opportunities for small-molecule inhibitors. In this review, we summarize the recent progress in the discovery of non-nucleoside HCV polymerase inhibitors with a focus on novel chemical matters, their clinical efficacy, safety and potential for combination therapy.

Systematic review: caspase-cleaved fragments of cytokeratin 18 - the promises and challenges of a biomarker for chronic liver disease

BACKGROUND

Biomarkers hold great promise for detecting chronic liver disease without the use of liver biopsy.

AIM

To review the usefulness of cytokeratin (CK) 18 fragments, a marker of hepatocyte apoptosis, to predict the presence of chronic liver injury.

METHODS

Available literature identified from PubMed was reviewed.

RESULTS

Levels of CK18 fragments have been shown to be elevated in hepatocellular carcinoma, viral hepatitis, alcoholic hepatitis, nonalcoholic fatty liver disease and cholestatic liver disease. In the setting of nonalcoholic fatty liver disease, CK18 fragments may distinguish nonalcoholic steatohepatitis from simple fatty liver.

CONCLUSIONS

Undoubtedly, the most promising application of CK18 fragments is currently in nonalcoholic fatty liver disease, and especially for distinguishing patients with nonalcoholic steatohepatitis vs. those with simple steatosis. Further investigations and technical improvements are required to cross the boundary from research to the clinical application of CK18 fragments as a marker of chronic liver disease.

Prospects for future therapy of HCV infection

Worldwide, HCV infection is a major cause of chronic liver disease and hepatocellular carcinoma and is often refractory to current antiviral treatments. The most effective therapy, pegylated interferon plus ribavirin, unfortunately eliminates virus only in approximately half of patients treated and is frequently poorly tolerated. The recent development of in vitro and in vivo HCV infection and replication models has resulted in breakthroughs in basic research toward the development of new antiviral agents. Currently, many therapeutic agents with different mechanisms of action are under development, and several are in late-phase clinical trials. Some of these drugs have shown promise when used in combination with the standard peginterferon and ribavirin, and others could constitute tablet-based combination therapies without standard therapy. This article reviews the current status of drug development, ongoing clinical trials and future perspectives in the field of HCV therapeutics.

New therapeutic approaches to hepatitis C virus

Year 201X will see a huge battle against hepatitis C virus (HCV) infection. HCV, a leading cause of end stage diseases and hepatocellular malignancies, is a negative legacy of the past in many regions worldwide, and has long been refractory to conventional treatments. The most effective peginterferons and ribavirin-based antiviral therapies can eliminate the virus in only half of patients treated, and the treatments are often poorly tolerated. Recently, the development of an HCV cell culture system has become a turning point of basic research. At present, novel therapeutic agents with different mechanisms of action are under development or on clinical trials. Some of these drugs have been proven to be effective when used with the conventional treatments, and may constitute antiviral therapies without being used in combination with interferons. This article reviews the current status of preclinical drug development, ongoing clinical trials, and near future perspectives in the field of HCV therapeutics.