The nonstructural 5A (NS5A) protein is a target for drug development against hepatitis C virus (HCV). Interestingly, the NS5A inhibitor daclatasvir (BMS-790052) caused a decrease in serum HCV RNA levels by about two orders of magnitude within 6 h of administration. However, NS5A has no known enzymatic functions, making it difficult to understand daclatasvir's mode of action (MOA) and to estimate its antiviral effectiveness. Modeling viral kinetics during therapy has provided important insights into the MOA and effectiveness of a variety of anti-HCV agents. Here, we show that understanding the effects of daclatasvir in vivo requires a multiscale model that incorporates drug effects on the HCV intracellular lifecycle, and we validated this approach with in vitro HCV infection experiments. The model predicts that daclatasvir efficiently blocks two distinct stages of the viral lifecycle, namely viral RNA synthesis and virion assembly/ secretion with mean effectiveness of 99% and 99.8%, respectively, and yields a more precise estimate of the serum HCV half-life, 45 min, i.e., around four times shorter than previous estimates. Intracellular HCV RNA in HCV-infected cells treated with daclatasvir and the HCV polymerase inhibitor NM107 showed a similar pattern of decline. However, daclatasvir treatment led to an immediate and rapid decline of extracellular HCV titers compared to a delayed (6-9 h) and slower decline with NM107, confirming an effect of daclatasvir on both viral replication and assembly/secretion. The multiscale modeling approach, validated with in vitro kinetic experiments, brings a unique conceptual framework for understanding the mechanism of action of a variety of agents in development for the treatment of HCV.direct-acting antiviral agents | mathematical modeling | viral dynamics H epatitis C virus (HCV) infection is a major health burden affecting about 150 million people worldwide (1) and ∼4.1 million in the United States (2), where it is the primary cause of liver cirrhosis and liver cancer (1). Until 2011, the most advanced antiviral therapy was pegylated interferon-α (IFN-α) plus ribavirin (Peg-IFN/RBV), with a cure rate of 50% or less in patients infected with HCV genotype 1, the most prevalent in the Western world.To obtain higher cure rates, drug development has focused mainly on inhibiting the function of nonstructural (NS) viral proteins with known enzymatic functions, such as the NS3-4A protease and the NS5B polymerase. Through the use of an innovative screening approach to search for nonenzymatic targets, daclatasvir (BMS-790052) was identified as a potent NS5A inhibitor (3). The functions of the NS5A protein are not fully elucidated, although in vitro studies suggest an essential role of NS5A in both viral replication (4-7) and assembly/release of infectious particles (8-11). The efficacy of daclatasvir as an antiviral agent was confirmed in a single ascending-dose study in which a mean 3.3-log 10 reduction in viral load 24 h after drug administration was observed in patients receiving a 1...

Background Cases of sustained-virological response (SVR or cure) after an ultra-short duration (≤27 days) of direct-acting antiviral (DAA)-based therapy, despite HCV being detected at end of treatment (EOT), have been reported. Established HCV mathematical models that predict the treatment duration required to achieve cure do not take into account the possibility that the infectivity of virus produced during treatment might be reduced. The aim of this study was to develop a new mathematical model that considers the fundamental and critical concept that HCV RNA in serum represents both infectious virus (Vi) and non-infectious virus (Vni) in order to explain the observation of cure with ultrashort DAA therapy. Methods Established HCV models were compared to the new mathematical model to retrospectively explain cure in 2 patients who achieved cure after 24 or 27 days of paritaprevir, ombitasvir, dasabuvir, ritonavir and ribavirin or sofosbuvir plus ribavirin, respectively. Results Fitting established models with measured longitudinal HCV viral loads indicated that in both cases, cure would not have been expected without an additional 3 to 6 weeks of therapy after the actual EOT. In contrast, the new model fits the observed outcome by considering that in addition to blocking Vi and Vni production (ε~0.998), these DAA + ribavirin treatments further enhanced the ratio of Vni to Vi, thus increasing the log(Vni/Vi) from 1 at pretreatment to 6 by EOT, which led to <1 infectious-virus particle in the extracellular body fluid (i.e., cure) prior to EOT. Conclusions This new model can explain cure after short duration of DAA+ribavirin therapy by suggesting that a minimum 6-fold increase of log(Vni/Vi) results from drug-induced enhancement of the Vni/Vi.

Deoxycytidine kinase (dCK) is a key enzyme in the nucleoside salvage pathway that is also required for the activation of several anticancer and antiviral nucleoside analog prodrugs. Additionally, dCK has been implicated in immune disorders and has been found to be overexpressed in several cancers. To allow the probing and modulation of dCK activity, a new class of small-molecule inhibitors of the enzyme were developed. Here, the structural characterization of four of these inhibitors in complex with human dCK is presented. The structures reveal that the compounds occupy the nucleoside-binding site and bind to the open form of dCK. Surprisingly, a slight variation in the nature of the substituent at the 5-position of the thiazole ring governs whether the active site of the enzyme is occupied by one or two inhibitor molecules. Moreover, this substituent plays a critical role in determining the affinity, improving it from >700 to 1.5 nM in the best binder. These structures lay the groundwork for future modifications that would result in even tighter binding and the correct placement of moieties that confer favorable pharmacodynamics and pharmacokinetic properties.