Widely used chemical genetic screens have greatly facilitated the identification of many antiviral agents. However, the regions of interaction and inhibitory mechanisms of many therapeutic candidates have yet to be elucidated. Previous chemical screens identified Daclatasvir (BMS-790052) as a potent nonstructural protein 5A (NS5A) inhibitor for Hepatitis C virus (HCV) infection with an unclear inhibitory mechanism. Here we have developed a quantitative high-resolution genetic (qHRG) approach to systematically map the drug-protein interactions between Daclatasvir and NS5A and profile genetic barriers to Daclatasvir resistance. We implemented saturation mutagenesis in combination with next-generation sequencing technology to systematically quantify the effect of every possible amino acid substitution in the drug-targeted region (domain IA of NS5A) on replication fitness and sensitivity to Daclatasvir. This enabled determination of the residues governing drug-protein interactions. The relative fitness and drug sensitivity profiles also provide a comprehensive reference of the genetic barriers for all possible single amino acid changes during viral evolution, which we utilized to predict clinical outcomes using mathematical models. We envision that this high-resolution profiling methodology will be useful for next-generation drug development to select drugs with higher fitness costs to resistance, and also for informing the rational use of drugs based on viral variant spectra from patients.
Submitter: Shu-Ching Ou
Submission Date: July 31, 2018, 4:43 p.m.
|Number of data points||3922|
|Assays/Quantities/Protocols||Experimental Assay: Relative fitness (under drug treatment) ; Experimental Assay: Relative fitness (in NS5A in virus replication) ; Experimental Assay: Relative fitness (in NS5A in virus replication, under 20 pM Daclatasvir treat)|
|Libraries||Selection coefficient in NS5A in virus replication ; Selection coefficient in NS5A in virus replication, under Daclatasvir treatment (20 pM) ; Fitness landscape fold change under Daclatasvir treatment (20 pM)|
|Structure ID||Release Date||Resolution||Structure Title|
|1YUY||2005-02-14T00:00:00+0000||1.9||HEPATITIS C VIRUS NS5B RNA-DEPENDENT RNA POLYMERASE GENOTYPE 2a|
|1YV2||2005-02-14T00:00:00+0000||2.5||Hepatitis C virus NS5B RNA-dependent RNA Polymerase genotype 2a|
|1YVX||2005-02-16T00:00:00+0000||2.0||Hepatitis C Virus RNA Polymerase Genotype 2a In Complex With Non- Nucleoside Analogue Inhibitor|
|1YVZ||2005-02-16T00:00:00+0000||2.2||Hepatitis C Virus RNA Polymerase Genotype 2a In Complex With Non- Nucleoside Analogue Inhibitor|
|2XWH||2010-11-03T00:00:00+0000||1.8||HCV-J6 NS5B polymerase structure at 1.8 Angstrom|
|4ADP||2012-01-02T00:00:00+0000||1.9||HCV-J6 NS5B POLYMERASE V405I MUTANT|
|2LIF||2011-08-29T00:00:00+0000||0||Solution Structure of KKGF|
|2LVG||2012-07-05T00:00:00+0000||0||NMR structure of HCV Non-structural protein AB, NS4B(1-40)|
|2XXD||2010-11-10T00:00:00+0000||1.88||HCV-JFH1 NS5B polymerase structure at 1.9 angstrom|