Asymmetric Binding to NS5A by Daclatasvir (BMS-790052) and Analogs Suggests Two Novel Modes of HCV Inhibition

Symmetric,
dimeric daclatasvir (BMS-790052) is the clinical lead
for a class of picomolar inhibitors of HCV replication. While specific,
resistance-bearing mutations at positions 31 and 93 of domain I strongly
suggest the viral NS5A as target, structural mechanism(s) for the
drugs’ activities and resistance remains unclear. Several previous
models suggested symmetric binding modes relative to the homodimeric
target; however, none can fully explain SAR details for this class.
We present semiautomated workflows to model potential receptor conformations
for docking. Surprisingly, ranking docked hits with our library-derived
3D-pharmacophore revealed two distinct asymmetric binding modes, at
a conserved poly-proline region between 31 and 93, consistent with
SAR. Interfering with protein–protein interactions at this
membrane interface can explain potent inhibition of replication–complex
formation, resistance, effects on lipid droplet distribution, and
virion release. These detailed interaction models and proposed mechanisms
of action will allow structure-based design of new NS5A directed compounds
with higher barriers to HCV resistance.