Molecular Dynamics-Ensemble Docking and Biophysical Studies for Structure-Based Identification of Non-Amino Acidic Ligands of DDAH‑1

Dimethylarginine
dimethylaminohydrolase-1 (DDAH-1) accounts
for
the catabolism of the endogenous inhibitors of nitric oxide (NO) synthases,
namely, ADMA (Nω,Nω-dimethyl-l-arginine) and NMMA (Nω-monomethyl-l-arginine). Inhibition
of DDAH-1 may prove a therapeutic benefit in diseases associated with
elevated nitric oxide (NO) levels by providing a tissue-specific increase
of ADMA and NMMA. In this work, we have used molecular dynamics to
generate a pool of DDAH-1 conformations in the apo and holo forms.
Ensemble docking has been instrumental in screening an in-house fragment-based
library of 824 compounds. Resulting virtual hits have been validated
for their binding activity to recombinant human DDAH-1 using microscale
thermophoresis (MST). As a key result, three non-amino acidic ligands
of DDAH-1 (VIS212, VIS268, VIS726) are identified with higher binding
efficiency index than ADMA. Amid these compounds, purpurogallin (VIS726)
proves a potent ligand of DDAH-1, showing a mixed behavior of enzymatic
inhibition in a biochemical assay. This finding widens the panel of
known molecular targets of purpurogallin and provides clues into the
molecular mechanisms of its cellular NO inhibition activity as well
as its anti-inflammatory and neuroprotective effects.