Structure-Based Drug Discovery of Non-SAM-Mimetic Bisubstrate Inhibitors against Nicotinamide N‑Methyltransferase

Nicotinamide N-methyltransferase (NNMT)
has emerged
as a regulator of cellular methylation, epigenetic remodeling, and
energy homeostasis. Its aberrant expression has been implicated in
cancer, metabolic disorders, and renal diseases. Although several
NNMT inhibitors have been reported, most lack selectivity, cellular
activity, or favorable pharmacokinetic properties. Here, we describe
the discovery and optimization of a novel non-SAM-mimetic bisubstrate
inhibitor of NNMT originating from high-throughput screening. Guided
by structure-based design, systematic modifications of hit compound 1 yielded lead compound 16 with over 1000-fold
improved potency (IC50 for compounds 1 and 16 = 10 μM and 0.0084 μM, respectively). Compound 16 exhibited sub-micromolar cell-based activity and high selectivity
for a subfamily of methyltransferases. In rodents, compound 16 exhibited pronounced renal distribution and moderate bioavailability,
while achieving dose-dependent renal NNMT inhibition in a renal fibrosis
model. These results highlight compound 16 as a promising
probe and a starting point for NNMT-targeted drug discovery.