Computer assisted discovery of novel nicotinamide phosphoribosyltransferase agonists to combat muscle atrophy

Nicotinamide adenine dinucleotide (NAD⁺) is a crucial cofactor for maintaining cellular homeostasis, and its level is strictly regulated by the rate-limiting enzyme nicotinamide phosphoribosyltransferase (NAMPT). Small molecule NAMPT agonists hold great potential to boost NAD⁺ level, while only few agonists were available currently. Herein, we established a rapid screening workflow for NAMPT agonists by integrating molecular docking and molecular dynamics simulations. In brief, the high-throughput docking was firstly performed on 1.3 million compounds from the ZINC20 Lead-like subset, and the top 20 candidates were further evaluated by all-atom molecular dynamics simulations and MM/GBSA assessments, ultimately identifying three potential candidates. Among them, 3,4-dihydro-1H-isoquinolin-2-yl-[4-(2H-tetrazol-5-yl)phenyl]methanone (DIPM) enhanced NAMPT enzymatic activity by approximately threefold at the concentration of 20 μM, with the EC₅₀ value of 3.366 μM and a maximum effect approximate 1.05-fold that of NAT. DIPM binds stably to NAMPT with a binding free energy of -30.86 kcal/mol. Its binding sites are located far from the catalytic active center of NAMPT and do not interfere with the substrate channel, indicating that DIPM activates NAMPT through an allosteric mechanism. DIPM (20 μM) elevated intracellular NAD⁺ levels by approximately twofold with no obvious toxicity in C2C12 myotubes. In a dexamethasone-induced C2C12 myotube atrophy model, DIPM (20 μM) restored myotube diameter, decreased the expression of atrophy markers Atrogin-1 and muscle ring finger 1 (MuRF1), and increased Myosin heavy chain (MyHC) expression. As a potent, low-toxic, non-competitive allosteric NAMPT agonist, DIPM represents a promising lead compound for treating conditions involving muscle wasting.

Allosteric activator; High-throughput docking; Molecular dynamics; Muscle atrophy; NAMPT.