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.

烟酰胺N-甲基转移酶（Nicotinamide N-methyltransferase, NNMT）已被证实为细胞甲基化、表观遗传重塑及能量稳态的关键调控因子。其异常表达与癌症、代谢紊乱及肾脏疾病的发生发展密切相关。尽管已有多款NNMT抑制剂被报道，但多数存在选择性不足、细胞活性欠佳或药代动力学特性不佳等缺陷。本研究报道了一款源自高通量筛选的新型非SAM模拟型双底物NNMT抑制剂的发现与优化路径。在结构导向设计的指导下，研究人员对命中化合物1进行系统性修饰，最终得到先导化合物16，其抑制效力提升超1000倍（化合物1与16的IC₅₀分别为10 μM与0.0084 μM）。化合物16展现出亚微摩尔级的细胞水平活性，且对特定甲基转移酶亚家族具有高选择性。在啮齿类动物实验中，化合物16表现出显著的肾脏分布特性与中等生物利用度，并在肾纤维化模型中实现了剂量依赖性的肾脏NNMT抑制作用。上述研究结果表明，化合物16是一款极具潜力的研究探针，同时可作为靶向NNMT的药物开发起点。