Department of Chemistry, Rikkyo University, Nishi-Ikebukuro, Toshima, Tokyo 171-8501, Japan.
Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan.
Biochem Biophys Res Commun. 2018 May 5;499(2):239-245. doi: 10.1016/j.bbrc.2018.03.135. Epub 2018 Mar 22.
Peroxisome proliferator-activated receptor-α (PPARα) is a ligand-activated transcription factor involved in the regulation of lipid homeostasis and improves hypertriglyceridemia. Pemafibrate is a novel selective PPARα modulator (SPPARMα) that activates PPARα transcriptional activity. Here, we computationally constructed the structure of the human PPARα in a complex with pemafibrate, along with that of hPPARα complexed with the classical fenofibrate, and studied their interactions quantitatively by using the first-principles calculations-based fragment molecular orbital (FMO) method. Comprehensive structural and protein-ligand binding elucidation along with the in vitro luciferase analysis let us to identify pemafibrate as a novel SPPARMα. Unlike known fibrate ligands, which bind only with the arm I of the Y-shaped ligand binding pocket, the Y-shaped pemafibrate binds to the entire cavity region. This lock and key nature causes enhanced induced fit in pemafibrate-ligated PPARα. Importantly, this selective modulator allosterically changes PPARα conformation to form a brand-new interface, which in turn binds to PPARα co-activator, PGC-1α, resulting in the full activation of PPARα. The structural basis for the potent effects of pemafibrate on PPARα transcriptional activity predicted by the in silico FMO methods was confirmed by in vitro luciferase assay for mutants. The unique binding mode of pemafibrate reveals a new pattern of nuclear receptor ligand recognition and suggests a novel basis for ligand design, offering cues for improving the binding affinity and selectivity of ligand for better clinical consequences. The findings explain the high affinity and efficacy of pemafibrate, which is expected to be in the clinical use soon.
过氧化物酶体增殖物激活受体-α（PPARα）是一种配体激活的转录因子，参与脂质稳态的调节，并改善高甘油三酯血症。非诺贝特是一种新型选择性过氧化物酶体增殖物激活受体-α 调节剂（SPPARMα），可激活 PPARα 的转录活性。在这里，我们通过使用基于第一性原理计算的片段分子轨道（FMO）方法，计算构建了人 PPARα 与 pemafibrate 复合物的结构，以及人 PPARα 与经典 fenofibrate 复合物的结构，并对它们的相互作用进行了定量研究。综合结构和蛋白质-配体结合阐明以及体外荧光素酶分析使我们能够将 pemafibrate 鉴定为新型 SPPARMα。与仅与 Y 形配体结合口袋的臂 I 结合的已知纤维酸配体不同，Y 形 pemafibrate 结合整个腔区域。这种锁和键性质导致 pemafibrate 结合的 PPARα 诱导契合增强。重要的是，这种选择性调节剂变构地改变 PPARα 的构象，形成一个全新的界面，进而与 PPARα 共激活剂 PGC-1α 结合，导致 PPARα 的完全激活。通过计算 FMO 方法预测的 pemafibrate 对 PPARα 转录活性的强大作用的结构基础通过突变体的体外荧光素酶测定得到了证实。pemafibrate 独特的结合模式揭示了核受体配体识别的新模式，并为配体设计提供了新的基础，为提高配体的结合亲和力和选择性以获得更好的临床效果提供了线索。这些发现解释了 pemafibrate 的高亲和力和功效，预计很快将在临床上使用。
