The c-Jun N-terminal kinase 3 (JNK3) signaling cascade is activated during cerebral ischemia leading to neuronal damage. The present study was carried out to identify and evaluate novel JNK3 inhibitors using in-silico and in-vitro approach. A total of 380 JNK3 inhibitors belonging to different organic groups was collected from the previously reported literature. These molecules were used to generate a pharmacophore model. This model was used to screen a chemical database (SPECS) to identify newer molecules with similar chemical features. The top 1000 hits molecules were then docked against the JNK3 enzyme coordinate following GLIDE rigid receptor docking (RRD) protocol. Best posed molecules of RRD were used during induced-fit docking (IFD), allowing receptor flexibility. Other computational predictions such as binding free energy, electronic configuration and ADME/tox were also calculated. Inferences from the best pharmacophore model suggested that, in order to have specific JNK3 inhibitory activity, the molecules must possess one H-bond donor, two hydrophobic and two ring features. Docking studies suggested that the main interaction between lead molecules and JNK3 enzyme consisted of hydrogen bond interaction with methionine 149 of the hinge region. It was also observed that the molecule with better MM-GBSA dG binding free energy, had greater correlation with JNK3 inhibition. Lead molecule (AJ-292-42151532) with the highest binding free energy (dG = 106.8 Kcal/mol) showed better efficacy than the SP600125 (reference JNK3 inhibitor) during cell-free JNK3 kinase assay (IC50 = 58.17 nM) and cell-based neuroprotective assay (EC50 = 7.5 µM).

中文翻译：

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通过基于结构的虚拟筛选和体外测定对潜在的 c-Jun N 端激酶 3 抑制剂进行鉴定和神经保护评估。

c-Jun N 末端激酶 3 (JNK3) 信号级联在脑缺血期间被激活，导致神经元损伤。本研究旨在使用计算机模拟和体外方法鉴定和评估新型 JNK3 抑制剂。从先前报道的文献中收集了总共380种属于不同有机基团的JNK3抑制剂。这些分子用于生成药效团模型。该模型用于筛选化学数据库 (SPECS)，以识别具有相似化学特征的新分子。然后按照 GLIDE 刚性受体对接 (RRD) 协议将前 1000 个命中分子对接 JNK3 酶坐标。在诱导拟合对接 (IFD) 过程中使用了 RRD 的最佳姿势分子，从而允许受体具有灵活性。其他计算预测，例如结合自由能，还计算了电子构型和 ADME/tox。最佳药效团模型的推论表明，为了具有特定的 JNK3 抑制活性，分子必须具有一个 H 键供体、两个疏水性和两个环特征。对接研究表明，先导分子与JNK3酶之间的主要相互作用由与铰链区甲硫氨酸149的氢键相互作用组成。还观察到具有更好 MM-GBSA dG 结合自由能的分子与 JNK3 抑制具有更大的相关性。在无细胞 JNK3 激酶测定 (IC50 = 58.17 nM) 和细胞-基于神经保护测定 (EC50 = 7.5 µM)。