In silico design, modelling and molecular mechanisms of Axl receptor tyrosine kinase inhibitors

A kinase domain from receptor tyrosine kinases (RTKs) regulate intracellular communications to control cellular metabolic activities. Some of the malignant cells have upregulated and overexpressed RTKs which are responsible for angiogenesis in many metastatic cancers. Axl RTK is present in most of the eukaryotic cells and all metastatic cancer cells have overexpressed Axl tyrosine kinase to trigger uncontrolled growth and angiogenesis in the malignant cells. The upregulated kinases can be inhibited in its active and inactive states in the presence of small organic molecule inhibitors. Kinase inhibitors have been discovered to arrest the signal transduction pathways in the malignant cells as a therapy and cure for cancer. In this work, small molecule databases were screened using the pharmacophore features of a macrocyclic inhibitor (7YS) taken as reference from the crystal structure of Axl kinase domain. Pharmacophore based virtual screening of small molecule libraries (CHEMBL32, ChemDiv, Chemspace, Mcule, MolProt, PubChem and Zinc), followed by molecular docking, molecular dynamics simulations, binding energies from MM-PBSA calculations and trajectory analysis as principal component analysis were studied. The molecular basis for the binding of macrocyclic inhibitor, ATP and seven screened hit molecules bound at Axl kinase domain in two different modes at catalytic and regulatory sites was analyzed.

受体酪氨酸激酶（Receptor Tyrosine Kinases, RTKs）的激酶结构域可调控细胞内信号传导，以控制细胞代谢活动。部分恶性细胞会出现受体酪氨酸激酶的上调与过表达，而这类异常表达的受体酪氨酸激酶是诸多转移性癌症血管生成的关键驱动因素。Axl受体酪氨酸激酶（Axl RTK）广泛表达于大多数真核细胞中，所有转移性癌细胞均会过表达Axl酪氨酸激酶，进而触发恶性细胞的失控增殖与血管生成。在有机小分子抑制剂存在的条件下，上调的激酶无论处于激活态还是失活态均可被抑制。研究表明，激酶抑制剂可通过阻断恶性细胞内的信号转导通路，实现癌症的治疗与治愈。本研究以Axl激酶结构域晶体结构来源的大环类抑制剂（7YS）的药效团特征为参考模板，对小分子数据库开展虚拟筛选。所筛选的小分子库包含CHEMBL32、ChemDiv、Chemspace、Mcule、MolProt、PubChem及Zinc，随后依次开展了分子对接、分子动力学模拟、MM-PBSA结合自由能计算以及采用主成分分析的轨迹分析等研究。本研究还分析了大环抑制剂、三磷酸腺苷（ATP）以及7个经筛选得到的命中分子，以两种不同结合模式分别结合于Axl激酶结构域催化位点与调节位点的分子结合机制。