Abstract：
Cyclin-dependent kinase 2 (CDK2) regulates cell cycle checkpoints in the synthesis and mitosis phases and plays a pivotal role in cancerous cell proliferation. The activation of CDK2, influenced by various protein signaling pathways, initiates the phosphorylation process. Due to its crucial role in carcinogenesis, CDK2 is a druggable hotspot target to suppress cancer cell proliferation. In this context, several studies have identified spirooxindoles as an effective class of CDK2 inhibitors. In the present study, three spirooxindoles (SOI1, SOI2, and SOI3) were studied to understand their inhibitory mechanism against CDK2 through a structure-based approach. Molecular docking and molecular dynamics (MD) simulations were performed to explore their interactions with CDK2 at the molecular level. The calculated binding free energy for the spirooxindole-based CDK2 inhibitors aligned well with experimental results regarding CDK2 inhibition. Energy decomposition (ED) analysis identified key binding residues, including I10, G11, T14, R36, F82, K89, L134, P155, T158, Y159, and T160, in the CDK2 active site and T-loop phosphorylation. Molecular mechanics (MM) energy was identified as the primary contributor to stabilizing inhibitor binding in the CDK2 protein structure. Furthermore, the analysis of binding affinity revealed that the inhibitor SOI1 binds more strongly to CDK2 compared to the other inhibitors under investigation. It demonstrated a robust interaction with the crucial residue T160 in the T-loop phosphorylation site, responsible for kinase activation. These insights into the inhibitory mechanism are anticipated to contribute to the development of potential CDK2 inhibitors using the spirooxindole scaffold.
摘要：
细胞周期蛋白依赖性激酶2（CDK2）在合成和有丝分裂阶段调节细胞周期检查点，并在癌细胞增殖中起关键作用。CDK2的激活，受各种蛋白质信号通路的影响，启动磷酸化过程。由于其在致癌过程中的关键作用，CDK2是抑制癌细胞增殖的药物热点靶标。在这种情况下，一些研究已经确定螺羟吲哚是一类有效的CDK2抑制剂。在本研究中,研究了三种螺羟吲哚（SOI1，SOI2和SOI3），以通过基于结构的方法了解它们对CDK2的抑制机制。进行分子对接和分子动力学(MD)模拟以探索它们在分子水平上与CDK2的相互作用。计算的基于螺羟吲哚的CDK2抑制剂的结合自由能与关于CDK2抑制的实验结果良好地一致。能量分解(ED)分析确定了关键结合残基，包括I10，G11，T14，R36，F82，K89，L134，P155，T158，Y159和T160，在CDK2活性位点和T环磷酸化。分子力学（MM）能量被认为是稳定CDK2蛋白结构中抑制剂结合的主要贡献者。此外，结合亲和力分析显示,与研究中的其他抑制剂相比,抑制剂SOI1与CDK2结合更强.它证明了与T环磷酸化位点中关键残基T160的强大相互作用，负责激酶激活。预期对抑制机制的这些见解有助于使用螺羟吲哚支架开发潜在的CDK2抑制剂。
