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探索 VEGFR-2 酪氨酸激酶抑制作用的结构要求:II 型,“DFG-out”抑制剂的结合位点分析。

Exploration of structural requirements for the inhibition of VEGFR-2 tyrosine kinase: Binding site analysis of type II, 'DFG-out' inhibitors.

机构信息

Department of Pharmaceutical Chemistry, Poona College of Pharmacy, Bharati Vidyapeeth (Deemed to be University), Pune, Maharashtra, India.

出版信息

J Biomol Struct Dyn. 2022 Aug;40(12):5712-5727. doi: 10.1080/07391102.2021.1872417. Epub 2021 Jan 18.

Abstract

The conserved three-dimensional structure of receptor tyrosine kinases (RTKs) has been varyingly observed in prokaryotes to humans that actively participate in the phosphorylation process of tyrosine residues in the protein, which results in the alteration of protein's function. Mutation and transcriptional or post-translational modifications lead to a deregulation of kinases, which ultimately fallout into the development of pathological conditions like cancer. The human genome encodes two kinds of tyrosine kinases: non-receptor tyrosine kinases (NRTKs) and receptor tyrosine kinases (RTKs). Among these kinases, VEGF/VEGFR-2 signaling cascade is an important target to develop novel small-molecule inhibitors for the therapy of abnormal angiogenesis incorporated with cancer. Due to advances in the knowledge of the catalytic domain and 'DFG-motif' region, selective 'DFG-in' (type I) and 'DFG-out' (type II) VEGFR-2/KDR inhibitors were successfully developed, and some are in different phases of a clinical trial. 'DFG-out' (inactive) confirmation has significant advantages over 'DFG-in' (active) confirmation concerning the affinity of the ATP at the catalytic domain. Further, in the catalytic domain, between front and back cleft, smaller gatekeeper residue (Val916) present; therefore, selectivity against VEGFR-2 could be precisely achieved. In this review, small molecule type II/'DFG-out' inhibitors, their conformation, interaction at receptor binding pocket, and structural requirements to inhibit VEGFR-2 at the molecular level are discussed.HighlightsVEGFR-2 is a type of membrane-bound receptor tyrosine kinases (RTKs) that regulates the process of vasculogenesis and angiogenesis.Small molecule first-generation type I, 'DFG-in' and second-generation type II, 'DFG-out' VEGFR-2 inhibitors exhibit clinical benefits in the treatment of aberrant angiogenesis associated with cancer.Molecular docking of FDA approved and novel type II inhibitors were performed using X-ray crystal structures of VEGFR-2; binding site analysis was carried out.Structural requirements for the inhibition of VEGFR-2 were identified.

摘要

受体酪氨酸激酶 (RTKs) 的保守三维结构在原核生物到人类中都有不同程度的观察,它们积极参与蛋白质中酪氨酸残基的磷酸化过程,导致蛋白质功能的改变。突变和转录或翻译后修饰导致激酶失活,最终导致癌症等病理状况的发展。人类基因组编码两种酪氨酸激酶:非受体酪氨酸激酶 (NRTKs) 和受体酪氨酸激酶 (RTKs)。在这些激酶中,VEGF/VEGFR-2 信号级联是开发用于治疗与癌症相关的异常血管生成的新型小分子抑制剂的重要靶点。由于对催化结构域和“DFG-motif”区域的认识不断提高,成功开发了选择性的“DFG-in”(I 型)和“DFG-out”(II 型)VEGFR-2/KDR 抑制剂,其中一些处于临床试验的不同阶段。与催化结构域中的“DFG-in”(活性)构象相比,“DFG-out”(非活性)构象在 ATP 与催化结构域的亲和力方面具有显著优势。此外,在催化结构域中,在前后裂隙之间存在较小的“门卫”残基(Val916);因此,可以精确实现对 VEGFR-2 的选择性。在这篇综述中,讨论了小分子 II 型/“DFG-out”抑制剂、它们的构象、在受体结合口袋中的相互作用以及在分子水平上抑制 VEGFR-2 的结构要求。

亮点

VEGFR-2 是一种膜结合受体酪氨酸激酶 (RTKs),它调节血管生成和血管生成的过程。

小分子第一代 I 型“DFG-in”和第二代 II 型“DFG-out”VEGFR-2 抑制剂在治疗与癌症相关的异常血管生成方面显示出临床益处。

使用 VEGFR-2 的 X 射线晶体结构对已批准的 FDA 和新型 II 型抑制剂进行分子对接;进行了结合位点分析。

确定了抑制 VEGFR-2 的结构要求。

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