Protein–ligand interaction-guided discovery of novel VEGFR-2 inhibitors

As an effective target in abnormal angiogenesis-related tumor treatment, VEGFR-2 has small-molecule inhibitors of various scaffolds being approved for treating diseases such as renal carcinoma, non-small cell lung cancer, etc. However, endogenous and acquired drug resistance are still considered to be the main contributors for the failure of VEGFR-2 clinical candidates. Therefore, development of novel VEGFR-2 inhibitors is still urgently needed in the market but also challenging. In this work, residues including Asp1046, Ile1025, HIS1026, Cys919 and Lys868 were identified as the most important residues for Hbonded interaction, while His1026, Asp1046, Glu885, Ile1025 and Leu840 exhibited critical role for the nonbonded interactions through a comprehensive analysis of protein–ligand interactions, which plays critical roles in the binding of compounds and targets. Guided by the analysis of binding interactions, a total of 10 novel VEGFR-2 inhibitors based on <i>N</i>-methyl-4-oxo-<i>N</i>-propyl-1,4-dihydroquinoline-2-carboxamide scaffold were discovered through fragment-based drug design and structure-based virtual screening, which expands the chemical space of current VEGFR-2 inhibitors. Biological activity evaluation showed that even though the enzymatic activity of these compounds against VEGFR-2 were inferior to that of the positive controls sorafenib and motesanib, compound I-10 showed moderate HepG2 cell inhibitory activity with an IC₅₀ value of 33.65 μM and eight compounds exhibited moderate or higher HUVEC inhibitory activity in the range of 19.54–57.98 μM compared to the controls. Particularly, the HUVEC inhibitory activity of compound I-6 (IC₅₀ = 19.54 μM) outperformed motesanib and can be used as starting points for further optimization and development for cancer treatment. Communicated by Ramaswamy H. Sarma

作为异常血管生成相关肿瘤治疗的有效靶点，血管内皮生长因子受体2（VEGFR-2）已有多款搭载不同母核结构的小分子抑制剂获批，用于肾癌、非小细胞肺癌等疾病的临床治疗。然而，内源性与获得性耐药仍被认为是VEGFR-2临床候选药物研发失败的核心诱因，因此市场对新型VEGFR-2抑制剂存在迫切需求，但相关研发仍极具挑战性。本研究通过对蛋白质-配体相互作用的全面解析，鉴定出天冬氨酸1046（Asp1046）、异亮氨酸1025（Ile1025）、组氨酸1026（His1026）、半胱氨酸919（Cys919）与赖氨酸868（Lys868）为介导氢键相互作用的关键残基；同时发现组氨酸1026（His1026）、天冬氨酸1046（Asp1046）、谷氨酸885（Glu885）、异亮氨酸1025（Ile1025）及亮氨酸840（Leu840）在非键相互作用中发挥核心作用，上述相互作用对化合物与靶点的结合具有决定性影响。基于上述结合相互作用的分析结果，本研究通过基于片段的药物设计与基于结构的虚拟筛选，共获得10款基于N-甲基-4-氧代-N-丙基-1,4-二氢喹啉-2-甲酰胺母核的新型VEGFR-2抑制剂，拓展了现有VEGFR-2抑制剂的化学空间。生物活性评价结果显示，尽管这些化合物对VEGFR-2的酶学活性不及阳性对照药索拉非尼（sorafenib）与莫特塞尼（motesanib），但化合物I-10对HepG2细胞表现出中等强度的抑制活性，其半抑制浓度（IC₅₀）为33.65 μM；另有8款化合物对人脐静脉内皮细胞（HUVEC）的抑制活性处于19.54~57.98 μM区间，其活性达到或优于对照药物。其中，化合物I-6的HUVEC抑制活性（IC₅₀=19.54 μM）优于莫特塞尼，可作为癌症治疗领域后续优化与开发的先导起始化合物。本文由Ramaswamy H. Sarma供稿。