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

Abstract

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 N-methyl-4-oxo-N-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

Graphical Abstract

Keywords:

• VEGFR-2 inhibitors
• protein–ligand interaction
• fragment-based drug design
• structure-based virtual screening

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This work was financially supported by National Natural Science Foundation of China (no. 81803370), Natural Science Foundation of Jiangsu Province (no. BK20180559), State Key Laboratory Innovation Research and Cultivation Fund (no. SKLNMZZCX201812) and ‘Double World-classes’ Construction Program of China Pharmaceutical University (no. CPU2018GF02).