Discovery of dual kinase inhibitors targeting VEGFR2 and FAK: structure-based pharmacophore modeling, virtual screening, and molecular docking studies

Abstract

VEGFR2 and FAK signaling pathways are interconnected and have synergistic effects on tumor angiogenesis, growth, and metastasis. Thus, instead of the conventional targeting of each of these proteins individually with a specific inhibitor, the present work aimed to discover novel dual inhibitors targeting both VEGFR2 and FAK exploiting their association. To this end, receptor-based pharmacophore modeling technique was opted to generate 3D pharmacophore models for VEGFR2 and FAK type II kinase inhibitors. The generated pharmacophore models were validated by assessing their ability to discriminate between active and decoy compounds in a pre-compiled test set of VEGFR2 and FAK active compounds and decoys. ZINCPharmer web tool was then used to screen the ZINC database purchasable subset using the validated pharmacophore models retrieving 42,616 hits for VEGFR2 and 28,475 hits for FAK. Subsequently, they were filtered using various filters leaving 13,023 and 6,832 survived compounds for VEGFR2 and FAK, respectively, with 124 common compounds. Based on molecular docking simulations, thirteen compounds were found to satisfy all necessary interactions with VEGFR2 and FAK kinase domains. Thus, they are predicted to have a possible dual VEGFR2/FAK inhibitory activity. Finally, SwissADME web tool showed that compound ZINC09875266 is not only promising in terms of binding pattern to our target kinases, but also in terms of pharmacokinetic properties.

Keywords: Angiogenesis; Cancer; FAK; Molecular docking; Multi-kinase inhibitors; Pharmacophore modelling; VEGFR2; Virtual screening.

Fig. 1

Examples for FDA approved multi-kinase inhibitors

Fig. 2

Examples for kinase inhibitors discovered using CADD approaches

Fig. 3

VEGFR2 (Query) and FAK (Subject) kinase domains amino acid sequence alignment using BLASTp (Aligned residues involved in type II kinase inhibition binding pattern are highlighted)

Fig. 4

Key structural features of type II kinase inhibitors

Fig. 5.

3D superimposition of VEGFR2 (PDB ID: 4ASD) and FAK (PDB ID: 4K9Y) protein structures with a close focus on the key residues at the ATP binding site (Hydrophobic region: grey; Polar regions: red)

Fig. 6

a The selected pharmacophore model for VEGFR2 inhibitors, VEGFR2_Ph4_109 (distances in Å) b VEGFR2_Ph4_109 mapped onto a VEGFR2 inhibitor

Fig. 7

a The selected pharmacophore model for FAK inhibitors, FAK_Ph4_12 (distances in Å) b FAK_Ph4_12 mapped onto an FAK inhibitor

Fig. 8

Virtual screening hit filtration for FAK and VEGFR2

Fig. 9

ZINC09875266 docked into FAK and VEGFR binding sites. a VEGFR 3D representation. b VEGFR2 2D representation. c FAK 3D representation. d FAK 2D representation

Fig. 10

SwissADME Boiled-Egg plot dividing the compounds into three regions: bad oral bioavailability (grey), good oral bioavailability (white), and BBB permeation (yellow). The highlighted points represent the compounds with desirable characters

Fig. 11

The chemical structure of the hit compound survived the pharmacokinetics filtration step