Discovery of Novel Multiangiogenic Agents Targeting VEGFR2, EphB4, FGFR-1, and TIE-2: Receptor-Based Pharmacophore Modeling, Virtual Screening, and Molecular Modeling Studies

Abstract

The angiogenesis phenomenon is crucial for the formation of new blood vessels in cancer cells. The cancerous cells' progress hampers other healthy cells. The main objective of this study is to explore and decipher multimodal natural compounds against VEGFR2, EphB4, FGFR-1, and TIE-2 drug targets to arrest angiogenesis and progression. The receptor-based pharmacophore modeling of VEGFR2, EphB4, FGFR-1, and TIE-2 was developed and validated through enrichment parameters. Further, the validated hypothesis allowed for screening druglike natural product databases such as SuperNatural 3.0, COCONUT, and LOTUS. The common pharmacophoric featured natural compounds were assessed for binding affinities using absolute end-point methods. Finally, density functional theory has been studied to understand the chemical reactivity and stability of the protein complexes. Among all of the screened natural compounds, 17 natural compounds were found to align accurately against validated pharmacophore models having higher fitness scores and align scores. Taking reference drugs sorafenib (VEGFR2), NVP-BHG712 (EphB4), pemiganitib (FGFR-1), and DP1919 (TIE-2), three promising natural compounds CNP0003920, CNP0243075, and CNP0211397 were concluded based on their end-point binding energies, binding interactions, molecular dynamics, and optimal pharmacokinetic and toxicity profiles. The density functional theory (DFT) results suggested that the identified compounds bound with protein complexes are stable. Our findings can represent a promising starting point for developing multimodal analogues VEGFR2, EphB4, FGFR-1, and TIE-2 proteins.

Figure 1

Rationale design strategy and potential mechanisms of multitarget anti-angiogenic agents targeting VEGFR2, EphB4, FGFR-1, and TIE-2.

Figure 2

Flowchart of virtual database preparations.

Figure 3

Workflow of phase screening for exploring common natural compounds.

Figure 4

Multiple sequence alignment of four receptor tyrosine kinases showing identical patterns highlighted in blue color.

Figure 5

Multiple sequence alignment of four receptor tyrosine kinases representing the glycine-rich loop, hinge region, catalytic lysine, conserved glutamate, gatekeeper, and DFG motif.

Figure 6

Superposition of the protein backbone VEGFR2, EphB4, FGFR-1, EphB4, and TIE-2, which are represented in salmon red, cyan, violet, and lime green colors, respectively.

Figure 7

Pairwise structural alignment of VEGFR2, FGFR-1, EphB4, and TIE-2. The protein structural alignments between (A) VEGFR2 and FGFR-1, (B) VEGFR2 and TIE-2, (C) VEGFR2 and EphB4, (D) EphB4 and FGFR-1, (E) FGFR-1 and TIE-2, and (F) EphB4 and TIE-2 are represented based on their RMSD.

Figure 8

Receptor-based pharmacophore hypothesis showing the features of (A) VEGFR2, (B) EphB4, (C) FGFR-1, and (D) TIE-2 complexes.

Figure 9

Developed residue-based pharmacophore (receptor–ligand cavity) hypothesis models of (A) VEGFR2, (B) EphB4, (C) FGFR-1, and (D) TIE-2 complexes.

Figure 10

Developed e-pharmacophore hypothesis alignment between all.

Figure 11

Redocked cocrystal conformers (in orange) superimposed on the cocrystallized ligands of (A) VEGFR2, (B) EphB4, (C) FGFR-1, and (D) TIE-2 PDB complexes.

Figure 12

Best-selected compounds for molecular dynamics and ADMET assessment.

Figure 13

Molecular interactions between CNP0003920 (in orange) with (A) VEGFR2, (B) EphB4, (C) FGFR-1, and (D) TIE-2 proteins.

Figure 14

Molecular interactions between CNP0243075 (black) with (A) VEGFR2, (B) EphB4, (C) FGFR-1, and (D) TIE-2 proteins.

Figure 15

Molecular interactions between CNP0211397 (in blue) and (A) VEGFR2, (B) EphB4, (C) FGFR-1, and (D) TIE-2 proteins.

Figure 16

Binding affinities of best-selected natural compounds and the standard control against (A) VEGFR2, (B) EphB4, (C) FGFR-1, and (D) TIE-2 proteins.

Figure 17

RMSD trajectories of CNP0003920, CNP0243075, and CNP0211397 complexed with (A) VEGFR2, (B) EphB4, (C) FGFR-1, and (D) TIE-2 proteins.

Figure 18

Frontier molecular orbitals of potent hits representing the electronic energies of the HOMO and LUMO. The energy gaps between the HOMO and the LUMO are represented on the arrow.