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Dear Editor, Tumor angiogenesis is regulated by the binding of VEGF to receptors (VEGFRs). The major mediator of tumor angiogenesis is VEGFA, more commonly referred to as VEGF. VEGFR1 binds VEGF with higher affinity (10 times) than VEGFR2. However, the role of the VEGFR1 in VEGF-mediated angiogenesis remains a mystery. In order to disrupt the VEGFB–VEGFA/VEGFR1D2 interaction as a tool to study the angiogenesis process, the first step was the generation of a second extracellular domain of the VEGFR1. Hence, His-tagged VEGFR1D2 was expressed and purified (Supplementary Fig. S1). The addressed protein could be used in biophysical, biological, and in vivo studies with an appropriate VEGF receptor binding peptide. Such a peptide could be designed and synthesized (Supplementary Figs. S1–S6) and (Supplementary Tables S1 and S2). The aim of this study was to develop a simplified system to enable the rational design of inhibitor of VEGFB–VEGFA/ VEGFR1D2 system (PDB ID:2XAC and 1FLT). Among large surface areas comprising five main interacting regions, a small peptide antagonist could be designed and only act at a single site covering a small surface area with high-affinity interaction. Here, we described designing such a peptide referred to as VGB3 using “protein contact atlas”, “LigPlot” and “PocketQuery”. VGB3 binds and neutralizes VEGFR1D2. A major binding site for VEGFR1D2 binding involves residues 60–67 (the loop region connecting β3 to β4), 62-PDDGL-66, and strand β7 (103–106) 102-ECRP-105 of VEGFB. In addition, to increase peptide half-life in circulation, a Cys residue was added to the C terminus to make the disulfide bond. The loop region has more numbers of acidic residues, which are highlighted by LigPlot and PocketQuery, and could be recognized as polar interactions with VEGFR1D2. In good agreement, Iyer et al. reported the similarity of interactions in all three receptor bound complexes of VEGFB–VEGFR1D2, VEGFA–VEGFR1D2, and PlGF–VEGFR1D2 by this acidic stretch of residues. It would be assumed that these polar interactions would play an important role in VEGFB:VEGFR1D2 complex. Next, the peptide was designed and synthesized by using a solid-phase peptide synthesis procedure. Accordingly, the mimetic decapeptide VGB3 introduced by this sequence; 2NH-Glu1-Cys2-Arg3Pro4-Pro5-Asp6-Asp7-Gly8-Leu9-Cys10-COOH. To gain structural information about the molecular interface of the bound VGB3 peptide, a structural model of VGB3/VEGFR1D2 complex has been generated using the ZDOCK web server. The binding energetic of VGB3/VEGFR1D2 was calculated and the free binding of energy value is −30.819 kcal/mol. The energetic analysis also supported this finding, that is, VGB3 can bind tightly to VEGFR1D2 as compared with free energy of binding for same antagonist target complexes. Analysis of the VGB3:VEGFR1D2 interface Ligplot+ and Pocketquery shows direct interactions between VGB3 and residues within the loop region connecting β3 to β4 and strand β7 of VEGFR1D2 (Fig. 1b). In the VGB3:VEGFR1D2 complex, the residues from this loop region make a total of 14 van der waals interactions with Pro143, Leu204, Phe172, Lys170, Pro173, Leu174, Lys171, Thr206, Glu208, Leu215, and Lys217 of VEGFR-1D2. The most van der Waals contacts were from hydrophobic residues such as Phe172 and Leu204 of VEGFR1D2 to Cys2, Arg3, Cys10, and Leu9 of VGB3. In order to highlight the crucial role of polar interaction in the loop region, Iyer et al. performed the mutation and the results indicated 67% of total interactions of VEGFB (a total of 12 interactions). Detailed comparison of full crystal structure VEGFB:VEGFR1D2 complex (PDB: 2XAC) and present derivative VGB3:VEGFR1D2 complex gives an insight as to why this might be the case. All active residues in interaction VGB3 to VEGFR1D2 are listed in Table S3, which includes mostly a network of van der Waals and polar contacts (Fig. 1a and Supplementary Table S3). Potential polar contacts can also be identified involving amide groups of the VEGFR1D2 surface and carboxyl group of side chains of the peptide. Subsequently, to verify the ability of VGB3 to form a complex with VEGFR1D2, microscale thermophoresis (MST) measurements were performed using a VEGFR1D2-labeled with VGB3 at increasing concentrations. As well as measuring the Kd between VGB3 and its receptor this functional test will also confirm whether the refolded protein VEGFR1D2 assumes the correct conformation. Fluorescently labeled VEGFR1D2 purified and titrated as 1:1 with VGB3. The curve for VGB3 vs VEGFR1D2 exhibited a dissociation constant (Kd) of 1.96 ± 0.69 μM (Fig. 1b). It should be noted that this binding constant is 40-fold lower than the Kd (Kd= ~50 nM) of VEGFA to the entire extracellular portion of VEGFR1. Previously, a tight association between VEGFR1 D2 and VEGF has also been reported (113pM). This difference between VGB3 and VEGF in affinity indicates that multiple regions of VEGF are required in the binding of VEGFR. However, the single digit micro molar affinity measured in MST indicates that the dominant portion of the binding interaction is mimicked by the VGB3 peptide.

signal transduction and targeted therapy

Molecular docking, synthesis and biological evaluation of Vascular Endothelial Growth Factor (VEGF) B based peptide as antiangiogenic agent targeting the second domain of the Vascular Endothelial Growth Factor Receptor 1 (VEGFR1D2) for anticancer application