Structural insights into molecular-targeting helix–loop–helix peptide against vascular endothelial growth factor-A

• Published in: Biochemical and biophysical research communications Vol. 734; p. 150749
• Main Authors: Michigami, Masataka, Notsu, Kunpei, Kamo, Masayuki, Hirokawa, Takatsugu, Kinoshita, Takayoshi, Inaka, Koji, Nakase, Ikuhiko, Fujii, Ikuo
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 19-11-2024
• Subjects: Helix–loop–helix; VEGF; X-ray crystal structure; VEGF; X-ray crystal structure; Helix–loop–helix
• ISSN: 0006-291X; 1090-2104; 1090-2104
• DOI: 10.1016/j.bbrc.2024.150749

Mid-sized binding peptides have recently emerged as a new therapeutic modality. A helix-loop-helix (HLH) peptide was designed as a scaffold for combinatorial peptide libraries. We screened the HLH peptide libraries against human vascular endothelial growth factor-A (VEGF) to generate a peptide, VS42-LR3, which inhibited VEGF/receptor interaction and suppressed tumor growth in a murine xenograft model of human colorectal cancer. Here, we report the first crystal structure of the HLH peptide in a complex with VEGF at high resolution using space-grown protein crystals. The X-ray structural analysis revealed that the monomeric VS42-LR3 adopted an HLH structure and bound to VEGF at the VEGF receptor-binding site. Interestingly, from the site-directed mutagenesis, thermodynamic analysis, and molecular dynamic simulations, it turned out that the loop region in the non-interacting surface to VEGF affected the structural rigidity of the whole HLH to increase the binding affinity. These findings provide valuable insights for the design of more structurally stable and higher affinity mid-sized binding peptides as well as HLH peptides, that could play a crucial role in advancing molecular-targeting therapies.
•The first crystal structure of an HLH peptide binding to VEGF at 1.5 Å resolution.•VS42-LR3 folded into the HLH structure and bound to VEGF as a monomer.•The non-interacting surface to VEGF affected to increase the binding affinity.