Computational screening of AI-derived cyclotides as putative VEGFR2 binders for wound-site angiogenesis

Abstract Chronic wounds represent a longstanding clinical problem due to impaired angiogenesis due to insufficient activation of vascular endothelial growth factor receptor 2 (VEGFR2). In this investigation, we used computational methods to evaluate the angiogenic potential of cycloviolacin O13, a cyclotide of plant origin, as a potential modulator of human VEGFR2. The receptor structure was obtained from Protein Data Bank and the structure was checked using ERRAT (81.176) along with Ramachandran analysis which resulted in 79.8% favored residues. Pocket inference showed the most suitable binding cavity to be Pocket 1. A curated library of twenty-five cyclotides was modelled using AlphaFold, of which cycloviolacin O13 showed the best interaction with VEGFR2 as judged by a HADDOCK score of -84.7 and a ligand root-mean-squared deviation of 0.8 nm. Molecular dynamics simulations over a period of 500 nanoseconds (ns) verified the stability of the VEGFR2-O13 complex in which root mean square deviation (RMSD) values were stabilized at 0.25–0.45 nm, compact radius of gyration and a permanent hydrogen bond network involving 200 to 260 hydrogen bonds. Dynamic cross-corr and principal component analyses supported the coordinated motions and a stable conformational response to peptide binding, and normal mode analysis suggested that low deformation and high mechanical resilience occur. The peptide alone also indicate to be quite rigid and structurally sound. Immuno-informatics evaluations found that cycloviolacin O13 was non-antigenic, non-allergenic and nontoxic, with immune simulations showing no adverse B- or T-cell response. These results identify cycloviolacin O13 as a structurally stable and immunologically low-risk lead that can form a persistent, dynamically stable complex with VEGFR2 at a predicted binding pocket. However, docking and MD simulations cannot determine whether this binding would be agonistic, antagonistic, or functionally neutral; therefore, experimental validation (e.g., VEGFR2 phosphorylation and downstream signaling assays in endothelial cells) is required to establish any effect on VEGFR2-mediated angiogenic signaling.