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Background <p>Acridine derivatives exhibit diverse biological activities, yet their potential to modulate angiogenesis remains underexplored. This study evaluated 9-phenyl acridine (ACPH) as a small-molecule ligand capable of engaging vascular endothelial growth factor (VEGF) and altering conformational features relevant to receptor recognition, with the working hypothesis that ACPH may modulate VEGF structural dynamics in regions involved in VEGF-VEGFR interaction rather than directly inhibiting receptor binding.</p> Methods <p>Structure-based binding was assessed using AutoDock, PatchDock, and GOLD, with VEGF as the molecular target. Complex stability and conformational effects were examined by 50-ns molecular dynamics simulations, including RMSD, residue-level flexibility, compactness, solvent exposure, and interaction energetics. Functional activity was evaluated using the chick embryo chorioallantoic membrane (CAM) assay at 0.04 nM, 0.4 nM, and 0.8 nM, with ImageJ-based quantification of vascular features over 24–48&#xa0;h.</p> Results <p>Docking consistently positioned ACPH within a VEGF pocket, with predicted contacts involving Phe36, Ile46, Phe47, and Lys48 (chain A) and Cys60, Cys61, Asn62, Asp63, Glu64, and Glu67 (chain B). Across simulations, ACPH association was associated with reduced conformational variability of VEGF, particularly in regions relevant to protein-protein interaction, supported by an estimated ligand-protein interaction energy of approximately − 26.77&#xa0;kcal/mol derived from trajectory-based and interpreted qualitatively rather than as a rigorous thermodynamic binding free energy. In ovo, ACPH exposure was associated with a dose-dependent reduction in CAM vascularization, with observable effects at 0.4 nM and more pronounced effects at 0.8 nM; however, this represents a phenotypic observation and does not establish VEGF-specific inhibition or a defined anti-angiogenic mechanism. Prolonged exposure at 0.8 nM was also associated with reduced embryo viability, indicating that non-specific toxicity may contribute at the highest dose.</p> Conclusions <p>Docking and MD simulations consistently positioned ACPH within a transient VEGF cavity and were associated with reduced conformational drift and residue-level fluctuations. In the CAM model, ACPH exposure was associated with dose-dependent vascular reduction, with reduced embryo viability at 0.8 nM suggesting possible non-specific toxicity; these findings warrant receptor-facing validation and cytotoxicity-controlled endothelial assays.</p>

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Acridine-derived small molecule associates with VEGF and is linked to reduced CAM vascularization: a combined in silico and CAM study

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年6月3日

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  • Sayantani Karmakar,
  • Shuvojit Moulik,
  • Semanti Ghosh,
  • Gunjan Uttam,
  • Ashwag Alsharidah,
  • Ranjay Kumar Choudhary,
  • Moattar Raza Rizvi

摘要

Background

Acridine derivatives exhibit diverse biological activities, yet their potential to modulate angiogenesis remains underexplored. This study evaluated 9-phenyl acridine (ACPH) as a small-molecule ligand capable of engaging vascular endothelial growth factor (VEGF) and altering conformational features relevant to receptor recognition, with the working hypothesis that ACPH may modulate VEGF structural dynamics in regions involved in VEGF-VEGFR interaction rather than directly inhibiting receptor binding.

Methods

Structure-based binding was assessed using AutoDock, PatchDock, and GOLD, with VEGF as the molecular target. Complex stability and conformational effects were examined by 50-ns molecular dynamics simulations, including RMSD, residue-level flexibility, compactness, solvent exposure, and interaction energetics. Functional activity was evaluated using the chick embryo chorioallantoic membrane (CAM) assay at 0.04 nM, 0.4 nM, and 0.8 nM, with ImageJ-based quantification of vascular features over 24–48 h.

Results

Docking consistently positioned ACPH within a VEGF pocket, with predicted contacts involving Phe36, Ile46, Phe47, and Lys48 (chain A) and Cys60, Cys61, Asn62, Asp63, Glu64, and Glu67 (chain B). Across simulations, ACPH association was associated with reduced conformational variability of VEGF, particularly in regions relevant to protein-protein interaction, supported by an estimated ligand-protein interaction energy of approximately − 26.77 kcal/mol derived from trajectory-based and interpreted qualitatively rather than as a rigorous thermodynamic binding free energy. In ovo, ACPH exposure was associated with a dose-dependent reduction in CAM vascularization, with observable effects at 0.4 nM and more pronounced effects at 0.8 nM; however, this represents a phenotypic observation and does not establish VEGF-specific inhibition or a defined anti-angiogenic mechanism. Prolonged exposure at 0.8 nM was also associated with reduced embryo viability, indicating that non-specific toxicity may contribute at the highest dose.

Conclusions

Docking and MD simulations consistently positioned ACPH within a transient VEGF cavity and were associated with reduced conformational drift and residue-level fluctuations. In the CAM model, ACPH exposure was associated with dose-dependent vascular reduction, with reduced embryo viability at 0.8 nM suggesting possible non-specific toxicity; these findings warrant receptor-facing validation and cytotoxicity-controlled endothelial assays.