Structural and dynamic investigation of Wnt inhibitor complexes with sulfobutyl ether-β-cyclodextrin using experimental and computational approaches

• LGK974 has low solubility, limiting its pharmaceutical use. • βSBECD complexation improves LGK974 solubility. • Structural studies elucidated LGK974:βSBECD interactions. • NMR (1D and 2D) mapped LGK974 binding site in βSBECD. • Molecular modeling confirmed stable host–guest geometry via hydrophobic forces. The Wnt signaling pathway is a key regulator of cell proliferation and differentiation, and its dysregulation has been implicated in various malignancies. LGK974, a small-molecule PORCN inhibitor, has demonstrated potent antitumor activity in preclinical models but suffers from extremely low aqueous solubility, limiting its pharmaceutical development. In this study, we explored the inclusion complexation of LGK974 with sulfobutyl ether-β-cyclodextrin (βSBECD) as a strategy to enhance its solubility and structural stability. A combination of 1D and 2D NMR techniques (¹H NMR, COSY, HSQC, HMBC, NOESY), high-resolution diffusion-ordered spectroscopy (HR-DOSY), FTIR-ATR spectroscopy and Raman spectroscopy were employed to characterize the interaction between LGK974 and βSBECD. NOESY and HR-DOSY experiments confirmed spatial proximity and co-diffusion of both components, indicating successful inclusion. Raman spectroscopy, exploring a guest-specific spectral region (1500–1700 cm⁻¹), revealed shifts and intensity decreases of LGK974 bands upon complexation, highlighting concentration-dependent encapsulation effects. Molecular docking and dynamics simulations supported these findings, showing a stable host–guest geometry driven by hydrophobic interactions. Together, these results provide molecular-level evidence of LGK974 encapsulation by βSBECD and highlight cyclodextrin-based carriers as a promising platform to improve the formulation and therapeutic potential of hydrophobic Wnt inhibitors.