Can Molecular Docking Predict Guest Orientation in β-Cyclodextrin? A Cross-Docking and DFT Refinement Study

Abstract

Molecular docking is widely used to predict cyclodextrin host–guest structures, yet its ability to reproduce the directional orientation of asymmetric guests within the β-cyclodextrin (β-CD) cavity has rarely been evaluated systematically. Here, 20 crystallographically characterized 1:1 β-CD complexes containing asymmetric 1,4-disubstituted benzene guests were selected from the Cambridge Structural Database. Each guest was docked into each of 20 experimentally derived β-CD conformations, yielding 7916 retained poses. Poses reproducing the crystallographic direction of inclusion were classified as Up, whereas the opposite orientation was classified as Down. Across the complete dataset, approximately 26% of poses were Up, with guest-dependent frequencies ranging from 5% to 83%. Importantly, only one β-CD conformation generated Up poses for all 20 guests, whereas the complete receptor set sampled at least one crystal-consistent pose for every compound. However, GlideScore-based orientation recovery was 65% for Top-1, 95% for Top-2, and 100% for Top-3, demonstrating that successful sampling does not necessarily ensure correct top-ranked prediction. Selected poses were subsequently optimized using dispersion-corrected DFT. DFT-based energetic ranking did not consistently favour the crystallographic orientation and could either decrease or increase guest heavy-atom RMSD. Overall, the results demonstrate that reliable validation of β-CD docking requires explicit separation of pose generation, pose ranking, energetic refinement, and structural similarity, and support the use of structurally diverse crystal-derived receptor sets to broaden orientational sampling.