In Silico Evaluation of the Effects of Temperature on the Affinity of the SV2C Ligand UCB-1A to SV2 Paralogs

MD simulations reproduced these observations, namely that ligand RMSD values at 37 °C showed that UCB-1A binding fluctuated markedly in the SV2A complex, with many trajectories exceeding the 3.0 Å stability cutoff, whereas UCB-1A remained relatively well-anchored in SV2C under the same conditions. Structural analysis showed that, while UCB-1A adopts a conserved binding pose across all paralogs stabilized by π–π stacking and a hydrogen bond with Asp, SV2C possesses a unique stabilizing feature.

In SV2C, Tyr298 is less exposed to the solvent and engages in a persistent hydrogen bond with Asparagine, a structural feature that reinforces pocket stability and limits temperature-induced destabilization. This interaction is absent in SV2A, consistent with its greater temperature sensitivity. Together, these findings provide a mechanistic explanation for the experimentally observed temperature independence of UCB-1A binding to SV2C.

More broadly, the results highlight the importance of incorporating physiologically relevant temperatures into SV2 ligand evaluation and demonstrate how combining experiments with simulations can uncover isoform-specific mechanisms of ligand recognition and stability.