Structure-based exploration of sevoflurane binding sites in cognition-related synaptotagmin-1

Synaptotagmin 1 (Syt1) is a Ca²⁺ sensor in the membrane of pre-synaptic axon terminal, which functions as an essential regulator of neurotransmitter release and hormone secretion and plays an important role in learning, memory and thinking. The sevoflurane, a general anaesthetics used widely in surgery, has been reported to modulate intracellular calcium flux and downstream neural events by targeting Syt1 C2A domain, exhibiting potential to reshape cognition. In order to explore the binding sites of sevoflurane in Syt1 C2A domain, we herein conducted a systematic computational investigation that integrated ligand pocket mapping, molecular docking calculations and molecular dynamics simulations to perform conformational sampling in the interaction space of sevoflurane with the domain. With the protocol, we were able to identify a number of ‘hotspots’ where sevoflurane can potentially bind to the domain. Subsequently, the location, geometry and physicochemical property of these putative binding sites were examined in detail using a variety of bioinformatics tools, from which three promising candidates were selected and investigated in vitro. Consequently, one was confirmed as specific binding site that can be bound tightly by sevoflurane ligand, while another was suggested to form a relatively weak, non-specific interaction with the ligand. This work would help to understand the molecular mechanism and biological implication underlying Syt1-sevoflurane recognition, and to design molecular aptamers to intervene with cognitive behaviour.