A Computational Workflow for Membrane Protein–Ligand Interaction Studies: Focus on α5-Containing GABA (A) Receptors

In neuropharmacology and drug development, in silico methods have become increasingly vital, particularly for studying receptor-ligand interactions at the molecular level. Membrane proteins such as GABA (A) receptors play a central role in neuronal signaling and are key targets for therapeutic intervention. While experimental techniques like electrophysiology and radioligand binding provide valuable functional data, they often fall short in resolving the structural complexity of membrane proteins and can be time-consuming, costly, and inaccessible in many research settings. This study presents a comprehensive computational workflow for investigating membrane protein-ligand interactions, demonstrated using the GABA (A) receptor α5β2γ2 subtype and mitragynine, an alkaloid from <i>Mitragyna speciosa</i> (Kratom), as a case study. The protocol includes homology modeling of the receptor based on a high-resolution template, followed by structure optimization and validation. Ligand docking is then used to predict binding sites and affinities at known modulatory interfaces. Finally, molecular dynamics (MD) simulations assess the stability and conformational dynamics of receptor-ligand complexes over time. Overall, this workflow offers a robust, reproducible approach for structural analysis of membrane protein-ligand interactions, supporting early-stage drug discovery and mechanistic studies across diverse membrane protein targets. Key features • Applicable to diverse membrane proteins, including ion channels and G protein-coupled receptors (GPCRs), facilitating ligand interactions and dynamic behavior in biologically relevant environments. • Supports the investigation of both natural and synthetic compounds targeting specific receptor subtypes within complex membrane systems. • Combines homology modeling, molecular docking, and molecular dynamics simulations to deliver comprehensive structural and functional insights. • Showcased with the GABA (A) α5β2γ2 receptor subtype and alkaloid from <i>Mitragyna speciosa</i>, with adaptability to a broad range of receptor-ligand systems.