In silico analysis of the multitarget potential of GlyT1 inhibitors in SLC6 transporters

Abstract

The solute carrier family 6 (SLC6) transporters are essential for regulating neurotransmitter homeostasis through the reuptake of amino acids and monoamines. Among them, the glycine transporter type 1 (GlyT1, SLC6A9) plays a central role in modulating NMDA receptor function and glutamatergic signaling. Despite their therapeutic relevance, the selectivity profiles of GlyT1 inhibitors remain poorly defined, raising concerns about off-target effects. In this study, we employed an integrative in silico approach combining homology modeling, molecular docking, consensus scoring, and molecular dynamics simulations to characterize the multitarget potential of GlyT1 inhibitors toward related SLC6 transporters—GlyT2, PROT, SERT, NET, and DAT. High-quality three-dimensional models were generated and validated through structural refinement and quality metrics. Consensus docking with DockThor, GOLD, and AutoDock Vina followed by Exponential Consensus Ranking (ECR) identified NFPS_2 as the most potent GlyT1 ligand (ECR = 1.896), forming π–π interactions with TYR99 and TRP279, while Org 24598_2 preferentially bound GlyT2, and Bitopertin showed high affinity for DAT. Molecular dynamics simulations (300 ns) confirmed the structural stability of all complexes (RMSD < 0.25 nm), with low residue fluctuations within the binding pockets and stable solvent exposure profiles. MMPBSA energy analyses revealed favorable binding free energies for GlyT1, NET, and DAT (ΔG ≈ −25 to −30 kcal/mol). These results demonstrate the intrinsic multitarget behavior of GlyT1 inhibitors, highlighting conserved interaction motifs within the SLC6 family. Collectively, our findings emphasize the importance of structure-guided optimization to improve selectivity and reduce potential off-target effects while maintaining therapeutic efficacy.