Analysis of Binding Determinants for Different Classes of Competitive and Noncompetitive Inhibitors of Glycine Transporters

Abstract

Glycine transporters are interesting therapeutic targets as they play significant roles in glycinergic and glutamatergic systems. The search for new selective inhibitors of particular types of glycine transporters (GlyT-1 and GlyT-2) with beneficial kinetics is hampered by limited knowledge about the spatial structure of these proteins. In this study, a pool of homology models of GlyT-1 and GlyT-2 in different conformational states was constructed using the crystal structures of related transporters from the SLC6 family and the recently revealed structure of GlyT-1 in the inward-open state, in order to investigate their binding sites. The binding mode of the known GlyT-1 and GlyT-2 inhibitors was determined using molecular docking studies, molecular dynamics simulations, and MM-GBSA free energy calculations. The results of this study indicate that two amino acids, Gly373 and Leu476 in GlyT-1 and the corresponding Ser479 and Thr582 in GlyT-2, are mainly responsible for the selective binding of ligands within the S1 site. Apart from these, one pocket of the S2 site, which lies between TM3 and TM10, may also be important. Moreover, selective binding of noncompetitive GlyT-1 inhibitors in the intracellular release pathway is affected by hydrophobic interactions with Ile399, Met382, and Leu158. These results can be useful in the rational design of new glycine transporter inhibitors with desired selectivity and properties in the future.

Glycine Transporter 1 Inhibitors: Predictions on Their Possible Mechanisms in the Development of Opioid Analgesic Tolerance

“…Several GlyT inhibitors have been described in the last two decades. Although they selectively inhibit either astrocytic GlyT1 or neuronal GlyT2, animal models of human disorders have also pointed to the need for non-selective GlyT inhibitors [85]. Modeling neuropathic pain in rats has indicated the involvement of both types of GlyTs in the pathological alterations of spinal cord neuronal circuitries [85][86][87][88].…”

Analysis of Different Binding Modes for Tiagabine within the GAT-1 Transporter

“…During the transport cycle, three main conformational states of transporters can be distinguished: an outward-open state, allowing for access to the S1 site for the substrate and ions from the extracellular side; an occluded state, where access to the S1 site is blocked from both sides of the membrane; and an inward-open state, allowing for the release of the substrate and ions into the cell [ 10 , 11 ]. Analysis of the available crystal structures of SLC6 proteins and the results of in silico studies revealed that competitive inhibitors bind with a high affinity to the S1 site, blocking the transporter in an outward-open state [ 6 , 7 , 12 , 13 , 14 , 15 , 16 ]. Within the vestibule of the transporter, an allosteric binding site (S2) was identified, in which, as observed for S-citalopram in SERT, additional ligand molecules can bind, thus modulating the affinity of ligands (including itself) that bind in the S1 site [ 8 , 17 , 18 ].…”