Homology modelling of the GABA transporter and analysis of tiagabine binding.
A homology model of the human GABA transporter (GAT-1) based on the recently reported crystal structures of the bacterial leucine transporter from Aquifex aeolicus (LeuT) was developed. The stability of the resulting model embedded in a membrane environment was analyzed by extensive molecular dynamics (MD) simulations. Based on docking studies and subsequent MD simulations of three compounds, the endogenous ligand GABA and two potent inhibitors, (R)-nipecotic acid and the anti-epilepsy drug tiagabine, various binding modes were identified and are discussed. Whereas GABA and (R)-nipecotic acid, which are both substrates, are stabilised with residues located deep inside the occluded state binding pocket (including residues Tyr 60 and Ser 396), tiagabine, which contains a large aliphatic side chain, is stabilised in a binding mode that extends from the substrate binding pocket (i.e., stabilised by Phe 294) to the extracellular vestibule, where the side chain is stabilised by aliphatic residues. The tiagabine binding mode, reaching from the substrate binding site to the extracellular vestibule, forces the side chain of Phe 294 to adopt a distinct conformation from that found in the occluded conformation of the transporter. Hence, in presence of tiagabine, GAT-1 is constrained in an open-to-out conformation. Our results may be of particular interest for the design of new GAT-1 inhibitors.
Skovstrup
Søren
S
Department of Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark.
Taboureau
Olivier
O
Bräuner-Osborne
Hans
H
Jørgensen
Flemming Steen
FS
D000595:Amino Acid Sequence; D000927:Anticonvulsants / Q000737:chemistry*; D001665:Binding Sites; D015195:Drug Design; D050485:GABA Plasma Membrane Transport Proteins / Q000737:chemistry*; D006801:Humans; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D009557:Nipecotic Acids / Q000737:chemistry*; D016415:Sequence Alignment; D040681:Structural Homology, Protein; D000078308:Tiagabine
D000927:Anticonvulsants; D050485:GABA Plasma Membrane Transport Proteins; D009557:Nipecotic Acids; C493413:SLC6A1 protein, human; C030278:nipecotic acid; D000078308:Tiagabine