Insights into Substrate and Inhibitor Selectivity among Human GLUT Transporters through Comparative Modeling and Molecular Docking

Abstract

The solute carrier 2 family is composed of 14 transporters, which are members of the major facilitator superfamily. Despite their high physiological importance, there are still many open questions concerning their function and specificity, and in some cases, their physiological substrate is still unknown. To understand the determinants of the substrate and inhibitor specificity, we modeled all human glucose transport carriers (GLUTs) and simulated their interaction with known ligands. Comparative modeling was performed with the @TOME-2 pipeline, employing multiple templates and providing an ensemble of models for each GLUT. We analyzed models in both outward-occluded and inward-open conformations, to compare exofacial and endofacial binding sites throughout the family and understand differences in susceptibility of GLUTs to the inhibitor cytochalasin B. Finally, we employed molecular docking and bioinformatics to identify residues likely critical for recognition of myo-inositol by GLUT13 and urate by GLUT9. These results provide insights into the molecular basis for the specificity for these substrates. In addition, we suggested a potential recognition site of glucosamine by GLUT11 to be evaluated in future experiments.

Figure 1

Disease-related mutations mapped to GLUT9 (A) and GLUT10 (B) models. Approximate locations of endofacial and exofacial binding sites are indicated with black and red dashed lines, respectively.

Figure 2

Molecular basis for cytochalasin B selectivity within the GLUT family. (A) Cytochalasin B (cytoB) chemical structure. (B) Binding mode of cytoB to GLUT1 (PDB 5EQI). (C–E) Comparative docking to GLUT5, 7, and 9, respectively, highlighting residue substitutions. Hydrogen bonds (distance cutoff = 3.5 Å) are shown as yellow dashed lines.

Figure 3

Molecular bases for the specific binding of myo-inositol to GLUT13. (A) Chemical structures of α-d-glucose and myo-inositol. (B) Glucose binding mode to GLUT3 (PDB 4ZW9). (C) myo-inositol binding mode to GLUT13; prediction based on docking with PLANTS. Highlighted residues (shown as sticks) are predicted to be important for ligand binding, either by their involvement in hydrogen bonds or through improvement of sterical complementarity. Hydrogen bonds (distance cutoff = 3.5 Å) are shown as yellow dashed lines. Visualization of myo-inositol docking to GLUT3 (D) and GLUT13 (E) with DSX online. Favorable and unfavorable potentials are shown as blue and red spheres, respectively. Favorable and unfavorable distances are shown as blue and red lines, respectively.

Figure 4

Molecular bases for urate specific binding of GLUT9. (A) Urate chemical structure. (B) urate binding mode to GLUT9, predicted by docking with PLANTS. Residues predicted to hydrogen-bond with the ligand or which differ from most GLUTs are highlighted residues shown as sticks. Hydrogen bonds (distance cutoff = 3.5 Å) are shown as yellow dashed lines. (C) Visualization of the docking result with DSX online. Favorable and unfavorable potentials are shown as blue and red spheres, respectively. Favorable and unfavorable distances are shown as blue and red lines, respectively. (D) superposition of GLUT9 (cyan) and GLUT1 (white) binding sites.

Figure 5

Predicted binding mode for putative GLUT11 substrates. (A) Chemical structures of docked ligands. Docking predicted poses for: (B) α-d-glucose, (C) d-glucosamine, and (D) N-acetyl-glucosamine thiazoline. GLUT11 is shown as a cartoon, with selected residues and ligands highlighted as sticks and colored by atom. Salt bridges and hydrogen bonds (distance cutoff = 3.5 Å) are shown as yellow dashed lines.