Molecular Modeling and Bioinformatics Analysis of Drug-Receptor Interactions in the System Formed by Glargine, Its Metabolite M1, the Insulin Receptor, and the IGF1 Receptor

Abstract

Introduction: Insulin and insulin-like growth factor type 1 (IGF1) regulate multiple physiological functions by acting on the insulin receptor (IR) and insulin-like growth factor type 1 receptor (IGF1R). The insulin analog glargine differs from insulin in three residues (Gly^A21, Arg^B31, Arg^B32), and it is converted to metabolite M1 (lacks residues Arg^B31 and Arg^B32) by in vivo processing. It is known that activation of these receptors modulates pathways related to metabolism, cell division, and growth. Though, the structures and structural basis of the glargine interaction with these receptors are not known.

Aim: To generate predictive structural models, and to analyze the drug/receptor interactions in the system formed by glargine, its metabolite M1, IR, and IGF1R by using bioinformatics tools.

Methods: Ligand/receptor models were built by homology modeling using SWISSMODEL, and surface interactions were analyzed using Discovery Studio® Visualizer. Target and hetero target sequences and appropriate template structures were used for modeling.

Results: Our glargine/IR and metabolite M1/IR models showed an overall symmetric T-shaped conformation and full occupancy with four ligand molecules. The glargine/IR model revealed that the glargine residues Arg^B31 and Arg^B32 fit in a hydrophilic region formed by the α-chain C-terminal helix (αCT) and the cysteine-rich region (CR) domain of this receptor, close to the CR residues Arg270-Arg271-Gln272 and αCT residue Arg717. Regarding IGF1R, homologous ligand/receptor models were further built assuming that the receptor is in a symmetrical T-shaped conformation and is fully occupied with four ligand molecules, similar to what we described for IR. Our glargine/IGF1R model showed the interaction of the glargine residues Arg^B31 and Arg^B32 with Glu264 and Glu305 in the CR domain of IGF1R.

Conclusion: Using bioinformatics tools and predictive modeling, our study provides a better understanding of the glargine/receptor interactions.

Keywords: IGF type 1 receptor; Insulin glargine; insulin receptor; molecular models; protein conformation; receptor protein-tyrosine kinases; theoretical models.

Figure 1.

Metabolite M1/IR model. IR ectodomain bound to four insulin molecules (center). Enlarged images of ligand binding site 1 (left) and ligand binding site 2 (right) are shown. Metabolite M1 is in green (A chain in light green; B chain in dark green). The two IR alpha subunits are in different colors: gray (α) and golden (α’). The apostrophe (’) indicates a site or domain in the IR α’-subunit. In site 1, metabolite M1 is in close contact with L1, CR, and FnIII-1’ domains of IR; in site 2, metabolite M1 makes contact with the FnIII-1 domain of IR. The quality parameters for this model are: GMQE of 0.73 (high precision between 0 and 1), QMEAN score of -1.57 (good quality score closer to 0, bad quality closer to -4), and RMSD of 0.29 Å (high similarity between 0 and 2 Å). GQME indicates Global Model Quality Estimate; IR, insulin receptor; QMEAN, Qualitative Model Energy Analysis; RMSD, root mean square deviation.

Figure 2.

Contact surfaces of metabolite M1 and glargine-bound IR models. (A) Metabolite M1/IR model, with the ligand (metabolite M1) shown in green (A chain in light green; B chain in dark green). (B) Glargine/IR model, with the ligand (glargine) in red (A chain in light red; B chain in dark red). The IR alpha subunits are in gray (α) and golden (α’). Apostrophe (’) indicates a site or domain in the IR α’-subunit. (C) Glargine/IR model contact surface shown with hydrophobic regions in brown color and hydrophilic regions in blue color. IR indicates insulin receptor.

Figure 3.

Insulin/IR model. Left: IR ectodomain bound to four ligand (insulin) molecules. Right: enlargement of ligand binding site 1. Insulin is shown in purple color (A chain in light purple; B chain in dark purple). The IR alpha subunits are in gray (α) and golden (α’). Apostrophe (’) indicates a site or domain in the IR α’-subunit. The quality parameters for this model are: GMQE of 0.73 (high precision between 0 and 1), QMEAN score of -1.49 (good quality score closer to 0, bad quality closer to -4), and RMSD of 0.20 Å (high similarity between 0 and 2 Å). GQME indicates Global Model Quality Estimate; IR, insulin receptor; QMEAN, Qualitative Model Energy Analysis; RMSD, root mean square deviation.

Figure 4.

Metabolite M1/IGF1R symmetric model. Center: IGF1R bound to four ligand (metabolite M1) molecules. Lower left: expanded view of the ligand binding site 1, where glargine M1 is seen in close contact with the IGF1R domains L1, CR, and FnIII-1.’ Lower right: expanded view of the ligand binding site 2, where glargine M1 makes contact with the IGF1R domain FnIII-1. Metabolite M1 is shown in green (A chain in light green; B chain in dark green). IGF1R alpha subunits are colored blue (α) and lavender (α’). Apostrophe (’) indicates a site or domain in the IR α’-subunit. The quality parameters for this model are: GMQE of 0.77 (high precision between 0 and 1), QMEAN score of -2.91 (good quality closer to 0, bad quality closer to -4), and RMSD of 0.35 Å (high similarity between 0 and 2 Å). GQME indicates Global Model Quality Estimate; IGF1R, insulin-like growth factor type 1 receptor; QMEAN, Qualitative Model Energy Analysis; RMSD, root mean square deviation.

Figure 5.

Contact surfaces of metabolite M1 and glargine-bound IGF1R symmetric models. (A) Metabolite M1/IGF1R model, where the metabolite M1 is shown in green (A chain in light green; B chain in dark green). (B) Glargine/IGF1R model, with glargine shown in red (A chain in light red; B chain in dark red). Receptor residues and structure are colored blue (α) and lavender (α’). Apostrophe (’) indicates a site or domain in the IR α’-subunit. IGF1R indicates insulin-like growth factor type 1 receptor.