Molecular Mechanisms Controlling Insulin Signaling: Computational and Bioinformatic Approaches رسالة ماجستير

Abstract

Background: Diabetes and insulin resistance are two major global public health issues, with a sever effect on the public welfare and general health. Novel targets for therapeutic interventions for these diseases can only be determined with better knowledge of the molecular mechanisms of insulin signaling. Phytochemicals, bioactive plant chemicals, have been found to alter insulin signaling pathways. The likelihood of these compounds interfering with critical inhibitory proteins in the insulin signaling pathway, namely Akt substrate of 160 kDa (AS160) and phosphatase and tensin homolog (PTEN) is an overly optimistic window of intervention. Computational and bioinformatics methods can shed light in understanding such kinds of molecular interaction. Aim: This study aims to understand the molecular interactions between six selected phytochemicals and key proteins in insulin signaling pathway (AS160 and PTEN). The goal is to study the potential therapeutic targets for the selected phytochemicals in the insulin signaling pathway to overcome insulin resistance. Methodology: A computational approach of molecular docking simulation and molecular dynamics (MD) simulations used to predict the binding affinity (binding free energy) and binding interaction of the selected six phytochemicals (3,4-dihydroxybenzoic acid, 4-methoxybenzoic acid, 3,4,5-trihydroxybenzoic acid, 2-hydroxy-4-methoxybenzoic acid, 4-hydroxybenzoic acid, and benzoic acid) with two key target proteins in insulin signaling pathway (AS160 and PTEN). Three dimensional (3D) structures of the phytochemicals obtained from PubChem database. Crystal structures for PTEN and AS160 were retrieved from the Protein Data Bank with PDB IDs 1D5R and 3QYB, respectively. Docking using AutoDockFR (ADFR) software was done to identify the binding modes and binding affinities of protein-phytochemical complexes. For MD simulations GROMACS was used to assess the binding stability and flexibility of the protein-phytochemical complexes over the time course. Results: Docking experiments revealed that the chosen phytochemicals exhibited greater binding affinities towards PTEN than AS160. Among the tested ligands, 3,4-dihydroxybenzoic acid and 2-hydroxy-4-methoxybenzoic acid both exhibited the highest affinities of -7.4 kcal/mol. MD simulations revealed that ligand-PTEN complexes were stable, especially with the above two phytochemicals, as their RMSD values were low. AS160-ligand complexes did not show stable interactions and possessed greater RMSD values. Hydrogen bonding analysis suggests that stability within the compound is due to methoxy and hydroxyl groups since stability in the complex declines dramatically in the absence of hydrogen bonding. Conclusion: Molecular docking and MD simulation studies helped in understanding the binding interactions between AS160 and PTEN with the selected phytochemicals. The results revealed a strong and stable interaction between several of these ligands and PTEN. Conversely, the AS160- ligands complexes showed an unstable and weak interaction. These results indicated that further studies in PTEN as a therapeutic target and the promising phytochemicals as inhibitors to treat diabetes are promising and worthwhile. However, studies on AS160 and the current iv phytochemicals need further editing and understanding options such as ligand improvement or alternative AS160 binding sites will be helpful to enhance the interactions