Computational Studies and Design of Novel Molecules as Potential Glycogen Synthase Kinase Inhibitors

Abstract

The present thesis titled “Computational Studies and Design of Novel Molecules as Potential Glycogen Synthase Kinase Inhibitors” is divided into 7 chapters as described in brief. Chapter 1 describes the disease condition associated with the over expression of GSK-3β enzyme, its structure, various strategies implemented for designing selective GSK-3β inhibitors and clinical status of GSK-3β inhibitors. Chapter 2 outlines the aim and objectives of the present work. The aim of the work is to identify new chemical moieties as GSK-3β inhibitors by rational drug design based on in-silico fragment-based and docking approach as well as to identify novel inhibitors via virtual screening of chemical databases. Chapter 3 covers detailed literature review of various class of compounds available as GSK-3β inhibitors. They are further classified based on their mode of inhibition as non-ATP competitive, substrate competitive and ATP-competitive GSK-3β inhibitors. A review on patent literature is also covered. Chapter 4 describes prediction of binding sites and druggability assessment of GSK-3β by SiteMap software tool. The ligand-binding characteristics and druggability of each site of GSK-3β was assessed with SiteScore (SScore) and Druggability score (Dscore) respectively. Eight sites were identified on the surface of GSK-3β. The ATP-binding site (pocket 1) and allosteric site (pocket 7) were predicted as top scoring sites of GSK-3β. Application of combined in-silico fragment-based and molecular docking approach yielded the design of new chemical series of allosteric pocket 7 targeted N1,3-disubstituted imidazolidin-2-one derivatives. These hits displayed strong H-bond and pi-stacking interactions with Ser236 and His173 residues. Application of virtual screening methodology based on structural features of Tideglusib; identified new heterocyclic compounds via shape-based similarity screening using ROCS followed by molecular docking, electrostatic similarity search using EON and pharmacophore feature-based searching and molecular dynamics simulation approach. Three virtual hits AO-476/41610153, AT-057/43486355 and AK-080/40907857 (ZINC4192390) were identified from the SPECS and ZINC database. Chapter 5 describes synthesis and characterization of 21 designed compounds under a series of N1,3-disubstituted imidazolidin-2-one derivatives. The final synthesized compounds were purified by 100 - 200 mesh silica gel by column chromatography. Structural characterization was carried through FT-IR, Mass (ESI-MS), 1H NMR and 13C NMR analysis. LC-MS analysis of compound 2d was also performed for confirmation of synthesized compound. Chapter 6 describes in-vitro screening of 24 test compounds and Tideglusib on GSK-3β target using ADP-GloTM Kinase assay. Assay standardization was performed to find the optimal concentration of GSK-3β (7.5 ng), ATP (10 μM) and substrate (2 μM) for the entire study. The inhibitory effect of test compounds and Tideglusib was studied. Compounds 1i, 1n, 2d and AO-476/41610153 have very weak inhibition on GSK-3β compared to the standard drug Tideglusib. Out of the four identified hits, compounds 1i and AO-476/41610153 showed the highest GLIDE XP scores in the allosteric and substrate sites of GSK-3β respectively. Here, our docking computations are in perfect agreement with the in-vitro results. Chapter 7 describes the summary and future prospects, which can be further explored with this study.