Discovery of Potential RAGE inhibitors using Receptor-Based Pharmacophore Modeling, High Throughput Virtual Screening and Docking Studies

Author(s): Harbinder Singh and Devendra K Agrawal

Receptor for Advanced Glycation End products (RAGE) is a transmembrane receptor that can bind to various endogenous and exogenous ligands and initiate the inflammatory downstream signaling pathways. So far RAGE has been involved in various disorders including cardiovascular and neurodegenerative diseases, cancer, and diabetes. Blocking the interactions between RAGE and its ligands is a therapeutic approach to treat these conditions. In this context, we effectively utilized the receptor-based-pharmacophore modeling to discover structurally diverse molecular compounds having potential to effectively bind with RAGE. Two pharmacophore models were developed on V-domain of RAGE using Phase application of Schrodinger suite. The developed pharmacophoric features were used for screening of 1.8 million drug-like molecules downloaded from ChEMBL database. The molecules were scrutinized according to their molecular weight as well as clogP values. Phase screening was performed to find out the molecules that matched the developed pharmacophoric features that were further selected to analyze their binding modes using high-throughput virtual screening, extra precision docking studies and MM-GBSA ΔG binding calculations. These analyses provided ten hit RAGE inhibitory molecules that can bind to two different shallow binding sites on the V-domain of RAGE. Among the obtained compounds two compounds ChEMBL501494 and ChEMBL4081874 were found with best binding free energies that proved their receptor-ligand complex stability within their respective binding cavity on RAGE. Therefore, these molecules could be utilized for further designing and optimizing the future class of potential RAGE inhibitors.