Integrating machine learning and high throughput screening for the discovery of allosteric AKT1 inhibitors

Evidence from clinical and experimental investigations reveals the role of Akt in oral Cancer, which has led to the development of therapeutic and pharmacological medications for inhibiting Akt protein. Despite prodigious effort, researchers are searching for new allosteric inhibitors as orthosteric inhibitors are non-selective and exert off-target effects. In the current study, we proposed an integrated computational workflow for identifying allosteric Akt1 inhibitors as this isoform is highly correlated with poor prognosis and survival. To achieve this objective, 84 classification QSAR models with six different machine learning algorithms were developed. The models created with RDKit_RF and RDKit_kstar outperformed internal and test set validation with an ROC of 0.98. The outperformed models were then used to screen Chembl, which contains over a million compounds, for Akt1 inhibitors. The Tanimoto similarity search approach identified the compounds structurally resembling Akt allosteric inhibitors. The filtered compounds were further subjected to docking phases, molecular dynamic simulation and mmpbsa to verify the binding mode of selected ones. All these analyses suggested hit 5 (CHEMBL3948083) as the potential allosteric inhibitor of Akt1 as the stability parameters, favourable binding affinity (-107.78 ± 11.56 KJ/mol) and ligand interaction were better in comparison to other compounds and reference compound. The residual analysis demonstrated that allosteric and isoform-specific residues such as Trp80 and Val270 contributed the larger energy for ligand binding. The proposed integrated approach in this study might achieve a futuristic outcome when employed in a pharmaceutical scheme different from the conventional method.Communicated by Ramaswamy H. Sarma.

AKT1; allosteric inhibitor; big data screening; machine learning classifiers; molecular dynamics simulation; similarity search.