You`re tasked with developing an inhibitor for a specific kinase within the pharmaceutical industry. Your team has already identified a compound that can moderate the kinase`s activity.
In using Auto DockTools and Autodock Vina to dock your compound with the kinase, the search area for docking is determined based on the active site of the kinase. This area is typically identified through structural information about the kinase, such as crystal structures or computational models. The search box is positioned to encompass the active site, allowing for potential interactions between your compound and the kinase.
Possible interactions between your compound and the kinase are assessed post-docking. These interactions may include hydrogen bonding, electrostatic interactions, and hydrophobic interactions. A detailed analysis with suitable images and labeling is provided to highlight these interactions.
The binding affinity of your compound and the kinase from docking is tabulated, providing quantitative data on their interaction strength.
Based on the docking results and medicinal chemistry knowledge, five changes are proposed to the molecule to explore structure-activity relationships (SAR) and enhance binding efficiency. These changes are illustrated on a target molecule, with explanations provided for each modification and the expected outcomes.