CHEM1110:A brief explanation of how you determine the search area for the docking, accompanied by a suitable picture to show where the search box is located with respect to the kinase in your docking.

You are working within the pharmaceutical industry, and you have been assigned a kinase to develop an inhibitor for. Your team has already found a compound that can moderate the activity of the kinase of interest

  • Using this information, use Auto DockTools and Autodock Vina to dock your compound with the kinase of interest. Your report should include

a) A brief explanation of how you determine the search area for the docking, accompanied by a suitable picture to show where the search box is located with respect to the kinase in your docking.

b) Description of possible interactions between your compound and the kinase that you have identified after docking, accompanied by a suitable picture(s) and labeling to highlight the interactions.

c) A table to show the binding affinity of your compound and the kinase from docking

  • Based on the results from the molecular docking, and also using your knowledge of medicinal chemistry, suggest FIVE changes you would make to the molecule in order to probe SAR and increase binding efficiency.To answer this question, please draw your target molecule, and highlight the proposed changes with a brief explanation as a note as to the reasons for the change with the suspected outcome(s). Your answer should be a maximum of ONE A4 page in length.