Using this information, use AutoDockTools and Autodock Vina

Posted: February 22nd, 2023

Please complete your coursework within a Microsoft Word document and submit your completed exercise through the Turnitin submission point found in the CHEM1110 Moodle
Please note that you can use the Nelson IT Labs for this docking and any other University study related activities.
Exercise
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 (for your kinase/compound paring, please look for your name in the Excel spreadsheet in the CHEM1110 Moodle shell – where you found this guidance).
1) Using this information, use AutoDockTools 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.

[Tips: To help you determine where the search area should be for the docking, you can go to the protein data bank, and search the PDB code of the kinase you are given. You will see a web page similar to the picture below, which contains information to describe your kinase target.

You can click “Ligand Interaction” which will bring you into a new page displaying where and how a drug molecule interacts with the kinase. You can use your mouse to rotate and zoom in/out to help you visualise the binding site.

Once you have a good understanding where the binding site should be, you need to adjust the dimensions, scaling factor and the centre of the search box in AutoDockTools based on this information. You need to make sure you define the search box correctly in your conf.txt file.

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

(c) A table to show the binding affinity of your compound and the kinase from docking
[20 marks]

2) 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, highlight the proposed changes (show the modification on the structure) with a brief explanation as a note as to the reasons for the change with suspected outcome(s). Your answer should be a maximum of ONE A4 page in length.
[20 marks]

You will also be assessed on the overall presentation and clarity of your submission.
[10 marks]
[Total 50 marks]
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Developing a Kinase Inhibitor: Using AutoDockTools and Autodock Vina for Docking

Introduction

As a member of the pharmaceutical industry, you have been tasked with developing an inhibitor for a kinase. This process requires a thorough understanding of the target kinase, its binding site, and potential interactions with compounds. In this exercise, you will use AutoDockTools and Autodock Vina to dock a compound with the kinase of interest and evaluate possible interactions. Based on the results, you will suggest changes to the molecule to improve binding efficiency.

Determining the Search Area for Docking

To determine the search area for docking, you should first go to the protein data bank and search for the PDB code of your kinase target. This will provide you with information about the structure of the kinase and the binding site. You can click on “Ligand Interaction” to see how a drug molecule interacts with the kinase. Use this information to adjust the dimensions, scaling factor, and center of the search box in AutoDockTools. Be sure to define the search box correctly in your conf.txt file.

Possible Interactions between Compound and Kinase

After docking, evaluate the possible interactions between your compound and the kinase. Use suitable pictures and labelling to highlight the interactions. Look for hydrogen bonds, electrostatic interactions, and hydrophobic interactions between the two molecules.

Table of Binding Affinity

Create a table to show the binding affinity of your compound and the kinase from docking. This will help you evaluate the strength of the interactions and potential for binding.

Suggested Changes to the Molecule

Based on the results of the molecular docking and your knowledge of medicinal chemistry, suggest five changes to the molecule to improve binding efficiency. Draw the target molecule and highlight proposed changes. Provide a brief explanation of the reasons for each change and suspected outcomes. Keep your answer to a maximum of one A4 page.

Using Nelson IT Labs for Docking

Remember to use the Nelson IT Labs for this docking and any other university study-related activities. This resource can help you complete your coursework within a Microsoft Word document and submit your completed exercise through the Turnitin submission point found in the CHEM1110 Moodle.

Developing a kinase inhibitor requires a thorough understanding of the target kinase and potential interactions with compounds. Using AutoDockTools and Autodock Vina for docking, you can evaluate the interactions between your compound and the kinase of interest. Based on the results, you can suggest changes to the molecule to improve binding efficiency. Remember to use the Nelson IT Labs for this and any other university-related activities.