CHM 357b - TOPICS IN BIOCHEMISTRY: PHARMACOLOGY

Computational  Drug Design - Session IV

You should still have four separate files for COX1 and COX2 without ligands, and for each of the ligands (salicylate and S58) alone, with all of these files generated from the superimposed COX1 and COX2 protein-ligand complexes.  In this session, we will

1. Edit salicylic acid in salicylate, and create the complex COX2-salicylate.
2. Minimize the energy of salicylate in COX2 binding site.
3. Edit S58 to modify its structure.
4. Fit it in COX2 binding site, and minimize its energy.
5. Compare the values of the potential energies of the complexes COX2-S58 and COX2-editedS58

1. Editing salicylic acid in salicylate, and create the complex COX2-salicylate.

At the physiologic pH, salicylic acid looses its proton, and thus becomes the ion salicylate. The negative charge of salicylate is involved in the stabilization of the binding, so before doing any energy calculation we should first edit salicylic acid in order to create this negative charge.

• Remember that it is always safer to work on one molecule at a time when editing!
• Open the MSF file for salicylic acid
• Under the Edit main menu, select Molecular Editor.
• Go to the appendix of the QUANTA tutorial to refresh your memories about the Molecular Editor
• Remove the acidic proton of salicylic acid, add a negative charge to one of the oxygens of the acid function and create 2 resonant bonds between each oxygen and the carbon atom they are linked to.
• Save the file for salicylate under a new name
• Open the file for COX2 and check that salicylate is approximately located at the binding site of COX2.
• Use Save as under File main menu to create a file for the complex COX2-salicylate.

Minimization will be explained at the beginning of the class, but as a reminder, carefully read the introduction of section 10 of the Quanta tutorial.

• Read part A of section 10 and  add polar hydrogens to the structure, using the Molecular Editor.
• Save the modified structure.
• Read part B and set the minimization options to 100 steps of the Adopted-Basis Newton Raphson. Don't forget to verify that PSF mode is on.
• Read part C and apply constraints to the whole protein, leaving only the ligand free.
• Read part D and launch the minimization calculation.
• Save the minimized structure under a new name.
• Turn all constraints off, and calculate the potential energy of both complexes, COX2-salicylate before and after minimization.

 From now on, it is your turn to imagine a/several modification(s) of S58 that could improve its specific binding to COX2.

• Remember that it is always safer to work on one molecule at a time when editing!
• Edit S58, modifying it in ways that you think could improve its binding to COX2.  (Eventually, especially if you are successful, we would like you to explain your choice.)  Use the Molecular Editor to make the modifications and don't forget to save the new structure under a different name.

You might have noticed that adding hydrogens in a long process. To avoid having to do it again, we are going to use the minimized COX2-salicylate complex whose protein part has been already edited in this way. This structure has not had any other modification because it was constrained during the COX2-salicylate complex minimization, and thus is identical to the original COX2 in terms of geometry.
 

• Open the minimized complex COX2-Salicylate and use Active Atoms to remove salicylate from the binding site. Save under a new meaningful name because this file will be used again in part 5
• Open your modified S58 and check that it is located at COX2 binding site.
• Read part C of section 10 and apply constraints to the whole protein, leaving only the ligand free.
• Read part D and launch the minimization calculation.
• Save the minimized structure under a new name.

• Turn all constraints off, and calculate the potential energy of the complex COX2-modifiedS58.
• Open the files for COX2 (the one created in part 4) and the native S58.
• Use Save As under File to recreate the initial complex COX2-nativeS58.
• Apply constraints to the whole protein, leaving only the ligand free, and  minimize the energy of the native S58 bound to COX2..
• Turn all constraints off and calculate the potential energy of the minimized complex COX2-nativeS58.
• Using those potential energy values, discuss the quality of the ligand you created in terms of selective binding to COX2, and affinity.

 

Reminder of some of last weeks questions:
 

• Salicylic acid binds to both COX1 and COX2.  Do you find any spatial conflicts with salicylic acid in the binding site of the COX1 or COX2 structures?  If not, what does this suggest?  If you do, can you explain this?
• In COX2, can you find any empty regions near the ligand binding site?  How big are they?  Can you think of a modification of S58 that might fit into the space?
• Are there any charged or polar groups in COX2 near the ligand binding site?  Can you think of a modification of S58 that might be complimentary to these groups?

• COX2 with bound S58 and a modified S58