2023 Denovo tutorial 1 with PDBID 4S0V

Introduction

This next section will walk you through the three options for DeNovo Design:

1. Generic DeNovo Design
2. Focused Fragment Design
3. DeNovo Refinement

and will be a continuation of the Virtual Screening tutorial. We will continue this work with #4s0v from the Protein Data Base.

Setting Up Your Environment

For this section we will need to create some more directories following this structure:

DeNovo Refinement

The DeNovo Refinement calculation/algorithm within DOCK is an interesting way to determine the effects on a ligand/protein interaction by changing part of the small molecule. For this tutorial we are going to change just a terminal ring on our ligand and see what different residues DOCK suggests we look into further.

The overall idea behind this refinement is to delete a portion of your ligand, replace the "stub" atom (or "anchor" atom) which is now not bonded to anything with a dummy atom, and ask DOCK to find an alternative.

1. Open the ligand minimized mol2 file we generated in the previous tutorial into Chimera.
2. Open the protein into the same session
3. Examine the binding site and choose a residue on the ligand that's pointing towards the inside of the binding site. For our protein this detailed section looks like:

We see an imidazole ring pointing towards the binding site so will choose to work with that. Select the protein and hide it from view.

1. Place your mouse over the atom connecting the ring to the rest of the ligand and note the atom and number. In this case it's N4.

• Step 5: Delete all the atoms from N4 to the end. Your ligand should now look something like:

• Step 6: Save a .mol2 file of your ligand in this configuration. Make sure to give it a new filename such as 4s0v_denovoRefinement.mol2
• Step 7: Open the .mol2 file. If you're on a UNIX system, you can use vi; if you're on a PC, you can use textedit. Locate the atom that will now be changed to a dummy atom:

• Step 8: Change the atom type to 'Du1' and the bond type to 'Du':

and save the file.

• Step 9: Open a new session in Chimera and load the modified mol2 file. The "dummy" atom should now be purple: