Prevent Docking Failures: Manual Ligand Preparation for Covalent Docking

When performing covalent docking, one of the most common sources of error stems from improper ligand preparation — especially when working with ligands already covalently bound in crystal structures. By default, automatic preparation tools may fail to reconstruct the originally unbound ligand structure. This can lead to incorrect docking poses or even docking failure. If you’re seeing unexpected behavior in your covalent docking simulations, manual ligand preparation might be the step you’re missing.

In this blog post, we’ll look at a specific example using the FITTED Suite for SAMSON, where we manually adjust the ligand’s bond order and hybridization for a covalent inhibitor before docking. This ensures a more realistic, physically meaningful docking result. The example comes from a simulation involving the 7KH ligand covalently bound to the sulfur atom of a CYS 25 residue in the 5MAJ protein (human cathepsin L).

Why Manual Ligand Preparation Matters

When starting from a structure with an already covalently bound ligand, you’re not starting with the ligand in its original, unbound form. That means your docking algorithm might “think” the ligand always has that covalent bond and miss its reactivity altogether.

Correcting this involves mimicking the unbound form of the ligand by:

  • Changing the bond order of the reactive atom to match the pre-reaction form (e.g. a triple bond for a nitrile group)
  • Setting the hybridization of atoms to match their correct chemical state pre-covalent bond

How to Manually Prepare Ligands in FITTED

In the case of 7KH 301, a known covalent inhibitor, the key reactive group is the nitrile bound to the C8 atom of the ligand. Here’s how to manually prepare it for covalent docking:

  • Select the C8 atom in the ligand. You can find it by typing 7KH 301 in the search bar of the Document view and expanding the atom list.
  • Set the bond between C8 and N7 to a triple bond.
  • Open the Inspector and change the hybridization of C8 and N7 to SP.

Changing bond order of C8-N7 bond to triple bond

Changing hybridization of C8, N7 atoms to SP

Why is this important? The docking algorithm in the FITTED Suite uses this configuration to determine reaction feasibility during covalent docking. If you leave the ligand in its already-reacted state, the scoring and placement may no longer represent realistic interactions with the receptor.

Additional Tips

  • Disable automatic ligand preparation in the FITTED Suite when using manually edited ligands. This prevents it from overwriting your changes.
  • Store modified ligands in custom groups to keep your document organized.
  • You can always inspect bond orders and hybridizations later by simply reselecting atoms and opening them in the Inspector.

This manual tweak takes just a minute but can save hours of confusing troubleshooting later. For anyone using reactive ligands, it’s a good habit to double-check that their chemical form matches what’s expected before the docking interaction begins.

To learn more about covalent docking and ligand preparation in SAMSON, view the full tutorial on the FITTED Suite documentation page.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.

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