Covalent docking is an essential technique for drug discovery projects targeting enzymes and other proteins with reactive residues. However, setting up a covalent docking experiment can be time-consuming and error-prone, especially if you need to adjust bond orders, assign atom hybridizations, and define specific binding sites manually.
If this sounds familiar, you might want to explore the covalent docking workflow provided in the FITTED Suite, a SAMSON Extension developed with Molecular Forecaster. In this post, we’ll walk you through the covalent docking part of a hands-on tutorial using the example of the human cathepsin L protein (5MAJ) covalently bound to a ligand (7KH 301).
Why covalent docking is tricky
In many docking platforms, setting up covalent docking requires modifying the original PDB structure manually, defining covalent warheads, and often scripting complex procedures. The SAMSON FITTED Suite extension helps simplify this by guiding you through an intuitive interface, while still preserving full control over chemical and structural adjustments.
Step-by-step: from structure to covalent complex
To get started:
- Load the system: Open the
5MAJ.samfile provided in the FITTED tutorial archive. - Check bonding and hybridization: If your ligand is already covalently bound in the crystal structure, you’ll need to set proper bond orders. In the tutorial example, the nitrile warhead forms a covalent bond with the sulfur of a cysteine residue. Set the
C8–N7bond to a triple bond prior to the reaction and adjustsphybridization for both atoms. - Set up receptor, ligand, and binding site: Use the FITTED Suite UI to define the receptor, ligand, and binding site. You can assign the binding site based on the bound ligand directly.
- Define covalent residue and optional catalytic base: Select the cysteine residue that forms the covalent bond (e.g.,
CYS 25) and an adjacent basic residue (e.g.,HIS 163) to assist in the simulated mechanism. - Set parameters and run: Choose “Covalent only” mode and configure the number of runs. Then press Dock.
Understanding the results
Once docking is complete, the results table will show your conformations. The top-scored poses are automatically imported into your SAMSON workspace. Notably, the docked ligand will include the part of the amino acid residue it reacts with, visually confirming covalent binding.
From here, you can use tools like the Protein-Ligand Interaction Analyzer or Hydrogen Bond Finder to evaluate your docked models further, looking at binding interactions and structural complementarity.
When would you use this?
This workflow is particularly useful if you’re designing irreversible inhibitors or targeting catalytic residues directly. The clear guidance inside the app and the SAMSON document structure make it easy to review and repeat experiments with minimal overhead.
To dive deeper and try it out yourself, visit the original documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.