Covalent docking is a powerful strategy in structure-based drug design, especially when targeting active sites with known reactive residues. However, setting things up properly — from hybridization to binding site specification — can be a major source of friction for molecular modelers.
What if your covalent inhibitor is already crystallized in complex with the target protein? You might assume this simplifies your workflow — and with the FITTED Suite for SAMSON, that’s mostly true. But there are still subtle steps you need to get right, like correctly assigning bond orders and hybridizations, or defining binding partners for proper covalent docking runs.
This post walks through a practical example from the SAMSON documentation: covalent self-docking with the human cathepsin L protein (PDB: 5MAJ) and a covalently bound ligand (7KH 301).
Why hybridization and bond orders matter
In covalent docking scenarios involving pre-bound ligands, it’s important to model the unreacted form of the ligand. This involves resetting the bond between the ligand and protein to its initial state (e.g., a triple bond in a nitrile group). In the 5MAJ complex, you’d need to:
- Change the
C8-N7bond back to a triple bond. - Assign sp hybridization to atoms
C8andN7.
This can be done in SAMSON using the bond editing tools or the Inspector. These manual tweaks are not optional: getting the chemistry right up front leads to more realistic docking results.
Specifying covalent docking parameters
Once the ligand’s structure is ready, open the FITTED Suite (via Home > Apps > Biology) and specify the key elements for docking:
- Receptor: Select the protein structure from the document and set it in the app.
- Binding Site: Use the pre-bound ligand (
7KH 301) to define the binding pocket. - Ligand: Set the edited ligand as the docking candidate. Be sure to uncheck the preparation option if you’ve manually changed its structure.
The most important covalent-specific step is identifying the residue involved in the covalent bond — here, CYS 25. You can select this residue directly or via a predefined group in the Document view. Additionally, a nearby basic atom, like ND1 in HIS 163, can be set to improve covalent docking precision (though this is optional).
Launching and visualizing results
Before docking:
- Set docking mode to Covalent only.
- Choose number of runs (e.g., 2 for quick testing).
- Define output folder for results.
Click Dock and relax — the FITTED Suite integrates side processes like PREPARE to handle hydrogens, tautomers, and bond cleaning automatically.
Once results are ready, the top-ranked pose is imported into your project. You can visualize the docking using secondary structure ribbons, highlight the new ligand pose, or analyze interactions using tools like the Protein-Ligand Interaction Analyzer and Hydrogen Bond Finder in SAMSON.
Takeaway
Proper covalent docking requires more than just launching an app — careful attention to ligand structure and correct selection of covalent partners is essential. Fortunately, SAMSON and the FITTED Suite make these processes highly visual and interactive, reducing trial-and-error and improving reproducibility.
To explore the full workflow and tools discussed in this post, refer to the complete SAMSON documentation: https://documentation.samson-connect.net/tutorials/fitted/fitted-suite/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.