When working with covalent inhibitors, many molecular modelers face uncertainty: preparing bond order, dealing with hybridization, and ensuring correct interaction setup can be complex and error-prone. If you’ve ever needed to dock covalent ligands (like irreversible inhibitors) but were unsure about the extra steps involved, you’re not alone.
Fortunately, the FITTED Suite in the SAMSON molecular design platform makes covalent docking streamlined and intuitive—even for newcomers. This post walks through the covalent docking process using the example of a covalently bound ligand from the 5MAJ PDB structure (human cathepsin L with a 7KH ligand).
Why covalent docking needs extra care
Unlike non-covalent docking, covalent docking requires special attention to atomic hybridization and specific reactive atoms since you’re modeling a bond formation between a ligand and a residue on the target protein.
With the FITTED Suite in SAMSON, you not only define the receptor, binding site, and ligand, but also specify the covalent residue and, optionally, a nearby basic atom—both essential for accurate modeling.
Steps to set up covalent docking
After launching SAMSON and opening the 5MAJ.sam file, here’s how you can prepare your system:
1. Adjust ligand hybridization and bonds
In this case, the 7KH 301 ligand is already covalently bound. It’s important to modify bond order manually before docking. Select the C8 atom and change the C8–N7 bond to a triple bond. Then, assign SP hybridization to these atoms using SAMSON’s Inspector panel.
2. Set the receptor
Select the protein structure 5MAJ and define this as the receptor. Default parameters (Protein macromolecule, keep water) are sufficient here.
3. Define the binding site
Use the bound ligand method: select the 7KH 301 ligand and use it to set the binding site center.
4. Set the ligand
Once more, select 7KH 301 from the structure and uncheck the Prepare ligand option to retain your manually adjusted bonds and hybridizations.
5. Configure docking as covalent
- Docking mode:
Covalent only - Number of runs: 2
- Set the covalent residue:
CYS 25(SG atom in the receptor) - Optionally, set a basic atom: e.g. the
ND1nitrogen in adjacentHIS 163
6. Run docking and analyze
Click the Dock button. After a few minutes, results appear in the results table and are inserted into the workspace. You’ll observe a ligand bound covalently to CYS 25 in 5MAJ_pro.
Why this matters
This workflow saves time and avoids trial-and-error when modeling irreversible inhibitors in drug discovery pipelines. FITTED’s integration in SAMSON is especially helpful for visualizing, validating, and analyzing covalent interactions, directly in 3D.
To learn more about the full tutorial, visit the original documentation page: Covalent and non-covalent protein-ligand docking with the Fitted Suite.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.