Covalent docking remains a critical step in the design of irreversible enzyme inhibitors and other chemically reactive compounds—but the technical challenges involved can often outweigh the benefit, especially for those new to the field. Setting up such systems manually can be time-consuming, error-prone, and confusing. Errors in hybridization, bond types, or missing parameters typically result in failed jobs or unreliable results.
Fortunately, the FITTED Suite SAMSON Extension offers a more guided approach for setting up both covalent and non-covalent docking. In this post, we’ll walk through how to easily carry out covalent docking using the example of the 5MAJ structure—a human cathepsin L protein covalently bound to its ligand 7KH 301.
Who is this for?
This guide is useful for researchers and students interested in structure-based drug design, particularly those focused on covalent inhibitors, who want to streamline their setup and analysis workflow using a modern molecular modeling platform.
What makes covalent docking difficult?
Unlike non-covalent docking, covalent docking involves explicitly modeling the chemical bond formation between a ligand and a reactive amino acid residue in the binding pocket. This means:
- Correctly assigning a hybridization state for specific atoms
- Adjusting bond orders to match the unbound ligand state
- Selecting both the covalent residue and optionally a nearby basic atom
How SAMSON simplifies covalent docking
Using the FITTED Suite extension in SAMSON, you can work directly with PDB structures, graphically modify hybridizations and bond orders, and set up a run using a simple interface.
Let’s look at the key steps:
🔬 Step 1: Adjust bond order and hybridization
You may need to change the bond order of atoms in the ligand back to their unbound state. In our example:
- Change the C8–N7 bond (in
7KH 301) to a triple bond - Set both atoms’ hybridization to
SP
This ensures the ligand geometry before docking reflects its unbound state.
🧬 Step 2: Set up in the FITTED Suite interface
- Set Receptor: Select
5MAJstructural model - Define Binding Site: Select the bound ligand
7KH 301 - Set Ligand: Select the same molecule, and make sure to uncheck “Prepare ligand” to preserve your manual changes
🔗 Step 3: Set covalent parameters
Here’s the key step: define the two atoms involved in the covalent bond:
- Set Covalent Residue: Select
CYS 25, which contributes the sulfur atom (SG) - Set Basic Atom (optional): Select the ND1 nitrogen from the adjacent
HIS 163residue
🚀 Step 4: Launch and review
Set the number of docking runs (e.g., 2), select Covalent only docking mode, and specify an output folder. Then click Dock.
The output includes both receptor and ligand in a processed form, with the ligand covalently attached through the expected bond.
Wrapping up
This covalent docking workflow avoids many of the pitfalls involving input misconfiguration. Whether you’re working on nitrile-based inhibitors or warheads targeting cysteines, visualization and data setup in SAMSON noticeably reduce the overhead of managing covalent systems.
To learn more about this workflow, please visit the full documentation here: FITTED Suite Tutorial.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.