DOCKovalent 3.7

DOCKovalent is the covalent docking version of DOCK. Originally implemented within DOCK 3.6, it was ported over to DOCK 3.7 on March 2015. The most current publication to cite DOCKovalent is:

"Covalent docking of large libraries for the discovery of chemical probes" Nir London, Rand M Miller, Shyam Krishnan, Kenji Uchida, John J Irwin, Oliv Eidam, Lucie Gibold, Peter Cimermančič, Richard Bonnet, Brian K Shoichet & Jack Taunton. Nature Chemical Biology 10, 1066–1072 (2014) doi:10.1038/nchembio.1666

Below are instructions on various aspects related to using this version of DOCKovalent. The running example for usage would be docking of cyanoacrylamides (doubly activated Michael's acceptors) to an active site cysteine in RSK2 kinase (PDB ID: 4d9t)

Custom Ligand / Library Generation

• To generate a single / few ligands:

• To generate a large library of ligands for covalent docking:

• Currently available covalent libraries (At the Shoichet lab / cluster 2)

Protein preparation

For covalent docking we need the structure (or a model) of a protein, a crystal ligand to define the binding site, and the identity of the residue for which we want to covalently dock.

• Download 4d9t.pdb
• Extract the protein (e.g. grep ^ATOM 4d9t.pdb > rec.pdb)
• Extract the crystal ligand (e..g grep "0JG A" 4d9t.pdb > xtal-lig.pdb)
• Execute the protein preparation script while indicating the covalent attachment point, in this case CYS 436

DOCK/proteins/blastermaster/blastermaster.py -r 4d9t.pdb --covalentResNum 436 --covalentResName CYS --covalentResAtoms HG

Note that if you want to dock to a Serine residue you also need to de-protonate the HG atom but for Lysine for instance you should remove all three protons: --covalentResNum 123 --covalentResName LYS --covalentResAtoms HZ1,HZ2,HZ3

The output of this script is an INDOCK file (see below), a "working" dir which contains temporary files that were generated during the preparation and a "dockfiles" dir that is required for the docking run (containing e.g. the scoring grids). One of the files that were automatically generated is dockfiles/matching_spheres.sph which for a covalent run would contain only three spheres corresponding to the three atoms in the protein preceding the covalent attachment point. E.g. for CYS these will be CA,CB,SG. Currently this is automatically generated for CYS/SER/LYS if you wish to dock to a different residue edit this file and input the coordinates of the corresponding atoms.

INDOCK parameters

By default covalent docking is turned off (weird right?) edit the INDOCK file to turn it on by changing dockovalent no -> yes

Description of parameters: bond_len - the 'ideal' covalent bond length len_range - what range around the ideal length should be sampled. len_step - at what increments should the bond length be sampled. So. e.g. for bond_len=1.8, len_range=0.1, len_step=0.05, the following lengths will be sampled: 1.7,1.75,1.8,1.85,1.9 Note that due to steric hindrance of 1-3 interactions DOCK will most of the time prefer the longest bond length possible, for this reason, currently it's advised to use len_range=0, len_step=0.1 (to avoid division by zero) and just set the ideal length correctly. With better modeling of the covalent energy this might be fixed.

bond_ang1 - the 'ideal' bond angle for CB-SG-Lig1 (look at length explantation above for ang1_range, and ang1_step) bond_ang2 - the 'ideal' bond angle for SG-Lig1-Lig2 (look at length explantation above for ang2_range, and ang2_step)

The default parameters for sampling (bond length and two bond angels are suitable for thioethers (e.g. when docking acrylamides to cysteines) these should be changed for different electrophile/nucleophile combinations. Some parameters you might want to use are listed below, but more work is being done in this vein as you read these lines.

Interpretation of the results

• Due to the ignorance of the scoring function to the covalent bond, scores tend to be higher than non covalent docking scores, even positive at times. As an example just covalently docking a methyl on to a cysteine without it clashing with anything will give a VDW score of ~+10. So positive VDW scores should not deter you from choosing what may look by eye like a good pose.

• Different electrophiles have different inherent reactivity. This is not taken into account in any way during the docking. The docked library should be matched to the application you are interested in. If you are looking for a non-toxic compound that may be active in cells you might consider unsubstituted acrylamides that are considered mild. If on the other hand you are looking for something that can label your protein in-vitro for crystallization studies Bromo-acetamide is very very reactive. Most of the covalent docking libraries were designed with fairly mild electrophiles but keep this consideration in mind when selecting which library to dock and which compounds to test.