I had a similar issue recently. I simply deleted the ligand atoms, restored any atoms on the receptor residue to which the ligand had been bound (if any), and set it to the highest predicted rotomer that didn't clash with any other receptor atoms.

I just had a look at 4F4Q and the highest probability rotomer for the cysteine residue is almost the same to what it is already. So I would suggest to just delete the ligand atoms, then prepare the receptor structure how you normally would.

Thank you Michael,

I wanted to do the same as you told, I deleted the ligand and receptor bond. Now can I place the reference ligand in the same cavity? What if I dock the reference ligand again? Will it be fine to take the docked pose as reference purpose?

Please answer

Thanks

Hi, If you want design a non-covalent ligand you can remove the covalent ligand bound to residue. After this you can adjust the protein by PPW (protein preparation wizard (Schrodinger) and perform 3-5ns of MD in order to relax the system without the covalent ligand. Subsequently you can use the active site from relaxed system for designing your non covalent ligand taking into account the key residues of pocket that must be targeted in order to inhibit the receptor. Moreover when you have in your hands the protein without covalent ligand and prepared as above mentioned you can perform an HTD (High-throughput Docking) for discovering potential non-covalent scaffolds that are able to inhibit the enzyme

regards

In docking softwares like Arguslab, you can make a copy of the covalently bound ligand and dock the copy on the protein structure using the coordinates of original ligand as binding site. Arguslab docking is not affected by previous ligand being in place. This has a added advantage that the protein is alreadily in its most favourable conformation while we perform docking. A root mean square deviation (RMSD) of less than 5 between consecutive docking runs should validate the model. Now further validate your docking model by docking structures of commonly known ligands of your target protein and correlating their docking energies with reported EC50 or reported biological activity. You can also examine the docked structures in three dimensions and postulate requirements for binding with the receptor. Then you would be free to make these changes in structure of your ligand and dock the new structures.

@Omprakash Tanwar, I assume it would be fine to use the ligand you deleted from the receptor structure to validate the receptor structure, as long as, again, you restore any atoms that should be there on the ligand.

Simone Brogi raises a good point, it's probably worthwhile doing some MD. I would have thought it would be better to do that with the reference ligand in place (but not covalently bonded) than without any ligand, but I am unsure on this...

Mr.Omprakash Tanwar

First you should find what are the active site amino acids bind with residues of ligand ( for covalent bond), then based on that you can design new compounds by changing the residues (H,NH2,OH,Halogens etc ),after design and selection , go for docking analyse the binding energies and also find out pose of receptor - ligand, analyse the results.

Thank you

Remember if you take a covalent ligand out and adjust the cysteine residue, no docking package will put it back non-covalently in exactly the same pose minus the bond, as the protein and ligand will clash at the sum of the vdw radii. Only by using a docking package which can use covalent constraints (e.g. GOLD and others) can you expect to reproduce the binding pose. Most docking packages fudge covalent inhibitors by ignoring/turning off steric and electronic clashes at the simulated "bond"

for instructions using GOLD see:

http://www.ccdc.cam.ac.uk/support/documentation/gold/3_2/doc/portable_html/gold_portable-3-049.html

In my view, The task is tricky. As suggested, U need the protein in a conformation which favors discovery of non-covalent ligands. So MD of the protein alone, would be the preferable choice to start the docking/screening process.

Once U prioritized the potential inhibitors, U can carry out MD of the protein-top hit complex(s) to re-score the docking results of the selected top hits.

Dear Omparkash Tanwar, have you worked on Vlife Molecular Design Suite(MDS) and that too latest version of its i.e. 4.2. Using this software your problem will no longer be a problem. Before texting you, I have tried it. In case of 4F4Q, the covalently bound BTZ043 can be easily removed as well as capable to redock it at its active site. The only concern need to be taken into consideration is while you extract the covalently bound ligand from the protein, you should not rotate the protein, it will change its conformations and disturb active site. After extraction, save your protein as apo protein and ligand as reference ligand. Then if you use the GRIP docking technology of VLife MDS 4.2, it will ask you for the reference ligand if any, enter this ref lig in place of mentioning cavity. The task will be completed. If you need any help in the use of the mentioned software, kindly let me know abd buzz me at [email protected] . May be i can help you virtually to get rid of this problem.