I have been working on certain protein-ligand interactions and have observed Tryptophan indole moiety is forming Pi-cation/Pi-Pi/Pi sigma with most of the ligands selected for studies. Is it matter of concern? Should I choose to study this pattern?
Dear Anuj
The interactions u observed called weak dispersive interactions can be possible in your case .so its not matter of concern
Hi Anuj,
Without seeing the data directly, there's probably a long answer to this. But for the moment, I'll stick with a short answer.
If the distances, angles, etc are consistent with reported non-bond interactions for pi-pi, pi-cation and pi-sigma for pi and aromatic systems, then you should not be concerned. In fact, it is likely that you are observing some favourable weak interactions that are consistent with other reported publications.
Here's a couple of very good overview papers that you might want to review, to satisfy yourself that you have valid stabilizing interactions between ligand and protein residue:
- Bissantz C., et al, "A Medicinal Chemist's Guide to Molecular Interactions", J. Med. Chem. 2010, 53, 5061–5084. DOI: 10.1021/jm100112j
- Kuhn B., et al. "Rationalizing Tight Ligand Binding through Cooperative Interaction Networks", J. Chem. Inf. Model. 2011, 51, 3180–3198. dx.doi.org/10.1021/ci200319e
- Marshall M.S., et al, "Potential Energy Curves for Cation-π Interactions: Off-Axis Configurations Are Also Attractive", J. Phys. Chem. A 2009, 113, 13628–13632. DOI: 10.1021/jp906086x
Regards,
A.
In the november or december issue of Accounts of Chemical Research you will find an interesting article about pi-cation interactions. Use ACS webpage to find it. Regards.
Thank You all. @Adrian Sir, Yor information was quiet useful. Thanks again
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