I am performing molecular docking for a peptide with a small molecule (ligand). After running the docking using AutoDock Vina, I visualize the docked position using LigPlot+ to identify hydrogen bonds and hydrophobic interactions. However, the LigPlot+ predicts some polar residues to participate in hydrophobic interactions with the ligand. Is this unacceptable to be reported?
Look at the specific atoms involved in the interaction: While the polar head groups of the longer side chains make polar interactions, the more proximal CH2 groups (Cbeta, Cgamma, Cdelta ...) e.g. of Lys, Arg, Gln can also be involved in hydrophobic interaction.
Greetings. Of course that is possible a interaction between polar residues and hydrophobic zones of the ligand. For example some carbonyl groups form van der Waals interactions with nonpolar atoms and also, sulfonyl groups from the ligand can form weak hydrogen bonds with C-alpha H donors. We have to remember that a dipole can polarize the electronic cloud from a hydrophobic atom (but remember that some of these interactions can only be taking account in a docking algorithm in a geometric way). You can see for example:
Bissantz, C., Kuhn, B., & Stahl, M. (2010). A medicinal chemist’s guide to molecular interactions. Journal of medicinal chemistry, 53(14), 5061-5084.
Thank you very much Dr. Annemarie Honegger for the clarification.
Thanks Edward Francisco Méndez Otálvaro for the clarification I will take a look at the paper!
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