Hello everyone
in designing cyclic peptide as an inhibitor how to identify the catalytic site residues that interact with peptide and how to choose the amino acids that making the cyclic peptide
One way is to use computational modeling such as proteochemometrics if you dont have the crystal structure of your target.
You can perform an empirical Alanine scan approach to evaluate the activity of your protein and thus identifying the critical residues in your inhibitor to get the maximum inhibition. Albeit it doesn´t give you the exact residues of your protein that are involved with the inhibitor interaction, you can get some nice hints about it nevertheless.
Your protein-target seems to be an enzyme if it has a catalytic site ? Do you know substrates ? And mechanism? All this should be useful.
If no structure is available, then cyclic mimetics of the substrate can be engineered (although there will be a lot of trial and error involved, so it's not really a rational design). Or screening as the last option.
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