I wanted to know, what changes will occur, if a replace or remove of a functional group of ligand at give specific site and put it on other position with that ligand, my ligand have steroids and lactone characteristics.
How it will affect the binding affinity it protein and what other changes will occur besides stability problem?
Functional groups are the important part of a particular chemical compound. If you replace it with another functional group, it may affect it's IC50 values, Ki, and binding affinity with the particular protein (either it may be enhanced or reduced). It may also have effect on the protein's stability and secondary structure. Biophysically, you can determine the secondary structure change by Circular dichroism. The kinetics of binding of ligand with the protein i.e. it's deltaG,deltaH and it's binding energy, you can determine with ITC, Fluorescence spectroscopy, and SPR. Stability of the protein and ligand complexes can be determined by Molecular dynamics simulations.
Computationally, you can determine the binding energy and Ki of the protein-ligand complex by Autodock and Glide.
Best Regards
You can change the functional groups cautiously such as add some acceptor groups where the receptor have donor groups or add positively protonated group (NH2) if the receptor has negative group like acid. If you will change like this your binding affinity will increase. But be careful about the clashes that can occur if you add more bulky groups.
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