identify-predict peptides targeted by antibody

Question

[TriS]

hi all

I'm trying to identify which peptide sequence is targeted by a commercially available antibody (pembrolizumab) that targets PD1. the various sequences of the antibody itself are available at the patent website and on IMGT.

from here I'm not sure how to proceed, does anybody have experience in this?

thanks

Answer 1

[ALchEmiXt]

Not sure if you can reverse engineer the binding epitope from the antibody sequence..... seems hard to do. Perhaps search for homologous antibodies of which the epitope is known?

An alternative strategy that could give you at least a clue on the epitope is looking at the antibody specificity:

• which protein variants does it still detect and which don't (fom literature or databases or company);
• the same if there are variants of the proteins that are detected or not, you could search for conserved regions using comparative bioinformatics;
• under which conditions can the antibody detect the target (ELISA is different from Western blot) giving a clue on conformational of discontinuous epitope (meaning non linear);

And perhaps more....