Low-throughput model design of protein folding inhibitors

The stabilization energy of proteins in their native conformation is not distributed uniformly among all the amino acids, but is concentrated in few (short) fragments, fragments which play a key role in the folding process and in the stability of the protein. Peptides displaying the same sequence as these key fragments can compete with the formation of the most important native contacts, destabilizing the protein and thus inhibiting its biological activity. We present an essentially automatic method to individuate such peptidic inhibitors based on a low-throughput screening of the fragments which build the target protein. The efficiency and generality of the method is tested on proteins Src-SH3, G, CI2, and HIV-1-PR with the help of a simplified computational model. In each of the cases studied, we find few peptides displaying strong inhibitory properties, properties which are quite robust with respect to point mutations. The possibility of implementing the method through low-throughput experimental screening of the target protein is discussed.