Methods of developing selective peptide antagonists
Methods and compositions related to the selective, specific disruption of multiple ligand-receptor signaling interactions, such as ligand-receptor interactions implicated in disease, are disclosed. These interactions may involve multiple cytokines in a single receptor family or multiple ligand receptor interactions from at least two distinct ligand-receptor families. The compositions may comprise polypeptides having composite sequences that comprise sequence fragments of two or more ligand binding sites. The methods and compositions may involve sequence fragments of two or more ligand binding sites that are arranged to conserve the secondary structure of each of the ligands from which the sequence fragments were taken.
1. A method of producing a therapeutic composite peptide(s) configured to inhibit the activity of at least two cytokines selected from a family of cytokines that bind to a common receptor, the method comprising the steps of:
using a computer to obtain amino acid sequences of the at least two cytokines from an amino acid sequence database;
generating 3D renditions of receptor binding interactions by one or both of the following methods:
performing computer-assisted docking simulations for one or more of the at least two cytokines binding to the common receptor based on the obtained amino acid sequences; and
analyzing the crystal structures of one or more of the at least two cytokines and the crystal structure of the common receptor;
identifying from the 3D renditions, specific amino acids and one or more structurally conserved regions responsible for the binding of each of the at least two cytokines to the common receptor;
designing candidate composite peptides that contain both the specific amino acids and the one or more structurally conserved regions responsible for the binding of each of the at least two cytokines;
screening the candidate composite peptides for thermodynamic stability and proper binding;
synthesizing by solid-phase peptide synthesis, biological synthesis, or both, the candidate composite peptide(s) that exhibit both thermodynamic stability and proper binding;
testing the synthesized candidate composite peptides for binding and biological activity to identify the therapeutic composite peptide(s);
repeating one or more of the above steps if needed, and
producing the therapeutic composite peptide(s).
2. The method of claim 1 , wherein the family of cytokines comprises the γc-family of cytokines.
3. The method of claim 1 , wherein the family of cytokines comprises the IL-6 family of cytokines.
4. The method of claim 1 , wherein the family of cytokines comprises the IL-17 family of cytokines.