Solution-phase affinity selection of inhibitors from combinatorial peptide libraries

Abstract

The present invention provides novel peptides (e.g., peptides, macrocyclic peptides, mini-proteins) that modulate protein-protein interactions or salts thereof, and methods of making and using the inventive peptides. In some embodiments, the peptides are high affinity inhibitors (e.g., KD of at most 100 nM, at most 10 nM, at most 1 nM) of a protein-protein interaction. In certain embodiments, these peptides interfere with p53-MDM2 binding interactions (e.g., by binding to MDM2 (GenBank® Gene ID: 4193)). In some embodiments, the peptides interfere with the dimerization of the C-terminal domain of the human immunodeficiency virus (HIV) capsid protein (C-CA), comprising residues 146-231 of the HIV capsid protein (e.g., by binding to the C-terminal domain of the HIV capsid protein (C-CA), thereby inhibiting the dimeric interface of HIV capsid protein, thereby inhibiting viral assembly). These inventive peptides were rapidly generated and identified using novel methods described herein comprising combinatorial peptide synthesis and / or solution affinity selection.

Description

RELATED APPLICATIONS[0001]This application claims priority under 35 U.S.C. § 119(e) to U.S. Provisional Patent Application, U.S. Ser. No. 62 / 593,861, filed Dec. 1, 2017, the entire contents of which is incorporated herein by reference.GOVERNMENT SUPPORT[0002]This invention was made with Government support under Grant No. N66001-14-2-4058 awarded by the Space and Naval Warfare Systems Center (SPAWAR). The Government has certain rights in this invention.BACKGROUND OF THE INVENTION[0003]Drugging protein-protein interactions (PPIs) has become a major center of focus in drug discovery. However, simple methods allowing for the rapid generation of scaffolds containing non-proteinogenic side chains, which would broaden the peptide structure and function space and would therefore facilitate the discovery of potent peptide-based PPI inhibitors, are lacking.[0004]Over the past 10 years, PPIs have been recognized as key targets in drug discovery [1]. In this regard peptide binders have the pote...

AI Technical Summary

Benefits of technology

[0032]“Stapling” or “hydrocarbon-stapling,” as used herein, may refer to a process by which to amino acids side chains in a peptide are used in order to covalently link one part of a peptide chain to another. For example, stapling may involve a process by which two terminally unsaturated amino acid side chains in a peptide chain react with each other in the presence of a ring closing metathesis catalyst to generate a C—C double bonded cross-link between the two amino acids (a “staple”). Stapling engenders constraint on a secondary structure, such as an alpha helical structure. The length and geometry of the cross-link can be optimized to improve the yield of the desired secondary structure content. The constraint provided can, for example, prevent the secondary structure to unfold and / or can reinforce the shape of the secondary structure, and thus makes the secondary structure more stable. Stapling may occur between two non-consecutive amino acids in a peptide chain. In certain embodiments, stapling may occur at i,i+3, i,i+4, and / or i,i+7 positions of the polypeptide.

Problems solved by technology

However, simple methods allowing for the rapid generation of scaffolds containing non-proteinogenic side chains, which would broaden the peptide structure and function space and would therefore facilitate the discovery of potent peptide-based PPI inhibitors, are lacking.

The latter are extremely attractive but are either not yet amenable to the use of large repertoires of non-canonical amino acids [8] or may suffer in their conventional format from screen complexity and false positives [9].

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