Peptide drug discovery has evolved over time with a focus on receptor and extracellular targets (1st wave) as well as intracellular targets (2nd wave). Ultimately the peptide modality, itself, has become a focus (3rd wave) to leverage super-diverse libraries, deep knowledge from structural biology and computational chemistry. This presentation will feature exploring drug space at the crossroad of alpha-helices and D-peptide modalities.

We’ve been using passively permeable macrocycles found in nature as therapeutics for decades. However, designing this property into synthetic cyclic peptides has proved to be challenging despite the myriad of screening and selection platforms available. This talk will explore how we leverage our platform to turn impermeable binders into passively permeable leads.

The protein-protein interaction of KEAP1 with Nrf2 is a target of high current interest that, due to the highly charged nature of the interface, poses special problems for inhibitor discovery. I will describe progress toward developing a cyclic peptide inhibitor of KEAP1, with emphasis on how we approached optimizing ring size, eliminating strain, occupying binding energy hot spots, and eliminating charged groups that hinder cell permeability.

Syrbactins, macrocyclic peptide natural products, are the basis of drug candidates for autoimmune disorders and multiple myeloma. They show irreversible, covalent proteasome modification, high specificity for particular proteasome catalytic subunits in cell culture, no off-targets in adverse drug reaction screens, and a good therapeutic index in animal models. We exploit the syrbactin macrocycle to predict, analyze, and control the 3D conformations of our drug candidates, which affect their proteasome selectivity.

We describe the proof of concept for macrocyclic peptides that inhibit BRAF through binding to the dimerization interface of the RAF kinases. Furthermore, we applied the REPLACE strategy to identify and optimize the peptides for BRAF affinity and increased drug-likeness. The compounds block paradoxical signaling resulting from aberrant activation of BRAF by ATP competitive drugs and thus, have potential as next-generation BRAF inhibitors for treating resistant melanomas.

E3 ligases are key regulators of the cell cycle and cell proliferation and important therapeutic targets. The proteins from which they are derived adopt extended, non-helical bioactive conformations, presenting challenges for the
rational design of chemical constraints. I will present our work on peptides designed to inhibit two E3 ligases. I will also discuss how we are exploiting our findings and methodologies for targeted protein degradation.

Cyclotides are ultra-stable peptides that are able to penetrate cells. This presentation will describe their membrane interactions and cell-penetrating ability, along with their ability to be loaded with epitopes for intracellular targets.

Current biologic drugs work almost exclusively against extracellular targets, because they cannot cross the cell membrane. We recently discovered a family of small amphipathic cyclic peptides as highly efficient cell-penetrating peptides (CPPs), which are capable of delivering a variety of cargo molecules into the cytosol of mammalian cells. In this presentation, I will discuss their mechanism of action, which involves endocytic uptake followed by efficient endosomal escape. I will next discuss how to leverage the cyclic CPPs to design intracellular biologics as next-generation therapeutics against previously intractable diseases, such as those caused by genetic mutations and aberrant protein-protein interactions (e.g., calcineurin-NFAT, Keap1-Nrf2, and beta-catenin-TCF interactions).

FAST is capable of screening ~5M assay points in 1 minute. We have used this to design and screen large libraries (10⁷ – 10⁹) of synthetic non-natural polymer macromolecules to routinely find nanomolar to sub-nanomolar binders to ‘undruggable’ targets, such as K-Ras and asialoglycoprotein receptor. With remarkable biological stability and extended in vivo PK half-life, these represent early examples of a new class of synthetic macromolecular modality for therapeutics discovery.

Cyclic peptides are an important tool for development of peptide therapeutics with cyclizations achieved several ways.  Here we describe several fully automated synthesis optimization methods, some using induction heating, for therapeutically relevant peptides including APY-d4 and RFP14 as well as Melanotan II, NYAD1 & Agardhipeptin A cyclic peptide sequences.