Developing macrocyclic binders against intracellular proteins and protein-protein interfaces remains a challenge with current methods and scaffolds. We recently developed computational methods to design peptides with enhanced membrane permeability and oral bioavailability. We are further integrating our computational methods with high-throughput peptide synthesis to design peptide binders for antibiotic, antiviral, and other therapeutic applications. Overall, these methods present avenues for binding intracellular targets currently considered "undruggable" or "difficult to drug."

To design passively membrane permeable bioactive macrocycles, chemists have resorted to N-methylated amino acids and/or unnatural amino acids. We replaced select amino acid residues by azole heterocycles in a stepwise manner, which vastly improved the lipophilicity and PAMPA permeability of macrocycles. NMR analysis and molecular dynamics demonstrated permeability did not linearly increase with the addition of heterocycles. This study paves a  way to discover privileged macrocyclic scaffolds for drug discovery.

Designing macrocycles for passive membrane permeability is a topic of intense research activity. Several different empirical and theoretical approaches have shown promise. I will discuss our recent machine-learning-based approaches for predicting macrocycle permeability, with emphasis on the idea that different classes of compound may have different permeation mechanisms available to them.

This lecture will discuss the development of efficient methods for the solid phase synthesis and on-resin screening of DNA-encoded libraries (DELs) of non-peptidic macrocycles. Because the macrocycles contain few amide N-H bonds, they display good intrinsic cell permeability. Stringent quality control measures have been established to ensure that almost all of the molecules in the library are indeed macrocyclic. Novel FACS-based screening methods to mine these libraries for highly selective target protein ligands, including molecular glue candidates, will be highlighted.

I will describe our method for synthesizing and screening ten-thousands of macrocyclic compounds at a picomole scale (S. Habeshian et al., Nat Commun. 13, 3823, 2022). Our new platform yields small cyclic peptides (< 700 Da) that have physicochemical properties suited to enter cells or for oral delivery.

The virtual chemical space that includes synthetically accessible macrocyclic peptides (MCPs) in the 1000-MW range is astronomical. While the proportion of those compounds that are cell permeable may be low, because the space is so vast, the total number of permeable MCPs above 1000 MW is high. I will describe high-throughput synthetic and analytical tools for the discovery of large, passively permeable MCP scaffolds toward ligands against challenging intracellular targets.

Circle Pharma has established an indication-agnostic peptide macrocycle discovery platform that combines structure-based design, physics-based permeability prediction, and semi-automated synthesis. The integrated workflow enables the rational exploration of vast chemical space to identify potent and permeable macrocycles in rapid iterative design cycles. This platform has produced orally bioavailable macrocyclic inhibitors of intracellular protein-protein interactions that demonstrate in vivo efficacy in mouse xenograft tumor models.

We identified lead macrocyclic compounds that are type IV kinase inhibitors and represent an ideal framework for conversion into next generation BRAF inhibitors. Despite the clinical success of B-Raf inhibitors like vemurafenib in treating metastatic melanoma, resistance has emerged through “paradoxical MEK/ERK signaling” where transactivation of one protomer occurs as a result of drug inhibition of the other partner in the activated dimer. We targeted the dimerization interface to overcome this problem.

Protagonist utilized its peptide technology platform for the de novo drug discovery of first and best-in-class drugs. The peptide technology platform produced novel peptides both oral and injectable clinical assets that include and not limited to rusfertide, PN-943, and PN-235. Will present the discovery and development of rusfertide (PTG-300), an hepcidin mimetic for the Treatment of Polycythemia Vera (PV).

This talk will highlight the discovery efforts from mRNA display screening hits to a tricyclic peptide PCSK9 inhibitor drug candidate, which demonstrated its pharmacodynamic effects similar to the FDA-approved, parenterally dosed anti-PCSK9 mAb, with the advantage of oral administration using lipidic dosing vehicle Labrasol.

I will discuss my lab's research which touches on macrocycles (DELs) and a strategy we patented for creating super pure DELs which should work out much better in DEL selections by improving signal:noise.

We design libraries of macrocycles aiming at generating better cell membrane permeability and apply to the RaPID selection against protein target of interest.

Targeted Protein Degradation has the potential to transform the treatment of disease. C4T’s TORPEDO platform enables the design of potent, selective, and orally available targeted protein degraders including monofunctional or MonoDAC degraders and heterobifunctional or BiDAC degraders and has delivered a robust pipeline of preclinical candidates. The presentation will discuss in vitro and in vivo strategies and challenges in the context of degrader drug discovery. As a case study, preclinical ADME properties of CFT8634, a potent, selective, and orally available BiDAC degrader of BRD9 for the treatment of SMARCB1-perturbed cancers will be discussed.

A platform to accelerate optimization of proteolysis targeting chimeras (PROTACs) has been developed using a direct-to-biology (D2B) approach focusing on linker effects. A large number of linker analogs, with varying length, polarity, and rigidity, were rapidly prepared and, without chromatographic purification, characterized in four cell-based assays by streamlining time-consuming steps in synthesis and purification. The expansive dataset informs on linker structure-activity relationships (SAR) for in-cell E3 ligase target engagement, degradation, permeability, and cell toxicity.

Synovial sarcoma is a rare, often aggressive malignancy with limited therapeutic options. In preclinical studies, FHD-609 has been shown to selectively degrade bromodomain-containing protein 9 (BRD9), taking advantage of a synthetic lethal relationship with the SS18-SSX translocation. The discovery and optimization of this first-in-class clinical compound will be described.