Scientists at New York University (NYU) and the New York University School of Medicine have used computer simulation tools to develop a new type of compound that blocks the interaction of proteins involved in driving drug-resistant prostate cancer. Rather than target the androgen receptor (AR), which is the main therapeutic target for prostate cancer, the new compound is designed to block the interaction between two proteins in the Wnt signaling pathway, which is commonly mutated in tumors from patients with metastatic prostate cancer. Early in vitro and in vivo tests showed that the macrocycle peptoid inhibited Wnt signaling by blocking the interaction between the ß-catenin and TCF (T-cell factor) transcription factors, and inhibited prostate cancer cell proliferation by up to 95%.

“Rather than continue making compounds that are just like older drugs, the focus of our work has been to rethink the definition of what a drug-like molecule can be,” says corresponding author Susan Logan, Ph.D., associate professor in the department of urology, at NYU School of Medicine. “We designed our peptoids specifically to hit targets that are currently ‘undruggable,’” such as those causing treatment-resistant prostate cancer,” adds co-lead author Kent Kirshenbaum, Ph.D., a professor at NYU’s department of chemistry.

The researchers report on the development of the compound, in Nature Communications, in a paper titled, “Design of Peptoid-peptide Macrocycles to Inhibit the β-catenin TCF Interaction in Prostate Cancer.”

Prostate cancer is the third most common cause of cancer-related death, and while patients with localized disease have a good prognosis, for those with metastatic disease the 5-year survival rate is just 30%, the authors write. Most prostate cancer drugs target the androgen receptor (AR), but the majority of patients treated using anti-androgens will eventually become resistant to therapy and their disease will progress to metastatic castration-resistant prostate cancer (mCRPC).

In the search for alternative prostate cancer targets researchers have investigated Wnt signaling, which is involved in transcriptional control of the androgen receptor. Studies have suggested that the Wnt signaling pathway is mutated in upwards of 20% of patients with mCRPC. Central to Wnt signaling is the binding of ß-catenin to the TCF family of transcription factors, which activates genes involved in cell proliferation and differentiation. However, as the team notes, “The Wnt pathway remains a tantalizing but elusive target for drug discovery.”

Protein-protein interactions (PPIs) provide the structural and functional basis for many key biological processes, the authors continue, but designing molecules that can inhibit PPIs involved in disease pathogenesis isn’t easy. “Small molecules may lack sufficient surface area to abrogate protein–protein binding effectively, as these interfaces are typically broad and flat,” the team notes. “In addition, peptides often lack desirable pharmacological characteristics and are readily susceptible to degradation in vivo.”

Some of these problems can be overcome by designing peptidomimetic oligomers, which the researchers note could represent an “attractive middle ground” between small molecules and large biomolecules. Foldamers, including a class of molecule known as peptoids, for example, are sequence-specific oligomers that can be designed to mimic the secondary structure shapes of biomolecules, and could represent potential therapeutic candidates. However, designing these molecules represents what the team acknowledges is “a formidable and intriguing challenge.”

The team used computational protein design approaches to generate macrocyclic peptoid-peptide hybrids that would target part of the ß-catenin molecule by folding into structures that are complementary to part of its surface that interacts with TCF, and so could prevent the two proteins from interacting.

The approach effectively involved joining the ends of a linear peptoid together to form cyclical structures, which resemble the hairpins that TCFs depend on to interact with ß-catenin. The most promising of these, which the team called macrocycle 13, inhibited Wnt and AR signaling in cultured cells, and was found to directly block ß-catenin:TCF protein interaction.

Tests showed that the compound blocked the proliferation of prostate cancer cells in vitro, by 95%, compared with untreated cancer cells, whereas the linear peptoid effected just a 40% reduction in cell growth. In vivo experiments in a zebrafish model showed that the compound inhibited Wnt signaling, without harming zebrafish embryo development. This zebrafish model demonstrates overactive Wnt signaling, and ß-catenin accumulation that stops the eyes and forebrain for developing. Treatment with the macrocycle peptoids rescued eye development by blocking the overactive ß-catenin:TCF interactions.

In vitro experiments also showed that macrocycle peptoids caused a reduction in AR pathway target gene expression, which the researchers suggest could be the result of either direct inhibition of β-catenin:AR interaction, or result indirectly through the reduction in Wnt signaling, which then decreases AR gene transcripts.

They acknowledge that further testing in mouse xenograft models of prostate cancer will be needed to determine the therapeutic potential of macrocycle 13, or modified versions of the compound. “In this study, we demonstrate how computational tools can facilitate the design of oligomers that target β-catenin and disrupt its interaction with TCF,” the authors state. “More generally, this study portends further computer-assisted discovery of increasingly complex folded oligomers to address the vast number of different PPI relevant to human disease.”

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