Researchers  have revealed in the greatest detail yet the workings of molecules called protein degraders which can be deployed to combat what have previously been regarded as "undruggable" diseases, including cancers and neurodegenerative diseases.

Protein degrader molecules are heralding a revolution in drug discovery, with more than 50 drugs of this type currently being tested in clinical trials for patients with diseases for which no other options exist.

Now researchers have revealed previously invisible levels of detail and understanding of how the protein degraders work, which in turn is allowing for even more targeted use of them at the molecular level.

They used a technique called cryo-electron microscopy (cryo-EM), which enables scientists to see how biomolecules move and interact with each other.

This works by flash-freezing proteins and using a focused electron beam and a high-resolution camera to generate millions of 2D images of the protein. They then used sophisticated software and artificial intelligence (AI) models which allowed them to generate 3D snapshots of the degrader drugs working in action.

Their latest research is published in the journal Science Advances and is expected to constitute a landmark contribution to research in the field of TPD and ubiquitin mechanisms.

They  have reached a level of detail where they can see how these protein degraders work and can be deployed to recruit the disease-causing protein  and target the 'bull's eye,' in molecular terms.

Protein degrader molecules work in a way that is fundamentally different from the way conventional drugs work. However, until recently the exact details of how this process works at the molecular level had remained elusive.

Proteins are typically a few nanometers large, which is 1 billionth of a meter, or 1 millionth of the width of a hair. So being able to 'see' them in action has not been possible, up until now.
Scientists have now been able to build a moving image of how it all happens, which means they can more specifically control the process with an incredible level of detail.
Proteins are essential for our cells to function properly, but when these do not work correctly they can cause disease.

Targeted protein degradation involves redirecting protein recycling systems in our cells to destroy the disease-causing proteins. Protein degraders work by capturing the disease-causing protein and making it stick like a glue to the cellular protein-recycling machinery, which then tags the protein as expired in order to destroy it.

The tag is a small protein called ubiquitin, which effectively gets fired at the disease-causing protein like a bullet. In order for the process to work effectively, ubiquitin must hit the right spots on the target protein so that it gets tagged effectively. The new work by the researchers enables them to see how the bullet hits the proverbial bull's eye.
Working with a protein degrader molecule called MZ1, which was developed in the Ciulli laboratory at Dundee, and using high-end mass spectrometry, they were able to identify exactly where on the target protein the vital "tags" are added.

The work shows how degrader drugs hold onto and position disease-causing proteins, making them good targets for receiving ubiquitin molecules (i.e., "ubiquitin-atable") which then leads to their destruction inside the cell.

Protein degradation efficiency and productivity is dependent on the degrader molecule's ability to hold tight onto the disease-causing protein, and in a position where it can most effectively act. This latest research paints a bull's eye and holds it steady enough for the molecule to be accurately targeted.

Charlotte Crowe et al, Mechanism of degrader-targeted protein ubiquitinability, Science Advances (2024). DOI: 10.1126/sciadv.ado6492. www.science.org/doi/10.1126/sciadv.ado6492

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Scientists discover chemical probes for previously 'undruggable' cancer target

Hormone-driven cancers, like those of the breast and prostate, often rely on a tricky-to-target protein called Forkhead box protein 1 (FOXA1). FOXA1 mutations can enable these types of cancers to grow and proliferate. Today, FOXA1 is notoriously difficult to block with drugs—but that may soon change.

Scientists have identified a crucial binding site on FOXA1 that could pave the way for future cancer treatments. The team's findings, which were published in Molecular Cell on October 15, 2024, also mapped out how tiny drug-like chemical compounds—called small molecules—interact with the protein.

While examining protein interactions on a large scale, investigators determined that small molecules could, in fact, interact with FOXA1.

FOXA1 had historically been considered undruggable. It's thought to lack the types of surfaces that small molecule drugs can bind to, which is likely why it's been so difficult to target the protein.

Researchers used two forms of activity-based protein profiling (ABPP) to capture protein activity on a global scale. The dual approach allowed them not only to determine whether a small molecule could bind to FOAX1 at all, but also to pinpoint the exact binding site.

They  are particularly interested in how certain genes are turned "on" and "off" by proteins called transcription factors, and how this leads to cell states that cause cancer. Transcription factors like FOXA1 bind to specific regions of DNA and control whether a gene is activated (turned "on") or repressed (turned "off"). This regulation is essential to how cells function and respond to changes—such as in the case of hormone-driven cancers, which often depend on FOXA1 to grow.

FOXA1 is a master regulator of gene control, or what scientists call a lineage-defining factor.  The investigators found a specific site on FOXA1 that can bind to small molecules, which is a tremendously important discovery since transcription factors like FOXA1 are not only attractive targets for cancer, but also many other diseases.

Because it's so rare to find a small molecule binding site on a transcription factor, the discovery was unexpected.

A common analogy is that drugs bind to proteins like keys inside a lock, but the prevailing attitude is that most transcription factors don't have binding sites to unlock. The binding site on FOXA1 is like a hidden lock; without the ABPP technology as it exists today, it's hard to imagine how scientists would have discovered it.

Another surprising finding: FOXA1 usually binds to a distinct sequence of DNA bases to control gene regulation—but binding FOXA1 to small molecules changed the sequences that it preferred, allowing the protein to target different genes than it normally would.

This discovery may help future researchers understand how such molecules affect gene regulation in cancer. If small molecules alter FOXA1's DNA preferences, they could influence which genes are turned on or off—potentially affecting cancer growth.

Researchers now found small molecules could impact FOXA1's ability to interpret the information written into the genome.

Furthermore, the team determined that certain mutations in FOXA1 affected areas close to where small molecules could attach to the protein. These mutations changed how FOXA1 interacted with DNA—in the exact same way that the small molecules did.

This suggests that a hotspot for cancer-associated mutations is also a hotspot for small molecule binding events.

Contrary to what they originally thought, the researchers found that small molecules couldn't just attach to FOXA1 on their own. Instead, they could only bind to FOXA1 when the protein was already bound to DNA sequences—meaning the effectiveness of small molecules as cancer treatments probably relies on FOXA1's interactions with DNA.

Sang Joon Won et al. Redirecting the pioneering function of FOXA1 with covalent small molecules, Molecular Cell (2024). DOI: 10.1016/j.molcel.2024.09.024. www.cell.com/molecular-cell/fu … 1097-2765(24)00780-9