The road to drugging the undruggable

When you imagine a drug at work in the body, what do you picture? A tiny assassin silently sneaking up on its protein target? An entire army of combatants swarming a gargantuan biomolecular enemy? However you envision it, these comparisons aren’t that far from the truth. With a bit of creativity, researchers at St. Jude are finding novel ways to design and develop therapeutics that go after disease from innovative angles.

If drug design was as easy as finding a small molecule that always hits its target like a skilled assassin, much of today’s biomolecular research wouldn’t be needed. Many (or most) illnesses are incredibly intricate puzzles with countless moving pieces, each linked together in a domino-like medley of cause and effect. The idea of a therapeutic that would work for broad swaths of disease, such as all cancers, is unrealistic in such a complex world. Even so, thanks to new biologic insights about human health and disease, drug design has hit new and extremely creative highs, with researchers turning their sights on pathways once considered “undruggable.” Scientists at St. Jude are at the forefront of finding ways to modify transcription and related processes to open the field of what is possible in therapeutics.

A golden age for chemistry

Transcription has long been considered an “undruggable” process. One of the fundamental mechanisms of our body, transcription, is how genetic information in DNA is copied into mRNA to be later translated into a protein. It is about as intricate a dance as any other mechanism the human body offers. The components that regulate this process are called transcription factors, and our genome encodes about 1,500 different ones. Any deregulation of these transcription factors, such as mutations, fusions, or deletions, results in aberrant behavior and has been attributed to numerous diseases, including cancer. Targeting transcription is a tall order, but researchers at St. Jude have answered the call.

“Chemistry has entered a golden age because so many mechanisms are now available for us to target specific sites in the body,” said Anang Shelat, PhD, St. Jude Department of Chemical Biology and Therapeutics.

Shelat has taken a keen interest in drugging transcription. “As I got more involved in transcription-related projects, I started to have my own ideas,” Shelat explained. “I recognized that making the molecules wasn’t enough. You needed someone to dedicate time to figure out what these molecules were doing.”

Betting on bromodomains

Scientists have directed significant research around transcription factors towards bromodomains, a structural feature of 46 proteins associated with transcriptional regulation. Both chemically and structurally, bromodomains are ideal drug targets, and in the past ten or so years, the floodgates opened on the creation of inhibitors to target them. However, in an ironic turn of events, the more bromodomains were targeted, the more we learned how ubiquitous they are throughout the body and the potential for unwanted side effects. JQ1 is one such bromodomain inhibitor, which has garnered significant attention amid a plethora of claims of its use in treating numerous diseases across the body.

“That was telling us that a wide-scale perturbation of gene expression was happening,” Shelat said. “That tends to cause a lot of stress in normal cells. So clinically, these inhibitors have struggled to progress because they have a lot of on-target but off-tissue toxicity.”

Compounding this is the concept of transcriptional plasticity, wherein a compensatory regulator replaces a transcription factor when selectively targeted by a drug. Like cutting off the head of the Hydra — two grow back in its place.

So, what do you do when you have promising therapeutics that are toxic to the cell at therapeutic concentrations (thanks to their target being so crucial to cellular function) and selective therapeutics that are too selective? Researchers at St. Jude, including Shelat and Martine Roussel, PhD, St. Jude Department of Tumor Cell Biology, sought a compromise between selectivity and effectiveness by trying combination therapy. Recently published in Molecular Cancer Therapeutics, the team examined the effect of combining partners from a panel of oncology drugs in treating recurrent medulloblastoma (a type of childhood brain tumor). Their results indicated that combining low doses of an inhibitor of the cyclin-dependent kinase family (which has its own off-target effects by itself) with the bromodomain inhibitor JQ1 significantly boosted efficacy against tumor growth.

Inspired by the activity of bromodomain inhibitors, Shelat and his colleagues in CBT sought to design more selective inhibitors. Published in Cancer Research in a hugely collaborative effort, they developed a series of inhibitors that targeted not just one bromodomain-containing protein but one particular bromodomain within that protein. The compounds, which target the bromodomain and extraterminal (BET) family of proteins, offer tremendous therapeutic promise.

“We have developed a molecule that shows reasonable selectivity, but importantly, the chemists here in Chemical Biology & Therapeutics made it very effective from a clinical perspective. Our compound isn’t as selective (as other bromodomain inhibitors), but it might work better in the body than what’s out there,” Shelat said.

Approaching from a new angle

When our genes are not actively being transcribed, they are usually found wound up in compact structures called nucleosomes. A nucleosome is the basic packaging unit of our DNA and consists of DNA wrapped tightly around proteins called histones. These nucleosomes are then further packaged until all the DNA in our genetic makeup (about 6 feet in length) can be snugly compartmentalized inside the nucleus of each of our cells. Before a gene can be transcribed, the nucleosome needs to be moved or dislodged for transcription factors to gain access to the gene of interest. This is a job served by chromatin remodelers.  

From a therapeutic standpoint, chromatin remodelers are a hot spot for drug targeting. Charles W. M. Roberts, MD, PhD, Executive Vice President and St. Jude Comprehensive Cancer Center director, led the charge early on and is a pioneer in the SWI/SNF family of remodelers, one of the first chromatin remodelers researchers targeted therapeutically to treat cancer. “I think there was a lot of interest in remodelers because they are involved in the opening and closing of actively transcribed genes,” Shelat said. “So, there’s a clear link to them for targeting transcription. In addition, there have been mutations and amplifications to them that pop up often in cancer.”

Current ongoing work from the Shelat lab has pointed to a link between neuroblastoma and a curious amplification of one particular gene involved in remodeling: the bromodomain PHD finger transcription factor (BPTF).

The bromodomain portions of a BPTF represent a clear target for researchers, but what about the PHD finger? PHDs are protein motifs (characteristic subunits) often expressed with bromodomains and function similarly by interacting with DNA during transcription. However, in the context of drug development, they are worlds apart.

“Bromodomains have been easy to target with small molecules. PHD domains have been terrible,” according to Shelat. “Generally, this is an interesting problem for us in chemical biology to figure out how to target these motifs.”

A massive collaboration across no less than eight labs at St. Jude, including Shelat’s, is ongoing to develop inhibitor screens for PHD domains of different oncoproteins. Through these screens, the researchers hope to determine the feasibility of targeting them. If successful, it may be possible to specifically target chromatin remodelers or include them in a combination therapy.

Molecular glues are the future?

Even with this relative arsenal at a doctor’s disposal, many diseases remain resistant to treatment. Each step taken in drug development reveals new layers of complexity. When conventional therapies offer no clear path to success, scientists at St. Jude find a new way.

Proteins, in general, have a life cycle, and when a protein has fulfilled its function and is no longer needed, it gets degraded. This degradation involves getting tagged with a ubiquitin molecule detected by proteases. These proteases break the protein down, returning it to its fundamental components. But what if we could hire this degradation machinery as our own personal mercenaries? That is what scientists at St. Jude are trying to do with developing a molecular glue library. In straightforward terms, molecular glues do just that: glue two different proteins together.

“These molecules can engage the degradation machinery but also interact with and target transcription factors,” Shelat said.

Despite being relatively new to the therapeutic world, molecular glues excite many people.

“Now we think about molecules that could effectively degrade the machinery of transcription or degrade some accessory protein involved in the stability of the proteins,” Shelat added. “We have a couple of screening campaigns using molecular glues, including one against Ewing sarcoma in particular.” This work targets the aberrant fusion of the Ewing sarcoma protein (EWS) and the transcription factor FLI1 found in approximately 90% of all Ewing sarcoma tumors.

Molecular glues are not just limited to degradation machinery; St. Jude researchers are also looking to commandeer other cellular processes to go after particular targets. Proteins are very often regulated by post-translational modifications such as phosphorylation (addition of a phosphate group to the protein), methylation (addition of a methyl group) or acetylation (addition of an acetyl group). The addition of these post-translational modifications can act as ON/OFF switches for cellular function. Controlling the regulation of such processes as transcription by hijacking these ON/OFF switches offers a largely unexplored route for therapy with enormous potential.

Therapeutic design has significantly advanced in recent years. Thanks to researchers like Shelat, and others at St. Jude, scientists are diving into cellular biology to target a variety of processes therapeutically. With these next-generation novel strategies gaining traction toward targeting undruggable pathways such as transcription, researchers are excited about what’s to come.