The behind-the-scenes chemistry driving drug discovery

If drug discovery were a film production, chemistry would have all the high-profile acting roles, and all the behind-the-scenes roles too. And while the spotlight shines brightest on the lead, they would be nowhere without that behind-the-scenes supporting effort that contributes to the final product. St. Jude researchers are using chemistry to explore every step of production in their search for the next generation of therapeutic stars.

Chemistry as the director

Hai Dao, PhD, St. Jude Department of Chemical Biology & Therapeutics, uses chemistry as biology’s director. His research focuses on nucleosomes, the fundamental units of chromatin, which are critical for DNA packaging and regulation. Nucleosomes consist of DNA wrapped around histone proteins. These structures undergo diverse modifications to determine which genes are turned on or off at any given time. Errors in this gene regulation are common drivers of pediatric cancers, making nucleosome-regulating mechanisms attractive therapeutic targets. However, drug discovery in this space is hampered by how laborious and time-consuming it is to obtain enough chromatin with varied modifications for the necessary screening experiments.

Dao’s lab pioneers methods to create nucleosomes and chromatin synthetically, rather than by painstakingly extracting them from cells. “To mimic the diverse chromatin landscape in cells, we want to examine chromatin regulation using as many flavors of histone modifications and DNA sequences as possible,” Dao says. “However, traditional methods are much too time-consuming to make this feasible. Instead, we are developing methods to make chromatin from scratch in only 30 minutes, cutting out a week of tedious purification and manipulation.” These synthetic nucleosomes are made in part by chemically synthesizing short peptides and then linking them together through a process called native chemical ligation. 

Having more well-defined nucleosomes makes understanding the impacts of modification more accessible, meaning Dao has increased scientists’ capacity to screen and identify useful compounds that target chromatin-based processes. “We think that this is going to be a game-changer for accelerating the high-throughput biochemical study of chromatin states and drug discovery,” Dao says. “Now we can shorten that discovery step into a reasonable time frame, which will accelerate the entire process.”

Chemistry as the producer

Using chemistry to optimize processes is central to the research of Daniel Blair, PhD, Department of Chemical Biology & Therapeutics. In Blair’s lab, chemistry functions as the producer, striving to solve problems with ever-increasing speed and efficiency. 

Quantity is one such problem, as large numbers of diverse chemical compounds are necessary for an effective drug screen. “Even amongst the many hundreds of thousands of molecules we have in the St. Jude compound collection, there’s a significant amount of untapped functional potential in all of those other molecules that you could make,” Blair explains. “We recognized early on that the major bottleneck throttling our capacity was analyzing what we had made.”

Published in Nature, Blair and his team addressed this by focusing only on a few known molecular fragments to simplify the identification of new chemicals. “Instead of having to create thousands and thousands of individual analyses, we could simplify that to a small handful, tens or hundreds at most, to create thousands of different molecules,” Blair says. “Being able to explore these molecules increases our access to large swaths of different types of chemicals.”

With their new analytical capabilities, the Blair lab synthesized 5,000 new chemicals, using 20,000 chemical reactions, while cutting their analysis from about two months to a single day. It was vital to make screens as reliable as possible, as the analysis can be performed before the compounds have a chance to decompose. “This strategy was really impactful in advancing our ability to search through molecules,” Blair says.

Blair plans to speed up chemical production and analysis even more. He cites one example of an experiment that would traditionally take 42 days, but could now be condensed to just seven hours. “Things that would otherwise be unimaginably cumbersome and take anywhere close to a third of a year of total analysis time, we don’t really bat an eyelid about doing now,” he says.

Chemistry as the screenwriter

All productions need a purpose, however. As Blair puts it, “It’s all well and good making lots of molecules, but if you haven’t got something to do with them, you’ve just made a lot of stuff.” Chemistry must also act as a screenwriter, exploring the potential for new stories, mechanisms and biology.

Tommaso Cupido, PhD, Department of Chemical Biology & Therapeutics, exemplifies this function particularly well. Cupido and his team are interested in inhibiting a class of enzymes called the DEAD-box RNA helicases, which are collectively involved in many steps of RNA processing and protein assembly. “These motor proteins are at least as old as cellular life and haven’t changed all that much in about 1.5 billion years of evolution,” Cupido says.

Cupido’s current focus is on a specific helicase that is a potential therapeutic target in pediatric cancer. However, finding a molecule that would be selective for just one of these enzymes has traditionally been exceptionally challenging. This lack of historical success meant Cupido and his team were forced to flip the script. 

“We had no idea what a molecule that targets these proteins would actually look like, and no structural information on how a compound would bind,” he explains. “There was no way for us to build on similarity to other molecules, which is the classical way to do it.”

Instead, the researchers looked to exploit a previously unknown aspect of the protein’s function, and in so doing, develop a new mechanistic story. “These proteins are extremely dynamic, so they adopt different shapes as they go through their activity cycles,” Cupido explains. “We told ourselves, maybe that’s what we have to pay attention to.”

The team screened relatively few compounds, but emphasized chemical diversity —  variety in the shapes, sizes and composition of the chemicals in their screening library. The more diverse compounds one screens, the greater the potential for finding a molecule with a new mechanism of action, or that acts on something that has never been targeted before. Eventually, this strategy paid off, and the researchers found a compound that targets a previously unknown state of the enzyme.

Like all first drafts, this hit compound was not perfect, but it gave Cupido and his team a starting point for further refinement. “This molecule is not great at all, it’s terrible in the beginning, but that’s the whole idea,” he says. “It gives us a chance, because the mechanism supports having selectivity and being able to target a dynamic protein.” Now with a promising molecule in hand, researchers can adjust its structure and activity to explore its biological story fully.

Together, these research efforts demonstrate the power of chemistry to drive drug discovery behind the scenes. Between making and analyzing vast collections of molecules, developing more efficient and accurate methods to find desirable compounds, and delving into their biological stories, chemistry does it all.

Lights, camera, (mechanism of) action!