Molecular Engines for Drug Synthesis

by Laura DeMassa ’21

Ithaca reminds Sophie G. Bender of her undergraduate years in Portland, Oregon: the good beer, quality coffee, and green trails—all of which owe their existence to the tireless labor of enzymes, the huge proteins that catalyze chemical reactions such as fermentation and photosynthesis.

“Enzymes are nature’s perfect little chemistry machines,” says Bender, a PhD student. “When a new, small molecule is added to an enzyme, so much can change from the resulting cascade of different protein interactions. Enzymes are unparalleled in their ability to carefully control the orientation and reactions of different molecules. With the right enzyme, you could make an otherwise very difficult reaction relatively easy.”

Enzymes have striking potential for medicine, Bender explains. Currently, it is uncommon for enzymes to be used in organic chemical reactions, such as those required for making medicine. Working in the lab of Todd K. Hyster, Chemistry and Chemical Biology, Bender aims to demonstrate the advantages of using enzymes in drug synthesis.

In traditional methods, molecules would be placed in a soup-like solution, and lab scientists would wait for them to collide or fragment to form the desired compound. With the advancement of modern medicine, greater precision and control were needed, and scientists began using catalysts—molecules that help position or orient the building block molecules to react more easily. Some catalysts are made using costly metals; and although they are effective, even these catalysts may rely on the building block molecules to tumble around and eventually bump into one another: an improvement, but one that still offers only a limited amount of control.

The Hyster lab hopes to achieve greater control by using enzymes as the catalysts that prompt reactions, a process called biocatalysis. Enzymes can precisely and quickly stitch or sever molecules for new drugs.

“We are trying to develop a set of tools that a pharmaceutical chemist could use to create new or modified drugs and mass-produce them. Our job is to find or design the right enzyme for a reaction and make it the best it can be at doing that reaction, so that eventually someone who needs that specific reaction to happen can turn to our work for the answer,” Bender says.

Using Enzymes to Synthesize Compounds

Enzymes are huge complexes of amino acids, made primarily of carbon, hydrogen, oxygen, and nitrogen, that are linked in long chains. The amino acids in a single enzyme may differ widely. Some are drawn to water, others are oily and hydrophobic. Some carry a positive charge, others are negative. The resulting attractions and repulsions cause the long chain of amino acids to fold over and into itself. As the molecule clumps up, certain amino acids pull together around a pocket—the enzyme’s active site—where molecules can attach, spurring a reaction.

“Our job is to find or design the right enzyme for a reaction and make it the best it can be at doing that reaction, so that eventually someone who needs that specific reaction to happen can turn to our work for the answer.”

The enzyme’s scaffolding of amino acids cradles incoming molecules in its pocket and holds them in such a way that dictates how the reaction will proceed, Bender explains.

By feeding specific DNA sequences to Escherichia coli cells, Bender grows many iterations of an enzyme with variations in its amino acid chain. In a process called site saturation mutagenesis, she makes ever-so-slight changes, like small mutations, that might increase the enzyme’s ability to catalyze. Once she has an advantageous mutation, she will compound the next, creating a double and then perhaps a triple mutation. Mutations may affect a variety of the enzyme’s qualities: its stability, its three-dimensional shape, or how it absorbs light. In effect, she mimics evolution to create an enzyme that is increasingly efficient at transforming the starting material, or molecules, into a desired product. The increased control and precision afforded by the enzyme’s genetically modified scaffolding ensures that the correct compound is synthesized.

Moreover, the Hyster lab has demonstrated that light can enable enzymes to perform novel functions. “We find that they can do unusual chemistry that is not seen in nature,” Bender says.

The Hyster lab experimented with shining light on Gluconobacter Ene-Reductase, or GluER, an enzyme that typically breaks double bonds into single bonds. The researchers found that light prompts GluER to have a larger repertoire of abilities, such as pasting molecules together and placing them into ring formations.

“Some of these transformations were entirely unknown and could open up new paths to making very difficult molecules and compounds,” Bender says.

These insights could prove indispensable for pharmaceutical chemists developing and mass-producing new drugs.

Building the Hyster Lab at Cornell

Bender first joined the Hyster lab in August 2020 when it was located at Princeton University. Six months later, the Hyster lab moved to Cornell and Bender chose to move as well, helping build the lab from a pile of boxes in Baker Laboratory.

“It felt very empowering to be one of the people who was trying to build our new space and deciding what all our new systems would look like,” Bender says. “It made me feel like an integral part of the lab.”

Bender’s work in the Chemistry and Chemical Biology department at Cornell extends beyond her lab work. She taught undergraduates in the lab section for “CHEM 2510: Introduction to Experimental Organic Chemistry” during her first semester on campus.

“I love teaching, and I want to teach chemistry for the rest of my life,” Bender says. “I love the process of breaking down an explanation so you know that somebody, even if they do not quite get it yet, they feel like they can get it.”

The Hyster lab has also taught Bender about how she meshes in collaborative settings.

“I have learned a lot about how I am as a team worker, getting to know everyone else in my lab and all their different ways of approaching problems,” Bender says. “No matter where I end up going in life, that kind of communication and interpersonal aspect of science is what keeps me going.”

Ultimately, Bender finds that her work with enzymes—feeding, testing, and monitoring them time and again—has given her an acute eye toward the nitty-gritty.

“I will forever be a better chemist because I have the knowledge of what is really happening granularly and what may be causing the problems I encounter,” she says.