FINDing new drug leads faster with DNA nanotechnology

DNA nanoswitch platform rapidly searches large libraries for molecules that change how different proteins interact, introducing unprecedented functionality and efficiency into drug screening.

By Benjamin Boettner

(BOSTON) — Researchers at the Wyss Institute at Harvard University, Boston Children’s Hospital, and Harvard Medical School (HMS) have developed FIND, a drug discovery platform that searches large libraries for molecules that modulate binding interactions between two proteins. FIND uses DNA nanoswitches to select drug candidates based on their effects on these protein-protein interactions, rather than simply whether they bind to a single target protein, giving it a key advantage over conventional binding-based screening.

In a study published in Science, the researchers used FIND to discover both small molecules and nanobodies, small antibody-like proteins, that promoted particular protein-protein interactions with relevance for different disorders.

Proteins often work by binding to other proteins, and changes in these interactions can contribute to disease. Such protein interactions are also targeted by some of the most successful drugs. For example, the diabetes drug Ozempic mimics the natural GLP-1 hormone and activates its receptor, helping regulate blood sugar and reduce appetite; and inhaled albuterol activates beta-2 adrenergic receptors on airway muscle cells, triggering signals through associated G proteins that relax these muscles and open the airways.

Many conventional drug screens test compounds individually in multi-well plates, with instruments measuring changes in purified proteins or cells. Pooled screens of encoded compound libraries can search much larger collections, but most conventional methods only identify molecules that bind to a target.

“Our idea was to build each experiment onto a single DNA molecule, so that many experiments could run in parallel in one tube,” said senior author Wesley Wong, Ph.D., an Associate Faculty member at the Wyss Institute, Associate Professor at HMS, and Investigator at Boston Children’s Hospital. “This gives us a high-throughput way to search for molecules that change how proteins work together.”

From a single switch to a molecular switchboard

FIND, short for Functional Interaction-based Nanoswitch Discovery, builds on DNA nanoswitches, a technology that Wong’s group first developed for single-molecule measurements and then adapted into a gel assay in 2015. Wong, who co-leads the Wyss Institute’s Molecular Robotics Initiative, and co-first authors Clinton Hansen, Ph.D., and Mark Lipstein, Ph.D., subsequently advanced the technology for drug discovery with other scientists at the Wyss Institute. Their “Lab-on-a-Molecule” project was supported by Northpond Labs, the research-and-development affiliate of Northpond Ventures, through its strategic alliance with the Wyss Institute.

DNA nanoswitches are programmable devices made from long strands of DNA. They switch between a linear shape, in which two attached potential protein partners are unbound, and a looped shape, in which the two proteins bind and bring two points on the DNA together. Compounds that promote this interaction increase the fraction of looped nanoswitches. The team separated these shapes using gel electrophoresis, a standard laboratory method for distinguishing pieces of DNA with different sizes and structures. Looped nanoswitches moved more slowly through the gel than linear ones, allowing them to be collected separately. To develop FIND, the team attached a candidate drug molecule to each nanoswitch using a flexible linker, along with a nucleic acid barcode that identified the candidate.

“Each candidate stays linked to the result of its own experiment,” said Lipstein, who worked on the project first as a graduate student in Wong’s group and then as a postdoctoral fellow. “We can then separate the nanoswitches by their response and sequence the barcodes to identify the molecules that were selected.”

Finding new leads

As one example, the researchers applied FIND to PPAR-gamma, a diabetes drug target that helps regulate insulin sensitivity and fat storage. Using a screening process that began with a 400-million-member DNA-encoded small-molecule library, they identified compounds that promoted the receptor’s interaction with a fragment of its partner protein CBP. These compounds also increased lipid accumulation in cultured cells, consistent with PPAR-gamma activation. FIND was thus able to uncover new compounds that modulate complex protein-protein interactions with the potential to be further developed into medicines.

The researchers also used FIND to discover a nanobody that modulated the interaction between SARS-CoV-2’s spike protein and its receptor on human cells, demonstrating its utility for finding new research tools for studying disease. In addition, the team validated their new drug discovery approach by recovering a known beta-2 adrenergic receptor activator that had been added to a mixture of barcoded controls.

“We can directly search for molecules that have the effect we want on a disease-related protein-protein interaction,” said Hansen, who was a postdoctoral fellow on Wong’s team and continued working on the project as an Instructor at HMS. “The molecules we find could become starting points for developing new medicines or useful research tools for understanding diseases.”

The technology has recently been licensed to a newly formed startup cofounded by members of the research team.

“This DNA nanoswitch-based drug discovery platform developed by Wesley Wong and his team at the Wyss institute, Harvard Medical School, and Boston Children’s Hospital, offers an entirely new ultra-high throughput approach to discovering drugs that modulate the myriad types of biological mechanisms that regulation cellular function, but currently are out of reach for conventional discovery tools. The success of the FIND project is also a testament to what the Wyss institute’s collaborative powers and innovative partnerships can achieve,” said Wyss Founding Director Donald Ingber, M.D., Ph.D., who is also the Judah Folkman Professor of Vascular Biology at Harvard Medical School and Boston Children’s Hospital, and the Hansjörg Wyss Professor of Biologically Inspired Engineering at Harvard John A. Paulson School of Engineering and Applied Sciences.

Other authors on the study are Sarah Erlandson and Andrew Kruse of HMS; Tobias Schwalbe and Peter Gmeiner of Friedrich-Alexander University Erlangen-Nürnberg, Germany; and Sylvie Bernier of the Wyss Institute.

The work was supported by the Wyss Institute at Harvard University and Boston Children’s Hospital; the National Institutes of Health’s National Institute of General Medical Sciences (under awards #R35GM119537 and #F31GM128233) and National Cancer Institute (under award #R01CA260415); as well as Takeda Pharmaceuticals; the Arnold and Mabel Beckman Foundation; a Smith Family Award; the Deutsche Forschungsgemeinschaft; and the Elite Network of Bavaria.

The content of this release is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

PRESS CONTACT

Wyss Institute for Biologically Inspired Engineering at Harvard University
Benjamin Boettner, benjamin.boettner@wyss.harvard.edu

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The Wyss Institute for Biologically Inspired Engineering at Harvard University (www.wyss.harvard.edu) is a research and development engine for disruptive innovation powered by biologically-inspired engineering with visionary people at its heart. Our mission is to transform healthcare and the environment by developing ground-breaking technologies that emulate the way Nature builds and accelerate their translation into commercial products through formation of startups and corporate partnerships to bring about positive near-term impact in the world. We accomplish this by breaking down the traditional silos of academia and barriers with industry, enabling our world-leading faculty to collaborate creatively across our focus areas of diagnostics, therapeutics, medtech, and sustainability. Our consortium partners encompass the leading academic institutions and hospitals in the Boston area and throughout the world, including Harvard’s Schools of Medicine, Engineering, Arts & Sciences and Design, Beth Israel Deaconess Medical Center, Brigham and Women’s Hospital, Boston Children’s Hospital, Dana–Farber Cancer Institute, Massachusetts General Hospital, the University of Massachusetts Medical School, Spaulding Rehabilitation Hospital, Boston University, Tufts University, Charité – Universitätsmedizin Berlin, University of Zürich, and Massachusetts Institute of Technology.