Synthetic DNA provides a safer blood clot treatment

As a key ingredient in PCR, short synthetic strands of DNA have helped revolutionize diagnostics. Keitaro Yoshimoto spent his years as a graduate student in molecular chemistry studying DNA’s potential as a bioanalytical reagent. However, when he started his lab at the University of Tokyo, Yoshimoto shifted focus: He wanted to see whether he could use synthetic DNA to design therapies as well.

Now in a recent study published in Molecular Therapy Nucleic Acids, Yoshimoto and his team used synthetic DNA strands known as aptamers to treat blood clots more effectively and safely than currently available treatments (1). His work could potentially lead to the first aptamer-based blood thinner to reach the market.

A man with black hair and a goatee, wearing a gray blazer over a checked button down. Trees and buildings are in soft focus in the background.

Keitaro Yoshimoto studies aptamer drug design at the University of Tokyo.

Credit: Keitaro Yoshimoto

Often life altering and potentially life threatening, blood clots have been the focus of aptamer drug development since scientists first conceived of aptamers (2). Whereas existing blood thinners run the risk of causing excessive bleeding and staying in the bloodstream too long, aptamers can bind their targets reversibly, and as DNA molecules, they are much easier to clear. Researchers have spent decades designing aptamers that bind thrombin, a serine protease that converts a blood-borne fibrinogen to a more gel-like fibrin and ultimately causes blood to clot. However, thrombin-binding aptamers have yet to make it through clinical trials.

According to Yoshimoto, this was partly because of the aptamer design process. When he first started his lab, the standard filtering protocol wasn’t robust enough. “Nonspecific binders [could] also be mixed into the samples. It [was] very difficult to identify good aptamer candidates,” he recalled. He spent his first few years improving the design process in the hopes of making a better thrombin binder. Ultimately, his team produced a uniquely-structured aptamer that bound more tightly to thrombin and prevented blood clotting in vitro for twice as long as previous attempts (3,4).

Without much experience in clinical research, Yoshimoto had to find an external collaborator to test his new aptamer in vivo. “That was our first trial: to make human communication,” he joked. Eventually, an invitation to speak at Nara Medical University (NMU) led him to NMU hematologist Asuka Sakata . “As I get older, I feel more and more richly that networking and human nature are important for researchers,” Yoshimoto said. “The most important point is to find a good collaborator.”

Yoshimoto was disappointed with the first in vivo experiments, where he and his collaborators compared their drug to the existing blood thinners argatroban and bivalirudin. “Our aptamer drug activity was higher but not so dramatically higher,” he said.

As I get older, I feel more and more richly that networking and human nature are important for researchers… The most important point is to find a good collaborator.
- Keitaro Yoshimoto, University of Tokyo

While looking for ways to improve this, Yoshimoto’s team came across previous work on bivalent aptamers, where researchers had used a non-aptamer DNA polymer to covalently link two aptamers, each targeting a distinct region of a target protein (5). They looked for thrombin binders that targeted other regions and found Thrombin Aptamer 29 (TBA29), which bound to a region on the side opposite their aptamer’s binding site. They linked TBA29 with their aptamer using different linkers, ultimately designing a collection of four bivalent aptamers. Both in human plasma and in their in vivo mouse model, their bivalent aptamers bound to thrombin 100 times more tightly and prevented blood clotting for up to 100 times longer than existing treatments.

“Bivalent aptamers have not been used in vivo before, and [Yoshimoto’s] show great performance,” said Günter Mayer, who was involved in the development of the first bivalent aptamers (5). Mayer is a chemical biologist at the University of Bonn and was not involved in the study.

Yoshimoto’s team compared their aptamers with Mayer’s and found that theirs prevented blood clotting twice as long. “I wish that we would have done [Yoshimoto’s experiment] before with our bivalent aptamers, but not every single step [can be done] at a time,” said Mayer.

Finally, Yoshimoto and his team successfully reversed the effect of their aptamers to allow blood clotting by introducing the complementary sequence of DNA. This was important because existing blood thinners can cause fatal excessive bleeding in a condition called heparin induced thrombocytopenia (HIT). Treating HIT typically requires an entirely separate drug. “This is a major advantage of aptamer drugs,” said Yoshimoto. “Once the aptamer is obtained, the complimentary chain can be used as a neutralizer.”

“Our [lab] members were very happy, but I am not satisfied with this situation,” said Yoshimoto. He expressed concerns about the bivalent aptamers’ half-lives, which showed little to no improvement over their unmodified aptamers. “We have to improve the aptamers’ performance, aptamers’ characteristics, to increase aptamer presence in the drug field.”

Yoshimoto’s team at LinkBIO is working to bring their bivalent aptamer drugs to market. He explained that this will be a tremendous challenge. In the 30 years since researchers began to work with aptamers, only two aptamer drugs have made it through clinical trials to approval, neither of which are thrombin binders. Ultimately, Yoshimoto hopes to show aptamers’ worth as a viable drug class. “This is my next objective: to improve the aptamer impression in the medical field,” he said.