An On/Off Switch for Drug Design

In theory, aptamers can specifically bind and modulate the activity of any protein for which they're designed.

Mar 28, 2005
David Secko(

© 2004 Nature Publishing Group

The aptamer binds to activated factor IX preventing proteolytic cleavage of factor X. In the presence of antidote, the aptamer is released from factor IXa. The aptamer is stabilized by a 3'-3'-linked deoxythymidine at the 3'-end and by 2'fluoro-2'deoxy modifications at every pyrimidine residue. It carries a cholesterol modification at the 5' end to increase plasma residence time. (From M. Famulok, Nat Biotechnol, 22:1373–4, 2004.)

In theory, aptamers can specifically bind and modulate the activity of any protein for which they're designed. Aptamers fold into three-dimensional structures, based on their oligonucleotide sequences, and like antibodies specifically target proteins, distinguishing them from antisense or RNA interference (RNAi). Currently, at least 23 aptamer-based therapeutic agents are under clinical development.1

"There is a huge potential in aptamers," says Bruce Sullenger of Duke University Medical Center. But like other oligonucleotide-based therapies, they do not cross cell boundaries very well, can be easily degraded, and may have short half-lives in the body. Nonetheless, their specificity, non-immunogenicity, temperature insensitivity, and the in vitro chemical selection process used to create them, have made the preclinical development of aptamers for niche markets appealing.

Another unique feature is now adding to the aptamer allure, namely the development of aptamer-antidote pairs. An oligonucleotide complementary to an aptamers' sequence can bind and inhibit aptamer function. "What I like about this concept is the logic that is behind aptamer-antidote pairs," says Michael Famulok, professor at the University of Bonn in Germany.


Sullenger and his colleagues have been working on a drug-antidote pair for anticoagulants. Requiring delicate balance between effective dose and overdose, anticoagulants are used after injury, surgery, or stroke, but dangerous side effects such as excessive bleeding may require blood transfusions. Heparin, now more than 70 years old, is still the most widely used anticoagulant today, because it has an antidote (protamine). "We have been very slow to progress towards new anticoagulants," says Edward Tuddenham, professor at Imperial College London.

In 2002, Sullenger, Christopher Rusconi (also at Regado Biosciences, Research Triangle Park, NC), and colleagues at Duke used systematic evolution of ligands by exponential enrichment (SELEX) to design an aptamer against coagulation factor IXa.2 The aptamer, called 9.3t, binds factor IXa and blocks the next step in the proteolytic cascade leading to clotting. The group has been able to extend the molecule's meager half-life to 1–1.5 hours in vivo in swine by adding a cholesterol group to its 5' end. But perhaps most importantly, the team developed an antidote to 9.3t, called 5-2, which can reverse more than 90% of 9.3t's activity in swine in 10 minutes. This reversal lasts at least one hour.

For now, aptamer targets are relatively limited, says Famulok. "I think that the first and maybe second generations of aptamer-based drugs will be restricted to extracellular targets," he says. Both Tuddenham and Famulok say the methodology for making aptamers should be applicable to other clotting factors and clinical drug targets in general. Indeed, aptamers are being designed to combat viral infection, inflammation, and angiogenesis.


Other proteins for which aptamers have been developed include E2F, components of HIV, and vascular endothelial growth factor (VEGF).1 In December 2004, the US Food and Drug Administration approved Macugen for treating macular degeneration. Developed by the New York company Eyetech in conjunction with Pfizer, Macugen is an aptamer against VEGF – an extracellular target that is well suited to inhibition – and it is the first aptamer-based drug to be approved. "We are excited about aptamers as a platform and want to make more," says Anthony Adamis, chief scientific officer at Eyetech.

Another aptamer, edifoligide (E2F decoy), is in Phase III clinical trials with Corgentech in San Francisco. Edifoligide is designed to inhibit E2F, which regulates cellular proliferation, and it is being used to prevent an increase in cell number during vein grafts (intimal hyperplasia),3 a leading cause of death after bypass surgery. The results of the Phase III trials are due out in a few weeks, says Michael Conte, from Brigham and Women's Hospital in Boston, who is running the trial.

Although aptamers are still expensive to make, the ability to use SELEX to evolve highly specific aptamers to chosen drug targets, and then pair these aptamers with antidotes, means that they can fill therapeutic needs where other techniques have failed, says Sullenger. Adamis agrees: "I think aptamers will turn out to be an important new class of drugs, similar to what antibodies are now."