On aptamers

OK, so it’s been awhile. I busted my arm, which made typing modestly difficult. I’ll gear up here with an easy (but still hopefully meaningful) one:

The word ‘aptamer’ comes from the Latin ‘aptus,’ to fit. Thus, this was meant to be a polymer (incongruously Greek) that ‘fit’ to its target. Of course, the origins of this word are not nearly as rational or pedantic as we like to make it seem. We’d developed in vitro selection methods (as had Larry Gold and Craig Tuerk), and were attempting to do some marketing. I have always liked inventing words (and concepts, although the precedence of one over the other is surprisingly random), but I must say I’m a bit of a piker at it. At the time I had a good friend, Nina Tovish, who regularly thrashed me, badly, in Scrabble. As a Yale Literature major, she is a true wordsmith. And thus it is that I formally credit Nina with the origin of the term ‘aptamer,’ although it is entirely possible that my memory is faulty and either Dave Bartel or Rachel Green did the honors over bridge one evening. Someone should now update Wikipedia, as my Blog undoubtedly counts as a verified ’source’ of information. The Internet looks into the void and sees itself. Anyway, I should point out that Nina’s word is much better than my front-runner, which was “Clingon,” and better still than the replies we got when we first started using it. “Adaptamer?” people would say.

I still like the term much better than “SELEX,” which is what Craig and Larry called the process of in vitro selection (when it wasn’t being called the Tuerk-o-matic). SELEX always sounded to me like something that you’d see on the back of a cereal box. Both words have now enjoyed a long run in the literature, while ‘aptazyme’ has generally faltered and been replaced by ‘riboswitch’ (good job, Ron Breaker).

Naming aside, and for those who did not know at the outset of this drabble, aptamers are selected nucleic acid binding species, the nucleic acid equivalent of antibodies. You take a large pool of random sequence information (often upwards of 10^15 species, dwarfing the diversity of the human immune system, at least in terms of numbers) You can select for one or more of these diverse species to bind to a thing, where the thing has been as small as zinc and as large as a rat tail. Having bound, the species can be eluted and amplified by traditional molecular biology trickery: reverse transcription, PCR, in vitro transcription. Multiple cycles of selection and amplification lead to the purification of those binding species with the highest affinities and specificities.

It is a cool technology, if I do say so myself. And all kudos go to Jack Szostak, who believed in it even when I didn’t. But in the end, all technologies must be brought to account, and one has to ask: what are aptamers good for? The answer is: so far, not much. They have an awesome research track record, and an absolutely shitty commercialization track record. One can argue over the scientific and / or business reasons for this, but to my mind the bottom line is this: aptamers aren’t as good as antibodies. My lab now works on both, often side-by-side, and I must say that antibodies kick ass. They bind roughly 10- to 100-fold better than aptamers in many cases, and work consistently under a variety of conditions. You can tout advantages for each (aptamers are smaller and more penetrable; aptamers can be reversibly denatured; aptamers are synthetically accessible, aptamers can be programmed to undergo conformational changes. In contrast, antibodies often have less background binding; antibodies frequently recognize denatured epitopes; antibodies can be easily adapted to standard analytical formats, like ELISA; antibodies can be raised against a greater range of targets). For different applications you can choose your poison. But in the end, antibodies bind better, and mostly that’s what makes the difference.

Until now.

I sometimes think that I’ve had a long-running feud with Larry Gold, but really it’s just a long-running conversation that sometimes gets testy. And I must say that Larry has now done something quite remarkable that gives aptamers a new life. You have to ask, why is it that antibodies are so much better than aptamers? The answer would likely be: they have more chemistry available to them. Cysteine has a sulfur; the branched chain amino acids provide many opportunities for specific hydrophobic interactions; lysine, arginine, an histidine bear positive charges that no self-respecting nucleic acid would countenance. Recognizing this, Bruce Eaton and others started years ago to develop amino acid-like nucleotides, where the nucleobases had side chains somewhat like the amino acids. This has finally reached an apotheosis in which Somalogic, the latest incarnation of an aptamer company, has developed literally thousands of aptamers with modified nucleotides that bind to their targets in the low nM to pM range. (see, for example, Gold et al. (2010), PLoS One, 5:e15004). And a shout-out to my pal Marty Stanton for the pipeline; awesome!

Thus beginneth the Second Coming of Aptamers. I would argue that the new side chains put aptamers on par with antibodies, finally, and that it is now a horse race. Now, business or other considerations may still handicap that race in various interesting ways, but at least the fundamental chemical properties of a replicating polyanion are not the limiting factor. From a biodefense point of view, this Second Coming should have an interesting impact. Like everything else in the defense community, aptamers fall in and out of favor as various generations of Program Managers come and go (the question of why there is no corporate memory in defense-related research can wait for another day). We’re probably on, what, the third cycle of favor now. But in part because the United States is so very good at turning its research apparatus on a dime, we’re bizarrely behind other countries that are still bullish on aptamers … because they paradoxically never really had the chance to be disappointed in them. In particular, I’m going to retire to Korea, not just because it is an amazingly beautiful country, but because I could probably live off of giving testimonials to the various institutes that work on aptamers. The increase in publications on aptamer biosensors from China is also stunning / staggering, depending on my mood.

It’s not clear who will win the horserace (either between biopoymers or countries), but it should be fun to watch and participate. Proteins have alot of tricks up their sleeves still, some of which I hope we’re going to help invent. But in the end, the Second Coming may not go to the swift, but to the greedy: the old aptamer patents have about reached their limits, and the new frontier will be the composition of matter surrounding the side chains. Somalogic has its favorites, but there’s still alot of chemical territory to be covered. And as I previously speculated regarding novel base-pairs, it’s possible that there will be patents that have national security implications, where the composition-of-matter of coveted side chains are owned by a single company or entity that excludes practice by others.


- originally posted on Sunday, March 6th, 2011