Aptamers

Ashley Edwards

Molecular Machines FYS

Aptamers

Aptamers show important promise in the medical field; eventually they might be able to treat a myriad of diseases from macular degeneration to HIV to cancer. Already there are drugs on the market that utilize aptamers, and there are many companies that are starting to take interest in these new potential treatment options because they are highly specialized and can be custom-made in a mere matter of months to target almost any molecule in the body. Aptamers are similar to antibodies in that they target protein-protein interactions, but differ in how they are made, the functions they perform, and the way in which they are used in medicines today.

Aptamers are micromolecules made up of nucleic acid that bind to a specific target molecule. They work by disrupting a specific protein interaction by direct competition with what usually binds to the target protein. They use the full range of bonding methods that proteins use, including hydrophobic interactions, charge-charge interactions, and hydrogen bonding. Aptamers are chemically synthesized and combine the best properties of antibodies and small molecules such as chemical stability, high affinity, and low immunogenicity.

In order to make an aptamer, a pool of individual nucleotides is placed in a test tube with the appropriate RNA or DNA polymerase. Since the aptamers are made up of nucleic acid, they can be written out symbolically on paper in a series of letters representing the nucleic acid (adenosine, thymine, guanine, cytosine, and uracil), just like DNA and RNA. Aptamers have individual three dimensional shapes so that they can fit tightly to a receptor protein like a lock and key. Once you have an incredibly large group of aptamers (in the millions), they must be selected for the specific target protein. They can show high specificity for their target protein, and can therefore discriminate between similar proteins.

The Systematic Evolution of Ligands by Exponential Enrichment (SELEX) is the method used to select aptamers for the target proteins. First, a starting library of nucleic acids is incubated with the protein target of interest. Next, the aptamers that bind to the target, which is usually a protein, but can be almost anything (even ATP), are separated from those which did not bond. The aptamers that bind are then amplified to create a library with those specific aptamers. The process is then repeated, since originally multiple aptamers might bind to the target protein, but after a couple of trials, there will usually be very few that consistently bind. Antibodies, on the other hand, are biologically expressed and not chemically synthesized like aptamers are which makes them more expensive and does not provide them with high stability in harsh environments. Antibodies are also not usually tested intracellularly, which makes them more likely to change once they are inserted into the body. Aptamers work on the outside of the cells, which makes it easier for their environment to be controlled and makes them easier to make, whereas antibodies enter the cell and therefore create many more obstacles to consider.

Once an aptamer that will bind to the target molecule is found, it can be used in a practical manner. Aptamers are usually used for one of two things; either function-blocking or escorting. Function-blocking aptamers disrupt the protein interaction by direct competition and can therefore interrupt the process of disease. HIV, for example, uses TAR RNA to help replicate itself and recruit other cells. An aptamer that mimics the TAR RNA, can compete with it for binding positions on the tat protein, which is what the TAR RNA of HIV binds to. By sequestering the tat protein from the HIV RNA, the aptamer can inhibit the replication of the virus and slow down or even stop the progression.

Escort aptamers are designed to deliver radionuclides, toxins, or cytotoxin agents to diseased tissues. In order to make an escort aptamer, an existing aptamer that has been shown, through the SELEX process to bind to the target protein, is used. The aptamer is truncated in a way that it will still bind to the target protein but will not have any effect. On the truncated parts, it is possible to attach almost anything organic that will react with the cell. In this way, aptamers can deliver many different things to the outside of the target molecules. They also show great promise in this area because of their rapid blood clearance and their high level of adaptability. The rapid blood clearance helps aptamers quickly leave the body. In tissues, aptamers can accumulate into high concentrations because they are taken in rapidly and the tissues retain them very well. The aptamers have a high level of specificity; they can differentiate normal from abnormal tissues, which shows that they could be capable of targeting cancerous cells.

Already, Eyetech Pharmaceuticals has come up with macugen, which is FDA approved and takes advantage of aptamers in treating macular degeneration (the disease that destroys the vision in the elderly). The drug uses an anti-VEGF aptamer that binds to the VEGF 165 protein that signals the growth of abnormal blood cells in the eye. Macugen blocks the binding of the VEGF to its receptor, and therefore prevents the growth of abnormal blood cells that cloud vision.

Many other companies are working on using aptamers in their drugs as well. The leading company in aptamer research is Archemix, which holds a number of patents on aptamer technique, and therefore has made quite a few handsome deals with various drug companies such as Pfizer, Nuvelo, Elan, and Merck KGaA. Basically, Archemix uses SELEX to select aptamers that bind to the proteins that are involved in the diseases that the drug companies wish to treat. Archemix then gives the drug company the right to mass-produce and market the drug in exchange for research funding upfront and milestone recognition, along with more compensation if the drug does well on the market.

Archemix recently announced the initiation of a clinical trial for a new anti-platelet aptamer that stops platelet-dependent clotting in only the targeted sites of the body, while keeping the rest of the platelet clotting normal. This could potentially help patients with life-threatening thrombosis, which causes the formations of clots in the bloodstream, inhibiting the flow of blood in the circulatory system. The formation of clots in the bloodstream can cause strokes and if it goes untreated, can cause death. This breakthrough drug could have enormous potential if the clinical trials go well, and would help promote the use of aptamers in many more medications that treat many different diseases. Archemix’s cooperation with Merck KGaA is all about finding treatments and/or identification of cancerous cells. If aptamers could be used to target every type of cancer cell, then the terminal cases could decrease dramatically, if not disappear completely.

Obviously, aptamers are on the up-and-coming medicinal wave, and in another decade, it is quite possible that almost every new drug will be made from aptamers. They show great promise in binding to almost any target molecule, and once targets are identified for diseases, the selection process for aptamers can begin. Unfortunately, some diseases seem to be more complex, and therefore simple competition with the target site might not be enough to stop the progression. Hopefully though, aptamers can make a huge difference in the diseases that do have target cells, and also be a key component in identifying diseased tissue through its escort capabilities. Archemix has already made huge leaps in the field of aptamer drugs, and the contracts with various drug companies will provide them with enough research funding to continue finding aptamers that will work to combat some serious and common diseases.

Literature Cited

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