Affibody Molecule Discovery and Uses

Affibodies are small molecules that have a high affinity towards a specific protein target. These useful molecules have applications in therapeutics, diagnostics, and biotechnology.

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Structure of an affibody

Affibody molecules consist of a three-helix bundle and the structure is similar to the IgG-binding domain of Protein A. Protein A is a protein which is present on the surface of the bacterium Staphylococcus aureus which binds to IgG.

Affibodies comprise 58 amino acids, and variations in 13 of these amino acids creates a large number of ligand variants in the affibody library. It is a relatively short peptide and the kinetics of its folding reaction are very fast.

Although affibodies mimic monoclonal antibodies, their size is significantly smaller than antibodies; an affibody is  6kDa, while antibodies are 150kDa. Despite its smaller size, the binding site and affinity of an affibody is similar to that of an antibody.

Advantages of affibodies compared to antibodies

Affibodies are simpler and smaller than antibodies, and are also more physically resilient. Affibodies can bear wide range of extreme variations in pH and temperature, making them more reliable for researchers. They can also fold within a cell. In this way, affibodies can conjugate with matrices, giving them applications in several fields, including affinity purification, protein detection, and sample preparation.

What are the therapeutic applications of affibodies?

Targeting payloads

An example of a payload is immunotoxins, which are hybrid proteins with an affinity moiety, mostly fragments of antibodies, and a toxin domain, from either bacterial or plant toxin. An immunotoxin construct containing a bacterial toxin and HER2 targeting affibody was created, as the toxin had been shown to have a therapeutic effect.

The inhibitory effect of this immunotoxin was analyzed in cancer cell lines that express different levels of HER2 on the cell. It was found that even 1pM of the immunotoxin was sufficient to suppress the synthesis of HER2 protein.

Redirecting particles

To increase the efficacy of a targeted drug, several drug molecules can be combined using particles. These particles consist of polymers, vesicular components, or viral particles. Due to the properties of affibodies, they can provide particles with specificity and affinity towards specific targets. Affibody along with chemical co-polymers can give rise to nanoparticle bioconjugates to target tumor cells.

A study found that particles carrying a cancer drug with an affibody targeting HER2 showed that the use of these targeted particles led to an increased uptake of the drug as well as increased cell killing in vitro.


Liposomes are small vesicles which can be used to carry drugs. . Using this method, the drug can be protected from elimination and degradation.

A recent study showed that affibodies can be used to target liposome to specific cells, by the use of a PEG moiety. This makes it easier for the affibody to integrate with the cell membrane. In the study, a cancer drug encased within a liposome was targeted successfully to tumor cells expressing EGFR, again leading to increased uptake and death of targeted cells.

Viral particles

Viruses, such as human adenoviruses have been used as vector for gene therapy in cancer. To improve their therapeutic potential, their binding properties need to be mutated to generate new specificity. Affibodies can be employed as retargeting ligands as they can fold correctly even in the reducing intracellular regions. Several studies have re-targeted viruses using affibodies.

Can affibodies be used in biotechnology?

Affibody can be used in affinity chromatography to purify proteins or target proteins, such as apolipoprotein, Taq polymerase, recombinant human factor VIII, or G protein of respiratory syncytial virus. They can be used to deplete human proteins, amyloid β peptide, human IgA from human serum, cerebrospinal fluid and plasma.

Affibodies have also  been used as affinity probes in micro-arrays of proteins. Another use of affibodies are as biosensors in FRET-based assays.

In one study, two different affibodies were used which had different affinities for human IgA and IgG. The target protein was then added to this mix, which subsequently bound to the protein. This resulted in a shift in the fluorescence and reduced FRET between acceptor and donor molecule.

Further Reading

Last Updated: Nov 21, 2018

Dr. Surat P

Written by

Dr. Surat P

Dr. Surat graduated with a Ph.D. in Cell Biology and Mechanobiology from the Tata Institute of Fundamental Research (Mumbai, India) in 2016. Prior to her Ph.D., Surat studied for a Bachelor of Science (B.Sc.) degree in Zoology, during which she was the recipient of an Indian Academy of Sciences Summer Fellowship to study the proteins involved in AIDs. She produces feature articles on a wide range of topics, such as medical ethics, data manipulation, pseudoscience and superstition, education, and human evolution. She is passionate about science communication and writes articles covering all areas of the life sciences.  


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