Hitting difficult targets with Affimer® technology

Despite having undoubtedly advanced life science research and disease treatment, antibodies are inherent with a number of issues which all too often fail to produce effective affinity reagents. Affimer reagents has been designed to overcome many of these problems. They show a greater range of pH and thermostability than antibodies, are smaller in size, and can be generated far more rapidly. Due to the failings and inability of previous affinity reagents to specifically target certain proteins much of the proteome is simply not investigated. One study found that of 20 million papers published between 1950 and 2009 more than 75% of protein research focused on just 10% of the proteins (link is external) that were known before the human genome was mapped. With research in such large areas of life science being stalled or neglected due to the lack of appropriate probes to target such molecules, the ability of Affimer reagents and biotherapeutics to shine a light on these until now ignored research avenues, offers new scope for understanding and the development of new solutions in biotechnology.

We have already created Affimer reagents to key targets in the ubiquitin proteasome system, to ubiquitin (link is external)itself and the K48 di-ubiquitin (link is external) linkage, and to the K6 (link is external) and K33 di-ubiquitin (link is external) linkages, to which there are no equivalent antibodies available. Targeting Affimer technology to the previously ‘impossible’ targets of the ubiquitin system opens up the possibilities of exploring these atypical ubiquitin chains to understand their intracellular function in health and disease. Ubiquitin chains, as there name suggests, are indeed ubiquitous within the different cells of the body and defects in the control mechanisms governing the ubiquitin system are associated with cancer and many other diseases. Yet despite their ubiquitous expression, chemical probes that target and can act to inhibit the molecular components of this system have not been available to researchers before, and have therefore prevented their investigation and hindered the progression of pharmaceutical products based on these targets into the drug pipeline.

The power of our Affimer technology has been further demonstrated in the development of binders to small molecules. Compounds with low molecular weight are not typically immunogenic, thus necessitating their conjugation to a carrier protein in order to raise an immune response and generate antibodies to the target. Unfortunately, the use of carrier molecules often results in the resulting antibodies being specific to the hapten-carrier molecule linker region rather than to the desired hapten. As Affimer technology is developed wholly in vitro it does not rely on an animal’s immune system and so targeting small molecules is not a problem. Screens against the anti-fungal agent posaconazole were able to identify a number of Affimer reagents that were all specific to this target yet showed a range of affinities. Additionally, we have developed Affimer proteins to peptide structures that are able to specifically distinguish between over twenty different peptidomimetic structures that vary only by side chains.

Up until now the lack of tools available to analyse these difficult targets has precluded researchers from studying them. The emergence of Affimer technology to enable researchers to investigate proteins of interest rather than examine proteins to which antibodies can be targeted has the potential to advance areas of research that have either been stranded or neglected due to the inability or deficiencies of exisiting affinity reagents, such as antibodies and aptamers.

hitting difficult targets with Affimers - data

An Affimer was generated to the small molecule fungicide posaconazole by binding it to a surface using a linker during screening. From eight candidates, seven were specific to posaconazole and not to the similar structured voriconazole, nor to the linker that was used. Affimer four in this screen showed no binding to the target.