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Predictive Reagent Antibody Replacement Technology

Periodic Reporting for period 2 - PRe-ART (Predictive Reagent Antibody Replacement Technology)

Reporting period: 2018-09-01 to 2020-02-29

Predictive Reagent Antibody Replacement Technology (PRe-ART) will create a foundational new technology platform to completely replace conventional antibody technology within medical diagnostics and basic life science research. In a multidisciplinary approach combining basic science, protein engineering and computational prediction, Pre-ART will generate non-antibody components which can be combined in an entirely modular fashion to create molecules that bind any peptide of choice. Such a biotechnological revolution is timely because of current failings in the reagent antibody market, after forty years still based on monoclonal antibodies (mAbs) to detect biomolecules, when 50% of all commercial reagent mAbs have been shown to not function correctly. By combining information science with directed evolution, PRe-ART will ultimately create an encyclopedia of predesigned and experimentally pre-selected modules (in a crude analogy, they can be thought of as biological Lego bricks) that may be combined, without any further experiment, to generate unique binding molecules that function as antibody replacements. It goes without saying that the conducted research takes deviations from this simple additivity fully into account.

Today, global spending on protein-binding reagents amounts to an estimated $ 1.6 billion worldwide, of which $ 700 million occur in the US. As only half of all antibodies are validated and functional, $ 800 million and $ 350 million respectively are misspent. We estimate that 50% of these reagents are used in public research institutions and the other 50% by private companies. Europe's pharma and biotech industries and renowned research institutions would enormously benefit from a technology that will increase quality of all detection reagents, and standardize and customize their production. Thus, PRe-ART has the potential to take over leadership in delivering protein-binding reagents for research in Europe, the US and beyond.
Significant progress could already be reached in four important areas.

First, in the structure determination of the scaffold. Many crystal structures have been determined which confirmed the general strategy of designing a stable scaffold which can be modified. Therefore, the fundamental building blocks exist, and this could be structurally verified.

Second, in the synthesis of new libraries. Using proprietary know-how, new libraries with carefully biased residue statistics were designed, produced, verified, characterized and successfully implemented in the next steps.,

Third, in developing selection technologies. While all three selection technologies, phage display, ribosome display and yeast display were investigated initially, yeast display was found to suit the project needs best. A very important break-through was reached in the first part of this project in that a novel method could be established which directed selection to the affinity of one single amino acid side chain.

Fourth, in computational design. A very important break-through was reached by creating a browsable atlas of related scaffold proteins, thereby accessing a wealth of structural data. This valuable resource can now form the basis of next-generation designs.
Reproducibility of biomedical research is in a crisis, a phenomenon affecting society as a whole, and poor reagent antibodies are a big part of this. As mentioned in the introduction, the situation with traditional monoclonal antibody detection reagents is not sustainable, as enormous amounts of public and private money are wasted on ill-characterized, non-renewable and poorly performing reagents. Moreover, the downstream costs of research, which cannot be reproduced based on such antibody data, has not even been taken into account. While recombinant reagents (with a defined sequence) have solved the first problem of molecular definition, they have not addressed the problem of the tedious individual generation of each reagent by individual panning experiments.

The PRe-ART vision is that mAbs for many applications in biological research will be replaced over the course of a decade by these designer molecules, with the potential to completely disrupt the industry selling low-quality commercial animal-derived reagent antibodies, and thus create a major new technology for biological research.

Thus, PRe-ART will ultimately contribute not only to the health and well-being of the EU citizen through improved diagnostic capability, but also to the economy of the EU through the development of myriad detection products, enabled by this foundational platform technology. The interdisciplinary PRe-ART project will achieve this goal by bringing together three leading labs from different fields, two of which are lead by women PIs, whose joint efforts will achieve this breakthrough S&T target. The PRe-ART project thus closely addresses all specific challenges of the call.
Concept of modular binding