Periodic Reporting for period 1 - BiodeCCodiNNg (Decoding novel reaction chemistries in biocatalysis – Training Europe’s next visionaries for a sustainable future)
Période du rapport: 2023-01-01 au 2024-12-31
Enzymes are environmentally friendly alternatives to traditional chemical processes - contributing to the goals of the European Green Deal and Europe's transition to a sustainable bio-based industry. The mission of BiodeCCodiNNg is to train 10 Doctoral Candidates (DCs) with an out-of-the-box and entrepreneurial mindset to expand the repertoire of enzymes for industrial biotechnology. A particular focus is on novel reactions that are not accessible with the existing enzymatic toolbox. In order to achieve this, BiodeCCodiNNg will leverage the beyond-state-of-the-art knowledge generated on C-C bond forming enzymes (CCzymes), while filling current gaps and addressing the paucity of knowledge on the largely untapped family of N-N bond forming enzymes (NNzymes). The BIODECCODING Doctoral Network will train and educate Europe's next 10 visionaries for a sustainable future on cutting-edge enzyme technology centered around N-N and C-C bond formation, addressing technology gaps, practical challenges and exploiting synthetic opportunities with huge innovation potential. This PhD program not only provides in-depth training in an interdisciplinary working environment, but also strengthens transferable skills training with strong industry participation. The objectives will be achieved through an interdisciplinary consortium of 19 leading academic and private organizations, providing the ideal environment to foster complementary expertise in drug discovery, enzyme catalysis and process development.
BiodeCCodiNNG focuses on new concepts for interdisciplinary and intersectoral research projects around the promising enzyme classes of CC- and NNzymes. Since NNzymes have not yet found their way into industrial applications, the development of biocatalyst platforms for N-N bond formation reactions is one of the main objectives. In addition, BiodeCCodiNNG's DCs focus on important reactions that cannot yet be achieved with enzymes, such as the Morita-Baylis-Hillman (MBH) reaction or formylation reactions (biocatalytic counterpart of Friedel-Crafts acylation). Finally, the DCs aim to elucidate missing structural and mechanistic knowledge to guide engineering efforts towards promiscuous biocatalysts. This research is accompanied by specially designed training of DCs and dissemination of results to the scientific community and the public. The research is divided into three scientific work packages focusing on enzyme discovery and characterization (WP1), structure elucidation and enzyme engineering (WP2), and reaction engineering and biocatalytic applications (WP3). After the BiodeCCodiNNg consortium successfully recruited its 10 highly talented young scientists, the first phase of the individual projects was dedicated to the establishment of the experimental systems and the experimental proof of concept. The DCs showed remarkable progress in taking the first steps towards the elucidation of novel CC- and NNzymes for the targeted reaction scope. In addition, several secondments to the academic partner universities and industrial partners as well as intensive discussions at project meetings with participants from the private sector and the Industrial Biotechnology Cluster allowed a clear orientation of the research towards innovation and technical implementation. The joint supervision structure of the project provided a framework for highly interdisciplinary research at the interface of drug discovery, enzyme engineering & catalysis and process development. Work on the development of a biocatalytic toolbox has led to the identification of several novel CC- and NNzymes, obtained through genome mining combined with bioinformatic analysis and biochemical characterization, or through the engineering of known protein scaffolds that now give rise to promiscuous C-C bond forming activities. In addition, structural and mechanistic features of NN- and CCzymes have been elucidated. In the second phase of BiodeCCodiNNg, this knowledge will be integrated into engineering efforts to induce or enhance promiscuous activities towards N-N bond formation, Friedel-Crafts acylation, MBH-type reactions, and other C-C bond forming reactions. Finally, the first examples of biocatalytic cascades have been developed and proof-of-concept as well as important kinetic evaluations for further performance improvement have been obtained. In the second phase of BiodeCCodiNNg, this knowledge will be used to combine the reactivities of NN- and CCzymes in biocatalytic cascades to access multifunctionalized pharmaceutical precursors and to demonstrate the potential of newly developed biocatalysts.
The growing world population, which is expected to reach ~11 billion by 2100, will increase the demand for chemicals, such as aging-related drugs, by a greater number of consumers. Therefore, the need for high quality intermediates produced by environmentally friendly technologies with low carbon dioxide emissions will be manifold. To this end, the implementation of novel biocatalysts and methods that use fewer reagents than established methods, increase the reusability of biocatalysts and reduce waste generation will contribute to cleaner, safer and less energy-intensive production routes, thereby contributing in the long term to reduced carbon dioxide emissions from fossil-based feedstocks and less waste-generating industries. This is where BiodeCCodiNNg comes in: the results of the research are expected to provide novel methodologies for the creation of tailor-made biocatalysts for the production of a wide range of CC- and NN-bonded products, leading to a variety of industrially relevant compounds that cannot be realized with the currently known enzyme diversity. More than 80% of chemical products are produced by catalytic reactions. Thus, the benefits of identifying novel biocatalysts for C-C and N-N bond formation that are not yet accessible through enzyme catalysis are manifold. The holistic approach to the development of novel biocatalysts for the targeted C-C and N-N bond formation reactions requires the combination of expertise in synthetic biology, biocatalysis, enzyme and process engineering, structural and computational biology, chemistry, analytics, and process design.
An integral part of BiodeCCodiNNg is therefore the intensive interaction with the private sector to facilitate cross-sector discussions and the exchange of ideas through secondments to the various industrial partners. The first phase of BiodeCCodiNNg has already demonstrated the usefulness of native and engineered CC- and NNzymes for the targeted reactions to produce valuable drug building blocks, along with important optimization steps to improve the enzymatic reactions. In the second phase, we expect the interdisciplinary collaboration to increase our understanding of the underlying structural and mechanistic features that determine how efficiently the novel CC- and NNzymes perform the desired reactions, and how they can be engineered to further advance the industrial implementation of the biocatalytic toolbox enzymes developed in BiodeCCodiNNg. Several publications are currently in preparation and more scientific results will be obtained in the coming period of BiodeCCodiNNg.
An integral part of BiodeCCodiNNg is therefore the intensive interaction with the private sector to facilitate cross-sector discussions and the exchange of ideas through secondments to the various industrial partners. The first phase of BiodeCCodiNNg has already demonstrated the usefulness of native and engineered CC- and NNzymes for the targeted reactions to produce valuable drug building blocks, along with important optimization steps to improve the enzymatic reactions. In the second phase, we expect the interdisciplinary collaboration to increase our understanding of the underlying structural and mechanistic features that determine how efficiently the novel CC- and NNzymes perform the desired reactions, and how they can be engineered to further advance the industrial implementation of the biocatalytic toolbox enzymes developed in BiodeCCodiNNg. Several publications are currently in preparation and more scientific results will be obtained in the coming period of BiodeCCodiNNg.