Periodic Reporting for period 5 - LightZymes (Evolution of artificial enzymes for light-driven reactions by implementing unnatural cofactors in protein scaffolds)
Reporting period: 2023-02-01 to 2024-01-31
Biotechnology is considered as one of the key-enabling technologies to create a sustainable, bio-based economy. Besides well-established applications of enzymes in food and laundry industry, enzyme catalysis is an especially powerful tool for the industrial production of fine chemicals (cosmetics, pharmaceuticals). Due to their selectivity, the formation of unwanted side products can be avoided. Furthermore, mild reaction conditions can be employed (room temperature and aqueous reaction media) accompanying with preventing of toxic reagents, and solvents as well as the use of heavy metals as catalysts. This makes enzymes very attractive for environmentally benign syntheses routes.
Although nature has demonstrated its great potential to evolve diverse enzymes to construct complex pathways, a limited set of enzymatic reactivities have been developed during evolution. Enzymes are composed out of 20 amino acids, which allow a restricted set of catalytic mechanisms. With the help of (a limited number of) small organic molecules – cofactors – nature expanded this range significantly. However, chemists often desire reactions that are not known in nature. The creation of non-natural enzymes with an expanded reaction scope is therefore an important step to increase the impact of biotechnology. An expanded collection of available enzymes will facilitate a greater contribution of biocatalysis in industrial synthesis, having an important economical and ecological potential. One example of desired but not yet available enzymatic reactions are transformations driven by light that can be catalyzed by small organic dyes. Light is a cheap and renewable energy source, which can fuel reactions that otherwise would need reagents providing high energy. Furthermore, light-driven reactions often enable a complementary range of reactivities, which cannot be obtained via classical chemical approaches. However, it is not possible to render photo-organo-catalyzed reactions stereoselective in most cases, which is a prerequisite for applying these reaction for the production of pharmaceutical ingredients or intermediate building blocks that are required at high optical purity.
Therefore, this research program aims to expand the chemical repertoire of naturally evolved enzymes for selective photocatalyzed conversions of small organic molecules. We want to combine the natural ability of enzymes to create selectivity to a catalyzed reaction by incorporating organic photocatalysts as non-natural cofactors. These hybrid proteins will then catalyse light-driven reactions, which are not known in nature. The protein scaffold is required to induce the desired selectivity to the reaction which is not observed if the photo catalyst is used alone. To this end, an important goal is to combine laboratory evolution and protein design methods to optimize these newly designed hybrid proteins. This requires work on the following subgoals: (i) to identify and establish model reaction, (ii) to employ and develop molecular techniques to integrate the small organic photocatalysts into the protein, (iii) to create and optimize the production of hybrid proteins in E. coli cells, (iv) to develop instrumental and high throughput analytics that facilitate the screening, (v) to create variants and identify ones with improved properties, and (vi) to optimize a selected reaction for preparative scale.
Although nature has demonstrated its great potential to evolve diverse enzymes to construct complex pathways, a limited set of enzymatic reactivities have been developed during evolution. Enzymes are composed out of 20 amino acids, which allow a restricted set of catalytic mechanisms. With the help of (a limited number of) small organic molecules – cofactors – nature expanded this range significantly. However, chemists often desire reactions that are not known in nature. The creation of non-natural enzymes with an expanded reaction scope is therefore an important step to increase the impact of biotechnology. An expanded collection of available enzymes will facilitate a greater contribution of biocatalysis in industrial synthesis, having an important economical and ecological potential. One example of desired but not yet available enzymatic reactions are transformations driven by light that can be catalyzed by small organic dyes. Light is a cheap and renewable energy source, which can fuel reactions that otherwise would need reagents providing high energy. Furthermore, light-driven reactions often enable a complementary range of reactivities, which cannot be obtained via classical chemical approaches. However, it is not possible to render photo-organo-catalyzed reactions stereoselective in most cases, which is a prerequisite for applying these reaction for the production of pharmaceutical ingredients or intermediate building blocks that are required at high optical purity.
Therefore, this research program aims to expand the chemical repertoire of naturally evolved enzymes for selective photocatalyzed conversions of small organic molecules. We want to combine the natural ability of enzymes to create selectivity to a catalyzed reaction by incorporating organic photocatalysts as non-natural cofactors. These hybrid proteins will then catalyse light-driven reactions, which are not known in nature. The protein scaffold is required to induce the desired selectivity to the reaction which is not observed if the photo catalyst is used alone. To this end, an important goal is to combine laboratory evolution and protein design methods to optimize these newly designed hybrid proteins. This requires work on the following subgoals: (i) to identify and establish model reaction, (ii) to employ and develop molecular techniques to integrate the small organic photocatalysts into the protein, (iii) to create and optimize the production of hybrid proteins in E. coli cells, (iv) to develop instrumental and high throughput analytics that facilitate the screening, (v) to create variants and identify ones with improved properties, and (vi) to optimize a selected reaction for preparative scale.
We studied several photocatalytic model reactions and evaluated their compatibility to proteins / biocatalysis. One example is the introduction of oxygen (as a ketone functional group) in simple hydrocarbons by a light-mediated reaction. This reaction was shown to be compatible with conditions of biocatalysis (e.g. the presence of enzymes, aqueous reaction environment). Moreover, we demonstrated that the photocatalytic reaction can be performed together with an enzyme reaction simultaneously in the same pot and - by utilizing different enzymes - various chiral products can be obtained in this cascade approach. The published results (Eur. J. Org. Chem. 2019, 80–84) are one of the first examples that this combination of photo- and enzyme catalysis is possible and fruitful. Optimization studies facilitated the application of an exemplary photobiocatalytic one-pot three step approach on preparative scale (manuscript in preparation).
For several other model reactions studied, we developed sensitive GC-MS analytics to quantify the formation and optical purity of the product. From a structure search of the Protein databank (PDB), a variety of potential scaffolds for constructing the envisioned hybrid proteins have been identified. The initial part of the project was mostly dedicated to the incorporation of the photoorganocatalyst benzophenone as ncAA, using the stop codon suppression method. Such unnatural proteins were successfully expressed in E. coli cells in decent amounts and purity. For the model reaction, the developed LightZymes produced the expected product in small amounts but failed to give the envisioned selectivity. As it turned out that enantioselectivity is difficult to control due to inherent reasons lying in the mechanism of the reaction, we focused on the incorporation of a newly selected photoorganocatalyst, thioxanthone. Via protein engineering, an amino acyl tRNA synthetase was developed that is capable of incorporating the synthesized thioxanthone-bearing amino acid into protein scaffolds. The developed Lightzymes bearing the thioxanthone moiety have been employed in different model reactions, to generate fluorescent products, specifically coumarins. This should facilitate the establishment of HTS assays, which can be applied for the evolution of activity and selectivity of the selected hybrid proteins.
For several other model reactions studied, we developed sensitive GC-MS analytics to quantify the formation and optical purity of the product. From a structure search of the Protein databank (PDB), a variety of potential scaffolds for constructing the envisioned hybrid proteins have been identified. The initial part of the project was mostly dedicated to the incorporation of the photoorganocatalyst benzophenone as ncAA, using the stop codon suppression method. Such unnatural proteins were successfully expressed in E. coli cells in decent amounts and purity. For the model reaction, the developed LightZymes produced the expected product in small amounts but failed to give the envisioned selectivity. As it turned out that enantioselectivity is difficult to control due to inherent reasons lying in the mechanism of the reaction, we focused on the incorporation of a newly selected photoorganocatalyst, thioxanthone. Via protein engineering, an amino acyl tRNA synthetase was developed that is capable of incorporating the synthesized thioxanthone-bearing amino acid into protein scaffolds. The developed Lightzymes bearing the thioxanthone moiety have been employed in different model reactions, to generate fluorescent products, specifically coumarins. This should facilitate the establishment of HTS assays, which can be applied for the evolution of activity and selectivity of the selected hybrid proteins.
In a collaboration project we published one of the first known combinations of organo-photo catalysis and biocatalysis and demonstrated the fruitful combination of these two disciplines (Eur. J. Org. Chem. 2019, 80–84). This is an important interdisciplinary achievement in the field of catalysis. Furthermore, we are now able to incorporate a thioxanthone bearing non-canonical amino acid into proteins. This will broaden the applicability of photobiocatalysis to novel types of reactions.