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Smart Biologics: Developing New Tools in Glycobiology

Periodic Reporting for period 4 - SWEETOOLS (Smart Biologics: Developing New Tools in Glycobiology)

Reporting period: 2020-08-01 to 2021-07-31

Sugars are ubiquitous molecules found throughout all kingdoms of life. Early studies contributed considerably to our appreciation of sugar functions by showing that abnormalities in the glycosylation can develop into pathogenesis and severe disease. Despite the crucial role of sugars in many biological events we still do not have adequate tools to decipher their complexity. To unveil the mysteries in the rapidly emerging field of sugar biology (glycobiology) we aim in this project to develop new tools that will help us to study and understand these important biomolecules. To realize this, we plan to construct unique bioconjugates, which will enable us to target various sugar processing enzymes with unprecedented selectivity. Our goal is to develop a new class of smart probes that will help us to answer fundamental questions in glycobiology. The outcomes of this project will significantly deepen our knowledge of glycoconjugates and in the long term, will allow for the design of efficient vaccines and for the development of better therapeutics.
Within this project, we have successfully elaborated several parts of the project proposal. In the first part devoted to the development of methodology for finding selective glycosidase inhibitors, we performed numerous optimizations of synthetic procedures to obtain the required compounds in sufficient amount and quality. Due to complications encountered in the subsequent screening experiments (and hit identification) using the glycosidases we decided to perform and optimize the procedure using more accessible/cheaper enzymes (carbonic anhydrases which are available within collaboration with another group from IOCB). These experiments provided us with important information about the efficiency and limitations of the methodology. By comparing different approaches (in situ click chemistry, synthetic and phage displayed libraries) we found that the phage display libraries lead to selection of better/more selective inhibitor-peptide conjugates. We plan to further expand the developed methodology to find selective inhibitors also for more challenging enzymes including sugar-processing enzymes. Toward this direction, we performed screening experiments of the peptide libraries using whole intact cells instead of purified proteins. In this way, the system will be closer to the natural situation where the target enzymes are located at the cell surface. We have also successfully solved the initial problems with hit peptide sequencing (usually done by Edman sequencing, which is time consuming and low throughput). We now use a ladder-based sequencing based MALDI-MS experiments where larger amounts of hit peptide sequences can be identified. This part of the project enabled the group to gain important experience and information that will be used beyond the ERC funded project. Our work on the comparison of three different selection processes (in situ click chemistry, synthetic and phage-displayed peptide libraries) is currently being summarized for publication.
We also moved forward in the second part of the project devoted to construction of glycopeptide libraries. After extensive optimizations, we are now able to produce sophisticated heteroglycopeptide libraries based on the proposed click reaction/deprotection steps. We have successfully performed screening of such libraries toward model protein (Concanavalin A) and initiated a collaboration where we aim at more interesting, cancer-related proteins (Galectins). First hit glycopeptide sequences have been identified and resynthesized and their binding properties were determined. The methodology will be also used to find new siglec ligands and cytokine mimetics and applied to cancer immunotherapy studies. manuscript describing our optimization study and application of the methodology toward selective galectin 3 inhibitors is under preparation.
To study glycoconjugates from a different perspective, we succeeded in the synthesis and metabolic incorporation of a new sugar derivative. In combination with the developed fluorogenic bioorthogonal reactions (published in due course), we were able to visualize and inspect glycoconjugates on live cells. In addition, the new derivative in combination with other known and complementary metabolic labeling strategies will enable us to perform studies devoted to identification of e.g. sugar-protein, protein-protein interactions in a cellular context. These experiments will deliver important insight into this type of cellular events at the molecular level.
Most importantly, a patent application on the methodology was submitted to European Patent Office. We believe that the methodology has significant translation potential as it enables selective and highly efficient modification of cell surfaces with different moieties. In contrast to genetically modified cells, the methodology enables attachment of non-encodable moieties to cell surfaces, which could significantly broaden the application potential. The resulting cell-surface modified cells can be used in bioimaging, for the construction of smart biomaterials, in regenerative medicine, as drug delivery systems, in immunotherapy and other biomedical applications.
Overall, the project delivered extremely valuable experience to the group and many projects will be further elaborated in the group. The main results were summarized in 8 publications in respected, international journals with several other publications being under preparation. The results were also presented on several conferences (e.g. The chemical biology society conference) and within invited lectures of the PI. Finally, we were able to develop a new methodology that has tremendous potential for practical use. We are currently exploring different ways of applying the method mainly for therapeutic and diagnostic purposes.
Our results are in good line with the outlined objectives. We have initiated and developed several new approaches to study the fascinating biology of glycoconjugates. We believe that this project delivered several new approaches to study, label and manipulate also other biomolecules and to investigate e.g. the mechanism of action of small molecule drugs. Moreover, our new methodology enabling modification of cell surfaces with various molecules could lead to better production of therapeutically-relevant cells (e.g. immune cells). Such cells could be used for e.g. navigating immune cells to cancer. In this way, the method would represent a real value for society as it could bring the adoptive cell therapy closer to a larger group of patients that will benefit from it.