Samenvatting

The coronavirus disease-19 (COVID-19) pandemic still poses serious threats to global public health. Therefore, the scientific community is desperately looking for suitable vaccines and pharmacological treatment options. This thesis completes the internship at Specs Compound Handling BV and describes the results of a part of the COVID-19-NMR project initiated at the Goethe University in Frankfurt. In this project, the method of fragment-based drug discovery (FBDD) was used, which has become an important tool for finding hit compounds for difficult targets. The first goal of the internship was the synthesis of spin labeled analogues of 19 small molecules (fragments). These fragments show high quality interactions with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA as previously detected by first-site NMR screening by the Goethe University of a library of 768 fragments. These spin labeled analogues allow for second-site NMR screening, that is, the detection of fragments that bind in the vicinity of the first labeled fragment. Three different organic reactions (Buchwald Hartwig amination, aromatic nucleophilic substitution and amide formation) were used to successfully introduce a TEMPO spin label for 16 first-site hit fragments. Of these reactions, aromatic nucleophilic substitution showed low yield or no products at all. The labeled fragments were submitted for second-site NMR screening. The preliminary second site screening results are promising because a major second-site hit was found in the presence of labeled compound 19, as seen by quenching of the NMR signal.
The second goal of the internship was to covalently link first-site and second-site fragments by means of a spacer. Because the second-site screening results emerged very recently, it was not possible to apply them in the synthesis of linked fragments. Therefore, as a proof of principle, an 8-step chemical route was developed to successfully link two different fragments. The length of the spacer between the two fragments was 9 atoms as determined by molecular modeling. The results show that the present FBDD approach may be promising in the development of inhibitor
drugs targeting the SARS-CoV-2 RNA .