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Welcome to the CNP18-DENVRdrp-VirtualScreen wiki!
This repository outlines one of several projects related to our efforts to identify a small molecular compound that binds to the Dengue virus RNA-dependent RNA polymerase (RdRp). This specific repository describes our efforts at identifying a possible hit molecule from the Enamine REAL library.
Below is a summary of the project, and the sidebar to the the right allows you to explore each step if the process further; linking to additional data, tables, and other overviews we might only reference below.
To get an overview of the READDI-AViDD project please read the Rules of Participation and Origins of the Project.
You can also explore Other Repositories related to Dengue RdRp campaign.
In mid-2023 we started a virtual screening campaign of the Enamine REAL space to help us identify new starting points for developing a probe that binds to Dengue RdRp. To guide the virtual screen, mutagenic studies supported the identification of highly conserved residues on the protein, and a previously unexplored pocket on the RdRp was identified. Using HIDDEN-GEM a preliminary library of ~1000 compounds was generated and of these 65 were send for initial testing.
This generated three hits that were used as starting point for further exploration. Initially, these showed only antiviral activity but later tests using a WaveDelta assay showed they are likely binding to RdRp. Before this data arrives a first tentative exploration for the three hits was selected from commercially available sources. These should provide information about what parts are important for binding and will guide future SAR exploration.
Additional data for these hits show that RA-3301 is the top compound due to its favorable antiviral replication activity (EC90), best Kd of the tested compounds, as well as favorable aggregation profile. The main issue that needs to be addressed with this compound is the very low solubility causing issues in some assays and that the CC50/EC50 < 5.
In Q1 of 2024, the first expansion was sent for testing and the results of these efforts are chelated on this page. In summary, initial single point data pointed at four compounds with potential activity. After dose-response determination, antiviral replication tests, and whole cell toxicity this was narrowed down to two analogues of RA-3301 that were of interest: RA-20636 and RA-20641.
Especially RA-20641 shows retained activity and CC50/EC50 > 5. Notably, in this compound the motif that presented as a possible PAIN in the parent compound has been removed. As the lower part of the RA-3301 seems to play a minor role for activity this allow us to use this part of the molecule overcome the issues with solubility.
Synthetic chemistry efforts have commenced to do a conservative SAR analysis of RA-3301 and RA-20636.
June 2024
- Expansion sent for testing in SPR at SGC Toronto
- Second expansion arriving soon at UCL
- Expansion sent for testing in gelbased assay in Gotte Lab
- Co-crystal efforts ongoing in Arnold Lab