The Story So Far - StructuralGenomicsConsortium/CNP25-CHIKV-nsP3-Macrodomain GitHub Wiki

The starting point for the project is the dataset derived from a crystallographic fragment screen vs the Chikungunya (CHIKV) nsP3 macrodomain carried out by Jasmin Aschenbrenner and Daren Fearon from the XChem team at Diamond Light Source in late 2023.

The aim of the project is to use these fragments to design a chemical probe binding to the CHIKV nsP3 macrodomain, particularly to the substrate (ADP-ribose) binding site including the catalytic residues. This enzyme is a promising antiviral target because catalytic mutations render viruses nonpathogenic 1, 2, 3. By finding molecules with high affinity for this site, the substrate wouldn't be able to bind and no reaction would occur so our aim is to inhibit the ADP-ribosylhydrolase activity of Chikungunya virus macrodomain not to kill the virus itself.

The importance of the macrodomain (MD)as a novel pharmaceutical target comes from its essential role in reading and earsing ADP-ribolysation 4, 5, 6, 7 because it possesses broad hydrolase activity towards mono-ADP-ribosylated (MAR) substrates of the mono-ADP-ribosyltransferases and it binds to the DNA, RNA as well 8, 9

The macrodomain (MD) hydrolase activity specifically removes the mono-ADP-ribose (MAR) moiety from the lysine residues in substrate proteins, therefore the inhibition of MAR hydrolase activity and ADP-ribose binding will slow the viral replication 10 and reduce the virus virulence 11. MD is also involved in the polyprotein processing, replication compartment formation and replication-transcription complex formation 12, 13

Here are a few fragments that have been identified so far by XChem which bind to the adenosine site of CHIKV nsP3 macrodomain: The images taken from our collaborator (XChem team) presentation.

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Using Fragmenstein and Knitwork generated various sets of merged compounds binding to different sits of the protein target, see the following picture:

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You can also see other few fragments which have also been identified by DLS team in different sites of CHIKV nsp3 macrodomainTarget meeting's slides-7 Dec 2023

A kick-off meeting was held Feb 5th 2024 to discuss the compounds screening and triage. The UCL team visited Diamond Light Source on 22nd March 2024 to discuss the possibility to use the algorithmic XChem tools for follow-up designs via fragment merging. The agreement took place and the curation of several compounds sets was carried out and led to nominate 85 compounds for purchase see here from REAL-ENAMINE on 24th April 2024 and to be shipped to Diamond for testing. 354 compounds were shortlisted for Chemist-assisted Robotics (CAR) which will be done at the Research Complex at Harwell (RCaH).

On 15th April 2024, the XChem team visited us at UCL to discuss different aspects of the project, particularly the automated chemistry for a big number of analogues to be done at RCaH.

We obtained all the required data: the data of the crystallography data that carried out by the DLS team and the GCI and TSA data which are carried out by Wenjie Chen- UCL team and antiviral assay data which is carried out by our collaborator's team at University of North Carolina (UNC): Marcia Sanders and Jack Sears.

The antiviral profiling of the compounds compounds is given at See here: https://github.com/StructuralGenomicsConsortium/CNP25-CHIKV-nsP3-Macrodomain/issues/7#issuecomment-2413906224

Overall workflow

of the project is presented in the figure below along with the suggested issue numbers that you can read for the expansion of each of the identified hits: image Click the links below to read about the work on the hits:

Issue #8: Hit expansion: RA-0188454 Issue #10: Hit expansion of RA-0188499 & RA-0188476 Issue #9: Hit expansion: RA-0188437 Issue #11: Hit expansion of RA-0188455 Issue#12: CAR
Pyrrole, tertrazole, thiazole variations by Hadia expansion 1 Expansion on the RHS variation on LHS variation on LHS amidation, Suzuki, SNAr, BH reactions
thiazole to trizole Expansion in the middle