04-Oct-2022
Two-and-a-half years have passed now and the SARS-CoV-2 pandemic is still ongoing, showing that we need to find long-lasting solutions to fight the virus and the constant appearance of new variants. Although vaccines have been developed that help control the pandemic and avoid the most severe forms of Covid-19, the high mutation rate of SARS-CoV-2 and the evolution of many variants make the development of vaccines that work for all variants extremely complicated. Further, some people cannot or do not want to be vaccinated, yet suffer from severe outbreak of the viral infection and need instant medication. Thus, there is a need to look for alternatives to vaccines. Small molecule anti-viral drugs are one handle that target conserved proteins of SARS-CoV2.
Even though several initiatives have already been undertaken to uncover drug targets, a more comprehensive approach looking for drugs that affect a broad range of SARS-CoV-2 proteins was lacking. The Covid-19 NMR consortium sought to set up a large NMR screen, looking for chemical fragment binding to 25 of the SARS-CoV-2 proteins which represents more than 80% of the viral proteome. These 25 proteins represent diverse protein types: proteases, replicase transcriptase and accessory proteins. Several NMR labs worldwide worked together to prepare milligram quantities of these 25 proteins in in high purity, which were then used for a comprehensive NMR screen in Frankfurt NMR center (BMRZ).
The library used for this screen is composed of 768 diverse, pure, soluble fragments that were screened for their binding affinity to the 25 SARS-CoV-2 proteins investigated. This screen led to the identification of 311 binders across the 25 target proteins.
Binders were identified for each of the target proteins, with the number of binders for each protein ranging from 2 to 154.
In parallel, complementary predictions were made using FTMap, a computational mapping server, to look at predicted chemical scaffold and ligand binding sites which showed striking correlation with the NMR experimental data (see Figure 1).
Figure1: Correlation between bioinformatic and experimental mapping of the binding site: the example of the nsp5 protease. The subsites of the active site are labelled as S1, S1 ́, S2 and S3. The crossclusters occupying the binding site are shown in grey sticks. The docked pose of binder 21 is shown in cyan. Mapping of the CSPs (chemical shift perturbations) on to the structure of nsp5 (in blue).
Finally, to validate the ligand binding sites predicted using FTMap, titration experiments using NMR were performed to determine the dissociation constants for a subset of targets.
Overall, this study allowed the discovery and description of new protein/ligand interactions of interest, and confirmed known interactions described using complementary approaches such as Crystallography screens. Ligands binding to SARS-CoV-2 proteins with key function in the virus life cycle could be central to the development of new drugs against the virus.
This initiative was undertaken by the Covid-19 NMR consortium, led by Professor Harald Schwalbe, the Instruct-ERIC Director, and benefited from the support of the CERM/CIRMMP centre of Instruct, as well as several European projects in which Instruct is involved such as iNEXT-discovery, BY-COVID and EOSC Future.
Read the full article here: Berg et al., Comprehensive Fragment Screening of the SARS-CoV-2 Proteome Explores Novel Chemical Space for Drug Development, Angew Chem Int Ed Engl (2022). doi: 10.1002/anie.202205858
