Identification and evaluation of small-molecule inhibitors against the dNTPase SAMHD1 via a comprehensive screening funnel

Zhang, S. M.; Paulin, C. B.; Michel, M.; Marttila, P.; Yagüe-Capilla, M.; Bwanika, H. C.; Shu, H.; Papagudi Vekatram, R.; Wiita, E.; Jemth, A.-S.; Almlöf, I.; Loseva, O.; Ortis, F.; Dirks, C.; Koolmeister, T.; Linde, E.; Lee, S.; Llona-Minguez, S.; Haraldsson, M.; Strömberg, K.; Homan, E. J.; Scobie, M.; Lundbäck, T.; Helleday, T.; Rudd, S. G.

doi:10.1101/2023.01.17.524275

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bioRxiv · 10.1101/2023.01.17.524275

Identification and evaluation of small-molecule inhibitors against the dNTPase SAMHD1 via a comprehensive screening funnel

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Abstract

Sterile alpha motif and histidine-aspartic acid domain containing protein-1 (SAMHD1) is a deoxynucleoside triphosphate (dNTP) triphosphohydrolase central to cellular nucleotide pool homeostasis. Recent literature has also demonstrated how SAMHD1 can detoxify chemotherapy metabolites thereby controlling their clinical responses. To further understand SAMHD1 biology and to investigate the potential of targeting this enzyme as a neoadjuvant to existing chemotherapies we set out to discover selective small molecule-based inhibitors of SAMHD1. Here we report a discovery pipeline encompassing a biochemical screening campaign and a set of complementary biochemical, biophysical, and cell-based readouts for further characterisation of the screen output. The identified hit compound TH6342 and its analogues, accompanied by their inactive negative control analogue TH7126, demonstrated specific, low M potency in inhibiting the hydrolysis of both natural substrates and nucleotide analogue therapeutics, shown using complementary enzyme-coupled and direct enzymatic activity assays. Their mode of inhibition was subsequently detailed by coupling kinetic studies with thermal shift assays, where TH6342 and analogues were shown to engage with pre-tetrameric SAMHD1 and deter the oligomerisation and allosteric activation of SAMHD1 without occupying nucleotide binding pockets. We further outline the development and application of multiple cellular assays for assessing cellular target engagement and associated functional effects, including CETSA and an in-cell dNTP hydrolase activity assay, which highlighted future optimisation strategies of this chemotype. In summary, with a novel mode of inhibition, TH6342 and analogues broaden the set of tool compounds available in deciphering SAMHD1 enzymology and functions, and furthermore, the discovery pipeline reported herein represents a thorough framework for future SAMHD1 inhibitor development. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=96 SRC="FIGDIR/small/524275v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@dc706forg.highwire.dtl.DTLVardef@59a9b4org.highwire.dtl.DTLVardef@9473e2org.highwire.dtl.DTLVardef@4427dc_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Zhang, S. M., Paulin, C. B., Michel, M., Marttila, P., Yagüe-Capilla, M., Bwanika, H. C., Shu, H., Papagudi Vekatram, R., Wiita, E., Jemth, A.-S., Almlöf, I., Loseva, O., Ortis, F., Dirks, C., Koolmeister, T., Linde, E., Lee, S., Llona-Minguez, S., Haraldsson, M., Strömberg, K., Homan, E. J., Scobie, M., Lundbäck, T., Helleday, T., Rudd, S. G.. 2023-01-18. Identification and evaluation of small-molecule inhibitors against the dNTPase SAMHD1 via a comprehensive screening funnel. https://doi.org/10.1101/2023.01.17.524275

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