Discovery of non-nucleoside inhibitors of the enterovirus D68 3D polymerase through crystallographic fragment and high-throughput biochemical screening

Biswas, I.; Wang, Q.; McCann, J. T.; Tchesnokov, E. P.; Nguyen, L.; Saini, M.; Cantero, J.; Revalde, J. L.; Gotte, M.; Renslo, A.; Neitz, R. J.; Arkin, M. R.; Arnold, E.; Ruiz, F. X.

doi:10.64898/2026.07.09.737532

bioRxiv · 10.64898/2026.07.09.737532

Discovery of non-nucleoside inhibitors of the enterovirus D68 3D polymerase through crystallographic fragment and high-throughput biochemical screening

Biswas, I.·Wang, Q.·McCann, J. T.·Tchesnokov, E. P.·Nguyen, L.·Saini, M.·Cantero, J.·Revalde, J. L.·Gotte, M.·Renslo, A.·Neitz, R. J.·Arkin, M. R.·Arnold, E.·Ruiz, F. X.

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Abstract

Enterovirus D68 (EV-D68) is a non-polio picornavirus that has caused increasing rates of severe respiratory illness and acute flaccid myelitis in children worldwide this century. There are no approved vaccines or antivirals for EV-D68. Thus, we conducted a crystallographic fragment screening (CFS) and a high-throughput screening (HTS) biochemical assay against the EV-D68 RNA-dependent RNA polymerase 3D (3Dpol) to identify ligandable sites and non-nucleoside compounds that can spearhead anti-enteroviral drug discovery. The CFS, involving 650 fragments, identified 68 hit compounds (~10% hit rate) distributed across 3Dpol, including the functionally relevant sites RNA template channel, Active site, and RNA primer channel, and the previously unknown "Thumb site II" and "Index-middle finger pocket". Inhibition assays confirmed that compounds binding to each site can inhibit EV-D68 3Dpol activity. The HTS, a fluorescence-based PicoGreen biochemical assay, permitted screening 50,000 compounds of the ChemBridge Premium Library (0.77% hit rate). After a second-round dose-response screening, we identified 5-aminoindazole as a promising scaffold that inhibits EV-D68 3Dpol, including hit-to-lead compound 727590, which displayed an IC50 value of 25 M and preliminary structure-activity relationships. These hits offer amenable starting points for discovery and development of non-nucleoside inhibitors and provide opportunities for structure-based drug design against enteroviruses. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=107 SRC="FIGDIR/small/737532v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@1a7cb78org.highwire.dtl.DTLVardef@11f4bb9org.highwire.dtl.DTLVardef@1a477e0org.highwire.dtl.DTLVardef@ba5391_HPS_FORMAT_FIGEXP M_FIG Created with biorender.com and PyMOL Molecular Graphics System, version 2.5.0. Schrodinger, LLC. C_FIG

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Biswas, I., Wang, Q., McCann, J. T., Tchesnokov, E. P., Nguyen, L., Saini, M., Cantero, J., Revalde, J. L., Gotte, M., Renslo, A., Neitz, R. J., Arkin, M. R., Arnold, E., Ruiz, F. X.. 2026-07-10. Discovery of non-nucleoside inhibitors of the enterovirus D68 3D polymerase through crystallographic fragment and high-throughput biochemical screening. https://doi.org/10.64898/2026.07.09.737532

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