Mechanistic Insights into Dengue Virus Inhibition by a Clinical Trial Compound NITD-688

Wang, Y.; Song, L.; Fernandes, L.; Wang, Y.-H.; Zou, J.; Franklin, S. J.; Hu, Y.; Palmer, L. K.; Yeung, J.; Barriga, D.; Russell, W. K.; Moquin, S. A.; Shi, P.-Y.; Skepper, C.; Xie, X.

doi:10.1101/2024.12.15.628546

bioRxiv · 10.1101/2024.12.15.628546

Mechanistic Insights into Dengue Virus Inhibition by a Clinical Trial Compound NITD-688

Wang, Y.·Song, L.·Fernandes, L.·Wang, Y.-H.·Zou, J.·Franklin, S. J.·Hu, Y.·Palmer, L. K.·Yeung, J.·Barriga, D.·Russell, W. K.·Moquin, S. A.·Shi, P.-Y.·Skepper, C.·Xie, X.

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Abstract

Dengue, caused by the dengue virus (DENV), presents a significant public health challenge with limited effective treatments. NITD-688 is a potent pan-serotype DENV inhibitor currently in Phase II clinical trials. However, its mechanism of action is not fully understood. Here, we present the molecular details of how NITD-688 inhibits DENV. NITD-688 binds directly to the nonstructural protein 4B (NS4B) with nanomolar affinities across all four DENV serotypes and specifically disrupts the interaction between NS4B and nonstructural protein 3 (NS3) without significantly changing the interactions between NS4B and other viral or host proteins. NS4B mutations that confer resistance to NITD-688 reduce both NITD-688 binding to NS4B and disruption of the NS4B/NS3 interaction. Specifically, NITD-688 blocks the interaction of NS3 with a cytosolic loop within NS4B. This inhibits the formation of new NS4B/NS3 complexes and disrupts pre-existing complexes in vitro and DENV-infected cells, ultimately inhibiting viral replication. Consistent with this mechanism, NITD-688 retains greater potency in cellular assays with delayed treatment compared to JNJ-1802, another NS4B inhibitor that has been studied in Phase II clinical trials. Together, these findings provide critical insights into the mechanism of action of NITD-688, facilitating the development of novel flavivirus NS4B inhibitors and informing future clinical interventions against DENV.

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Wang, Y., Song, L., Fernandes, L., Wang, Y.-H., Zou, J., Franklin, S. J., Hu, Y., Palmer, L. K., Yeung, J., Barriga, D., Russell, W. K., Moquin, S. A., Shi, P.-Y., Skepper, C., Xie, X.. 2024-12-15. Mechanistic Insights into Dengue Virus Inhibition by a Clinical Trial Compound NITD-688. https://doi.org/10.1101/2024.12.15.628546

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