Dataset Information

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

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 nonstructural protein 4B (NS4B) with nanomolar affinities across all four DENV serotypes. This binding specifically disrupts the interaction between NS4B and nonstructural protein 3 (NS3), without affecting interactions with other viral or host proteins. NITD-688-resistant mutations in NS4B reduce NITD-688 binding to NS4B and its disruption of the NS4B/NS3 interaction. Mechanistically, NITD-688 blocks the interaction of NS3 with a cytosolic loop within NS4B and disrupts both the formation and pre-existing NS4B/NS3 complexes in vitro and in DENV-infected cells, ultimately inhibiting viral replication. This characteristic enables NITD-688 to remain effective even with delayed treatment, distinguishing it from JNJ-1802, another clinically studied NS4B inhibitor. Moreover, combining NITD-688 with either JNJ-1802 or an NS5 polymerase inhibitor synergistically inhibits DENV-2 infection. 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.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human) Dengue Virus

TISSUE(S): Cell Culture, Early Embryonic Cell

SUBMITTER: Lee Palmer

LAB HEAD: William Russell

PROVIDER: PXD053801 | Pride | 2025-10-06

REPOSITORIES: Pride

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			Action	DRS
	22jan24_S7-12_Xxie_aur_e_lp_19jan24_071.mgf	Mgf
	22jan24_S7-12_Xxie_aur_e_lp_19jan24_071.mzML	Mzml
	22jan24_S7-12_Xxie_aur_e_lp_19jan24_071.mzid.gz	Mzid
	22jan24_S7-12_Xxie_aur_e_lp_19jan24_071.xlsx	Xlsx
	22jan24_Xxie_NS4B-tagged.fasta	Fasta

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Mechanistic insights into dengue virus inhibition by a clinical trial compound NITD-688.

Wang Yan Y Sun Long L Fernandes Luciana L Wang Yu-Hsiu YH Zou Jing J Franklin Samuel J SJ Hu Yanping Y Palmer Lee K LK Yeung Jason J Barriga Daniela D Russell William K WK Moquin Stephanie A SA Shi Pei-Yong PY Skepper Colin C Xie Xuping X

Proceedings of the National Academy of Sciences of the United States of America 20250328 13

Dengue, caused by the dengue virus (DENV), presents a significant public health challenge with limited effective treatments. NITD-688 is a potent panserotype 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 interactio ...[more]

PMID: 40153462

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Project description:Dengue virus (DENV) infection is associated with a range of clinical manifestations, from self-limiting dengue fever (DF) to life-threatening dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS). Although DENV-specific CD4 T cells are capable of producing inflammatory cytokines and can acquire cytotoxic functions in previously DENV-exposed individuals, much less is known related to DENV-specific CD4 T cells during acute DENV infection and disease. In this study, we set out to characterize the immune signatures of DENV-specific CD4 T cells during acute infection and investigate whether DENV-specific CD4 T cell response differs between DF and DHF. Previous studies suggest that increased IL-10 level in the blood is associated with severe dengue disease. Here we show evidence of DENV-specific IL-10-producing CD4 T cells during acute DENV infection. More specifically, an IL-10+IFN-γ+ double positive (DP) CD4 T cell population was prominent in acute hospitalized DENV cases but disappeared at the convalescent stage. RNA-sequencing analysis revealed that these cells were associated with gene signatures that marginally overlapped with previously identified signatures of cytotoxic CD4 T cells and type 1 regulatory T (Tr1)-like cells. However, the majority of the genes differentially expressed by DP cells were not related to cytotoxic CD4 T cells or Tr1-like cells. These genes include IL-21, IL-22, CD86, CD109, and CCR1, which are involved in T cell activation, function, cytokine signaling, and migration. Notably, the magnitude of DP cell response was higher in DHF than DF, whereas the gene expression profile of DP cells was similar between DF and DHF. Finally, our data show that DENV-specific DP cells are largely homogeneous based on the expression of 31 selected markers. Overall, this study reveals unique phenotypes of virus-specific IL-10/IFN-γ co-producing CD4 cells and indicates that the quantity but not quality of these cells may be positively correlated with dengue disease severity.

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