A Novel Indole Derivative Targets Orthoflavivirus Non-structural NS1 Protein

A novel indole derivative targets orthoflavivirus NS1 protein, exhibits antiviral effect, and alleviates viral pathogenesis

Clinical Relevance

Emerging and resurging orthoflaviviruses (formerly known as flaviviruses) continue to pose a major global public health and socioeconomic challenge. Each year, these viruses infect an estimated 400 million people and cause a wide range of diseases, from visceral and neurological disorders to devastating congenital abnormalities. Transmitted primarily by mosquitoes and ticks, orthoflaviviruses are highly capable of expanding into new geographic regions, underscoring the urgent need for effective countermeasures. Vaccines and antiviral therapies remain the cornerstone of viral disease control. However, despite decades of research, no antiviral drug has yet received clinical approval for the treatment of

several orthoflaviviral diseases including dengue and zika. Vaccine development for dengue has also proven particularly challenging due to the structural complexity of viral proteins and concerns regarding antibody-dependent enhancement (ADE). Notably, a recombinant live-attenuated tetravalent vaccine against dengue virus (DENV) demonstrated a favorable safety profile in a randomized, controlled phase 2b clinical trial. Nevertheless, its overall efficacy reached only 30.2%, highlighting the substantial hurdles that remain and the pressing need for innovative strategies to combat these particular orthoflaviviral diseases.

Rationale of Targeting Orthoflavivirus NS1 and Preliminary Evidence

Orthoflavivirus non-structural protein 1 (NS1) was first identified in 1970 in the serum and brain extracts of DENV-infected mice as a soluble complement-fixing protein (SCF), also referred to as gp48, and was later renamed NS1. NS1, a ~352 amino acid glycoprotein, exists intracellularly as monomers and membrane-associated homodimers, while hexameric NS1 is secreted extracellularly. NS1 plays multifaceted roles in viral replication, immune evasion, and pathogenesis such as vascular leakage. Moreover, its high conservation across orthoflaviviruses makes it an attractive target for broad-spectrum antiviral development.

Using computational approaches and a custom chemical structure database, I designed several novel NS1-targeting indole derivatives, including YS261017NS1, which has a molecular weight of 503.5 g/mol. Molecular docking predicted interactions between YS261017NS1 (Shown in blue) and several orthoflavivirus NS1 residues, including C291 and R336 (Fig. A). Previous study has demonstrated that these residues are critical for viral replication. This inhibitor exhibited a relatively low predicted binding free energy for NS1 and favorable water solubility (LogP = 3.12). To evaluate its antiviral potential, I conducted preliminary studies using YS-NS1W-im, a structural fragment representing approximately one-third of the parent molecule and containing an indole scaffold consisting of a benzene ring fused to a five-membered nitrogen-containing ring. Treatment with YS-NS1W-im inhibited replication of both DENV-2 and Zika virus (ZIKV) in human endothelial cells (Fig. B). Notably, YS-NS1W-im did not affect cell proliferation or induce apoptosis at concentrations up to 100 µM, suggesting minimal interaction with cellular proteins (Fig. C). Furthermore, YS-NS1W-im significantly reduced DENV-associated endothelial hyperpermeability in a solute flux assay (Fig. D). Consistent with these findings, the compound also showed protective effects against DENV NS1-induced vascular leakage in vivo. Treatment with YS-NS1W-im markedly decreased NS1-induced systemic vascular leakage, particularly in the liver, brain, and lungs (Fig. E). Importantly, this NS1-targeting small molecule can be chemically synthesized (schematic synthesis not shown).

Take-Home Hypothesis & Clinical Implication

YS261017NS1, an indole-based compound, may inhibit orthoflavivirus infection and reduce endothelial hyperpermeability by targeting viral NS1. Although further optimization is required for YS261017NS1, these preliminary findings underscore the potential of class of indole as promising candidates for the development of therapeutics against viral infections.

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Dr. Yogy Simanjuntak-HyVir

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