Huerta, L. | bioRxiv Science

bioRxiv2026

Substrate and target selectivity of 4'-fluoroadenosine against viral and host polymerases

Developing safe and effective treatments against emerging RNA viruses is an important goal in pandemic preparedness efforts. 4'-fluorouridine (4'-FlU) is a broad-spectrum antiviral that was shown to inhibit viral RNA-dependent RNA polymerases (RdRps). Given its notable range of antiviral activity, this class of nucleoside analogs warrants further investigation. Here, we studied the antiviral activity and underlying mechanism of inhibition of 4'-fluoroadenosine (4'-FlA). Like 4'-FlU, 4'-FlA demonstrates a broad-spectrum of antiviral activity against eight prototypic viruses representing diverse families. Enzyme kinetics show that the triphosphate (4'-FlA-TP) is efficiently incorporated by viral RdRps. A cryo-EM structure of RdRp of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in complex with double-stranded RNA and the incorporated monophosphate (4'-FlA-MP) characterizes interactions at the active site. The incorporated analog elicits heterogeneous inhibition patterns in primer extension reactions. In contrast, templates with embedded 4'-FlA-MP inhibit incorporation of complementary UTP across the viral RdRps. However, incorporation of 4'-FIA-TP is not limited to viral polymerases and likewise includes human mitochondrial RNA polymerase. These results demonstrate the general potential for 4'-fluorinated nucleotides as antiviral drugs and guide the development of more selective derivatives for medical use in appropriate settings.

microbiology↗

bioRxiv2017

A quantitative network modeling approach to evaluate the role of cytokine combinations on CD4+ T cell differentiation, partial polarization, and plasticity

Diverse cellular polarization states with different phenotypes and functions are derived from the differentiation of activated CD4+ T naive lymphocytes in the presence of particular cytokines. In addition, conversion of polarized cells to phenotypes different from that originally induced has been documented, highlighting the capacity of the immune response for adaptation to changing circumstances. In a recent study, we proposed a minimal Boolean regulatory network of CD4+ T differentiation that incorporates transcription factors, signaling pathways, and autocrine and exogenous cytokines. The qualitative model effectively reproduced the main polarized phenotypes of CD4+ T cells and several of the plasticity events reported in the literature. Yet, the amount and the expression of cytokines relative to expression of other factors influence CD4+ T cell transitions. In this paper, we have extended the Boolean network to a continuous model that allows us to assess the effect of quantitative differences in the concentrations and combinations of exogenous and endogenous cytokines, as well as diverse levels of transcription factors expression, in order to assess the role of intracellular and extracellular components in CD4+ T differentiation and plasticity. Interestingly, the model predicts either abrupt or gradual differentiation patterns between observed phenotypes depending on critical concentrations of single or multiple environmental cytokines. Plastic changes induced by environmental cytokines were observed in conditions of partial phenotype polarization in the Th1/Th2 transition. On the other hand, the Th17/iTreg transition was highly dependent on cytokine concentrations in the environment. Thus, modeling shows how the concentration of exogenous factors, the degree of initial polarization, and cell heterogeneity, may determine the differentiation and plasticity capacity of CD4+ T cells. The model and results presented here are useful to further understand system-level mechanisms underlying observed patterns of CD4+ T differentiation and plasticity.

systems biology↗