Gangotia, D. | Search bioRxiv

bioRxiv2023

Inhibition of potassium ion channels reduces Semliki Forest virus genome replication

IntroductionSemliki forest virus (SFV) is a model virus used to investigate the Alphavirus genus, which includes human pathogens Chikungunya virus and Ross River virus. Viruses harness cellular machinery to facilitate various steps of their replicative cycles. Ion channels are one group of cellular proteins required for the efficient replication of some viruses, including Influenza A viruses, Ebola virus and members of the Betacoronavirus genus. This study focussed on understanding SFVs requirement for functional ion channels during replication. MethodsThe effect of ion channel inhibitors on in vitro SFV infections was measured to investigate the contribution of ion channels in its replication cycle. ResultsIn vitro SFV infections carried out in the presence or absence of different ion channel inhibitors showed broad-range K+ channel inhibitors reproducibly attenuated virus replication and reduced its cytotoxicity in two mammalian cell lines. These broad-range K+ channel inhibitors disrupted an early, post-entry step causing a delay or reduction in SFV protein and RNA synthesis. Screens using inhibitors of specific K+ channel families showed that two-pore domain K+ channel (2pK) inhibitors attenuated SFV replication. Confocal microscopy revealed decreased detection of dsRNA and SFV protein in the presence of inhibitor but no change in RNA and protein colocalisation, which would indicate disruption of replication complexes. Broad-range K+ and 2pK inhibitors decreased viral RNA replication and transcription from the subgenomic promoter. ConclusionsK+ channel inhibitors attenuate in vitro SFV replication by inhibiting an early, post-entry step of virus replication, potentially RNA synthesis. ImportanceNo antiviral therapies have been approved for clinical use against diseases caused by members of the Alphavirus genus. Work presented in this manuscript shows for the first time that SFV genome replication and virus induced cytotoxicity can be reduced in vitro by treating infected cells with K+ channel inhibitors. This work provides the basis for investigating the effectiveness of K+ channel inhibitors against other alphaviruses both in vitro and in vivo and, because many ion channel inhibiting drugs are already in clinical use, rapid repurposing against alphavirus infections would be possible.

microbiology↗

bioRxiv2021

In silico DNA codon optimization of the variant antigen-encoding genes of diverse strains of Nipah virus

Due to an increase in human and wildlife interaction, more and more zoonotic diseases are emerging. A prime example of this is the emergence of the Nipah virus (NiV). Due to high rate of mortality specifically in India and Bangladesh, there is an urgent need for accelerated research for NiV involving the development of vaccines or drugs. The genome of NiV consists of six genes (N, P, M, F, G and L) encoding yielding nucleoprotein, phosphoprotein, matrix, fusion, glycoprotein and large RNA polymerase. We have used these six genes for in silico assessment of DNA codon optimization in Escherichia coli. It was observed that the codon adaptation index (CAI) and GC content of the genes in optimized DNA were enhanced significantly as compared to wild-type strain. On an average, CAI and GC content of N gene in optimized DNA was enhanced by 2.3 (135.1%) and 1.2(9.9 %) fold respectively, while in P/V/C it was increased by 2.0 (98.3 %) and 1.1(7.8%) fold respectively. Further, the CAI and GC content in optimized DNA of M gene and F gene was enhanced by 2.0(99.0%) and 1.1(7.2%) fold respectively for gene M and 2.4(142.5 %), 1.2(15.4%) fold respectively for gene F. Gene G showed an increase of 2.1(114.8 %) fold for CAI, 1.1(11.2%) fold for GC content and gene L showed an increase of 2.4(143.7%) fold for CAI, 1.2(17.2%) fold for GC content. Our result demonstrates that the optimized genes could be useful for better expression in host without any truncated proteins and also useful for protein folding and function.

bioinformatics↗