Dataset of high-throughput ligand screening against the RNA Packaging Signals regulating Hepatitis B Virus nucleocapsid formation

Multiple ssRNA viruses which infect bacteria, plants or humans use RNA Packaging Signal (PS)-mediated regulation during assembly to package their genomes faithfully and efficiently. PSs typically comprise short nucleotide recognition motifs, most often presented in the unpaired region of RNA stem-loops, and often bind their cognate coat proteins (CPs) with nanomolar affinity. PSs identified to date are resilient in the face of the typical error prone replication of their virus-coded polymerases, making them potential drug targets. An immobilised array of small molecular weight, drug-like compounds was panned against a fluorescently-labelled oligonucleotide encompassing the most conserved Hepatitis B Virus (HBV) PS, PS1, known to be a major determinant in nucleocapsid formation. This identified > 70 compounds that bind PS1 uniquely in the array. The commercially available 66 of these were tested for their potential effect(s) on HBV nucleocapsid-like particle (NCP) assembly in vitro , which identified potent assembly in-hibitors. Here, we describe a high-throughput screen for such effects using employing fluorescence anisotropy in a 96-well microplate format. HBV genomic RNAs (gRNA) , short oligonucleotides encompassing PS1 were 5 ' labelled with an Alexa Fluor 488 dye. Excess (with respect to stoichio-metric T = 4 NCP formation) HBV core protein (Cp) dimers were titrated robotically into solutions containing each of these RNAs stepwise, using a Biomek 4000 liquid handling robot. The anisotropy values of these mixtures were moni-tored using a POLARstar microplate reader. NCP-like struc-tures were challenged with RNase A to identify reactions that did not result in complete NCP formation. The results imply that similar to 50% of the compounds prevent complete NCP formation, highlighting both PS-meditated assembly and the PS-binding compounds as potential directly-acting anti-virals with a novel molecular target. Importantly, this method al-lows high-throughput in vitro screening for assembly in-hibitors in this major human pathogen. (C) 2022 Published by Elsevier Inc.

Automated summary

Multiple ssRNA viruses use RNA Packaging Signal (PS)-mediated regulation during assembly to package their genomes, and PS-binding compounds have the potential to be directly-acting antivirals. This study identified over 70 compounds that uniquely bind to the PS of Hepatitis B Virus (HBV) and tested them for their inhibitory effect on HBV nucleocapsid-like particle (NCP) assembly. The results highlight the importance of PS-mediated assembly and suggest the PS-binding compounds as potential drug targets.