Guan, J. S. | Search bioRxiv

bioRxiv2022

In silico repurposed drugs against monkeypox virus

Monkeypox is an emerging epidemic of concern. The disease is caused by the monkeypox virus and an increasing global incidence with a 2022 outbreak that has spread to Europe amid the COVID-19 pandemic. The new outbreak is associated with novel, previously undiscovered mutations a nd variants. Currently the US Food and Drug Administration (FDA) approved poxvirus treatment involves use of tecovirimat. However, there is limited pharmacopoeia otherwise, and limited research interest in monkeypox. In this study, virtual screening and molecular dynamics were employed to explore the potential repurposing of multiple drugs previously approved by the FDA or other jurisdictions for other applications. Several drugs are predicted to tightly bind to viral proteins which are crucial in viral replication, including molecules which show high potential for binding the monkeypox D13L capsid protein, whose inhibition has previously been demonstrated to suppress viral replication.

bioinformatics↗

bioRxiv2021

Bacteria.guru: comparative transcriptomics and co-expression database for bacterial pathogens

SummaryThe bacterial kingdom comprises unicellular prokaryotes able to establish symbioses from mutualism to parasitism. To combat bacterial pathogenicity, we need an enhanced understanding of gene function and regulation, which will mediate the development of novel antimicrobials. Gene expression can predict gene function, but there lacks a database enabling expansive inter- and intraspecific exploration of gene expression profiles and co-expression networks for bacteria. To address this, we integrated the genomic and transcriptomic data of the 17 most notorious and studied bacterial pathogens, creating bacteria.guru, an interactive database that can identify, visualize, and compare gene expression profiles, co-expression networks, functionally enriched clusters, and gene families across species. Through illustrating antibiotic resistance mechanisms in P. aeruginosa, we demonstrate that bacteria.guru could potentially aid the discovery of multi-faceted antibiotic targets. Hence, we believe bacteria.guru will facilitate future bacterial research. AvailabilityThe database and co-expression networks are freely available from https://bacteria.guru/. The sample annotations are found in the supplemental data.

bioinformatics↗