Binding of a pyrimidine RNA base-mimic to SARS-CoV-2 non-structural protein 9

Dene R Littler; Biswaranjan Mohanty; Shea A Lowery; Rhys N Colson; Benjamin S Gully; Stanley Perlman; Martin J Scanlon; Jamie Rossjohn

doi:10.1016/j.jbc.2021.101018

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Binding of a pyrimidine RNA base-mimic to SARS-CoV-2 non-structural protein 9

Journal article

Open access

Peer reviewed

Binding of a pyrimidine RNA base-mimic to SARS-CoV-2 non-structural protein 9

Dene R Littler, Biswaranjan Mohanty, Shea A Lowery, Rhys N Colson, Benjamin S Gully, Stanley Perlman, Martin J Scanlon and Jamie Rossjohn

The Journal of biological chemistry, Vol.297(3), 101018

07/28/2021

DOI: 10.1016/j.jbc.2021.101018

PMCID: PMC8317483

PMID: 34331944

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Abstract

The coronaviral non-structural protein 9 (Nsp9) is essential for viral replication; it is the primary substrate of Nsp12’s pseudokinase domain within the viral replication transcription complex, an association that also recruits other components during different stages of RNA reproduction. In the unmodified state, Nsp9 forms an obligate homodimer via an essential GxxxG protein-interaction motif, but its ssRNA-binding mechanism remains unknown. Using structural biological techniques, here we show that a base-mimicking compound identified from a small molecule fragment screen engages Nsp9 via a tetrameric Pi-Pi stacking interaction that induces the formation of a parallel trimer-of-dimers. This oligomerization mechanism allows an interchange of “latching” N-termini, the charges of which contribute to a series of electropositive channels that suggests a potential interface for viral RNA. The identified pyrrolo-pyrimidine compound may also serve as a potential starting point for the development of compounds seeking to probe Nsp9’s role within SARS-CoV-2 replication.

fragment-screen

Nsp9

oligonucleotide binding

replicase

SARS-CoV-2

COVID-19 pandemic

coronavirus

Details

Title: Subtitle: Binding of a pyrimidine RNA base-mimic to SARS-CoV-2 non-structural protein 9
Creators: Dene R Littler - Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
Biswaranjan Mohanty - Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria, 3052, Australia
Shea A Lowery - Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa, USA
Rhys N Colson - Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
Benjamin S Gully - Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
Stanley Perlman - Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa, USA
Martin J Scanlon - Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria, 3052, Australia
Jamie Rossjohn - Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
Resource Type: Journal article
Publication Details: The Journal of biological chemistry, Vol.297(3), 101018
DOI: 10.1016/j.jbc.2021.101018
PMID: 34331944
PMCID: PMC8317483
NLM abbreviation: J Biol Chem
ISSN: 0021-9258
eISSN: 1083-351X
Publisher: Elsevier Inc
Grant note: DOI: 10.13039/501100000923, name: Australian Research Council; DOI: 10.13039/501100000947, name: Australian Cancer Research Foundation
Language: English
Date published: 07/28/2021
Academic Unit: Microbiology and Immunology; Stead Family Department of Pediatrics; Iowa Neuroscience Institute; Infectious Disease (Pediatrics)
Record Identifier: 9984117145202771

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