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Front Immunol ; 13: 812393, 2022.
Article in English | MEDLINE | ID: covidwho-1858006


CD8+ T cells are a pivotal part of the immune response to viruses, playing a key role in disease outcome and providing long-lasting immunity to conserved pathogen epitopes. Understanding CD8+ T cell immunity in humans is complex due to CD8+ T cell restriction by highly polymorphic Human Leukocyte Antigen (HLA) proteins, requiring T cell epitopes to be defined for different HLA allotypes across different ethnicities. Here we evaluate strategies that have been developed to facilitate epitope identification and study immunogenic T cell responses. We describe an immunopeptidomics approach to sequence HLA-bound peptides presented on virus-infected cells by liquid chromatography with tandem mass spectrometry (LC-MS/MS). Using antigen presenting cell lines that stably express the HLA alleles characteristic of Indigenous Australians, this approach has been successfully used to comprehensively identify influenza-specific CD8+ T cell epitopes restricted by HLA allotypes predominant in Indigenous Australians, including HLA-A*24:02 and HLA-A*11:01. This is an essential step in ensuring high vaccine coverage and efficacy in Indigenous populations globally, known to be at high risk from influenza disease and other respiratory infections.

Influenza Vaccines , Influenza, Human , Australia , CD8-Positive T-Lymphocytes , Chromatography, Liquid , Epitopes, T-Lymphocyte , HLA Antigens , Histocompatibility Antigens Class I , Histocompatibility Antigens Class II , Humans , Tandem Mass Spectrometry
J Biol Chem ; 297(6): 101362, 2021 12.
Article in English | MEDLINE | ID: covidwho-1751075


The Nsp9 replicase is a conserved coronaviral protein that acts as an essential accessory component of the multi-subunit viral replication/transcription complex. Nsp9 is the predominant substrate for the essential nucleotidylation activity of Nsp12. Compounds specifically interfering with this viral activity would facilitate its study. Using a native mass-spectrometry-based approach to screen a natural product library for Nsp9 binders, we identified an ent-kaurane natural product, oridonin, capable of binding to purified SARS-CoV-2 Nsp9 with micromolar affinities. By determining the crystal structure of the Nsp9-oridonin complex, we showed that oridonin binds through a conserved site near Nsp9's C-terminal GxxxG-helix. In enzymatic assays, oridonin's binding to Nsp9 reduces its potential to act as substrate for Nsp12's Nidovirus RdRp-Associated Nucleotidyl transferase (NiRAN) domain. We also showed using in vitro cellular assays oridonin, while cytotoxic at higher doses has broad antiviral activity, reducing viral titer following infection with either SARS-CoV-2 or, to a lesser extent, MERS-CoV. Accordingly, these preliminary findings suggest that the oridonin molecular scaffold may have the potential to be developed into an antiviral compound to inhibit the function of Nsp9 during coronaviral replication.

Antiviral Agents/pharmacology , COVID-19/drug therapy , Diterpenes, Kaurane/pharmacology , RNA-Binding Proteins/metabolism , SARS-CoV-2/drug effects , Viral Nonstructural Proteins/metabolism , Virus Replication/drug effects , Animals , Antiviral Agents/chemistry , Binding Sites/drug effects , Biological Products/chemistry , Biological Products/pharmacology , COVID-19/metabolism , COVID-19/virology , Chlorocebus aethiops , Diterpenes, Kaurane/chemistry , Humans , Molecular Docking Simulation , RNA-Binding Proteins/chemistry , SARS-CoV-2/chemistry , SARS-CoV-2/physiology , Vero Cells , Viral Nonstructural Proteins/chemistry
Proteomics ; 21(17-18): e2100036, 2021 09.
Article in English | MEDLINE | ID: covidwho-1162932


SARS-CoV-2 has caused a significant ongoing pandemic worldwide. A number of studies have examined the T cell mediated immune responses against SARS-CoV-2, identifying potential T cell epitopes derived from the SARS-CoV-2 proteome. Such studies will aid in identifying targets for vaccination and immune monitoring. In this study, we applied tandem mass spectrometry and proteomic techniques to a library of ∼40,000 synthetic peptides, in order to generate a large dataset of SARS-CoV-2 derived peptide MS/MS spectra. On this basis, we built an online knowledgebase, termed virusMS (, to document, annotate and analyse these synthetic peptides and their spectral information. VirusMS incorporates a user-friendly interface to facilitate searching, browsing and downloading the database content. Detailed annotations of the peptides, including experimental information, peptide modifications, predicted peptide-HLA (human leukocyte antigen) binding affinities, and peptide MS/MS spectral data, are provided in virusMS.

COVID-19 , SARS-CoV-2 , Humans , Peptides , Proteomics , Tandem Mass Spectrometry