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O'Donoghue S, Earley B, Johnston D, McCabe MS, Kim JW, Taylor JF, Duffy C, Lemon K, McMenamy M, Cosby SL, Morris DW, Waters SM. Whole blood transcriptome analysis in dairy calves experimentally challenged with bovine herpesvirus 1 (BoHV-1) and comparison to a bovine respiratory syncytial virus (BRSV) challenge. Front Genet 2023; 14:1092877. [PMID: 36873940 PMCID: PMC9981960 DOI: 10.3389/fgene.2023.1092877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 01/25/2023] [Indexed: 02/19/2023] Open
Abstract
Bovine herpesvirus 1 (BoHV-1), is associated with several clinical syndromes in cattle, among which bovine respiratory disease (BRD) is of particular significance. Despite the importance of the disease, there is a lack of information on the molecular response to infection via experimental challenge with BoHV-1. The objective of this study was to investigate the whole-blood transcriptome of dairy calves experimentally challenged with BoHV-1. A secondary objective was to compare the gene expression results between two separate BRD pathogens using data from a similar challenge study with BRSV. Holstein-Friesian calves (mean age (SD) = 149.2 (23.8) days; mean weight (SD) = 174.6 (21.3) kg) were either administered BoHV-1 inoculate (1 × 107/mL × 8.5 mL) (n = 12) or were mock challenged with sterile phosphate buffered saline (n = 6). Clinical signs were recorded daily from day (d) -1 to d 6 (post-challenge), and whole blood was collected in Tempus RNA tubes on d six post-challenge for RNA-sequencing. There were 488 differentially expressed (DE) genes (p < 0.05, False Discovery rate (FDR) < 0.10, fold change ≥2) between the two treatments. Enriched KEGG pathways (p < 0.05, FDR <0.05); included Influenza A, Cytokine-cytokine receptor interaction and NOD-like receptor signalling. Significant gene ontology terms (p < 0.05, FDR <0.05) included defence response to virus and inflammatory response. Genes that are highly DE in key pathways are potential therapeutic targets for the treatment of BoHV-1 infection. A comparison to data from a similar study with BRSV identified both similarities and differences in the immune response to differing BRD pathogens.
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Affiliation(s)
- Stephanie O'Donoghue
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Meath, Ireland.,Discipline of Biochemistry, National University of Ireland, Galway, Ireland
| | - Bernadette Earley
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Meath, Ireland
| | - Dayle Johnston
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Meath, Ireland
| | - Matthew S McCabe
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Meath, Ireland
| | - Jae Woo Kim
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States
| | - Jeremy F Taylor
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States
| | - Catherine Duffy
- Veterinary Sciences Division, Agri-Food and Biosciences Institute, Stormont, Belfast, Northern Ireland
| | - Ken Lemon
- Veterinary Sciences Division, Agri-Food and Biosciences Institute, Stormont, Belfast, Northern Ireland
| | - Michael McMenamy
- Veterinary Sciences Division, Agri-Food and Biosciences Institute, Stormont, Belfast, Northern Ireland
| | - S Louise Cosby
- Veterinary Sciences Division, Agri-Food and Biosciences Institute, Stormont, Belfast, Northern Ireland
| | - Derek W Morris
- Discipline of Biochemistry, National University of Ireland, Galway, Ireland
| | - Sinéad M Waters
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Meath, Ireland
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Ferguson TEG, Reihill JA, Martin SL, Walker B. Novel inhibitors and activity-based probes targeting serine proteases. Front Chem 2022; 10:1006618. [PMID: 36247662 PMCID: PMC9555310 DOI: 10.3389/fchem.2022.1006618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 08/18/2022] [Indexed: 11/13/2022] Open
Abstract
Serine proteases play varied and manifold roles in important biological, physiological, and pathological processes. These include viral, bacterial, and parasitic infection, allergic sensitization, tumor invasion, and metastasis. The use of activity-based profiling has been foundational in pinpointing the precise roles of serine proteases across this myriad of processes. A broad range of serine protease-targeted activity-based probe (ABP) chemotypes have been developed and we have recently introduced biotinylated and "clickable" peptides containing P1 N-alkyl glycine arginine N-hydroxy succinimidyl (NHS) carbamates as ABPs for detection/profiling of trypsin-like serine proteases. This present study provides synthetic details for the preparation of additional examples of this ABP chemotype, which function as potent irreversible inhibitors of their respective target serine protease. We describe their use for the activity-based profiling of a broad range of serine proteases including trypsin, the trypsin-like protease plasmin, chymotrypsin, cathepsin G, and neutrophil elastase (NE), including the profiling of the latter protease in clinical samples obtained from patients with cystic fibrosis.
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Affiliation(s)
| | | | | | - Brian Walker
- Biomolecular Sciences Research Group, School of Pharmacy, Queen’s University Belfast, Belfast, United Kingdom
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Nutho B, Rungrotmongkol T. Binding recognition of substrates in NS2B/NS3 serine protease of Zika virus revealed by molecular dynamics simulations. J Mol Graph Model 2019; 92:227-235. [DOI: 10.1016/j.jmgm.2019.08.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 06/21/2019] [Accepted: 08/01/2019] [Indexed: 10/26/2022]
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Nutho B, Mulholland AJ, Rungrotmongkol T. Quantum Mechanics/Molecular Mechanics (QM/MM) Calculations Support a Concerted Reaction Mechanism for the Zika Virus NS2B/NS3 Serine Protease with Its Substrate. J Phys Chem B 2019; 123:2889-2903. [PMID: 30845796 DOI: 10.1021/acs.jpcb.9b02157] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Zika virus (ZIKV) is mainly transmitted to humans by Aedes species mosquitoes and is associated with serious pathological disorders including microcephaly in newborns and Guillain-Barré syndrome in adults. Currently, there is no vaccine or anti-ZIKV drug available for preventing or controlling ZIKV infection. An attractive drug target for ZIKV treatment is a two-compartment (NS2B/NS3) serine protease that processes viral polyprotein during infection. Here, conventional molecular dynamics simulations of the ZIKV protease in complex with peptide substrate (TGKRS) sequence at the C-terminus of NS2B show that the substrate is in the active conformation for the cleavage reaction by ZIKV protease. Hybrid quantum mechanics/molecular mechanics (QM/MM) umbrella sampling simulations (PM6/ff14SB) of acylation results reveal that proton transfer from S135 to H51 and nucleophilic attack on the substrate by S135 are concerted. The rate-limiting step involves the formation of a tetrahedral intermediate. In addition, the single-point energy QM/MM calculations, precisely at the level of coupled cluster theory (LCCSD(T)/(aug)-cc-pVTZ), were performed to correct the potential energy profiles for the first step of the acylation process. The average computed activation barrier at this level of theory is 16.3 kcal mol-1. Therefore, the computational approaches presented here are helpful for further designing of NS2B/NS3 inhibitors based on transition-state analogues.
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Affiliation(s)
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Bristol BS8 1TS , U.K
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