Antiviral drug design based on structural insights into the N-terminal domain and C-terminal domain of the SARS-CoV-2 nucleocapsid protein

Luan, Xiaodong; Li, Xinming; Li, Yufan; Su, Gengchen; Yin, Wanchao; Jiang, Yi; Xu, Ning; Wang, Rui; Wang, Cheng; Ye, Jin; Zhang, Leike; Xu, Hao; Xue, Yi; Zhang, Shuyang

doi:10.1016/j.scib.2022.10.021

Cited by 22 publications

(18 citation statements)

References 43 publications

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“…They suggest the interaction as little-specific and preferential binding to rely on the ssRNA nature 8 . In line with this, a recently solved complex structure with a short, unrelated dsRNA reveals the NTD to interact exclusively – and thus non-specifically – with the phosphate backbone, giving no hint at drivers for specificity 42 . A study by Redzic et al showed NTD binding to both ss and stem-looped RNA by NMR, indicating a preference for a GU-rich single strand, but taking into account the context of NTD-flanking IDRs 40 .…”

Section: Introductionmentioning

confidence: 98%

“…Surprisingly little is known about specific RNA-recognition by N. Studies have used intentionally short, random or bulk RNAs to derive determinants of preferences with very heterogeneous/contradictive outcome 8 , 11 , 19 , 38 – 42 . Thus, N target RNA selectivity has remained enigmatic seeing the large pool of RNAs in an infected cell, but likely involves multivalency as the basis for high affinity 26 .…”

Section: Introductionmentioning

confidence: 99%

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The preference signature of the SARS-CoV-2 Nucleocapsid NTD for its 5’-genomic RNA elements

et al. 2023

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The nucleocapsid protein (N) of SARS-CoV-2 plays a pivotal role during the viral life cycle. It is involved in RNA transcription and accounts for packaging of the large genome into virus particles. N manages the enigmatic balance of bulk RNA-coating versus precise RNA-binding to designated cis-regulatory elements. Numerous studies report the involvement of its disordered segments in non-selective RNA-recognition, but how N organizes the inevitable recognition of specific motifs remains unanswered. We here use NMR spectroscopy to systematically analyze the interactions of N’s N-terminal RNA-binding domain (NTD) with individual cis RNA elements clustering in the SARS-CoV-2 regulatory 5’-genomic end. Supported by broad solution-based biophysical data, we unravel the NTD RNA-binding preferences in the natural genome context. We show that the domain’s flexible regions read the intrinsic signature of preferred RNA elements for selective and stable complex formation within the large pool of available motifs.

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Section: Introductionmentioning

confidence: 98%

Section: Introductionmentioning

confidence: 99%

The preference signature of the SARS-CoV-2 Nucleocapsid NTD for its 5’-genomic RNA elements

et al. 2023

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“…In addition to the full-length CryoEM structure [2], several X-Ray structures have been reported for isolated N or C terminal domains [46] [47] [48] [49] [50], and one NMR structure of the “linker region”, residues 191-262 [3] which shows interactions with the viral protein NSP3.…”

Section: Resultsmentioning

confidence: 99%

Efficient overexpression and purification of SARS-CoV-2 Nucleocapsid proteins inEscherichia coli

Brudenell,

Pohare,

Zafred

et al. 2024

Preprint

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The fundamental biology of Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid protein (Ncap), its use in diagnostic assays and its potential application as a vaccine component have received considerable attention since the outbreak of the Covid19 pandemic in late 2019. Here we report the scalable expression and purification of soluble, immunologically active, SARS-CoV-2 Ncap inEscherichia coli. Codon-optimised synthetic genes encoding the original Ncap sequence and four common variants with an N-terminal 6His affinity tag (sequence MHHHHHHG) were cloned into an inducible expression vector carrying a regulated bacteriophage T5 synthetic promoter controlled bylacoperator binding sites. The constructs were used to express Ncap proteins and protocols developed which allow efficient production of purified Ncap with yields of over 200 mg per litre of culture media. These proteins were deployed in ELISA assays to allow comparison of their responses to human sera. Our results suggest that there was no detectable difference between the 6His-tagged and untagged original Ncap proteins but there may be a slight loss of sensitivity of sera to other Ncap isolates.

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“…Antibodies targeting the S327 amino acid might exhibit reduced effectiveness in neutralizing the virus carrying the S327L mutation 60 . Consequently, the body's immune response may encounter challenges in effectively combating the infection, potentially leading to more severe disease outcomes 61 .…”

Section: Nucleocapsid (N)mentioning

confidence: 99%

Bridging Computational Predictions and Empirical Data: Insights into SARS-CoV-2 Mutational Impacts and Evolution

Shaukat,

Nguyen,

Hsu

et al. 2024

Preprint

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The emergence of SARS-CoV-2 has unleashed a global health crisis, demanding advanced research into its genomic mutations and their consequences. Our study combines computational models and empirical validation to predict the effects of these mutations, aiming to understand their impact on the virus's behaviour, including its transmissibility and immune escape mechanisms. Utilising advanced prediction tools, we analysed mutations across the virus's genome, focusing on changes to both structural and non-structural proteins. This approach identified key mutations likely to influence protein functionality and the virus's evolution. Our findings, integrating computational predictions with real-world data, offer insights into SARS-CoV-2's evolutionary path and its implications for developing vaccines and therapies. We highlight the necessity of ongoing genomic surveillance and the combined use of computational and empirical methods to stay ahead of viral mutations. This study not only deepens our understanding of SARS-CoV-2 but also lays groundwork for future research on viral evolution and pandemic response strategies, emphasizing our approach's potential to inform public health decisions and research priorities.

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Antiviral drug design based on structural insights into the N-terminal domain and C-terminal domain of the SARS-CoV-2 nucleocapsid protein

Cited by 22 publications

References 43 publications

The preference signature of the SARS-CoV-2 Nucleocapsid NTD for its 5’-genomic RNA elements

The preference signature of the SARS-CoV-2 Nucleocapsid NTD for its 5’-genomic RNA elements

Efficient overexpression and purification of SARS-CoV-2 Nucleocapsid proteins inEscherichia coli

Bridging Computational Predictions and Empirical Data: Insights into SARS-CoV-2 Mutational Impacts and Evolution

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