Evaluation of inhibitory efficacy of plantaricin JK against NSP1 from SARS-CoV-2 by in silico methods

Aspects of Molecular Medicine, Journal Year: 2025, Volume and Issue: unknown, P. 100080 - 100080

Published: March 1, 2025

Language: Английский

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Revealing druggable cryptic pockets in the Nsp1 of SARS-CoV-2 and other β-coronaviruses by simulations and crystallography

eLife, Journal Year: 2022, Volume and Issue: 11

Published: Nov. 22, 2022

Non-structural protein 1 (Nsp1) is a main pathogenicity factor of α- and β-coronaviruses. Nsp1 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) suppresses the host gene expression by sterically blocking 40S ribosomal subunits promoting mRNA degradation. This mechanism leads to downregulation translation-mediated innate immune response in cells, ultimately mediating observed evasion capabilities SARS-CoV-2. Here, combining extensive molecular dynamics simulations, fragment screening crystallography, we reveal druggable pockets Nsp1. Structural computational solvent mapping analyses indicate partial crypticity these newly discovered binding sites. The results fragment-based via X-ray crystallography confirm druggability major pocket Finally, show how targeting this could disrupt Nsp1-mRNA complex open novel avenue design new inhibitors for other Nsp1s present homologous

Language: Английский

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SARS-CoV2 Nsp1 is a metal-dependent DNA and RNA endonuclease

BioMetals, Journal Year: 2024, Volume and Issue: unknown

Published: March 28, 2024

Abstract Over recent years, we have been living under a pandemic, caused by the rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV2). One major virulence factors Coronaviruses is Non-structural protein 1 (Nsp1), known to suppress host cells translation machinery, allowing virus produce its own proteins, propagate and invade new cells. To unveil molecular mechanisms SARS-CoV2 Nsp1, addressed biochemical biophysical properties in presence calcium, magnesium manganese. Our findings indicate that solution monomer binds both manganese with high affinity. Surprisingly, our results show Nsp1 alone displays metal-dependent endonucleolytic activity towards RNA DNA, regardless ribosome. These as nuclease within family. Furthermore, double variant R124A/K125A presents no for RNA, although it retains suggesting distinct binding sites DNA RNA. Thus, present first time, evidence activities are modulated different metals, which proposed play an important role during viral infection. This research contributes significantly understanding action Coronaviruses.

Language: Английский

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Interaction of SARS-CoV-2 with host cells and antibodies: experiment and simulation

Chemical Society Reviews, Journal Year: 2023, Volume and Issue: 52(18), P. 6497 - 6553

Published: Jan. 1, 2023

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of devastating global COVID-19 pandemic announced by WHO in March 2020.

Language: Английский

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An Evolutionarily Conserved Strategy for Ribosome Binding and Host Translation Inhibition by β-coronavirus Non-structural Protein 1

Journal of Molecular Biology, Journal Year: 2023, Volume and Issue: 435(20), P. 168259 - 168259

Published: Sept. 1, 2023

Language: Английский

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Structural biology of SARS-CoV-2 leader protein (nsp1)

Crystallography Reviews, Journal Year: 2024, Volume and Issue: unknown, P. 1 - 17

Published: April 15, 2024

Following infection, SARS-CoV-2's leader protein nsp1 is the very first viral to be expressed. Its sequence highly conserved among different SARS-CoV-2 strains, indicating its vital function that makes it a promising target for drugs and vaccination. Nsp1 takes over host cell expression machinery facilitate production of virions by binding ribosome obstructing any but proteins. To date, 28 structures obtained cryo-electron microscopy X-ray diffraction have been published, showing protein's structural features as well number interactions with ribosomes. has also shown interfere immune response pathways connected cytokine storm causing organ damage failure in COVID-19 patients.

Language: Английский

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High-Confidence Placement of Fragments into Electron Density Using Anomalous Diffraction—A Case Study Using Hits Targeting SARS-CoV-2 Non-Structural Protein 1

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(13), P. 11197 - 11197

Published: July 7, 2023

The identification of multiple simultaneous orientations small molecule inhibitors binding to a protein target is common challenge. It has recently been reported that the conformational heterogeneity ligands widely underreported in Protein Data Bank, which likely impede optimal exploitation improve affinity these ligands. Significantly less even known about for fragments (<300 Da), although this information would be essential subsequent fragment optimisation using growing, linking or merging and rational structure-based design. Here, we use hits SARS-CoV-2 non-structural 1 (nsp1) N-terminal domain propose general procedure unambiguously identifying 2-dimensional containing either sulphur chloro substituents within wavelength range most tunable beamlines. By measuring datasets at two energies, beamline operating vacuum optimised data collection very low X-ray show anomalous signal can used identify and/or verify conformations. Although specific case identified positions chlorine bound their target, are confident work further expanded additional atoms ions often occur fragments. Finally, our improvements understanding will also serve nsp1

Language: Английский

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Structural Insights into SARS-CoV-2 Nonstructural Protein 1 Interaction with Human Cyclophilin and FKBP1 to Regulate Interferon Production

The Journal of Physical Chemistry Letters, Journal Year: 2024, Volume and Issue: 15(4), P. 919 - 924

Published: Jan. 19, 2024

The ongoing coronavirus disease 2019 (COVID-19) pandemic caused by the SARS-CoV-2 and perpetual rise of new variants warrant investigation molecular structural details infection process modulation host defense viral proteins. This Letter reports combined experimental computational approaches to provide key insights into functional basis Nsp1's association with different cyclophilins FKBPs in regulating COVID-19 infection. We demonstrated real-time stability dynamics Nsp1-CypA/FKBP1A complex investigated repurposing potential inhibitors that could block these interactions. Overall, we provided inhibitory role Nsp1 downstream interferon production, a aspect for prevents or related family corona virus

Language: Английский

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High-confidence placement of low-occupancy fragments into electron density using the anomalous signal of sulfur and halogen atoms

Acta Crystallographica Section D Structural Biology, Journal Year: 2024, Volume and Issue: 80(6), P. 451 - 463

Published: June 1, 2024

Fragment-based drug design using X-ray crystallography is a powerful technique to enable the development of new lead compounds, or probe molecules, against biological targets. This study addresses need determine fragment binding orientations for low-occupancy fragments with incomplete electron density, an essential step before further molecule. Halogen atoms play multiple roles in discovery due their unique combination electronegativity, steric effects and hydrophobic properties. Fragments incorporating halogen serve as promising starting points hit-to-lead they often establish bonds target proteins, potentially enhancing affinity selectivity, well counteracting resistance. Here, aim was unambiguously identify hits SARS-CoV-2 nonstructural protein 1 (nsp1) which contain sulfur and/or chlorine, bromine iodine substituents. The carefully selected nsp1 analogue were focused on by employing anomalous scattering combined Pan-Dataset Density Analysis (PanDDA). Anomalous difference Fourier maps derived from diffraction data collected at both standard long-wavelength X-rays compared. discrepancies observed iodine-containing different energies attributed site-specific radiation-damage stemming strong absorption I atoms, likely cause cleavage C-I bond. A reliable effective data-collection strategy containing while mitigating radiation damage presented.

Language: Английский

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In vitroreconstitution of SARS CoV-2 Nsp1-induced mRNA cleavage reveals the key roles of the N-terminal domain of Nsp1 and the RRM domain of eIF3g

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: May 26, 2023

SARS CoV-2 nonstructural protein 1 (Nsp1) is the major pathogenesis factor that inhibits host translation using a dual strategy of impairing initiation and inducing endonucleolytic cleavage cellular mRNAs. To investigate mechanism cleavage, we reconstituted it in vitro on β-globin, EMCV IRES CrPV mRNAs use unrelated mechanisms. In all instances, required Nsp1 only canonical translational components (40S subunits factors), arguing against involvement putative RNA endonuclease. Requirements for factors differed these mRNAs, reflecting their requirements ribosomal attachment. Cleavage mRNA was supported by minimal set consisting 40S eIF3g's RRM domain. The site located coding region 18 nucleotides downstream from entrance indicating occurs solvent side subunit. Mutational analysis identified positively charged surface Nsp1's N-terminal domain (NTD) above mRNA-binding channel contain residues essential cleavage. These were three highlighting general roles Nsp1-NTD per se, irrespective mode

Language: Английский

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