Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(2)

Published: Jan. 4, 2023

The nonstructural protein 3 (NSP3) of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) contains a conserved macrodomain enzyme (Mac1) that is critical for pathogenesis and lethality. While small-molecule inhibitors Mac1 have great therapeutic potential, at outset COVID-19 pandemic, there were no well-validated this nor, indeed, family, making target pharmacological orphan. Here, we report structure-based discovery development several different chemical scaffolds exhibiting low- to sub-micromolar affinity through iterations computer-aided design, structural characterization by ultra-high-resolution crystallography, binding evaluation. Potent designed with in silico fragment linkage ultra-large library docking over 450 million molecules. Both techniques leverage computational exploration tangible space are applicable other orphans. Overall, 160 ligands 119 discovered, 153 Mac1-ligand complex crystal structures determined, typically 1 Å resolution or better. Our analyses discovered selective cell-permeable molecules, unexpected ligand-mediated conformational changes within active site, key inhibitor motifs will template future drug against Mac1.

Language: Английский

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Neutralization escape, infectivity, and membrane fusion of JN.1-derived SARS-CoV-2 SLip, FLiRT, and KP.2 variants

Cell Reports, Journal Year: 2024, Volume and Issue: 43(8), P. 114520 - 114520

Published: July 17, 2024

Highlights•SLip, FLiRT, and KP.2 are poorly neutralized by bivalent-vaccinated sera•XBB.1.5-vaccinated hamster JN.1 patient sera SLip, KP.2•S mutations R346T, L455S, F456L alter ACE2 binding neutralization epitopes•SLip, spikes exhibit less fusion processing relative to JN.1SummaryWe investigate JN.1-derived subvariants for antibodies in vaccinated individuals, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected patients, or class III monoclonal antibody S309. Compared JN.1, KP.2, especially FLiRT increased resistance BA.2.86/JN.1-wave convalescent human sera. XBB.1.5 monovalent-vaccinated robustly neutralize but have reduced efficiency SLip. All resistant S309 show decreased infectivity, cell-cell fusion, spike JN.1. Modeling reveals that L455S SLip reduce ACE2, while R346T strengthens it. These three mutations, alongside D339H, key epitopes spike, likely explaining the sensitivity of these neutralization. Our findings highlight suggest future vaccine formulations should consider as an immunogen, although current monovalent could still offer adequate protection.Graphical abstract

Language: Английский

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Characteristics of JN.1-derived SARS-CoV-2 subvariants SLip, FLiRT, and KP.2 in neutralization escape, infectivity and membrane fusion

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: May 21, 2024

SARS-CoV-2 variants derived from the immune evasive JN.1 are on rise worldwide. Here, we investigated JN.1-derived subvariants SLip, FLiRT, and KP.2 for their ability to be neutralized by antibodies in bivalent-vaccinated human sera, XBB.1.5 monovalent-vaccinated hamster sera people infected during BA.2.86/JN.1 wave, class III monoclonal antibody (Mab) S309. We found that compared parental JN.1, SLip KP.2, especially exhibit increased resistance COVID-19 BA.2.86/JN.1-wave convalescent sera. Interestingly, monovalent vaccinated robustly FLiRT but had reduced efficiency SLip. These were resistant neutralization Mab In addition, aspects of spike protein biology including infectivity, cell-cell fusion processing, these subvariants, a decreased infectivity membrane relative correlating with processing. Homology modeling revealed L455S F456L mutations local hydrophobicity hence its binding ACE2. contrast, additional R346T mutation strengthened conformational support receptor-binding motif, thus counteracting effects F456L. three mutations, alongside D339H, which is present all sublineages, alter epitopes targeted therapeutic Mabs, I S309, explaining sensitivity Together, our findings provide insight into newly emerged suggest future vaccine formulations should consider as immunogen, although current could still offer adequate protection.

Language: Английский

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PARP14 and PARP9/DTX3L regulate interferon-induced ADP-ribosylation

The EMBO Journal, Journal Year: 2024, Volume and Issue: 43(14), P. 2929 - 2953

Published: June 4, 2024

Language: Английский

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DELTEX E3 ligases ubiquitylate ADP-ribosyl modification on protein substrates

Science Advances, Journal Year: 2022, Volume and Issue: 8(40)

Published: Oct. 5, 2022

Ubiquitylation had been considered limited to protein lysine residues, but other substrates have recently emerged. Here, we show that DELTEX E3 ligases specifically target the 3′ hydroxyl of adenosine diphosphate (ADP)–ribosyl moiety can be linked a protein, thus generating hybrid ADP-ribosyl-ubiquitin modification. Unlike known hydroxyl-specific E3s, which proceed via covalent E3~ubiqutin intermediate, enzymes are RING E3s stimulate direct ubiquitin transfer from E2~ubiquitin onto substrate. However, DELTEXes follow previously unidentified paradigm for whereby ligase not only forms scaffold also provides catalytic residues activate acceptor. Comparative analysis hydroxyl-ubiquitylating active sites points recurring use histidine residue, which, in is potentiated by glutamate triad-like manner. In addition, determined hydrolase specificity profile this modification, identifying human and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) could reverse it cells.

Language: Английский

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The molecular mechanism of SARS-CoV-2 evading host antiviral innate immunity

Virology Journal, Journal Year: 2022, Volume and Issue: 19(1)

Published: March 19, 2022

The newly identified Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has resulted in a global health emergency (COVID-19) because of its rapid spread and high mortality. Since the virus epidemic, many pathogenic mechanisms have been revealed, virus-related vaccines successfully developed applied clinical practice. However, pandemic is still developing, new mutations are emerging. Virus pathogenicity closely related to immune status host. As innate immunity body's first defense against viruses, understanding inhibitory effect SARS-CoV-2 on great significance for determining target antiviral intervention. This review summarizes molecular mechanism by which escapes host system, including suppressing production blocking adaptive priming. Here, one hand, we devoted ourselves summarizing combined action cells, cytokines, chemokines fine-tune outcome infection immunopathogenesis. On other focused effects immunity, enhancing viral adhesion, increasing rate invasion, inhibiting transcription translation immune-related mRNA, cellular mRNA degradation, protein transmembrane transport. underlying should provide theoretical support developing future targeted drugs SARS-CoV-2. Nevertheless, completely virus, people's it process growth, various studies also being carried out. Although strive make our as inclusive possible, there may be incompleteness.

Language: Английский

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NAD+ in COVID-19 and viral infections

Trends in Immunology, Journal Year: 2022, Volume and Issue: 43(4), P. 283 - 295

Published: Feb. 11, 2022

Language: Английский

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Treatment of SARS-CoV-2-induced pneumonia with NAD+ and NMN in two mouse models

Cell Discovery, Journal Year: 2022, Volume and Issue: 8(1)

Published: April 29, 2022

The global COVID-19 epidemic has spread rapidly around the world and caused death of more than 5 million people. It is urgent to develop effective strategies treat patients. Here, we revealed that SARS-CoV-2 infection resulted in dysregulation genes associated with NAD+ metabolism, immune response, cell mice, similar We therefore investigated effect treatment its intermediate (NMN) found pneumonia phenotypes, including excessive inflammatory infiltration, hemolysis, embolization SARS-CoV-2-infected lungs were significantly rescued. Cell was suppressed substantially by NMN supplementation. More strikingly, supplementation can protect 30% aged mice infected lethal mouse-adapted from death. Mechanically, or partially rescued disturbed gene expression metabolism infection. Thus, our vivo mouse study supports trials for treating patients targeting pathway.

Language: Английский

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SARS-CoV-2 Mac1 is required for IFN antagonism and efficient virus replication in cell culture and in mice

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(35)

Published: Aug. 22, 2023

Several coronavirus (CoV) encoded proteins are being evaluated as targets for antiviral therapies COVID-19. Included in these drug is the conserved macrodomain, or Mac1, an ADP-ribosylhydrolase and ADP-ribose binding protein a small domain at N terminus of nonstructural 3. Utilizing point mutant recombinant viruses, Mac1 was shown to be critical both murine hepatitis virus (MHV) severe acute respiratory syndrome (SARS)-CoV virulence. However, potential target, it imperative understand how complete deletion impacts replication pathogenesis different CoVs. To this end, we created bacterial artificial chromosomes (BACs) containing deletions (ΔMac1) MHV, MERS-CoV, SARS-CoV-2. While were unable recover infectious from MHV MERS-CoV ΔMac1 BACs, SARS-CoV-2 readily recovered BAC transfection, indicating stark difference requirement between Furthermore, replicated near wild-type levels multiple cell lines susceptible infection. mouse model infection, quickly cleared causing minimal pathology without any morbidity. induced increased interferon (IFN) IFN-stimulated gene expression culture mice, that blocks IFN responses which may contribute its attenuation. infection also led reduction inflammatory monocytes neutrophils. These results demonstrate only minimally replication, unlike but required unique target.

Language: Английский

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Protein post-translational modification in SARS-CoV-2 and host interaction

Frontiers in Immunology, Journal Year: 2023, Volume and Issue: 13

Published: Jan. 13, 2023

SARS-CoV-2 can cause lung diseases, such as pneumonia and acute respiratory distress syndrome, multi-system dysfunction. Post-translational modifications (PTMs) related to are conservative pathogenic, the common PTMs glycosylation, phosphorylation, acylation. The glycosylation of mainly occurs on spike (S) protein, which mediates entry virus into cells through interaction with angiotensin-converting enzyme 2. utilizes glycans cover its epitopes evade immune response S protein. Phosphorylation nucleocapsid (N) protein improves selective binding viral RNA promotes replication transcription, thereby increasing load in host. Succinylated N membrane(M) proteins synergistically affect particle assembly. regulates affinity for other genome acetylation. acetylated envelope (E) interacts bromodomain-containing 2/4 influence host response. Both palmitoylation myristoylation sites infectivity. Papain-like protease is a domain NSP3 that dysregulates inflammation by deubiquitination impinges IFN-I antiviral responses deISGylation. Ubiquitination ORF7a inhibits IFN-α signaling blocking STAT2 phosphorylation. methylation inhibit formation stress granules promote RNA, promoting production particles. macrodomain reverse ADP-ribosylation proteins, cascade IFN core, intracellular SARS-CoV-2. On whole, have fundamental roles entry, replication, assembly, Mutations various variants, lead changes at corresponding sites, different biological effects. In this paper, we reviewed effects cells, whose application inform strategies inhibiting infection facilitating treatment vaccine development COVID-19.

Language: Английский

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