Crystal structure of Nsp15 endoribonuclease <scp>NendoU</scp> from <scp>SARS‐CoV</scp>‐2

Kim, Young Chang; Jedrzejczak, R.; Maltseva, N.; Wilamowski, Mateusz; Endres, M.; Godzik, Adam; Michalska, K.; Joachimiak, A.

doi:10.1002/pro.3873

Cited by 328 publications

(299 citation statements)

References 42 publications

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“…The enzyme cleaves efficiently eicosamer 5'GAACU¯CAU¯GGACCU¯U¯GGCAG3' at all four uridine sites ( Fig. 1), as well as synthetic EndoU substrate ( 5′-6-FAM-dArU¯dAdA -6-TAMRA-3′ ) 8 in the presence of Mn 2+ and the reaction rate increases with metal ion concentration. The cleavage of the eicosamer seems to show no sequence preference as 5'CU¯C, 5'AU¯G, 5'CU¯U and 5'UU¯G are recognized and cut, especially at higher manganese concentration ( Fig.…”

Section: Nsp15 Nuclease Activitymentioning

confidence: 92%

Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2

Kim

Wower

Maltseva

et al. 2020

Preprint

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SARS-CoV-2 Nsp15 is a uridylate-specific endoribonuclease with C-terminal catalytic domain belonging to the EndoU family. It degrades the polyuridine extensions in (−) sense strand of viral RNA and some non-translated RNA on (+) sense strand. This activity seems to be responsible for the interference with the innate immune response and evasion of host pattern recognition. Nsp15 is highly conserved in coronaviruses suggesting that its activity is important for virus replication. Here we report first structures with bound nucleotides and show that SARS-CoV-2 Nsp15 specifically recognizes U in a pattern previously predicted for EndoU. In the presence of manganese ions, the enzyme cleaves unpaired RNAs. Inhibitors of Nsp15 have been reported but not actively pursued into therapeutics. The current COVID-19 pandemic brought to attention the repurposing of existing drugs and the rapid identification of new antiviral compounds. Tipiracil is an FDA approved drug that is used with trifluridine in the treatment of colorectal cancer. Here, we combine crystallography, biochemical and whole cell assays, and show that this compound inhibits SARS-CoV-2 Nsp15 and interacts with the uridine binding pocket of the enzyme’s active site, providing basis for the uracil scaffold-based drug development.

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Section: Nsp15 Nuclease Activitymentioning

confidence: 92%

Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2

Kim

Wower

Maltseva

et al. 2020

Preprint

Self Cite

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“…There was an attempt to design a theoretical model of a carbon nanotube-UNA drug matrix to block the entry of human immunodeficiency virus (HIV) [86]. Moreover, a recent document demonstrated that UNA has the potential to strongly interact with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Nsp15, an endoribonuclease which is essential for the lifecycle of coronaviruses [87,88]. Molecular docking and dynamics analyses show that UNA is predicted to bind stably with the catalytic residues of SARS-CoV-2 Nsp15 via hydrogen bonds, suggesting that UNA may represent one of drug candidates to inhibit replication of SARS-CoV-2, the virus responsible for the coronavirus disease 2019 (COVID-19) pandemic.…”

Section: Antiviral Effectsmentioning

confidence: 99%

Therapeutic Potential of Ursonic Acid: Comparison with Ursolic Acid

Son

Lee

2020

Biomolecules

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Plants have been used as drugs to treat human disease for centuries. Ursonic acid (UNA) is a naturally occurring pentacyclic triterpenoid extracted from certain medicinal herbs such as Ziziphus jujuba. Since the pharmacological effects and associated mechanisms of UNA are not well-known, in this work, we attempt to introduce the therapeutic potential of UNA with a comparison to ursolic acid (ULA), a well-known secondary metabolite, for beneficial effects. UNA has a keto group at the C-3 position, which may provide a critical difference for the varied biological activities between UNA and ULA. Several studies previously showed that UNA exerts pharmaceutical effects similar to, or stronger than, ULA, with UNA significantly decreasing the survival and proliferation of various types of cancer cells. UNA has potential to exert inhibitory effects in parasitic protozoa that cause several tropical diseases. UNA also exerts other potential effects, including antihyperglycemic, anti-inflammatory, antiviral, and antioxidant activities. Of note, a recent study highlighted the suppressive potential of UNA against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Molecular modifications of UNA may enhance bioavailability, which is crucial for in vivo and clinical studies. In conclusion, UNA has promising potential to be developed in anticancer and antiprotozoan pharmaceuticals. In-depth investigations may increase the possibility of UNA being developed as a novel reagent for chemotherapy.

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“…Third, conformational B-cell epitopes were predicted with DiscoTope2 on molecular structures of SARS-CoV-2 proteins 8 . The unprecedented speed at which experimental SARS-CoV-2 structures have been solved and deposited in the PDB allowed us to predict epitopes on 13 proteins (Table S3) [9][10][11][12] . Coverage was further extended to all proteins except E envelope protein, ORF9b and ORF14, by including high-quality homology models obtained with the Robetta platform and ab-initio models from the CASP-commons competition ( Table S3) 13,14 .…”

Section: Epitope Predictionsmentioning

confidence: 99%

In silico detection of SARS-CoV-2 specific B-cell epitopes and validation in ELISA for serological diagnosis of COVID-19

Phan

Subramanian

Kim

et al. 2020

Preprint

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Rapid generation of diagnostics is paramount to understand epidemiology and to control the spread of emerging infectious diseases such as COVID-19. Computational methods to predict serodiagnostic epitopes that are specific for the pathogen could help accelerate the development of new diagnostics. A systematic survey of 27 SARS-CoV-2 proteins was conducted to assess whether existing B-cell epitope prediction methods, combined with comprehensive mining of sequence databases and structural data, could predict whether a particular protein would be suitable for serodiagnosis. Nine of the predictions were validated with recombinant SARS-CoV-2 proteins in the ELISA format using plasma and sera from patients with SARS-CoV-2 infection, and a further 11 predictions were compared to the recent literature. Results appeared to be in agreement with 12 of the predictions, in disagreement with 3, while a further 5 were deemed inconclusive. We showed that two of our top five candidates, the N-terminal fragment of the nucleoprotein and the receptor-binding domain of the spike protein, have the highest sensitivity and specificity and signal-to-noise ratio for detecting COVID-19 sera/plasma by ELISA. Mixing the two antigens together for coating ELISA plates led to a sensitivity of 94% (N=80 samples from persons with RT-PCR confirmed SARS-CoV2 infection), and a specificity of 97.2% (N=106 control samples).

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Crystal structure of Nsp15 endoribonuclease NendoU from SARS‐CoV‐2

Cited by 328 publications

References 42 publications

Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2

Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2

Therapeutic Potential of Ursonic Acid: Comparison with Ursolic Acid

In silico detection of SARS-CoV-2 specific B-cell epitopes and validation in ELISA for serological diagnosis of COVID-19

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