Profile of Andrea Rinaldo

Gabrielsen, Paul

doi:10.1073/pnas.1401995111

Cited by 4 publications

(7 citation statements)

References 11 publications

(6 reference statements)

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“…It is likely that the interaction between Nsp8 and Nsp15 may provide a possible explanation (i.e., the direct interaction might induce a conformational change in Nsp15). Indeed, the SARS-CoV Nsp7/Nsp8 complex may bind RNA and has been shown to confer RNA binding ability to SARS-CoV Nsp12 (22,23). We speculate, therefore, that Nsp8 or the Nsp7/Nsp8 complex may increase NendoU activity by enhancing the RNA binding ability of Nsp15.…”

Section: Discussionmentioning

confidence: 89%

Structural and Biochemical Characterization of Endoribonuclease Nsp15 Encoded by Middle East Respiratory Syndrome Coronavirus

Zhang

Yan

et al. 2018

J Virol

112

127

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Nonstructural protein 15 (Nsp15) encoded by coronavirus (CoV) is a nidoviral uridylate-specific endoribonuclease (NendoU) that plays an essential role in the life cycle of the virus. Structural information on this crucial protein from the Middle East respiratory syndrome CoV (MERS-CoV), which is lethally pathogenic and has caused severe respiratory diseases worldwide, is lacking. Here, we determined the crystal structure of MERS-CoV Nsp15 at a 2.7-Å resolution and performed the relevant biochemical assays to study how NendoU activity is regulated. Although the overall structure is conserved, MERS-CoV Nsp15 shows unique and novel features compared to its homologs. Serine substitution of residue F285, which harbors an aromatic side chain that disturbs RNA binding compared with that of other homologs, increases catalytic activity. Mutations of residues residing on the oligomerization interfaces that distort hexamerization, namely, N38A, Y58A, and N157A, decrease thermostability, decrease affinity of binding with RNA, and reduce the NendoU activity of Nsp15. In contrast, mutant D39A exhibits increased activity and a higher substrate binding capacity. Importantly, Nsp8 was found to interact with both monomeric and hexameric Nsp15. The Nsp7/Nsp8 complex displays a higher binding affinity for Nsp15. Furthermore, Nsp8 and the Nsp7/Nsp8 complex also enhance the NendoU activity of hexameric Nsp15 Taking the findings together, this work first provides evidence on how the activity of Nsp15 may be functionally mediated by catalytic residues, oligomeric assembly, RNA binding efficiency, or the possible association with other nonstructural proteins. The lethally pathogenic Middle East respiratory syndrome coronavirus (MERS-CoV) and the severe acute respiratory syndrome coronavirus (SARS-CoV) pose serious threats to humans. Endoribonuclease Nsp15 encoded by coronavirus plays an important role in viral infection and pathogenesis. This study determines the structure of MERS-CoV Nsp15 and demonstrates how the catalytic activity of this protein is potentially mediated, thereby providing structural and functional evidence for developing antiviral drugs. We also hypothesize that the primase-like protein Nsp8 and the Nsp7/Nsp8 complex may interact with Nsp15 and affect enzymatic activity. This contributes to the understanding of the association of Nsp15 with the viral replication and transcription machinery.

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Section: Discussionmentioning

confidence: 89%

Structural and Biochemical Characterization of Endoribonuclease Nsp15 Encoded by Middle East Respiratory Syndrome Coronavirus

Zhang

Yan

et al. 2018

J Virol

112

127

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show abstract

“…It is a vital enzyme for coronavirus replication. In complex with nsp 7 and nsp 8 as co-factors, this protein is greatly stimulated to perform polymerase activity [ 2 , 37 ]. Homology studies revealed that the SARS-COV nsp 12 shared several kinase catalytic residues with protein kinases [ 22 ] therefore suggesting potential nucleotide-binding site within the enzyme domain and nucleotidyl transfer [ 25 ] function.…”

Section: Resultsmentioning

confidence: 99%

Molecular docking and ADMET studies of Allium cepa, Azadirachta indica and Xylopia aethiopica isolates as potential anti-viral drugs for Covid-19

et al. 2021

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Plants are repository of important constituents with proven efficacy against many human diseases including viral diseases. The antiviral activity of many plants including Azadirachta indica, Xylopia aethiopica and Allium cepa has been reported. The novel coronavirus disease is no exception among viral diseases in which plant compounds could serve as potent antagonist. Therefore, our study investigated the inhibitory potentials of Azadirachta indica and Xylopia aethiopica isolates against SARS-CoV-2 viral accessory proteins and the host serine protease. The protein data (SARS-CoV-2 Papain like protease (PLpro) (PDB: 6wx4), Chymotrypsin-like main protease (3CLpro) (PDB:6YB7), SARS-CoV nsp 12 (PDB: 6nus), Host cell protease (TMPRSS1) (PDB:5ce1) were obtained from the protein data bank (PDB), while the SDS format of each Ligands were obtained from Pubchem database. Molecular docking analysis was performed with Auto Dock Vina 1.5.6 and visualization of the interaction between the ligands and protein was done with discovery studio 2019. The ADMET prediction of pharmacokinetics and toxicity properties of the ligands was obtained using vNN Web Server. Our result showed that all the plant isolates demonstrated negative Gibb’s free energy, indicating good binding affinity for both the viral and host protein. Overall, twenty-three of the forty-seven isolates showed good binding affinity comparable with dexamethasone that was used as reference drug. Although many of the compounds have good binding affinity for the viral and host proteins, based on the ADMET prediction, only Azadironic acid, Nimbionone, Nimbionol and Nimocinol all from A. indica could serve as potential drug candidate with good pharmacokinetics and toxicity profile. This study provides an insight into potential inhibitors and novel drug candidates for SARS-CoV-2. Further studies will look forward into the wet laboratory validation of Azadironic acid, Nimbionone, Nimbionol and Nimocinol against corona virus disease. Supplementary Information The online version contains supplementary material available at 10.1007/s13337-021-00682-7.

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“…The SARS-CoV (betacoronavirus) nsp7 protein structure (83-amino acid) was determined using both NMR [ 62 ] and X-ray crystallography with a hexadecameric supercomplex consisting of recombinant nsp7 and nsp8 [ 63 ]. Reverse-genetic studies aimed at particular residues within SARS-CoV nsp7 verified the significance of this protein for the virus replication [ 64 ], even though the effect of single point mutations was less than predicted based on the in vitro biochemical characterization of the RNA-binding properties of protein complexes containing nsp7. The nsp7-fold includes four helices with quiet different position and spatial orientation, suggesting that the protein's configuration is mainly affected by the interaction with nsp8 [ 65 ].…”

Section: Non-structural Proteins (Nsps) Of Coronavirusesmentioning

confidence: 99%

“…Biochemistry and reverse genetics studies pointed to an important role in RNA synthesis for SARS-CoV nsp8 residues K58, P183, and R190 ( Fig. 1 c), replacing which was lethal to SARS-CoV whereas P183 and R190 residues were presumed to be involved in interactions with nsp12, while K58 may be critical for interactions with nsp8–RNA [ 64 ]. The amino acid sequence alignment for nsp8 of SARS-CoV-2 compared to other human coronaviruses is shown in Fig.…”

Section: Non-structural Proteins (Nsps) Of Coronavirusesmentioning

confidence: 99%

“…The CoV genome encodes two replicase polyproteins pp1a and pp1ab to support effective replication, which is processed proteolytically into 16 non-structural proteins (nsps) [ 21 , 91 , 92 ] that assemble into the membrane-associated replication-transcription complexes (RTCs), to drive viral genome replication and translation. The RNA-dependent RNA polymerase (nsp12) and the helicase (nsp13) are main components of RTC [ 28 , 29 , 64 ]. Positive stranded RNA viruses with a genome greater than 7 kb have been shown to encode helicases [ 93 , 94 ] that are classified into six super-families (SF1-SF6) and participate in almost every aspect of nucleic acid metabolism [ 95 ].…”

Section: Non-structural Proteins (Nsps) Of Coronavirusesmentioning

confidence: 99%

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Structural and functional insights into non-structural proteins of coronaviruses

Rohaim

Naggar

Clayton

et al. 2021

Microbial Pathogenesis

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Profile of Andrea Rinaldo

Cited by 4 publications

References 11 publications

Structural and Biochemical Characterization of Endoribonuclease Nsp15 Encoded by Middle East Respiratory Syndrome Coronavirus

Structural and Biochemical Characterization of Endoribonuclease Nsp15 Encoded by Middle East Respiratory Syndrome Coronavirus

Molecular docking and ADMET studies of Allium cepa, Azadirachta indica and Xylopia aethiopica isolates as potential anti-viral drugs for Covid-19

Structural and functional insights into non-structural proteins of coronaviruses

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