Crystal structure of SARS-CoV-2 nsp10/nsp16 2′-O-methylase and its implication on antiviral drug design

Lin, Sheng; Chen, Hua; Ye, Fei; Chen, Zimin; Yang, Fulun; Zheng, Yue; Cao, Yu; Qiao, Juan; Yang, Shengyong; Lu, Guangwen

doi:10.1038/s41392-020-00241-4

Cited by 87 publications

(76 citation statements)

References 4 publications

(8 reference statements)

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“…However, this domain was found to be essential for the viability of SARS-CoV-2 (and also MERS) Y96 targets both the nsp10-nsp14 and nsp10-nsp16 interactions in SARS-CoV [24]. The same seems to be valid for SARS-CoV-2 based in our results in vitro and on the crystal structure of the nsp10-nsp16 complex recently solved [41]. An alanine substitution in the residue S72 of nsp10, which has also been reported to be involved in SARS-CoV nsp10-nsp16 and nsp10-nsp14 interactions [24], resulted in a total loss of SARS-CoV-2 nsp10 ability to stimulate the exoribonucleolytic activity of nsp14.…”

Section: Discussionsupporting

confidence: 77%

New targets for drug design: Importance of nsp14/nsp10 complex formation for the 3’-5’ exoribonucleolytic activity on SARS-CoV-2

Saramago

Bárria

Costa

et al. 2021

Preprint

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus has triggered a global pandemic with devastating consequences for health-care and social-economic systems. Thus, the understanding of fundamental aspects of SARS-CoV-2 is of extreme importance.In this work, we have focused our attention on the viral ribonuclease (RNase) nsp14, since this protein was considered one of the most interferon antagonists from SARS-CoV-2, and affects viral replication. This RNase is a multifunctional protein that harbors two distinct activities, an N-terminal 3’-to-5’ exoribonuclease (ExoN) and a C-terminal N7-methyltransferase (N7-MTase), both with critical roles in coronaviruses life cycle. Namely, SARS-CoV-2 nsp14 ExoN knockout mutants are non-viable, indicating nsp14 as a prominent target for the development of antiviral drugs.Nsp14 ExoN activity is stimulated through the interaction with the nsp10 protein, which has a pleiotropic function during viral replication. In this study, we have performed the first biochemical characterization of the complex nsp14-nsp10 from SARS-CoV-2. Here we confirm the 3’-5’ exoribonuclease and MTase activities of nsp14 in this new Coronavirus, and the critical role of nsp10 in upregulating the nsp14 ExoN activity in vitro. Furthermore, we demonstrate that SARS-CoV-2 nsp14 N7-MTase activity is functionally independent of the ExoN activity. The nsp14 MTase activity also seems to be independent of the presence of nsp10 cofactor, contrarily to nsp14 ExoN.Until now, there is no available structure for the SARS-CoV-2 nsp14-nsp10 complex. As such, we have modelled the SARS-CoV-2 nsp14-nsp10 complex based on the 3D structure of the complex from SARS-CoV (PDB ID 5C8S). We also have managed to map key nsp10 residues involved in its interaction with nsp14, all of which are also shown to be essential for stimulation of the nsp14 ExoN activity. This reinforces the idea that a stable interaction between nsp10 and nsp14 is strictly required for the nsp14-mediated ExoN activity of SARS-CoV-2, as observed for SARS-CoV.We have studied the role of conserved DEDD catalytic residues of SARS-CoV-2 nsp14 ExoN. Our results show that motif I of ExoN domain is essential for the nsp14 function contrasting to the functionality of these conserved catalytic residues in SARS-CoV, and in the Middle East respiratory syndrome coronavírus (MERS). The differences here revealed can have important implications regarding the specific pathogenesis of SARS-CoV-2.The nsp10-nsp14 interface is a recognized attractive target for antivirals against SARS-CoV-2 and other coronaviruses. This work has unravelled a basis for discovering inhibitors targeting the specific amino acids here reported, in order to disrupt the assembly of this complex and interfere with coronaviruses replication.

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Section: Discussionsupporting

confidence: 77%

New targets for drug design: Importance of nsp14/nsp10 complex formation for the 3’-5’ exoribonucleolytic activity on SARS-CoV-2

Saramago

Bárria

Costa

et al. 2021

Preprint

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“…Thus, in order to ensure an accurate approach for drug discovery, we present a comprehensive study of the first structures of the SARS-CoV-2 2′- O -MTase complex that were publicly available to the scientific community. In addition to the structures reported here, similar structures of the nsp16-nsp10 complex have subsequently been determined by other groups; including structures with SAM [PDB codes 6W61 ( 37 ), 7BQ7 ( 38 ), 7C2I, and 7C2J ( 39 )] and with SFG [PDB code 6YZ1, ( 34 )]. Independently, another structure of nsp16-nsp10 in complex with m 7 GpppA + SAM was also deposited [PDB code 6WKS ( 35 )] but released subsequent to our structure (PDB code 6WQ3).…”

Section: Discussionsupporting

confidence: 62%

High-resolution structures of the SARS-CoV-2 2′- O -methyltransferase reveal strategies for structure-based inhibitor design

et al. 2020

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There are currently no antiviral therapies specific for SARS-CoV-2, the virus responsible for the global pandemic disease COVID-19. To facilitate structure-based drug design, we conducted an x-ray crystallographic study of the SARS-CoV-2 nsp16-nsp10 2′-O-methyltransferase complex, which methylates Cap-0 viral mRNAs to improve viral protein translation and to avoid host immune detection. We determined the structures for nsp16-nsp10 heterodimers bound to the methyl donor S-adenosylmethionine (SAM), the reaction product S-adenosylhomocysteine (SAH), or the SAH analog sinefungin (SFG). We also solved structures for nsp16-nsp10 in complex with the methylated Cap-0 analog m7GpppA and either SAM or SAH. Comparative analyses between these structures and published structures for nsp16 from other betacoronaviruses revealed flexible loops in open and closed conformations at the m7GpppA-binding pocket. Bound sulfates in several of the structures suggested the location of the ribonucleic acid backbone phosphates in the ribonucleotide-binding groove. Additional nucleotide-binding sites were found on the face of the protein opposite the active site. These various sites and the conserved dimer interface could be exploited for the development of antiviral inhibitors.

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“…Because of this, mutation of the KDKE has been shown to ablate 2′-O-MTase activity and attenuate various aspects of in [41,63,64]. In heterodimeric complexes, NSP10 is essential by acting as a cofactor for NSP16 methylase [50,52,53,60,65]. Previous research also confirmed that SARS-CoV-2 NSP10 is highly conserved in SARS-CoV [38].…”

Section: Comparison Of the Nsp16 And Nsp10 Of Various Human Coronavirmentioning

confidence: 89%

NSP16 2′-O-MTase in Coronavirus Pathogenesis: Possible Prevention and Treatments Strategies

Chang

Chen

2021

Viruses

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Several life-threatening viruses have recently appeared, including the coronavirus, infecting a variety of human and animal hosts and causing a range of diseases like human upper respiratory tract infections. They not only cause serious human and animal deaths, but also cause serious public health problems worldwide. Currently, seven species are known to infect humans, namely SARS-CoV-2, MERS-CoV, SARS-CoV, HCoV-229E, HCoV-NL63, HCoV-OC43, and HCoV-HKU1. The coronavirus nonstructural protein 16 (NSP16) structure is similar to the 5′-end capping system of mRNA used by eukaryotic hosts and plays a vital role in evading host immunity response and protects the nascent viral mRNA from degradation. NSP16 is also well-conserved among related coronaviruses and requires its binding partner NSP10 to activate its enzymatic activity. With the continued threat of viral emergence highlighted by human coronaviruses and SARS-CoV-2, mutant strains continue to appear, affecting the highly conserved NSP16: this provides a possible therapeutic approach applicable to any novel coronavirus. To this end, current information on the 2′-O-MTase activity mechanism, the differences between NSP16 and NSP10 in human coronaviruses, and the current potential prevention and treatment strategies related to NSP16 are summarized in this review.

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Crystal structure of SARS-CoV-2 nsp10/nsp16 2′-O-methylase and its implication on antiviral drug design

Cited by 87 publications

References 4 publications

New targets for drug design: Importance of nsp14/nsp10 complex formation for the 3’-5’ exoribonucleolytic activity on SARS-CoV-2

New targets for drug design: Importance of nsp14/nsp10 complex formation for the 3’-5’ exoribonucleolytic activity on SARS-CoV-2

High-resolution structures of the SARS-CoV-2 2′- O -methyltransferase reveal strategies for structure-based inhibitor design

NSP16 2′-O-MTase in Coronavirus Pathogenesis: Possible Prevention and Treatments Strategies

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