High-resolution structures of the SARS-CoV-2 2′- O -methyltransferase reveal strategies for structure-based inhibitor design
Abstract
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.
- Authors:
-
[1];
[1];
[1];
[1];
[1];
[2];
[1]
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA., Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA.
- Northwestern Synchrotron Research Center, Life Sciences Collaborative Access Team, Northwestern University, Argonne, IL 60439, USA.
- Publication Date:
- Research Org.:
- Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1668455
- Alternate Identifier(s):
- OSTI ID: 1671118
- Grant/Contract Number:
- AC02-06CH11357
- Resource Type:
- Published Article
- Journal Name:
- Science Signaling
- Additional Journal Information:
- Journal Name: Science Signaling Journal Volume: 13 Journal Issue: 651; Journal ID: ISSN 1945-0877
- Publisher:
- American Association for the Advancement of Science (AAAS)
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 60 APPLIED LIFE SCIENCES
Citation Formats
Rosas-Lemus, Monica, Minasov, George, Shuvalova, Ludmilla, Inniss, Nicole L., Kiryukhina, Olga, Brunzelle, Joseph, and Satchell, Karla J. F. High-resolution structures of the SARS-CoV-2 2′- O -methyltransferase reveal strategies for structure-based inhibitor design. United States: N. p., 2020.
Web. doi:10.1126/scisignal.abe1202.
Rosas-Lemus, Monica, Minasov, George, Shuvalova, Ludmilla, Inniss, Nicole L., Kiryukhina, Olga, Brunzelle, Joseph, & Satchell, Karla J. F. High-resolution structures of the SARS-CoV-2 2′- O -methyltransferase reveal strategies for structure-based inhibitor design. United States. https://doi.org/10.1126/scisignal.abe1202
Rosas-Lemus, Monica, Minasov, George, Shuvalova, Ludmilla, Inniss, Nicole L., Kiryukhina, Olga, Brunzelle, Joseph, and Satchell, Karla J. F. Tue .
"High-resolution structures of the SARS-CoV-2 2′- O -methyltransferase reveal strategies for structure-based inhibitor design". United States. https://doi.org/10.1126/scisignal.abe1202.
@article{osti_1668455,
title = {High-resolution structures of the SARS-CoV-2 2′- O -methyltransferase reveal strategies for structure-based inhibitor design},
author = {Rosas-Lemus, Monica and Minasov, George and Shuvalova, Ludmilla and Inniss, Nicole L. and Kiryukhina, Olga and Brunzelle, Joseph and Satchell, Karla J. F.},
abstractNote = {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.},
doi = {10.1126/scisignal.abe1202},
journal = {Science Signaling},
number = 651,
volume = 13,
place = {United States},
year = {2020},
month = {9}
}
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Works referenced in this record:
Coronavirus Nsp10, a Critical Co-factor for Activation of Multiple Replicative Enzymes
journal, July 2014
- Bouvet, Mickaël; Lugari, Adrien; Posthuma, Clara C.
- Journal of Biological Chemistry, Vol. 289, Issue 37
Crystal structure of SARS-CoV-2 nsp10/nsp16 2′-O-methylase and its implication on antiviral drug design
journal, July 2020
- Lin, Sheng; Chen, Hua; Ye, Fei
- Signal Transduction and Targeted Therapy, Vol. 5, Issue 1
New LIC vectors for production of proteins from genes containing rare codons
journal, September 2013
- Eschenfeldt, William H.; Makowska-Grzyska, Magdalena; Stols, Lucy
- Journal of Structural and Functional Genomics, Vol. 14, Issue 4
The Architecture of SARS-CoV-2 Transcriptome
journal, May 2020
- Kim, Dongwan; Lee, Joo-Yeon; Yang, Jeong-Sun
- Cell, Vol. 181, Issue 4
Crystal Structure of Nonstructural Protein 10 from the Severe Acute Respiratory Syndrome Coronavirus Reveals a Novel Fold with Two Zinc-Binding Motifs
journal, August 2006
- Joseph, Jeremiah S.; Saikatendu, Kumar Singh; Subramanian, Vanitha
- Journal of Virology, Vol. 80, Issue 16
Overview of the CCP 4 suite and current developments
journal, March 2011
- Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D.
- Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
mRNA capping: biological functions and applications
journal, June 2016
- Ramanathan, Anand; Robb, G. Brett; Chan, Siu-Hong
- Nucleic Acids Research, Vol. 44, Issue 16
Identification of Novel Subgenomic RNAs and Noncanonical Transcription Initiation Signals of Severe Acute Respiratory Syndrome Coronavirus
journal, May 2005
- Hussain, Snawar; Pan, Ji'an; Chen, Yu
- Journal of Virology, Vol. 79, Issue 9
Crystal Structure and Functional Analysis of the SARS-Coronavirus RNA Cap 2′-O-Methyltransferase nsp10/nsp16 Complex
journal, May 2011
- Decroly, Etienne; Debarnot, Claire; Ferron, François
- PLoS Pathogens, Vol. 7, Issue 5
FATCAT: a web server for flexible structure comparison and structure similarity searching
journal, July 2004
- Ye, Y.; Godzik, A.
- Nucleic Acids Research, Vol. 32, Issue Web Server
Heightened Innate Immune Responses in the Respiratory Tract of COVID-19 Patients
journal, June 2020
- Zhou, Zhuo; Ren, Lili; Zhang, Li
- Cell Host & Microbe, Vol. 27, Issue 6
Mutational Analysis of Encephalitozoon cuniculi mRNA Cap (Guanine-N7) Methyltransferase, Structure of the Enzyme Bound to Sinefungin, and Evidence That Cap Methyltransferase Is the Target of Sinefungin's Antifungal Activity
journal, September 2006
- Zheng, Sushuang; Hausmann, Stéphane; Liu, Quansheng
- Journal of Biological Chemistry, Vol. 281, Issue 47
Dodecamer Structure of Severe Acute Respiratory Syndrome Coronavirus Nonstructural Protein nsp10
journal, August 2006
- Su, Dan; Lou, Zhiyong; Sun, Fei
- Journal of Virology, Vol. 80, Issue 16
Structural analysis of human 2′-O-ribose methyltransferases involved in mRNA cap structure formation
journal, January 2014
- Smietanski, Miroslaw; Werner, Maria; Purta, Elzbieta
- Nature Communications, Vol. 5, Issue 1
Genome-Wide Analysis of Protein-Protein Interactions and Involvement of Viral Proteins in SARS-CoV Replication
journal, October 2008
- Pan, Ji'An; Peng, Xiaoxue; Gao, Yajing
- PLoS ONE, Vol. 3, Issue 10
Structural basis of RNA cap modification by SARS-CoV-2
journal, July 2020
- Viswanathan, Thiruselvam; Arya, Shailee; Chan, Siu-Hong
- Nature Communications, Vol. 11, Issue 1
COVID-19: Emergence, Spread, Possible Treatments, and Global Burden
journal, May 2020
- Keni, Raghuvir; Alexander, Anila; Nayak, Pawan Ganesh
- Frontiers in Public Health, Vol. 8
Functional screen reveals SARS coronavirus nonstructural protein nsp14 as a novel cap N7 methyltransferase
journal, February 2009
- Chen, Y.; Cai, H.; Pan, J.
- Proceedings of the National Academy of Sciences, Vol. 106, Issue 9
Crystallization and diffraction analysis of the SARS coronavirus nsp10–nsp16 complex
journal, February 2011
- Debarnot, Claire; Imbert, Isabelle; Ferron, François
- Acta Crystallographica Section F Structural Biology and Crystallization Communications, Vol. 67, Issue 3
PDBFlex: exploring flexibility in protein structures
journal, November 2015
- Hrabe, Thomas; Li, Zhanwen; Sedova, Mayya
- Nucleic Acids Research, Vol. 44, Issue D1
Biochemical and Structural Insights into the Mechanisms of SARS Coronavirus RNA Ribose 2′-O-Methylation by nsp16/nsp10 Protein Complex
journal, October 2011
- Chen, Yu; Su, Ceyang; Ke, Min
- PLoS Pathogens, Vol. 7, Issue 10
The non-structural protein Nsp10 of mouse hepatitis virus binds zinc ions and nucleic acids
journal, June 2006
- Matthes, Nele; Mesters, Jeroen R.; Coutard, Bruno
- FEBS Letters, Vol. 580, Issue 17
Comparing SARS-CoV-2 with SARS-CoV and influenza pandemics
journal, September 2020
- Petersen, Eskild; Koopmans, Marion; Go, Unyeong
- The Lancet Infectious Diseases, Vol. 20, Issue 9
mRNA Cap-1 Methyltransferase in the SARS Genome
journal, June 2003
- von Grotthuss, Marcin; Wyrwicz, Lucjan S.; Rychlewski, Leszek
- Cell, Vol. 113, Issue 6
Compounds with Therapeutic Potential against Novel Respiratory 2019 Coronavirus
journal, March 2020
- Martinez, Miguel Angel
- Antimicrobial Agents and Chemotherapy, Vol. 64, Issue 5
Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan
journal, January 2020
- Chan, Jasper Fuk-Woo; Kok, Kin-Hang; Zhu, Zheng
- Emerging Microbes & Infections, Vol. 9, Issue 1
Molecular basis for specific viral RNA recognition and 2′-O-ribose methylation by the dengue virus nonstructural protein 5 (NS5)
journal, November 2015
- Zhao, Yongqian; Soh, Tingjin Sherryl; Lim, Siew Pheng
- Proceedings of the National Academy of Sciences, Vol. 112, Issue 48
Binding of the Methyl Donor S-Adenosyl-l-Methionine to Middle East Respiratory Syndrome Coronavirus 2′-O-Methyltransferase nsp16 Promotes Recruitment of the Allosteric Activator nsp10
journal, December 2016
- Aouadi, Wahiba; Blanjoie, Alexandre; Vasseur, Jean-Jacques
- Journal of Virology, Vol. 91, Issue 5
Multiple Enzymatic Activities Associated with Severe Acute Respiratory Syndrome Coronavirus Helicase
journal, June 2004
- Ivanov, Konstantin A.; Thiel, Volker; Dobbe, Jessika C.
- Journal of Virology, Vol. 78, Issue 11
Discovery of an RNA virus 3'->5' exoribonuclease that is critically involved in coronavirus RNA synthesis
journal, March 2006
- Minskaia, E.; Hertzig, T.; Gorbalenya, A. E.
- Proceedings of the National Academy of Sciences, Vol. 103, Issue 13
HKL -3000: the integration of data reduction and structure solution – from diffraction images to an initial model in minutes
journal, July 2006
- Minor, Wladek; Cymborowski, Marcin; Otwinowski, Zbyszek
- Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 8
MolProbity : all-atom structure validation for macromolecular crystallography
journal, December 2009
- Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J.
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1
Coot model-building tools for molecular graphics
journal, November 2004
- Emsley, Paul; Cowtan, Kevin
- Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132
Deciphering key features in protein structures with the new ENDscript server
journal, April 2014
- Robert, Xavier; Gouet, Patrice
- Nucleic Acids Research, Vol. 42, Issue W1
Molecular Mapping of the RNA Cap 2′- O -Methyltransferase Activation Interface between Severe Acute Respiratory Syndrome Coronavirus nsp10 and nsp16
journal, August 2010
- Lugari, Adrien; Betzi, Stephane; Decroly, Etienne
- Journal of Biological Chemistry, Vol. 285, Issue 43
REFMAC 5 for the refinement of macromolecular crystal structures
journal, March 2011
- Murshudov, Garib N.; Skubák, Pavol; Lebedev, Andrey A.
- Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
Methyltransferase Inhibitors: Competing with, or Exploiting the Bound Cofactor
journal, December 2019
- Ferreira de Freitas, Renato; Ivanochko, Danton; Schapira, Matthieu
- Molecules, Vol. 24, Issue 24
An interactive web-based dashboard to track COVID-19 in real time
journal, May 2020
- Dong, Ensheng; Du, Hongru; Gardner, Lauren
- The Lancet Infectious Diseases, Vol. 20, Issue 5
Structural analysis of the SARS-CoV-2 methyltransferase complex involved in RNA cap creation bound to sinefungin
journal, July 2020
- Krafcikova, Petra; Silhan, Jan; Nencka, Radim
- Nature Communications, Vol. 11, Issue 1
Recognition of RNA Cap in the Wesselsbron Virus NS5 Methyltransferase Domain: Implications for RNA-Capping Mechanisms in Flavivirus
journal, January 2009
- Bollati, Michela; Milani, Mario; Mastrangelo, Eloise
- Journal of Molecular Biology, Vol. 385, Issue 1
A less laborious approach to the high-throughput production of recombinant proteins in Escherichia coli using 2-liter plastic bottles
journal, June 2003
- Sanville Millard, Cynthia; Stols, Lucy; Quartey, Pearl
- Protein Expression and Purification, Vol. 29, Issue 2
Many paths to methyltransfer: a chronicle of convergence
journal, June 2003
- Schubert, Heidi L.; Blumenthal, Robert M.; Cheng, Xiaodong
- Trends in Biochemical Sciences, Vol. 28, Issue 6
Molecular mechanisms of coronavirus RNA capping and methylation
journal, February 2016
- Chen, Yu; Guo, Deyin
- Virologica Sinica, Vol. 31, Issue 1
Molecular target of the antileishmanial action of sinefungin.
journal, October 1987
- Nolan, L. L.
- Antimicrobial Agents and Chemotherapy, Vol. 31, Issue 10
Optimal description of a protein structure in terms of multiple groups undergoing TLS motion
journal, March 2006
- Painter, Jay; Merritt, Ethan A.
- Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 4
Genome Composition and Divergence of the Novel Coronavirus (2019-nCoV) Originating in China
journal, March 2020
- Wu, Aiping; Peng, Yousong; Huang, Baoying
- Cell Host & Microbe, Vol. 27, Issue 3
Continuous and Discontinuous RNA Synthesis in Coronaviruses
journal, November 2015
- Sola, Isabel; Almazán, Fernando; Zúñiga, Sonia
- Annual Review of Virology, Vol. 2, Issue 1
Coronavirus nsp10/nsp16 Methyltransferase Can Be Targeted by nsp10-Derived Peptide In Vitro and In Vivo To Reduce Replication and Pathogenesis
journal, June 2015
- Wang, Yi; Sun, Ying; Wu, Andong
- Journal of Virology, Vol. 89, Issue 16
Zoonotic origins of human coronaviruses
journal, January 2020
- Ye, Zi-Wei; Yuan, Shuofeng; Yuen, Kit-San
- International Journal of Biological Sciences, Vol. 16, Issue 10
A SARS-CoV-2 protein interaction map reveals targets for drug repurposing
journal, April 2020
- Gordon, David E.; Jang, Gwendolyn M.; Bouhaddou, Mehdi
- Nature, Vol. 583, Issue 7816
Phaser crystallographic software
journal, July 2007
- McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
- Journal of Applied Crystallography, Vol. 40, Issue 4