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Mertinkus KR, Grün JT, Altincekic N, Bains JK, Ceylan B, Ferner JP, Frydman L, Fürtig B, Hengesbach M, Hohmann KF, Hymon D, Kim J, Knezic B, Novakovic M, Oxenfarth A, Peter SA, Qureshi NS, Richter C, Scherf T, Schlundt A, Schnieders R, Schwalbe H, Stirnal E, Sudakov A, Vögele J, Wacker A, Weigand JE, Wirmer-Bartoschek J, Martin MAW, Wöhnert J. 1H, 13C and 15N chemical shift assignment of the stem-loops 5b + c from the 5'-UTR of SARS-CoV-2. Biomol NMR Assign 2022; 16:17-25. [PMID: 35178672 PMCID: PMC8853908 DOI: 10.1007/s12104-021-10053-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/16/2021] [Indexed: 06/14/2023]
Abstract
The ongoing pandemic of the respiratory disease COVID-19 is caused by the SARS-CoV-2 (SCoV2) virus. SCoV2 is a member of the Betacoronavirus genus. The 30 kb positive sense, single stranded RNA genome of SCoV2 features 5'- and 3'-genomic ends that are highly conserved among Betacoronaviruses. These genomic ends contain structured cis-acting RNA elements, which are involved in the regulation of viral replication and translation. Structural information about these potential antiviral drug targets supports the development of novel classes of therapeutics against COVID-19. The highly conserved branched stem-loop 5 (SL5) found within the 5'-untranslated region (5'-UTR) consists of a basal stem and three stem-loops, namely SL5a, SL5b and SL5c. Both, SL5a and SL5b feature a 5'-UUUCGU-3' hexaloop that is also found among Alphacoronaviruses. Here, we report the extensive 1H, 13C and 15N resonance assignment of the 37 nucleotides (nts) long sequence spanning SL5b and SL5c (SL5b + c), as basis for further in-depth structural studies by solution NMR spectroscopy.
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Affiliation(s)
- Klara R Mertinkus
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - J Tassilo Grün
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Herzl St. 234, 760001, Rehovot, Israel
| | - Nadide Altincekic
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Jasleen Kaur Bains
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Betül Ceylan
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Jan-Peter Ferner
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Lucio Frydman
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Herzl St. 234, 760001, Rehovot, Israel
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Katharina F Hohmann
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Daniel Hymon
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Jihyun Kim
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Herzl St. 234, 760001, Rehovot, Israel
| | - Božana Knezic
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Mihajlo Novakovic
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Herzl St. 234, 760001, Rehovot, Israel
- Institute for Biochemistry, ETH Zürich, Hönggerbergring 64, 8093, Zürich, Switzerland
| | - Andreas Oxenfarth
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Stephen A Peter
- Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287, Darmstadt, Germany
| | | | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Tali Scherf
- Department of Chemical Research Support, Weizmann Institute of Science, Herzl St. 234, 760001, Rehovot, Israel
| | - Andreas Schlundt
- Institute for Molecular Biosciences, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Robbin Schnieders
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Deutero GmbH, Am Ring 29, 56288, Kastellaun, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany.
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany.
| | - Elke Stirnal
- Institute for Molecular Biosciences, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Alexey Sudakov
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Jennifer Vögele
- Institute for Molecular Biosciences, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Anna Wacker
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Julia E Weigand
- Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287, Darmstadt, Germany
| | - Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Maria A Wirtz Martin
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Jens Wöhnert
- Institute for Molecular Biosciences, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
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Sreeramulu S, Richter C, Berg H, Wirtz Martin MA, Ceylan B, Matzel T, Adam J, Altincekic N, Azzaoui K, Bains JK, Blommers MJJ, Ferner J, Fürtig B, Göbel M, Grün JT, Hengesbach M, Hohmann KF, Hymon D, Knezic B, Martins JN, Mertinkus KR, Niesteruk A, Peter SA, Pyper DJ, Qureshi NS, Scheffer U, Schlundt A, Schnieders R, Stirnal E, Sudakov A, Tröster A, Vögele J, Wacker A, Weigand JE, Wirmer‐Bartoschek J, Wöhnert J, Schwalbe H. Exploring the Druggability of Conserved RNA Regulatory Elements in the SARS‐CoV‐2 Genome. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103693] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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3
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Sreeramulu S, Richter C, Berg H, Wirtz Martin MA, Ceylan B, Matzel T, Adam J, Altincekic N, Azzaoui K, Bains JK, Blommers MJJ, Ferner J, Fürtig B, Göbel M, Grün JT, Hengesbach M, Hohmann KF, Hymon D, Knezic B, Martins JN, Mertinkus KR, Niesteruk A, Peter SA, Pyper DJ, Qureshi NS, Scheffer U, Schlundt A, Schnieders R, Stirnal E, Sudakov A, Tröster A, Vögele J, Wacker A, Weigand JE, Wirmer‐Bartoschek J, Wöhnert J, Schwalbe H. Exploring the Druggability of Conserved RNA Regulatory Elements in the SARS-CoV-2 Genome. Angew Chem Int Ed Engl 2021; 60:19191-19200. [PMID: 34161644 PMCID: PMC8426693 DOI: 10.1002/anie.202103693] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 06/03/2021] [Indexed: 12/12/2022]
Abstract
SARS-CoV-2 contains a positive single-stranded RNA genome of approximately 30 000 nucleotides. Within this genome, 15 RNA elements were identified as conserved between SARS-CoV and SARS-CoV-2. By nuclear magnetic resonance (NMR) spectroscopy, we previously determined that these elements fold independently, in line with data from in vivo and ex-vivo structural probing experiments. These elements contain non-base-paired regions that potentially harbor ligand-binding pockets. Here, we performed an NMR-based screening of a poised fragment library of 768 compounds for binding to these RNAs, employing three different 1 H-based 1D NMR binding assays. The screening identified common as well as RNA-element specific hits. The results allow selection of the most promising of the 15 RNA elements as putative drug targets. Based on the identified hits, we derive key functional units and groups in ligands for effective targeting of the RNA of SARS-CoV-2.
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4
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Wacker A, Weigand JE, Akabayov SR, Altincekic N, Bains JK, Banijamali E, Binas O, Castillo-Martinez J, Cetiner E, Ceylan B, Chiu LY, Davila-Calderon J, Dhamotharan K, Duchardt-Ferner E, Ferner J, Frydman L, Fürtig B, Gallego J, Grün JT, Hacker C, Haddad C, Hähnke M, Hengesbach M, Hiller F, Hohmann KF, Hymon D, de Jesus V, Jonker H, Keller H, Knezic B, Landgraf T, Löhr F, Luo L, Mertinkus KR, Muhs C, Novakovic M, Oxenfarth A, Palomino-Schätzlein M, Petzold K, Peter SA, Pyper DJ, Qureshi NS, Riad M, Richter C, Saxena K, Schamber T, Scherf T, Schlagnitweit J, Schlundt A, Schnieders R, Schwalbe H, Simba-Lahuasi A, Sreeramulu S, Stirnal E, Sudakov A, Tants JN, Tolbert BS, Vögele J, Weiß L, Wirmer-Bartoschek J, Wirtz Martin MA, Wöhnert J, Zetzsche H. Correction to 'Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy'. Nucleic Acids Res 2021; 49:7204-7205. [PMID: 34161581 PMCID: PMC8266613 DOI: 10.1093/nar/gkab568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Anna Wacker
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Julia E Weigand
- Department of Biology, Technical University of Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Sabine R Akabayov
- Faculty of Chemistry, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Nadide Altincekic
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Jasleen Kaur Bains
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Elnaz Banijamali
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum 9B, Solnavägen 9, 17177 Stockholm, Sweden
| | - Oliver Binas
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | | | - Erhan Cetiner
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Betül Ceylan
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Liang-Yuan Chiu
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | | | | | | | - Jan Ferner
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Lucio Frydman
- Faculty of Chemistry, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - José Gallego
- School of Medicine, Catholic University of Valencia, C/Quevedo 2, 46001 Valencia, Spain
| | - J Tassilo Grün
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Carolin Hacker
- Signals GmbH & Co. KG, Graf-von-Stauffenberg-Allee 83, 60438 Frankfurt/M, Germany
| | - Christina Haddad
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Martin Hähnke
- Signals GmbH & Co. KG, Graf-von-Stauffenberg-Allee 83, 60438 Frankfurt/M, Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Fabian Hiller
- Signals GmbH & Co. KG, Graf-von-Stauffenberg-Allee 83, 60438 Frankfurt/M, Germany
| | - Katharina F Hohmann
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Daniel Hymon
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Vanessa de Jesus
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Henry Jonker
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | | | - Bozana Knezic
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Tom Landgraf
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Frank Löhr
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Le Luo
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum 9B, Solnavägen 9, 17177 Stockholm, Sweden
| | - Klara R Mertinkus
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Christina Muhs
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Mihajlo Novakovic
- Faculty of Chemistry, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Andreas Oxenfarth
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | | | - Katja Petzold
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum 9B, Solnavägen 9, 17177 Stockholm, Sweden
| | - Stephen A Peter
- Department of Biology, Technical University of Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Dennis J Pyper
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Nusrat S Qureshi
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Magdalena Riad
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum 9B, Solnavägen 9, 17177 Stockholm, Sweden
| | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Krishna Saxena
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Tatjana Schamber
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Tali Scherf
- Faculty of Chemistry, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Judith Schlagnitweit
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum 9B, Solnavägen 9, 17177 Stockholm, Sweden
| | | | - Robbin Schnieders
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Alvaro Simba-Lahuasi
- School of Medicine, Catholic University of Valencia, C/Quevedo 2, 46001 Valencia, Spain
| | - Sridhar Sreeramulu
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Elke Stirnal
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Alexey Sudakov
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | | | - Blanton S Tolbert
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | | | | | - Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Maria A Wirtz Martin
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | | | - Heidi Zetzsche
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
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5
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Wacker A, Weigand JE, Akabayov SR, Altincekic N, Bains JK, Banijamali E, Binas O, Castillo-Martinez J, Cetiner E, Ceylan B, Chiu LY, Davila-Calderon J, Dhamotharan K, Duchardt-Ferner E, Ferner J, Frydman L, Fürtig B, Gallego J, Grün JT, Hacker C, Haddad C, Hähnke M, Hengesbach M, Hiller F, Hohmann KF, Hymon D, de Jesus V, Jonker H, Keller H, Knezic B, Landgraf T, Löhr F, Luo L, Mertinkus KR, Muhs C, Novakovic M, Oxenfarth A, Palomino-Schätzlein M, Petzold K, Peter SA, Pyper DJ, Qureshi NS, Riad M, Richter C, Saxena K, Schamber T, Scherf T, Schlagnitweit J, Schlundt A, Schnieders R, Schwalbe H, Simba-Lahuasi A, Sreeramulu S, Stirnal E, Sudakov A, Tants JN, Tolbert BS, Vögele J, Weiß L, Wirmer-Bartoschek J, Wirtz Martin MA, Wöhnert J, Zetzsche H. Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy. Nucleic Acids Res 2020; 48:12415-12435. [PMID: 33167030 PMCID: PMC7736788 DOI: 10.1093/nar/gkaa1013] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 09/08/2020] [Accepted: 10/14/2020] [Indexed: 12/24/2022] Open
Abstract
The current pandemic situation caused by the Betacoronavirus SARS-CoV-2 (SCoV2) highlights the need for coordinated research to combat COVID-19. A particularly important aspect is the development of medication. In addition to viral proteins, structured RNA elements represent a potent alternative as drug targets. The search for drugs that target RNA requires their high-resolution structural characterization. Using nuclear magnetic resonance (NMR) spectroscopy, a worldwide consortium of NMR researchers aims to characterize potential RNA drug targets of SCoV2. Here, we report the characterization of 15 conserved RNA elements located at the 5' end, the ribosomal frameshift segment and the 3'-untranslated region (3'-UTR) of the SCoV2 genome, their large-scale production and NMR-based secondary structure determination. The NMR data are corroborated with secondary structure probing by DMS footprinting experiments. The close agreement of NMR secondary structure determination of isolated RNA elements with DMS footprinting and NMR performed on larger RNA regions shows that the secondary structure elements fold independently. The NMR data reported here provide the basis for NMR investigations of RNA function, RNA interactions with viral and host proteins and screening campaigns to identify potential RNA binders for pharmaceutical intervention.
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Affiliation(s)
- Anna Wacker
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Julia E Weigand
- Department of Biology, Technical University of Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Sabine R Akabayov
- Faculty of Chemistry, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Nadide Altincekic
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Jasleen Kaur Bains
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Elnaz Banijamali
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum 9B, Solnavägen 9, 17177 Stockholm, Sweden
| | - Oliver Binas
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | | | - Erhan Cetiner
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Betül Ceylan
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Liang-Yuan Chiu
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | | | | | | | - Jan Ferner
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Lucio Frydman
- Faculty of Chemistry, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - José Gallego
- School of Medicine, Catholic University of Valencia, C/Quevedo 2, 46001 Valencia, Spain
| | - J Tassilo Grün
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Carolin Hacker
- Signals GmbH & Co. KG, Graf-von-Stauffenberg-Allee 83, 60438 Frankfurt/M, Germany
| | - Christina Haddad
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Martin Hähnke
- Signals GmbH & Co. KG, Graf-von-Stauffenberg-Allee 83, 60438 Frankfurt/M, Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Fabian Hiller
- Signals GmbH & Co. KG, Graf-von-Stauffenberg-Allee 83, 60438 Frankfurt/M, Germany
| | - Katharina F Hohmann
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Daniel Hymon
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Vanessa de Jesus
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Henry Jonker
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | | | - Bozana Knezic
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Tom Landgraf
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Frank Löhr
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Le Luo
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum 9B, Solnavägen 9, 17177 Stockholm, Sweden
| | - Klara R Mertinkus
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Christina Muhs
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Mihajlo Novakovic
- Faculty of Chemistry, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Andreas Oxenfarth
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | | | - Katja Petzold
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum 9B, Solnavägen 9, 17177 Stockholm, Sweden
| | - Stephen A Peter
- Department of Biology, Technical University of Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Dennis J Pyper
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Nusrat S Qureshi
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Magdalena Riad
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum 9B, Solnavägen 9, 17177 Stockholm, Sweden
| | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Krishna Saxena
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Tatjana Schamber
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Tali Scherf
- Faculty of Chemistry, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Judith Schlagnitweit
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Biomedicum 9B, Solnavägen 9, 17177 Stockholm, Sweden
| | | | - Robbin Schnieders
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Alvaro Simba-Lahuasi
- School of Medicine, Catholic University of Valencia, C/Quevedo 2, 46001 Valencia, Spain
| | - Sridhar Sreeramulu
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Elke Stirnal
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Alexey Sudakov
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | | | - Blanton S Tolbert
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA
| | | | | | - Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | - Maria A Wirtz Martin
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
| | | | - Heidi Zetzsche
- Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 7, 60438 Frankfurt/M., Germany
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