X-Ray Structure and Inhibition of 3C-like Protease from Porcine Epidemic Diarrhea Virus
Identifieur interne : 000652 ( Pmc/Checkpoint ); précédent : 000651; suivant : 000653X-Ray Structure and Inhibition of 3C-like Protease from Porcine Epidemic Diarrhea Virus
Auteurs : Sarah E. St. John ; Brandon J. Anson ; Andrew D. MesecarSource :
- Scientific Reports [ 2045-2322 ] ; 2016.
Abstract
Porcine epidemic diarrhea virus (PEDV) is a coronavirus that infects pigs and can have mortality rates approaching 100% in piglets, causing serious economic impact. The 3C-like protease (3CLpro) is essential for the coronaviral life cycle and is an appealing target for the development of therapeutics. We report the expression, purification, crystallization and 2.10 Å X-ray structure of 3CLpro from PEDV. Analysis of the PEDV 3CLpro structure and comparison to other coronaviral 3CLpro’s from the same alpha-coronavirus phylogeny shows that the overall structures and active site architectures across 3CLpro’s are conserved, with the exception of a loop that comprises the protease S2 pocket. We found a known inhibitor of severe acute respiratory syndrome coronavirus (SARS-CoV) 3CLpro, (
Url:
DOI: 10.1038/srep25961
PubMed: 27173881
PubMed Central: 4865815
Affiliations:
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St. John</name><affiliation><nlm:aff id="Aff1"><institution-wrap><institution-id institution-id-type="GRID">grid.169077.e</institution-id><institution-id institution-id-type="ISNI">0000 0004 1937 2197</institution-id><institution>Department of Chemistry,</institution><institution>Purdue University,</institution></institution-wrap>West Lafayette, Indiana USA</nlm:aff><wicri:noCountry code="subfield">Indiana USA</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff2"><institution-wrap><institution-id institution-id-type="GRID">grid.169077.e</institution-id><institution-id institution-id-type="ISNI">0000 0004 1937 2197</institution-id><institution>Centers for Cancer Research & Drug Discovery, Purdue University,</institution></institution-wrap>West Lafayette, Indiana USA</nlm:aff><wicri:noCountry code="subfield">Indiana USA</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff3"><institution-wrap><institution-id institution-id-type="GRID">grid.169077.e</institution-id><institution-id institution-id-type="ISNI">0000 0004 1937 2197</institution-id><institution>Department of Biological Sciences,</institution><institution>Purdue University,</institution></institution-wrap>West Lafayette, Indiana USA</nlm:aff><wicri:noCountry code="subfield">Indiana USA</wicri:noCountry></affiliation></author><author><name sortKey="Anson, Brandon J" sort="Anson, Brandon J" uniqKey="Anson B" first="Brandon J." last="Anson">Brandon J. 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St. John</name><affiliation><nlm:aff id="Aff1"><institution-wrap><institution-id institution-id-type="GRID">grid.169077.e</institution-id><institution-id institution-id-type="ISNI">0000 0004 1937 2197</institution-id><institution>Department of Chemistry,</institution><institution>Purdue University,</institution></institution-wrap>West Lafayette, Indiana USA</nlm:aff><wicri:noCountry code="subfield">Indiana USA</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff2"><institution-wrap><institution-id institution-id-type="GRID">grid.169077.e</institution-id><institution-id institution-id-type="ISNI">0000 0004 1937 2197</institution-id><institution>Centers for Cancer Research & Drug Discovery, Purdue University,</institution></institution-wrap>West Lafayette, Indiana USA</nlm:aff><wicri:noCountry code="subfield">Indiana USA</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff3"><institution-wrap><institution-id institution-id-type="GRID">grid.169077.e</institution-id><institution-id institution-id-type="ISNI">0000 0004 1937 2197</institution-id><institution>Department of Biological Sciences,</institution><institution>Purdue University,</institution></institution-wrap>West Lafayette, Indiana USA</nlm:aff><wicri:noCountry code="subfield">Indiana USA</wicri:noCountry></affiliation></author><author><name sortKey="Anson, Brandon J" sort="Anson, Brandon J" uniqKey="Anson B" first="Brandon J." last="Anson">Brandon J. Anson</name><affiliation><nlm:aff id="Aff3"><institution-wrap><institution-id institution-id-type="GRID">grid.169077.e</institution-id><institution-id institution-id-type="ISNI">0000 0004 1937 2197</institution-id><institution>Department of Biological Sciences,</institution><institution>Purdue University,</institution></institution-wrap>West Lafayette, Indiana USA</nlm:aff><wicri:noCountry code="subfield">Indiana USA</wicri:noCountry></affiliation></author><author><name sortKey="Mesecar, Andrew D" sort="Mesecar, Andrew D" uniqKey="Mesecar A" first="Andrew D." last="Mesecar">Andrew D. Mesecar</name><affiliation><nlm:aff id="Aff1"><institution-wrap><institution-id institution-id-type="GRID">grid.169077.e</institution-id><institution-id institution-id-type="ISNI">0000 0004 1937 2197</institution-id><institution>Department of Chemistry,</institution><institution>Purdue University,</institution></institution-wrap>West Lafayette, Indiana USA</nlm:aff><wicri:noCountry code="subfield">Indiana USA</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff2"><institution-wrap><institution-id institution-id-type="GRID">grid.169077.e</institution-id><institution-id institution-id-type="ISNI">0000 0004 1937 2197</institution-id><institution>Centers for Cancer Research & Drug Discovery, Purdue University,</institution></institution-wrap>West Lafayette, Indiana USA</nlm:aff><wicri:noCountry code="subfield">Indiana USA</wicri:noCountry></affiliation><affiliation><nlm:aff id="Aff3"><institution-wrap><institution-id institution-id-type="GRID">grid.169077.e</institution-id><institution-id institution-id-type="ISNI">0000 0004 1937 2197</institution-id><institution>Department of Biological Sciences,</institution><institution>Purdue University,</institution></institution-wrap>West Lafayette, Indiana USA</nlm:aff><wicri:noCountry code="subfield">Indiana USA</wicri:noCountry></affiliation></author></analytic><series><title level="j">Scientific Reports</title><idno type="eISSN">2045-2322</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Porcine epidemic diarrhea virus (PEDV) is a coronavirus that infects pigs and can have mortality rates approaching 100% in piglets, causing serious economic impact. The 3C-like protease (3CL<sup>pro</sup>) is essential for the coronaviral life cycle and is an appealing target for the development of therapeutics. We report the expression, purification, crystallization and 2.10 Å X-ray structure of 3CL<sup>pro</sup> from PEDV. Analysis of the PEDV 3CL<sup>pro</sup> structure and comparison to other coronaviral 3CL<sup>pro</sup>’s from the same alpha-coronavirus phylogeny shows that the overall structures and active site architectures across 3CL<sup>pro</sup>’s are conserved, with the exception of a loop that comprises the protease S<sub>2</sub> pocket. We found a known inhibitor of severe acute respiratory syndrome coronavirus (SARS-CoV) 3CL<sup>pro</sup>, (<italic>R</italic>)-<bold>16</bold>, to have inhibitor activity against PEDV 3CL<sup>pro</sup>, despite that SARS-3CL<sup>pro</sup> and PEDV 3CL<sup>pro</sup> share only 45.4% sequence identity. Structural comparison reveals that the majority of residues involved in (<italic>R</italic>)-<bold>16</bold> binding to SARS-3CL<sup>pro</sup> are conserved in PEDV-3CL<sup>pro</sup>; however, the sequence variation and positional difference in the loop forming the S<sub>2</sub> pocket may account for large observed difference in IC<sub>50</sub> values. This work advances our understanding of the subtle, but important, differences in coronaviral 3CL<sup>pro</sup> architecture and contributes to the broader structural knowledge of coronaviral 3CL<sup>pro</sup>’s.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Debouck, P" uniqKey="Debouck P">P Debouck</name></author><author><name sortKey="Pensaert, M" uniqKey="Pensaert M">M Pensaert</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wood, En" uniqKey="Wood E">EN Wood</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hofmann, M" uniqKey="Hofmann M">M Hofmann</name></author><author><name sortKey="Wyler, R" uniqKey="Wyler R">R Wyler</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Egberink, Hf" uniqKey="Egberink H">HF Egberink</name></author><author><name sortKey="Ederveen, J" uniqKey="Ederveen J">J Ederveen</name></author><author><name sortKey="Callebaut, P" uniqKey="Callebaut P">P Callebaut</name></author><author><name sortKey="Horzinek, Mc" uniqKey="Horzinek M">MC Horzinek</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Utiger, A" uniqKey="Utiger A">A Utiger</name></author><author><name sortKey="Tobler, K" uniqKey="Tobler K">K Tobler</name></author><author><name sortKey="Bridgen, A" uniqKey="Bridgen A">A Bridgen</name></author><author><name sortKey="Ackermann, M" uniqKey="Ackermann M">M Ackermann</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Song, D" uniqKey="Song D">D Song</name></author><author><name sortKey="Park, B" uniqKey="Park B">B Park</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Stevenson, Gw" uniqKey="Stevenson G">GW Stevenson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Zhang, Q" uniqKey="Zhang Q">Q Zhang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Paarlberg, P" uniqKey="Paarlberg P">P Paarlberg</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kocherhans, R" uniqKey="Kocherhans R">R Kocherhans</name></author><author><name sortKey="Bridgen, A" uniqKey="Bridgen A">A Bridgen</name></author><author><name sortKey="Ackermann, M" uniqKey="Ackermann M">M Ackermann</name></author><author><name sortKey="Tobler, K" uniqKey="Tobler K">K Tobler</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Barrila, J" uniqKey="Barrila J">J Barrila</name></author><author><name sortKey="Bacha, U" uniqKey="Bacha U">U Bacha</name></author><author><name sortKey="Freire, E" uniqKey="Freire E">E Freire</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Anand, K" uniqKey="Anand K">K Anand</name></author><author><name sortKey="Ziebuhr, J" uniqKey="Ziebuhr J">J Ziebuhr</name></author><author><name sortKey="Wadhwani, P" uniqKey="Wadhwani P">P Wadhwani</name></author><author><name sortKey="Mesters, Jr" uniqKey="Mesters J">JR Mesters</name></author><author><name sortKey="Hilgenfeld, R" uniqKey="Hilgenfeld R">R Hilgenfeld</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lee, Cc" uniqKey="Lee C">CC Lee</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="St John, Se" uniqKey="St John S">SE St John</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jacobs, J" uniqKey="Jacobs J">J Jacobs</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Anand, K" uniqKey="Anand K">K Anand</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yang, Ht" uniqKey="Yang H">HT Yang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kim, Y" uniqKey="Kim Y">Y Kim</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hsu, Mf" uniqKey="Hsu M">MF Hsu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Xu, T" uniqKey="Xu T">T Xu</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Mesecar, Ad" uniqKey="Mesecar A">AD Mesecar</name></author><author><name sortKey="Stoddard, Bl" uniqKey="Stoddard B">BL Stoddard</name></author><author><name sortKey="Koshland, De" uniqKey="Koshland D">DE Koshland</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Otwinowski, Z" uniqKey="Otwinowski Z">Z Otwinowski</name></author><author><name sortKey="Minor, W" uniqKey="Minor W">W Minor</name></author><author><name sortKey="Jr C W, Carter" uniqKey="Jr C W C">Carter Jr. C.W.</name></author><author><name sortKey="Sweet, Rm" uniqKey="Sweet R">RM Sweet</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Adams, Pd" uniqKey="Adams P">PD Adams</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Emsley, P" uniqKey="Emsley P">P Emsley</name></author><author><name sortKey="Lohkamp, B" uniqKey="Lohkamp B">B Lohkamp</name></author><author><name sortKey="Scott, Wg" uniqKey="Scott W">WG Scott</name></author><author><name sortKey="Cowtan, K" uniqKey="Cowtan K">K Cowtan</name></author></analytic></biblStruct></listBibl></div1></back></TEI><pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Sci Rep</journal-id><journal-id journal-id-type="iso-abbrev">Sci Rep</journal-id><journal-title-group><journal-title>Scientific Reports</journal-title></journal-title-group><issn pub-type="epub">2045-2322</issn><publisher><publisher-name>Nature Publishing Group UK</publisher-name><publisher-loc>London</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">27173881</article-id><article-id pub-id-type="pmc">4865815</article-id><article-id pub-id-type="publisher-id">BFsrep25961</article-id><article-id pub-id-type="doi">10.1038/srep25961</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>X-Ray Structure and Inhibition of 3C-like Protease from Porcine Epidemic Diarrhea Virus</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>St. John</surname><given-names>Sarah E.</given-names></name><xref ref-type="aff" rid="Aff1">1</xref><xref ref-type="aff" rid="Aff2">2</xref><xref ref-type="aff" rid="Aff3">3</xref></contrib><contrib contrib-type="author"><name><surname>Anson</surname><given-names>Brandon J.</given-names></name><xref ref-type="aff" rid="Aff3">3</xref></contrib><contrib contrib-type="author"><name><surname>Mesecar</surname><given-names>Andrew D.</given-names></name><address><email>amesecar@purdue.edu</email></address><xref ref-type="aff" rid="Aff1">1</xref><xref ref-type="aff" rid="Aff2">2</xref><xref ref-type="aff" rid="Aff3">3</xref></contrib><aff id="Aff1"><label>1</label><institution-wrap><institution-id institution-id-type="GRID">grid.169077.e</institution-id><institution-id institution-id-type="ISNI">0000 0004 1937 2197</institution-id><institution>Department of Chemistry,</institution><institution>Purdue University,</institution></institution-wrap>West Lafayette, Indiana USA</aff><aff id="Aff2"><label>2</label><institution-wrap><institution-id institution-id-type="GRID">grid.169077.e</institution-id><institution-id institution-id-type="ISNI">0000 0004 1937 2197</institution-id><institution>Centers for Cancer Research & Drug Discovery, Purdue University,</institution></institution-wrap>West Lafayette, Indiana USA</aff><aff id="Aff3"><label>3</label><institution-wrap><institution-id institution-id-type="GRID">grid.169077.e</institution-id><institution-id institution-id-type="ISNI">0000 0004 1937 2197</institution-id><institution>Department of Biological Sciences,</institution><institution>Purdue University,</institution></institution-wrap>West Lafayette, Indiana USA</aff></contrib-group><pub-date pub-type="epub"><day>13</day><month>5</month><year>2016</year></pub-date><pub-date pub-type="pmc-release"><day>13</day><month>5</month><year>2016</year></pub-date><pub-date pub-type="collection"><year>2016</year></pub-date><volume>6</volume><elocation-id>25961</elocation-id><history><date date-type="received"><day>11</day><month>2</month><year>2016</year></date><date date-type="accepted"><day>26</day><month>4</month><year>2016</year></date></history><permissions><copyright-statement>© The Author(s) 2016</copyright-statement><license license-type="OpenAccess"><license-p>This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</ext-link></license-p></license></permissions><abstract id="Abs1"><p>Porcine epidemic diarrhea virus (PEDV) is a coronavirus that infects pigs and can have mortality rates approaching 100% in piglets, causing serious economic impact. The 3C-like protease (3CL<sup>pro</sup>) is essential for the coronaviral life cycle and is an appealing target for the development of therapeutics. We report the expression, purification, crystallization and 2.10 Å X-ray structure of 3CL<sup>pro</sup> from PEDV. Analysis of the PEDV 3CL<sup>pro</sup> structure and comparison to other coronaviral 3CL<sup>pro</sup>’s from the same alpha-coronavirus phylogeny shows that the overall structures and active site architectures across 3CL<sup>pro</sup>’s are conserved, with the exception of a loop that comprises the protease S<sub>2</sub> pocket. We found a known inhibitor of severe acute respiratory syndrome coronavirus (SARS-CoV) 3CL<sup>pro</sup>, (<italic>R</italic>)-<bold>16</bold>, to have inhibitor activity against PEDV 3CL<sup>pro</sup>, despite that SARS-3CL<sup>pro</sup> and PEDV 3CL<sup>pro</sup> share only 45.4% sequence identity. Structural comparison reveals that the majority of residues involved in (<italic>R</italic>)-<bold>16</bold> binding to SARS-3CL<sup>pro</sup> are conserved in PEDV-3CL<sup>pro</sup>; however, the sequence variation and positional difference in the loop forming the S<sub>2</sub> pocket may account for large observed difference in IC<sub>50</sub> values. This work advances our understanding of the subtle, but important, differences in coronaviral 3CL<sup>pro</sup> architecture and contributes to the broader structural knowledge of coronaviral 3CL<sup>pro</sup>’s.</p></abstract><kwd-group kwd-group-type="npg-subject"><title>Subject terms</title><kwd>Drug discovery</kwd><kwd>X-ray crystallography</kwd></kwd-group><custom-meta-group><custom-meta><meta-name>issue-copyright-statement</meta-name><meta-value>© The Author(s) 2016</meta-value></custom-meta></custom-meta-group></article-meta></front></pmc><affiliations><list></list><tree><noCountry><name sortKey="Anson, Brandon J" sort="Anson, Brandon J" uniqKey="Anson B" first="Brandon J." last="Anson">Brandon J. Anson</name><name sortKey="Mesecar, Andrew D" sort="Mesecar, Andrew D" uniqKey="Mesecar A" first="Andrew D." last="Mesecar">Andrew D. Mesecar</name><name sortKey="St John, Sarah E" sort="St John, Sarah E" uniqKey="St John S" first="Sarah E." last="St. John">Sarah E. 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