Molecular docking and dynamics simulation of FDA approved drugs with the main protease from 2019 novel coronavirus
Identifieur interne : 000177 ( Pmc/Checkpoint ); précédent : 000176; suivant : 000178Molecular docking and dynamics simulation of FDA approved drugs with the main protease from 2019 novel coronavirus
Auteurs : Hasanain Abdulhameed Odhar [Iraq] ; Salam Waheed Ahjel [Iraq] ; Ali A. Mohammed Ali Albeer [Iraq] ; Ahmed Fadhil Hashim [Iraq] ; Ali Mahmood Rayshan [Iraq] ; Suhad Sami Humadi [Iraq]Source :
- Bioinformation [ 0973-8894 ] ; 2020.
Abstract
Design and development of an effective drug to combat the 2019 novel coronavirus remains a challenge. Therefore, it is of interest to study the binding features of 1615 FDA approved drugs with the recently known 2019-nCoV main protease structure having high sequence homology with that from SARS-CoV. We document the binding features of top 10 drugs with the target protein. We further report that Conivaptan and Azelastine are mainly involved in hydrophobic interactions with active site residues. Both drugs can maintain close proximity to the binding pocket of main protease during simulation. However, these data need further in vitro and in vivo evaluation to repurpose these two drugs against 2019-nCoV.
Url:
DOI: 10.6026/97320630016236
PubMed: NONE
PubMed Central: 7147498
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Molecular docking and dynamics simulation of FDA approved drugs with the main protease from 2019 novel coronavirus</title><author><name sortKey="Odhar, Hasanain Abdulhameed" sort="Odhar, Hasanain Abdulhameed" uniqKey="Odhar H" first="Hasanain Abdulhameed" last="Odhar">Hasanain Abdulhameed Odhar</name><affiliation wicri:level="1"><nlm:aff id="A1">Department of pharmacy, Al-Zahrawi University College, Karbala, Iraq</nlm:aff><country xml:lang="fr">Iraq</country><wicri:regionArea>Department of pharmacy, Al-Zahrawi University College, Karbala</wicri:regionArea><wicri:noRegion>Karbala</wicri:noRegion></affiliation></author><author><name sortKey="Ahjel, Salam Waheed" sort="Ahjel, Salam Waheed" uniqKey="Ahjel S" first="Salam Waheed" last="Ahjel">Salam Waheed Ahjel</name><affiliation wicri:level="1"><nlm:aff id="A1">Department of pharmacy, Al-Zahrawi University College, Karbala, Iraq</nlm:aff><country xml:lang="fr">Iraq</country><wicri:regionArea>Department of pharmacy, Al-Zahrawi University College, Karbala</wicri:regionArea><wicri:noRegion>Karbala</wicri:noRegion></affiliation></author><author><name sortKey="Albeer, Ali A Mohammed Ali" sort="Albeer, Ali A Mohammed Ali" uniqKey="Albeer A" first="Ali A. Mohammed Ali" last="Albeer">Ali A. Mohammed Ali Albeer</name><affiliation wicri:level="1"><nlm:aff id="A1">Department of pharmacy, Al-Zahrawi University College, Karbala, Iraq</nlm:aff><country xml:lang="fr">Iraq</country><wicri:regionArea>Department of pharmacy, Al-Zahrawi University College, Karbala</wicri:regionArea><wicri:noRegion>Karbala</wicri:noRegion></affiliation></author><author><name sortKey="Hashim, Ahmed Fadhil" sort="Hashim, Ahmed Fadhil" uniqKey="Hashim A" first="Ahmed Fadhil" last="Hashim">Ahmed Fadhil Hashim</name><affiliation wicri:level="1"><nlm:aff id="A1">Department of pharmacy, Al-Zahrawi University College, Karbala, Iraq</nlm:aff><country xml:lang="fr">Iraq</country><wicri:regionArea>Department of pharmacy, Al-Zahrawi University College, Karbala</wicri:regionArea><wicri:noRegion>Karbala</wicri:noRegion></affiliation></author><author><name sortKey="Rayshan, Ali Mahmood" sort="Rayshan, Ali Mahmood" uniqKey="Rayshan A" first="Ali Mahmood" last="Rayshan">Ali Mahmood Rayshan</name><affiliation wicri:level="1"><nlm:aff id="A1">Department of pharmacy, Al-Zahrawi University College, Karbala, Iraq</nlm:aff><country xml:lang="fr">Iraq</country><wicri:regionArea>Department of pharmacy, Al-Zahrawi University College, Karbala</wicri:regionArea><wicri:noRegion>Karbala</wicri:noRegion></affiliation></author><author><name sortKey="Humadi, Suhad Sami" sort="Humadi, Suhad Sami" uniqKey="Humadi S" first="Suhad Sami" last="Humadi">Suhad Sami Humadi</name><affiliation wicri:level="1"><nlm:aff id="A1">Department of pharmacy, Al-Zahrawi University College, Karbala, Iraq</nlm:aff><country xml:lang="fr">Iraq</country><wicri:regionArea>Department of pharmacy, Al-Zahrawi University College, Karbala</wicri:regionArea><wicri:noRegion>Karbala</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmc">7147498</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7147498</idno><idno type="RBID">PMC:7147498</idno><idno type="doi">10.6026/97320630016236</idno><idno type="pmid">NONE</idno><date when="2020">2020</date><idno type="wicri:Area/Pmc/Corpus">000E36</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000E36</idno><idno type="wicri:Area/Pmc/Curation">000E36</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000E36</idno><idno type="wicri:Area/Pmc/Checkpoint">000177</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000177</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Molecular docking and dynamics simulation of FDA approved drugs with the main protease from 2019 novel coronavirus</title><author><name sortKey="Odhar, Hasanain Abdulhameed" sort="Odhar, Hasanain Abdulhameed" uniqKey="Odhar H" first="Hasanain Abdulhameed" last="Odhar">Hasanain Abdulhameed Odhar</name><affiliation wicri:level="1"><nlm:aff id="A1">Department of pharmacy, Al-Zahrawi University College, Karbala, Iraq</nlm:aff><country xml:lang="fr">Iraq</country><wicri:regionArea>Department of pharmacy, Al-Zahrawi University College, Karbala</wicri:regionArea><wicri:noRegion>Karbala</wicri:noRegion></affiliation></author><author><name sortKey="Ahjel, Salam Waheed" sort="Ahjel, Salam Waheed" uniqKey="Ahjel S" first="Salam Waheed" last="Ahjel">Salam Waheed Ahjel</name><affiliation wicri:level="1"><nlm:aff id="A1">Department of pharmacy, Al-Zahrawi University College, Karbala, Iraq</nlm:aff><country xml:lang="fr">Iraq</country><wicri:regionArea>Department of pharmacy, Al-Zahrawi University College, Karbala</wicri:regionArea><wicri:noRegion>Karbala</wicri:noRegion></affiliation></author><author><name sortKey="Albeer, Ali A Mohammed Ali" sort="Albeer, Ali A Mohammed Ali" uniqKey="Albeer A" first="Ali A. Mohammed Ali" last="Albeer">Ali A. Mohammed Ali Albeer</name><affiliation wicri:level="1"><nlm:aff id="A1">Department of pharmacy, Al-Zahrawi University College, Karbala, Iraq</nlm:aff><country xml:lang="fr">Iraq</country><wicri:regionArea>Department of pharmacy, Al-Zahrawi University College, Karbala</wicri:regionArea><wicri:noRegion>Karbala</wicri:noRegion></affiliation></author><author><name sortKey="Hashim, Ahmed Fadhil" sort="Hashim, Ahmed Fadhil" uniqKey="Hashim A" first="Ahmed Fadhil" last="Hashim">Ahmed Fadhil Hashim</name><affiliation wicri:level="1"><nlm:aff id="A1">Department of pharmacy, Al-Zahrawi University College, Karbala, Iraq</nlm:aff><country xml:lang="fr">Iraq</country><wicri:regionArea>Department of pharmacy, Al-Zahrawi University College, Karbala</wicri:regionArea><wicri:noRegion>Karbala</wicri:noRegion></affiliation></author><author><name sortKey="Rayshan, Ali Mahmood" sort="Rayshan, Ali Mahmood" uniqKey="Rayshan A" first="Ali Mahmood" last="Rayshan">Ali Mahmood Rayshan</name><affiliation wicri:level="1"><nlm:aff id="A1">Department of pharmacy, Al-Zahrawi University College, Karbala, Iraq</nlm:aff><country xml:lang="fr">Iraq</country><wicri:regionArea>Department of pharmacy, Al-Zahrawi University College, Karbala</wicri:regionArea><wicri:noRegion>Karbala</wicri:noRegion></affiliation></author><author><name sortKey="Humadi, Suhad Sami" sort="Humadi, Suhad Sami" uniqKey="Humadi S" first="Suhad Sami" last="Humadi">Suhad Sami Humadi</name><affiliation wicri:level="1"><nlm:aff id="A1">Department of pharmacy, Al-Zahrawi University College, Karbala, Iraq</nlm:aff><country xml:lang="fr">Iraq</country><wicri:regionArea>Department of pharmacy, Al-Zahrawi University College, Karbala</wicri:regionArea><wicri:noRegion>Karbala</wicri:noRegion></affiliation></author></analytic><series><title level="j">Bioinformation</title><idno type="ISSN">0973-8894</idno><idno type="eISSN">0973-2063</idno><imprint><date when="2020">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Design and development of an effective drug to combat the 2019 novel coronavirus remains a challenge. Therefore, it is of interest to study the binding features of 1615 FDA approved
drugs with the recently known 2019-nCoV main protease structure having high sequence homology with that from SARS-CoV. We document the binding features of top 10 drugs with the target
protein. We further report that Conivaptan and Azelastine are mainly involved in hydrophobic interactions with active site residues. Both drugs can maintain close proximity to the binding
pocket of main protease during simulation. However, these data need further in vitro and in vivo evaluation to repurpose these two drugs against 2019-nCoV.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey=" Weiss, Sr" uniqKey=" Weiss S">SR Weiss</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey=" Masters, Ps" uniqKey=" Masters P">PS Masters</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey=" Kuiken, T" uniqKey=" Kuiken T">T Kuiken</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey=" Raj, Vs" uniqKey=" Raj V">VS Raj</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey=" Graham, Rl" uniqKey=" Graham R">RL Graham</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey=" Drexler, Jf" uniqKey=" Drexler J">JF Drexler</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey=" Azhar, Ei" uniqKey=" Azhar E">EI Azhar</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey=" Huang, C" uniqKey=" Huang C">C Huang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey=" Lu, R" uniqKey=" Lu R">R Lu</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey=" Assiri, A" uniqKey=" Assiri A">A Assiri</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey=" Lee, N" uniqKey=" Lee N">N Lee</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey=" Li, Q" uniqKey=" Li Q">Q Li</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey=" Wan, Y" uniqKey=" Wan Y">Y Wan</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey=" Pettersen, Ef" uniqKey=" Pettersen E">EF Pettersen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey=" Hilgenfeld, R" uniqKey=" Hilgenfeld R">R Hilgenfeld</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey=" Wang, F" uniqKey=" Wang F">F Wang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey=" Yang, H" uniqKey=" Yang H">H Yang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey=" Meng, Ec" uniqKey=" Meng E">EC Meng</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey=" Sterling, T" uniqKey=" Sterling T">T Sterling</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey=" Trott, O" uniqKey=" Trott O">O Trott</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey=" Morris, Gm" uniqKey=" Morris G">GM Morris</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey=" Krieger, E" uniqKey=" Krieger E">E Krieger</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey=" Liu, X" uniqKey=" Liu X">X Liu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey=" Krieger, E" uniqKey=" Krieger E">E Krieger</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey=" Krieger, E" uniqKey=" Krieger E">E Krieger</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey=" Maier, Ja" uniqKey=" Maier J">JA Maier</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey=" Jakalian, A" uniqKey=" Jakalian A">A Jakalian</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey=" Wang, J" uniqKey=" Wang J">J Wang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey=" Hornak, V" uniqKey=" Hornak V">V Hornak</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey=" Essmann, U" uniqKey=" Essmann U">U Essmann</name></author></analytic></biblStruct><biblStruct></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">Bioinformation</journal-id><journal-id journal-id-type="iso-abbrev">Bioinformation</journal-id><journal-id journal-id-type="publisher-id">Bioinformation</journal-id><journal-title-group><journal-title>Bioinformation</journal-title></journal-title-group><issn pub-type="ppub">0973-8894</issn><issn pub-type="epub">0973-2063</issn><publisher><publisher-name>Biomedical Informatics</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmc">7147498</article-id><article-id pub-id-type="publisher-id">97320630016236</article-id><article-id pub-id-type="doi">10.6026/97320630016236</article-id><article-categories><subj-group subj-group-type="heading"><subject>Editorial</subject></subj-group></article-categories><title-group><article-title>Molecular docking and dynamics simulation of FDA approved drugs with the main protease from 2019 novel coronavirus</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Odhar</surname><given-names>Hasanain Abdulhameed</given-names></name><xref ref-type="aff" rid="A1">1</xref><xref ref-type="corresp" rid="COR1">*</xref></contrib><contrib contrib-type="author"><name><surname>Ahjel</surname><given-names>Salam Waheed</given-names></name><xref ref-type="aff" rid="A1">1</xref></contrib><contrib contrib-type="author"><name><surname>Albeer</surname><given-names>Ali A.Mohammed Ali</given-names></name><xref ref-type="aff" rid="A1">1</xref></contrib><contrib contrib-type="author"><name><surname>Hashim</surname><given-names>Ahmed Fadhil</given-names></name><xref ref-type="aff" rid="A1">1</xref></contrib><contrib contrib-type="author"><name><surname>Rayshan</surname><given-names>Ali Mahmood</given-names></name><xref ref-type="aff" rid="A1">1</xref></contrib><contrib contrib-type="author"><name><surname>Humadi</surname><given-names>Suhad Sami</given-names></name><xref ref-type="aff" rid="A1">1</xref></contrib><aff id="A1"><label>1</label>Department of pharmacy, Al-Zahrawi University College, Karbala, Iraq</aff></contrib-group><author-notes><corresp id="COR1"><label>*</label>Hasanain Abdulhameed Odhar <email>hodhar3@gmail.com</email></corresp></author-notes><pub-date pub-type="collection"><year>2020</year></pub-date><pub-date pub-type="epub"><day>31</day><month>3</month><year>2020</year></pub-date><volume>16</volume><issue>3</issue><fpage>236</fpage><lpage>244</lpage><history><date date-type="received"><day>28</day><month>2</month><year>2020</year></date><date date-type="rev-recd"><day>10</day><month>3</month><year>2020</year></date><date date-type="accepted"><day>20</day><month>3</month><year>2020</year></date></history><permissions><copyright-statement>© 2020 Biomedical Informatics</copyright-statement><copyright-year>2020</copyright-year><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/3.0/"><license-p>This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.</license-p></license></permissions><abstract><p>Design and development of an effective drug to combat the 2019 novel coronavirus remains a challenge. Therefore, it is of interest to study the binding features of 1615 FDA approved
drugs with the recently known 2019-nCoV main protease structure having high sequence homology with that from SARS-CoV. We document the binding features of top 10 drugs with the target
protein. We further report that Conivaptan and Azelastine are mainly involved in hydrophobic interactions with active site residues. Both drugs can maintain close proximity to the binding
pocket of main protease during simulation. However, these data need further in vitro and in vivo evaluation to repurpose these two drugs against 2019-nCoV.</p></abstract><kwd-group><kwd>2019-nCoV</kwd><kwd>main protease</kwd><kwd>repurposing</kwd><kwd>docking</kwd><kwd>dynamics simulation</kwd></kwd-group></article-meta></front><floats-group><table-wrap id="T1" position="float"><label>Table 1</label><caption><title>Binding pockets prediction for chain A of 2019-nCoV main protease crystal.</title></caption><table frame="hsides" rules="groups"><thead><tr><td rowspan="1" colspan="1">Pocket No.</td><td rowspan="1" colspan="1">Volume (A<sup>3</sup>)</td><td rowspan="1" colspan="1">Surface area (A<sup>2</sup>)</td><td rowspan="1" colspan="1">Druggability score</td></tr></thead><tbody><tr><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">702.27</td><td rowspan="1" colspan="1">842.81</td><td rowspan="1" colspan="1">0.77</td></tr><tr><td rowspan="1" colspan="1">2</td><td rowspan="1" colspan="1">374.59</td><td rowspan="1" colspan="1">757.16</td><td rowspan="1" colspan="1">0.74</td></tr><tr><td rowspan="1" colspan="1">3</td><td rowspan="1" colspan="1">330.18</td><td rowspan="1" colspan="1">518.79</td><td rowspan="1" colspan="1">0.56</td></tr></tbody></table></table-wrap><table-wrap id="T2" position="float"><label>Table 2</label><caption><title>Chemical and clinical characteristics of the top ten drugs as screened virtually against 2019-nCoV main protease. These drugs were ranked according to their minimum
binding energy to main protease crystal of 2019-nCoV.</title></caption><table frame="hsides" rules="groups"><thead><tr><td rowspan="1" colspan="1">No.</td><td rowspan="1" colspan="1">Generic name</td><td rowspan="1" colspan="1">Molecular formula</td><td rowspan="1" colspan="1">Binding energy (Kcal/mol)</td><td rowspan="1" colspan="1">Indication [<xref rid="R41" ref-type="bibr">41</xref>]</td><td rowspan="1" colspan="1">Legal status [<xref rid="R41" ref-type="bibr">41</xref>]</td></tr></thead><tbody><tr><td rowspan="1" colspan="1">1</td><td rowspan="1" colspan="1">Perampanel</td><td rowspan="1" colspan="1">C23H15N3O</td><td rowspan="1" colspan="1">-8.8</td><td rowspan="1" colspan="1">Epilepsy</td><td rowspan="1" colspan="1">POM</td></tr><tr><td rowspan="1" colspan="1">2</td><td rowspan="1" colspan="1">Conivaptan</td><td rowspan="1" colspan="1">C32H26N4O2</td><td rowspan="1" colspan="1">-8.6</td><td rowspan="1" colspan="1">Hyponatremia</td><td rowspan="1" colspan="1">POM</td></tr><tr><td rowspan="1" colspan="1">3</td><td rowspan="1" colspan="1">Sonidegib</td><td rowspan="1" colspan="1">C26H26F3N3O3</td><td rowspan="1" colspan="1">-8.5</td><td rowspan="1" colspan="1">Basal-cell carcinoma</td><td rowspan="1" colspan="1">POM</td></tr><tr><td rowspan="1" colspan="1">4</td><td rowspan="1" colspan="1">Azelastine</td><td rowspan="1" colspan="1">C22H24ClN3O</td><td rowspan="1" colspan="1">-8.4</td><td rowspan="1" colspan="1">Allergy</td><td rowspan="1" colspan="1">POM</td></tr><tr><td rowspan="1" colspan="1">5</td><td rowspan="1" colspan="1">Idelalisib</td><td rowspan="1" colspan="1">C22H18FN7O</td><td rowspan="1" colspan="1">-8.1</td><td rowspan="1" colspan="1">Leukemia and </td><td rowspan="1" colspan="1">POM</td></tr><tr><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1">lymphoma</td><td rowspan="1" colspan="1"></td></tr><tr><td rowspan="1" colspan="1">6</td><td rowspan="1" colspan="1">Suvorexant</td><td rowspan="1" colspan="1">C23H23ClN6O2</td><td rowspan="1" colspan="1">-8.1</td><td rowspan="1" colspan="1">Insomnia</td><td rowspan="1" colspan="1">POM</td></tr><tr><td rowspan="1" colspan="1">7</td><td rowspan="1" colspan="1">Olaparib</td><td rowspan="1" colspan="1">C24H23FN4O3</td><td rowspan="1" colspan="1">-8</td><td rowspan="1" colspan="1">Ovarian, breast and</td><td rowspan="1" colspan="1">POM</td></tr><tr><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"></td><td rowspan="1" colspan="1"> pancreatic cancers</td><td rowspan="1" colspan="1"></td></tr><tr><td rowspan="1" colspan="1">8</td><td rowspan="1" colspan="1">Ponatinib</td><td rowspan="1" colspan="1">C29H27F3N6O</td><td rowspan="1" colspan="1">-8</td><td rowspan="1" colspan="1">Leukemia</td><td rowspan="1" colspan="1">POM</td></tr><tr><td rowspan="1" colspan="1">9</td><td rowspan="1" colspan="1">Loxapine</td><td rowspan="1" colspan="1">C18H18ClN3O</td><td rowspan="1" colspan="1">-7.6</td><td rowspan="1" colspan="1">Schizophrenia</td><td rowspan="1" colspan="1">POM</td></tr><tr><td rowspan="1" colspan="1">10</td><td rowspan="1" colspan="1">Tolvaptan</td><td rowspan="1" colspan="1">C26H25ClN2O3</td><td rowspan="1" colspan="1">-7.5</td><td rowspan="1" colspan="1">Hyponatremia</td><td rowspan="1" colspan="1">POM</td></tr></tbody></table></table-wrap><fig id="F1" position="float"><label>Figure 1</label><caption><p>A three-dimensional cartoon representation for chain A of 2019-nCoV main protease crystal. The C-terminus is colored as red while N-terminus is colored as blue. We have used
the recently released Mpro crystal with code 6LU7 [<xref rid="R19" ref-type="bibr">19</xref>]. We have employed UCSF chimera version 1.13.1 for image processing and rendering
[<xref rid="R20" ref-type="bibr">20</xref>].</p></caption><graphic xlink:href="97320630016236F1"></graphic></fig><fig id="F2" position="float"><label>Figure 2</label><caption><p>Superimposition of chain A for 2019-nCoV Mpro (blue color) with chain A for SARS-CoV Mpro (red color).</p></caption><graphic xlink:href="97320630016236F2"></graphic></fig><fig id="F3" position="float"><label>Figure 3</label><caption><p>Sequence alignment output for 2019-nCoV Mpro chain A with the reference SARS-CoV Mpro chain A. The RMSD: ca represents the root-mean-square deviation for variation in each
column.</p></caption><graphic xlink:href="97320630016236F3"></graphic></fig><fig id="F4" position="float"><label>Figure 4</label><caption><p>Predicted binding pockets within chain A of 2019-nCoV main protease crystal.</p></caption><graphic xlink:href="97320630016236F4"></graphic></fig><fig id="F5" position="float"><label>Figure 5</label><caption><p>Chemical structures for the top ten drugs with least binding energy as screened virtually against 2019-nCoV Mpro crystal.</p></caption><graphic xlink:href="97320630016236F5"></graphic></fig><fig id="F6" position="float"><label>Figure 6</label><caption><p>Two-dimensional representation for docking of (A) Conivaptan and (B) Azelastine against 2019-nCoV main protease crystal. The colored discs represent active site residues,
while dashed lines refer to interaction bonds.</p></caption><graphic xlink:href="97320630016236F6"></graphic></fig><fig id="F7" position="float"><label>Figure 7</label><caption><p>Potential energy versus simulation time plot for (A) Conivaptan-Mpro complex and (B) Azelastine-Mpro complex. Energy is expressed as KJ/ mol.</p></caption><graphic xlink:href="97320630016236F7"></graphic></fig><fig id="F8" position="float"><label>Figure 8</label><caption><p>Interactions plot between Mpro active site residues and (A) Conivaptan or (B) Azelastine during 7 nanoseconds period of simulation.</p></caption><graphic xlink:href="97320630016236F8"></graphic></fig><fig id="F9" position="float"><label>Figure 9</label><caption><p>Ligand movement RMSD as a function of simulation period. Plot (A) is for Conivaptan movement while plot (B) is for Azelastine movement.</p></caption><graphic xlink:href="97320630016236F9"></graphic></fig><fig id="F10" position="float"><label>Figure 10</label><caption><p>Ligand conformation RMSD as a function of simulation period. Plot (A) is for Conivaptan conformational changes while plot (B) is for Azelastine conformational changes.</p></caption><graphic xlink:href="97320630016236F10"></graphic></fig></floats-group></pmc><affiliations><list><country><li>Iraq</li></country></list><tree><country name="Iraq"><noRegion><name sortKey="Odhar, Hasanain Abdulhameed" sort="Odhar, Hasanain Abdulhameed" uniqKey="Odhar H" first="Hasanain Abdulhameed" last="Odhar">Hasanain Abdulhameed Odhar</name></noRegion><name sortKey="Ahjel, Salam Waheed" sort="Ahjel, Salam Waheed" uniqKey="Ahjel S" first="Salam Waheed" last="Ahjel">Salam Waheed Ahjel</name><name sortKey="Albeer, Ali A Mohammed Ali" sort="Albeer, Ali A Mohammed Ali" uniqKey="Albeer A" first="Ali A. Mohammed Ali" last="Albeer">Ali A. Mohammed Ali Albeer</name><name sortKey="Hashim, Ahmed Fadhil" sort="Hashim, Ahmed Fadhil" uniqKey="Hashim A" first="Ahmed Fadhil" last="Hashim">Ahmed Fadhil Hashim</name><name sortKey="Humadi, Suhad Sami" sort="Humadi, Suhad Sami" uniqKey="Humadi S" first="Suhad Sami" last="Humadi">Suhad Sami Humadi</name><name sortKey="Rayshan, Ali Mahmood" sort="Rayshan, Ali Mahmood" uniqKey="Rayshan A" first="Ali Mahmood" last="Rayshan">Ali Mahmood Rayshan</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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