174 lines
15 KiB
XML
174 lines
15 KiB
XML
<document id="52A4C49C0F9CCDF9728555F97C91934F" ID-DOI="10.1016/j.phytochem.2021.113018" ID-ISSN="1873-3700" ID-Zenodo-Dep="8234792" IM.illustrations_approvedBy="carolina" IM.materialsCitations_approvedBy="felipe" IM.metadata_approvedBy="felipe" IM.tables_approvedBy="carolina" IM.taxonomicNames_approvedBy="carolina" IM.treatments_approvedBy="carolina" checkinTime="1691688826009" checkinUser="felipe" docAuthor="Yang, Yupei, Liu, Yongbei, Yu, Huanghe, Xie, Qingling, Wang, Bin, Jiang, Sai, Su, Wei, Mao, Yu, Li, Bin, Peng, Caiyun, Jian, Yuqing & Wang, Wei" docDate="2022" docId="F109879FFFE4FF9DFFBEF9795FD6FBCF" docLanguage="en" docName="Phytochemistry.194.113018.pdf" docOrigin="Phytochemistry (113018) 194" docSource="http://dx.doi.org/10.1016/j.phytochem.2021.113018" docStyle="DocumentStyle:F36D69FC8B198FBE91029DF9C24697D3.5:Phytochemistry.2020-.journal_article" docStyleId="F36D69FC8B198FBE91029DF9C24697D3" docStyleName="Phytochemistry.2020-.journal_article" docStyleVersion="5" docTitle="Kadsura coccinea A. C. Sm." docType="treatment" docVersion="2" lastPageNumber="8" masterDocId="0D30FFE7FFE3FF9AFFDAFFB25B44FFAC" masterDocTitle="Sesquiterpenes from Kadsura coccinea attenuate rheumatoid arthritis-related inflammation by inhibiting the NF-κB and JAK 2 / STAT 3 signal pathways" masterLastPageNumber="9" masterPageNumber="1" pageNumber="8" updateTime="1692106775550" updateUser="ExternalLinkService">
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<mods:title id="B1E7752273397E61F84F7F02F8E33154">Sesquiterpenes from Kadsura coccinea attenuate rheumatoid arthritis-related inflammation by inhibiting the NF-κB and JAK 2 / STAT 3 signal pathways</mods:title>
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<mods:namePart id="AD4AA6E2EA705A39762FEFB63442CA96">Yang, Yupei</mods:namePart>
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<mods:namePart id="DDB90F1B263DFE08A9EB0BE33588801F">Liu, Yongbei</mods:namePart>
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<mods:namePart id="C6FABB267F58FEE05E34A1D5DABCFC2F">Yu, Huanghe</mods:namePart>
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<mods:namePart id="AACE1B7691AE077EA51373E021A4B482">Xie, Qingling</mods:namePart>
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<mods:namePart id="48B6F53076F8F46C91C9699539765F12">Wang, Bin</mods:namePart>
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<mods:namePart id="A6B028C2B24E4D368BB1E600558593E5">Jiang, Sai</mods:namePart>
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<mods:namePart id="62FECD844CB29A8ABA21C2E0C0FB1BD7">Su, Wei</mods:namePart>
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<mods:namePart id="0EE5224CA2A91968094F70E0B3836C64">Mao, Yu</mods:namePart>
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<mods:namePart id="1271D30A62CA4B4A4831BCD36702D071">Li, Bin</mods:namePart>
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<mods:namePart id="993313633D52E34FDF5CB9F0EE44BE15">Peng, Caiyun</mods:namePart>
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<mods:namePart id="080A0E4AC4B29061A0ED51044CAFD968">Jian, Yuqing</mods:namePart>
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<mods:namePart id="7BDE2A9AFF2524673166F4B74EF82445">Wang, Wei</mods:namePart>
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<mods:date id="A957D82B1F394D59233DDEBA3CDAE498">2022</mods:date>
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<mods:title id="B5E6FD0129876DB1115F1A11BB9E7EB6">113018</mods:title>
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<mods:number id="2C29151B09287D367478EFBCFB988A5D">2022-02-28</mods:number>
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<mods:number id="40FABBC034F7EC12D3D48E38DA248B04">194</mods:number>
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<mods:start id="CC3BC353CC8467D4EF8994A23AE67EE8">1</mods:start>
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<mods:url id="F08E3FA4468956936BB67FCA9EA9A14D">http://dx.doi.org/10.1016/j.phytochem.2021.113018</mods:url>
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<treatment id="F109879FFFE4FF9DFFBEF9795FD6FBCF" ID-DOI="http://doi.org/10.5281/zenodo.8249906" ID-Zenodo-Dep="8249906" LSID="urn:lsid:plazi:treatment:F109879FFFE4FF9DFFBEF9795FD6FBCF" httpUri="http://treatment.plazi.org/id/F109879FFFE4FF9DFFBEF9795FD6FBCF" lastPageNumber="8" pageId="7" pageNumber="8">
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<emphasis id="4BD4EA9BFFE4FF9DFFBEF97959B5F972" bold="true" box="[100,753,1739,1759]" italics="true" pageId="7" pageNumber="8">
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5.9. Target prediction analysis of the active compounds from
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<taxonomicName id="BEA04D0AFFE4FF9DFD48F97959B5F972" ID-CoL="3QXWG" ID-ENA="124780" authority="(Lem.) A. C. Sm." authorityName="A. C. Sm." baseAuthorityName="Lem." box="[658,753,1739,1758]" class="Magnoliopsida" family="Schisandraceae" genus="Kadsura" kingdom="Plantae" order="Austrobaileyales" pageId="7" pageNumber="8" phylum="Tracheophyta" rank="species" species="coccinea">K.coccinea</taxonomicName>
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</emphasis>
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</paragraph>
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<subSubSection id="31BA6502FFE4FF9DFF5EF8B15FD6FBCF" pageId="7" pageNumber="8" type="description">
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<paragraph id="791F3689FFE4FF9DFF5EF8B158CCFF73" blockId="7.[100,770,1795,1982]" lastBlockId="7.[818,1487,148,223]" pageId="7" pageNumber="8">
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Active compounds
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<emphasis id="4BD4EA9BFFE4FF9DFEEDF8B15A07F8BA" bold="true" box="[311,323,1795,1814]" pageId="7" pageNumber="8">2</emphasis>
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,
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<emphasis id="4BD4EA9BFFE4FF9DFE95F8B15A1FF8BA" bold="true" box="[335,347,1795,1814]" pageId="7" pageNumber="8">6</emphasis>
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,
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<emphasis id="4BD4EA9BFFE4FF9DFEBDF8B15AC4F8BA" bold="true" box="[359,384,1795,1814]" pageId="7" pageNumber="8">11</emphasis>
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,
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<emphasis id="4BD4EA9BFFE4FF9DFE51F8B15A8CF8BA" bold="true" box="[395,456,1795,1815]" pageId="7" pageNumber="8">13–14</emphasis>
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,
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<emphasis id="4BD4EA9BFFE4FF9DFE09F8B15AA8F8BA" bold="true" box="[467,492,1795,1814]" pageId="7" pageNumber="8">16</emphasis>
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, and
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<emphasis id="4BD4EA9BFFE4FF9DFDFBF8B15919F8BA" bold="true" box="[545,605,1795,1815]" pageId="7" pageNumber="8">18–20</emphasis>
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were selected for the target prediction analysis based on the
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<emphasis id="4BD4EA9BFFE4FF9DFDD4F8AD5915F89E" bold="true" box="[526,593,1823,1842]" italics="true" pageId="7" pageNumber="8">in vitro</emphasis>
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anti-RA and anti-inflammatory activities screening results. The Swiss Target Prediction (https://www.swisstargetprediction.ch/) database (Gfeller et al., 2014) was used to retrieve the predicted gene targets for the selected nine active compounds. The sdf format of the optimized structure of each compound was uploaded to the Swiss Target Prediction online platform for screening, with the screening condition limited to “
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<taxonomicName id="BEA04D0AFFE4FF9DFA99FF265EFBFF0B" authorityName="Linnaeus" authorityYear="1758" box="[1347,1471,148,167]" class="Mammalia" family="Hominidae" genus="Homo" kingdom="Animalia" order="Primates" pageId="7" pageNumber="8" phylum="Chordata" rank="species" species="sapiens">
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<emphasis id="4BD4EA9BFFE4FF9DFA99FF265EFBFF0B" bold="true" box="[1347,1471,148,167]" italics="true" pageId="7" pageNumber="8">Homo sapiens</emphasis>
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</taxonomicName>
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”. High probability targets were selected after the elimination of duplicate contents.
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</paragraph>
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<paragraph id="791F3689FFE4FF9DFCE8FEB45F00FEB5" blockId="7.[818,1092,262,281]" box="[818,1092,262,281]" pageId="7" pageNumber="8">
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<heading id="225781E5FFE4FF9DFCE8FEB45F00FEB5" bold="true" box="[818,1092,262,281]" fontSize="36" level="1" pageId="7" pageNumber="8" reason="1">
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<emphasis id="4BD4EA9BFFE4FF9DFCE8FEB45F00FEB5" bold="true" box="[818,1092,262,281]" italics="true" pageId="7" pageNumber="8">5.10. Prediction of RA targets</emphasis>
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</heading>
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</paragraph>
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<paragraph id="791F3689FFE4FF9DFC8BFE8C583CFE55" blockId="7.[818,1487,318,505]" pageId="7" pageNumber="8">
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The potential therapeutic targets for RA were searched in online disease databases, GeneCards (http://www.genecards.org/) (Stelzer et al., 2016) and MalaCards (https://www.malacards.org/) (Rappaport et al., 2017). The search term was “rheumatoid arthritis”, followed by further filtering using the conditions “gene” and “
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<taxonomicName id="BEA04D0AFFE4FF9DFACDFE1C5ED7FE6C" authorityName="Linnaeus" authorityYear="1758" box="[1303,1427,429,449]" class="Mammalia" family="Hominidae" genus="Homo" kingdom="Animalia" order="Primates" pageId="7" pageNumber="8" phylum="Chordata" rank="species" species="sapiens">
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<emphasis id="4BD4EA9BFFE4FF9DFACDFE1C5ED7FE6C" bold="true" box="[1303,1427,429,449]" italics="true" pageId="7" pageNumber="8">Homo sapiens</emphasis>
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</taxonomicName>
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”. The prediction targets from the two databases were combined as the final RA targets.
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</paragraph>
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<paragraph id="791F3689FFE4FF9DFCE8FD925E30FD9E" blockId="7.[818,1396,543,563]" box="[818,1396,543,563]" pageId="7" pageNumber="8">
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<heading id="225781E5FFE4FF9DFCE8FD925E30FD9E" bold="true" box="[818,1396,543,563]" fontSize="36" level="1" pageId="7" pageNumber="8" reason="1">
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<emphasis id="4BD4EA9BFFE4FF9DFCE8FD925E30FD9E" bold="true" box="[818,1396,543,563]" italics="true" pageId="7" pageNumber="8">5.11. Construction of protein-protein interactions (PPI) network</emphasis>
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</heading>
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</paragraph>
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<paragraph id="791F3689FFE4FF9DFC8BFDE55ED5FD12" blockId="7.[818,1487,599,702]" pageId="7" pageNumber="8">The common RA active compounds prediction targets were uploaded into STRING (https://string-db.org/cgi/input.pl) to build the PPI network interaction (Szklarczyk et al., 2016). The PPI network was then constructed and visualized using the Cytoscape V3.6.0 software.</paragraph>
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<paragraph id="791F3689FFE4FF9DFCE8FD575FBFFD54" blockId="7.[818,1275,741,760]" box="[818,1275,741,760]" pageId="7" pageNumber="8">
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<heading id="225781E5FFE4FF9DFCE8FD575FBFFD54" bold="true" box="[818,1275,741,760]" fontSize="36" level="1" pageId="7" pageNumber="8" reason="1">
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<emphasis id="4BD4EA9BFFE4FF9DFCE8FD575FBFFD54" bold="true" box="[818,1275,741,760]" italics="true" pageId="7" pageNumber="8">5.12. Pathway and functional enrichment analysis</emphasis>
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</heading>
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</paragraph>
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<paragraph id="791F3689FFE4FF9DFC8BFCAF5FD6FBCF" blockId="7.[818,1488,797,1123]" pageId="7" pageNumber="8">
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The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) enrichment analyses of the active compounds were done to investigate the potential signaling pathways and biological processes regulated by these compounds. The enrichment results were then visualized using Bioinformatics (http://www.bioinformatics.com. cn/). KEGG pathway analysis is a prominent analysis tool in network pharmacology that aids in the understanding of drug action mechanisms in disease. On the other hand, GO enrichment analysis identifies the biological processes (BP), molecular functions (MF), and cellular components (CC) of the target compounds. The top 20 GO enrichments and KEGG pathways with higher counts based on a significance threshold of
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<emphasis id="4BD4EA9BFFE4FF9DFCE8FBE25810FBCF" box="[818,852,1104,1123]" italics="true" pageId="7" pageNumber="8">
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<emphasis id="4BD4EA9BFFE4FF9DFCE8FBE2587AFBCF" bold="true" box="[818,830,1104,1123]" italics="true" pageId="7" pageNumber="8">P</emphasis>
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<
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</emphasis>
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0.05 were then further analyzed.
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</paragraph>
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</subSubSection>
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</treatment>
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