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| ==An Ligand-observed Mass Spectrometry-based Approach Integrated into the Fragment Based Lead Discovery Pipeline== | | ==An Ligand-observed Mass Spectrometry-based Approach Integrated into the Fragment Based Lead Discovery Pipeline== |
| <StructureSection load='4ty9' size='340' side='right' caption='[[4ty9]], [[Resolution|resolution]] 2.78Å' scene=''> | | <StructureSection load='4ty9' size='340' side='right'caption='[[4ty9]], [[Resolution|resolution]] 2.78Å' scene=''> |
| == Structural highlights == | | == Structural highlights == |
| <table><tr><td colspan='2'>[[4ty9]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/9hepc 9hepc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TY9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4TY9 FirstGlance]. <br> | | <table><tr><td colspan='2'>[[4ty9]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Hepacivirus_C Hepacivirus C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TY9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4TY9 FirstGlance]. <br> |
| </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3B0:5-(TRIFLUOROMETHYL)PYRIDIN-2-AMINE'>3B0</scene></td></tr> | | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.78Å</td></tr> |
| <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4txf|4txf]], [[4txs|4txs]], [[4tya|4tya]], [[4tyb|4tyb]], [[4ty8|4ty8]]</td></tr> | | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3B0:5-(TRIFLUOROMETHYL)PYRIDIN-2-AMINE'>3B0</scene></td></tr> |
| <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ty9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ty9 OCA], [http://pdbe.org/4ty9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ty9 RCSB], [http://www.ebi.ac.uk/pdbsum/4ty9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ty9 ProSAT]</span></td></tr> | | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4ty9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ty9 OCA], [https://pdbe.org/4ty9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ty9 RCSB], [https://www.ebi.ac.uk/pdbsum/4ty9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ty9 ProSAT]</span></td></tr> |
| </table> | | </table> |
| <div style="background-color:#fffaf0;">
| | == Function == |
| == Publication Abstract from PubMed == | | [https://www.uniprot.org/uniprot/D0PY27_9HEPC D0PY27_9HEPC] |
| In fragment-based lead discovery (FBLD), a cascade combining multiple orthogonal technologies is required for reliable detection and characterization of fragment binding to the target. Given the limitations of the mainstream screening techniques, we presented a ligand-observed mass spectrometry approach to expand the toolkits and increase the flexibility of building a FBLD pipeline especially for tough targets. In this study, this approach was integrated into a FBLD program targeting the HCV RNA polymerase NS5B. Our ligand-observed mass spectrometry analysis resulted in the discovery of 10 hits from a 384-member fragment library through two independent screens of complex cocktails and a follow-up validation assay. Moreover, this MS-based approach enabled quantitative measurement of weak binding affinities of fragments which was in general consistent with SPR analysis. Five out of the ten hits were then successfully translated to X-ray structures of fragment-bound complexes to lay a foundation for structure-based inhibitor design. With distinctive strengths in terms of high capacity and speed, minimal method development, easy sample preparation, low material consumption and quantitative capability, this MS-based assay is anticipated to be a valuable addition to the repertoire of current fragment screening techniques.
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| A ligand-observed mass spectrometry approach integrated into the fragment based lead discovery pipeline.,Chen X, Qin S, Chen S, Li J, Li L, Wang Z, Wang Q, Lin J, Yang C, Shui W Sci Rep. 2015 Feb 10;5:8361. doi: 10.1038/srep08361. PMID:25666181<ref>PMID:25666181</ref>
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| From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| </div>
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| <div class="pdbe-citations 4ty9" style="background-color:#fffaf0;"></div>
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| == References ==
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| <references/>
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| __TOC__ | | __TOC__ |
| </StructureSection> | | </StructureSection> |
| [[Category: Chen, S]] | | [[Category: Hepacivirus C]] |
| [[Category: Chen, X]] | | [[Category: Large Structures]] |
| [[Category: Lin, J]] | | [[Category: Chen S]] |
| [[Category: Qin, S]] | | [[Category: Chen X]] |
| [[Category: Shui, W]] | | [[Category: Lin J]] |
| [[Category: Yang, C]] | | [[Category: Qin S]] |
| [[Category: Ns5b]] | | [[Category: Shui W]] |
| [[Category: Tranaferase-transferase inhibitor complex]] | | [[Category: Yang C]] |