5k5m: Difference between revisions
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==Co-Crystal Structure of Dengue Virus Serotype 2 RNA Dependent RNA Polymerase with Compound 27== | ==Co-Crystal Structure of Dengue Virus Serotype 2 RNA Dependent RNA Polymerase with Compound 27== | ||
<StructureSection load='5k5m' size='340' side='right' caption='[[5k5m]], [[Resolution|resolution]] 2.01Å' scene=''> | <StructureSection load='5k5m' size='340' side='right'caption='[[5k5m]], [[Resolution|resolution]] 2.01Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5k5m]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K5M OCA]. For a <b>guided tour on the structure components</b> use [http:// | <table><tr><td colspan='2'>[[5k5m]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Dengue_virus_2 Dengue virus 2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K5M OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5K5M FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=68T:5-[5-(3-HYDROXYPROP-1-YN-1-YL)THIOPHEN-2-YL]-2,4-DIMETHOXY-N-[(3-METHOXYPHENYL)SULFONYL]BENZAMIDE'>68T</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=68T:5-[5-(3-HYDROXYPROP-1-YN-1-YL)THIOPHEN-2-YL]-2,4-DIMETHOXY-N-[(3-METHOXYPHENYL)SULFONYL]BENZAMIDE'>68T</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http:// | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5k5m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k5m OCA], [http://pdbe.org/5k5m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k5m RCSB], [http://www.ebi.ac.uk/pdbsum/5k5m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k5m ProSAT]</span></td></tr> | ||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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</div> | </div> | ||
<div class="pdbe-citations 5k5m" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 5k5m" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[RNA polymerase 3D structures|RNA polymerase 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Dengue virus 2]] | |||
[[Category: Large Structures]] | |||
[[Category: Arora, R]] | [[Category: Arora, R]] | ||
[[Category: Benson, T E]] | [[Category: Benson, T E]] | ||
Revision as of 12:20, 25 June 2020
Co-Crystal Structure of Dengue Virus Serotype 2 RNA Dependent RNA Polymerase with Compound 27Co-Crystal Structure of Dengue Virus Serotype 2 RNA Dependent RNA Polymerase with Compound 27
Structural highlights
Publication Abstract from PubMedFlaviviruses comprise major emerging pathogens such as dengue virus (DENV) or Zika virus (ZIKV). The flavivirus RNA genome is replicated by the RNA-dependent-RNA polymerase (RdRp) domain of non-structural protein 5 (NS5). This essential enzymatic activity renders the RdRp attractive for antiviral therapy. NS5 synthesizes viral RNA via a "de novo" initiation mechanism. Crystal structures of the flavivirus RdRp revealed a "closed" conformation reminiscent of a pre-initiation state, with a well ordered priming loop that extrudes from the thumb subdomain into the dsRNA exit tunnel, close to the "GDD" active site. To-date, no allosteric pockets have been identified for the RdRp, and compound screening campaigns did not yield suitable drug candidates. Using fragment-based screening via X-ray crystallography, we found a fragment that bound to a pocket of the apo-DENV RdRp close to its active site (termed "N pocket"). Structure-guided improvements yielded DENV pan-serotype inhibitors of the RdRp de novo initiation activity with nano-molar potency that also impeded elongation activity at micro-molar concentrations. Inhibitors exhibited mixed inhibition kinetics with respect to competition with the RNA or GTP substrate. The best compounds have EC50 values of 1-2 muM against all four DENV serotypes in cell culture assays. Genome-sequencing of compound-resistant DENV replicons, identified amino acid changes that mapped to the N pocket. Since inhibitors bind at the thumb/palm interface of the RdRp, this class of compounds is proposed to hinder RdRp conformational changes during its transition from initiation to elongation. This is the first report of a class of pan-serotype and cell-active DENV RdRp inhibitors. Given the evolutionary conservation of residues lining the N pocket, these molecules offer insights to treat other serious conditions caused by flaviviruses. Potent Allosteric Dengue Virus NS5 Polymerase Inhibitors: Mechanism of Action and Resistance Profiling.,Lim SP, Noble CG, Seh CC, Soh TS, El Sahili A, Chan GK, Lescar J, Arora R, Benson T, Nilar S, Manjunatha U, Wan KF, Dong H, Xie X, Shi PY, Yokokawa F PLoS Pathog. 2016 Aug 8;12(8):e1005737. doi: 10.1371/journal.ppat.1005737., eCollection 2016 Aug. PMID:27500641[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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