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==Crystal structure of Ebolavirus glycoprotein in complex with inhibitor 118a==
==Crystal structure of Ebolavirus glycoprotein in complex with inhibitor 118a==
<StructureSection load='6hro' size='340' side='right' caption='[[6hro]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
<StructureSection load='6hro' size='340' side='right'caption='[[6hro]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6hro]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HRO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HRO FirstGlance]. <br>
<table><tr><td colspan='2'>[[6hro]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ebola_virus_-_Mayinga,_Zaire,_1976 Ebola virus - Mayinga, Zaire, 1976]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HRO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6HRO FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=GKZ:1-[2-[4-[4-(4-chlorophenyl)-3-methyl-1~{H}-pyrazol-5-yl]-3-oxidanyl-phenoxy]ethyl]piperidin-1-ium-4-carboxamide'>GKZ</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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]] 2.3&#8491;</td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=GKZ:1-[2-[4-[4-(4-chlorophenyl)-3-methyl-1~{H}-pyrazol-5-yl]-3-oxidanyl-phenoxy]ethyl]piperidin-1-ium-4-carboxamide'>GKZ</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=6hro FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hro OCA], [http://pdbe.org/6hro PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6hro RCSB], [http://www.ebi.ac.uk/pdbsum/6hro PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6hro 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=6hro FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hro OCA], [https://pdbe.org/6hro PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6hro RCSB], [https://www.ebi.ac.uk/pdbsum/6hro PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6hro ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[[http://www.uniprot.org/uniprot/VGP_EBOZM VGP_EBOZM]] GP1 is responsible for binding to the receptor(s) on target cells. Interacts with CD209/DC-SIGN and CLEC4M/DC-SIGNR which act as cofactors for virus entry into the host cell. Binding to CD209 and CLEC4M, which are respectively found on dendritic cells (DCs), and on endothelial cells of liver sinusoids and lymph node sinuses, facilitate infection of macrophages and endothelial cells. These interactions not only facilitate virus cell entry, but also allow capture of viral particles by DCs and subsequent transmission to susceptible cells without DCs infection (trans infection). Binding to the macrophage specific lectin CLEC10A also seem to enhance virus infectivity. Interaction with FOLR1/folate receptor alpha may be a cofactor for virus entry in some cell types, although results are contradictory. Members of the Tyro3 receptor tyrosine kinase family also seem to be cell entry factors in filovirus infection. Once attached, the virions are internalized through clathrin-dependent endocytosis and/or macropinocytosis. After internalization of the virus into the endosomes of the host cell, proteolysis of GP1 by two cysteine proteases, CTSB/cathepsin B and CTSL/cathepsin L presumably induces a conformational change of GP2, unmasking its fusion peptide and initiating membranes fusion.<ref>PMID:10932225</ref> <ref>PMID:12050398</ref> <ref>PMID:16051836</ref> <ref>PMID:15681442</ref> <ref>PMID:16603527</ref> <ref>PMID:16775318</ref> <ref>PMID:20862315</ref> <ref>PMID:20202662</ref>  GP2 acts as a class I viral fusion protein. Under the current model, the protein has at least 3 conformational states: pre-fusion native state, pre-hairpin intermediate state, and post-fusion hairpin state. During viral and target cell membrane fusion, the coiled coil regions (heptad repeats) assume a trimer-of-hairpins structure, positioning the fusion peptide in close proximity to the C-terminal region of the ectodomain. The formation of this structure appears to drive apposition and subsequent fusion of viral and target cell membranes. Responsible for penetration of the virus into the cell cytoplasm by mediating the fusion of the membrane of the endocytosed virus particle with the endosomal membrane. Low pH in endosomes induces an irreversible conformational change in GP2, releasing the fusion hydrophobic peptide.<ref>PMID:10932225</ref> <ref>PMID:12050398</ref> <ref>PMID:16051836</ref> <ref>PMID:15681442</ref> <ref>PMID:16603527</ref> <ref>PMID:16775318</ref> <ref>PMID:20862315</ref> <ref>PMID:20202662</ref>  GP1,2 mediates endothelial cell activation and decreases endothelial barrier function. Mediates activation of primary macrophages. At terminal stages of the viral infection, when its expression is high, GP1,2 down-modulates the expression of various host cell surface molecules that are essential for immune surveillance and cell adhesion. Down-modulates integrins ITGA1, ITGA2, ITGA3, ITGA4, ITGA5, ITGA6, ITGAV and ITGB1. GP1,2 alters the cellular recycling of the dimer alpha-V/beta-3 via a dynamin-dependent pathway. Decrease in the host cell surface expression of various adhesion molecules may lead to cell detachment, contributing to the disruption of blood vessel integrity and hemorrhages developed during Ebola virus infection (cytotoxicity). This cytotoxicity appears late in the infection, only after the massive release of viral particles by infected cells. Down-modulation of host MHC-I, leading to altered recognition by immune cells, may explain the immune suppression and inflammatory dysfunction linked to Ebola infection. Also down-modulates EGFR surface expression.<ref>PMID:10932225</ref> <ref>PMID:12050398</ref> <ref>PMID:16051836</ref> <ref>PMID:15681442</ref> <ref>PMID:16603527</ref> <ref>PMID:16775318</ref> <ref>PMID:20862315</ref> <ref>PMID:20202662</ref>  GP2delta is part of the complex GP1,2delta released by host ADAM17 metalloprotease. This secreted complex may play a role in the pathogenesis of the virus by efficiently blocking the neutralizing antibodies that would otherwise neutralize the virus surface glycoproteins GP1,2. Might therefore contribute to the lack of inflammatory reaction seen during infection in spite the of extensive necrosis and massive virus production. GP1,2delta does not seem to be involved in activation of primary macrophages.<ref>PMID:10932225</ref> <ref>PMID:12050398</ref> <ref>PMID:16051836</ref> <ref>PMID:15681442</ref> <ref>PMID:16603527</ref> <ref>PMID:16775318</ref> <ref>PMID:20862315</ref> <ref>PMID:20202662</ref> 
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
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</div>
</div>
<div class="pdbe-citations 6hro" style="background-color:#fffaf0;"></div>
<div class="pdbe-citations 6hro" style="background-color:#fffaf0;"></div>
==See Also==
*[[Glycoprotein GP 3D structures|Glycoprotein GP 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Ren, J]]
[[Category: Ebola virus - Mayinga, Zaire, 1976]]
[[Category: Stuart, D I]]
[[Category: Large Structures]]
[[Category: Zhao, Y]]
[[Category: Ren J]]
[[Category: Ebola glycoprotein]]
[[Category: Stuart DI]]
[[Category: Natural compound]]
[[Category: Zhao Y]]
[[Category: Structure-based in silico screening]]

Latest revision as of 11:01, 17 October 2024

Crystal structure of Ebolavirus glycoprotein in complex with inhibitor 118aCrystal structure of Ebolavirus glycoprotein in complex with inhibitor 118a

Structural highlights

6hro is a 2 chain structure with sequence from Ebola virus - Mayinga, Zaire, 1976. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.3Å
Ligands:, , , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

Potent Ebolavirus (EBOV) inhibitors will help to curtail outbreaks such as that which occurred in 2014-16 in West Africa. EBOV has on its surface a single glycoprotein (GP) critical for viral entry and membrane fusion. Recent high resolution complexes of EBOV GP with a variety of approved drugs revealed that binding to a common cavity prevented fusion of the virus and endosomal membranes, inhibiting virus infection. We performed docking experiments, screening a database of natural compounds to identify those likely to bind at this site. Using both inhibition assays of HIV-1-derived pseudovirus cell entry and structural analyses of the complexes of the compounds with GP we show here that two of these compounds attach in the common binding cavity, out of eight tested. In both cases two molecules bind in the cavity. The two compounds are chemically similar but the tighter binder has an additional chlorine atom that forms good halogen bonds to the protein and achieves an IC50 of 50 nM, making it the most potent GP-binding EBOV inhibitor yet identified, validating our screening approach for the discovery of novel anti-viral compounds.

Structure-based In Silico Screening Identifies a Potent Ebolavirus Inhibitor from a Traditional Chinese Medicine Library.,Shaikh F, Zhao Y, Alvarez L, Iliopoulou M, Lohans CT, Schofield CJ, Padilla-Parra S, Siu SWI, Fry E, Ren J, Stuart DI J Med Chem. 2019 Feb 20. doi: 10.1021/acs.jmedchem.8b01328. PMID:30785281[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Shaikh F, Zhao Y, Alvarez L, Iliopoulou M, Lohans CT, Schofield CJ, Padilla-Parra S, Siu SWI, Fry E, Ren J, Stuart DI. Structure-based In Silico Screening Identifies a Potent Ebolavirus Inhibitor from a Traditional Chinese Medicine Library. J Med Chem. 2019 Feb 20. doi: 10.1021/acs.jmedchem.8b01328. PMID:30785281 doi:http://dx.doi.org/10.1021/acs.jmedchem.8b01328

6hro, resolution 2.30Å

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