6piy - Revision history

OCA at 07:30, 11 October 2023

OCA — Wed, 11 Oct 2023 07:30:21 GMT

←Older revision		Revision as of 07:30, 11 October 2023
Line 3:		Line 3:
	<StructureSection load='6piy' size='340' side='right'caption='[[6piy]], [[Resolution\|resolution]] 1.86Å' scene=''>		<StructureSection load='6piy' size='340' side='right'caption='[[6piy]], [[Resolution\|resolution]] 1.86Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6piy]] is a 1 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=6PIY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6PIY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6piy]] is a 1 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=6PIY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PIY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=OMS:1-methylcyclobutyl+[(2R,6S,12Z,13aS,14aR,16aS)-2-[(7-methoxy-3-methylquinoxalin-2-yl)oxy]-14a-{[(1-methylcyclopropyl)sulfonyl]carbamoyl}-5,16-dioxo-1,2,3,5,6,7,8,9,10,11,13a,14,14a,15,16,16a-hexadecahydrocyclopropa[e]pyrrolo[1,2-a][1,4]diazacyclopentadecin-6-yl]carbamate'>OMS</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.862Å</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6piy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6piy OCA], [~~http~~://pdbe.org/6piy PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6piy RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6piy PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6piy ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=OMS:1-methylcyclobutyl+[(2R,6S,12Z,13aS,14aR,16aS)-2-[(7-methoxy-3-methylquinoxalin-2-yl)oxy]-14a-{[(1-methylcyclopropyl)sulfonyl]carbamoyl}-5,16-dioxo-1,2,3,5,6,7,8,9,10,11,13a,14,14a,15,16,16a-hexadecahydrocyclopropa[e]pyrrolo[1,2-a][1,4]diazacyclopentadecin-6-yl]carbamate'>OMS</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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'>[https://proteopedia.org/fgij/fg.htm?mol=6piy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6piy OCA], [https://pdbe.org/6piy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6piy RCSB], [https://www.ebi.ac.uk/pdbsum/6piy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6piy ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A0B4WYC6_9HEPC A0A0B4WYC6_9HEPC]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 18:		Line 21:

	==See Also==		==See Also==
-	*[[Virus ~~proteases~~ 3D ~~strutures~~\|Virus ~~proteases~~ 3D ~~strutures~~]]	+	*[[Virus protease 3D structures\|Virus protease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Hepacivirus C]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Schiffer~~, C A~~]]	+	[[Category: Schiffer CA]]
-	[[Category: Zephyr, J]]	+	[[Category: Zephyr J]]
-	~~[[Category: Drug resistance]]~~	+
-	~~[[Category: Hepatitis c virus]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Hydrolase-hydrolase inhibitor complex]]~~	+
-	~~[[Category: Ns3/4a protease]]~~	+
-	~~[[Category: Protease inhibitor~~]]	+

OCA at 10:06, 16 September 2020

OCA — Wed, 16 Sep 2020 10:06:28 GMT

←Older revision		Revision as of 10:06, 16 September 2020
Line 3:		Line 3:
	<StructureSection load='6piy' size='340' side='right'caption='[[6piy]], [[Resolution\|resolution]] 1.86Å' scene=''>		<StructureSection load='6piy' size='340' side='right'caption='[[6piy]], [[Resolution\|resolution]] 1.86Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6piy]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PIY OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6PIY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6piy]] is a 1 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=6PIY OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6PIY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=OMS:1-methylcyclobutyl+[(2R,6S,12Z,13aS,14aR,16aS)-2-[(7-methoxy-3-methylquinoxalin-2-yl)oxy]-14a-{[(1-methylcyclopropyl)sulfonyl]carbamoyl}-5,16-dioxo-1,2,3,5,6,7,8,9,10,11,13a,14,14a,15,16,16a-hexadecahydrocyclopropa[e]pyrrolo[1,2-a][1,4]diazacyclopentadecin-6-yl]carbamate'>OMS</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=OMS:1-methylcyclobutyl+[(2R,6S,12Z,13aS,14aR,16aS)-2-[(7-methoxy-3-methylquinoxalin-2-yl)oxy]-14a-{[(1-methylcyclopropyl)sulfonyl]carbamoyl}-5,16-dioxo-1,2,3,5,6,7,8,9,10,11,13a,14,14a,15,16,16a-hexadecahydrocyclopropa[e]pyrrolo[1,2-a][1,4]diazacyclopentadecin-6-yl]carbamate'>OMS</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6piy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6piy OCA], [http://pdbe.org/6piy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6piy RCSB], [http://www.ebi.ac.uk/pdbsum/6piy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6piy ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6piy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6piy OCA], [http://pdbe.org/6piy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6piy RCSB], [http://www.ebi.ac.uk/pdbsum/6piy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6piy ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Hepatitis C virus (HCV) infects millions of people worldwide, causing chronic liver disease that can lead to cirrhosis, hepatocellular carcinoma, and liver transplant. In the last several years, the advent of direct-acting antivirals, including NS3/4A protease inhibitors (PIs), has remarkably improved treatment outcomes of HCV-infected patients. However, selection of resistance-associated substitutions and polymorphisms among genotypes can lead to drug resistance and in some cases treatment failure. A proactive strategy to combat resistance is to constrain PIs within evolutionarily conserved regions in the protease active site. Designing PIs using the substrate envelope is a rational strategy to decrease the susceptibility to resistance by using the constraints of substrate recognition. We successfully designed two series of HCV NS3/4A PIs to leverage unexploited areas in the substrate envelope to improve potency, specifically against resistance-associated substitutions at D168. Our design strategy achieved better resistance profiles over both the FDA-approved NS3/4A PI grazoprevir and the parent compound against the clinically relevant D168A substitution. Crystallographic structural analysis and inhibition assays confirmed that optimally filling the substrate envelope is critical to improve inhibitor potency while avoiding resistance. Specifically, inhibitors that enhanced hydrophobic packing in the S4 pocket and avoided an energetically frustrated pocket performed the best. Thus, the HCV substrate envelope proved to be a powerful tool to design robust PIs, offering a strategy that can be translated to other targets for rational design of inhibitors with improved potency and resistance profiles.IMPORTANCE Despite significant progress, hepatitis C virus (HCV) continues to be a major health problem with millions of people infected worldwide and thousands dying annually due to resulting complications. Recent antiviral combinations can achieve >95% cure, but late diagnosis, low access to treatment, and treatment failure due to drug resistance continue to be roadblocks against eradication of the virus. We report the rational design of two series of HCV NS3/4A protease inhibitors with improved resistance profiles by exploiting evolutionarily constrained regions of the active site using the substrate envelope model. Optimally filling the S4 pocket is critical to avoid resistance and improve potency. Our results provide drug design strategies to avoid resistance that are applicable to other quickly evolving viral drug targets.
		+
		+	Avoiding Drug Resistance by Substrate Envelope-Guided Design: Toward Potent and Robust HCV NS3/4A Protease Inhibitors.,Matthew AN, Zephyr J, Nageswara Rao D, Henes M, Kamran W, Kosovrasti K, Hedger AK, Lockbaum GJ, Timm J, Ali A, Kurt Yilmaz N, Schiffer CA mBio. 2020 Mar 31;11(2). pii: mBio.00172-20. doi: 10.1128/mBio.00172-20. PMID:32234812<ref>PMID:32234812</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6piy" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Virus proteases 3D strutures\|Virus proteases 3D strutures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:45, 4 March 2020

OCA — Wed, 04 Mar 2020 06:45:59 GMT

←Older revision		Revision as of 06:45, 4 March 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6piy is ON HOLD until Paper Publication~~	+	==Crystal structure of HCV NS3/4A D168A protease in complex with P4-2 (NR02-61)==
-		+	<StructureSection load='6piy' size='340' side='right'caption='[[6piy]], [[Resolution\|resolution]] 1.86Å' scene=''>
-	~~Authors: Zephyr, J., Schiffer, C.A.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6piy]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PIY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PIY FirstGlance]. <br>
-	~~Description:~~ Crystal structure of HCV NS3/4A D168A protease in complex with P4-2 (NR02-61)	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=OMS:1-methylcyclobutyl+[(2R,6S,12Z,13aS,14aR,16aS)-2-[(7-methoxy-3-methylquinoxalin-2-yl)oxy]-14a-{[(1-methylcyclopropyl)sulfonyl]carbamoyl}-5,16-dioxo-1,2,3,5,6,7,8,9,10,11,13a,14,14a,15,16,16a-hexadecahydrocyclopropa[e]pyrrolo[1,2-a][1,4]diazacyclopentadecin-6-yl]carbamate'>OMS</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<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=6piy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6piy OCA], [http://pdbe.org/6piy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6piy RCSB], [http://www.ebi.ac.uk/pdbsum/6piy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6piy ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Schiffer, C A]]
	[[Category: Zephyr, J]]		[[Category: Zephyr, J]]
-	[[Category: ~~Schiffer, C.A~~]]	+	[[Category: Drug resistance]]
		+	[[Category: Hepatitis c virus]]
		+	[[Category: Hydrolase]]
		+	[[Category: Hydrolase-hydrolase inhibitor complex]]
		+	[[Category: Ns3/4a protease]]
		+	[[Category: Protease inhibitor]]

OCA at 08:57, 17 July 2019

OCA — Wed, 17 Jul 2019 08:57:45 GMT

←Older revision		Revision as of 08:57, 17 July 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6piy is ON HOLD	+	The entry 6piy is ON HOLD until Paper Publication

	Authors: Zephyr, J., Schiffer, C.A.		Authors: Zephyr, J., Schiffer, C.A.

OCA: Protected "6piy" [edit=sysop:move=sysop]

OCA — Wed, 03 Jul 2019 04:25:34 GMT

Protected "6piy" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:25, 3 July 2019

OCA: New page: '''Unreleased structure''' The entry 6piy is ON HOLD Authors: Zephyr, J., Schiffer, C.A. Description: Crystal structure of HCV NS3/4A D168A protease in complex with P4-2 (NR02-61) [[Ca...

OCA — Wed, 03 Jul 2019 04:25:32 GMT

New page: '''Unreleased structure''' The entry 6piy is ON HOLD Authors: Zephyr, J., Schiffer, C.A. Description: Crystal structure of HCV NS3/4A D168A protease in complex with P4-2 (NR02-61) [[Ca...

New page

'''Unreleased structure'''

The entry 6piy is ON HOLD

Authors: Zephyr, J., Schiffer, C.A.

Description: Crystal structure of HCV NS3/4A D168A protease in complex with P4-2 (NR02-61)
[[Category: Unreleased Structures]]
[[Category: Zephyr, J]]
[[Category: Schiffer, C.A]]