8gfk - Revision history

OCA at 10:49, 22 May 2024

2024-05-22T10:49:57Z

←Older revision		Revision as of 10:49, 22 May 2024
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	The effect of mutations of the catalytic dyad residues of SARS-CoV-2 main protease (MPro(WT)) on the thermodynamics of binding of covalent inhibitors comprising nitrile [nirmatrelvir (NMV), NBH2], aldehyde (GC373), and ketone (BBH1) warheads to MPro is examined together with room temperature X-ray crystallography. When lacking the nucleophilic C145, NMV binding is approximately 400-fold weaker corresponding to 3.5 kcal/mol and 13.3 degrees C decrease in free energy (DeltaG) and thermal stability (T(m)), respectively, relative to MPro(WT). The H41A mutation results in a 20-fold increase in the dissociation constant (K(d)), and 1.7 kcal/mol and 1.4 degrees C decreases in DeltaG and T(m), respectively. Increasing the pH from 7.2 to 8.2 enhances NMV binding to MPro(H41A), whereas no significant change is observed in binding to MPro(WT). Structures of the four inhibitor complexes with MPro(1-304/C145A) show that the active site geometries of the complexes are nearly identical to that of MPro(WT) with the nucleophilic sulfur of C145 positioned to react with the nitrile or the carbonyl carbon. These results support a two-step mechanism for the formation of the covalent complex involving an initial non-covalent binding followed by a nucleophilic attack by the thiolate anion of C145 on the warhead carbon. Noncovalent inhibitor ensitrelvir (ESV) exhibits a binding affinity to MPro(WT) that is similar to NMV but differs in its thermodynamic signature from NMV. The binding of ESV to MPro(C145A) also results in a significant, but smaller, increase in K(d) and decrease in DeltaG and T(m), relative to NMV.		The effect of mutations of the catalytic dyad residues of SARS-CoV-2 main protease (MPro(WT)) on the thermodynamics of binding of covalent inhibitors comprising nitrile [nirmatrelvir (NMV), NBH2], aldehyde (GC373), and ketone (BBH1) warheads to MPro is examined together with room temperature X-ray crystallography. When lacking the nucleophilic C145, NMV binding is approximately 400-fold weaker corresponding to 3.5 kcal/mol and 13.3 degrees C decrease in free energy (DeltaG) and thermal stability (T(m)), respectively, relative to MPro(WT). The H41A mutation results in a 20-fold increase in the dissociation constant (K(d)), and 1.7 kcal/mol and 1.4 degrees C decreases in DeltaG and T(m), respectively. Increasing the pH from 7.2 to 8.2 enhances NMV binding to MPro(H41A), whereas no significant change is observed in binding to MPro(WT). Structures of the four inhibitor complexes with MPro(1-304/C145A) show that the active site geometries of the complexes are nearly identical to that of MPro(WT) with the nucleophilic sulfur of C145 positioned to react with the nitrile or the carbonyl carbon. These results support a two-step mechanism for the formation of the covalent complex involving an initial non-covalent binding followed by a nucleophilic attack by the thiolate anion of C145 on the warhead carbon. Noncovalent inhibitor ensitrelvir (ESV) exhibits a binding affinity to MPro(WT) that is similar to NMV but differs in its thermodynamic signature from NMV. The binding of ESV to MPro(C145A) also results in a significant, but smaller, increase in K(d) and decrease in DeltaG and T(m), relative to NMV.

-	Contribution of the catalytic dyad of SARS-CoV-2 main protease to binding covalent and noncovalent inhibitors.,Kovalevsky A, Aniana A, Coates L, Bonnesen PV, Nashed NT, Louis JM J Biol Chem. 2023 ~~Jun 2~~;299(7):104886. doi: 10.1016/j.jbc.2023.104886. PMID:37271339<ref>PMID:37271339</ref>	+	Contribution of the catalytic dyad of SARS-CoV-2 main protease to binding covalent and noncovalent inhibitors.,Kovalevsky A, Aniana A, Coates L, Bonnesen PV, Nashed NT, Louis JM J Biol Chem. 2023 Jul;299(7):104886. doi: 10.1016/j.jbc.2023.104886. Epub 2023 , Jun 2. PMID:37271339<ref>PMID:37271339</ref>

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

OCA at 07:23, 12 July 2023

2023-07-12T07:23:20Z

←Older revision		Revision as of 07:23, 12 July 2023
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-	'''Unreleased structure'''

-	~~The entry~~ 8gfk is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Room temperature X-ray structure of truncated SARS-CoV-2 main protease C145A mutant, residues 1-304==
		+	<StructureSection load='8gfk' size='340' side='right'caption='[[8gfk]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8gfk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Severe_acute_respiratory_syndrome_coronavirus_2 Severe acute respiratory syndrome coronavirus 2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8GFK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8GFK FirstGlance]. <br>
		+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2Å</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=8gfk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8gfk OCA], [https://pdbe.org/8gfk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8gfk RCSB], [https://www.ebi.ac.uk/pdbsum/8gfk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8gfk ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/R1AB_SARS2 R1AB_SARS2] Multifunctional protein involved in the transcription and replication of viral RNAs. Contains the proteinases responsible for the cleavages of the polyprotein.[UniProtKB:P0C6X7] Inhibits host translation by interacting with the 40S ribosomal subunit. The nsp1-40S ribosome complex further induces an endonucleolytic cleavage near the 5'UTR of host mRNAs, targeting them for degradation. Viral mRNAs are not susceptible to nsp1-mediated endonucleolytic RNA cleavage thanks to the presence of a 5'-end leader sequence and are therefore protected from degradation. By suppressing host gene expression, nsp1 facilitates efficient viral gene expression in infected cells and evasion from host immune response.[UniProtKB:P0C6X7] May play a role in the modulation of host cell survival signaling pathway by interacting with host PHB and PHB2. Indeed, these two proteins play a role in maintaining the functional integrity of the mitochondria and protecting cells from various stresses.[UniProtKB:P0C6X7] Responsible for the cleavages located at the N-terminus of the replicase polyprotein. In addition, PL-PRO possesses a deubiquitinating/deISGylating activity and processes both 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains from cellular substrates. Participates together with nsp4 in the assembly of virally-induced cytoplasmic double-membrane vesicles necessary for viral replication. Antagonizes innate immune induction of type I interferon by blocking the phosphorylation, dimerization and subsequent nuclear translocation of host IRF3. Prevents also host NF-kappa-B signaling.[UniProtKB:P0C6X7] Participates in the assembly of virally-induced cytoplasmic double-membrane vesicles necessary for viral replication.[UniProtKB:P0C6X7] Cleaves the C-terminus of replicase polyprotein at 11 sites. Recognizes substrates containing the core sequence [ILMVF]-Q-\|-[SGACN] (PubMed:32198291). Also able to bind an ADP-ribose-1''-phosphate (ADRP).[UniProtKB:P0C6X7]<ref>PMID:32198291</ref> Plays a role in the initial induction of autophagosomes from host reticulum endoplasmic. Later, limits the expansion of these phagosomes that are no longer able to deliver viral components to lysosomes.[UniProtKB:P0C6X7] Forms a hexadecamer with nsp8 (8 subunits of each) that may participate in viral replication by acting as a primase. Alternatively, may synthesize substantially longer products than oligonucleotide primers.[UniProtKB:P0C6X7] Forms a hexadecamer with nsp7 (8 subunits of each) that may participate in viral replication by acting as a primase. Alternatively, may synthesize substantially longer products than oligonucleotide primers.[UniProtKB:P0C6X7] May participate in viral replication by acting as a ssRNA-binding protein.[UniProtKB:P0C6X7] Plays a pivotal role in viral transcription by stimulating both nsp14 3'-5' exoribonuclease and nsp16 2'-O-methyltransferase activities. Therefore plays an essential role in viral mRNAs cap methylation.[UniProtKB:P0C6X7] Responsible for replication and transcription of the viral RNA genome.[UniProtKB:P0C6X7] Multi-functional protein with a zinc-binding domain in N-terminus displaying RNA and DNA duplex-unwinding activities with 5' to 3' polarity. Activity of helicase is dependent on magnesium.[UniProtKB:P0C6X7] Enzyme possessing two different activities: an exoribonuclease activity acting on both ssRNA and dsRNA in a 3' to 5' direction and a N7-guanine methyltransferase activity. Acts as a proofreading exoribonuclease for RNA replication, thereby lowering The sensitivity of the virus to RNA mutagens.[UniProtKB:P0C6X7] Mn(2+)-dependent, uridylate-specific enzyme, which leaves 2'-3'-cyclic phosphates 5' to the cleaved bond.[UniProtKB:P0C6X7] Methyltransferase that mediates mRNA cap 2'-O-ribose methylation to the 5'-cap structure of viral mRNAs. N7-methyl guanosine cap is a prerequisite for binding of nsp16. Therefore plays an essential role in viral mRNAs cap methylation which is essential to evade immune system.[UniProtKB:P0C6X7]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The effect of mutations of the catalytic dyad residues of SARS-CoV-2 main protease (MPro(WT)) on the thermodynamics of binding of covalent inhibitors comprising nitrile [nirmatrelvir (NMV), NBH2], aldehyde (GC373), and ketone (BBH1) warheads to MPro is examined together with room temperature X-ray crystallography. When lacking the nucleophilic C145, NMV binding is approximately 400-fold weaker corresponding to 3.5 kcal/mol and 13.3 degrees C decrease in free energy (DeltaG) and thermal stability (T(m)), respectively, relative to MPro(WT). The H41A mutation results in a 20-fold increase in the dissociation constant (K(d)), and 1.7 kcal/mol and 1.4 degrees C decreases in DeltaG and T(m), respectively. Increasing the pH from 7.2 to 8.2 enhances NMV binding to MPro(H41A), whereas no significant change is observed in binding to MPro(WT). Structures of the four inhibitor complexes with MPro(1-304/C145A) show that the active site geometries of the complexes are nearly identical to that of MPro(WT) with the nucleophilic sulfur of C145 positioned to react with the nitrile or the carbonyl carbon. These results support a two-step mechanism for the formation of the covalent complex involving an initial non-covalent binding followed by a nucleophilic attack by the thiolate anion of C145 on the warhead carbon. Noncovalent inhibitor ensitrelvir (ESV) exhibits a binding affinity to MPro(WT) that is similar to NMV but differs in its thermodynamic signature from NMV. The binding of ESV to MPro(C145A) also results in a significant, but smaller, increase in K(d) and decrease in DeltaG and T(m), relative to NMV.

-	~~Authors:~~ Kovalevsky, A., Coates, L.	+	Contribution of the catalytic dyad of SARS-CoV-2 main protease to binding covalent and noncovalent inhibitors.,Kovalevsky A, Aniana A, Coates L, Bonnesen PV, Nashed NT, Louis JM J Biol Chem. 2023 Jun 2;299(7):104886. doi: 10.1016/j.jbc.2023.104886. PMID:37271339<ref>PMID:37271339</ref>

-	~~Description: Room temperature X-ray structure~~ of ~~truncated SARS~~-~~CoV~~-~~2 main protease C145A mutant, residues 1-304~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: Coates, L]]	+	<div class="pdbe-citations 8gfk" style="background-color:#fffaf0;"></div>
-	[[Category: Kovalevsky, A]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Severe acute respiratory syndrome coronavirus 2]]
		+	[[Category: Coates L]]
		+	[[Category: Kovalevsky A]]

OCA at 05:40, 22 March 2023

2023-03-22T05:40:41Z

←Older revision		Revision as of 05:40, 22 March 2023
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8gfk is ON HOLD	+	The entry 8gfk is ON HOLD until Paper Publication

	Authors: Kovalevsky, A., Coates, L.		Authors: Kovalevsky, A., Coates, L.

OCA: Protected "8gfk" [edit=sysop:move=sysop]

2023-03-15T07:52:19Z

Protected "8gfk" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:52, 15 March 2023

OCA: New page: '''Unreleased structure''' The entry 8gfk is ON HOLD Authors: Kovalevsky, A., Coates, L. Description: Room temperature X-ray structure of truncated SARS-CoV-2 main protease C145A mutan...

2023-03-15T07:52:16Z

New page: '''Unreleased structure''' The entry 8gfk is ON HOLD Authors: Kovalevsky, A., Coates, L. Description: Room temperature X-ray structure of truncated SARS-CoV-2 main protease C145A mutan...

New page

'''Unreleased structure'''

The entry 8gfk is ON HOLD

Authors: Kovalevsky, A., Coates, L.

Description: Room temperature X-ray structure of truncated SARS-CoV-2 main protease C145A mutant, residues 1-304
[[Category: Unreleased Structures]]
[[Category: Coates, L]]
[[Category: Kovalevsky, A]]