8aad - Revision history

OCA at 13:37, 1 February 2024

2024-02-01T13:37:00Z

← Older revision		Revision as of 13:37, 1 February 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[8aad]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8AAD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8AAD FirstGlance]. <br>		<table><tr><td colspan='2'>[[8aad]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8AAD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8AAD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=LKO:16,17-dimethoxy-21-(2-pyridin-4-ylethyl)-5,7-dioxa-13$l^{4}-azapentacyclo[11.8.0.0^{2,10}.0^{4,8}.0^{15,20}]henicosa-1(13),2,4(8),9,14,16,18,20-octaene'>LKO</scene></td></tr>		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.04Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=LKO:16,17-dimethoxy-21-(2-pyridin-4-ylethyl)-5,7-dioxa-13$l^{4}-azapentacyclo[11.8.0.0^{2,10}.0^{4,8}.0^{15,20}]henicosa-1(13),2,4(8),9,14,16,18,20-octaene'>LKO</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=8aad FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8aad OCA], [https://pdbe.org/8aad PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8aad RCSB], [https://www.ebi.ac.uk/pdbsum/8aad PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8aad 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=8aad FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8aad OCA], [https://pdbe.org/8aad PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8aad RCSB], [https://www.ebi.ac.uk/pdbsum/8aad PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8aad ProSAT]</span></td></tr>
	</table>		</table>

OCA at 08:17, 7 December 2022

2022-12-07T08:17:32Z

← Older revision		Revision as of 08:17, 7 December 2022
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	~~The entry~~ 8aad is ~~ON HOLD until Paper~~ Publication		==Two carbons pendant pyridine derivative of the natural alkaloid Berberine as Human Telomeric G-quadruplex Binder==
			<StructureSection load='8aad' size='340' side='right'caption='[[8aad]], [[Resolution\|resolution]] 2.04Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[8aad]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8AAD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8AAD FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=LKO:16,17-dimethoxy-21-(2-pyridin-4-ylethyl)-5,7-dioxa-13$l^{4}-azapentacyclo[11.8.0.0^{2,10}.0^{4,8}.0^{15,20}]henicosa-1(13),2,4(8),9,14,16,18,20-octaene'>LKO</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=8aad FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8aad OCA], [https://pdbe.org/8aad PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8aad RCSB], [https://www.ebi.ac.uk/pdbsum/8aad PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8aad ProSAT]</span></td></tr>
			</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			The interaction between the series of berberine derivatives 1-5 (NAX071, NAX120, NAX075, NAX077 and NAX079) and human telomeric G-quadruplexes (G4), which are able to inhibit the Telomerase enzyme's activity in malignant cells, was investigated. The derivatives bear a pyridine moiety connected by a hydrocarbon linker of varying length (n = 1-5, with n number of aliphatic carbon atoms) to the C13 position of the parent berberine. As for the G4s, both bimolecular 5'-TAGGGTTAGGGT-3' (Tel12) and monomolecular 5'-TAGGGTTAGGGTTAGGGTTAGGG-3' (Tel23) DNA oligonucleotides were considered. Spectrophotometric titrations, melting tests, X-ray diffraction solid state analysis and in silico molecular dynamics (MD) simulations were used to describe the different systems. The results were compared in search of structure-activity relationships. The analysis pointed out the formation of 1:1 complexes between Tel12 and all ligands, whereas both 1:1 and 2:1 ligand/G4 stoichiometries were found for the adduct formed by NAX071 (n = 1). Tel12, with tetrads free from the hindrance by the loop, showed a higher affinity. The details of the different binding geometries were discussed, highlighting the importance of H-bonds given by the berberine benzodioxole group and a correlation between the strength of binding and the hydrocarbon linker length. Theoretical (MD) and experimental (X-ray) structural studies evidence the possibility for the berberine core to interact with one or both G4 strands, depending on the constraints given by the linker length, thus affecting the G4 stabilization effect.

	~~Authors~~: ~~Ferraroni~~, M., Bazzicalupi, C., ~~Gratteri~~, P., Papi, F.		Probing the Efficiency of 13-Pyridylalkyl Berberine Derivatives to Human Telomeric G-Quadruplexes Binding: Spectroscopic, Solid State and In Silico Analysis.,Bazzicalupi C, Bonardi A, Biver T, Ferraroni M, Papi F, Savastano M, Lombardi P, Gratteri P Int J Mol Sci. 2022 Nov 14;23(22):14061. doi: 10.3390/ijms232214061. PMID:36430540<ref>PMID:36430540</ref>

	~~Description: Two carbons pendant pyridine derivative~~ of the ~~natural alkaloid Berberine as Human Telomeric G~~-~~quadruplex Binder~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	[[Category: ~~Unreleased~~ Structures]]		</div>
	[[Category: Bazzicalupi, C]]		<div class="pdbe-citations 8aad" style="background-color:#fffaf0;"></div>
	[[Category: Ferraroni, M]]		== References ==
	[[Category: Gratteri, P]]		<references/>
	[[Category: Papi, F]]		__TOC__
			</StructureSection>
			[[Category: Homo sapiens]]
			[[Category: Large Structures]]
			[[Category: Bazzicalupi C]]
			[[Category: Ferraroni M]]
			[[Category: Gratteri P]]
			[[Category: Papi F]]

OCA at 03:51, 10 August 2022

2022-08-10T03:51:12Z

← Older revision		Revision as of 03:51, 10 August 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 8aad is ON HOLD		The entry 8aad is ON HOLD until Paper Publication

	Authors: Ferraroni, M., Bazzicalupi, C., Gratteri, P., Papi, F.		Authors: Ferraroni, M., Bazzicalupi, C., Gratteri, P., Papi, F.
Line 7:		Line 7:
	Description: Two carbons pendant pyridine derivative of the natural alkaloid Berberine as Human Telomeric G-quadruplex Binder		Description: Two carbons pendant pyridine derivative of the natural alkaloid Berberine as Human Telomeric G-quadruplex Binder
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
			[[Category: Bazzicalupi, C]]
			[[Category: Ferraroni, M]]
	[[Category: Gratteri, P]]		[[Category: Gratteri, P]]
	~~[[Category: Ferraroni, M]]~~
	[[Category: Papi, F]]		[[Category: Papi, F]]
	~~[[Category: Bazzicalupi, C]]~~

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

2022-07-06T15:07:18Z

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

← Older revision	Revision as of 15:07, 6 July 2022
(No difference)

OCA: New page: '''Unreleased structure''' The entry 8aad is ON HOLD Authors: Ferraroni, M., Bazzicalupi, C., Gratteri, P., Papi, F. Description: Two carbons pendant pyridine derivative of the natural...

2022-07-06T15:07:17Z

New page: '''Unreleased structure''' The entry 8aad is ON HOLD Authors: Ferraroni, M., Bazzicalupi, C., Gratteri, P., Papi, F. Description: Two carbons pendant pyridine derivative of the natural...

New page

'''Unreleased structure'''

The entry 8aad is ON HOLD

Authors: Ferraroni, M., Bazzicalupi, C., Gratteri, P., Papi, F.

Description: Two carbons pendant pyridine derivative of the natural alkaloid Berberine as Human Telomeric G-quadruplex Binder
[[Category: Unreleased Structures]]
[[Category: Gratteri, P]]
[[Category: Ferraroni, M]]
[[Category: Papi, F]]
[[Category: Bazzicalupi, C]]