5uoq - Revision history

OCA at 14:28, 6 March 2024

OCA — Wed, 06 Mar 2024 14:28:27 GMT

←Older revision		Revision as of 14:28, 6 March 2024
Line 3:		Line 3:
	<StructureSection load='5uoq' size='340' side='right'caption='[[5uoq]], [[Resolution\|resolution]] 2.61Å' scene=''>		<StructureSection load='5uoq' size='340' side='right'caption='[[5uoq]], [[Resolution\|resolution]] 2.61Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5uoq]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Foamv Foamv~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UOQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5UOQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5uoq]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_spumaretrovirus Human spumaretrovirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UOQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5UOQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8G1:(3R)-8-[(3-CHLORO-4-FLUOROPHENYL)METHYL]-6-HYDROXY-1,5,7-TRIOXO-1,2,3,5,7,8,9,10-OCTAHYDRO-2H-SPIRO[IMIDAZO[5,1-A][2,6]NAPHTHYRIDINE-3,1-INDENE]-7-CARBONITRILE'>8G1</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.61Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5uop\|5uop]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8G1:(3R)-8-[(3-CHLORO-4-FLUOROPHENYL)METHYL]-6-HYDROXY-1,5,7-TRIOXO-1,2,3,5,7,8,9,10-OCTAHYDRO-2H-SPIRO[IMIDAZO[5,1-A][2,6]NAPHTHYRIDINE-3,1-INDENE]-7-CARBONITRILE'>8G1</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pol ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11963 FOAMV])~~</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=5uoq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uoq OCA], [https://pdbe.org/5uoq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5uoq RCSB], [https://www.ebi.ac.uk/pdbsum/5uoq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5uoq 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=5uoq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uoq OCA], [~~http~~://pdbe.org/5uoq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5uoq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5uoq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5uoq ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/POL_FOAMV POL_FOAMV]] The aspartyl protease activity mediates proteolytic cleavages of Gag and Pol polyproteins. The reverse transcriptase (RT) activity converts the viral RNA genome into dsDNA in the cytoplasm, shortly after virus entry into the cell (early reverse transcription) or after proviral DNA transcription (late reverse transcription). RT consists of a DNA polymerase activity that can copy either DNA or RNA templates, and a ribonuclease H (RNase H) activity that cleaves the RNA strand of RNA-DNA heteroduplexes in a partially processive 3' to 5' endonucleasic mode. Conversion of viral genomic RNA into dsDNA requires many steps. A tRNA-Lys1,2 binds to the primer-binding site (PBS) situated at the 5'-end of the viral RNA. RT uses the 3' end of the tRNA primer to perform a short round of RNA-dependent minus-strand DNA synthesis. The reading proceeds through the U5 region and ends after the repeated (R) region which is present at both ends of viral RNA. The portion of the RNA-DNA heteroduplex is digested by the RNase H, resulting in a ssDNA product attached to the tRNA primer. This ssDNA/tRNA hybridizes with the identical R region situated at the 3' end of viral RNA. This template exchange, known as minus-strand DNA strong stop transfer, can be either intra- or intermolecular. RT uses the 3' end of this newly synthesized short ssDNA to perform the RNA-dependent minus-strand DNA synthesis of the whole template. RNase H digests the RNA template except for a polypurine tract (PPT) situated at the 5'-end and near the center of the genome. It is not clear if both polymerase and RNase H activities are simultaneous. RNase H probably can proceed both in a polymerase-dependent (RNA cut into small fragments by the same RT performing DNA synthesis) and a polymerase-independent mode (cleavage of remaining RNA fragments by free RTs). Secondly, RT performs DNA-directed plus-strand DNA synthesis using the PPT that has not been removed by RNase H as primer. PPT and tRNA primers are then removed by RNase H. The 3' and 5' ssDNA PBS regions hybridize to form a circular dsDNA intermediate. Strand displacement synthesis by RT to the PBS and PPT ends produces a blunt ended, linear dsDNA copy of the viral genome that includes long terminal repeats (LTRs) at both ends (By similarity). Integrase catalyzes viral DNA integration into the host chromosome, by performing a series of DNA cutting and joining reactions. This enzyme activity takes place after virion entry into a cell and reverse transcription of the RNA genome in dsDNA. The first step in the integration process is 3' processing. This step requires a complex comprising at least the viral genome, matrix protein, and integrase. This complex is called the pre-integration complex (PIC). The integrase protein removes 2 nucleotides from the 3' end of the viral DNA right (U5) end, leaving the left (U3) intact. In the second step, the PIC enters cell nucleus. This process is mediated through the integrase and allows the virus to infect both dividing (nuclear membrane disassembled) and G1/S-arrested cells (active translocation), but with no viral gene expression in the latter. In the third step, termed strand transfer, the integrase protein joins the previously processed 3' ends to the 5' ends of strands of target cellular DNA at the site of integration. It is however not clear how integration then proceeds to resolve the asymmetrical cleavage of viral DNA (By similarity).	+	[https://www.uniprot.org/uniprot/POL_FOAMV POL_FOAMV] The aspartyl protease activity mediates proteolytic cleavages of Gag and Pol polyproteins. The reverse transcriptase (RT) activity converts the viral RNA genome into dsDNA in the cytoplasm, shortly after virus entry into the cell (early reverse transcription) or after proviral DNA transcription (late reverse transcription). RT consists of a DNA polymerase activity that can copy either DNA or RNA templates, and a ribonuclease H (RNase H) activity that cleaves the RNA strand of RNA-DNA heteroduplexes in a partially processive 3' to 5' endonucleasic mode. Conversion of viral genomic RNA into dsDNA requires many steps. A tRNA-Lys1,2 binds to the primer-binding site (PBS) situated at the 5'-end of the viral RNA. RT uses the 3' end of the tRNA primer to perform a short round of RNA-dependent minus-strand DNA synthesis. The reading proceeds through the U5 region and ends after the repeated (R) region which is present at both ends of viral RNA. The portion of the RNA-DNA heteroduplex is digested by the RNase H, resulting in a ssDNA product attached to the tRNA primer. This ssDNA/tRNA hybridizes with the identical R region situated at the 3' end of viral RNA. This template exchange, known as minus-strand DNA strong stop transfer, can be either intra- or intermolecular. RT uses the 3' end of this newly synthesized short ssDNA to perform the RNA-dependent minus-strand DNA synthesis of the whole template. RNase H digests the RNA template except for a polypurine tract (PPT) situated at the 5'-end and near the center of the genome. It is not clear if both polymerase and RNase H activities are simultaneous. RNase H probably can proceed both in a polymerase-dependent (RNA cut into small fragments by the same RT performing DNA synthesis) and a polymerase-independent mode (cleavage of remaining RNA fragments by free RTs). Secondly, RT performs DNA-directed plus-strand DNA synthesis using the PPT that has not been removed by RNase H as primer. PPT and tRNA primers are then removed by RNase H. The 3' and 5' ssDNA PBS regions hybridize to form a circular dsDNA intermediate. Strand displacement synthesis by RT to the PBS and PPT ends produces a blunt ended, linear dsDNA copy of the viral genome that includes long terminal repeats (LTRs) at both ends (By similarity). Integrase catalyzes viral DNA integration into the host chromosome, by performing a series of DNA cutting and joining reactions. This enzyme activity takes place after virion entry into a cell and reverse transcription of the RNA genome in dsDNA. The first step in the integration process is 3' processing. This step requires a complex comprising at least the viral genome, matrix protein, and integrase. This complex is called the pre-integration complex (PIC). The integrase protein removes 2 nucleotides from the 3' end of the viral DNA right (U5) end, leaving the left (U3) intact. In the second step, the PIC enters cell nucleus. This process is mediated through the integrase and allows the virus to infect both dividing (nuclear membrane disassembled) and G1/S-arrested cells (active translocation), but with no viral gene expression in the latter. In the third step, termed strand transfer, the integrase protein joins the previously processed 3' ends to the 5' ends of strands of target cellular DNA at the site of integration. It is however not clear how integration then proceeds to resolve the asymmetrical cleavage of viral DNA (By similarity).
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	HIV integrase strand transfer inhibitors (InSTIs) represent an important class of antiviral therapeutics with proven efficacy and excellent tolerability for the treatment of HIV infections. In 2007, Raltegravir became the first marketed strand transfer inhibitor pioneering the way to a first-line therapy for treatment-naive patients. Challenges with this class of therapeutics remain, including frequency of the dosing regimen and the genetic barrier to resistance. To address these issues, research towards next-generation integrase inhibitors has focused on imparting potency against RAL-resistent mutants and improving pharmacokinetic profiles. Herein, we detail medicinal chemistry efforts on a novel class of 2-pyridinone aminal InSTIs, inpsired by MK-0536, which led to the discovery of important lead molecules for our program. Systematic optimization carried out at the amide and aminal positions on the periphery of the core provided the necessary balance of antiviral activity and physiochemical properties. These efforts led to a novel aminal lead compound with the desired virological profile and preclinical pharmacokinetic profile to support a once-daily human dose prediction.	+
-		+
-	Discovery and optimization of 2-pyridinone aminal integrase strand transfer inhibitors for the treatment of HIV.,Schreier JD, Embrey MW, Raheem IT, Barbe G, Campeau LC, Dubost D, McCabe Dunn J, Grobler J, Hartingh TJ, Hazuda DJ, Klein D, Miller MD, Moore KP, Nguyen N, Pajkovic N, Powell DA, Rada V, Sanders JM, Sisko J, Steele TG, Wai J, Walji A, Xu M, Coleman PJ Bioorg Med Chem Lett. 2017 Feb 20. pii: S0960-894X(17)30172-5. doi:, 10.1016/j.bmcl.2017.02.039. PMID:28285916<ref>PMID:28285916</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5uoq" style="background-color:#fffaf0;"></div>~~	+

	==See Also==		==See Also==
	*[[Retroviral integrase 3D structures\|Retroviral integrase 3D structures]]		*[[Retroviral integrase 3D structures\|Retroviral integrase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Foamv~~]]	+	[[Category: Human spumaretrovirus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Klein~~, D J]]~~	+	[[Category: Klein DJ]]
-	~~[[Category: Dna integration]]~~	+
-	~~[[Category: Recombination-inhibitor-dna complex]]~~	+
-	~~[[Category: Transferase-dna complex]]~~	+
-	~~[[Category: Transferase-dna-inhibitor complex]]~~	+
-	~~[[Category: Viral protein~~]]	+

OCA at 12:40, 23 September 2020

OCA — Wed, 23 Sep 2020 12:40:51 GMT

←Older revision		Revision as of 12:40, 23 September 2020
Line 1:		Line 1:

	==CRYSTAL STRUCTURE OF THE PROTOTYPE FOAMY VIRUS INTASOME WITH A 2- PYRIDINONE AMINAL INHIBITOR (COMPOUND 31)==		==CRYSTAL STRUCTURE OF THE PROTOTYPE FOAMY VIRUS INTASOME WITH A 2- PYRIDINONE AMINAL INHIBITOR (COMPOUND 31)==
-	<StructureSection load='5uoq' size='340' side='right' caption='[[5uoq]], [[Resolution\|resolution]] 2.61Å' scene=''>	+	<StructureSection load='5uoq' size='340' side='right'caption='[[5uoq]], [[Resolution\|resolution]] 2.61Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5uoq]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UOQ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5UOQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5uoq]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Foamv Foamv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UOQ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5UOQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8G1:(3R)-8-[(3-CHLORO-4-FLUOROPHENYL)METHYL]-6-HYDROXY-1,5,7-TRIOXO-1,2,3,5,7,8,9,10-OCTAHYDRO-2H-SPIRO[IMIDAZO[5,1-A][2,6]NAPHTHYRIDINE-3,1-INDENE]-7-CARBONITRILE'>8G1</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=8G1:(3R)-8-[(3-CHLORO-4-FLUOROPHENYL)METHYL]-6-HYDROXY-1,5,7-TRIOXO-1,2,3,5,7,8,9,10-OCTAHYDRO-2H-SPIRO[IMIDAZO[5,1-A][2,6]NAPHTHYRIDINE-3,1-INDENE]-7-CARBONITRILE'>8G1</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5uop\|5uop]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5uop\|5uop]]</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=5uoq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uoq OCA], [http://pdbe.org/5uoq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5uoq RCSB], [http://www.ebi.ac.uk/pdbsum/5uoq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5uoq ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pol ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11963 FOAMV])</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=5uoq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uoq OCA], [http://pdbe.org/5uoq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5uoq RCSB], [http://www.ebi.ac.uk/pdbsum/5uoq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5uoq ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5uoq" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5uoq" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Retroviral integrase 3D structures\|Retroviral integrase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Foamv]]
		+	[[Category: Large Structures]]
	[[Category: Klein, D J]]		[[Category: Klein, D J]]
	[[Category: Dna integration]]		[[Category: Dna integration]]

OCA at 14:05, 29 March 2017

OCA — Wed, 29 Mar 2017 14:05:41 GMT

←Older revision		Revision as of 14:05, 29 March 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The entry ~~5uoq~~ is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==CRYSTAL STRUCTURE OF THE PROTOTYPE FOAMY VIRUS INTASOME WITH A 2- PYRIDINONE AMINAL INHIBITOR (COMPOUND 31)==
		+	<StructureSection load='5uoq' size='340' side='right' caption='[[5uoq]], [[Resolution\|resolution]] 2.61Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5uoq]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UOQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UOQ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=8G1:(3R)-8-[(3-CHLORO-4-FLUOROPHENYL)METHYL]-6-HYDROXY-1,5,7-TRIOXO-1,2,3,5,7,8,9,10-OCTAHYDRO-2H-SPIRO[IMIDAZO[5,1-A][2,6]NAPHTHYRIDINE-3,1-INDENE]-7-CARBONITRILE'>8G1</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5uop\|5uop]]</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=5uoq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uoq OCA], [http://pdbe.org/5uoq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5uoq RCSB], [http://www.ebi.ac.uk/pdbsum/5uoq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5uoq ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/POL_FOAMV POL_FOAMV]] The aspartyl protease activity mediates proteolytic cleavages of Gag and Pol polyproteins. The reverse transcriptase (RT) activity converts the viral RNA genome into dsDNA in the cytoplasm, shortly after virus entry into the cell (early reverse transcription) or after proviral DNA transcription (late reverse transcription). RT consists of a DNA polymerase activity that can copy either DNA or RNA templates, and a ribonuclease H (RNase H) activity that cleaves the RNA strand of RNA-DNA heteroduplexes in a partially processive 3' to 5' endonucleasic mode. Conversion of viral genomic RNA into dsDNA requires many steps. A tRNA-Lys1,2 binds to the primer-binding site (PBS) situated at the 5'-end of the viral RNA. RT uses the 3' end of the tRNA primer to perform a short round of RNA-dependent minus-strand DNA synthesis. The reading proceeds through the U5 region and ends after the repeated (R) region which is present at both ends of viral RNA. The portion of the RNA-DNA heteroduplex is digested by the RNase H, resulting in a ssDNA product attached to the tRNA primer. This ssDNA/tRNA hybridizes with the identical R region situated at the 3' end of viral RNA. This template exchange, known as minus-strand DNA strong stop transfer, can be either intra- or intermolecular. RT uses the 3' end of this newly synthesized short ssDNA to perform the RNA-dependent minus-strand DNA synthesis of the whole template. RNase H digests the RNA template except for a polypurine tract (PPT) situated at the 5'-end and near the center of the genome. It is not clear if both polymerase and RNase H activities are simultaneous. RNase H probably can proceed both in a polymerase-dependent (RNA cut into small fragments by the same RT performing DNA synthesis) and a polymerase-independent mode (cleavage of remaining RNA fragments by free RTs). Secondly, RT performs DNA-directed plus-strand DNA synthesis using the PPT that has not been removed by RNase H as primer. PPT and tRNA primers are then removed by RNase H. The 3' and 5' ssDNA PBS regions hybridize to form a circular dsDNA intermediate. Strand displacement synthesis by RT to the PBS and PPT ends produces a blunt ended, linear dsDNA copy of the viral genome that includes long terminal repeats (LTRs) at both ends (By similarity). Integrase catalyzes viral DNA integration into the host chromosome, by performing a series of DNA cutting and joining reactions. This enzyme activity takes place after virion entry into a cell and reverse transcription of the RNA genome in dsDNA. The first step in the integration process is 3' processing. This step requires a complex comprising at least the viral genome, matrix protein, and integrase. This complex is called the pre-integration complex (PIC). The integrase protein removes 2 nucleotides from the 3' end of the viral DNA right (U5) end, leaving the left (U3) intact. In the second step, the PIC enters cell nucleus. This process is mediated through the integrase and allows the virus to infect both dividing (nuclear membrane disassembled) and G1/S-arrested cells (active translocation), but with no viral gene expression in the latter. In the third step, termed strand transfer, the integrase protein joins the previously processed 3' ends to the 5' ends of strands of target cellular DNA at the site of integration. It is however not clear how integration then proceeds to resolve the asymmetrical cleavage of viral DNA (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	HIV integrase strand transfer inhibitors (InSTIs) represent an important class of antiviral therapeutics with proven efficacy and excellent tolerability for the treatment of HIV infections. In 2007, Raltegravir became the first marketed strand transfer inhibitor pioneering the way to a first-line therapy for treatment-naive patients. Challenges with this class of therapeutics remain, including frequency of the dosing regimen and the genetic barrier to resistance. To address these issues, research towards next-generation integrase inhibitors has focused on imparting potency against RAL-resistent mutants and improving pharmacokinetic profiles. Herein, we detail medicinal chemistry efforts on a novel class of 2-pyridinone aminal InSTIs, inpsired by MK-0536, which led to the discovery of important lead molecules for our program. Systematic optimization carried out at the amide and aminal positions on the periphery of the core provided the necessary balance of antiviral activity and physiochemical properties. These efforts led to a novel aminal lead compound with the desired virological profile and preclinical pharmacokinetic profile to support a once-daily human dose prediction.

-	~~Authors~~:	+	Discovery and optimization of 2-pyridinone aminal integrase strand transfer inhibitors for the treatment of HIV.,Schreier JD, Embrey MW, Raheem IT, Barbe G, Campeau LC, Dubost D, McCabe Dunn J, Grobler J, Hartingh TJ, Hazuda DJ, Klein D, Miller MD, Moore KP, Nguyen N, Pajkovic N, Powell DA, Rada V, Sanders JM, Sisko J, Steele TG, Wai J, Walji A, Xu M, Coleman PJ Bioorg Med Chem Lett. 2017 Feb 20. pii: S0960-894X(17)30172-5. doi:, 10.1016/j.bmcl.2017.02.039. PMID:28285916<ref>PMID:28285916</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5uoq" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Klein, D J]]
		+	[[Category: Dna integration]]
		+	[[Category: Recombination-inhibitor-dna complex]]
		+	[[Category: Transferase-dna complex]]
		+	[[Category: Transferase-dna-inhibitor complex]]
		+	[[Category: Viral protein]]

OCA at 19:15, 15 March 2017

OCA — Wed, 15 Mar 2017 19:15:03 GMT

←Older revision		Revision as of 19:15, 15 March 2017
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5uoq is ON HOLD	+	The entry 5uoq is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5uoq" [edit=sysop:move=sysop]

OCA — Thu, 09 Mar 2017 14:44:32 GMT

Protected "5uoq" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:44, 9 March 2017

OCA: New page: '''Unreleased structure''' The entry 5uoq is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Thu, 09 Mar 2017 14:44:31 GMT

New page: '''Unreleased structure''' The entry 5uoq is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5uoq is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]