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5a00

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Revision as of 07:48, 18 May 2023

Structure of human PARP1 catalytic domain bound to an isoindolinone inhibitor

Structural highlights

5a00 is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PARP1_HUMAN Involved in the base excision repair (BER) pathway, by catalyzing the poly(ADP-ribosyl)ation of a limited number of acceptor proteins involved in chromatin architecture and in DNA metabolism. This modification follows DNA damages and appears as an obligatory step in a detection/signaling pathway leading to the reparation of DNA strand breaks. Mediates the poly(ADP-ribosyl)ation of APLF and CHFR. Positively regulates the transcription of MTUS1 and negatively regulates the transcription of MTUS2/TIP150. With EEF1A1 and TXK, forms a complex that acts as a T-helper 1 (Th1) cell-specific transcription factor and binds the promoter of IFN-gamma to directly regulate its transcription, and is thus involved importantly in Th1 cytokine production.^[1] ^[2] ^[3] ^[4]

Publication Abstract from PubMed

The nuclear protein poly(ADP-ribose) polymerase-1 (PARP-1) has a well-established role in the signaling and repair of DNA and is a prominent target in oncology, as testified by the number of candidates in clinical testing. However all current compounds unselectively target both PARP-1 and its closest isoform PARP-2. The goal of our program was to find a PARP-1 selective inhibitor that would potentially mitigate toxicities arising from cross-inhibition of PARP-2. Thus, an HTS campaign on the proprietary Nerviano Medical Sciences (NMS) chemical collection, followed by SAR optimization around the unselective isoindolinone-4-carboxamide hits 10a and 10b, allowed us to subsequently discover 2-[1-(4,4-difluorocyclohexyl)piperidin-4-yl]-6-fluoro-3-oxo-2,3-dihydro-1H-isoind ole-4-carboxamide (NMS-P118, 20by). NMS-P118 proved to be a potent, orally available and highly selective PARP-1 inhibitor endowed with excellent ADME and pharmacokinetic profiles and high efficacy in vivo both as a single agent and in combination with temozolomide, in MDA-MB-436 and CAPAN-1 xenograft models, respectively. High resolution X-ray diffraction co-crystal structures of 20by with both PARP-1 and PARP-2 catalytic domain proteins allowed rationalization of the observed selectivity.

Discovery of 2-[1-(4,4-difluorocyclohexyl)piperidin-4-yl]-6-fluoro-3-oxo-2,3-dihydro-1H-isoind ole-4-carboxamide (NMS-P118): a Potent, Orally Available and Highly Selective PARP-1 Inhibitor for Cancer Therapy.,Papeo GM, Posteri H, Borghi D, Busel AA, Caprera F, Casale E, Ciomei M, Cirla A, Corti E, D'Anello M, Fasolini M, Forte B, Galvani A, Isacchi A, Khvat A, Krasavin MY, Lupi R, Orsini P, Perego R, Pesenti E, Pezzetta D, Rainoldi S, Riccardi-Sirtori F, Scolaro A, Sola F, Zuccotto F, Felder ER, Donati D, Montagnoli A J Med Chem. 2015 Jul 29. PMID:26222319^[5]

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

References

↑ Maruyama T, Nara K, Yoshikawa H, Suzuki N. Txk, a member of the non-receptor tyrosine kinase of the Tec family, forms a complex with poly(ADP-ribose) polymerase 1 and elongation factor 1alpha and regulates interferon-gamma gene transcription in Th1 cells. Clin Exp Immunol. 2007 Jan;147(1):164-75. PMID:17177976 doi:10.1111/j.1365-2249.2006.03249.x
↑ Ahel I, Ahel D, Matsusaka T, Clark AJ, Pines J, Boulton SJ, West SC. Poly(ADP-ribose)-binding zinc finger motifs in DNA repair/checkpoint proteins. Nature. 2008 Jan 3;451(7174):81-5. doi: 10.1038/nature06420. PMID:18172500 doi:10.1038/nature06420
↑ Reinemund J, Seidel K, Steckelings UM, Zaade D, Klare S, Rompe F, Katerbaum M, Schacherl J, Li Y, Menk M, Schefe JH, Goldin-Lang P, Szabo C, Olah G, Unger T, Funke-Kaiser H. Poly(ADP-ribose) polymerase-1 (PARP-1) transcriptionally regulates angiotensin AT2 receptor (AT2R) and AT2R binding protein (ATBP) genes. Biochem Pharmacol. 2009 Jun 15;77(12):1795-805. doi: 10.1016/j.bcp.2009.02.025., Epub 2009 Mar 19. PMID:19344625 doi:10.1016/j.bcp.2009.02.025
↑ Ahel D, Horejsi Z, Wiechens N, Polo SE, Garcia-Wilson E, Ahel I, Flynn H, Skehel M, West SC, Jackson SP, Owen-Hughes T, Boulton SJ. Poly(ADP-ribose)-dependent regulation of DNA repair by the chromatin remodeling enzyme ALC1. Science. 2009 Sep 4;325(5945):1240-3. doi: 10.1126/science.1177321. Epub 2009 Aug, 6. PMID:19661379 doi:10.1126/science.1177321
↑ Papeo GM, Posteri H, Borghi D, Busel AA, Caprera F, Casale E, Ciomei M, Cirla A, Corti E, D'Anello M, Fasolini M, Forte B, Galvani A, Isacchi A, Khvat A, Krasavin MY, Lupi R, Orsini P, Perego R, Pesenti E, Pezzetta D, Rainoldi S, Riccardi-Sirtori F, Scolaro A, Sola F, Zuccotto F, Felder ER, Donati D, Montagnoli A. Discovery of 2-[1-(4,4-difluorocyclohexyl)piperidin-4-yl]-6-fluoro-3-oxo-2,3-dihydro-1H-isoind ole-4-carboxamide (NMS-P118): a Potent, Orally Available and Highly Selective PARP-1 Inhibitor for Cancer Therapy. J Med Chem. 2015 Jul 29. PMID:26222319 doi:http://dx.doi.org/10.1021/acs.jmedchem.5b00680

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5a00"

@@ Line 1: / Line 1: @@
 ==Structure of human PARP1 catalytic domain bound to an isoindolinone inhibitor==
-<StructureSection load='5a00' size='340' side='right'  caption='[[5a00]], [[Resolution|resolution]] 2.75&Aring;' scene=''>
+<StructureSection load='5a00' size='340' side='right'caption='[[5a00]], [[Resolution|resolution]] 2.75&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5a00]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5A00 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5A00 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5a00]] 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=5A00 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5A00 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=D7N:2-[1-(4,4-DIFLUOROCYCLOHEXYL)-PIPERIDIN-4-YL]-6-FLUORO-3-OXO-2,3-DIHYDRO-1H-ISOINDOLE-4-CARBOXAMIDE'>D7N</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=D7N:2-[1-(4,4-DIFLUOROCYCLOHEXYL)-PIPERIDIN-4-YL]-6-FLUORO-3-OXO-2,3-DIHYDRO-1H-ISOINDOLE-4-CARBOXAMIDE'>D7N</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4zzx|4zzx]], [[4zzy|4zzy]], [[4zzz|4zzz]]</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=5a00 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5a00 OCA], [https://pdbe.org/5a00 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5a00 RCSB], [https://www.ebi.ac.uk/pdbsum/5a00 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5a00 ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/NAD(+)_ADP-ribosyltransferase NAD(+) ADP-ribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.30 2.4.2.30] </span></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=5a00 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5a00 OCA], [http://pdbe.org/5a00 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5a00 RCSB], [http://www.ebi.ac.uk/pdbsum/5a00 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5a00 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/PARP1_HUMAN PARP1_HUMAN]] Involved in the base excision repair (BER) pathway, by catalyzing the poly(ADP-ribosyl)ation of a limited number of acceptor proteins involved in chromatin architecture and in DNA metabolism. This modification follows DNA damages and appears as an obligatory step in a detection/signaling pathway leading to the reparation of DNA strand breaks. Mediates the poly(ADP-ribosyl)ation of APLF and CHFR. Positively regulates the transcription of MTUS1 and negatively regulates the transcription of MTUS2/TIP150. With EEF1A1 and TXK, forms a complex that acts as a T-helper 1 (Th1) cell-specific transcription factor and binds the promoter of IFN-gamma to directly regulate its transcription, and is thus involved importantly in Th1 cytokine production.<ref>PMID:17177976</ref> <ref>PMID:18172500</ref> <ref>PMID:19344625</ref> <ref>PMID:19661379</ref>
+[https://www.uniprot.org/uniprot/PARP1_HUMAN PARP1_HUMAN] Involved in the base excision repair (BER) pathway, by catalyzing the poly(ADP-ribosyl)ation of a limited number of acceptor proteins involved in chromatin architecture and in DNA metabolism. This modification follows DNA damages and appears as an obligatory step in a detection/signaling pathway leading to the reparation of DNA strand breaks. Mediates the poly(ADP-ribosyl)ation of APLF and CHFR. Positively regulates the transcription of MTUS1 and negatively regulates the transcription of MTUS2/TIP150. With EEF1A1 and TXK, forms a complex that acts as a T-helper 1 (Th1) cell-specific transcription factor and binds the promoter of IFN-gamma to directly regulate its transcription, and is thus involved importantly in Th1 cytokine production.<ref>PMID:17177976</ref> <ref>PMID:18172500</ref> <ref>PMID:19344625</ref> <ref>PMID:19661379</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 20: @@
 ==See Also==
-*[[Poly (ADP-ribose) polymerase|Poly (ADP-ribose) polymerase]]
+*[[Poly(ADP-ribose) polymerase 3D structures|Poly(ADP-ribose) polymerase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
-[[Category: Borghi, D]]
+[[Category: Large Structures]]
-[[Category: Busel, A A]]
+[[Category: Borghi D]]
-[[Category: Caprera, F]]
+[[Category: Busel AA]]
-[[Category: Casale, E]]
+[[Category: Caprera F]]
-[[Category: Ciomei, M]]
+[[Category: Casale E]]
-[[Category: Cirla, A]]
+[[Category: Ciomei M]]
-[[Category: Corti, E]]
+[[Category: Cirla A]]
-[[Category: DAnello, M]]
+[[Category: Corti E]]
-[[Category: Donati, D]]
+[[Category: DAnello M]]
-[[Category: Fasolini, M]]
+[[Category: Donati D]]
-[[Category: Felder, E R]]
+[[Category: Fasolini M]]
-[[Category: Forte, B]]
+[[Category: Felder ER]]
-[[Category: Galvani, A]]
+[[Category: Forte B]]
-[[Category: Isacchi, A]]
+[[Category: Galvani A]]
-[[Category: Khvat, A]]
+[[Category: Isacchi A]]
-[[Category: Krasavin, M Y]]
+[[Category: Khvat A]]
-[[Category: Lupi, R]]
+[[Category: Krasavin MY]]
-[[Category: Montagnoli, A]]
+[[Category: Lupi R]]
-[[Category: Orsini, P]]
+[[Category: Montagnoli A]]
-[[Category: Papeo, G]]
+[[Category: Orsini P]]
-[[Category: Perego, R]]
+[[Category: Papeo G]]
-[[Category: Pesenti, E]]
+[[Category: Perego R]]
-[[Category: Pezzetta, D]]
+[[Category: Pesenti E]]
-[[Category: Posteri, H]]
+[[Category: Pezzetta D]]
-[[Category: Rainoldi, S]]
+[[Category: Posteri H]]
-[[Category: RiccardiSirtori, F]]
+[[Category: Rainoldi S]]
-[[Category: Scolaro, A]]
+[[Category: RiccardiSirtori F]]
-[[Category: Sola, F]]
+[[Category: Scolaro A]]
-[[Category: Zuccotto, F]]
+[[Category: Sola F]]
-[[Category: Artd1]]
+[[Category: Zuccotto F]]
-[[Category: Human parp1]]
-[[Category: Transferase]]

5a00

From Proteopedia

Revision as of 07:48, 18 May 2023

Structure of human PARP1 catalytic domain bound to an isoindolinone inhibitor

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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