1
|
Jiang S, Ren J, Zhang Q, Liu W, Liu H, Xu Q, Tian X, Zhang CY. Construction of a Dendritic Nanoassembly-Based Fluorescent Biosensor for Electrostatic Interaction-Independent and Label-Free Measurement of Human Poly(ADP-ribose) Polymerase 1 in Lung Tissues. Anal Chem 2023; 95:11815-11822. [PMID: 37489894 DOI: 10.1021/acs.analchem.3c02376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Poly(ADP-ribose) polymerase 1 (PARP-1) is responsible for catalyzing the creation of poly(ADP-ribose) polymer and involved in DNA replication and repair. Sensitive measurement of PARP-1 is critical for clinical diagnosis. However, the conventional electrostatic attraction-based PAPR-1 assays usually involve laborious procedures, poor sensitivity, and false positives. Herein, we demonstrate the construction of a dendritic nanoassembly-based fluorescent biosensor for electrostatic interaction-independent and label-free measurement of human PARP-1 in lung tumor tissues. When PARP-1 is present, the specific double-stranded DNA (dsDNA)-activated PARP-1 transfers the ADP-ribosyl group from nicotinamide adenine dinucleotide (NAD+)/biotinylated NAD+ to the PARP-1 itself, resulting in the formation of biotinylated dsDNA-PARP-1-PAR polymer bioconjugates that can be captured by magnetic beads. Upon the addition of TdT, APE1, and NH2-modified T-rich probe, the captured dsDNAs with dual 3'-OH termini initiate TdT-activated APE1-mediated hyperbranched amplification to produce abundant dendritic DNA nanoassemblies that can be stained by SYBR Green I to generate a high fluorescence signal. This biosensor is characterized by a template-free, electrostatic interaction-independent, high sensitivity, and label-free assay. It enables rapid (less than 3 h) measurement of PARP-1 with a limit of detection of 4.37 × 10-8 U/μL and accurate measurement of cellular PARP-1 activity with single-cell sensitivity. Moreover, it is capable of screening potential inhibitors and discriminating the PARP-1 level in normal person tissues and lung cancer patient tissues, with great potential in PARP-1-related clinical diagnosis and drug discovery.
Collapse
Affiliation(s)
- Su Jiang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Jingyi Ren
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Qian Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Wenjing Liu
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Hao Liu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Qinfeng Xu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Xiaorui Tian
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| |
Collapse
|
2
|
Kurgina TA, Moor NA, Kutuzov MM, Lavrik OI. The HPF1-dependent histone PARylation catalyzed by PARP2 is specifically stimulated by an incised AP site-containing BER DNA intermediate. DNA Repair (Amst) 2022; 120:103423. [DOI: 10.1016/j.dnarep.2022.103423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 10/27/2022] [Accepted: 10/29/2022] [Indexed: 11/03/2022]
|
3
|
Kurgina TA, Shram SI, Kutuzov MM, Abramova TV, Shcherbakova TA, Maltseva EA, Poroikov VV, Lavrik OI, Švedas VK, Nilov DK. Inhibitory Effects of 7-Methylguanine and Its Metabolite 8-Hydroxy-7-Methylguanine on Human Poly(ADP-Ribose) Polymerase 1. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:823-831. [PMID: 36171646 DOI: 10.1134/s0006297922080132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/23/2022] [Accepted: 05/23/2022] [Indexed: 06/16/2023]
Abstract
Previously, we have found that a nucleic acid metabolite, 7-methylguanine (7mGua), produced in the body can have an inhibitory effect on the poly(ADP-ribose) polymerase 1 (PARP1) enzyme, an important pharmacological target in anticancer therapy. In this work, using an original method of analysis of PARP1 activity based on monitoring fluorescence anisotropy, we studied inhibitory properties of 7mGua and its metabolite, 8-hydroxy-7-methylguanine (8h7mGua). Both compounds inhibited PARP1 enzymatic activity in a dose-dependent manner, however, 8h7mGua was shown to be a stronger inhibitor. The IC50 values for 8h7mGua at different concentrations of the NAD+ substrate were found to be 4 times lower, on average, than those for 7mGua. The more efficient binding of 8h7mGua in the PARP1 active site is explained by the presence of an additional hydrogen bond with the Glu988 catalytic residue. Experimental and computational studies did not reveal the effect of 7mGua and 8h7mGua on the activity of other DNA repair enzymes, indicating selectivity of their inhibitory action.
Collapse
Affiliation(s)
- Tatyana A Kurgina
- Institute of Chemical Biology and Fundamental Medicine, Russian Academy of Sciences, Siberian Branch, Novosibirsk, 630090, Russia
| | - Stanislav I Shram
- Institute of Molecular Genetics of National Research Center "Kurchatov Institute", Moscow, 123182, Russia
| | - Mikhail M Kutuzov
- Institute of Chemical Biology and Fundamental Medicine, Russian Academy of Sciences, Siberian Branch, Novosibirsk, 630090, Russia
| | - Tatyana V Abramova
- Institute of Chemical Biology and Fundamental Medicine, Russian Academy of Sciences, Siberian Branch, Novosibirsk, 630090, Russia
| | - Tatyana A Shcherbakova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Ekaterina A Maltseva
- Institute of Chemical Biology and Fundamental Medicine, Russian Academy of Sciences, Siberian Branch, Novosibirsk, 630090, Russia
| | | | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Russian Academy of Sciences, Siberian Branch, Novosibirsk, 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Vytas K Švedas
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia
- Research Computing Center, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Dmitry K Nilov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
| |
Collapse
|
4
|
Abstract
PARP is an important target in the treatment of cancers, particularly in patients with breast, ovarian, or prostate cancer that have compromised homologous recombination repair (i.e., BRCA−/−). This review about inhibitors of PARP (PARPi) is for readers interested in the development of next-generation drugs for the treatment of cancer, providing insights into structure–activity relationships, in vitro vs. in vivo potency, PARP trapping, and synthetic lethality. Selective inhibitors of PARP1 and PARP2 (PARP1/2) are used to treat cancer patients with deficiencies in the repair of DNA via homologous recombination. Here we provide a perspective on the reported potencies of the most studied of these inhibitors (olaparib, talazoparib, niraparib, rucaparib, and veliparib) in vitro and in vivo and how these numbers relate to the known structures of these inhibitors bound to the active sites of PARP1 and PARP2. We suggest that the phenomenon of PARP trapping is primarily due to the inhibition of the catalytic activity of PARP1 and that the basis for the higher potency of talazoparib compared to the other inhibitors lies in its more extensive network of interactions with conserved residues in the active site. We also consider the potential role of the recently characterized protein “Histone PARylation Factor 1” (HPF1), which interacts with PARP1/2 to form a shared active site, for the design of the next generation of inhibitors of PARP1/2.
Collapse
|
5
|
Alemasova EE, Naumenko KN, Sukhanova MV, Lavrik OI. Role of YB-1 in Regulation of Poly(ADP-Ribosylation) Catalyzed by Poly(ADP-Ribose) Polymerases. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:S32-S0. [PMID: 35501985 DOI: 10.1134/s0006297922140048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/14/2021] [Accepted: 09/17/2021] [Indexed: 06/14/2023]
Abstract
Poly(ADP-ribosyl)ation is a post-translational modification of proteins that performs an essential regulatory function in the cellular response to DNA damage. The key enzyme synthesizing poly(ADP-ribose) (PAR) in the cells is poly(ADP-ribose) polymerase 1 (PARP1). Understanding the mechanisms of the PARP1 activity regulation within the cells is necessary for development of the PARP1-targeted antitumor therapy. This review is devoted to the studies of the role of the RNA-binding protein YB-1 in the PARP1-catalyzed PARylation. The mechanisms of PARP1 activity stimulation by YB-1 protein can possibly be extended to other RNA-binding proteins involved in the maintenance of the genome stability.
Collapse
Affiliation(s)
- Elizaveta E Alemasova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Konstantin N Naumenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Maria V Sukhanova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
- Novosibirsk State University, Novosibirsk, 630090, Russia
| |
Collapse
|
6
|
Rudolph J, Muthurajan UM, Palacio M, Mahadevan J, Roberts G, Erbse AH, Dyer PN, Luger K. The BRCT domain of PARP1 binds intact DNA and mediates intrastrand transfer. Mol Cell 2021; 81:4994-5006.e5. [PMID: 34919819 PMCID: PMC8769213 DOI: 10.1016/j.molcel.2021.11.014] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 09/15/2021] [Accepted: 11/12/2021] [Indexed: 12/18/2022]
Abstract
PARP1 is a key player in the response to DNA damage and is the target of clinical inhibitors for the treatment of cancers. Binding of PARP1 to damaged DNA leads to activation wherein PARP1 uses NAD+ to add chains of poly(ADP-ribose) onto itself and other nuclear proteins. PARP1 also binds abundantly to intact DNA and chromatin, where it remains enzymatically inactive. We show that intact DNA makes contacts with the PARP1 BRCT domain, which was not previously recognized as a DNA-binding domain. This binding mode does not result in the concomitant reorganization and activation of the catalytic domain. We visualize the BRCT domain bound to nucleosomal DNA by cryogenic electron microscopy and identify a key motif conserved from ancestral BRCT domains for binding phosphates on DNA and phospho-peptides. Finally, we demonstrate that the DNA-binding properties of the BRCT domain contribute to the "monkey-bar mechanism" that mediates DNA transfer of PARP1.
Collapse
Affiliation(s)
- Johannes Rudolph
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Uma M Muthurajan
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Megan Palacio
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Jyothi Mahadevan
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Genevieve Roberts
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Annette H Erbse
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Pamela N Dyer
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Karolin Luger
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA; Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80309, USA.
| |
Collapse
|
7
|
Abstract
The SNF2 family ATPase Amplified in Liver Cancer 1 (ALC1) is the only chromatin remodeling enzyme with a poly(ADP-ribose) (PAR) binding macrodomain. ALC1 functions together with poly(ADP-ribose) polymerase PARP1 to remodel nucleosomes. Activation of ALC1 cryptic ATPase activity and the subsequent nucleosome remodeling requires binding of its macrodomain to PAR chains synthesized by PARP1 and NAD+ A key question is whether PARP1 has a role(s) in ALC1-dependent nucleosome remodeling beyond simply synthesizing the PAR chains needed to activate the ALC1 ATPase. Here, we identify PARP1 separation-of-function mutants that activate ALC1 ATPase but do not support nucleosome remodeling by ALC1. Investigation of these mutants has revealed multiple functions for PARP1 in ALC1-dependent nucleosome remodeling and provides insights into its multifaceted role in chromatin remodeling.
Collapse
|
8
|
Bell NAW, Haynes PJ, Brunner K, de Oliveira TM, Flocco MM, Hoogenboom BW, Molloy JE. Single-molecule measurements reveal that PARP1 condenses DNA by loop stabilization. SCIENCE ADVANCES 2021; 7:7/33/eabf3641. [PMID: 34380612 PMCID: PMC8357241 DOI: 10.1126/sciadv.abf3641] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 06/22/2021] [Indexed: 05/11/2023]
Abstract
Poly(ADP-ribose) polymerase 1 (PARP1) is an abundant nuclear enzyme that plays important roles in DNA repair, chromatin organization and transcription regulation. Although binding and activation of PARP1 by DNA damage sites has been extensively studied, little is known about how PARP1 binds to long stretches of undamaged DNA and how it could shape chromatin architecture. Here, using single-molecule techniques, we show that PARP1 binds and condenses undamaged, kilobase-length DNA subject to sub-piconewton mechanical forces. Stepwise decondensation at high force and DNA braiding experiments show that the condensation activity is due to the stabilization of DNA loops by PARP1. PARP inhibitors do not affect the level of condensation of undamaged DNA but act to block condensation reversal for damaged DNA in the presence of NAD+ Our findings suggest a mechanism for PARP1 in the organization of chromatin structure.
Collapse
Affiliation(s)
- Nicholas A W Bell
- The Francis Crick Institute, London NW1 1AT, UK.
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK
| | - Philip J Haynes
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK
- Molecular Sciences Research Hub, Department of Chemistry, Imperial College London, London W12 0BZ, UK
- Department of Physics and Astronomy, University College London, London WC1E 6BT, UK
| | - Katharina Brunner
- The Francis Crick Institute, London NW1 1AT, UK
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Taiana Maia de Oliveira
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Maria M Flocco
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Bart W Hoogenboom
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK
- Department of Physics and Astronomy, University College London, London WC1E 6BT, UK
| | | |
Collapse
|
9
|
Kutuzov MM, Belousova EA, Kurgina TA, Ukraintsev AA, Vasil’eva IA, Khodyreva SN, Lavrik OI. The contribution of PARP1, PARP2 and poly(ADP-ribosyl)ation to base excision repair in the nucleosomal context. Sci Rep 2021; 11:4849. [PMID: 33649352 PMCID: PMC7921663 DOI: 10.1038/s41598-021-84351-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 02/11/2021] [Indexed: 01/31/2023] Open
Abstract
The regulation of repair processes including base excision repair (BER) in the presence of DNA damage is implemented by a cellular signal: poly(ADP-ribosyl)ation (PARylation), which is catalysed by PARP1 and PARP2. Despite ample studies, it is far from clear how BER is regulated by PARPs and how the roles are distributed between the PARPs. Here, we investigated the effects of PARP1, PARP2 and PARylation on activities of the main BER enzymes (APE1, DNA polymerase β [Polβ] and DNA ligase IIIα [LigIIIα]) in combination with BER scaffold protein XRCC1 in the nucleosomal context. We constructed nucleosome core particles with midward- or outward-oriented damage. It was concluded that in most cases, the presence of PARP1 leads to the suppression of the activities of APE1, Polβ and to a lesser extent LigIIIα. PARylation by PARP1 attenuated this effect to various degrees depending on the enzyme. PARP2 had an influence predominantly on the last stage of BER: DNA sealing. Nonetheless, PARylation by PARP2 led to Polβ inhibition and to significant stimulation of LigIIIα activities in a NAD+-dependent manner. On the basis of the obtained and literature data, we suggest a hypothetical model of the contribution of PARP1 and PARP2 to BER.
Collapse
Affiliation(s)
- M. M. Kutuzov
- grid.415877.80000 0001 2254 1834Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia
| | - E. A. Belousova
- grid.415877.80000 0001 2254 1834Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia
| | - T. A. Kurgina
- grid.415877.80000 0001 2254 1834Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia ,grid.4605.70000000121896553Novosibirsk State University, Novosibirsk, Russia
| | - A. A. Ukraintsev
- grid.415877.80000 0001 2254 1834Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia
| | - I. A. Vasil’eva
- grid.415877.80000 0001 2254 1834Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia
| | - S. N. Khodyreva
- grid.415877.80000 0001 2254 1834Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia
| | - O. I. Lavrik
- grid.415877.80000 0001 2254 1834Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia ,grid.4605.70000000121896553Novosibirsk State University, Novosibirsk, Russia
| |
Collapse
|
10
|
Rudolph J, Roberts G, Luger K. Histone Parylation factor 1 contributes to the inhibition of PARP1 by cancer drugs. Nat Commun 2021; 12:736. [PMID: 33531508 PMCID: PMC7854685 DOI: 10.1038/s41467-021-20998-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 01/05/2021] [Indexed: 01/30/2023] Open
Abstract
Poly-(ADP-ribose) polymerase 1 and 2 (PARP1 and PARP2) are key enzymes in the DNA damage response. Four different inhibitors (PARPi) are currently in the clinic for treatment of ovarian and breast cancer. Recently, histone PARylation Factor 1 (HPF1) has been shown to play an essential role in the PARP1- and PARP2-dependent poly-(ADP-ribosylation) (PARylation) of histones, by forming a complex with both enzymes and altering their catalytic properties. Given the proximity of HPF1 to the inhibitor binding site both PARPs, we hypothesized that HPF1 may modulate the affinity of inhibitors toward PARP1 and/or PARP2. Here we demonstrate that HPF1 significantly increases the affinity for a PARP1 - DNA complex of some PARPi (i.e., olaparib), but not others (i.e., veliparib). This effect of HPF1 on the binding affinity of Olaparib also holds true for the more physiologically relevant PARP1 - nucleosome complex but does not extend to PARP2. Our results have important implications for the interpretation of PARP inhibition by current PARPi as well as for the design and analysis of the next generation of clinically relevant PARP inhibitors.
Collapse
Affiliation(s)
- Johannes Rudolph
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, 80309, USA
| | - Genevieve Roberts
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, 80309, USA
| | - Karolin Luger
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, 80309, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
| |
Collapse
|
11
|
Naumenko KN, Sukhanova MV, Hamon L, Kurgina TA, Alemasova EE, Kutuzov MM, Pastré D, Lavrik OI. Regulation of Poly(ADP-Ribose) Polymerase 1 Activity by Y-Box-Binding Protein 1. Biomolecules 2020; 10:E1325. [PMID: 32947956 PMCID: PMC7565162 DOI: 10.3390/biom10091325] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/07/2020] [Accepted: 09/10/2020] [Indexed: 12/23/2022] Open
Abstract
Y-box-binding protein 1 (YB-1) is a multifunctional positively charged protein that interacts with DNA or RNA and poly(ADP-ribose) (PAR). YB-1 is poly(ADP-ribosyl)ated and stimulates poly(ADP-ribose) polymerase 1 (PARP1) activity. Here, we studied the mechanism of YB-1-dependent PAR synthesis by PARP1 in vitro using biochemical and atomic force microscopy assays. PAR synthesis activity of PARP1 is known to be facilitated by co-factors such as Mg2+. However, in contrast to an Mg2+-dependent reaction, the activation of PARP1 by YB-1 is accompanied by overall up-regulation of protein PARylation and shortening of the PAR polymer. Therefore, YB-1 and cation co-factors stimulated PAR synthesis in divergent ways. PARP1 autoPARylation in the presence of YB-1 as well as trans-PARylation of YB-1 are greatly affected by the type of damaged DNA, suggesting that PARP1 activation depends on the formation of a PARP1-YB-1-DNA ternary complex. An unstructured C-terminal part of YB-1 involved in an interaction with PAR behaves similarly to full-length YB-1, indicating that both DNA and PAR binding are involved in the stimulation of PARP1 activity by YB-1. Thus, YB-1 is likely linked to the regulation of PARylation events in cells via an interaction with PAR and damaged DNA.
Collapse
Affiliation(s)
- Konstantin N. Naumenko
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 630090 Novosibirsk, Russia; (K.N.N.); (M.V.S.); (T.A.K.); (E.E.A.); (M.M.K.)
| | - Mariya V. Sukhanova
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 630090 Novosibirsk, Russia; (K.N.N.); (M.V.S.); (T.A.K.); (E.E.A.); (M.M.K.)
| | - Loic Hamon
- Laboratoire Structure-Activité des Biomolécules Normales et Pathologiques, University of Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France; (L.H.); (D.P.)
| | - Tatyana A. Kurgina
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 630090 Novosibirsk, Russia; (K.N.N.); (M.V.S.); (T.A.K.); (E.E.A.); (M.M.K.)
- Department of Molecular Biology, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Elizaveta E. Alemasova
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 630090 Novosibirsk, Russia; (K.N.N.); (M.V.S.); (T.A.K.); (E.E.A.); (M.M.K.)
| | - Mikhail M. Kutuzov
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 630090 Novosibirsk, Russia; (K.N.N.); (M.V.S.); (T.A.K.); (E.E.A.); (M.M.K.)
| | - David Pastré
- Laboratoire Structure-Activité des Biomolécules Normales et Pathologiques, University of Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France; (L.H.); (D.P.)
| | - Olga I. Lavrik
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 630090 Novosibirsk, Russia; (K.N.N.); (M.V.S.); (T.A.K.); (E.E.A.); (M.M.K.)
- Department of Molecular Biology, Novosibirsk State University, 630090 Novosibirsk, Russia
| |
Collapse
|
12
|
Nilov D, Maluchenko N, Kurgina T, Pushkarev S, Lys A, Kutuzov M, Gerasimova N, Feofanov A, Švedas V, Lavrik O, Studitsky VM. Molecular Mechanisms of PARP-1 Inhibitor 7-Methylguanine. Int J Mol Sci 2020; 21:ijms21062159. [PMID: 32245127 PMCID: PMC7139824 DOI: 10.3390/ijms21062159] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 03/12/2020] [Accepted: 03/17/2020] [Indexed: 12/11/2022] Open
Abstract
7-Methylguanine (7-MG), a natural compound that inhibits DNA repair enzyme poly(ADP-ribose) polymerase 1 (PARP-1), can be considered as a potential anticancer drug candidate. Here we describe a study of 7-MG inhibition mechanism using molecular dynamics, fluorescence anisotropy and single-particle Förster resonance energy transfer (spFRET) microscopy approaches to elucidate intermolecular interactions between 7-MG, PARP-1 and nucleosomal DNA. It is shown that 7-MG competes with substrate NAD+ and its binding in the PARP-1 active site is mediated by hydrogen bonds and nonpolar interactions with the Gly863, Ala898, Ser904, and Tyr907 residues. 7-MG promotes formation of the PARP-1–nucleosome complexes and suppresses DNA-dependent PARP-1 automodification. This results in nonproductive trapping of PARP-1 on nucleosomes and likely prevents the removal of genotoxic DNA lesions.
Collapse
Affiliation(s)
- Dmitry Nilov
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Lenin Hills 1, bldg. 40, 119991 Moscow, Russia;
- Correspondence: (D.N.); (V.M.S.)
| | - Natalya Maluchenko
- Lomonosov Moscow State University, Biology Faculty, Lenin Hills 1, bldg. 12, 119992 Moscow, Russia; (N.M.); (A.L.); (N.G.); (A.F.)
| | - Tatyana Kurgina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentiev avenue 8, 630090 Novosibirsk, Russia; (T.K.); (M.K.); (O.L.)
- Novosibirsk State University, Pirogov str. 2, 630090 Novosibirsk, Russia
| | - Sergey Pushkarev
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Lenin Hills 1, bldg. 73, 119991 Moscow, Russia;
| | - Alexandra Lys
- Lomonosov Moscow State University, Biology Faculty, Lenin Hills 1, bldg. 12, 119992 Moscow, Russia; (N.M.); (A.L.); (N.G.); (A.F.)
| | - Mikhail Kutuzov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentiev avenue 8, 630090 Novosibirsk, Russia; (T.K.); (M.K.); (O.L.)
| | - Nadezhda Gerasimova
- Lomonosov Moscow State University, Biology Faculty, Lenin Hills 1, bldg. 12, 119992 Moscow, Russia; (N.M.); (A.L.); (N.G.); (A.F.)
| | - Alexey Feofanov
- Lomonosov Moscow State University, Biology Faculty, Lenin Hills 1, bldg. 12, 119992 Moscow, Russia; (N.M.); (A.L.); (N.G.); (A.F.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya str. 16/10, 117997 Moscow, Russia
| | - Vytas Švedas
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Lenin Hills 1, bldg. 40, 119991 Moscow, Russia;
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Lenin Hills 1, bldg. 73, 119991 Moscow, Russia;
| | - Olga Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentiev avenue 8, 630090 Novosibirsk, Russia; (T.K.); (M.K.); (O.L.)
- Novosibirsk State University, Pirogov str. 2, 630090 Novosibirsk, Russia
| | - Vasily M. Studitsky
- Lomonosov Moscow State University, Biology Faculty, Lenin Hills 1, bldg. 12, 119992 Moscow, Russia; (N.M.); (A.L.); (N.G.); (A.F.)
- Fox Chase Cancer Center, Cottman Avenue 333, Philadelphia, PA 19111-2497, USA
- Correspondence: (D.N.); (V.M.S.)
| |
Collapse
|
13
|
Impact of PARP1, PARP2 & PARP3 on the Base Excision Repair of Nucleosomal DNA. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1241:47-57. [PMID: 32383115 DOI: 10.1007/978-3-030-41283-8_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
DNA is constantly attacked by different damaging agents; therefore, it requires frequent repair. On the one hand, the base excision repair (BER) system is responsible for the repair of the most frequent DNA lesions. On the other hand, the formation of poly(ADP-ribose) is one of the main DNA damage response reactions that is catalysed by members of the PARP family. PARP1, which belongs to the PARP family and performs approximately 90% of PAR synthesis in cells, could be considered a main regulator of the BER process. Most of the experimental data concerning BER investigation have been obtained using naked DNA. However, in the context of the eukaryotic cell, DNA is compacted in the nucleus, and the lowest compaction level is represented by the nucleosome. Thus, the organization of DNA into the nucleosome impacts the DNA-protein interactions that are involved in BER processes. Poly(ADP-ribosyl)ation (PARylation) is thought to regulate the initiation of the BER process at the chromatin level. In this review, we focus on the mechanisms involved in BER in the nucleosomal context and the potential effect of PARylation, which is catalysed by DNA-dependent PARP1, PARP2 and PARP3 proteins, on this process.
Collapse
|
14
|
Design, Synthesis and Molecular Modeling Study of Conjugates of ADP and Morpholino Nucleosides as A Novel Class of Inhibitors of PARP-1, PARP-2 and PARP-3. Int J Mol Sci 2019; 21:ijms21010214. [PMID: 31892271 PMCID: PMC6982223 DOI: 10.3390/ijms21010214] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/23/2019] [Accepted: 12/24/2019] [Indexed: 12/12/2022] Open
Abstract
We report on the design, synthesis and molecular modeling study of conjugates of adenosine diphosphate (ADP) and morpholino nucleosides as potential selective inhibitors of poly(ADP-ribose)polymerases-1, 2 and 3. Sixteen dinucleoside pyrophosphates containing natural heterocyclic bases as well as 5-haloganeted pyrimidines, and mimicking a main substrate of these enzymes, nicotinamide adenine dinucleotide (NAD+)-molecule, have been synthesized in a high yield. Morpholino nucleosides have been tethered to the β-phosphate of ADP via a phosphoester or phosphoramide bond. Screening of the inhibiting properties of these derivatives on the autopoly(ADP-ribosyl)ation of PARP-1 and PARP-2 has shown that the effect depends upon the type of nucleobase as well as on the linkage between ADP and morpholino nucleoside. The 5-iodination of uracil and the introduction of the P–N bond in NAD+-mimetics have shown to increase inhibition properties. Structural modeling suggested that the P–N bond can stabilize the pyrophosphate group in active conformation due to the formation of an intramolecular hydrogen bond. The most active NAD+ analog against PARP-1 contained 5-iodouracil 2ʹ-aminomethylmorpholino nucleoside with IC50 126 ± 6 μM, while in the case of PARP-2 it was adenine 2ʹ-aminomethylmorpholino nucleoside (IC50 63 ± 10 μM). In silico analysis revealed that thymine and uracil-based NAD+ analogs were recognized as the NAD+-analog that targets the nicotinamide binding site. On the contrary, the adenine 2ʹ-aminomethylmorpholino nucleoside-based NAD+ analogs were predicted to identify as PAR-analogs that target the acceptor binding site of PARP-2, representing a novel molecular mechanism for selective PARP inhibition. This discovery opens a new avenue for the rational design of PARP-1/2 specific inhibitors.
Collapse
|
15
|
Alemasova EE, Lavrik OI. Poly(ADP-ribosyl)ation by PARP1: reaction mechanism and regulatory proteins. Nucleic Acids Res 2019; 47:3811-3827. [PMID: 30799503 PMCID: PMC6486540 DOI: 10.1093/nar/gkz120] [Citation(s) in RCA: 271] [Impact Index Per Article: 54.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 02/04/2019] [Accepted: 02/14/2019] [Indexed: 12/18/2022] Open
Abstract
Poly(ADP-ribosyl)ation (PARylation) is posttranslational modification of proteins by linear or branched chains of ADP-ribose units, originating from NAD+. The central enzyme for PAR production in cells and the main target of poly(ADP-ribosyl)ation during DNA damage is poly(ADP-ribose) polymerase 1 (PARP1). PARP1 ability to function as a catalytic and acceptor protein simultaneously made a considerable contribution to accumulation of contradictory data. This topic is directly related to other questions, such as the stoichiometry of PARP1 molecules in auto-modification reaction, direction of the chain growth during PAR elongation and functional coupling of PARP1 with PARylation targets. Besides DNA damage necessary for the folding of catalytically active PARP1, other mechanisms appear to be required for the relevant intensity and specificity of PARylation reaction. Indeed, in recent years, PARP research has been enriched by the discovery of novel PARP1 interaction partners modulating its enzymatic activity. Understanding the details of PARP1 catalytic mechanism and its regulation is especially important in light of PARP-targeted therapy and may significantly aid to PARP inhibitors drug design. In this review we summarize old and up-to-date literature to clarify several points concerning PARylation mechanism and discuss different ways for regulation of PAR synthesis by accessory proteins reported thus far.
Collapse
Affiliation(s)
- Elizaveta E Alemasova
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk 630090, Russia
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk 630090, Russia.,Novosibirsk State University, Novosibirsk 630090, Russia
| |
Collapse
|
16
|
The multifunctional protein YB-1 potentiates PARP1 activity and decreases the efficiency of PARP1 inhibitors. Oncotarget 2018; 9:23349-23365. [PMID: 29805738 PMCID: PMC5955111 DOI: 10.18632/oncotarget.25158] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 04/02/2018] [Indexed: 02/06/2023] Open
Abstract
Y-box-binding protein 1 (YB-1) is a multifunctional cellular factor overexpressed in tumors resistant to chemotherapy. An intrinsically disordered structure together with a high positive charge peculiar to YB-1 allows this protein to function in almost all cellular events related to nucleic acids including RNA, DNA and poly(ADP-ribose) (PAR). In the present study we show that YB-1 acts as a potent poly(ADP-ribose) polymerase 1 (PARP1) cofactor that can reduce the efficiency of PARP1 inhibitors. Similarly to that of histones or polyamines, stimulatory effect of YB-1 on the activity of PARP1 was significantly higher than the activator potential of Mg2+ and was independent of the presence of EDTA. The C-terminal domain of YB-1 proved to be indispensable for PARP1 stimulation. We also found that functional interactions of YB-1 and PARP1 can be mediated and regulated by poly(ADP-ribose).
Collapse
|