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Kelly M, Dietz C, Kasson S, Zhang Y, Holtzman MJ, Kim IK. Deltex family E3 ligases specifically ubiquitinate the terminal ADP-ribose of poly(ADP-ribosyl)ation. Biochem Biophys Res Commun 2024; 720:150101. [PMID: 38749191 PMCID: PMC11219154 DOI: 10.1016/j.bbrc.2024.150101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 04/24/2024] [Accepted: 05/10/2024] [Indexed: 06/01/2024]
Abstract
Poly(ADP-ribose) polymerases (PARPs) are critical to regulating cellular activities, such as the response to DNA damage and cell death. PARPs catalyze a reversible post-translational modification (PTM) in the form of mono- or poly(ADP-ribosyl)ation. This type of modification is known to form a ubiquitin-ADP-ribose (Ub-ADPR) conjugate that depends on the actions of Deltex family of E3 ubiquitin ligases (DTXs). In particular, DTXs add ubiquitin to the 3'-OH of adenosine ribose' in ADP-ribose, which effectively sequesters ubiquitin and impedes ubiquitin-dependent signaling. Previous work demonstrates DTX function for ubiquitination of protein-free ADPR, mono-ADP-ribosylated peptides, and ADP-ribosylated nucleic acids. However, the dynamics of DTX-mediated ubiquitination of poly(ADP-ribosyl)ation remains to be defined. Here we show that the ADPR ubiquitination function is not found in other PAR-binding E3 ligases and is conserved across DTX family members. Importantly, DTXs specifically target poly(ADP-ribose) chains for ubiquitination that can be cleaved by PARG, the primary eraser of poly(ADP-ribose), leaving the adenosine-terminal ADPR unit conjugated to ubiquitin. Our collective results demonstrate the DTXs' specific ubiquitination of the adenosine terminus of poly(ADP-ribosyl)ation and suggest the unique Ub-ADPR conjugation process as a basis for PARP-DTX control of cellular activities.
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Affiliation(s)
- Matthew Kelly
- Division of Biochemistry, Department of Chemistry, University of Cincinnati, 301 Clifton Ct, Cincinnati, OH, 45221, USA
| | - Chase Dietz
- Division of Biochemistry, Department of Chemistry, University of Cincinnati, 301 Clifton Ct, Cincinnati, OH, 45221, USA
| | - Samuel Kasson
- Division of Biochemistry, Department of Chemistry, University of Cincinnati, 301 Clifton Ct, Cincinnati, OH, 45221, USA
| | - Yong Zhang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO, 63110, USA
| | - Michael J Holtzman
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO, 63110, USA
| | - In-Kwon Kim
- Division of Biochemistry, Department of Chemistry, University of Cincinnati, 301 Clifton Ct, Cincinnati, OH, 45221, USA.
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2
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Khizer H, Maryam A, Ansari A, Ahmad MS, Khalid RR. Leveraging shape screening and molecular dynamics simulations to optimize PARP1-Specific chemo/radio-potentiators for antitumor drug design. Arch Biochem Biophys 2024; 756:110010. [PMID: 38642632 DOI: 10.1016/j.abb.2024.110010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 04/02/2024] [Accepted: 04/17/2024] [Indexed: 04/22/2024]
Abstract
PARP1 plays a pivotal role in DNA repair within the base excision pathway, making it a promising therapeutic target for cancers involving BRCA mutations. Current study is focused on the discovery of PARP inhibitors with enhanced selectivity for PARP1. Concurrent inhibition of PARP1 with PARP2 and PARP3 affects cellular functions, potentially causing DNA damage accumulation and disrupting immune responses. In step 1, a virtual library of 593 million compounds has been screened using a shape-based screening approach to narrow down the promising scaffolds. In step 2, hierarchical docking approach embedded in Schrödinger suite was employed to select compounds with good dock score, drug-likeness and MMGBSA score. Analysis supplemented with decomposition energy, molecular dynamics (MD) simulations and hydrogen bond frequency analysis, pinpointed that active site residues; H862, G863, R878, M890, Y896 and F897 are crucial for specific binding of ZINC001258189808 and ZINC000092332196 with PARP1 as compared to PARP2 and PARP3. The binding of ZINC000656130962, ZINC000762230673, ZINC001332491123, and ZINC000579446675 also revealed interaction involving two additional active site residues of PARP1, namely N767 and E988. Weaker or no interaction was observed for these residues with PARP2 and PARP3. This approach advances our understanding of PARP-1 specific inhibitors and their mechanisms of action, facilitating the development of targeted therapeutics.
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Affiliation(s)
- Hifza Khizer
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Arooma Maryam
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Adnan Ansari
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Sajjad Ahmad
- School of Chemical Engineering, Hebei University of Technology, Tianjin, 300401, PR China
| | - Rana Rehan Khalid
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan.
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De Silva WGM, Sequeira VB, Yang C, Dixon KM, Holland AJA, Mason RS, Rybchyn MS. 1,25-Dihydroxyvitamin D 3 Suppresses UV-Induced Poly(ADP-Ribose) Levels in Primary Human Keratinocytes, as Detected by a Novel Whole-Cell ELISA. Int J Mol Sci 2024; 25:5583. [PMID: 38891771 PMCID: PMC11171802 DOI: 10.3390/ijms25115583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/13/2024] [Accepted: 05/16/2024] [Indexed: 06/21/2024] Open
Abstract
Photoprotective properties of 1,25-dihydroxyvitamin D3 (1,25(OH)2D3) to reduce UV-induced DNA damage have been established in several studies. UV-induced DNA damage in skin such as single or double strand breaks is known to initiate several cellular mechanisms including activation of poly(ADP-ribose) (pADPr) polymerase-1 (PARP-1). DNA damage from UV also increases extracellular signal-related kinase (ERK) phosphorylation, which further increases PARP activity. PARP-1 functions by using cellular nicotinamide adenine dinucleotide (NAD+) to synthesise pADPr moieties and attach these to target proteins involved in DNA repair. Excessive PARP-1 activation following cellular stress such as UV irradiation may result in excessive levels of cellular pADPr. This can also have deleterious effects on cellular energy levels due to depletion of NAD+ to suboptimal levels. Since our previous work indicated that 1,25(OH)2D3 reduced UV-induced DNA damage in part through increased repair via increased energy availability, the current study investigated the effect of 1,25(OH)2D3 on UV-induced PARP-1 activity using a novel whole-cell enzyme- linked immunosorbent assay (ELISA) which quantified levels of the enzymatic product of PARP-1, pADPr. This whole cell assay used around 5000 cells per replicate measurement, which represents a 200-400-fold decrease in cell requirement compared to current commercial assays that measure in vitro pADPr levels. Using our assay, we observed that UV exposure significantly increased pADPr levels in human keratinocytes, while 1,25(OH)2D3 significantly reduced levels of UV-induced pADPr in primary human keratinocytes to a similar extent as a known PARP-1 inhibitor, 3-aminobenzamide (3AB). Further, both 1,25(OH)2D3 and 3AB as well as a peptide inhibitor of ERK-phosphorylation significantly reduced DNA damage in UV-exposed keratinocytes. The current findings support the proposal that reduction in pADPr levels may be critical for the function of 1,25(OH)2D3 in skin to reduce UV-induced DNA damage.
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Affiliation(s)
| | - Vanessa Bernadette Sequeira
- Department of Physiology, School of Medical Sciences and Bosch Institute, The University of Sydney, Sydney, NSW 2006, Australia
| | - Chen Yang
- Department of Physiology, School of Medical Sciences and Bosch Institute, The University of Sydney, Sydney, NSW 2006, Australia
| | - Katie Marie Dixon
- Department of Anatomy and Histology and Bosch Institute, The University of Sydney, Sydney, NSW 2006, Australia;
| | - Andrew J. A. Holland
- Douglas Cohen Department of Paediatric Surgery, The Children’s Hospital at Westmead Clinical School, The Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Rebecca Sara Mason
- Department of Physiology, School of Medical Sciences and Bosch Institute, The University of Sydney, Sydney, NSW 2006, Australia
- School of Life and Environmental Sciences and Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
| | - Mark Stephen Rybchyn
- Department of Physiology, School of Medical Sciences and Bosch Institute, The University of Sydney, Sydney, NSW 2006, Australia
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4
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Wu S, Yao X, Sun W, Jiang K, Hao J. Exploration of poly (ADP-ribose) polymerase inhibitor resistance in the treatment of BRCA1/2-mutated cancer. Genes Chromosomes Cancer 2024; 63:e23243. [PMID: 38747337 DOI: 10.1002/gcc.23243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 04/19/2024] [Indexed: 05/21/2024] Open
Abstract
Breast cancer susceptibility 1/2 (BRCA1/2) genes play a crucial role in DNA damage repair, yet mutations in these genes increase the susceptibility to tumorigenesis. Exploiting the synthetic lethality mechanism between BRCA1/2 mutations and poly(ADP-ribose) polymerase (PARP) inhibition has led to the development and clinical approval of PARP inhibitor (PARPi), representing a milestone in targeted therapy for BRCA1/2 mutant tumors. This approach has paved the way for leveraging synthetic lethality in tumor treatment strategies. Despite the initial success of PARPis, resistance to these agents diminishes their efficacy in BRCA1/2-mutant tumors. Investigations into PARPi resistance have identified replication fork stability and homologous recombination repair as key factors sensitive to PARPis. Additionally, studies suggest that replication gaps may also confer sensitivity to PARPis. Moreover, emerging evidence indicates a correlation between PARPi resistance and cisplatin resistance, suggesting a potential overlap in the mechanisms underlying resistance to both agents. Given these findings, it is imperative to explore the interplay between replication gaps and PARPi resistance, particularly in the context of platinum resistance. Understanding the impact of replication gaps on PARPi resistance may offer insights into novel therapeutic strategies to overcome resistance mechanisms and enhance the efficacy of targeted therapies in BRCA1/2-mutant tumors.
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Affiliation(s)
- Shuyi Wu
- School of Life Sciences, Zhejiang Chinese Medicine University, HangZhou, China
| | - Xuanjie Yao
- The Fourth Clinical Medical College, Zhejiang Chinese Medicine University, HangZhou, China
| | - Weiwei Sun
- School of Life Sciences, Zhejiang Chinese Medicine University, HangZhou, China
| | - Kaitao Jiang
- School of Life Sciences, Zhejiang Chinese Medicine University, HangZhou, China
| | - Jie Hao
- School of Life Sciences, Zhejiang Chinese Medicine University, HangZhou, China
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Dai Y, Lin J, Chen X, Ren J, Wu C, Shen H, Li X, Yu J, Jiang B, Yu L. NAMPT/NAD +/PARP1 Pathway Regulates CFA-Induced Inflammatory Pain via NF-κB Signaling in Rodents. Adv Biol (Weinh) 2024; 8:e2400028. [PMID: 38463014 DOI: 10.1002/adbi.202400028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/26/2024] [Indexed: 03/12/2024]
Abstract
Emerging evidence has implicated nicotinamide adenine dinucleotide (NAD+) metabolism in various inflammatory diseases. In the study, the role of NAD+ metabolism in Complete Freund's Adjuvant (CFA)-evoked inflammatory pain and the underlying mechanisms are investigated. The study demonstrated that CFA induced upregulation of nicotinamide phosphoribosyltransferase (NAMPT) in dorsal root ganglia (DRG) without significant changes in the spinal cord. Inhibition of NAMPT expression by intrathecal injection of NAMPT siRNA alleviated CFA-induced pain-like behavior, decreased NAD+ contents in DRG, and lowered poly-(ADP-ribose) polymerase 1 (PARP1) activity levels. These effects are all reversed by the supplement of nicotinamide mononucleotide (NMN). Inhibition of PARP1 expression by intrathecal injection of PARP1 siRNA alleviated CFA-induced pain-like behavior, while elevated NAD+ levels of DRG. The analgesic effect of inhibiting NAMPT/NAD+/PARP1 axis can be attributed to the downregulation of the NF-κB/IL-1β inflammatory pathway. Double immunofluorescence staining showed that the expression of NAMPT/NAD+/PARP1 axis is restricted to DRG neurons. In conclusion, PARP1 activation in response to CFA stimulation, fueled by NAMPT-derived NAD+, mediates CFA-induced inflammatory pain through NF-κB/IL-1β inflammatory pathway.
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Affiliation(s)
- Yi Dai
- Department of Anesthesiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, China
| | - Jiaqi Lin
- East Hospital Affiliated to Tongji University, Shanghai, 200000, China
| | - Xiangde Chen
- Department of Anesthesiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, China
| | - Jinxuan Ren
- Department of Anesthesiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, China
| | - Chengwei Wu
- Department of Anesthesiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, China
- Lishui Municipal Central Hospital, Lishui, 323000, China
| | - Huihui Shen
- Department of Anesthesiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, China
| | - Xue Li
- Department of Anesthesiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, China
| | - Jing Yu
- Department of Anesthesiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, China
| | - Baochun Jiang
- Department of Anesthesiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, China
| | - Lina Yu
- Department of Anesthesiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310009, China
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6
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Burtscher ML, Gade S, Garrido-Rodriguez M, Rutkowska A, Werner T, Eberl HC, Petretich M, Knopf N, Zirngibl K, Grandi P, Bergamini G, Bantscheff M, Fälth-Savitski M, Saez-Rodriguez J. Network integration of thermal proteome profiling with multi-omics data decodes PARP inhibition. Mol Syst Biol 2024; 20:458-474. [PMID: 38454145 PMCID: PMC10987601 DOI: 10.1038/s44320-024-00025-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/13/2024] [Accepted: 02/20/2024] [Indexed: 03/09/2024] Open
Abstract
Complex disease phenotypes often span multiple molecular processes. Functional characterization of these processes can shed light on disease mechanisms and drug effects. Thermal Proteome Profiling (TPP) is a mass-spectrometry (MS) based technique assessing changes in thermal protein stability that can serve as proxies of functional protein changes. These unique insights of TPP can complement those obtained by other omics technologies. Here, we show how TPP can be integrated with phosphoproteomics and transcriptomics in a network-based approach using COSMOS, a multi-omics integration framework, to provide an integrated view of transcription factors, kinases and proteins with altered thermal stability. This allowed us to recover consequences of Poly (ADP-ribose) polymerase (PARP) inhibition in ovarian cancer cells on cell cycle and DNA damage response as well as interferon and hippo signaling. We found that TPP offers a complementary perspective to other omics data modalities, and that its integration allowed us to obtain a more complete molecular overview of PARP inhibition. We anticipate that this strategy can be used to integrate functional proteomics with other omics to study molecular processes.
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Affiliation(s)
- Mira L Burtscher
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany
- Cellzome, a GSK company, Heidelberg, Germany
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | | | - Martin Garrido-Rodriguez
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | | | | | | | | | - Katharina Zirngibl
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany
- Cellzome, a GSK company, Heidelberg, Germany
| | | | | | | | | | - Julio Saez-Rodriguez
- Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany.
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7
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Abugable AA, Antar S, El-Khamisy SF. Chromosomal single-strand break repair and neurological disease: Implications on transcription and emerging genomic tools. DNA Repair (Amst) 2024; 135:103629. [PMID: 38266593 DOI: 10.1016/j.dnarep.2024.103629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 12/21/2023] [Accepted: 01/04/2024] [Indexed: 01/26/2024]
Abstract
Cells are constantly exposed to various sources of DNA damage that pose a threat to their genomic integrity. One of the most common types of DNA breaks are single-strand breaks (SSBs). Mutations in the repair proteins that are important for repairing SSBs have been reported in several neurological disorders. While several tools have been utilised to investigate SSBs in cells, it was only through recent advances in genomics that we are now beginning to understand the architecture of the non-random distribution of SSBs and their impact on key cellular processes such as transcription and epigenetic remodelling. Here, we discuss our current understanding of the genome-wide distribution of SSBs, their link to neurological disorders and summarise recent technologies to investigate SSBs at the genomic level.
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Affiliation(s)
- Arwa A Abugable
- School of Biosciences, Firth Court, University of Sheffield, Sheffield, UK; The healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK
| | - Sarah Antar
- School of Biosciences, Firth Court, University of Sheffield, Sheffield, UK; The healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK; Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Mansoura University, Egypt
| | - Sherif F El-Khamisy
- School of Biosciences, Firth Court, University of Sheffield, Sheffield, UK; The healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK; Institute of Cancer Therapeutics, Faculty of Life Sciences, University of Bradford, Bradford, UK.
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Khodyreva SN, Ilina ES, Dyrkheeva NS, Kochetkova AS, Yamskikh AA, Maltseva EA, Malakhova AA, Medvedev SP, Zakian SM, Lavrik OI. A Knockout of Poly(ADP-Ribose) Polymerase 1 in a Human Cell Line: An Influence on Base Excision Repair Reactions in Cellular Extracts. Cells 2024; 13:302. [PMID: 38391916 PMCID: PMC10886765 DOI: 10.3390/cells13040302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/24/2024] [Accepted: 02/01/2024] [Indexed: 02/24/2024] Open
Abstract
Base excision repair (BER) is the predominant pathway for the removal of most forms of hydrolytic, oxidative, and alkylative DNA lesions. The precise functioning of BER is achieved via the regulation of each step by regulatory/accessory proteins, with the most important of them being poly(ADP-ribose) polymerase 1 (PARP1). PARP1's regulatory functions extend to many cellular processes including the regulation of mRNA stability and decay. PARP1 can therefore affect BER both at the level of BER proteins and at the level of their mRNAs. Systematic data on how the PARP1 content affects the activities of key BER proteins and the levels of their mRNAs in human cells are extremely limited. In this study, a CRISPR/Cas9-based technique was used to knock out the PARP1 gene in the human HEK 293FT line. The obtained cell clones with the putative PARP1 deletion were characterized by several approaches including PCR analysis of deletions in genomic DNA, Sanger sequencing of genomic DNA, quantitative PCR analysis of PARP1 mRNA, Western blot analysis of whole-cell-extract (WCE) proteins with anti-PARP1 antibodies, and PAR synthesis in WCEs. A quantitative PCR analysis of mRNAs coding for BER-related proteins-PARP2, uracil DNA glycosylase 2, apurinic/apyrimidinic endonuclease 1, DNA polymerase β, DNA ligase III, and XRCC1-did not reveal a notable influence of the PARP1 knockout. The corresponding WCE catalytic activities evaluated in parallel did not differ significantly between the mutant and parental cell lines. No noticeable effect of poly(ADP-ribose) synthesis on the activity of the above WCE enzymes was revealed either.
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Affiliation(s)
- Svetlana N. Khodyreva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia; (E.S.I.); (N.S.D.); (A.S.K.); (A.A.Y.); (E.A.M.); (A.A.M.); (S.P.M.); (S.M.Z.)
| | - Ekaterina S. Ilina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia; (E.S.I.); (N.S.D.); (A.S.K.); (A.A.Y.); (E.A.M.); (A.A.M.); (S.P.M.); (S.M.Z.)
- Faculty of Natural Sciences, Novosibirsk State University, 2 Pirogova Str., Novosibirsk 630090, Russia
| | - Nadezhda S. Dyrkheeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia; (E.S.I.); (N.S.D.); (A.S.K.); (A.A.Y.); (E.A.M.); (A.A.M.); (S.P.M.); (S.M.Z.)
- Faculty of Natural Sciences, Novosibirsk State University, 2 Pirogova Str., Novosibirsk 630090, Russia
| | - Alina S. Kochetkova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia; (E.S.I.); (N.S.D.); (A.S.K.); (A.A.Y.); (E.A.M.); (A.A.M.); (S.P.M.); (S.M.Z.)
| | - Alexandra A. Yamskikh
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia; (E.S.I.); (N.S.D.); (A.S.K.); (A.A.Y.); (E.A.M.); (A.A.M.); (S.P.M.); (S.M.Z.)
- Faculty of Natural Sciences, Novosibirsk State University, 2 Pirogova Str., Novosibirsk 630090, Russia
| | - Ekaterina A. Maltseva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia; (E.S.I.); (N.S.D.); (A.S.K.); (A.A.Y.); (E.A.M.); (A.A.M.); (S.P.M.); (S.M.Z.)
| | - Anastasia A. Malakhova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia; (E.S.I.); (N.S.D.); (A.S.K.); (A.A.Y.); (E.A.M.); (A.A.M.); (S.P.M.); (S.M.Z.)
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia
| | - Sergey P. Medvedev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia; (E.S.I.); (N.S.D.); (A.S.K.); (A.A.Y.); (E.A.M.); (A.A.M.); (S.P.M.); (S.M.Z.)
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia
| | - Suren M. Zakian
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia; (E.S.I.); (N.S.D.); (A.S.K.); (A.A.Y.); (E.A.M.); (A.A.M.); (S.P.M.); (S.M.Z.)
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia
| | - Olga I. Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia; (E.S.I.); (N.S.D.); (A.S.K.); (A.A.Y.); (E.A.M.); (A.A.M.); (S.P.M.); (S.M.Z.)
- Faculty of Natural Sciences, Novosibirsk State University, 2 Pirogova Str., Novosibirsk 630090, Russia
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9
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Kanev PB, Atemin A, Stoynov S, Aleksandrov R. PARP1 roles in DNA repair and DNA replication: The basi(c)s of PARP inhibitor efficacy and resistance. Semin Oncol 2024; 51:2-18. [PMID: 37714792 DOI: 10.1053/j.seminoncol.2023.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 08/10/2023] [Indexed: 09/17/2023]
Abstract
Genome integrity is under constant insult from endogenous and exogenous sources. In order to cope, eukaryotic cells have evolved an elaborate network of DNA repair that can deal with diverse lesion types and exhibits considerable functional redundancy. PARP1 is a major sensor of DNA breaks with established and putative roles in a number of pathways within the DNA repair network, including repair of single- and double-strand breaks as well as protection of the DNA replication fork. Importantly, PARP1 is the major target of small-molecule PARP inhibitors (PARPi), which are employed in the treatment of homologous recombination (HR)-deficient tumors, as the latter are particularly susceptible to the accumulation of DNA damage due to an inability to efficiently repair highly toxic double-strand DNA breaks. The clinical success of PARPi has fostered extensive research into PARP biology, which has shed light on the involvement of PARP1 in various genomic transactions. A major goal within the field has been to understand the relationship between catalytic inhibition and PARP1 trapping. The specific consequences of inhibition and trapping on genomic stability as a basis for the cytotoxicity of PARP inhibitors remain a matter of debate. Finally, PARP inhibition is increasingly recognized for its capacity to elicit/modulate anti-tumor immunity. The clinical potential of PARP inhibition is, however, hindered by the development of resistance. Hence, extensive efforts are invested in identifying factors that promote resistance or sensitize cells to PARPi. The current review provides a summary of advances in our understanding of PARP1 biology, the mechanistic nature, and molecular consequences of PARP inhibition, as well as the mechanisms that give rise to PARPi resistance.
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Affiliation(s)
- Petar-Bogomil Kanev
- Laboratory of Genomic Stability, Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Aleksandar Atemin
- Laboratory of Genomic Stability, Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Stoyno Stoynov
- Laboratory of Genomic Stability, Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria.
| | - Radoslav Aleksandrov
- Laboratory of Genomic Stability, Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria.
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10
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Bourlon MT, Valdez P, Castro E. Development of PARP inhibitors in advanced prostate cancer. Ther Adv Med Oncol 2024; 16:17588359231221337. [PMID: 38205078 PMCID: PMC10777773 DOI: 10.1177/17588359231221337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/29/2023] [Indexed: 01/12/2024] Open
Abstract
The relatively high prevalence of alterations in the homologous recombination repair (HRR) pathway described in advanced prostate cancer provides a unique opportunity to develop therapeutic strategies that take advantage of the decreased tumor ability to repair DNA damage. Poly ADP-ribose polymerase (PARP) inhibitors have been demonstrated to improve the outcomes of metastatic castration-resistant prostate cancer (mCRPC) patients with HRR defects, particularly in those with BRCA1/2 alterations. To expand the benefit of PARPi to patients without detectable HRR alterations, multiple studies are addressing potential synergies between PARP inhibition (PARPi) and androgen receptor pathway inhibitors (ARSi), radiation, radioligand therapy, chemotherapy, or immunotherapy, and these strategies are also being evaluated in the hormone-sensitive setting. In this review, we summarize the development of PARPi in prostate cancer, the potential synergies, and combinations being investigated as well as the future directions of PARPi for the management of the disease.
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Affiliation(s)
- Maria Teresa Bourlon
- Hemato-Oncology Department, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Paola Valdez
- Hemato-Oncology Department, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Elena Castro
- Department of Medical Oncology, Hospital Universitario 12 de Octubre, Av. Cordoba s/n, 28041, Madrid, Spain
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11
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Caldecott KW. Causes and consequences of DNA single-strand breaks. Trends Biochem Sci 2024; 49:68-78. [PMID: 38040599 DOI: 10.1016/j.tibs.2023.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/20/2023] [Accepted: 11/03/2023] [Indexed: 12/03/2023]
Abstract
DNA single-strand breaks (SSBs) are among the most common lesions arising in human cells, with tens to hundreds of thousands arising in each cell, each day. Cells have efficient mechanisms for the sensing and repair of these ubiquitous DNA lesions, but the failure of these processes to rapidly remove SSBs can lead to a variety of pathogenic outcomes. The threat posed by unrepaired SSBs is illustrated by the existence of at least six genetic diseases in which SSB repair (SSBR) is defective, all of which are characterised by neurodevelopmental and/or neurodegenerative pathology. Here, I review current understanding of how SSBs arise and impact on critical molecular processes, such as DNA replication and gene transcription, and their links to human disease.
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Affiliation(s)
- Keith W Caldecott
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, UK.
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12
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Wu Y, Wu M, Zheng X, Yu H, Mao X, Jin Y, Wang Y, Pang A, Zhang J, Zeng S, Xu T, Chen Y, Zhang B, Lin N, Dai H, Wang Y, Yao X, Dong X, Huang W, Che J. Discovery of a potent and selective PARP1 degrader promoting cell cycle arrest via intercepting CDC25C-CDK1 axis for treating triple-negative breast cancer. Bioorg Chem 2024; 142:106952. [PMID: 37952486 DOI: 10.1016/j.bioorg.2023.106952] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/26/2023] [Accepted: 10/28/2023] [Indexed: 11/14/2023]
Abstract
PARP1 is a multifaceted component of DNA repair and chromatin remodeling, making it an effective therapeutic target for cancer therapy. The recently reported proteolytic targeting chimera (PROTAC) could effectively degrade PARP1 through the ubiquitin-proteasome pathway, expanding the therapeutic application of PARP1 blocking. In this study, a series of nitrogen heterocyclic PROTACs were designed and synthesized through ternary complex simulation analysis based on our previous work. Our efforts have resulted in a potent PARP1 degrader D6 (DC50 = 25.23 nM) with high selectivity due to nitrogen heterocyclic linker generating multiple interactions with the PARP1-CRBN PPI surface, specifically. Moreover, D6 exhibited strong cytotoxicity to triple negative breast cancer cell line MDA-MB-231 (IC50 = 1.04 µM). And the proteomic results showed that the antitumor mechanism of D6 was found that intensifies DNA damage by intercepting the CDC25C-CDK1 axis to halt cell cycle transition in triple-negative breast cancer cells. Furthermore, in vivo study, D6 showed a promising PK property with moderate oral absorption activity. And D6 could effectively inhibit tumor growth (TGI rate = 71.4 % at 40 mg/kg) without other signs of toxicity in MDA-MB-321 tumor-bearing mice. In summary, we have identified an original scaffold and potent PARP1 PROTAC that provided a novel intervention strategy for the treatment of triple-negative breast cancer.
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Affiliation(s)
- Yiquan Wu
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Mingfei Wu
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiaoli Zheng
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou 310058, China
| | - Hengyuan Yu
- Key Laboratory of Advanced Drug Delivery Systems of Zhejiang Province, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xinfei Mao
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuyuan Jin
- Key Laboratory of Neuropsychiatric Drug Research of Zhejiang Province, Hangzhou Medical College, Hangzhou 310058, China
| | - Yanhong Wang
- Department of Pharmacy, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, Zhejiang, China
| | - Ao Pang
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jingyu Zhang
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shenxin Zeng
- Key Laboratory of Neuropsychiatric Drug Research of Zhejiang Province, Hangzhou Medical College, Hangzhou 310058, China
| | - Tengfei Xu
- Key Laboratory of Advanced Drug Delivery Systems of Zhejiang Province, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yong Chen
- Key Laboratory of Advanced Drug Delivery Systems of Zhejiang Province, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Bo Zhang
- Department of Clinical Pharmacology, Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, China
| | - Nengming Lin
- Department of Clinical Pharmacology, Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, China
| | - Haibin Dai
- Department of Pharmacy, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, Zhejiang, China
| | - Yuwei Wang
- Centre for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macau 999078, China
| | - Xiaojun Yao
- College of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang 712046, China
| | - Xiaowu Dong
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; Department of Pharmacy, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, Zhejiang, China
| | - Wenhai Huang
- Key Laboratory of Neuropsychiatric Drug Research of Zhejiang Province, Hangzhou Medical College, Hangzhou 310058, China.
| | - Jinxin Che
- Hangzhou Institute of Innovative Medicine, Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
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13
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Fu X, Li P, Zhou Q, He R, Wang G, Zhu S, Bagheri A, Kupfer G, Pei H, Li J. Mechanism of PARP inhibitor resistance and potential overcoming strategies. Genes Dis 2024; 11:306-320. [PMID: 37588193 PMCID: PMC10425807 DOI: 10.1016/j.gendis.2023.02.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/27/2023] [Accepted: 02/02/2023] [Indexed: 08/18/2023] Open
Abstract
PARP inhibitors (PARPi) are a kind of cancer therapy that targets poly (ADP-ribose) polymerase. PARPi is the first clinically approved drug to exert synthetic lethality by obstructing the DNA single-strand break repair process. Despite the significant therapeutic effect in patients with homologous recombination (HR) repair deficiency, innate and acquired resistance to PARPi is a main challenge in the clinic. In this review, we mainly discussed the underlying mechanisms of PARPi resistance and summarized the promising solutions to overcome PARPi resistance, aiming at extending PARPi application and improving patient outcomes.
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Affiliation(s)
- Xiaoyu Fu
- Department of Oncology, Georgetown Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, China
| | - Ping Li
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, China
| | - Qi Zhou
- Department of Oncology, Georgetown Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, China
| | - Ruyuan He
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, China
| | - Guannan Wang
- Department of Oncology, Georgetown Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Shiya Zhu
- Department of Oncology, Georgetown Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Amir Bagheri
- Department of Oncology, Georgetown Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Gary Kupfer
- Department of Oncology, Georgetown Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Huadong Pei
- Department of Oncology, Georgetown Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Juanjuan Li
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, China
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14
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Laspata N, Muoio D, Fouquerel E. Multifaceted Role of PARP1 in Maintaining Genome Stability Through Its Binding to Alternative DNA Structures. J Mol Biol 2024; 436:168207. [PMID: 37481154 DOI: 10.1016/j.jmb.2023.168207] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/28/2023] [Accepted: 07/12/2023] [Indexed: 07/24/2023]
Abstract
Alternative DNA structures that differ from the canonical B-form of DNA can arise from repetitive sequences and play beneficial roles in many cellular processes such as gene regulation and chromatin organization. However, they also threaten genomic stability in several ways including mutagenesis and collisions with replication and/or transcription machinery, which lead to genomic instability that is associated with human disease. Thus, the careful regulation of non-B-DNA structure formation and resolution is crucial for the maintenance of genome integrity. Several protein factors have been demonstrated to associate with alternative DNA structures to facilitate their removal, one of which is the ADP-ribose transferase (ART) PARP1 (also called ADP-ribosyltransferase diphtheria toxin-like 1 or ARTD1), a multifaceted DNA repair enzyme that recognizes single- and double-stranded DNA breaks and synthesizes chains of poly (ADP-ribose) (PAR) to recruit DNA repair proteins. It is now well appreciated that PARP1 recognizes several nucleic acid structures beyond DNA lesions, including stalled replication forks, DNA hairpins and cruciforms, R-loops, and DNA G-quadruplexes (G4 DNA). In this review, we summarize the current evidence of a direct association of PARP1 with each of these aforementioned alternative DNA structures, as well as discuss the role of PARP1 in the prevention of non-B-DNA structure-induced genetic instability. We will focus on the mechanisms of the recognition and binding by PARP1 to each alternative structure and the structure-based stimulation of PARP1 catalytic activity upon binding. Finally, we will discuss some of the outstanding gaps in the literature and offer speculative insight for questions that remain to be experimentally addressed.
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Affiliation(s)
- Natalie Laspata
- UPMC Hillman Cancer Center, University of Pittsburgh Cancer Institute, Department of Pharmacology and Chemical Biology, Pittsburgh, PA 15232, USA; Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Daniela Muoio
- UPMC Hillman Cancer Center, University of Pittsburgh Cancer Institute, Department of Pharmacology and Chemical Biology, Pittsburgh, PA 15232, USA
| | - Elise Fouquerel
- UPMC Hillman Cancer Center, University of Pittsburgh Cancer Institute, Department of Pharmacology and Chemical Biology, Pittsburgh, PA 15232, USA.
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15
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Kellett T, Noor R, Zhou Q, Esquer H, Sala R, Stojanovic P, Rudolph J, Luger K, LaBarbera DV. HTS discovery of PARP1-HPF1 complex inhibitors in cancer. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2023; 28:394-401. [PMID: 37844763 PMCID: PMC10872402 DOI: 10.1016/j.slasd.2023.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/09/2023] [Accepted: 10/11/2023] [Indexed: 10/18/2023]
Abstract
PARP1/2 inhibitors (PARPi) are effective clinically used drugs for the treatment of cancers with BRCA deficiencies. PARPi have had limited success and applicability beyond BRCA deficient cancers, and their effect is diminished by resistance mechanisms. The recent discovery of Histone PARylation Factor (HPF1) and the role it plays in the PARylation reaction by forming a shared active site with PARP1 raises the possibility that novel inhibitors that target the PARP1-HPF1 complex can be identified. Herein we describe a simple and cost-effective high-throughput screening (HTS) method aimed at discovering inhibitors of the PARP1-HPF1 complex. Upon HTS validation, we first applied this method to screen a small PARP-focused library of compounds and then scale up our approach using robotic automation to conduct a pilot screen of 10,000 compounds and validating >100 hits. This work demonstrates for the first time the capacity to discover potent inhibitors of the PARP1-HPF1 complex, which may have utility as probes to better understand the DNA damage response and as therapeutics for cancer.
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Affiliation(s)
- Timothy Kellett
- Department of Pharmaceutical Sciences, The Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus (CU AMC), Aurora, CO, USA
| | - Rida Noor
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Qiong Zhou
- Department of Pharmaceutical Sciences, The Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus (CU AMC), Aurora, CO, USA; The CU AMC Center for Drug Discovery, Aurora, CO, USA
| | - Hector Esquer
- Department of Pharmaceutical Sciences, The Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus (CU AMC), Aurora, CO, USA; The CU AMC Center for Drug Discovery, Aurora, CO, USA
| | - Rita Sala
- Department of Pharmaceutical Sciences, The Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus (CU AMC), Aurora, CO, USA
| | - Petra Stojanovic
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Johannes Rudolph
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Karolin Luger
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA; Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA.
| | - Daniel V LaBarbera
- Department of Pharmaceutical Sciences, The Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus (CU AMC), Aurora, CO, USA; The CU AMC Center for Drug Discovery, Aurora, CO, USA; The University of Colorado Cancer Center, Aurora, CO, USA.
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16
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Stephens EN, Zhang XN, Lam AT, Li J, Pei H, Louie SG, Wang CCC, Zhang Y. A ribose-functionalized NAD + with versatile activity for ADP-ribosylation. Chem Commun (Camb) 2023; 59:13843-13846. [PMID: 37921487 PMCID: PMC10841986 DOI: 10.1039/d3cc04343f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
An NAD+ featuring an adenosyl 4'-azido functions as a general substrate for poly-ADP-ribose polymerases. Its derived mono- and poly-ADP-ribosylated proteins can be adequately recognized by distinct ADP-ribosylation-specific readers. This molecule represents the first ribose-functionalized NAD+ with versatile activities across different ADP-ribosyltransferases and provides insight into developing new probes for ADP-ribosylation.
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Affiliation(s)
- Elisa N Stephens
- Department of Pharmacology and Pharmaceutical Sciences, Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089, USA.
| | - Xiao-Nan Zhang
- Department of Pharmacology and Pharmaceutical Sciences, Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089, USA.
| | - Albert T Lam
- Department of Pharmacology and Pharmaceutical Sciences, Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089, USA.
| | - Jiawei Li
- Department of Pharmacology and Pharmaceutical Sciences, Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089, USA.
| | - Hua Pei
- Titus Family Department of Clinical Pharmacy, Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Stan G Louie
- Titus Family Department of Clinical Pharmacy, Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA
| | - Clay C C Wang
- Department of Pharmacology and Pharmaceutical Sciences, Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089, USA.
- Department of Chemistry, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Yong Zhang
- Department of Pharmacology and Pharmaceutical Sciences, Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089, USA.
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA
- Department of Chemistry, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA 90089, USA
- Research Center for Liver Diseases, University of Southern California, Los Angeles, CA 90089, USA
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17
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Tayanloo-Beik A, Hamidpour SK, Nikkhah A, Arjmand R, Mafi AR, Rezaei-Tavirani M, Larijani B, Gilany K, Arjmand B. DNA Damage Responses, the Trump Card of Stem Cells in the Survival Game. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023. [PMID: 37923882 DOI: 10.1007/5584_2023_791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2023]
Abstract
Stem cells, as a group of undifferentiated cells, are enriched with self-renewal and high proliferative capacity, which have attracted the attention of many researchers as a promising approach in the treatment of many diseases over the past years. However, from the cellular and molecular point of view, the DNA repair system is one of the biggest challenges in achieving therapeutic goals through stem cell technology. DNA repair mechanisms are an advantage for stem cells that are constantly multiplying to deal with various types of DNA damage. However, this mechanism can be considered a trump card in the game of cell survival and treatment resistance in cancer stem cells, which can hinder the curability of various types of cancer. Therefore, getting a deep insight into the DNA repair system can bring researchers one step closer to achieving major therapeutic goals. The remarkable thing about the DNA repair system is that this system is not only under the control of genetic factors, but also under the control of epigenetic factors. Therefore, it is necessary to investigate the role of the DNA repair system in maintaining the survival of cancer stem cells from both aspects.
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Affiliation(s)
- Akram Tayanloo-Beik
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Amirabbas Nikkhah
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Rasta Arjmand
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Ahmad Rezazadeh Mafi
- Department of Radiation Oncology, Imam Hossein Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Bagher Larijani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical sciences, Tehran, Iran
| | - Kambiz Gilany
- Integrative Oncology Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
- Reproductive Immunology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Babak Arjmand
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.
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18
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Mateos-Pujante A, Jiménez MC, Andreu I. Assessment of the PARP inhibitor talazoparib photosafety profile. Biomed Pharmacother 2023; 167:115593. [PMID: 37793275 DOI: 10.1016/j.biopha.2023.115593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/06/2023] Open
Abstract
Talazoparib (TLZ) is a poly(adenosine diphosphate [ADP]-ribose) polymerase inhibitor employed for the treatment of breast cancer. This drug displays an absorption band in the UVA region, and therefore investigation of the possible phototoxic side-effects associated to its administration results of enormous relevance. In this context, we describe here a photochemical and photobiological study to ascertain the photosafety profile of TLZ. Concerning transient species, the singlet and triplet excited states of TLZ were detected by fluorescence (λmax em = 440 nm) and laser flash photolysis experiments (λmax abs = 400 nm), respectively. Remarkably, TLZ irradiation with UVA light in aqueous solution resulted in formation of a stable photooxidated product, TLZ-P, whose absorption band is extended until the visible region. From in vitro experiments, phototoxicity was revealed for the parent drug by neutral red uptake (NRU) assays, with a PIF value of ca 7; besides, TLZ induced formation of reactive oxygen species (ROS) and produced significant damage to both proteins and DNA. By contrast, the singlet and triplet excited states of TLZ-P were not detected, and no photodamage was observed in the NRU experiments. Overall, the results indicate that TLZ induces phototoxicity, whereas its photoproduct exhibits photosafety.
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Affiliation(s)
- Alejandro Mateos-Pujante
- Departamento de Química, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain; Unidad Mixta de Investigación Universitat Politècnica de València -Instituto de Investigación Sanitaria (IIS) La Fe, Hospital Universitari i Politècnic La Fe, Avenida de Fernando Abril Martorell 106, 46026 Valencia, Spain
| | - M Consuelo Jiménez
- Departamento de Química, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain; Unidad Mixta de Investigación Universitat Politècnica de València -Instituto de Investigación Sanitaria (IIS) La Fe, Hospital Universitari i Politècnic La Fe, Avenida de Fernando Abril Martorell 106, 46026 Valencia, Spain.
| | - Inmaculada Andreu
- Departamento de Química, Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain; Unidad Mixta de Investigación Universitat Politècnica de València -Instituto de Investigación Sanitaria (IIS) La Fe, Hospital Universitari i Politècnic La Fe, Avenida de Fernando Abril Martorell 106, 46026 Valencia, Spain.
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19
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Grand RJ. SARS-CoV-2 and the DNA damage response. J Gen Virol 2023; 104:001918. [PMID: 37948194 PMCID: PMC10768691 DOI: 10.1099/jgv.0.001918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023] Open
Abstract
The recent coronavirus disease 2019 (COVID-19) pandemic was caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 is characterized by respiratory distress, multiorgan dysfunction and, in some cases, death. The virus is also responsible for post-COVID-19 condition (commonly referred to as 'long COVID'). SARS-CoV-2 is a single-stranded, positive-sense RNA virus with a genome of approximately 30 kb, which encodes 26 proteins. It has been reported to affect multiple pathways in infected cells, resulting, in many cases, in the induction of a 'cytokine storm' and cellular senescence. Perhaps because it is an RNA virus, replicating largely in the cytoplasm, the effect of SARS-Cov-2 on genome stability and DNA damage responses (DDRs) has received relatively little attention. However, it is now becoming clear that the virus causes damage to cellular DNA, as shown by the presence of micronuclei, DNA repair foci and increased comet tails in infected cells. This review considers recent evidence indicating how SARS-CoV-2 causes genome instability, deregulates the cell cycle and targets specific components of DDR pathways. The significance of the virus's ability to cause cellular senescence is also considered, as are the implications of genome instability for patients suffering from long COVID.
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Affiliation(s)
- Roger J. Grand
- Institute for Cancer and Genomic Science, The Medical School, University of Birmingham, Birmingham, UK
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20
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Chen H, Hu Y, Zhuang Z, Wang D, Ye Z, Jing J, Cheng X. Advancements and Obstacles of PARP Inhibitors in Gastric Cancer. Cancers (Basel) 2023; 15:5114. [PMID: 37958290 PMCID: PMC10647262 DOI: 10.3390/cancers15215114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 10/10/2023] [Accepted: 10/12/2023] [Indexed: 11/15/2023] Open
Abstract
Gastric cancer (GC) is a common and aggressive cancer of the digestive system, exhibiting high aggressiveness and significant heterogeneity. Despite advancements in improving survival rates over the past few decades, GC continues to carry a worrisome prognosis and notable mortality. As a result, there is an urgent need for novel therapeutic approaches to address GC. Recent targeted sequencing studies have revealed frequent mutations in DNA damage repair (DDR) pathway genes in many GC patients. These mutations lead to an increased reliance on poly (adenosine diphosphate-ribose) polymerase (PARP) for DNA repair, making PARP inhibitors (PARPi) a promising treatment option for GC. This article presents a comprehensive overview of the rationale and development of PARPi, highlighting its progress and challenges in both preclinical and clinical research for treating GC.
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Affiliation(s)
- Hongjie Chen
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China; (H.C.); (Y.H.); (D.W.)
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China;
| | - Yangchan Hu
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China; (H.C.); (Y.H.); (D.W.)
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China;
| | - Zirui Zhuang
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China;
- School of Molecular Medicine, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences (UCAS), Hangzhou 310024, China
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Dingyi Wang
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China; (H.C.); (Y.H.); (D.W.)
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China;
| | - Zu Ye
- Department of Gastric Surgery, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China;
- Zhejiang Key Laboratory of Prevention, Diagnosis and Therapy of Upper Gastrointestinal Cancer, Hangzhou 310022, China
| | - Ji Jing
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China;
- Zhejiang Key Laboratory of Prevention, Diagnosis and Therapy of Upper Gastrointestinal Cancer, Hangzhou 310022, China
| | - Xiangdong Cheng
- Department of Gastric Surgery, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China;
- Zhejiang Key Laboratory of Prevention, Diagnosis and Therapy of Upper Gastrointestinal Cancer, Hangzhou 310022, China
- Zhejiang Provincial Research Center for Upper Gastrointestinal Tract Cancer, Zhejiang Cancer Hospital, Hangzhou 310022, China
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21
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Salbaum JM, Stone KP, Kruger C, Kappen C. Differential responses to maternal diabetes in embryo and visceral yolk sac. Front Cell Dev Biol 2023; 11:1273641. [PMID: 37928898 PMCID: PMC10620973 DOI: 10.3389/fcell.2023.1273641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 10/02/2023] [Indexed: 11/07/2023] Open
Abstract
Introduction: Maternal diabetes during pregnancy is well known to be associated with a higher risk for structural birth defects in the offspring. Recent searches for underlying mechanisms have largely focused on aberrant processes in the embryo itself, although prior research in rodent models implicated dysfunction also of the visceral yolk sac. The objective of our research was to investigate both tissues within the conceptus simultaneously. Methods: We conducted unbiased transcriptome profiling by RNA sequencing on pairs of individual yolk sacs and their cognate embryos, using the non-obese diabetic (NOD) mouse model. The analysis was performed at gestational day 8.5 on morphologically normal specimen to circumvent confounding by defective development. Results: Even with large sample numbers (n = 33 in each group), we observed considerable variability of gene expression, primarily driven by exposure to maternal diabetes, and secondarily by developmental stage of the embryo. Only a moderate number of genes changed expression in the yolk sac, while in the embryo, the exposure distinctly influenced the relationship of gene expression levels to developmental progression, revealing a possible role for altered cell cycle regulation in the response. Also affected in embryos under diabetic conditions were genes involved in cholesterol biosynthesis and NAD metabolism pathways. Discussion: Exposure to maternal diabetes during gastrulation changes transcriptomic profiles in embryos to a substantially greater effect than in the corresponding yolk sacs, indicating that despite yolk sac being of embryonic origin, different mechanisms control transcriptional activity in these tissues. The effects of maternal diabetes on expression of many genes that are correlated with developmental progression (i.e. somite stage) highlight the importance of considering developmental maturity in the interpretation of transcriptomic data. Our analyses identified cholesterol biosynthesis and NAD metabolism as novel pathways not previously implicated in diabetic pregnancies. Both NAD and cholesterol availability affect a wide variety of cellular signaling processes, and can be modulated by diet, implying that prevention of adverse outcomes from diabetic pregnancies may require broad interventions, particularly in the early stages of pregnancy.
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Affiliation(s)
- J. Michael Salbaum
- Department of Regulation of Gene Expression, Pennington Biomedical Research Center, Louisiana State University System, Baton Rouge, LA, United States
| | - Kirsten P. Stone
- Department of Developmental Biology, Pennington Biomedical Research Center, Louisiana State University System, Baton Rouge, LA, United States
| | - Claudia Kruger
- Department of Developmental Biology, Pennington Biomedical Research Center, Louisiana State University System, Baton Rouge, LA, United States
| | - Claudia Kappen
- Department of Developmental Biology, Pennington Biomedical Research Center, Louisiana State University System, Baton Rouge, LA, United States
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22
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Pei J, Zhang J, Wang XD, Kim C, Yu Y, Cong Q. Impact of Asp/Glu-ADP-ribosylation on protein-protein interaction and protein function. Proteomics 2023; 23:e2200083. [PMID: 36453556 PMCID: PMC10362910 DOI: 10.1002/pmic.202200083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/12/2022] [Accepted: 11/10/2022] [Indexed: 12/04/2022]
Abstract
PARylation plays critical role in regulating multiple cellular processes such as DNA damage response and repair, transcription, RNA processing, and stress response. More than 300 human proteins have been found to be modified by PARylation on acidic residues, that is, Asp (D) and Glu (E). We used the deep-learning tool AlphaFold to predict protein-protein interactions (PPIs) and their interfaces for these proteins based on coevolution signals from joint multiple sequence alignments (MSAs). AlphaFold predicted 260 confident PPIs involving PARylated proteins, and about one quarter of these PPIs have D/E-PARylation sites in their predicted PPI interfaces. AlphaFold predictions offer novel insights into the mechanisms of PARylation regulations by providing structural details of the PPI interfaces. D/E-PARylation sites have a preference to occur in coil regions and disordered regions, and PPI interfaces containing D/E-PARylation sites tend to occur between short linear sequence motifs in disordered regions and globular domains. The hub protein PCNA is predicted to interact with more than 20 proteins via the common PIP box motif and the structurally variable flanking regions. D/E-PARylation sites were found in the interfaces of key components of the RNA transcription and export complex, the SF3a spliceosome complex, and H/ACA and C/D small nucleolar ribonucleoprotein complexes, suggesting that systematic PARylation have a profound effect in regulating multiple RNA-related processes such as RNA nuclear export, splicing, and modification. Finally, PARylation of SUMO2 could modulate its interaction with CHAF1A, thereby representing a potential mechanism for the cross-talk between PARylation and SUMOylation in regulation of chromatin remodeling.
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Affiliation(s)
- Jimin Pei
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jing Zhang
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xu-Dong Wang
- Department of Molecular Pharmacology and Therapeutics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Chiho Kim
- Department of Molecular Pharmacology and Therapeutics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Yonghao Yu
- Department of Molecular Pharmacology and Therapeutics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Qian Cong
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
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23
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Lewicky JD, Martel AL, Gupta MR, Roy R, Rodriguez GM, Vanderhyden BC, Le HT. Conventional DNA-Damaging Cancer Therapies and Emerging cGAS-STING Activation: A Review and Perspectives Regarding Immunotherapeutic Potential. Cancers (Basel) 2023; 15:4127. [PMID: 37627155 PMCID: PMC10453198 DOI: 10.3390/cancers15164127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/10/2023] [Accepted: 08/11/2023] [Indexed: 08/27/2023] Open
Abstract
Many traditional cancer treatments such as radiation and chemotherapy are known to induce cellular DNA damage as part of their cytotoxic activity. The cGAS-STING signaling axis, a key member of the DNA damage response that acts as a sensor of foreign or aberrant cytosolic DNA, is helping to rationalize the DNA-damaging activity of these treatments and their emerging immunostimulatory capacity. Moreover, cGAS-STING, which is attracting considerable attention for its ability to promote antitumor immune responses, may fundamentally be able to address many of the barriers limiting the success of cancer immunotherapy strategies, including the immunosuppressive tumor microenvironment. Herein, we review the traditional cancer therapies that have been linked with cGAS-STING activation, highlighting their targets with respect to their role and function in the DNA damage response. As part of the review, an emerging "chemoimmunotherapy" concept whereby DNA-damaging agents are used for the indirect activation of STING is discussed as an alternative to the direct molecular agonism strategies that are in development, but have yet to achieve clinical approval. The potential of this approach to address some of the inherent and emerging limitations of cGAS-STING signaling in cancer immunotherapy is also discussed. Ultimately, it is becoming clear that in order to successfully employ the immunotherapeutic potential of the cGAS-STING axis, a balance between its contrasting antitumor and protumor/inflammatory activities will need to be achieved.
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Affiliation(s)
- Jordan D. Lewicky
- Health Sciences North Research Institute, 56 Walford Road, Sudbury, ON P3E 2H2, Canada; (J.D.L.); (A.L.M.)
| | - Alexandrine L. Martel
- Health Sciences North Research Institute, 56 Walford Road, Sudbury, ON P3E 2H2, Canada; (J.D.L.); (A.L.M.)
| | - Mukul Raj Gupta
- Glycosciences and Nanomaterial Laboratory, Université du Québec à Montréal, Succ. Centre-Ville, Montréal, QC H3C 3P8, Canada; (M.R.G.); (R.R.)
| | - René Roy
- Glycosciences and Nanomaterial Laboratory, Université du Québec à Montréal, Succ. Centre-Ville, Montréal, QC H3C 3P8, Canada; (M.R.G.); (R.R.)
| | - Galaxia M. Rodriguez
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, 501 Smyth Rd., Ottawa, ON K1H 8L6, Canada; (G.M.R.); (B.C.V.)
- Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Rd., Ottawa, ON K1H 8M5, Canada
| | - Barbara C. Vanderhyden
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, 501 Smyth Rd., Ottawa, ON K1H 8L6, Canada; (G.M.R.); (B.C.V.)
- Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Rd., Ottawa, ON K1H 8M5, Canada
| | - Hoang-Thanh Le
- Health Sciences North Research Institute, 56 Walford Road, Sudbury, ON P3E 2H2, Canada; (J.D.L.); (A.L.M.)
- Medicinal Sciences Division, NOSM University, 935 Ramsey Lake Road, Sudbury, ON P3E 2C6, Canada
- School of Natural Sciences, Laurentian University, 935 Ramsey Lake Road, Sudbury, ON P3E 2C6, Canada
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24
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Stojanovic P, Luger K, Rudolph J. Slow Dissociation from the PARP1-HPF1 Complex Drives Inhibitor Potency. Biochemistry 2023; 62:2382-2390. [PMID: 37531469 PMCID: PMC10433523 DOI: 10.1021/acs.biochem.3c00243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/13/2023] [Indexed: 08/04/2023]
Abstract
PARP1, upon binding to damaged DNA, is activated to perform poly ADP-ribosylation (PARylation) on itself and other proteins, which leads to relaxation of chromatin and recruitment of DNA repair factors. HPF1 was recently discovered as a protein cofactor of PARP1 that directs preferential PARylation of histones over other targets by contributing to and altering the PARP1 active site. Inhibitors of PARP1 (PARPi) are used in the treatment of BRCA-/- cancers, but the basis for their potency in cells, especially in the context of HPF1, is not fully understood. Here, we demonstrate the simple one-step association for eight different PARPi to PARP1 with measured rates of association (kon) of 0.8-6 μM-1 s-1. We find only minor differences in these on rates when comparing PARP1 with the PARP1-HPF1 complex. By characterizing the rates of dissociation (koff) and the binding constants (KD) for two more recently discovered PARPi, we find, for example, that saruparib has a half-life for dissociation of 22.5 h and fluzoparib has higher affinity for PARP1 in the presence of HPF1, just like the structurally related compound olaparib. By using the measured KD and kon to calculate koff, we find that the potency of PARPi in cells correlates best with the koff from the PARP1-HPF1 complex. Our data suggest that dissociation of a drug compound from the PARP1-HPF1 complex should be the parameter of choice for guiding the development of next-generation PARPi.
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Affiliation(s)
- Petra Stojanovic
- Department
of Biochemistry, University of Colorado
Boulder, Boulder, Colorado 80309, United States
| | - Karolin Luger
- Department
of Biochemistry, University of Colorado
Boulder, Boulder, Colorado 80309, United States
- Howard
Hughes Medical Institute, University of
Colorado Boulder, Boulder, Colorado 80309, United States
| | - Johannes Rudolph
- Department
of Biochemistry, University of Colorado
Boulder, Boulder, Colorado 80309, United States
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25
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Miller AL, James RE, Harvey AR, Trifunović D, Carvalho LS. The role of epigenetic changes in the pathology and treatment of inherited retinal diseases. Front Cell Dev Biol 2023; 11:1224078. [PMID: 37601102 PMCID: PMC10436478 DOI: 10.3389/fcell.2023.1224078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/20/2023] [Indexed: 08/22/2023] Open
Abstract
Elucidation of the cellular changes that occur in degenerating photoreceptors of people with inherited retinal diseases (IRDs) has been a focus for many research teams, leading to numerous theories on how these changes affect the cell death process. What is clearly emerging from these studies is that there are common denominators across multiple models of IRD, regardless of the underlying genetic mutation. These common markers could open avenues for broad neuroprotective therapeutics to prevent photoreceptor loss and preserve functional vision. In recent years, the role of epigenetic modifications contributing to the pathology of IRDs has been a particular point of interest, due to many studies noting changes in these epigenetic modifications, which coincide with photoreceptor cell death. This review will discuss the two broad categories of epigenetic changes, DNA methylation and histone modifications, that have received particular attention in IRD models. We will review the altered epigenetic regulatory events that are believed to contribute to cell death in IRDs and discuss the therapeutic potential of targeting these alterations.
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Affiliation(s)
- Annie L. Miller
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Crawley, WA, Australia
- Retinal Genomics and Therapy Laboratory, Lions Eye Institute, Nedlands, WA, Australia
| | - Rebekah E. James
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Crawley, WA, Australia
- Retinal Genomics and Therapy Laboratory, Lions Eye Institute, Nedlands, WA, Australia
| | - Alan R. Harvey
- Retinal Genomics and Therapy Laboratory, Lions Eye Institute, Nedlands, WA, Australia
- School of Human Sciences, The University of Western Australia, Crawley, WA, Australia
- Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia
| | - Dragana Trifunović
- Institute for Ophthalmic Research, Tubingen University, Tübingen, Germany
| | - Livia S. Carvalho
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Crawley, WA, Australia
- Retinal Genomics and Therapy Laboratory, Lions Eye Institute, Nedlands, WA, Australia
- Department of Optometry and Vision Sciences, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC, Australia
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26
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Lovsund T, Mashayekhi F, Fitieh A, Stafford J, Ismail IH. Unravelling the Role of PARP1 in Homeostasis and Tumorigenesis: Implications for Anti-Cancer Therapies and Overcoming Resistance. Cells 2023; 12:1904. [PMID: 37508568 PMCID: PMC10378431 DOI: 10.3390/cells12141904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/14/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Detailing the connection between homeostatic functions of enzymatic families and eventual progression into tumorigenesis is crucial to our understanding of anti-cancer therapies. One key enzyme group involved in this process is the Poly (ADP-ribose) polymerase (PARP) family, responsible for an expansive number of cellular functions, featuring members well established as regulators of DNA repair, genomic stability and beyond. Several PARP inhibitors (PARPi) have been approved for clinical use in a range of cancers, with many more still in trials. Unfortunately, the occurrence of resistance to PARPi therapy is growing in prevalence and requires the introduction of novel counter-resistance mechanisms to maintain efficacy. In this review, we summarize the updated understanding of the vast homeostatic functions the PARP family mediates and pin the importance of PARPi therapies as anti-cancer agents while discussing resistance mechanisms and current up-and-coming counter-strategies for countering such resistance.
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Affiliation(s)
- Taylor Lovsund
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta, 11560 University Avenue, Edmonton, AB T6G 1Z2, Canada
| | - Fatemeh Mashayekhi
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta, 11560 University Avenue, Edmonton, AB T6G 1Z2, Canada
| | - Amira Fitieh
- Department of Biophysics, Faculty of Science, Cairo University, Giza 12613, Egypt
| | - James Stafford
- Department of Biological Sciences, Faculty of Science, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Ismail Hassan Ismail
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta, 11560 University Avenue, Edmonton, AB T6G 1Z2, Canada
- Department of Biophysics, Faculty of Science, Cairo University, Giza 12613, Egypt
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27
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Wan A, Zhang G, Ma D, Zhang Y, Qi X. An overview of the research progress of BRCA gene mutations in breast cancer. Biochim Biophys Acta Rev Cancer 2023; 1878:188907. [PMID: 37172654 DOI: 10.1016/j.bbcan.2023.188907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 04/14/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023]
Abstract
The breast cancer susceptibility gene (BRCA) is an important tumor suppressor gene, including BRCA1 and BRCA2, a biomarker that assesses the risk of breast cancer and influences a patient's individualized treatment options. BRCA1/2 mutation (BRCAm) increases the risk of breast cancer. However, breast-conserving surgery is still an option for BRCAm, and prophylactic mastectomy and nipple-sparing mastectomy may also reduce the risk of breast cancer. BRCAm is sensitive to Poly (ADP-ribose) polymerase inhibitor (PARPi) therapy due to specific types of DNA repair defects, and its combination with other DNA damage pathway inhibitors and endocrine therapy and immunotherapy are also used for the treatment of BRCAm breast cancer. The current treatment and research progress of BRCA1/2 mutant breast cancer in this review provides a basis for the individualized treatment of patients with this type of breast cancer.
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Affiliation(s)
- Andi Wan
- Department of Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing, China
| | - Guozhi Zhang
- Department of Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing, China
| | - Dandan Ma
- Department of Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing, China
| | - Yi Zhang
- Department of Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing, China
| | - Xiaowei Qi
- Department of Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing, China.
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28
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Duma L, Ahel I. The function and regulation of ADP-ribosylation in the DNA damage response. Biochem Soc Trans 2023; 51:995-1008. [PMID: 37171085 PMCID: PMC10317172 DOI: 10.1042/bst20220749] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/27/2023] [Accepted: 05/02/2023] [Indexed: 05/13/2023]
Abstract
ADP-ribosylation is a post-translational modification involved in DNA damage response (DDR). In higher organisms it is synthesised by PARP 1-3, DNA strand break sensors. Recent advances have identified serine residues as the most common targets for ADP-ribosylation during DDR. To ADP-ribosylate serine, PARPs require an accessory factor, HPF1 which completes the catalytic domain. Through ADP-ribosylation, PARPs recruit a variety of factors to the break site and control their activities. However, the timely removal of ADP-ribosylation is also key for genome stability and is mostly performed by two hydrolases: PARG and ARH3. Here, we describe the key writers, readers and erasers of ADP-ribosylation and their contribution to the mounting of the DDR. We also discuss the use of PARP inhibitors in cancer therapy and the ways to tackle PARPi treatment resistance.
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Affiliation(s)
- Lena Duma
- Sir William Dunn School of Pathology, University of Oxford, Oxford, U.K
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, U.K
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29
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Tisseverasinghe S, Bahoric B, Anidjar M, Probst S, Niazi T. Advances in PARP Inhibitors for Prostate Cancer. Cancers (Basel) 2023; 15:cancers15061849. [PMID: 36980735 PMCID: PMC10046616 DOI: 10.3390/cancers15061849] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/12/2023] [Accepted: 03/14/2023] [Indexed: 03/30/2023] Open
Abstract
Poly-adenosine diphosphate-ribose polymerase plays an essential role in cell function by regulating apoptosis, genomic stability and DNA repair. PARPi is a promising drug class that has gained significant traction in the last decade with good outcomes in different cancers. Several trials have sought to test its effectiveness in metastatic castration resistant prostate cancer (mCRPC). We conducted a comprehensive literature review to evaluate the current role of PARPi in this setting. To this effect, we conducted queries in the PubMed, Embase and Cochrane databases. We reviewed and compared all major contemporary publications on the topic. In particular, recent phase II and III studies have also demonstrated the benefits of olaparib, rucaparib, niraparib, talazoparib in CRPC. Drug effectiveness has been assessed through radiological progression or overall response. Given the notion of synthetic lethality and potential synergy with other oncological therapies, several trials are looking to integrate PARPi in combined therapies. There remains ongoing controversy on the need for genetic screening prior to treatment initiation as well as the optimal patient population, which would benefit most from PARPi. PARPi is an important asset in the oncological arsenal for mCRPC. New combinations with PARPi may improve outcomes in earlier phases of prostate cancer.
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Affiliation(s)
| | - Boris Bahoric
- Department of Radiation Oncology, McGill University, Montreal, QC H3A 0G4, Canada
| | - Maurice Anidjar
- Department of Urology, McGill University, Montreal, QC H3A 0G4, Canada
| | - Stephan Probst
- Department of Nuclear Medicine, McGill University, Montreal, QC H3A 0G4, Canada
| | - Tamim Niazi
- Department of Radiation Oncology, McGill University, Montreal, QC H3A 0G4, Canada
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30
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New Approaches in Early-Stage NSCL Management: Potential Use of PARP Inhibitors and Immunotherapy Combination. Int J Mol Sci 2023; 24:ijms24044044. [PMID: 36835456 PMCID: PMC9961654 DOI: 10.3390/ijms24044044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/05/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023] Open
Abstract
Lung cancer is the second most common cancer in the world, being the first cause of cancer-related mortality. Surgery remains the only potentially curative treatment for Non-Small Cell Lung Cancer (NSCLC), but the recurrence risk remains high (30-55%) and Overall Survival (OS) is still lower than desirable (63% at 5 years), even with adjuvant treatment. Neoadjuvant treatment can be helpful and new therapies and pharmacologic associations are being studied. Immune Checkpoint Inhibitors (ICI) and PARP inhibitors (PARPi) are two pharmacological classes already in use to treat several cancers. Some pre-clinical studies have shown that its association can be synergic and this is being studied in different settings. Here, we review the PARPi and ICI strategies in cancer management and the information will be used to develop a clinical trial to evaluate the potential of PARPi association with ICI in early-stage neoadjuvant setting NSCLC.
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31
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Dutta S, Ganguly A, Chatterjee K, Spada S, Mukherjee S. Targets of Immune Escape Mechanisms in Cancer: Basis for Development and Evolution of Cancer Immune Checkpoint Inhibitors. BIOLOGY 2023; 12:biology12020218. [PMID: 36829496 PMCID: PMC9952779 DOI: 10.3390/biology12020218] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/22/2023] [Accepted: 01/27/2023] [Indexed: 02/03/2023]
Abstract
Immune checkpoint blockade (ICB) has emerged as a novel therapeutic tool for cancer therapy in the last decade. Unfortunately, a small number of patients benefit from approved immune checkpoint inhibitors (ICIs). Therefore, multiple studies are being conducted to find new ICIs and combination strategies to improve the current ICIs. In this review, we discuss some approved immune checkpoints, such as PD-L1, PD-1, and CTLA-4, and also highlight newer emerging ICIs. For instance, HLA-E, overexpressed by tumor cells, represents an immune-suppressive feature by binding CD94/NKG2A, on NK and T cells. NKG2A blockade recruits CD8+ T cells and activates NK cells to decrease the tumor burden. NKG2D acts as an NK cell activating receptor that can also be a potential ICI. The adenosine A2A and A2B receptors, CD47-SIRPα, TIM-3, LAG-3, TIGIT, and VISTA are targets that also contribute to cancer immunoresistance and have been considered for clinical trials. Their antitumor immunosuppressive functions can be used to develop blocking antibodies. PARPs, mARTs, and B7-H3 are also other potential targets for immunosuppression. Additionally, miRNA, mRNA, and CRISPR-Cas9-mediated immunotherapeutic approaches are being investigated with great interest. Pre-clinical and clinical studies project these targets as potential immunotherapeutic candidates in different cancer types for their robust antitumor modulation.
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Affiliation(s)
- Shovan Dutta
- The Center for Immunotherapy & Precision Immuno-Oncology (CITI), Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Anirban Ganguly
- Department of Biochemistry, All India Institute of Medical Sciences, Deoghar 814152, India
| | | | - Sheila Spada
- Department of Radiation Oncology, Weill Cornell Medicine, New York, NY 10065, USA
- Correspondence: (S.S.); (S.M.)
| | - Sumit Mukherjee
- Department of Cardiothoracic and Vascular Surgery, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Correspondence: (S.S.); (S.M.)
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32
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Löffler T, Krüger A, Zirak P, Winterhalder MJ, Müller AL, Fischbach A, Mangerich A, Zumbusch A. Influence of chain length and branching on poly(ADP-ribose)-protein interactions. Nucleic Acids Res 2023; 51:536-552. [PMID: 36625274 PMCID: PMC9881148 DOI: 10.1093/nar/gkac1235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 11/16/2022] [Accepted: 12/10/2022] [Indexed: 01/11/2023] Open
Abstract
Hundreds of proteins interact with poly(ADP-ribose) (PAR) via multiple PAR interaction motifs, thereby regulating their physico-chemical properties, sub-cellular localizations, enzymatic activities, or protein stability. Here, we present a targeted approach based on fluorescence correlation spectroscopy (FCS) to characterize potential structure-specific interactions of PAR molecules of defined chain length and branching with three prime PAR-binding proteins, the tumor suppressor protein p53, histone H1, and the histone chaperone APLF. Our study reveals complex and structure-specific PAR-protein interactions. Quantitative Kd values were determined and binding affinities for all three proteins were shown to be in the nanomolar range. We report PAR chain length dependent binding of p53 and H1, yet chain length independent binding of APLF. For all three PAR binders, we found a preference for linear over hyperbranched PAR. Importantly, protein- and PAR-structure-specific binding modes were revealed. Thus, while the H1-PAR interaction occurred largely on a bi-molecular 1:1 basis, p53-and potentially also APLF-can form complex multivalent PAR-protein structures. In conclusion, our study gives detailed and quantitative insight into PAR-protein interactions in a solution-based setting at near physiological buffer conditions. The results support the notion of protein and PAR-structure-specific binding modes that have evolved to fit the purpose of the respective biochemical functions and biological contexts.
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Affiliation(s)
| | | | - Peyman Zirak
- Department of Chemistry, Universität Konstanz, Konstanz D-78457, Germany
| | | | - Anna-Lena Müller
- Department of Chemistry, Universität Konstanz, Konstanz D-78457, Germany
| | - Arthur Fischbach
- Department of Biology, Universität Konstanz, Konstanz D-78457, Germany
| | - Aswin Mangerich
- To whom correspondence should be addressed. Tel: +49 33200 88 5301;
| | - Andreas Zumbusch
- Correspondence may also be addressed to Andreas Zumbusch. Tel: +49 7531 882027;
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Krishnan Muthaiah VP, Kaliyappan K, Mahajan SD. Poly ADP-Ribose Polymerase-1 inhibition by 3-aminobenzamide recuperates HEI-OC1 auditory hair cells from blast overpressure-induced cell death. Front Cell Dev Biol 2023; 11:1047308. [PMID: 36949771 PMCID: PMC10025353 DOI: 10.3389/fcell.2023.1047308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 01/30/2023] [Indexed: 03/08/2023] Open
Abstract
Introduction: Poly ADP-Ribose Polymerase-1 (PARP1), a DNA repair enzyme is implicated as a key molecule in the pathogenesis of several neurodegenerative disorders. Traumatic insults inducing oxidative stress results in its over-activation causing inflammation and cell death (Parthanatos). As PARP1 inhibition is known to reduce oxidative stress, we hypothesized that PARP1 inhibition by a known inhibitor 3-aminobenzamide (3AB) might recuperate the damage in an in vitro model of blast injury using HEI-OC1 cells (mouse auditory hair cells). Methods: Here, we evaluated the protective effect of 3AB on HEI-OC1 cells following single and repetitive blast overpressures (BOPs). Results: We found that inhibition of PARP1 b 3AB inhibits the PARP1 enzyme and its action of a post-translational modification i.e. formation of Poly ADP-Ribose Polymers which leads to massive ATP depletion. PARP inhibition (3AB treatment) reduced the oxidative stress (4HNE, a marker of lipid peroxidation, and 8OHdG, a marker of oxidative DNA damage) in cells exposed to single/repetitive BOPS through up-regulation of Nrf2, a transcriptional regulator of antioxidant defense and the GCLC, a rate limiting enzyme in the synthesis of glutathione. Discussion: Overall, we found that PARP inhibition by 3AB helps to maintain the viability of BOP-exposed auditory hair cells by recuperating the ATP pool from both mitochondrial and glycolytic sources.
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Affiliation(s)
- Vijaya Prakash Krishnan Muthaiah
- Department of Rehabilitation Sciences, School of Public Health and Health Professions, University at Buffalo, Buffalo, NY, United States
- *Correspondence: Vijaya Prakash Krishnan Muthaiah,
| | - Kathiravan Kaliyappan
- Department of Rehabilitation Sciences, School of Public Health and Health Professions, University at Buffalo, Buffalo, NY, United States
| | - Supriya D. Mahajan
- Department of Medicine, Division of Allergy, Immunology and Rheumatology, State University of New York at Buffalo, Clinical Translational Research Center, Buffalo, NY, United States
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Zhu T, Zheng JY, Huang LL, Wang YH, Yao DF, Dai HB. Human PARP1 substrates and regulators of its catalytic activity: An updated overview. Front Pharmacol 2023; 14:1137151. [PMID: 36909172 PMCID: PMC9995695 DOI: 10.3389/fphar.2023.1137151] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 02/09/2023] [Indexed: 02/25/2023] Open
Abstract
Poly (ADP-ribose) polymerase 1 (PARP1) is a key DNA damage sensor that is recruited to damaged sites after DNA strand breaks to initiate DNA repair. This is achieved by catalyzing attachment of ADP-ribose moieties, which are donated from NAD+, on the amino acid residues of itself or other acceptor proteins. PARP inhibitors (PARPi) that inhibit PARP catalytic activity and induce PARP trapping are commonly used for treating BRCA1/2-deficient breast and ovarian cancers through synergistic lethality. Unfortunately, resistance to PARPi frequently occurs. In this review, we present the novel substrates and regulators of the PARP1-catalyzed poly (ADP-ribosyl)ation (PARylatison) that have been identified in the last 3 years. The overall aim is the presentation of protein interactions of potential therapeutic intervention for overcoming the resistance to PARPi.
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Affiliation(s)
- Tao Zhu
- Department of Pharmacy, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ju-Yan Zheng
- Institute of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
| | - Ling-Ling Huang
- Department of Pharmacy, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yan-Hong Wang
- Department of Pharmacy, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Di-Fei Yao
- Department of Pharmacy, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hai-Bin Dai
- Department of Pharmacy, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Rudolph J, Luger K. Analyzing PARP1 Activity: Small Molecule Reactants and Attached Chains of Poly (ADP-Ribose). Methods Mol Biol 2022; 2609:61-73. [PMID: 36515829 DOI: 10.1007/978-1-0716-2891-1_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We describe a method for analyzing multiple products of PARylation by PARP1 and/or PARP2 using high-pressure liquid chromatography. The method quantitates the small molecules NAD+ (the substrate), nicotinamide (the byproduct of PARylation or hydrolysis of NAD+), and ADPR, the product of NAD+ hydrolysis. The method also quantitates the products of PARylation following digestion of the PAR chains into "ends," "middles," and "branches." This method is useful for dissecting both the activity and the partitioning of PARylation products between different outcomes (i.e., long chains vs. short chains, PARylation vs. hydrolysis).
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Affiliation(s)
- Johannes Rudolph
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Karolin Luger
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA. .,Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA.
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36
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Li R, Luo R, Luo Y, Hou Y, Wang J, Zhang Q, Chen X, Hu L, Zhou J. Biological function, mediate cell death pathway and their potential regulated mechanisms for post-mortem muscle tenderization of PARP1: A review. Front Nutr 2022; 9:1093939. [PMID: 36590225 PMCID: PMC9797534 DOI: 10.3389/fnut.2022.1093939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 11/30/2022] [Indexed: 12/23/2022] Open
Abstract
Tenderness is a key attribute of meat quality that affects consumers' willingness to purchase meat. Changes in the physiological environment of skeletal muscles following slaughter can disrupt the balance of redox homeostasis and may lead to cell death. Excessive accumulation of reactive oxygen species (ROS) in the myocytes causes DNA damage and activates poly ADP-ribose polymerase 1 (PARP1), which is involved in different intracellular metabolic pathways and is known to affect muscle tenderness during post-slaughter maturation. There is an urgent requirement to summarize the related research findings. Thus, this paper reviews the current research on the protein structure of PARP1 and its metabolism and activation, outlines the mechanisms underlying the function of PARP1 in regulating muscle tenderness through cysteine protease 3 (Caspase-3), oxidative stress, heat shock proteins (HSPs), and energy metabolism. In addition, we describe the mechanisms of PARP1 in apoptosis and necrosis pathways to provide a theoretical reference for enhancing the mature technology of post-mortem muscle tenderization.
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Affiliation(s)
- Rong Li
- School of Food and Wine, Ningxia University, Yinchuan, China,National R & D Center for Mutton Processing, Yinchuan, China
| | - Ruiming Luo
- School of Food and Wine, Ningxia University, Yinchuan, China,National R & D Center for Mutton Processing, Yinchuan, China
| | - Yulong Luo
- School of Food and Wine, Ningxia University, Yinchuan, China,National R & D Center for Mutton Processing, Yinchuan, China,*Correspondence: Yulong Luo,
| | - Yanru Hou
- School of Food and Wine, Ningxia University, Yinchuan, China,National R & D Center for Mutton Processing, Yinchuan, China
| | - Jinxia Wang
- School of Food and Wine, Ningxia University, Yinchuan, China,National R & D Center for Mutton Processing, Yinchuan, China
| | - Qian Zhang
- School of Food and Wine, Ningxia University, Yinchuan, China,National R & D Center for Mutton Processing, Yinchuan, China
| | - Xueyan Chen
- School of Food and Wine, Ningxia University, Yinchuan, China,National R & D Center for Mutton Processing, Yinchuan, China
| | - Lijun Hu
- School of Food and Wine, Ningxia University, Yinchuan, China
| | - Julong Zhou
- School of Food and Wine, Ningxia University, Yinchuan, China
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Arnold MR, Langelier MF, Gartrell J, Kirby IT, Sanderson DJ, Bejan DS, Šileikytė J, Sundalam SK, Nagarajan S, Marimuthu P, Duell AK, Shelat AA, Pascal JM, Cohen MS. Allosteric regulation of DNA binding and target residence time drive the cytotoxicity of phthalazinone-based PARP-1 inhibitors. Cell Chem Biol 2022; 29:1694-1708.e10. [PMID: 36493759 DOI: 10.1016/j.chembiol.2022.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 08/31/2022] [Accepted: 11/14/2022] [Indexed: 12/13/2022]
Abstract
Allosteric coupling between the DNA binding site to the NAD+-binding pocket drives PARP-1 activation. This allosteric communication occurs in the reverse direction such that NAD+ mimetics can enhance PARP-1's affinity for DNA, referred to as type I inhibition. The cellular effects of type I inhibition are unknown, largely because of the lack of potent, membrane-permeable type I inhibitors. Here we identify the phthalazinone inhibitor AZ0108 as a type I inhibitor. Unlike the structurally related inhibitor olaparib, AZ0108 induces replication stress in tumorigenic cells. Synthesis of analogs of AZ0108 revealed features of AZ0108 that are required for type I inhibition. One analog, Pip6, showed similar type I inhibition of PARP-1 but was ∼90-fold more cytotoxic than AZ0108. Washout experiments suggest that the enhanced cytotoxicity of Pip6 compared with AZ0108 is due to prolonged target residence time on PARP-1. Pip6 represents a new class of PARP-1 inhibitors that may have unique anticancer properties.
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Affiliation(s)
- Moriah R Arnold
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, 3181 SW Sam Jackson Pk. Rd., Portland, OR 97210, USA
| | - Marie-France Langelier
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Jessica Gartrell
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ilsa T Kirby
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, 3181 SW Sam Jackson Pk. Rd., Portland, OR 97210, USA
| | - Daniel J Sanderson
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, 3181 SW Sam Jackson Pk. Rd., Portland, OR 97210, USA
| | - Daniel S Bejan
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, 3181 SW Sam Jackson Pk. Rd., Portland, OR 97210, USA
| | - Justina Šileikytė
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, 3181 SW Sam Jackson Pk. Rd., Portland, OR 97210, USA
| | - Sunil K Sundalam
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, 3181 SW Sam Jackson Pk. Rd., Portland, OR 97210, USA
| | - Shanthi Nagarajan
- Medicinal Chemistry Core, Oregon Health & Science University, Portland, OR 97210, USA
| | - Parthiban Marimuthu
- Structural Bioinformatics Laboratory, Åbo Akademi University, Faculty of Science and Engineering, 20520 Turku, Finland
| | - Anna K Duell
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, 3181 SW Sam Jackson Pk. Rd., Portland, OR 97210, USA
| | - Anang A Shelat
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - John M Pascal
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Michael S Cohen
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, 3181 SW Sam Jackson Pk. Rd., Portland, OR 97210, USA.
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Pillay N, Mariotti L, Zaleska M, Inian O, Jessop M, Hibbs S, Desfosses A, Hopkins PCR, Templeton CM, Beuron F, Morris EP, Guettler S. Structural basis of tankyrase activation by polymerization. Nature 2022; 612:162-169. [PMID: 36418402 PMCID: PMC9712121 DOI: 10.1038/s41586-022-05449-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 10/13/2022] [Indexed: 11/25/2022]
Abstract
The poly-ADP-ribosyltransferase tankyrase (TNKS, TNKS2) controls a wide range of disease-relevant cellular processes, including WNT-β-catenin signalling, telomere length maintenance, Hippo signalling, DNA damage repair and glucose homeostasis1,2. This has incentivized the development of tankyrase inhibitors. Notwithstanding, our knowledge of the mechanisms that control tankyrase activity has remained limited. Both catalytic and non-catalytic functions of tankyrase depend on its filamentous polymerization3-5. Here we report the cryo-electron microscopy reconstruction of a filament formed by a minimal active unit of tankyrase, comprising the polymerizing sterile alpha motif (SAM) domain and its adjacent catalytic domain. The SAM domain forms a novel antiparallel double helix, positioning the protruding catalytic domains for recurring head-to-head and tail-to-tail interactions. The head interactions are highly conserved among tankyrases and induce an allosteric switch in the active site within the catalytic domain to promote catalysis. Although the tail interactions have a limited effect on catalysis, they are essential to tankyrase function in WNT-β-catenin signalling. This work reveals a novel SAM domain polymerization mode, illustrates how supramolecular assembly controls catalytic and non-catalytic functions, provides important structural insights into the regulation of a non-DNA-dependent poly-ADP-ribosyltransferase and will guide future efforts to modulate tankyrase and decipher its contribution to disease mechanisms.
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Affiliation(s)
- Nisha Pillay
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Laura Mariotti
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Mariola Zaleska
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Oviya Inian
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Matthew Jessop
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Sam Hibbs
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Ambroise Desfosses
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Paul C R Hopkins
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Catherine M Templeton
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK
| | - Fabienne Beuron
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
| | - Edward P Morris
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK
| | - Sebastian Guettler
- Division of Structural Biology, The Institute of Cancer Research (ICR), London, UK.
- Division of Cancer Biology, The Institute of Cancer Research (ICR), London, UK.
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Shi D, Pang Q, Qin Q, Yao X, Yao X, Yu Y. Discovery of novel anti-tumor compounds targeting PARP-1 with induction of autophagy through in silico and in vitro screening. Front Pharmacol 2022; 13:1026306. [PMID: 36353483 PMCID: PMC9638114 DOI: 10.3389/fphar.2022.1026306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/13/2022] [Indexed: 11/16/2022] Open
Abstract
Poly (ADP-ribose) polymerase 1 (PARP-1) is a critical enzyme involved in DNA damage repair and recombination, and shows great potential for drug development in the treatment of cancers with defective DNA repair. The anti-tumor activities of PARP-1 inhibitors are regulated by both inhibition activities and allosteric mechanisms of PARP-1, and may also be involved in an autophagy-mediated process. Screening PARP-1 inhibitors with potential allosteric mechanisms and induced autophagy process could achieve elevated potency toward cancer cell killing. In this study, we tried to discover novel anti-tumor compounds targeting PARP-1 by computer simulations and in vitro screening. In order to filter PARP-1 inhibitors that could affect the folding state of the helix domain (HD) on PARP-1, the free energy contribution of key residues on HD were systematically analyzed using the ligand-binding crystal structures and integrated into in silico screening workflow for the selection of 20 pick-up compounds. Four compounds (Chemdiv codes: 8012-0567, 8018-6529, 8018-7168, 8018-7603) were proved with above 40% inhibitory ratio targeting PARP-1 under 20 μM, and further performed binding mode prediction and dynamic effect evaluation by molecular dynamics simulation. Further in vitro assays showed that compounds 8018-6529 and 8018-7168 could inhibit the growth of the human colorectal cancer cell (HCT-116) with IC50 values of 4.30 and 9.29 μM and were accompanied with an induced autophagy process. Taken together, we discover two novel anti-tumor compounds that target PARP-1 with an induced autophagy process and provide potential hit compounds for the anti-cancer drug development.
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Affiliation(s)
- Danfeng Shi
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, Guangzhou, China
- *Correspondence: Yang Yu, ; Danfeng Shi,
| | - Qianqian Pang
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, Guangzhou, China
| | - Qianyu Qin
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, Guangzhou, China
| | - Xinsheng Yao
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, Guangzhou, China
| | - Xiaojun Yao
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau, China
| | - Yang Yu
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, Guangzhou, China
- *Correspondence: Yang Yu, ; Danfeng Shi,
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Maluchenko N, Koshkina D, Korovina A, Studitsky V, Feofanov A. Interactions of PARP1 Inhibitors with PARP1-Nucleosome Complexes. Cells 2022; 11:cells11213343. [PMID: 36359739 PMCID: PMC9658683 DOI: 10.3390/cells11213343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/12/2022] [Accepted: 10/19/2022] [Indexed: 11/23/2022] Open
Abstract
Inhibitors (PARPi) of poly(ADP-ribose-)polymerase-1 (PARP1) are used in antitumor therapy; their cytotoxicity correlates with the efficiency of PARP1 trapping in cell chromatin. Previous studies have demonstrated the PARPi-induced trapping of PARP1 on DNA, although details of the mechanism remain controversial. Here, the interactions of PARP1-nucleosome complexes with PARPi, olaparib (Ola), talazoparib (Tala), and veliparib (Veli) were studied. PARPi trap PARP1 on nucleosomes without affecting the structure of PARP1-nucleosome complexes. The efficiency of PARP1 trapping on nucleosomes increases in the order of Tala>Ola>>Veli, recapitulating the relative trapping efficiencies of PARPi in cells, but different from the relative potency of PARPi to inhibit the catalytic activity of PARP1. The efficiency of PARP1 trapping on nucleosomes correlates with the level of inhibition of auto-PARylation, which otherwise promotes the dissociation of PARP1-nucleosome complexes. The trapping efficiencies of Tala and Ola (but not Veli) are additionally modulated by the enhanced PARP1 binding to nucleosomes. The dissociation of PARP1-nucleosome complexes occurs without a loss of histones and leads to the restoration of the intact structure of nucleosomal DNA. The data suggest that the chromatin structure can considerably affect the efficiency of the PARPi action.
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Affiliation(s)
- Natalya Maluchenko
- Biology Faculty, Lomonosov Moscow State University, 119234 Moscow, Russia
- Correspondence: (N.M.); (A.F.)
| | - Darya Koshkina
- Biology Faculty, Lomonosov Moscow State University, 119234 Moscow, Russia
- Institute of Gene Biology RAS, 34/5 Vavilov Str., 119334 Moscow, Russia
| | - Anna Korovina
- Biology Faculty, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Vasily Studitsky
- Biology Faculty, Lomonosov Moscow State University, 119234 Moscow, Russia
- Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Alexey Feofanov
- Biology Faculty, Lomonosov Moscow State University, 119234 Moscow, Russia
- Institute of Gene Biology RAS, 34/5 Vavilov Str., 119334 Moscow, Russia
- Correspondence: (N.M.); (A.F.)
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Chan CY, Hopkins SL, Guibbal F, Pacelli A, Baguña Torres J, Mosley M, Lau D, Isenegger P, Chen Z, Wilson TC, Dias G, Hueting R, Gouverneur V, Cornelissen B. Correlation between molar activity, injection mass and uptake of the PARP targeting radiotracer [ 18F]olaparib in mouse models of glioma. EJNMMI Res 2022; 12:67. [PMID: 36210377 PMCID: PMC9548459 DOI: 10.1186/s13550-022-00940-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 09/30/2022] [Indexed: 11/10/2022] Open
Abstract
PURPOSE Radiopharmaceuticals targeting poly(ADP-ribose) polymerase (PARP) have emerged as promising agents for cancer diagnosis and therapy. PARP enzymes are expressed in both cancerous and normal tissue. Hence, the injected mass, molar activity and potential pharmacological effects are important considerations for the use of radiolabelled PARP inhibitors for diagnostic and radionuclide therapeutic applications. Here, we performed a systematic evaluation by varying the molar activity of [18F]olaparib and the injected mass of [TotalF]olaparib to investigate the effects on tumour and normal tissue uptake in two subcutaneous human glioblastoma xenograft models. METHODS [18F]Olaparib uptake was evaluated in the human glioblastoma models: in vitro on U251MG and U87MG cell lines, and in vivo on tumour xenograft-bearing mice, after administration of [TotalF]olaparib (varying injected mass: 0.04-8.0 µg, and molar activity: 1-320 GBq/μmol). RESULTS Selective uptake of [18F]olaparib was demonstrated in both models. Tumour uptake was found to be dependent on the injected mass of [TotalF]olaparib (µg) but not the molar activity. An injected mass of 1 μg resulted in the highest tumour uptake (up to 6.9 ± 1.3%ID/g), independent of the molar activity. In comparison, both the lower and higher injected masses of [TotalF]olaparib resulted in lower relative tumour uptake (%ID/g; P < 0.05). Ex vivo analysis of U87MG xenograft sections showed that the heterogeneity in [18F]olaparib intratumoural uptake correlated with PARP1 expression. Substantial upregulation of PARP1-3 expression was observed after administration of [TotalF]olaparib (> 0.5 µg). CONCLUSION Our findings show that the injected mass of [TotalF]olaparib has significant effects on tumour uptake. Moderate injected masses of PARP inhibitor-derived radiopharmaceuticals may lead to improved relative tumour uptake and tumour-to-background ratio for cancer diagnosis and radionuclide therapy.
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Affiliation(s)
- Chung Ying Chan
- CRUK/MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Off Roosevelt Drive, Oxford, OX3 7LJ UK
| | - Samantha L. Hopkins
- CRUK/MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Off Roosevelt Drive, Oxford, OX3 7LJ UK
| | - Florian Guibbal
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, South Parks Road, Oxford, OX1 3TA UK
| | - Anna Pacelli
- CRUK/MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Off Roosevelt Drive, Oxford, OX3 7LJ UK
| | - Julia Baguña Torres
- CRUK/MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Off Roosevelt Drive, Oxford, OX3 7LJ UK
| | - Michael Mosley
- CRUK/MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Off Roosevelt Drive, Oxford, OX3 7LJ UK
| | - Doreen Lau
- CRUK/MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Off Roosevelt Drive, Oxford, OX3 7LJ UK
| | - Patrick Isenegger
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, South Parks Road, Oxford, OX1 3TA UK
| | - Zijun Chen
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, South Parks Road, Oxford, OX1 3TA UK
| | - Thomas C. Wilson
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, South Parks Road, Oxford, OX1 3TA UK
| | - Gemma Dias
- CRUK/MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Off Roosevelt Drive, Oxford, OX3 7LJ UK
| | - Rebekka Hueting
- CRUK/MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Off Roosevelt Drive, Oxford, OX3 7LJ UK
| | - Véronique Gouverneur
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, South Parks Road, Oxford, OX1 3TA UK
| | - Bart Cornelissen
- CRUK/MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Off Roosevelt Drive, Oxford, OX3 7LJ UK
- Department of Nuclear Medicine and Molecular Imaging, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
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Xue H, Bhardwaj A, Yin Y, Fijen C, Ephstein A, Zhang L, Ding X, Pascal JM, VanArsdale TL, Rothenberg E. A two-step mechanism governing PARP1-DNA retention by PARP inhibitors. SCIENCE ADVANCES 2022; 8:eabq0414. [PMID: 36070389 PMCID: PMC9451145 DOI: 10.1126/sciadv.abq0414] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
PARP inhibitors (PARPi) have emerged as promising cancer therapeutics capable of targeting specific DNA repair pathways, but their mechanism of action with respect to PARP1-DNA retention remains unclear. Here, we developed single-molecule assays to directly monitor the retention of PARP1 on DNA lesions in real time. Our study reveals a two-step mechanism by which PARPi modulate the retention of PARP1 on DNA lesions, consisting of a primary step of catalytic inhibition via binding competition with NAD+ followed by an allosteric modulation of bound PARPi. While clinically relevant PARPi exhibit distinct allosteric modulation activities that can either increase retention of PARP1 on DNA or induce its release, their retention potencies are predominantly determined by their ability to outcompete NAD+ binding. These findings provide a mechanistic basis for improved PARPi selection according to their characteristic activities and enable further development of more potent inhibitors.
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Affiliation(s)
- Huijun Xue
- Department of Biochemistry and Molecular Pharmacology and Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Amit Bhardwaj
- Department of Biochemistry and Molecular Pharmacology and Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Yandong Yin
- Department of Biochemistry and Molecular Pharmacology and Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Carel Fijen
- Department of Biochemistry and Molecular Pharmacology and Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Anastasiya Ephstein
- Department of Biochemistry and Molecular Pharmacology and Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Lianglin Zhang
- Oncology Research and Development, Pfizer Inc., La Jolla, CA 92121, USA
| | - Xia Ding
- Oncology Research and Development, Pfizer Inc., La Jolla, CA 92121, USA
| | - John M. Pascal
- Département de Biochimie and Médecine Moléculaire, Faculté de Médecine, Université de Montréal, Montréal QC H3C 3J7, Canada
| | - Todd L. VanArsdale
- Oncology Research and Development, Pfizer Inc., La Jolla, CA 92121, USA
- Corresponding author. (T.V.); (E.R.)
| | - Eli Rothenberg
- Department of Biochemistry and Molecular Pharmacology and Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
- Corresponding author. (T.V.); (E.R.)
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43
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Caldecott KW. DNA single-strand break repair and human genetic disease. Trends Cell Biol 2022; 32:733-745. [PMID: 35643889 DOI: 10.1016/j.tcb.2022.04.010] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 04/13/2022] [Accepted: 04/22/2022] [Indexed: 12/15/2022]
Abstract
DNA single-strand breaks (SSBs) are amongst the commonest DNA lesions arising in cells, with many tens of thousands induced in each cell each day. SSBs arise not only from exposure to intracellular and environmental genotoxins but also as intermediates of normal DNA metabolic processes, such as the removal of torsional stress in DNA by topoisomerase enzymes and the epigenetic regulation of gene expression by DNA base excision repair (BER). If not rapidly detected and repaired, SSBs can result in RNA polymerase stalling, DNA replication fork collapse, and hyperactivation of the SSB sensor protein poly(ADP-ribose) polymerase 1 (PARP1). The potential impact of unrepaired SSBs is illustrated by the existence of genetic diseases in which proteins involved in SSB repair (SSBR) are mutated, and which are typified by hereditary neurodevelopmental and/or neurodegenerative disease. Here, I review our current understanding of SSBR and its impact on human neurological disease, with a focus on recent developments and concepts.
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Affiliation(s)
- Keith W Caldecott
- Genome Damage and Stability Centre, School of Life Sciences, Science Park Road, University of Sussex, Falmer, Brighton BN1 9RQ, UK.
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44
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Almeleebia TM, Ahamad S, Ahmad I, Alshehri A, Alkhathami AG, Alshahrani MY, Asiri MA, Saeed A, Siddiqui JA, Yadav DK, Saeed M. Identification of PARP12 Inhibitors By Virtual Screening and Molecular Dynamics Simulations. Front Pharmacol 2022; 13:847499. [PMID: 36016564 PMCID: PMC9395932 DOI: 10.3389/fphar.2022.847499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Accepted: 04/27/2022] [Indexed: 11/13/2022] Open
Abstract
Poly [adenosine diphosphate (ADP)-ribose] polymerases (PARPs) are members of a family of 17 enzymes that performs several fundamental cellular processes. Aberrant activity (mutation) in PARP12 has been linked to various diseases including inflammation, cardiovascular disease, and cancer. Herein, a large library of compounds (ZINC-FDA database) has been screened virtually to identify potential PARP12 inhibitor(s). The best compounds were selected on the basis of binding affinity scores and poses. Molecular dynamics (MD) simulation and binding free energy calculation (MMGBSA) were carried out to delineate the stability and dynamics of the resulting complexes. To this end, root means deviations, relative fluctuation, atomic gyration, compactness, covariance, residue-residue contact map, and free energy landscapes were studied. These studies have revealed that compounds ZINC03830332, ZINC03830554, and ZINC03831186 are promising agents against mutated PARP12.
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Affiliation(s)
- Tahani M. Almeleebia
- Department of Clinical Pharmacy, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | | | - Irfan Ahmad
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Ahmad Alshehri
- College of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Ali G. Alkhathami
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Mohammad Y. Alshahrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Mohammed A. Asiri
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Amir Saeed
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail, Saudi Arabia
- Department of Medical Microbiology, Faculty of Medical Laboratory Sciences, University of Medical Sciences and Technology, Khartoum, Sudan
| | - Jamshaid Ahmad Siddiqui
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | - Dharmendra K. Yadav
- Department of Pharmacy, Gachon Institute of Pharmaceutical Sciences, College of Pharmacy, Gachon University of Medicine and Science, Incheon, South Korea
- *Correspondence: Mohd Saeed, ; Dharmendra K. Yadav,
| | - Mohd Saeed
- Department of Biology, College of Sciences, University of Hail, Hail, Saudi Arabia
- *Correspondence: Mohd Saeed, ; Dharmendra K. Yadav,
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45
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Hu J, Liang P, Jin D, Fan R, Xie X, Liu C, Jiang Q, Gao L. Poly (ADP-ribose) polymerase inhibitors (PARPi) for advanced malignancies with multiple DNA-repair genetic aberrations. Expert Rev Anticancer Ther 2022; 22:717-723. [PMID: 35679134 DOI: 10.1080/14737140.2022.2088513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Poly (ADP-ribose) polymerase inhibitors (PARPi) have been approved for the treatment of advanced tumors with defects in genes involved in homologous recombination repair (HRR), including cancers of the prostate, pancreas, breast, and ovary. In these advanced tumors, PARPi afford 'synthetic lethality' by blocking the PARP-associated repair pathway in cancer cells with HRR genetic mutations, resulting in chromosome instability and cellular apoptosis. According to the synthetic lethality theory, patients with a greater burden of genetic alterations, in proportion (relative quantity) or category, would have more satisfactory outcomes after PARPi administration. However, this issue remains obscure based on the existing sporadic evidence. AREAS COVERED We summarize the therapeutic effects of PARPi in advanced tumors with multiple HRR genetic mutations, and attempted to compare these results with those obtained for cancers with a single mutation. EXPERT OPINION Limited evidence has provided a possibly encouraging response to PARPi among patients carrying multiple HRR genetic mutations compared with those with a single mutation (although the treatment effect was negative in some patients). Further research is needed to understand the role of PARPi in tumor cells with multiple HRR genetic mutations.
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Affiliation(s)
- Jian Hu
- Department of Urology, The Second Affiliated Hospital of Chongqing Medical University, Chong Qing, China
| | - Peihe Liang
- Department of Urology, The Second Affiliated Hospital of Chongqing Medical University, Chong Qing, China
| | - Dachun Jin
- Department of Urology, Daping Hospital/Army Medical Center of PLA, Army Medical University
| | - Runze Fan
- Department of Urology, The Second Affiliated Hospital of Chongqing Medical University, Chong Qing, China
| | - Xiaodu Xie
- Department of Urology, The Second Affiliated Hospital of Chongqing Medical University, Chong Qing, China
| | - Chuan Liu
- Department of Urology, The Second Affiliated Hospital of Chongqing Medical University, Chong Qing, China
| | - Qing Jiang
- Department of Urology, The Second Affiliated Hospital of Chongqing Medical University, Chong Qing, China
| | - Liang Gao
- Department of Urology, The Second Affiliated Hospital of Chongqing Medical University, Chong Qing, China
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46
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Ying Z, Qi D, Chaoran W, Min H, Miao W, Qin L. PARP inhibitors rising as an epoch-making strategy in first-line maintenance therapy of ovarian cancer: A systematic review and meta-analysis. Cancer Invest 2022; 40:889-900. [PMID: 35686725 DOI: 10.1080/07357907.2022.2088780] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Background To illustrate the accurate location of PARP inhibitor (PARPi) as the first-line maintenance therapy in advanced ovarian cancer (AOC).Methods Search for eligible studies and calculate clinical outcomes.Results PARPi as a first-line maintenance treatment significantly prolonged the BRCAmut population and the HRD positive population.Conclusion PARPi as first-line maintenance therapy significantly improves the PFS in AOC, especially in the BRCAmut and HRD positive populations. PARPi has been becoming the standard first-line maintenance therapy for AOC.
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Affiliation(s)
- Zhang Ying
- Department of Oncology, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Du Qi
- Department of Oncology, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Wang Chaoran
- Department of Oncology, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Hu Min
- Biochemistry and Molecular Biology, Basic Medicine College, Shanxi Medical University, Taiyuan, 050001, China
| | - Wang Miao
- Department of Oncology, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Li Qin
- Department of Oncology, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
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A Long-Lasting PARP1-Activation Mediates Signal-Induced Gene Expression. Cells 2022; 11:cells11091576. [PMID: 35563882 PMCID: PMC9101275 DOI: 10.3390/cells11091576] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/26/2022] [Accepted: 05/04/2022] [Indexed: 02/04/2023] Open
Abstract
This overview presents recent evidence for a long-lasting PARP1 activation by a variety of signal transduction mechanisms, mediating signal-induced gene expression and chromatin remodeling. This mode of PARP1 activation has been reported in a variety of cell types, under physiological conditions. In this mechanism, PARP1 is not transiently activated by binding to DNA breaks. Moreover, damaged DNA interfered with this long-lasting PARP1 activation.
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48
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Wanderley CWS, Correa TS, Scaranti M, Cunha FQ, Barroso-Sousa R. Targeting PARP1 to Enhance Anticancer Checkpoint Immunotherapy Response: Rationale and Clinical Implications. Front Immunol 2022; 13:816642. [PMID: 35572596 PMCID: PMC9094400 DOI: 10.3389/fimmu.2022.816642] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 03/25/2022] [Indexed: 11/13/2022] Open
Abstract
Reinvigorating the antitumor immune response using immune checkpoint inhibitors (ICIs) has revolutionized the treatment of several malignancies. However, extended use of ICIs has resulted in a cancer-specific response. In tumors considered to be less immunogenic, the response rates were low or null. To overcome resistance and improve the beneficial effects of ICIs, novel strategies focused on ICI-combined therapies have been tested. In particular, poly ADP-ribose polymerase inhibitors (PARPi) are a class of agents with potential for ICI combined therapy. PARPi impairs single-strand break DNA repair; this mechanism involves synthetic lethality in tumor cells with deficient homologous recombination. More recently, novel evidence indicated that PAPRi has the potential to modulate the antitumor immune response by activating antigen-presenting cells, infiltrating effector lymphocytes, and upregulating programmed death ligand-1 in tumors. This review covers the current advances in the immune effects of PARPi, explores the potential rationale for combined therapy with ICIs, and discusses ongoing clinical trials.
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Affiliation(s)
- Carlos Wagner S. Wanderley
- Center for Research in Inflammatory Diseases (CRID), Ribeirao Preto Medical School, Ribeirao Preto, Brazil
- Department of Pharmacology, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, Brazil
| | | | | | - Fernando Queiroz Cunha
- Center for Research in Inflammatory Diseases (CRID), Ribeirao Preto Medical School, Ribeirao Preto, Brazil
- Department of Pharmacology, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, Brazil
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Muoio D, Laspata N, Fouquerel E. Functions of ADP-ribose transferases in the maintenance of telomere integrity. Cell Mol Life Sci 2022; 79:215. [PMID: 35348914 PMCID: PMC8964661 DOI: 10.1007/s00018-022-04235-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/03/2022] [Accepted: 03/07/2022] [Indexed: 12/21/2022]
Abstract
The ADP-ribose transferase (ART) family comprises 17 enzymes that catalyze mono- or poly-ADP-ribosylation, a post-translational modification of proteins. Present in all subcellular compartments, ARTs are implicated in a growing number of biological processes including DNA repair, replication, transcription regulation, intra- and extra-cellular signaling, viral infection and cell death. Five members of the family, PARP1, PARP2, PARP3, tankyrase 1 and tankyrase 2 are mainly described for their crucial functions in the maintenance of genome stability. It is well established that the most describedrole of PARP1, 2 and 3 is the repair of DNA lesions while tankyrases 1 and 2 are crucial for maintaining the integrity of telomeres. Telomeres, nucleoprotein complexes located at the ends of eukaryotic chromosomes, utilize their unique structure and associated set of proteins to orchestrate the mechanisms necessary for their own protection and replication. While the functions of tankyrases 1 and 2 at telomeres are well known, several studies have also brought PARP1, 2 and 3 to the forefront of telomere protection. The singular quality of the telomeric environment has highlighted protein interactions and molecular pathways distinct from those described throughout the genome. The aim of this review is to provide an overview of the current knowledge on the multiple roles of PARP1, PARP2, PARP3, tankyrase 1 and tankyrase 2 in the maintenance and preservation of telomere integrity.
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Affiliation(s)
- Daniela Muoio
- UPMC Cancer Institute and Department of Pharmacology and Chemical Biology at the University of Pittsburgh, Hillman Cancer Center, 5115 Centre Avenue, Pittsburgh, PA, 15213, USA
| | - Natalie Laspata
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 S. 10th street, Philadelphia, PA, 19107, USA
| | - Elise Fouquerel
- UPMC Cancer Institute and Department of Pharmacology and Chemical Biology at the University of Pittsburgh, Hillman Cancer Center, 5115 Centre Avenue, Pittsburgh, PA, 15213, USA.
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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.
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