1
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Shanmugam N, Chatterjee S, Cisneros GA. Impact of a Cancer-Associated Mutation on Poly(ADP-ribose) Polymerase1 Inhibition. J Phys Chem B 2025; 129:2175-2186. [PMID: 39962867 PMCID: PMC12005076 DOI: 10.1021/acs.jpcb.4c07960] [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: 02/26/2025]
Abstract
Poly(ADP-ribose) polymerase1 (PARP1) plays a vital role in DNA repair, and its inhibition in cancer cells may cause cell apoptosis. In this study, we investigated the effects of a PARP1 variant, V762A, which is strongly associated with several cancers in humans, on the inhibition of PARP1 by three FDA-approved inhibitors: niraparib, rucaparib, and talazoparib. Specifically, we compared the inhibition of the mutant to that of wild-type (WT) PARP1. Additionally, we investigated how the mutation influences the binding of these inhibitors to PARP1. Our work suggests that while mutant PARP1 exhibits only minor differences in residual fluctuations, backbone deviations, and residue motion correlations compared to the WT under niraparib and rucaparib inhibitions, it shows significant and distinct differences in these features when inhibited by talazoparib. Among the three inhibitions, talazoparib inhibition uniquely lowers the average residue fluctuations in the mutant than the WT including lower fluctuations of mutant's N- and C-terminal residues in the catalytic domain, conserved H-Y-E traid residues, and donor loop (D-loop) residues which are important for catalysis more effectively than other inhibitions. However, talazoparib also significantly enhances destabilizing interactions between the mutation site in the HD domain in the mutant than WT. Further, among the three inhibitions, talazoparib inhibition uniquely and significantly disrupts the functional fluctuations of terminal regions in the mutant, which are otherwise present in the WT. The mutation and inhibition do not significantly affect PARP1's essential dynamics. Lastly, these inhibitors bind to the V762A mutant more effectively than to the WT, with similar binding free energies between them.
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Affiliation(s)
- Neel Shanmugam
- Department of Chemistry, University of North Texas, Denton, Texas 76201, United States; Present Address: Department of Computer Science, Columbia University, New York, New York 10027, United States
| | - Shubham Chatterjee
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas 75080, United States
| | - G. Andrés Cisneros
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas 75080, United States; Department of Physics, University of Texas at Dallas, Richardson, Texas 75080, United States
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2
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Skouras P, Markouli M, Papadatou I, Piperi C. Targeting epigenetic mechanisms of resistance to chemotherapy in gliomas. Crit Rev Oncol Hematol 2024; 204:104532. [PMID: 39406277 DOI: 10.1016/j.critrevonc.2024.104532] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Accepted: 10/09/2024] [Indexed: 10/19/2024] Open
Abstract
Glioma, an aggressive type of brain tumors of glial origin is highly heterogeneous, posing significant treatment challenges due to its intrinsic resistance to conventional therapeutic schemes. It is characterized by an interplay between epigenetic and genetic alterations in key signaling pathways which further endorse their resistance potential. Aberrant DNA methylation patterns, histone modifications and non-coding RNAs may alter the expression of genes associated with drug response and cell survival, induce gene silencing or deregulate key pathways contributing to glioma resistance. There is evidence that epigenetic plasticity enables glioma cells to adapt dynamically to therapeutic schemes and allow the formation of drug-resistant subpopulations. Furthermore, the tumor microenvironment adds an extra input on epigenetic regulation, increasing the complexity of resistance mechanisms. Herein, we discuss epigenetic changes conferring to drug resistance mechanisms in gliomas in order to delineate novel therapeutic targets and potential approaches that will enable personalized treatment.
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Affiliation(s)
- Panagiotis Skouras
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, Athens 11527, Greece; 1st Department of Neurosurgery, Evangelismos Hospital, National and Kapodistrian University of Athens, Greece.
| | - Mariam Markouli
- Department of Medicine, Boston Medical Center, Boston University School of Medicine, Boston, MA 02118, USA.
| | - Ioanna Papadatou
- University Research Institute for the Study of Genetic & Malignant Disorders in Childhood, "Aghia Sophia" Children's Hospital, National and Kapodistrian University of Athens, Athens 11527, Greece.
| | - Christina Piperi
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, Athens 11527, Greece.
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3
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Wu K, Karapetyan E, Schloss J, Vadgama J, Wu Y. Advancements in small molecule drug design: A structural perspective. Drug Discov Today 2023; 28:103730. [PMID: 37536390 PMCID: PMC10543554 DOI: 10.1016/j.drudis.2023.103730] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 07/19/2023] [Accepted: 07/27/2023] [Indexed: 08/05/2023]
Abstract
In this review, we outline recent advancements in small molecule drug design from a structural perspective. We compare protein structure prediction methods and explore the role of the ligand binding pocket in structure-based drug design. We examine various structural features used to optimize drug candidates, including functional groups, stereochemistry, and molecular weight. Computational tools such as molecular docking and virtual screening are discussed for predicting and optimizing drug candidate structures. We present examples of drug candidates designed based on their molecular structure and discuss future directions in the field. By effectively integrating structural information with other valuable data sources, we can improve the drug discovery process, leading to the identification of novel therapeutics with improved efficacy, specificity, and safety profiles.
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Affiliation(s)
- Ke Wu
- Division of Cancer Research and Training, Department of Internal Medicine, Charles R. Drew University of Medicine and Science, David Geffen UCLA School of Medicine and UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA 90095, USA
| | - Eduard Karapetyan
- Division of Cancer Research and Training, Department of Internal Medicine, Charles R. Drew University of Medicine and Science, David Geffen UCLA School of Medicine and UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA 90095, USA
| | - John Schloss
- Division of Cancer Research and Training, Department of Internal Medicine, Charles R. Drew University of Medicine and Science, David Geffen UCLA School of Medicine and UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA 90095, USA; School of Pharmacy, American University of Health Sciences, Signal Hill, CA 90755, USA
| | - Jaydutt Vadgama
- Division of Cancer Research and Training, Department of Internal Medicine, Charles R. Drew University of Medicine and Science, David Geffen UCLA School of Medicine and UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA 90095, USA; School of Pharmacy, American University of Health Sciences, Signal Hill, CA 90755, USA.
| | - Yong Wu
- Division of Cancer Research and Training, Department of Internal Medicine, Charles R. Drew University of Medicine and Science, David Geffen UCLA School of Medicine and UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA 90095, USA.
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4
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Bou Zerdan M, Atoui A, Hijazi A, Basbous L, Abou Zeidane R, Alame SM, Assi HI. Latest updates on cellular and molecular biomarkers of gliomas. Front Oncol 2022; 12:1030366. [PMID: 36425564 PMCID: PMC9678906 DOI: 10.3389/fonc.2022.1030366] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 10/05/2022] [Indexed: 03/05/2024] Open
Abstract
Gliomas are the most common central nervous system malignancies, compromising almost 80% of all brain tumors and is associated with significant mortality. The classification of gliomas has shifted from basic histological perspective to one that is based on molecular biomarkers. Treatment of this type of tumors consists currently of surgery, chemotherapy and radiation therapy. During the past years, there was a limited development of effective glioma diagnostics and therapeutics due to multiple factors including the presence of blood-brain barrier and the heterogeneity of this type of tumors. Currently, it is necessary to highlight the advantage of molecular diagnosis of gliomas to develop patient targeted therapies based on multiple oncogenic pathway. In this review, we will evaluate the development of cellular and molecular biomarkers for the diagnosis of gliomas and the impact of these diagnostic tools for better tailored and targeted therapies.
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Affiliation(s)
- Maroun Bou Zerdan
- Department of Internal Medicine, State University of New York (SUNY) Upstate Medical University, Syracuse, NY, United States
| | - Ali Atoui
- Hematology-Oncology Division, Internal Medicine Department, American University of Beirut Medical Center, Beirut, Lebanon
| | - Ali Hijazi
- Hematology-Oncology Division, Internal Medicine Department, American University of Beirut Medical Center, Beirut, Lebanon
| | - Lynn Basbous
- Hematology-Oncology Division, Internal Medicine Department, American University of Beirut Medical Center, Beirut, Lebanon
| | - Reine Abou Zeidane
- Hematology-Oncology Division, Internal Medicine Department, American University of Beirut Medical Center, Beirut, Lebanon
| | - Saada M Alame
- Department of Pediatrics, Faculty of Medicine, Lebanese University, Beirut, Lebanon
| | - Hazem I Assi
- Hematology-Oncology Division, Internal Medicine Department, American University of Beirut Medical Center, Beirut, Lebanon
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5
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Perez J, Twigg CAI, Guan W, Thomas SN. Proteomic Analysis Reveals Low-Dose PARP Inhibitor-Induced Differential Protein Expression in BRCA1-Mutated High-Grade Serous Ovarian Cancer Cells. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:242-250. [PMID: 34958553 PMCID: PMC8824432 DOI: 10.1021/jasms.1c00215] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 10/12/2021] [Accepted: 10/12/2021] [Indexed: 06/14/2023]
Abstract
High-grade serous ovarian cancer (HGSOC) is the most common form of ovarian cancer diagnosed in patients worldwide. Patients with BRCA1/2-mutated HGSOC have benefited from targeted treatments such as poly(ADP-ribose) polymerase inhibitors (PARPi). Despite the initial success of PARPi-based ovarian cancer treatment regimens, approximately 70% of patients with ovarian cancer relapse and the 5-year survival rate remains at 30%. PARPi exhibit variable treatment efficacy and toxicity profiles. Furthermore, the off-target effects of PARP inhibition have not yet been fully elucidated, warranting further study of these classes of molecules in the context of HGSOC treatment. Highly reproducible quantitative mass spectrometry-based proteomic workflows have been developed for the analysis of tumor tissues and cell lines. To detect the off-target effects of PARP inhibition, we conducted a quantitative mass spectrometry-based proteomic analysis of a BRCA1-mutated HGSOC cell line treated with low doses of two PARPi, niraparib and rucaparib. Our goal was to identify PARPi-induced protein signaling pathway alterations toward a more comprehensive elucidation of the mechanism of action of PARPi beyond the DNA damage response pathway. A significant enrichment of nuclear and nucleoplasm proteins that are involved in protein binding was observed in the rucaparib-treated cells. Shared upregulated proteins between niraparib and rucaparib treatment demonstrated RNA II pol promoter-associated pathway enrichment in transcription regulation. Pathway enrichment analyses also revealed off-target effects in the Golgi apparatus and the ER. The results from our mass spectrometry-based proteomic analysis highlights notable off-target effects produced by low-dose treatment of BRCA1-mutated HGSOC cells treated with rucaparib or niraparib.
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Affiliation(s)
- Jesenia
M. Perez
- Microbiology,
Immunology, and Cancer Biology Graduate Program, University of Minnesota School of Medicine, Minneapolis, Minnesota 55455, United States
| | - Carly A. I. Twigg
- Department
of Laboratory Medicine and Pathology, University
of Minnesota School of Medicine, Minneapolis, Minnesota 55455, United States
| | - Weihua Guan
- Division
of Biostatistics, University of Minnesota
School of Public Health, Minneapolis, Minnesota 55455, United States
| | - Stefani N. Thomas
- Department
of Laboratory Medicine and Pathology, University
of Minnesota School of Medicine, Minneapolis, Minnesota 55455, United States
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6
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Wu Q, Berglund AE, Etame AB. The Impact of Epigenetic Modifications on Adaptive Resistance Evolution in Glioblastoma. Int J Mol Sci 2021; 22:8324. [PMID: 34361090 PMCID: PMC8347012 DOI: 10.3390/ijms22158324] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 07/25/2021] [Accepted: 07/30/2021] [Indexed: 02/06/2023] Open
Abstract
Glioblastoma (GBM) is a highly lethal cancer that is universally refractory to the standard multimodal therapies of surgical resection, radiation, and chemotherapy treatment. Temozolomide (TMZ) is currently the best chemotherapy agent for GBM, but the durability of response is epigenetically dependent and often short-lived secondary to tumor resistance. Therapies that can provide synergy to chemoradiation are desperately needed in GBM. There is accumulating evidence that adaptive resistance evolution in GBM is facilitated through treatment-induced epigenetic modifications. Epigenetic alterations of DNA methylation, histone modifications, and chromatin remodeling have all been implicated as mechanisms that enhance accessibility for transcriptional activation of genes that play critical roles in GBM resistance and lethality. Hence, understanding and targeting epigenetic modifications associated with GBM resistance is of utmost priority. In this review, we summarize the latest updates on the impact of epigenetic modifications on adaptive resistance evolution in GBM to therapy.
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Affiliation(s)
- Qiong Wu
- Department of Neuro-Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, USA;
| | - Anders E. Berglund
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, USA;
| | - Arnold B. Etame
- Department of Neuro-Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, USA;
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7
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Wasyluk W, Zwolak A. PARP Inhibitors: An Innovative Approach to the Treatment of Inflammation and Metabolic Disorders in Sepsis. J Inflamm Res 2021; 14:1827-1844. [PMID: 33986609 PMCID: PMC8110256 DOI: 10.2147/jir.s300679] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/19/2021] [Indexed: 12/19/2022] Open
Abstract
Sepsis is not only a threat to the health of individual patients but also presents a serious epidemiological problem. Despite intensive research, modern sepsis therapy remains based primarily on antimicrobial treatment and supporting the functions of failing organs. Finding a cure for sepsis represents a great and as yet unfulfilled need in modern medicine. Research results indicate that the activity of poly (adenosine diphosphate (ADP)-ribose) polymerase (PARP) may play an important role in the inflammatory response and the cellular metabolic disorders found in sepsis. Mechanisms by which PARP-1 may contribute to inflammation and metabolic disorders include effects on the regulation of gene expression, impaired metabolism, cell death, and the release of alarmins. These findings suggest that inhibition of this enzyme may be a promising solution for the treatment of sepsis. In studies using experimental sepsis models, inhibition of PARP-1 has been shown to ameliorate the inflammatory response and increase survival. This action was described, among others, for olaparib, a PARP-1 inhibitor approved for use in oncology. While the results of current research are promising, the use of PARP inhibitors in non-oncological diseases raises some concerns, mainly related to the enzyme's role in deoxyribonucleic acid (DNA) repair. However, the results of studies on experimental models indicate the effectiveness of even short-term PARP-1 inhibition and do not confirm concerns regarding its impact on the integrity of nuclear DNA. Current research presents PARP inhibition as a potential solution for the treatment of sepsis and indicates the need for further research.
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Affiliation(s)
- Weronika Wasyluk
- Chair of Internal Medicine and Department of Internal Medicine in Nursing, Faculty of Health Sciences, Medical University of Lublin, Lublin, Poland.,Doctoral School, Medical University of Lublin, Lublin, Poland
| | - Agnieszka Zwolak
- Chair of Internal Medicine and Department of Internal Medicine in Nursing, Faculty of Health Sciences, Medical University of Lublin, Lublin, Poland
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8
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Pavlović M, Tadić A, Gligorijević N, Poljarević J, Petrović T, Dojčinović B, Savić A, Radulović S, Grgurić-Šipka S, Aranđelović S. Synthesis, chemical characterization, PARP inhibition, DNA binding and cellular uptake of novel ruthenium(II)-arene complexes bearing benzamide derivatives in human breast cancer cells. J Inorg Biochem 2020; 210:111155. [PMID: 32768729 DOI: 10.1016/j.jinorgbio.2020.111155] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/03/2020] [Accepted: 06/11/2020] [Indexed: 10/24/2022]
Abstract
Inhibitors of poly(ADP-ribose) polymerase-1 (PARP-1) showed remarkable clinical efficacy in BRCA-mutated tumors. Based on the rational drug design, derivatives of PARP inhibitor 3-aminobenzamide (3-AB), 2-amino-4-methylbenzamide (L1) and 3-amino-N-methylbenzamide (L2), were coordinated to the ruthenium(II) ion, to form potential drugs affecting DNA and inhibiting PARP enzyme. The four conjugated complexes of formula: C1 [(ƞ6-toluene)Ru(L1)Cl]PF6, C2 [(ƞ6-p-cymene)Ru(L1)Cl]PF6, C3 [(ƞ6-toluene)Ru(L2)Cl2] and C4 [(ƞ6-p-cymene)Ru(L2)Cl2], have been synthesized and characterized. Colorimetric 3-(4.5-dimethylthiazol-2-yl)-2.5-diphenyltetrazolium bromide (MTT) assay showed the highest antiproliferative activity of C1 in HCC1937, MDA-MB-231, and MCF-7 breast cancer cells. Efficiency of inhibition of PARP-1 enzymatic activity in vitro decreased in order: C2 > C4 > 3-AB>C1 > C3. ICP-MS study of intracellular accumulation and distribution in BRCA1-mutated HCC1937 revealed that C1-C4 entered cells within 24 h. The complex C1 showed the highest intracellular accumulation, nuclear-targeting properties, and exhibited the highest DNA binding (39.2 ± 0.6 pg of Ru per μg of DNA) that resulted in the cell cycle arrest in the S phase.
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Affiliation(s)
- Marijana Pavlović
- Department of Experimental Oncology, Institute for Oncology and Radiology of Serbia, Pasterova 14, 11000 Belgrade, Serbia
| | - Ana Tadić
- Department of General and Inorganic Chemistry, University of Belgrade-Faculty of Chemistry, Studentski trg 12-16, 11000 Belgrade, Serbia
| | - Nevenka Gligorijević
- Department of Experimental Oncology, Institute for Oncology and Radiology of Serbia, Pasterova 14, 11000 Belgrade, Serbia
| | - Jelena Poljarević
- Department of General and Inorganic Chemistry, University of Belgrade-Faculty of Chemistry, Studentski trg 12-16, 11000 Belgrade, Serbia.
| | - Tamara Petrović
- Department of General and Inorganic Chemistry, University of Belgrade-Faculty of Chemistry, Studentski trg 12-16, 11000 Belgrade, Serbia
| | - Biljana Dojčinović
- Centre of Chemistry Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Studentski trg 12-16, 11000 Belgrade, Serbia
| | - Aleksandar Savić
- Department of General and Inorganic Chemistry, University of Belgrade-Faculty of Chemistry, Studentski trg 12-16, 11000 Belgrade, Serbia
| | - Siniša Radulović
- Department of Experimental Oncology, Institute for Oncology and Radiology of Serbia, Pasterova 14, 11000 Belgrade, Serbia
| | - Sanja Grgurić-Šipka
- Department of General and Inorganic Chemistry, University of Belgrade-Faculty of Chemistry, Studentski trg 12-16, 11000 Belgrade, Serbia.
| | - Sandra Aranđelović
- Department of Experimental Oncology, Institute for Oncology and Radiology of Serbia, Pasterova 14, 11000 Belgrade, Serbia
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9
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The Modified Phenanthridine PJ34 Unveils an Exclusive Cell-Death Mechanism in Human Cancer Cells. Cancers (Basel) 2020; 12:cancers12061628. [PMID: 32575437 PMCID: PMC7352794 DOI: 10.3390/cancers12061628] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 06/15/2020] [Indexed: 12/17/2022] Open
Abstract
This overview summarizes recent data disclosing the efficacy of the PARP inhibitor PJ34 in exclusive eradication of a variety of human cancer cells without impairing healthy proliferating cells. Its cytotoxic activity in cancer cells is attributed to the insertion of specific un-repairable anomalies in the structure of their mitotic spindle, leading to mitotic catastrophe cell death. This mechanism paves the way to a new concept of cancer therapy.
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10
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Makhov P, Uzzo RG, Tulin AV, Kolenko VM. Histone-dependent PARP-1 inhibitors: A novel therapeutic modality for the treatment of prostate and renal cancers. Urol Oncol 2020; 39:312-315. [PMID: 32402770 DOI: 10.1016/j.urolonc.2020.04.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 04/02/2020] [Accepted: 04/09/2020] [Indexed: 12/13/2022]
Abstract
Clinical interest in poly(ADP-ribose) polymerase 1 (PARP-1) has increased over the past decade with the recognition of its roles in transcription regulation, DNA repair, epigenetic bookmarking, and chromatin restructuring. A number of PARP-1 inhibitors demonstrating clinical efficacy against tumors of various origins have emerged in recent years. These inhibitors have been essentially designed as nicotinamide adenine dinucleotide (NAD+) mimetics. However, because NAD+ is utilized by many enzymes other than PARP-1, NAD+ competitors tend to produce certain off-target effects. To overcome the limitation of NAD-like PARP-1 inhibitors, we have developed a new class of PARP-1 inhibitors that specifically targets the histone-dependent route of PARP-1 activation, a mechanism of activation that is unique to PARP-1. Novel histone-dependent inhibitors are highly specific for PARP-1 and demonstrate promising in vitro and in vivo efficacy against prostate and renal tumors. Our findings suggest that novel PARP-1 inhibitors have strong therapeutic potential for the treatment of urological tumors.
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Affiliation(s)
- Peter Makhov
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA
| | - Robert G Uzzo
- Department of Surgical Oncology, Fox Chase Cancer Center, Philadelphia, PA
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11
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Zhou Y, Tang S, Chen T, Niu MM. Structure-Based Pharmacophore Modeling, Virtual Screening, Molecular Docking and Biological Evaluation for Identification of Potential Poly (ADP-Ribose) Polymerase-1 (PARP-1) Inhibitors. Molecules 2019; 24:E4258. [PMID: 31766720 PMCID: PMC6930522 DOI: 10.3390/molecules24234258] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/13/2019] [Accepted: 11/20/2019] [Indexed: 01/28/2023] Open
Abstract
Poly (ADP-ribose) polymerase-1 (PARP-1) plays critical roles in many biological processes and is considered as a potential target for anticancer therapy. Although some PARP-1 inhibitors have been reported, their clinical application in cancer therapy is limited by some shortcomings such as weak affinity, low selectivity and adverse side effects. To identify highly potent and selective PARP-1 inhibitors, an integrated protocol that combines pharmacophore mapping, virtual screening and molecular docking was constructed. It was then used as a screening query to identify potent leads with unknown scaffolds from an in-house database. Finally, four retrieved compounds were selected for biological evaluation. Biological testing indicated that the four compounds showed strong inhibitory activities on the PARP-1 (IC50 < 0.2 μM). MTT assay confirmed that compounds 1-4 inhibited the growth of human lung cancer A549 cells in a dose-dependent manner. The obtained compounds from this study may be potential leads for PARP-1 inhibition in the treatment of cancer.
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Affiliation(s)
| | | | | | - Miao-Miao Niu
- Department of Pharmaceutical Analysis, State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China; (Y.Z.); (S.T.); (T.C.)
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12
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Visochek L, Atias D, Spektor I, Castiel A, Golan T, Cohen-Armon M. The phenanthrene derivative PJ34 exclusively eradicates human pancreatic cancer cells in xenografts. Oncotarget 2019; 10:6269-6282. [PMID: 31692907 PMCID: PMC6817443 DOI: 10.18632/oncotarget.27268] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 09/10/2019] [Indexed: 11/25/2022] Open
Abstract
Recent reports demonstrate an exclusive eradication of a variety of human cancer cells by the modified phenanthridine PJ34. Their eradication during mitosis is attributed to PJ34 preventing NuMA clustering in the mitotic spindle poles of human malignant cells, which is crucial for their normal mitosis. Here, the effect of PJ34 is tested in cell cultures and xenografts of human pancreas ductal adenocarcinoma. Evidence is presented for a substantial reduction (80-90%) of PANC1 cancer cells in xenografts, measured 30 days after the treatment with PJ34 has been terminated. Benign cells infiltrated into the PANC1 tumors (stroma) were not affected. Growth, weight gain and behavior of the treated nude mice were not impaired during, and 30 days after the treatment with PJ34. The efficient eradication of malignant cells in human pancreas cancer xenografts presents a new model of pancreas cancer treatment.
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Affiliation(s)
- Leonid Visochek
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Dikla Atias
- Oncology Institute, Sheba Medical Center, Ramat Gan 53621, Israel
| | - Itay Spektor
- Oncology Institute, Sheba Medical Center, Ramat Gan 53621, Israel
| | - Asher Castiel
- Oncology Institute, Sheba Medical Center, Ramat Gan 53621, Israel
| | - Talia Golan
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel.,Oncology Institute, Sheba Medical Center, Ramat Gan 53621, Israel
| | - Malka Cohen-Armon
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel.,Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv 69978, Israel
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13
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Karpova Y, Wu C, Divan A, McDonnell ME, Hewlett E, Makhov P, Gordon J, Ye M, Reitz AB, Childers WE, Skorski T, Kolenko V, Tulin AV. Non-NAD-like PARP-1 inhibitors in prostate cancer treatment. Biochem Pharmacol 2019; 167:149-162. [PMID: 30880062 PMCID: PMC6702078 DOI: 10.1016/j.bcp.2019.03.021] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 03/13/2019] [Indexed: 01/03/2023]
Abstract
In our previous studies of the molecular mechanisms of poly(ADP-ribose) polymerase 1 (PARP-1)-mediated transcriptional regulation we identified a novel class of PARP-1 inhibitors targeting the histone-dependent route of PARP-1 activation. Because histone-dependent activation is unique to PARP-1, non-NAD-like PARP-1 inhibitors have the potential to bypass the off-target effects of classical NAD-dependent PARP-1 inhibitors, such as olaparib, veliparib, and rucaparib. Furthermore, our recently published studies demonstrate that, compared to NAD-like PARP-1 inhibitors that are used clinically, the non-NAD-like PARP-1 inhibitor 5F02 exhibited superior antitumor activity in cell and animal models of human prostate cancer (PC). In this study, we further evaluated the antitumor activity of 5F02 and several of its novel analogues against PC cells. In contrast to NAD-like PARP-1 inhibitors, non-NAD-like PARP-1 inhibitors demonstrated efficacy against androgen-dependent and -independent routes of androgen receptor signaling activation. Our experiments reveal that methylation of the quaternary ammonium salt and the presence of esters were critical for the antitumor activity of 5F02 against PC cells. In addition, we examined the role of a related regulatory protein of PARP-1, called Poly(ADP-ribose) glycohydrolase (PARG), in prostate carcinogenesis. Our study reveals that PARG expression is severely disrupted in PC cells, which is associated with decreased integrity and localization of Cajal bodies (CB). Overall, the results of our study strengthen the justification for using non-NAD-like PARP-1 inhibitors as a novel therapeutic strategy for the treatment of advanced prostate cancer.
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Affiliation(s)
| | - Chao Wu
- Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Ali Divan
- University of North Dakota, Grand Forks, ND, United States
| | - Mark E McDonnell
- Fox Chase Chemical Diversity Center, Inc., Philadelphia, PA, United States
| | - Elizabeth Hewlett
- Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, PA, United States
| | - Peter Makhov
- Fox Chase Cancer Center, Philadelphia, PA, United States
| | - John Gordon
- Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, PA, United States
| | - Min Ye
- Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, PA, United States
| | - Allen B Reitz
- Fox Chase Chemical Diversity Center, Inc., Philadelphia, PA, United States
| | - Wayne E Childers
- Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, PA, United States
| | - Tomasz Skorski
- Department of Microbiology and Immunology and Fels Institute for Cancer Research and Molecular Biology, Temple University Lewis Katz School of Medicine, Philadelphia, PA, United States
| | | | - Alexei V Tulin
- University of North Dakota, Grand Forks, ND, United States.
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14
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Kumar C, P.T.V. L, Arunachalam A. Structure based pharmacophore study to identify possible natural selective PARP-1 trapper as anti-cancer agent. Comput Biol Chem 2019; 80:314-323. [DOI: 10.1016/j.compbiolchem.2019.04.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 04/29/2019] [Accepted: 04/30/2019] [Indexed: 02/06/2023]
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15
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Cohen-Armon M, Yeheskel A, Pascal JM. Signal-induced PARP1-Erk synergism mediates IEG expression. Signal Transduct Target Ther 2019; 4:8. [PMID: 30993015 PMCID: PMC6459926 DOI: 10.1038/s41392-019-0042-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 01/10/2019] [Accepted: 03/06/2019] [Indexed: 12/14/2022] Open
Abstract
A recently disclosed Erk-induced PARP1 activation mechanism mediates the expression of immediate early genes (IEGs) in response to a variety of extra- and intracellular signals implicated in memory acquisition, development and proliferation. Here, we review this mechanism, which is initiated by stimulation-induced binding of PARP1 to phosphorylated Erk translocated into the nucleus. This binding maintains long-lasting synergistic activity of these proteins, which offers a new pattern for targeted therapy.
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Affiliation(s)
- Malka Cohen-Armon
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, 69978 Israel
- Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv, 69978 Israel
| | - Adva Yeheskel
- Bioinformatics Unit, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, 69978 Israel
| | - John M. Pascal
- Department of Biochemistry and Molecular Medicine, University of Montreal, Québec, Canada
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16
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Jain PG, Patel BD. Medicinal chemistry approaches of poly ADP-Ribose polymerase 1 (PARP1) inhibitors as anticancer agents - A recent update. Eur J Med Chem 2019; 165:198-215. [PMID: 30684797 DOI: 10.1016/j.ejmech.2019.01.024] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 12/28/2018] [Accepted: 01/11/2019] [Indexed: 12/14/2022]
Abstract
Poly (ADP-ribose) Polymerase1 (PARP1) is a member of 17 membered PARP family having diversified biological functions such as synthetic lethality, DNA repair, apoptosis, necrosis, histone binding etc. It is primarily a chromatin-bound nuclear enzyme that gets activated by DNA damage. It binds to DNA signal- and double-strand breaks, does parylation of target proteins (using NAD+ as a substrate) like histones and other DNA repair proteins and modifies them as a part of DNA repair mechanism. Inhibition of PARP1 prevents the DNA repair and leads to cell death. Clinically, PARP1 Inhibitors have shown their potential in treating BRCAm breast and ovarian cancers and trials are going on for the treatment of other solid tumors like pancreatic, prostate, colorectal etc. as a single agent or in combination. There are currently three FDA approved PARP1 inhibitors namely Olaparib, Rucaparib and Niraparib in the market while Veliparib and Talazoparib are in the late stage of clinical development. All these molecules are nonselective PARP1 inhibitors with concurrent inhibition of PARP2 with similar potency. In addition, resistance to marketed PARP1 inhibitors has been reported. Overall, looking at the success rate of PARP1 inhibitors into various solid tumors, there is an urge of a novel and selective PARP1 inhibitors. This review provides an update on various newer heterocyclic PARP1 inhibitors reported in last three years along with their structural design strategies. We classified them into two main chemical classes; NAD analogues and non-NAD analogues and discussed the medicinal chemistry approaches of each class. To understand the structural features required for in-silico designing of next-generation PARP1 inhibitors, we also reported the crucial amino acid interactions of these inhibitors at the target site. Thus, present review provides the insight on recent development on new lead structures as PARP1 inhibitors, their SAR, an overview of in-vitro and in-vivo screening methods, current challenges and opinion on future designing of more selective and safe PARP1 inhibitors.
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Affiliation(s)
- Priyancy G Jain
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat, 382481, India
| | - Bhumika D Patel
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat, 382481, India.
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17
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Zakharenko AL, Lebedeva NA, Lavrik OI. DNA Repair Enzymes as Promising Targets in Oncotherapy. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2018. [DOI: 10.1134/s1068162017060140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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Visochek L, Castiel A, Mittelman L, Elkin M, Atias D, Golan T, Izraeli S, Peretz T, Cohen-Armon M. Exclusive destruction of mitotic spindles in human cancer cells. Oncotarget 2017; 8:20813-20824. [PMID: 28209915 PMCID: PMC5400547 DOI: 10.18632/oncotarget.15343] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 01/31/2017] [Indexed: 12/15/2022] Open
Abstract
We identified target proteins modified by phenanthrenes that cause exclusive eradication of human cancer cells. The cytotoxic activity of the phenanthrenes in a variety of human cancer cells is attributed by these findings to post translational modifications of NuMA and kinesins HSET/kifC1 and kif18A. Their activity prevented the binding of NuMA to α-tubulin and kinesins in human cancer cells, and caused aberrant spindles. The most efficient cytotoxic activity of the phenanthridine PJ34, caused significantly smaller aberrant spindles with disrupted spindle poles and scattered extra-centrosomes and chromosomes. Concomitantly, PJ34 induced tumor growth arrest of human malignant tumors developed in athymic nude mice, indicating the relevance of its activity for cancer therapy.
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Affiliation(s)
- Leonid Visochek
- The Neufeld Cardiac Research Institute, Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Asher Castiel
- Cancer Research Center, Sheba Medical Center, Ramat Gan 53621, Israel
| | - Leonid Mittelman
- The Imaging Unit, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Michael Elkin
- Sharett Oncology Institute, Hadassah Medical Center, Ein-Kerem, Jerusalem 91120, Israel
| | - Dikla Atias
- Cancer Research Center, Sheba Medical Center, Ramat Gan 53621, Israel
| | - Talia Golan
- Cancer Research Center, Sheba Medical Center, Ramat Gan 53621, Israel
| | - Shai Izraeli
- Cancer Research Center, Sheba Medical Center, Ramat Gan 53621, Israel.,The Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Tamar Peretz
- Sharett Oncology Institute, Hadassah Medical Center, Ein-Kerem, Jerusalem 91120, Israel
| | - Malka Cohen-Armon
- The Neufeld Cardiac Research Institute, Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel.,Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv 69978, Israel
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19
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Ferri M, Liscio P, Carotti A, Asciutti S, Sardella R, Macchiarulo A, Camaioni E. Targeting Wnt-driven cancers: Discovery of novel tankyrase inhibitors. Eur J Med Chem 2017; 142:506-522. [PMID: 29107427 DOI: 10.1016/j.ejmech.2017.09.030] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 09/15/2017] [Accepted: 09/16/2017] [Indexed: 01/11/2023]
Abstract
Recent years have seen substantially heightened interest in the discovery of tankyrase inhibitors (TNKSi) as new promising anticancer agents. In this framework, the aim of this review article is focused on the description of potent TNKSi also endowed with disruptor activity toward the Wnt/β-catenin signaling pathway. Beginning with an overview of the most characterized TNKSi deriving from several drug design approaches and classifying them on the basis of the molecular interactions with the target, we discuss only those ones acting against Wnt cancer cell lines. In addition, comprehensive structure property relationships (SPR) emerging from the hit evolution processes and preclinical results are provided. We then review the most promising TNKSi hitherto reported in literature, acting in vivo models of Wnt-driven cancers. Some outlooks on current issues and future directions in this field are also discussed.
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Affiliation(s)
- Martina Ferri
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - Paride Liscio
- TES Pharma, Via P. Togliatti 22bis, 06073 Terrioli, Corciano, Italy
| | - Andrea Carotti
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - Stefania Asciutti
- Icahn School of Medicine at Mount Sinai, Department of Oncological Sciences, 1425 Madison Ave, New York, NY 10029 USA
| | - Roccaldo Sardella
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - Antonio Macchiarulo
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - Emidio Camaioni
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy.
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20
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Gong C, Yang L, Zhou J, Guo X, Zhuang Z. Possible role of PAPR-1 in protecting human HaCaT cells against cytotoxicity of SiO2 nanoparticles. Toxicol Lett 2017; 280:213-221. [DOI: 10.1016/j.toxlet.2017.07.213] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 06/28/2017] [Accepted: 07/04/2017] [Indexed: 12/14/2022]
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21
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Ordway GA, Szebeni A, Hernandez LJ, Crawford JD, Szebeni K, Chandley MJ, Burgess KC, Miller C, Bakkalbasi E, Brown RW. Antidepressant-Like Actions of Inhibitors of Poly(ADP-Ribose) Polymerase in Rodent Models. Int J Neuropsychopharmacol 2017; 20:994-1004. [PMID: 29016792 PMCID: PMC5716178 DOI: 10.1093/ijnp/pyx068] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 07/28/2017] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Many patients suffering from depressive disorders are refractory to treatment with currently available antidepressant medications, while many more exhibit only a partial response. These factors drive research to discover new pharmacological approaches to treat depression. Numerous studies demonstrate evidence of inflammation and elevated oxidative stress in major depression. Recently, major depression has been shown to be associated with elevated levels of DNA oxidation in brain cells, accompanied by increased gene expression of the nuclear base excision repair enzyme, poly(ADP-ribose) polymerase-1. Given these findings and evidence that drugs that inhibit poly(ADP-ribose) polymerase-1 activity have antiinflammatory and neuroprotective properties, the present study was undertaken to examine the potential antidepressant properties of poly(ADP-ribose) polymerase inhibitors. METHODS Two rodent models, the Porsolt swim test and repeated exposure to psychological stressors, were used to test the poly(ADP-ribose) polymerase inhibitor, 3-aminobenzamide, for potential antidepressant activity. Another poly(ADP-ribose) polymerase inhibitor, 5-aminoisoquinolinone, was also tested. RESULTS Poly(ADP-ribose) polymerase inhibitors produced antidepressant-like effects in the Porsolt swim test, decreasing immobility time, and increasing latency to immobility, similar to the effects of fluoxetine. In addition, 3-aminobenzamide treatment increased sucrose preference and social interaction times relative to vehicle-treated control rats following repeated exposure to combined social defeat and unpredictable stress, mediating effects similar to fluoxetine treatment. CONCLUSIONS The poly(ADP-ribose) polymerase inhibitors 3-aminobenzamide and 5-aminoisoquinolinone exhibit antidepressant-like activity in 2 rodent stress models and uncover poly(ADP-ribose) polymerase as a unique molecular target for the potential development of a novel class of antidepressants.
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Affiliation(s)
- Gregory A Ordway
- Department of Biomedical Sciences (Drs Ordway and Szebeni, Ms Hernandez, Drs Crawford and Szebeni, Ms Burgess, and Dr Brown) and Department of Psychiatry and Behavioral Sciences (Dr Ordway), James H. Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee; Department of Health Sciences, College of Public Health, East Tennessee State University, Johnson City, Tennessee (Dr Chandley); DS Therapeutics, Houston, Texas (Dr Miller and Dr Bakkalbasi),Correspondence: Gregory A. Ordway, PhD, East Tennessee State University, PO Box 70577, Johnson City, 37614 ()
| | - Attila Szebeni
- Department of Biomedical Sciences (Drs Ordway and Szebeni, Ms Hernandez, Drs Crawford and Szebeni, Ms Burgess, and Dr Brown) and Department of Psychiatry and Behavioral Sciences (Dr Ordway), James H. Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee; Department of Health Sciences, College of Public Health, East Tennessee State University, Johnson City, Tennessee (Dr Chandley); DS Therapeutics, Houston, Texas (Dr Miller and Dr Bakkalbasi)
| | - Liza J Hernandez
- Department of Biomedical Sciences (Drs Ordway and Szebeni, Ms Hernandez, Drs Crawford and Szebeni, Ms Burgess, and Dr Brown) and Department of Psychiatry and Behavioral Sciences (Dr Ordway), James H. Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee; Department of Health Sciences, College of Public Health, East Tennessee State University, Johnson City, Tennessee (Dr Chandley); DS Therapeutics, Houston, Texas (Dr Miller and Dr Bakkalbasi)
| | - Jessica D Crawford
- Department of Biomedical Sciences (Drs Ordway and Szebeni, Ms Hernandez, Drs Crawford and Szebeni, Ms Burgess, and Dr Brown) and Department of Psychiatry and Behavioral Sciences (Dr Ordway), James H. Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee; Department of Health Sciences, College of Public Health, East Tennessee State University, Johnson City, Tennessee (Dr Chandley); DS Therapeutics, Houston, Texas (Dr Miller and Dr Bakkalbasi)
| | - Katalin Szebeni
- Department of Biomedical Sciences (Drs Ordway and Szebeni, Ms Hernandez, Drs Crawford and Szebeni, Ms Burgess, and Dr Brown) and Department of Psychiatry and Behavioral Sciences (Dr Ordway), James H. Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee; Department of Health Sciences, College of Public Health, East Tennessee State University, Johnson City, Tennessee (Dr Chandley); DS Therapeutics, Houston, Texas (Dr Miller and Dr Bakkalbasi)
| | - Michelle J Chandley
- Department of Biomedical Sciences (Drs Ordway and Szebeni, Ms Hernandez, Drs Crawford and Szebeni, Ms Burgess, and Dr Brown) and Department of Psychiatry and Behavioral Sciences (Dr Ordway), James H. Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee; Department of Health Sciences, College of Public Health, East Tennessee State University, Johnson City, Tennessee (Dr Chandley); DS Therapeutics, Houston, Texas (Dr Miller and Dr Bakkalbasi)
| | - Katherine C Burgess
- Department of Biomedical Sciences (Drs Ordway and Szebeni, Ms Hernandez, Drs Crawford and Szebeni, Ms Burgess, and Dr Brown) and Department of Psychiatry and Behavioral Sciences (Dr Ordway), James H. Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee; Department of Health Sciences, College of Public Health, East Tennessee State University, Johnson City, Tennessee (Dr Chandley); DS Therapeutics, Houston, Texas (Dr Miller and Dr Bakkalbasi)
| | - Corwin Miller
- Department of Biomedical Sciences (Drs Ordway and Szebeni, Ms Hernandez, Drs Crawford and Szebeni, Ms Burgess, and Dr Brown) and Department of Psychiatry and Behavioral Sciences (Dr Ordway), James H. Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee; Department of Health Sciences, College of Public Health, East Tennessee State University, Johnson City, Tennessee (Dr Chandley); DS Therapeutics, Houston, Texas (Dr Miller and Dr Bakkalbasi)
| | - Erol Bakkalbasi
- Department of Biomedical Sciences (Drs Ordway and Szebeni, Ms Hernandez, Drs Crawford and Szebeni, Ms Burgess, and Dr Brown) and Department of Psychiatry and Behavioral Sciences (Dr Ordway), James H. Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee; Department of Health Sciences, College of Public Health, East Tennessee State University, Johnson City, Tennessee (Dr Chandley); DS Therapeutics, Houston, Texas (Dr Miller and Dr Bakkalbasi)
| | - Russell W Brown
- Department of Biomedical Sciences (Drs Ordway and Szebeni, Ms Hernandez, Drs Crawford and Szebeni, Ms Burgess, and Dr Brown) and Department of Psychiatry and Behavioral Sciences (Dr Ordway), James H. Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee; Department of Health Sciences, College of Public Health, East Tennessee State University, Johnson City, Tennessee (Dr Chandley); DS Therapeutics, Houston, Texas (Dr Miller and Dr Bakkalbasi)
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22
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Baptista SJ, Silva MMC, Moroni E, Meli M, Colombo G, Dinis TCP, Salvador JAR. Novel PARP-1 Inhibitor Scaffolds Disclosed by a Dynamic Structure-Based Pharmacophore Approach. PLoS One 2017; 12:e0170846. [PMID: 28122037 PMCID: PMC5266331 DOI: 10.1371/journal.pone.0170846] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 01/11/2017] [Indexed: 12/20/2022] Open
Abstract
PARP-1 inhibition has been studied over the last decades for the treatment of various diseases. Despite the fact that several molecules act as PARP-1 inhibitors, a reduced number of compounds are used in clinical practice. To identify new compounds with a discriminatory PARP-1 inhibitory function, explicit-solvent molecular dynamics simulations using different inhibitors bound to the PARP-1 catalytic domain were performed. The representative structures obtained were used to generate structure-based pharmacophores, taking into account the dynamic features of receptor-ligand interactions. Thereafter, a virtual screening of compound databases using the pharmacophore models obtained was performed and the hits retrieved were subjected to molecular docking-based scoring. The drug-like molecules featuring the best ranking were evaluated for their PARP-1 inhibitory activity and IC50 values were calculated for the top scoring docked compounds. Altogether, three new PARP-1 inhibitor chemotypes were identified.
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Affiliation(s)
- Salete J. Baptista
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Maria M. C. Silva
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Elisabetta Moroni
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Milano, Italy
| | - Massimiliano Meli
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Milano, Italy
| | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Milano, Italy
- * E-mail: (GC); (JARS)
| | - Teresa C. P. Dinis
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
| | - Jorge A. R. Salvador
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- * E-mail: (GC); (JARS)
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23
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Thomas C, Ji Y, Lodhi N, Kotova E, Pinnola AD, Golovine K, Makhov P, Pechenkina K, Kolenko V, Tulin AV. Non-NAD-Like poly(ADP-Ribose) Polymerase-1 Inhibitors effectively Eliminate Cancer in vivo. EBioMedicine 2016; 13:90-98. [PMID: 27727003 PMCID: PMC5264309 DOI: 10.1016/j.ebiom.2016.10.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 10/03/2016] [Accepted: 10/03/2016] [Indexed: 01/29/2023] Open
Abstract
The clinical potential of PARP-1 inhibitors has been recognized >10years ago, prompting intensive research on their pharmacological application in several branches of medicine, particularly in oncology. However, natural or acquired resistance of tumors to known PARP-1 inhibitors poses a serious problem for their clinical implementation. Present study aims to reignite clinical interest to PARP-1 inhibitors by introducing a new method of identifying highly potent inhibitors and presenting the largest known collection of structurally diverse inhibitors. The majority of PARP-1 inhibitors known to date have been developed as NAD competitors. NAD is utilized by many enzymes other than PARP-1, resulting in a trade-off trap between their specificity and efficacy. To circumvent this problem, we have developed a new strategy to blindly screen a small molecule library for PARP-1 inhibitors by targeting a highly specific rout of its activation. Based on this screen, we present a collection of PARP-1 inhibitors and provide their structural classification. In addition to compounds that show structural similarity to NAD or known PARP-1 inhibitors, the screen identified structurally new non-NAD-like inhibitors that block PARP-1 activity in cancer cells with greater efficacy and potency than classical PARP-1 inhibitors currently used in clinic. These non-NAD-like PARP-1 inhibitors are effective against several types of human cancer xenografts, including kidney, prostate, and breast tumors in vivo. Our pre-clinical testing of these inhibitors using laboratory animals has established a strong foundation for advancing the new inhibitors to clinical trials.
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Affiliation(s)
- Colin Thomas
- Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Yingbiao Ji
- Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Niraj Lodhi
- Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Elena Kotova
- Fox Chase Cancer Center, Philadelphia, PA, United States
| | | | | | - Peter Makhov
- Fox Chase Cancer Center, Philadelphia, PA, United States
| | | | | | - Alexei V Tulin
- Fox Chase Cancer Center, Philadelphia, PA, United States.
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24
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Xu J, Wang H, Won SJ, Basu J, Kapfhamer D, Swanson RA. Microglial activation induced by the alarmin S100B is regulated by poly(ADP-ribose) polymerase-1. Glia 2016; 64:1869-78. [PMID: 27444121 DOI: 10.1002/glia.23026] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Revised: 06/19/2016] [Accepted: 06/21/2016] [Indexed: 11/11/2022]
Abstract
Brain injury resulting from stroke or trauma can be exacerbated by the release of proinflammatory cytokines, proteases, and reactive oxygen species by activated microglia. The microglial activation resulting from brain injury is mediated in part by alarmins, which are signaling molecules released from damaged cells. The nuclear enzyme poly(ADP-ribose) polymerase-1 (PARP-1) has been shown to regulate microglial activation after brain injury, and here we show that signaling effects of the alarmin S100B are regulated by PARP-1. S100B is a protein localized predominantly to astrocytes. Exogenous S100B added to primary microglial cultures induced a rapid change in microglial morphology, upregulation of IL-1β, TNFα, and iNOS gene expression, and release of matrix metalloproteinase 9 and nitric oxide. Most, though not all of these effects were attenuated in PARP-1(-/-) microglia and in wild-type microglia treated with the PARP inhibitor, veliparib. Microglial activation and gene expression changes induced by S100B injected directly into brain were likewise attenuated by PARP-1 inhibition. The anti-inflammatory effects of PARP-1 inhibitors in acutely injured brain may thus be mediated in part through effects on S100B signaling pathways. GLIA 2016;64:1869-1878.
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Affiliation(s)
- Jianguo Xu
- Department of Neurosurgery, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, Jiangsu Province, People's Repubic of China.,Department of Neurology, University of California San Francisco and San Francisco Veterans Affairs Medical Center, San Francisco, California
| | - Handong Wang
- Department of Neurosurgery, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, Jiangsu Province, People's Repubic of China
| | - Seok Joon Won
- Department of Neurology, University of California San Francisco and San Francisco Veterans Affairs Medical Center, San Francisco, California
| | - Jayinee Basu
- Department of Neurology, University of California San Francisco and San Francisco Veterans Affairs Medical Center, San Francisco, California
| | - David Kapfhamer
- Department of Neurology, University of California San Francisco and San Francisco Veterans Affairs Medical Center, San Francisco, California
| | - Raymond A Swanson
- Department of Neurology, University of California San Francisco and San Francisco Veterans Affairs Medical Center, San Francisco, California.
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25
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Gavande NS, VanderVere-Carozza PS, Hinshaw HD, Jalal SI, Sears CR, Pawelczak KS, Turchi JJ. DNA repair targeted therapy: The past or future of cancer treatment? Pharmacol Ther 2016; 160:65-83. [PMID: 26896565 DOI: 10.1016/j.pharmthera.2016.02.003] [Citation(s) in RCA: 280] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The repair of DNA damage is a complex process that relies on particular pathways to remedy specific types of damage to DNA. The range of insults to DNA includes small, modest changes in structure including mismatched bases and simple methylation events to oxidized bases, intra- and interstrand DNA crosslinks, DNA double strand breaks and protein-DNA adducts. Pathways required for the repair of these lesions include mismatch repair, base excision repair, nucleotide excision repair, and the homology directed repair/Fanconi anemia pathway. Each of these pathways contributes to genetic stability, and mutations in genes encoding proteins involved in these pathways have been demonstrated to promote genetic instability and cancer. In fact, it has been suggested that all cancers display defects in DNA repair. It has also been demonstrated that the ability of cancer cells to repair therapeutically induced DNA damage impacts therapeutic efficacy. This has led to targeting DNA repair pathways and proteins to develop anti-cancer agents that will increase sensitivity to traditional chemotherapeutics. While initial studies languished and were plagued by a lack of specificity and a defined mechanism of action, more recent approaches to exploit synthetic lethal interaction and develop high affinity chemical inhibitors have proven considerably more effective. In this review we will highlight recent advances and discuss previous failures in targeting DNA repair to pave the way for future DNA repair targeted agents and their use in cancer therapy.
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Affiliation(s)
- Navnath S Gavande
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | | | - Hilary D Hinshaw
- Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - Shadia I Jalal
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - Catherine R Sears
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | | | - John J Turchi
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, United States; NERx Biosciences, Indianapolis, IN 46202, United States; Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, United States.
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