1
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Gomatam A, Hirlekar BU, Singh KD, Murty US, Dixit VA. Improved QSAR models for PARP-1 inhibition using data balancing, interpretable machine learning, and matched molecular pair analysis. Mol Divers 2024; 28:2135-2152. [PMID: 38374474 DOI: 10.1007/s11030-024-10809-9] [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: 10/17/2023] [Accepted: 01/07/2024] [Indexed: 02/21/2024]
Abstract
The poly (ADP-ribose) polymerase-1 (PARP-1) enzyme is an important target in the treatment of breast cancer. Currently, treatment options include the drugs Olaparib, Niraparib, Rucaparib, and Talazoparib; however, these drugs can cause severe side effects including hematological toxicity and cardiotoxicity. Although in silico models for the prediction of PARP-1 activity have been developed, the drawbacks of these models include low specificity, a narrow applicability domain, and a lack of interpretability. To address these issues, a comprehensive machine learning (ML)-based quantitative structure-activity relationship (QSAR) approach for the informed prediction of PARP-1 activity is presented. Classification models built using the Synthetic Minority Oversampling Technique (SMOTE) for data balancing gave robust and predictive models based on the K-nearest neighbor algorithm (accuracy 0.86, sensitivity 0.88, specificity 0.80). Regression models were built on structurally congeneric datasets, with the models for the phthalazinone class and fused cyclic compounds giving the best performance. In accordance with the Organization for Economic Cooperation and Development (OECD) guidelines, a mechanistic interpretation is proposed using the Shapley Additive Explanations (SHAP) to identify the important topological features to differentiate between PARP-1 actives and inactives. Moreover, an analysis of the PARP-1 dataset revealed the prevalence of activity cliffs, which possibly negatively impacts the model's predictive performance. Finally, a set of chemical transformation rules were extracted using the matched molecular pair analysis (MMPA) which provided mechanistic insights and can guide medicinal chemists in the design of novel PARP-1 inhibitors.
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Affiliation(s)
- Anish Gomatam
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, (NIPER Guwahati), Department of Pharmaceuticals, Ministry of Chemicals and Fertilizers, Govt. of India, Sila Katamur (Halugurisuk), Dist: Kamrup, P.O.: Changsari, Guwahati, Assam, 781101, India
| | - Bhakti Umesh Hirlekar
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, (NIPER Guwahati), Department of Pharmaceuticals, Ministry of Chemicals and Fertilizers, Govt. of India, Sila Katamur (Halugurisuk), Dist: Kamrup, P.O.: Changsari, Guwahati, Assam, 781101, India
| | - Krishan Dev Singh
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, (NIPER Guwahati), Department of Pharmaceuticals, Ministry of Chemicals and Fertilizers, Govt. of India, Sila Katamur (Halugurisuk), Dist: Kamrup, P.O.: Changsari, Guwahati, Assam, 781101, India
| | - Upadhyayula Suryanarayana Murty
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, (NIPER Guwahati), Department of Pharmaceuticals, Ministry of Chemicals and Fertilizers, Govt. of India, Sila Katamur (Halugurisuk), Dist: Kamrup, P.O.: Changsari, Guwahati, Assam, 781101, India
| | - Vaibhav A Dixit
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, (NIPER Guwahati), Department of Pharmaceuticals, Ministry of Chemicals and Fertilizers, Govt. of India, Sila Katamur (Halugurisuk), Dist: Kamrup, P.O.: Changsari, Guwahati, Assam, 781101, India.
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2
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El Hassab MA, El-Hafeez AAA, Almahli H, Elsayed ZM, Eldehna WM, Hassan GS, Abou-Seri SM. Phthalimide-tethered isatins as novel poly(ADP-ribose) polymerase inhibitors: Design, synthesis, biological evaluations, and molecular modeling investigations. Arch Pharm (Weinheim) 2024; 357:e2300599. [PMID: 38100160 DOI: 10.1002/ardp.202300599] [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: 10/14/2023] [Revised: 11/20/2023] [Accepted: 11/23/2023] [Indexed: 03/03/2024]
Abstract
Humanity is currently facing various diseases with significant mortality rates, particularly those associated with malignancies. Numerous enzymes and proteins have been identified as highly promising targets for the treatment of cancer. The poly(ADP-ribose) polymerases (PARPs) family comprises 17 members which are essential in DNA damage repair, allowing the survival of cancer cells. Unlike other PARP family members, PARP-1 and, to a lesser extent, PARP-2 show more than 90% activity in response to DNA damage. PARP-1 levels were shown to be elevated in various tumor cells, including breast, lung, ovarian, and prostate cancer and melanomas. Accordingly, novel series of phthalimide-tethered isatins (6a-n, 10a-e, and 11a-e) were synthesized as potential PARP-1 inhibitors endowed with anticancer activity. All the synthesized molecules were assessed against PARP-1, where compounds 6f and 10d showed nanomolar activities with IC50 = 15.56 ± 2.85 and 13.65 ± 1.42 nM, respectively. Also, the assessment of the antiproliferative effects of the synthesized isatins was conducted on four cancer cell lines: leukemia (K-562), liver (HepG2), and breast (MCF-7 and HCC1937) cancers. Superiorly, compounds 6f and 10d demonstrated submicromolar IC50 values against breast cancer MCF-7 (IC50 = 0.92 ± 0.18 and 0.67 ± 0.12 µM, respectively) and HCC1937 (IC50 = 0.88 ± 0.52 and 0.53 ± 0.11 µM, respectively) cell lines. In addition, compounds 6f and 10d induced arrest in the G2/M phase of the cell cycle as compared to untreated cells. Finally, in silico studies, including docking and molecular dynamic simulations, were performed to justify the biological results.
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Affiliation(s)
- Mahmoud A El Hassab
- Department of Medicinal Chemistry, Faculty of Pharmacy, King Salman International University (KSIU), Ras Sudr, South Sinai, Egypt
| | - Amer Ali Abd El-Hafeez
- Cancer Biology Department, Pharmacology and Experimental Oncology Unit, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Hadia Almahli
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Zainab M Elsayed
- Scientific Research and Innovation Support Unit, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Wagdy M Eldehna
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
- School of Biotechnology, Badr University in Cairo, Badr City, Egypt
| | - Ghaneya S Hassan
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
- Pharmaceutical Chemistry Department, School of Pharmacy, Badr University in Cairo (BUC), Badr City, Egypt
| | - Sahar M Abou-Seri
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
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3
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Zhang X, Pang W, Li T, Lin T, Yuan J, Xu S. Design, synthesis, and biological activity evaluation of new tankyrase-2 directed inhibitors. Chem Biol Drug Des 2024; 103:e14360. [PMID: 37814809 DOI: 10.1111/cbdd.14360] [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: 05/13/2023] [Revised: 09/05/2023] [Accepted: 09/12/2023] [Indexed: 10/11/2023]
Abstract
A new series of flavonoids and quinolone derivatives were designed, synthesized and, evaluated for their biological activity. Among them, compound 14e showed better inhibition potency against TNKS2 in comparison with G007-LK, one of the most potent preclinical stage TNKS inhibitor. Molecular docking results showed that 14e occupied both the adenosine and nicotinamide pockets and formed a hydrogen bond with Met1054 of TNKS2. This study provides a lead for the design and discovery of potent and selective TNKS2 inhibitors.
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Affiliation(s)
- Xiaoli Zhang
- College of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai, China
| | - Wan Pang
- College of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai, China
| | - Tang Li
- College of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai, China
| | - Taofeng Lin
- College of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai, China
| | - Juanchan Yuan
- College of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai, China
| | - Songhui Xu
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, China
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4
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Thakur A, Rana M, Ritika, Mathew J, Nepali S, Pan CH, Liou JP, Nepali K. Small molecule tractable PARP inhibitors: Scaffold construction approaches, mechanistic insights and structure activity relationship. Bioorg Chem 2023; 141:106893. [PMID: 37783100 DOI: 10.1016/j.bioorg.2023.106893] [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: 08/09/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 10/04/2023]
Abstract
Diverse drug design strategies viz. molecular hybridization, substituent installation, scaffold hopping, isosteric replacement, high-throughput screening, induction and separation of chirality, structure modifications of phytoconstituents and use of structural templates have been exhaustively leveraged in the last decade to load the chemical toolbox of PARP inhibitors. Resultantly, numerous promising scaffolds have been pinpointed that in turn have led to the resuscitation of the credence to PARP inhibitors as cancer therapeutics. This review briefly presents the physiological functions of PARPs, the pharmacokinetics, and pharmacodynamics, and the interaction profiles of FDA-approved PARP inhibitors. Comprehensively covered is the section on the drug design strategies employed by drug discovery enthusiasts for furnishing PARP inhibitors. The impact of structural variations in the template of designed scaffolds on enzymatic and cellular activity (structure-activity relationship studies) has been discussed. The insights gained through the biological evaluation such as profiling of physicochemical properties andin vitroADME properties, PK assessments, and high-dose pharmacology are covered.
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Affiliation(s)
- Amandeep Thakur
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei 110031, Taiwan
| | - Mandeep Rana
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei 110031, Taiwan
| | - Ritika
- College of Medicine, Taipei Medical University, Taipei 110031, Taiwan
| | - Jacob Mathew
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 106335, Taiwan
| | - Sanya Nepali
- Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, India
| | - Chun-Hsu Pan
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei 110031, Taiwan; Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taiwan
| | - Jing Ping Liou
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei 110031, Taiwan; Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taiwan
| | - Kunal Nepali
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei 110031, Taiwan; Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taiwan.
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5
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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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6
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Murthy S, Nizi MG, Maksimainen MM, Massari S, Alaviuhkola J, Lippok BE, Vagaggini C, Sowa ST, Galera-Prat A, Ashok Y, Venkannagari H, Prunskaite-Hyyryläinen R, Dreassi E, Lüscher B, Korn P, Tabarrini O, Lehtiö L. [1,2,4]Triazolo[3,4- b]benzothiazole Scaffold as Versatile Nicotinamide Mimic Allowing Nanomolar Inhibition of Different PARP Enzymes. J Med Chem 2023; 66:1301-1320. [PMID: 36598465 PMCID: PMC9884089 DOI: 10.1021/acs.jmedchem.2c01460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We report [1,2,4]triazolo[3,4-b]benzothiazole (TBT) as a new inhibitor scaffold, which competes with nicotinamide in the binding pocket of human poly- and mono-ADP-ribosylating enzymes. The binding mode was studied through analogues and cocrystal structures with TNKS2, PARP2, PARP14, and PARP15. Based on the substitution pattern, we were able to identify 3-amino derivatives 21 (OUL243) and 27 (OUL232) as inhibitors of mono-ARTs PARP7, PARP10, PARP11, PARP12, PARP14, and PARP15 at nM potencies, with 27 being the most potent PARP10 inhibitor described to date (IC50 of 7.8 nM) and the first PARP12 inhibitor ever reported. On the contrary, hydroxy derivative 16 (OUL245) inhibits poly-ARTs with a selectivity toward PARP2. The scaffold does not possess inherent cell toxicity, and the inhibitors can enter cells and engage with the target protein. This, together with favorable ADME properties, demonstrates the potential of TBT scaffold for future drug development efforts toward selective inhibitors against specific enzymes.
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Affiliation(s)
- Sudarshan Murthy
- Faculty
of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu90220, Finland
| | - Maria Giulia Nizi
- Department
of Pharmaceutical Sciences, University of
Perugia, Perugia06123, Italy
| | - Mirko M. Maksimainen
- Faculty
of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu90220, Finland
| | - Serena Massari
- Department
of Pharmaceutical Sciences, University of
Perugia, Perugia06123, Italy
| | - Juho Alaviuhkola
- Faculty
of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu90220, Finland
| | - Barbara E. Lippok
- Institute
of Biochemistry and Molecular Biology, RWTH
Aachen University, Aachen52074, Germany
| | - Chiara Vagaggini
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, SienaI-53100, Italy
| | - Sven T. Sowa
- Faculty
of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu90220, Finland
| | - Albert Galera-Prat
- Faculty
of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu90220, Finland
| | - Yashwanth Ashok
- Faculty
of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu90220, Finland
| | - Harikanth Venkannagari
- Faculty
of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu90220, Finland
| | | | - Elena Dreassi
- Department
of Biotechnology, Chemistry and Pharmacy, University of Siena, SienaI-53100, Italy
| | - Bernhard Lüscher
- Institute
of Biochemistry and Molecular Biology, RWTH
Aachen University, Aachen52074, Germany
| | - Patricia Korn
- Institute
of Biochemistry and Molecular Biology, RWTH
Aachen University, Aachen52074, Germany
| | - Oriana Tabarrini
- Department
of Pharmaceutical Sciences, University of
Perugia, Perugia06123, Italy,
| | - Lari Lehtiö
- Faculty
of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu90220, Finland,
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7
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Vaishali M. Patil. Role of CSF1R Inhibitor Pexidartinib for the Treatment of Cancer. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2022. [DOI: 10.1134/s1068162023010223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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8
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Marmouset V, Decroocq J, Garciaz S, Etienne G, Belhabri A, Bertoli S, Gastaud L, Simand C, Chantepie S, Uzunov M, Genthon A, Berthon C, Chiche E, Dumas PY, Vargaftig J, Salmeron G, Lemasle E, Tavernier E, Delage J, Loirat M, Morineau N, Blanc-Durand F, Pautier P, Vergé V, Auger N, Thomas M, Stefani L, Lepelley M, Boyer T, Thepot S, Gourin MP, Bourquard P, Duchmann M, Morice PM, Michallet M, Adès L, Fenaux P, Récher C, Dombret H, Pagès A, Marzac C, Leary A, Micol JB. Therapy-related Myeloid Neoplasms Following PARP Inhibitors: Real-life Experience. Clin Cancer Res 2022; 28:5211-5220. [PMID: 36201165 DOI: 10.1158/1078-0432.ccr-22-1622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/27/2022] [Accepted: 10/04/2022] [Indexed: 01/24/2023]
Abstract
PURPOSE To provide insights into the diagnosis and management of therapy-related myeloid neoplasms (t-MN) following PARP inhibitors (PARPi). EXPERIMENTAL DESIGN In a French cancer center, we identified and described the profiles of 13 t-MN diagnosed among 37 patients with ovarian cancer referred to hematology consultation for cytopenia under PARPi. Next, we described these 13 t-MN post-PARPi among 37 t-MN post ovarian cancer according to PARPi exposure. Finally, we described 69 t-MN post-PARPi in a national cohort. RESULTS From 2016 to 2021, cumulative incidence of t-MN was 3.5% (13/373) among patients with ovarian cancer treated with PARPi. At time of hematologic consultation, patients with t-MN had a longer PARPi exposure (9 vs. 3 months, P = 0.01), lower platelet count (74 vs. 173 G/L, P = 0.0005), and more cytopenias (2 vs. 1, P = 0.0005). Compared with t-MN not exposed to PARPi, patients with t-MN-PARPi had more BRCA1/2 germline mutation (61.5% vs. 0%, P = 0.03) but similar overall survival (OS). In the national cohort, most t-MN post-PARPi had a complex karyotype (61%) associated with a high rate of TP53 mutation (71%). Median OS was 9.6 months (interquartile range, 4-14.6). In multivariate analysis, a longer time between end of PARPi and t-MN (HR, 1.046; P = 0.02), olaparib compared with other PARPi (HR, 5.82; P = 0.003) and acute myeloid leukemia (HR, 2.485; P = 0.01) were associated with shorter OS. CONCLUSIONS In a large series, we described a high incidence of t-MN post-PARPi associated with unfavorable cytogenetic and molecular abnormalities leading to poor OS. Early detection is crucial, particularly in cases of delayed cytopenia.
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Affiliation(s)
- Vincent Marmouset
- Department of Hematology, Gustave Roussy, Université Paris-Saclay, Villejuif, France
- Interception Program, Personalized Cancer Prevention Center, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Justine Decroocq
- Assistance Publique-Hôpitaux de Paris, Centre-Université de Paris, Service d'Hématologie Clinique, Hôpital Cochin, Paris, France
| | - Sylvain Garciaz
- Institut Paoli Calmettes, Marseille, France
- Cancer Research Center of Marseille, INSERM U1068, Aix-Marseille University, Marseille, France
| | | | - Amine Belhabri
- Department of Oncology, Centre Leon Berard, Lyon, France
| | - Sarah Bertoli
- Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, Université Toulouse III Paul Sabatier, Toulouse, France
| | | | - Célestine Simand
- Department of Hematology, Institute for Cancer Strasbourg-Europe (ICANS), Strasbourg University, Strasbourg, France
| | - Sylvain Chantepie
- Department of Clinical Hematology, Caen University Hospital, Caen, France
| | - Madalina Uzunov
- Service d'hématologie adulte, Hôpital Pitié-Salpêtrière, Paris, France
| | - Alexis Genthon
- Department of Clinical Hematology, Saint Antoine Hospital, Sorbonne University, INSERM UMR-S 938, Paris, France
| | - Céline Berthon
- Department of Hematology, CHU Lille, Lille, France
- University of Lille, CNRS, Inserm, CHU Lille, IRCL, UMR9020 - UMR1277 - Canther - Cancer heterogeneity, plasticity and resistance to therapies, Lille, France
| | | | - Pierre-Yves Dumas
- CHU Bordeaux, Service d'Hématologie Clinique et de Thérapie Cellulaire, Bordeaux, France
| | | | | | - Emilie Lemasle
- Département d'hématologie, Hôpital Henri Becquerel, Rouen, France
| | - Emmanuelle Tavernier
- Hématologie, Institut de Cancérologie-Hématologie Universitaire de Saint Etienne, France
| | - Jérémy Delage
- Département d'hématologie clinique, Saint Eloi, Montpellier, France
| | - Marion Loirat
- Service d'hématologie, Hôpital Saint Nazaire, Saint-Nazaire, France
| | | | - Félix Blanc-Durand
- Department of Oncology, Gustave Roussy, Université Paris-Saclay, Villejuif, France
- INSERM U981, Villejuif, France
- Interception Program, Personalized Cancer Prevention Center, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Patricia Pautier
- Department of Oncology, Gustave Roussy, Université Paris-Saclay, Villejuif, France
- INSERM U981, Villejuif, France
- Interception Program, Personalized Cancer Prevention Center, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Véronique Vergé
- Department of Biology, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Nathalie Auger
- Department of Biology, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | | | | | - Marion Lepelley
- Centre Régional de Pharmacovigilance - Addictovigilance, CHU de Grenoble-Alpes, France
| | - Thomas Boyer
- Laboratoire d'Hématologie, Centre Hospitalier Universitaire d'Amiens, Amiens, France
| | | | | | | | - Matthieu Duchmann
- Université de Paris, Génomes, Biologie Cellulaire et Thérapeutique Unité (U)944, INSERM, Centre National de la Recherche Scientifique (CNRS), Paris, France
| | - Pierre-Marie Morice
- Department of Clinical Hematology, Caen University Hospital, Caen, France
- UNICAEN, INSERM U1086 ANTICIPE (Interdisciplinary Research Unit for Cancer Prevention and Treatment), Normandie University, Caen, France
| | | | - Lionel Adès
- Hématologie Sénior Hôpital Saint Louis, Assistance publique hôpitaux de paris, and Université de Paris Cité, Paris, France
| | - Pierre Fenaux
- Hématologie Sénior Hôpital Saint Louis, Assistance publique hôpitaux de paris, and Université de Paris Cité, Paris, France
| | - Christian Récher
- Centre Hospitalier Universitaire de Toulouse, Institut Universitaire du Cancer de Toulouse Oncopole, Université Toulouse III Paul Sabatier, Toulouse, France
| | - Hervé Dombret
- Adult Hematology Department, Saint-Louis Hospital, APHP, URP3518, Institut de Recherche Saint-Louis, Université de Paris, Paris, France
| | - Arnaud Pagès
- Bureau de Biostatistique et d'Épidémiologie - Gustave Roussy Équipe Oncostat - CESP U1018 - Inserm, France
| | - Christophe Marzac
- Department of Biology, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Alexandra Leary
- Department of Oncology, Gustave Roussy, Université Paris-Saclay, Villejuif, France
- INSERM U981, Villejuif, France
- Interception Program, Personalized Cancer Prevention Center, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Jean-Baptiste Micol
- Department of Hematology, Gustave Roussy, Université Paris-Saclay, Villejuif, France
- Interception Program, Personalized Cancer Prevention Center, Gustave Roussy, Université Paris-Saclay, Villejuif, France
- INSERM U1287, Gustave Roussy, Université Paris-Saclay, Villejuif, France
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9
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Nizi M, Maksimainen MM, Lehtiö L, Tabarrini O. Medicinal Chemistry Perspective on Targeting Mono-ADP-Ribosylating PARPs with Small Molecules. J Med Chem 2022; 65:7532-7560. [PMID: 35608571 PMCID: PMC9189837 DOI: 10.1021/acs.jmedchem.2c00281] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Indexed: 12/13/2022]
Abstract
Major advances have recently defined functions for human mono-ADP-ribosylating PARP enzymes (mono-ARTs), also opening up potential applications for targeting them to treat diseases. Structural biology combined with medicinal chemistry has allowed the design of potent small molecule inhibitors which typically bind to the catalytic domain. Most of these inhibitors are at the early stages, but some have already a suitable profile to be used as chemical tools. One compound targeting PARP7 has even progressed to clinical trials. In this review, we collect inhibitors of mono-ARTs with a typical "H-Y-Φ" motif (Φ = hydrophobic residue) and focus on compounds that have been reported as active against one or a restricted number of enzymes. We discuss them from a medicinal chemistry point of view and include an analysis of the available crystal structures, allowing us to craft a pharmacophore model that lays the foundation for obtaining new potent and more specific inhibitors.
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Affiliation(s)
- Maria
Giulia Nizi
- Department
of Pharmaceutical Sciences, University of
Perugia, 06123 Perugia, Italy
| | - Mirko M. Maksimainen
- Faculty
of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 5400 Oulu, Finland
| | - Lari Lehtiö
- Faculty
of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, 5400 Oulu, Finland
| | - Oriana Tabarrini
- Department
of Pharmaceutical Sciences, University of
Perugia, 06123 Perugia, Italy
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10
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Taayoshi F, Iraji A, Moazzam A, Soleimani M, Asadi M, Pedrood K, Akbari M, Salehabadi H, Larijani B, Adibpour N, Mahdavi M. Synthesis, molecular docking, and cytotoxicity of quinazolinone and dihydroquinazolinone derivatives as cytotoxic agents. BMC Chem 2022; 16:35. [PMID: 35585608 PMCID: PMC9118628 DOI: 10.1186/s13065-022-00825-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 05/05/2022] [Indexed: 11/10/2022] Open
Abstract
Background Cancer is the most cause of morbidity and mortality, and a major public health problem worldwide. In this context, two series of quinazolinone 5a–e and dihydroquinazolinone 10a–f compounds were designed, synthesized as cytotoxic agents. Methodology All derivatives (5a–e and 10a–f) were synthesized via straightforward pathways and elucidated by FTIR, 1H-NMR, CHNS elemental analysis, as well as the melting point. All the compounds were evaluated for their in vitro cytotoxicity effects using the MTT assay against two human cancer cell lines (MCF-7 and HCT-116) using doxorubicin as the standard drug. The test derivatives were additionally docked into the PARP10 active site using Gold software. Results and discussion Most of the synthesized compounds, especially 5a and 10f were found to be highly potent against both cell lines. Synthesized compounds demonstrated IC50 in the range of 4.87–205.9 μM against HCT-116 cell line and 14.70–98.45 μM against MCF-7 cell line compared with doxorubicin with IC50 values of 1.20 and 1.08 μM after 72 h, respectively, indicated the plausible activities of the synthesized compounds. Conclusion The compounds quinazolinone 5a–e and dihydroquinazolinone 10a–f showed potential activity against cancer cell lines which can lead to rational drug designing of the cytotoxic agents. Supplementary Information The online version contains supplementary material available at 10.1186/s13065-022-00825-x.
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Affiliation(s)
- Fahimeh Taayoshi
- Department of Medicinal Chemistry, School of Pharmacy, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Aida Iraji
- Stem Cells Technology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.,Central Research Laboratory, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ali Moazzam
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Meysam Soleimani
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Hamadan University of Medical Science Hamadan, Hamedan, Iran
| | - Mehdi Asadi
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Sciences, Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Keyvan Pedrood
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Mosayeb Akbari
- Department of Medicinal Chemistry, School of Pharmacy, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Hafezeh Salehabadi
- Department of Medicinal Chemistry, School of Pharmacy, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Bagher Larijani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Neda Adibpour
- Department of Medicinal Chemistry, School of Pharmacy, Zanjan University of Medical Sciences, Zanjan, Iran.
| | - Mohammad Mahdavi
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.
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11
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Mashimo M, Kita M, Uno A, Nii M, Ishihara M, Honda T, Gotoh-Kinoshita Y, Nomura A, Nakamura H, Murayama T, Kizu R, Fujii T. Tankyrase Regulates Neurite Outgrowth through Poly(ADP-ribosyl)ation-Dependent Activation of β-Catenin Signaling. Int J Mol Sci 2022; 23:ijms23052834. [PMID: 35269974 PMCID: PMC8911479 DOI: 10.3390/ijms23052834] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 02/28/2022] [Accepted: 03/02/2022] [Indexed: 12/17/2022] Open
Abstract
Poly(ADP-ribosyl)ation is a post-translational modification of proteins by transferring poly(ADP-ribose) (PAR) to acceptor proteins by the action of poly(ADP-ribose) polymerase (PARP). Two tankyrase (TNKS) isoforms, TNK1 and TNK2 (TNKS1/2), are ubiquitously expressed in mammalian cells and participate in diverse cellular functions, including wnt/β-catenin signaling, telomere maintenance, glucose metabolism and mitosis regulation. For wnt/β-catenin signaling, TNKS1/2 catalyze poly(ADP-ribosyl)ation of Axin, a key component of the β-catenin degradation complex, which allows Axin’s ubiquitination and subsequent degradation, thereby activating β-catenin signaling. In the present study, we focused on the functions of TNKS1/2 in neuronal development. In primary hippocampal neurons, TNKS1/2 were detected in the soma and neurites, where they co-localized with PAR signals. Treatment with XAV939, a selective TNKS1/2 inhibitor, suppressed neurite outgrowth and synapse formation. In addition, XAV939 also suppressed norepinephrine uptake in PC12 cells, a rat pheochromocytoma cell line. These effects likely resulted from the inhibition of β-catenin signaling through the stabilization of Axin, which suggests TNKS1/2 enhance Axin degradation by modifying its poly(ADP-ribosyl)ation, thereby stabilizing wnt/β-catenin signaling and, in turn, promoting neurite outgrowth and synapse formation.
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Affiliation(s)
- Masato Mashimo
- Department of Pharmacology, Faculty of Pharmaceutical Sciences, Doshisha Women’s College of Liberal Arts, Kyotanabe 610-0395, Japan; (M.K.); (A.U.); (M.N.); (M.I.); (A.N.); (T.F.)
- Correspondence:
| | - Momoko Kita
- Department of Pharmacology, Faculty of Pharmaceutical Sciences, Doshisha Women’s College of Liberal Arts, Kyotanabe 610-0395, Japan; (M.K.); (A.U.); (M.N.); (M.I.); (A.N.); (T.F.)
| | - Arina Uno
- Department of Pharmacology, Faculty of Pharmaceutical Sciences, Doshisha Women’s College of Liberal Arts, Kyotanabe 610-0395, Japan; (M.K.); (A.U.); (M.N.); (M.I.); (A.N.); (T.F.)
| | - Moe Nii
- Department of Pharmacology, Faculty of Pharmaceutical Sciences, Doshisha Women’s College of Liberal Arts, Kyotanabe 610-0395, Japan; (M.K.); (A.U.); (M.N.); (M.I.); (A.N.); (T.F.)
| | - Moe Ishihara
- Department of Pharmacology, Faculty of Pharmaceutical Sciences, Doshisha Women’s College of Liberal Arts, Kyotanabe 610-0395, Japan; (M.K.); (A.U.); (M.N.); (M.I.); (A.N.); (T.F.)
| | - Takuya Honda
- Laboratory of Chemical Pharmacology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan; (T.H.); (H.N.); (T.M.)
| | - Yuka Gotoh-Kinoshita
- Department of Clinical Pharmacy, Faculty of Pharmaceutical Sciences, Doshisha Women’s College of Liberal Arts, Kyotanabe 610-0395, Japan; (Y.G.-K.); (R.K.)
| | - Atsuo Nomura
- Department of Pharmacology, Faculty of Pharmaceutical Sciences, Doshisha Women’s College of Liberal Arts, Kyotanabe 610-0395, Japan; (M.K.); (A.U.); (M.N.); (M.I.); (A.N.); (T.F.)
| | - Hiroyuki Nakamura
- Laboratory of Chemical Pharmacology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan; (T.H.); (H.N.); (T.M.)
| | - Toshihiko Murayama
- Laboratory of Chemical Pharmacology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan; (T.H.); (H.N.); (T.M.)
| | - Ryoichi Kizu
- Department of Clinical Pharmacy, Faculty of Pharmaceutical Sciences, Doshisha Women’s College of Liberal Arts, Kyotanabe 610-0395, Japan; (Y.G.-K.); (R.K.)
| | - Takeshi Fujii
- Department of Pharmacology, Faculty of Pharmaceutical Sciences, Doshisha Women’s College of Liberal Arts, Kyotanabe 610-0395, Japan; (M.K.); (A.U.); (M.N.); (M.I.); (A.N.); (T.F.)
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12
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Oliveira JL, Greipp PT, Rangan A, Jatoi A, Nguyen PL. Myeloid malignancies in cancer patients treated with poly(ADP-ribose) polymerase (PARP) inhibitors: a case series. Blood Cancer J 2022; 12:11. [PMID: 35078980 PMCID: PMC8789926 DOI: 10.1038/s41408-022-00607-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 11/03/2021] [Indexed: 11/08/2022] Open
Affiliation(s)
| | - Patricia T Greipp
- Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, USA
| | - Aruna Rangan
- Division of Hematopathology, Mayo Clinic, Rochester, MN, USA
| | - Aminah Jatoi
- Division of Medical Oncology, Mayo Clinic, Rochester, MN, USA.
| | - Phuong L Nguyen
- Division of Hematopathology, Mayo Clinic, Rochester, MN, USA
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13
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Hindi NN, Elsakrmy N, Ramotar D. The base excision repair process: comparison between higher and lower eukaryotes. Cell Mol Life Sci 2021; 78:7943-7965. [PMID: 34734296 PMCID: PMC11071731 DOI: 10.1007/s00018-021-03990-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 09/08/2021] [Accepted: 10/14/2021] [Indexed: 01/01/2023]
Abstract
The base excision repair (BER) pathway is essential for maintaining the stability of DNA in all organisms and defects in this process are associated with life-threatening diseases. It is involved in removing specific types of DNA lesions that are induced by both exogenous and endogenous genotoxic substances. BER is a multi-step mechanism that is often initiated by the removal of a damaged base leading to a genotoxic intermediate that is further processed before the reinsertion of the correct nucleotide and the restoration of the genome to a stable structure. Studies in human and yeast cells, as well as fruit fly and nematode worms, have played important roles in identifying the components of this conserved DNA repair pathway that maintains the integrity of the eukaryotic genome. This review will focus on the components of base excision repair, namely, the DNA glycosylases, the apurinic/apyrimidinic endonucleases, the DNA polymerase, and the ligases, as well as other protein cofactors. Functional insights into these conserved proteins will be provided from humans, Saccharomyces cerevisiae, Drosophila melanogaster, and Caenorhabditis elegans, and the implications of genetic polymorphisms and knockouts of the corresponding genes.
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Affiliation(s)
- Nagham Nafiz Hindi
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Doha, Qatar
| | - Noha Elsakrmy
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Doha, Qatar
| | - Dindial Ramotar
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Doha, Qatar.
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14
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Safrygin A, Zhmurov P, Dar'in D, Silonov S, Kasatkina M, Zonis Y, Gureev M, Krasavin M. 1-Oxo-3,4-dihydroisoquinoline-4-carboxamides as novel druglike inhibitors of poly(ADP-ribose) polymerase (PARP) with favourable ADME characteristics. J Enzyme Inhib Med Chem 2021; 36:1968-1983. [PMID: 34482781 PMCID: PMC8425678 DOI: 10.1080/14756366.2021.1972993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2022] Open
Abstract
A novel 3,4-dihydroisoquinol-1-one-4-carboxamide scaffold was designed as the basis for the development of novel inhibitors of poly(ADP-ribose) polymerase (PARP). Synthesis of 3,4-dihydroisoquinol-1-one-4-carboxylic acids was achieved using the previously developed protocol based on the modified Castagnoli-Cushman reaction of homophthalic anhydrides and 1,3,5-triazinanes as formaldimine synthetic equivalents. Employment of 2,4-dimethoxy groups on the nitrogen atom of the latter allowed preparation of 2,3-unsubatituted 3,4-dihydroquinolone core building blocks. Iterative synthesis and in vitro biological testing of the amides resulting from the amidation of these carboxylic acids allowed not only drawing important structure-activity generalisations (corroborated by in silico docking simulation) but also the identification of the lead compound, 4-([1,4'-bipiperidine]-1'-carbonyl)-7-fluoro-3,4-dihydroisoquinolin-1(2H)-one, as the candidate for further preclinical development. The lead compound as well as its des-fluoro analog were compared to the approved PARP1 inhibitor, anticancer drug Olaparib, in terms of their molecular characteristics defining druglikeness as well as experimentally determined ADME parameters. The newly developed series demonstrated clear advantages over Olaparib in terms of molecular weight, hydrophilicity, human liver microsomal and plasma stability as well as plasma protein binding. Further preclinical investigation of the lead compound is highly warranted.
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Affiliation(s)
| | - Petr Zhmurov
- Saint Petersburg State University, Saint Petersburg, Russian Federation
| | - Dmitry Dar'in
- Saint Petersburg State University, Saint Petersburg, Russian Federation
| | | | | | - Yulia Zonis
- JSC BIOCAD, Saint Petersburg, Russian Federation
| | - Maxim Gureev
- Digital Biodesign and Personalized Healthcare Research Center, Sechenov First Moscow State Medical University, Moscow, Russian Federation
| | - Mikhail Krasavin
- Saint Petersburg State University, Saint Petersburg, Russian Federation.,Immanuel Kant Baltic Federal University, Kaliningrad, Russian Federation
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