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Dyrkheeva NS, Zakharenko AL, Malakhova AA, Okorokova LS, Shtokalo DN, Medvedev SP, Tupikin AA, Kabilov MR, Lavrik OI. Transcriptomic analysis of HEK293A cells with a CRISPR/Cas9-mediated TDP1 knockout. Biochim Biophys Acta Gen Subj 2024; 1868:130616. [PMID: 38621596 DOI: 10.1016/j.bbagen.2024.130616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 03/21/2024] [Accepted: 04/01/2024] [Indexed: 04/17/2024]
Abstract
Tyrosyl-DNA phosphodiesterase 1 (TDP1) is a human DNA repair protein. It is a member of the phospholipase D family based on structural similarity. TDP1 is a key enzyme of the repair of stalled topoisomerase 1 (TOP1)-DNA complexes. Previously, with the CRISPR/Cas9 method, we obtained HEK293A cells with a homozygous knockout of the TDP1 gene and used the TDP1 knockout cells as a cellular model for studying mechanisms of action of an anticancer therapy. In the present work, we hypothesized that the TDP1 knockout would alter the expression of DNA repair-related genes. By transcriptomic analysis, we investigated for the first time the effect of the TDP1 gene knockout on genes' expression changes in the human HEK293A cell line. We obtained original data implying a role of TDP1 in other processes besides the repair of the DNA-TOP1 complex. Differentially expressed gene analysis revealed that TDP1 may participate in cell adhesion and communication, spermatogenesis, mitochondrial function, neurodegeneration, a cytokine response, and the MAPK signaling pathway.
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Affiliation(s)
- Nadezhda S Dyrkheeva
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia.
| | - Alexandra L Zakharenko
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia.
| | - Anastasia A Malakhova
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia; Federal research center Institute of Cytology and Genetics, SB RAS, 10 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia.
| | | | - Dmitry N Shtokalo
- AcademGene LLC, 6 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia; A.P. Ershov Institute of Informatics Systems, SB RAS, 6 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia.
| | - Sergey P Medvedev
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia; Federal research center Institute of Cytology and Genetics, SB RAS, 10 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia.
| | - Alexey A Tupikin
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia.
| | - Marsel R Kabilov
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia.
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Akad. Lavrentyeva Ave., Novosibirsk 630090, Russia.
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Beyer GV, Hueser S, Li R, Manika D, Lee M, Chan CHF, Howe JR, Ear PH. Gastroenteropancreatic neuroendocrine carcinoma tumor spheroid drug screen reveals vulnerability to tyrosyl-DNA phosphodiesterase 1 inhibitors. Surgery 2024; 175:605-612. [PMID: 37914572 PMCID: PMC10872605 DOI: 10.1016/j.surg.2023.08.044] [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: 05/16/2023] [Revised: 07/26/2023] [Accepted: 08/08/2023] [Indexed: 11/03/2023]
Abstract
BACKGROUND Gastroenteropancreatic neuroendocrine carcinomas are rare neoplasms with no effective treatments and poor prognosis. Few reliable preclinical models exist for the study of gastroenteropancreatic neuroendocrine carcinomas, limiting investigation of novel treatments. We used tumor spheroids from our recently established gastroenteropancreatic neuroendocrine carcinoma patient-derived xenograft models to systematically screen for compounds with diverse structures to identify potential new categories of therapeutic agents that can target gastroenteropancreatic neuroendocrine carcinomas. METHODS Tumor spheroids were derived from our NEC913 and NEC1452 gastroenteropancreatic neuroendocrine carcinoma patient-derived xenograft models. Gastroenteropancreatic neuroendocrine carcinoma spheroids were screened against a library of 885 compounds from the National Cancer Institute Diversity Set VII collection. Cell viability was measured via AlamarBlue assay. After identification of potential therapeutic compounds, synergy screening of a selected group with temozolomide and doxorubicin was performed, and these combinations were further analyzed for γH2AX and phosphorylated-ERK proteins. RESULTS We identified 16 compounds that inhibit over 75% of gastroenteropancreatic neuroendocrine carcinoma spheroid survival. Seven are inhibitors of tyrosyl-DNA phosphodiesterase 1, a DNA repair enzyme working closely with the topoisomerase I complex. When combined with temozolomide or doxorubicin, the tyrosyl-DNA phosphodiesterase 1 inhibitor cytarabine increased the cytotoxic effects of these drugs on NEC1452 cells which was further evidenced by increasing γH2AX and decreasing phosphorylated-ERK in combination treatment compared to temozolomide alone. CONCLUSION Both NEC913 and NEC1452 gastroenteropancreatic neuroendocrine carcinoma spheroid lines are useful preclinical models for drug testing. Our library screen revealed these gastroenteropancreatic neuroendocrine carcinoma spheroids are highly sensitive to a novel class of anti-cancer drugs that target nuclear genome stability.
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Affiliation(s)
- Gabriella V Beyer
- Department of Surgery, University of Iowa Carver College of Medicine, Iowa City, IA
| | - Sophia Hueser
- Department of Surgery, University of Iowa Carver College of Medicine, Iowa City, IA
| | - Rachel Li
- Department of Surgery, University of Iowa Carver College of Medicine, Iowa City, IA
| | - Deeraj Manika
- Department of Surgery, University of Iowa Carver College of Medicine, Iowa City, IA
| | - Minhyuk Lee
- Department of Surgery, University of Iowa Carver College of Medicine, Iowa City, IA
| | - Carlos H F Chan
- Department of Surgery, University of Iowa Carver College of Medicine, Iowa City, IA; Holden Comprehensive Cancer Center, University of Iowa Hospitals and Clinics, Iowa City, IA
| | - James R Howe
- Department of Surgery, University of Iowa Carver College of Medicine, Iowa City, IA; Holden Comprehensive Cancer Center, University of Iowa Hospitals and Clinics, Iowa City, IA
| | - Po Hien Ear
- Department of Surgery, University of Iowa Carver College of Medicine, Iowa City, IA; Holden Comprehensive Cancer Center, University of Iowa Hospitals and Clinics, Iowa City, IA.
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Sharma NK, Bahot A, Sekar G, Bansode M, Khunteta K, Sonar PV, Hebale A, Salokhe V, Sinha BK. Understanding Cancer's Defense against Topoisomerase-Active Drugs: A Comprehensive Review. Cancers (Basel) 2024; 16:680. [PMID: 38398072 PMCID: PMC10886629 DOI: 10.3390/cancers16040680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 02/02/2024] [Indexed: 02/25/2024] Open
Abstract
In recent years, the emergence of cancer drug resistance has been one of the crucial tumor hallmarks that are supported by the level of genetic heterogeneity and complexities at cellular levels. Oxidative stress, immune evasion, metabolic reprogramming, overexpression of ABC transporters, and stemness are among the several key contributing molecular and cellular response mechanisms. Topo-active drugs, e.g., doxorubicin and topotecan, are clinically active and are utilized extensively against a wide variety of human tumors and often result in the development of resistance and failure to therapy. Thus, there is an urgent need for an incremental and comprehensive understanding of mechanisms of cancer drug resistance specifically in the context of topo-active drugs. This review delves into the intricate mechanistic aspects of these intracellular and extracellular topo-active drug resistance mechanisms and explores the use of potential combinatorial approaches by utilizing various topo-active drugs and inhibitors of pathways involved in drug resistance. We believe that this review will help guide basic scientists, pre-clinicians, clinicians, and policymakers toward holistic and interdisciplinary strategies that transcend resistance, renewing optimism in the ongoing battle against cancer.
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Affiliation(s)
- Nilesh Kumar Sharma
- Cancer and Translational Research Centre Dr. D.Y. Patil Biotechnology & Bioinformatics Institute, Dr. D.Y. Patil Vidyapeeth, Pune 411033, Maharashtra, India; (N.K.S.); (A.B.); (G.S.); (M.B.); (K.K.); (P.V.S.); (A.H.); (V.S.)
| | - Anjali Bahot
- Cancer and Translational Research Centre Dr. D.Y. Patil Biotechnology & Bioinformatics Institute, Dr. D.Y. Patil Vidyapeeth, Pune 411033, Maharashtra, India; (N.K.S.); (A.B.); (G.S.); (M.B.); (K.K.); (P.V.S.); (A.H.); (V.S.)
| | - Gopinath Sekar
- Cancer and Translational Research Centre Dr. D.Y. Patil Biotechnology & Bioinformatics Institute, Dr. D.Y. Patil Vidyapeeth, Pune 411033, Maharashtra, India; (N.K.S.); (A.B.); (G.S.); (M.B.); (K.K.); (P.V.S.); (A.H.); (V.S.)
| | - Mahima Bansode
- Cancer and Translational Research Centre Dr. D.Y. Patil Biotechnology & Bioinformatics Institute, Dr. D.Y. Patil Vidyapeeth, Pune 411033, Maharashtra, India; (N.K.S.); (A.B.); (G.S.); (M.B.); (K.K.); (P.V.S.); (A.H.); (V.S.)
| | - Kratika Khunteta
- Cancer and Translational Research Centre Dr. D.Y. Patil Biotechnology & Bioinformatics Institute, Dr. D.Y. Patil Vidyapeeth, Pune 411033, Maharashtra, India; (N.K.S.); (A.B.); (G.S.); (M.B.); (K.K.); (P.V.S.); (A.H.); (V.S.)
| | - Priyanka Vijay Sonar
- Cancer and Translational Research Centre Dr. D.Y. Patil Biotechnology & Bioinformatics Institute, Dr. D.Y. Patil Vidyapeeth, Pune 411033, Maharashtra, India; (N.K.S.); (A.B.); (G.S.); (M.B.); (K.K.); (P.V.S.); (A.H.); (V.S.)
| | - Ameya Hebale
- Cancer and Translational Research Centre Dr. D.Y. Patil Biotechnology & Bioinformatics Institute, Dr. D.Y. Patil Vidyapeeth, Pune 411033, Maharashtra, India; (N.K.S.); (A.B.); (G.S.); (M.B.); (K.K.); (P.V.S.); (A.H.); (V.S.)
| | - Vaishnavi Salokhe
- Cancer and Translational Research Centre Dr. D.Y. Patil Biotechnology & Bioinformatics Institute, Dr. D.Y. Patil Vidyapeeth, Pune 411033, Maharashtra, India; (N.K.S.); (A.B.); (G.S.); (M.B.); (K.K.); (P.V.S.); (A.H.); (V.S.)
| | - Birandra Kumar Sinha
- Mechanistic Toxicology Branch, Division of Translational Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC 27709, USA
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Kornienko TE, Chepanova AA, Zakharenko AL, Filimonov AS, Luzina OA, Dyrkheeva NS, Nikolin VP, Popova NA, Salakhutdinov NF, Lavrik OI. Enhancement of the Antitumor and Antimetastatic Effect of Topotecan and Normalization of Blood Counts in Mice with Lewis Carcinoma by Tdp1 Inhibitors-New Usnic Acid Derivatives. Int J Mol Sci 2024; 25:1210. [PMID: 38279210 PMCID: PMC10816808 DOI: 10.3390/ijms25021210] [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: 11/22/2023] [Revised: 01/10/2024] [Accepted: 01/16/2024] [Indexed: 01/28/2024] Open
Abstract
Tyrosyl-DNA phosphodiesterase 1 (Tdp1) is an important DNA repair enzyme and one of the causes of tumor resistance to topoisomerase 1 inhibitors such as topotecan. Inhibitors of this Tdp1 in combination with topotecan may improve the effectiveness of therapy. In this work, we synthesized usnic acid derivatives, which are hybrids of its known derivatives: tumor sensitizers to topotecan. New compounds inhibit Tdp1 in the micromolar and submicromolar concentration range; some of them enhance the effect of topotecan on the metabolic activity of cells of various lines according to the MTT test. One of the new compounds (compound 7) not only sensitizes Krebs-2 and Lewis carcinomas of mice to the action of topotecan, but also normalizes the state of the peripheral blood of mice, which is disturbed in the presence of a tumor. Thus, the synthesized substances may be the prototype of a new class of additional therapy for cancer.
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Affiliation(s)
- Tatyana E. Kornienko
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., Novosibirsk 630090, Russia; (T.E.K.); (A.A.C.); (N.S.D.); (O.I.L.)
| | - Arina A. Chepanova
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., Novosibirsk 630090, Russia; (T.E.K.); (A.A.C.); (N.S.D.); (O.I.L.)
| | - Alexandra L. Zakharenko
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., Novosibirsk 630090, Russia; (T.E.K.); (A.A.C.); (N.S.D.); (O.I.L.)
| | - Aleksandr S. Filimonov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk 630090, Russia; (A.S.F.); (O.A.L.); (N.F.S.)
| | - Olga A. Luzina
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk 630090, Russia; (A.S.F.); (O.A.L.); (N.F.S.)
| | - Nadezhda S. Dyrkheeva
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., Novosibirsk 630090, Russia; (T.E.K.); (A.A.C.); (N.S.D.); (O.I.L.)
| | - Valeriy P. Nikolin
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10, Akademika Lavrentieva Ave., Novosibirsk 630090, Russia; (V.P.N.); (N.A.P.)
| | - Nelly A. Popova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10, Akademika Lavrentieva Ave., Novosibirsk 630090, Russia; (V.P.N.); (N.A.P.)
| | - Nariman F. Salakhutdinov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk 630090, Russia; (A.S.F.); (O.A.L.); (N.F.S.)
| | - Olga I. Lavrik
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., Novosibirsk 630090, Russia; (T.E.K.); (A.A.C.); (N.S.D.); (O.I.L.)
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Okhina AA, Kornienko TE, Rogachev AD, Luzina OA, Popova NA, Nikolin VP, Zakharenko AL, Dyrkheeva NS, Pokrovsky AG, Salakhutdinov NF, Lavrik OI. Pharmacokinetic study of Tdp1 inhibitor resulted in a significant increase in antitumor effect in the treatment of Lewis lung carcinoma in mice by its combination with topotecan. J Pharm Biomed Anal 2023; 236:115731. [PMID: 37741072 DOI: 10.1016/j.jpba.2023.115731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/17/2023] [Accepted: 09/16/2023] [Indexed: 09/25/2023]
Abstract
We have previously shown that the Tdp1 inhibitor, enamine derivative of usnic acid, the agent OL9-116, enhances the antitumor activity of topotecan. In the present study, we developed and validated LC-MS/MS method for the quantification of OL9-116 in mouse whole blood and studied pharmacokinetics of the agent. The substance OL9-116 was shown to be stable in the whole blood in vitro. Sample preparation included two steps: mixing 10 µL of a blood sample with 10 µL of 0.2 M ZnSO4 aqueous solution, followed by protein precipitation with 100 µL of acetonitrile containing internal standard. Quantification of the compound was performed using SCIEX 6500 QTRAP mass spectrometer in MRM mode following chromatographic separation on a C8 reversed-phase column. The method was validated in terms of selectivity, linearity, accuracy, precision, recovery, and stability of the prepared sample. When the agent OL9-116 was administered intragastrically at a dose of 150 mg/kg, the maximum concentration in the blood (about 5000 ng/mL) was reached after 2-4 h followed by the distribution and elimination of the compound. A study of the antitumor activity of a combination of OL9-116 and topotecan against Lewis lung carcinoma revealed that administration of topotecan 3 h after OL9-116 resulted in the most pronounced antitumor effect compared to simultaneous or individual administration of both compounds.
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Affiliation(s)
- Alina A Okhina
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry of the Siberian Branch of Russian Academy of Sciences, Lavrent'ev ave., 9, Novosibirsk 630090, Russia; Novosibirsk State University, Pirogov St., 2, Novosibirsk 630090, Russia
| | - Tatyana E Kornienko
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of Russian Academy of Sciences, Lavrent'ev ave., 8, Novosibirsk 630090, Russia
| | - Artem D Rogachev
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry of the Siberian Branch of Russian Academy of Sciences, Lavrent'ev ave., 9, Novosibirsk 630090, Russia; Novosibirsk State University, Pirogov St., 2, Novosibirsk 630090, Russia
| | - Olga A Luzina
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry of the Siberian Branch of Russian Academy of Sciences, Lavrent'ev ave., 9, Novosibirsk 630090, Russia
| | - Nelly A Popova
- Novosibirsk State University, Pirogov St., 2, Novosibirsk 630090, Russia; Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Lavrent'ev ave., 10, Novosibirsk 630090, Russia
| | - Valery P Nikolin
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Lavrent'ev ave., 10, Novosibirsk 630090, Russia
| | - Alexandra L Zakharenko
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of Russian Academy of Sciences, Lavrent'ev ave., 8, Novosibirsk 630090, Russia
| | - Nadezhda S Dyrkheeva
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of Russian Academy of Sciences, Lavrent'ev ave., 8, Novosibirsk 630090, Russia
| | - Andrey G Pokrovsky
- Novosibirsk State University, Pirogov St., 2, Novosibirsk 630090, Russia
| | - Nariman F Salakhutdinov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry of the Siberian Branch of Russian Academy of Sciences, Lavrent'ev ave., 9, Novosibirsk 630090, Russia
| | - Olga I Lavrik
- Novosibirsk State University, Pirogov St., 2, Novosibirsk 630090, Russia; Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of Russian Academy of Sciences, Lavrent'ev ave., 8, Novosibirsk 630090, Russia.
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Anticevic I, Otten C, Vinkovic L, Jukic L, Popovic M. Tyrosyl-DNA phosphodiesterase 1 (TDP1) and SPRTN protease repair histone 3 and topoisomerase 1 DNA-protein crosslinks in vivo. Open Biol 2023; 13:230113. [PMID: 37788708 PMCID: PMC10547559 DOI: 10.1098/rsob.230113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 08/14/2023] [Indexed: 10/05/2023] Open
Abstract
DNA-protein crosslinks (DPCs) are frequent and damaging DNA lesions that affect all DNA transactions, which in turn can lead to the formation of double-strand breaks, genomic instability and cell death. At the organismal level, impaired DPC repair (DPCR) is associated with cancer, ageing and neurodegeneration. Despite the severe consequences of DPCs, little is known about the processes underlying repair pathways at the organism level. SPRTN is a protease that removes most cellular DPCs during replication, whereas tyrosyl-DNA phosphodiesterase 1 repairs one of the most abundant enzymatic DPCs, topoisomerase 1-DPC (TOP1-DPC). How these two enzymes repair DPCs at the organism level is currently unknown. We perform phylogenetic, syntenic, structural and expression analysis to compare tyrosyl-DNA phosphodiesterase 1 (TDP1) orthologues between human, mouse and zebrafish. Using the zebrafish animal model and human cells, we demonstrate that TDP1 and SPRTN repair endogenous, camptothecin- and formaldehyde-induced DPCs, including histone H3- and TOP1-DPCs. We show that resolution of H3-DNA crosslinks depends on upstream proteolysis by SPRTN and subsequent peptide removal by TDP1 in RPE1 cells and zebrafish embryos, whereas SPRTN and TDP1 function in different pathways in the repair of endogenous TOP1-DPCs and total DPCs. Furthermore, we have found increased TDP2 expression in TDP1-deficient cells and embryos. Understanding the role of TDP1 in DPCR at the cellular and organismal levels could provide an impetus for the development of new drugs and combination therapies with TOP1-DPC inducing drugs.
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Affiliation(s)
- Ivan Anticevic
- Department for Marine and Environmental Research, Laboratory for Molecular Ecotoxicology, Institute Ruder Boskovic, Zagreb, Croatia
| | - Cecile Otten
- Department for Marine and Environmental Research, Laboratory for Molecular Ecotoxicology, Institute Ruder Boskovic, Zagreb, Croatia
| | - Luka Vinkovic
- Department for Marine and Environmental Research, Laboratory for Molecular Ecotoxicology, Institute Ruder Boskovic, Zagreb, Croatia
| | - Luka Jukic
- Department for Marine and Environmental Research, Laboratory for Molecular Ecotoxicology, Institute Ruder Boskovic, Zagreb, Croatia
| | - Marta Popovic
- Department for Marine and Environmental Research, Laboratory for Molecular Ecotoxicology, Institute Ruder Boskovic, Zagreb, Croatia
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Okhina AA, Rogachev AD, Kovaleva KS, Yarovaya OI, Khotskina AS, Zavyalov EL, Vatsadze SZ, Pokrovsky AG, Salakhutdinov NF. Development of an LC-MS/MS-based method for quantification and pharmacokinetics study on SCID mice of a dehydroabietylamine-adamantylamine conjugate, a promising inhibitor of the DNA repair enzyme. J Pharm Biomed Anal 2023; 234:115507. [PMID: 37331915 DOI: 10.1016/j.jpba.2023.115507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/10/2023] [Accepted: 06/04/2023] [Indexed: 06/20/2023]
Abstract
Earlier, it was found that the agent KS-389, a conjugate of dehydroabietylamine and 1-aminoadamantane, possess inhibiting activity with regard to Tdp1. It this study, LC-MS/MS-based methods of quantification of KS-389 in mice blood and several organs (brain, liver and kidney) were developed and validated. Validation of the methods was performed according to the guidelines of U.S. Food and Drug Administration and European Medicines Agency in terms of selectivity, linearity, accuracy, precision, recovery, matrix effect, stability and carry-over. Dried blood spots (DBS) method was used for blood sample preparation. HPLC separation was performed on a reversed-phase column; the total analysis time was 12 min. Mass spectral detection was performed on a 6500 QTRAP mass spectrometer in multiple reaction monitoring mode. Transitions 463.5→135.1/107.2 and 336.2→332.2/176.2 were scanned for KS-389 and 2,5-bis(4-diethylaminophenyl)-1,3,4-oxadiazole used as the internal standard, respectively. Pharmacokinetics of the compound as well as its distribution in the organs were studied on SCID mice after intraperitoneal administration of the substance at a dose of 5 mg/kg, and it was found that its maximum concentration in blood is reached in 1-1.5 h and was 80 ng/mL. The maximum concentration in all organs is reached after the same time and is approximately 1500 ng/g and 1100 ng/g in liver and kidney, respectively. This is the first report on the pharmacokinetics of Tdp1 inhibitor based on dehydroabietylamine and 1-aminoadamantane after a single administration to mice. Also, the substance was found to be able to penetrate the blood-brain barrier which is important for, and its maximum concentration was c.a. 25-30 ng/g. These results are important for glioma treatment and make it promising for this purpose.
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Affiliation(s)
- Alina A Okhina
- Department of Medicinal Chemistry, N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Acad. Lavrentiev Ave., 9, Novosibirsk 630090, Russia; Zelman Institute for Medicine and Psychology, Novosibirsk State University, Pirogov Str., 2, Novosibirsk 630090, Russia
| | - Artem D Rogachev
- Department of Medicinal Chemistry, N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Acad. Lavrentiev Ave., 9, Novosibirsk 630090, Russia; Zelman Institute for Medicine and Psychology, Novosibirsk State University, Pirogov Str., 2, Novosibirsk 630090, Russia.
| | - Kseniya S Kovaleva
- Department of Medicinal Chemistry, N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Acad. Lavrentiev Ave., 9, Novosibirsk 630090, Russia
| | - Olga I Yarovaya
- Department of Medicinal Chemistry, N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Acad. Lavrentiev Ave., 9, Novosibirsk 630090, Russia; Zelman Institute for Medicine and Psychology, Novosibirsk State University, Pirogov Str., 2, Novosibirsk 630090, Russia
| | - Anna S Khotskina
- Institute of Cytology and Genetics, Acad. Lavrentiev Ave., 10, Novosibirsk 630090, Russia
| | - Evgeniy L Zavyalov
- Institute of Cytology and Genetics, Acad. Lavrentiev Ave., 10, Novosibirsk 630090, Russia
| | - Sergey Z Vatsadze
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninski pr., 47, 119991 Moscow, Russia
| | - Andrey G Pokrovsky
- Zelman Institute for Medicine and Psychology, Novosibirsk State University, Pirogov Str., 2, Novosibirsk 630090, Russia
| | - Nariman F Salakhutdinov
- Department of Medicinal Chemistry, N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Acad. Lavrentiev Ave., 9, Novosibirsk 630090, Russia; Zelman Institute for Medicine and Psychology, Novosibirsk State University, Pirogov Str., 2, Novosibirsk 630090, Russia
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Yang H, Qin C, Wu M, Wang FT, Wang W, Agama K, Pommier Y, Hu DX, An LK. Synthesis and Biological Activities of 11- and 12-Substituted Benzophenanthridinone Derivatives as DNA Topoisomerase IB and Tyrosyl-DNA Phosphodiesterase 1 Inhibitors. ChemMedChem 2023; 18:e202200593. [PMID: 36932053 PMCID: PMC10233710 DOI: 10.1002/cmdc.202200593] [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: 11/04/2022] [Revised: 03/06/2023] [Indexed: 03/19/2023]
Abstract
Herein, a series of 11- or 12-substituted benzophenanthridinone derivatives was designed and synthesized for the discovery of dual topoisomerase IB (TOP1) and tyrosyl-DNA phosphodiesterase 1 (TDP1) inhibitors. Enzyme-based assays indicated that two compounds 12 and 38 showed high TOP1 inhibitory potency (+++), and four compounds 35, 37, 39 and 43 showed good TDP1 inhibition with IC50 values ranging from 10 to 18 μM. 38 could induce cellular TOP1cc formation, resulting in the highest cytotoxicity against HCT-116 cells (0.25 μM). The most potent TDP1 inhibitor 43 (10 μM) could induce cellular TDP1cc formation and enhance topotecan-induced DNA damage and showed strong synergistic cytotoxicity with topotecan in both MCF-7 and MCF-7/TDP1 cells.
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Affiliation(s)
- Hao Yang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P. R. China
- School of Pharmacy, Ningxia Medical University, Yinchuan, 750004, P. R. China
| | - Chao Qin
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P. R. China
| | - Min Wu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P. R. China
| | - Fang-Ting Wang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P. R. China
| | - Wenjie Wang
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Keli Agama
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yves Pommier
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - De-Xuan Hu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P. R. China
| | - Lin-Kun An
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P. R. China
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou, 510006, P. R. China
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9
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Bhattacharjee S, Richardson JM, Das BB. Fluorescence-resonance-energy-transfer-based assay to estimate modulation of TDP1 activity through arginine methylation. STAR Protoc 2023; 4:102218. [PMID: 37058403 PMCID: PMC10139991 DOI: 10.1016/j.xpro.2023.102218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/15/2023] [Accepted: 03/13/2023] [Indexed: 04/15/2023] Open
Abstract
Tyrosyl DNA phosphodiesterase (TDP1) is a DNA repair enzyme that hydrolyzes the phosphotyrosyl linkage between 3'-DNA-protein crosslinks such as stalled topoisomerase 1 cleavage complexes (Top1cc). Here, we present a fluorescence-resonance-energy-transfer-(FRET) based assay to estimate modulation of TDP1 activity through arginine methylation. We describe steps for TDP1 expression and purification and estimating TDP1 activity using fluorescence-quenched probes mimicking Top1cc. We then detail data analysis of real-time TDP1 activity and screening of TDP1-selective inhibitors. For complete details on the use and execution of this protocol, please refer to Bhattacharjee et al. (2022).1.
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Affiliation(s)
- Sangheeta Bhattacharjee
- Laboratory of Molecular Biology, School of Biological Sciences, Indian Association for the Cultivation of Science, 2A & B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Julia M Richardson
- Institute of Quantitative Biology, Biochemistry, and Biotechnology, School of Biological Sciences, University of Edinburgh, The King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Benu Brata Das
- Laboratory of Molecular Biology, School of Biological Sciences, Indian Association for the Cultivation of Science, 2A & B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India.
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10
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TDP1-independent pathways in the process and repair of TOP1-induced DNA damage. Nat Commun 2022; 13:4240. [PMID: 35869071 PMCID: PMC9307636 DOI: 10.1038/s41467-022-31801-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 06/29/2022] [Indexed: 11/15/2022] Open
Abstract
Anticancer drugs, such as camptothecin (CPT), trap topoisomerase I (TOP1) on DNA and form TOP1 cleavage complexes (TOP1cc). Alternative repair pathways have been suggested in the repair of TOP1cc. However, how these pathways work with TDP1, a key repair enzyme that specifically hydrolyze the covalent bond between TOP1 catalytic tyrosine and the 3’-end of DNA and contribute to the repair of TOP1cc is poorly understood. Here, using unbiased whole-genome CRISPR screens and generation of co-deficient cells with TDP1 and other genes, we demonstrate that MUS81 is an important factor that mediates the generation of excess double-strand breaks (DSBs) in TDP1 KO cells. APEX1/2 are synthetic lethal with TDP1. However, deficiency of APEX1/2 does not reduce DSB formation in TDP1 KO cells. Together, our data suggest that TOP1cc can be either resolved directly by TDP1 or be converted into DSBs and repaired further by the Homologous Recombination (HR) pathway. Here the authors find that MUS81 mediates excess DNA double strand break (DSB) generation in TDP1 KO cells after camptothecin treatment. They show that TOP1 cleavage complexes can be either resolved directly by TDP1 or be converted into DSBs and repaired further by the Homologous Recombination pathway.
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11
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A Review of Medicinal Plants of the Himalayas with Anti-Proliferative Activity for the Treatment of Various Cancers. Cancers (Basel) 2022; 14:cancers14163898. [PMID: 36010892 PMCID: PMC9406073 DOI: 10.3390/cancers14163898] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/04/2022] [Accepted: 08/06/2022] [Indexed: 12/17/2022] Open
Abstract
Simple Summary Drugs are used to treat cancer. Most drugs available in the market are chemosynthetic drugs and have side effects on the patient during and after the treatment, in addition to cancer itself. For instance, hair loss, loss of skin color and texture, loss of energy, nausea, infertility, etc. To overcome these side effects, naturally obtained drugs from medicinal plants are preferred. Our review paper aims to encourage the study of anticancer medicinal plants by giving detailed information on thirty-three medicinal plants and parts that constitute the phytochemicals responsible for the treatment of cancer. The development of plant-based drugs could be a game changer in treating cancer as well as boosting the immune system. Abstract Cancer is a serious and significantly progressive disease. Next to cardiovascular disease, cancer has become the most common cause of mortality in the entire world. Several factors, such as environmental factors, habitual activities, genetic factors, etc., are responsible for cancer. Many cancer patients seek alternative and/or complementary treatments because of the high death rate linked with cancer and the adverse side effects of chemotherapy and radiation therapy. Traditional medicine has a long history that begins with the hunt for botanicals to heal various diseases, including cancer. In the traditional medicinal system, several plants used to treat diseases have many bioactive compounds with curative capability, thereby also helping in disease prevention. Plants also significantly contributed to the modern pharmaceutical industry throughout the world. In the present review, we have listed 33 medicinal plants with active and significant anticancer activity, as well as their anticancer compounds. This article will provide a basic set of information for researchers interested in developing a safe and nontoxic active medicinal plant-based treatment for cancer. The research will give a scientific foundation for the traditional usage of these medicinal herbs to treat cancer.
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12
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Yang H, Wang FT, Wu M, Wang W, Agama K, Pommier Y, An LK. Synthesis of 11-aminoalkoxy substituted benzophenanthridine derivatives as tyrosyl-DNA phosphodiesterase 1 inhibitors and their anticancer activity. Bioorg Chem 2022; 123:105789. [PMID: 35429714 PMCID: PMC10557912 DOI: 10.1016/j.bioorg.2022.105789] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/02/2022] [Accepted: 03/31/2022] [Indexed: 11/19/2022]
Abstract
Tyrosyl-DNA phosphodiesterase 1 (TDP1) is an enzyme that repairs DNA lesions caused by the trapping of DNA topoisomerase IB (TOP1)-DNA break-associated crosslinks. TDP1 inhibitors have synergistic effect with TOP1 inhibitors in cancer cells and can overcome cancer cell resistance to TOP1 inhibitors. Here, we report the synthesis of 11-aminoalkoxy substituted benzophenanthridine derivatives as selective TDP1 inhibitors and show that six compounds 14, 16, 18, 20, 25 and 27 exhibit high TDP1 inhibition potency. The most potent TDP1 inhibitor 14 (IC50 = 1.7 ± 0.24 μM) induces cellular TDP1cc formation and shows synergistic effect with topotecan in four human cancer cell lines MCF-7, A549, H460 and HepG2.
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Affiliation(s)
- Hao Yang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Fang-Ting Wang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Min Wu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Wenjie Wang
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - Keli Agama
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - Yves Pommier
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - Lin-Kun An
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Guangzhou 510006, China.
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13
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Pyranodipyran Derivatives with Tyrosyl DNA Phosphodiesterase 1 Inhibitory Activities and Fluorescent Properties from Aspergillus sp. EGF 15-0-3. Mar Drugs 2022; 20:md20030211. [PMID: 35323510 PMCID: PMC8954640 DOI: 10.3390/md20030211] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/09/2022] [Accepted: 03/13/2022] [Indexed: 12/02/2022] Open
Abstract
Four new benzodipyran racemates, namely (±)-aspergiletals A–D (3–6), representing a rare pyrano[4,3-h]chromene scaffold were isolated together with eurotiumide G (1) and eurotiumide F (2) from the soft-coral-derived fungus Aspergillus sp. EGF 15-0-3. All the corresponding optically pure enantiomers were successfully separated by a chiral HPLC column. The structures and configurations of all the compounds were elucidated based on the combination of NMR and HRESIMS data, chiral separation, single-crystal X-ray diffraction, quantum chemical 13C NMR, and electronic circular dichroism calculations. Meanwhile, the structure of eurotiumide G was also revised. The TDP1 inhibitor activities and photophysical properties of the obtained compounds were evaluated. In the TDP1 inhibition assay, as a result of synergy between (+)-6 and (−)-6, (±)-6 displayed strong inhibitory activity to TDP1 with IC50 values of 6.50 ± 0.73 μM. All compounds had a large Stokes shift and could be utilized for elucidating the mode of bioactivities by fluorescence imaging.
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14
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Zhang L, Chen C, Fu J, Lilley B, Berlinicke C, Hansen B, Ding D, Wang G, Wang T, Shou D, Ye Y, Mulligan T, Emmerich K, Saxena MT, Hall KR, Sharrock AV, Brandon C, Park H, Kam TI, Dawson VL, Dawson TM, Shim JS, Hanes J, Ji H, Liu JO, Qian J, Ackerley DF, Rohrer B, Zack DJ, Mumm JS. Large-scale phenotypic drug screen identifies neuroprotectants in zebrafish and mouse models of retinitis pigmentosa. eLife 2021; 10:e57245. [PMID: 34184634 PMCID: PMC8425951 DOI: 10.7554/elife.57245] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 06/28/2021] [Indexed: 11/25/2022] Open
Abstract
Retinitis pigmentosa (RP) and associated inherited retinal diseases (IRDs) are caused by rod photoreceptor degeneration, necessitating therapeutics promoting rod photoreceptor survival. To address this, we tested compounds for neuroprotective effects in multiple zebrafish and mouse RP models, reasoning drugs effective across species and/or independent of disease mutation may translate better clinically. We first performed a large-scale phenotypic drug screen for compounds promoting rod cell survival in a larval zebrafish model of inducible RP. We tested 2934 compounds, mostly human-approved drugs, across six concentrations, resulting in 113 compounds being identified as hits. Secondary tests of 42 high-priority hits confirmed eleven lead candidates. Leads were then evaluated in a series of mouse RP models in an effort to identify compounds effective across species and RP models, that is, potential pan-disease therapeutics. Nine of 11 leads exhibited neuroprotective effects in mouse primary photoreceptor cultures, and three promoted photoreceptor survival in mouse rd1 retinal explants. Both shared and complementary mechanisms of action were implicated across leads. Shared target tests implicated parp1-dependent cell death in our zebrafish RP model. Complementation tests revealed enhanced and additive/synergistic neuroprotective effects of paired drug combinations in mouse photoreceptor cultures and zebrafish, respectively. These results highlight the value of cross-species/multi-model phenotypic drug discovery and suggest combinatorial drug therapies may provide enhanced therapeutic benefits for RP patients.
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Affiliation(s)
- Liyun Zhang
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
| | - Conan Chen
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
| | - Jie Fu
- The Center for Nanomedicine, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
| | - Brendan Lilley
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
| | - Cynthia Berlinicke
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
| | - Baranda Hansen
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
| | - Ding Ding
- Department of Biostatistics, Johns Hopkins UniversityBaltimoreUnited States
| | - Guohua Wang
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
| | - Tao Wang
- The Center for Nanomedicine, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
- School of Chemistry, Xuzhou College of Industrial TechnologyXuzhouChina
- College of Light Industry and Food Engineering, Nanjing Forestry UniversityNanjingChina
| | - Daniel Shou
- The Center for Nanomedicine, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
| | - Ying Ye
- The Center for Nanomedicine, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
| | - Timothy Mulligan
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
| | - Kevin Emmerich
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
- Department of Genetic Medicine, Johns Hopkins UniversityBaltimoreUnited States
| | - Meera T Saxena
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
| | - Kelsi R Hall
- School of Biological Sciences, Victoria University of WellingtonWellingtonNew Zealand
| | - Abigail V Sharrock
- Department of Biostatistics, Johns Hopkins UniversityBaltimoreUnited States
- School of Biological Sciences, Victoria University of WellingtonWellingtonNew Zealand
| | - Carlene Brandon
- Department of Ophthalmology, Medical University of South CarolinaCharlestonUnited States
| | - Hyejin Park
- Department of Neurology, Johns Hopkins UniversityBaltimoreUnited States
| | - Tae-In Kam
- Department of Neurology, Johns Hopkins UniversityBaltimoreUnited States
- Institute for Cell Engineering, Johns Hopkins UniversityBaltimoreUnited States
| | - Valina L Dawson
- Department of Neurology, Johns Hopkins UniversityBaltimoreUnited States
- Institute for Cell Engineering, Johns Hopkins UniversityBaltimoreUnited States
- Department of Pharmacology and Molecular Sciences, Johns Hopkins UniversityBaltimoreUnited States
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins UniversityBaltimoreUnited States
| | - Ted M Dawson
- Department of Neurology, Johns Hopkins UniversityBaltimoreUnited States
- Institute for Cell Engineering, Johns Hopkins UniversityBaltimoreUnited States
- Department of Pharmacology and Molecular Sciences, Johns Hopkins UniversityBaltimoreUnited States
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins UniversityBaltimoreUnited States
| | - Joong Sup Shim
- Faculty of Health Sciences, University of Macau, TaipaMacauChina
| | - Justin Hanes
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
- The Center for Nanomedicine, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
| | - Hongkai Ji
- Department of Biostatistics, Johns Hopkins UniversityBaltimoreUnited States
| | - Jun O Liu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins UniversityBaltimoreUnited States
- Department of Oncology, Johns Hopkins UniversityBaltimoreUnited States
| | - Jiang Qian
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
| | - David F Ackerley
- School of Biological Sciences, Victoria University of WellingtonWellingtonNew Zealand
| | - Baerbel Rohrer
- Department of Ophthalmology, Medical University of South CarolinaCharlestonUnited States
| | - Donald J Zack
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
- The Center for Nanomedicine, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
- Department of Genetic Medicine, Johns Hopkins UniversityBaltimoreUnited States
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins UniversityBaltimoreUnited States
- Department of Molecular Biology and Genetics, Johns Hopkins UniversityBaltimoreUnited States
| | - Jeff S Mumm
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
- The Center for Nanomedicine, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
- Department of Genetic Medicine, Johns Hopkins UniversityBaltimoreUnited States
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins UniversityBaltimoreUnited States
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15
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Hu DX, Tang WL, Zhang Y, Yang H, Wang W, Agama K, Pommier Y, An LK. Synthesis of Methoxy-, Methylenedioxy-, Hydroxy-, and Halo-Substituted Benzophenanthridinone Derivatives as DNA Topoisomerase IB (TOP1) and Tyrosyl-DNA Phosphodiesterase 1 (TDP1) Inhibitors and Their Biological Activity for Drug-Resistant Cancer. J Med Chem 2021; 64:7617-7629. [PMID: 34008967 PMCID: PMC10087287 DOI: 10.1021/acs.jmedchem.1c00318] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
As a recently discovered DNA repair enzyme, tyrosyl-DNA phosphodiesterase 1 (TDP1) removes topoisomerase IB (TOP1)-mediated DNA protein cross-links. Inhibiting TDP1 can potentiate the cytotoxicity of TOP1 inhibitors and overcome cancer cell resistance to TOP1 inhibitors. On the basis of our previous study, herein we report the synthesis of benzophenanthridinone derivatives as TOP1 and TDP1 inhibitors. Seven compounds (C2, C4, C5, C7, C8, C12, and C14) showed a robust TOP1 inhibitory activity (+++ or ++++), and four compounds (A13, C12, C13, and C26) showed a TDP1 inhibition (half-maximal inhibitory concentration values of 15 or 19 μM). We also show that the dual TOP1 and TDP1 inhibitor C12 induces both cellular TOP1cc, TDP1cc formation and DNA damage, resulting in cancer cell apoptosis at a sub-micromolar concentration. In addition, C12 showed an enhanced activity in drug-resistant MCF-7/TDP1 cancer cells and was synergistic with topotecan in both MCF-7 and MCF-7/TDP1 cells.
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Affiliation(s)
- De-Xuan Hu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Wen-Lin Tang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Yu Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Hao Yang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Wenjie Wang
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda 20892, Maryland, United States
| | - Keli Agama
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda 20892, Maryland, United States
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda 20892, Maryland, United States
| | - Lin-Kun An
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China.,Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Guangzhou 510006, China
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16
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Milanović ŽB, Dimić DS, Avdović EH, Milenković DA, Marković JD, Klisurić OR, Trifunović SR, Marković ZS. Synthesis and comprehensive spectroscopic (X-ray, NMR, FTIR, UV–Vis), quantum chemical and molecular docking investigation of 3-acetyl-4‑hydroxy‑2-oxo-2H-chromen-7-yl acetate. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129256] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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17
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Salomatina OV, Popadyuk II, Zakharenko AL, Zakharova OD, Chepanova AA, Dyrkheeva NS, Komarova NI, Reynisson J, Anarbaev RO, Salakhutdinov NF, Lavrik OI, Volcho KP. Deoxycholic acid as a molecular scaffold for tyrosyl-DNA phosphodiesterase 1 inhibition: A synthesis, structure-activity relationship and molecular modeling study. Steroids 2021; 165:108771. [PMID: 33221302 DOI: 10.1016/j.steroids.2020.108771] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/05/2020] [Accepted: 11/14/2020] [Indexed: 02/08/2023]
Abstract
Para-Bromoanilides of deoxycholic acid with various functional groups on the steroid scaffold were designed as promising tyrosyl-DNA phosphodiesterase 1 (Tdp1) inhibitors. Tdp1 is a DNA repair enzyme, involved in removing DNA damage caused by topoisomerase I poisons; an important class of anticancer drugs. Thus, reducing the activity of Tdp1 can increase the efficacy of anticancer drugs in current use. Inhibitory activity in the low micromolar and submicromolar concentrations was observed with 3,12-dimethoxy para-bromoanilide 17 being the most active with an IC50 value of 0.27 μM. The activity of N-methyl para-bromoanilides was 3-4.8 times lower than of the corresponding para-bromoanilides. Increased potency of the ligands was seen with higher molecular weight and log P values. The ligands were evaluated for their cytotoxic potential in a panel of tumor cell lines; all were nontoxic to the A549 pulmonary adenocarcinoma cell line. However, derivatives containing a hydroxyl group at the 12th position were more toxic than their 12-hydroxyl group counterparts (acetoxy-, oxo- and methoxy- group) against HCT-116 human colon and HepG2 hepatocellular carcinomas. In addition, an N-methyl substitution led to an increase in toxicity for the HCT-116 and HepG2 cell lines. The excellent activity as well as low cytotoxicity, derivative 17 can be considered as a lead compound for further development.
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Affiliation(s)
- Oksana V Salomatina
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS, 9, Lavrent'ev Ave., Novosibirsk 630090, Russian Federation.
| | - Irina I Popadyuk
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS, 9, Lavrent'ev Ave., Novosibirsk 630090, Russian Federation
| | - Alexandra L Zakharenko
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8, Lavrent'ev Ave., Novosibirsk 630090, Russian Federation
| | - Olga D Zakharova
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8, Lavrent'ev Ave., Novosibirsk 630090, Russian Federation
| | - Arina A Chepanova
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8, Lavrent'ev Ave., Novosibirsk 630090, Russian Federation
| | - Nadezhda S Dyrkheeva
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8, Lavrent'ev Ave., Novosibirsk 630090, Russian Federation
| | - Nina I Komarova
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS, 9, Lavrent'ev Ave., Novosibirsk 630090, Russian Federation
| | - Jóhannes Reynisson
- School of Pharmacy and Bioengineering, Keele University, Hornbeam Building, Staffordshire ST5 5BG, UK
| | - Rashid O Anarbaev
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8, Lavrent'ev Ave., Novosibirsk 630090, Russian Federation
| | - Nariman F Salakhutdinov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS, 9, Lavrent'ev Ave., Novosibirsk 630090, Russian Federation
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8, Lavrent'ev Ave., Novosibirsk 630090, Russian Federation
| | - Konstantin P Volcho
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS, 9, Lavrent'ev Ave., Novosibirsk 630090, Russian Federation
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18
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Baglini E, Salerno S, Barresi E, Robello M, Da Settimo F, Taliani S, Marini AM. Multiple Topoisomerase I (TopoI), Topoisomerase II (TopoII) and Tyrosyl-DNA Phosphodiesterase (TDP) inhibitors in the development of anticancer drugs. Eur J Pharm Sci 2021; 156:105594. [DOI: 10.1016/j.ejps.2020.105594] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 10/07/2020] [Accepted: 10/08/2020] [Indexed: 02/08/2023]
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19
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Dyrkheeva N, Anarbaev R, Lebedeva N, Kuprushkin M, Kuznetsova A, Kuznetsov N, Rechkunova N, Lavrik O. Human Tyrosyl-DNA Phosphodiesterase 1 Possesses Transphosphooligonucleotidation Activity With Primary Alcohols. Front Cell Dev Biol 2020; 8:604732. [PMID: 33425909 PMCID: PMC7786179 DOI: 10.3389/fcell.2020.604732] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/05/2020] [Indexed: 12/20/2022] Open
Abstract
Human tyrosyl-DNA phosphodiesterase 1 (TDP1) belongs to the phospholipase D superfamily, whose members contain paired catalytic histidine and lysine residues within two conserved motifs and hydrolyze phosphodiester bonds. TDP1 is a DNA repair enzyme that processes 3′ DNA end blocking lesions and a wide range of synthetic DNA adducts as a substrate. TDP1 hydrolyzes DNA-adducts via two coordinated SN2 nucleophilic attacks mediated by the action of two histidine residues and leads to the formation of the covalent intermediate. Hydrolysis of this intermediate is proposed to be carried out by a water molecule that is activated by the His493 residue acting as a general base. It was known that phospholipase D enzymes are able to catalyze not only hydrolysis but also a transphosphatidylation reaction in the presence of primary alcohols in which they transfer the substrate to the alcohol instead of water. Here, we first demonstrated that TDP1 is able to undergo a “transphosphooligonucleotidation” reaction, transferring the substrate residue to the alcohol, thus inducing the formation of covalent DNA adducts with different primary alcohol residues. Such adducts can be accumulated in the conditions of high concentration of alcohol. We demonstrated that glycerol residue was efficiently cleaved from the 3′-end by TDP1 but not by its mutant form associated with the disease spinocerebellar ataxia with axonal neuropathy. Therefore, the second reaction step can be carried out not only by a water molecule but also by the other small nucleophilic molecules, e.g., glycerol and ethanol. Thus, in some cases, TDP1 can be regarded not only as a repair enzyme but also as a source of DNA damage especially in the case of mutation. Such damages can make a negative contribution to the stability of cell vitality.
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Affiliation(s)
- Nadezhda Dyrkheeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Rashid Anarbaev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Natalia Lebedeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Maxim Kuprushkin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexandra Kuznetsova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Nikita Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Nadejda Rechkunova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Olga Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
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20
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Mutti G, Raveane A, Pagano A, Bertolini F, Semino O, Balestrazzi A, Macovei A. Plant TDP1 (Tyrosyl-DNA Phosphodiesterase 1): A Phylogenetic Perspective and Gene Expression Data Mining. Genes (Basel) 2020; 11:E1465. [PMID: 33297410 PMCID: PMC7762302 DOI: 10.3390/genes11121465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/02/2020] [Accepted: 12/03/2020] [Indexed: 01/28/2023] Open
Abstract
The TDP1 (tyrosyl-DNA phosphodiesterase 1) enzyme removes the non-specific covalent intermediates between topoisomerase I and DNA, thus playing a crucial role in preventing DNA damage. While mammals possess only one TDP1 gene, in plants two genes (TDP1α and TDP1β) are present constituting a small gene subfamily. These display a different domain structure and appear to perform non-overlapping functions in the maintenance of genome integrity. Namely, the HIRAN domain identified in TDP1β is involved in the interaction with DNA during the recognition of stalled replication forks. The availability of transcriptomic databases in a growing variety of experimental systems provides new opportunities to fill the current gaps of knowledge concerning the evolutionary origin and the specialized roles of TDP1 genes in plants. Whereas a phylogenetic approach has been used to track the evolution of plant TDP1 protein, transcriptomic data from a selection of representative lycophyte, eudicots, and monocots have been implemented to explore the transcriptomic dynamics in different tissues and a variety of biotic and abiotic stress conditions. While the phylogenetic analysis indicates that TDP1α is of non-plant origin and TDP1β is plant-specific originating in ancient vascular plants, the gene expression data mining comparative analysis pinpoints for tissue- and stress-specific responses.
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Affiliation(s)
- Giacomo Mutti
- Department of Biology and Biotechnology ‘L. Spallanzani’, University of Pavia, via Ferrata 9, 27100 Pavia, Italy; (G.M.); (A.P.); (O.S.); (A.B.)
| | - Alessandro Raveane
- Department of Biology and Biotechnology ‘L. Spallanzani’, University of Pavia, via Ferrata 9, 27100 Pavia, Italy; (G.M.); (A.P.); (O.S.); (A.B.)
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, via Ripamonti 435, 20141 Milan, Italy;
| | - Andrea Pagano
- Department of Biology and Biotechnology ‘L. Spallanzani’, University of Pavia, via Ferrata 9, 27100 Pavia, Italy; (G.M.); (A.P.); (O.S.); (A.B.)
| | - Francesco Bertolini
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, via Ripamonti 435, 20141 Milan, Italy;
| | - Ornella Semino
- Department of Biology and Biotechnology ‘L. Spallanzani’, University of Pavia, via Ferrata 9, 27100 Pavia, Italy; (G.M.); (A.P.); (O.S.); (A.B.)
| | - Alma Balestrazzi
- Department of Biology and Biotechnology ‘L. Spallanzani’, University of Pavia, via Ferrata 9, 27100 Pavia, Italy; (G.M.); (A.P.); (O.S.); (A.B.)
| | - Anca Macovei
- Department of Biology and Biotechnology ‘L. Spallanzani’, University of Pavia, via Ferrata 9, 27100 Pavia, Italy; (G.M.); (A.P.); (O.S.); (A.B.)
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21
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Krumpe LRH, Wilson BAP, Marchand C, Sunassee SN, Bermingham A, Wang W, Price E, Guszczynski T, Kelley JA, Gustafson KR, Pommier Y, Rosengren KJ, Schroeder CI, O'Keefe BR. Recifin A, Initial Example of the Tyr-Lock Peptide Structural Family, Is a Selective Allosteric Inhibitor of Tyrosyl-DNA Phosphodiesterase I. J Am Chem Soc 2020; 142:21178-21188. [PMID: 33263997 DOI: 10.1021/jacs.0c10418] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Tyrosyl-DNA phosphodiesterase 1 (TDP1) is a molecular target for the sensitization of cancer cells to the FDA-approved topoisomerase inhibitors topotecan and irinotecan. High-throughput screening of natural product extract and fraction libraries for inhibitors of TDP1 activity resulted in the discovery of a new class of knotted cyclic peptides from the marine sponge Axinella sp. Bioassay-guided fractionation of the source extract resulted in the isolation of the active component which was determined to be an unprecedented 42-residue cysteine-rich peptide named recifin A. The native NMR structure revealed a novel fold comprising a four strand antiparallel β-sheet and two helical turns stabilized by a complex disulfide bond network that creates an embedded ring around one of the strands. The resulting structure, which we have termed the Tyr-lock peptide family, is stabilized by a tyrosine residue locked into three-dimensional space. Recifin A inhibited the cleavage of phosphodiester bonds by TDP1 in a FRET assay with an IC50 of 190 nM. Enzyme kinetics studies revealed that recifin A can specifically modulate the enzymatic activity of full-length TDP1 while not affecting the activity of a truncated catalytic domain of TDP1 lacking the N-terminal regulatory domain (Δ1-147), suggesting an allosteric binding site for recifin A on the regulatory domain of TDP1. Recifin A represents both the first of a unique structural class of knotted disulfide-rich peptides and defines a previously unseen mechanism of TDP1 inhibition that could be productively exploited for potential anticancer applications.
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Affiliation(s)
- Lauren R H Krumpe
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States.,Molecular Targets Program, Center for Cancer Research, NCI-Frederick, NIH, Frederick, Maryland 21702, United States
| | - Brice A P Wilson
- Molecular Targets Program, Center for Cancer Research, NCI-Frederick, NIH, Frederick, Maryland 21702, United States
| | - Christophe Marchand
- Developmental Therapeutics Branch, Laboratory of Molecular Pharmacology, NCI, NIH, Bethesda, Maryland 20892, United States
| | - Suthananda N Sunassee
- Molecular Targets Program, Center for Cancer Research, NCI-Frederick, NIH, Frederick, Maryland 21702, United States
| | - Alun Bermingham
- Molecular Targets Program, Center for Cancer Research, NCI-Frederick, NIH, Frederick, Maryland 21702, United States
| | - Wenjie Wang
- Developmental Therapeutics Branch, Laboratory of Molecular Pharmacology, NCI, NIH, Bethesda, Maryland 20892, United States
| | - Edmund Price
- Molecular Targets Program, Center for Cancer Research, NCI-Frederick, NIH, Frederick, Maryland 21702, United States
| | - Tad Guszczynski
- Molecular Targets Program, Center for Cancer Research, NCI-Frederick, NIH, Frederick, Maryland 21702, United States
| | - James A Kelley
- Chemical Biology Laboratory, Center for Cancer Research, NCI-Frederick, NIH, Frederick, Maryland 21702, United States
| | - Kirk R Gustafson
- Molecular Targets Program, Center for Cancer Research, NCI-Frederick, NIH, Frederick, Maryland 21702, United States
| | - Yves Pommier
- Developmental Therapeutics Branch, Laboratory of Molecular Pharmacology, NCI, NIH, Bethesda, Maryland 20892, United States
| | - K Johan Rosengren
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Christina I Schroeder
- Chemical Biology Laboratory, Center for Cancer Research, NCI-Frederick, NIH, Frederick, Maryland 21702, United States.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Barry R O'Keefe
- Molecular Targets Program, Center for Cancer Research, NCI-Frederick, NIH, Frederick, Maryland 21702, United States.,Natural Products Branch, Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Frederick, Maryland 21702, United States
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22
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Design, Synthesis, and Biological Investigation of Novel Classes of 3-Carene-Derived Potent Inhibitors of TDP1. Molecules 2020; 25:molecules25153496. [PMID: 32751997 PMCID: PMC7436013 DOI: 10.3390/molecules25153496] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/29/2020] [Accepted: 07/31/2020] [Indexed: 12/02/2022] Open
Abstract
Two novel structural types of tyrosyl-DNA phosphodiesterase 1 (TDP1) inhibitors with hexahydroisobenzofuran 11 and 3-oxabicyclo [3.3.1]nonane 12 scaffolds were discovered. These monoterpene-derived compounds were synthesized through preliminary isomerization of (+)-3-carene to (+)-2-carene followed by reaction with heteroaromatic aldehydes. All the compounds inhibit the TDP1 enzyme at micro- and submicromolar levels, with the most potent compound having an IC50 value of 0.65 μM. TDP1 is an important DNA repair enzyme and a promising target for the development of new chemosensitizing agents. A panel of isogenic clones of the HEK293FT cell line knockout for the TDP1 gene was created using the CRISPR-Cas9 system. Cytotoxic effects of topotecan (Tpc) and non-cytotoxic compounds of the new structures were investigated separately and jointly in the TDP1 gene knockout cells. For two TDP1 inhibitors, 11h and 12k, a synergistic effect was observed with Tpc in the HEK293FT cells but was not found in TDP1 −/− cells. Thus, it is likely that the synergistic effect is caused by inhibition of TDP1. Synergy was also found for 11h in other cancer cell lines. Thus, sensitizing cancer cells using a non-cytotoxic drug can enhance the efficacy of currently used pharmaceuticals and, concomitantly, reduce toxic side effects.
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23
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Xiao LG, Zhang Y, Zhang HL, Li D, Gu Q, Tang GH, Yu Q, An LK. Spiroconyone A, a new phytosterol with a spiro [5,6] ring system from Conyza japonica. Org Biomol Chem 2020; 18:5130-5136. [PMID: 32379263 DOI: 10.1039/d0ob00666a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Spiroconyone A (1), the first rearranged phytosterol featuring an unusual spiro [5,6] ring system, and nine known compounds (2-10) were isolated from the aerial parts of Conyza japonica. The structure of 1 was elucidated through spectroscopic methods, and its absolute configuration was determined by single-crystal X-ray diffraction analysis. Enzyme-based assay revealed that spiroconyone A showed weak TDP1 inhibition and compounds 7 and 10 showed TDP1 inhibition with IC50 values of 36 μM and 16 μM, respectively. MTT assay indicated that 7 and 10 showed a strong synergistic effect with the clinical TOP1 inhibitor topotecan in MCF-7 cells. Compound 5 displayed the most potent cytotoxicity against MCF-7 cells with a GI50 value of 3.3 μM. Furthermore, a hypothetical biosynthetic pathway for 1 was proposed. This work provides valuable information that the secondary metabolites from Conyza japonica could be developed as anticancer agents.
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Affiliation(s)
- Long-Gao Xiao
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China.
| | - Yu Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China.
| | - Hong-Li Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China.
| | - Ding Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China.
| | - Qiong Gu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China.
| | - Gui-Hua Tang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China.
| | - Qian Yu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China. and Clinical Pharmacy (School of Integrative Pharmacy, Institute of Integrative Pharmaceutical Research), Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Lin-Kun An
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China. and Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Guangzhou, 510006, China
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24
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Zhang HL, Zhang Y, Yan XL, Xiao LG, Hu DX, Yu Q, An LK. Secondary metabolites from Isodon ternifolius (D. Don) Kudo and their anticancer activity as DNA topoisomerase IB and Tyrosyl-DNA phosphodiesterase 1 inhibitors. Bioorg Med Chem 2020; 28:115527. [PMID: 32345458 DOI: 10.1016/j.bmc.2020.115527] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/17/2020] [Accepted: 04/20/2020] [Indexed: 12/21/2022]
Abstract
Based on DNA topoisomerase IB (TOP1) and tyrosyl-DNA phosphodiesterase 1 (TDP1) inhibition of the ethanol extract of the roots of Isodon ternifolius (D. Don) Kudo (Labiatae), its secondary metabolites has been studied. Two new compounds, an ent-abietane diterpenoid isodopene A (1) and a 2,3-seco-triterpene isodopene B (13), along with 25 known compounds were isolated. Their structures were elucidated by spectroscopic analysis and theoretical calculations. The enzyme-based assays indicated that 1 and 13 showed strong (+++) and moderate (++) TOP1 inhibition, respectively. Two chalcone derivatives 11 and 12 were firstly found as dual TDP1 and TOP1 natural inhibitors, and showed synergistic effect with the clinical TOP1 inhibitors topotecan in MCF-7 cells. Compounds 8, 16, and 22 acted as TOP1 catalytic inhibitors with equipotent TOP1 inhibition to camptothecin (++++). Compounds 7 and 8 exhibited significant cytotoxicity against MCF-7, A549, and HCT116 cells with GI50 values in the range of 2.2-4.8 μM. This work would provide valuable information that secondary metabolites from I. ternifolius could be developed as anticancer agents.
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Affiliation(s)
- Hong-Li Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Yu Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Xue-Long Yan
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Long-Gao Xiao
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - De-Xuan Hu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Qian Yu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China; Clinical Pharmacy (School of Integrative Pharmacy, Institute of Integrative Pharmaceutical Research), Guangdong Pharmaceutical University, Guangzhou 510006, China.
| | - Lin-Kun An
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Guangzhou 510006, China.
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25
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Vibrational spectroscopic studies (FTIR and FT-Raman) and molecular dynamics analysis of industry inspired 3-amino-4-hydroxybenzene sulfonic acid. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127579] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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26
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Mozhaitsev ES, Zakharenko AL, Suslov EV, Korchagina DV, Zakharova OD, Vasil'eva IA, Chepanova AA, Black E, Patel J, Chand R, Reynisson J, Leung IKH, Volcho KP, Salakhutdinov NF, Lavrik OI. Novel Inhibitors of DNA Repair Enzyme TDP1 Combining Monoterpenoid and Adamantane Fragments. Anticancer Agents Med Chem 2020; 19:463-472. [PMID: 30523770 DOI: 10.2174/1871520619666181207094243] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 11/06/2018] [Accepted: 11/20/2018] [Indexed: 01/30/2023]
Abstract
BACKGROUND AND OBJECTIVE The DNA repair enzyme tyrosyl-DNA-phosphodiesterase 1 (TDP1) is a current inhibition target to improve the efficacy of cancer chemotherapy. Previous studies showed that compounds combining adamantane and monoterpenoid fragments are active against TDP1 enzyme. This investigation is focused on the synthesis of monoterpenoid derived esters of 1-adamantane carboxylic acid as TDP1 inhibitors. METHODS New esters were synthesized by the interaction between 1-adamantane carboxylic acid chloride and monoterpenoid alcohols. The esters were tested against TDP1 and its binding to the enzyme was modeling. RESULTS 13 Novel ester-based TDP1 inhibitors were synthesized with yields of 21-94%; of these, nine esters had not been previously described. A number of the esters were found to inhibit TDP1, with IC50 values ranging from 0.86-4.08 µM. Molecular modelling against the TDP1 crystal structure showed a good fit of the active esters in the catalytic pocket, explaining their potency. A non-toxic dose of ester, containing a 3,7- dimethyloctanol fragment, was found to enhance the cytotoxic effect of topotecan, a clinically used anti-cancer drug, against the human lung adenocarcinoma cell line A549. CONCLUSION The esters synthesized were found to be active against TDP1 in the lower micromolar concentration range, with these findings being corroborated by molecular modeling. Simultaneous action of the ester synthesized from 3,7-dimethyloctanol-1 and topotecan revealed a synergistic effect.
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Affiliation(s)
- Evgenii S Mozhaitsev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of Russian Academy of Sciences, 9, Lavrentiev Ave., Novosibirsk, 630090, Russian Federation
| | - Alexandra L Zakharenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8, Lavrentiev Ave., Novosibirsk, 630090, Russian Federation
| | - Evgeniy V Suslov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of Russian Academy of Sciences, 9, Lavrentiev Ave., Novosibirsk, 630090, Russian Federation
| | - Dina V Korchagina
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of Russian Academy of Sciences, 9, Lavrentiev Ave., Novosibirsk, 630090, Russian Federation
| | - Olga D Zakharova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8, Lavrentiev Ave., Novosibirsk, 630090, Russian Federation
| | - Inna A Vasil'eva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8, Lavrentiev Ave., Novosibirsk, 630090, Russian Federation
| | - Arina A Chepanova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8, Lavrentiev Ave., Novosibirsk, 630090, Russian Federation
| | - Ellena Black
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand
| | - Jinal Patel
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand
| | - Raina Chand
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand
| | - Jóhannes Reynisson
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand
| | - Ivanhoe K H Leung
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand
| | - Konstantin P Volcho
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of Russian Academy of Sciences, 9, Lavrentiev Ave., Novosibirsk, 630090, Russian Federation.,Novosibirsk State University, 2, Pirogova Str., Novosibirsk, 630090, Russian Federation
| | - Nariman F Salakhutdinov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of Russian Academy of Sciences, 9, Lavrentiev Ave., Novosibirsk, 630090, Russian Federation.,Novosibirsk State University, 2, Pirogova Str., Novosibirsk, 630090, Russian Federation
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8, Lavrentiev Ave., Novosibirsk, 630090, Russian Federation.,Novosibirsk State University, 2, Pirogova Str., Novosibirsk, 630090, Russian Federation
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27
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Lountos GT, Zhao XZ, Kiselev E, Tropea JE, Needle D, Pommier Y, Burke TR, Waugh DS. Identification of a ligand binding hot spot and structural motifs replicating aspects of tyrosyl-DNA phosphodiesterase I (TDP1) phosphoryl recognition by crystallographic fragment cocktail screening. Nucleic Acids Res 2019; 47:10134-10150. [PMID: 31199869 DOI: 10.1093/nar/gkz515] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 05/20/2019] [Accepted: 06/11/2019] [Indexed: 02/02/2023] Open
Abstract
Tyrosyl DNA-phosphodiesterase I (TDP1) repairs type IB topoisomerase (TOP1) cleavage complexes generated by TOP1 inhibitors commonly used as anticancer agents. TDP1 also removes DNA 3' end blocking lesions generated by chain-terminating nucleosides and alkylating agents, and base oxidation both in the nuclear and mitochondrial genomes. Combination therapy with TDP1 inhibitors is proposed to synergize with topoisomerase targeting drugs to enhance selectivity against cancer cells exhibiting deficiencies in parallel DNA repair pathways. A crystallographic fragment screening campaign against the catalytic domain of TDP1 was conducted to identify new lead compounds. Crystal structures revealed two fragments that bind to the TDP1 active site and exhibit inhibitory activity against TDP1. These fragments occupy a similar position in the TDP1 active site as seen in prior crystal structures of TDP1 with bound vanadate, a transition state mimic. Using structural insights into fragment binding, several fragment derivatives have been prepared and evaluated in biochemical assays. These results demonstrate that fragment-based methods can be a highly feasible approach toward the discovery of small-molecule chemical scaffolds to target TDP1, and for the first time, we provide co-crystal structures of small molecule inhibitors bound to TDP1, which could serve for the rational development of medicinal TDP1 inhibitors.
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Affiliation(s)
- George T Lountos
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Xue Zhi Zhao
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Evgeny Kiselev
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Joseph E Tropea
- Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Danielle Needle
- Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Yves Pommier
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Terrence R Burke
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - David S Waugh
- Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
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28
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Mamontova EM, Zakharenko AL, Zakharova OD, Dyrkheeva NS, Volcho KP, Reynisson J, Arabshahi HJ, Salakhutdinov NF, Lavrik OI. Identification of novel inhibitors for the tyrosyl-DNA-phosphodiesterase 1 (Tdp1) mutant SCAN1 using virtual screening. Bioorg Med Chem 2019; 28:115234. [PMID: 31831297 DOI: 10.1016/j.bmc.2019.115234] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 11/21/2019] [Accepted: 11/21/2019] [Indexed: 10/25/2022]
Abstract
Spinocerebellar ataxia syndrome with axonal neuropathy (SCAN1) is a debilitating neurological disease that is caused by the mutation the Tyrosyl-DNA phosphodiesterase 1 (TDP1) DNA repair enzyme. The crucial His493 in TDP1's binding site is replaced with an arginine amino acid residue rendering the enzyme dysfunctional. A virtual screen was performed against the homology model of SCAN1 and seventeen compounds were identified and tested in a novel SCAN1 specific biochemical assay. Six compounds showed activity with IC50 values between 3.5 and 25.1 µM. The most active ligand 5 (3.5 µM) is a dicoumarin followed by a close structural analogue 6 at 6.0 µM. A less potent series of β-carbolines (14 and 15) was found with potency in the mid-teens. According to molecular modelling an excellent fit for the active ligands into the binding pocket is predicted. To the best of our knowledge, data on inhibitors of the mutant form of TDP1 has not been reported previously. The virtual hits were also tested for wild type TDP1 activity and all six SCAN1 inhibitors are potent for the former, e.g., ligand 5 has a measured IC50 at 99 nM. In the last decade, TDP1 is considered as a promising target for adjuvant therapy against cancer in combination with Topoisomerase 1 poisons. The active ligands are mostly non-toxic to cancer cell lines A-549, T98G and MCF-7 as well as the immortalized WI-38 human fetal lung cells. Furthermore, ligands 5 and 7, show promising synergy in conjunction with topotecan, a clinically used topoisomerase 1 anticancer drug. The active ligands 5, 7, 14 and 15 have a good balance of the physicochemical properties required for oral bioavailability making the excellent candidates for further development.
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Affiliation(s)
- E M Mamontova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8, Lavrentiev Ave., Novosibirsk 630090, Russian Federation; Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russian Federation
| | - A L Zakharenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8, Lavrentiev Ave., Novosibirsk 630090, Russian Federation
| | - O D Zakharova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8, Lavrentiev Ave., Novosibirsk 630090, Russian Federation
| | - N S Dyrkheeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8, Lavrentiev Ave., Novosibirsk 630090, Russian Federation
| | - K P Volcho
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russian Federation; N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of Russian Academy of Sciences, 9, Lavrentiev Ave., Novosibirsk 630090, Russian Federation
| | - J Reynisson
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand; School of Pharmacy and Bioengineering, Keele University, Hornbeam Building, Staffordshire ST5 5BG, United Kingdom
| | - H J Arabshahi
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland 1142, New Zealand
| | - N F Salakhutdinov
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russian Federation; N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of Russian Academy of Sciences, 9, Lavrentiev Ave., Novosibirsk 630090, Russian Federation
| | - O I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8, Lavrentiev Ave., Novosibirsk 630090, Russian Federation.
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29
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Kovaleva K, Oleshko O, Mamontova E, Yarovaya O, Zakharova O, Zakharenko A, Kononova A, Dyrkheeva N, Cheresiz S, Pokrovsky A, Lavrik O, Salakhutdinov N. Dehydroabietylamine Ureas and Thioureas as Tyrosyl-DNA Phosphodiesterase 1 Inhibitors That Enhance the Antitumor Effect of Temozolomide on Glioblastoma Cells. JOURNAL OF NATURAL PRODUCTS 2019; 82:2443-2450. [PMID: 31430155 DOI: 10.1021/acs.jnatprod.8b01095] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A new class of tyrosyl-DNA phosphodiesterase 1 (TDP1) inhibitors was found among resin acid derivatives. Several novel ureas and thioureas derived from dehydroabietylamine were synthesized and tested for TDP1 inhibition. The synthesized compounds showed IC50 values in the range of 0.1 to 3.7 μM and demonstrated low cytotoxicity against the human tumor cell lines U-937, U-87MG, MDA-MB, SK-Mel8, A-549, MCF7, T98G, and SNB19. Several compounds showed enhancement of the cytotoxic activity of the alkylating agent temozolomide, which is used as a first line therapy against glioblastoma (GBM), in the GBM cell lines U-87MG and SNB19.
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Affiliation(s)
- Kseniya Kovaleva
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences , Novosibirsk , 630090 , Russian Federation
- Novosibirsk State University , Novosibirsk , 630090 , Russian Federation
| | - Olga Oleshko
- Novosibirsk State University , Novosibirsk , 630090 , Russian Federation
| | - Evgeniya Mamontova
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences , Novosibirsk , 630090 , Russian Federation
| | - Olga Yarovaya
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences , Novosibirsk , 630090 , Russian Federation
- Novosibirsk State University , Novosibirsk , 630090 , Russian Federation
| | - Olga Zakharova
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences , Novosibirsk , 630090 , Russian Federation
| | - Alexandra Zakharenko
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences , Novosibirsk , 630090 , Russian Federation
| | - Alena Kononova
- Novosibirsk State University , Novosibirsk , 630090 , Russian Federation
| | - Nadezhda Dyrkheeva
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences , Novosibirsk , 630090 , Russian Federation
| | - Sergey Cheresiz
- Novosibirsk State University , Novosibirsk , 630090 , Russian Federation
- State Scientific Research Institute of Physiology and Basic Medicine , P.O. Box 237, Novosibirsk , 630117 , Russian Federation
| | - Andrey Pokrovsky
- Novosibirsk State University , Novosibirsk , 630090 , Russian Federation
| | - Olga Lavrik
- Novosibirsk State University , Novosibirsk , 630090 , Russian Federation
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences , Novosibirsk , 630090 , Russian Federation
| | - Nariman Salakhutdinov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences , Novosibirsk , 630090 , Russian Federation
- Novosibirsk State University , Novosibirsk , 630090 , Russian Federation
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30
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Gutiérrez-Corbo C, Álvarez-Velilla R, Reguera RM, García-Estrada C, Cushman M, Balaña-Fouce R, Pérez-Pertejo Y. Topoisomerase IB poisons induce histone H2A phosphorylation as a response to DNA damage in Leishmania infantum. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2019; 11:39-48. [PMID: 31563118 PMCID: PMC6796659 DOI: 10.1016/j.ijpddr.2019.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 09/16/2019] [Accepted: 09/17/2019] [Indexed: 02/07/2023]
Abstract
DNA topoisomerases are considered consolidated druggable targets against diseases produced by trypanosomatids. Several reports indicated that indenoisoquinolines, a family of non-camptothecinic based topoisomerase poisons, have a strong leishmanicidal effect both in vitro and in vivo in murine models of visceral leishmaniasis. The antileishmanial effect of the indenoisoquinolines implies several mechanisms that include the stabilization of the cleavage complex, histone H2A phosphorylation and DNA fragmentation. A series of 20 compounds with the indenoisoquinoline scaffold and several substituents at positions N6, C3, C8 and C9, were tested both in promastigotes and in intramacrophage splenic amastigotes obtained from an experimental murine infection. The antileishmanial effect of most of these compounds was within the micromolar or submicromolar range. In addition, the introduction of an N atom in the indenoisoquinoline ring (7-azaindenoisoquinolines) produced the highest selectivity index along with strong DNA topoisomerase IB inhibition, histone H2A phosphorylation and DNA-topoisomerase IB complex stabilization. This report shows for the first time the effect of a series of synthetic indenoisoquinolines on histone H2A phosphorylation, which represents a primary signal of double stranded DNA break in genus Leishmania. N-6 indenoisoquinoline derivatives show strong antileishmanial activity. Indenoisoquinolines arrest Leishmania cell-cycle in S phase. Inhibition of leishmanial TopIB by indenoisoquinolines induces DNA fragmentation. Leishmanial H2A histone is phosphorylated at the Thr128 in response to DNA damage.
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Affiliation(s)
- Camino Gutiérrez-Corbo
- Departamento de Ciencias Biomédicas, Universidad de León, Campus de Vegazana S/n, 24071, León, Spain
| | - Raquel Álvarez-Velilla
- Departamento de Ciencias Biomédicas, Universidad de León, Campus de Vegazana S/n, 24071, León, Spain
| | - Rosa M Reguera
- Departamento de Ciencias Biomédicas, Universidad de León, Campus de Vegazana S/n, 24071, León, Spain
| | - Carlos García-Estrada
- INBIOTEC (Instituto de Biotecnología de León), Avda. Real 1 - Parque Científico de León, 24006, León, Spain
| | - Mark Cushman
- Department of Medicinal Chemistry, and Molecular Pharmacology, College of Pharmacy, The Purdue Center for Cancer Research, Purdue University, Lafayette, IN, USA
| | - Rafael Balaña-Fouce
- Departamento de Ciencias Biomédicas, Universidad de León, Campus de Vegazana S/n, 24071, León, Spain
| | - Yolanda Pérez-Pertejo
- Departamento de Ciencias Biomédicas, Universidad de León, Campus de Vegazana S/n, 24071, León, Spain.
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31
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Kawale AS, Povirk LF. Tyrosyl-DNA phosphodiesterases: rescuing the genome from the risks of relaxation. Nucleic Acids Res 2019; 46:520-537. [PMID: 29216365 PMCID: PMC5778467 DOI: 10.1093/nar/gkx1219] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 11/29/2017] [Indexed: 12/13/2022] Open
Abstract
Tyrosyl–DNA Phosphodiesterases 1 (TDP1) and 2 (TDP2) are eukaryotic enzymes that clean-up after aberrant topoisomerase activity. While TDP1 hydrolyzes phosphotyrosyl peptides emanating from trapped topoisomerase I (Top I) from the 3′ DNA ends, topoisomerase 2 (Top II)-induced 5′-phosphotyrosyl residues are processed by TDP2. Even though the canonical functions of TDP1 and TDP2 are complementary, they exhibit little structural or sequence similarity. Homozygous mutations in genes encoding these enzymes lead to the development of severe neurodegenerative conditions due to the accumulation of transcription-dependent topoisomerase cleavage complexes underscoring the biological significance of these enzymes in the repair of topoisomerase–DNA lesions in the nervous system. TDP1 can promiscuously process several blocked 3′ ends generated by DNA damaging agents and nucleoside analogs in addition to hydrolyzing 3′-phosphotyrosyl residues. In addition, deficiency of these enzymes causes hypersensitivity to anti-tumor topoisomerase poisons. Thus, TDP1 and TDP2 are promising therapeutic targets and their inhibitors are expected to significantly synergize the effects of current anti-tumor therapies including topoisomerase poisons and other DNA damaging agents. This review covers the structural aspects, biology and regulation of these enzymes, along with ongoing developments in the process of discovering safe and effective TDP inhibitors.
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Affiliation(s)
- Ajinkya S Kawale
- Department of Pharmacology and Toxicology and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Lawrence F Povirk
- Department of Pharmacology and Toxicology and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
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32
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Zakharenko A, Dyrkheeva N, Lavrik O. Dual DNA topoisomerase 1 and tyrosyl-DNA phosphodiesterase 1 inhibition for improved anticancer activity. Med Res Rev 2019; 39:1427-1441. [PMID: 31004352 DOI: 10.1002/med.21587] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 03/26/2019] [Accepted: 04/02/2019] [Indexed: 12/22/2022]
Abstract
Tyrosyl-DNA phosphodiesterase 1 (Tdp1) is a DNA repair enzyme that catalyzes the hydrolysis of the phosphodiester bond in the DNA-topoisomerase 1 (Top1) covalent complex and repairs some other 3'-end DNA adducts. Currently, Tdp1 functions as an important target in cancer drug design owing to its ability to break down various DNA adducts induced by chemotherapeutics. Tdp1 inhibitors may sensitize tumor cells to the action of Top1 poisons, thereby potentiating their effects. This mini-review summarizes findings from studies reporting the combined inhibition of Top1 and Tdp1. Two different approaches have been considered for developing such drug precursors.
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Affiliation(s)
- Alexandra Zakharenko
- Laboratory of Bioorganic Chemistry of Enzymes, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Nadezhda Dyrkheeva
- Laboratory of Bioorganic Chemistry of Enzymes, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Olga Lavrik
- Laboratory of Bioorganic Chemistry of Enzymes, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russian Federation
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33
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Aghamiri S, Jafarpour A, Gomari MM, Ghorbani J, Rajabibazl M, Payandeh Z. siRNA nanotherapeutics: a promising strategy for anti‐HBV therapy. IET Nanobiotechnol 2019; 13:457-463. [PMCID: PMC8676379 DOI: 10.1049/iet-nbt.2018.5286] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 11/18/2018] [Accepted: 01/28/2019] [Indexed: 07/31/2023] Open
Abstract
Chronic hepatitis B (CHB) is the most common cause of hepatocellular carcinoma (HCC) and liver cirrhosis worldwide. In spite of the numerous advances in the treatment of CHB, drugs and vaccines have failed because of many factors like complexity, resistance, toxicity, and heavy cost. New RNA interference (RNAi)‐based technologies have developed innovative strategies to target Achilles' heel of the several hazardous diseases involving cancer, some genetic disease, autoimmune illnesses, and viral disorders particularly hepatitis B virus (HBV) infections. Naked siRNA delivery has serious challenges including failure to cross the cell membrane, susceptibility to the enzymatic digestion, and excretion by renal filtration, which ideally can be addressed by nanoparticle‐mediated delivery systems. cccDNA formation is a significant problem in obtaining HBV infections complete cure because of strength, durability, and lack of proper immune response. Nano‐siRNA drugs have a great potential to address this problem by silencing specific genes which are involved in cccDNA formation. In this article, the authors describe siRNA nanocarrier‐mediated delivery systems as a promising new strategy for HBV infections therapy. Simultaneously, the authors completely represent the clinical trials which use these strategies for treatment of the HBV infections.
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Affiliation(s)
- Shahin Aghamiri
- Student research committeeDepartment of Medical BiotechnologySchool of Advanced Technologies in MedicineShahid Beheshti University of Medical SciencesTehranIran
| | - Ali Jafarpour
- Students' Scientific Research CenterVirology DivisionDepartment of PathobiologySchool of Public HealthTehran University of Medical SciencesTehranIran
| | | | - Jaber Ghorbani
- Department of Medical BiotechnologySchool of Advanced Technologies in MedicineTehran University of Medical SciencesTehranIran
| | - Masoumeh Rajabibazl
- Department of Clinical BiochemistryFaculty of MedicineShahid Beheshti University of Medical SciencesTehranIran
- Department of Tissue Engineering and Applied Cell SciencesSchool of Advanced Technologies in MedicineShahid Beheshti University of Medical SciencesTehranIran
| | - Zahra Payandeh
- Immunology Research CenterTabriz University of Medical SciencesTabrizIran
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34
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Mozhaitsev E, Suslov E, Demidova Y, Korchagina D, Volcho K, Zakharenko A, Vasil'eva I, Kupryushkin M, Chepanova A, Ayine-Tora DM, Reynisson J, Salakhutdinov N, Lavrik O. The Development of Tyrosyl-DNA Phosphodyesterase 1 (TDP1) Inhibitors Based on the Amines Combining Aromatic/Heteroaromatic and Monoterpenoid Moieties. LETT DRUG DES DISCOV 2019. [DOI: 10.2174/1570180816666181220121042] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Background:
Inhibition of the DNA repair enzyme, tyrosyl-DNA phosphodiesterase 1
(TDP1), may increase the efficacy of cancer drugs that cause damage to tumor cell DNA. Among
the known TDP1 inhibitors, there are compounds containing moieties of natural substances, e.g.,
monoterpenoids. In this work, we synthesized several compounds containing aromatic/
heteroaromatic amines and monoterpenoid groups and assessed their TDP1 inhibition potential.
Methods:
Structures of all the synthesized compounds were confirmed by 1H and 13C NMR as well
as HRMS. The TDP1 inhibitory activity of the amines was determined by real-time fluorescence
oligonucleotide biosensor.
Results:
The synthesized secondary amines had TDP1 inhibitory activity IC50 in the range of
0.79-9.2 µM. The highest activity was found for (–)-myrtenal derivatives containing p-bromoaniline
or m-(trifluoromethyl)aniline residue.
Conclusion:
We synthesized 22 secondary amines; of these, 17 amines are novel chemical structures.
Many of the amines inhibit TDP1 activity in the low micromolar range. Therefore, these
compounds are promising for further study of their antiproliferative activity in conjunction with
DNA damaging drugs.
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Affiliation(s)
- Evgenii Mozhaitsev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Novosibirsk-630090, Russian Federation
| | - Evgenii Suslov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Novosibirsk-630090, Russian Federation
| | - Yuliya Demidova
- Boreskov Institute of Catalysis, Siberian Branch of the Russian Academy of Sciences, Novosibirsk-630090, Russian Federation
| | - Dina Korchagina
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Novosibirsk-630090, Russian Federation
| | - Konstantin Volcho
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Novosibirsk-630090, Russian Federation
| | - Alexandra Zakharenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Inna Vasil'eva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Maksim Kupryushkin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Arina Chepanova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | | | - Jóhannes Reynisson
- School of Chemical Sciences, The University of Auckland, Auckland-1142, New Zealand
| | - Nariman Salakhutdinov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Novosibirsk-630090, Russian Federation
| | - Olga Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
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Ikram N, Mirza MU, Vanmeert M, Froeyen M, Salo-Ahen OMH, Tahir M, Qazi A, Ahmad S. Inhibition of Oncogenic Kinases: An In Vitro Validated Computational Approach Identified Potential Multi-Target Anticancer Compounds. Biomolecules 2019; 9:E124. [PMID: 30925835 PMCID: PMC6523505 DOI: 10.3390/biom9040124] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 03/20/2019] [Accepted: 03/21/2019] [Indexed: 12/16/2022] Open
Abstract
Tumorigenesis in humans is a multistep progression that imitates genetic changes leading to cell transformation and malignancy. Oncogenic kinases play a central role in cancer progression, rendering them putative targets for the design of anti-cancer drugs. The presented work aims to identify the potential multi-target inhibitors of oncogenic receptor tyrosine kinases (RTKs) and serine/threonine kinases (STKs). For this, chemoinformatics and structure-based virtual screening approaches were combined with an in vitro validation of lead hits on both cancerous and non-cancerous cell lines. A total of 16 different kinase structures were screened against ~739,000 prefiltered compounds using diversity selection, after which the top hits were filtered for promising pharmacokinetic properties. This led to the identification of 12 and 9 compounds against RTKs and STKs, respectively. Molecular dynamics (MD) simulations were carried out to better comprehend the stability of the predicted hit kinase-compound complexes. Two top-ranked compounds against each kinase class were tested in vitro for cytotoxicity, with compound F34 showing the most promising inhibitory activity in HeLa, HepG2, and Vero cell lines with IC50 values of 145.46 μM, 175.48 μM, and 130.52 μM, respectively. Additional docking of F34 against various RTKs was carried out to support potential multi-target inhibition. Together with reliable MD simulations, these results suggest the promising potential of identified multi-target STK and RTK scaffolds for further kinase-specific anti-cancer drug development toward combinatorial therapies.
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Affiliation(s)
- Nazia Ikram
- Institute of Molecular Biology and Biotechnology, The University of Lahore, 54000 Lahore, Pakistan.
| | - Muhammad Usman Mirza
- Centre for Research in Molecular Medicine, The University of Lahore, 54000 Lahore, Pakistan.
- Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, University of Leuven, B-3000 Leuven, Belgium.
| | - Michiel Vanmeert
- Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, University of Leuven, B-3000 Leuven, Belgium.
| | - Matheus Froeyen
- Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, University of Leuven, B-3000 Leuven, Belgium.
| | - Outi M H Salo-Ahen
- Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, FI-20520 Turku, Finland.
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Pharmacy, Åbo Akademi University, FI-20520 Turku, Finland.
| | - Muhammad Tahir
- Centre for Research in Molecular Medicine, The University of Lahore, 54000 Lahore, Pakistan.
| | - Aamer Qazi
- Centre for Research in Molecular Medicine, The University of Lahore, 54000 Lahore, Pakistan.
| | - Sarfraz Ahmad
- Institute of Pharmaceutical Sciences, Riphah University, 54000 Lahore, Pakistan.
- Department of Chemistry, Faculty of Sciences, University Malaya, 59100, Kuala Lumpur, Malaysia.
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36
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Arshad F, Khan MF, Akhtar W, Alam MM, Nainwal LM, Kaushik SK, Akhter M, Parvez S, Hasan SM, Shaquiquzzaman M. Revealing quinquennial anticancer journey of morpholine: A SAR based review. Eur J Med Chem 2019; 167:324-356. [PMID: 30776694 DOI: 10.1016/j.ejmech.2019.02.015] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 01/24/2019] [Accepted: 02/04/2019] [Indexed: 02/07/2023]
Abstract
Morpholine, a six-membered heterocycle containing one nitrogen and one oxygen atom, is a moiety of great significance. It forms an important intermediate in many industrial and organic syntheses. Morpholine containing drugs are of high therapeutic value. Its wide array of pharmacological activity includes anti-diabetic, anti-emetic, growth stimulant, anti-depressant, bronchodilator and anticancer. Multi-drug resistance in cancer cases have emerged in the last few years and have led to the failure of many chemotherapeutic drugs. Newer treatment methods and drugs are being developed to overcome this problem. Target based drug discovery is an effective method to develop novel anticancer drugs. To develop newer drugs, previously reported work needs to be studied. Keeping this in mind, last five year's literature on morpholine used as anticancer agents has been reviewed and summarized in the paper herein.
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Affiliation(s)
- Fatima Arshad
- Drug Design & Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India
| | - Mohemmed Faraz Khan
- Drug Design & Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India
| | - Wasim Akhtar
- Drug Design & Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India
| | - Mohammad Mumtaz Alam
- Drug Design & Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India
| | - Lalit Mohan Nainwal
- Drug Design & Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India
| | - Sumit Kumar Kaushik
- Drug Design & Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India
| | - Mymoona Akhter
- Drug Design & Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India
| | - Suhel Parvez
- Department of Toxicology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, 110062, India
| | | | - Mohammad Shaquiquzzaman
- Drug Design & Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India.
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37
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Zhang Y, Wang Z, Li D, Zang W, Zhu H, Wu P, Mei Y, Liang Y. A polysaccharide from Antrodia cinnamomea mycelia exerts antitumor activity through blocking of TOP1/TDP1-mediated DNA repair pathway. Int J Biol Macromol 2018; 120:1551-1560. [DOI: 10.1016/j.ijbiomac.2018.09.162] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 09/09/2018] [Accepted: 09/25/2018] [Indexed: 12/20/2022]
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38
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Komarova AO, Drenichev MS, Dyrkheeva NS, Kulikova IV, Oslovsky VE, Zakharova OD, Zakharenko AL, Mikhailov SN, Lavrik OI. Novel group of tyrosyl-DNA-phosphodiesterase 1 inhibitors based on disaccharide nucleosides as drug prototypes for anti-cancer therapy. J Enzyme Inhib Med Chem 2018; 33:1415-1429. [PMID: 30191738 PMCID: PMC6136360 DOI: 10.1080/14756366.2018.1509210] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 07/06/2018] [Accepted: 08/04/2018] [Indexed: 02/03/2023] Open
Abstract
A new class of tyrosyl-DNA phosphodiesterase 1 (TDP1) inhibitors based on disaccharide nucleosides was identified. TDP1 plays an essential role in the resistance of cancer cells to currently used antitumour drugs based on Top1 inhibitors such as topotecan and irinotecan. The most effective inhibitors investigated in this study have IC50 values (half-maximal inhibitory concentration) in 0.4-18.5 µM range and demonstrate relatively low own cytotoxicity along with significant synergistic effect in combination with anti-cancer drug topotecan. Moreover, kinetic parameters of the enzymatic reaction and fluorescence anisotropy were measured using different types of DNA-biosensors to give a sufficient insight into the mechanism of inhibitor's action.
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Affiliation(s)
- Anastasia O. Komarova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russian Federation
| | - Mikhail S. Drenichev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation
| | - Nadezhda S. Dyrkheeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Irina V. Kulikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation
| | - Vladimir E. Oslovsky
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation
| | - Olga D. Zakharova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Alexandra L. Zakharenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Sergey N. Mikhailov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation
| | - Olga I. Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russian Federation
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39
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Al-Hrout A, Chaiboonchoe A, Khraiwesh B, Murali C, Baig B, El-Awady R, Tarazi H, Alzahmi A, Nelson DR, Greish YE, Ramadan W, Salehi-Ashtiani K, Amin A. Safranal induces DNA double-strand breakage and ER-stress-mediated cell death in hepatocellular carcinoma cells. Sci Rep 2018; 8:16951. [PMID: 30446676 PMCID: PMC6240095 DOI: 10.1038/s41598-018-34855-0] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 10/26/2018] [Indexed: 12/21/2022] Open
Abstract
Poor prognoses remain the most challenging aspect of hepatocellular carcinoma (HCC) therapy. Consequently, alternative therapeutics are essential to control HCC. This study investigated the anticancer effects of safranal against HCC using in vitro, in silico, and network analyses. Cell cycle and immunoblot analyses of key regulators of cell cycle, DNA damage repair and apoptosis demonstrated unique safranal-mediated cell cycle arrest at G2/M phase at 6 and 12 h, and at S-phase at 24 h, and a pronounced effect on DNA damage machinery. Safranal also showed pro-apoptotic effect through activation of both intrinsic and extrinsic initiator caspases; indicating ER stress-mediated apoptosis. Gene set enrichment analysis provided consistent findings where UPR is among the top terms of up-regulated genes in response to safranal treatment. Thus, proteins involved in ER stress were regulated through safranal treatment to induce UPR in HepG2 cells.
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Affiliation(s)
- Ala'a Al-Hrout
- Biology Department, College of Science, UAE University, P.O. Box 15551, Al-Ain, UAE
| | - Amphun Chaiboonchoe
- Laboratory of Algal, Synthetic, and Systems Biology, Division of Science and Math, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, UAE
| | - Basel Khraiwesh
- Laboratory of Algal, Synthetic, and Systems Biology, Division of Science and Math, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, UAE
- Center for Genomics and Systems Biology (CGSB), Division of Science, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, UAE
| | - Chandraprabha Murali
- Biology Department, College of Science, UAE University, P.O. Box 15551, Al-Ain, UAE
| | - Badriya Baig
- Biology Department, College of Science, UAE University, P.O. Box 15551, Al-Ain, UAE
| | - Raafat El-Awady
- College of Pharmacy and Sharjah Institute for Medical Research, University of Sharjah, Sharjah, UAE
| | - Hamadeh Tarazi
- College of Pharmacy and Sharjah Institute for Medical Research, University of Sharjah, Sharjah, UAE
| | - Amnah Alzahmi
- Laboratory of Algal, Synthetic, and Systems Biology, Division of Science and Math, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, UAE
| | - David R Nelson
- Laboratory of Algal, Synthetic, and Systems Biology, Division of Science and Math, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, UAE
| | | | - Wafaa Ramadan
- College of Pharmacy and Sharjah Institute for Medical Research, University of Sharjah, Sharjah, UAE
| | - Kourosh Salehi-Ashtiani
- Laboratory of Algal, Synthetic, and Systems Biology, Division of Science and Math, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, UAE.
- Center for Genomics and Systems Biology (CGSB), Division of Science, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, UAE.
| | - Amr Amin
- Biology Department, College of Science, UAE University, P.O. Box 15551, Al-Ain, UAE.
- Zoology Department, Cairo University, Giza, Egypt.
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40
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Zhang XR, Wang HW, Tang WL, Zhang Y, Yang H, Hu DX, Ravji A, Marchand C, Kiselev E, Ofori-Atta K, Agama K, Pommier Y, An LK. Discovery, Synthesis, and Evaluation of Oxynitidine Derivatives as Dual Inhibitors of DNA Topoisomerase IB (TOP1) and Tyrosyl-DNA Phosphodiesterase 1 (TDP1), and Potential Antitumor Agents. J Med Chem 2018; 61:9908-9930. [PMID: 30336023 DOI: 10.1021/acs.jmedchem.8b00639] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Tyrosyl-DNA phosphodiesterase 1 (TDP1) is a recently discovered enzyme repairing DNA lesions resulting from stalled topoisomerase IB (TOP1)-DNA covalent complex. Inhibiting TDP1 in conjunction with TOP1 inhibitors can boost the action of the latter. Herein, we report the discovery of the natural product oxynitidine scaffold as a novel chemotype for the development of TOP1 and TDP1 inhibitors. Three kinds of analogues, benzophenanthridinone, dihydrobenzophenanthridine, and benzophenanthridine derivatives, were synthesized and evaluated for both TOP1 and TDP1 inhibition and cytotoxicity. Analogue 19a showed high TOP1 inhibition (+++) and induced the formation of cellular TOP1cc and DNA damage, resulting in cancer cells apoptosis at nanomolar concentration range. In vivo studies indicated that 19a exhibits antitumor efficiency in HCT116 xenograft model. 41a exhibited additional TDP1 inhibition with IC50 value of 7 μM and synergistic effect with camptothecin in MCF-7 cells. This work will facilitate future efforts for the discovery of natural product-based TOP1 and TDP1 inhibitors.
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Affiliation(s)
- Xiao-Ru Zhang
- School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , China
| | - Hao-Wen Wang
- School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , China
| | - Wen-Lin Tang
- School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , China
| | - Yu Zhang
- School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , China
| | - Hui Yang
- School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , China
| | - De-Xuan Hu
- School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , China
| | - Azhar Ravji
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Christophe Marchand
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Evgeny Kiselev
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Kwabena Ofori-Atta
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Keli Agama
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Lin-Kun An
- School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , China
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41
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Zakharenko AL, Mozhaitsev ES, Suslov EV, Korchagina DV, Volcho KP, Salakhutdinov NF, Lavrik OI. Synthesis and Inhibitory Properties of Imines Containing Monoterpenoid and Adamantane Fragments Against DNA Repair Enzyme Tyrosyl-DNA Phosphodiesterase 1 (Tdp1). Chem Nat Compd 2018. [DOI: 10.1007/s10600-018-2443-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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42
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Zakharova O, Luzina O, Zakharenko A, Sokolov D, Filimonov A, Dyrkheeva N, Chepanova A, Ilina E, Ilyina A, Klabenkova K, Chelobanov B, Stetsenko D, Zafar A, Eurtivong C, Reynisson J, Volcho K, Salakhutdinov N, Lavrik O. Synthesis and evaluation of aryliden- and hetarylidenfuranone derivatives of usnic acid as highly potent Tdp1 inhibitors. Bioorg Med Chem 2018; 26:4470-4480. [PMID: 30076000 DOI: 10.1016/j.bmc.2018.07.039] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 07/19/2018] [Accepted: 07/22/2018] [Indexed: 10/28/2022]
Abstract
Tyrosyl-DNA phosphodiesterase 1 (Tdp1) is a repair enzyme for stalled DNA-topoisomerase 1 (Top 1) cleavage complexes and other 3'-end DNA lesions. Tdp1 is a promising target for anticancer therapy, since it can repair DNA lesions caused by Top1 inhibitors leading to drug resistance. Hence, Tdp1 inhibition should result in synergistic effect with Top1 inhibitors. Twenty nine derivatives of (+)-usnic acid were tested for in vitro Tdp1 inhibitory activity using a fluorescent-based assay. Excellent activity was obtained, with derivative 6m demonstrating the lowest IC50 value of 25 nM. The established efficacy was verified using a gel-based assay, which gave close results to that of the fluorescent assay. In addition, molecular modeling in the Tdp1 substrate binding pocket suggested plausible binding modes for the active analogues. The synergistic effect of the Tdp1 inhibitors with topotecan, a Top1 poison in clinical use, was tested in two human cell lines, A-549 and HEK-293. Compounds 6k and 6x gave very promising results. In particular, 6x has a low cytotoxicity and an IC50 value of 63 nM, making it a valuable lead compound for the development of potent Tdp1 inhibitors for clinical use.
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Affiliation(s)
- Olga Zakharova
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russian Federation
| | - Olga Luzina
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russian Federation
| | - Alexandra Zakharenko
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russian Federation
| | - Dmitry Sokolov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russian Federation
| | - Alexandr Filimonov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russian Federation; Novosibirsk State University, Novosibirsk 630090, Russian Federation
| | - Nadezhda Dyrkheeva
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russian Federation
| | - Arina Chepanova
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russian Federation
| | - Ekaterina Ilina
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russian Federation
| | - Anna Ilyina
- Novosibirsk State University, Novosibirsk 630090, Russian Federation
| | | | - Boris Chelobanov
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russian Federation; Novosibirsk State University, Novosibirsk 630090, Russian Federation
| | - Dmitry Stetsenko
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russian Federation
| | - Ayesha Zafar
- School of Chemical Sciences, University of Auckland, New Zealand
| | | | | | - Konstantin Volcho
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russian Federation; Novosibirsk State University, Novosibirsk 630090, Russian Federation
| | - Nariman Salakhutdinov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russian Federation; Novosibirsk State University, Novosibirsk 630090, Russian Federation
| | - Olga Lavrik
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russian Federation; Novosibirsk State University, Novosibirsk 630090, Russian Federation.
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43
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Salomatina OV, Popadyuk II, Zakharenko AL, Zakharova OD, Fadeev DS, Komarova NI, Reynisson J, Arabshahi HJ, Chand R, Volcho KP, Salakhutdinov NF, Lavrik OI. Novel Semisynthetic Derivatives of Bile Acids as Effective Tyrosyl-DNA Phosphodiesterase 1 Inhibitors. Molecules 2018; 23:molecules23030679. [PMID: 29562592 PMCID: PMC6017735 DOI: 10.3390/molecules23030679] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 03/14/2018] [Accepted: 03/16/2018] [Indexed: 12/20/2022] Open
Abstract
An Important task in the treatment of oncological and neurodegenerative diseases is the search for new inhibitors of DNA repair system enzymes. Tyrosyl-DNA phosphodiesterase 1 (Tdp1) is one of the DNA repair system enzymes involved in the removal of DNA damages caused by topoisomerase I inhibitors. Thus, reducing the activity of Tdp1 can increase the effectiveness of currently used anticancer drugs. We describe here a new class of semisynthetic small molecule Tdp1 inhibitors based on the bile acid scaffold that were originally identified by virtual screening. The influence of functional groups of bile acids (hydroxy and acetoxy groups in the steroid framework and amide fragment in the side chain) on inhibitory activity was investigated. In vitro studies demonstrate the ability of the semisynthetic derivatives to effectively inhibit Tdp1 with IC50 up to 0.29 µM. Furthermore, an excellent fit is realized for the ligands when docked into the active site of the Tdp1 enzyme.
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Affiliation(s)
- Oksana V Salomatina
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS, acad. Lavrentjev ave. 9, Novosibirsk 630090, Russia.
| | - Irina I Popadyuk
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS, acad. Lavrentjev ave. 9, Novosibirsk 630090, Russia.
| | - Alexandra L Zakharenko
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, SB RAS, acad. Lavrentjev ave. 8, Novosibirsk 630090, Russia.
| | - Olga D Zakharova
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, SB RAS, acad. Lavrentjev ave. 8, Novosibirsk 630090, Russia.
| | - Dmitriy S Fadeev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS, acad. Lavrentjev ave. 9, Novosibirsk 630090, Russia.
| | - Nina I Komarova
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS, acad. Lavrentjev ave. 9, Novosibirsk 630090, Russia.
| | - Jóhannes Reynisson
- School of Chemical Sciences, University of Auckland, Auckland 1142, New Zealand.
| | - H John Arabshahi
- School of Chemical Sciences, University of Auckland, Auckland 1142, New Zealand.
| | - Raina Chand
- School of Chemical Sciences, University of Auckland, Auckland 1142, New Zealand.
| | - Konstantin P Volcho
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS, acad. Lavrentjev ave. 9, Novosibirsk 630090, Russia.
- Novosibirsk State University, Pirogova str. 2, Novosibirsk 630090, Russia.
| | - Nariman F Salakhutdinov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS, acad. Lavrentjev ave. 9, Novosibirsk 630090, Russia.
- Novosibirsk State University, Pirogova str. 2, Novosibirsk 630090, Russia.
| | - Olga I Lavrik
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, SB RAS, acad. Lavrentjev ave. 8, Novosibirsk 630090, Russia.
- Novosibirsk State University, Pirogova str. 2, Novosibirsk 630090, Russia.
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44
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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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45
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Flett FJ, Ruksenaite E, Armstrong LA, Bharati S, Carloni R, Morris ER, Mackay CL, Interthal H, Richardson JM. Structural basis for DNA 3'-end processing by human tyrosyl-DNA phosphodiesterase 1. Nat Commun 2018; 9:24. [PMID: 29295983 PMCID: PMC5750209 DOI: 10.1038/s41467-017-02530-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 12/06/2017] [Indexed: 11/15/2022] Open
Abstract
Tyrosyl-DNA phosphodiesterase (Tdp1) is a DNA 3'-end processing enzyme that repairs topoisomerase 1B-induced DNA damage. We use a new tool combining site-specific DNA-protein cross-linking with mass spectrometry to identify Tdp1 interactions with DNA. A conserved phenylalanine (F259) of Tdp1, required for efficient DNA processing in biochemical assays, cross-links to defined positions in DNA substrates. Crystal structures of Tdp1-DNA complexes capture the DNA repair machinery after 3'-end cleavage; these reveal how Tdp1 coordinates the 3'-phosphorylated product of nucleosidase activity and accommodates duplex DNA. A hydrophobic wedge splits the DNA ends, directing the scissile strand through a channel towards the active site. The F259 side-chain stacks against the -3 base pair, delimiting the junction of duplexed and melted DNA, and fixes the scissile strand in the channel. Our results explain why Tdp1 cleavage is non-processive and provide a molecular basis for DNA 3'-end processing by Tdp1.
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Affiliation(s)
- Fiona J Flett
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, The King's Buildings, Roger Land Building, Alexander Crum Brown Road, Edinburgh, EH9 3FF, UK
| | - Emilija Ruksenaite
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, The King's Buildings, Max Born Crescent, Edinburgh, EH9 3BF, UK
| | - Lee A Armstrong
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, The King's Buildings, Max Born Crescent, Edinburgh, EH9 3BF, UK
| | - Shipra Bharati
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, The King's Buildings, Max Born Crescent, Edinburgh, EH9 3BF, UK
| | - Roberta Carloni
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, The King's Buildings, Roger Land Building, Alexander Crum Brown Road, Edinburgh, EH9 3FF, UK
| | - Elizabeth R Morris
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, The King's Buildings, Max Born Crescent, Edinburgh, EH9 3BF, UK
| | - C Logan Mackay
- EaStCHEM School of Chemistry, University of Edinburgh, The King's Buildings, David Brewster Road, Edinburgh, EH9 3FJ, UK
| | - Heidrun Interthal
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, The King's Buildings, Roger Land Building, Alexander Crum Brown Road, Edinburgh, EH9 3FF, UK.
| | - Julia M Richardson
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, The King's Buildings, Max Born Crescent, Edinburgh, EH9 3BF, UK.
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46
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Barakat A, Islam MS, Ghawas HM, Al-Majid AM, El-Senduny FF, Badria FA, Elshaier YAM, Ghabbour HA. Substituted spirooxindole derivatives as potent anticancer agents through inhibition of phosphodiesterase 1. RSC Adv 2018; 8:14335-14346. [PMID: 35540737 PMCID: PMC9079959 DOI: 10.1039/c8ra02358a] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Accepted: 04/02/2018] [Indexed: 12/02/2022] Open
Abstract
Spirooxindole is a promising chemo therapeutic agent. Possible targets include cancers of the liver, prostate, lung, stomach, colon, and breast. Here, we demonstrate a one-pot three-component reaction via a [3 + 2] cycloaddition/ring contraction sequence of a dipolarophile (activated alkene) with in situ-generated azomethine ylide (1,3-dipoles) without the use of any catalyst. The reaction provides efficient access to synthetically useful and biologically important spirooxindoles in high yield (69–94%) with high diastereoselectivity. The synthesized compounds were subjected to cytotoxicity evaluation using colorectal cancer (HCT-116), hepatocellular carcinoma (HepG2), and prostate cancer (PC-3) cells. Compounds 4i, 4j, and 4k showed potent cytotoxic activity and high selectivity against HCT-116 cells when compared to cisplatin. Meanwhile compound 4d retained high cytotoxic activity and selectivity against HepG2 and PC-3 cells in comparison to cisplatin. The mechanism of compound 4d was further studied using phosphodiesterase 1 enzyme and showed 74.2% inhibitory activity. A possible binding mode for compound 4d to PDE-1 was investigated by molecular modeling using OpenEye software. Pose predictions for the active compounds were demonstrated by ROCS alignments. Compound 4d has a special geometry and differs from other active compounds. Spirooxindole is a promising chemo therapeutic agent. Possible targets include cancers of the liver, prostate, lung, stomach, colon, and breast.![]()
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Affiliation(s)
- Assem Barakat
- Department of Chemistry
- College of Science
- King Saud University
- Riyadh 11451
- Saudi Arabia
| | | | - Hussien Mansur Ghawas
- Department of Chemistry
- College of Science
- King Saud University
- Riyadh 11451
- Saudi Arabia
| | | | | | - Farid A. Badria
- Department of Pharmacognosy
- Faculty of Pharmacy
- Mansoura University
- Mansoura 35516
- Egypt
| | - Yaseen A. M. M. Elshaier
- Pharmaceutical Organic Chemistry Department
- Faculty of Pharmacy
- Al-Azhar University
- Assuit 71524
- Egypt
| | - Hazem A. Ghabbour
- Department of Pharmaceutical Chemistry
- College of Pharmacy
- King Saud University
- Riyadh 11451
- Saudi Arabia
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47
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Zhang Y, Li D, Wang Z, Zang W, Rao P, Liang Y, Mei Y. Alpha-terpineol affects synthesis and antitumor activity of triterpenoids fromAntrodia cinnamomeamycelia in solid-state culture. Food Funct 2018; 9:6517-6525. [DOI: 10.1039/c8fo02079e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
To enhance production ofAntrodia cinnamomeatriterpenoids (ACTs) from mycelia in solid-state culture, α-terpineol was added to the medium as an elicitor at an optimal concentration of 0.05 mL L−1.
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Affiliation(s)
- Yutian Zhang
- State Key Laboratory of Agricultural Microbiology
- College of Life Science and Technology
- Huazhong Agricultural University
- Wuhan 430070
- P. R. China
| | - Diying Li
- State Key Laboratory of Agricultural Microbiology
- College of Life Science and Technology
- Huazhong Agricultural University
- Wuhan 430070
- P. R. China
| | - Zhuo Wang
- State Key Laboratory of Agricultural Microbiology
- College of Life Science and Technology
- Huazhong Agricultural University
- Wuhan 430070
- P. R. China
| | - Wanting Zang
- State Key Laboratory of Agricultural Microbiology
- College of Life Science and Technology
- Huazhong Agricultural University
- Wuhan 430070
- P. R. China
| | - Pan Rao
- State Key Laboratory of Agricultural Microbiology
- College of Life Science and Technology
- Huazhong Agricultural University
- Wuhan 430070
- P. R. China
| | - Yunxiang Liang
- State Key Laboratory of Agricultural Microbiology
- College of Life Science and Technology
- Huazhong Agricultural University
- Wuhan 430070
- P. R. China
| | - Yuxia Mei
- State Key Laboratory of Agricultural Microbiology
- College of Life Science and Technology
- Huazhong Agricultural University
- Wuhan 430070
- P. R. China
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48
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Ponomarev KY, Suslov EV, Zakharenko AL, Zakharova OD, Rogachev AD, Korchagina DV, Zafar A, Reynisson J, Nefedov AA, Volcho KP, Salakhutdinov NF, Lavrik OI. Aminoadamantanes containing monoterpene-derived fragments as potent tyrosyl-DNA phosphodiesterase 1 inhibitors. Bioorg Chem 2017; 76:392-399. [PMID: 29248742 DOI: 10.1016/j.bioorg.2017.12.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 11/28/2017] [Accepted: 12/01/2017] [Indexed: 12/17/2022]
Abstract
The ability of a number of nitrogen-containing compounds that simultaneously carry the adamantane and monoterpene moieties to inhibit Tdp1, an important enzyme of the DNA repair system, is studied. Inhibition of this enzyme has the potential to overcome chemotherapeutic resistance of some tumor types. Compound (+)-3c synthesized from 1-aminoadamantane and (+)-myrtenal, and compound 4a produced from 2-aminoadamantane and citronellal were found to be most potent as they inhibited Tdp1 with IC50 values of 6 and 3.5 µM, respectively. These compounds proved to have low cytotoxicity in colon HCT-116 and lung A-549 human tumor cell lines (CC50 > 50 µM). It was demonstrated that compound 4a at 10 µM enhanced cytotoxicity of topotecan, a topoisomerase 1 poison in clinical use, against HCT-116 more than fivefold and to a lesser extent of 1.5 increase in potency for A-549.
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Affiliation(s)
- Konstantin Yu Ponomarev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk 630090, Russian Federation
| | - Evgeniy V Suslov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk 630090, Russian Federation
| | - Alexandra L Zakharenko
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., Novosibirsk 630090, Russian Federation
| | - Olga D Zakharova
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., Novosibirsk 630090, Russian Federation
| | - Artem D Rogachev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk 630090, Russian Federation; Novosibirsk State University, 2, Pirogova Str., Novosibirsk 630090, Russian Federation
| | - Dina V Korchagina
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk 630090, Russian Federation
| | - Ayesha Zafar
- School of Chemical Sciences, University of Auckland, New Zealand
| | | | - Andrey A Nefedov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk 630090, Russian Federation; Novosibirsk State University, 2, Pirogova Str., Novosibirsk 630090, Russian Federation
| | - Konstantin P Volcho
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk 630090, Russian Federation; Novosibirsk State University, 2, Pirogova Str., Novosibirsk 630090, Russian Federation
| | - Nariman F Salakhutdinov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk 630090, Russian Federation; Novosibirsk State University, 2, Pirogova Str., Novosibirsk 630090, Russian Federation
| | - Olga I Lavrik
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., Novosibirsk 630090, Russian Federation; Novosibirsk State University, 2, Pirogova Str., Novosibirsk 630090, Russian Federation.
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49
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Lohavanichbutr P, Sakoda LC, Amos CI, Arnold SM, Christiani DC, Davies MPA, Field JK, Haura EB, Hung RJ, Kohno T, Landi MT, Liu G, Liu Y, Marcus MW, O'Kane GM, Schabath MB, Shiraishi K, Slone SA, Tardón A, Yang P, Yoshida K, Zhang R, Zong X, Goodman GE, Weiss NS, Chen C. Common TDP1 Polymorphisms in Relation to Survival among Small Cell Lung Cancer Patients: A Multicenter Study from the International Lung Cancer Consortium. Clin Cancer Res 2017; 23:7550-7557. [PMID: 28974547 DOI: 10.1158/1078-0432.ccr-17-1401] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 07/12/2017] [Accepted: 09/28/2017] [Indexed: 11/16/2022]
Abstract
Purpose: DNA topoisomerase inhibitors are commonly used for treating small-cell lung cancer (SCLC). Tyrosyl-DNA phosphodiesterase (TDP1) repairs DNA damage caused by this class of drugs and may therefore influence treatment outcome. In this study, we investigated whether common TDP1 single-nucleotide polymorphisms (SNP) are associated with overall survival among SCLC patients.Experimental Design: Two TDP1 SNPs (rs942190 and rs2401863) were analyzed in 890 patients from 10 studies in the International Lung Cancer Consortium (ILCCO). The Kaplan-Meier method and Cox regression analyses were used to evaluate genotype associations with overall mortality at 36 months postdiagnosis, adjusting for age, sex, race, and tumor stage.Results: Patients homozygous for the minor allele (GG) of rs942190 had poorer survival compared with those carrying AA alleles, with a HR of 1.36 [95% confidence interval (CI): 1.08-1.72, P = 0.01), but no association with survival was observed for patients carrying the AG genotype (HR = 1.04, 95% CI, 0.84-1.29, P = 0.72). For rs2401863, patients homozygous for the minor allele (CC) tended to have better survival than patients carrying AA alleles (HR = 0.79; 95% CI, 0.61-1.02, P = 0.07). Results from the Genotype Tissue Expression (GTEx) Project, the Encyclopedia of DNA Elements (ENCODE), and the ePOSSUM web application support the potential function of rs942190.Conclusions: We found the rs942190 GG genotype to be associated with relatively poor survival among SCLC patients. Further investigation is needed to confirm the result and to determine whether this genotype may be a predictive marker for treatment efficacy of DNA topoisomerase inhibitors. Clin Cancer Res; 23(24); 7550-7. ©2017 AACR.
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Affiliation(s)
- Pawadee Lohavanichbutr
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Lori C Sakoda
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Christopher I Amos
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire
| | - Susanne M Arnold
- Division of Medical Oncology, University of Kentucky Markey Cancer Center, Lexington, Kentucky
| | - David C Christiani
- Department of Environmental Health, Harvard School of Public Health, Boston, Massachusetts
| | - Michael P A Davies
- Roy Castle Lung Cancer Research Programme, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - John K Field
- Roy Castle Lung Cancer Research Programme, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Eric B Haura
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Research Institute, Tokyo, Japan
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland
| | - Geoffrey Liu
- Department of Medical Oncology, Princess Margaret Cancer Center and University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Yi Liu
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Michael W Marcus
- Roy Castle Lung Cancer Research Programme, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Grainne M O'Kane
- Department of Medical Oncology, Princess Margaret Cancer Center and University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Matthew B Schabath
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Kouya Shiraishi
- Division of Genome Biology, National Cancer Research Institute, Tokyo, Japan
| | - Stacey A Slone
- Biostatistics and Bioinformatics Shared Resource Facility, University of Kentucky Markey Cancer Center, Lexington, Kentucky
| | - Adonina Tardón
- CIBER Epidemiology and Public Health (CIBER-ESP), Health Research Institute Carlos III, Madrid, Spain.,University Institute of Oncology, University of Oviedo, Oviedo, Asturias, Spain
| | - Ping Yang
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Kazushi Yoshida
- Division of Genome Biology, National Cancer Research Institute, Tokyo, Japan
| | - Ruyang Zhang
- Department of Environmental Health, Harvard School of Public Health, Boston, Massachusetts
| | - Xuchen Zong
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Gary E Goodman
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Noel S Weiss
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington
| | - Chu Chen
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington. .,Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington.,Department of Otolaryngology: Head and Neck Surgery, School of Medicine, University of Washington, Seattle, Washington
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50
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Sanni DM, Fatoki TH, Kolawole AO, Akinmoladun AC. Xeronine structure and function: computational comparative mastery of its mystery. In Silico Pharmacol 2017; 5:8. [PMID: 28955650 DOI: 10.1007/s40203-017-0028-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 08/22/2017] [Indexed: 12/18/2022] Open
Abstract
Morinda citrifolia (Noni) fruit has a long history of dietary use in tropical regions of the world. Pharmacological properties that have been attributed to the fruit include anti-inflammatory, anti-cancer, and antioxidant properties. Xeronine, a small alkaloid which has been patented (US4543212) is one of the bioactive compounds of Noni fruit, which is believed to be capable of modifying the molecular structure of specific inactive proteins thereby regulating proper folding to active enzymes. Despite reports of the potential of Xeronine as therapeutic agent, its presence is controversial and its structure has not been explored. In this study, standard chemoinformatics tools and servers such as ChemSketch, ChemMine, Swisstargetprediction, SwissADME and Swisssimilarity have been employed to predict its possible structure. In addition, synthetic xeronine structures based on the known bioactive components of Noni fruit were designed. Results showed that the hypothetical structure of xeronine provided by the patent inventor is a mystery based on its <5% probable protein targets and no similarity match to the US Food and Drug Administration (FDA) approved drugs and experimental compounds by in silico evaluation. By constrast, final designed xeronine structure possess all the features that were described in the patent document, and has >40% probable protein targets related to neurodegenerative diseases such as Alzheimer's disease (AD), which possibly justifies the key function stated in the patent.
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Affiliation(s)
- David Morakinyo Sanni
- Enzyme Biotechnology and Bioinformatics Unit, Department of Biochemistry, Federal University of Technology, PMB 704 Akure, Nigeria
| | - Toluwase Hezekiah Fatoki
- Enzyme Biotechnology and Bioinformatics Unit, Department of Biochemistry, Federal University of Technology, PMB 704 Akure, Nigeria
| | - Ayodele Oluseyi Kolawole
- Enzyme Biotechnology and Bioinformatics Unit, Department of Biochemistry, Federal University of Technology, PMB 704 Akure, Nigeria
| | - Afolabi Clement Akinmoladun
- Biochemical Pharmacology and Toxicology Unit, Department of Biochemistry, Federal University of Technology, PMB 704 Akure, Nigeria
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