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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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2
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Zakharenko AL, Luzina OA, Chepanova AA, Dyrkheeva NS, Salakhutdinov NF, Lavrik OI. Natural Products and Their Derivatives as Inhibitors of the DNA Repair Enzyme Tyrosyl-DNA Phosphodiesterase 1. Int J Mol Sci 2023; 24:ijms24065781. [PMID: 36982848 PMCID: PMC10051138 DOI: 10.3390/ijms24065781] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 02/22/2023] [Accepted: 03/14/2023] [Indexed: 03/30/2023] Open
Abstract
Tyrosyl-DNA phosphodiesterase 1 (TDP1) is an important repair enzyme that removes various covalent adducts from the 3' end of DNA. Particularly, covalent complexes of topoisomerase 1 (TOP1) with DNA stabilized by DNA damage or by various chemical agents are an examples of such adducts. Anticancer drugs such as the TOP1 poisons topotecan and irinotecan are responsible for the stabilization of these complexes. TDP1 neutralizes the effect of these anticancer drugs, eliminating the DNA adducts. Therefore, the inhibition of TDP1 can sensitize tumor cells to the action of TOP1 poisons. This review contains information about methods for determining the TDP1 activity, as well as describing the inhibitors of these enzyme derivatives of natural biologically active substances, such as aminoglycosides, nucleosides, polyphenolic compounds, and terpenoids. Data on the efficiency of combined inhibition of TOP1 and TDP1 in vitro and in vivo are presented.
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Affiliation(s)
- 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
| | - 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
| | - 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
| | - 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
| | - 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
| | - 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
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3
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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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4
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In Vitro and In Silico Studies of Human Tyrosyl-DNA Phosphodiesterase 1 (Tdp1) Inhibition by Stereoisomeric Forms of Lipophilic Nucleosides: The Role of Carbohydrate Stereochemistry in Ligand-Enzyme Interactions. Molecules 2022; 27:molecules27082433. [PMID: 35458631 PMCID: PMC9024977 DOI: 10.3390/molecules27082433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/03/2022] [Accepted: 04/06/2022] [Indexed: 12/10/2022] Open
Abstract
Inhibition of human DNA repair enzyme tyrosyl-DNA phosphodiesterase 1 (Tdp1) by different chiral lipophilic nucleoside derivatives was studied. New Tdp1 inhibitors were found in the series of the studied compounds with IC50 = 2.7–6.7 μM. It was shown that D-lipophilic nucleoside derivatives manifested higher inhibition activity than their L-analogs, and configuration of the carbohydrate moiety can influence the mechanism of Tdp1 inhibition.
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Salomatina OV, Dyrkheeva NS, Popadyuk II, Zakharenko AL, Ilina ES, Komarova NI, Reynisson J, Salakhutdinov NF, Lavrik OI, Volcho KP. New Deoxycholic Acid Derived Tyrosyl-DNA Phosphodiesterase 1 Inhibitors Also Inhibit Tyrosyl-DNA Phosphodiesterase 2. Molecules 2021; 27:molecules27010072. [PMID: 35011303 PMCID: PMC8746696 DOI: 10.3390/molecules27010072] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 12/04/2022] Open
Abstract
A series of deoxycholic acid (DCA) amides containing benzyl ether groups on the steroid core were tested against the tyrosyl-DNA phosphodiesterase 1 (TDP1) and 2 (TDP2) enzymes. In addition, 1,2,4- and 1,3,4-oxadiazole derivatives were synthesized to study the linker influence between a para-bromophenyl moiety and the steroid scaffold. The DCA derivatives demonstrated promising inhibitory activity against TDP1 with IC50 in the submicromolar range. Furthermore, the amides and the 1,3,4-oxadiazole derivatives inhibited the TDP2 enzyme but at substantially higher concentration. Tryptamide 5 and para-bromoanilide 8 derivatives containing benzyloxy substituent at the C-3 position and non-substituted hydroxy group at C-12 on the DCA scaffold inhibited both TDP1 and TDP2 as well as enhanced the cytotoxicity of topotecan in non-toxic concentration in vitro. According to molecular modeling, ligand 5 is anchored into the catalytic pocket of TDP1 by one hydrogen bond to the backbone of Gly458 as well as by π–π stacking between the indolyl rings of the ligand and Tyr590, resulting in excellent activity. It can therefore be concluded that these derivatives contribute to the development of specific TDP1 and TDP2 inhibitors for adjuvant therapy against cancer in combination with topoisomerase poisons.
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Affiliation(s)
- Oksana V. Salomatina
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS, 9, Lavrent’ev Ave., 630090 Novosibirsk, Russia; (O.V.S.); (I.I.P.); (N.I.K.); (N.F.S.)
| | - Nadezhda S. Dyrkheeva
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8, Lavrent’ev Ave., 630090 Novosibirsk, Russia; (N.S.D.); (A.L.Z.); (E.S.I.); (O.I.L.)
| | - Irina I. Popadyuk
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS, 9, Lavrent’ev Ave., 630090 Novosibirsk, Russia; (O.V.S.); (I.I.P.); (N.I.K.); (N.F.S.)
| | - Alexandra L. Zakharenko
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8, Lavrent’ev Ave., 630090 Novosibirsk, Russia; (N.S.D.); (A.L.Z.); (E.S.I.); (O.I.L.)
| | - Ekaterina S. Ilina
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8, Lavrent’ev Ave., 630090 Novosibirsk, Russia; (N.S.D.); (A.L.Z.); (E.S.I.); (O.I.L.)
| | - Nina I. Komarova
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS, 9, Lavrent’ev Ave., 630090 Novosibirsk, Russia; (O.V.S.); (I.I.P.); (N.I.K.); (N.F.S.)
| | - Jóhannes Reynisson
- School of Pharmacy and Bioengineering, Keele University, Staffordshire ST5 5BG, UK;
| | - Nariman F. Salakhutdinov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS, 9, Lavrent’ev Ave., 630090 Novosibirsk, Russia; (O.V.S.); (I.I.P.); (N.I.K.); (N.F.S.)
| | - Olga I. Lavrik
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8, Lavrent’ev Ave., 630090 Novosibirsk, Russia; (N.S.D.); (A.L.Z.); (E.S.I.); (O.I.L.)
| | - Konstantin P. Volcho
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS, 9, Lavrent’ev Ave., 630090 Novosibirsk, Russia; (O.V.S.); (I.I.P.); (N.I.K.); (N.F.S.)
- Correspondence:
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6
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A Dual-Sensor-Based Screening System for In Vitro Selection of TDP1 Inhibitors. SENSORS 2021; 21:s21144832. [PMID: 34300575 PMCID: PMC8309759 DOI: 10.3390/s21144832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/09/2021] [Accepted: 07/13/2021] [Indexed: 12/22/2022]
Abstract
DNA sensors can be used as robust tools for high-throughput drug screening of small molecules with the potential to inhibit specific enzymes. As enzymes work in complex biological pathways, it is important to screen for both desired and undesired inhibitory effects. We here report a screening system utilizing specific sensors for tyrosyl-DNA phosphodiesterase 1 (TDP1) and topoisomerase 1 (TOP1) activity to screen in vitro for drugs inhibiting TDP1 without affecting TOP1. As the main function of TDP1 is repair of TOP1 cleavage-induced DNA damage, inhibition of TOP1 cleavage could thus reduce the biological effect of the TDP1 drugs. We identified three new drug candidates of the 1,5-naphthyridine and 1,2,3,4-tetrahydroquinolinylphosphine sulfide families. All three TDP1 inhibitors had no effect on TOP1 activity and acted synergistically with the TOP1 poison SN-38 to increase the amount of TOP1 cleavage-induced DNA damage. Further, they promoted cell death even with low dose SN-38, thereby establishing two new classes of TDP1 inhibitors with clinical potential. Thus, we here report a dual-sensor screening approach for in vitro selection of TDP1 drugs and three new TDP1 drug candidates that act synergistically with TOP1 poisons.
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7
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The synthesis of furoquinolinedione and isoxazoloquinolinedione derivatives as selective Tyrosyl-DNA phosphodiesterase 2 (TDP2) inhibitors. Bioorg Chem 2021; 111:104881. [PMID: 33839584 PMCID: PMC9893515 DOI: 10.1016/j.bioorg.2021.104881] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/17/2021] [Accepted: 03/28/2021] [Indexed: 02/04/2023]
Abstract
Based on our previous study on the development of the furoquinolinedione and isoxazoloquinolinedione TDP2 inhibitors, the further structure-activity relationship (SAR) was studied in this work. A series of furoquinolinedione and isoxazoloquinolinedione derivatives were synthesized and tested for enzyme inhibitions. Enzyme-based assays indicated that isoxazoloquinolinedione derivatives selectively showed high TDP2 inhibitory activity at sub-micromolar range, as well as furoquinolinedione derivatives at low micromolar range. The most potent 3-(3,4-dimethoxyphenyl)isoxazolo[4,5-g]quinoline-4,9-dione (70) showed TDP2 inhibitory activity with IC50 of 0.46 ± 0.15 μM. This work will facilitate future efforts for the discovery of isoxazoloquinolinedione TDP2 selective inhibitors.
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8
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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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9
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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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10
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Khomenko TM, Zakharenko AL, Chepanova AA, Ilina ES, Zakharova OD, Kaledin VI, Nikolin VP, Popova NA, Korchagina DV, Reynisson J, Chand R, Ayine-Tora DM, Patel J, Leung IKH, Volcho KP, Salakhutdinov NF, Lavrik OI. Promising New Inhibitors of Tyrosyl-DNA Phosphodiesterase I (Tdp 1) Combining 4-Arylcoumarin and Monoterpenoid Moieties as Components of Complex Antitumor Therapy. Int J Mol Sci 2019; 21:ijms21010126. [PMID: 31878088 PMCID: PMC6982354 DOI: 10.3390/ijms21010126] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 12/19/2019] [Accepted: 12/20/2019] [Indexed: 12/26/2022] Open
Abstract
Tyrosyl-DNA phosphodiesterase 1 (Tdp1) is an important DNA repair enzyme in humans, and a current and promising inhibition target for the development of new chemosensitizing agents due to its ability to remove DNA damage caused by topoisomerase 1 (Top1) poisons such as topotecan and irinotecan. Herein, we report our work on the synthesis and characterization of new Tdp1 inhibitors that combine the arylcoumarin (neoflavonoid) and monoterpenoid moieties. Our results showed that they are potent Tdp1 inhibitors with IC50 values in the submicromolar range. In vivo experiments with mice revealed that compound 3ba (IC50 0.62 µM) induced a significant increase in the antitumor effect of topotecan on the Krebs-2 ascites tumor model. Our results further strengthen the argument that Tdp1 is a druggable target with the potential to be developed into a clinically-potent adjunct therapy in conjunction with Top1 poisons.
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Affiliation(s)
- Tatyana M. Khomenko
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, 9 acad. Lavrentjev ave., 630090 Novosibirsk, Russia; (T.M.K.); (D.V.K.); (N.F.S.)
| | - Alexandra L. Zakharenko
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, 8, acad. Lavrentjev ave., 630090 Novosibirsk, Russia; (A.L.Z.); (A.A.C.); (E.S.I.); (O.D.Z.); (O.I.L.)
| | - Arina A. Chepanova
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, 8, acad. Lavrentjev ave., 630090 Novosibirsk, Russia; (A.L.Z.); (A.A.C.); (E.S.I.); (O.D.Z.); (O.I.L.)
| | - Ekaterina S. Ilina
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, 8, acad. Lavrentjev ave., 630090 Novosibirsk, Russia; (A.L.Z.); (A.A.C.); (E.S.I.); (O.D.Z.); (O.I.L.)
| | - Olga D. Zakharova
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, 8, acad. Lavrentjev ave., 630090 Novosibirsk, Russia; (A.L.Z.); (A.A.C.); (E.S.I.); (O.D.Z.); (O.I.L.)
| | - Vasily I. Kaledin
- Institute of Cytology and Genetics, 10, acad. Lavrentjev Ave., 630090 Novosibirsk, Russian; (V.I.K.); (V.P.N.); (N.A.P.)
| | - Valeriy P. Nikolin
- Institute of Cytology and Genetics, 10, acad. Lavrentjev Ave., 630090 Novosibirsk, Russian; (V.I.K.); (V.P.N.); (N.A.P.)
| | - Nelly A. Popova
- Institute of Cytology and Genetics, 10, acad. Lavrentjev Ave., 630090 Novosibirsk, Russian; (V.I.K.); (V.P.N.); (N.A.P.)
- Novosibirsk State University, V. Zelman Institute for Medicine and Psychology and Department of Natural Sciences, 2, Pirogova str., 630090 Novosibirsk, Russia
| | - Dina V. Korchagina
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, 9 acad. Lavrentjev ave., 630090 Novosibirsk, Russia; (T.M.K.); (D.V.K.); (N.F.S.)
| | - Jóhannes Reynisson
- School of Pharmacy and Bioengineering, Keele University, Hornbeam Building, Staffordshire ST5 5BG, UK;
| | - Raina Chand
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, 1142 Auckland, New Zealand; (R.C.); (D.M.A.-T.); (J.P.); (I.K.H.L.)
| | - Daniel M. Ayine-Tora
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, 1142 Auckland, New Zealand; (R.C.); (D.M.A.-T.); (J.P.); (I.K.H.L.)
| | - Jinal Patel
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, 1142 Auckland, New Zealand; (R.C.); (D.M.A.-T.); (J.P.); (I.K.H.L.)
| | - Ivanhoe K. H. Leung
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, 1142 Auckland, New Zealand; (R.C.); (D.M.A.-T.); (J.P.); (I.K.H.L.)
| | - Konstantin P. Volcho
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, 9 acad. Lavrentjev ave., 630090 Novosibirsk, Russia; (T.M.K.); (D.V.K.); (N.F.S.)
- Novosibirsk State University, V. Zelman Institute for Medicine and Psychology and Department of Natural Sciences, 2, Pirogova str., 630090 Novosibirsk, Russia
- Correspondence:
| | - Nariman F. Salakhutdinov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, 9 acad. Lavrentjev ave., 630090 Novosibirsk, Russia; (T.M.K.); (D.V.K.); (N.F.S.)
- Novosibirsk State University, V. Zelman Institute for Medicine and Psychology and Department of Natural Sciences, 2, Pirogova str., 630090 Novosibirsk, Russia
| | - Olga I. Lavrik
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, 8, acad. Lavrentjev ave., 630090 Novosibirsk, Russia; (A.L.Z.); (A.A.C.); (E.S.I.); (O.D.Z.); (O.I.L.)
- Novosibirsk State University, V. Zelman Institute for Medicine and Psychology and Department of Natural Sciences, 2, Pirogova str., 630090 Novosibirsk, Russia
- Department of Physical and Chemical Biology and Biotechnology, Altai State University, 61, Lenina Ave., 656049 Barnaul, Russia
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11
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Brettrager EJ, van Waardenburg RC. Targeting Tyrosyl-DNA phosphodiesterase I to enhance toxicity of phosphodiester linked DNA-adducts. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2019; 2:1153-1163. [PMID: 31875206 PMCID: PMC6929713 DOI: 10.20517/cdr.2019.91] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 11/19/2019] [Accepted: 11/29/2019] [Indexed: 06/10/2023]
Abstract
Our genomic DNA is under constant assault from endogenous and exogenous sources, which needs to be resolved to maintain cellular homeostasis. The eukaryotic DNA repair enzyme Tyrosyl-DNA phosphodiesterase I (Tdp1) catalyzes the hydrolysis of phosphodiester bonds that covalently link adducts to DNA-ends. Tdp1 utilizes two catalytic histidines to resolve a growing list of DNA-adducts. These DNA-adducts can be divided into two groups: small adducts, including oxidized nucleotides, RNA, and non-canonical nucleoside analogs, and large adducts, such as (drug-stabilized) topoisomerase- DNA covalent complexes or failed Schiff base reactions as occur between PARP1 and DNA. Many Tdp1 substrates are generated by chemotherapeutics linking Tdp1 to cancer drug resistance, making a compelling argument to develop small molecules that target Tdp1 as potential novel therapeutic agents. Tdp1's unique catalytic cycle, which is centered on the formation of Tdp1-DNA covalent reaction intermediate, allows for two principally different targeting strategies: (1) catalytic inhibition of Tdp1 catalysis to prevent Tdp1-mediated repair of DNA-adducts that enhances the effectivity of chemotherapeutics; and (2) poisoning of Tdp1 by stabilization of the Tdp1- DNA covalent reaction intermediate, which would increase the half-life of a potentially toxic DNA-adduct by preventing its resolution, analogous to topoisomerase targeted poisons such as topotecan or etoposide. The catalytic Tdp1 mutant that forms the molecular basis of the autosomal recessive neurodegenerative disease spinocerebellar ataxia with axonal neuropathy best illustrates this concept; however, no small molecules have been reported for this strategy. Herein, we concisely discuss the development of Tdp1 catalytic inhibitors and their results.
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Affiliation(s)
- Evan J. Brettrager
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL 35294-0019, USA
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12
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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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13
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The Development of Tyrosyl-DNA Phosphodiesterase 1 Inhibitors. Combination of Monoterpene and Adamantine Moieties via Amide or Thioamide Bridges. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9132767] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Eleven amide and thioamide derivatives with monoterpene and adamantine substituents were synthesised. They were tested for their activity against the tyrosyl-DNA phosphodiesterase 1 DNA (Tdp1) repair enzyme with the most potent compound 47a, having an IC50 value of 0.64 M. When tested in the A-549 lung adenocarcinoma cell line, no or very limited cytotoxic effect was observed for the ligands. However, in conjunction with topotecan, a well-established Topoisomerase 1 (Top1) poison in clinical use against cancer, derivative 46a was very cytotoxic at 5 M concentration, displaying strong synergism. This effect was only seen for 46a (IC50—3.3 M) albeit some other ligands had better IC50 values. Molecular modelling into the catalytic site of Tdp1 predicted plausible binding mode of 46a, effectively blocking access to the catalytic site.
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14
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Tombak EM, Männik A, Burk RD, Le Grand R, Ustav E, Ustav M. The molecular biology and HPV drug responsiveness of cynomolgus macaque papillomaviruses support their use in the development of a relevant in vivo model for antiviral drug testing. PLoS One 2019; 14:e0211235. [PMID: 30682126 PMCID: PMC6347367 DOI: 10.1371/journal.pone.0211235] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 01/09/2019] [Indexed: 01/29/2023] Open
Abstract
Due to the extreme tissue and species restriction of the papillomaviruses (PVs), there is a great need for animal models that accurately mimic PV infection in humans for testing therapeutic strategies against human papillomaviruses (HPVs). In this study, we present data that demonstrate that in terms of gene expression during initial viral DNA amplification, Macaca fascicularis PV (MfPV) types 5 and 8 appear to be similar to mucosal oncogenic HPVs, while MfPV1 (isolated from skin) resembles most high-risk cutaneous beta HPVs (HPV5). Similarities were also observed in replication properties during the initial amplification phase of the MfPV genomes. We demonstrate that high-risk mucosal HPV-specific inhibitors target the transient replication of the MfPV8 genomes, which indicates that similar pathways are used by the high-risk HPVs and MfPVs during their genome replication. Taking all into account, we propose that Macaca fascicularis may serve as a highly relevant model for preclinical tests designed to evaluate therapeutic strategies against HPV-associated lesions.
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Affiliation(s)
- Eva-Maria Tombak
- University of Tartu, Institute of Technology, Tartu, Estonia
- Icosagen Cell Factory Ltd., Eerika tee 1, Õssu, Kambja, Tartumaa, Estonia
| | - Andres Männik
- University of Tartu, Institute of Technology, Tartu, Estonia
- Icosagen Cell Factory Ltd., Eerika tee 1, Õssu, Kambja, Tartumaa, Estonia
| | - Robert D. Burk
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, New York, United States of America
- Department of Pediatrics (Genetics), Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, New York, United States of America
- Department of Microbiology & Immunology, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, New York, United States of America
- Department of Obstetrics, Gynecology & Women's Health, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, New York, United States of America
| | - Roger Le Grand
- CEA, Université Paris Sud, INSERM U1184, Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department / IBFJ, Fontenay-aux-Roses, France
| | - Ene Ustav
- University of Tartu, Institute of Technology, Tartu, Estonia
| | - Mart Ustav
- University of Tartu, Institute of Technology, Tartu, Estonia
- Icosagen Cell Factory Ltd., Eerika tee 1, Õssu, Kambja, Tartumaa, Estonia
- Estonian Academy of Sciences, Tallinn, Estonia
- * E-mail:
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15
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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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16
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Zakharenko AL, Luzina OA, Sokolov DN, Kaledin VI, Nikolin VP, Popova NA, Patel J, Zakharova OD, Chepanova AA, Zafar A, Reynisson J, Leung E, Leung IKH, Volcho KP, Salakhutdinov NF, Lavrik OI. Novel tyrosyl-DNA phosphodiesterase 1 inhibitors enhance the therapeutic impact of topoteсan on in vivo tumor models. Eur J Med Chem 2018; 161:581-593. [PMID: 30396105 DOI: 10.1016/j.ejmech.2018.10.055] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 10/18/2018] [Accepted: 10/22/2018] [Indexed: 02/07/2023]
Abstract
The druggability of the tyrosyl-DNA phosphodiesterase 1 (Tdp1) enzyme was investigated in conjunction with topoisomerase 1 inhibition. A novel class of thiazole, aminothiazole and hydrazonothiazole usnic acid derivatives was synthesized and evaluated as Tdp1 inhibitors and their ability to sensitize tumors to topotecan, a topoisomerase inhibitor in clinical use. Of all the compounds tested, four hydrazinothiazole derivatives, 20c, 20d, 20h and 20i, inhibited the enzyme in the nanomolar range. The activity of the compounds was verified by affinity experiments as well as supported by molecular modelling. The most effective Tdp1 inhibitor, 20d, was ton-toxic and increased the effect of topotecan both in vitro and in vivo in the Lewis lung carcinoma model. Furthermore, 20d showed significant increase in the antitumor and antimetastatic effect of topotecan in mice. The results presented here justify compound 20d to be considered as a drug lead for antitumor therapy.
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Affiliation(s)
- A 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
| | - O A Luzina
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk, 630090, Russian Federation
| | - D N Sokolov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk, 630090, Russian Federation
| | - V I Kaledin
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10, Akademika Lavrentieva Ave., Novosibirsk, 630090, Russian Federation
| | - V P Nikolin
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10, Akademika Lavrentieva Ave., Novosibirsk, 630090, Russian Federation
| | - N A Popova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10, Akademika Lavrentieva Ave., Novosibirsk, 630090, Russian Federation; Novosibirsk State University, Pirogova str. 1, Novosibirsk, 630090, Russian Federation
| | - J Patel
- School of Chemical Sciences, The University of Auckland, New Zealand
| | - O 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
| | - A A Chepanova
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., Novosibirsk, 630090, Russian Federation
| | - A Zafar
- School of Chemical Sciences, The University of Auckland, New Zealand
| | - J Reynisson
- School of Chemical Sciences, The University of Auckland, New Zealand
| | - E Leung
- Auckland Cancer Society Research Centre and Department of Molecular Medicine and Pathology, The University of Auckland, New Zealand
| | - I K H Leung
- School of Chemical Sciences, The University of Auckland, New Zealand
| | - K P Volcho
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk, 630090, Russian Federation; Novosibirsk State University, Pirogova str. 1, Novosibirsk, 630090, Russian Federation
| | - N F Salakhutdinov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk, 630090, Russian Federation; Novosibirsk State University, Pirogova str. 1, Novosibirsk, 630090, Russian Federation
| | - O 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, Pirogova str. 1, Novosibirsk, 630090, Russian Federation.
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17
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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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18
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Yu LM, Hu Z, Chen Y, Ravji A, Lopez S, Plescia CB, Yu Q, Yang H, Abdelmalak M, Saha S, Agama K, Kiselev E, Marchand C, Pommier Y, An LK. Synthesis and structure-activity relationship of furoquinolinediones as inhibitors of Tyrosyl-DNA phosphodiesterase 2 (TDP2). Eur J Med Chem 2018; 151:777-796. [PMID: 29677635 DOI: 10.1016/j.ejmech.2018.04.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 04/08/2018] [Accepted: 04/10/2018] [Indexed: 10/17/2022]
Abstract
Tyrosyl-DNA phosphodiesterase 2 (TDP2) is a recently discovered enzyme specifically repairing topoisomerase II (TOP2)-mediated DNA damage. It has been shown that inhibition of TDP2 synergize with TOP2 inhibitors. Herein, we report the discovery of the furoquinolinedione chemotype as a suitable skeleton for the development of selective TDP2 inhibitors. Compound 1 was identified as a TDP2 inhibitor as a result of screening our in-house compound library for compounds selective for TDP2 vs. TDP1. Further SAR studies provide several selective TDP2 inhibitors at low-micromolar range. The most potent compound 74 shows inhibitory activity with IC50 of 1.9 and 2.1 μM against recombinant TDP2 and TDP2 in whole cell extracts (WCE), respectively.
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Affiliation(s)
- Le-Mao Yu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Zhu Hu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Yu Chen
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Azhar Ravji
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, United States
| | - Sophia Lopez
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, United States
| | - Caroline B Plescia
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, United States
| | - Qian Yu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Hui Yang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Monica Abdelmalak
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, United States
| | - Sourav Saha
- 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
| | - Evgeny Kiselev
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, United States
| | - Christophe Marchand
- 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.
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19
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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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20
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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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21
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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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22
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Jun JH, Kumar V, Dexheimer TS, Wedlich I, Nicklaus MC, Pommier Y, Malhotra SV. Synthesis, anti-cancer screening and tyrosyl-DNA phosphodiesterase 1 (Tdp1) inhibition activity of novel piperidinyl sulfamides. Eur J Pharm Sci 2018; 111:337-348. [PMID: 29037996 PMCID: PMC8087116 DOI: 10.1016/j.ejps.2017.10.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Revised: 10/06/2017] [Accepted: 10/11/2017] [Indexed: 10/18/2022]
Abstract
Novel piperidinyl-based sulfamide derivatives were designed and synthesized through various synthetic routes. Anticancer activities of these sulfamides were evaluated by phenotypic screening on National Cancer Institute's 60 human tumor cell lines (NCI-60). Preliminary screening at 10μM concentration showed that piperidinyl sulfamide aminoester 26 (NSC 749204) was sensitive to most of the cell lines in the panel. Further dose-response studies showed that 26 was highly selective for inhibition of colon cancer cell lines with minimum GI50=1.88μM for COLO-205 and maximum GI50=11.1μM for SW-620 cells. These newly synthesized sulfamides were also screening for their Tdp1 inhibition activity. Compound 18 (NSC 750706) showed significant inhibition of Tdp1 with IC50=23.7μM. Molecular-docking studies showed that 18 bind to Tdp1 in its binding pocket similar to a known Tdp1 inhibitor.
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Affiliation(s)
- Jung Ho Jun
- Department of Chemistry, University of Kansas, KS 66045, USA
| | - Vineet Kumar
- Department of Radiation Oncology, Stanford University, 3165 Porter Drive, Palo Alto, CA 94304, USA
| | - Thomas S Dexheimer
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Iwona Wedlich
- Chemical Biology Laboratory, Frederick National Laboratory for Cancer Research, 376 Boyles Street, Frederick, MD 21702, USA
| | - Marc C Nicklaus
- Chemical Biology Laboratory, Frederick National Laboratory for Cancer Research, 376 Boyles Street, Frederick, MD 21702, USA
| | - Yves Pommier
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sanjay V Malhotra
- Department of Radiation Oncology, Stanford University, 3165 Porter Drive, Palo Alto, CA 94304, USA.
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23
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Tian LW, Feng Y, Tran TD, Shimizu Y, Pfeifer T, Vu HT, Quinn RJ. Achyrodimer F, a tyrosyl-DNA phosphodiesterase I inhibitor from an Australian fungus of the family Cortinariaceae. Bioorg Med Chem Lett 2017; 27:4007-4010. [PMID: 28797798 DOI: 10.1016/j.bmcl.2017.07.062] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 07/15/2017] [Accepted: 07/24/2017] [Indexed: 11/24/2022]
Abstract
Mass-guided isolation of the dichloromethane/methanol extracts from a specimen of teleomorphic fungus of the family Cortinariaceae resulted in the identification of a new dimeric cyclobutane metabolite, achyrodimer F (1), along with the monomers hispidin (2) and bisnoryangonin (3). Their structures were determined by NMR and MS data analyses. Density Function Theory (DFT) NMR calculations was employed to confirm the chemical structure of achyrodimer F. Compound 1 inhibited tyrosyl-DNA phosphodiesterase I with an IC50 value of 1μM.
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Affiliation(s)
- Li-Wen Tian
- Griffith Institute for Drug Discovery, Griffith University, Brisbane QLD 4111, Australia
| | - Yunjiang Feng
- Griffith Institute for Drug Discovery, Griffith University, Brisbane QLD 4111, Australia
| | - Trong D Tran
- Griffith Institute for Drug Discovery, Griffith University, Brisbane QLD 4111, Australia
| | - Yoko Shimizu
- Centre for Drug Research and Development, Vancouver, British Columbia V6T1Z3, Canada
| | - Tom Pfeifer
- Centre for Drug Research and Development, Vancouver, British Columbia V6T1Z3, Canada
| | - Hoan T Vu
- Griffith Institute for Drug Discovery, Griffith University, Brisbane QLD 4111, Australia
| | - Ronald J Quinn
- Griffith Institute for Drug Discovery, Griffith University, Brisbane QLD 4111, Australia.
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24
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Bermingham A, Price E, Marchand C, Chergui A, Naumova A, Whitson EL, Krumpe LRH, Goncharova EI, Evans JR, McKee TC, Henrich CJ, Pommier Y, O'Keefe BR. Identification of Natural Products That Inhibit the Catalytic Function of Human Tyrosyl-DNA Phosphodiesterase (TDP1). SLAS DISCOVERY 2017; 22:1093-1105. [PMID: 28697309 DOI: 10.1177/2472555217717200] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Tyrosyl-DNA phosphodiesterase 1 (TDP1) is an enzyme crucial for cleavage of the covalent topoisomerase 1-DNA complex, an intermediate in DNA repair. TDP1 plays a role in reversing inhibition of topoisomerase I by camptothecins, a series of potent and effective inhibitors used in the treatment of colorectal, ovarian, and small-cell lung cancers. It is hypothesized that inhibition of TDP1 activity may enhance camptothecin sensitivity in tumors. Here, we describe the design, development, and execution of a novel assay to identify inhibitors of TDP1 present in natural product extracts. The assay was designed to address issues with fluorescent "nuisance" molecules and to minimize the detection of false-positives caused by polyphenolic molecules known to nonspecifically inhibit enzyme activity. A total of 227,905 purified molecules, prefractionated extracts, and crude natural product extracts were screened. This yielded 534 initial positives (0.23%). Secondary prioritization reduced this number to 117 (0.05% final hit rate). Several novel inhibitors have been identified showing micromolar affinity for human TDP1, including halenaquinol sulfate, a pentacyclic hydroquinone from the sponge Xestospongia sp.
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Affiliation(s)
- Alun Bermingham
- Molecular Targets Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Edmund Price
- Molecular Targets Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Christophe Marchand
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Adel Chergui
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Alena Naumova
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Emily L Whitson
- Molecular Targets Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Lauren R H Krumpe
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory, Frederick, MD, USA
| | | | | | - Tawnya C McKee
- Molecular Targets Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Curtis J Henrich
- Molecular Targets Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA.,Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory, Frederick, MD, USA
| | - Yves Pommier
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Barry R O'Keefe
- Molecular Targets Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA.,Natural Products Branch, Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
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25
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Wang P, Elsayed MSA, Plescia CB, Ravji A, Redon CE, Kiselev E, Marchand C, Zeleznik O, Agama K, Pommier Y, Cushman M. Synthesis and Biological Evaluation of the First Triple Inhibitors of Human Topoisomerase 1, Tyrosyl-DNA Phosphodiesterase 1 (Tdp1), and Tyrosyl-DNA Phosphodiesterase 2 (Tdp2). J Med Chem 2017; 60:3275-3288. [PMID: 28418653 DOI: 10.1021/acs.jmedchem.6b01565] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Tdp1 and Tdp2 are two tyrosyl-DNA phosphodiesterases that can repair damaged DNA resulting from topoisomerase inhibitors and a variety of other DNA-damaging agents. Both Tdp1 and Tdp2 inhibition could hypothetically potentiate the cytotoxicities of topoisomerase inhibitors. This study reports the successful structure-based design and synthesis of new 7-azaindenoisoquinolines that act as triple inhibitors of Top1, Tdp1, and Tdp2. Enzyme inhibitory data and cytotoxicity data from human cancer cell cultures establish that modification of the lactam side chain of the 7-azaindenoisoquinolines can modulate their inhibitory potencies and selectivities vs Top1, Tdp1, and Tdp2. Molecular modeling of selected target compounds bound to Top1, Tdp1, and Tdp2 was used to design the inhibitors and facilitate the structure-activity relationship analysis. The monitoring of DNA damage by γ-H2AX foci formation in human PBMCs (lymphocytes) and acute lymphoblastic leukemia CCRF-CEM cells documented significantly more DNA damage in the cancer cells vs normal cells.
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Affiliation(s)
- Ping Wang
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, and the Purdue Center for Cancer Research, Purdue University , West Lafayette, Indiana 47907, United States
| | - Mohamed S A Elsayed
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, and the Purdue Center for Cancer Research, Purdue University , West Lafayette, Indiana 47907, United States
| | - Caroline B Plescia
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Institutes of Health, Bethesda , Frederick, Maryland 20892, United States
| | - Azhar Ravji
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Institutes of Health, Bethesda , Frederick, Maryland 20892, United States
| | - Christophe E Redon
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Institutes of Health, Bethesda , Frederick, Maryland 20892, United States
| | - Evgeny Kiselev
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Institutes of Health, Bethesda , Frederick, Maryland 20892, United States
| | - Christophe Marchand
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Institutes of Health, Bethesda , Frederick, Maryland 20892, United States
| | - Olga Zeleznik
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Institutes of Health, Bethesda , Frederick, Maryland 20892, United States
| | - Keli Agama
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Institutes of Health, Bethesda , Frederick, Maryland 20892, United States
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Institutes of Health, Bethesda , Frederick, Maryland 20892, United States
| | - Mark Cushman
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, and the Purdue Center for Cancer Research, Purdue University , West Lafayette, Indiana 47907, United States
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26
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Gushchina I, Nilov D, Zakharenko A, Lavrik O, Švedas V. Structure Modeling of Human Tyrosyl-DNA Phosphodiesterase 1 and Screening for Its Inhibitors. Acta Naturae 2017; 9:59-66. [PMID: 28740727 PMCID: PMC5509001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Indexed: 11/15/2022] Open
Abstract
The DNA repair enzyme tyrosyl-DNA phosphodiesterase 1 (Tdp1) represents a potential molecular target for anticancer therapy. A human Tdp1 model has been constructed using the methods of quantum and molecular mechanics, taking into account the ionization states of the amino acid residues in the active site and their interactions with the substrate and competitive inhibitors. The oligonucleotide- and phosphotyrosine-binding cavities important for the inhibitor design have been identified in the enzyme's active site. The developed molecular model allowed us to uncover new Tdp1 inhibitors whose sulfo group is capable of occupying the position of the 3'-phosphate group of the substrate and forming hydrogen bonds with Lys265, Lys495, and other amino acid residues in the phosphotyrosine binding site.
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Affiliation(s)
- I.V. Gushchina
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Lenin Hills 1, bldg. 73, Moscow, 119991, Russia
| | - D.K. Nilov
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Lenin Hills 1 , bldg. 40, Moscow, 119991, Russia
| | - A.L. Zakharenko
- Institute of Chemical Biology and Fundamental Medicine, Russian Academy of Sciences, Siberian Branch, Lavrentiev avenue 8, Novosibirsk, 630090, Russia
| | - O.I. Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Russian Academy of Sciences, Siberian Branch, Lavrentiev avenue 8, Novosibirsk, 630090, Russia
- Altai State University, Lenin avenue 61, Barnaul, 656049, Russia
| | - V.K. Švedas
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Lenin Hills 1, bldg. 73, Moscow, 119991, Russia
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Lenin Hills 1 , bldg. 40, Moscow, 119991, Russia
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27
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Zakharenko AL, Luzina OA, Sokolov DN, Zakharova OD, Rakhmanova ME, Chepanova AA, Dyrkheeva NS, Lavrik OI, Salakhutdinov NF. Usnic acid derivatives are effective inhibitors of tyrosyl-DNA phosphodiesterase 1. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2017. [DOI: 10.1134/s1068162017010125] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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28
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Identification of several high-risk HPV inhibitors and drug targets with a novel high-throughput screening assay. PLoS Pathog 2017; 13:e1006168. [PMID: 28182794 PMCID: PMC5300127 DOI: 10.1371/journal.ppat.1006168] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Accepted: 01/05/2017] [Indexed: 12/19/2022] Open
Abstract
Human papillomaviruses (HPVs) are oncogenic viruses that cause numerous different cancers as well as benign lesions in the epithelia. To date, there is no effective cure for an ongoing HPV infection. Here, we describe the generation process of a platform for the development of anti-HPV drugs. This system consists of engineered full-length HPV genomes that express reporter genes for evaluation of the viral copy number in all three HPV replication stages. We demonstrate the usefulness of this system by conducting high-throughput screens to identify novel high-risk HPV-specific inhibitors. At least five of the inhibitors block the function of Tdp1 and PARP1, which have been identified as essential cellular proteins for HPV replication and promising candidates for the development of antivirals against HPV and possibly against HPV-related cancers. Human papillomaviruses are causative agents of many different cancers; they are most commonly associated with cervical cancer which leads to about quarter of a million deaths each year. Regardless of extensive studies for decades there is no specific cure against HPV infection. During this research, we have engineered modified HPV marker genomes that express Renilla luciferase reporter gene which expression level correlates directly with viral genome copy number. We have used such modified HPV genome in high-throughput screening of NCI Diversity Set IV chemical library and have identified a number of novel high-risk HPV-specific chemical compounds and drug targets. Such Renilla-expressing marker genomes could be used in various cell systems suitable for HPV replication studies to conduct high-throughput screens and quantify viral genome copy number quickly and effectively.
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29
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Laev SS, Salakhutdinov NF, Lavrik OI. Tyrosyl-DNA phosphodiesterase inhibitors: Progress and potential. Bioorg Med Chem 2016; 24:5017-5027. [PMID: 27687971 DOI: 10.1016/j.bmc.2016.09.045] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 08/30/2016] [Accepted: 09/18/2016] [Indexed: 10/21/2022]
Abstract
DNA topoisomerases are essential during transcription and replication. The therapeutic mechanism of action of topoisomerase inhibitors is enzyme poisoning rather than catalytic inhibition. Tyrosyl-DNA phosphodiesterases 1 or 2 were found as DNA repair enzymes hydrolyzing the covalent bond between the tyrosyl residue of topoisomerases I or II and the 3'- or 5'-phosphate groups in DNA, respectively. Tyrosyl-DNA phosphodiesterase 1 is a key enzyme in DNA repair machinery and a promising target for antitumor and neurodegenerative therapy. Inhibitors of tyrosyl-DNA phosphodiesterase 1 could act synergistically with topoisomerase I inhibitors and thereby potentiate the effects of topoisomerase I poisons. Tyrosyl-DNA phosphodiesterase 2 is an enzyme that specifically repairs DNA damages induced by topoisomerase II poisons and causes resistance to these drugs. Selective inhibition of tyrosyl-DNA phosphodiesterase 2 may be a novel approach to overcome intrinsic or acquired resistance to topoisomerase II-targeted drug therapy. Thus, agents that inhibit tyrosyl-DNA phosphodiesterases 1 and 2 have many applications in biochemical and physiological research and they have the potential to become anticancer and antiviral drugs. The structures, mechanism of action and therapeutic rationale of tyrosyl-DNA phosphodiesterase inhibitors and their development for combinations with topoisomerase inhibitors and DNA damaging agents are discussed.
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Affiliation(s)
- Sergey S Laev
- Vorozhtsov Institute of Organic Chemistry, Siberian Division, Russian Academy of Sciences, pr. akademika Lavrent'eva 9, Novosibirsk 630090, Russian Federation.
| | - Nariman F Salakhutdinov
- Vorozhtsov Institute of Organic Chemistry, Siberian Division, Russian Academy of Sciences, pr. akademika Lavrent'eva 9, Novosibirsk 630090, Russian Federation; Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russian Federation
| | - Olga I Lavrik
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russian Federation; Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Division, Russian Academy of Sciences, pr. akademika Lavrent'eva 8, Novosibirsk 630090, Russian Federation
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30
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Zakharenko AL, Ponomarev KU, Suslov EV, Korchagina DV, Volcho KP, Vasil'eva IA, Salakhutdinov NF, Lavrik OI. [Inhibitory Properties of Nitrogen-Containing Adamantane Derivatives with Monoterpenoid Fragments Against Tyrosyl-DNA Phosphodiesterase I]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2016; 41:731-6. [PMID: 27125028 DOI: 10.1134/s1068162015060199] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
It was found that compounds combining diazaadamantane and monoterpenoid fragments are potent inhibitors of new structural type of human recombinant DNA repair enzyme Tyrosyl-DNA phosphodiesterase I (Tdp1). It was demonstrated that the inhibition efficiency depended on the length and flexibility of the aliphatic chain of the substituent.
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31
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Beck DE, Abdelmalak M, Lv W, Reddy PVN, Tender GS, O'Neill E, Agama K, Marchand C, Pommier Y, Cushman M. Discovery of potent indenoisoquinoline topoisomerase I poisons lacking the 3-nitro toxicophore. J Med Chem 2015; 58:3997-4015. [PMID: 25909279 DOI: 10.1021/acs.jmedchem.5b00303] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
3-Nitroindenoisoquinoline human topoisomerase IB (Top1) poisons have potent antiproliferative effects on cancer cells. The undesirable nitro toxicophore could hypothetically be replaced by other functional groups that would retain the desired biological activities and minimize potential safety risks. Eleven series of indenoisoquinolines bearing 3-nitro bioisosteres were synthesized. The molecules were evaluated in the Top1-mediated DNA cleavage assay and in the National Cancer Institute's 60 cell line cytotoxicity assay. The data reveal that fluorine and chlorine may substitute for the 3-nitro group with minimal loss of Top1 poisoning activity. The new information gained from these efforts can be used to design novel indenoisoquinolines with improved safety.
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Affiliation(s)
- Daniel E Beck
- †Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, and the Purdue Center for Cancer Research, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Monica Abdelmalak
- ‡Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NCI-Frederick, Frederick, Maryland 21702, United States
| | - Wei Lv
- †Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, and the Purdue Center for Cancer Research, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - P V Narasimha Reddy
- †Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, and the Purdue Center for Cancer Research, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Gabrielle S Tender
- ‡Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NCI-Frederick, Frederick, Maryland 21702, United States
| | - Elizaveta O'Neill
- †Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, and the Purdue Center for Cancer Research, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Keli Agama
- ‡Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NCI-Frederick, Frederick, Maryland 21702, United States
| | - Christophe Marchand
- ‡Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NCI-Frederick, Frederick, Maryland 21702, United States
| | - Yves Pommier
- ‡Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NCI-Frederick, Frederick, Maryland 21702, United States
| | - Mark Cushman
- †Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, and the Purdue Center for Cancer Research, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
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32
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Nguyen TX, Abdelmalak M, Marchand C, Agama K, Pommier Y, Cushman M. Synthesis and biological evaluation of nitrated 7-, 8-, 9-, and 10-hydroxyindenoisoquinolines as potential dual topoisomerase I (Top1)-tyrosyl-DNA phosphodiesterase I (TDP1) inhibitors. J Med Chem 2015; 58:3188-208. [PMID: 25811317 PMCID: PMC7747014 DOI: 10.1021/acs.jmedchem.5b00136] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The structure-activity relationships and hit-to-lead optimization of dual Top1-TDP1 inhibitors in the indenoisoquinoline drug class were investigated. A series of nitrated 7-, 8-, 9-, and 10-hydroxyindenoisoquinolines were synthesized and evaluated. Several compounds displayed potent dual Top1-TDP1 inhibition. The 9-hydroxy series exhibited potencies and cytotoxicities vs Top1 that surpassed those of camptothecin (CPT), the natural alkaloid that is being used as a standard in the Top1-mediated DNA cleavage assay. One member of this series was a more potent Top1 inhibitor at a concentration of 5 nM and produced a more stable ternary drug-DNA-Top1 cleavage complex than CPT.
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Affiliation(s)
- Trung Xuan Nguyen
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, and the Purdue Center for Cancer Research, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Monica Abdelmalak
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892-4255, United States
| | - Christophe Marchand
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892-4255, United States
| | - Keli Agama
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892-4255, United States
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892-4255, United States
| | - Mark Cushman
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, and the Purdue Center for Cancer Research, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
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Zakharenko A, Khomenko T, Zhukova S, Koval O, Zakharova O, Anarbaev R, Lebedeva N, Korchagina D, Komarova N, Vasiliev V, Reynisson J, Volcho K, Salakhutdinov N, Lavrik O. Synthesis and biological evaluation of novel tyrosyl-DNA phosphodiesterase 1 inhibitors with a benzopentathiepine moiety. Bioorg Med Chem 2015; 23:2044-52. [PMID: 25819333 DOI: 10.1016/j.bmc.2015.03.020] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2014] [Revised: 03/02/2015] [Accepted: 03/05/2015] [Indexed: 01/28/2023]
Abstract
Tyrosyl-DNA phosphodiesterase 1 (TDP1) is a promising target for antitumor therapy based on Top1 poison-mediated DNA damage. Several novel benzopentathiepines were synthesized and tested as inhibitors of TDP1 using a new oligonucleotide-based fluorescence assay. The benzopentathiepines have IC₅₀ values in the range of 0.2-6.0 μM. According to the molecular modeling, the conformational flexibility of the dibutylamine group of the most effective inhibitor (3d) allows it to occupy an advantageous position for effective binding compared to its cyclic counterparts. The study of cytotoxicity of these compounds revealed that all compounds cause an apoptotic cell death in MCF-7 and Hep G2 cells. Therefore the new class of very effective inhibitors of TDP1 was elaborated.
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Affiliation(s)
- Alexandra 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
| | - Tatyana Khomenko
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk 630090, Russian Federation; Novosibirsk State University, Pirogova 2, Novosibirsk 630090, Russian Federation
| | - Svetlana Zhukova
- Altai State University, 61, Lenina Ave., Barnaul 656049, Russian Federation
| | - Olga Koval
- 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, Pirogova 2, Novosibirsk 630090, Russian Federation
| | - Olga 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
| | - Rashid Anarbaev
- 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, Pirogova 2, Novosibirsk 630090, Russian Federation
| | - Natalya Lebedeva
- 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, Pirogova 2, Novosibirsk 630090, Russian Federation
| | - Dina Korchagina
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk 630090, Russian Federation
| | - Nina Komarova
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk 630090, Russian Federation
| | - Vladimir Vasiliev
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk 630090, Russian Federation
| | | | - Konstantin Volcho
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk 630090, Russian Federation; Novosibirsk State University, Pirogova 2, Novosibirsk 630090, Russian Federation
| | - Nariman Salakhutdinov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk 630090, Russian Federation; Novosibirsk State University, Pirogova 2, Novosibirsk 630090, Russian Federation.
| | - Olga 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, Pirogova 2, Novosibirsk 630090, Russian Federation.
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Comeaux EQ, van Waardenburg RCAM. Tyrosyl-DNA phosphodiesterase I resolves both naturally and chemically induced DNA adducts and its potential as a therapeutic target. Drug Metab Rev 2014; 46:494-507. [PMID: 25327705 DOI: 10.3109/03602532.2014.971957] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
DNA is subject to a wide range of insults, resulting from endogenous and exogenous sources that need to be metabolized/resolved to maintain genome integrity. Tyrosyl-DNA phosphodiesterase I (Tdp1) is a eukaryotic DNA repair enzyme that catalyzes the removal of covalent 3'-DNA adducts. As a phospholipase D superfamily member Tdp1 utilizes two catalytic histidines each within a His-Lys-Asn motif. Tdp1 was discovered for its ability to hydrolyze the 3'-phospho-tyrosyl that in the cell covalently links DNA Topoisomerase I (Topo1) and DNA. Tdp1's list of substrates has since grown and can be divided into two groups: protein-DNA adducts, such as camptothecin stabilized Topo1-DNA adducts, and modified nucleotides, including oxidized nucleotides and chain terminating nucleoside analogs. Since many of Tdp1's substrates are generated by clinically relevant chemotherapeutics, Tdp1 became a therapeutic target for molecularly targeted small molecules. Tdp1's unique catalytic cycle allows for two different targeting strategies: (1) the intuitive inhibition of Tdp1 catalysis to prevent Tdp1-mediated repair of chemotherapeutically induced DNA adducts, thereby enhancing their toxicity and (2) stabilization of the Tdp1-DNA covalent reaction intermediate, prevents resolution of Tdp1-DNA adduct and increases the half-life of this potentially toxic DNA adduct. This concept is best illustrated by a catalytic Tdp1 mutant that forms the molecular basis of the autosomal recessive neurodegenerative disease spinocerebellar ataxia with axonal neuropathy, and results in an increased stability of its Tdp1-DNA reaction intermediate. Here, we will discuss Tdp1 catalysis from a structure-function perspective, Tdp1 substrates and Tdp1 potential as a therapeutic target.
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Affiliation(s)
- Evan Q Comeaux
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham , Birmingham, AL , USA
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35
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Dean RA, Fam HK, An J, Choi K, Shimizu Y, Jones SJM, Boerkoel CF, Interthal H, Pfeifer TA. Identification of a putative Tdp1 inhibitor (CD00509) by in vitro and cell-based assays. ACTA ACUST UNITED AC 2014; 19:1372-82. [PMID: 25117203 DOI: 10.1177/1087057114546551] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Mutations of DNA repair pathways contribute to tumorigenesis and provide a therapeutic target for synthetic lethal interactions in tumor cells. Given that tyrosyl-DNA phosphodiesterase 1 (Tdp1) repairs stalled topoisomerase-I DNA complexes, we hypothesized that inhibition of Tdp1 has synthetic lethal effects in some cancers. To test this, we screened tumor arrays for Tdp1 expression and observed that Tdp1 is expressed in many tumors, including more than 90% of human breast tumors. Subsequent chemical screening identified putative Tdp1 inhibitors. Treatment of control human mammary epithelial cells and the breast cancer cell line MCF-7 with compound CD00509 preferentially sensitized MCF-7 cells to camptothecin and decreased cell proliferation 25% more than camptothecin treatment alone. This suggests that CD00509 specifically targeted Tdp1 in vitro, and CD00509 increased the sensitivity of wild-type murine embryonic fibroblasts (MEFs) to camptothecin to a degree comparable to that of Tdp1(-/-) MEFs. In addition, consistent with poly ADP-ribose polymerase-1 (PARP-1) collaborating with Tdp1 in DNA repair, combined Tdp1 and PARP-1 inhibition was more detrimental to MCF-7 cells than either treatment alone, whereas the combination was not additively harmful to control mammary cells. We conclude that targeting Tdp1 in anticancer therapy preferentially enhances the sensitivity of some breast cancer cells to camptothecin and may be an effective adjuvant for breast cancer therapy.
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Affiliation(s)
- Richard A Dean
- Centre for Drug Research and Development, Vancouver, BC, Canada
| | - Hok Khim Fam
- Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Jianghong An
- Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada
| | - Kunho Choi
- Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Yoko Shimizu
- Centre for Drug Research and Development, Vancouver, BC, Canada
| | - Steven J M Jones
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Cornelius F Boerkoel
- Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Heidrun Interthal
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Tom A Pfeifer
- Centre for Drug Research and Development, Vancouver, BC, Canada
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Marchand C, Huang SYN, Dexheimer TS, Lea WA, Mott BT, Chergui A, Naumova A, Stephen AG, Rosenthal AS, Rai G, Murai J, Gao R, Maloney DJ, Jadhav A, Jorgensen WL, Simeonov A, Pommier Y. Biochemical assays for the discovery of TDP1 inhibitors. Mol Cancer Ther 2014; 13:2116-26. [PMID: 25024006 DOI: 10.1158/1535-7163.mct-13-0952] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Drug screening against novel targets is warranted to generate biochemical probes and new therapeutic drug leads. TDP1 and TDP2 are two DNA repair enzymes that have yet to be successfully targeted. TDP1 repairs topoisomerase I-, alkylation-, and chain terminator-induced DNA damage, whereas TDP2 repairs topoisomerase II-induced DNA damage. Here, we report the quantitative high-throughput screening (qHTS) of the NIH Molecular Libraries Small Molecule Repository using recombinant human TDP1. We also developed a secondary screening method using a multiple loading gel-based assay where recombinant TDP1 is replaced by whole cell extract (WCE) from genetically engineered DT40 cells. While developing this assay, we determined the importance of buffer conditions for testing TDP1, and most notably the possible interference of phosphate-based buffers. The high specificity of endogenous TDP1 in WCE allowed the evaluation of a large number of hits with up to 600 samples analyzed per gel via multiple loadings. The increased stringency of the WCE assay eliminated a large fraction of the initial hits collected from the qHTS. Finally, inclusion of a TDP2 counter-screening assay allowed the identification of two novel series of selective TDP1 inhibitors.
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Affiliation(s)
- Christophe Marchand
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute;
| | - Shar-yin N Huang
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute
| | - Thomas S Dexheimer
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Bethesda
| | - Wendy A Lea
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Bethesda
| | - Bryan T Mott
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Bethesda
| | - Adel Chergui
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute
| | - Alena Naumova
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute
| | - Andrew G Stephen
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland; and
| | - Andrew S Rosenthal
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Bethesda
| | - Ganesha Rai
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Bethesda
| | - Junko Murai
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute
| | - Rui Gao
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute
| | - David J Maloney
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Bethesda
| | - Ajit Jadhav
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Bethesda
| | | | - Anton Simeonov
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Bethesda
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute;
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Abstract
TDP1 and TDP2 were discovered and named based on the fact they process 3'- and 5'-DNA ends by excising irreversible protein tyrosyl-DNA complexes involving topoisomerases I and II, respectively. Yet, both enzymes have an extended spectrum of activities. TDP1 not only excises trapped topoisomerases I (Top1 in the nucleus and Top1mt in mitochondria), but also repairs oxidative damage-induced 3'-phosphoglycolates and alkylation damage-induced DNA breaks, and excises chain terminating anticancer and antiviral nucleosides in the nucleus and mitochondria. The repair function of TDP2 is devoted to the excision of topoisomerase II- and potentially topoisomerases III-DNA adducts. TDP2 is also essential for the life cycle of picornaviruses (important human and bovine pathogens) as it unlinks VPg proteins from the 5'-end of the viral RNA genome. Moreover, TDP2 has been involved in signal transduction (under the former names of TTRAP or EAPII). The DNA repair partners of TDP1 include PARP1, XRCC1, ligase III and PNKP from the base excision repair (BER) pathway. By contrast, TDP2 repair functions are coordinated with Ku and ligase IV in the non-homologous end joining pathway (NHEJ). This article summarizes and compares the biochemistry, functions, and post-translational regulation of TDP1 and TDP2, as well as the relevance of TDP1 and TDP2 as determinants of response to anticancer agents. We discuss the rationale for developing TDP inhibitors for combinations with topoisomerase inhibitors (topotecan, irinotecan, doxorubicin, etoposide, mitoxantrone) and DNA damaging agents (temozolomide, bleomycin, cytarabine, and ionizing radiation), and as novel antiviral agents.
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Affiliation(s)
- Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Building 37, Room 5068, NIH, Bethesda, MD 20892, USA.
| | - Shar-yin N Huang
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Building 37, Room 5068, NIH, Bethesda, MD 20892, USA
| | - Rui Gao
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Building 37, Room 5068, NIH, Bethesda, MD 20892, USA
| | - Benu Brata Das
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Building 37, Room 5068, NIH, Bethesda, MD 20892, USA; Laboratory of Molecular Biology, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Junko Murai
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Building 37, Room 5068, NIH, Bethesda, MD 20892, USA; Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku 606-8501, Japan
| | - Christophe Marchand
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Building 37, Room 5068, NIH, Bethesda, MD 20892, USA
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Lv PC, Agama K, Marchand C, Pommier Y, Cushman M. Design, synthesis, and biological evaluation of O-2-modified indenoisoquinolines as dual topoisomerase I-tyrosyl-DNA phosphodiesterase I inhibitors. J Med Chem 2014; 57:4324-36. [PMID: 24800942 PMCID: PMC4033654 DOI: 10.1021/jm500294a] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
![]()
Tyrosyl-DNA
phosphodiesterase I (TDP1) repairs stalled topoisomerase
I (Top1)–DNA covalent complexes and has been proposed to be
a promising and attractive target for cancer treatment. Inhibitors
of TDP1 could conceivably act synergistically with Top1 inhibitors
and thereby potentiate the effects of Top1 poisons. This study describes
the successful design and synthesis of 2-position-modified indenoisoquinolines
as dual Top1–TDP1 inhibitors using a structure-based drug design
approach. Enzyme inhibition studies indicate that indenoisoquinolines
modified at the 2-position with three-carbon side chains ending with
amino substituents show both promising Top1 and TDP1 inhibitory activity.
Molecular modeling of selected target compounds bound to Top1 and
TDP1 was used to rationalize the enzyme inhibition results and structure–activity
relationship analysis.
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Affiliation(s)
- Peng-Cheng Lv
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, and the Purdue Center for Cancer Research, Purdue University , West Lafayette, Indiana 47907, United States
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Sirivolu VR, Vernekar SKV, Marchand C, Naumova A, Chergui A, Renaud A, Stephen AG, Chen F, Sham YY, Pommier Y, Wang Z. 5-Arylidenethioxothiazolidinones as inhibitors of tyrosyl-DNA phosphodiesterase I. J Med Chem 2012; 55:8671-84. [PMID: 23006064 DOI: 10.1021/jm3008773] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tyrosyl-DNA phosphodiesterase I (Tdp1) is a cellular enzyme that repairs the irreversible topoisomerase I (Top1)-DNA complexes and confers chemotherapeutic resistance to Top1 inhibitors. Inhibiting Tdp1 provides an attractive approach to potentiating clinically used Top1 inhibitors. However, despite recent efforts in studying Tdp1 as a therapeutic target, its inhibition remains poorly understood and largely underexplored. We describe herein the discovery of arylidene thioxothiazolidinone as a scaffold for potent Tdp1 inhibitors based on an initial tyrphostin lead compound 8. Through structure-activity relationship (SAR) studies we demonstrated that arylidene thioxothiazolidinones inhibit Tdp1 and identified compound 50 as a submicromolar inhibitor of Tdp1 (IC₅₀ = 0.87 μM). Molecular modeling provided insight into key interactions essential for observed activities. Some derivatives were also active against endogenous Tdp1 in whole cell extracts. These findings contribute to advancing the understanding on Tdp1 inhibition.
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Affiliation(s)
- Venkata Ramana Sirivolu
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, Minnesota 55455, USA
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Nguyen TX, Morrell A, Conda-Sheridan M, Marchand C, Agama K, Bermingam A, Stephen AG, Chergui A, Naumova A, Fisher R, O’Keefe BR, Pommier Y, Cushman M. Synthesis and biological evaluation of the first dual tyrosyl-DNA phosphodiesterase I (Tdp1)-topoisomerase I (Top1) inhibitors. J Med Chem 2012; 55:4457-78. [PMID: 22536944 PMCID: PMC3350798 DOI: 10.1021/jm300335n] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Substances with dual tyrosyl-DNA phosphodiesterase I-topoisomerase I inhibitory activity in one low molecular weight compound would constitute a unique class of anticancer agents that could potentially have significant advantages over drugs that work against the individual enzymes. The present study demonstrates the successful synthesis and evaluation of the first dual Top1-Tdp1 inhibitors, which are based on the indenoisoquinoline chemotype. One bis(indenoisoquinoline) had significant activity against human Tdp1 (IC(50) = 1.52 ± 0.05 μM), and it was also equipotent to camptothecin as a Top1 inhibitor. Significant insights into enzyme-drug interactions were gained via structure-activity relationship studies of the series. The present results also document the failure of the previously reported sulfonyl ester pharmacophore to confer Tdp1 inhibition in this indenoisoquinoline class of inhibitors even though it was demonstrated to work well for the steroid NSC 88915 (7). The current study will facilitate future efforts to optimize dual Top1-Tdp1 inhibitors.
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Affiliation(s)
- Trung Xuan Nguyen
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, and the Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907
| | - Andrew Morrell
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, and the Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907
| | - Martin Conda-Sheridan
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, and the Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907
| | - Christophe Marchand
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892-4255
| | - Keli Agama
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892-4255
| | - Alun Bermingam
- Molecular Targets Laboratory, Center for Cancer Research, National Cancer Institute, NCI-Frederick, Frederick, Maryland 217023
| | - Andrew G. Stephen
- Protein Chemistry Laboratory, Advanced Technology Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702
| | - Adel Chergui
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892-4255
| | - Alena Naumova
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892-4255
| | - Robert Fisher
- Protein Chemistry Laboratory, Advanced Technology Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702
| | - Barry R. O’Keefe
- Molecular Targets Laboratory, Center for Cancer Research, National Cancer Institute, NCI-Frederick, Frederick, Maryland 217023
| | - Yves Pommier
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892-4255
| | - Mark Cushman
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, and the Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907
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Takagi M, Ueda JY, Hwang JH, Hashimoto J, Izumikawa M, Murakami H, Sekido Y, Shin-ya K. Tyrosyl-DNA phosphodiesterase 1 inhibitor from an anamorphic fungus. JOURNAL OF NATURAL PRODUCTS 2012; 75:764-767. [PMID: 22390627 DOI: 10.1021/np2007389] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Tyrosyl-DNA phosphodiesterase 1 (Tdp1) is an enzyme that catalyzes hydrolysis of 3'-phosphotyrosyl bonds and is involved in repair of irreversible topoisomerase I (Top1)-DNA covalent complexes. Tdp1 inhibitors are regarded as potential cancer therapeutics in combination with Top1 inhibitors, which are currently used to treat human cancers. While screening for Tdp1 inhibitors, we discovered a novel compound, JBIR-21 (1), from the culture of an anamorphic fungus, RF-13305. The structure of 1 was established by extensive NMR and MS analyses. Compound 1 showed inhibitory activity against Tdp1 (IC(50) value, 18 μM) and cytotoxic activity against cancer cell lines (IC(50) values, 3.5-13 μM). Compound 1 also exhibited antitumor activity in a mouse xenograft model without adverse effects.
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Affiliation(s)
- Motoki Takagi
- Biomedicinal Information Research Center (BIRC), Japan Biological Informatics Consortium (JBIC), 2-4-7 Aomi, Tokyo 135-0064, Japan.
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Rich RL, Myszka DG. Survey of the 2009 commercial optical biosensor literature. J Mol Recognit 2012; 24:892-914. [PMID: 22038797 DOI: 10.1002/jmr.1138] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We took a different approach to reviewing the commercial biosensor literature this year by inviting 22 biosensor users to serve as a review committee. They set the criteria for what to expect in a publication and ultimately decided to use a pass/fail system for selecting which papers to include in this year's reference list. Of the 1514 publications in 2009 that reported using commercially available optical biosensor technology, only 20% passed their cutoff. The most common criticism the reviewers had with the literature was that "the biosensor experiments could have been done better." They selected 10 papers to highlight good experimental technique, data presentation, and unique applications of the technology. This communal review process was educational for everyone involved and one we will not soon forget.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT, USA
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Abstract
Inhibitors of topoisomerase I (Top1) that result in stalled Top1 cleavage complexes (Top1cc) are commonly employed against cancer. Combination chemotherapy with DNA repair inhibitors can potentially improve response to these widely used chemotherapeutics. One line of inquiry focuses on inhibitors of tyrosyl-DNA phosphodiesterase 1 (Tdp1), a repair enzyme for Top1cc. Tdp1 catalyzes the hydrolysis of DNA adducts covalently linked to the 3'-phosphate of DNA, including Top1-derived peptides and also 3'-phosphoglycolates. Tdp1 inhibitors should synergize not only with Top1-targeting drugs (camptothecins, indenoisoquinolines), but also with bleomycin, topoisomerase II (Top2) inhibitors (etoposide, doxorubicin) and DNA alkylating agents. Here, we summarize the structure-activity relationship obtained from the reported Tdp1 inhibitors. Better understanding of Top1cc repair in vivo coupled with detailed structural studies on Tdp1-inhibitor interaction will be crucial in guiding the rational design of Tdp1 inhibitors.
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Affiliation(s)
- Shar-yin N. Huang
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892
| | - Yves Pommier
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892
| | - Christophe Marchand
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892
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Hettiarachchi G, Nguyen D, Wu J, Lucas D, Ma D, Isaacs L, Briken V. Toxicology and drug delivery by cucurbit[n]uril type molecular containers. PLoS One 2010; 5:e10514. [PMID: 20463906 PMCID: PMC2865549 DOI: 10.1371/journal.pone.0010514] [Citation(s) in RCA: 189] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Accepted: 04/13/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Many drug delivery systems are based on the ability of certain macrocyclic compounds - such as cyclodextrins (CDs) - to act as molecular containers for pharmaceutical agents in water. Indeed beta-CD and its derivatives have been widely used in the formulation of hydrophobic pharmaceuticals despite their poor abilities to act as a molecular container (e.g., weak binding (K(a)<10(4) M(-1)) and their challenges toward chemical functionalization. Cucurbit[n]urils (CB[n]) are a class of molecular containers that bind to a variety of cationic and neutral species with high affinity (K(a)>10(4) M(-1)) and therefore show great promise as a drug delivery system. METHODOLOGY In this study we investigated the toxicology, uptake, and bioactivity of two cucurbit[n]urils (CB[5] and CB[7]) and three CB[n]-type containers (Pentamer 1, methyl hexamer 2, and phenyl hexamer 3). All five containers demonstrated high cell tolerance at concentrations of up to 1 mM in cell lines originating from kidney, liver or blood tissue using assays for metabolic activity and cytotoxicity. Furthermore, the CB[7] molecular container was efficiently internalized by macrophages indicating their potential for the intracellular delivery of drugs. Bioactivity assays showed that the first-line tuberculosis drug, ethambutol, was as efficient in treating mycobacteria infected macrophages when loaded into CB[7] as when given in the unbound form. This result suggests that CB[7]-bound drug molecules can be released from the container to find their intracellular target. CONCLUSION Our study reveals very low toxicity of five members of the cucurbit[n]uril family of nanocontainers. It demonstrates the uptake of containers by cells and intracellular release of container-loaded drugs. These results provide initial proof-of-concept towards the use of CB[n] molecular containers as an advanced drug delivery system.
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Affiliation(s)
- Gaya Hettiarachchi
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
| | - Duc Nguyen
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
| | - Jing Wu
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, United States of America
| | - Derick Lucas
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, United States of America
| | - Da Ma
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, United States of America
| | - Lyle Isaacs
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, United States of America
| | - Volker Briken
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
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Virtual screening using ligand-based pharmacophores for inhibitors of human tyrosyl-DNA phospodiesterase (hTdp1). Bioorg Med Chem 2010; 18:2347-2355. [PMID: 30025429 DOI: 10.1016/j.bmc.2010.02.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Human tyrosyl-DNA phosphodiesterase (hTdp1) inhibitors have become a major area of drug research and structure-based design since they have been shown to work synergistically with camptothecin (CPT) and selectively in cancer cells. The pharmacophore features of 14hTdp1 inhibitors were used as a filter to screen the ChemNavigator iResearch Library of about 27 million purchasable samples. Docking of the inhibitors and hits obtained from virtual screening was performed into a structural model of hTdp1 based on a high resolution X-ray crystal structure of human Tdp1 in complex with vanadate, DNA and a human topoisomerase I (Top1)-derived peptide (PDB code: 1NOP). We present and discuss in some detail 46 compounds matching the three-dimensional arrangement of the pharmacophoric features. The presented novel chemotypes may provide new scaffolds for developing inhibitors of Tdp1.
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Weidlich IE, Dexheimer T, Marchand C, Antony S, Pommier Y, Nicklaus MC. Inhibitors of human tyrosyl-DNA phospodiesterase (hTdp1) developed by virtual screening using ligand-based pharmacophores. Bioorg Med Chem 2009; 18:182-9. [PMID: 19963390 DOI: 10.1016/j.bmc.2009.11.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2009] [Revised: 10/31/2009] [Accepted: 11/03/2009] [Indexed: 11/19/2022]
Abstract
Human tyrosyl-DNA phosphodiesterase (hTdp1) inhibitors have become a major area of drug research and structure-based design since they have been shown to work synergistically with camptothecin (CPT) and selectively in cancer cells. The pharmacophore features of 14 hTdp1 inhibitors were used as a filter to screen the ChemNavigator iResearch Library of about 27 million purchasable samples. Docking of the inhibitors and hits obtained from virtual screening was performed into a structural model of hTdp1 based on a high resolution X-ray crystal structure of human Tdp1 in complex with vanadate, DNA and a human topoisomerase I (TopI)-derived peptide (PDB code: 1NOP). A total of 46 compounds matching the three-dimensional arrangement of the pharmacophoric features were assayed. Using a high-throughput screening assay, we have identified an 1H-indol-3-yl-acetic acid derivative as a potent Tdp1 inhibitor with an IC(50) value of 7.94 microM. The obtained novel chemotype may provide a new scaffold for developing inhibitors of Tdp1.
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Affiliation(s)
- Iwona E Weidlich
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS, Frederick, MD 21702, USA
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