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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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Zhao XZ, Wang W, Lountos GT, Kiselev E, Tropea JE, Needle D, Pommier Y, Burke TR. Identification of multidentate tyrosyl-DNA phosphodiesterase 1 (TDP1) inhibitors that simultaneously access the DNA, protein and catalytic-binding sites by oxime diversification. RSC Chem Biol 2023; 4:334-343. [PMID: 37181631 PMCID: PMC10170656 DOI: 10.1039/d2cb00230b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/26/2023] [Indexed: 03/29/2023] Open
Abstract
Tyrosyl-DNA phosphodiesterase 1 (TDP1) is a member of the phospholipase D family that can downregulate the anticancer effects of the type I topoisomerase (TOP1) inhibitors by hydrolyzing the 3'-phosphodiester bond between DNA and the TOP1 residue Y723 in the critical stalled intermediate that is the foundation of TOP1 inhibitor mechanism of action. Thus, TDP1 antagonists are attractive as potential enhancers of TOP1 inhibitors. However, the open and extended nature of the TOP1-DNA substrate-binding region has made the development of TDP1 inhibitors extremely challenging. In this study, starting from our recently identified small molecule microarray (SMM)-derived TDP1-inhibitory imidazopyridine motif, we employed a click-based oxime protocol to extend the parent platform into the DNA and TOP1 peptide substrate-binding channels. We applied one-pot Groebke-Blackburn-Bienayme multicomponent reactions (GBBRs) to prepare the needed aminooxy-containing substrates. By reacting these precursors with approximately 250 aldehydes in microtiter format, we screened a library of nearly 500 oximes for their TDP1 inhibitory potencies using an in vitro florescence-based catalytic assay. Select hits were structurally explored as their triazole- and ether-based isosteres. We obtained crystal structures of two of the resulting inhibitors bound to the TDP1 catalytic domain. The structures reveal that the inhibitors form hydrogen bonds with the catalytic His-Lys-Asn triads ("HKN" motifs: H263, K265, N283 and H493, K495, N516), while simultaneously extending into both the substrate DNA and TOP1 peptide-binding grooves. This work provides a structural model for developing multivalent TDP1 inhibitors capable of binding in a tridentate fashion with a central component situated within the catalytic pocket and extensions that project into both the DNA and TOP1 peptide substrate-binding regions.
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Affiliation(s)
- Xue Zhi Zhao
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health Frederick MD USA
| | - Wenjie Wang
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health Bethesda MD USA
| | - George T Lountos
- Basic Science Program, Frederick National Laboratory for Cancer Research Frederick MD USA
| | - Evgeny Kiselev
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health Bethesda MD USA
| | - Joseph E Tropea
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute Frederick MD USA
| | - Danielle Needle
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute Frederick MD USA
| | - Yves Pommier
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health Bethesda MD USA
| | - Terrence R Burke
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health Frederick MD USA
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3
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Zhou M, Sun J, Yu Z, Wu Z, Li W, Liu G, Ma L, Wang R, Tang Y. Investigation of Anti-Alzheimer's Mechanisms of Sarsasapogenin Derivatives by Network-Based Combining Structure-Based Methods. J Chem Inf Model 2023; 63:2881-2894. [PMID: 37104820 DOI: 10.1021/acs.jcim.3c00018] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Alzheimer's disease (AD), a neurodegenerative disease with no cure, affects millions of people worldwide and has become one of the biggest healthcare challenges. Some investigated compounds play anti-AD roles at the cellular or the animal level, but their molecular mechanisms remain unclear. In this study, we designed a strategy combining network-based and structure-based methods together to identify targets for anti-AD sarsasapogenin derivatives (AAs). First, we collected drug-target interactions (DTIs) data from public databases, constructed a global DTI network, and generated drug-substructure associations. After network construction, network-based models were built for DTI prediction. The best bSDTNBI-FCFP_4 model was further used to predict DTIs for AAs. Second, a structure-based molecular docking method was employed for rescreening the prediction results to obtain more credible target proteins. Finally, in vitro experiments were conducted for validation of the predicted targets, and Nrf2 showed significant evidence as the target of anti-AD compound AA13. Moreover, we analyzed the potential mechanisms of AA13 for the treatment of AD. Generally, our combined strategy could be applied to other novel drugs or compounds and become a useful tool in identification of new targets and elucidation of disease mechanisms. Our model was deployed on our NetInfer web server (http://lmmd.ecust.edu.cn/netinfer/).
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Affiliation(s)
- Moran Zhou
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Jiamin Sun
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zhuohang Yu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zengrui Wu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Weihua Li
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Guixia Liu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Lei Ma
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Rui Wang
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yun Tang
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
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4
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Wang Y, Shi N, He Y, Li Y, Zheng Q. A direct approach toward investigating DNA-ligand interactions via surface-enhanced Raman spectroscopy combined with molecular dynamics simulations. Phys Chem Chem Phys 2023; 25:2153-2160. [PMID: 36562542 DOI: 10.1039/d2cp04566d] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Small molecules that interfere with DNA replication can trigger genomic instability, which makes these molecules valuable in the search for anticancer drugs. Thus, interactions between DNA and its ligands at the molecular level are of great significance. In the present study, a new method based on surface-enhanced Raman spectroscopy (SERS) combined with molecular dynamics simulations has been proposed for analyzing the interactions between DNA and its ligands. The SERS signals of DNA hairpins (ST: d(CGACCAACGTGTCGCCTGGTCG), AP1: d(CGCACAACGTGTCGCCTGTGCG)), pure argininamide, and their complexes, were obtained, and the characteristic peak sites of the DNA secondary structure and argininamide ligand-binding region were analyzed. Molecular dynamics calculations predicted that argininamide binds to the 8C and 9G bases of AP1 via hydrogen bonding. Our method successfully detected the changes of SERS fingerprint peaks of hydrogen bonds and bases between argininamide and DNA hairpin bases, and their binding sites and action modes were consistent with the predicted results of the molecular dynamics simulations. This SERS technology combined with the molecular dynamics simulation detection platform provides a general analysis tool, with the advantage of effective, rapid, and sensitive detection. This platform can obtain sufficient molecular level conformational information to provide avenues for rapid drug screening and promote progress in several fields, including targeted drug design.
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Affiliation(s)
- Yunpeng Wang
- College of Pharmacy, Research Center for Innovative Technology of Pharmaceutical Analysis, Harbin Medical University, Harbin, Heilongjiang, 150081, China.
| | - Na Shi
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, 130023, China.
| | - Yingying He
- College of Pharmacy, Research Center for Innovative Technology of Pharmaceutical Analysis, Harbin Medical University, Harbin, Heilongjiang, 150081, China.
| | - Yang Li
- College of Pharmacy, Research Center for Innovative Technology of Pharmaceutical Analysis, Harbin Medical University, Harbin, Heilongjiang, 150081, China.
| | - Qingchuan Zheng
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, 130023, China.
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5
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Burke, Jr TR. Meet the Editorial Board Member. Curr Med Chem 2022. [DOI: 10.2174/092986732932220816152125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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6
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Zhao XZ, Wang W, Lountos GT, Tropea JE, Needle D, Pommier Y, Burke TR. Phosphonic acid-containing inhibitors of tyrosyl-DNA phosphodiesterase 1. Front Chem 2022; 10:910953. [PMID: 36051621 PMCID: PMC9424690 DOI: 10.3389/fchem.2022.910953] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
Tyrosyl-DNA phosphodiesterase 1 (TDP1) repairs stalled type I topoisomerase (TOP1)-DNA complexes by hydrolyzing the phosphodiester bond between the TOP1 Y723 residue and the 3′-phosphate of its DNA substrate. Although TDP1 antagonists could potentially reduce the dose of TOP1 inhibitors needed to achieve effective anticancer effects, the development of validated TDP1 inhibitors has proven to be challenging. This may, in part, be due to the open and extended nature of the TOP1 substrate binding region. We have previously reported imidazopyrazines and imidazopyridines that can inhibit TDP1 catalytic function in vitro. We solved the TDP1 crystal structures with bound inhibitors of this class and found that the dicarboxylic acid functionality within the N-(3,4-dicarboxyphenyl)-2-diphenylimidazo [1,2-a]pyridin-3-amine platform overlaps with aspects of phosphoryl substrate recognition. Yet phosphonic acids could potentially better-replicate cognate TOP1-DNA substrate binding interactions than carboxylic acids. As reported herein, we designed phosphonic acid-containing variants of our previously reported carboxylic acid-containing imidazopyrazine and imidazopyridine inhibitors and effected their synthesis using one-pot Groebke–Blackburn–Bienayme multicomponent reactions. We obtained crystal structures of TDP1 complexed with a subset of inhibitors. We discuss binding interactions of these inhibitors within the context of phosphate-containing substrate and carboxylic acid-based inhibitors. These compounds represent a new structural class of small molecule ligands that mimic aspects of the 3′-processed substrate that results from TDP1 catalysis.
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Affiliation(s)
- Xue Zhi Zhao
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, United States
- *Correspondence: Xue Zhi Zhao,
| | - Wenjie Wang
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - George T. Lountos
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Joseph E. Tropea
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States
| | - Danielle Needle
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Terrence R. Burke
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, United States
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7
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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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8
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Pyranodipyran Derivatives with Tyrosyl DNA Phosphodiesterase 1 Inhibitory Activities and Fluorescent Properties from Aspergillus sp. EGF 15-0-3. Mar Drugs 2022; 20:md20030211. [PMID: 35323510 PMCID: PMC8954640 DOI: 10.3390/md20030211] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/09/2022] [Accepted: 03/13/2022] [Indexed: 12/02/2022] Open
Abstract
Four new benzodipyran racemates, namely (±)-aspergiletals A–D (3–6), representing a rare pyrano[4,3-h]chromene scaffold were isolated together with eurotiumide G (1) and eurotiumide F (2) from the soft-coral-derived fungus Aspergillus sp. EGF 15-0-3. All the corresponding optically pure enantiomers were successfully separated by a chiral HPLC column. The structures and configurations of all the compounds were elucidated based on the combination of NMR and HRESIMS data, chiral separation, single-crystal X-ray diffraction, quantum chemical 13C NMR, and electronic circular dichroism calculations. Meanwhile, the structure of eurotiumide G was also revised. The TDP1 inhibitor activities and photophysical properties of the obtained compounds were evaluated. In the TDP1 inhibition assay, as a result of synergy between (+)-6 and (−)-6, (±)-6 displayed strong inhibitory activity to TDP1 with IC50 values of 6.50 ± 0.73 μM. All compounds had a large Stokes shift and could be utilized for elucidating the mode of bioactivities by fluorescence imaging.
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9
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Leung E, Patel J, Hollywood JA, Zafar A, Tomek P, Barker D, Pilkington LI, van Rensburg M, Langley RJ, Helsby NA, Squire CJ, Baguley BC, Denny WA, Reynisson J, Leung IKH. Validating TDP1 as an Inhibition Target for the Development of Chemosensitizers for Camptothecin-Based Chemotherapy Drugs. Oncol Ther 2021; 9:541-556. [PMID: 34159519 PMCID: PMC8593127 DOI: 10.1007/s40487-021-00158-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 06/03/2021] [Indexed: 12/01/2022] Open
Abstract
Cancer chemotherapy sensitizers hold the key to maximizing the potential of standard anticancer treatments. We have a long-standing interest in developing and validating inhibitors of the DNA repair enzyme tyrosyl-DNA phosphodiesterase 1 (TDP1) as chemosensitizers for topoisomerase I poisons such as topotecan. Herein, by using thieno[2,3-b]pyridines, a class of TDP1 inhibitors, we showed that the inhibition of TDP1 can restore sensitivity to topotecan, results that are supported by TDP1 knockout cell experiments using CRISPR/Cas9. However, we also found that the restored sensitivity towards topoisomerase I inhibitors is likely regulated by multiple complementary DNA repair pathways. Our results showed that one of these pathways is likely modulated by PARP1, although it is also possible that other redundant and partially overlapping pathways may be involved in the DNA repair process. Our work thus raises the prospect of targeting multiple DNA repair pathways to increase the sensitivity to topoisomerase I inhibitors.
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Affiliation(s)
- Euphemia Leung
- Auckland Cancer Society Research Centre, School of Medical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand. .,Department of Molecular Medicine and Pathology, School of Medical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand. .,Maurice Wilkins Centre for Molecular Biodiscovery, 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
| | - Jennifer A Hollywood
- Department of Molecular Medicine and Pathology, School of Medical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand
| | - Ayesha Zafar
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand
| | - Petr Tomek
- Auckland Cancer Society Research Centre, School of Medical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand
| | - David Barker
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand.,The MacDiarmid Institute for Advanced Materials and Nanotechnology, Victoria University of Wellington, PO Box 600, Wellington, 6140, New Zealand
| | - Lisa I Pilkington
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand
| | - Michelle van Rensburg
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand
| | - Ries J Langley
- Department of Molecular Medicine and Pathology, School of Medical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand
| | - Nuala A Helsby
- Department of Molecular Medicine and Pathology, School of Medical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand
| | - Christopher J Squire
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand.,School of Biological Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand
| | - Bruce C Baguley
- Auckland Cancer Society Research Centre, School of Medical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand
| | - William A Denny
- Auckland Cancer Society Research Centre, School of Medical 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. .,School of Pharmacy and Bioengineering, Keele University, Staffordshire, ST5 5BG, UK.
| | - Ivanhoe K H Leung
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand. .,School of Chemical Sciences, The University of Auckland, Private Bag 92019, Victoria Street West, Auckland, 1142, New Zealand. .,School of Chemistry, The University of Melbourne, Parkville, VIC, 3010, Australia. .,Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, 3010, Australia.
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10
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Novel Tdp1 Inhibitors Based on Adamantane Connected with Monoterpene Moieties via Heterocyclic Fragments. Molecules 2021; 26:molecules26113128. [PMID: 34073771 PMCID: PMC8197275 DOI: 10.3390/molecules26113128] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/14/2021] [Accepted: 05/21/2021] [Indexed: 01/23/2023] Open
Abstract
Tyrosyl-DNA phosphodiesterase 1 (Tdp1) is a promising target for anticancer therapy due to its ability to counter the effects topoisomerase 1 (Top1) poison, such as topotecan, thus, decreasing their efficacy. Compounds containing adamantane and monoterpenoid residues connected via 1,2,4-triazole or 1,3,4-thiadiazole linkers were synthesized and tested against Tdp1. All the derivatives exhibited inhibition at low micromolar or nanomolar concentrations with the most potent inhibitors having IC50 values in the 0.35–0.57 µM range. The cytotoxicity was determined in the HeLa, HCT-116 and SW837 cancer cell lines; moderate CC50 (µM) values were seen from the mid-teens to no effect at 100 µM. Furthermore, citral derivative 20c, α-pinene-derived compounds 20f, 20g and 25c, and the citronellic acid derivative 25b were found to have a sensitizing effect in conjunction with topotecan in the HeLa cervical cancer and colon adenocarcinoma HCT-116 cell lines. The ligands are predicted to bind in the catalytic pocket of Tdp1 and have favorable physicochemical properties for further development as a potential adjunct therapy with Top1 poisons.
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11
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Gladkova ED, Chepanova AA, Ilina ES, Zakharenko AL, Reynisson J, Luzina OA, Volcho KP, Lavrik OI, Salakhutdinov NF. Discovery of Novel Sultone Fused Berberine Derivatives as Promising Tdp1 Inhibitors. Molecules 2021; 26:molecules26071945. [PMID: 33808389 PMCID: PMC8037669 DOI: 10.3390/molecules26071945] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 12/18/2022] Open
Abstract
A new type of berberine derivatives was obtained by the reaction of berberrubine with aliphatic sulfonyl chlorides. The new polycyclic compounds have a sultone ring condensed to C and D rings of a protoberberine core. The reaction conditions were developed to facilitate the formation of sultones with high yields without by-product formation. Thus, it was shown that the order of addition of reagents affects the composition of the reaction products: when sulfochlorides are added to berberrubine, their corresponding 9-O-sulfonates are predominantly formed; when berberrubine is added to pre-generated sulfenes, sultones are the only products. The reaction was shown to proceed stereo-selectively and the cycle configuration was confirmed by 2D NMR spectroscopy. The inhibitory activity of the synthesized sultones and their 12-brominated analogs against the DNA-repair enzyme tyrosyl-DNA phosphodiesterase 1 (Tdp1), an important target for a potential antitumor therapy, was studied. All derivatives were active in the micromolar and submicromolar range, in contrast to the acyclic analogs and 9-O-sulfonates, which were inactive. The significance of the sultone cycle and bromine substituent in binding with the enzyme was confirmed using molecular modeling. The active inhibitors are mostly non-toxic to the HeLa cancer cell line, and several ligands show synergy with topotecan, a topoisomerase 1 poison in clinical use. Thus, novel berberine derivatives can be considered as candidates for adjuvant therapy against cancer.
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Affiliation(s)
- Elizaveta D. Gladkova
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (E.D.G.); (K.P.V.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova str. 1, 630090 Novosibirsk, Russia
| | - Arina A. Chepanova
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.A.C.); (E.S.I.); (A.L.Z.); (O.I.L.)
| | - Ekaterina S. Ilina
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.A.C.); (E.S.I.); (A.L.Z.); (O.I.L.)
| | - Alexandra L. Zakharenko
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.A.C.); (E.S.I.); (A.L.Z.); (O.I.L.)
| | - Jóhannes Reynisson
- School of Pharmacy and Bioengineering, Keele University, Hornbeam Building, Staffordshire ST5 5BG, UK;
| | - Olga A. Luzina
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (E.D.G.); (K.P.V.)
- Correspondence: (O.A.L.); (N.F.S.)
| | - Konstantin P. Volcho
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (E.D.G.); (K.P.V.)
| | - Olga I. Lavrik
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.A.C.); (E.S.I.); (A.L.Z.); (O.I.L.)
| | - Nariman F. Salakhutdinov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (E.D.G.); (K.P.V.)
- Correspondence: (O.A.L.); (N.F.S.)
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12
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Zhao Z, Wu X, He F, Xiang C, Feng X, Bai X, Liu X, Zhao J, Takeda S, Qing Y. Critical roles of Rad54 in tolerance to apigenin-induced Top1-mediated DNA damage. Exp Ther Med 2021; 21:505. [PMID: 33791014 DOI: 10.3892/etm.2021.9936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 07/07/2020] [Indexed: 02/05/2023] Open
Abstract
Apigenin (APG), a flavone sub-class of flavonoids, possesses a diverse range of biological activities, including anti-cancer and anti-inflammatory effects. Previous studies identified the genotoxicity of APG in certain cancer cells, which may be associated with its anticancer effect. However, the DNA damage repair mechanism induced by APG has remained elusive. In order to clarify the molecular mechanisms, the present study determined the toxicity of APG to the wild-type (WT) DT40 chicken B-lymphocyte cell line, as well as to DT40 cells with deletions in various DNA repair genes, and their sensitivities were compared. It was demonstrated that cells deficient of Rad54, a critical homologous recombination gene, were particularly sensitive to APG. Cell-cycle analysis demonstrated that APG caused an increase in the G2/M-phase population of Rad54- / - cells that was greater than that in WT cells. Furthermore, it was demonstrated by immunofluorescence assay that Rad54- / - cells exhibited significantly increased numbers of γ-phosphorylated H2AX variant histone foci and chromosomal aberrations compared to the WT cells in response to APG. Of note, the in vitro complex of enzyme assay indicated that APG induced increased topoisomerase I (Top1) covalent protein DNA complex in Rad54- / - cells compared to WT cells. Finally, these results were verified using the TK6 human lymphoblastoid cell line and it was demonstrated that, as for DT40 cells, Rad54 deficiency sensitized TK6 cells to APG. The present study demonstrated that Rad54 was involved in the repair of APG-induced DNA damage, which was associated with Top1 inhibition.
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Affiliation(s)
- Zilu Zhao
- Department of Pharmacology, Key Laboratory of Drug-Targeting and Drug Delivery Systems of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Xiaohua Wu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Fang He
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Cuifang Xiang
- Department of Pharmacology, Key Laboratory of Drug-Targeting and Drug Delivery Systems of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Xiaoyu Feng
- Department of Pharmacology, Key Laboratory of Drug-Targeting and Drug Delivery Systems of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Xin Bai
- Department of Pharmacology, Key Laboratory of Drug-Targeting and Drug Delivery Systems of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Xin Liu
- Department of Pharmacology, Key Laboratory of Drug-Targeting and Drug Delivery Systems of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Jingxia Zhao
- Department of Pharmacology, Key Laboratory of Drug-Targeting and Drug Delivery Systems of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Yong Qing
- Department of Pharmacology, Key Laboratory of Drug-Targeting and Drug Delivery Systems of the Education Ministry, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041, P.R. China
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13
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Zhao XZ, Kiselev E, Lountos GT, Wang W, Tropea JE, Needle D, Hilimire TA, Schneekloth JS, Waugh DS, Pommier Y, Burke TR. Small molecule microarray identifies inhibitors of tyrosyl-DNA phosphodiesterase 1 that simultaneously access the catalytic pocket and two substrate binding sites. Chem Sci 2021; 12:3876-3884. [PMID: 34163656 PMCID: PMC8179437 DOI: 10.1039/d0sc05411a] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Tyrosyl-DNA phosphodiesterase 1 (TDP1) is a member of the phospholipase D family of enzymes, which catalyzes the removal of both 3′- and 5′-DNA phosphodiester adducts. Importantly, it is capable of reducing the anticancer effects of type I topoisomerase (TOP1) inhibitors by repairing the stalled covalent complexes of TOP1 with DNA. It achieves this by promoting the hydrolysis of the phosphodiester bond between the Y723 residue of human TOP1 and the 3′-phosphate of its DNA substrate. Blocking TDP1 function is an attractive means of enhancing the efficacy of TOP1 inhibitors and overcoming drug resistance. Previously, we reported the use of an X-ray crystallographic screen of more than 600 fragments to identify small molecule variations on phthalic acid and hydroxyquinoline motifs that bind within the TDP1 catalytic pocket. Yet, the majority of these compounds showed limited (millimolar) TDP1 inhibitory potencies. We now report examining a 21 000-member library of drug-like Small Molecules in Microarray (SMM) format for their ability to bind Alexa Fluor 647 (AF647)-labeled TDP1. The screen identified structurally similar N,2-diphenylimidazo[1,2-a]pyrazin-3-amines as TDP1 binders and catalytic inhibitors. We then explored the core heterocycle skeleton using one-pot Groebke–Blackburn–Bienayme multicomponent reactions and arrived at analogs having higher inhibitory potencies. Solving TDP1 co-crystal structures of a subset of compounds showed their binding at the TDP1 catalytic site, while mimicking substrate interactions. Although our original fragment screen differed significantly from the current microarray protocol, both methods identified ligand–protein interactions containing highly similar elements. Importantly inhibitors identified through the SMM approach show competitive inhibition against TDP1 and access the catalytic phosphate-binding pocket, while simultaneously providing extensions into both the substrate DNA and peptide-binding channels. As such, they represent a platform for further elaboration of trivalent ligands, that could serve as a new genre of potent TDP1 inhibitors. Using small molecule microarray TDP1 inhibitors have been identified that bind in a trivalent mode.![]()
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Affiliation(s)
- Xue Zhi Zhao
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute Frederick MD USA
| | - Evgeny Kiselev
- Developmental Therapeutics Branch, Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute Bethesda MD USA
| | - George T Lountos
- Basic Science Program, Frederick National Laboratory for Cancer Research Frederick MD USA
| | - Wenjie Wang
- Developmental Therapeutics Branch, Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute Bethesda MD USA
| | - Joseph E Tropea
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute Frederick MD USA
| | - Danielle Needle
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute Frederick MD USA
| | - Thomas A Hilimire
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute Frederick MD USA
| | - John S Schneekloth
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute Frederick MD USA
| | - David S Waugh
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute Frederick MD USA
| | - Yves Pommier
- Developmental Therapeutics Branch, Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute Bethesda MD USA
| | - Terrence R Burke
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute Frederick MD USA
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14
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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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15
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Chen F, Chen L, Liang W, Zhang Z, Li J, Zheng W, Zhu Z, Zhu J, Zhao Y. Identification and confirmation of 14-3-3 ζ as a novel target of ginsenosides in brain tissues. J Ginseng Res 2020; 45:465-472. [PMID: 34295206 PMCID: PMC8282492 DOI: 10.1016/j.jgr.2020.12.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 11/11/2020] [Accepted: 12/23/2020] [Indexed: 12/21/2022] Open
Abstract
Background Ginseng can help regulate brain excitability, promote learning and memory, and resist cerebral ischemia in the central nervous system. Ginsenosides are the major effective compounds of Ginseng, but their protein targets in the brain have not been determined. Methods We screened proteins that interact with the main components of ginseng (ginsenosides) by affinity chromatography and identified the 14-3-3 ζ protein as a potential target of ginsenosides in brain tissues. Results Biolayer interferometry (BLI) analysis showed that 20(S)-protopanaxadiol (PPD), a ginseng saponin metabolite, exhibited the highest direct interaction to the 14-3-3 ζ protein. Subsequently, BLI kinetics analysis and isothermal titration calorimetry (ITC) assay showed that PPD specifically bound to the 14-3-3 ζ protein. The cocrystal structure of the 14-3-3 ζ protein-PPD complex showed that the main interactions occurred between the residues R56, R127, and Y128 of the 14-3-3 ζ protein and a portion of PPD. Moreover, mutating any of the above residues resulted in a significant decrease of affinity between PPD and the 14-3-3 ζ protein. Conclusion Our results indicate the 14-3-3 ζ protein is the target of PPD, a ginsenoside metabolite. Crystallographic and mutagenesis studies suggest a direct interaction between PPD and the 14-3-3 ζ protein. This finding can help in the development of small-molecular compounds that bind to the 14-3-3 ζ protein on the basis of the structure of dammarane-type triterpenoid.
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Affiliation(s)
- Feiyan Chen
- Research and Innovation Center, College of Traditional Chinese Medicine Integrated Chinese and Western Medicine College, Nanjing University of Chinese Medicine, Nanjing, China.,Department of Cell Biology and Medical Genetics, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Lin Chen
- Department of Physiology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Weifeng Liang
- Department of Cell Biology and Medical Genetics, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Zhengguang Zhang
- Department of Cell Biology and Medical Genetics, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jiao Li
- Department of Cell Biology and Medical Genetics, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Wan Zheng
- Department of Cell Biology and Medical Genetics, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Zhu Zhu
- Department of Pharmacology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jiapeng Zhu
- Department of Cell Biology and Medical Genetics, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yunan Zhao
- Department of Pathology and Pathophysiology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
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16
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Krumpe LRH, Wilson BAP, Marchand C, Sunassee SN, Bermingham A, Wang W, Price E, Guszczynski T, Kelley JA, Gustafson KR, Pommier Y, Rosengren KJ, Schroeder CI, O'Keefe BR. Recifin A, Initial Example of the Tyr-Lock Peptide Structural Family, Is a Selective Allosteric Inhibitor of Tyrosyl-DNA Phosphodiesterase I. J Am Chem Soc 2020; 142:21178-21188. [PMID: 33263997 DOI: 10.1021/jacs.0c10418] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Tyrosyl-DNA phosphodiesterase 1 (TDP1) is a molecular target for the sensitization of cancer cells to the FDA-approved topoisomerase inhibitors topotecan and irinotecan. High-throughput screening of natural product extract and fraction libraries for inhibitors of TDP1 activity resulted in the discovery of a new class of knotted cyclic peptides from the marine sponge Axinella sp. Bioassay-guided fractionation of the source extract resulted in the isolation of the active component which was determined to be an unprecedented 42-residue cysteine-rich peptide named recifin A. The native NMR structure revealed a novel fold comprising a four strand antiparallel β-sheet and two helical turns stabilized by a complex disulfide bond network that creates an embedded ring around one of the strands. The resulting structure, which we have termed the Tyr-lock peptide family, is stabilized by a tyrosine residue locked into three-dimensional space. Recifin A inhibited the cleavage of phosphodiester bonds by TDP1 in a FRET assay with an IC50 of 190 nM. Enzyme kinetics studies revealed that recifin A can specifically modulate the enzymatic activity of full-length TDP1 while not affecting the activity of a truncated catalytic domain of TDP1 lacking the N-terminal regulatory domain (Δ1-147), suggesting an allosteric binding site for recifin A on the regulatory domain of TDP1. Recifin A represents both the first of a unique structural class of knotted disulfide-rich peptides and defines a previously unseen mechanism of TDP1 inhibition that could be productively exploited for potential anticancer applications.
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Affiliation(s)
- Lauren R H Krumpe
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States.,Molecular Targets Program, Center for Cancer Research, NCI-Frederick, NIH, Frederick, Maryland 21702, United States
| | - Brice A P Wilson
- Molecular Targets Program, Center for Cancer Research, NCI-Frederick, NIH, Frederick, Maryland 21702, United States
| | - Christophe Marchand
- Developmental Therapeutics Branch, Laboratory of Molecular Pharmacology, NCI, NIH, Bethesda, Maryland 20892, United States
| | - Suthananda N Sunassee
- Molecular Targets Program, Center for Cancer Research, NCI-Frederick, NIH, Frederick, Maryland 21702, United States
| | - Alun Bermingham
- Molecular Targets Program, Center for Cancer Research, NCI-Frederick, NIH, Frederick, Maryland 21702, United States
| | - Wenjie Wang
- Developmental Therapeutics Branch, Laboratory of Molecular Pharmacology, NCI, NIH, Bethesda, Maryland 20892, United States
| | - Edmund Price
- Molecular Targets Program, Center for Cancer Research, NCI-Frederick, NIH, Frederick, Maryland 21702, United States
| | - Tad Guszczynski
- Molecular Targets Program, Center for Cancer Research, NCI-Frederick, NIH, Frederick, Maryland 21702, United States
| | - James A Kelley
- Chemical Biology Laboratory, Center for Cancer Research, NCI-Frederick, NIH, Frederick, Maryland 21702, United States
| | - Kirk R Gustafson
- Molecular Targets Program, Center for Cancer Research, NCI-Frederick, NIH, Frederick, Maryland 21702, United States
| | - Yves Pommier
- Developmental Therapeutics Branch, Laboratory of Molecular Pharmacology, NCI, NIH, Bethesda, Maryland 20892, United States
| | - K Johan Rosengren
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Christina I Schroeder
- Chemical Biology Laboratory, Center for Cancer Research, NCI-Frederick, NIH, Frederick, Maryland 21702, United States.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Barry R O'Keefe
- Molecular Targets Program, Center for Cancer Research, NCI-Frederick, NIH, Frederick, Maryland 21702, United States.,Natural Products Branch, Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Frederick, Maryland 21702, United States
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17
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The First Berberine-Based Inhibitors of Tyrosyl-DNA Phosphodiesterase 1 (Tdp1), an Important DNA Repair Enzyme. Int J Mol Sci 2020; 21:ijms21197162. [PMID: 32998385 PMCID: PMC7582571 DOI: 10.3390/ijms21197162] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/22/2020] [Accepted: 09/26/2020] [Indexed: 12/17/2022] Open
Abstract
A series of berberine and tetrahydroberberine sulfonate derivatives were prepared and tested against the tyrosyl-DNA phosphodiesterase 1 (Tdp1) DNA-repair enzyme. The berberine derivatives inhibit the Tdp1 enzyme in the low micromolar range; this is the first reported berberine based Tdp1 inhibitor. A structure–activity relationship analysis revealed the importance of bromine substitution in the 12-position on the tetrahydroberberine scaffold. Furthermore, it was shown that the addition of a sulfonate group containing a polyfluoroaromatic moiety at position 9 leads to increased potency, while most of the derivatives containing an alkyl fragment at the same position were not active. According to the molecular modeling, the bromine atom in position 12 forms a hydrogen bond to histidine 493, a key catalytic residue. The cytotoxic effect of topotecan, a clinically important topoisomerase 1 inhibitor, was doubled in the cervical cancer HeLa cell line by derivatives 11g and 12g; both displayed low toxicity without topotecan. Derivatives 11g and 12g can therefore be used for further development to sensitize the action of clinically relevant Topo1 inhibitors.
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18
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Luzina O, Filimonov A, Zakharenko A, Chepanova A, Zakharova O, Ilina E, Dyrkheeva N, Likhatskaya G, Salakhutdinov N, Lavrik O. Usnic Acid Conjugates with Monoterpenoids as Potent Tyrosyl-DNA Phosphodiesterase 1 Inhibitors. JOURNAL OF NATURAL PRODUCTS 2020; 83:2320-2329. [PMID: 32786885 DOI: 10.1021/acs.jnatprod.9b01089] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Hybrid molecules created from different pharmacophores of natural and synthetic equivalents are successfully used in pharmaceutical practice. One promising target for anticancer therapy is tyrosyl-DNA phosphodiesterase 1 (Tdp1) because it can repair DNA lesions caused by DNA-topoisomerase 1 (Top1) inhibitors, resulting in drug resistance. In this study, new hybrid compounds were synthesized by combining the pharmacophoric moiety of a set of natural compounds with inhibitory properties against Tdp1, particularly, phenolic usnic acid and a set of different monoterpenoid fragments. These fragments were connected through a hydrazinothiazole linker. The inhibitory properties of the new compounds mainly depended on the structure of the terpenoid moieties. The two most potent compounds, 9a and 9b, were synthesized from citral and citronellal, which contain acyclic fragments with IC50 values in the range of 10-16 nM. Some synthesized derivatives showed low cytotoxicity against HeLa cells and increased the effect of the Top1 inhibitor topotecan in vitro by three to seven times. These derivatives may be considered as potential agents for the development of anticancer therapies when combined with Top1 inhibitors.
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Affiliation(s)
- Olga Luzina
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russian Federation
| | - Alexander 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
| | - Alexandra Zakharenko
- 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
| | - Olga Zakharova
- 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
| | - Nadezhda Dyrkheeva
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russian Federation
| | - Galina Likhatskaya
- Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of Russian Academy of Sciences, Vladivostok, 690022, 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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19
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Tsuda M, Kitamasu K, Kumagai C, Sugiyama K, Nakano T, Ide H. Tyrosyl-DNA phosphodiesterase 2 (TDP2) repairs topoisomerase 1 DNA-protein crosslinks and 3'-blocking lesions in the absence of tyrosyl-DNA phosphodiesterase 1 (TDP1). DNA Repair (Amst) 2020; 91-92:102849. [PMID: 32460231 DOI: 10.1016/j.dnarep.2020.102849] [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: 12/20/2019] [Revised: 03/19/2020] [Accepted: 03/23/2020] [Indexed: 01/29/2023]
Abstract
Topoisomerase I (TOP1) resolves DNA topology during replication and transcription. The enzyme forms an intermediate TOP1 cleavage complex (TOP1cc) through transient TOP1-DNA-protein crosslinks. Camptothecin is a frontline anticancer agent that freezes this reaction intermediate, leading to the generation of irreversible TOP1ccs that act as 3'-blocking lesions. It is widely accepted that TOP1cc is repaired via a two-step pathway involving proteasomal degradation of TOP1cc to the crosslinked peptide, followed by removal of the TOP1cc-derived peptide from DNA by tyrosyl-DNA phosphodiesterase 1 (TDP1). In the present study, we developed an assay system to estimate repair kinetics of TOP1cc separately in the first and second steps, using monoclonal antibodies against the TOP1 protein and the TOP1 catalytic site peptide-DNA complex, respectively. Although TDP1-deficient (TDP1-/-) TK6 cells had normal kinetics of the first step, a delay in the kinetics of the second step was observed relative to that in wild-type cells. Tyrosyl-DNA phosphodiesterase 2 (TDP2) reportedly promotes the repair of TOP1-induced DNA damage in the absence of TDP1. The present assays additionally demonstrated that TDP2 promotes the second, but not the first, step of TOP1cc repair in the absence of TDP1. We also analyzed sensitivities of TK6 cells with deficiencies in TDP1 and/or TDP2 to agents that produce 3' -blocking lesions. These experiments showed that TDP1-/-TDP2-/- cells were more sensitive to the agents Azidothymidine (zidovudine), Cytarabine, Abacavir, Gemcitabine, and Trifluridine than TDP1-/- or TDP2-/- cells. Taken together, our findings confirm the roles of TDP2 in the repair of 3'-blocking lesions.
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Affiliation(s)
- Masataka Tsuda
- Program of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8526, Japan.
| | - Kaito Kitamasu
- Program of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Chiho Kumagai
- Program of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Kazuya Sugiyama
- Program of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Toshiaki Nakano
- DNA Damage Chemistry Research Group, Institute for Quantum Life Science, National Institutes of Quantum and Radiological Science and Technology, 8-1-7 Umemidai, Kizugawa-shi, Kyoto 619-0215, Japan
| | - Hiroshi Ide
- Program of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8526, Japan.
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Sun Y, Saha S, Wang W, Saha LK, Huang SYN, Pommier Y. Excision repair of topoisomerase DNA-protein crosslinks (TOP-DPC). DNA Repair (Amst) 2020; 89:102837. [PMID: 32200233 DOI: 10.1016/j.dnarep.2020.102837] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/22/2020] [Accepted: 02/25/2020] [Indexed: 12/13/2022]
Abstract
Topoisomerases are essential enzymes solving DNA topological problems such as supercoils, knots and catenanes that arise from replication, transcription, chromatin remodeling and other nucleic acid metabolic processes. They are also the targets of widely used anticancer drugs (e.g. topotecan, irinotecan, enhertu, etoposide, doxorubicin, mitoxantrone) and fluoroquinolone antibiotics (e.g. ciprofloxacin and levofloxacin). Topoisomerases manipulate DNA topology by cleaving one DNA strand (TOP1 and TOP3 enzymes) or both in concert (TOP2 enzymes) through the formation of transient enzyme-DNA cleavage complexes (TOPcc) with phosphotyrosyl linkages between DNA ends and the catalytic tyrosyl residue of the enzymes. Failure in the self-resealing of TOPcc results in persistent TOPcc (which we refer it to as topoisomerase DNA-protein crosslinks (TOP-DPC)) that threaten genome integrity and lead to cancers and neurodegenerative diseases. The cell prevents the accumulation of topoisomerase-mediated DNA damage by excising TOP-DPC and ligating the associated breaks using multiple pathways conserved in eukaryotes. Tyrosyl-DNA phosphodiesterases (TDP1 and TDP2) cleave the tyrosyl-DNA bonds whereas structure-specific endonucleases such as Mre11 and XPF (Rad1) incise the DNA phosphodiester backbone to remove the TOP-DPC along with the adjacent DNA segment. The proteasome and metalloproteases of the WSS1/Spartan family typify proteolytic repair pathways that debulk TOP-DPC to make the peptide-DNA bonds accessible to the TDPs and endonucleases. The purpose of this review is to summarize our current understanding of how the cell excises TOP-DPC and why, when and where the cell recruits one specific mechanism for repairing topoisomerase-mediated DNA damage, acquiring resistance to therapeutic topoisomerase inhibitors and avoiding genomic instability, cancers and neurodegenerative diseases.
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Affiliation(s)
- Yilun Sun
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Sourav Saha
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Wenjie Wang
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Liton Kumar Saha
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Shar-Yin Naomi Huang
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States.
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21
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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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22
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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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23
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Filimonov AS, Chepanova AA, Luzina OA, Zakharenko AL, Zakharova OD, Ilina ES, Dyrkheeva NS, Kuprushkin MS, Kolotaev AV, Khachatryan DS, Patel J, Leung IK, Chand R, Ayine-Tora DM, Reynisson J, Volcho KP, Salakhutdinov NF, Lavrik OI. New Hydrazinothiazole Derivatives of Usnic Acid as Potent Tdp1 Inhibitors. Molecules 2019; 24:molecules24203711. [PMID: 31619021 PMCID: PMC6832265 DOI: 10.3390/molecules24203711] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/12/2019] [Accepted: 10/12/2019] [Indexed: 11/16/2022] Open
Abstract
Tyrosyl-DNA phosphodiesterase 1 (Tdp1) is a promising therapeutic target in cancer therapy. Combination chemotherapy using Tdp1 inhibitors as a component can potentially improve therapeutic response to many chemotherapeutic regimes. A new set of usnic acid derivatives with hydrazonothiazole pharmacophore moieties were synthesized and evaluated as Tdp1 inhibitors. Most of these compounds were found to be potent inhibitors with IC50 values in the low nanomolar range. The activity of the compounds was verified by binding experiments and supported by molecular modeling. The ability of the most effective inhibitors, used at non-toxic concentrations, to sensitize tumors to the anticancer drug topotecan was also demonstrated. The order of administration of the inhibitor and topotecan on their synergistic effect was studied, suggesting that prior or simultaneous introduction of the inhibitor with topotecan is the most effective.
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Affiliation(s)
- Aleksander S. Filimonov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.S.F.); (O.A.L.); (N.F.S.)
- Novosibirsk State University, Pirogova str. 1, 630090 Novosibirsk, Russia
| | - Arina A. Chepanova
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.A.C.); (A.L.Z.); (O.D.Z.); (E.S.I.); (N.S.D.); (M.S.K.)
| | - Olga A. Luzina
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.S.F.); (O.A.L.); (N.F.S.)
| | - Alexandra L. Zakharenko
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.A.C.); (A.L.Z.); (O.D.Z.); (E.S.I.); (N.S.D.); (M.S.K.)
| | - Olga D. Zakharova
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.A.C.); (A.L.Z.); (O.D.Z.); (E.S.I.); (N.S.D.); (M.S.K.)
| | - Ekaterina S. Ilina
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.A.C.); (A.L.Z.); (O.D.Z.); (E.S.I.); (N.S.D.); (M.S.K.)
| | - Nadezhda S. Dyrkheeva
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.A.C.); (A.L.Z.); (O.D.Z.); (E.S.I.); (N.S.D.); (M.S.K.)
| | - Maxim S. Kuprushkin
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.A.C.); (A.L.Z.); (O.D.Z.); (E.S.I.); (N.S.D.); (M.S.K.)
| | - Anton V. Kolotaev
- The Federal State Unitary Enterprise, Institute of Chemical Reagents and High Purity Chemical Substances of National Research Centre, Kurchatov Institute, 107076 Moscow, Russia; (A.V.K.); (D.S.K.)
| | - Derenik S. Khachatryan
- The Federal State Unitary Enterprise, Institute of Chemical Reagents and High Purity Chemical Substances of National Research Centre, Kurchatov Institute, 107076 Moscow, Russia; (A.V.K.); (D.S.K.)
| | - Jinal Patel
- School of Chemical Sciences, The University of Auckland, Auckland 1142, New Zealand; (J.P.); (R.C.); (D.M.A.-T.)
| | - Ivanhoe K.H. Leung
- School of Chemical Sciences, The University of Auckland, Auckland 1142, New Zealand; (J.P.); (R.C.); (D.M.A.-T.)
| | - Raina Chand
- School of Chemical Sciences, The University of Auckland, Auckland 1142, New Zealand; (J.P.); (R.C.); (D.M.A.-T.)
| | - Daniel M. Ayine-Tora
- School of Chemical Sciences, The University of Auckland, Auckland 1142, New Zealand; (J.P.); (R.C.); (D.M.A.-T.)
| | - Johannes Reynisson
- School of Pharmacy and Bioengineering, Keele University, Hornbeam Building, Staffordshire ST5 5BG, UK;
| | - Konstantin P. Volcho
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.S.F.); (O.A.L.); (N.F.S.)
- Novosibirsk State University, Pirogova str. 1, 630090 Novosibirsk, Russia
- Correspondence: (K.P.V.); (O.I.L.); Tel.: +7-383-3308870 (K.P.V.); + 7-383-3635195 (O.I.L.)
| | - Nariman F. Salakhutdinov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.S.F.); (O.A.L.); (N.F.S.)
- Novosibirsk State University, Pirogova str. 1, 630090 Novosibirsk, Russia
| | - Olga I. Lavrik
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., 630090 Novosibirsk, Russia; (A.S.F.); (O.A.L.); (N.F.S.)
- Novosibirsk State University, Pirogova str. 1, 630090 Novosibirsk, Russia
- Correspondence: (K.P.V.); (O.I.L.); Tel.: +7-383-3308870 (K.P.V.); + 7-383-3635195 (O.I.L.)
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24
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Wang W, Rodriguez-Silva M, Acanda de la Rocha AM, Wolf AL, Lai Y, Liu Y, Reinhold WC, Pommier Y, Chambers JW, Tse-Dinh YC. Tyrosyl-DNA Phosphodiesterase 1 and Topoisomerase I Activities as Predictive Indicators for Glioblastoma Susceptibility to Genotoxic Agents. Cancers (Basel) 2019; 11:cancers11101416. [PMID: 31547492 PMCID: PMC6827102 DOI: 10.3390/cancers11101416] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/06/2019] [Accepted: 09/19/2019] [Indexed: 02/06/2023] Open
Abstract
Glioblastoma (GBM) patients have an estimated survival of ~15 months with treatment, and the standard of care only modestly enhances patient survival. Identifying biomarkers representing vulnerabilities may allow for the selection of efficacious chemotherapy options to address personalized variations in GBM tumors. Irinotecan targets topoisomerase I (TOP1) by forming a ternary DNA-TOP1 cleavage complex (TOP1cc), inducing apoptosis. Tyrosyl-DNA phosphodiesterase 1 (TDP1) is a crucial repair enzyme that may reduce the effectiveness of irinotecan. We treated GBM cell lines with increasing concentrations of irinotecan and compared the IC50 values. We found that the TDP1/TOP1 activity ratio had the strongest correlation (Pearson correlation coefficient R = 0.972, based on the average from three sets of experiments) with IC50 values following irinotecan treatment. Increasing the TDP1/TOP1 activity ratio by the ectopic expression of wild-type TDP1 increased in irinotecan IC50, while the expression of the TDP1 catalytic-null mutant did not alter the susceptibility to irinotecan. The TDP1/TOP1 activity ratio may be a new predictive indicator for GBM vulnerability to irinotecan, allowing for the selection of individual patients for irinotecan treatment based on risk-benefit. Moreover, TDP1 inhibitors may be a novel combination treatment with irinotecan to improve GBM patient responsiveness to genotoxic chemotherapies.
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Affiliation(s)
- Wenjie Wang
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA.
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.
| | - Monica Rodriguez-Silva
- Department of Environmental Health Sciences, Florida International University, Miami, FL 33199, USA.
| | | | - Aizik L Wolf
- Department of Neurosurgery, Miami Neuroscience Center at Larkin, South Miami, FL 33143, USA.
| | - Yanhao Lai
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA.
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.
| | - Yuan Liu
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA.
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.
| | - William C Reinhold
- Developmental Therapeutic Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA.
| | - Yves Pommier
- Developmental Therapeutic Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892 USA.
| | - Jeremy W Chambers
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA.
- Department of Environmental Health Sciences, Florida International University, Miami, FL 33199, USA.
| | - Yuk-Ching Tse-Dinh
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA.
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA.
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