1
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Haro-Moreno JM, Cabello-Yeves PJ, Garcillán-Barcia MP, Zakharenko A, Zemskaya TI, Rodriguez-Valera F. A novel and diverse group of Candidatus Patescibacteria from bathypelagic Lake Baikal revealed through long-read metagenomics. Environ Microbiome 2023; 18:12. [PMID: 36823661 PMCID: PMC9948471 DOI: 10.1186/s40793-023-00473-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Lake Baikal, the world's deepest freshwater lake, contains important numbers of Candidatus Patescibacteria (formerly CPR) in its deepest reaches. However, previously obtained CPR metagenome-assembled genomes recruited very poorly indicating the potential of other groups being present. Here, we have applied for the first time a long-read (PacBio CCS) metagenomic approach to analyze in depth the Ca. Patescibacteria living in the bathypelagic water column of Lake Baikal at 1600 m. RESULTS The retrieval of nearly complete 16S rRNA genes before assembly has allowed us to detect the presence of a novel and a likely endemic group of Ca. Patescibacteria inhabiting bathypelagic Lake Baikal. This novel group seems to possess extremely high intra-clade diversity, precluding complete genomes' assembly. However, read binning and scaffolding indicate that these microbes are similar to other Ca. Patescibacteria (i.e. parasites or symbionts), although they seem to carry more anabolic pathways, likely reflecting the extremely oligotrophic habitat they inhabit. The novel bins have not been found anywhere, but one of the groups appears in small amounts in an oligotrophic and deep alpine Lake Thun. We propose this novel group be named Baikalibacteria. CONCLUSION The recovery of 16S rRNA genes via long-read metagenomics plus the use of long-read binning to uncover highly diverse "hidden" groups of prokaryotes are key strategies to move forward in ecogenomic microbiology. The novel group possesses enormous intraclade diversity akin to what happens with Ca. Patescibacteria at the interclade level, which is remarkable in an environment that has changed little in the last 25 million years.
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Affiliation(s)
- Jose M Haro-Moreno
- Evolutionary Genomics Group, Departamento Producción Vegetal y Microbiología, Universidad Miguel Hernández, Apartado 18, San Juan de Alicante, 03550, Alicante, Spain
| | - Pedro J Cabello-Yeves
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, 46980, Paterna, Valencia, Spain
| | - M Pilar Garcillán-Barcia
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-Consejo Superior de Investigaciones Científicas, Santander, Spain
| | - Alexandra Zakharenko
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Tamara I Zemskaya
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento Producción Vegetal y Microbiología, Universidad Miguel Hernández, Apartado 18, San Juan de Alicante, 03550, Alicante, Spain.
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2
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Oganyan K, Musaelyan A, Lapin S, Kupenskaya T, Svechkova A, Belyaev M, Zakharenko A, Orlov S. 63P Molecular markers as predictors of response to perioperative FLOT chemotherapy in gastric cancer. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.09.064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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3
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Musaelyan A, Lapin S, Nazarov V, Vorobyev S, Zakharenko A, Orlov S. 10P Clinical and morphological pattern of malignant tumors with microsatellite instability (MSI). Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.08.2006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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4
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Zakharenko A, Smagulova S. Search engine optimization as a tool to increase the competitiveness of pharmaceutical companies in modern conditions. E-Management 2020. [DOI: 10.26425/2658-3445-2020-2-32-39] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Search engine optimization (SEO), which is currently actively used by the majority of pharmaceutical companies all over the world, is one of the most relevant digital marketing technologies. The features of the SEO in pharmaceutical companies as one of the modern tools of digital marketing have been considered in the article.Most of the companies, which operate in the natural sciences, are several years behind in development from other industries, due to the low level of SEO strategy application. As a result, the marketing budgets of pharmaceutical companies are focused on maintaining traditional classical approaches in the field of marketing. This bias in the budget arises mainly from the underestimation of the role of the SEO strategy in the organization’s activities by the majority of pharmaceutical companies. Companies should clearly understand how significant is the impact of digitalization on their activity in modern conditions. SEO is much broader than using search queries and meta tags. Due to implementing digital tools, it is possible to create “social signals” for attracting a new target audience.It has been noted in the article that search algorithms, developed by search platforms, change very often, and it is necessary to constantly monitor and improve them. Moreover, SEO is required to help people to find the content that best matches their intended goal, rather than to misinform them by showing inappropriate pages with matched search keywords in search results.Competition among the largest companies is constantly increasing in the global pharmaceutical market, and the use of digital marketing tools, such as SEO, will allow companies to change radically the situation. As a result of the research, recommendations for the effective use of SEO as one of the digital marketing tools in the business of pharmaceutical companies have been proposed. Finally, the conclusions about the increasing the role of digital marketing in modern conditions have been made.
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5
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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. J Nat Prod 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] [What about the content of this article? (0)] [Affiliation(s)] [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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6
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Kovaleva K, Oleshko O, Mamontova E, Yarovaya O, Zakharova O, Zakharenko A, Kononova A, Dyrkheeva N, Cheresiz S, Pokrovsky A, Lavrik O, Salakhutdinov N. Dehydroabietylamine Ureas and Thioureas as Tyrosyl-DNA Phosphodiesterase 1 Inhibitors That Enhance the Antitumor Effect of Temozolomide on Glioblastoma Cells. J Nat Prod 2019; 82:2443-2450. [PMID: 31430155 DOI: 10.1021/acs.jnatprod.8b01095] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A new class of tyrosyl-DNA phosphodiesterase 1 (TDP1) inhibitors was found among resin acid derivatives. Several novel ureas and thioureas derived from dehydroabietylamine were synthesized and tested for TDP1 inhibition. The synthesized compounds showed IC50 values in the range of 0.1 to 3.7 μM and demonstrated low cytotoxicity against the human tumor cell lines U-937, U-87MG, MDA-MB, SK-Mel8, A-549, MCF7, T98G, and SNB19. Several compounds showed enhancement of the cytotoxic activity of the alkylating agent temozolomide, which is used as a first line therapy against glioblastoma (GBM), in the GBM cell lines U-87MG and SNB19.
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Affiliation(s)
- Kseniya Kovaleva
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences , Novosibirsk , 630090 , Russian Federation
- Novosibirsk State University , Novosibirsk , 630090 , Russian Federation
| | - Olga Oleshko
- Novosibirsk State University , Novosibirsk , 630090 , Russian Federation
| | - Evgeniya Mamontova
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences , Novosibirsk , 630090 , Russian Federation
| | - Olga Yarovaya
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences , Novosibirsk , 630090 , Russian Federation
- Novosibirsk State University , Novosibirsk , 630090 , Russian Federation
| | - Olga Zakharova
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences , Novosibirsk , 630090 , Russian Federation
| | - Alexandra Zakharenko
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences , Novosibirsk , 630090 , Russian Federation
| | - Alena Kononova
- Novosibirsk State University , Novosibirsk , 630090 , Russian Federation
| | - Nadezhda Dyrkheeva
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences , Novosibirsk , 630090 , Russian Federation
| | - Sergey Cheresiz
- Novosibirsk State University , Novosibirsk , 630090 , Russian Federation
- State Scientific Research Institute of Physiology and Basic Medicine , P.O. Box 237, Novosibirsk , 630117 , Russian Federation
| | - Andrey Pokrovsky
- Novosibirsk State University , Novosibirsk , 630090 , Russian Federation
| | - Olga Lavrik
- Novosibirsk State University , Novosibirsk , 630090 , Russian Federation
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences , Novosibirsk , 630090 , Russian Federation
| | - Nariman Salakhutdinov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences , Novosibirsk , 630090 , Russian Federation
- Novosibirsk State University , Novosibirsk , 630090 , Russian Federation
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7
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Zakharenko A, Dyrkheeva N, Lavrik O. Dual DNA topoisomerase 1 and tyrosyl-DNA phosphodiesterase 1 inhibition for improved anticancer activity. Med Res Rev 2019; 39:1427-1441. [PMID: 31004352 DOI: 10.1002/med.21587] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 03/26/2019] [Accepted: 04/02/2019] [Indexed: 12/22/2022]
Abstract
Tyrosyl-DNA phosphodiesterase 1 (Tdp1) is a DNA repair enzyme that catalyzes the hydrolysis of the phosphodiester bond in the DNA-topoisomerase 1 (Top1) covalent complex and repairs some other 3'-end DNA adducts. Currently, Tdp1 functions as an important target in cancer drug design owing to its ability to break down various DNA adducts induced by chemotherapeutics. Tdp1 inhibitors may sensitize tumor cells to the action of Top1 poisons, thereby potentiating their effects. This mini-review summarizes findings from studies reporting the combined inhibition of Top1 and Tdp1. Two different approaches have been considered for developing such drug precursors.
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Affiliation(s)
- Alexandra Zakharenko
- Laboratory of Bioorganic Chemistry of Enzymes, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Nadezhda Dyrkheeva
- Laboratory of Bioorganic Chemistry of Enzymes, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Olga Lavrik
- Laboratory of Bioorganic Chemistry of Enzymes, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russian Federation
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8
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Mozhaitsev E, Suslov E, Demidova Y, Korchagina D, Volcho K, Zakharenko A, Vasil'eva I, Kupryushkin M, Chepanova A, Ayine-Tora DM, Reynisson J, Salakhutdinov N, Lavrik O. The Development of Tyrosyl-DNA Phosphodyesterase 1 (TDP1) Inhibitors Based on the Amines Combining Aromatic/Heteroaromatic and Monoterpenoid Moieties. LETT DRUG DES DISCOV 2019. [DOI: 10.2174/1570180816666181220121042] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Background:
Inhibition of the DNA repair enzyme, tyrosyl-DNA phosphodiesterase 1
(TDP1), may increase the efficacy of cancer drugs that cause damage to tumor cell DNA. Among
the known TDP1 inhibitors, there are compounds containing moieties of natural substances, e.g.,
monoterpenoids. In this work, we synthesized several compounds containing aromatic/
heteroaromatic amines and monoterpenoid groups and assessed their TDP1 inhibition potential.
Methods:
Structures of all the synthesized compounds were confirmed by 1H and 13C NMR as well
as HRMS. The TDP1 inhibitory activity of the amines was determined by real-time fluorescence
oligonucleotide biosensor.
Results:
The synthesized secondary amines had TDP1 inhibitory activity IC50 in the range of
0.79-9.2 µM. The highest activity was found for (–)-myrtenal derivatives containing p-bromoaniline
or m-(trifluoromethyl)aniline residue.
Conclusion:
We synthesized 22 secondary amines; of these, 17 amines are novel chemical structures.
Many of the amines inhibit TDP1 activity in the low micromolar range. Therefore, these
compounds are promising for further study of their antiproliferative activity in conjunction with
DNA damaging drugs.
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Affiliation(s)
- Evgenii Mozhaitsev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Novosibirsk-630090, Russian Federation
| | - Evgenii Suslov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Novosibirsk-630090, Russian Federation
| | - Yuliya Demidova
- Boreskov Institute of Catalysis, Siberian Branch of the Russian Academy of Sciences, Novosibirsk-630090, Russian Federation
| | - Dina Korchagina
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Novosibirsk-630090, Russian Federation
| | - Konstantin Volcho
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Novosibirsk-630090, Russian Federation
| | - Alexandra Zakharenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Inna Vasil'eva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Maksim Kupryushkin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Arina Chepanova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | | | - Jóhannes Reynisson
- School of Chemical Sciences, The University of Auckland, Auckland-1142, New Zealand
| | - Nariman Salakhutdinov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Novosibirsk-630090, Russian Federation
| | - Olga Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
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9
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Dyrkheeva N, Luzina O, Filimonov A, Zakharova O, Ilina E, Zakharenko A, Kuprushkin M, Nilov D, Gushchina I, Švedas V, Salakhutdinov N, Lavrik O. Inhibitory Effect of New Semisynthetic Usnic Acid Derivatives on Human Tyrosyl-DNA Phosphodiesterase 1. Planta Med 2019; 85:103-111. [PMID: 30142660 DOI: 10.1055/a-0681-7069] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Usnic acid, a lichen secondary metabolite produced by a whole number of lichens, has attracted the interest of researchers owing to its broad range of biological activity, including antiviral, antibiotic, anticancer properties, and it possessing a certain toxicity. The synthesis of new usnic acid derivatives and the investigation of their biological activity may lead to the discovery of compounds with better pharmacological and toxicity profiles. In this context, a series of new usnic acid derivatives comprising a terpenoid moiety were synthesized, and their ability to inhibit the catalytic activity of the human DNA repair enzyme tyrosyl-DNA phosphodiesterase 1 was investigated. The most potent compounds (15A, 15B, 15G: , and 16A, 16B, 16G: ) had IC50 values in the range of 0.33 - 2.7 µM. The inhibitory properties were mainly dependent on the flexibility and length of the terpenoid moiety, but not strongly dependent on the configuration of the asymmetric centers. The synthesized derivatives showed low cytotoxicity against human cell lines in an MTT assay. They could be used as a basis for the development of more effective anticancer therapies when combined with topoisomerase 1 inhibitors.
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Affiliation(s)
- Nadezhda Dyrkheeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Olga Luzina
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Aleksandr Filimonov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
- Novosibirsk State University, Novosibirsk, Russian Federation
| | - Olga Zakharova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Ekaterina Ilina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Alexandra Zakharenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Maxim Kuprushkin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Dmitry Nilov
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Moscow, Russian Federation
| | - Irina Gushchina
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, Russian Federation
| | - Vytas Švedas
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Moscow, Russian Federation
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, Russian Federation
| | - Nariman Salakhutdinov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
- Novosibirsk State University, Novosibirsk, Russian Federation
| | - Olga Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
- Novosibirsk State University, Novosibirsk, Russian Federation
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10
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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11
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Zakharenko A, Luzina O, Koval O, Nilov D, Gushchina I, Dyrkheeva N, Švedas V, Salakhutdinov N, Lavrik O. Tyrosyl-DNA Phosphodiesterase 1 Inhibitors: Usnic Acid Enamines Enhance the Cytotoxic Effect of Camptothecin. J Nat Prod 2016; 79:2961-2967. [PMID: 27933897 DOI: 10.1021/acs.jnatprod.6b00979] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Tyrosyl-DNA phosphodiesterase 1 (TDP1) is a repair enzyme for stalled DNA-topoisomerase 1 (Top1) cleavage complexes and other 3'-end DNA lesions. TDP1 is a perspective target for anticancer therapy based on Top1-poison-mediated DNA damage. Several novel usnic acid derivatives with an enamine moiety have been synthesized and tested as inhibitors of TDP1. The enamines of usnic acid showed IC50 values in the range of 0.16 to 2.0 μM. These compounds revealed moderate cytotoxicity against human tumor MCF-7 cells. These new compounds enhanced the cytotoxicity of the established Top1 poison camptothecin by an order of magnitude.
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Affiliation(s)
- Alexandra Zakharenko
- 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
| | - Olga Koval
- 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
| | | | | | - Nadezhda Dyrkheeva
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences , Novosibirsk, 630090, Russian Federation
| | | | - Nariman Salakhutdinov
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences , Novosibirsk, 630090, Russian Federation
- Novosibirsk State University , Novosibirsk, 630090, Russian Federation
| | - 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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Khomenko T, Zakharenko A, Odarchenko T, Arabshahi HJ, Sannikova V, Zakharova O, Korchagina D, Reynisson J, Volcho K, Salakhutdinov N, Lavrik O. New inhibitors of tyrosyl-DNA phosphodiesterase I (Tdp 1) combining 7-hydroxycoumarin and monoterpenoid moieties. Bioorg Med Chem 2016; 24:5573-5581. [PMID: 27658793 DOI: 10.1016/j.bmc.2016.09.016] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 07/31/2016] [Accepted: 09/08/2016] [Indexed: 11/27/2022]
Abstract
A number of derivatives of 7-hydroxycoumarins containing aromatic or monoterpene substituents at hydroxy-group were synthesized based on a hit compound from a virtual screen. The ability of these compounds to inhibit tyrosyl-DNA phosphodiesterase I (Tdp 1), important target for anti-cancer therapy, was studied for the first time. It was found that the 7-hydroxycoumarin derivatives with monoterpene pinene moiety are effective inhibitors of Tdp 1 with the most active derivative (+)-25c with IC50 value of 0.675μM. This compound has low cytotoxicity (CC50>100μM) when tested against human cancer cells which is crucial for presupposed application in combination with clinically established anticancer drugs. The ability of the new compounds to enhance the cytotoxicity of camptothecin, an established topoisomerase 1 poison, was demonstrated.
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Affiliation(s)
- 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
| | - 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 Odarchenko
- 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
| | | | - Victoriya Sannikova
- 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
| | - 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
| | | | - 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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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: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Zakharenko A, Sokolov D, Luzina O, Sukhanova M, Khodyreva S, Zakharova O, Salakhutdinov N, Lavrik O. Influence of usnic acid and its derivatives on the activity of mammalian poly(ADP-ribose)polymerase 1 and DNA polymerase β. Med Chem 2012; 8:883-93. [PMID: 22741606 DOI: 10.2174/157340612802084225] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 04/17/2012] [Accepted: 04/26/2012] [Indexed: 11/22/2022]
Abstract
The influence of a number of usnic acid derivatives on auto(polyADP-ribosyl)ation catalyzed by PARP1 and DNA synthesis catalyzed by DNA polymerase β was studied. The derivatives of usnic acid containing aromatic substituents were shown to be moderate inhibitors of PARP1. The presence of both usnic acid tricyclic structure and aromatic substituent at any position of the molecule is a key factor for the inhibitory action. In the case of DNA polymerase β, no relationship between the structure and inhibitory properties has been found with the only exception. Derivatives with modified ring A showed mild activation of DNA synthesis catalyzed by DNA polymerase β.
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Affiliation(s)
- Alexandra Zakharenko
- Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospect Lavrentieva 8, Novosibirsk, 630090, Russia
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