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Krochtová K, Janovec L, Bogárová V, Halečková A, Kožurková M. Interaction of 3,9-disubstituted acridine with single stranded poly(rA), double stranded poly(rAU) and triple stranded poly(rUAU): molecular docking - A spectroscopic tandem study. Chem Biol Interact 2024; 394:110965. [PMID: 38552767 DOI: 10.1016/j.cbi.2024.110965] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/12/2024] [Accepted: 03/16/2024] [Indexed: 04/10/2024]
Abstract
RNA plays an important role in many biological processes which are crucial for cell survival, and it has been suggested that it may be possible to inhibit individual processes involved in many diseases by targeting specific sequences of RNA. The aim of this work is to determine the affinity of novel 3,9-disubstited acridine derivative 1 with three different RNA molecules, namely single stranded poly(rA), double stranded homopolymer poly(rAU) and triple stranded poly(rUAU). The results of the absorption titration assays show that the binding constant of the novel derivative to the RNA molecules was in the range of 1.7-6.2 × 104 mol dm-3. The fluorescence and circular dichroism titration assays revealed considerable changes. The most significant results in terms of interpreting the nature of the interactions were the melting temperatures of the RNA samples in complexes with the 1. In the case of poly(rA), denaturation resulted in a self-structure formation; increased stabilization was observed for poly(rAU), while the melting points of the ligand-poly(rUAU) complex showed significant destabilization as a result of the interaction. The principles of molecular mechanics were applied to propose the non-bonded interactions within the binding complex, pentariboadenylic acid and acridine ligand as the study model. Initial molecular docking provided the input structure for advanced simulation techniques. Molecular dynamics simulation and cluster analysis reveal π - π stacking and the hydrogen bonds formation as the main forces that can stabilize the binding complex. Subsequent MM-GBSA calculations showed negative binding enthalpy accompanied the complex formation and proposed the most preferred conformation of the interaction complex.
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Affiliation(s)
- Kristína Krochtová
- Department of Biochemistry, Institute of Chemistry, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 041 54, Košice, Slovak Republic
| | - Ladislav Janovec
- Department of Organic Chemistry, Institute of Chemistry, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 041 54, Košice, Slovak Republic
| | - Viktória Bogárová
- Department of Biochemistry, Institute of Chemistry, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 041 54, Košice, Slovak Republic
| | - Annamária Halečková
- Department of Organic Chemistry, Institute of Chemistry, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 041 54, Košice, Slovak Republic
| | - Mária Kožurková
- Department of Biochemistry, Institute of Chemistry, Faculty of Science, Pavol Jozef Šafárik University in Košice, Šrobárova 2, 041 54, Košice, Slovak Republic.
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Hudáková T, Šemeláková M, Očenáš P, Kožurková M, Krochtová K, Sovová S, Tóthová Z, Guľášová Z, Popelka P, Solár P. Chili pepper extracts, capsaicin, and dihydrocapsaicin as potential anticancer agents targeting topoisomerases. BMC Complement Med Ther 2024; 24:96. [PMID: 38383414 PMCID: PMC10880293 DOI: 10.1186/s12906-024-04394-5] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 02/07/2024] [Indexed: 02/23/2024] Open
Abstract
DNA topoisomerases regulate conformational changes in DNA topology during normal cell growth, such as replication, transcription, recombination, and repair, and may be targeted for anticancer drugs. A DNA topology assay was used to investigate DNA-damaging/protective activities of extracts from Habanero Red (HR), Habanero Maya Red (HMR), Trinidad Moruga Scorpion (TMS), Jalapeno (J), Serrano pepper (SP), Habanero Red Savina (HRS), Bhut Jolokia (BJ), and Jamaica Rosso (JR) peppers, demonstrating their inhibitory effect on the relaxation of pBR by Topo I. DNA topoisomerase II (Topo II) is proven therapeutic target of anticancer drugs. Complete inhibition of Topo II was observed for samples TMS, HR, and HMR. Extracts J and SP had the lowest capsaicin and dihydrocapsaicin content compared to other peppers. HR, HMR, TMS, J, S, HRS, BJ, JR extracts showed the anticancer effect, examined by MTS and xCell assay on the in vitro culture of human colon carcinoma cell line HCT116.
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Affiliation(s)
- Terézia Hudáková
- Department of Medical Biology, Faculty of Medicine, Pavol Jozef Šafárik University in Košice, Trieda SNP 1, 040 11, Košice, Slovakia
| | - Martina Šemeláková
- Department of Medical Biology, Faculty of Medicine, Pavol Jozef Šafárik University in Košice, Trieda SNP 1, 040 11, Košice, Slovakia
| | - Peter Očenáš
- Department of Chemistry, Biochemistry and Biophysics, University of Veterinary Medicine and Pharmacy in Košice, Komenského 73, 041 81, Košice, Slovakia
| | - Mária Kožurková
- Department of Biochemistry, Faculty of Science, Pavol Jozef Šafárik University in Košice, Moyzesova 11, 040 01, Košice, Slovakia
| | - Kristína Krochtová
- Department of Biochemistry, Faculty of Science, Pavol Jozef Šafárik University in Košice, Moyzesova 11, 040 01, Košice, Slovakia
| | - Simona Sovová
- Department of Biochemistry, Faculty of Science, Pavol Jozef Šafárik University in Košice, Moyzesova 11, 040 01, Košice, Slovakia
| | - Zuzana Tóthová
- Department of Medical Biology, Faculty of Medicine, Pavol Jozef Šafárik University in Košice, Trieda SNP 1, 040 11, Košice, Slovakia
| | - Zuzana Guľášová
- Center of Clinical and Preclinical Research MEDIPARK, Faculty of Medicine, Pavol Jozef Šafárik University in Košice, Trieda SNP 1, 040 11, Košice, Slovakia
| | - Peter Popelka
- Department of Food Hygiene, Technology and Safety, University of Veterinary Medicine and Pharmacy in Košice, Komenského 73, 041 81, Košice, Slovakia
| | - Peter Solár
- Department of Medical Biology, Faculty of Medicine, Pavol Jozef Šafárik University in Košice, Trieda SNP 1, 040 11, Košice, Slovakia.
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Krochtová K, Halečková A, Janovec L, Blizniaková M, Kušnírová K, Kožurková M. Novel 3,9-Disubstituted Acridines with Strong Inhibition Activity against Topoisomerase I: Synthesis, Biological Evaluation and Molecular Docking Study. Molecules 2023; 28:1308. [PMID: 36770975 PMCID: PMC9921529 DOI: 10.3390/molecules28031308] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023] Open
Abstract
A series of novel 3,9-disubstituted acridines were synthesized and their biological potential was investigated. The synthetic plan consists of eight reaction steps, which produce the final products, derivatives 17a-17j, in a moderate yield. The principles of cheminformatics and computational chemistry were applied in order to study the relationship between the physicochemical properties of the 3,9-disubstituted acridines and their biological activity at a cellular and molecular level. The selected 3,9-disubstituted acridine derivatives were studied in the presence of DNA using spectroscopic (UV-Vis, circular dichroism, and thermal denaturation) and electrophoretic (nuclease activity, relaxation and unwinding assays for topoisomerase I and decatenation assay for topoisomerase IIα) methods. Binding constants (2.81-9.03 × 104 M-1) were calculated for the derivatives from the results of the absorption titration spectra. The derivatives were found to have caused the inhibition of both topoisomerase I and topoisomerase IIα. Molecular docking simulations suggested a different way in which the acridines 17a-17j can interact with topoisomerase I versus topoisomerase IIα. A strong correlation between the lipophilicity of the derivatives and their ability to stabilize the intercalation complex was identified for all of the studied agents. Acridines 17a-17j were also subjected to in vitro screening conducted by the Developmental Therapeutic Program of the National Cancer Institute (NCI) against a panel of 60 cancer cell lines. The strongest biological activity was displayed by aniline acridine 17a (MCF7-GI50 18.6 nM) and N,N-dimethylaniline acridine 17b (SR-GI50 38.0 nM). The relationship between the cytostatic activity of the most active substances (derivatives 17a, 17b, and 17e-17h) and their values of KB, LogP, ΔS°, and δ was also investigated. Due to the fact that a significant correlation was only found in the case of charge density, δ, it is possible to assume that the cytostatic effect might be dependent upon the structural specificity of the acridine derivatives.
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Affiliation(s)
- Kristína Krochtová
- Department of Biochemistry, Faculty of Science, Pavol Jozef Šafárik University in Košice, Moyzesova 11, 040 01 Košice, Slovakia
| | - Annamária Halečková
- Department of Organic Chemistry, Faculty of Science, Pavol Jozef Šafárik University in Košice, Moyzesova 11, 040 01 Košice, Slovakia
| | - Ladislav Janovec
- Department of Organic Chemistry, Faculty of Science, Pavol Jozef Šafárik University in Košice, Moyzesova 11, 040 01 Košice, Slovakia
| | - Michaela Blizniaková
- Department of Biochemistry, Faculty of Science, Pavol Jozef Šafárik University in Košice, Moyzesova 11, 040 01 Košice, Slovakia
| | - Katarína Kušnírová
- Department of Organic Chemistry, Faculty of Science, Pavol Jozef Šafárik University in Košice, Moyzesova 11, 040 01 Košice, Slovakia
| | - Mária Kožurková
- Department of Biochemistry, Faculty of Science, Pavol Jozef Šafárik University in Košice, Moyzesova 11, 040 01 Košice, Slovakia
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Budovská M, Krochtová K, Michalková R, Mojžiš J. Aminoanalogues of isobrassinin, erucalexin and isocyclobrassinin: Synthesis and evaluation of the antiproliferative and cytotoxic properties. Tetrahedron 2022. [DOI: 10.1016/j.tet.2022.132898] [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: 11/28/2022]
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Budovská M, Krochtová K, Kuba M, Tischlerová V, Mojžiš J. Synthesis and cytotoxicity evaluation of novel 5-fluorinated indoles. J Fluor Chem 2021. [DOI: 10.1016/j.jfluchem.2021.109879] [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]
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