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Bocian W, Naumczuk B, Urbanowicz M, Sitkowski J, Bednarek E, Wiktorska K, Pogorzelska A, Wielgus E, Kozerski L. Insight on the Interaction between the Camptothecin Derivative and DNA Oligomer Mimicking the Target of Topo I Inhibitors. Molecules 2022; 27:molecules27206946. [PMID: 36296539 PMCID: PMC9612166 DOI: 10.3390/molecules27206946] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 11/23/2022] Open
Abstract
The understanding of the mechanism of Topo I inhibition by organic ligands is a crucial source of information that has led to the design of more effective and safe pharmaceuticals in oncological chemotherapy. The vast number of inhibitors that have been studied in this respect over the last decades have enabled the creation of a concept of an ‘interfacial inhibitor’, thereby describing the machinery of Topo I inhibition. The central module of action of this machinery is the interface of a Topo I/DNA/inhibitor ternary complex. Most of the ‘interfacial inhibitors’ are primarily kinetic inhibitors that form molecular complexes with an “on–off” rate timing; therefore, all of the contacts between the inhibitor and both the enzyme and the DNA are essential to keep the complex stable and reduce the “off rate”. To test this hypothesis, we designed the compound using a C-9-(N-(2′-hydroxyethyl)amino)methyl substituent in an SN38 core, with a view that a flexible substituent may bind inside the nick of a model of the DNA and stabilize the complex, leading to a reduction in the “off rate” of a ligand in a potential ternary complex in vivo. Using docking analysis and molecular dynamics, free energy calculations on the level of the MM-PBSA and MM-GBSA model, here we presented the in silico-calculated structure of a ternary complex involving the studied compound 1. This confirmed our suggestion that compound 1 is situated in a groove of the nicked DNA model in a few conformations. The number of hydrogen bonds between the components of a ternary complex was established, which strengthens the complex and supports our view. The docking analysis and free energy calculations for the receptor structures which were obtained in the MD simulations of the ternary complex 1/DNA/Topo I show that the binding constant is stronger than it was for similar complexes with TPT, CPT, and SN38, which are commonly considered as strong Topo I inhibitors. The binary complex structure 1/DNA was calculated and compared with the experimental results of a complex that was in a solution. The analysis of the cross-peaks in NOESY spectra allowed us to assign the dipolar interactions between the given protons in the calculated structures. A DOSY experiment in the solution confirmed the strong binding of a ligand in a binary complex, having a Ka of 746 mM−1, which was compared with a Ka of 3.78 mM−1 for TPT. The MALDI-ToF MS showed the presence of the biohybrid, thus evidencing the occurrence of DNA alkylation by compound 1. Because of it having a strong molecular complex, alkylation is the most efficient way to reduce the “on–off” timing as it acts as a tool that causes the cog to brake in a working gear, and this is this activity we want to highlight in our contribution. Finally, the Topo I inhibition test showed a lower IC50 of the studied compound than it did for CPT and SN38.
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Affiliation(s)
| | - Beata Naumczuk
- National Medicines Institute, 00-725 Warsaw, Poland
- Institute of Organic Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland
- Correspondence: ; Tel.: +48-22-8514371 (ext. 318)
| | | | | | | | | | | | - Ewelina Wielgus
- Centre of Molecular and Macromolecular Studies, Polish Academy of Science, 90-363 Lodz, Poland
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Bocian W, Naumczuk B, Urbanowicz M, Sitkowski J, Bierczyńska-Krzysik A, Bednarek E, Wiktorska K, Milczarek M, Kozerski L. The Mode of SN38 Derivatives Interacting with Nicked DNA Mimics Biological Targeting of Topo I Poisons. Int J Mol Sci 2021; 22:ijms22147471. [PMID: 34299090 PMCID: PMC8303725 DOI: 10.3390/ijms22147471] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/08/2021] [Accepted: 07/08/2021] [Indexed: 11/16/2022] Open
Abstract
The compounds 7-ethyl-9-(N-methylamino)methyl-10-hydroxycamptothecin (2) and 7-ethyl-9-(N-morpholino)methyl-10-hydroxycamptothecin (3) are potential topoisomerase I poisons. Moreover, they were shown to have favorable anti-neoplastic effects on several tumor cell lines. Due to these properties, the compounds are being considered for advancement to the preclinical development stage. To gain better insights into the molecular mechanism with the biological target, here, we conducted an investigation into their interactions with model nicked DNA (1) using different techniques. In this work, we observed the complexity of the mechanism of action of the compounds 2 and 3, in addition to their decomposition products: compound 4 and SN38. Using DOSY experiments, evidence of the formation of strongly bonded molecular complexes of SN38 derivatives with DNA duplexes was provided. The molecular modeling based on cross-peaks from the NOESY spectrum also allowed us to assign the geometry of a molecular complex of DNA with compound 2. Confirmation of the alkylation reaction of both compounds was obtained using MALDI–MS. Additionally, in the case of 3, alkylation was confirmed in the recording of cross-peaks in the 1H/13C HSQC spectrum of 13C-enriched compound 3. In this work, we showed that the studied compounds—parent compounds 2 and 3, and their potential metabolite 4 and SN38—interact inside the nick of 1, either forming the molecular complex or alkylating the DNA nitrogen bases. In order to confirm the influence of the studied compounds on the topoisomerase I relaxation activity of supercoiled DNA, the test was performed based upon the measurement of the fluorescence of DNA stain which can differentiate between supercoiled and relaxed DNA. The presented results confirmed that studied SN38 derivatives effectively block DNA relaxation mediated by Topo I, which means that they stop the machinery of Topo I activity.
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Affiliation(s)
- Wojciech Bocian
- National Medicines Institute, 00-725 Warsaw, Poland; (W.B.); (M.U.); (J.S.); (E.B.); (K.W.); (M.M.); (L.K.)
| | - Beata Naumczuk
- National Medicines Institute, 00-725 Warsaw, Poland; (W.B.); (M.U.); (J.S.); (E.B.); (K.W.); (M.M.); (L.K.)
- Institute of Organic Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland
- Correspondence: ; Tel.: +48-22-8514371 (ext. 318)
| | - Magdalena Urbanowicz
- National Medicines Institute, 00-725 Warsaw, Poland; (W.B.); (M.U.); (J.S.); (E.B.); (K.W.); (M.M.); (L.K.)
| | - Jerzy Sitkowski
- National Medicines Institute, 00-725 Warsaw, Poland; (W.B.); (M.U.); (J.S.); (E.B.); (K.W.); (M.M.); (L.K.)
| | | | - Elżbieta Bednarek
- National Medicines Institute, 00-725 Warsaw, Poland; (W.B.); (M.U.); (J.S.); (E.B.); (K.W.); (M.M.); (L.K.)
| | - Katarzyna Wiktorska
- National Medicines Institute, 00-725 Warsaw, Poland; (W.B.); (M.U.); (J.S.); (E.B.); (K.W.); (M.M.); (L.K.)
| | - Małgorzata Milczarek
- National Medicines Institute, 00-725 Warsaw, Poland; (W.B.); (M.U.); (J.S.); (E.B.); (K.W.); (M.M.); (L.K.)
| | - Lech Kozerski
- National Medicines Institute, 00-725 Warsaw, Poland; (W.B.); (M.U.); (J.S.); (E.B.); (K.W.); (M.M.); (L.K.)
- Institute of Organic Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland
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Naumczuk B, Sitkowski J, Bocian W, Stolarska M, Bednarek E, Kozerski L. A NMR study of binding the metabolite of SN38 derivatives to a model nicked DNA decamer mimicking target of Topo I inhibitors. Bioorg Chem 2021; 107:104631. [PMID: 33476866 DOI: 10.1016/j.bioorg.2021.104631] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 12/10/2020] [Accepted: 01/03/2021] [Indexed: 02/07/2023]
Abstract
In this account we present NMR based results of the interaction of 7-ethyl-9-hydroxymethyl-10-hydroxycamptothecin (1), a derivative of SN38, with a model nicked DNA decamer mimicking the wild type DNA target of Topoisomerase I inhibitors from the camptothecin family. The title compound 1 can be considered a main metabolite of phase I in the metabolic pathway of camptothecin derivatives bearing the alkylamino substituent. Therefore, its pharmacodynamic properties are of interest. It was established by DOSY (Diffusion Ordered Spectroscopy) that compound 1 forms a fairly stable molecular complex with a model nicked DNA decamer with affinity constant Ka 3.02 mM-1. The analysis of NOESY experiments revealed intermolecular cross peaks and mutual induced shifts on both interacting components allowing the conclusion that guest molecule 1 is stacking the nitrogen bases inside the nick. MD (Molecular Dynamics) analysis of four possible inclusions of 1 inside the nick allows establishing the detailed geometry of a complex. Two conformations are suggested as the ones best representing the results of molecular modeling reconciled with experimental NOESY results. The aromatic core of both structures is stacking the nitrogen bases in a nick facing the unbroken strand with ring A. The protons in ring E interact with ribose protons of edge bases of a nick. In conclusion, it can be asserted that SN38 derivative 1 can effectively bind the molecular target of Topo I enzyme and play a role as a Topo I inhibitor.
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Affiliation(s)
- Beata Naumczuk
- National Medicines Institute, Warsaw, Poland; Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland.
| | - Jerzy Sitkowski
- National Medicines Institute, Warsaw, Poland; Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | | | | | | | - Lech Kozerski
- National Medicines Institute, Warsaw, Poland; Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
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Naumczuk B, Bocian W, Sitkowski J, Kawęcki R, Kozerski L. Solvent-dependent regioselectivity of 2′-deoxyadenosine alkylation by 9-aminomethyl derivatives of SN38. NEW J CHEM 2019. [DOI: 10.1039/c9nj04828f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The investigated compounds in DMSO solution unexpectedly alkylate the N9 nitrogen of 2′-deoxyadenosine, whereas the N6 nitrogen atom is alkylated in water solution.
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Affiliation(s)
- B. Naumczuk
- National Medicines Institute
- Chełmska 30/34
- Poland
- Institute of Organic Chemistry
- Polish Academy of Sciences
| | - W. Bocian
- National Medicines Institute
- Chełmska 30/34
- Poland
| | - J. Sitkowski
- National Medicines Institute
- Chełmska 30/34
- Poland
- Institute of Organic Chemistry
- Polish Academy of Sciences
| | - R. Kawęcki
- University of Natural Sciences and Humanities
- Faculty of Science
- 3 Maja 54
- Poland
| | - L. Kozerski
- National Medicines Institute
- Chełmska 30/34
- Poland
- Institute of Organic Chemistry
- Polish Academy of Sciences
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Naumczuk B, Kawęcki R, Bocian W, Bednarek E, Sitkowski J, Kozerski L. Regioselective alkylation reaction of the 2′-deoxyctidine with 9-aminomethyl derivatives of SN38. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2018.08.096] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Abstract
DNA-damaging agents, such as methylating agents, chloroethylating agents and platinum-based agents, have been extensively used as anticancer drugs. However, the side effects, high toxicity, lack of selectivity and resistance severely limit their clinical applications. In recent years, a strategy combining a DNA-damaging agent with a bioactive molecule (e.g., enzyme inhibitors) or carrier (e.g., steroid hormone and DNA intercalators) to produce a new 'combi-molecule' with improved efficacy or selectivity has been attempted to overcome these drawbacks. The combi-molecule simultaneously acts on two targets and is expected to possess better potency than the parent compounds. Many studies have shown DNA-damaging combi-molecules exhibiting excellent anticancer activity in vitro and in vivo. This review focuses on the development of combi-molecules, which possess increased DNA-damaging potency, anticancer efficacy and tumor selectivity and reduced side reactions than the parent compounds. The future opportunities and challenges in the discovery of combi-molecules were also discussed.
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Naumczuk B, Kawęcki R, Bocian W, Bednarek E, Sitkowski J, Kozerski L. Preliminary study of mechanism of action of SN38 derivatives. Physicochemical data, evidence of interaction and alkylation of DNA octamer d(GCGATCGC) 2. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:128-136. [PMID: 27575369 DOI: 10.1002/mrc.4508] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 08/17/2016] [Accepted: 08/26/2016] [Indexed: 06/06/2023]
Abstract
The synthesis of water-soluble SN38 derivatives is presented, and their stability in solutions used during drug development studies has been investigated. A preliminary study of mechanism of action of 9-aminomethyl SN38 is presented. Using NMR techniques, the interaction of the oligomer d(GCGATCGC)2 is studied, showing that the terminal GC base pairs are the main site of interaction. Using pulsed field gradient spin echo and mass spectroscopy, evidence of a spontaneous alkylation reaction of the DNA oligomer with SN38 derivatives is presented. A proposed mechanism of reaction is suggested. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Beata Naumczuk
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Robert Kawęcki
- University of Natural Sciences and Humanities, Siedlce, Poland
| | - Wojciech Bocian
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
- National Medicines Institute, Warsaw, Poland
| | | | - Jerzy Sitkowski
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
- National Medicines Institute, Warsaw, Poland
| | - Lech Kozerski
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
- National Medicines Institute, Warsaw, Poland
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Naumczuk B, Wiktorska K, Lubelska K, Kawęcki R, Bocian W, Bednarek E, Sitkowski J, Chilmonczyk Z, Kozerski L. New generation of camptothecin derivatives spontaneously alkylating DNA. NEW J CHEM 2016. [DOI: 10.1039/c6nj01217e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The IC50 values of new derivatives 2(a–e) for blood and lung cancer cells are comparable to SN38, and a few orders of magnitude higher than for irinotecan.
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Affiliation(s)
- Beata Naumczuk
- Institute of Organic Chemistry
- Polish Academy of Sciences
- Kasprzaka 44
- Poland
| | | | | | | | - Wojciech Bocian
- Institute of Organic Chemistry
- Polish Academy of Sciences
- Kasprzaka 44
- Poland
- National Medicines Institute
| | | | - Jerzy Sitkowski
- Institute of Organic Chemistry
- Polish Academy of Sciences
- Kasprzaka 44
- Poland
- National Medicines Institute
| | | | - Lech Kozerski
- Institute of Organic Chemistry
- Polish Academy of Sciences
- Kasprzaka 44
- Poland
- National Medicines Institute
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