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Matić J, Piotrowski P, Vrban L, Kobetić R, Vianello R, Jurić I, Fabijanić I, Pernar Kovač M, Brozovic A, Piantanida I, Schmuck C, Radić Stojković M. Distinctive Nucleic Acid Recognition by Lysine-Embedded Phenanthridine Peptides. Int J Mol Sci 2024; 25:4866. [PMID: 38732083 PMCID: PMC11084427 DOI: 10.3390/ijms25094866] [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: 03/28/2024] [Revised: 04/25/2024] [Accepted: 04/27/2024] [Indexed: 05/13/2024] Open
Abstract
Three new phenanthridine peptide derivatives (19, 22, and 23) were synthesized to explore their potential as spectrophotometric probes for DNA and RNA. UV/Vis and circular dichroism (CD) spectra, mass spectroscopy, and computational analysis confirmed the presence of intramolecular interactions in all three compounds. Computational analysis revealed that compounds alternate between bent and open conformations, highlighting the latter's crucial influence on successful polynucleotide recognition. Substituting one glycine with lysine in two regioisomers (22, 23) resulted in stronger binding interactions with DNA and RNA than for a compound containing two glycines (19), thus emphasizing the importance of lysine. The regioisomer with lysine closer to the phenanthridine ring (23) exhibited a dual and selective fluorimetric response with non-alternating AT and ATT polynucleotides and induction of triplex formation from the AT duplex. The best binding constant (K) with a value of 2.5 × 107 M-1 was obtained for the interaction with AT and ATT polynucleotides. Furthermore, apart from distinguishing between different types of ds-DNA and ds-RNA, the same compound could recognize GC-rich DNA through distinct induced CD signals.
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Affiliation(s)
- Josipa Matić
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (J.M.); (R.K.); (I.J.); (I.F.); (I.P.)
| | - Patryciusz Piotrowski
- Institute for Organic Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany; (P.P.)
| | - Lucija Vrban
- Laboratory for the Computational Design and Synthesis of Functional Materials, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (L.V.); (R.V.)
| | - Renata Kobetić
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (J.M.); (R.K.); (I.J.); (I.F.); (I.P.)
| | - Robert Vianello
- Laboratory for the Computational Design and Synthesis of Functional Materials, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (L.V.); (R.V.)
| | - Ivona Jurić
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (J.M.); (R.K.); (I.J.); (I.F.); (I.P.)
| | - Ivana Fabijanić
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (J.M.); (R.K.); (I.J.); (I.F.); (I.P.)
| | - Margareta Pernar Kovač
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (M.P.K.); (A.B.)
| | - Anamaria Brozovic
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (M.P.K.); (A.B.)
| | - Ivo Piantanida
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (J.M.); (R.K.); (I.J.); (I.F.); (I.P.)
| | - Carsten Schmuck
- Institute for Organic Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany; (P.P.)
| | - Marijana Radić Stojković
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (J.M.); (R.K.); (I.J.); (I.F.); (I.P.)
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Zafar MN, Butt AM, Chaudhry GES, Perveen F, Nazar MF, Masood S, Dalebrook AF, Mughal EU, Sumrra SH, Sung YY, Muhammad TST, Wright LJ. Pd(II) complexes with chelating N-(1-alkylpyridin-4(1H)-ylidene)amide (PYA) ligands: Synthesis, characterization and evaluation of anticancer activity. J Inorg Biochem 2021; 224:111590. [PMID: 34507110 DOI: 10.1016/j.jinorgbio.2021.111590] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 08/17/2021] [Accepted: 08/18/2021] [Indexed: 01/12/2023]
Abstract
The bidentate N-(1-Alkylpyridin-4(1H)-ylidene)amide (PYA) pro-ligands [H2LBn][Cl]2 (2), and [H2LMe][TfO]2 (3) were prepared by simple alkylation reactions of the known compound, N,N-di(pyridin-4-yl)oxalamide (H2L, 1). The Pd(II) complexes, [Pd(LBn)2][Cl]2 (4), [Pd(LMe)2][Cl][TfO] (5), Pd(LBn)Cl2 (6) and Pd(LMe)Cl2 (7) were synthesized through reactions between these pro-ligands and suitable Pd(II) substrates in the presence of base. The molecular structures of 3 and 6 were obtained by single crystal X-ray structure determinations. Studies of the experimental and computational DNA binding interactions of the compounds 1-7 revealed that overall 4 and 6 have the largest values for the binding parameters Kb and ΔGbo. The results showed a good correlation with the steric and electronic parameters obtained by quantitative structure activity relationship (QSAR) studies. In-vitro cytotoxicity studies against four different cell lines showed that the human breast cancer cell lines MCF-7, T47D and cervical cancer cell line HeLa had either higher or similar sensitivities towards 4, 6 and 2, respectively, compared to cisplatin. In general, the cytotoxicity of the compounds, represented by IC50 values, decreased in the order 4 > 6 > 2 > 5 > 3 > 1 > 7 in cancer cell lines. Apoptosis contributed significantly to the cytotoxic effects of these anticancer agents as evaluated by apoptosis studies.
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Affiliation(s)
| | - Abdul Mannan Butt
- Department of Chemistry, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Gul-E-Saba Chaudhry
- Institute of Marine Biotechnology, Universiti Malaysia, Terengganu 21030, Malaysia
| | - Fouzia Perveen
- RCMS, National University of Science and Technology, Islamabad 44000, Pakistan
| | - Muhammad Faizan Nazar
- Division of Science and Technology, Department of Chemistry, University of Education Lahore, Multan Campus 60700, Pakistan
| | - Sara Masood
- Department of Chemistry, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | | | | | | | - Yeong Yik Sung
- Institute of Marine Biotechnology, Universiti Malaysia, Terengganu 21030, Malaysia
| | | | - Leonard James Wright
- School of Chemical Sciences, University of Auckland, Auckland 1010, New Zealand.
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Zubair M, Sirajuddin M, Ullah K, Haider A, Perveen F, Hussain I, Ali S, Tahir MN. Synthesis, structural peculiarities, theoretical study and biological evaluation of newly designed O-Vanillin based azomethines. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127574] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Qamar S, Akhter Z, Yousuf S, Bano H, Perveen F. Synthesis, structural characterization, DNA binding and antioxidant studies of 4,4′-Nitrophenoxyaniline derived azo dyes. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.07.069] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Munir N, Masood S, Liaqat F, Tahir MN, Yousuf S, Kalsoom S, Mughal EU, Sumrra SH, Maalik A, Zafar MN. Synthesis of new Pro-PYE ligands as co-catalysts toward Pd-catalyzed Heck-Mizoroki cross coupling reactions. RSC Adv 2019; 9:37986-38000. [PMID: 35541803 PMCID: PMC9075740 DOI: 10.1039/c9ra07912b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 11/07/2019] [Indexed: 11/25/2022] Open
Abstract
The present research work describes the synthesis of five new ligands containing pyridinium amine, [H2L1][OTf]2-[H2L5][I]2 from two new precursors, [P3 Et][I] and [P2 Me][CF3SO3]. The structure elucidations of the compounds were confirmed by multinuclear NMR (1H, 13C), FT-IR and by single crystal XRD techniques. Theoretical DFT studies were carried out to get better insight into the electronic levels and structural features of all the molecules. These synthesized new Pro-PYE ligands [H2L1][OTf]2-[H2L5][I]2 were found to be significantly active as co-catalysts for Pd(CH3CO2)2 toward Heck-Mizoroki coupling reactions with wide substrate scope in the order of [H2L1][OTf]2 ≫ [H2L2][OTf]2 > [H2L3][OTf]2 > [H2L4][OTf]2 > [H2L5][I]2.
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Affiliation(s)
- Naima Munir
- Department of Chemistry, Quaid-i-Azam University Islamabad-45320 Pakistan +923314503061
| | - Sara Masood
- Department of Chemistry, Quaid-i-Azam University Islamabad-45320 Pakistan +923314503061
| | - Faroha Liaqat
- Department of Chemistry, Quaid-i-Azam University Islamabad-45320 Pakistan +923314503061
| | | | - Sammer Yousuf
- H. E. J. Research Institute of Chemistry, International Centre for Chemical and Biological Sciences, University of Karachi 75270 Pakistan
| | - Saima Kalsoom
- Centre for Interdisciplinary Research in Basic Sciences (CIRBS), International Islamic University Islamabad Pakistan
| | | | | | - Aneela Maalik
- Department of Chemistry, COMSATS University Islamabad, Islamabad Campus Park Road Islamabad-45550 Pakistan +923335490834
| | - Muhammad Naveed Zafar
- Department of Chemistry, Quaid-i-Azam University Islamabad-45320 Pakistan +923314503061
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Zafar MN, Masood S, Chaudhry GES, Muhammad TST, Dalebrook AF, Nazar MF, Malik FP, Mughal EU, Wright LJ. Synthesis, characterization and anti-cancer properties of water-soluble bis(PYE) pro-ligands and derived palladium(ii) complexes. Dalton Trans 2019; 48:15408-15418. [PMID: 31393494 DOI: 10.1039/c9dt01923e] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The two cationic palladium(ii) complexes, [Pd(Len)2][OTf]2 (4) and [Pd(Lphen)2][OTf]2 (5), were synthesized by treatment of bis(benzonitrile)dichloropalladium(ii) with [H2Len][OTf]2 (2) or [H2Lphen][OTf]2 (3), respectively, in the presence of a weak base. The pro-ligands 2 and 3 were synthesized by melt reactions between N-methyl-4-chloropyridinium triflate (1) and the amines ethylenediamine or phenylenediamine, respectively. The water-soluble compounds 2-5 were fully characterized, including by single-crystal X-ray crystal structure determinations for 2-4. UV-Vis and fluorescence spectroscopy were used to study the binding interactions of 2-5 with CT-DNA. The spectroscopic data suggested the presence of intercalative and groove binding modes and this was supported by molecular docking studies. The in vitro cytotoxicity studies (IC50 values) showed that the human breast cancer cell lines MCF-7 and T47D were more sensitive towards 3, 4 and 5 than cisplatin. The cytotoxicity of the new compounds decreased in the order 5 > 4 > 3 > 2. Furthermore, the annexin V-FITC staining method strongly suggested the presence of phosphatidylserine (PS) on the outer membrane of the treated cells, which is a hallmark of apoptosis.
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