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Shereef HA, Moemen YS, Elshami FI, El-Nahas AM, Shaban SY, van Eldik R. DNA Binding and Cleavage, Stopped-Flow Kinetic, Mechanistic, and Molecular Docking Studies of Cationic Ruthenium(II) Nitrosyl Complexes Containing “NS4” Core. Molecules 2023; 28:molecules28073028. [PMID: 37049792 PMCID: PMC10095794 DOI: 10.3390/molecules28073028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/24/2023] [Accepted: 03/24/2023] [Indexed: 03/31/2023] Open
Abstract
This work aimed to evaluate in vitro DNA binding mechanistically of cationic nitrosyl ruthenium complex [RuNOTSP]+ and its ligand (TSPH2) in detail, correlate the findings with cleavage activity, and draw conclusions about the impact of the metal center. Theoretical studies were performed for [RuNOTSP]+, TSPH2, and its anion TSP−2 using DFT/B3LYP theory to calculate optimized energy, binding energy, and chemical reactivity. Since nearly all medications function by attaching to a particular protein or DNA, the in vitro calf thymus DNA (ctDNA) binding studies of [RuNOTSP]+ and TSPH2 with ctDNA were examined mechanistically using a variety of biophysical techniques. Fluorescence experiments showed that both compounds effectively bind to ctDNA through intercalative/electrostatic interactions via the DNA helix’s phosphate backbone. The intrinsic binding constants (Kb), (2.4 ± 0.2) × 105 M−1 ([RuNOTSP]+) and (1.9 ± 0.3) × 105 M−1 (TSPH2), as well as the enhancement dynamic constants (KD), (3.3 ± 0.3) × 104 M−1 ([RuNOTSP]+) and (2.6 ± 0.2) × 104 M−1 (TSPH2), reveal that [RuNOTSP]+ has a greater binding propensity for DNA compared to TSPH2. Stopped-flow investigations showed that both [RuNOTSP]+ and TSPH2 bind through two reversible steps: a fast second-order binding, followed by a slow first-order isomerization reaction via a static quenching mechanism. For the first and second steps of [RuNOTSP]+ and TSPH2, the detailed binding parameters were established. The total binding constants for [RuNOTSP]+ (Ka = 43.7 M−1, Kd = 2.3 × 10−2 M−1, ΔG0 = −36.6 kJ mol−1) and TSPH2 (Ka = 15.1 M−1, Kd = 66 × 10−2 M, ΔG0 = −19 kJ mol−1) revealed that the relative reactivity is approximately ([RuNOTSP]+)/(TSPH2) = 3/1. The significantly negative ΔG0 values are consistent with a spontaneous binding reaction to both [RuNOTSP]+ and TSPH2, with the former being very favorable. The findings showed that the Ru(II) center had an effect on the reaction rate but not on the mechanism and that the cationic [RuNOTSP]+ was a more highly effective DNA binder than the ligand TSPH2 via strong electrostatic interaction with the phosphate end of DNA. Because of its higher DNA binding affinity, cationic [RuNOTSP]+ demonstrated higher cleavage efficiency towards the minor groove of pBR322 DNA via the hydrolytic pathway than TSPH2, revealing the synergy effect of TSPH2 in the form of the complex. Furthermore, the mode of interaction of both compounds with ctDNA has also been supported by molecular docking.
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Affiliation(s)
- Hadeer A. Shereef
- Chemistry Department, Faculty of Science, Menoufia University, Shebin El-Kom 32512, Egypt
- Clinical Pathology Department, University Hospital, Menoufia University, Shebin El-Kom 32512, Egypt
| | - Yasmine S. Moemen
- Clinical Pathology Department, National Liver Institute, Menoufia University, Shebin El-Kom 32512, Egypt
| | - Fawzia I. Elshami
- Chemistry Department, Faculty of Science, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
| | - Ahmed M. El-Nahas
- Chemistry Department, Faculty of Science, Menoufia University, Shebin El-Kom 32512, Egypt
| | - Shaban Y. Shaban
- Chemistry Department, Faculty of Science, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
- Correspondence: (S.Y.S.); (R.v.E.)
| | - Rudi van Eldik
- Department of Chemistry and Pharmacy, University of Erlangen-Nuremberg, 91058 Erlangen, Germany
- Faculty of Chemistry, Nicolaus Copernicus University in Torun, 87-100 Torun, Poland
- Correspondence: (S.Y.S.); (R.v.E.)
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Inci D, Aydin R, Zorlu Y. Affinity of a new copper(II) complex to DNA/BSA and antioxidant/radical scavenging activities: crystal structure of [Cu(4,7-diphenyl-1,10-phenanthroline)(leucine)(NO3)(H2O)]. J COORD CHEM 2016. [DOI: 10.1080/00958972.2016.1213390] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Duygu Inci
- Faculty of Arts and Sciences, Department of Chemistry, Uludag University, Bursa, Turkey
| | - Rahmiye Aydin
- Faculty of Arts and Sciences, Department of Chemistry, Uludag University, Bursa, Turkey
| | - Yunus Zorlu
- Department of Chemistry, Gebze Technical University, Gebze, Turkey
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Shahabadi N, Fatahi A. Multispectroscopic DNA-binding studies of a tris-chelate nickel(II) complex containing 4,7-diphenyl 1,10-phenanthroline ligands. J Mol Struct 2010. [DOI: 10.1016/j.molstruc.2010.02.048] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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