1
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Głuszyńska A, Kosman J, Chuah SS, Hoffmann M, Haider S. Carbazole Derivatives Binding to Bcl-2 Promoter Sequence G-quadruplex. Pharmaceuticals (Basel) 2024; 17:912. [PMID: 39065762 PMCID: PMC11279778 DOI: 10.3390/ph17070912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 07/04/2024] [Accepted: 07/05/2024] [Indexed: 07/28/2024] Open
Abstract
In this study, we used ultraviolet-visible (UV-Vis), fluorescence, and circular dichroism (CD) techniques, as well as molecular modeling, to probe the interactions between carbazole derivatives and the G-quadruplex structure formed in the promoter region of gene Bcl-2. This gene is a rational target for anticancer therapy due to its high expression in a variety of tumors as well as resistance to chemotherapy-induced apoptosis. We employed a sequence with a specific dual G-to-T mutation that may form a mixed-type hybrid G-quadruplex structure in the Bcl-2 P1 promoter region. The three tested carbazole compounds differing in substitution on the nitrogen atom of carbazole interact with the Bcl-2 G-quadruplex by the same binding mode with the very comparable binding affinities in the order of 105 M-1. During absorption and fluorescence measurements, large changes in the ligand spectra were observed at higher G4 concentrations. The spectrophotometric titration results showed a two-step complex formation between the ligands and the G-quadruplex in the form of initial hypochromicity followed by hyperchromicity with a bathochromic shift. The strong fluorescence enhancement of ligands was observed after binding to the DNA. All of the used analytical techniques, as well as molecular modeling, suggested the π-π interaction between carbazole ligands and a guanine tetrad of the Bcl-2 G-quadruplex. Molecular modeling has shown differences in the interaction between each of the ligands and the tested G-quadruplex, which potentially had an impact on the binding strength.
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Affiliation(s)
- Agata Głuszyńska
- Department of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614 Poznań, Poland;
| | - Joanna Kosman
- Department of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614 Poznań, Poland;
- Laboratory of Molecular Assays and Imaging, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Shang Shiuan Chuah
- School of Pharmacy, University College London, London WC1N 1AX, UK (S.H.)
| | - Marcin Hoffmann
- Department of Quantum Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614 Poznań, Poland;
| | - Shozeb Haider
- School of Pharmacy, University College London, London WC1N 1AX, UK (S.H.)
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2
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Ghosal S, Bag S, Chinnadurai RK, Mukherjee M, Pramanik G, Bhowmik S. Investigating the preferential interaction between imatinib mesylate and VEGF G-quadruplex DNA as therapeutic strategies for cancer treatment: Biophysical and molecular modelling approaches. Comput Biol Med 2024; 177:108683. [PMID: 38838555 DOI: 10.1016/j.compbiomed.2024.108683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 05/27/2024] [Accepted: 05/30/2024] [Indexed: 06/07/2024]
Abstract
G-Quadruplex DNA (GQ-DNA) is one of the most important non-canonical nucleic acid structures. GQ-DNA forming sequences are present in different crucial genomic regions and are abundant in promoter regions of several oncogenes. Therefore, GQ-DNA is an important target for anticancer drugs and hence binding interactions between GQ-DNA and small molecule ligands are of great importance. Since GQ-DNA is a highly polymorphic structure, it is important to identify ligand molecules which preferentially target a particular quadruplex sequence. In this present study, we have used a FDA approved drug called imatinib mesylate (ligand) which is a selective tyrosine kinase inhibitor, successfully used for the treatment of chronic myelogenous leukaemia, gastrointestinal stromal tumours. Different spectroscopic techniques as well as molecular docking investigations and molecular simulations have been used to explore the interaction between imatinib mesylate with VEGF GQ DNA structures along with duplex DNA, C-Myc, H-Telo GQ DNA. We found that imatinib mesylate shows preferential interaction towards VEGF GQ DNA compared to C-Myc, H-Telo GQ and duplex DNA. Imatinib mesylate seems to be an efficient ligand for VEGF GQ DNA, suggesting that it might be used to regulate the expression of genes in cancerous cells.
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Affiliation(s)
- Souvik Ghosal
- Mahatma Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth (Deemed to be University), Pondy-Cuddalore Main Road, Pillaiyarkuppam, Pondicherry, 607402, India
| | - Sagar Bag
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, A.P.C. Road, Kolkata, 700009, India
| | - Raj Kumar Chinnadurai
- Mahatma Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth (Deemed to be University), Pondy-Cuddalore Main Road, Pillaiyarkuppam, Pondicherry, 607402, India
| | - Moupriya Mukherjee
- UGC-DAE Consortium for Scientific Research, Kolkata Centre, Sector III, LB-8, Bidhan Nagar, Kolkata, 700 106, India
| | - Goutam Pramanik
- UGC-DAE Consortium for Scientific Research, Kolkata Centre, Sector III, LB-8, Bidhan Nagar, Kolkata, 700 106, India
| | - Sudipta Bhowmik
- Mahatma Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth (Deemed to be University), Pondy-Cuddalore Main Road, Pillaiyarkuppam, Pondicherry, 607402, India; Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, A.P.C. Road, Kolkata, 700009, India.
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3
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Cai JH, Yang DY, Zhang JJ, Tan JH, Huang ZS, Chen SB. Constructing triazole-modified quinazoline derivatives as selective c-MYC G-quadruplex ligands and potent anticancer agents through click chemistry. Bioorg Chem 2024; 144:107173. [PMID: 38335759 DOI: 10.1016/j.bioorg.2024.107173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 01/26/2024] [Accepted: 01/31/2024] [Indexed: 02/12/2024]
Abstract
c-MYC is a hallmark of various cancers, playing a critical role in promoting tumorigenesis. The formation of G-quadruplex (G4) in the c-MYC promoter region significantly suppresses its expression. Therefore, developing small-molecule ligands to stabilize c-MYC G4 formation and subsequentially suppress c-MYC expression is an attractive topic for c-MYC-driven cancer therapy. However, achieving selective ligands for c-MYC G4 poses challenges. In this study, we developed a series of triazole-modified quinazoline (TMQ) derivatives as potential c-MYC G4 ligands and c-MYC transcription inhibitors from 4-anilinoquinazoline lead 7a using click chemistry. Importantly, the c-MYC G4 stabilizing ability and antiproliferation activity were well correlated among these new derivatives, particularly in the c-MYC highly expressed colorectal cancer cell line HCT116. Among them, compound A6 exhibited good selectivity in stabilizing c-MYC G4 and in suppressing c-MYC transcription better than 7a. This compound induced G4 formation, selectively inhibited G4-related c-MYC transcription and suppressed the progression of HCT116 cells. These findings identify a new c-MYC transcription inhibitor and provide new insights for optimizing c-MYC G4-targeting ligands.
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Affiliation(s)
- Jiong-Heng Cai
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Dan-Yan Yang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Jun-Jie Zhang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Jia-Heng Tan
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhi-Shu Huang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China.
| | - Shuo-Bin Chen
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China.
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4
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Andregic N, Weaver C, Basu S. The binding of a c-MYC promoter G-quadruplex to neurotransmitters: An analysis of G-quadruplex stabilization using DNA melting, fluorescence spectroscopy, surface-enhanced Raman scattering and molecular docking. Biochim Biophys Acta Gen Subj 2023; 1867:130473. [PMID: 37778448 DOI: 10.1016/j.bbagen.2023.130473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/14/2023] [Accepted: 09/28/2023] [Indexed: 10/03/2023]
Abstract
The interactions of several neurotransmitter and neural hormone molecules with the c-MYC G-quadruplex DNA sequence were analyzed using a combination of spectroscopic and computational techniques. The interactions between indole, catecholamine, and amino acid neurotransmitters and DNA sequences could potentially add to the understanding of the role of G-quadruplex structures play in various diseases. Also, the interaction of the DNA sequence derived from the nuclear hypersensitivity element (NHE) III1 region of c-MYC oncogene (Pu22), 5'-TGAGGGTGGGTAGGGTGGGTAA-3', has added significance in that these molecules may promote or inhibit the formation of G-quadruplex DNA which could lead to the development of promising drugs for anticancer therapy. The results showed that these molecules did not disrupt G-quadruplex formation even in the absence of quadruplex-stabilizing cations. There was also evidence of concentration-dependent binding and high binding affinities based on the Stern-Volmer model, and thermodynamically favorable interactions in the form of hydrogen-bonding and interactions involving the π system of the aromatic neurotransmitters.
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Affiliation(s)
- Nicole Andregic
- Department of Biology, Susquehanna University, 514 University Avenue, Selinsgrove, PA 17870, USA
| | - Caitlin Weaver
- Department of Biology, Susquehanna University, 514 University Avenue, Selinsgrove, PA 17870, USA
| | - Swarna Basu
- Department of Chemistry, Susquehanna University, 514 University Avenue, Selinsgrove, PA 17870, USA.
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5
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Bahls B, Aljnadi IM, Emídio R, Mendes E, Paulo A. G-Quadruplexes in c-MYC Promoter as Targets for Cancer Therapy. Biomedicines 2023; 11:biomedicines11030969. [PMID: 36979947 PMCID: PMC10046398 DOI: 10.3390/biomedicines11030969] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/09/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
Cancer is a societal burden demanding innovative approaches. A major problem with the conventional chemotherapeutic agents is their strong toxicity and other side effects due to their poor selectivity. Uncontrolled proliferation of cancer cells is due to mutations, deletions, or amplifications in genes (oncogenes) encoding for proteins that regulate cell growth and division, such as transcription factors, for example, c-MYC. The direct targeting of the c-MYC protein has been attempted but so far unsuccessfully, as it lacks a definite binding site for the modulators. Meanwhile, another approach has been explored since the discovery that G-quadruplex secondary DNA structures formed in the guanine-rich sequences of the c-MYC promoter region can downregulate the transcription of this oncogene. Here, we will overview the major achievements made in the last decades towards the discovery of a new class of anticancer drugs targeting G-quadruplexes in the c-MYC promoter of cancer cells.
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Affiliation(s)
- Bárbara Bahls
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal
| | - Israa M Aljnadi
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal
| | - Rita Emídio
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal
| | - Eduarda Mendes
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal
| | - Alexandra Paulo
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal
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6
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Xu P, Yuan L, Wang K, Pan B, Ye Y, Lu K. Interaction of bifunctional peptide-carbazole complexes with DNA and antimicrobial activity. Int J Biol Macromol 2023; 237:124070. [PMID: 36940762 DOI: 10.1016/j.ijbiomac.2023.124070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/24/2023] [Accepted: 03/05/2023] [Indexed: 03/23/2023]
Abstract
Two peptide-carbazole conjugates, CTAT and CNLS, were designed and synthesized using carbazole Schiff base to modify the cell membrane penetrating peptide TAT (47-57) and the nuclear localization peptide NLS at the N terminus. The interaction with ctDNA was investigated by multispectral and agarose gel electrophoresis. And the effects of CNLS and CTAT on the G-quadruplex structure were explored by circular dichroism titration experiments. The results show that both CTAT and CNLS interact with ctDNA in a minor groove binding manner. Both conjugates bind more tightly to DNA than the individual substances CIBA, TAT and NLS. In addition, CTAT and CNLS are capable of unfolding parallel G-quadruplex structures and are potential G-quadruplex unfolding agents. Finally, broth microdilution was performed to test the antimicrobial activity of the peptides. The results showed that CTAT and CNLS had a 4-fold increase in antimicrobial activity compared with the parent peptides TAT and NLS. They could exert antimicrobial activity by disrupting the integrity of cell membrane bilayer and binding to DNA, and could be used as novel antimicrobial peptides for the development of novel antimicrobial antibiotics.
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Affiliation(s)
- Ping Xu
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
| | - Libo Yuan
- College of Chemistry and Chemical Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Ke Wang
- College of Chemistry and Chemical Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Boyuan Pan
- College of Chemistry and Chemical Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Yong Ye
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
| | - Kui Lu
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China; School of Chemical Engineering and Food Science, Zhengzhou University of Technology, Zhengzhou 450044, China.
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7
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Wang Z, Liu W, Li G, Wang J, Zhao B, Huang P, Mei W. Ruthenium(II) Complexes Coupled by Erianin via a Flexible Carbon Chain as a Potential Stabilizer of c-myc G-Quadruplex DNA. Molecules 2023; 28:molecules28041529. [PMID: 36838516 PMCID: PMC9958891 DOI: 10.3390/molecules28041529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/08/2023] Open
Abstract
Herein, two novel ruthenium(II) complexes coupled by erianin via a flexible carbon chain, [Ru(phen)2(L1-(CH2)4-erianin)](ClO4)2 (L1 = 2-(2-(tri-fluoromethyphenyl))-imidazo [4,5f][1-10]phenanthroline (1) and [Ru(phen)2(L2-(CH2)4-eria)](ClO4)2 (L2 = 2-(4-(tri-fluoromethyphenyl))-imidazo [4,5f][1,10]phenanthroline (2), have been synthesized and investigated as a potential G-quadruplex(G4) DNA stabilizer. Both complexes, especially 2, can bind to c-myc G4 DNA with high affinity by electronic spectra, and the binding constant calculated for 1 and 2 is about 15.1 and 2.05 × 107 M-1, respectively. This was further confirmed by the increase in fluorescence intensity for both complexes. Moreover, the positive band at 265 nm in the CD spectra of c-myc G4 DNA decreased treated with 2, indicating that 2 may bind to c-myc G4 DNA through extern groove binding mode. Furthermore, fluorescence resonance energy transfer (FRET) assay indicated that the melting point of c-myc G4 DNA treated with 1 and 2 increased 15.5 and 16.5 °C, respectively. Finally, molecular docking showed that 1 can bind to c-myc G4 DNA in the extern groove formed by base pairs G7-G9 and G22-A24, and 2 inserts into the small groove of c-myc G4 DNA formed by base pairs T19-A24. In summary, these ruthenium(II) complexes, especially 2, can be developed as potential c-myc G4 DNA stabilizers and will be exploited as potential anticancer agents in the future.
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Affiliation(s)
- Zhixiang Wang
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Wentao Liu
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Guohu Li
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Jiacheng Wang
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Bin Zhao
- Department of Southern Pharmacy, Guangdong Jiangmen Chinese Medical, Jiangmen 510047, China
- Correspondence: (B.Z.); (W.M.)
| | - Peishan Huang
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Wenjie Mei
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
- Guangdong Province Engineering Technology Centre for Molecular Probe and Bio-Medical Imaging, Guangzhou 510006, China
- Correspondence: (B.Z.); (W.M.)
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8
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Alexander A, Sumohan Pillai A, Sri Varalakshmi G, Ananthi N, Pal H, V. M. V. Enoch I, Sayed M. G-Quadruplex binding affinity variation on molecular encapsulation of ligands by porphyrin-tethered cyclodextrin. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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9
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Savva L, Fossépré M, Keramidas O, Themistokleous A, Rizeq N, Panagiotou N, Leclercq M, Nicolaidou E, Surin M, Hayes SC, Georgiades SN. Gaining Insights on the Interactions of a Class of Decorated (2-([2,2'-Bipyridin]-6-yl)phenyl)platinum Compounds with c-Myc Oncogene Promoter G-Quadruplex and Other DNA Structures. Chemistry 2022; 28:e202201497. [PMID: 35726630 PMCID: PMC9804160 DOI: 10.1002/chem.202201497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Indexed: 01/05/2023]
Abstract
Organometallic molecules offer some of the most promising scaffolds for interaction with G-quadruplex nucleic acids. We report the efficient synthesis of a family of organoplatinum(II) complexes, featuring a 2-([2,2'-bipyridin]-6-yl)phenyl tridentate (N∧ N∧ C) ligand, that incorporates peripheral side-chains aiming at enhancing and diversifying its interaction capabilities. These include a di-isopropyl carbamoyl amide, a morpholine ethylenamide, two enantiomeric proline imides and an oxazole. The binding affinities of the Pt-complexes were evaluated via UV-vis and fluorescence titrations, against 5 topologically-distinct DNA structures, including c-myc G-quadruplex, two telomeric (22AG) G-quadruplexes, a duplex (ds26) and a single-stranded (polyT) DNA. All compounds exhibited binding selectivity in favour of c-myc, with association constants (Ka ) in the range of 2-5×105 M-1 , lower affinity for both folds of 22AG and for ds26 and negligible affinity for polyT. Remarkable emission enhancements (up to 200-fold) upon addition of excess DNA were demonstrated by a subset of the compounds with c-myc, providing a basis for optical selectivity, since optical response to all other tested DNAs was low. A c-myc DNA-melting experiment showed significant stabilizing abilities for all compounds, with the most potent binder, the morpholine-Pt-complex, exhibiting a ΔTm >30 °C, at 1 : 5 DNA-to-ligand molar ratio. The same study implied contributions of the diverse side-chains to helix stabilization. To gain direct evidence of the nature of the interactions, mixtures of c-myc with the four most promising compounds were studied via UV Resonance Raman (UVRR) spectroscopy, which revealed end-stacking binding mode, combined with interactions of side-chains with loop nucleobase residues. Docking simulations were conducted to provide insights into the binding modes for the same four Pt-compounds, suggesting that the binding preference for two alternative orientations of the c-myc G-quadruplex thymine 'cap' ('open' vs. 'closed'), as well as the relative contributions to affinity from end-stacking and H-bonding, are highly dependent on the nature of the interacting Pt-complex side-chain.
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Affiliation(s)
- Loukiani Savva
- Department of ChemistryUniversity of Cyprus1 Panepistimiou Avenue, Aglandjia2109NicosiaCyprus
| | - Mathieu Fossépré
- Laboratory for Chemistry of Novel MaterialsUniversity of Mons – UMONS20 Place du ParcB-7000MonsBelgium
| | - Odysseas Keramidas
- Department of ChemistryUniversity of Cyprus1 Panepistimiou Avenue, Aglandjia2109NicosiaCyprus
| | | | - Natalia Rizeq
- Department of ChemistryUniversity of Cyprus1 Panepistimiou Avenue, Aglandjia2109NicosiaCyprus
| | - Nikos Panagiotou
- Department of ChemistryUniversity of Cyprus1 Panepistimiou Avenue, Aglandjia2109NicosiaCyprus
| | - Maxime Leclercq
- Laboratory for Chemistry of Novel MaterialsUniversity of Mons – UMONS20 Place du ParcB-7000MonsBelgium
| | - Eliana Nicolaidou
- Department of ChemistryUniversity of Cyprus1 Panepistimiou Avenue, Aglandjia2109NicosiaCyprus
| | - Mathieu Surin
- Laboratory for Chemistry of Novel MaterialsUniversity of Mons – UMONS20 Place du ParcB-7000MonsBelgium
| | - Sophia C. Hayes
- Department of ChemistryUniversity of Cyprus1 Panepistimiou Avenue, Aglandjia2109NicosiaCyprus
| | - Savvas N. Georgiades
- Department of ChemistryUniversity of Cyprus1 Panepistimiou Avenue, Aglandjia2109NicosiaCyprus
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10
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Li ML, Yuan JM, Yuan H, Wu BH, Huang SL, Li QJ, Ou TM, Wang HG, Tan JH, Li D, Chen SB, Huang ZS. Design, Synthesis, and Evaluation of New Sugar-Substituted Imidazole Derivatives as Selective c-MYC Transcription Repressors Targeting the Promoter G-Quadruplex. J Med Chem 2022; 65:12675-12700. [PMID: 36121464 DOI: 10.1021/acs.jmedchem.2c00467] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
c-MYC is a key driver of tumorigenesis. Repressing the transcription of c-MYC by stabilizing the G-quadruplex (G4) structure with small molecules is a potential strategy for cancer therapy. Herein, we designed and synthesized 49 new derivatives by introducing carbohydrates to our previously developed c-MYC G4 ligand 1. Among these compounds, 19a coupled with a d-glucose 1,2-orthoester displayed better c-MYC G4 binding, stabilization, and protein binding disruption abilities than 1. Our further evaluation indicated that 19a blocked c-MYC transcription by targeting the promoter G4, leading to c-MYC-dependent cancer cell death in triple-negative breast cancer cell MDA-MB-231. Also, 19a significantly inhibited tumor growth in the MDA-MB-231 mouse xenograft model accompanied by c-MYC downregulation. Notably, the safety of 19a was dramatically improved compared to 1. Our findings indicated that 19a could become a promising anticancer candidate, which suggested that introducing carbohydrates to improve the G4-targeting and antitumor activity is a feasible option.
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Affiliation(s)
- Mao-Lin Li
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Jing-Mei Yuan
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Hao Yuan
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Bi-Han Wu
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Shi-Liang Huang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Qing-Jiang Li
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Tian-Miao Ou
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Hong-Gen Wang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Jia-Heng Tan
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Ding Li
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Shuo-Bin Chen
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhi-Shu Huang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
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11
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Wang M, Zhang F, Luo Y, Shuo L, Wang MQ. DPA-Substituted Carbazole Derivative as a Fluorescent Ligand for G4 DNA. Chem Biodivers 2022; 19:e202200061. [PMID: 35762741 DOI: 10.1002/cbdv.202200061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 06/17/2022] [Indexed: 11/07/2022]
Abstract
Herein a conjugated dipicolylamine/carbazole (Car-DPA) molecule was designed and synthesized to enhance the performance for the application as a G4 fluorescent ligand. This ligand has been found to display distinct and specific fluorescence enhancements in the presence of various G4 DNA structures, but limited with ssDNA or dsDNAs. The detail binding characteristics of the ligand with c-MYC G4 DNA were investigated by fluorescence, UV/VIS absorption, CD spectroscopy, and molecular docking. The present study demonstrated that Car-DPA bound to c-MYC G4s with a two-step complex formation, in which the binding mode appeared to be end-stacking. Confocal fluorescence images indicated that ligand Car-DPA could locate in nucleus, which is quite prominent from the cellular internalization studies.
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Affiliation(s)
- Ming Wang
- College of Mechanical Engineering and Automation, Shandong Institute of Petrochemical Technology, Dongying, 257001, P. R. China
| | - Feng Zhang
- College of Mechanic and Electronic Engineering, China University of Petroleum (East China), Qingdao, 266580, P. R. China.,Shengli Oil Field Petroleum Engineering Technology Research Institute Sinopec, Dongying, 257000, P. R. China
| | - Yang Luo
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, P. R. China
| | - Li Shuo
- School of Chemical Engineering, Chongqing University of Technology, Chongqing, 400054, P. R. China
| | - Ming-Qi Wang
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, P. R. China
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12
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Venkata Suseela Y, Sengupta P, Roychowdhury T, Panda S, Talukdar S, Chattopadhyay S, Chatterjee S, Govindaraju T. Targeting Oncogene Promoters and Ribosomal RNA Biogenesis by G-Quadruplex Binding Ligands Translate to Anticancer Activity. ACS BIO & MED CHEM AU 2022; 2:125-139. [PMID: 37101746 PMCID: PMC10114666 DOI: 10.1021/acsbiomedchemau.1c00039] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
G-Quadruplex (GQ) nucleic acids are promising therapeutic targets in anticancer research due to their structural robustness, polymorphism, and gene-regulatory functions. Here, we presented the structure-activity relationship of carbazole-based monocyanine ligands using region-specific functionalization with benzothiazole (TCA and TCZ), lepidine (LCA and LCZ), and quinaldine (QCA and QCZ) acceptor moieties and evaluated their binding profiles with different oncogenic GQs. Their differential turn-on fluorescence emission upon GQ binding confirmed the GQ-to-duplex selectivity of all carbazole ligands, while the isothermal titration calorimetry results showed selective interactions of TCZ and TCA to c-MYC and BCL-2 GQs, respectively. The aldehyde group in TCA favors stacking interactions with the tetrad of BCL-2 GQ, whereas TCZ provides selective groove interactions with c-MYC GQ. Dual-luciferase assay and chromatin immunoprecipitation (ChIP) showed that these molecules interfere with the recruitment of specific transcription factors at c-MYC and BCL-2 promoters and stabilize the promoter GQ structures to inhibit their constitutive transcription in cancer cells. Their intrinsic turn-on fluorescence response with longer lifetimes upon GQ binding allowed real-time visualization of GQ structures at subcellular compartments. Confocal microscopy revealed the uptake of these ligands in the nucleoli, resulting in nucleolar stress. ChIP studies further confirmed the inhibition of Nucleolin occupancy at multiple GQ-enriched regions of ribosomal DNA (rDNA) promoters, which arrested rRNA biogenesis. Therefore, carbazole ligands act as the "double-edged swords" to arrest c-MYC and BCL-2 overexpression as well as rRNA biogenesis, triggering synergistic inhibition of multiple oncogenic pathways and apoptosis in cancer cells.
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Affiliation(s)
- Yelisetty Venkata Suseela
- Bioorganic
Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, P.O., Bengaluru, Karnataka 560064, India
| | - Pallabi Sengupta
- Department
of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kankurgachi, Kolkata 700054, India
| | - Tanaya Roychowdhury
- Cancer
Biology and Inflammatory Disorder Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Suman Panda
- Department
of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kankurgachi, Kolkata 700054, India
| | - Sangita Talukdar
- Bioorganic
Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, P.O., Bengaluru, Karnataka 560064, India
| | - Samit Chattopadhyay
- Cancer
Biology and Inflammatory Disorder Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Subhrangsu Chatterjee
- Department
of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kankurgachi, Kolkata 700054, India
| | - Thimmaiah Govindaraju
- Bioorganic
Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, P.O., Bengaluru, Karnataka 560064, India
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13
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Mohamed HI, Gao C, Gui Z, Song Z, Wei D. A novel fluorescent probe with a pyrazolo[4,3- c]quinoline core selectively recognizes c-MYC promoter G-quadruplexes. NEW J CHEM 2022. [DOI: 10.1039/d1nj00098e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An aptamer combined with a c-MYC-selective fluorophore could work as the fluorescent core of nucleic acid mimics of fluorescent proteins to locate and image functional biomolecules in cells.
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Affiliation(s)
- Hany I. Mohamed
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Hubei Hongshan Laboratory, Interdisciplinary Sciences Institute, National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- Chemistry Department, Faculty of Science, Benha University, Benha 13518, Egypt
| | - Chao Gao
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Zhikun Gui
- College of Science, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Zibing Song
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Hubei Hongshan Laboratory, Interdisciplinary Sciences Institute, National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- College of Science, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Dengguo Wei
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Hubei Hongshan Laboratory, Interdisciplinary Sciences Institute, National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China
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14
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Piperine analogs arrest c-myc gene leading to downregulation of transcription for targeting cancer. Sci Rep 2021; 11:22909. [PMID: 34824301 PMCID: PMC8617303 DOI: 10.1038/s41598-021-01529-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/28/2021] [Indexed: 11/08/2022] Open
Abstract
G-quadruplex (G4) structures are considered a promising therapeutic target in cancer. Since Ayurveda, Piperine has been known for its medicinal properties. Piperine shows anticancer properties by stabilizing the G4 motif present upstream of the c-myc gene. This gene belongs to a group of proto-oncogenes, and its aberrant transcription drives tumorigenesis. The transcriptional regulation of the c-myc gene is an interesting approach for anticancer drug design. The present study employed a chemical similarity approach to identify Piperine similar compounds and analyzed their interaction with cancer-associated G-quadruplex motifs. Among all Piperine analogs, PIP-2 exhibited strong selectivity, specificity, and affinity towards c-myc G4 DNA as elaborated through biophysical studies such as fluorescence emission, isothermal calorimetry, and circular dichroism. Moreover, our biophysical observations are supported by molecular dynamics analysis and cellular-based studies. Our study showed that PIP-2 showed higher toxicity against the A549 lung cancer cell line but lower toxicity towards normal HEK 293 cells, indicating increased efficacy of the drug at the cellular level. Biological evaluation assays such as TFP reporter assay, quantitative real-time PCR (qRT- PCR), and western blotting suggest that the Piperine analog-2 (PIP-2) stabilizes the G-quadruplex motif located at the promoter site of c-myc oncogene and downregulates its expression. In conclusion, Piperine analog PIP-2 may be used as anticancer therapeutics as it affects the c-myc oncogene expression via G-quadruplex mediated mechanism.
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15
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Müller D, Saha P, Panda D, Dash J, Schwalbe H. Insights from Binding on Quadruplex Selective Carbazole Ligands. Chemistry 2021; 27:12726-12736. [PMID: 34138492 PMCID: PMC8518889 DOI: 10.1002/chem.202101866] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Indexed: 01/11/2023]
Abstract
Polymorphic G-quadruplex (G4) secondary DNA structures have received increasing attention in medicinal chemistry owing to their key involvement in the regulation of the maintenance of genomic stability, telomere length homeostasis and transcription of important proto-oncogenes. Different classes of G4 ligands have been developed for the potential treatment of several human diseases. Among them, the carbazole scaffold with appropriate side chain appendages has attracted much interest for designing G4 ligands. Because of its large and rigid π-conjugation system and ease of functionalization at three different positions, a variety of carbazole derivatives have been synthesized from various natural or synthetic sources for potential applications in G4-based therapeutics and biosensors. Herein, we provide an updated close-up of the literatures on carbazole-based G4 ligands with particular focus given on their detailed binding insights studied by NMR spectroscopy. The structure-activity relationships and the opportunities and challenges of their potential applications as biosensors and therapeutics are also discussed. This review will provide an overall picture of carbazole ligands with remarkable G4 topological preference, fluorescence properties and significant bioactivity; portraying carbazole as a very promising scaffold for assembling G4 ligands with a range of novel functional applications.
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Affiliation(s)
- Diana Müller
- Institute of Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Goethe University FrankfurtMax-von-Laue Strasse 7Frankfurt am Main60438Germany
| | - Puja Saha
- School of Chemical SciencesIndian Association for the Cultivation of ScienceJadavpurKolkata-700032India
| | - Deepanjan Panda
- School of Chemical SciencesIndian Association for the Cultivation of ScienceJadavpurKolkata-700032India
| | - Jyotirmayee Dash
- School of Chemical SciencesIndian Association for the Cultivation of ScienceJadavpurKolkata-700032India
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Goethe University FrankfurtMax-von-Laue Strasse 7Frankfurt am Main60438Germany
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16
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Chaudhuri R, Fatma K, Dash J. Regulation of gene expression by targeting DNA secondary structures. J CHEM SCI 2021. [DOI: 10.1007/s12039-021-01898-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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17
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Desai N, Shah V, Datta B. Assessing G4-Binding Ligands In Vitro and in Cellulo Using Dimeric Carbocyanine Dye Displacement Assay. Molecules 2021; 26:molecules26051400. [PMID: 33807659 PMCID: PMC7961521 DOI: 10.3390/molecules26051400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 01/31/2021] [Accepted: 02/24/2021] [Indexed: 12/05/2022] Open
Abstract
G-quadruplexes (G4) are the most actively studied non-canonical secondary structures formed by contiguous repeats of guanines in DNA or RNA strands. Small molecule mediated targeting of G-quadruplexes has emerged as an attractive tool for visualization and stabilization of these structures inside the cell. Limited number of DNA and RNA G4-selective assays have been reported for primary ligand screening. A combination of fluorescence spectroscopy, AFM, CD, PAGE, and confocal microscopy have been used to assess a dimeric carbocyanine dye B6,5 for screening G4-binding ligands in vitro and in cellulo. The dye B6,5 interacts with physiologically relevant DNA and RNA G4 structures, resulting in fluorescence enhancement of the molecule as an in vitro readout for G4 selectivity. Interaction of the dye with G4 is accompanied by quadruplex stabilization that extends its use in primary screening of G4 specific ligands. The molecule is cell permeable and enables visualization of quadruplex dominated cellular regions of nucleoli using confocal microscopy. The dye is displaced by quarfloxin in live cells. The dye B6,5 shows remarkable duplex to quadruplex selectivity in vitro along with ligand-like stabilization of DNA G4 structures. Cell permeability and response to RNA G4 structures project the dye with interesting theranostic potential. Our results validate that B6,5 can serve the dual purpose of visualization of DNA and RNA G4 structures and screening of G4 specific ligands, and adds to the limited number of probes with such potential.
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Affiliation(s)
- Nakshi Desai
- Department of Biological Engineering, Indian Institute of Technology, Gandhinagar 382355, India; (N.D.); (V.S.)
| | - Viraj Shah
- Department of Biological Engineering, Indian Institute of Technology, Gandhinagar 382355, India; (N.D.); (V.S.)
| | - Bhaskar Datta
- Department of Biological Engineering, Indian Institute of Technology, Gandhinagar 382355, India; (N.D.); (V.S.)
- Department of Chemistry, Indian Institute of Technology, Gandhinagar, Gandhinagar 382355, India
- Correspondence: ; Tel.: +91-79-2395-2427; Fax: +91-79-2397-2622
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18
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Singu PS, Chilakamarthi U, Mahadik NS, Keerti B, Valipenta N, Mokale SN, Nagesh N, Kumbhare RM. Benzimidazole-1,2,3-triazole hybrid molecules: synthesis and study of their interaction with G-quadruplex DNA. RSC Med Chem 2021; 12:416-429. [PMID: 34046624 DOI: 10.1039/d0md00414f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/12/2021] [Indexed: 12/18/2022] Open
Abstract
A series of new benzimidazole-1,2,3-triazole hybrid derivatives have been synthesized via 'click' reaction and evaluated for their in vitro cytotoxicity as well as DNA binding affinity. MTT assay showed that all the six compounds are cytotoxic to PC3 and B16-F10 cancer cell lines. Though all the compounds showed moderate interaction with G4, c-Myc promoter DNA and dsDNA, 4f exhibited selective interaction with G-quadruplex DNA over duplex DNA as demonstrated by spectroscopic experiments like UV-vis spectroscopy, fluorescence spectroscopy, CD spectroscopy, thermal melting and fluorescence lifetime experiments. They also confirm the G-quadruplex DNA stabilizing potential of 4f. Viscosity measurements also confirm that 4f exhibits high G-quadruplex DNA selectivity over duplex DNA. Docking studies supported the spectroscopic observations. Cell cycle analysis showed that 4f induces G2/M phase arrest and induces apoptosis. Hence, from these experimental results it is evident that compound 4f may be a G-quadruplex DNA groove binding molecule with anticancer activity.
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Affiliation(s)
- Padma S Singu
- Department of Fluoro-Agrochemicals, CSIR-Indian Institute of Chemical Technology Tarnaka Hyderabad 500007 India .,Academy of Scientific and Innovative Research (AcSIR) Ghaziabad India
| | - Ushasri Chilakamarthi
- Polymers and Functional Materials Division, CSIR-Indian Institute of Chemical Technology Hyderabad-500007 India
| | - Namita S Mahadik
- Applied Biology Division, CSIR-Indian Institute of Chemical Technology Hyderabad-500007 India
| | - Bhamidipati Keerti
- Applied Biology Division, CSIR-Indian Institute of Chemical Technology Hyderabad-500007 India
| | - Narasimhulu Valipenta
- Department of Fluoro-Agrochemicals, CSIR-Indian Institute of Chemical Technology Tarnaka Hyderabad 500007 India .,Academy of Scientific and Innovative Research (AcSIR) Ghaziabad India
| | - Santosh N Mokale
- Y. B. Chavan College of Pharmacy Dr. Rafiq Zakaria Campus Aurangabad-431001 India
| | - Narayana Nagesh
- Medical Biotechnology Complex, CSIR-Centre for Cellular and Molecular Biology ANNEXE II, Uppal Road Hyderabad 500007 India
| | - Ravindra M Kumbhare
- Department of Fluoro-Agrochemicals, CSIR-Indian Institute of Chemical Technology Tarnaka Hyderabad 500007 India .,Academy of Scientific and Innovative Research (AcSIR) Ghaziabad India
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19
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Ghamri M, Harkati D, Belaidi S, Boudergua S, Said RB, Linguerri R, Chambaud G, Hochlaf M. Carbazole derivatives containing chalcone analogues targeting topoisomerase II inhibition: First principles characterization and QSAR modelling. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 242:118724. [PMID: 32769058 DOI: 10.1016/j.saa.2020.118724] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/29/2020] [Accepted: 07/04/2020] [Indexed: 06/11/2023]
Abstract
Recently, a series of carbazole derivatives containing chalcone analogues (CDCAs) were synthetized as potent anticancer agents and apoptosis inducers. These compounds target the inhibition of topoisomerase II and present cytotoxic activities. After comparison to experiment, we validated the use of B3LYP, a density functional theory-based approach, to describe the structure and molecular properties of the carbazole subunit and CDCAs compounds of interest. Then, we derived relationships between the chemical descriptors and activity of these carbazole derivatives using multi-parameter optimization and quantitative structure activity relationships (QSAR) approaches. For the QSAR studies, we used multiple linear regression and artificial neural network statistical modelling. Our predicted activities are in good agreement with the experimental ones. We found that the most important parameter influencing the activity of the considered compounds is the octanol-water partition coefficient, highlighting the importance of flexibility as a key molecular parameter to favor cell membrane crossing and enhance the action of these CDCAs against topoisomerase II. Our results provide useful guidelines for designing new oral active CDCAs medicaments for cytotoxic inhibition.
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Affiliation(s)
- M Ghamri
- University of Biskra, Group of Computational and Pharmaceutical Chemistry, LMCE Laboratory, 07000 Biskra, Algeria; Université Gustave Eiffel, COSYS/LISIS, 5 Bd Descartes, 77454, Champs sur Marne, France
| | - D Harkati
- University of Biskra, Group of Computational and Pharmaceutical Chemistry, LMCE Laboratory, 07000 Biskra, Algeria
| | - S Belaidi
- University of Biskra, Group of Computational and Pharmaceutical Chemistry, LMCE Laboratory, 07000 Biskra, Algeria.
| | - S Boudergua
- University of Biskra, Group of Computational and Pharmaceutical Chemistry, LMCE Laboratory, 07000 Biskra, Algeria
| | - R Ben Said
- Department of Chemistry, College of Science and Arts, Qassim University, Ar Rass, Saudi Arabia.
| | - R Linguerri
- Université Gustave Eiffel, COSYS/LISIS, 5 Bd Descartes, 77454, Champs sur Marne, France
| | - G Chambaud
- Université Gustave Eiffel, COSYS/LISIS, 5 Bd Descartes, 77454, Champs sur Marne, France
| | - M Hochlaf
- Université Gustave Eiffel, COSYS/LISIS, 5 Bd Descartes, 77454, Champs sur Marne, France.
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20
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Gouda AS, Przypis Ł, Walczak K, Jørgensen PT, Wengel J. Carbazole modified oligonucleotides: synthesis, hybridization studies and fluorescence properties. Org Biomol Chem 2020; 18:6935-6948. [PMID: 32936176 DOI: 10.1039/d0ob01553a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Synthesis of the novel thiophenyl carbazole phosphoramidite DNA building block 5 was accomplished in four steps using a Suzuki-Miyaura cross-coupling reaction from the core carbazole and it was seamlessly accommodated into a 9-mer DNA-based oligonucleotide by incorporation at the flanking 5'-end in combination with a central insertion of an LNA-T nucleotide. The carbazole-containing oligonucleotide was combined in different duplex hybrids, which were characterized by thermal denaturation, circular dichroism and fluorescence studies. The carbazole monomer modulates the duplex stability in various ways. Thus, monomer Z increased the thermal stability of the 9-mer towards the complementary 9-mer/15-mer DNA duplex by 4.2 °C. Furthermore, indications of its intercalation into the duplex were obtained by modeling studies and robust decreases in fluorescence emission intensities upon duplex formation. In contrast, no clear intercalating tendency was corroborated for monomer Z within the DNA/RNA hybrid duplex as indicated by moderate quenching of the fluorescence and similar duplex thermal stabilities relative to the corresponding control duplex. The recognition efficiencies of the carbazole modified oligonucleotide toward single nucleotide mismatches were studied with two 15-mer model targets (DNA and RNA). For both systems, mismatches positioned at the juxtaposition of the carbazole monomer showed pronounced deceases in thermal denaturation temperature. Steady-state fluorescence emission studies of all mismatched duplexes with incorporation of Z monomer typically displayed efficient fluorescence quenching.
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Affiliation(s)
- Alaa S Gouda
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
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21
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Human MYC G-quadruplex: From discovery to a cancer therapeutic target. Biochim Biophys Acta Rev Cancer 2020; 1874:188410. [PMID: 32827579 DOI: 10.1016/j.bbcan.2020.188410] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/21/2020] [Accepted: 07/21/2020] [Indexed: 02/06/2023]
Abstract
Overexpression of the MYC oncogene is a molecular hallmark of both cancer initiation and progression. Targeting MYC is a logical and effective cancer therapeutic strategy. A special DNA secondary structure, the G-quadruplex (G4), is formed within the nuclease hypersensitivity element III1 (NHE III1) region, located upstream of the MYC gene's P1 promoter that drives the majority of its transcription. Targeting such G4 structures has been a focus of anticancer therapies in recent decades. Thus, a comprehensive review of the MYC G4 structure and its role as a potential therapeutic target is timely. In this review, we first outline the discovery of the MYC G4 structure and evidence of its formation in vitro and in cells. Then, we describe the functional role of G4 in regulating MYC gene expression. We also summarize three types of MYC G4-interacting proteins that can promote, stabilize and unwind G4 structures. Finally, we discuss G4-binding molecules and the anticancer activities of G4-stabilizing ligands, including small molecular compounds and peptides, and assess their potential as novel anticancer therapeutics.
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22
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Zou L, Li H, Liu M, Zhao W, Wang S. Enhancement Effect of Zn-Arsenazo III Complex for G-quadruplex DNA Stability of Proto-oncogene Promoter Telomeres. LETT DRUG DES DISCOV 2020. [DOI: 10.2174/1570180816666191112154141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Controlling the structure of proto-oncogene telomeres is very important in
antitumor therapy. There are relationships between G-quadruplex DNA and the growth of tumor cell.
Methods:
In this study, spectroscopic, cyclic voltammetry and viscosity methods were employed to
investigate the interaction between Zn-Arsenazo Ⅲ complex and G-quadruplex DNA by using 4S
Green Plus Nucleic Acid Stain as a spectral probe in PBS buffer. The binding ratios were n Arsenazo Ⅲ
: n Zn(Ⅱ) = 5:1 for Zn-Arsenazo Ⅲ complex and n Zn- Arsenazo Ⅲ : n G-quadruplex DNA = 8:1 for Zn-Arsenazo
Ⅲ-G-quadruplex DNA. The bonding constants (Kθ
298.15K=4.44x105 L·mol-1, Kθ
308.15K= 1.00x105
L·mol-1, Kθ
318.15K= 1.04x106 L·mol-1) were obtained by double reciprocal method at different temperatures, Which was found that the interaction between Zn-Arsenazo Ⅲ complex and Gquadruplex
DNA was driven by enthalpy. Furthermore, the research further confirmed that the interaction
mode between Zn-Arsenazo Ⅲ complex and G-quadruplex DNA was a mixed binding
which involved intercalation and non-intercalation interaction.
Results and Conclusion:
Together these findings also have corroborated the application of stabilizing
ligands and intervening with their function for target G-quadruplexes in a cellular context.
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Affiliation(s)
- Liyuan Zou
- Key Laboratory of Functional Small Organic Molecule, Ministry of Education, College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, China
| | - Hongbo Li
- Key Laboratory of Functional Small Organic Molecule, Ministry of Education, College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, China
| | - Mingbin Liu
- Key Laboratory of Functional Small Organic Molecule, Ministry of Education, College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, China
| | - Weihua Zhao
- Key Laboratory of Functional Small Organic Molecule, Ministry of Education, College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, China
| | - Suqin Wang
- Key Laboratory of Functional Small Organic Molecule, Ministry of Education, College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, China
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23
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Phthalocyanines for G-quadruplex aptamers binding. Bioorg Chem 2020; 100:103920. [PMID: 32413624 DOI: 10.1016/j.bioorg.2020.103920] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 05/05/2020] [Accepted: 05/06/2020] [Indexed: 01/02/2023]
Abstract
The G-quadruplex (G4)-forming sequence within the AS1411 derivatives with alternative nucleobases and backbones can improve the chemical and biological properties of AS1411. Zn(II) phthalocyanine (ZnPc) derivatives have potential as high-affinity G4 ligands because they have similar size and shape to the G-quartets. The interactions of four Zn(II) phthalocyanines with the G4 AS1411 aptamer and its derivatives were determined by biophysical techniques, molecular docking and gel electrophoresis. Cell viability assay was carried out to evaluate the antiproliferative effects of Zn(II) phthalocyanines and complexes. CD experiments showed structural changes after addition of ZnPc 4, consistent with multiple binding modes and conformations shown by NMR and gel electrophoresis. CD melting confirmed that ZnPc 2 and ZnPc 4, both containing eight positive charges, are able to stabilize the AT11 G4 structure (ΔTm > 30 °C and 18.5 °C, respectively). Molecular docking studies of ZnPc 3 and ZnPc 4 suggested a preferential binding to the 3'- and 5'-end, respectively, of the AT11 G4. ZnPc 3 and its AT11 and AT11-L0 complexes revealed pronounced cytotoxic effect against cervical cancer cells and no cytotoxicity to normal human cells. Zn(II) phthalocyanines provide the basis for the development of effective therapeutic agents as G4 ligands.
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24
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Verma S, Ghuge SA, Ravichandiran V, Ranjan N. Spectroscopic studies of Thioflavin-T binding to c-Myc G-quadruplex DNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 212:388-395. [PMID: 30703662 DOI: 10.1016/j.saa.2018.12.044] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 11/16/2018] [Accepted: 12/22/2018] [Indexed: 05/29/2023]
Abstract
G-quadruplexes are well-known DNA secondary structures which can be formed both within the DNA and the RNA sequences of the human genome. While many functions of G-quadruplex during cell regulatory events are still unknown, a number of reports have established their role in finding new cancer therapies. In this report, we provide a detailed account of Thioflavin T (ThT) interacting with a promoter gene (c-Myc) which has relevance in several types of human cancers. Using a variety of spectroscopic techniques, we have shown that the binding of ThT is selective to c-Myc G-quadruplex only, having poor interactions with the duplex DNA sequences. UV-Visible titration experiments show that binding involves stacking interactions which were further corroborated by CD experiments. Fluorescence studies showed that the binding of ThT to c-Myc G-quadruplex results in a large increase in the fluorescence emission spectrum of c-Myc G-quadruplex while the same to duplex DNAs was much poor. Binding of ThT to c-Myc G-quadruplex results in thermal stabilization of the quadruplex DNA by up to 7.4 °C and Job plot experiments demonstrated the presence of 1:1 and 2:1 ligand to quadruplex complexes. Finally, the docking study suggested that ThT stacks with the guanine bases in one of the grooves which is in agreement with the CD studies. These results are expected to provide leads into the design of new ThT analogs and derivatives for enhancing the stability and selectivity of new G-quadruplex targeting ligands.
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Affiliation(s)
- Smita Verma
- National Institute of Pharmaceutical Education and Research, ITI Compound, Raebareli 229010, India; National Institute of Pharmaceutical Education and Research, Kolkata, Maniktala Main Road, Kolkata 700054, India
| | - Sandip A Ghuge
- TERI-Deakin Nanobiotechnology Research Center, Sustainable Agriculture Division, The Energy and Resources Institute, New Delhi 110003, India
| | - V Ravichandiran
- National Institute of Pharmaceutical Education and Research, Kolkata, Maniktala Main Road, Kolkata 700054, India
| | - Nihar Ranjan
- National Institute of Pharmaceutical Education and Research, ITI Compound, Raebareli 229010, India.
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Practical Microwave Synthesis of Carbazole Aldehydes for the Development of DNA-Binding Ligands. Molecules 2019; 24:molecules24050965. [PMID: 30857275 PMCID: PMC6429063 DOI: 10.3390/molecules24050965] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 02/25/2019] [Accepted: 03/06/2019] [Indexed: 01/28/2023] Open
Abstract
Microwave formylation of carbazole derivatives was investigated and 3-monoaldehydes were obtained in high yield. A potential DNA-binding ligand, 3-[(3-ethyl)-2-vinylbenzothiazolium]-9-N-ethyl carbazole iodide, was synthesized and characterized including spectral properties (UV-Vis absorption and fluorescence spectra). The binding selectivity and affinity of three carbazole ligands for double-stranded and G-quadruplex DNA structures were studied using a competitive dialysis method in sodium- and potassium-containing buffer solutions.
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Binding Study of the Fluorescent Carbazole Derivative with Human Telomeric G-Quadruplexes. Molecules 2018; 23:molecules23123154. [PMID: 30513661 PMCID: PMC6321567 DOI: 10.3390/molecules23123154] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 11/28/2018] [Accepted: 11/29/2018] [Indexed: 01/04/2023] Open
Abstract
The carbazole ligand 3 was synthesized, characterized and its binding interactions with human telomeric (22HT) G-quadruplex DNA in Na+ and K+-containing buffer were investigated by ultraviolet-visible (UV-Vis) spectrophotometry, fluorescence, circular dichroism (CD) spectroscopy, and DNA melting. The results showed that the studied carbazole ligand interacted and stabilized the intramolecular G-quadruplexes formed by the telomeric sequence in the presence of sodium and potassium ions. In the UV-Vis titration experiments a two-step complex formation between ligand and G-quadruplex was observed. Very low fluorescence intensity of the carbazole derivative in Tris HCl buffer in the presence of the NaCl or KCl increased significantly after addition of the 22HT G4 DNA. Binding stoichiometry of the ligand/G-quadruplex was investigated with absorbance-based Job plots. Carbazole ligand binds 22HT with about 2:1 stoichiometry in the presence of sodium and potassium ions. The binding mode appeared to be end-stacking with comparable binding constants of ~105 M−1 as determined from UV-Vis and fluorescence titrations data. The carbazole ligand is able to induce formation of G4 structure of 22HT in the absence of salt, which was proved by CD spectroscopy and melting studies. The derivative of carbazole 3 shows significantly higher cytotoxicity against breast cancer cells then for non-tumorigenic breast epithelial cells. The cytotoxic activity of ligand seems to be not associated with telomerase inhibition.
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Bhattacharjee S, Chakraborty S, Chorell E, Sengupta PK, Bhowmik S. Importance of the hydroxyl substituents in the B-ring of plant flavonols on their preferential binding interactions with VEGF G-quadruplex DNA: Multi-spectroscopic and molecular modeling studies. Int J Biol Macromol 2018; 118:629-639. [PMID: 29953891 DOI: 10.1016/j.ijbiomac.2018.06.115] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 06/22/2018] [Accepted: 06/23/2018] [Indexed: 10/28/2022]
Abstract
G-quadruplex (G4) structures are known to be promising anticancer drug targets and flavonols (an important class of flavonoids) are small molecules reported to possess several health-promoting properties including those of anticancer activities. In this work, we explored the interactions of the structurally related plant flavonols kaempferol (KAE; 3,5,7,4'OH flavone) and morin (MOR; 3,5,7,2',4'OH flavone) with various G4-DNA sequences along with duplex DNA using a combination of spectroscopic and molecular docking studies. Our results revealed that KAE shows preferential interaction with VEGF G4-DNA in comparison to the other G4 sequences and duplex DNA. Moreover, KAE enhances the thermal stability of VEGF G4-DNA. In contrast, MOR exhibits an appreciably weaker level of interaction with both duplex and various G4-DNAs, with no significant structural specificity. The contrasting DNA binding behaviors suggest a crucial role of the 2'OH substituent in the B-ring of flavonol moiety. While KAE is relatively planar, MOR adopts a significantly non-planar conformation attributable to steric hindrance from the additional 2'OH substituent. This small structural difference is apparently very important for the ability of KAE and MOR to interact with VEGF G4-DNA. Thus, KAE (but not MOR) appears to be an effective ligand for VEGF G4-DNA, opening up possibilities of its application for regulation of gene expression in cancer cells.
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Affiliation(s)
- Snehasish Bhattacharjee
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92 Acharya Prafulla Chandra Road, Kolkata 700009, India
| | - Sandipan Chakraborty
- Department of Microbiology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata 700019, India
| | - Erik Chorell
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
| | - Pradeep K Sengupta
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92 Acharya Prafulla Chandra Road, Kolkata 700009, India.
| | - Sudipta Bhowmik
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92 Acharya Prafulla Chandra Road, Kolkata 700009, India.
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Głuszyńska A, Juskowiak B, Kuta-Siejkowska M, Hoffmann M, Haider S. Carbazole Derivatives' Binding to c-KIT G-Quadruplex DNA. Molecules 2018; 23:E1134. [PMID: 29747481 PMCID: PMC6099540 DOI: 10.3390/molecules23051134] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 04/25/2018] [Accepted: 05/07/2018] [Indexed: 11/17/2022] Open
Abstract
The binding affinities of three carbazole derivatives to the intramolecular G-quadruplex (GQ) DNA formed by the sequence 5′-AGGGAGGGCGCTGGGAGGAGGG-3′, derived from the c-KIT 1 oncogene region, were investigated. All carbazole cationic ligands that differed in the substituents on the nitrogen atom were able to stabilize G-quadruplex, as demonstrated using UV-Vis, fluorescence and CD spectroscopic techniques as well as molecular modeling. The spectrophotometric titration results showed spectral features characteristic of these ligands-bathochromic shifts and initial hypochromicity followed by hyperchromicity at higher GQ concentrations. All free carbazole ligands exhibited modest fluorescent properties, but after binding to the DNA the fluorescence intensity increased significantly. The binding affinities of carbazole ligands to the c-KIT 1 DNA were comparable showing values in the order of 10⁵ M−1. Molecular modeling highlights the differences in interactions between each particular ligand and studied G-quadruplex, which potentially influenced binding strength. Obtained results relevant that all three investigated ligands have stabilization properties on studied G-quadruplex.
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Affiliation(s)
- Agata Głuszyńska
- Laboratory of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Umultowska Street 89b, 61-614 Poznań, Poland.
| | - Bernard Juskowiak
- Laboratory of Bioanalytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Umultowska Street 89b, 61-614 Poznań, Poland.
| | - Martyna Kuta-Siejkowska
- Laboratory of Quantum Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Umultowska Street 89b, 61-614 Poznań, Poland.
| | - Marcin Hoffmann
- Laboratory of Quantum Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Umultowska Street 89b, 61-614 Poznań, Poland.
| | - Shozeb Haider
- School of Pharmacy, University College London, London WC1N 1AX, UK.
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