1
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Sun JW, Zou J, Zheng Y, Yuan H, Xie YZY, Wang XN, Ou TM. Design, synthesis, and evaluation of novel quindoline derivatives with fork-shaped side chains as RNA G-quadruplex stabilizers for repressing oncogene NRAS translation. Eur J Med Chem 2024; 271:116406. [PMID: 38688064 DOI: 10.1016/j.ejmech.2024.116406] [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: 02/03/2024] [Revised: 03/25/2024] [Accepted: 04/09/2024] [Indexed: 05/02/2024]
Abstract
NRAS mutation is the second most common oncogenic factor in cutaneous melanoma. Inhibiting NRAS translation by stabilizing the G-quadruplex (G4) structure with small molecules seems to be a potential strategy for cancer therapy due to the NRAS protein's lack of a druggable pocket. To enhance the effects of previously reported G4 stabilizers quindoline derivatives, we designed and synthesized a novel series of quindoline derivatives with fork-shaped side chains by introducing (alkylamino)alkoxy side chains. Panels of experimental results showed that introducing a fork-shaped (alkylamino)alkoxy side chain could enhance the stabilizing abilities of the ligands against NRAS RNA G-quadruplexes and their anti-melanoma activities. One of them, 10b, exhibited good antitumor activity in the NRAS-mutant melanoma xenograft mouse model, showing the therapeutic potential of this kind of compounds.
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Affiliation(s)
- Jia-Wei Sun
- School of Pharmaceutical Sciences, State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou, 510006, China
| | - Jing Zou
- School of Pharmaceutical Sciences, State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou, 510006, China
| | - Ying Zheng
- School of Pharmaceutical Sciences, State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou, 510006, China
| | - Hao Yuan
- School of Pharmaceutical Sciences, State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou, 510006, China
| | - Yuan-Ze-Yu Xie
- School of Pharmaceutical Sciences, State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou, 510006, China
| | - Xiao-Na Wang
- School of Pharmaceutical Sciences, State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou, 510006, China
| | - Tian-Miao Ou
- School of Pharmaceutical Sciences, State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou, 510006, China.
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2
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Tomlovich RA, Lash TD. Synthesis, Spectroscopic Properties, and Metalation of 3-Alkoxybenziporphyrins. Molecules 2024; 29:1903. [PMID: 38675721 PMCID: PMC11054816 DOI: 10.3390/molecules29081903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 04/15/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024] Open
Abstract
A series of 5-alkoxy-1,3-benzenedicarbaldehydes and related dimers were prepared in three steps from dimethyl 5-hydroxyisophthalate. Acid catalyzed condensation of the dialdehydes with a tripyrrane dicarboxylic acid, followed by oxidation with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone, afforded good yields of 3-alkoxybenziporphyrins, although dimeric tetraaldehydes failed to give isolatable porphyrinoid products. Proton NMR spectroscopy gave no indication of an aromatic ring current, but addition of trifluoroacetic acid resulted in the formation of dications that exhibited weakly diatropic characteristics. Spectroscopic titration with TFA demonstrated that stepwise protonation took place, generating monocationic and dicationic species. 3-Alkoxybenziporphyrins reacted with nickel(II) or palladium(II) acetate to give the related nickel(II) or palladium(II) complexes. These stable organometallic derivatives showed increased diatropic properties that were most pronounced for the palladium(II) complexes. These unique porphyrinoids provide further insights into the properties of benziporphyrins.
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Affiliation(s)
| | - Timothy D. Lash
- Department of Chemistry, Illinois State University, Normal, IL 61790-4160, USA;
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3
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Kumari A, Pandav K, Nath M, Barthwal R, Peddinti RK. Recognition of human telomeric G-quadruplex DNA by 1,5-disubstituted diethyl-amido anthraquinone derivative in different ion environments causing thermal stabilization and apoptosis. J Biomol Struct Dyn 2024:1-17. [PMID: 38174595 DOI: 10.1080/07391102.2023.2298733] [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: 10/09/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024]
Abstract
Ligand binding to G-quadruplex (G4) structures at human telomeric DNA ends promotes thermal stabilization, disrupting the interaction of the telomerase enzyme, which is found active in 80-85% of cancers and serves as a molecular marker. Anthraquinone compounds are well-known G-quadruplex (G4) binders that inhibit telomerase and induce apoptosis in cancer cells. Our current investigation is based on 1,5-bis[3-(diethylamino)propionamido]anthracene-9,10-dione, a derivative of anthraquinone and its binding characterization with two different human telomeric DNA structures, wHTel26 and HTel22, in the effect of K+ and Na+ by using an array of biophysical, calorimetry, molecular docking and cell viability assay techniques. Binding constants (Kb) in the range of ∼105-107 M-1 and stoichiometries of 1:1, 2:1 & 4:1 were obtained from the absorbance, fluorescence, and circular dichroism study. Remarkable hypochromism (55, 97%) and ∼17 nm shift in absorbance, fluorescence quenching (95, 97%), the unaltered value of fluorescence lifetime, restoration of Circular Dichroism bands, absence of ICD band, indicated the external groove binding/binding somewhere at loops. This is also evident in molecular docking results, the ligand binds to groove forming base (G4, G5, G24, T25) and in the vicinity to TTA loop (G14, G15, T17) bases of wHTel26 and HTel22, respectively. Thermal stabilization induced by ligand was found greater in Na+ ion (27.5 °C) than (19.1 °C) in K+ ion. Ligand caused cell toxicity in MCF-7 cancer cell lines with an IC50 value of ∼8.4 µM. The above findings suggest the ligand, 1,5-bis[3-(diethylamino)propionamido]anthracene-9,10-dione could be a potent anticancer drug candidate and has great therapeutic implications.Binding of disubstituted amido anthraquinone derivative, 1,5-bis[3-(diethylamino)propionamido]anthracene-9,10-dione to human telomere HTel22 antiparallel conformation induced thermal stabilization.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anjana Kumari
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Kumud Pandav
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Mala Nath
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Ritu Barthwal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Rama Krishna Peddinti
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
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4
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Roy S, Bhattacharya S. An in silico approach to evaluate the bindings of natural flavonoids and RNA-DNA hybrids. J Biomol Struct Dyn 2023:1-8. [PMID: 37922129 DOI: 10.1080/07391102.2023.2275184] [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: 08/08/2023] [Accepted: 10/20/2023] [Indexed: 11/05/2023]
Abstract
Flavonoids, low molecular weight polyphenolic compounds, are important natural products that belong to plant secondary metabolites. They have diverse biomedical applications such as antioxidative, anti-inflammatory, enzyme inhibitory, antimutagenic, anticarcinogenic, aromatase inhibitory effects, etc. Some of the flavonoids have been exported for bindings with certain DNA and tRNA structures both experimentally and computationally. RNA-DNA hybrid (RDH) falls into an important category of noncanonical nucleic acid structures that have many important biological functions. We have investigated the interaction of RDH structures with some of the dietary flavonoids with the aid of computational methods such as docking and molecular dynamics simulation. The presence of the - OH group on the ligand and the availability of a proper binding pocket in the macromolecule are the two main factors driving the binding preference. Thus, this computationally guided report explains the binding of the flavonoids with RDH structures to assist the researchers in designing noncanonical nucleic acid-targeted drug molecules.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Soma Roy
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata, India
| | - Santanu Bhattacharya
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata, India
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, India
- Department of Chemistry, Indian Institute of Science, Education & Research, Tirupati, India
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5
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Dey A, Anand K, Singh A, Prasad R, Barthwal R. MOSR and NDHA Genes Comprising G-Quadruplex as Promising Therapeutic Targets against Mycobacterium tuberculosis: Molecular Recognition by Mitoxantrone Suppresses Replication and Gene Regulation. Genes (Basel) 2023; 14:978. [PMID: 37239338 PMCID: PMC10217741 DOI: 10.3390/genes14050978] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/19/2022] [Accepted: 04/18/2023] [Indexed: 05/28/2023] Open
Abstract
Occurrence of non-canonical G-quadruplex (G4) DNA structures in the genome have been recognized as key factors in gene regulation and several other cellular processes. The mosR and ndhA genes involved in pathways of oxidation sensing regulation and ATP generation, respectively, make Mycobacterium tuberculosis (Mtb) bacteria responsible for oxidative stress inside host macrophage cells. Circular Dichroism spectra demonstrate stable hybrid G4 DNA conformations of mosR/ndhA DNA sequences. Real-time binding of mitoxantrone to G4 DNA with an affinity constant ~105-107 M-1, leads to hypochromism with a red shift of ~18 nm, followed by hyperchromism in the absorption spectra. The corresponding fluorescence is quenched with a red shift ~15 nm followed by an increase in intensity. A change in conformation of the G4 DNA accompanies the formation of multiple stoichiometric complexes with a dual binding mode. The external binding of mitoxantrone with a partial stacking with G-quartets and/or groove binding induces significant thermal stabilization, ~20-29 °C in ndhA/mosR G4 DNA. The interaction leads to a two/four-fold downregulation of transcriptomes of mosR/ndhA genes apart from the suppression of DNA replication by Taq polymerase enzyme, establishing the role of mitoxantrone in targeting G4 DNA, as an alternate strategy for effective anti-tuberculosis action in view of deadly multi-drug resistant tuberculosis disease causing bacterial strains t that arise from existing therapeutic treatments.
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Affiliation(s)
- Arpita Dey
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Kushi Anand
- Centre for Infectious Disease Research, Indian Institute of Science, Bengaluru 560012, Karnataka, India
| | - Amit Singh
- Centre for Infectious Disease Research, Indian Institute of Science, Bengaluru 560012, Karnataka, India
| | - Ramasare Prasad
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Ritu Barthwal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
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6
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Roy S, Maiti B, Banerjee N, Kaulage MH, Muniyappa K, Chatterjee S, Bhattacharya S. New Xanthone Derivatives as Potent G-Quadruplex Binders for Developing Anti-Cancer Therapeutics. ACS Pharmacol Transl Sci 2023; 6:546-566. [PMID: 37082748 PMCID: PMC10111628 DOI: 10.1021/acsptsci.2c00205] [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: 10/23/2022] [Indexed: 04/22/2023]
Abstract
Xanthone is an important scaffold for various medicinally relevant compounds. However, it has received scant attention in the design of agents that are cytotoxic to cancer cells via targeting the stabilization of G-quadruplex (G4) nucleic acids. Specific G4 DNA recognition against double-stranded (ds) DNA is receiving epoch-making interest for the development of G4-mediated anticancer agents. Toward this goal, we have synthesized xanthone-based derivatives with various functionalized side-arm substituents that exhibited significant selectivity for G4 DNA as compared to dsDNA. The specific interaction has been demonstrated by performing various biophysical experiments. Based on the computational study as well as the competitive ligand binding assay, it is inferred that the potent compounds exhibit an end-stacking mode of binding with G4 DNA. Additionally, compound-induced conformational changes in the flanking nucleotides form the binding pocket for effective interaction. Selective action of the compounds on cancer cells suggests their effectiveness as potent anti-cancer agents. This study promotes the importance of structure-based screening approaches to get molecular insights for new scaffolds toward desired specific recognition of non-canonical G4 DNA structures.
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Affiliation(s)
- Soma Roy
- Department
of Organic Chemistry, Indian Institute of
Science, Bangalore 560012, India
- School
of Applied & Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Bappa Maiti
- School
of Applied & Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Nilanjan Banerjee
- Department
of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700054, India
| | - Mangesh H. Kaulage
- Department
of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Kalappa Muniyappa
- Department
of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Subhrangsu Chatterjee
- Department
of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700054, India
| | - Santanu Bhattacharya
- Department
of Organic Chemistry, Indian Institute of
Science, Bangalore 560012, India
- School
of Applied & Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
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7
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Ghosh S, De D, Banerjee V, Biswas S, Ghosh U. High throughput screening of a new fluorescent G-quadruplex ligand having telomerase inhibitory activity in human A549 cells. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2023:1-22. [PMID: 36919622 DOI: 10.1080/15257770.2023.2188220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Identification of a new G-quadruplex ligand having anti-telomerase activity would be a promising strategy for cancer therapy. The screened compound from ZINC database using docking studies was experimentally verified for its binding with three different telomeric G-quadruplex DNA sequences and anti-telomerase activity in A549 cells. Identified compound is an intrinsic fluorescent molecule, permeable to live cells and has a higher affinity to 22AG out of three different telomeric G-quadruplex DNA. It showed cytotoxicity and a significant reduction of telomerase activity in human A549 cells at a very low dose. So, this compound has a good anti-cancer effect.
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Affiliation(s)
- Sourav Ghosh
- Department of Biochemistry & Biophysics, University of Kalyani, Kalyani, India
| | - Debapriya De
- Department of Biochemistry & Biophysics, University of Kalyani, Kalyani, India
| | - Victor Banerjee
- Department of Biochemistry & Biophysics, University of Kalyani, Kalyani, India
| | - Soumyajit Biswas
- Department of Biochemistry & Biophysics, University of Kalyani, Kalyani, India
| | - Utpal Ghosh
- Department of Biochemistry & Biophysics, University of Kalyani, Kalyani, India
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8
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Roy S, Chakraborty N, Maiti B, Muniyappa K, Bhattacharya S. Design and Synthesis of Xanthone Analogues Conjugated with Aza-aromatic Substituents as Promising G-Quadruplex Stabilizing Ligands and their Selective Cancer Cell Cytotoxic Action. Chembiochem 2023; 24:e202200609. [PMID: 36455103 DOI: 10.1002/cbic.202200609] [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: 10/24/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022]
Abstract
We have examined the stabilization of higher-order noncanonical G-quadruplex (G4) DNA structures formed by the G-rich sequences in the promoter region of oncogenes such as c-MYC, c-KIT, VEGF and BCl2 by newly synthesized, novel nitrogen-containing aromatics conjugated to xanthone moiety. Compounds with N-heterocyclic substituents such as pyridine (XNiso), benzimidazole (XBIm), quinoxaline (XQX) and fluorophore dansyl (XDan) showed greater effectiveness in stabilizing the G4 DNA as well as selective cytotoxicity for cancer cells (mainly A549) over normal cells both in terms of UV-Vis spectral titrations and cytotoxicity assay. Both fluorescence spectral titrimetric measurements and circular dichroism (CD) melting experiments further substantiated the G4 stabilization phenomenon by these small-molecular ligands. In addition, these compounds could induce the formation of parallel G4 structures in the absence of any added salt condition in Tris⋅HCl buffer at 25 °C. In a polymerase stop assay, the formation of stable G4 structures in the promoter of oncogenes and halting of DNA synthesis in the presence of the above-mentioned compounds was demonstrated by using oncogene promoter as the DNA synthesis template. Apoptosis-mediated cell death of the cancer cells was proved by Annexin V-PI dual staining assay and cell-cycle arrest occurred in the S phase of the cell cycles. The plausible mode of binding involves the stacking of the xanthone core on the G4 DNA plane with the possibility of interaction with the 5'-overhang as indicated by molecular dynamics simulation studies.
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Affiliation(s)
- Soma Roy
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, 560012, India.,School of Applied & Interdisciplinary Sciences Indian Association for the Cultivation of Science, Kolkata, 700032, India
| | - Nirmal Chakraborty
- School of Applied & Interdisciplinary Sciences Indian Association for the Cultivation of Science, Kolkata, 700032, India
| | - Bappa Maiti
- School of Applied & Interdisciplinary Sciences Indian Association for the Cultivation of Science, Kolkata, 700032, India
| | - Kalappa Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Santanu Bhattacharya
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, 560012, India.,School of Applied & Interdisciplinary Sciences Indian Association for the Cultivation of Science, Kolkata, 700032, India
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9
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Jin M, Li J, Chen Y, Zhao J, Zhang J, Zhang Z, Du P, Zhang L, Lu X. Near-Infrared Small Molecule as a Specific Fluorescent Probe for Ultrasensitive Recognition of Antiparallel Human Telomere G-Quadruplexes. ACS APPLIED MATERIALS & INTERFACES 2021; 13:32743-32752. [PMID: 34228441 DOI: 10.1021/acsami.1c07101] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
In the past 10 years, many fluorescent probes have been developed to recognize G-quadruplexes (G4s) since G4s play an important role in biological systems. However, the selectivity and sensitivity of existing probes for G4s limit their further applications. Herein, we design and synthesize a new probe (TOVJ) by introducing 9-vinyljulolidine into TO. The new probe exhibits almost no fluorescence in an aqueous solution. Upon interacting with G4s, especially the antiparallel G4s, the fluorescence intensity was greatly enhanced (maximum 2742-fold) with a large Stokes shift of 198 nm and the maximum emission peak at 694 nm (near-infrared region). TOVJ showed high sensitivity and selectivity to G4s over other DNA topologies (ssDNA/dsDNA), especially to antiparallel G4s. For antiparallel human telomere G4 detection, the limits of detection of Hum24 and 22AG Na+ were as low as 164 and 231 pM, respectively. This indicates that TOVJ is a highly sensitive fluorescence sensor that can be effectively used for antiparallel human telomere G4 detection. The result of live-cell imaging showed that TOVJ could enter live cells and locate in the mitochondria.
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Affiliation(s)
- Ming Jin
- Tianjin Key Laboratory of Molecular Optoelectronic, Department of Chemistry, Tianjin University, Tianjin 300072, People's Republic of China
| | - Jing Li
- Tianjin Key Laboratory of Molecular Optoelectronic, Department of Chemistry, Tianjin University, Tianjin 300072, People's Republic of China
| | - Yang Chen
- Tianjin Key Laboratory of Molecular Optoelectronic, Department of Chemistry, Tianjin University, Tianjin 300072, People's Republic of China
| | - Jie Zhao
- Tianjin Key Laboratory of Molecular Optoelectronic, Department of Chemistry, Tianjin University, Tianjin 300072, People's Republic of China
| | - Jiahui Zhang
- Tianjin Key Laboratory of Molecular Optoelectronic, Department of Chemistry, Tianjin University, Tianjin 300072, People's Republic of China
| | - Zhen Zhang
- Tianjin Key Laboratory of Molecular Optoelectronic, Department of Chemistry, Tianjin University, Tianjin 300072, People's Republic of China
| | - Peiyao Du
- Tianjin Key Laboratory of Molecular Optoelectronic, Department of Chemistry, Tianjin University, Tianjin 300072, People's Republic of China
| | - Libing Zhang
- Tianjin Key Laboratory of Molecular Optoelectronic, Department of Chemistry, Tianjin University, Tianjin 300072, People's Republic of China
| | - Xiaoquan Lu
- Key Laboratory of Bioelectrochemistry and Environmental Analysis of Gansu Province, College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou 730070, People's Republic of China
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Roy S, Ali A, Bhattacharya S. Theoretical Insight into the Library Screening Approach for Binding of Intermolecular G-Quadruplex RNA and Small Molecules through Docking and Molecular Dynamics Simulation Studies. J Phys Chem B 2021; 125:5489-5501. [PMID: 34029082 DOI: 10.1021/acs.jpcb.0c10991] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The interactions of intermolecular G-quadruplex RNA and small molecules have been investigated by computational studies. Various anthraquinone, bisbenzimidazole, and carbazole-benzimidazole based ligands have shown a distinct preference to G-quadruplex structures as opposed to the corresponding duplex forms of DNA that were docked with telomeric G-quadruplex RNA. The comparative binding study of such ligands with G-quadruplex (G4) RNA showed higher binding affinities toward carbazole-benzimidazole ligands than those of the anthraquinone and bisbenzimidazole based ligands. A molecular dynamics simulation study was used to examine quadruplex-ligand interactions. Analysis of the binding free energy indicated the formation of the thermodynamically favorable RNA-ligand complex. The formation of several H-bonding interactions and the change of the solvent accessible surface area (SASA) also support the effective binding of the carbazole-benzimidazole ligands with G4 RNA structures. Thus, the library screening approach has assisted in getting a structure-activity relationship for the selected small molecules toward the G-quadruplex RNA binding, which can be applied in the targeting of G-quadruplex RNA medicated anticancer therapeutics.
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Affiliation(s)
- Soma Roy
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Asfa Ali
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Santanu Bhattacharya
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India.,School of Applied & Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata, West Bengal 700032, India
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11
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Roy S, Ali A, Kamra M, Muniyappa K, Bhattacharya S. Specific stabilization of promoter G-Quadruplex DNA by 2,6-disubstituted amidoanthracene-9,10-dione based dimeric distamycin analogues and their selective cancer cell cytotoxicity. Eur J Med Chem 2020; 195:112202. [PMID: 32302880 DOI: 10.1016/j.ejmech.2020.112202] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/19/2020] [Accepted: 03/01/2020] [Indexed: 10/24/2022]
Abstract
We have designed and synthesized anthraquinone containing compounds which have oligopyrrole side chains of varying lengths. These compounds stabilized the G-quadruplex DNA formed in the promoter regions of c-MYC oncogenes selectively over the duplex DNA. These observations were recorded using UV-vis spectroscopic titrations, fluorescence measurements and circular dichroism (CD) spectral titrations. The potency of the compounds to stabilize the G4 DNA has been shown from the thermal denaturation experiments. The compound interacts with c-MYC G-quadruplex DNA through stacking mode as obtained from ethidium bromide displacement assay, cyclic voltammetric titration, and docking experiments. Molecular modeling studies suggested that the stacking of the anthraquinone moiety over the G-tetrad of the G4 structures are responsible for the stability of such quadruplex secondary structure. Furthermore, polymerase stop assay also supported the formation of stable G4 structures in the presence of the above-mentioned compounds. The compounds have shown selective cancer cell (HeLa and HEK293T) cytotoxicity over normal cells (NIH3T3 and HDFa) under in vitro conditions as determined from MTT based cell viability assay. Apoptosis was found to be the mechanistic pathway underlying the cancer cell cytotoxicity as obtained from Annexin V-FITC and PI dual staining assay which was further substantiated by nuclear morphological changes as observed by AO/EB dual staining assay. Cellular morphological changes, as well as nuclear condensation and fragmentation upon treatment with these compounds, were observed under bright field and confocal microscopy.
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Affiliation(s)
- Soma Roy
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Asfa Ali
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Mohini Kamra
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Kalappa Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Santanu Bhattacharya
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, 560012, India; School of Applied & Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata, 700032, India.
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12
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Chen X, Tang WJ, Shi JB, Liu MM, Liu XH. Therapeutic strategies for targeting telomerase in cancer. Med Res Rev 2019; 40:532-585. [PMID: 31361345 DOI: 10.1002/med.21626] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/12/2019] [Accepted: 07/16/2019] [Indexed: 12/13/2022]
Abstract
Telomere and telomerase play important roles in abnormal cell proliferation, metastasis, stem cell maintenance, and immortalization in various cancers. Therefore, designing of drugs targeting telomerase and telomere is of great significance. Over the past two decades, considerable knowledge regarding telomere and telomerase has been accumulated, which provides theoretical support for the design of therapeutic strategies such as telomere elongation. Therefore, the development of telomere-based therapies such as nucleoside analogs, non-nucleoside small molecules, antisense technology, ribozymes, and dominant negative human telomerase reverse transcriptase are being prioritized for eradicating a majority of tumors. While the benefits of telomere-based therapies are obvious, there is a need to address the limitations of various therapeutic strategies to improve the possibility of clinical applications. In this study, current knowledge of telomere and telomerase is discussed, and therapeutic strategies based on recent research are reviewed.
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Affiliation(s)
- Xing Chen
- School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, People's Republic of China
| | - Wen-Jian Tang
- School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, People's Republic of China
| | - Jing Bo Shi
- School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, People's Republic of China
| | - Ming Ming Liu
- School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, People's Republic of China
| | - Xin-Hua Liu
- School of Pharmacy, Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, People's Republic of China
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13
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Sullivan HJ, Readmond C, Radicella C, Persad V, Fasano TJ, Wu C. Binding of Telomestatin, TMPyP4, BSU6037, and BRACO19 to a Telomeric G-Quadruplex-Duplex Hybrid Probed by All-Atom Molecular Dynamics Simulations with Explicit Solvent. ACS OMEGA 2018; 3:14788-14806. [PMID: 30555989 PMCID: PMC6289566 DOI: 10.1021/acsomega.8b01574] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Accepted: 09/11/2018] [Indexed: 06/09/2023]
Abstract
A promising anticancer therapeutic strategy is the stabilization of telomeric G-quadruplexes using G-quadruplex-binding small molecules. Although many G-quadruplex-specific ligands have been developed, their low potency and selectivity to G-quadruplexes over duplex remains unsolved. Recently, a crystal structure of a telomeric 3' quadruplex-duplex hybrid was reported and the quadruplex-duplex interface was suggested to a good target to address the issues. However, there are no high-resolution complex structures reported for G-quadruplex ligands except for a docked BSU6037. In this study, molecular dynamic (MD) binding simulations with a free ligand were used to study binding poses and dynamics of four representative ligands: telomestatin, TMPyP4, BSU6037, and BRACO19. The MD data showed that BSU6037 was able to fully intercalate into the interface whereas TMPyP4 and BRACO19 could only maintain partial intercalation into the interface and telomestatin only binds at the quadruplex and duplex ends. Both linear ligands, BSU6037 and BRACO19, were able to interact with the interface, yet they were not selective over duplex DNA. The DNA geometry, binding modes, and binding pathways were systematically characterized, and the binding energy was calculated and compared for each system. The interaction of the ligands to the interface was by the means of an induced-fit binding mechanism rather than a lock-key mechanism, consisting of the DNA unfolding at the interface to allow entrance of the drug and then the refolding and repacking of the DNA and the ligand to further stabilize the G-quadruplex. On the basis of the findings in this study, modifications were suggested to optimize the interface binding for TMPyp4 and telomestatin.
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Affiliation(s)
- Holli-Joi Sullivan
- Chemistry
& Biochemistry and Department of Molecular & Cellular Biosciences, College of Science and Mathematics, Rowan University, Glassboro, New Jersey 08028, United States
| | - Carolyn Readmond
- Chemistry
& Biochemistry and Department of Molecular & Cellular Biosciences, College of Science and Mathematics, Rowan University, Glassboro, New Jersey 08028, United States
| | - Christina Radicella
- Chemistry
& Biochemistry and Department of Molecular & Cellular Biosciences, College of Science and Mathematics, Rowan University, Glassboro, New Jersey 08028, United States
| | - Victoria Persad
- Chemistry
& Biochemistry and Department of Molecular & Cellular Biosciences, College of Science and Mathematics, Rowan University, Glassboro, New Jersey 08028, United States
| | - Thomas J. Fasano
- Chemistry
& Biochemistry and Department of Molecular & Cellular Biosciences, College of Science and Mathematics, Rowan University, Glassboro, New Jersey 08028, United States
| | - Chun Wu
- Chemistry
& Biochemistry and Department of Molecular & Cellular Biosciences, College of Science and Mathematics, Rowan University, Glassboro, New Jersey 08028, United States
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14
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Carella A, Roviello V, Iannitti R, Palumbo R, La Manna S, Marasco D, Trifuoggi M, Diana R, Roviello GN. Evaluating the biological properties of synthetic 4-nitrophenyl functionalized benzofuran derivatives with telomeric DNA binding and antiproliferative activities. Int J Biol Macromol 2018; 121:77-88. [PMID: 30261256 DOI: 10.1016/j.ijbiomac.2018.09.153] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/12/2018] [Accepted: 09/24/2018] [Indexed: 11/25/2022]
Abstract
Four 4-nitrophenyl-functionalized benzofuran (BF1, BF2) and benzodifuran (BDF1, BDF2) compounds were synthesized by a convenient route based on the Craven reaction. All the compounds underwent a detailed chemical-physical characterization to evaluate their structural, thermal and optical properties. An investigation on the therapeutic potential of the reported compounds was performed by analyzing their antiproliferative activity on prostatic tumour cells (PC-3). In both classes of compounds, anticancer potential is in direct correlation with the lipophilicity. From our study it emerged that antiproliferative activity was higher for benzofuran derivatives as compared to benzodifuran systems. Moreover, we report a mechanistic study relative to the most promising molecule, i.e. the apolar benzofuran BF1, that relates the antiproliferative properties found in our investigation to its ability to bind telomeric DNA (proven by CD and fluorescence techniques on tel22 G4 DNA), and highlights its unexpected impact on cell cycle progression.
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Affiliation(s)
- Antonio Carella
- University of Naples Federico II, Department of Chemical Sciences, Via Cintia 21, I-80126 Naples, Italy
| | - Valentina Roviello
- Analytical Chemistry for the Environment and CeSMA (Advanced Metrologic Service Center), University of Naples Federico II, Corso N. Protopisani, 80146 Naples, Italy
| | - Roberta Iannitti
- CNR, Institute of Biostructure and Bioimaging - (Via Mezzocannone Site and Headquarters), 80134 Naples, Italy
| | - Rosanna Palumbo
- CNR, Institute of Biostructure and Bioimaging - (Via Mezzocannone Site and Headquarters), 80134 Naples, Italy
| | - Sara La Manna
- University of Naples Federico II, Department of Pharmacy, Via Mezzocannone 16, 80134 Naples, Italy
| | - Daniela Marasco
- CNR, Institute of Biostructure and Bioimaging - (Via Mezzocannone Site and Headquarters), 80134 Naples, Italy; University of Naples Federico II, Department of Pharmacy, Via Mezzocannone 16, 80134 Naples, Italy
| | - Marco Trifuoggi
- University of Naples Federico II, Department of Chemical Sciences, Via Cintia 21, I-80126 Naples, Italy
| | - Rosita Diana
- University of Naples Federico II, Department of Chemical Sciences, Via Cintia 21, I-80126 Naples, Italy
| | - Giovanni N Roviello
- CNR, Institute of Biostructure and Bioimaging - (Via Mezzocannone Site and Headquarters), 80134 Naples, Italy.
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15
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Xie X, Reznichenko O, Chaput L, Martin P, Teulade-Fichou MP, Granzhan A. Topology-Selective, Fluorescent “Light-Up” Probes for G-Quadruplex DNA Based on Photoinduced Electron Transfer. Chemistry 2018; 24:12638-12651. [DOI: 10.1002/chem.201801701] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Indexed: 12/26/2022]
Affiliation(s)
- Xiao Xie
- CNRS UMR9187, INSERM U1196; Institut Curie; PSL Research University; 91405 Orsay France
- CNRS UMR9187, INSERM U1196; Université Paris Sud, Université Paris-Saclay; 91405 Orsay France
| | - Oksana Reznichenko
- CNRS UMR9187, INSERM U1196; Institut Curie; PSL Research University; 91405 Orsay France
- CNRS UMR9187, INSERM U1196; Université Paris Sud, Université Paris-Saclay; 91405 Orsay France
| | - Ludovic Chaput
- CNRS UMR9187, INSERM U1196; Institut Curie; PSL Research University; 91405 Orsay France
- CNRS UMR9187, INSERM U1196; Université Paris Sud, Université Paris-Saclay; 91405 Orsay France
- CNRS UPR2301; Institut de Chimie des Substances Naturelles (ICSN); 91198 Gif-sur-Yvette France
| | - Pascal Martin
- ITODYS, CNRS UMR7086; Université Paris Diderot; 75205 Paris France
| | - Marie-Paule Teulade-Fichou
- CNRS UMR9187, INSERM U1196; Institut Curie; PSL Research University; 91405 Orsay France
- CNRS UMR9187, INSERM U1196; Université Paris Sud, Université Paris-Saclay; 91405 Orsay France
| | - Anton Granzhan
- CNRS UMR9187, INSERM U1196; Institut Curie; PSL Research University; 91405 Orsay France
- CNRS UMR9187, INSERM U1196; Université Paris Sud, Université Paris-Saclay; 91405 Orsay France
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16
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Al-Mughaid H, Al-Zoubi RM, Khazaaleh M, Grindley TB. Assembly and inhibitory activity of monovalent mannosides terminated with aromatic methyl esters: The effect of naphthyl groups. Carbohydr Res 2017; 446-447:76-84. [PMID: 28549256 DOI: 10.1016/j.carres.2017.03.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 03/13/2017] [Accepted: 03/16/2017] [Indexed: 10/19/2022]
Abstract
A series of monovalent α-D-mannoside ligands terminated with aromatic methyl esters have been synthesized in excellent yields using the Cu(I) catalyzed azide-alkyne 1,3-dipolar cycloaddition ("click chemistry"). These mannosides were designed to have a unique aglycone moiety (tail) that combines a triazole ring attached to aromatic methyl esters via a six carbon alkyl chain. The mannose unit of these ligands was linked at the ortho, meta, and para positions of substituted methyl benzoates and 1-, 3-, and 6-substituted methyl 2-napthaoates. In hemagglutination assays, ligands (32A-38A) showed better inhibitory activities than the standard inhibitor, methyl α-D-mannopyranoside. Overall, the naphthyl-based mannoside ligand (37A) showed the best activity and therefore merits further development.
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Affiliation(s)
- Hussein Al-Mughaid
- Department of Chemistry, Jordan University of Science and Technology, PO Box 3030, Irbid 22110, Jordan; Department of Chemistry, Dalhousie University, Halifax, NS, B3H 4J3, Canada.
| | - Raed M Al-Zoubi
- Department of Chemistry, Jordan University of Science and Technology, PO Box 3030, Irbid 22110, Jordan
| | - Maha Khazaaleh
- Department of Chemistry, Jordan University of Science and Technology, PO Box 3030, Irbid 22110, Jordan
| | - T Bruce Grindley
- Department of Chemistry, Dalhousie University, Halifax, NS, B3H 4J3, Canada.
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17
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Ali A, Kamra M, Roy S, Muniyappa K, Bhattacharya S. Enhanced G-Quadruplex DNA Stabilization and Telomerase Inhibition by Novel Fluorescein Derived Salen and Salphen Based Ni(II) and Pd(II) Complexes. Bioconjug Chem 2017; 28:341-352. [PMID: 28165710 DOI: 10.1021/acs.bioconjchem.6b00433] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Metal based salen complexes have been considered as an important scaffold toward targeting of DNA structures. In the present work, we have synthesized nickel(II) and palladium(II) salen and salphen complexes by using readily available fluorescein as the backbone to provide an extended aromatic surface. The metal complexes exhibit affinity toward the human telomeric G-quadruplex DNA with promising inhibition of telomerase activity. This has been ascertained by their efficiency in the long term cell proliferation assay which showed significant cancer cell toxicity in the presence of the metal complexes. Confocal microscopy showed cellular internalization followed by localization in the nucleus and mitochondria. Considerable population at the sub-G1 phase of the cell cycle showed cell death via apoptotic pathway.
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Affiliation(s)
| | | | | | | | - Santanu Bhattacharya
- Director's Research Unit, Indian Association for the Cultivation of Science , Kolkata 700 032, India
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18
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Padmapriya K, Barthwal R. NMR based structural studies decipher stacking of the alkaloid coralyne to terminal guanines at two different sites in parallel G-quadruplex DNA, [d(TTGGGGT)]4 and [d(TTAGGGT)]4. Biochim Biophys Acta Gen Subj 2017; 1861:37-48. [DOI: 10.1016/j.bbagen.2016.11.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 10/13/2016] [Accepted: 11/08/2016] [Indexed: 01/15/2023]
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19
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Padmapriya K, Barthwal R. Binding of the alkaloid coralyne to parallel G-quadruplex DNA [d(TTGGGGT)]4 studied by multi-spectroscopic techniques. Biophys Chem 2016; 219:49-58. [DOI: 10.1016/j.bpc.2016.09.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Revised: 08/17/2016] [Accepted: 09/17/2016] [Indexed: 11/16/2022]
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20
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Ali A, Kamra M, Roy S, Muniyappa K, Bhattacharya S. Novel Oligopyrrole Carboxamide based Nickel(II) and Palladium(II) Salens, Their Targeting of Human G-Quadruplex DNA, and Selective Cancer Cell Toxicity. Chem Asian J 2016; 11:2542-54. [DOI: 10.1002/asia.201600655] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 07/16/2016] [Indexed: 01/22/2023]
Affiliation(s)
- Asfa Ali
- Department of Organic Chemistry; Indian Institute of Science; Bangalore 560 012 India
| | - Mohini Kamra
- Department of Organic Chemistry; Indian Institute of Science; Bangalore 560 012 India
| | - Soma Roy
- Department of Organic Chemistry; Indian Institute of Science; Bangalore 560 012 India
| | - K. Muniyappa
- Department of Biochemistry; Indian Institute of Science; Bangalore 560 012 India
| | - Santanu Bhattacharya
- Department of Organic Chemistry; Indian Institute of Science; Bangalore 560 012 India
- Director's Research Unit; Indian Association for the Cultivation of Science; Kolkata 700 032 India
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21
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Recent advances in targeting the telomeric G-quadruplex DNA sequence with small molecules as a strategy for anticancer therapies. Future Med Chem 2016; 8:1259-90. [PMID: 27442231 DOI: 10.4155/fmc-2015-0017] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Human telomeric DNA (hTelo), present at the ends of chromosomes to protect their integrity during cell division, comprises tandem repeats of the sequence d(TTAGGG) which is known to form a G-quadruplex secondary structure. This unique structural formation of DNA is distinct from the well-known helical structure that most genomic DNA is thought to adopt, and has recently gained prominence as a molecular target for new types of anticancer agents. In particular, compounds that can stabilize the intramolecular G-quadruplex formed within the human telomeric DNA sequence can inhibit the activity of the enzyme telomerase which is known to be upregulated in tumor cells and is a major contributor to their immortality. This provides the basis for the discovery and development of small molecules with the potential for selective toxicity toward tumor cells. This review summarizes the various families of small molecules reported in the literature that have telomeric quadruplex stabilizing properties, and assesses the potential for compounds of this type to be developed as novel anticancer therapies. A future perspective is also presented, emphasizing the need for researchers to adopt approaches that will allow the discovery of molecules with more drug-like properties in order to improve the chances of lead molecules reaching the clinic in the next decade.
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22
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Sheu SY, Huang CH, Zhou JK, Yang DY. Relative stability of G-quadruplex structures: Interactions between the human Bcl2 promoter region and derivatives of carbazole and diphenylamine. Biopolymers 2016; 101:1038-50. [PMID: 24723333 DOI: 10.1002/bip.22497] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 04/07/2014] [Accepted: 04/07/2014] [Indexed: 01/24/2023]
Abstract
The bcl2 promoter region forms a G-quadruplex structure, which is a crucial target for anticancer drug development. In this study, we provide theoretical predictions of the stability of different G-quadruplex folds of the 23-mer bcl2 promoter region and G-quadruplex ligand. We take into account the whole G-quadruplex structure, including bound-cations and solvent effects, in order to compute the ligand binding free energy using molecular dynamics simulation. Two series of the carbazole and diphenylamine derivatives are used to screen for the most potent drug in terms of stabilization. The energy analysis identifies the predominant energy components affecting the stability of the various different G-quadruplex folds. The energy associated with the stability of the G-quadruplex-K(+) structures obtained displays good correlation with experimental Tm measurements. We found that loop orientation has an intrinsic influence on G-quadruplex stability and that the basket structure is the most stable. Furthermore, parallel loops are the most effective drug binding site. Our studies also demonstrate that rigidity and planarity are the key structural elements of a drug that stabilizes the G-quadruplex structure. BMVC-4 is the most potential G-quadruplex ligand. This approach demonstrates significant promise and should benefit drug design.
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Affiliation(s)
- Sheh-Yi Sheu
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, 112, Taiwan; Institute of Biomedical informatics, National Yang-Ming University, Taipei, 112, Taiwan
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23
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Maji B, Kumar K, Muniyappa K, Bhattacharya S. New dimeric carbazole-benzimidazole mixed ligands for the stabilization of human telomeric G-quadruplex DNA and as telomerase inhibitors. A remarkable influence of the spacer. Org Biomol Chem 2016; 13:8335-48. [PMID: 26149178 DOI: 10.1039/c5ob00675a] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The development of G-quadruplex (G4) DNA binding small molecules has become an important strategy for selectively targeting cancer cells. Herein, we report the design and evolution of a new kind of carbazole-based benzimidazole dimers for their efficient telomerase inhibition activity. Spectroscopic titrations reveal the ligands high affinity toward the G4 DNA with significantly higher selectivity over duplex-DNA. The electrophoretic mobility shift assay shows that the ligands efficiently promote the formation of G4 DNA even at a lower concentration of the stabilizing K(+) ions. The TRAP-LIG assay demonstrates the ligand's potential telomerase inhibition activity and also establishes that the activity proceeds via G4 DNA stabilization. An efficient nuclear internalization of the ligands in several common cancer cells (HeLa, HT1080, and A549) also enabled differentiation between normal HFF cells in co-cultures of cancer and normal ones. The ligands induce significant apoptotic response and antiproliferative activity toward cancer cells selectively when compared to the normal cells.
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Affiliation(s)
- Basudeb Maji
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560 012, India.
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24
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Zhang L, Zhang K, Rauf S, Dong D, Liu Y, Li J. Single-Molecule Analysis of Human Telomere Sequence Interactions with G-quadruplex Ligand. Anal Chem 2016; 88:4533-40. [DOI: 10.1021/acs.analchem.6b00555] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Ling Zhang
- Department
of Chemistry,
Beijing Key Laboratory for Analytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China
| | - Kaixiang Zhang
- Department
of Chemistry,
Beijing Key Laboratory for Analytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China
| | - Sana Rauf
- Department
of Chemistry,
Beijing Key Laboratory for Analytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China
| | - Duo Dong
- Department
of Chemistry,
Beijing Key Laboratory for Analytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China
| | - Yang Liu
- Department
of Chemistry,
Beijing Key Laboratory for Analytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China
| | - Jinghong Li
- Department
of Chemistry,
Beijing Key Laboratory for Analytical Methods and Instrumentation, Tsinghua University, Beijing 100084, China
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25
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Tripathi S, Pradeep TP, Barthwal R. Molecular Recognition of Parallel DNA Quadruplex d(TTAGGGT)4by Mitoxantrone: Binding with 1:2 Stoichiometry Leading to Thermal Stabilization and Telomerase Inhibition. Chembiochem 2016; 17:554-60. [DOI: 10.1002/cbic.201500588] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Indexed: 01/28/2023]
Affiliation(s)
- Sweta Tripathi
- Department of Biotechnology; Indian Institute of Technology Roorkee; Roorkee 247667 India
| | | | - Ritu Barthwal
- Department of Biotechnology; Indian Institute of Technology Roorkee; Roorkee 247667 India
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26
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Synthesis of symmetrical and unsymmetrical 1,3-diheteroarylbenzenes through palladium-catalyzed direct arylation of benzene-1,3-disulfonyl dichloride and 3-bromobenzenesulfonyl chlorides. Tetrahedron 2015. [DOI: 10.1016/j.tet.2015.10.082] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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27
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Hegde M, Sharath Kumar KS, Thomas E, Ananda H, Raghavan SC, Rangappa KS. A novel benzimidazole derivative binds to the DNA minor groove and induces apoptosis in leukemic cells. RSC Adv 2015. [DOI: 10.1039/c5ra16605e] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
In the present study, we have synthesized various benzimidazole derivatives, evaluated their potential to act as DNA minor groove binder and tested their chemotherapeutic efficacy.
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Affiliation(s)
- Mahesh Hegde
- Department of Studies in Chemistry
- Manasagangotri, University of Mysore
- Mysuru-570006, India
| | | | - Elizabeth Thomas
- Department of Biochemistry
- Indian Institute of Science
- Bangalore-560012, India
| | - Hanumappa Ananda
- Department of Studies in Chemistry
- Manasagangotri, University of Mysore
- Mysuru-570006, India
| | - Sathees C. Raghavan
- Department of Biochemistry
- Indian Institute of Science
- Bangalore-560012, India
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28
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Ali A, Bansal M, Bhattacharya S. Ligand 5,10,15,20-tetra(N-methyl-4-pyridyl)porphine (TMPyP4) prefers the parallel propeller-type human telomeric G-quadruplex DNA over its other polymorphs. J Phys Chem B 2014; 119:5-14. [PMID: 25526532 DOI: 10.1021/jp505792z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The binding of ligand 5,10,15,20-tetra(N-methyl-4-pyridyl)porphine (TMPyP4) with telomeric and genomic G-quadruplex DNA has been extensively studied. However, a comparative study of interactions of TMPyP4 with different conformations of human telomeric G-quadruplex DNA, namely, parallel propeller-type (PP), antiparallel basket-type (AB), and mixed hybrid-type (MH) G-quadruplex DNA, has not been done. We considered all the possible binding sites in each of the G-quadruplex DNA structures and docked TMPyP4 to each one of them. The resultant most potent sites for binding were analyzed from the mean binding free energy of the complexes. Molecular dynamics simulations were then carried out, and analysis of the binding free energy of the TMPyP4-G-quadruplex complex showed that the binding of TMPyP4 with parallel propeller-type G-quadruplex DNA is preferred over the other two G-quadruplex DNA conformations. The results obtained from the change in solvent excluded surface area (SESA) and solvent accessible surface area (SASA) also support the more pronounced binding of the ligand with the parallel propeller-type G-quadruplex DNA.
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Affiliation(s)
- Asfa Ali
- Department of Organic Chemistry, Indian Institute of Science , Bangalore 560 012, India
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29
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Maji B, Kumar K, Kaulage M, Muniyappa K, Bhattacharya S. Design and Synthesis of New Benzimidazole–Carbazole Conjugates for the Stabilization of Human Telomeric DNA, Telomerase Inhibition, and Their Selective Action on Cancer Cells. J Med Chem 2014; 57:6973-88. [DOI: 10.1021/jm500427n] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Basudeb Maji
- Department of Organic
Chemistry, Indian Institute of Science, Bangalore, Karnataka 560 012, India
| | - Krishan Kumar
- Department of Organic
Chemistry, Indian Institute of Science, Bangalore, Karnataka 560 012, India
| | - Mangesh Kaulage
- Department of Organic
Chemistry, Indian Institute of Science, Bangalore, Karnataka 560 012, India
- Department
of Biochemistry, Indian Institute of Science, Bangalore, Karnataka 560 012, India
| | - K. Muniyappa
- Department
of Biochemistry, Indian Institute of Science, Bangalore, Karnataka 560 012, India
| | - Santanu Bhattacharya
- Department of Organic
Chemistry, Indian Institute of Science, Bangalore, Karnataka 560 012, India
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, Karnataka 560 012, India
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30
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DNA binders in clinical trials and chemotherapy. Bioorg Med Chem 2014; 22:4506-21. [DOI: 10.1016/j.bmc.2014.05.030] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2014] [Revised: 05/09/2014] [Accepted: 05/14/2014] [Indexed: 01/09/2023]
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31
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Song D, Yang W, Qin T, Wu L, Liu K, Su H. Explicit Differentiation of G-Quadruplex/Ligand Interactions: Triplet Excited States as Sensitive Reporters. J Phys Chem Lett 2014; 5:2259-2266. [PMID: 26279544 DOI: 10.1021/jz501040a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We report a new transient spectral method utilizing triplet excited state as sensitive reporters to monitor and differentiate the multiplex G-quadruplex/ligand interactions in a single assay, which is a difficult task and usually requires a combination of several techniques. From a systematic study on the interactions of porphyrin (TMPyP4) with each telomeric G-quadruplex: AG3(T2AG3)3, G2T2G2TGTG2T2G2, (G4T4G4)2, and (TG4T)4, it is convincingly shown that the ligand triplet decay lifetimes are sensitive to the local bound microenvironment within G-quadruplexes, from which the coexisting binding modes of end-stacking, intercalation, and sandwich are distinguished and their respective contribution are determined. The complete scenario of mixed interaction modes is thus revealed, shedding light on the past controversial issues. Additional control experiments demonstrate the sensitivity of this triplet reporter method, which can even capture the binding behavior change as the G-quadruplex structures are adjusted by Na(+) or K(+).
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Affiliation(s)
- Di Song
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Wen Yang
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Tingxiao Qin
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Lidan Wu
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Kunhui Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Hongmei Su
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
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32
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Jin B, Zhang X, Zheng W, Liu X, Zhou J, Zhang N, Wang F, Shangguan D. Dicyanomethylene-Functionalized Squaraine as a Highly Selective Probe for Parallel G-Quadruplexes. Anal Chem 2014; 86:7063-70. [DOI: 10.1021/ac501619v] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Bing Jin
- Beijing
National Laboratory for Molecular Sciences, Key Laboratory of Analytical
Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Zhang
- Beijing
National Laboratory for Molecular Sciences, Key Laboratory of Analytical
Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Zheng
- Beijing
National Laboratory for Molecular Sciences, Key Laboratory of Analytical
Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiangjun Liu
- Beijing
National Laboratory for Molecular Sciences, Key Laboratory of Analytical
Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Jin Zhou
- Beijing
National Laboratory for Molecular Sciences, Key Laboratory of Analytical
Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Nan Zhang
- Beijing
National Laboratory for Molecular Sciences, Key Laboratory of Analytical
Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fuyi Wang
- Beijing
National Laboratory for Molecular Sciences, Key Laboratory of Analytical
Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Dihua Shangguan
- Beijing
National Laboratory for Molecular Sciences, Key Laboratory of Analytical
Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
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33
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Maji B, Bhattacharya S. Advances in the molecular design of potential anticancer agents via targeting of human telomeric DNA. Chem Commun (Camb) 2014; 50:6422-38. [DOI: 10.1039/c4cc00611a] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Telomerase is an attractive drug target to develop new generation drugs against cancer.
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Affiliation(s)
- Basudeb Maji
- Department of Organic Chemistry
- Indian Institute of Science
- Bangalore-560012, India
| | - Santanu Bhattacharya
- Department of Organic Chemistry
- Indian Institute of Science
- Bangalore-560012, India
- Chemical Biology Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
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34
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Zhou J, Chang A, Wang L, Liu Y, Liu X, Shangguan D. Effects of side chains on DNA binding, cell permeability, nuclear localization and cytotoxicity of 4-aminonaphthalimides. Org Biomol Chem 2014; 12:9207-15. [DOI: 10.1039/c4ob01274g] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The guanidinoethyl group increases DNA binding, and decreases the cell permeability and cytotoxity; the dimethylaminopropyl group enhances the cell permeability and cytotoxity.
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Affiliation(s)
- Jin Zhou
- Beijing National Laboratory for Molecular Sciences
- Key Laboratory of Analytical Chemistry for Living Biosystems
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing, 100190, China
| | - Ang Chang
- Beijing National Laboratory for Molecular Sciences
- Key Laboratory of Analytical Chemistry for Living Biosystems
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing, 100190, China
| | - Linlin Wang
- Beijing National Laboratory for Molecular Sciences
- Key Laboratory of Analytical Chemistry for Living Biosystems
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing, 100190, China
| | - Ying Liu
- Beijing National Laboratory for Molecular Sciences
- Key Laboratory of Analytical Chemistry for Living Biosystems
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing, 100190, China
| | - Xiangjun Liu
- Beijing National Laboratory for Molecular Sciences
- Key Laboratory of Analytical Chemistry for Living Biosystems
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing, 100190, China
| | - Dihua Shangguan
- Beijing National Laboratory for Molecular Sciences
- Key Laboratory of Analytical Chemistry for Living Biosystems
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing, 100190, China
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35
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Jin B, Zhang X, Zheng W, Liu X, Qi C, Wang F, Shangguan D. Fluorescence light-up probe for parallel G-quadruplexes. Anal Chem 2013; 86:943-52. [PMID: 24354276 DOI: 10.1021/ac403676x] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Putative G-quadruplex-forming sequences (PQS) are highly prevalent in human genome; however, the structures and functions of most PQSs in genome are poorly understood. Therefore, selective recognition of certain types of G-quadruplexes (G4s) is important for the study of G4s. A new light up fluorescent probe, BPBC composed of benzimidazole and carbazole moieties was designed and synthesized. BPBC possesses a crescent-shaped π-conjugated planar core that is slightly larger than the dimension of the G-quartet plane in G4s. This structure endows BPBC with excellent selectivity to parallel G4s. BPBC exhibits almost no fluorescence in the aqueous buffer condition, its fluorescence increases approximately 330-1800-fold in the presence of parallel G4s but only about 30-fold in the presence of single/double-stranded (ss/ds) DNA and 30-110-fold in the presence of antiparallel G4s. Binding studies indicate that the highly selective fluorescent response of BPBC arises from end-stack binding model to G-quartet.
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Affiliation(s)
- Bing Jin
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
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36
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Biver T. Stabilisation of non-canonical structures of nucleic acids by metal ions and small molecules. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2013.04.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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37
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Kumar V, Anslyn EV. A Selective Turn-On Fluorescent Sensor for Sulfur Mustard Simulants. J Am Chem Soc 2013; 135:6338-44. [DOI: 10.1021/ja401845e] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Vinod Kumar
- Department of Chemistry
and Biochemistry, The University of Texas at Austin, Austin, Texas 78712,
United States
| | - Eric V. Anslyn
- Department of Chemistry
and Biochemistry, The University of Texas at Austin, Austin, Texas 78712,
United States
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38
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He JH, Liu HY, Li Z, Tan JH, Ou TM, Huang SL, An LK, Li D, Gu LQ, Huang ZS. New quinazoline derivatives for telomeric G-quadruplex DNA: effects of an added phenyl group on quadruplex binding ability. Eur J Med Chem 2013; 63:1-13. [PMID: 23454529 DOI: 10.1016/j.ejmech.2013.01.051] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 01/19/2013] [Accepted: 01/24/2013] [Indexed: 01/06/2023]
Abstract
To improve the selectivity of indoloquinoline or benzofuroquinoline derivatives, we previously reported several quinazoline derivatives [17]. These compounds could mimic a tetracyclic aromatic system through intramolecular hydrogen bond. Studies showed that these quinazoline derivatives were effective and selective telomeric G-quadruplex ligands. With this encouragement, here we synthesized a series of N-(2-(quinazolin-2-yl)phenyl)benzamide (QPB) compounds as modified quinazoline derivatives. In this modification, a phenyl group was introduced to the aromatic core. The evaluation results showed that part of QPB derivatives had stronger binding ability and better selectivity for telomeric G-quadruplex DNA than LZ-11, the most potential compound of reported quinazoline derivatives. Furthermore, telomerase inhibition of QPB derivatives and their cellular effects were studied.
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Affiliation(s)
- Jin-Hui He
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, People's Republic of China
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39
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Bianco S, Musetti C, Krapcho AP, Palumbo M, Sissi C. Ni2+ and Cu2+ complexes of a phenanthroline-based ligand bind to G-quadruplexes at non-overlapping sites. Chem Commun (Camb) 2013; 49:8057-9. [DOI: 10.1039/c3cc44382e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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40
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Beyramabadi SA, Morsali A, Vahidi SH. DFT characterization of 1-acetylpiperazinyl-dithiocarbamate ligand and its transition metal complexes. J STRUCT CHEM+ 2012. [DOI: 10.1134/s0022476612040087] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
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41
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Paul A, Maji B, Misra SK, Jain AK, Muniyappa K, Bhattacharya S. Stabilization and structural alteration of the G-quadruplex DNA made from the human telomeric repeat mediated by Tröger's base based novel benzimidazole derivatives. J Med Chem 2012; 55:7460-71. [PMID: 22827615 DOI: 10.1021/jm300442r] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Ligand-induced stabilization of the G-quadruplex DNA structure derived from the single-stranded 3'-overhang of the telomeric DNA is an attractive strategy for the inhibition of the telomerase activity. The agents that can induce/stabilize a DNA sequence into a G-quadruplex structure are therefore potential anticancer drugs. Herein we present the first report of the interactions of two novel bisbenzimidazoles (TBBz1 and TBBz2) based on Tröger's base skeleton with the G-quadruplex DNA (G4DNA). These Tröger's base molecules stabilize the G4DNA derived from a human telomeric sequence. Evidence of their strong interaction with the G4DNA has been obtained from CD spectroscopy, thermal denaturation, and UV-vis titration studies. These ligands also possess significantly higher affinity toward the G4DNA over the duplex DNA. The above results obtained are in excellent agreement with the biological activity, measured in vitro using a modified TRAP assay. Furthermore, the ligands are selectively more cytotoxic toward the cancerous cells than the corresponding noncancerous cells. Computational studies suggested that the adaptive scaffold might allow these ligands to occupy not only the G-quartet planes but also the grooves of the G4DNA.
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Affiliation(s)
- Ananya Paul
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560 012, India
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42
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Binding of gemini bisbenzimidazole drugs with human telomeric G-quadruplex dimers: effect of the spacer in the design of potent telomerase inhibitors. PLoS One 2012; 7:e39467. [PMID: 22737240 PMCID: PMC3380826 DOI: 10.1371/journal.pone.0039467] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Accepted: 05/21/2012] [Indexed: 11/19/2022] Open
Abstract
The study of anticancer agents that act via stabilization of telomeric G-quadruplex DNA (G4DNA) is important because such agents often inhibit telomerase activity. Several types of G4DNA binding ligands are known. In these studies, the target structures often involve a single G4 DNA unit formed by short DNA telomeric sequences. However, the 3′-terminal single-stranded human telomeric DNA can form higher-order structures by clustering consecutive quadruplex units (dimers or n-mers). Herein, we present new synthetic gemini (twin) bisbenzimidazole ligands, in which the oligo-oxyethylene spacers join the two bisbenzimidazole units for the recognition of both monomeric and dimeric G4DNA, derived from d(T2AG3)4 and d(T2AG3)8 human telomeric DNA, respectively. The spacer between the two bisbenzimidazoles in the geminis plays a critical role in the G4DNA stability. We report here (i) synthesis of new effective gemini anticancer agents that are selectively more toxic towards the cancer cells than the corresponding normal cells; (ii) formation and characterization of G4DNA dimers in solution as well as computational construction of the dimeric G4DNA structures. The gemini ligands direct the folding of the single-stranded DNA into an unusually stable parallel-stranded G4DNA when it was formed in presence of the ligands in KCl solution and the gemini ligands show spacer length dependent potent telomerase inhibition properties.
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43
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Jain AK, Paul A, Maji B, Muniyappa K, Bhattacharya S. Dimeric 1,3-Phenylene-bis(piperazinyl benzimidazole)s: Synthesis and Structure–Activity Investigations on their Binding with Human Telomeric G-Quadruplex DNA and Telomerase Inhibition Properties. J Med Chem 2012; 55:2981-93. [DOI: 10.1021/jm200860b] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Akash K Jain
- Department
of Organic Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Ananya Paul
- Department
of Organic Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Basudeb Maji
- Department
of Organic Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - K. Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Santanu Bhattacharya
- Department
of Organic Chemistry, Indian Institute of Science, Bangalore 560012, India
- Chemical Biology Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560012, India
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44
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Visualizing the Quadruplex: From Fluorescent Ligands to Light-Up Probes. Top Curr Chem (Cham) 2012; 330:111-77. [DOI: 10.1007/128_2012_346] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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45
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Jain AK, Bhattacharya S. Interaction of G-Quadruplexes with Nonintercalating Duplex-DNA Minor Groove Binding Ligands. Bioconjug Chem 2011; 22:2355-68. [DOI: 10.1021/bc200268a] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Akash K. Jain
- Department
of Organic Chemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Santanu Bhattacharya
- Department
of Organic Chemistry, Indian Institute of Science, Bangalore 560 012, India
- Chemical Biology Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560 012, India
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46
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Largy E, Hamon F, Rosu F, Gabelica V, De Pauw E, Guédin A, Mergny JL, Teulade-Fichou MP. Tridentate N-Donor Palladium(II) Complexes as Efficient Coordinating Quadruplex DNA Binders. Chemistry 2011; 17:13274-83. [DOI: 10.1002/chem.201102300] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Indexed: 11/05/2022]
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47
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Murat P, Singh Y, Defrancq E. Methods for investigating G-quadruplex DNA/ligand interactions. Chem Soc Rev 2011; 40:5293-307. [PMID: 21720638 DOI: 10.1039/c1cs15117g] [Citation(s) in RCA: 191] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
DNA is considered an important target for drug design and development. Until recently, the focus was on double-stranded (duplex) DNA structures. However, it has now been shown that single stranded DNA can fold into hairpin, triplex, i-motif and G-quadruplex structures. The more interesting G-quadruplex DNA structures comprise four strands of stacked guanine (G)-tetrads formed by the coplanar arrangement of four guanines, held together by Hoogsteen bonds. The DNA sequences with potential to form G-quadruplex structures are found at the chromosomal extremities (i.e. the telomeres) and also at the intra-chromosomal region (i.e. oncogenic promoters) in several important oncogenes. The formation of G-quadruplex structures is considered to have important consequences at the cellular level and such structures have been evoked in the control of expression of certain genes involved in carcinogenesis (c-myc, c-kit, K-ras etc.) as well as in the perturbation of telomeric organization. It has been shown that the formation of quadruplexes inhibits the telomere extension by the telomerase enzyme, which is up-regulated in cancer cells. Therefore, G-quadruplex structures are an important target for drug design and development and there is a huge interest in design and development of small molecules (ligands) to target these structures. A large number of so-called G-quadruplex ligands, displaying varying degrees of affinity and more importantly selectivity (i.e. the ability to interact only with quadruplex-DNA and not duplex-DNA), have been reported. Access to efficient and robust in vitro assays is needed to effectively monitor and quantify the G-quadruplex DNA/ligand interactions. This tutorial review provides an overview of G-quadruplex ligands and biophysical techniques available to monitor such interactions.
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Affiliation(s)
- Pierre Murat
- Department of Chemistry, The University of Cambridge, Cambridge CB2 1EW, UK.
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48
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Largy E, Hamon F, Teulade-Fichou MP. Development of a high-throughput G4-FID assay for screening and evaluation of small molecules binding quadruplex nucleic acid structures. Anal Bioanal Chem 2011; 400:3419-27. [PMID: 21528379 DOI: 10.1007/s00216-011-5018-z] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Revised: 04/08/2011] [Accepted: 04/12/2011] [Indexed: 11/25/2022]
Abstract
G4-FID (G-quadruplex fluorescent intercalator displacement) is a simple and fast method that allows to evaluate the affinity of a compound for G-quadruplex DNA and its selectivity towards duplex DNA. This assay is based on the loss of fluorescence of thiazole orange (TO) upon competitive displacement from DNA by a putative ligand. We describe here the development of a high-throughput version of this assay performed in 96-well microplates, and fully transposable to 384-well microplates. The test was calibrated with a set of G-quadruplex ligands characterized for their ability to bind quadruplex within a large range of affinity. The comparison of the results obtained in microplates and in cuvettes was conducted indicating a full agreement. Additionally, the spectral range of the test was enlarged using two other fluorescent on/off probes whose absorption are red-shifted (TO-PRO-3) and blue-shifted (Hoechst 33258) as compared to that of TO. These labels enable to screen a large diversity of compounds with various optical properties, which was exemplified by evaluation of affinity and selectivity of the porphyrin TMPyP4 that could not be evaluated previously. Altogether, our study demonstrates that the HT-G4-FID assay offers the possibility to label a large variety of G-quadruplexes of biological interest and should enable screening of collections of putative G4-ligands of high structural diversity. It thus represents a powerful tool to bring into light new ligands able to discriminate between quadruplexes of different structures.
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Affiliation(s)
- Eric Largy
- Institut Curie, CNRS UMR-176, Centre Universitaire, Orsay, France
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