1
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Banerjee N, Chatterjee O, Roychowdhury T, Basu D, Dutta A, Chowdhury M, Dastidar SG, Chatterjee S. Sequence driven interaction of amino acids in de-novo designed peptides determines c-Myc G-quadruplex unfolding inducing apoptosis in cancer cells. Biochim Biophys Acta Gen Subj 2023; 1867:130267. [PMID: 36334788 DOI: 10.1016/j.bbagen.2022.130267] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 10/21/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022]
Abstract
c-MYC proto-oncogene harbors a putative G-quadruplex structure (Pu27) at the NHEIII1 domain, which can shuffle between transcriptional inhibitor quadruplex and transcriptionally active duplex. In cancer cells this quadruplex destabilization is preferred and NHEIII1 domain assume a duplex topology thereby inducing c-MYC overexpression and tumorigenesis. Hence, the c-MYC quadruplex acts as an excellent target for anti-cancer therapy. Though researcher have tried to develop G-quadruplex targeted small molecules, work with G-quadruplex targeting peptides is very limited. Here we present a peptide that can bind to c-MYC quadruplex, destabilize the tetrad core, and permit the formation of a substantially different structure from the quartet core seen in the canonical G-quadruplexes. Such conformation potentially acted as a roadblock for transcription factors thereby reducing cMYC expression. This event sensitizes the cancer cell to activate apoptotic cascade via the c-MYC-VEGF-A-BCL2 axis. This study provides a detailed insight into the peptide-quadruplex interface that encourages better pharmacophore design to target dynamic quadruplex structure. We believe that our results will contribute to the development, characterization, and optimization of G-quadruplex binding peptides for potential clinical application.
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Affiliation(s)
- Nilanjan Banerjee
- Department of Biophysics, Bose Institute, Unified Academic campus, EN-80, Sector V, Kolkata 700091, India
| | - Oishika Chatterjee
- Department of Biophysics, Bose Institute, Unified Academic campus, EN-80, Sector V, Kolkata 700091, India
| | - Tanaya Roychowdhury
- Cancer Biology and Inflammatory Disorder Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700032, India
| | - Debadrita Basu
- Division of Bioinformatics, Bose Institute, Unified Academic campus, EN-80, Sector V, Kolkata 700091, India
| | - Anindya Dutta
- Department of Biophysics, Bose Institute, Unified Academic campus, EN-80, Sector V, Kolkata 700091, India
| | - Madhurima Chowdhury
- Department of Biophysics, Bose Institute, Unified Academic campus, EN-80, Sector V, Kolkata 700091, India
| | - Shubhra Ghosh Dastidar
- Division of Bioinformatics, Bose Institute, Unified Academic campus, EN-80, Sector V, Kolkata 700091, India
| | - Subhrangsu Chatterjee
- Department of Biophysics, Bose Institute, Unified Academic campus, EN-80, Sector V, Kolkata 700091, India.
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2
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Kundu N, Sharma T, Kaur S, Singh M, Kumar V, Sharma U, Jain A, Shankaraswamy J, Miyoshi D, Saxena S. Significant structural change in human c-Myc promoter G-quadruplex upon peptide binding in potassium. RSC Adv 2022; 12:7594-7604. [PMID: 35424772 PMCID: PMC8982240 DOI: 10.1039/d2ra00535b] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 03/02/2022] [Indexed: 01/25/2023] Open
Abstract
We selected the G-quadruplex motif located in the nuclease-hypersensitive elements (NHE) III1 region of the c-Myc promoter and for the first time performed its interaction studies with a designed peptide (QW10). Our CD results showed that the peptide bound to the c-Myc G-quadruplex and induced a significant blue shift in the positive peak of 20 nm in KCl alone or with 40wt% PEG200 or 20wt% PEG8000 in comparison to NaCl. Our Native Gel results confirmed that peptide binding destabilized the duplex and stabilized the unimolecular G-quadruplex and not binding to i-motif. UV thermal results confirmed destabilization of bimolecular structure and stabilization of unimolecular G-quadruplex. QW10 showed preferential binding towards c-MYC promoter G4 with binding constant (K b) values of the order of 0.05 ± 0.2 μM, 0.12 ± 0.1 μM and 0.05 ± 0.3 μM for complexes in K+ alone or 40wt% PEG 200 or 20wt% PEG 8000 respectively. QW10 showed preferential cytotoxicity with IC50 values of 11.10 μM and 6.44 μM after 72 and 96 hours' incubation on Human Breast Carcinoma MDA-MB 231 cells and was found to be non-toxic with Human Embryonic Kidney (HEK-1) cells. Interestingly, we observed reduction of c-Myc gene expression by 2.5 fold due to QW10 binding and stabilizing c-MYC G4. Our study for the first time provides an expanded overview of significant structural change in human c-Myc promoter G-quadruplex upon peptide binding in potassium.
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Affiliation(s)
- Nikita Kundu
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Structural Biology Lab Sector-125, Expressway Highway Noida 201313 India +91-120-4735600
| | - Taniya Sharma
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Structural Biology Lab Sector-125, Expressway Highway Noida 201313 India +91-120-4735600
| | - Sarvpreet Kaur
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Structural Biology Lab Sector-125, Expressway Highway Noida 201313 India +91-120-4735600
| | - Mamta Singh
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University Uttar Pradesh Noida 201313 India
| | - Vinit Kumar
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University Uttar Pradesh Noida 201313 India
| | - Uttam Sharma
- Department of Animal Sciences, Central University of Punjab Bathinda India
| | - Aklank Jain
- Department of Animal Sciences, Central University of Punjab Bathinda India
| | - Jadala Shankaraswamy
- Department of Fruit Science, College of Horticulture, Mojerla, Sri Konda Laxman Telangana State Horticultural University 509382 Telangana India
| | - Daisuke Miyoshi
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe Hyogo 650-0047 Japan
| | - Sarika Saxena
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Structural Biology Lab Sector-125, Expressway Highway Noida 201313 India +91-120-4735600
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3
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Devi G, Winnerdy FR, Ang JCY, Lim KW, Phan AT. Four-Layered Intramolecular Parallel G-Quadruplex with Non-Nucleotide Loops: An Ultra-Stable Self-Folded DNA Nano-Scaffold. ACS NANO 2022; 16:533-540. [PMID: 34927423 DOI: 10.1021/acsnano.1c07630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A four-stranded scaffold of nucleic acids termed G-quadruplex (G4) has found growing applications in nano- and biotechnology. Propeller loops are a hallmark of the most stable intramolecular parallel-stranded G4s. To date, propeller loops have been observed to span only a maximum of three G-tetrad layers. Going beyond that would allow creation of more stable scaffolds useful for building robust nanodevices. Here we investigate the formation of propeller loops spanning more than three layers. We show that native nucleotide sequences are incompatible toward this goal, and we report on synthetic non-nucleotide linkers that form a propeller loop across four layers. With the established linkers, we constructed a four-layered intramolecular parallel-stranded G4, which exhibited ultrahigh thermal stability. Control on loop design would augment the toolbox toward engineering of G4-based nanoscaffolds for diverse applications.
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Affiliation(s)
- Gitali Devi
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Fernaldo Richtia Winnerdy
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Jason Cheng Yu Ang
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Kah Wai Lim
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore 636921, Singapore
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4
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Komůrková D, Svobodová Kovaříková A, Bártová E. G-Quadruplex Structures Colocalize with Transcription Factories and Nuclear Speckles Surrounded by Acetylated and Dimethylated Histones H3. Int J Mol Sci 2021; 22:1995. [PMID: 33671470 PMCID: PMC7922289 DOI: 10.3390/ijms22041995] [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: 01/20/2021] [Revised: 02/11/2021] [Accepted: 02/15/2021] [Indexed: 12/26/2022] Open
Abstract
G-quadruplexes (G4s) are four-stranded helical structures that regulate several nuclear processes, including gene expression and telomere maintenance. We observed that G4s are located in GC-rich (euchromatin) regions and outside the fibrillarin-positive compartment of nucleoli. Genomic regions around G4s were preferentially H3K9 acetylated and H3K9 dimethylated, but H3K9me3 rarely decorated G4 structures. We additionally observed the variability in the number of G4s in selected human and mouse cell lines. We found the highest number of G4s in human embryonic stem cells. We observed the highest degree of colocalization between G4s and transcription factories, positive on the phosphorylated form of RNA polymerase II (RNAP II). Similarly, a high colocalization rate was between G4s and nuclear speckles, enriched in pre-mRNA splicing factor SC-35. PML bodies, the replication protein SMD1, and Cajal bodies colocalized with G4s to a lesser extent. Thus, G4 structures seem to appear mainly in nuclear compartments transcribed via RNAP II, and pre-mRNA is spliced via the SC-35 protein. However, α-amanitin, an inhibitor of RNAP II, did not affect colocalization between G4s and transcription factories as well as G4s and SC-35-positive domains. In addition, irradiation by γ-rays did not change a mutual link between G4s and DNA repair proteins (G4s/γH2AX, G4s/53BP1, and G4s/MDC1), accumulated into DNA damage foci. Described characteristics of G4s seem to be the manifestation of pronounced G4s stability that is likely maintained not only via a high-order organization of these structures but also by a specific histone signature, including H3K9me2, responsible for chromatin compaction.
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Affiliation(s)
| | | | - Eva Bártová
- Institute of Biophysics of the Czech Academy of Sciences, Department of Molecular Cytology and Cytometry, Královopolská 135, 612 65 Brno, Czech Republic; (D.K.); (A.S.K.)
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5
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Abstract
Several decades elapsed between the first descriptions of G-quadruplex nucleic acid structures (G4s) assembled in vitro and the emergence of experimental findings indicating that such structures can form and function in living systems. A large body of evidence now supports roles for G4s in many aspects of nucleic acid biology, spanning processes from transcription and chromatin structure, mRNA processing, protein translation, DNA replication and genome stability, and telomere and mitochondrial function. Nonetheless, it must be acknowledged that some of this evidence is tentative, which is not surprising given the technical challenges associated with demonstrating G4s in biology. Here I provide an overview of evidence for G4 biology, focusing particularly on the many potential pitfalls that can be encountered in its investigation, and briefly discuss some of broader biological processes that may be impacted by G4s including cancer.
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Affiliation(s)
- F. Brad Johnson
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
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6
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Maity A, Winnerdy FR, Chang WD, Chen G, Phan AT. Intra-locked G-quadruplex structures formed by irregular DNA G-rich motifs. Nucleic Acids Res 2020; 48:3315-3327. [PMID: 32100003 PMCID: PMC7102960 DOI: 10.1093/nar/gkaa008] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 12/30/2019] [Accepted: 02/24/2020] [Indexed: 12/14/2022] Open
Abstract
G-rich DNA sequences with tracts of three or more continuous guanines (G≥3) are known to have high propensity to adopt stable G-quadruplex (G4) structures. Bioinformatic analyses suggest high prevalence of G-rich sequences with short G-tracts (G≤2) in the human genome. However, due to limited structural studies, the folding principles of such sequences remain largely unexplored and hence poorly understood. Here, we present the solution NMR structure of a sequence named AT26 consisting of irregularly spaced G2 tracts and two isolated single guanines. The structure is a four-layered G4 featuring two bi-layered blocks, locked between themselves in an unprecedented fashion making it a stable scaffold. In addition to edgewise and propeller-type loops, AT26 also harbors two V-shaped loops: a 2-nt V-shaped loop spanning two G-tetrad layers and a 0-nt V-shaped loop spanning three G-tetrad layers, which are named as VS- and VR-loop respectively, based on their distinct structural features. The intra-lock motif can be a basis for extending the G-tetrad core and a very stable intra-locked G4 can be formed by a sequence with G-tracts of various lengths including several G2 tracts. Findings from this study will aid in understanding the folding of G4 topologies from sequences containing irregularly spaced multiple short G-tracts.
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Affiliation(s)
- Arijit Maity
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Fernaldo Richtia Winnerdy
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Weili Denyse Chang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Gang Chen
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, Singapore 636921, Singapore
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7
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Sengupta P, Banerjee N, Roychowdhury T, Dutta A, Chattopadhyay S, Chatterjee S. Site-specific amino acid substitution in dodecameric peptides determines the stability and unfolding of c-MYC quadruplex promoting apoptosis in cancer cells. Nucleic Acids Res 2019; 46:9932-9950. [PMID: 30239898 PMCID: PMC6212778 DOI: 10.1093/nar/gky824] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 09/11/2018] [Indexed: 12/11/2022] Open
Abstract
c-MYC proto-oncogene harbours a transcription-inhibitory quadruplex-forming scaffold (Pu27) upstream P1 promoter providing anti-neoplastic therapeutic target. Previous reports showed the binding profile of human Cathelicidin peptide (LL37) and telomeric G-quadruplex. Here, we truncated the quadruplex-binding domain of LL37 to prepare a small library of peptides through site-specific amino acid substitution. We investigated the intracellular selectivity of peptides for Pu27 over other oncogenic quadruplexes and their role in c-MYC promoter repression by dual-luciferase assays. We analysed their thermodynamics of binding reactions with c-MYC quadruplex isomers (Pu27, Myc22, Pu19) by Isothermal Titration Calorimetry. We discussed how amino acid substitutions and peptide helicity enhanced/weakened their affinities for c-MYC quadruplexes and characterized specific non-covalent inter-residual interactions determining their selectivity. Solution NMR structure indicated that KR12C, the best peptide candidate, selectively stabilized the 5′-propeller loop of c-MYC quadruplex by arginine-driven electrostatic-interactions at the sugar-phosphate backbone while KR12A peptide destabilized the quadruplex inducing a single-stranded hairpin-like conformation. Chromatin immunoprecipitations envisaged that KR12C and KR12A depleted and enriched Sp1 and NM23-H2 (Nucleoside diphosphate kinase) occupancy at Pu27 respectively supporting their regulation in stabilizing and unfolding c-MYC quadruplex in MCF-7 cells. We deciphered that selective arresting of c-MYC transcription by KR12C triggered apoptotic-signalling pathway via VEGF-A-BCL-2 axis.
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Affiliation(s)
- Pallabi Sengupta
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700054, India
| | - Nilanjan Banerjee
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), 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
| | - Anindya Dutta
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700054, 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), Kolkata 700054, India
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8
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Sengupta P, Bhattacharya A, Sa G, Das T, Chatterjee S. Truncated G-Quadruplex Isomers Cross-Talk with the Transcription Factors To Maintain Homeostatic Equilibria in c-MYC Transcription. Biochemistry 2019; 58:1975-1991. [PMID: 30920805 DOI: 10.1021/acs.biochem.9b00030] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The nuclease hypersensitive element III1 (NHE III1) upstream c-MYC promoter harbors a transcription-silencing G-quadruplex (Pu27) element. Dynamic turnover of various transcription factors (TFs) across Pu27 to control c-MYC transcription homeostasis is enigmatic. Here, we reveal that native Pu27 evolves truncated G-quadruplex isomers (Pu19, Pu22, Pu24, and Pu25) in cells that are optimal intracellular targets of specific TFs in a sequence- and structure-dependent manner. Nuclear magnetic resonance and isothermal titration calorimetry envisaged that NM23-H2 (nucleoside diphosphate kinase) and nucleolin induce conformational fluctuations in Pu27 to sample specific conformationally restricted conformer(s). Structural investigations revealed that the flanking guanines at 5'-Pu27 control solvent exposure at G-quartets upon NM23-H2 and nucleolin binding driving Pu27 unfolding and folding, respectively. Transient chromatin immunoprecipitations confirmed that NM23-H2 drives the conformation switch to Pu24 that outcompetes nucleolin recruitment. Similarly, nucleolin arrests Pu27 in the Pu22 conformer minimizing NM23-H2 binding at Pu27. hnRNPK (heterogeneous nuclear ribonucleoprotein K) positively regulates NM23-H2 and nucleolin association at Pu27 despite their antagonism. On the basis of these results, we simulated the transcription kinetics in a feed-forward loop in which the transcription output responds to hnRNPK-induced early activation via NM23-H2 association, which favors Pu24 formation at NHE III1 reducing nucleolin occupancy and driving quadruplex unfolding to initiate transcription. NM23-H2 further promotes hnRNPK deposition across NHE III1 altering Pu27 plasticity that finally enriches the nucleolin abundance to drive Pu22 formation and weaken NM23-H2 binding to extinguish transcription. This mechanism involves three positive feedback loops (NM23-H2-hnRNPK, NM23-H2-CNBP, and hnRNPK-nucleolin) and one negative feedback loop (NM23-H2-nucleolin) controlling optimal turnover and residence time of TFs at Pu27 to homeostatically regulate c-MYC transcription.
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Affiliation(s)
- Pallabi Sengupta
- Department of Biophysics , Bose Institute , P 1/12, C. I. T. Road, Scheme-VIIM , Kolkata 700054 , West Bengal , India
| | - Apoorva Bhattacharya
- Division of Molecular Medicine , Bose Institute , P 1/12, C. I. T. Road, Scheme-VIIM , Kolkata 700054 , West Bengal , India
| | - Gaurisankar Sa
- Division of Molecular Medicine , Bose Institute , P 1/12, C. I. T. Road, Scheme-VIIM , Kolkata 700054 , West Bengal , India
| | - Tanya Das
- Division of Molecular Medicine , Bose Institute , P 1/12, C. I. T. Road, Scheme-VIIM , Kolkata 700054 , West Bengal , India
| | - Subhrangsu Chatterjee
- Department of Biophysics , Bose Institute , P 1/12, C. I. T. Road, Scheme-VIIM , Kolkata 700054 , West Bengal , India
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9
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Bakalar B, Heddi B, Schmitt E, Mechulam Y, Phan AT. A Minimal Sequence for Left-Handed G-Quadruplex Formation. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201812628] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Blaž Bakalar
- School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore 637371 Singapore
- School of Biological Sciences; Nanyang Technological University; Singapore 637551 Singapore
| | - Brahim Heddi
- School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore 637371 Singapore
- Laboratoire de Biologie et Pharmacologie Appliquée, CNRS; Ecole Normale Supérieure Paris-Saclay; 94235 Cachan France
| | - Emmanuelle Schmitt
- Laboratoire de Biochimie, UMR 7654, CNRS; Ecole Polytechnique; 91128 Palaiseau France
| | - Yves Mechulam
- Laboratoire de Biochimie, UMR 7654, CNRS; Ecole Polytechnique; 91128 Palaiseau France
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore 637371 Singapore
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10
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Bakalar B, Heddi B, Schmitt E, Mechulam Y, Phan AT. A Minimal Sequence for Left-Handed G-Quadruplex Formation. Angew Chem Int Ed Engl 2019; 58:2331-2335. [PMID: 30481397 DOI: 10.1002/anie.201812628] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Indexed: 12/20/2022]
Abstract
Recently, we observed the first example of a left-handed G-quadruplex structure formed by natural DNA, named Z-G4. We analysed the Z-G4 structure and inspected its primary 28-nt sequence in order to identify motifs that convey the unique left-handed twist. Using circular dichroism spectroscopy, NMR spectroscopy, and X-ray crystallography, we revealed a minimal sequence motif of 12 nt (GTGGTGGTGGTG) for formation of the left-handed DNA G-quadruplex, which is found to be highly abundant in the human genome. A systematic analysis of thymine loop mutations revealed a moderate sequence tolerance, which would further broaden the space of sequences prone to left-handed G-quadruplex formation.
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Affiliation(s)
- Blaž Bakalar
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Brahim Heddi
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore.,Laboratoire de Biologie et Pharmacologie Appliquée, CNRS, Ecole Normale Supérieure Paris-Saclay, 94235, Cachan, France
| | - Emmanuelle Schmitt
- Laboratoire de Biochimie, UMR 7654, CNRS, Ecole Polytechnique, 91128, Palaiseau, France
| | - Yves Mechulam
- Laboratoire de Biochimie, UMR 7654, CNRS, Ecole Polytechnique, 91128, Palaiseau, France
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore
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11
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Do NQ, Chung WJ, Truong THA, Heddi B, Phan AT. G-quadruplex structure of an anti-proliferative DNA sequence. Nucleic Acids Res 2017; 45:7487-7493. [PMID: 28549181 PMCID: PMC5499593 DOI: 10.1093/nar/gkx274] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 05/24/2017] [Indexed: 01/06/2023] Open
Abstract
AGRO100 (also known as AS1411) is a G-rich oligonucleotide that has long been established as a potent anti-cancer aptamer. However, the structure of AGRO100 remained unresolved, due to the co-existence of multiple different G-quadruplex conformations. We identified a DNA sequence named AT11, derived from AGRO100, which formed a single major G-quadruplex conformation and exhibited a similar anti-proliferative activity as AGRO100. The solution structure of AT11 revealed a four-layer G-quadruplex comprising of two propeller-type parallel-stranded subunits connected through a central linker. The stacking between the two subunits occurs at the 3΄-end of the first block and the 5΄-end of the second block. The structure of the anti-proliferative DNA sequence AT11 will allow greater understanding on the G-quadruplex folding principles and aid in structural optimization of anti-proliferative oligonucleotides.
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Affiliation(s)
- Ngoc Quang Do
- School of Physical and Mathematical Sciences.,School of Biological Sciences, Nanyang Technological University, Singapore
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12
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Zou BQ, Qin QP, Bai YX, Cao QQ, Zhang Y, Liu YC, Chen ZF, Liang H. Synthesis and antitumor mechanism of a new iron(iii) complex with 5,7-dichloro-2-methyl-8-quinolinol as ligands. MEDCHEMCOMM 2017; 8:633-639. [PMID: 30108780 PMCID: PMC6072324 DOI: 10.1039/c6md00644b] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Accepted: 01/26/2017] [Indexed: 11/21/2022]
Abstract
A new iron(iii) complex with 5,7-dichloro-2-methyl-8-quinolinol (HClMQ) as ligands, i.e., [Fe(ClMQ)2Cl] (1), was synthesized and evaluated for its anticancer activity. Compared to the HClMQ ligand, complex 1 showed a higher cytotoxicity towards a series of tumor cell lines, including Hep-G2, BEL-7404, NCI-H460, A549, and T-24, with IC50 values in the range of 5.04-14.35 μM. Notably, the Hep-G2 cell line was the most sensitive to complex 1. Mechanistic studies indicated that complex 1 is a telomerase inhibitor targeting c-myc G-quadruplex DNA and can trigger cell apoptosis via inducing cell cycle arrest and DNA damage.
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Affiliation(s)
- Bi-Qun Zou
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources , School of Chemistry & Pharmaceutical Sciences , Guangxi Normal University , Guilin , Guangxi 541004 , P. R. China . ; ; ; ; Tel: +86 773 2120958
- Department of Chemistry , Guilin Normal College , Guilin , Guangxi 541001 , P. R. China
| | - Qi-Pin Qin
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources , School of Chemistry & Pharmaceutical Sciences , Guangxi Normal University , Guilin , Guangxi 541004 , P. R. China . ; ; ; ; Tel: +86 773 2120958
| | - Yu-Xia Bai
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources , School of Chemistry & Pharmaceutical Sciences , Guangxi Normal University , Guilin , Guangxi 541004 , P. R. China . ; ; ; ; Tel: +86 773 2120958
| | - Qian-Qian Cao
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources , School of Chemistry & Pharmaceutical Sciences , Guangxi Normal University , Guilin , Guangxi 541004 , P. R. China . ; ; ; ; Tel: +86 773 2120958
| | - Ye Zhang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources , School of Chemistry & Pharmaceutical Sciences , Guangxi Normal University , Guilin , Guangxi 541004 , P. R. China . ; ; ; ; Tel: +86 773 2120958
- Department of Chemistry , Guilin Normal College , Guilin , Guangxi 541001 , P. R. China
- College of Pharmacy , Guilin Medical University , North Ring 2rd Road 109 , Guilin 541004 , P. R. China
| | - Yan-Cheng Liu
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources , School of Chemistry & Pharmaceutical Sciences , Guangxi Normal University , Guilin , Guangxi 541004 , P. R. China . ; ; ; ; Tel: +86 773 2120958
| | - Zhen-Feng Chen
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources , School of Chemistry & Pharmaceutical Sciences , Guangxi Normal University , Guilin , Guangxi 541004 , P. R. China . ; ; ; ; Tel: +86 773 2120958
| | - Hong Liang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources , School of Chemistry & Pharmaceutical Sciences , Guangxi Normal University , Guilin , Guangxi 541004 , P. R. China . ; ; ; ; Tel: +86 773 2120958
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13
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Yang F, Sun X, Wang L, Li Q, Guan A, Shen G, Tang Y. Selective recognition of c-myc promoter G-quadruplex and down-regulation of oncogene c-myc transcription in human cancer cells by 3,8a-disubstituted indolizinone. RSC Adv 2017. [DOI: 10.1039/c7ra09870g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Indolizinone could selectively recognize c-myc promoter G-quadruplex.
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Affiliation(s)
- Fengmin Yang
- National Laboratory for Molecular Sciences
- Center for Molecular Sciences
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry Chinese Academy of Sciences
- Beijing
| | - Xin Sun
- National Laboratory for Molecular Sciences
- Center for Molecular Sciences
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry Chinese Academy of Sciences
- Beijing
| | - Lixia Wang
- National Laboratory for Molecular Sciences
- Center for Molecular Sciences
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry Chinese Academy of Sciences
- Beijing
| | - Qian Li
- National Laboratory for Molecular Sciences
- Center for Molecular Sciences
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry Chinese Academy of Sciences
- Beijing
| | - Aijiao Guan
- National Laboratory for Molecular Sciences
- Center for Molecular Sciences
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry Chinese Academy of Sciences
- Beijing
| | - Gang Shen
- National Laboratory for Molecular Sciences
- Center for Molecular Sciences
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry Chinese Academy of Sciences
- Beijing
| | - Yalin Tang
- National Laboratory for Molecular Sciences
- Center for Molecular Sciences
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry Chinese Academy of Sciences
- Beijing
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14
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Rezzoug F, Thomas SD, Rouchka EC, Miller DM. Discovery of a Family of Genomic Sequences Which Interact Specifically with the c-MYC Promoter to Regulate c-MYC Expression. PLoS One 2016; 11:e0161588. [PMID: 27551915 PMCID: PMC4995011 DOI: 10.1371/journal.pone.0161588] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/08/2016] [Indexed: 12/14/2022] Open
Abstract
G-quadruplex forming sequences are particularly enriched in the promoter regions of eukaryotic genes, especially of oncogenes. One of the most well studied G-quadruplex forming sequences is located in the nuclease hypersensitive element (NHE) III1 of the c-MYC promoter region. The oncoprotein c-MYC regulates a large array of genes which play important roles in growth regulation and metabolism. It is dysregulated in >70% of human cancers. The silencer NHEIII1 located upstream of the P1 promoter regulates up-to 80% of c-MYC transcription and includes a G-quadruplex structure (Pu27) that is required for promoter inhibition. We have identified, for the first time, a family of seventeen G-quadruplex-forming motifs with >90% identity with Pu27, located on different chromosomes throughout the human genome, some found near or within genes involved in stem cell maintenance or neural cell development. Notably, all members of the Pu27 family interact specifically with NHEIII1 sequence, in vitro. Crosslinking studies demonstrate that Pu27 oligonucleotide binds specifically to the C-rich strand of the NHEIII1 resulting in the G-quadruplex structure stabilization. Pu27 homologous sequences (Pu27-HS) significantly inhibit leukemic cell lines proliferation in culture. Exposure of U937 cells to the Pu27-HS induces cell growth inhibition associated with cell cycle arrest that is most likely due to downregulation of c-MYC expression at the RNA and/or protein levels. Expression of SOX2, another gene containing a Pu27-HS, was affected by Pu27-HS treatment as well. Our data suggest that the oligonucleotides encoding the Pu27 family target complementary DNA sequences in the genome, including those of the c-MYC and SOX2 promoters. This effect is most likely cell type and cell growth condition dependent. The presence of genomic G-quadruplex-forming sequences homologous to Pu27 of c-MYC silencer and the fact that they interact specifically with the parent sequence suggest a common regulatory mechanism for genes whose promoters contain these sequences.
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Affiliation(s)
- Francine Rezzoug
- James Graham Brown Cancer Center, Department of Medicine, University of Louisville, Louisville Kentucky, United States of America
- * E-mail: (FR); (DMM)
| | - Shelia D. Thomas
- James Graham Brown Cancer Center, Department of Medicine, University of Louisville, Louisville Kentucky, United States of America
| | - Eric C. Rouchka
- Department of Computer Engineering and Computer Science, Speed School of Engineering, University of Louisville, Kentucky, United States of America
| | - Donald M. Miller
- James Graham Brown Cancer Center, Department of Medicine, University of Louisville, Louisville Kentucky, United States of America
- * E-mail: (FR); (DMM)
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15
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Qin QP, Chen ZF, Shen WY, Jiang YH, Cao D, Li YL, Xu QM, Liu YC, Huang KB, Liang H. Synthesis of a platinum(II) complex with 2-(4-methoxy-phenyl) imidazo [4,5-f]-[1,10] phenanthrolin and study of its antitumor activity. Eur J Med Chem 2014; 89:77-87. [PMID: 25462228 DOI: 10.1016/j.ejmech.2014.10.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 09/23/2014] [Accepted: 10/08/2014] [Indexed: 11/28/2022]
Abstract
A new platinum(II) complex of [Pt(II)(L) (pn)]Cl·2H2O (1) (pn = 1,3-propanediamine) with 2-(4-methoxy-phenyl)imidazo [4,5-f]-[1,10]phenanthrolin (H-L) was synthesized and characterized. In complex 1, the platinum adopts a four-coordinated square planar geometry. Complex 1 exhibited selective cytotoxicity against NCI-H460, BEL-7402, SK-OV-3, SK-OV-3/DDP and HeLa cell lines with IC50 values in the micromolar range (9.7-35.8 μM), but low cytotoxicity toward normal human liver HL-7702 cells. Complex 1 caused HeLa cell cycle arrest at S phase and it induced HeLa apoptosis by the activation of caspase-3/9. Various experiments showed that complex 1 preferred to bind with G-quadruplex in c-myc. Taken together, we found that complex 1 exerted its antitumor activity mainly via inhibiting telomerase by interaction with c-myc quadruplex and activation of caspase-3/9.
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Affiliation(s)
- Qi-Pin Qin
- State Key Laboratory Cultivation Base for the Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry & Pharmacy of Guangxi Normal University, Yucai Road 15, Guilin 541004, PR China
| | - Zhen-Feng Chen
- State Key Laboratory Cultivation Base for the Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry & Pharmacy of Guangxi Normal University, Yucai Road 15, Guilin 541004, PR China.
| | - Wen-Ying Shen
- State Key Laboratory Cultivation Base for the Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry & Pharmacy of Guangxi Normal University, Yucai Road 15, Guilin 541004, PR China
| | - Yan-Hua Jiang
- State Key Laboratory Cultivation Base for the Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry & Pharmacy of Guangxi Normal University, Yucai Road 15, Guilin 541004, PR China
| | - Dong Cao
- State Key Laboratory Cultivation Base for the Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry & Pharmacy of Guangxi Normal University, Yucai Road 15, Guilin 541004, PR China
| | - Yu-Lan Li
- State Key Laboratory Cultivation Base for the Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry & Pharmacy of Guangxi Normal University, Yucai Road 15, Guilin 541004, PR China
| | - Qing-Min Xu
- State Key Laboratory Cultivation Base for the Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry & Pharmacy of Guangxi Normal University, Yucai Road 15, Guilin 541004, PR China
| | - Yan-Cheng Liu
- State Key Laboratory Cultivation Base for the Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry & Pharmacy of Guangxi Normal University, Yucai Road 15, Guilin 541004, PR China
| | - Ke-Bin Huang
- State Key Laboratory Cultivation Base for the Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry & Pharmacy of Guangxi Normal University, Yucai Road 15, Guilin 541004, PR China
| | - Hong Liang
- State Key Laboratory Cultivation Base for the Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry & Pharmacy of Guangxi Normal University, Yucai Road 15, Guilin 541004, PR China.
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16
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Agarwal T, Lalwani MK, Kumar S, Roy S, Chakraborty TK, Sivasubbu S, Maiti S. Morphological Effects of G-Quadruplex Stabilization Using a Small Molecule in Zebrafish. Biochemistry 2014; 53:1117-24. [DOI: 10.1021/bi4009352] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tani Agarwal
- CSIR-Institute of Genomics and Integrative
Biology, , Mall Road, New Delhi 110 007, India
| | - Mukesh Kumar Lalwani
- CSIR-Institute of Genomics and Integrative
Biology, , Mall Road, New Delhi 110 007, India
| | - Santosh Kumar
- CSIR-Institute of Genomics and Integrative
Biology, , Mall Road, New Delhi 110 007, India
| | - Saumya Roy
- CSIR-Indian Institute of Chemical
Technology, , Hyderabad 500 007, India
| | - Tushar Kanti Chakraborty
- CSIR-Indian Institute of Chemical
Technology, , Hyderabad 500 007, India
- Department
of Organic Chemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Sridhar Sivasubbu
- CSIR-Institute of Genomics and Integrative
Biology, , Mall Road, New Delhi 110 007, India
| | - Souvik Maiti
- CSIR-Institute of Genomics and Integrative
Biology, , Mall Road, New Delhi 110 007, India
- CSIR-National Chemical Laboratory, Pune 411008, India
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17
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Do NQ, Phan AT. Monomer-dimer equilibrium for the 5'-5' stacking of propeller-type parallel-stranded G-quadruplexes: NMR structural study. Chemistry 2012; 18:14752-9. [PMID: 23019076 DOI: 10.1002/chem.201103295] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Indexed: 01/24/2023]
Abstract
Guanine-rich sequence motifs, which contain tracts of three consecutive guanines connected by single non-guanine nucleotides, are abundant in the human genome and can form a robust G-quadruplex structure with high stability. Herein, by using NMR spectroscopy, we investigate the equilibrium between monomeric and 5'-5' stacked dimeric propeller-type G-quadruplexes that are formed by DNA sequences containing GGGT motifs. We show that the monomer-dimer equilibrium depends on a number of parameters, including the DNA concentration, DNA flanking sequences, the concentration and type of cations, and the temperature. We report on the high-definition structure of a simple monomeric G-quadruplex containing three single-residue loops, which could serve as a reference for propeller-type G-quadruplex structures in solution.
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Affiliation(s)
- Ngoc Quang Do
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
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18
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Liao SR, Zhou CX, Wu WB, Ou TM, Tan JH, Li D, Gu LQ, Huang ZS. 12-N-Methylated 5,6-dihydrobenzo[c]acridine derivatives: a new class of highly selective ligands for c-myc G-quadruplex DNA. Eur J Med Chem 2012; 53:52-63. [PMID: 22513122 DOI: 10.1016/j.ejmech.2012.03.034] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2012] [Revised: 03/16/2012] [Accepted: 03/17/2012] [Indexed: 11/19/2022]
Abstract
12-N-Methylated and non-methylated 5,6-dihydrobenzo[c]acridine derivatives were designed and synthesized as new series of c-myc G-quadruplex binding ligands. Their interactions with c-myc G-quadruplex were evaluated using fluorescence resonance energy transfer (FRET) melting assay, circular dichroism (CD) spectroscopy, surface plasmon resonance (SPR), polymerase chain reaction (PCR) stop assay, and molecular modeling. Compared with the non-methylated derivatives, 12-N-methylated derivatives had stronger binding affinity and stabilizing ability to c-myc G-quadruplex structure, and could more effectively stack on the G-quartet surface. All these derivatives had high selectivity for c-myc G-quadruplex DNA over duplex DNA. The reverse transcription (RT) PCR assay showed that compound 21c could down-regulate transcription of c-myc gene in Ramos cell line containing NHE III(1) element, but had no effect in CA46 cell line with NHE III(1) element removed.
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Affiliation(s)
- Sheng-Rong Liao
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou University City, Waihuan East Road 132, Guangzhou 510006, People's Republic of China
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19
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Chen WJ, Zhou CX, Yao PF, Wang XX, Tan JH, Li D, Ou TM, Gu LQ, Huang ZS. Disubstituted 1,8-dipyrazolcarbazole derivatives as a new type of c-myc G-quadruplex binding ligands. Bioorg Med Chem 2012; 20:2829-36. [PMID: 22484007 DOI: 10.1016/j.bmc.2012.03.031] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2012] [Revised: 03/13/2012] [Accepted: 03/14/2012] [Indexed: 11/19/2022]
Abstract
A series of 1,8-dipyrazolcarbazole (DPC) derivatives (6a-6d, 7a-7d) designed as G-quadruplex ligands have been synthesized and characterized. The FRET-melting and SPR results showed that the DPC derivatives could well recognize G-quadruplex with strong discrimination against the duplex DNA. In addition, the DPC derivatives showed much stronger stabilization activities and binding affinities for c-myc G-quadruplex rather than telomeric G-quadruplex. Therefore, their interactions with c-myc G-quadruplex were further explored by means of CD spectroscopy, PCR-stop assay, and molecular modeling. In cellular studies, all compounds showed strong cytotoxicity against cancer cells, while weak cytotoxicity towards normal cells. RT-PCR assay showed that compound 7b could down-regulate c-myc gene expression in Ramos cell line, while had no effect on c-myc expression in CA46 cell line with NHE III(1) element removed, indicating its effective binding with G-quadruplex on c-myc oncogene in vivo.
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Affiliation(s)
- Wei-Jia Chen
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, People's Republic of China
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20
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Lech CJ, Cheow Lim JK, Wen Lim JM, Amrane S, Heddi B, Phan AT. Effects of site-specific guanine C8-modifications on an intramolecular DNA G-quadruplex. Biophys J 2012; 101:1987-98. [PMID: 22004753 DOI: 10.1016/j.bpj.2011.08.049] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2011] [Revised: 08/15/2011] [Accepted: 08/19/2011] [Indexed: 10/16/2022] Open
Abstract
Understanding the fundamentals of G-quadruplex formation is important both for targeting G-quadruplexes formed by natural sequences and for engineering new G-quadruplexes with desired properties. Using a combination of experimental and computational techniques, we have investigated the effects of site-specific substitution of a guanine with C8-modified guanine derivatives, including 8-bromo-guanine, 8-O-methyl-guanine, 8-amino-guanine, and 8-oxo-guanine, within a well-defined (3 + 1) human telomeric G-quadruplex platform. The effects of substitutions on the stability of the G-quadruplex were found to depend on the type and position of the modification among different guanines in the structure. An interesting modification-dependent NMR chemical-shift effect was observed across basepairing within a guanine tetrad. This effect was reproduced by ab initio quantum mechanical computations, which showed that the observed variation in imino proton chemical shift is largely influenced by changes in hydrogen-bond geometry within the guanine tetrad.
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21
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Do NQ, Lim KW, Teo MH, Heddi B, Phan AT. Stacking of G-quadruplexes: NMR structure of a G-rich oligonucleotide with potential anti-HIV and anticancer activity. Nucleic Acids Res 2011; 39:9448-57. [PMID: 21840903 PMCID: PMC3241632 DOI: 10.1093/nar/gkr539] [Citation(s) in RCA: 145] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
G-rich oligonucleotides T30695 (or T30923), with the sequence of (GGGT)4, and T40214, with the sequence of (GGGC)4, have been reported to exhibit anti-HIV and anticancer activity. Here we report on the structure of a dimeric G-quadruplex adopted by a derivative of these sequences in K+ solution. It comprises two identical propeller-type parallel-stranded G-quadruplex subunits each containing three G-tetrad layers that are stacked via the 5′-5′ interface. We demonstrated control over the stacking of the two monomeric subunits by sequence modifications. Our analysis of possible structures at the stacking interface provides a general principle for stacking of G-quadruplexes, which could have implications for the assembly and recognition of higher-order G-quadruplex structures.
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Affiliation(s)
- Ngoc Quang Do
- School of Physical and Mathematical Sciences and School of Biological Sciences, Nanyang Technological University, Singapore
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22
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Ou TM, Lin J, Lu YJ, Hou JQ, Tan JH, Chen SH, Li Z, Li YP, Li D, Gu LQ, Huang ZS. Inhibition of cell proliferation by quindoline derivative (SYUIQ-05) through its preferential interaction with c-myc promoter G-quadruplex. J Med Chem 2011; 54:5671-9. [PMID: 21774525 DOI: 10.1021/jm200062u] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
G-Quadruplex is a special DNA secondary structure and present in many important regulatory regions in human genome, such as the telomeric end and the promoters of some oncogenes. Specially, different forms of G-quadruplexes exist in telomeric DNA and c-myc promoter and play important roles in the pathway of cell proliferation and senescence. The effects of G-quadruplex ligands for either telomeric or c-myc G-quadruplex in vitro have been widely studied, but the specificity of these effects in vivo is still unknown. In the present research, various experiments were carried out to study the effect of G-quadruplex ligand SYUIQ-05 on tumor cell lines and the mechanism of this effect. Our results showed that it preferred to bind with G-quadruplex in c-myc and had rather insignificant effect on G-quadruplex in telomere. Therefore, it is possible that this compound had its antitumor activity for cancer cells mainly through its interaction with c-myc quadruplex.
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Affiliation(s)
- Tian-Miao Ou
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, Waihuan East Road 132, Guangzhou 510006, People's Republic of China
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23
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Chen JLY, Sperry J, Ip NY, Brimble MA. Natural products targeting telomere maintenance. MEDCHEMCOMM 2011. [DOI: 10.1039/c0md00241k] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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24
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Agarwal T, Roy S, Chakraborty TK, Maiti S. Selective Targeting of G-Quadruplex Using Furan-Based Cyclic Homooligopeptides: Effect on c-MYC Expression. Biochemistry 2010; 49:8388-97. [DOI: 10.1021/bi1005927] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Tani Agarwal
- Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR, Mall Road, New Delhi 110 007, India
| | - Saumya Roy
- Indian Institute of Chemical Technology, CSIR, Hyderabad 500 007, India
| | - Tushar Kanti Chakraborty
- Indian Institute of Chemical Technology, CSIR, Hyderabad 500 007, India
- Central Drug Research Institute, CSIR, Lucknow 226 001, India
| | - Souvik Maiti
- Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR, Mall Road, New Delhi 110 007, India
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25
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Shalaby T, von Bueren AO, Hürlimann ML, Fiaschetti G, Castelletti D, Masayuki T, Nagasawa K, Arcaro A, Jelesarov I, Shin-ya K, Grotzer M. Disabling c-Myc in childhood medulloblastoma and atypical teratoid/rhabdoid tumor cells by the potent G-quadruplex interactive agent S2T1-6OTD. Mol Cancer Ther 2010; 9:167-79. [PMID: 20053783 DOI: 10.1158/1535-7163.mct-09-0586] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We investigated here the effects of S2T1-6OTD, a novel telomestatin derivative that is synthesized to target G-quadruplex-forming DNA sequences, on a representative panel of human medulloblastoma (MB) and atypical teratoid/rhabdoid (AT/RT) childhood brain cancer cell lines. S2T1-6OTD proved to be a potent c-Myc inhibitor through its high-affinity physical interaction with the G-quadruplex structure in the c-Myc promoter. Treatment with S2T1-6OTD reduced the mRNA and protein expressions of c-Myc and hTERT, which is transcriptionally regulated by c-Myc, and decreased the activities of both genes. In remarkable contrast to control cells, short-term (72-hour) treatment with S2T1-6OTD resulted in a dose- and time-dependent antiproliferative effect in all MB and AT/RT brain tumor cell lines tested (IC(50), 0.25-0.39 micromol/L). Under conditions where inhibition of both proliferation and c-Myc activity was observed, S2T1-6OTD treatment decreased the protein expression of the cell cycle activator cyclin-dependent kinase 2 and induced cell cycle arrest. Long-term treatment (5 weeks) with nontoxic concentrations of S2T1-6OTD resulted in a time-dependent (mainly c-Myc-dependent) telomere shortening. This was accompanied by cell growth arrest starting on day 28 followed by cell senescence and induction of apoptosis on day 35 in all of the five cell lines investigated. On in vivo animal testing, S2T1-6OTD may well represent a novel therapeutic strategy for childhood brain tumors.
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Affiliation(s)
- Tarek Shalaby
- Department of Oncology, University Children's Hospital Zurich, Zurich, Switzerland
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26
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Johnson JE, Cao K, Ryvkin P, Wang LS, Johnson FB. Altered gene expression in the Werner and Bloom syndromes is associated with sequences having G-quadruplex forming potential. Nucleic Acids Res 2009; 38:1114-22. [PMID: 19966276 PMCID: PMC2831322 DOI: 10.1093/nar/gkp1103] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The human Werner and Bloom syndromes (WS and BS) are caused by deficiencies in the WRN and BLM RecQ helicases, respectively. WRN, BLM and their Saccharomyces cerevisiae homologue Sgs1, are particularly active in vitro in unwinding G-quadruplex DNA (G4-DNA), a family of non-canonical nucleic acid structures formed by certain G-rich sequences. Recently, mRNA levels from loci containing potential G-quadruplex-forming sequences (PQS) were found to be preferentially altered in sgs1Δ mutants, suggesting that G4-DNA targeting by Sgs1 directly affects gene expression. Here, we extend these findings to human cells. Using microarrays to measure mRNAs obtained from human fibroblasts deficient for various RecQ family helicases, we observe significant associations between loci that are upregulated in WS or BS cells and loci that have PQS. No such PQS associations were observed for control expression datasets, however. Furthermore, upregulated genes in WS and BS showed no or dramatically reduced associations with sequences similar to PQS but that have considerably reduced potential to form intramolecular G4-DNA. These findings indicate that, like Sgs1, WRN and BLM can regulate transcription globally by targeting G4-DNA.
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Affiliation(s)
- Jay E Johnson
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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27
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Role for G-quadruplex RNA binding by Epstein-Barr virus nuclear antigen 1 in DNA replication and metaphase chromosome attachment. J Virol 2009; 83:10336-46. [PMID: 19656898 DOI: 10.1128/jvi.00747-09] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Latent infection by Epstein-Barr virus (EBV) requires both replication and maintenance of the viral genome. EBV nuclear antigen 1 (EBNA1) is a virus-encoded protein that is critical for the replication and maintenance of the genome during latency in proliferating cells. We have previously demonstrated that EBNA1 recruits the cellular origin recognition complex (ORC) through an RNA-dependent interaction with EBNA1 linking region 1 (LR1) and LR2. We now show that LR1 and LR2 bind to G-rich RNA that is predicted to form G-quadruplex structures. Several chemically distinct G-quadruplex-interacting drugs disrupted the interaction between EBNA1 and ORC. The G-quadruplex-interacting compound BRACO-19 inhibited EBNA1-dependent stimulation of viral DNA replication and preferentially blocked proliferation of EBV-positive cells relative to EBV-negative cell lines. BRACO-19 treatment also disrupted the ability of EBNA1 to tether to metaphase chromosomes, suggesting that maintenance function is also mediated through G-quadruplex recognition. These findings suggest that the EBNA1 replication and maintenance function uses a common G-quadruplex binding capacity of LR1 and LR2, which may be targetable by small-molecule inhibitors.
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28
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Bates PJ, Laber DA, Miller DM, Thomas SD, Trent JO. Discovery and development of the G-rich oligonucleotide AS1411 as a novel treatment for cancer. Exp Mol Pathol 2009; 86:151-64. [PMID: 19454272 PMCID: PMC2716701 DOI: 10.1016/j.yexmp.2009.01.004] [Citation(s) in RCA: 593] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2008] [Indexed: 02/07/2023]
Abstract
Certain guanine-rich (G-rich) DNA and RNA molecules can associate intermolecularly or intramolecularly to form four stranded or "quadruplex" structures, which have unusual biophysical and biological properties. Several synthetic G-rich quadruplex-forming oligodeoxynucleotides have recently been investigated as therapeutic agents for various human diseases. We refer to these biologically active G-rich oligonucleotides as aptamers because their activities arise from binding to protein targets via shape-specific recognition (analogous to antibody-antigen binding). As therapeutic agents, the G-rich aptamers may have some advantages over monoclonal antibodies and other oligonucleotide-based approaches. For example, quadruplex oligonucleotides are non-immunogenic, heat stable and they have increased resistance to serum nucleases and enhanced cellular uptake compared to unstructured sequences. In this review, we describe the characteristics and activities of G-rich oligonucleotides. We also give a personal perspective on the discovery and development of AS1411, an antiproliferative G-rich phosphodiester oligonucleotide that is currently being tested as an anticancer agent in Phase II clinical trials. This molecule functions as an aptamer to nucleolin, a multifunctional protein that is highly expressed by cancer cells, both intracellularly and on the cell surface. Thus, the serendipitous discovery of the G-rich oligonucleotides also led to the identification of nucleolin as a new molecular target for cancer therapy.
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Affiliation(s)
- Paula J Bates
- James Graham Brown Cancer Center, Department of Medicine, University of Louisville, Louisville, Kentucky 40202, USA.
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Arora A, Nair DR, Maiti S. Effect of flanking bases on quadruplex stability and Watson-Crick duplex competition. FEBS J 2009; 276:3628-40. [PMID: 19490117 DOI: 10.1111/j.1742-4658.2009.07082.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Guanine-rich DNA sequences have the ability to fold into four-stranded structures called G-quadruplexes, and are considered as promising anticancer targets. Although the G-quadruplex structure is composed of quartets and interspersed loops, in the genome it is also flanked on each side by numerous bases. The effect of loop length and composition on quadruplex conformation and stability has been well investigated in the past, but the effect of flanking bases on quadruplex stability and Watson-Crick duplex competition has not been addressed. We have studied in detail the effect of flanking bases on quadruplex stability and on duplex formation by the G-quadruplex in the presence of complementary strands using the quadruplex-forming sequence located in the promoter region of the c-kit oncogene. The results obtained from CD, thermal difference spectrum and UV melting demonstrated the effect of flanking bases on quadruplex structure and stability. With the increase in flank length, the increase in the more favorable DeltaH(vH) is accompanied by a striking increase in the unfavorable DeltaS(vH), which resulted in a decrease in the overall DeltaG(vH) of quadruplex formation. Furthermore, CD, fluorescence and isothermal titration calorimetry studies demonstrated that the propensity to attain quadruplex structure decreases with increasing flank length.
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Affiliation(s)
- Amit Arora
- Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, Council for Scientific and Industrial Research, Delhi, India
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Kumar N, Maiti S. A thermodynamic overview of naturally occurring intramolecular DNA quadruplexes. Nucleic Acids Res 2008; 36:5610-22. [PMID: 18757890 PMCID: PMC2553590 DOI: 10.1093/nar/gkn543] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Loop length and its composition are important for the structural and functional versatility of quadruplexes. To date studies on the loops have mainly concerned model sequences compared with naturally occurring quadruplex sequences which have diverse loop lengths and compositions. Herein, we have characterized 36 quadruplex-forming sequences from the promoter regions of various proto-oncogenes using CD, UV and native gel electrophoresis. We examined folding topologies and determined the thermodynamic profile for quadruplexes varying in total loop length (5–18 bases) and composition. We found that naturally occurring quadruplexes have variable thermodynamic stabilities (ΔG37) ranging from −1.7 to −15.6 kcal/mol. Overall, our results suggest that both loop length and its composition affect quadruplex structure and thermodynamics, thus making it difficult to draw generalized correlations between loop length and thermodynamic stability. Additionally, we compared the thermodynamic stability of quadruplexes and their respective duplexes to understand quadruplex–duplex competition. Our findings invoke a discussion on whether biological function is associated with quadruplexes with lower thermodynamic stability which undergo facile formation and disruption, or by quadruplexes with high thermodynamic stability.
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Affiliation(s)
- Niti Kumar
- Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110 007, India
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31
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Qin Y, Hurley LH. Structures, folding patterns, and functions of intramolecular DNA G-quadruplexes found in eukaryotic promoter regions. Biochimie 2008; 90:1149-71. [PMID: 18355457 DOI: 10.1016/j.biochi.2008.02.020] [Citation(s) in RCA: 373] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2008] [Accepted: 02/22/2008] [Indexed: 12/16/2022]
Abstract
In its simplest form, a DNA G-quadruplex is a four-stranded DNA structure that is composed of stacked guanine tetrads. G-quadruplex-forming sequences have been identified in eukaryotic telomeres, as well as in non-telomeric genomic regions, such as gene promoters, recombination sites, and DNA tandem repeats. Of particular interest are the G-quadruplex structures that form in gene promoter regions, which have emerged as potential targets for anticancer drug development. Evidence for the formation of G-quadruplex structures in living cells continues to grow. In this review, we examine recent studies on intramolecular G-quadruplex structures that form in the promoter regions of some human genes in living cells and discuss the biological implications of these structures. The identification of G-quadruplex structures in promoter regions provides us with new insights into the fundamental aspects of G-quadruplex topology and DNA sequence-structure relationships. Progress in G-quadruplex structural studies and the validation of the biological role of these structures in cells will further encourage the development of small molecules that target these structures to specifically modulate gene transcription.
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Affiliation(s)
- Yong Qin
- College of Pharmacy, 1703 E. Mabel, University of Arizona, Tucson, AZ 85721, USA
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32
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Johnson JE, Smith JS, Kozak ML, Johnson FB. In vivo veritas: using yeast to probe the biological functions of G-quadruplexes. Biochimie 2008; 90:1250-63. [PMID: 18331848 DOI: 10.1016/j.biochi.2008.02.013] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2007] [Accepted: 02/07/2008] [Indexed: 12/20/2022]
Abstract
Certain guanine-rich sequences are capable of forming higher order structures known as G-quadruplexes. Moreover, particular genomic regions in a number of highly divergent organisms are enriched for such sequences, raising the possibility that G-quadruplexes form in vivo and affect cellular processes. While G-quadruplexes have been rigorously studied in vitro, whether these structures actually form in vivo and what their roles might be in the context of the cell have remained largely unanswered questions. Recent studies suggest that G-quadruplexes participate in the regulation of such varied processes as telomere maintenance, transcriptional regulation and ribosome biogenesis. Here we review studies aimed at elucidating the in vivo functions of quadruplex structures, with a particular focus on findings in yeast. In addition, we discuss the utility of yeast model systems in the study of the cellular roles of G-quadruplexes.
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Affiliation(s)
- Jay E Johnson
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
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Arvanitis C, Bendapudi PK, Bachireddy P, Felsher DW. Identifying critical signaling molecules for the treatment of cancer. Recent Results Cancer Res 2007; 172:5-24. [PMID: 17607933 DOI: 10.1007/978-3-540-31209-3_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Constadina Arvanitis
- Department of Medicine, Stanford University School of Medicine, CA 94305-5151, USA
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Ou TM, Lu YJ, Zhang C, Huang ZS, Wang XD, Tan JH, Chen Y, Ma DL, Wong KY, Tang JCO, Chan ASC, Gu LQ. Stabilization of G-quadruplex DNA and down-regulation of oncogene c-myc by quindoline derivatives. J Med Chem 2007; 50:1465-74. [PMID: 17346034 DOI: 10.1021/jm0610088] [Citation(s) in RCA: 247] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Stabilization of G-quadruplex structures in the promoter region of certain oncogenes is an emerging field in anticancer drug design. Human c-myc gene is one of these oncogenes, and G-quadruplexes have been proven to be the transcriptional controller of this gene. In the present study, the interaction of quindoline derivatives with G-quadruplexes in c-myc was investigated. The experimental results indicated that these derivatives have the ability to induce/stabilize the G-quadruplexes in c-myc, which lead to down-regulation of the c-myc in the Hep G2 cell line. It was found that derivatives with terminal amino groups in their side chains would selectively bind to the isomers with the double nucleotide loops in the absence of K+. Molecular modeling studies revealed the binding mode between the derivatives and the G-quadruplexes is end-stacking at the 3'-position, and the positively charged side chain on the quindoline derivatives may contribute to the selectivity to certain loop isomers of topological quadruplexes as well as the improved stabilization action.
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Affiliation(s)
- Tian-Miao Ou
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510080, People's Republic of China
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Yin F, Liu J, Deng X, Wang J. Effects of Triethylene Tetraamine on the G-quadruplex Structure in the Human c-myc Promoter. ACTA ACUST UNITED AC 2007; 141:669-74. [PMID: 17339229 DOI: 10.1093/jb/mvm069] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
The increasing data show that a parallel G-quadruplex structure formed by the element of nuclease-hypersensitivity element III(1) (NHE III(1)) in the P1 promoter of c-myc functions as a transcriptional repressor. Triethylene tetraamine has exhibited interesting properties of stabilizing both inter- and intra-molecular G-quadruplex structures and telomerase-inhibitory potency. Here, we present evidences showing that triethylene tetraamine facilitates the formation of G-quadruplex structure by the NHE III(1) element, and inhibits the expression of c-myc in HeLa cells.
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Affiliation(s)
- Fei Yin
- Research Center of Pharmaceutical Chemistry & Chemobiology, Chongqing Technology and Business University, Chongqing 400067, China
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Abstract
Myc expression is deregulated in a wide range of human cancers and is often associated with aggressive, poorly differentiated tumors. The Myc protein is a transcription factor that regulates a variety of cellular processes including cell growth and proliferation, cell-cycle progression, transcription, differentiation, apoptosis, and cell motility. Potential strategies that either inhibit the growth promoting effect of Myc and/or activate its pro-apoptotic function are presently being explored. In this review, we give an overview of Myc activation in human tumors and discuss current strategies aimed at targeting Myc for cancer treatment. Such therapies could have potential in combination with mechanistically different cytotoxic drugs to combat and eradicate tumors cells.
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Affiliation(s)
- Marina Vita
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
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De Armond R, Wood S, Sun D, Hurley LH, Ebbinghaus SW. Evidence for the presence of a guanine quadruplex forming region within a polypurine tract of the hypoxia inducible factor 1alpha promoter. Biochemistry 2006; 44:16341-50. [PMID: 16331995 DOI: 10.1021/bi051618u] [Citation(s) in RCA: 228] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The promoter of the hypoxia inducible factor 1 alpha (HIF-1alpha) gene has a polypurine/polypyrimidine tract (-65 to -85) overlapping or adjacent to several putative transcription factor binding sites, and we found that mutagenesis of this region diminished basal HIF-1alpha expression. Oligonucleotides representing this region of the HIF-1alpha promoter were analyzed by electrophoretic mobility shift, chemical probing, circular dichroism, and DNA polymerase arrest assays. The guanine-rich strand was found to form a parallel, unimolecular quadruplex in the presence of potassium that was further stabilized by two known quadruplex binding compounds, the cationic porphyrin TmPyP4 and the natural product telomestatin, while TmPyP2, a positional isomer of TmPyP4, did not stabilize quadruplex formation. These data suggest that a quadruplex structure may form in a region of the HIF-1alpha promoter that regulates basal HIF-1alpha expression.
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Affiliation(s)
- Richard De Armond
- Arizona Cancer Center, University of Arizona, 1515 North Campbell Avenue, Tucson, Arizona 85724-5024, USA
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Ponzielli R, Katz S, Barsyte-Lovejoy D, Penn LZ. Cancer therapeutics: targeting the dark side of Myc. Eur J Cancer 2005; 41:2485-501. [PMID: 16243519 DOI: 10.1016/j.ejca.2005.08.017] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The potent Myc oncoprotein plays a pivotal role as a regulator of tumorigenesis in numerous human cancers of diverse origin. Experimental evidence shows that inhibiting Myc significantly halts tumour cell growth and proliferation. This review summarises recent progress in understanding the function of Myc as a transcription factor, with emphasis on key protein interactions and target gene regulation. In addition, major advances in drug development aimed at eliminating Myc are described, including antisense and triple helix forming oligonucleotides, porphyrins and siRNA. Future anti-Myc strategies are also discussed that inhibit Myc at the level of expression and/or function. Targeting the dark side of Myc with novel therapeutic agents promises to have a profound impact in combating cancer.
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Affiliation(s)
- Romina Ponzielli
- Ontario Cancer Institute/Princess Margaret Hospital, Department of Medical Biophysics, University of Toronto, 610 University Avenue, Toronto, Ont., Canada M5G 2M9
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39
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Affiliation(s)
- Ali Hachem
- University of Maryland Greenebaum Cancer Center, 9-011 BRB, 655 West Baltimore St, Baltimore MD 21201, USA
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40
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Nelson SM, Ferguson LR, Denny WA. Demonstration by Real-Time Polymerase Chain Reaction that Cellular DNA Alkylation by Novel Aminoindoline Compounds Affects Expression of the Protooncogene c-myc. Chem Res Toxicol 2005; 18:239-48. [PMID: 15720128 DOI: 10.1021/tx049852t] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Aminoindolines, analogues of the potent DNA alkylating agent seco-CBI-TMI, bind to and alkylate in the minor groove of AT-rich DNA in vitro. Here we extend the in vitro mechanism of action studies by treating cells in culture and examining the DNA binding patterns within AT-rich regions of the protooncogene locus c-myc, using a real-time polymerase chain reaction (PCR) stop assay. In addition, real-time reverse transcriptase (RT) PCR is used to examine the immediate effects of drug treatment on c-myc expression. These analyses demonstrate a concentration and time dependence for DNA alkylation at the chosen sites within the c-myc locus, as well as a prompt and significant downregulation of c-myc expression. While downregulation of this important growth regulator is likely not the only consequence of aminoindoline treatment, these studies begin to address the cellular pathways that are involved in the potent cytotoxic effects observed and provide insights for the future development of anticancer drugs of this class.
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Affiliation(s)
- Stephanie M Nelson
- Auckland Cancer Society Research Centre, School of Medical Sciences, The University of Auckland, Private Bag 92019, Auckland 10000, New Zealand.
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41
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Lemarteleur T, Gomez D, Paterski R, Mandine E, Mailliet P, Riou JF. Stabilization of the c-myc gene promoter quadruplex by specific ligands' inhibitors of telomerase. Biochem Biophys Res Commun 2004; 323:802-8. [PMID: 15381071 DOI: 10.1016/j.bbrc.2004.08.150] [Citation(s) in RCA: 176] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2004] [Indexed: 11/29/2022]
Abstract
A parallel G-quadruplex structure was recently identified in the NHE III(1) element of the c-myc gene promoter that functioned as a transcriptional repressor. Different series of telomeric G-quadruplex interacting ligands reported to block telomerase activity were evaluated in a new PCR stop assay on the c-myc quadruplex (Pu22myc). Results indicated that the cationic porphyrin TMPyP4 previously described to stabilize c-myc quadruplex and to cause transcription inhibition efficiently inhibited the assay but with a narrow selectivity when parallel experiments were performed with an oligonucleotide (Pu22mu) containing mutations in the guanine repeat which is unable to form a quadruplex. Other ligands presented potent inhibitory properties with IC(50) in the submicromolar range. 307A, a new 2,6-pyridin-dicarboxamide derivative was found to present the highest selectivity as compared to Pu22mu oligonucleotide (>90-fold). Comparison with telomeric G-quadruplex using TRAP-G4 and PCR stop assays also indicated that ligands 307A, telomestatin, and TMPyP4 are equipotent against both c-myc and telomeric sequences while other ligands displayed some partial selectivity (2- to 6-fold) towards one of these sequences. This work provides evidence that G-quadruplex ligands reported as telomerase inhibitors efficiently stabilized c-myc promoter intramolecular quadruplex and may also potentially be used to inhibit c-myc gene transcription in tumor cells.
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Affiliation(s)
- Thibault Lemarteleur
- Laboratoire d'Onco-Pharmacologie, JE 2428, UFR de Pharmacie, Université de Reims Champagne-Ardenne, 51096 Reims, France
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Maiti S, Chaudhury NK, Chowdhury S. Hoechst 33258 binds to G-quadruplex in the promoter region of human c-myc. Biochem Biophys Res Commun 2003; 310:505-12. [PMID: 14521939 DOI: 10.1016/j.bbrc.2003.09.052] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In vitro binding of Hoechst 33258 to the promoter region of human c-myc, d(GG GGAGGG TGG GGA GGG TGG GGA AGG TGG GG) which forms G-quadruplex, both in vitro and in vivo in the presence of metal ions, was investigated by equilibrium absorption, fluorescence, and kinetic surface plasmon resonance methods. Hypochromic effect in UV absorption spectra and blue shift in fluorescence emission maxima of Hoechst in the presence of quadruplex revealed that Hoechst binds to the quadruplex. Analysis of UV and fluorescence titration data revealed that Hoechst binds to quadruplex with binding affinity of the order of 10(6). Anisotropy measurements and higher lifetime obtained from time-resolved decay experiments revealed that quadruplex-bound Hoechst is rotationally restricted in a less polar environment than the bulk buffer medium. From surface plasmon resonance studies, we obtained kinetic association (k(a)) and dissociation (k(d)) of 1.23+/-0.04 x 10(5)M(-1)s(-1) and 0.686+/-0.009 s(-1), respectively. As Hoechst is known to bind A-T-rich region of duplex DNA, here we propose the likelihood of Hoechst interacting with the AAGGT loop of the quadruplex.
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Affiliation(s)
- Souvik Maiti
- Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110007, India.
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Siddiqui-Jain A, Grand CL, Bearss DJ, Hurley LH. Direct evidence for a G-quadruplex in a promoter region and its targeting with a small molecule to repress c-MYC transcription. Proc Natl Acad Sci U S A 2002; 99:11593-8. [PMID: 12195017 PMCID: PMC129314 DOI: 10.1073/pnas.182256799] [Citation(s) in RCA: 1759] [Impact Index Per Article: 80.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The nuclease hypersensitivity element III(1) upstream of the P1 promoter of c-MYC controls 85-90% of the transcriptional activation of this gene. We have demonstrated that the purine-rich strand of the DNA in this region can form two different intramolecular G-quadruplex structures, only one of which seems to be biologically relevant. This biologically relevant structure is the kinetically favored chair-form G-quadruplex, which is destabilized when mutated with a single G --> A transition, resulting in a 3-fold increase in basal transcriptional activity of the c-MYC promoter. The cationic porphyrin TMPyP4, which has been shown to stabilize this G-quadruplex structure, is able to suppress further c-MYC transcriptional activation. These results provide compelling evidence that a specific G-quadruplex structure formed in the c-MYC promoter region functions as a transcriptional repressor element. Furthermore, we establish the principle that c-MYC transcription can be controlled by ligand-mediated G-quadruplex stabilization.
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44
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Neidle S, Parkinson G. Telomere maintenance as a target for anticancer drug discovery. Nat Rev Drug Discov 2002; 1:383-93. [PMID: 12120414 DOI: 10.1038/nrd793] [Citation(s) in RCA: 511] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Maintenance of telomeres--specialized complexes that protect the ends of chromosomes--is undertaken by the enzyme complex telomerase, which is a key factor that is activated in more than 80% of cancer cells that have been examined so far, but is absent in most normal cells. So, targeting telomere-maintenance mechanisms could potentially half tumour growth across a broad spectrum of tumour types, with little cytotoxic effect outside tumours. Here, we describe the current understanding of telomere biology, and the application of this knowledge to the development of anticancer drugs.
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Affiliation(s)
- Stephen Neidle
- CRC Biomolecular Structure Unit, Chester Beatty Laboratories, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK.
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