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Ghosh D, Pratihar S, Govindaraju T. Designer tryptophan-rich peptide modulates structural dynamics of HIF-1α DNA i-motif DNA. J Pept Sci 2024; 30:e3601. [PMID: 38591712 DOI: 10.1002/psc.3601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/12/2024] [Accepted: 03/16/2024] [Indexed: 04/10/2024]
Abstract
Cytosine-rich DNA sequences can fold into intercalated motifs known as i-motifs, through noncanonical hydrogen bonding interactions. Molecular probes can provide valuable insights into the conformational stability and potential cellular functions of i-motifs. W5K5, a decapeptide composed of alternating tryptophan (W) and lysine (K) units, has been identified as a lead candidate to modulate the structural dynamics of the hypoxia-inducible factor 1-alpha (HIF-1α) DNA i-motif. This finding is expected to facilitate the rational design of peptide-based probes for studying the structure and functional dynamics of i-motifs.
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Affiliation(s)
- Debasis Ghosh
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru, Karnataka, India
| | - Sumon Pratihar
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru, Karnataka, India
| | - Thimmaiah Govindaraju
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru, Karnataka, India
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2
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Wang J, Wang S, Zhang J, Ji D, Huang ZS, Li D. Regulation of VEGF gene expression by bisacridine derivative through promoter i-motif for cancer treatment. Biochim Biophys Acta Gen Subj 2024; 1868:130631. [PMID: 38685534 DOI: 10.1016/j.bbagen.2024.130631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 04/12/2024] [Accepted: 04/19/2024] [Indexed: 05/02/2024]
Abstract
BACKGROUND Vascular endothelial growth factor (VEGF) is overexpressed in most malignant tumors, which has important impact on tumor angiogenesis and development. Its gene promoter i-motif structure formed by C-rich sequence can regulate gene expression, which is a promising new target for anti-tumor therapy. METHODS We screened various compounds and studied their effects on VEGF through extensive experiments, including SPR, MST, TO displacement, FRET, CD, ESI-MS, NMR, MTT, clone formation, qPCR, Western blot, dual-luciferase reporter assay, immunofluorescence, cell scrape, apoptosis, transwell assay, and animal model. RESULTS After extensive screening, bisacridine derivative B09 was found to have selective binding and stabilization to VEGF promoter i-motif, which could down-regulate VEGF gene expression. B09 showed potent inhibition on MCF-7 and HGC-27 cell proliferation and metastasis. B09 significantly inhibited tumor growth in xenograft mice model with HGC-27 cells, showing decreased VEGF expression analyzed through immunohistochemistry. CONCLUSION B09 could specifically regulate VEGF gene expression, possibly through interacting with promoter i-motif structure. As a lead compound, B09 could be further developed for innovative anti-cancer agent targeting VEGF.
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Affiliation(s)
- Jing Wang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, Guangzhou, PR China
| | - Siyi Wang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, Guangzhou, PR China
| | - Jiahui Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, Guangzhou, PR China
| | - Dongsheng Ji
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, Guangzhou, PR China
| | - Zhi-Shu Huang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, Guangzhou, PR China
| | - Ding Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, Guangzhou, PR China.
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3
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Tao S, Run Y, Monchaud D, Zhang W. i-Motif DNA: identification, formation, and cellular functions. Trends Genet 2024:S0168-9525(24)00133-1. [PMID: 38902139 DOI: 10.1016/j.tig.2024.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 05/29/2024] [Accepted: 05/29/2024] [Indexed: 06/22/2024]
Abstract
An i-motif (iM) is a four-stranded (quadruplex) DNA structure that folds from cytosine (C)-rich sequences. iMs can fold under many different conditions in vitro, which paves the way for their formation in living cells. iMs are thought to play key roles in various DNA transactions, notably in the regulation of genome stability, gene transcription, mRNA translation, DNA replication, telomere and centromere functions, and human diseases. We summarize the different techniques used to assess the folding of iMs in vitro and provide an overview of the internal and external factors that affect their formation and stability in vivo. We describe the possible biological relevance of iMs and propose directions towards their use as target in biology.
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Affiliation(s)
- Shentong Tao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production (CIC-MCP), Nanjing Agricultural University, 1 Weigang, Nanjing, Jiangsu 210095, China
| | - Yonghang Run
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production (CIC-MCP), Nanjing Agricultural University, 1 Weigang, Nanjing, Jiangsu 210095, China
| | - David Monchaud
- Institut de Chimie Moleculaire de l'Université de Bourgogne (ICMUB), Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 6302, Université Bourgogne Franche Comté (UBFC), Dijon, France
| | - Wenli Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production (CIC-MCP), Nanjing Agricultural University, 1 Weigang, Nanjing, Jiangsu 210095, China.
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Sengupta P, Jamroskovic J, Sabouri N. A beginner's handbook to identify and characterize i-motif DNA. Methods Enzymol 2023; 695:45-70. [PMID: 38521590 DOI: 10.1016/bs.mie.2023.11.001] [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] [Indexed: 03/25/2024]
Abstract
Genomic DNA exhibits an innate ability to manifest diverse sequence-dependent secondary structures, serving crucial functions in gene regulation and cellular equilibrium. While extensive research has confirmed the formation of G-quadruplex structures by guanine-rich sequences in vitro and in cells, recent investigations have turned the quadruplex community's attention to the cytosine (C)-rich complementary strands that can adopt unique tetra-stranded conformation, termed as intercalated motif or i-motif. I-motifs are stabilized by hemi-protonated C:CH+ base pairs under acidic conditions. Initially, the in vivo occurrence of i-motifs was underestimated because their formation is favored at non-physiological pH. However, groundbreaking research utilizing the structure-specific iMab antibody and high-throughput sequencing have recently detected their conserved dispersion throughout the genome, challenging previous assumptions. Given the evolving nature of this research field, it becomes imperative to conduct independent in vitro experiments aimed at identifying potential i-motif formation in C-rich sequences and consolidating the findings to address the properties of i-motifs. This chapter serves as an introductory guide for the swift identification of novel i-motifs, where we present an experimental framework for investigating and characterizing i-motif sequences in vitro. In this chapter, we selected a synthetic oligonucleotide (C7T3) sequence and outlined appropriate methodologies for annealing the i-motif structure into suitable buffers. Then, we validated its formation by CD (Circular Dichroism) and NMR (Nuclear Magnetic Resonance) spectroscopy. Finally, we provided a thorough account of the step-by-step procedures to investigate the effect of i-motif formation on the stalling or retardation of DNA replication using high resolution primer extension assays.
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Affiliation(s)
- Pallabi Sengupta
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Jan Jamroskovic
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Nasim Sabouri
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden.
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Romano F, Di Porzio A, Iaccarino N, Riccardi G, Di Lorenzo R, Laneri S, Pagano B, Amato J, Randazzo A. G-quadruplexes in cancer-related gene promoters: from identification to therapeutic targeting. Expert Opin Ther Pat 2023; 33:745-773. [PMID: 37855085 DOI: 10.1080/13543776.2023.2271168] [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: 06/26/2023] [Accepted: 10/11/2023] [Indexed: 10/20/2023]
Abstract
INTRODUCTION Guanine-rich DNA sequences can fold into four-stranded noncanonical secondary structures called G-quadruplexes (G4s) which are widely distributed in functional regions of the human genome, such as telomeres and gene promoter regions. Compelling evidence suggests their involvement in key genome functions such as gene expression and genome stability. Notably, the abundance of G4-forming sequences near transcription start sites suggests their potential involvement in regulating oncogenes. AREAS COVERED This review provides an overview of current knowledge on G4s in human oncogene promoters. The most representative G4-binding ligands have also been documented. The objective of this work is to present a comprehensive overview of the most promising targets for the development of novel and highly specific anticancer drugs capable of selectively impacting the expression of individual or a limited number of genes. EXPERT OPINION Modulation of G4 formation by specific ligands has been proposed as a powerful new tool to treat cancer through the control of oncogene expression. Actually, most of G4-binding small molecules seem to simultaneously target a range of gene promoter G4s, potentially influencing several critical driver genes in cancer, thus producing significant therapeutic benefits.
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Affiliation(s)
- Francesca Romano
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Anna Di Porzio
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Nunzia Iaccarino
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | | | | | - Sonia Laneri
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
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Das S, Takahashi S, Ohyama T, Bhowmik S, Sugimoto N. Theranostic approach to specifically targeting the interloop region of BCL2 i-motif DNA by crystal violet. Sci Rep 2023; 13:14338. [PMID: 37658102 PMCID: PMC10474294 DOI: 10.1038/s41598-023-39407-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/25/2023] [Indexed: 09/03/2023] Open
Abstract
Ligands that recognise specific i-motif DNAs are helpful in cancer diagnostics and therapeutics, as i-motif formation can cause cancer. Although the loop regions of i-motifs are promising targets for ligands, the interaction between a ligand and the loop regions based on sequence information remains unexplored. Herein, we investigated the loop regions of various i-motif DNAs to determine whether these regions specifically interact with fluorescent ligands. Crystal violet (CV), a triphenylmethane dye, exhibited strong fluorescence with the i-motif derived from the promoter region of the human BCL2 gene in a sequence- and structure-specific manner. Our systematic sequence analysis indicated that CV was bound to the site formed by the first and third loops through inter-loop interactions between the guanine bases present in these loops. As the structural stability of the BCL2 i-motif was unaffected by CV, the local stabilisation of the loops by CV could inhibit the interaction of transcription factors with these loops, repressing the BCL2 expression of MCF-7 cells. Our finding suggests that the loops of the i-motif can act as a novel platform for the specific binding of small molecules; thus, they could be utilised for the theranostics of diseases associated with i-motif DNAs.
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Affiliation(s)
- Sinjan Das
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan
| | - Shuntaro Takahashi
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan
| | - Tatsuya Ohyama
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan
| | - Sudipta Bhowmik
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, A.P.C Road, Kolkata, 700009, India
- Mahatma Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth (Deemed to be University), Pondy-Cuddalore Main Road, Pillayarkuppam, Pondicherry, 607402, India
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan.
- Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan.
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Dong J, Willner I. Transient Transcription Machineries Modulate Dynamic Functions of G-Quadruplexes: Temporal Regulation of Biocatalytic Circuits, Gene Replication and Transcription. Angew Chem Int Ed Engl 2023; 62:e202307898. [PMID: 37380611 DOI: 10.1002/anie.202307898] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 06/30/2023]
Abstract
Native G-quadruplex-regulated temporal biocatalytic circuits, gene polymerization, and transcription processes are emulated by biomimetic, synthetically engineered transcription machineries coupled to reconfigurable G-quadruplex nanostructures. These are addressed by the following example: (i) A reaction module demonstrates the fuel-triggered transcription machinery-guided transient synthesis of G-quadruplex nanostructures. (ii) A dynamically triggered and modulated transcription machinery that guides the temporal separation and reassembly of the anti-thrombin G-quadruplex aptamer/thrombin complex is introduced, and the transient thrombin-catalyzed coagulation of fibrinogen is demonstrated. (iii) A dynamically fueled transient transcription machinery for the temporal activation of G-quadruplex-topologically blocked gene polymerization circuits is introduced. (iv) Transcription circuits revealing G-quadruplex-promoted or G-quadruplex-inhibited cascaded transcription machineries are presented. Beyond advancing the rapidly developing field of dynamically modulated G-quadruplex DNA nanostructures, the systems introduce potential therapeutic applications.
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Affiliation(s)
- Jiantong Dong
- The Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Itamar Willner
- The Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
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Luo X, Zhang J, Gao Y, Pan W, Yang Y, Li X, Chen L, Wang C, Wang Y. Emerging roles of i-motif in gene expression and disease treatment. Front Pharmacol 2023; 14:1136251. [PMID: 37021044 PMCID: PMC10067743 DOI: 10.3389/fphar.2023.1136251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 02/27/2023] [Indexed: 03/22/2023] Open
Abstract
As non-canonical nucleic acid secondary structures consisting of cytosine-rich nucleic acids, i-motifs can form under certain conditions. Several i-motif sequences have been identified in the human genome and play important roles in biological regulatory functions. Due to their physicochemical properties, these i-motif structures have attracted attention and are new targets for drug development. Herein, we reviewed the characteristics and mechanisms of i-motifs located in gene promoters (including c-myc, Bcl-2, VEGF, and telomeres), summarized various small molecule ligands that interact with them, and the possible binding modes between ligands and i-motifs, and described their effects on gene expression. Furthermore, we discussed diseases closely associated with i-motifs. Among these, cancer is closely associated with i-motifs since i-motifs can form in some regions of most oncogenes. Finally, we introduced recent advances in the applications of i-motifs in multiple areas.
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Affiliation(s)
| | | | | | | | | | | | | | - Chang Wang
- *Correspondence: Chang Wang, ; Yuqing Wang,
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9
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Li Z, Wang J, Willner B, Willner I. Topologically Triggered Dynamic DNA Frameworks. Isr J Chem 2023. [DOI: 10.1002/ijch.202300013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Affiliation(s)
- Zhenzhen Li
- The Institute of Chemistry The Center for Nanoscience and Nanotechnology The Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Jianbang Wang
- The Institute of Chemistry The Center for Nanoscience and Nanotechnology The Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Bilha Willner
- The Institute of Chemistry The Center for Nanoscience and Nanotechnology The Hebrew University of Jerusalem Jerusalem 91904 Israel
| | - Itamar Willner
- The Institute of Chemistry The Center for Nanoscience and Nanotechnology The Hebrew University of Jerusalem Jerusalem 91904 Israel
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10
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Gong X, Lin X, Wang S, Ji D, Shu B, Huang ZS, Li D. Regulation of c-Kit gene transcription selectively by bisacridine derivative through promoter dual i-motif structures. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194912. [PMID: 36754277 DOI: 10.1016/j.bbagrm.2023.194912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 01/16/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023]
Abstract
BACKGROUND c-Kit protein is a signal transduction protein involved in multiple signal pathways, which play an important role in a variety of cellular events such as cell proliferation, apoptosis and differentiation. Special DNA secondary structures on the promoter of c-Kit gene, including G-quadruplex and i-motif structures, could act as "molecular switch" for gene transcriptional regulation, which are potentially important target for development of new anti-cancer drugs. METHODS We screened and evaluated the effect of compounds on c-Kit through several experiments, including SPR, FRET, CD, MST, NMR, dual-luciferase reporter assay, Western blot, qPCR, immunofluorescence, MTT assay, colony formation, cell scrape, cell apoptosis, cell cycle analysis, and transwell assay. RESULTS After extensive screening, we found that bisacridine derivative B05 had selective binding and stabilization to dual i-motif structures on c-Kit gene promoter, which could down-regulate c-Kit gene transcription and translation, resulting in inhibition of cell proliferation and metastasis. B05 exhibited potent anti-tumor activity on HGC-27 cells, and strongly suppressed tumor growth in HGC-27 xenograft mice model. CONCLUSIONS B05 could interact with c-Kit promoter dual i-motif structures with excellent selectivity, which make it possible for selective regulation of gene transcription and translation. B05 could be further developed for selective anti-cancer agent targeting c-Kit promoter i-motifs. GENERAL SIGNIFICANCE i-Motifs on different proto-oncogene promoters are diversified, and especially binding of dual i-motifs on the same promoter simultaneously could significantly down-regulate gene transcription with decreased dosage, and therefore increasing the selectivity. This new strategy shed bight light on development of selective DNA-targeting ligands.
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Affiliation(s)
- Xue Gong
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, Guangzhou, PR China
| | - Xiaomin Lin
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, Guangzhou, PR China
| | - Siyi Wang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, Guangzhou, PR China
| | - Dongsheng Ji
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, Guangzhou, PR China
| | - Bing Shu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, Guangzhou, PR China; School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, PR China
| | - Zhi-Shu Huang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, Guangzhou, PR China
| | - Ding Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, Guangzhou, PR China.
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Yang T, Xu Q, Chen J, Jia PK, Xie BB, Wang D, Zhou X, Shao Y. Selectively Identifying Exposed-over-Unexposed C-C + Pairs in Human Telomeric i-Motif Structures with Length-Dependent Polymorphism. Anal Chem 2022; 94:14994-15001. [PMID: 36263663 DOI: 10.1021/acs.analchem.2c02875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The i-motif structure (iM) has attracted much attention, because of its in vivo bioactivity and wide in vitro applications such as DNA-based switches. Herein, the length-dependent folding of cytosine-rich repeats of the human telomeric 5'-(CCCTAA)n-1CCC-3' (iM-n, where n = 2-8) was fully explored. We found that iM-4, iM-5, and iM-8 mainly form the intramolecular monomer iM structures, while a tetramolecular structure populates only for iM-3. However, iM-6 and iM-7 have the potential to fold as well into the dimeric iM structures besides the monomer ones. The natural hypericin (Hyp) was used as the polymorphism-selective probe to recognize the iM structures. Interestingly, only iM-3, iM-6, and iM-7 can efficiently switch on the Hyp fluorescence by specifically binding with the outmost C-C+ base pairs that are exposed directly to solution. However, other iM structures that fold in a way with a coverage of the outmost C-C+ pairs by loop sequences are totally unavailable for the Hyp binding. Theoretical modeling indicates that adaptive π-π and cation-π interactions contribute to the Hyp recognition toward the exposed C-C+ pairs. This specific iM recognition can be boosted by a photocatalytic DNAzyme construct. Our work provides a reliable fluorescence method to selectively explore the polymorphism of iM structures.
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Affiliation(s)
- Tong Yang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, People's Republic of China
| | - Qiuda Xu
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, People's Republic of China
| | - Jiahui Chen
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, People's Republic of China
| | - Pei-Ke Jia
- Hangzhou Institute of Advanced Studies, Zhejiang Normal University, 1108 Gengwen Road, Hangzhou 311231, Zhejiang, People's Republic of China
| | - Bin-Bin Xie
- Hangzhou Institute of Advanced Studies, Zhejiang Normal University, 1108 Gengwen Road, Hangzhou 311231, Zhejiang, People's Republic of China
| | - Dandan Wang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, People's Republic of China
| | - Xiaoshun Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, People's Republic of China
| | - Yong Shao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, People's Republic of China
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Chen L, Dickerhoff J, Sakai S, Yang D. DNA G-Quadruplex in Human Telomeres and Oncogene Promoters: Structures, Functions, and Small Molecule Targeting. Acc Chem Res 2022; 55:2628-2646. [PMID: 36054116 PMCID: PMC9937053 DOI: 10.1021/acs.accounts.2c00337] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
DNA G-quadruplex secondary structures formed in guanine-rich human telomeres and oncogene promoters are functionally important and have emerged as a promising new class of cancer-specific drug targets. These globular intramolecular structures are stabilized by K+ or Na+ and form readily under physiological solution conditions. Moreover, G-quadruplexes are epigenetic features and can alter chromatin structure and function together with interactive proteins. Here, we discuss our efforts over the last two decades to understand the structures and functions of DNA G-quadruplexes formed in key oncogene promoters and human telomeres and their interactions with small molecules. Using high-field NMR spectroscopy, we determined the high-resolution structures of physiologically relevant telomeric G-quadruplexes in K+ solution with a major form (hybrid-2) and a minor form (hybrid-1), as well as a two-tetrad intermediate. The intrinsic structural polymorphism of telomeric DNA may be important for the biology of human telomeres, and we proposed a model for the interconversion. More recently, we have worked on G-quadruplexes of MYC, BCL2, PDGFR-β, VEGF, and k-RAS oncogene promoters. We determined the structure of the major G-quadruplex formed in the MYC promoter, a prototype for parallel G-quadruplexes. It is the first example of the parallel-stranded G3NG3 structure motif with a 1-nt loop, which is prevalent in promoter sequences and likely evolutionarily selected to initiate folding. Remarkably, the parallel MYC promoter G-quadruplexes are highly stable. Additionally, we determined the molecular structures of G-quadruplexes formed in human BCL2, VEGF, and PDGFR-β promoters, each adopting a unique structure. For example, the BCL2 promoter contains distinct interchangeable G-quadruplexes in two adjacent regions, suggesting precise regulation by different proteins. The PDGFR-β promoter adopts unique "broken-strand" and vacancy G-quadruplexes, which can be recognized by cellular guanine metabolites for a potential regulatory role.Structural information on G-quadruplexes in complex with small-molecules is critical for understanding specific recognition and structure-based rational drug design. Our studies show that many G-quadruplexes contain unique structural features such as capping and loop structures, allowing specific recognition by drugs and protein. This represents a paradigm shift in understanding DNA as a drug target: Rather than a uniform, nonselective binding site in duplex DNA, the G-quadruplex is being pursued as a new class of selectively targetable drug receptors. We focus on targeting the biologically relevant MYC promoter G-quadruplex (MycG4) with small molecules and have determined its first and additional drug complex structures. Very recently, we have discovered clinically tested indenoisoquinolines as strong MycG4 binders and potent MYC inhibitors. We have also discovered drugs targeting the unique dGMP-bound-vG4 formed in the PDGFR-β promoter. Moreover, we determined the complex structures of the first small molecules that specifically recognize the physiologically relevant human telomeric G-quadruplexes. Unlike the previously recognized dogma that the optimal G-quadruplex ligands are large aromatic or cyclic compounds, our results suggest that smaller asymmetric compounds with appropriate functional groups are better choices to specifically bind G-quadruplexes. This body of work lays a strong foundation for future work aimed at understanding the cellular functions of G-quadruplexes and G-quadruplex-targeted drug design.
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Affiliation(s)
- Luying Chen
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Jonathan Dickerhoff
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Saburo Sakai
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
- Biogeochemistry Research Center, Japan Agency for Marine-Earth Science and Technology, 2-15, Natsushima-cho, Yokosuka-city, Kanagawa 237-0061, Japan
| | - Danzhou Yang
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
- Purdue Center for Cancer Research, Purdue University, 201 University Street, West Lafayette, Indiana 47907, United States
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
- Purdue Institute for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, Indiana 47907, United States
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Panczyk T, Nieszporek J, Nieszporek K. Molecular Dynamics Simulations of Interactions between Human Telomeric i-Motif Deoxyribonucleic Acid and Functionalized Graphene. J Phys Chem B 2022; 126:6671-6681. [PMID: 36036695 PMCID: PMC9465685 DOI: 10.1021/acs.jpcb.2c04327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/08/2022] [Indexed: 11/30/2022]
Abstract
The work deals with molecular dynamics (MD) simulations of protonated, human telomeric i-motif deoxyribonucleic acid (DNA) with functionalized graphene. We studied three different graphene sheets: unmodified graphene with hydrogen atoms attached to their edges and two functionalized ones. The functionalization of graphene edge consists in attaching partially protonated or dissociated amine and carboxyl groups. We found that in all cases the protonated i-motif adsorbs strongly on the graphene surface. The biased MD simulations showed that the work necessary to drag the i-motif out from amine-doped graphene is about twice larger than that in other cases. In general, the system i-motif/amine-doped graphene stands out from the rest, e.g., in this case, the i-motif adsorbs its side with 3' and 5' ends oriented in the opposite to surface direction. In other cases, the DNA fragment is adsorbed to graphene by 3' and 5' ends. In all cases, the adsorption on graphene influences the i-motif internal structure by changing the distances between i-motif strands as well as stretching or shortening the DNA chain, but only in the case of amine-doped graphene the adsorption affects internal H-bonds formed between nucleotides inside the i-motif structure.
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Affiliation(s)
- Tomasz Panczyk
- Institute
of Catalysis and Surface Chemistry, Polish Academy of Sciences, ul. Niezapominajek 8, Cracow 30239, Poland
| | - Jolanta Nieszporek
- Department
of Analytical Chemistry, Institute of Chemical
Sciences, Faculty of Chemistry, Maria Curie-Sklodowska University, pl. Maria Curie-Sklodowska 3, Lublin 20031, Poland
| | - Krzysztof Nieszporek
- Department
of Theoretical Chemistry, Institute of Chemical
Sciences, Faculty of Chemistry, Maria Curie-Sklodowska University, pl. Maria Curie-Sklodowska 3, Lublin 20031, Poland
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14
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Shen Z, Zheng R, Yang H, Xing S, Jin X, Yan H, Zhu J, Mei Y, Lin F, Zheng X. G-quadruplex stabilizer Tetra-Pt(bpy) disrupts telomere maintenance and impairs FAK-mediated migration of telomerase-positive cells. Int J Biol Macromol 2022; 213:858-870. [PMID: 35697164 DOI: 10.1016/j.ijbiomac.2022.06.015] [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: 03/29/2022] [Revised: 05/18/2022] [Accepted: 06/05/2022] [Indexed: 11/05/2022]
Abstract
G-quadruplex regulates a wide spectrum of biological processes, including telomere maintenance, DNA replication and transcription. The development of small molecules to selectively target G-quadruplex and their application remain hotspots in cancer therapy. Here, we explored the biological effect of G-quadruplexes stabilizer Tetra-Pt(bpy) in telomerase-positive cancer cells. Telomere maintenance was evaluated by telomerase repeat amplification protocol, chromosome orientation fluorescence in situ hybridization and telomere restriction fragment assays. We found that Tetra-Pt(bpy) accelerates telomere shortening through dual inhibition of telomerase activity and telomere sister chromatin exchanges mediated by telomeric G-quadruplexes. Consequently, Tetra-Pt(bpy)-treated cancer cells became enriched with extremely short telomeres and produced a strong telomeric DNA damage response following long-term treatment, leading to cell proliferation inhibition and senescence. Experimental evidence from RNA seq and cell migration-related assays showed that Tetra-Pt(bpy) decreased cell-matrix adhesion and inhibited the migration of non-senescent tumor cells. Mechanistically, Tetra-Pt(bpy) induced the formation of G-quadruplexes in focal adhesion kinase (FAK)-encoding gene PTK2, resulting in FAK transcription inhibition. Tetra-Pt(bpy) reduced xenograft tumor formation and inhibited tumor cell growth and migration in mice. This study further elucidates the function of G-quadruplexes in the human genome and reveals the potential of Tetra-Pt(bpy) as a novel chemotherapeutic agent for targeting telomerase-positive cancer cells.
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Affiliation(s)
- Zhe Shen
- Chemical Biology Research Center at School of Pharmaceutical Sciences, Wenzhou Medical University, 1210 University Town, Wenzhou 325035, Zhejiang, China
| | - Ruiling Zheng
- Chemical Biology Research Center at School of Pharmaceutical Sciences, Wenzhou Medical University, 1210 University Town, Wenzhou 325035, Zhejiang, China
| | - Huamao Yang
- Chemical Biology Research Center at School of Pharmaceutical Sciences, Wenzhou Medical University, 1210 University Town, Wenzhou 325035, Zhejiang, China
| | - Sunhui Xing
- Chemical Biology Research Center at School of Pharmaceutical Sciences, Wenzhou Medical University, 1210 University Town, Wenzhou 325035, Zhejiang, China
| | - Xiangxiang Jin
- Chemical Biology Research Center at School of Pharmaceutical Sciences, Wenzhou Medical University, 1210 University Town, Wenzhou 325035, Zhejiang, China
| | - Hao Yan
- Chemical Biology Research Center at School of Pharmaceutical Sciences, Wenzhou Medical University, 1210 University Town, Wenzhou 325035, Zhejiang, China
| | - Jufan Zhu
- Department of Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang, China
| | - Yanan Mei
- Chemical Biology Research Center at School of Pharmaceutical Sciences, Wenzhou Medical University, 1210 University Town, Wenzhou 325035, Zhejiang, China
| | - Feng Lin
- Department of Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang, China; Department of Gynecology, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang, China.
| | - Xiaohui Zheng
- Chemical Biology Research Center at School of Pharmaceutical Sciences, Wenzhou Medical University, 1210 University Town, Wenzhou 325035, Zhejiang, China.
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15
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Swafford K, Acharya B, Xu YZ, Raney T, McCrury M, Saha D, Frett B, Kendrick S. Targeting a Novel G-Quadruplex in the CARD11 Oncogene Promoter with Naptho(2,1-b)furan-1-ethanol,2-nitro- Requires the Nitro Group. Genes (Basel) 2022; 13:genes13071144. [PMID: 35885931 PMCID: PMC9321325 DOI: 10.3390/genes13071144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 06/17/2022] [Accepted: 06/21/2022] [Indexed: 02/04/2023] Open
Abstract
The aggressive nature of the activated B cell such as (ABC) subtype of diffuse large B cell (DLBCL) is frequently associated with altered B cell Receptor (BCR) signaling through the activation of key components including the scaffolding protein, CARD11. Most inhibitors, such as ibrutinib, target downstream BCR kinases with often modest and temporary responses for DLBCL patients. Here, we pursue an alternative strategy to target the BCR pathway by leveraging a novel DNA secondary structure to repress transcription. We discovered that a highly guanine (G)-rich element within the CARD11 promoter forms a stable G-quadruplex (G4) using circular dichroism and polymerase stop biophysical techniques. We then identified a small molecule, naptho(2,1-b)furan-1-ethanol,2-nitro- (NSC373981), from a fluorescence-resonance energy transfer-based screen that stabilized CARD11 G4 and inhibited CARD11 transcription in DLBCL cells. In generating and testing analogs of NSC373981, we determined that the nitro group is likely essential for the downregulation of CARD11 and interaction with CARD11 G4, and the removal of the ethanol side chain enhanced this activity. Of note, the expression of BCL2 and MYC, two other key oncogenes in DLBCL pathology with known promoter G4 structures, were often concurrently repressed with NSC373981 and the highly potent R158 analog. Our findings highlight a novel approach to treat aggressive DLBCL by silencing CARD11 gene expression that warrants further investigation.
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Affiliation(s)
- Kennith Swafford
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (K.S.); (Y.-Z.X.); (T.R.); (M.M.)
| | - Baku Acharya
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (B.A.); (D.S.)
| | - Ying-Zhi Xu
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (K.S.); (Y.-Z.X.); (T.R.); (M.M.)
| | - Thomas Raney
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (K.S.); (Y.-Z.X.); (T.R.); (M.M.)
| | - Mason McCrury
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (K.S.); (Y.-Z.X.); (T.R.); (M.M.)
| | - Debasmita Saha
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (B.A.); (D.S.)
| | - Brendan Frett
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (B.A.); (D.S.)
- Correspondence: (B.F.); (S.K.); Tel.: +1-501-526-0893 (B.F.); +1-501-526-6000 (ext. 25122) (S.K.)
| | - Samantha Kendrick
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; (K.S.); (Y.-Z.X.); (T.R.); (M.M.)
- Correspondence: (B.F.); (S.K.); Tel.: +1-501-526-0893 (B.F.); +1-501-526-6000 (ext. 25122) (S.K.)
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16
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Yang T, Peng S, Zeng R, Xu Q, Zheng X, Wang D, Zhou X, Shao Y. Visible light-driven i-motif-based DNAzymes. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 270:120845. [PMID: 35016065 DOI: 10.1016/j.saa.2021.120845] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 12/04/2021] [Accepted: 12/29/2021] [Indexed: 06/14/2023]
Abstract
DNA foldings provide variant possibilities to develop DNAzymes with remarkable catalytic performance. In spite of fruitful reports on G-quadruplex DNAzymes, four-stranded cytosine-rich i-motifs have not been explored as the potential skeletons of DNAzymes. In this work, we developed a visible light-driven DNAzyme based on human telomeric i-motifs using a natural photosensitizer of hypericin (Hyp) as the cofactor and dissolved oxygen as the oxidant source. The i-motif folding in acidic solution caused the distal thymine overhangs at the 3' and 5' ends to approach each other to provide a favorable binding site for Hyp via an interaction of fully complementary hydrogen bonding. However, the i-motifs without the distal overhangs or with the inappropriate overhang length and the base identity exhibited no binding with Hyp. The binding event converted Hyp from the fully dark state to the emissive state under visible light illumination. Subsequently, the excited Hyp had an opportunity to transfer energy to dissolved oxygen. Resultantly, singlet oxygen (1O2) was generated to initiate the substrate oxidation. The catalytic performance of the DNAzyme can be improved using a long-lived mediator. Our developed i-motif-based DNAzyme can be driven by almost the whole range of visible lights, suggesting broad applications in the photocatalytic fields, for example, as an alternative strategy in developing biodevices.
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Affiliation(s)
- Tong Yang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Shuzhen Peng
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Ruidi Zeng
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Qiuda Xu
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Xiong Zheng
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Dandan Wang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Xiaoshun Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Yong Shao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China.
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17
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Development of a Smart Fluorescent Probe Specifically Interacting with C-Myc I-Motif. Int J Mol Sci 2022; 23:ijms23073872. [PMID: 35409230 PMCID: PMC8998492 DOI: 10.3390/ijms23073872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 03/27/2022] [Accepted: 03/28/2022] [Indexed: 11/17/2022] Open
Abstract
I-motifs play key regulatory roles in biological processes, holding great potential as attractive therapeutic targets. In the present study, we developed a novel fluorescent probe G59 with strong and selective binding to the c-myc gene promoter i-motif. G59 had an i-motif-binding carbazole moiety conjugated with naphthalimide fluorescent groups. G59 could differentiate the c-myc i-motif from other DNA structures through selective activation of its fluorescence, with its apparent visualization in solution. The smart probe G59 showed excellent sensitivity, with a low fluorescent detection limit of 154 nM and effective stabilization to the c-myc i-motif. G59 could serve as a rapid and sensitive probe for label-free screening of selective c-myc i-motif binding ligands under neutral crowding conditions. To the best of our knowledge, G59 is the first fluorescent probe with high sensitivity for recognizing the i-motif structure and screening for selective binding ligands.
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18
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Stability and context of intercalated motifs (i-motifs) for biological applications. Biochimie 2022; 198:33-47. [PMID: 35259471 DOI: 10.1016/j.biochi.2022.03.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 02/21/2022] [Accepted: 03/03/2022] [Indexed: 11/24/2022]
Abstract
DNA is naturally dynamic and can self-assemble into alternative secondary structures including the intercalated motif (i-motif), a four-stranded structure formed in cytosine-rich DNA sequences. Until recently, i-motifs were thought to be unstable in physiological cellular environments. Studies demonstrating their existence in the human genome and role in gene regulation are now shining light on their biological relevance. Herein, we review the effects of epigenetic modifications on i-motif structure and stability, and biological factors that affect i-motif formation within cells. Furthermore, we highlight recent progress in targeting i-motifs with structure-specific ligands for biotechnology and therapeutic purposes.
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19
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Kretzmann JA, Irving KL, Smith NM, Evans CW. Modulating gene expression in breast cancer via DNA secondary structure and the CRISPR toolbox. NAR Cancer 2022; 3:zcab048. [PMID: 34988459 PMCID: PMC8693572 DOI: 10.1093/narcan/zcab048] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/26/2021] [Accepted: 12/01/2021] [Indexed: 12/11/2022] Open
Abstract
Breast cancer is the most commonly diagnosed malignancy in women, and while the survival prognosis of patients with early-stage, non-metastatic disease is ∼75%, recurrence poses a significant risk and advanced and/or metastatic breast cancer is incurable. A distinctive feature of advanced breast cancer is an unstable genome and altered gene expression patterns that result in disease heterogeneity. Transcription factors represent a unique therapeutic opportunity in breast cancer, since they are known regulators of gene expression, including gene expression involved in differentiation and cell death, which are themselves often mutated or dysregulated in cancer. While transcription factors have traditionally been viewed as 'undruggable', progress has been made in the development of small-molecule therapeutics to target relevant protein-protein, protein-DNA and enzymatic active sites, with varying levels of success. However, non-traditional approaches such as epigenetic editing, transcriptional control via CRISPR/dCas9 systems, and gene regulation through non-canonical nucleic acid secondary structures represent new directions yet to be fully explored. Here, we discuss these new approaches and current limitations in light of new therapeutic opportunities for breast cancers.
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Affiliation(s)
- Jessica A Kretzmann
- Laboratory for Biomolecular Nanotechnology, Department of Physics, Technical University of Munich, Am Coulombwall 4a, 85748 Garching, Germany
| | - Kelly L Irving
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Hwy, Crawley, WA 6009, Australia
| | - Nicole M Smith
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Hwy, Crawley, WA 6009, Australia
| | - Cameron W Evans
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Hwy, Crawley, WA 6009, Australia
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20
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Chen JN, He YD, Liang HT, Cai TT, Chen Q, Zheng KW. Regulation of PDGFR-β gene expression by targeting the G-vacancy bearing G-quadruplex in promoter. Nucleic Acids Res 2021; 49:12634-12643. [PMID: 34850916 PMCID: PMC8682790 DOI: 10.1093/nar/gkab1154] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/14/2021] [Accepted: 11/09/2021] [Indexed: 12/31/2022] Open
Abstract
G-quadruplex is an essential element in gene transcription that serves as a promising drug target. Guanine-vacancy-bearing G-quadruplex (GVBQ) is a newly identified G-quadruplex that has distinct structural features from the canonical G-quadruplex. Potential GVBQ-forming motifs are widely distributed in gene promoter regions. However, whether GVBQ can form in genomic DNA and be an effective target for manipulating gene expression is unknown. Using photo-crosslinking, dimethyl sulfate footprinting, exonuclease digestion and in vitro transcription, we demonstrated the formation of a GVBQ in the G-rich nuclease hypersensitivity element within the human PDGFR-β gene promoter region in both single-stranded and double-stranded DNA. The formation of GVBQ in dsDNA could be induced by negative supercoiling created by downstream transcription. We also found that the PDGFR-β GVBQ was specifically recognized and stabilized by a new synthetic porphyrin guanine conjugate (mPG). Targeting the PDGFR-β GVBQ in human cancer cells using the mPG could specifically alter PDGFR-β gene expression. Our work illustrates that targeting GVBQ with mPG in human cells can regulate the expression level of a specific gene, thus indicating a novel strategy for drug development.
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Affiliation(s)
- Juan-Nan Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Guangzhou 510006, P.R. China
| | - Yi-de He
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Guangzhou 510006, P.R. China.,School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, P.R. China
| | - Hui-Ting Liang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Guangzhou 510006, P.R. China
| | - Ting-Ting Cai
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Guangzhou 510006, P.R. China
| | - Qi Chen
- School of Public Health (Shenzhen), Sun Yat-Sen University, Guangzhou 510006, P.R. China
| | - Ke-Wei Zheng
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Guangzhou 510006, P.R. China
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21
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Di Porzio A, Galli U, Amato J, Zizza P, Iachettini S, Iaccarino N, Marzano S, Santoro F, Brancaccio D, Carotenuto A, De Tito S, Biroccio A, Pagano B, Tron GC, Randazzo A. Synthesis and Characterization of Bis-Triazolyl-Pyridine Derivatives as Noncanonical DNA-Interacting Compounds. Int J Mol Sci 2021; 22:11959. [PMID: 34769387 PMCID: PMC8584640 DOI: 10.3390/ijms222111959] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/31/2021] [Accepted: 11/01/2021] [Indexed: 02/07/2023] Open
Abstract
Besides the well-known double-helical conformation, DNA is capable of folding into various noncanonical arrangements, such as G-quadruplexes (G4s) and i-motifs (iMs), whose occurrence in gene promoters, replication origins, and telomeres highlights the breadth of biological processes that they might regulate. Particularly, previous studies have reported that G4 and iM structures may play different roles in controlling gene transcription. Anyway, molecular tools able to simultaneously stabilize/destabilize those structures are still needed to shed light on what happens at the biological level. Herein, a multicomponent reaction and a click chemistry functionalization were combined to generate a set of 31 bis-triazolyl-pyridine derivatives which were initially screened by circular dichroism for their ability to interact with different G4 and/or iM DNAs and to affect the thermal stability of these structures. All the compounds were then clustered through multivariate data analysis, based on such capability. The most promising compounds were subjected to a further biophysical and biological characterization, leading to the identification of two molecules simultaneously able to stabilize G4s and destabilize iMs, both in vitro and in living cells.
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Affiliation(s)
- Anna Di Porzio
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (A.D.P.); (J.A.); (N.I.); (S.M.); (F.S.); (D.B.); (A.C.); (B.P.)
| | - Ubaldina Galli
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Largo Donegani 2/3, 28100 Novara, Italy;
| | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (A.D.P.); (J.A.); (N.I.); (S.M.); (F.S.); (D.B.); (A.C.); (B.P.)
| | - Pasquale Zizza
- Oncogenomic and Epigenetic Unit, IRCCS-Regina Elena National Cancer Institute, 00144 Rome, Italy; (P.Z.); (S.I.); (A.B.)
| | - Sara Iachettini
- Oncogenomic and Epigenetic Unit, IRCCS-Regina Elena National Cancer Institute, 00144 Rome, Italy; (P.Z.); (S.I.); (A.B.)
| | - Nunzia Iaccarino
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (A.D.P.); (J.A.); (N.I.); (S.M.); (F.S.); (D.B.); (A.C.); (B.P.)
| | - Simona Marzano
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (A.D.P.); (J.A.); (N.I.); (S.M.); (F.S.); (D.B.); (A.C.); (B.P.)
| | - Federica Santoro
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (A.D.P.); (J.A.); (N.I.); (S.M.); (F.S.); (D.B.); (A.C.); (B.P.)
| | - Diego Brancaccio
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (A.D.P.); (J.A.); (N.I.); (S.M.); (F.S.); (D.B.); (A.C.); (B.P.)
| | - Alfonso Carotenuto
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (A.D.P.); (J.A.); (N.I.); (S.M.); (F.S.); (D.B.); (A.C.); (B.P.)
| | - Stefano De Tito
- Molecular Cell Biology of Autophagy, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK;
- Institute of Experimental Endocrinology and Oncology, National Research Council, 80131 Naples, Italy
| | - Annamaria Biroccio
- Oncogenomic and Epigenetic Unit, IRCCS-Regina Elena National Cancer Institute, 00144 Rome, Italy; (P.Z.); (S.I.); (A.B.)
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (A.D.P.); (J.A.); (N.I.); (S.M.); (F.S.); (D.B.); (A.C.); (B.P.)
| | - Gian Cesare Tron
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Largo Donegani 2/3, 28100 Novara, Italy;
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (A.D.P.); (J.A.); (N.I.); (S.M.); (F.S.); (D.B.); (A.C.); (B.P.)
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22
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Wang YH, Yang QF, Lin X, Chen D, Wang ZY, Chen B, Han HY, Chen HD, Cai KC, Li Q, Yang S, Tang YL, Li F. G4LDB 2.2: a database for discovering and studying G-quadruplex and i-Motif ligands. Nucleic Acids Res 2021; 50:D150-D160. [PMID: 34718746 PMCID: PMC8728129 DOI: 10.1093/nar/gkab952] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/29/2021] [Accepted: 10/02/2021] [Indexed: 11/14/2022] Open
Abstract
Noncanonical nucleic acid structures, such as G-quadruplex (G4) and i-Motif (iM), have attracted increasing research interests because of their unique structural and binding properties, as well as their important biological activities. To date, thousands of small molecules that bind to varying G4/iM structures have been designed, synthesized and tested for diverse chemical and biological uses. Because of the huge potential and increasing research interests on G4-targeting ligands, we launched the first G4 ligand database G4LDB in 2013. Here, we report a new version, termed G4LDB 2.2 (http://www.g4ldb.com), with upgrades in both content and function. Currently, G4LDB2.2 contains >3200 G4/iM ligands, ∼28 500 activity entries and 79 G4–ligand docking models. In addition to G4 ligand library, we have also added a brand new iM ligand library to G4LDB 2.2, providing a comprehensive view of quadruplex nucleic acids. To further enhance user experience, we have also redesigned the user interface and optimized the database structure and retrieval mechanism. With these improvements, we anticipate that G4LDB 2.2 will serve as a comprehensive resource and useful research toolkit for researchers across wide scientific communities and accelerate discovering and validating better binders and drug candidates.
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Affiliation(s)
- Yu-Huan Wang
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu610064, China
| | - Qian-Fan Yang
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu610064, China
| | - Xiao Lin
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu610064, China
| | - Die Chen
- West China School of Pharmacy, Sichuan University, Chengdu610041, China
| | - Zhi-Yin Wang
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu610064, China
| | - Bin Chen
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu610064, China
| | - Hua-Yi Han
- West China School of Pharmacy, Sichuan University, Chengdu610041, China
| | - Hao-Di Chen
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu610064, China
| | - Kai-Cong Cai
- College of Chemistry and Materials Science, Fujian Provincial Key Laboratory of Advanced Materials Oriented Chemical Engineering, Fujian Normal University, Fuzhou350007, China
| | - Qian Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Shu Yang
- West China School of Pharmacy, Sichuan University, Chengdu610041, China
| | - Ya-Lin Tang
- Beijing National Laboratory for Molecular Sciences (BNLMS), Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Feng Li
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu610064, China
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Wang KB, Dickerhoff J, Yang D. Solution Structure of Ternary Complex of Berberine Bound to a dGMP-Fill-In Vacancy G-Quadruplex Formed in the PDGFR-β Promoter. J Am Chem Soc 2021; 143:16549-16555. [PMID: 34586799 DOI: 10.1021/jacs.1c06200] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The G-quadruplexes (G4s) formed in the PDGFR-β gene promoter are transcriptional modulators and amenable to small-molecule targeting. Berberine (BER), a clinically important natural isoquinoline alkaloid, has gained increasing attention due to its potential as anticancer drug. We previously showed that the PDGFR-β gene promoter forms a unique vacancy G4 (vG4) that can be filled in and stabilized by guanine metabolites, such as dGMP. Herein, we report the high-resolution NMR structure of a ternary complex of berberine bound to the dGMP-fill-in PDGFR-β vG4 in potassium solution. This is the first small-molecule complex structure of a fill-in vG4. This ternary complex has a 2:1:1 binding stoichiometry with a berberine molecule bound at each the 5'- and 3'-end of the 5'-dGMP-fill-in PDGFR-β vG4. Each berberine recruits the adjacent adenine residue from the 5'- or 3'-flanking sequence to form a "quasi-triad plane" that covers the external G-tetrad of the fill-in vG4, respectively. Significantly, berberine covers and stabilizes the fill-in dGMP. The binding of berberine involves both π-stacking and electrostatic interactions, and the fill-in dGMP is covered and well-protected by berberine. The NMR structure can guide rational design of berberine analogues that target the PDGFR-β vG4 or dGMP-fill-in vG4. Moreover, our structure provides a molecular basis for designing small-molecule guanine conjugates to target vG4s.
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24
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Xi D, Cui M, Zhou X, Zhuge X, Ge Y, Wang Y, Zhang S. Nanopore-Based Single-Molecule Investigation of DNA Sequences with Potential to Form i-Motif Structures. ACS Sens 2021; 6:2691-2699. [PMID: 34237940 DOI: 10.1021/acssensors.1c00712] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
i-Motifs are DNA secondary structures present in cytosine-rich sequences. These structures are formed in regulatory regions of the human genome and play key regulatory roles. The investigation of sequences capable of forming i-motif structures at the single-molecule level is highly important. In this study, we used α-hemolysin nanopores to systematically study a series of DNA sequences at the nanometer scale by providing structure-dependent signature current signals to gain in-sights into the i-motif DNA sequence and structural stability. Increasing the length of the cytosine tract in a range of 3-10 nucleobases resulted in a longer translocation time through the pore, indicating improved stability. Changing the loop sequence and length in the sequences did not affect the formation of the i-motif structure but changed its stability. Importantly, the application of all-atom molecular dynamics simulations revealed the structural morphology of all sequences. Based on these results, we postulated a folding rule for i-motif formation, suggesting that thousands of cytosine-rich sequences in the human genome might fold into i-motif structures. Many of these were found in locations where structure formation is likely to play regulatory roles. These findings provide insights into the application of nanopores as a powerful tool for discovering potential i-motif-forming sequences and lay a foundation for future studies exploring the biological roles of i-motifs.
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Affiliation(s)
- Dongmei Xi
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Life Sciences, Linyi University, Linyi 276005, P. R. China
| | - Mengjie Cui
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
| | - Xin Zhou
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
| | - Xiao Zhuge
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
| | - Yaxian Ge
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
| | - Ying Wang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Life Sciences, Linyi University, Linyi 276005, P. R. China
| | - Shusheng Zhang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
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25
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G-Quadruplex in Gene Encoding Large Subunit of Plant RNA Polymerase II: A Billion-Year-Old Story. Int J Mol Sci 2021; 22:ijms22147381. [PMID: 34299001 PMCID: PMC8306923 DOI: 10.3390/ijms22147381] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/24/2021] [Accepted: 07/05/2021] [Indexed: 12/12/2022] Open
Abstract
G-quadruplexes have long been perceived as rare and physiologically unimportant nucleic acid structures. However, several studies have revealed their importance in molecular processes, suggesting their possible role in replication and gene expression regulation. Pathways involving G-quadruplexes are intensively studied, especially in the context of human diseases, while their involvement in gene expression regulation in plants remains largely unexplored. Here, we conducted a bioinformatic study and performed a complex circular dichroism measurement to identify a stable G-quadruplex in the gene RPB1, coding for the RNA polymerase II large subunit. We found that this G-quadruplex-forming locus is highly evolutionarily conserved amongst plants sensu lato (Archaeplastida) that share a common ancestor more than one billion years old. Finally, we discussed a new hypothesis regarding G-quadruplexes interacting with UV light in plants to potentially form an additional layer of the regulatory network.
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26
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Sanchez-Martin V, Soriano M, Garcia-Salcedo JA. Quadruplex Ligands in Cancer Therapy. Cancers (Basel) 2021; 13:3156. [PMID: 34202648 PMCID: PMC8267697 DOI: 10.3390/cancers13133156] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/18/2021] [Accepted: 06/20/2021] [Indexed: 02/07/2023] Open
Abstract
Nucleic acids can adopt alternative secondary conformations including four-stranded structures known as quadruplexes. To date, quadruplexes have been demonstrated to exist both in human chromatin DNA and RNA. In particular, quadruplexes are found in guanine-rich sequences constituting G-quadruplexes, and in cytosine-rich sequences forming i-Motifs as a counterpart. Quadruplexes are associated with key biological processes ranging from transcription and translation of several oncogenes and tumor suppressors to telomeres maintenance and genome instability. In this context, quadruplexes have prompted investigations on their possible role in cancer biology and the evaluation of small-molecule ligands as potential therapeutic agents. This review aims to provide an updated close-up view of the literature on quadruplex ligands in cancer therapy, by grouping together ligands for DNA and RNA G-quadruplexes and DNA i-Motifs.
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Affiliation(s)
- Victoria Sanchez-Martin
- Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain;
- Microbiology Unit, Biosanitary Research Institute IBS, University Hospital Virgen de las Nieves, 18014 Granada, Spain
- Department of Biochemistry, Molecular Biology III and Immunology, University of Granada, 18016 Granada, Spain
| | - Miguel Soriano
- Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain;
- Centre for Intensive Mediterranean Agrosystems and Agri-Food Biotechnology (CIAMBITAL), University of Almeria, 04001 Almeria, Spain
| | - Jose Antonio Garcia-Salcedo
- Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain;
- Microbiology Unit, Biosanitary Research Institute IBS, University Hospital Virgen de las Nieves, 18014 Granada, Spain
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27
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Chaudhuri R, Fatma K, Dash J. Regulation of gene expression by targeting DNA secondary structures. J CHEM SCI 2021. [DOI: 10.1007/s12039-021-01898-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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28
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Zhang M, Wei Z, Gong X, Li X, Kang S, Wang J, Liu B, Huang ZS, Li D. Syntheses and evaluation of acridone-naphthalimide derivatives for regulating oncogene PDGFR-β expression. Bioorg Med Chem 2021; 34:116042. [PMID: 33561716 DOI: 10.1016/j.bmc.2021.116042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 01/12/2021] [Accepted: 01/20/2021] [Indexed: 01/30/2023]
Abstract
Upregulation of platelet-derived growth factor receptor β (PDGFR-β) has been found to be associated with development of various types of cancers, which has become an attractive target for anti-tumor treatment. Previously, we have synthesized and studied an acridone derivative B19, which can selectively bind to and stabilize oncogene c-myc promoter i-motif, resulting in down-regulation of c-myc transcription and translation, however its effect on tumor cells apoptosis requires improvement. In the present study, we synthesized a variety of B19 derivatives containing a known anti-cancer fluorescent chromophore naphthalimide for the purpose of enhancing anti-cancer activity. After screening, we found that acridone-naphthalimide derivative WZZ02 could selectively stabilize PDGFR-β promoter G-quadruplex and destabilize its corresponding i-motif structure, without significant interaction to other oncogenes promoter G-quadruplex and i-motif. WZZ02 down-regulated PDGFR-β gene transcription and translation in a dose-dependent manner, possibly due to above interactions. WZZ02 could significantly inhibit cancer cell proliferation, and induce cell apoptosis and cycle arrest. WZZ02 exhibited tumor growth inhibition activity in MCF-7 xenograft tumor model, which could be due to its binding interactions with PDGFR-β promoter G-quadruplex and i-motif. Our results suggested that WZZ02 as a dual G-quadruplex/i-motif binder could be effective on both oncogene replication and transcription, which could become a promising lead compound for further development with improved potency and selectivity. The wide properties for the derivatives of 1,8-naphthalimide could facilitate further in-depth mechanistic studies of WZZ02 through various fluorescent physical and chemical methods, which could help to further understand the function of PDGFR-β gene promoter G-quadruplex and i-motif.
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Affiliation(s)
- Meiling Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, 132 Waihuan East Road, Guangzhou 510006, PR China
| | - Zuzhuang Wei
- School of Pharmaceutical Sciences, Sun Yat-sen University, 132 Waihuan East Road, Guangzhou 510006, PR China
| | - Xue Gong
- School of Pharmaceutical Sciences, Sun Yat-sen University, 132 Waihuan East Road, Guangzhou 510006, PR China
| | - Xiaoya Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, 132 Waihuan East Road, Guangzhou 510006, PR China
| | - Shuangshuang Kang
- School of Pharmaceutical Sciences, Sun Yat-sen University, 132 Waihuan East Road, Guangzhou 510006, PR China
| | - Jing Wang
- School of Pharmaceutical Sciences, Sun Yat-sen University, 132 Waihuan East Road, Guangzhou 510006, PR China
| | - Bobo Liu
- School of Pharmaceutical Sciences, Sun Yat-sen University, 132 Waihuan East Road, Guangzhou 510006, PR China
| | - Zhi-Shu Huang
- School of Pharmaceutical Sciences, Sun Yat-sen University, 132 Waihuan East Road, Guangzhou 510006, PR China
| | - Ding Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, 132 Waihuan East Road, Guangzhou 510006, PR China.
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Synthesis and Biological Evaluation of Oleanolic Acid Derivatives as Selective Vascular Endothelial Growth Factor Promoter i-Motif Ligands. Int J Mol Sci 2021; 22:ijms22041711. [PMID: 33567767 PMCID: PMC7915724 DOI: 10.3390/ijms22041711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/04/2021] [Accepted: 02/04/2021] [Indexed: 12/01/2022] Open
Abstract
Vascular endothelial growth factor (VEGF) is an angiogenic growth factor and plays a key role in tumor progression. The C-rich DNA sequence of VEGF promoter can form i-motif structure, which is a potential target for the development of novel anticancer agents. However, there is a limited number of chemotypes as the selective ligands of VEGF promoter i-motif, which leaves much room for development. Herein, we report the discovery of the natural oleanolic acid scaffold as a novel chemotype for the development of selective ligands of VEGF i-motif. A series of oleanolic acid derivatives as VEGF promoter i-motif ligands were synthesized. Subsequent evaluations showed that 3c could selectively bind to and stabilize VEGF promoter i-motif without significant binding to G-quadruplex, duplex DNA, and other oncogene i-motifs. Cell-based assays indicated that 3c could effectively downregulate VEGF gene transcription and expression in MCF-7 cells, inhibit tumor cells proliferation and migration, and induce cancer cells apoptosis. This work provides evidence of VEGF promoter i-motif as an anticancer target and will facilitate future efforts for the discovery of oleanolic acid-based selective ligands of VEGF promoter i-motif.
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30
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Pal S, Paul S. An in silico investigation of the binding modes and pathway of APTO-253 on c-KIT G-quadruplex DNA. Phys Chem Chem Phys 2021; 23:3361-3376. [PMID: 33502401 DOI: 10.1039/d0cp05210h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The stability of c-KIT G-quadruplex DNA via ligands has been a significant concern in the growing field of cancer therapy. Thus, it is very important to understand the mechanism behind the high binding affinity of the small drug molecules on the c-KIT G-quadruplex DNA. In this study, we have investigated the binding mode and pathway of the APTO-253 ligand on the c-KIT G-quadruplex DNA employing a total of 10 μs all atom molecular dynamics simulations and further 8.82 μs simulations via the umbrella sampling method using both OL15 and BSC1 latest force fields for DNA structures. From the cluster structure analysis, mainly three binding pathways i.e., top, bottom and side loop stacking modes are identified. Moreover, RMSD, RMSF and 2D-RMSD values indicate that the c-KIT G-quadruplex DNA and APTO-253 molecules are stable throughout the simulation run. Furthermore, the number of hydrogen bonds in each tetrad and the distance between the two central K+ cations confirm that the c-KIT G-quadruplex DNA maintains its conformation in the process of complex formation with the APTO-253 ligand. The binding free energies and the minimum values in the potential of mean forces suggest that the binding processes are energetically favorable. Furthermore, we have found that the bottom stacking mode is the most favorable binding mode among all the three modes for the OL15 force field. However, for the BSC1 force field, both the top and bottom binding modes of the APTO-253 ligand in c-KIT G-quadruplex DNA are comparable to each other. To investigate the driving force for the complex formation, we have noticed that the van der Waals (vdW) and π-π stacking interactions are mainly responsible. Our detailed studies provide useful information for the discovery of novel drugs in the field of stabilization of G-quadruplex DNAs.
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Affiliation(s)
- Saikat Pal
- Department of Chemistry, Indian Institute of Technology, Guwahati Assam, 781039, India.
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31
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Brown SL, Kendrick S. The i-Motif as a Molecular Target: More Than a Complementary DNA Secondary Structure. Pharmaceuticals (Basel) 2021; 14:ph14020096. [PMID: 33513764 PMCID: PMC7911047 DOI: 10.3390/ph14020096] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/20/2021] [Accepted: 01/22/2021] [Indexed: 12/25/2022] Open
Abstract
Stretches of cytosine-rich DNA are capable of adopting a dynamic secondary structure, the i-motif. When within promoter regions, the i-motif has the potential to act as a molecular switch for controlling gene expression. However, i-motif structures in genomic areas of repetitive nucleotide sequences may play a role in facilitating or hindering expansion of these DNA elements. Despite research on the i-motif trailing behind the complementary G-quadruplex structure, recent discoveries including the identification of a specific i-motif antibody are pushing this field forward. This perspective reviews initial and current work characterizing the i-motif and providing insight into the biological function of this DNA structure, with a focus on how the i-motif can serve as a molecular target for developing new therapeutic approaches to modulate gene expression and extension of repetitive DNA.
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32
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Saha P, Panda D, Paul R, Dash J. A DNA nanosensor for monitoring ligand-induced i-motif formation. Org Biomol Chem 2021; 19:1965-1969. [DOI: 10.1039/d1ob00248a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A GNP-based DNA nanosensor has been developed that identifies i-motif inducing ligands at physiological pH from a chemical library.
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Affiliation(s)
- Puja Saha
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata-700032
- India
| | - Deepanjan Panda
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata-700032
- India
| | - Raj Paul
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata-700032
- India
| | - Jyotirmayee Dash
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Kolkata-700032
- India
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33
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Sanchez-Martin V, Lopez-Pujante C, Soriano-Rodriguez M, Garcia-Salcedo JA. An Updated Focus on Quadruplex Structures as Potential Therapeutic Targets in Cancer. Int J Mol Sci 2020; 21:ijms21238900. [PMID: 33255335 PMCID: PMC7734589 DOI: 10.3390/ijms21238900] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/13/2020] [Accepted: 11/20/2020] [Indexed: 02/06/2023] Open
Abstract
Non-canonical, four-stranded nucleic acids secondary structures are present within regulatory regions in the human genome and transcriptome. To date, these quadruplex structures include both DNA and RNA G-quadruplexes, formed in guanine-rich sequences, and i-Motifs, found in cytosine-rich sequences, as their counterparts. Quadruplexes have been extensively associated with cancer, playing an important role in telomere maintenance and control of genetic expression of several oncogenes and tumor suppressors. Therefore, quadruplex structures are considered attractive molecular targets for cancer therapeutics with novel mechanisms of action. In this review, we provide a general overview about recent research on the implications of quadruplex structures in cancer, firstly gathering together DNA G-quadruplexes, RNA G-quadruplexes as well as DNA i-Motifs.
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Affiliation(s)
- Victoria Sanchez-Martin
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016 Granada, Spain; (V.S.-M.); (C.L.-P.)
- Microbiology Unit, University Hospital Virgen de las Nieves, Biosanitary Research Institute IBS, Granada, 18014 Granada, Spain
- Department of Biochemistry, Molecular Biology III and Immunology, University of Granada, 18016 Granada, Spain
| | - Carmen Lopez-Pujante
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016 Granada, Spain; (V.S.-M.); (C.L.-P.)
| | - Miguel Soriano-Rodriguez
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016 Granada, Spain; (V.S.-M.); (C.L.-P.)
- Centre for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAMBITAL), University of Almeria, 04001 Almeria, Spain
- Correspondence: (M.S.-R.); (J.A.G.-S.); Tel.: +34-958715500 (M.S.-R.); +34-958715500 (J.A.G.-S.)
| | - Jose A. Garcia-Salcedo
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016 Granada, Spain; (V.S.-M.); (C.L.-P.)
- Microbiology Unit, University Hospital Virgen de las Nieves, Biosanitary Research Institute IBS, Granada, 18014 Granada, Spain
- Correspondence: (M.S.-R.); (J.A.G.-S.); Tel.: +34-958715500 (M.S.-R.); +34-958715500 (J.A.G.-S.)
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34
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Zhang X, Zhang Y, Zhang W. Dynamic topology of double-stranded telomeric DNA studied by single-molecule manipulation in vitro. Nucleic Acids Res 2020; 48:6458-6470. [PMID: 32496520 PMCID: PMC7337930 DOI: 10.1093/nar/gkaa479] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 05/17/2020] [Accepted: 05/27/2020] [Indexed: 12/18/2022] Open
Abstract
The dynamic topological structure of telomeric DNA is closely related to its biological function; however, no such structural information on full-length telomeric DNA has been reported due to difficulties synthesizing long double-stranded telomeric DNA. Herein, we developed an EM-PCR and TA cloning-based approach to synthesize long-chain double-stranded tandem repeats of telomeric DNA. Using mechanical manipulation assays based on single-molecule atomic force microscopy, we found that mechanical force can trigger the melting of double-stranded telomeric DNA and the formation of higher-order structures (G-quadruplexes or i-motifs). Our results show that only when both the G-strand and C-strand of double-stranded telomeric DNA form higher-order structures (G-quadruplexes or i-motifs) at the same time (e.g. in the presence of 100 mM KCl under pH 4.7), that the higher-order structure(s) can remain after the external force is removed. The presence of monovalent K+, single-wall carbon nanotubes (SWCNTs), acidic conditions, or short G-rich fragments (∼30 nt) can shift the transition from dsDNA to higher-order structures. Our results provide a new way to regulate the topology of telomeric DNA.
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Affiliation(s)
- Xiaonong Zhang
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130012, People's Republic of China
| | - Yingqi Zhang
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130012, People's Republic of China
| | - Wenke Zhang
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun 130012, People's Republic of China
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35
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Kuang G, Zhang M, Kang S, Hu D, Li X, Wei Z, Gong X, An LK, Huang ZS, Shu B, Li D. Syntheses and Evaluation of New Bisacridine Derivatives for Dual Binding of G-Quadruplex and i-Motif in Regulating Oncogene c-myc Expression. J Med Chem 2020; 63:9136-9153. [PMID: 32787078 DOI: 10.1021/acs.jmedchem.9b01917] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The c-myc oncogene is an important regulator for cell growth and differentiation, and its aberrant overexpression is closely related to the occurrence and development of various cancers. Thus, the suppression of c-myc transcription and expression has been investigated for cancer treatment. In this study, various new bisacridine derivatives were synthesized and evaluated for their binding with c-myc promoter G-quadruplex and i-motif. We found that a9 could bind to and stabilize both G-quadruplex and i-motif, resulting in the downregulation of c-myc gene transcription. a9 could inhibit cancer cell proliferation and induce SiHa cell apoptosis and cycle arrest. a9 exhibited tumor growth inhibition activity in a SiHa xenograft tumor model, which might be related to its binding with c-myc promoter G-quadruplex and i-motif. Our results suggested that a9 as a dual G-quadruplex/i-motif binder could be effective in both oncogene replication and transcription and become a promising lead compound for further development with improved potency and selectivity.
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Affiliation(s)
- Guotao Kuang
- School of Pharmaceutical Sciences, Sun Yat-sen University, 132 Waihuan East Road, Guangzhou 510006, P. R. China
| | - Meiling Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, 132 Waihuan East Road, Guangzhou 510006, P. R. China
| | - Shuangshuang Kang
- School of Pharmaceutical Sciences, Sun Yat-sen University, 132 Waihuan East Road, Guangzhou 510006, P. R. China
| | - Dexuan Hu
- School of Pharmaceutical Sciences, Sun Yat-sen University, 132 Waihuan East Road, Guangzhou 510006, P. R. China
| | - Xiaoya Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, 132 Waihuan East Road, Guangzhou 510006, P. R. China
| | - Zuzhuang Wei
- School of Pharmaceutical Sciences, Sun Yat-sen University, 132 Waihuan East Road, Guangzhou 510006, P. R. China
| | - Xue Gong
- School of Pharmaceutical Sciences, Sun Yat-sen University, 132 Waihuan East Road, Guangzhou 510006, P. R. China
| | - Lin-Kun An
- School of Pharmaceutical Sciences, Sun Yat-sen University, 132 Waihuan East Road, Guangzhou 510006, P. R. China
| | - Zhi-Shu Huang
- School of Pharmaceutical Sciences, Sun Yat-sen University, 132 Waihuan East Road, Guangzhou 510006, P. R. China
| | - Bing Shu
- School of Pharmaceutical Sciences, Sun Yat-sen University, 132 Waihuan East Road, Guangzhou 510006, P. R. China.,School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, P. R. China
| | - Ding Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, 132 Waihuan East Road, Guangzhou 510006, P. R. China
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36
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Zhou Z, Fan D, Willner I. Modeling Gene Expression Instability by Programmed and Switchable Polymerization/Nicking DNA Nanomachineries. ACS NANO 2020; 14:5046-5052. [PMID: 32250590 DOI: 10.1021/acsnano.0c01583] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Models for gene expression instability by noncanonical DNA-nanostructures are introduced. The systems consist of a promoter-template scaffold that acts as a polymerization/nicking machinery that models, in the presence of polymerase/Nt.BbvCI and dNTPs, the autonomous synthesis of displaced strands mimicking the native "genes". Incorporation of noncanonical DNA structures into the scaffolds consisting of Sr2+-ion-stabilized G-quadruplexes, T-A·T triplexes, or ATP-aptamer complexes results in the perturbation of the polymerization/nicking DNA machineries and the synthesis of displaced strands-"genes" exhibiting other structures. By the dissociation of the noncanonical blockage units, the regeneration of the synthesis of the original intact displaced strands-"genes" is demonstrated. The study introduces conceptual means to eliminate destructive gene expression instability pathways.
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Affiliation(s)
- Zhixin Zhou
- Institute of Chemistry, The Minerva Center for Biohybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Daoqing Fan
- Institute of Chemistry, The Minerva Center for Biohybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Itamar Willner
- Institute of Chemistry, The Minerva Center for Biohybrid Complex Systems, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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37
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Wang KB, Dickerhoff J, Wu G, Yang D. PDGFR-β Promoter Forms a Vacancy G-Quadruplex that Can Be Filled in by dGMP: Solution Structure and Molecular Recognition of Guanine Metabolites and Drugs. J Am Chem Soc 2020; 142:5204-5211. [PMID: 32101424 DOI: 10.1021/jacs.9b12770] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Aberrant expression of PDGFR-β is associated with a number of diseases. The G-quadruplexes (G4s) formed in PDGFR-β gene promoter are transcriptional modulators and amenable to small molecule targeting. The major G4 formed in the PDGFR-β gene promoter was previously shown to have a broken G-strand. Herein, we report that the PDGFR-β gene promoter sequence forms a vacancy G-quadruplex (vG4) which can be filled in and stabilized by physiologically relevant guanine metabolites, such as dGMP, GMP, and cGMP, as well as guanine-derivative drugs. We determined the NMR structure of the dGMP-fill-in PDGFR-β vG4 in K+ solution. This is the first structure of a guanine-metabolite-fill-in vG4 based on a human gene promoter sequence. Our structure and systematic analysis elucidate the contributions of Hoogsten hydrogen bonds, sugar, and phosphate moieties to the specific G-vacancy fill-in. Intriguingly, an equilibrium of 3'- and 5'-end vG4s is present in the PDGFR-β promoter sequence, and dGMP favors the 5'-end fill-in. Guanine metabolites and drugs were tested and showed a conserved selectivity for the 5'-vacancy, except for cGMP. cGMP binds both the 3'- and 5'-end vG4s and forms two fill-in G4s with similar population. Significantly, guanine metabolites are involved in many physiological and pathological processes in human cells; thus, our results provide a structural basis to understand their potential regulatory functions by interaction with promoter vG4s. Moreover, the NMR structure can guide rational design of ligands that target the PDGFR-β vG4.
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38
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Deng M, Li M, Mao X, Li F, Zuo X. Nucleic Acid Nanoprobes for Biosensor Development in Complex Matrices. Chem Res Chin Univ 2020. [DOI: 10.1007/s40242-020-9073-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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39
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Saha P, Panda D, Müller D, Maity A, Schwalbe H, Dash J. In situ formation of transcriptional modulators using non-canonical DNA i-motifs. Chem Sci 2020; 11:2058-2067. [PMID: 32180928 PMCID: PMC7047845 DOI: 10.1039/d0sc00514b] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 01/28/2020] [Indexed: 12/14/2022] Open
Abstract
Herein, i-motif DNA-immobilized magnetic nanoparticles are used as templates to promote the in situ cycloaddition generating specific binders for i-motifs.
Non-canonical DNA i-motifs and G-quadruplexes are postulated as genetic switches for the transcriptional regulation of proto-oncogenes. However, in comparison to G-quadruplexes, the therapeutic potential of i-motifs is less explored. The development of i-motif selective ligands by conventional approaches is challenging due to the structural complexity of i-motifs. The target guided synthetic (TGS) approach involving in situ cycloaddition could provide specific ligands for these dynamic DNA structures. Herein, we have used i-motif forming C-rich DNA and their complementary G-quadruplex forming DNA sequences of c-MYC and BCL2 promoter regions as well as a control self-complementary duplex DNA sequence as the templates to generate selective ligands from a pool of reactive azide–alkyne building blocks. In our approach, thiolated DNA targets are immobilized on the surface of gold-coated iron nanoparticles to enable efficient isolation of the newly generated ligands from the solution mixture by simple magnetic decantation. The combinatorial in situ cycloaddition generated cell-membrane permeable triazole leads for respective DNA targets (c-MYC and BCL2 i-motifs and G-quadruplexes) that selectively promote their formation. In vitro cellular studies reveal that the c-MYC i-motif and G-quadruplex leads downregulate c-MYC gene expression whereas the BCL2 i-motif lead upregulates and the BCL2 G-quadruplex lead represses BCL2 gene expression. The TGS strategy using i-motif DNA nanotemplates represents a promising platform for the direct in situ formation of i-motif specific ligands for therapeutic intervention.
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Affiliation(s)
- Puja Saha
- School of Chemical Sciences , Indian Association for the Cultivation of Science , Jadavpur , Kolkata-700032 , India .
| | - Deepanjan Panda
- School of Chemical Sciences , Indian Association for the Cultivation of Science , Jadavpur , Kolkata-700032 , India .
| | - Diana Müller
- Institute of Organic Chemistry and Chemical Biology , Center for Biomolecular Magnetic Resonance (BMRZ) , Goethe University , Max-von-Laue Strasse 7 , Frankfurt , D-60438 , Germany
| | - Arunabha Maity
- School of Chemical Sciences , Indian Association for the Cultivation of Science , Jadavpur , Kolkata-700032 , India .
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical Biology , Center for Biomolecular Magnetic Resonance (BMRZ) , Goethe University , Max-von-Laue Strasse 7 , Frankfurt , D-60438 , Germany
| | - Jyotirmayee Dash
- School of Chemical Sciences , Indian Association for the Cultivation of Science , Jadavpur , Kolkata-700032 , India .
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40
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Fleming AM, Burrows CJ. Interplay of Guanine Oxidation and G-Quadruplex Folding in Gene Promoters. J Am Chem Soc 2020; 142:1115-1136. [PMID: 31880930 PMCID: PMC6988379 DOI: 10.1021/jacs.9b11050] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Living in an oxygen atmosphere demands an ability to thrive in the presence of reactive oxygen species (ROS). Aerobic organisms have successfully found solutions to the oxidative threats imposed by ROS by evolving an elaborate detoxification system, upregulating ROS during inflammation, and utilizing ROS as messenger molecules. In this Perspective, recent studies are discussed that demonstrate ROS as signaling molecules for gene regulation by combining two emergent properties of the guanine (G) heterocycle in DNA, namely, oxidation sensitivity and a propensity for G-quadruplex (G4) folding, both of which depend upon sequence context. In human gene promoters, this results from an elevated 5'-GG-3' dinucleotide frequency and GC enrichment near transcription start sites. Oxidation of DNA by ROS drives conversion of G to 8-oxo-7,8-dihydroguanine (OG) to mark target promoters for base excision repair initiated by OG-glycosylase I (OGG1). Sequence-dependent mechanisms for gene activation are available to OGG1 to induce transcription. Either OGG1 releases OG to yield an abasic site driving formation of a non-canonical fold, such as a G4, to be displayed to apurinic/apyrimidinic 1 (APE1) and stalling on the fold to recruit activating factors, or OGG1 binds OG and facilitates activator protein recruitment. The mechanisms described drive induction of stress response, DNA repair, or estrogen-induced genes, and these pathways are novel potential anticancer targets for therapeutic intervention. Chemical concepts provide a framework to discuss the regulatory or possible epigenetic potential of the OG modification in DNA, in which DNA "damage" and non-canonical folds collaborate to turn on or off gene expression. The next steps for scientific discovery in this growing field are discussed.
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Affiliation(s)
- Aaron M. Fleming
- 315 South 1400 East, Dept. of Chemistry, University of Utah, Salt Lake City, UT 84112-0850, USA
| | - Cynthia J. Burrows
- 315 South 1400 East, Dept. of Chemistry, University of Utah, Salt Lake City, UT 84112-0850, USA
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41
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Somkuti J, Molnár OR, Smeller L. Revealing unfolding steps and volume changes of human telomeric i-motif DNA. Phys Chem Chem Phys 2020; 22:23816-23823. [DOI: 10.1039/d0cp03894f] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The i-motif structure of the human telomeric DNA was destabilized by pressure and unfolded with a negative volume change.
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Affiliation(s)
- Judit Somkuti
- Department of Biophysics and Radiation Biology
- Semmelweis University
- Tuzolto utca 37-47 1094
- Hungary
| | - Orsolya Réka Molnár
- Department of Biophysics and Radiation Biology
- Semmelweis University
- Tuzolto utca 37-47 1094
- Hungary
| | - László Smeller
- Department of Biophysics and Radiation Biology
- Semmelweis University
- Tuzolto utca 37-47 1094
- Hungary
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42
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A DNA Polymerase Stop Assay for Characterization of G-Quadruplex Formation and Identification of G-Quadruplex-Interactive Compounds. Methods Mol Biol 2019. [PMID: 31444752 DOI: 10.1007/978-1-4939-9666-7_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
Guanine-rich DNA sequences are able to spontaneously fold into G-quadruplex structures in the presence of certain metal cations. In the human genome, the majority of DNA G-quadruplexes form at the telomeres and regulatory regions of cancer-related genes. The formation of these structures is implicated in nuclear processes involving DNA, including transcription, DNA replication, and DNA repair. In the past few decades, small molecules which can stabilize these structures have been shown to suppress the telomere extension and to inhibit oncogene transcription. Therefore, DNA G-quadruplexes are thought to be attractive targets for new anticancer therapies. In this chapter, we describe step by step a DNA polymerase extension method for the characterization of G-quadruplex formation and identification of G-quadruplex-interactive compounds. This method is based on the principle that DNA polymerase is incapable to resolve G-quadruplex structure and pauses at 3'-end of the G-quadruplex forming region when it transverses to the 5'-end of the template. Results from the DNA polymerase stop assay can provide the basis for further studies aimed at elucidating the major G-quadruplexes formed by sequences consisting of more than four runs of contiguous guanines, as well as the specificity of G-quadruplex-interactive molecules in binding different G-quadruplex topologies.
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43
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Weldon C, Dacanay JG, Gokhale V, Boddupally PVL, Behm-Ansmant I, Burley GA, Branlant C, Hurley LH, Dominguez C, Eperon IC. Specific G-quadruplex ligands modulate the alternative splicing of Bcl-X. Nucleic Acids Res 2019; 46:886-896. [PMID: 29156002 PMCID: PMC5778605 DOI: 10.1093/nar/gkx1122] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 10/26/2017] [Indexed: 12/23/2022] Open
Abstract
Sequences with the potential to form RNA G-quadruplexes (G4s) are common in mammalian introns, especially in the proximity of the 5′ splice site (5′SS). However, the difficulty of demonstrating that G4s form in pre-mRNA in functional conditions has meant that little is known about their effects or mechanisms of action. We have shown previously that two G4s form in Bcl-X pre-mRNA, one close to each of the two alternative 5′SS. If these G4s affect splicing but are in competition with other RNA structures or RNA binding proteins, then ligands that stabilize them would increase the proportion of Bcl-X pre-mRNA molecules in which either or both G4s had formed, shifting Bcl-X splicing. We show here that a restricted set of G4 ligands do affect splicing, that their activity and specificity are strongly dependent on their structures and that they act independently at the two splice sites. One of the ligands, the ellipticine GQC-05, antagonizes the major 5′SS that expresses the anti-apoptotic isoform of Bcl-X and activates the alternative 5′SS that expresses a pro-apoptotic isoform. We propose mechanisms that would account for these see-saw effects and suggest that these effects contribute to the ability of GQC-05 to induce apoptosis.
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Affiliation(s)
- Carika Weldon
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Justine G Dacanay
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Vijay Gokhale
- College of Pharmacy and College of Pharmacy and BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
| | - Peda Venkat L Boddupally
- Fluoroorganic Division, CSIR-Indian Institute of Chemical Technology, Hyderabad, Telangana 500 007, India
| | - Isabelle Behm-Ansmant
- IMoPA (Ingénierie Moléculaire et Physiopathologie Articulaire), UMR 7365 CNRS-UL, Biopôle de l'Université de Lorraine, 9 Avenue de la Forêt de Haye, 54505 Vandoeuvre-lès-Nancy, France
| | - Glenn A Burley
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1XL, UK
| | - Christiane Branlant
- IMoPA (Ingénierie Moléculaire et Physiopathologie Articulaire), UMR 7365 CNRS-UL, Biopôle de l'Université de Lorraine, 9 Avenue de la Forêt de Haye, 54505 Vandoeuvre-lès-Nancy, France
| | - Laurence H Hurley
- College of Pharmacy and College of Pharmacy and BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA.,Arizona Cancer Center, University of Arizona, Tucson, AZ 85724, USA
| | - Cyril Dominguez
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Ian C Eperon
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Leicester LE1 7RH, UK
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44
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Dvoráková Z, Renciuk D, Kejnovská I, Školáková P, Bednárová K, Sagi J, Vorlícková M. i-Motif of cytosine-rich human telomere DNA fragments containing natural base lesions. Nucleic Acids Res 2019; 46:1624-1634. [PMID: 29378012 PMCID: PMC5829569 DOI: 10.1093/nar/gky035] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 01/15/2018] [Indexed: 12/01/2022] Open
Abstract
i-Motif (iM) is a four stranded DNA structure formed by cytosine-rich sequences, which are often present in functionally important parts of the genome such as promoters of genes and telomeres. Using electronic circular dichroism and UV absorption spectroscopies and electrophoretic methods, we examined the effect of four naturally occurring DNA base lesions on the folding and stability of the iM formed by the human telomere DNA sequence (C3TAA)3C3T. The results demonstrate that the TAA loop lesions, the apurinic site and 8-oxoadenine substituting for adenine, and the 5-hydroxymethyluracil substituting for thymine only marginally disturb the formation of iM. The presence of uracil, which is formed by enzymatic or spontaneous deamination of cytosine, shifts iM formation towards substantially more acidic pH values and simultaneously distinctly reduces iM stability. This effect depends on the position of the damage sites in the sequence. The results have enabled us to formulate additional rules for iM formation.
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Affiliation(s)
- Zuzana Dvoráková
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Daniel Renciuk
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Iva Kejnovská
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Petra Školáková
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Klára Bednárová
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Janos Sagi
- Rimstone Laboratory, RLI, Carlsbad, CA 92010, USA
| | - Michaela Vorlícková
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
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45
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Wang KB, Elsayed MSA, Wu G, Deng N, Cushman M, Yang D. Indenoisoquinoline Topoisomerase Inhibitors Strongly Bind and Stabilize the MYC Promoter G-Quadruplex and Downregulate MYC. J Am Chem Soc 2019; 141:11059-11070. [PMID: 31283877 DOI: 10.1021/jacs.9b02679] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
MYC is one of the most important oncogenes and is overexpressed in the majority of cancers. G-Quadruplexes are noncanonical four-stranded DNA secondary structures that have emerged as attractive cancer-specific molecular targets for drug development. The G-quadruplex formed in the proximal promoter region of the MYC oncogene (MycG4) has been shown to be a transcriptional silencer that is amenable to small-molecule targeting for MYC suppression. Indenoisoquinolines are human topoisomerase I inhibitors in clinical testing with improved physicochemical and biological properties as compared to the clinically used camptothecin anticancer drugs topotecan and irinotecan. However, some indenoisoquinolines with potent anticancer activity do not exhibit strong topoisomerase I inhibition, suggesting a separate mechanism of action. Here, we report that anticancer indenoisoquinolines strongly bind and stabilize MycG4 and lower MYC expression levels in cancer cells, using various biochemical, biophysical, computer modeling, and cell-based methods. Significantly, a large number of active indenoisoquinolines cause strong MYC downregulation in cancer cells. Structure-activity relationships of MycG4 recognition by indenoisoquinolines are investigated. In addition, the analysis of indenoisoquinoline analogues for their MYC-inhibitory activity, topoisomerase I-inhibitory activity, and anticancer activity reveals a synergistic effect of MYC inhibition and topoisomerase I inhibition on anticancer activity. Therefore, this study uncovers a novel mechanism of action of indenoisoquinolines as a new family of drugs targeting the MYC promoter G-quadruplex for MYC suppression. Furthermore, the study suggests that dual targeting of MYC and topoisomerase I may serve as a novel strategy for anticancer drug development.
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Affiliation(s)
- Kai-Bo Wang
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy , Purdue University , 575 W Stadium Avenue , West Lafayette , Indiana 47907 , United States
| | - Mohamed S A Elsayed
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy , Purdue University , 575 W Stadium Avenue , West Lafayette , Indiana 47907 , United States
| | - Guanhui Wu
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy , Purdue University , 575 W Stadium Avenue , West Lafayette , Indiana 47907 , United States
| | - Nanjie Deng
- Department of Chemistry and Physical Sciences , Pace University , 1 Pace Plaza , New York , New York 10038 , United States
| | - Mark Cushman
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy , Purdue University , 575 W Stadium Avenue , West Lafayette , Indiana 47907 , United States.,Purdue Center for Cancer Research , 201 S University Street , West Lafayette , Indiana 47906 , United States.,Purdue Institute for Drug Discovery , 720 Clinic Drive , West Lafayette , Indiana 47907 , United States
| | - Danzhou Yang
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy , Purdue University , 575 W Stadium Avenue , West Lafayette , Indiana 47907 , United States.,Purdue Center for Cancer Research , 201 S University Street , West Lafayette , Indiana 47906 , United States.,Purdue Institute for Drug Discovery , 720 Clinic Drive , West Lafayette , Indiana 47907 , United States
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46
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Abou Assi H, Garavís M, González C, Damha MJ. i-Motif DNA: structural features and significance to cell biology. Nucleic Acids Res 2019; 46:8038-8056. [PMID: 30124962 PMCID: PMC6144788 DOI: 10.1093/nar/gky735] [Citation(s) in RCA: 233] [Impact Index Per Article: 46.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 08/13/2018] [Indexed: 12/20/2022] Open
Abstract
The i-motif represents a paradigmatic example of the wide structural versatility of nucleic acids. In remarkable contrast to duplex DNA, i-motifs are four-stranded DNA structures held together by hemi- protonated and intercalated cytosine base pairs (C:C+). First observed 25 years ago, and considered by many as a mere structural oddity, interest in and discussion on the biological role of i-motifs have grown dramatically in recent years. In this review we focus on structural aspects of i-motif formation, the factors leading to its stabilization and recent studies describing the possible role of i-motifs in fundamental biological processes.
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Affiliation(s)
- Hala Abou Assi
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
| | - Miguel Garavís
- Instituto de Química Física 'Rocasolano', CSIC, C/Serrano 119, 28006 Madrid, Spain
| | - Carlos González
- Instituto de Química Física 'Rocasolano', CSIC, C/Serrano 119, 28006 Madrid, Spain
| | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
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47
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Ducani C, Bernardinelli G, Högberg B, Keppler BK, Terenzi A. Interplay of Three G-Quadruplex Units in the KIT Promoter. J Am Chem Soc 2019; 141:10205-10213. [PMID: 31244182 DOI: 10.1021/jacs.8b12753] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The proto-oncogene KIT encodes for a tyrosine kinase receptor, which is a clinically validated target for treating gastrointestinal stromal tumors. The KIT promoter contains a G-rich domain within a relatively long sequence potentially able to form three adjacent G-quadruplex (G4) units, namely, K2, SP, and K1. These G4 domains have been studied mainly as single quadruplex units derived from short truncated sequences and are currently considered promising targets for anticancer drugs, alternatively to the encoded protein. Nevertheless, the information reported so far does not contemplate the interplay between those neighboring G4s in the context of the whole promoter, possibly thwarting drug-discovery efforts. Here we report the structural and functional study of the KIT promoter core sequence, in both single- and double-stranded forms, which includes all three predicted G4 units. By preventing the formation of alternatively one or two G4 units and by combining biophysical techniques and biological assays, we show for the first time that these quadruplexes cannot be analyzed independently, but they are correlated to each other. Our data suggest that, while K2 and K1 G-rich sequences retain the ability to fold into parallel G4 motifs within a long sequence, the SP G-rich domain contributes to G4 structure only together with K2. Remarkably, we have found that, in the context of a dynamic equilibrium between the three G4 units, the G4 formed by K1 has the most significant influence on the structure stability and on the biological role of the whole promoter.
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Affiliation(s)
- Cosimo Ducani
- Department of Medical Biochemistry and Biophysics , Karolinska Institutet , Stockholm 171 65 , Sweden
| | - Giulio Bernardinelli
- Department of Medical Biochemistry and Biophysics , Karolinska Institutet , Stockholm 171 65 , Sweden
| | - Björn Högberg
- Department of Medical Biochemistry and Biophysics , Karolinska Institutet , Stockholm 171 65 , Sweden
| | - Bernhard K Keppler
- Institute of Inorganic Chemistry , University of Vienna , Waehringerstrasse 42 , A-1090 Vienna , Austria
| | - Alessio Terenzi
- Institute of Inorganic Chemistry , University of Vienna , Waehringerstrasse 42 , A-1090 Vienna , Austria
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48
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Taladriz-Sender A, Campbell E, Burley GA. Splice-switching small molecules: A new therapeutic approach to modulate gene expression. Methods 2019; 167:134-142. [PMID: 31203161 DOI: 10.1016/j.ymeth.2019.06.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 06/10/2019] [Accepted: 06/11/2019] [Indexed: 12/12/2022] Open
Abstract
Manipulating alternative RNA splicing events with small molecules is emerging as a viable mechanism for the development of therapeutics. A salient challenge in the field is understanding the molecular determinants defining the selectivity of splice-switching events and their mechanisms of action. In this review, the current state-of-the-art in splice-switching small molecules is described. Three examples of splice-switching small molecules are presented, and the differences in their modes of action compared.
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Affiliation(s)
- Andrea Taladriz-Sender
- Department of Pure and Applied Chemistry, University of Strathclyde. Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Emma Campbell
- Department of Pure and Applied Chemistry, University of Strathclyde. Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Glenn A Burley
- Department of Pure and Applied Chemistry, University of Strathclyde. Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom.
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49
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Novel 11-Substituted Ellipticines as Potent Anticancer Agents with Divergent Activity against Cancer Cells. Pharmaceuticals (Basel) 2019; 12:ph12020090. [PMID: 31207878 PMCID: PMC6631919 DOI: 10.3390/ph12020090] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 06/09/2019] [Accepted: 06/12/2019] [Indexed: 11/17/2022] Open
Abstract
Ellipticines have well documented anticancer activity, in particular with substitution at the 1-, 2-, 6- and 9-positions. However, due to limitations in synthesis and coherent screening methodology the full SAR profile of this anticancer class has not yet been achieved. In order to address this shortfall, we have set out to explore the anticancer activity of this potent natural product by substitution. We currently describe the synthesis of novel 11-substituted ellipticines with two specific derivatives showing potency and diverging cellular growth effects.
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50
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Sun Y, Ji Y, Wang D, Wang J, Liu D. Stabilization of an intermolecular i-motif by lipid modification of cytosine-oligodeoxynucleotides. Org Biomol Chem 2019; 16:4857-4863. [PMID: 29926887 DOI: 10.1039/c8ob00920a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This paper describes the stabilization of an intermolecular i-motif by lipophilic modification on the 3'-terminus of oligonucleotides. The hydrophobic aliphatic chain connected at the 3'-terminus of a trinucleotide (dC)3 promoted the formation of an i-motif and significantly enhanced the quadruplex's stability. The impact of lipophilic modification on i-motif's thermal stability was studied by UV-thermal denaturation melting experiments and isothermal titration calorimetry. We found that alkyl chains containing more than 14 carbon atoms could elevate the i-motif structure's stability in a wide range of pH and concentrations.
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Affiliation(s)
- Yawei Sun
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering, China University of Petroleum (Huadong), Qingdao, 258000, China.
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