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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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2
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Structural insight into the bulge-containing KRAS oncogene promoter G-quadruplex bound to berberine and coptisine. Nat Commun 2022; 13:6016. [PMID: 36224201 PMCID: PMC9556435 DOI: 10.1038/s41467-022-33761-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 09/30/2022] [Indexed: 12/08/2022] Open
Abstract
KRAS is one of the most highly mutated oncoproteins, which is overexpressed in various human cancers and implicated in poor survival. The G-quadruplex formed in KRAS oncogene promoter (KRAS-G4) is a transcriptional modulator and amenable to small molecule targeting. However, no available KRAS-G4-ligand complex structure has yet been determined, which seriously hinders the structure-based rational design of KRAS-G4 targeting drugs. In this study, we report the NMR solution structures of a bulge-containing KRAS-G4 bound to berberine and coptisine, respectively. The determined complex structure shows a 2:1 binding stoichiometry with each compound recruiting the adjacent flacking adenine residue to form a "quasi-triad plane" that stacks over the two external G-tetrads. The binding involves both π-stacking and electrostatic interactions. Moreover, berberine and coptisine significantly lowered the KRAS mRNA levels in cancer cells. Our study thus provides molecular details of ligand interactions with KRAS-G4 and is beneficial for the design of specific KRAS-G4-interactive drugs.
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Ferino A, Marquevielle J, Choudhary H, Cinque G, Robert C, Bourdoncle A, Picco R, Mergny JL, Salgado GF, Xodo LE. hnRNPA1/UP1 Unfolds KRAS G-Quadruplexes and Feeds a Regulatory Axis Controlling Gene Expression. ACS OMEGA 2021; 6:34092-34106. [PMID: 34926957 PMCID: PMC8675163 DOI: 10.1021/acsomega.1c05538] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 11/12/2021] [Indexed: 05/20/2023]
Abstract
Recent studies have proven that the genetic landscape of pancreatic cancer is dominated by the KRAS oncogene. Its transcription is controlled by a G-rich motif (called 32R) located immediately upstream of the TSS. 32R may fold into a G-quadruplex (G4) in equilibrium between two G4 conformers: G9T (T M = 61.2 °C) and G25T (T M = 54.7 °C). We found that both G4s bind to hnRNPA1 and its proteolytic fragment UP1, promoting several contacts with the RRM protein domains. 1D NMR analysis of DNA imino protons shows that, upon binding to UP1, G25T is readily unfolded at both 5' and 3' tetrads, while G9T is only partially unfolded. The impact of hnRNPA1 on KRAS expression was determined by comparing Panc-1 cells with two Panc-1 knockout cell lines in which hnRNPA1 was deleted by the CRISPR/Cas9 technology. The results showed that the expression of KRAS is inhibited in the knockout cell lines, indicating that hnRNPA1 is essential for the transcription of KRAS. In addition, the knockout cell lines, compared to normal Panc-1 cells, show a dramatic decrease in cell growth and capacity of colony formation. Pull-down and Western blot experiments indicate that conformer G25T is a better platform than conformer G9T for the assembly of the transcription preinitiation complex with PARP1, Ku70, MAZ, and hnRNPA1. Together, our data prove that hnRNPA1, being a key transcription factor for the activation of KRAS, can be a new therapeutic target for the rational design of anticancer strategies.
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Affiliation(s)
- Annalisa Ferino
- Department
of Medicine, Laboratory of Biochemistry, P.le Kolbe 4; Udine 33100, Italy
| | - Julien Marquevielle
- ARNA
Laboratory, Université de Bordeaux, Inserm U1212, CNRS UMR 5320, IECB, 2 rue Robert Escarpit, Pessac 33607, France
| | - Himanshi Choudhary
- Department
of Medicine, Laboratory of Biochemistry, P.le Kolbe 4; Udine 33100, Italy
| | - Giorgio Cinque
- Department
of Medicine, Laboratory of Biochemistry, P.le Kolbe 4; Udine 33100, Italy
| | - Coralie Robert
- ARNA
Laboratory, Université de Bordeaux, Inserm U1212, CNRS UMR 5320, IECB, 2 rue Robert Escarpit, Pessac 33607, France
| | - Anne Bourdoncle
- ARNA
Laboratory, Université de Bordeaux, Inserm U1212, CNRS UMR 5320, IECB, 2 rue Robert Escarpit, Pessac 33607, France
| | - Raffaella Picco
- Department
of Medicine, Laboratory of Biochemistry, P.le Kolbe 4; Udine 33100, Italy
| | - Jean-Louis Mergny
- ARNA
Laboratory, Université de Bordeaux, Inserm U1212, CNRS UMR 5320, IECB, 2 rue Robert Escarpit, Pessac 33607, France
- Laboratoire
d’Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Route de Saclay, Palaiseau Cedex 91128, France
| | - Gilmar F. Salgado
- ARNA
Laboratory, Université de Bordeaux, Inserm U1212, CNRS UMR 5320, IECB, 2 rue Robert Escarpit, Pessac 33607, France
| | - Luigi E. Xodo
- Department
of Medicine, Laboratory of Biochemistry, P.le Kolbe 4; Udine 33100, Italy
- luigi.xodo@uniud.it
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D’Aria F, Pagano B, Petraccone L, Giancola C. KRAS Promoter G-Quadruplexes from Sequences of Different Length: A Physicochemical Study. Int J Mol Sci 2021; 22:ijms22010448. [PMID: 33466280 PMCID: PMC7795837 DOI: 10.3390/ijms22010448] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/23/2020] [Accepted: 12/31/2020] [Indexed: 11/16/2022] Open
Abstract
DNA G-quadruplexes (G4s) form in relevant genomic regions and intervene in several biological processes, including the modulation of oncogenes expression, and are potential anticancer drug targets. The human KRAS proto-oncogene promoter region contains guanine-rich sequences able to fold into G4 structures. Here, by using circular dichroism and differential scanning calorimetry as complementary physicochemical methodologies, we compared the thermodynamic stability of the G4s formed by a shorter and a longer version of the KRAS promoter sequence, namely 5′-AGGGCGGTGTGGGAATAGGGAA-3′ (KRAS 22RT) and 5′-AGGGCGGTGTGGGAAGAGGGAAGAGGGGGAGG-3′ (KRAS 32R). Our results show that the unfolding mechanism of KRAS 32R is more complex than that of KRAS 22RT. The different thermodynamic stability is discussed based on the recently determined NMR structures. The binding properties of TMPyP4 and BRACO-19, two well-known G4-targeting anticancer compounds, to the KRAS G4s were also investigated. The present physicochemical study aims to help in choosing the best G4 target for potential anticancer drugs.
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Affiliation(s)
- Federica D’Aria
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (F.D.); (B.P.)
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (F.D.); (B.P.)
| | - Luigi Petraccone
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 4, 80126 Naples, Italy;
| | - Concetta Giancola
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy; (F.D.); (B.P.)
- Correspondence:
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Marquevielle J, Robert C, Lagrabette O, Wahid M, Bourdoncle A, Xodo LE, Mergny JL, Salgado GF. Structure of two G-quadruplexes in equilibrium in the KRAS promoter. Nucleic Acids Res 2020; 48:9336-9345. [PMID: 32432667 PMCID: PMC7498360 DOI: 10.1093/nar/gkaa387] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 04/27/2020] [Accepted: 05/15/2020] [Indexed: 12/13/2022] Open
Abstract
KRAS is one of the most mutated oncogenes and still considered an undruggable target. An alternative strategy would consist in targeting its gene rather than the protein, specifically the formation of G-quadruplexes (G4) in its promoter. G4 are secondary structures implicated in biological processes, which can be formed among G-rich DNA (or RNA) sequences. Here we have studied the major conformations of the commonly known KRAS 32R, or simply 32R, a 32 residue sequence within the KRAS Nuclease Hypersensitive Element (NHE) region. We have determined the structure of the two major stable conformers that 32R can adopt and which display slow equilibrium (>ms) with each other. By using different biophysical methods, we found that the nucleotides G9, G25, G28 and G32 are particularly implicated in the exchange between these two conformations. We also showed that a triad at the 3' end further stabilizes one of the G4 conformations, while the second conformer remains more flexible and less stable.
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Affiliation(s)
- Julien Marquevielle
- European Institute of Chemistry and Biology (IECB), ARNA laboratory, INSERM U1212 - CNRS UMR 5320, University of Bordeaux, France
| | - Coralie Robert
- European Institute of Chemistry and Biology (IECB), ARNA laboratory, INSERM U1212 - CNRS UMR 5320, University of Bordeaux, France
| | - Olivier Lagrabette
- European Institute of Chemistry and Biology (IECB), ARNA laboratory, INSERM U1212 - CNRS UMR 5320, University of Bordeaux, France
| | - Mona Wahid
- European Institute of Chemistry and Biology (IECB), ARNA laboratory, INSERM U1212 - CNRS UMR 5320, University of Bordeaux, France
| | - Anne Bourdoncle
- European Institute of Chemistry and Biology (IECB), ARNA laboratory, INSERM U1212 - CNRS UMR 5320, University of Bordeaux, France
| | - Luigi E Xodo
- Department of Medicine, Laboratory of Biochemistry, 33100 Udine, Italy
| | - Jean-Louis Mergny
- European Institute of Chemistry and Biology (IECB), ARNA laboratory, INSERM U1212 - CNRS UMR 5320, University of Bordeaux, France
| | - Gilmar F Salgado
- European Institute of Chemistry and Biology (IECB), ARNA laboratory, INSERM U1212 - CNRS UMR 5320, University of Bordeaux, France
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6
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Cogoi S, Ferino A, Miglietta G, Pedersen EB, Xodo LE. The regulatory G4 motif of the Kirsten ras (KRAS) gene is sensitive to guanine oxidation: implications on transcription. Nucleic Acids Res 2019; 46:661-676. [PMID: 29165690 PMCID: PMC5778462 DOI: 10.1093/nar/gkx1142] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 10/31/2017] [Indexed: 01/10/2023] Open
Abstract
KRAS is one of the most mutated genes in human cancer. It is controlled by a G4 motif located upstream of the transcription start site. In this paper, we demonstrate that 8-oxoguanine (8-oxoG), being more abundant in G4 than in non-G4 regions, is a new player in the regulation of this oncogene. We designed oligonucleotides mimicking the KRAS G4-motif and found that 8-oxoG impacts folding and stability of the G-quadruplex. Dimethylsulphate-footprinting showed that the G-run carrying 8-oxoG is excluded from the G-tetrads and replaced by a redundant G-run in the KRAS G4-motif. Chromatin immunoprecipitation revealed that the base-excision repair protein OGG1 is recruited to the KRAS promoter when the level of 8-oxoG in the G4 region is raised by H2O2. Polyacrylamide gel electrophoresis evidenced that OGG1 removes 8-oxoG from the G4-motif in duplex, but when folded it binds to the G-quadruplex in a non-productive way. We also found that 8-oxoG enhances the recruitment to the KRAS promoter of MAZ and hnRNP A1, two nuclear factors essential for transcription. All this suggests that 8-oxoG in the promoter G4 region could have an epigenetic potential for the control of gene expression.
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Affiliation(s)
- Susanna Cogoi
- Department of Medicine, University of Udine, 33100 Udine, Italy
| | - Annalisa Ferino
- Department of Medicine, University of Udine, 33100 Udine, Italy
| | | | - Erik B Pedersen
- Nucleic Acid Center, Institute of Physics and Chemistry, University of Southern Denmark, DK-5230 Odense, Denmark
| | - Luigi E Xodo
- Department of Medicine, University of Udine, 33100 Udine, Italy
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7
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Abstract
G-quadruplexes (G4s) have become one of the most exciting nucleic acid secondary structures. A noncanonical, four-stranded structure formed in guanine-rich DNA and RNA sequences, G-quadruplexes can readily form under physiologically relevant conditions and are globularly folded structures. DNA is widely recognized as a double-helical structure essential in genetic information storage. However, only ~3% of the human genome is expressed in protein; RNA and DNA may form noncanonical secondary structures that are functionally important. G-quadruplexes are one such example which have gained considerable attention for their formation and regulatory roles in biologically significant regions, such as human telomeres, oncogene-promoter regions, replication initiation sites, and 5'- and 3'-untranslated region (UTR) of mRNA. They are shown to be a regulatory motif in a number of critical cellular processes including gene transcription, translation, replication, and genomic stability. G-quadruplexes are also found in nonhuman genomes, particularly those of human pathogens. Therefore, G-quadruplexes have emerged as a new class of molecular targets for drug development. In addition, there is considerable interest in the use of G-quadruplexes for biomaterials, biosensors, and biocatalysts. The First International Meeting on Quadruplex DNA was held in 2007, and the G-quadruplex field has been growing dramatically over the last decade. The methods used to study G-quadruplexes have been essential to the rapid progress in our understanding of this exciting nucleic acid secondary structure.
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Affiliation(s)
- Danzhou Yang
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, Purdue Center for Cancer Research, Purdue Institute for Drug Discovery, West Lafayette, IN USA
| | - Clement Lin
- Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN USA
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8
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Fluorescent light-up acridine orange derivatives bind and stabilize KRAS-22RT G-quadruplex. Biochimie 2018; 144:144-152. [DOI: 10.1016/j.biochi.2017.11.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Accepted: 11/06/2017] [Indexed: 01/17/2023]
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9
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Kaiser CE, Van Ert NA, Agrawal P, Chawla R, Yang D, Hurley LH. Insight into the Complexity of the i-Motif and G-Quadruplex DNA Structures Formed in the KRAS Promoter and Subsequent Drug-Induced Gene Repression. J Am Chem Soc 2017; 139:8522-8536. [PMID: 28570076 PMCID: PMC5978000 DOI: 10.1021/jacs.7b02046] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Activating KRAS mutations frequently occur in pancreatic, colorectal, and lung adenocarcinomas. While many attempts have been made to target oncogenic KRAS, no clinically useful therapies currently exist. Most efforts to target KRAS have focused on inhibiting the mutant protein; a less explored approach involves targeting KRAS at the transcriptional level. The promoter element of the KRAS gene contains a GC-rich nuclease hypersensitive site with three potential DNA secondary structure-forming regions. These are referred to as the Near-, Mid-, and Far-regions, on the basis of their proximity to the transcription start site. As a result of transcription-induced negative superhelicity, these regions can open up to form unique DNA secondary structures: G-quadruplexes on the G-rich strand and i-motifs on the C-rich strand. While the G-quadruplexes have been well characterized, the i-motifs have not been investigated as thoroughly. Here we show that the i-motif that forms in the C-rich Mid-region is the most stable and exists in a dynamic equilibrium with a hybrid i-motif/hairpin species and an unfolded hairpin species. The transcription factor heterogeneous nuclear ribonucleoprotein K (hnRNP K) was found to bind selectively to the i-motif species and to positively modulate KRAS transcription. Additionally, we identified a benzophenanthridine alkaloid that dissipates the hairpin species and destabilizes the interaction of hnRNP K with the Mid-region i-motif. This same compound stabilizes the three existing KRAS G-quadruplexes. The combined effect of the compound on the Mid-region i-motif and the G-quadruplexes leads to downregulation of KRAS gene expression. This dual i-motif/G-quadruplex-interactive compound presents a new mechanism to modulate gene expression.
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Affiliation(s)
- Christine E. Kaiser
- College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
| | - Natalie A. Van Ert
- College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
| | - Prashansa Agrawal
- College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
| | - Reena Chawla
- BIO5 Institute, University of Arizona, Tucson, Arizona 85721, United States
| | - Danzhou Yang
- College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
- University of Arizona Cancer Center, University of Arizona, Tucson, Arizona 85724, United States
- BIO5 Institute, University of Arizona, Tucson, Arizona 85721, United States
| | - Laurence H. Hurley
- College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
- University of Arizona Cancer Center, University of Arizona, Tucson, Arizona 85724, United States
- BIO5 Institute, University of Arizona, Tucson, Arizona 85721, United States
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10
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Kerkour A, Marquevielle J, Ivashchenko S, Yatsunyk LA, Mergny JL, Salgado GF. High-resolution three-dimensional NMR structure of the KRAS proto-oncogene promoter reveals key features of a G-quadruplex involved in transcriptional regulation. J Biol Chem 2017; 292:8082-8091. [PMID: 28330874 DOI: 10.1074/jbc.m117.781906] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 03/15/2017] [Indexed: 12/13/2022] Open
Abstract
Non-canonical base pairing within guanine-rich DNA and RNA sequences can produce G-quartets, whose stacking leads to the formation of a G-quadruplex (G4). G4s can coexist with canonical duplex DNA in the human genome and have been suggested to suppress gene transcription, and much attention has therefore focused on studying G4s in promotor regions of disease-related genes. For example, the human KRAS proto-oncogene contains a nuclease-hypersensitive element located upstream of the major transcription start site. The KRAS nuclease-hypersensitive element (NHE) region contains a G-rich element (22RT; 5'-AGGGCGGTGTGGGAATAGGGAA-3') and encompasses a Myc-associated zinc finger-binding site that regulates KRAS transcription. The NEH region therefore has been proposed as a target for new drugs that control KRAS transcription, which requires detailed knowledge of the NHE structure. In this study, we report a high-resolution NMR structure of the G-rich element within the KRAS NHE. We found that the G-rich element forms a parallel structure with three G-quartets connected by a four-nucleotide loop and two short one-nucleotide double-chain reversal loops. In addition, a thymine bulge is found between G8 and G9. The loops of different lengths and the presence of a bulge between the G-quartets are structural elements that potentially can be targeted by small chemical ligands that would further stabilize the structure and interfere or block transcriptional regulators such as Myc-associated zinc finger from accessing their binding sites on the KRAS promoter. In conclusion, our work suggests a possible new route for the development of anticancer agents that could suppress KRAS expression.
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Affiliation(s)
- Abdelaziz Kerkour
- From the Université Bordeaux, INSERM, CNRS, ARNA laboratory, European Institute of Chemistry and Biology, U1212, UMR 5320, 2 Rue Robert Escarpit, 33000 Pessac, France and
| | - Julien Marquevielle
- From the Université Bordeaux, INSERM, CNRS, ARNA laboratory, European Institute of Chemistry and Biology, U1212, UMR 5320, 2 Rue Robert Escarpit, 33000 Pessac, France and
| | - Stefaniia Ivashchenko
- From the Université Bordeaux, INSERM, CNRS, ARNA laboratory, European Institute of Chemistry and Biology, U1212, UMR 5320, 2 Rue Robert Escarpit, 33000 Pessac, France and
| | - Liliya A Yatsunyk
- From the Université Bordeaux, INSERM, CNRS, ARNA laboratory, European Institute of Chemistry and Biology, U1212, UMR 5320, 2 Rue Robert Escarpit, 33000 Pessac, France and.,Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania 19081
| | - Jean-Louis Mergny
- From the Université Bordeaux, INSERM, CNRS, ARNA laboratory, European Institute of Chemistry and Biology, U1212, UMR 5320, 2 Rue Robert Escarpit, 33000 Pessac, France and
| | - Gilmar F Salgado
- From the Université Bordeaux, INSERM, CNRS, ARNA laboratory, European Institute of Chemistry and Biology, U1212, UMR 5320, 2 Rue Robert Escarpit, 33000 Pessac, France and
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11
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Lipid-modified G4-decoy oligonucleotide anchored to nanoparticles: delivery and bioactivity in pancreatic cancer cells. Sci Rep 2016; 6:38468. [PMID: 27929127 PMCID: PMC5144097 DOI: 10.1038/srep38468] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 11/10/2016] [Indexed: 12/28/2022] Open
Abstract
KRAS is mutated in >90% of pancreatic ductal adenocarcinomas. As its inactivation leads to tumour regression, mutant KRAS is considered an attractive target for anticancer drugs. In this study we report a new delivery strategy for a G4-decoy oligonucleotide that sequesters MAZ, a transcription factor essential for KRAS transcription. It is based on the use of palmitoyl-oleyl-phosphatidylcholine (POPC) liposomes functionalized with lipid-modified G4-decoy oligonucleotides and a lipid-modified cell penetrating TAT peptide. The potency of the strategy in pancreatic cancer cells is demonstrated by cell cytometry, confocal microscopy, clonogenic and qRT-PCR assays.
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12
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Critical role of hnRNP A1 in activating KRAS transcription in pancreatic cancer cells: A molecular mechanism involving G4 DNA. Biochim Biophys Acta Gen Subj 2016; 1861:1389-1398. [PMID: 27888145 DOI: 10.1016/j.bbagen.2016.11.031] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 11/17/2016] [Accepted: 11/20/2016] [Indexed: 01/31/2023]
Abstract
KRAS is one of the most mutated genes in human cancer. Its crucial role in the tumourigenesis of pancreatic ductal adenocarcinoma (PDAC) has been widely demonstrated. As this deadly cancer does not sufficiently respond to conventional chemotherapies, it is important to increase our knowledge of pancreatic cancer biology, in particular how oncogenic KRAS is regulated. The promoter of KRAS contains a GA-element composed of runs of guanines that fold into a G4 structure. This unusual DNA conformation is recognized by several nuclear proteins, including MAZ and hnRNP A1. Recent data have revealed that KRAS is interconnected to ILK and hnRNP A1 in a circuitry that enables pancreatic cancer cells to maintain an aggressive phenotype. The present review illustrates recent advances on how KRAS is regulated in pancreatic cancer cells, focusing on the formation of G4 structures in the KRAS promoter and their interaction with hnRNP A1. The newly discovered KRAS-ILK-hnRNP A1 regulatory loop is discussed, emphasizing its potential as a therapeutic target for PDAC-specific molecules. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.
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13
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Cogoi S, Xodo LE. G4 DNA in ras genes and its potential in cancer therapy. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:663-74. [PMID: 26855080 DOI: 10.1016/j.bbagrm.2016.02.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 01/24/2016] [Accepted: 02/02/2016] [Indexed: 02/07/2023]
Abstract
It is now well established that in the human genome the canonical double helix coexists with folded G-quadruplex structures that are known to have important biological functions. In this review we summarize the current knowledge on quadruplex formation in the promoters of the ras genes that are mutated in about 30% of all human cancers. We describe the nuclear proteins that recognize these unusual DNA structures and discuss their function in transcription. We also examine the formation of G-quadruplexes in the 5'-untranslated region of the ras transcripts and conclude this review by reporting strategies that use either ras G-quadruplexes or proteins recognizing the ras G-quadruplexes as targets of anticancer small molecules.
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Affiliation(s)
- Susanna Cogoi
- Department of Medical and Biological Sciences, University of Udine, P.le Kolbe 4, 33100 Udine, Italy.
| | - Luigi E Xodo
- Department of Medical and Biological Sciences, University of Udine, P.le Kolbe 4, 33100 Udine, Italy.
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14
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Podbevšek P, Plavec J. KRAS promoter oligonucleotide with decoy activity dimerizes into a unique topology consisting of two G-quadruplex units. Nucleic Acids Res 2015; 44:917-25. [PMID: 26656490 PMCID: PMC4737153 DOI: 10.1093/nar/gkv1359] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 11/23/2015] [Indexed: 12/31/2022] Open
Abstract
Mutations of the KRAS proto-oncogene are associated with several tumor types, which is why it is being considered as a target for anti-cancer drug development. The human KRAS promoter contains a nuclease hypersensitive element (NHE), which can bind to nuclear proteins and is believed to form G-quadruplex structures. Previous studies showed that a 32-nt oligonucleotide (32R-3n) mimicking the KRAS NHE can reduce gene transcription by sequestering MAZ, a crucial transcription factor. Here we show that 32R-3n has to dimerize in order to fold into a G-quadruplex structure. Individual 5′- and 3′-end G-quadruplex units are formed and both feature a symmetric head-to-head topology with edge-type loops. The MAZ binding sequence is located within the 3′-end unit. Nuclear magnetic resonance data complemented by CD and UV spectra show that nucleotides of the MAZ binding G-rich motif are dynamic and could be available for sequence or structure based recognition. Both stable G-quadruplex structures could protect 5′- and 3′-ends of 32R-3n and enhance its anti-cancer activity. Single stranded genomic KRAS NHE including nucleotides flanking the 32R-3n sequence could favor a different monomeric fold, which remains unknown.
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Affiliation(s)
- Peter Podbevšek
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia EN-FIST Centre of Excellence, Trg OF 13, SI-1000 Ljubljana, Slovenia
| | - Janez Plavec
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia EN-FIST Centre of Excellence, Trg OF 13, SI-1000 Ljubljana, Slovenia Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
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15
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Morgan RK, Batra H, Gaerig VC, Hockings J, Brooks TA. Identification and characterization of a new G-quadruplex forming region within the kRAS promoter as a transcriptional regulator. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:235-45. [PMID: 26597160 DOI: 10.1016/j.bbagrm.2015.11.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 11/13/2015] [Accepted: 11/17/2015] [Indexed: 10/22/2022]
Abstract
kRAS is one of the most prevalent oncogenic aberrations. It is either upregulated or mutationally activated in a multitude of cancers, including pancreatic, lung, and colon cancers. While a significant effort has been made to develop drugs that target kRAS, their clinical activity has been disappointing due to a variety of mechanistic hurdles. The presented works describe a novel mechanism and molecular target to downregulate kRAS expression--a previously undescribed G-quadruplex (G4) secondary structure within the proximal promoter acting as a transcriptional silencer. There are three distinct guanine-rich regions within the core kRAS promoter, including a previously examined region (G4near). Of these regions, the most distal region does not form an inducible and stable structure, whereas the two more proximal regions (termed near and mid) do form strong G4s. G4near is predominantly a tri-stacked structure with a discontinuous guanine run incorporated; G4mid consists of seven distinct runs of continuous guanines and forms numerous competing isoforms, including a stable three-tetrad stacked mixed parallel and antiparallel loop structures with longer loops of up to 10 nucleotides. Comprehensive analysis of the regulation of transcription by higher order structures has revealed that the guanine-rich region in the middle of the core promoter, termed G4mid, is a stronger repressor of promoter activity than G4near. Using the extensive guanine-rich region of the kRAS core promoter, and particularly the G4mid structure, as the primary target, future drug discovery programs will have potential to develop a potent, specifically targeted small molecule to be used in the treatment of pancreatic, ovarian, lung, and colon cancers.
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Affiliation(s)
- Rhianna K Morgan
- School of Pharmacy, Department of BioMolecular Sciences, Division of Pharmacology, University of Mississippi, University, MS 38677, USA
| | - Harshul Batra
- School of Pharmacy, Department of BioMolecular Sciences, Division of Pharmacology, University of Mississippi, University, MS 38677, USA
| | - Vanessa C Gaerig
- College of Pharmacy, Department of Pharmacology and Toxicology, The University of Arizona, Tucson, AZ 85721, USA
| | - Jennifer Hockings
- School of Pharmacy, Department of BioMolecular Sciences, Division of Pharmacology, University of Mississippi, University, MS 38677, USA
| | - Tracy A Brooks
- School of Pharmacy, Department of BioMolecular Sciences, Division of Pharmacology, University of Mississippi, University, MS 38677, USA.
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16
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Brito H, Martins AC, Lavrado J, Mendes E, Francisco AP, Santos SA, Ohnmacht SA, Kim NS, Rodrigues CMP, Moreira R, Neidle S, Borralho PM, Paulo A. Targeting KRAS Oncogene in Colon Cancer Cells with 7-Carboxylate Indolo[3,2-b]quinoline Tri-Alkylamine Derivatives. PLoS One 2015; 10:e0126891. [PMID: 26024321 PMCID: PMC4449006 DOI: 10.1371/journal.pone.0126891] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 04/08/2015] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND A guanine-rich strand within the promoter of the KRAS gene can fold into an intra-molecular G-quadruplex structure (G4), which has an important role in the regulation of KRAS transcription. We have previously identified indolo[3,2-b]quinolines with a 7-carboxylate group and three alkylamine side chains (IQ3A) as effective G4 stabilizers and promising selective anticancer leads. Herein we investigated the anticancer mechanism of action of these compounds, which we hypothesized due to stabilization of the G4 sequence in the KRAS promoter and subsequent down-regulation of gene expression. METHODOLOGY/PRINCIPAL FINDINGS IQ3A compounds showed greater stabilization of G4 compared to duplex DNA structures and reduced KRAS promoter activity in a dual luciferase reporter assay. Moreover, IQ3A compounds showed high anti-proliferative activity in HCT116 and SW620 colon cancer cells (IC50 < 2.69 μM), without eliciting cell death in non-malignant HEK293T human embryonic kidney, and human colon fibroblasts CCD18co. IQ3A compounds significantly reduced KRAS mRNA and protein steady-state levels at IC50 concentrations, and increased p53 protein steady-state levels and cell death by apoptosis in HCT116 cells (mut KRAS, wt p53). Furthermore, KRAS silencing in HCT116 p53 wild-type (p53(+/+)) and null (p53(-/-)) isogenic cell lines induced a higher level of cell death, and a higher IQ3A-induced cell death in HCT116 p53(+/+) compared to HCT116 p53(-/-). CONCLUSIONS Herein we provide evidence that G4 ligands such as IQ3A compounds can target G4 motifs present in KRAS promoter, down-regulate the expression of the mutant KRAS gene through inhibition of transcription and translation, and induce cell death by apoptosis in colon cancer cell lines. Thus, targeting KRAS at the genomic level with G4 ligands may be a new anticancer therapy strategy for colon cancer.
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Affiliation(s)
- Hugo Brito
- Cell Function and Therapeutic Targeting Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Ana Cláudia Martins
- Medicinal Chemistry Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - João Lavrado
- Medicinal Chemistry Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Eduarda Mendes
- Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Ana Paula Francisco
- Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Sofia A. Santos
- Medicinal Chemistry Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA 02114, United States of America
| | - Stephan A. Ohnmacht
- UCL School of Pharmacy, University College London, 29/39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Nam-Soon Kim
- Medical Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-333, Republic of Korea
| | - Cecília M. P. Rodrigues
- Cell Function and Therapeutic Targeting Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Rui Moreira
- Medicinal Chemistry Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Stephen Neidle
- UCL School of Pharmacy, University College London, 29/39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Pedro M. Borralho
- Cell Function and Therapeutic Targeting Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
- * E-mail: (PMB); (AP)
| | - Alexandra Paulo
- Medicinal Chemistry Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
- * E-mail: (PMB); (AP)
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17
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Lavrado J, Brito H, Borralho PM, Ohnmacht SA, Kim NS, Leitão C, Pisco S, Gunaratnam M, Rodrigues CMP, Moreira R, Neidle S, Paulo A. KRAS oncogene repression in colon cancer cell lines by G-quadruplex binding indolo[3,2-c]quinolines. Sci Rep 2015; 5:9696. [PMID: 25853628 PMCID: PMC5382548 DOI: 10.1038/srep09696] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Accepted: 03/05/2015] [Indexed: 01/29/2023] Open
Abstract
KRAS is one of the most frequently mutated oncogenes in human cancer, yet remaining undruggable. To explore a new therapeutic strategy, a library of 5-methyl-indolo[3,2-c]quinoline derivatives (IQc) with a range of alkyldiamine side chains was designed to target DNA and RNA G-quadruplexes (G4) in the promoter and 5′-UTR mRNA of the KRAS gene. Biophysical experiments showed that di-substituted IQc compounds are potent and selective KRAS G4 stabilizers. They preferentially inhibit the proliferation of KRAS mutant cancer cell lines (0.22 < IC50 < 4.80 μM), down-regulate KRAS promoter activity in a luciferase reporter assay, and reduce both KRAS mRNA and p21KRAS steady-state levels in mutant KRAS colon cancer cell lines. Additionally, IQcs induce cancer cell death by apoptosis, explained in part by their capacity to repress KRAS expression. Overall, the results suggest that targeting mutant KRAS at the gene level with G4 binding small molecules is a promising anticancer strategy.
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Affiliation(s)
- João Lavrado
- Medicinal Chemistry Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Hugo Brito
- Cell Function and Therapeutic Targeting Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Pedro M Borralho
- Cell Function and Therapeutic Targeting Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Stephan A Ohnmacht
- The School of Pharmacy, University College London. 29/39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Nam-Soon Kim
- Medical Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-333, Republic of Korea
| | - Clara Leitão
- The School of Pharmacy, University College London. 29/39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Sílvia Pisco
- The School of Pharmacy, University College London. 29/39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Mekala Gunaratnam
- The School of Pharmacy, University College London. 29/39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Cecília M P Rodrigues
- Cell Function and Therapeutic Targeting Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Rui Moreira
- Medicinal Chemistry Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Stephen Neidle
- The School of Pharmacy, University College London. 29/39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Alexandra Paulo
- Medicinal Chemistry Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
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18
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Lavrado J, Borralho PM, Ohnmacht SA, Castro RE, Rodrigues CMP, Moreira R, dos Santos DJVA, Neidle S, Paulo A. Synthesis, G-quadruplex stabilisation, docking studies, and effect on cancer cells of indolo[3,2-b]quinolines with one, two, or three basic side chains. ChemMedChem 2013; 8:1648-61. [PMID: 23960016 DOI: 10.1002/cmdc.201300288] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Indexed: 11/07/2022]
Abstract
G-quadruplex (G4) DNA structures in telomeres and oncogenic promoter regions are potential targets for cancer therapy, and G4 ligands have been shown to modulate telomerase activity and oncogene transcription. Herein we report the synthesis and G4 thermal stabilisation effects, determined by FRET melting assays, of 20 indolo[3,2-b]quinolines mono-, di-, and trisubstituted with basic side chains. Molecular modelling studies were also performed in an attempt to rationalise the ligands' binding poses with G4. Overall, the results suggest that ligand binding and G4 DNA thermal stabilisation increase with an N5-methyl or a 7-carboxylate group and propylamine side chains, whereas selectivity between G4 and duplex DNA appears to be modulated by the number and relative position of basic side chains. From all the indoloquinoline derivatives studied, the novel trisubstituted compounds 3 d and 4 d, bearing a 7-(aminoalkyl)carboxylate side chain, stand out as the most promising compounds; they show high G4 thermal stabilisation (ΔTm values between 17 and 8 °C) with an inter-G4 ΔTm trend of Hsp90A>KRas21R≈F21T>c-Kit2, 10-fold selectivity for G4 over duplex DNA, and 100-fold selectivity for the HCT116 cancer cell line (IC50 and IC90: <10 μM) over primary rat hepatocytes. Compounds 3 d and 4 d also decreased protein expression levels of Hsp90 and KRas in HCT116 cancer cells.
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Affiliation(s)
- João Lavrado
- Medicinal Chemistry Group, Research Institute for Medicines and Pharmaceutical Sciences, Faculty of Pharmacy, University of Lisbon, Av. Prof. Gama Pinto, 1649-003 Lisbon (Portugal)
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19
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Cogoi S, Zorzet S, Rapozzi V, Géci I, Pedersen EB, Xodo LE. MAZ-binding G4-decoy with locked nucleic acid and twisted intercalating nucleic acid modifications suppresses KRAS in pancreatic cancer cells and delays tumor growth in mice. Nucleic Acids Res 2013; 41:4049-64. [PMID: 23471001 PMCID: PMC3627599 DOI: 10.1093/nar/gkt127] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
KRAS mutations are primary genetic lesions leading to pancreatic cancer. The promoter of human KRAS contains a nuclease-hypersensitive element (NHE) that can fold in G4-DNA structures binding to nuclear proteins, including MAZ (myc-associated zinc-finger). Here, we report that MAZ activates KRAS transcription. To knockdown oncogenic KRAS in pancreatic cancer cells, we designed oligonucleotides that mimic one of the G-quadruplexes formed by NHE (G4-decoys). To increase their nuclease resistance, two locked nucleic acid (LNA) modifications were introduced at the 3'-end, whereas to enhance the folding and stability, two polycyclic aromatic hydrocarbon units (TINA or AMANY) were inserted internally, to cap the quadruplex. The most active G4-decoy (2998), which had two para-TINAs, strongly suppressed KRAS expression in Panc-1 cells. It also repressed their metabolic activity (IC50 = 520 nM), and it inhibited cell growth and colony formation by activating apoptosis. We finally injected 2998 and control oligonucleotides 5153, 5154 (2 nmol/mouse) intratumorally in SCID mice bearing a Panc-1 xenograft. After three treatments, 2998 reduced tumor xenograft growth by 64% compared with control and increased the Kaplan-Meier median survival time by 70%. Together, our data show that MAZ-specific G4-decoys mimicking a KRAS quadruplex are promising for pancreatic cancer therapy.
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Affiliation(s)
- Susanna Cogoi
- Department of Medical and Biological Sciences, School of Medicine, P.le Kolbe 4, 33100 Udine, Italy
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