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Clowes SR, Ali Y, Astley OR, Răsădean DM, Pantoş GD. The Influence of Chirality on the β-Amino-Acid Naphthalenediimides/G-Quadruplex DNA Interaction. Molecules 2023; 28:7291. [PMID: 37959711 PMCID: PMC10647805 DOI: 10.3390/molecules28217291] [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: 09/05/2023] [Revised: 10/23/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
G-quadruplexes (G4s) have been identified as a potential alternative chemotherapy target. A series of eight β-amino acid derived naphthalenediimides (NDI) were screened against a series of oncogenic G4 sequences: c-KIT1, h-TELO, and TBA. Three sets of enantiomers were investigated to further our understanding of the effect of point chirality on G4 stabilisation. Enantioselective binding behaviour was observed with both c-KIT1 and h-TELO. Docking studies using GNINA and UV-vis titrations were employed to better understand this selective binding behaviour.
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Affiliation(s)
| | | | | | | | - G. Dan Pantoş
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
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2
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Banerjee N, Chatterjee O, Roychowdhury T, Basu D, Dutta A, Chowdhury M, Dastidar SG, Chatterjee S. Sequence driven interaction of amino acids in de-novo designed peptides determines c-Myc G-quadruplex unfolding inducing apoptosis in cancer cells. Biochim Biophys Acta Gen Subj 2023; 1867:130267. [PMID: 36334788 DOI: 10.1016/j.bbagen.2022.130267] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 10/21/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022]
Abstract
c-MYC proto-oncogene harbors a putative G-quadruplex structure (Pu27) at the NHEIII1 domain, which can shuffle between transcriptional inhibitor quadruplex and transcriptionally active duplex. In cancer cells this quadruplex destabilization is preferred and NHEIII1 domain assume a duplex topology thereby inducing c-MYC overexpression and tumorigenesis. Hence, the c-MYC quadruplex acts as an excellent target for anti-cancer therapy. Though researcher have tried to develop G-quadruplex targeted small molecules, work with G-quadruplex targeting peptides is very limited. Here we present a peptide that can bind to c-MYC quadruplex, destabilize the tetrad core, and permit the formation of a substantially different structure from the quartet core seen in the canonical G-quadruplexes. Such conformation potentially acted as a roadblock for transcription factors thereby reducing cMYC expression. This event sensitizes the cancer cell to activate apoptotic cascade via the c-MYC-VEGF-A-BCL2 axis. This study provides a detailed insight into the peptide-quadruplex interface that encourages better pharmacophore design to target dynamic quadruplex structure. We believe that our results will contribute to the development, characterization, and optimization of G-quadruplex binding peptides for potential clinical application.
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Affiliation(s)
- Nilanjan Banerjee
- Department of Biophysics, Bose Institute, Unified Academic campus, EN-80, Sector V, Kolkata 700091, India
| | - Oishika Chatterjee
- Department of Biophysics, Bose Institute, Unified Academic campus, EN-80, Sector V, Kolkata 700091, India
| | - Tanaya Roychowdhury
- Cancer Biology and Inflammatory Disorder Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700032, India
| | - Debadrita Basu
- Division of Bioinformatics, Bose Institute, Unified Academic campus, EN-80, Sector V, Kolkata 700091, India
| | - Anindya Dutta
- Department of Biophysics, Bose Institute, Unified Academic campus, EN-80, Sector V, Kolkata 700091, India
| | - Madhurima Chowdhury
- Department of Biophysics, Bose Institute, Unified Academic campus, EN-80, Sector V, Kolkata 700091, India
| | - Shubhra Ghosh Dastidar
- Division of Bioinformatics, Bose Institute, Unified Academic campus, EN-80, Sector V, Kolkata 700091, India
| | - Subhrangsu Chatterjee
- Department of Biophysics, Bose Institute, Unified Academic campus, EN-80, Sector V, Kolkata 700091, India.
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3
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Monsen RC, Maguire JM, DeLeeuw LW, Chaires JB, Trent JO. Drug discovery of small molecules targeting the higher-order hTERT promoter G-quadruplex. PLoS One 2022; 17:e0270165. [PMID: 35709230 PMCID: PMC9202945 DOI: 10.1371/journal.pone.0270165] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/03/2022] [Indexed: 12/15/2022] Open
Abstract
DNA G-quadruplexes (G4s) are now widely accepted as viable targets in the pursuit of anticancer therapeutics. To date, few small molecules have been identified that exhibit selectivity for G4s over alternative forms of DNA, such as the ubiquitous duplex. We posit that the lack of current ligand specificity arises for multiple reasons: G4 atomic models are often small, monomeric, single quadruplex structures with few or no druggable pockets; targeting G-tetrad faces frequently results in the enrichment of extended electron-deficient polyaromatic end-pasting scaffolds; and virtual drug discovery efforts often under-sample chemical search space. We show that by addressing these issues we can enrich for non-standard molecular templates that exhibit high selectivity towards G4s over other forms of DNA. We performed an extensive virtual screen against the higher-order hTERT core promoter G4 that we have previously characterized, targeting 12 of its unique loop and groove pockets using libraries containing 40 million drug-like compounds for each screen. Using our drug discovery funnel approach, which utilizes high-throughput fluorescence thermal shift assay (FTSA) screens, microscale thermophoresis (MST), and orthogonal biophysical methods, we have identified multiple unique G4 binding scaffolds. We subsequently used two rounds of catalogue-based SAR to increase the affinity of a disubstituted 2-aminoethyl-quinazoline that stabilizes the higher-order hTERT G-quadruplex by binding across its G4 junctional sites. We show selectivity of its binding affinity towards hTERT is virtually unaffected in the presence of near-physiological levels of duplex DNA, and that this molecule downregulates hTERT transcription in breast cancer cells.
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Affiliation(s)
- Robert C. Monsen
- UofL Health Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
| | - Jon M. Maguire
- UofL Health Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
| | - Lynn W. DeLeeuw
- UofL Health Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
| | - Jonathan B. Chaires
- UofL Health Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
- Department of Medicine, University of Louisville, Louisville, Kentucky, United States of America
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, Kentucky, United States of America
- * E-mail: (JBC); (JOT)
| | - John O. Trent
- UofL Health Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
- Department of Medicine, University of Louisville, Louisville, Kentucky, United States of America
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, Kentucky, United States of America
- * E-mail: (JBC); (JOT)
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Calatayud DG, Neophytou S, Nicodemou E, Giuffrida SG, Ge H, Pascu SI. Nano-Theranostics for the Sensing, Imaging and Therapy of Prostate Cancers. Front Chem 2022; 10:830133. [PMID: 35494646 PMCID: PMC9039169 DOI: 10.3389/fchem.2022.830133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 03/16/2022] [Indexed: 01/28/2023] Open
Abstract
We highlight hereby recent developments in the emerging field of theranostics, which encompasses the combination of therapeutics and diagnostics in a single entity aimed for an early-stage diagnosis, image-guided therapy as well as evaluation of therapeutic outcomes of relevance to prostate cancer (PCa). Prostate cancer is one of the most common malignancies in men and a frequent cause of male cancer death. As such, this overview is concerned with recent developments in imaging and sensing of relevance to prostate cancer diagnosis and therapeutic monitoring. A major advantage for the effective treatment of PCa is an early diagnosis that would provide information for an appropriate treatment. Several imaging techniques are being developed to diagnose and monitor different stages of cancer in general, and patient stratification is particularly relevant for PCa. Hybrid imaging techniques applicable for diagnosis combine complementary structural and morphological information to enhance resolution and sensitivity of imaging. The focus of this review is to sum up some of the most recent advances in the nanotechnological approaches to the sensing and treatment of prostate cancer (PCa). Targeted imaging using nanoparticles, radiotracers and biomarkers could result to a more specialised and personalised diagnosis and treatment of PCa. A myriad of reports has been published literature proposing methods to detect and treat PCa using nanoparticles but the number of techniques approved for clinical use is relatively small. Another facet of this report is on reviewing aspects of the role of functional nanoparticles in multimodality imaging therapy considering recent developments in simultaneous PET-MRI (Positron Emission Tomography-Magnetic Resonance Imaging) coupled with optical imaging in vitro and in vivo, whilst highlighting feasible case studies that hold promise for the next generation of dual modality medical imaging of PCa. It is envisaged that progress in the field of imaging and sensing domains, taken together, could benefit from the biomedical implementation of new synthetic platforms such as metal complexes and functional materials supported on organic molecular species, which can be conjugated to targeting biomolecules and encompass adaptable and versatile molecular architectures. Furthermore, we include hereby an overview of aspects of biosensing methods aimed to tackle PCa: prostate biomarkers such as Prostate Specific Antigen (PSA) have been incorporated into synthetic platforms and explored in the context of sensing and imaging applications in preclinical investigations for the early detection of PCa. Finally, some of the societal concerns around nanotechnology being used for the detection of PCa are considered and addressed together with the concerns about the toxicity of nanoparticles–these were aspects of recent lively debates that currently hamper the clinical advancements of nano-theranostics. The publications survey conducted for this review includes, to the best of our knowledge, some of the most recent relevant literature examples from the state-of-the-art. Highlighting these advances would be of interest to the biomedical research community aiming to advance the application of theranostics particularly in PCa diagnosis and treatment, but also to those interested in the development of new probes and methodologies for the simultaneous imaging and therapy monitoring employed for PCa targeting.
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Affiliation(s)
- David G. Calatayud
- Department of Chemistry, University of Bath, Bath, United Kingdom
- Department of Electroceramics, Instituto de Ceramica y Vidrio - CSIC, Madrid, Spain
- *Correspondence: Sofia I. Pascu, ; David G. Calatayud,
| | - Sotia Neophytou
- Department of Chemistry, University of Bath, Bath, United Kingdom
| | - Eleni Nicodemou
- Department of Chemistry, University of Bath, Bath, United Kingdom
| | | | - Haobo Ge
- Department of Chemistry, University of Bath, Bath, United Kingdom
| | - Sofia I. Pascu
- Department of Chemistry, University of Bath, Bath, United Kingdom
- Centre of Therapeutic Innovations, University of Bath, Bath, United Kingdom
- *Correspondence: Sofia I. Pascu, ; David G. Calatayud,
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5
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Structured Waters Mediate Small Molecule Binding to G-Quadruplex Nucleic Acids. Pharmaceuticals (Basel) 2021; 15:ph15010007. [PMID: 35056064 PMCID: PMC8781208 DOI: 10.3390/ph15010007] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 01/24/2023] Open
Abstract
The role of G-quadruplexes in human cancers is increasingly well-defined. Accordingly, G-quadruplexes can be suitable drug targets and many small molecules have been identified to date as G-quadruplex binders, some using computer-based design methods and co-crystal structures. The role of bound water molecules in the crystal structures of G-quadruplex-small molecule complexes has been analyzed in this study, focusing on the water arrangements in several G-quadruplex ligand complexes. One is the complex between the tetrasubstituted naphthalene diimide compound MM41 and a human intramolecular telomeric DNA G-quadruplex, and the others are in substituted acridine bimolecular G-quadruplex complexes. Bridging water molecules form most of the hydrogen-bond contacts between ligands and DNA in the parallel G-quadruplex structures examined here. Clusters of structured water molecules play essential roles in mediating between ligand side chain groups/chromophore core and G-quadruplex. These clusters tend to be conserved between complex and native G-quadruplex structures, suggesting that they more generally serve as platforms for ligand binding, and should be taken into account in docking and in silico studies.
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6
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Sanchez-Martin V, Schneider DA, Ortiz-Gonzalez M, Soriano-Lerma A, Linde-Rodriguez A, Perez-Carrasco V, Gutierrez-Fernandez J, Cuadros M, González C, Soriano M, Garcia-Salcedo JA. Targeting ribosomal G-quadruplexes with naphthalene-diimides as RNA polymerase I inhibitors for colorectal cancer treatment. Cell Chem Biol 2021; 28:1590-1601.e4. [PMID: 34166611 DOI: 10.1016/j.chembiol.2021.05.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/05/2021] [Accepted: 05/27/2021] [Indexed: 12/11/2022]
Abstract
Guanine quadruplexes (G4s) are non-canonical nucleic acid structures commonly found in regulatory genomic regions. G4 targeting has emerged as a therapeutic approach in cancer. We have screened naphthalene-diimides (NDIs), a class of G4 ligands, in a cellular model of colorectal cancer (CRC). Here, we identify the leading compound T5 with a potent and selective inhibition of cell growth by high-affinity binding to G4s in ribosomal DNA, impairing RNA polymerase I (Pol I) elongation. Consequently, T5 induces a rapid inhibition of Pol I transcription, nucleolus disruption, proteasome-dependent Pol I catalytic subunit A degradation and autophagy. Moreover, we attribute the higher selectivity of carbohydrate-conjugated T5 for tumoral cells to its preferential uptake through the overexpressed glucose transporter 1. Finally, we succinctly demonstrate that T5 could be explored as a therapeutic agent in a patient cohort with CRC. Therefore, we report a mode of action for these NDIs involving ribosomal G4 targeting.
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Affiliation(s)
- Victoria Sanchez-Martin
- GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, Granada 18016, Spain; Microbiology Unit, Biosanitary Research Institute IBS.Granada, University Hospital Virgen de las Nieves, Granada 18014, Spain; Department of Biochemistry, Molecular Biology III and Immunology, University of Granada, Granada 18016, Spain
| | - David A Schneider
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Matilde Ortiz-Gonzalez
- GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, Granada 18016, Spain; Centre for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAIMBITAL), University of Almeria, Almeria 04001, Spain
| | - Ana Soriano-Lerma
- GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, Granada 18016, Spain; Department of Physiology, University of Granada, Granada 18011, Spain
| | - Angel Linde-Rodriguez
- GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, Granada 18016, Spain; Microbiology Unit, Biosanitary Research Institute IBS.Granada, University Hospital Virgen de las Nieves, Granada 18014, Spain
| | - Virginia Perez-Carrasco
- GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, Granada 18016, Spain; Microbiology Unit, Biosanitary Research Institute IBS.Granada, University Hospital Virgen de las Nieves, Granada 18014, Spain
| | - Jose Gutierrez-Fernandez
- Microbiology Unit, Biosanitary Research Institute IBS.Granada, University Hospital Virgen de las Nieves, Granada 18014, Spain; Department of Microbiology, University of Granada, Granada 18011, Spain
| | - Marta Cuadros
- GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, Granada 18016, Spain; Department of Biochemistry, Molecular Biology III and Immunology, University of Granada, Granada 18016, Spain
| | - Carlos González
- Instituto de Química Física "Rocasolano", CSIC, Madrid 28006, Spain
| | - Miguel Soriano
- GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, Granada 18016, Spain; Centre for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAIMBITAL), University of Almeria, Almeria 04001, Spain
| | - Jose A Garcia-Salcedo
- GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, Granada 18016, Spain; Microbiology Unit, Biosanitary Research Institute IBS.Granada, University Hospital Virgen de las Nieves, Granada 18014, Spain.
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7
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Santos T, Salgado GF, Cabrita EJ, Cruz C. G-Quadruplexes and Their Ligands: Biophysical Methods to Unravel G-Quadruplex/Ligand Interactions. Pharmaceuticals (Basel) 2021; 14:769. [PMID: 34451866 PMCID: PMC8401999 DOI: 10.3390/ph14080769] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 07/31/2021] [Accepted: 08/03/2021] [Indexed: 12/12/2022] Open
Abstract
Progress in the design of G-quadruplex (G4) binding ligands relies on the availability of approaches that assess the binding mode and nature of the interactions between G4 forming sequences and their putative ligands. The experimental approaches used to characterize G4/ligand interactions can be categorized into structure-based methods (circular dichroism (CD), nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography), affinity and apparent affinity-based methods (surface plasmon resonance (SPR), isothermal titration calorimetry (ITC) and mass spectrometry (MS)), and high-throughput methods (fluorescence resonance energy transfer (FRET)-melting, G4-fluorescent intercalator displacement assay (G4-FID), affinity chromatography and microarrays. Each method has unique advantages and drawbacks, which makes it essential to select the ideal strategies for the biological question being addressed. The structural- and affinity and apparent affinity-based methods are in several cases complex and/or time-consuming and can be combined with fast and cheap high-throughput approaches to improve the design and development of new potential G4 ligands. In recent years, the joint use of these techniques permitted the discovery of a huge number of G4 ligands investigated for diagnostic and therapeutic purposes. Overall, this review article highlights in detail the most commonly used approaches to characterize the G4/ligand interactions, as well as the applications and types of information that can be obtained from the use of each technique.
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Affiliation(s)
- Tiago Santos
- CICS-UBI—Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal;
| | - Gilmar F. Salgado
- ARNA Laboratory, Université de Bordeaux, Inserm U1212, CNRS UMR 5320, IECB, 33607 Pessac, France;
| | - Eurico J. Cabrita
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal;
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
| | - Carla Cruz
- CICS-UBI—Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal;
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8
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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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9
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Lousen B, Pedersen SK, Răsădean DM, Pantoş GD, Pittelkow M. Triggering G-Quadruplex Conformation Switching with [7]Helicenes. Chemistry 2021; 27:6064-6069. [PMID: 33326174 DOI: 10.1002/chem.202004990] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Indexed: 12/14/2022]
Abstract
The dynamic interplay between two types of chiral structures; fully conjugated racemic hetero[7]helicenes and DNA strands prone to fold into G-quadruplex structures is described. Both the [7]helicenes and the G-quadruplex DNA structures exist in more than one conformation in solution. We show that the structures interact with and stabilise each other, mutually amplifying and stabilising certain conformations at increased temperatures. The [7]helicene ligands L1 and L2 stabilise the parallel conformation of k-ras significantly, whereas hybrid (K+ ) and antiparallel (Na+ ) h-telo G-quadruplexes are stabilised upon conformational switching into altered G-quadruplex conformations. Both L1 and L2 induce parallel G-quadruplexes from hybrid structures (K+ ) and L1 induces hybrid G-quadruplexes from antiparallel conformations (Na+ ). Enantioselective binding of one helicene enantiomer is observed for helicene ligand L2, and VTCD melting experiments are used to estimate the racemisation barrier of the helicene.
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Affiliation(s)
- Bodil Lousen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
| | - Stephan K Pedersen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
| | - Dora M Răsădean
- Department of Chemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - G Dan Pantoş
- Department of Chemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Michael Pittelkow
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
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10
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Andreeva DV, Tikhomirov AS, Shchekotikhin AE. Ligands of G-quadruplex nucleic acids. RUSSIAN CHEMICAL REVIEWS 2021. [DOI: 10.1070/rcr4968] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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11
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Zhirov AM, Kovalev DA, Ulshina DV, Pisarenko SV, Demidov OP, Borovlev IV. Diazapyrenes: interaction with nucleic acids and biological activity. Chem Heterocycl Compd (N Y) 2020; 56:674-693. [PMID: 32836316 PMCID: PMC7366485 DOI: 10.1007/s10593-020-02717-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 11/26/2019] [Indexed: 12/22/2022]
Abstract
The review summarizes data on the practical aspects of the interaction of nucleic acids with diazapyrene derivatives. The information on biological activity is given and the probable mechanisms underlying the action of diazapyrenes are analyzed. It contains 119 references.
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Affiliation(s)
- Andrey M. Zhirov
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya St, Stavropol, 355035 Russia
| | - Dmitry A. Kovalev
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya St, Stavropol, 355035 Russia
| | - Diana V. Ulshina
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya St, Stavropol, 355035 Russia
| | - Sergey V. Pisarenko
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya St, Stavropol, 355035 Russia
| | - Oleg P. Demidov
- North Caucasus Federal University, 1a Pushkina St, Stavropol, 355017 Russia
| | - Ivan V. Borovlev
- North Caucasus Federal University, 1a Pushkina St, Stavropol, 355017 Russia
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12
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Fik-Jaskółka MA, Mkrtchyan AF, Saghyan AS, Palumbo R, Belter A, Hayriyan LA, Simonyan H, Roviello V, Roviello GN. Spectroscopic and SEM evidences for G4-DNA binding by a synthetic alkyne-containing amino acid with anticancer activity. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 229:117884. [PMID: 31927477 DOI: 10.1016/j.saa.2019.117884] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/26/2019] [Accepted: 12/01/2019] [Indexed: 06/10/2023]
Abstract
Herein, we present a spectroscopic (CD and UV) and SEM study of a phenylalanine derivative carrying a terminal alkyne moiety and indicated by us CF3IIIPhe, with particular attention to its interaction with Cu(II) cation and some biological macromolecules, as well as a preliminary evaluation of its effect on cancerous cells. CD spectroscopy evidenced the ability of CF3IIIPhe to interact with tel26 and c-myc, two quadruplex DNA (G4 DNA) models explored in this study. Other CD and UV studies revealed the ability of the unnatural amino acid to form aggregates in aqueous solution, to bind Cu(II) cation, and to interact with bovine serum albumin (BSA). Cellular studies demonstrated CF3IIIPhe antiproliferative activity on PC3 cells. Its ability to bind telomeric DNA was verified with tel26 by CD investigation and SEM analysis, that revealed a noteworthy change in DNA morphology (mainly based on nanosphere structures) by CF3IIIPhe, confirming its G4-DNA binding ability already evidenced by spectroscopy.
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Affiliation(s)
- Marta A Fik-Jaskółka
- Department of Bioinorganic Chemistry, Faculty of Chemistry, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego Str. 8, 61-614 Poznan, Poland; Centre for Advanced Technologies, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego Str. 10, 61-614 Poznań, Poland; Istituto di Biostrutture e Bioimmagini IBB - CNR, Via Mezzocannone 16, I-80134 Naples, Italy
| | - Anna F Mkrtchyan
- Scientific and Production Center "Armbiotechnology" of NAS RA, 14 Gyurjyan Str., 0056 Yerevan, Armenia; Institute of Pharmacy, Yerevan State University, 1 Alex Manoogian Str., 0025 Yerevan, Armenia
| | - Ashot S Saghyan
- Scientific and Production Center "Armbiotechnology" of NAS RA, 14 Gyurjyan Str., 0056 Yerevan, Armenia; Institute of Pharmacy, Yerevan State University, 1 Alex Manoogian Str., 0025 Yerevan, Armenia
| | - Rosanna Palumbo
- Istituto di Biostrutture e Bioimmagini IBB - CNR, Via Mezzocannone 16, I-80134 Naples, Italy
| | - Agnieszka Belter
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Liana A Hayriyan
- Scientific and Production Center "Armbiotechnology" of NAS RA, 14 Gyurjyan Str., 0056 Yerevan, Armenia; Institute of Pharmacy, Yerevan State University, 1 Alex Manoogian Str., 0025 Yerevan, Armenia
| | - Hayarpi Simonyan
- Institute of Pharmacy, Yerevan State University, 1 Alex Manoogian Str., 0025 Yerevan, Armenia
| | - Valentina Roviello
- Department of Chemical, Materials and Industrial Production Engineering (DICMaPI), University of Naples Federico II, Piazzale V. Tecchio 80, 80125 Naples, Italy
| | - Giovanni N Roviello
- Istituto di Biostrutture e Bioimmagini IBB - CNR, Via Mezzocannone 16, I-80134 Naples, Italy.
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13
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Dhamodharan V, Pradeepkumar PI. Specific Recognition of Promoter G-Quadruplex DNAs by Small Molecule Ligands and Light-up Probes. ACS Chem Biol 2019; 14:2102-2114. [PMID: 31532996 DOI: 10.1021/acschembio.9b00475] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
G-Quadruplexes (G4s) are four-stranded nucleic acid structures whose underlying G-rich sequences are present across the chromosome and transcriptome. These highly structured elements are known to regulate many key biological functions such as replication, transcription, translation, and genomic stability, thereby providing an additional layer of gene regulation. G4s are structurally dynamic and diverse, and they can fold into numerous topologies. They are potential targets for small molecules, which can modulate their functions. To this end, myriad classes of small molecules have been developed and studied for their ability to bind and stabilize these unique structures. Though many of them can selectively target G4s over duplex DNA, only a few of them can distinguish one G4 topology from others. Design and development of G4-specific ligands are challenging owing to the subtle structural variations among G4 structures. However, screening assays and computational methods have identified a few classes of ligands that preferentially or specifically target the G4 topology of interest over others. This review focuses on the small molecules and fluorescent probes that specifically target human promoter G4s associated with oncogenes. Targeting promoter G4s could circumvent the issues such as undruggability and development of drug resistance associated with the protein targets. The ligands discussed here highlight that development of G4-specific ligands is an achievable goal in spite of the limited structural data available. The future goal is to pursue the development of G4-specific ligands endowed with drug-like properties for G4-based therapeutics and diagnostics.
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Affiliation(s)
- V. Dhamodharan
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
- Okinawa Institute of Science and Technology Graduate University, Okinawa 9040495, Japan
| | - P. I. Pradeepkumar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
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14
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Pathak P, Yao W, Hook KD, Vik R, Winnerdy FR, Brown JQ, Gibb BC, Pursell ZF, Phan AT, Jayawickramarajah J. Bright G-Quadruplex Nanostructures Functionalized with Porphyrin Lanterns. J Am Chem Soc 2019; 141:12582-12591. [PMID: 31322869 DOI: 10.1021/jacs.9b03250] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The intricate arrangement of numerous and closely placed chromophores on nanoscale scaffolds can lead to key photonic applications ranging from optical waveguides and antennas to signal-enhanced fluorescent sensors. In this regard, the self-assembly of dye-appended DNA sequences into programmed photonic architectures is promising. However, the dense packing of dyes can result in not only compromised DNA assembly (leading to ill-defined structures and precipitates) but also to essentially nonfluorescent systems (due to π-π aggregation). Here, we introduce a two-step "tether and mask" strategy wherein large porphyrin dyes are first attached to short G-quadruplex-forming sequences and then reacted with per-O-methylated β-cyclodextrin (PMβCD) caps, to form supramolecular synthons featuring the porphyrin fluor fixed into a masked porphyrin lantern (PL) state, due to intramolecular host-guest interactions in water. The PL-DNA sequences can then be self-assembled into cyclic architectures or unprecedented G-wires tethered with hundreds of porphyrin dyes. Importantly, despite the closely arrayed PL units (∼2 nm), the dyes behave as bright chromophores (up to 180-fold brighter than the analogues lacking the PMβCD masks). Since other self-assembling scaffolds, dyes, and host molecules can be used in this modular approach, this work lays out a general strategy for the bottom-up aqueous self-assembly of bright nanomaterials containing densely packed dyes.
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Affiliation(s)
- Pravin Pathak
- Department of Chemistry , Tulane University , 2015 Percival Stern Hall , New Orleans , Louisiana 70118 , United States
| | - Wei Yao
- Department of Chemistry , Tulane University , 2015 Percival Stern Hall , New Orleans , Louisiana 70118 , United States
| | - Katherine Delaney Hook
- Department of Biochemistry and Molecular Biology , Tulane University , New Orleans , Louisiana 70112 , United States
| | - Ryan Vik
- Department of Chemistry , Tulane University , 2015 Percival Stern Hall , New Orleans , Louisiana 70118 , United States
| | - Fernaldo Richtia Winnerdy
- School of Physical and Mathematical Sciences , Nanyang Technological University , Singapore 637371 , Singapore
| | - Jonathon Quincy Brown
- Department of Biomedical Engineering , Tulane University , New Orleans , Louisiana 70118 , United States
| | - Bruce C Gibb
- Department of Chemistry , Tulane University , 2015 Percival Stern Hall , New Orleans , Louisiana 70118 , United States
| | - Zachary F Pursell
- Department of Biochemistry and Molecular Biology , Tulane University , New Orleans , Louisiana 70112 , United States
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences , Nanyang Technological University , Singapore 637371 , Singapore
| | - Janarthanan Jayawickramarajah
- Department of Chemistry , Tulane University , 2015 Percival Stern Hall , New Orleans , Louisiana 70118 , United States
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15
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Moghaddam KG, de Vries AH, Marrink SJ, Faraji S. Binding of quinazolinones to c-KIT G-quadruplex; an interplay between hydrogen bonding and π-π stacking. Biophys Chem 2019; 253:106220. [PMID: 31302375 DOI: 10.1016/j.bpc.2019.106220] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/04/2019] [Accepted: 07/04/2019] [Indexed: 12/18/2022]
Abstract
Stabilization of G-quadruplex structures in the c-KIT promoter with the aid of ligands has become an area of great interest in potential cancer therapeutics. Understanding the binding process between ligands and G-quadruplex is essential for a discovery of selective ligands with high binding affinity to G-quadruplex. In the present work, binding mechanisms of 4-quinazolinones to c-KIT G-quadruplex were investigated theoretically by means of molecular dynamics (MD) simulations. To explore the binding affinity of ligands, binding free energy calculations were performed using the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method. We demonstrate that the key interactions in G-quadruplex-ligand complexes are π-π stacking and hydrogen bond interactions. However, neither of these two interactions alone determines the stability of the G-quadruplex-ligand complexes; rather, it is the result of an intricate interplay between the two. To further examine the nature of the binding, a free energy decomposition analysis at residue level was carried out. The results clearly demonstrate the crucial roles of two hot spot residues (DG4 and DG8) for the binding of ligands to c-KIT G-quadruplex, and highlight the importance of the planar aromatic moiety of ligands in G-quadruplex stabilization via π-π stacking interactions. Our study can assist in the design of new derivatives of 4-quinazolinone with high binding affinity for c-KIT G-quadruplex.
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Affiliation(s)
| | - Alex H de Vries
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - Shirin Faraji
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands.
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16
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Importance of Chiral Recognition in Designing Metal-Free Ligands for G-Quadruplex DNA. Molecules 2019; 24:molecules24081473. [PMID: 30991655 PMCID: PMC6514905 DOI: 10.3390/molecules24081473] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 04/08/2019] [Accepted: 04/11/2019] [Indexed: 01/26/2023] Open
Abstract
Four pairs of amino acid-functionalized naphthalenediimide enantiomers (d- and l-lysine derived NDIs) were screened toward G-quadruplex forming sequences in telomeres (h-TELO) and oncogene promoters: c-KIT1, c-KIT2, k-RAS and BCL-2. This is the first study to address the effect of point chirality toward G-quadruplex DNA stabilization using purely small organic molecules. Enantioselective behavior toward the majority of ligands was observed, particularly in the case of parallel conformations of c-KIT2 and k-RAS. Additionally, Nε-Boc-l-Lys-NDI and Nε-Boc-d-Lys-NDI discriminate between quadruplexes with parallel and hybrid topologies, which has not previously been observed with enantiomeric ligands.
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17
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Naphthalene Diimides as Multimodal G-Quadruplex-Selective Ligands. Molecules 2019; 24:molecules24030426. [PMID: 30682828 PMCID: PMC6384834 DOI: 10.3390/molecules24030426] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 01/11/2019] [Accepted: 01/22/2019] [Indexed: 02/03/2023] Open
Abstract
G-quadruplexes are four-stranded nucleic acids structures that can form in guanine-rich sequences. Following the observation that G-quadruplexes are particularly abundant in genomic regions related to cancer, such as telomeres and oncogenes promoters, several G-quadruplex-binding molecules have been developed for therapeutic purposes. Among them, naphthalene diimide derivatives have reported versatility, consistent selectivity and high affinity toward the G-quadruplex structures. In this review, we present the chemical features, synthesis and peculiar optoelectronic properties (absorption, emission, redox) that make naphtalene diimides so versatile for biomedical applications. We present the latest developments on naphthalene diimides as G-quadruplex ligands, focusing on their ability to bind G-quadruplexes at telomeres and oncogene promoters with consequent anticancer activity. Their different binding modes (reversible versus irreversible/covalent) towards G-quadruplexes and their additional use as antimicrobial agents are also presented and discussed.
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18
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Ng AWH, Au‐Yeung HY. Molecular Links and Knots from Naphthalenediimide: A Balance of Weak Interactions. Chem Asian J 2019; 14:1602-1612. [DOI: 10.1002/asia.201801681] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Antony Wing Hung Ng
- Department of ChemistryThe University of Hong Kong Pokfulam Road Hong Kong P. R. China
| | - Ho Yu Au‐Yeung
- Department of ChemistryThe University of Hong Kong Pokfulam Road Hong Kong P. R. China
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19
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Asamitsu S, Bando T, Sugiyama H. Ligand Design to Acquire Specificity to Intended G-Quadruplex Structures. Chemistry 2018; 25:417-430. [PMID: 30051593 DOI: 10.1002/chem.201802691] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 07/14/2018] [Indexed: 12/17/2022]
Abstract
A G-quadruplex is a nucleic acid secondary structure that is adopted by guanine-rich sequences, and is considered to be relevant in various pharmacological and biological contexts. G-Quadruplexes have also attracted great attention in the field of DNA nanotechnology because of their extremely high thermal stability and the availability of many defined structures. To date, a large repertory of DNA/RNA G-quadruplex-interactive ligands has been developed by numerous laboratories. Several relevant reviews have also been published that have helped researchers to grasp the full scope of G-quadruplex research from its outset to the present. This review focuses on the G-quadruplex ligands that allow targeting of specific G-quadruplexes. Moreover, unique ligands, successful methodologies, and future perspectives in relation to specific G-quadruplex recognition are also addressed.
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Affiliation(s)
- Sefan Asamitsu
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo, Kyoto, 606-8502, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo, Kyoto, 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo, Kyoto, 606-8502, Japan.,Institute for Integrated Cell-Material Science (WPI-iCeMS), Kyoto University, Sakyo, Kyoto, 606-8501, Japan
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20
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Rubio‐Magnieto J, Kajouj S, Di Meo F, Fossépré M, Trouillas P, Norman P, Linares M, Moucheron C, Surin M. Binding Modes and Selectivity of Ruthenium Complexes to Human Telomeric DNA G‐Quadruplexes. Chemistry 2018; 24:15577-15588. [DOI: 10.1002/chem.201802147] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 07/12/2018] [Indexed: 02/05/2023]
Affiliation(s)
- Jenifer Rubio‐Magnieto
- Laboratory for Chemistry of Novel Materials Center for Innovation in Materials and Polymers University of Mons-UMONS 20 Place du Parc 7000 Mons Belgium
- Current address: Bioinspired Supramolecular Chemistry and Materials group Departament de Química Inorgànica i Orgànica Universitat Jaume I Avda Sos Baynat s/n E-12071 Castelló Spain
| | - Sofia Kajouj
- Chimie Organique et Photochimie CP160/08 Université libre de Bruxelles 50 avenue F. D. Roosevelt 1050 Bruxelles Belgium
| | - Florent Di Meo
- INSERM U1248 IPPRITT University of Limoges School of Pharmacy 2 rue du Dr. Marcland 87025 Limoges France
| | - Mathieu Fossépré
- Laboratory for Chemistry of Novel Materials Center for Innovation in Materials and Polymers University of Mons-UMONS 20 Place du Parc 7000 Mons Belgium
| | - Patrick Trouillas
- INSERM U1248 IPPRITT University of Limoges School of Pharmacy 2 rue du Dr. Marcland 87025 Limoges France
- RCPTM Palacký University Faculty of Sciences Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Patrick Norman
- Department of Theoretical Chemistry and Biology School of Engineering Sciences in Chemistry Biotechnology and Health KTH Royal Institute of Technology SE-106 91 Stockholm Sweden
| | - Mathieu Linares
- Department of Theoretical Chemistry and Biology School of Engineering Sciences in Chemistry Biotechnology and Health KTH Royal Institute of Technology SE-106 91 Stockholm Sweden
- Swedish e-Science Research Centre (SeRC) KTH Royal Institute of Technology 104 50 Stockholm Sweden
| | - Cécile Moucheron
- Chimie Organique et Photochimie CP160/08 Université libre de Bruxelles 50 avenue F. D. Roosevelt 1050 Bruxelles Belgium
| | - Mathieu Surin
- Laboratory for Chemistry of Novel Materials Center for Innovation in Materials and Polymers University of Mons-UMONS 20 Place du Parc 7000 Mons Belgium
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21
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Marchetti C, Zyner KG, Ohnmacht SA, Robson M, Haider SM, Morton JP, Marsico G, Vo T, Laughlin-Toth S, Ahmed AA, Di Vita G, Pazitna I, Gunaratnam M, Besser RJ, Andrade ACG, Diocou S, Pike JA, Tannahill D, Pedley RB, Evans TRJ, Wilson WD, Balasubramanian S, Neidle S. Targeting Multiple Effector Pathways in Pancreatic Ductal Adenocarcinoma with a G-Quadruplex-Binding Small Molecule. J Med Chem 2018; 61:2500-2517. [PMID: 29356532 PMCID: PMC5867665 DOI: 10.1021/acs.jmedchem.7b01781] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Indexed: 12/11/2022]
Abstract
Human pancreatic ductal adenocarcinoma (PDAC) involves the dysregulation of multiple signaling pathways. A novel approach to the treatment of PDAC is described, involving the targeting of cancer genes in PDAC pathways having over-representation of G-quadruplexes, using the trisubstituted naphthalene diimide quadruplex-binding compound 2,7-bis(3-morpholinopropyl)-4-((2-(pyrrolidin-1-yl)ethyl)amino)benzo[ lmn][3,8]phenanthroline-1,3,6,8(2 H,7 H)-tetraone (CM03). This compound has been designed by computer modeling, is a potent inhibitor of cell growth in PDAC cell lines, and has anticancer activity in PDAC models, with a superior profile compared to gemcitabine, a commonly used therapy. Whole-transcriptome RNA-seq methodology has been used to analyze the effects of this quadruplex-binding small molecule on global gene expression. This has revealed the down-regulation of a large number of genes, rich in putative quadruplex elements and involved in essential pathways of PDAC survival, metastasis, and drug resistance. The changes produced by CM03 represent a global response to the complexity of human PDAC and may be applicable to other currently hard-to-treat cancers.
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Affiliation(s)
- Chiara Marchetti
- UCL
School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, U.K.
| | - Katherine G. Zyner
- Cancer
Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, U.K.
| | - Stephan A. Ohnmacht
- UCL
School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, U.K.
| | - Mathew Robson
- Cancer
Research UK Cancer Centre, UCL Cancer Institute, University College London, London WC1E 6BT, U.K.
| | - Shozeb M. Haider
- UCL
School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, U.K.
| | - Jennifer P. Morton
- Cancer
Research UK, Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD U.K.
- Institute
of Cancer Sciences. University of Glasgow, Glasgow G12 8QQ, U.K.
| | - Giovanni Marsico
- Cancer
Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, U.K.
| | - Tam Vo
- Department
of Chemistry and Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30303-3083, United States
| | - Sarah Laughlin-Toth
- Department
of Chemistry and Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30303-3083, United States
| | - Ahmed A. Ahmed
- UCL
School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, U.K.
| | - Gloria Di Vita
- UCL
School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, U.K.
| | - Ingrida Pazitna
- UCL
School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, U.K.
| | - Mekala Gunaratnam
- UCL
School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, U.K.
| | - Rachael J. Besser
- UCL
School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, U.K.
| | - Ana C. G. Andrade
- UCL
School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, U.K.
| | - Seckou Diocou
- UCL
Cancer Institute, University College London, London WC1E 6BT, U.K.
| | - Jeremy A. Pike
- Cancer
Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, U.K.
| | - David Tannahill
- Cancer
Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, U.K.
| | - R. Barbara Pedley
- UCL
Cancer Institute, University College London, London WC1E 6BT, U.K.
| | - T. R. Jeffry Evans
- Cancer
Research UK, Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD U.K.
- Institute
of Cancer Sciences. University of Glasgow, Glasgow G12 8QQ, U.K.
| | - W. David Wilson
- Department
of Chemistry and Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30303-3083, United States
| | - Shankar Balasubramanian
- Cancer
Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, U.K.
- Department
of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
- The
School of Clinical Medicine, University
of Cambridge, Cambridge CB2 0SP, U.K.
| | - Stephen Neidle
- UCL
School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, U.K.
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