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Pratihar S, Bhat S V V, Bhagavath KK, Govindaraju T. Unambiguous Detection of LTR-III G-Quadruplex in the HIV Genome Using a Tailored Fluorogenic Probe-based Assay. Anal Chem 2024; 96:15834-15839. [PMID: 39314132 DOI: 10.1021/acs.analchem.4c03374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
The noncanonical conformations within the genomes of viral pathogens is of significant diagnostic value, due to their unique secondary structures and interactions with specific fluorogenic molecules. In particular, adaptation of the G-quadruplex (GQ) conformation by the specific gene sequence leads to distinct topological features, resulting in unique binding sites that are crucial for the selective recognition of human immunodeficiency virus (HIV) by small molecules. Leveraging the selective fluorescence response of a benzobisthiazole-based fluorogenic probe to the LTR-III GQ target, we developed a GQ-based diagnostic platform for HIV detection. The successful fluorescence recognition of an amplified 176-nucleotide genomic segment harboring the LTR-III GQ, facilitated by pH-controlled GQ-targeted reliable conformational polymorphism (GQ-RCP), validates this method as an effective GQ-topology-targeted diagnostic tool for HIV.
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Affiliation(s)
- Sumon Pratihar
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bengaluru, 560064 Karnataka, India
| | - Vasudhar Bhat S V
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bengaluru, 560064 Karnataka, India
| | - Krithi K Bhagavath
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bengaluru, 560064 Karnataka, India
| | - Thimmaiah Govindaraju
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bengaluru, 560064 Karnataka, India
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2
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Pratihar S, Venkatesh R, Mattath MN, Govindaraju T. Identification and detection of conserved G-quadruplex in monkeypox virus using conformation specific fluorogenic probe. Chem Commun (Camb) 2024. [PMID: 39344814 DOI: 10.1039/d4cc03726j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Identifying distinct noncanonical structures in pathogenic genomes is crucial for developing new diagnostic tools. This study uncovers stable G-quadruplex (GQ) structures in conserved DNA sequences unique to the monkeypox virus (MPV). Furthermore, we developed a method for the detection of target GQ using a fluorogenic probe.
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Affiliation(s)
- Sumon Pratihar
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, P.O., Bengaluru, 560064 Karnataka, India.
| | - Ramjayakumar Venkatesh
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, P.O., Bengaluru, 560064 Karnataka, India.
| | - Mohamed Nabeel Mattath
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, P.O., Bengaluru, 560064 Karnataka, India.
| | - Thimmaiah Govindaraju
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, P.O., Bengaluru, 560064 Karnataka, India.
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3
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Ghosh D, Pratihar S, Govindaraju T. Designer tryptophan-rich peptide modulates structural dynamics of HIF-1α DNA i-motif DNA. J Pept Sci 2024; 30:e3601. [PMID: 38591712 DOI: 10.1002/psc.3601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/12/2024] [Accepted: 03/16/2024] [Indexed: 04/10/2024]
Abstract
Cytosine-rich DNA sequences can fold into intercalated motifs known as i-motifs, through noncanonical hydrogen bonding interactions. Molecular probes can provide valuable insights into the conformational stability and potential cellular functions of i-motifs. W5K5, a decapeptide composed of alternating tryptophan (W) and lysine (K) units, has been identified as a lead candidate to modulate the structural dynamics of the hypoxia-inducible factor 1-alpha (HIF-1α) DNA i-motif. This finding is expected to facilitate the rational design of peptide-based probes for studying the structure and functional dynamics of i-motifs.
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Affiliation(s)
- Debasis Ghosh
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru, Karnataka, India
| | - Sumon Pratihar
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru, Karnataka, India
| | - Thimmaiah Govindaraju
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru, Karnataka, India
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4
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Figueiredo J, Mergny JL, Cruz C. G-quadruplex ligands in cancer therapy: Progress, challenges, and clinical perspectives. Life Sci 2024; 340:122481. [PMID: 38301873 DOI: 10.1016/j.lfs.2024.122481] [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: 10/26/2023] [Revised: 01/20/2024] [Accepted: 01/29/2024] [Indexed: 02/03/2024]
Abstract
Guanine-rich sequences can form G-quadruplexes (G4) in living cells, making these structures promising anti-cancer targets. Compounds able to recognize these structures have been investigated as potential anticancer drugs; however, no G4 binder has yet been approved in the clinic. Here, we describe G4 ligands structure-activity relationships, in vivo effects as well as clinical trials. Addressing G4 ligand characteristics, targeting challenges, and structure-activity relationships, this review provides insights into the development of potent and selective G4-targeting molecules for therapeutic applications.
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Affiliation(s)
- Joana Figueiredo
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
| | - Jean-Louis Mergny
- Laboratoire d'Optique et Biosciences, Institut Polytechnique de Paris, CNRS, INSERM, Université Paris-Saclay, 91128 Palaiseau cedex, France; Institute of Biophysics of the CAS, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic.
| | - Carla Cruz
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal; Departamento de Química, Faculdade de Ciências, Universidade da Beira Interior, Rua Marquês de Ávila e Bolama, 6201-001 Covilhã, Portugal.
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5
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Figueiredo J, Djavaheri-Mergny M, Ferret L, Mergny JL, Cruz C. Harnessing G-quadruplex ligands for lung cancer treatment: A comprehensive overview. Drug Discov Today 2023; 28:103808. [PMID: 38414431 DOI: 10.1016/j.drudis.2023.103808] [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: 08/26/2023] [Revised: 10/19/2023] [Accepted: 10/24/2023] [Indexed: 02/29/2024]
Abstract
Lung cancer (LC) remains a leading cause of mortality worldwide, and new therapeutic strategies are urgently needed. One such approach revolves around the utilization of four-stranded nucleic acid secondary structures, known as G-quadruplexes (G4), which are formed by G-rich sequences. Ligands that bind selectively to G4 structures present a promising strategy for regulating crucial cellular processes involved in the progression of LC, rendering them potent agents for lung cancer treatment. In this review, we offer a summary of recent advancements in the development of G4 ligands capable of targeting specific genes associated with the development and progression of lung cancer.
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Affiliation(s)
- Joana Figueiredo
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, 6200-506 Covilhã, Portugal
| | - Mojgan Djavaheri-Mergny
- Centre de Recherche des Cordeliers, INSERM UMRS 1138, Sorbonne Université, Université Paris Cité, Equipe Labellisée par la Ligue contre le Cancer, Institut Universitaire de France, 75006 Paris, France; Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, 94805 Villejuif, France
| | - Lucille Ferret
- Centre de Recherche des Cordeliers, INSERM UMRS 1138, Sorbonne Université, Université Paris Cité, Equipe Labellisée par la Ligue contre le Cancer, Institut Universitaire de France, 75006 Paris, France; Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, 94805 Villejuif, France; Faculté de Médecine, Université de Paris Saclay, Paris, France
| | - Jean-Louis Mergny
- Laboratoire d'Optique et Biosciences, Institut Polytechnique de Paris, CNRS, INSERM, Université Paris-Saclay, 91120 Palaiseau, France.
| | - Carla Cruz
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, 6200-506 Covilhã, Portugal; Departamento de Química, Faculdade de Ciências da Universidade da Beira Interior, Rua Marquês de Ávila e Bolama, 6201-001 Covilhã, Portugal.
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6
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Pratihar S, Bhagavath KK, Govindaraju T. Small molecules and conjugates as theranostic agents. RSC Chem Biol 2023; 4:826-849. [PMID: 37920393 PMCID: PMC10619134 DOI: 10.1039/d3cb00073g] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 08/28/2023] [Indexed: 11/04/2023] Open
Abstract
Theranostics, the integration of therapy and diagnostics into a single entity for the purpose of monitoring disease progression and treatment response. Diagnostics involves identifying specific characteristics of a disease, while therapeutics refers to the treatment of the disease based on this identification. Advancements in medicinal chemistry and technology have led to the development of drug modalities that provide targeted therapeutic effects while also providing real-time updates on disease progression and treatment. The inclusion of imaging in therapy has significantly improved the prognosis of devastating diseases such as cancer and neurodegeneration. Currently, theranostic treatment approaches are based on nuclear medicine, while nanomedicine and a wide diversity of macromolecular systems such as gels, polymers, aptamers, and dendrimer-based agents are being developed for the purpose. Theranostic agents have significant roles to play in both early-stage drug development and clinical-stage therapeutic-containing drug candidates. This review will briefly outline the pros and cons of existing and evolving theranostic approaches before comprehensively discussing the role of small molecules and their conjugates.
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Affiliation(s)
- Sumon Pratihar
- Bioorganic Chemistry Laboratory, New Chemistry Unit, and School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR) Jakkur P.O. Bengaluru 560064 Karnataka India
| | - Krithi K Bhagavath
- Bioorganic Chemistry Laboratory, New Chemistry Unit, and School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR) Jakkur P.O. Bengaluru 560064 Karnataka India
| | - Thimmaiah Govindaraju
- Bioorganic Chemistry Laboratory, New Chemistry Unit, and School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR) Jakkur P.O. Bengaluru 560064 Karnataka India
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7
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Beč A, Racané L, Žonja L, Persoons L, Daelemans D, Starčević K, Vianello R, Hranjec M. Biological evaluation of novel amidino substituted coumarin-benzazole hybrids as promising therapeutic agents. RSC Med Chem 2023; 14:957-968. [PMID: 37252100 PMCID: PMC10214388 DOI: 10.1039/d3md00055a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 03/27/2023] [Indexed: 04/06/2024] Open
Abstract
Herein we present the design and the synthesis of novel substituted coumarin-benzimidazole/benzothiazole hybrids bearing a cyclic amidino group on the benzazole core as biologically active agents. All prepared compounds were evaluated for their in vitro antiviral and antioxidative activity as well as for their in vitro antiproliferative activity against a panel of several human cancer cell lines. Coumarin-benzimidazole hybrid 10 (EC50 9.0-43.8 μM) displayed the most promising broad spectrum antiviral activity, while two other coumarin-benzimidazole hybrids 13 and 14 showed the highest antioxidative capacity in the ABTS assay, superior to the reference standard BHT (IC50 0.17 and 0.11 mM, respectively). Computational analysis supported these results and demonstrated that these hybrids benefit from the high C-H hydrogen atom releasing tendency of the cationic amidine unit, and the pronounced ease with which they can liberate an electron, promoted by the electron-donating diethylamine group on the coumarin core. The coumarin ring substitution at position 7 with a N,N-diethylamino group also caused a significant enhancement of the antiproliferative activity, with the most active compounds being derivatives with a 2-imidazolinyl amidine group 13 (IC50 0.3-1.9 μM) and benzothiazole derivative with a hexacyclic amidine group 18 (IC50 1.3-2.0 μM).
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Affiliation(s)
- Anja Beč
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb Marulićev trg 19 HR-10000 Zagreb Croatia
| | - Livio Racané
- Department of Applied Chemistry, Faculty of Textile Technology, University of Zagreb Prilaz baruna Filipovića 28a 10000 Zagreb Croatia
| | - Lucija Žonja
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb Marulićev trg 19 HR-10000 Zagreb Croatia
| | - Leentje Persoons
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute Leuven Belgium
| | - Dirk Daelemans
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute Leuven Belgium
| | - Kristina Starčević
- Department of Chemistry and Biochemistry, Faculty of Veterinary Medicine, University of Zagreb Heinzelova 55 HR-10000 Zagreb Croatia
| | - Robert Vianello
- Laboratory for the Computational Design and Synthesis of Functional Materials, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute Zagreb Croatia
| | - Marijana Hranjec
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb Marulićev trg 19 HR-10000 Zagreb Croatia
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8
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Zhang R, Hao L, Chen P, Zhang G, Liu N. Multifunctional small-molecule theranostic agents for tumor-specific imaging and targeted chemotherapy. Bioorg Chem 2023; 137:106576. [PMID: 37182421 DOI: 10.1016/j.bioorg.2023.106576] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 04/17/2023] [Accepted: 04/26/2023] [Indexed: 05/16/2023]
Abstract
Cancer is one of the leading causes of death worldwide. Although great progress has been achieved in cancer diagnosis and treatment, novel therapies are still urgently needed to increase the efficacy and reduce the side effects of conventional therapies. Personalized medicine involves administering patients drugs that are specific to the characteristics of their tumors, and has significantly reduced side effects and increased overall survival rates. Multifunctional theranostic drugs are designed to combine diagnostic and therapeutic functions into a single molecule, which reduces the number of drugs administered to patients and increases patient compliance, and have shown great potential in propelling personalized medicine. This review focuses on multifunctional small-molecule theranostic agents for tumor-specific imaging and targeted chemotherapy, with a particular emphasis placed on highlighting design strategies and application in vitro or in vivo. The challenges and future perspectives of multifunctional small molecules are also discussed.
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Affiliation(s)
- Renshuai Zhang
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266071, China
| | - Li Hao
- Department of Gerontology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan 528051, China
| | - Pengwei Chen
- Hainan Key Laboratory for ReseCarch and Development of Natural Products from Li Folk Medicine, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
| | - Gang Zhang
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266071, China.
| | - Ning Liu
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266071, China.
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9
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Singh M, Gupta R, Comez L, Paciaroni A, Rani R, Kumar V. BCL2 G quadruplex-binding small molecules: Current status and prospects for the development of next-generation anticancer therapeutics. Drug Discov Today 2022; 27:2551-2561. [PMID: 35709931 DOI: 10.1016/j.drudis.2022.06.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 06/01/2022] [Accepted: 06/08/2022] [Indexed: 11/03/2022]
Abstract
B cell lymphoma 2 (BCL2) overexpression in a range of human tumors is often related to chemotherapy resistance and poor prognosis. GC-rich regions upstream of the P1 promoter in human BCL2 can form G-quadruplex (G4) structures through the stacking of four Hoogsteen-paired guanine bases. Stabilizing the G4 fold implies the inhibition of BCL2 expression and, thus, small molecules that selectively bind to the G4 are promising anticancer candidates. In this review, we discuss the structural aspects, binding affinity, selectivity, and biological activity of well-characterized BCL2 G4 binding ligands in vitro and in vivo. We also explore future directions in the research and development of G4-based anticancer therapeutics.
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Affiliation(s)
- Mamta Singh
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University, Noida, UP, 201303, India
| | - Rajat Gupta
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University, Noida, UP, 201303, India
| | - Lucia Comez
- IOM-CNR National Research Council, Via Pascoli, Perugia I-06123, Italy
| | - Alessandro Paciaroni
- Department of Physics and Geology, University of Perugia, via Pascoli, 06123, Italy
| | - Reshma Rani
- Drug Discovery Unit, Jubilant Biosys Ltd, Sector 58, Noida, UP 201301, India.
| | - Vinit Kumar
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University, Noida, UP, 201303, India.
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10
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Venkata Suseela Y, Sengupta P, Roychowdhury T, Panda S, Talukdar S, Chattopadhyay S, Chatterjee S, Govindaraju T. Targeting Oncogene Promoters and Ribosomal RNA Biogenesis by G-Quadruplex Binding Ligands Translate to Anticancer Activity. ACS BIO & MED CHEM AU 2022; 2:125-139. [PMID: 37101746 PMCID: PMC10114666 DOI: 10.1021/acsbiomedchemau.1c00039] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
G-Quadruplex (GQ) nucleic acids are promising therapeutic targets in anticancer research due to their structural robustness, polymorphism, and gene-regulatory functions. Here, we presented the structure-activity relationship of carbazole-based monocyanine ligands using region-specific functionalization with benzothiazole (TCA and TCZ), lepidine (LCA and LCZ), and quinaldine (QCA and QCZ) acceptor moieties and evaluated their binding profiles with different oncogenic GQs. Their differential turn-on fluorescence emission upon GQ binding confirmed the GQ-to-duplex selectivity of all carbazole ligands, while the isothermal titration calorimetry results showed selective interactions of TCZ and TCA to c-MYC and BCL-2 GQs, respectively. The aldehyde group in TCA favors stacking interactions with the tetrad of BCL-2 GQ, whereas TCZ provides selective groove interactions with c-MYC GQ. Dual-luciferase assay and chromatin immunoprecipitation (ChIP) showed that these molecules interfere with the recruitment of specific transcription factors at c-MYC and BCL-2 promoters and stabilize the promoter GQ structures to inhibit their constitutive transcription in cancer cells. Their intrinsic turn-on fluorescence response with longer lifetimes upon GQ binding allowed real-time visualization of GQ structures at subcellular compartments. Confocal microscopy revealed the uptake of these ligands in the nucleoli, resulting in nucleolar stress. ChIP studies further confirmed the inhibition of Nucleolin occupancy at multiple GQ-enriched regions of ribosomal DNA (rDNA) promoters, which arrested rRNA biogenesis. Therefore, carbazole ligands act as the "double-edged swords" to arrest c-MYC and BCL-2 overexpression as well as rRNA biogenesis, triggering synergistic inhibition of multiple oncogenic pathways and apoptosis in cancer cells.
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Affiliation(s)
- Yelisetty Venkata Suseela
- Bioorganic
Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, P.O., Bengaluru, Karnataka 560064, India
| | - Pallabi Sengupta
- Department
of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kankurgachi, Kolkata 700054, India
| | - Tanaya Roychowdhury
- Cancer
Biology and Inflammatory Disorder Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Suman Panda
- Department
of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kankurgachi, Kolkata 700054, India
| | - Sangita Talukdar
- Bioorganic
Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, P.O., Bengaluru, Karnataka 560064, India
| | - Samit Chattopadhyay
- Cancer
Biology and Inflammatory Disorder Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Subhrangsu Chatterjee
- Department
of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kankurgachi, Kolkata 700054, India
| | - Thimmaiah Govindaraju
- Bioorganic
Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, P.O., Bengaluru, Karnataka 560064, India
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11
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Sakamoto T, Yu Z, Otani Y. Dual-Color Fluorescence Switch-On Probe for Imaging G-Quadruplex and Double-Stranded DNA in Living Cells. Anal Chem 2022; 94:4269-4276. [PMID: 35234461 DOI: 10.1021/acs.analchem.1c04804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A tripodal quinone-cyanine dye having one donor and three acceptors, that is, one quinone and three N-methylbenzothiazolium moieties, QCy(MeBT)3, was synthesized by simple Knoevenagel condensation between 2-hydroxybenzene-1,3,5-tricarbaldehyde and N-methyl-2-methylbenzothiazolium iodide. The 700 nm (λex, 570 nm) and 600 nm (λex, 470 nm) fluorescence emission of QCy(MeBT)3 was significantly and individually enhanced with the addition of G-quadruplex (G4) DNA and double-stranded DNA (dsDNA), respectively. The results of docking simulations and the response against the viscosity change revealed that the dual-fluorescence response was caused by the difference in the binding mode of QCy(MeBT)3 depending on the DNA structure. The results of fluorescence microscopy imaging experiments using QCy(MeBT)3 suggested that G4 DNAs and dsDNAs in the cell nucleus can be imaged with near-infrared (NIR, 700 nm) and red (600 nm) fluorescence emissions. Furthermore, pyridostatin-induced G4 formation in the living cells can be imaged with NIR fluorescence. The results indicated that QCy(MeBT)3 has huge potential to be a NIR-fluorescent molecular probe for analyzing the structural dynamics of nucleic acids in living cells with a normal fluorescence microscope.
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Affiliation(s)
- Takashi Sakamoto
- Faculty of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan.,Graduate School of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan
| | - Zehui Yu
- Faculty of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan
| | - Yuto Otani
- Graduate School of Systems Engineering, Wakayama University, 930 Sakaedani, Wakayama 640-8510, Japan
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12
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Kretzmann JA, Irving KL, Smith NM, Evans CW. Modulating gene expression in breast cancer via DNA secondary structure and the CRISPR toolbox. NAR Cancer 2022; 3:zcab048. [PMID: 34988459 PMCID: PMC8693572 DOI: 10.1093/narcan/zcab048] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/26/2021] [Accepted: 12/01/2021] [Indexed: 12/11/2022] Open
Abstract
Breast cancer is the most commonly diagnosed malignancy in women, and while the survival prognosis of patients with early-stage, non-metastatic disease is ∼75%, recurrence poses a significant risk and advanced and/or metastatic breast cancer is incurable. A distinctive feature of advanced breast cancer is an unstable genome and altered gene expression patterns that result in disease heterogeneity. Transcription factors represent a unique therapeutic opportunity in breast cancer, since they are known regulators of gene expression, including gene expression involved in differentiation and cell death, which are themselves often mutated or dysregulated in cancer. While transcription factors have traditionally been viewed as 'undruggable', progress has been made in the development of small-molecule therapeutics to target relevant protein-protein, protein-DNA and enzymatic active sites, with varying levels of success. However, non-traditional approaches such as epigenetic editing, transcriptional control via CRISPR/dCas9 systems, and gene regulation through non-canonical nucleic acid secondary structures represent new directions yet to be fully explored. Here, we discuss these new approaches and current limitations in light of new therapeutic opportunities for breast cancers.
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Affiliation(s)
- Jessica A Kretzmann
- Laboratory for Biomolecular Nanotechnology, Department of Physics, Technical University of Munich, Am Coulombwall 4a, 85748 Garching, Germany
| | - Kelly L Irving
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Hwy, Crawley, WA 6009, Australia
| | - Nicole M Smith
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Hwy, Crawley, WA 6009, Australia
| | - Cameron W Evans
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Hwy, Crawley, WA 6009, Australia
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13
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Xu J, Jiang R, He H, Ma C, Tang Z. Recent advances on G-quadruplex for biosensing, bioimaging and cancer therapy. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116257] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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14
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Moorthy H, Govindaraju T. Dendrimer Architectonics to Treat Cancer and Neurodegenerative Diseases with Implications in Theranostics and Personalized Medicine. ACS APPLIED BIO MATERIALS 2021; 4:1115-1139. [PMID: 35014470 DOI: 10.1021/acsabm.0c01319] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Integration of diagnostic and therapeutic functions in a single platform namely theranostics has become a cornerstone for personalized medicine. Theranostics platform facilitates noninvasive detection and treatment while allowing the monitoring of disease progression and therapeutic efficacy in case of chronic conditions of cancer and Alzheimer's disease (AD). Theranostic tools function by themselves or with the aid of carrier, viz. liposomes, micelles, polymers, or dendrimers. The dendrimer architectures (DA) are well-characterized molecular nanoobjects with a large number of terminal functional groups to enhance solubility and offer multivalency and multifunctional properties. Various noninvasive diagnostic tools like magnetic resonance imaging (MRI), computed tomography (CT), gamma scintigraphy, and optical techniques have been accomplished utilizing DAs for simultaneous imaging and drug delivery. Obstacles in the formulation design, drug loading, payload delivery, biocompatibility, overcoming cellular membrane and blood-brain barrier (BBB), and systemic circulation remain a bottleneck in translational efforts. This review focuses on the diagnostic, therapeutic and theranostic potential of DA-based nanocarriers in treating cancer and neurodegenerative disorders like AD and Parkinson's disease (PD), among others. In view of the inverse relationship between cancer and AD, designing suitable DA-based theranostic nanodrug with high selectivity has tremendous implications in personalized medicine to treat cancer and neurodegenerative disorders.
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Affiliation(s)
- Hariharan Moorthy
- Bioorganic Chemistry Laboratory, New Chemistry Unit and The School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur P. O., Bengaluru, Karnataka 560064, India
| | - Thimmaiah Govindaraju
- Bioorganic Chemistry Laboratory, New Chemistry Unit and The School of Advanced Materials (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur P. O., Bengaluru, Karnataka 560064, India
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Liu LY, Zhao Y, Zhang N, Wang KN, Tian M, Pan Q, Lin W. Ratiometric Fluorescence Imaging for the Distribution of Nucleic Acid Content in Living Cells and Human Tissue Sections. Anal Chem 2021; 93:1612-1619. [PMID: 33381958 DOI: 10.1021/acs.analchem.0c04064] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The misregulation of nucleic acids behavior leads to cell dysfunction and induces serious diseases. A ratiometric fluorescence probe is a powerful tool to study the dynamic behavior and function relationships of nucleic acids. However, currently, no such effective probe has been reported for in situ, real-time tracking of nucleic acids in living cells and tissue sections. Herein, the unique probe named QPP-AS was rationally designed for ratiometric fluorescence response to nucleic acids through skillful regulation of the intramolecular charge-transfer capabilities of the electron acceptor and donor. Encouraged by the advantages of the selective nucleic acid response, ideal biocompatibility, and high signal-to-noise ratio, QPP-AS has been applied for in situ, real-time ratiometric fluorescence imaging of nucleic acids in living cells for the first time. Furthermore, we have demonstrated that QPP-AS is capable of visualizing the dynamic behavior of nucleic acids during different cellular processes (e.g., cell division and apoptosis) by ratiometric fluorescence imaging. More significantly, QPP-AS has been successfully used for ratiometric fluorescence imaging of nucleic acids in human tissue sections, which provides not only the cell contour, nuclear morphology, and nuclear-plasma ratio but also the nucleic acid content information and may greatly improve accuracy in clinicopathological diagnosis.
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Affiliation(s)
- Liu-Yi Liu
- Shunde Hospital of Southern Medical University (The First People's Hospital of Shunde), Foshan, Guangdong 528308, P.R. China.,MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Yuping Zhao
- Institute of Optical Materials and Chemical Biology, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi 530004, P.R. China.,Institute of Fluorescent Probes for Biological Imaging, School of Chemistry and Chemical Engineering, School of Materials Science and Engineering, University of Jinan, Jinan, Shandong 250022, P.R. China
| | - Nan Zhang
- Department of Physiology, Zhongshan School of Medicine, Sun Yat-Sen University, 74 Zhongshan Road 2, Guangzhou 510080, P.R. China
| | - Kang-Nan Wang
- Shunde Hospital of Southern Medical University (The First People's Hospital of Shunde), Foshan, Guangdong 528308, P.R. China.,MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Minggang Tian
- Institute of Fluorescent Probes for Biological Imaging, School of Chemistry and Chemical Engineering, School of Materials Science and Engineering, University of Jinan, Jinan, Shandong 250022, P.R. China
| | - Qiling Pan
- Shunde Hospital of Southern Medical University (The First People's Hospital of Shunde), Foshan, Guangdong 528308, P.R. China
| | - Weiying Lin
- Institute of Optical Materials and Chemical Biology, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi 530004, P.R. China.,Institute of Fluorescent Probes for Biological Imaging, School of Chemistry and Chemical Engineering, School of Materials Science and Engineering, University of Jinan, Jinan, Shandong 250022, P.R. China
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