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Yan MP, Wee CE, Yen KP, Stevens A, Wai LK. G-quadruplex ligands as therapeutic agents against cancer, neurological disorders and viral infections. Future Med Chem 2023; 15:1987-2009. [PMID: 37933551 DOI: 10.4155/fmc-2023-0202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023] Open
Abstract
G-quadruplexes (G4s) within the human genome have undergone extensive molecular investigation, with a strong focus on telomeres, gene promoters and repetitive regulatory sequences. G4s play central roles in regulating essential biological processes, including telomere maintenance, replication, transcription and translation. Targeting these molecular processes with G4-binding ligands holds substantial therapeutic potential in anticancer treatments and has also shown promise in treating neurological, skeletal and muscular disorders. The presence of G4s in bacterial and viral genomes also suggests that G4-binding ligands could be a critical tool in fighting infections. This review provides an overview of the progress and applications of G4-binding ligands, their proposed mechanisms of action, challenges faced and prospects for their utilization in anticancer treatments, neurological disorders and antiviral activities.
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Affiliation(s)
- Mock Phooi Yan
- Centre for Drug & Herbal Development, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, Kuala Lumpur, 50300, Malaysia
| | - Chua Eng Wee
- Centre for Drug & Herbal Development, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, Kuala Lumpur, 50300, Malaysia
| | - Khor Poh Yen
- Faculty Pharmacy & Health Sciences, Universiti Kuala Lumpur, Royal College of Medicine Perak, 3, Jalan Greentown, Ipoh, Perak, 30450, Malaysia
| | - Aaron Stevens
- Department of Pathology & Molecular Medicine, University of Otago, Wellington, 6021, New Zealand
| | - Lam Kok Wai
- Centre for Drug & Herbal Development, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, Kuala Lumpur, 50300, Malaysia
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2
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Jamaluddin ND, Mazlan NF, Tan LL, Yusof NYM, Khalid B. G-quadruplex microspheres-based optical RNA biosensor for arthropod-borne virus pathogen detection: A proof-of-concept with dengue serotype 2. Int J Biol Macromol 2021; 199:1-9. [PMID: 34922999 DOI: 10.1016/j.ijbiomac.2021.12.047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 11/16/2022]
Abstract
Dengue virus (DENV) is a positive-sense single-stranded RNA virus and that the detection of viral RNA itself is highly desirable, which can be achieved by using RNA biosensor diagnostic method. Herein, acrylic micropolymer-based optical RNA biosensor was developed by binding anionic copper(II) phthalocyanine (CPC) planar aromatic ligand to the G-quadruplex DNA probe via end-stacking with π-system of the guanine (G) quartet, and a blue coloration was developed on the G-quadruplex microspheres. Hybridization of G-quadruplex DNA probe with target DENV serotype 2 (DENV2) RNA unfolded the G-quadruplex, and rendering release of the CPC planar optical label, causing discoloration of the G-quadruplex microbiosensor. Optical characterization of the RNA biosensor was performed by means of fiber optic reflectance spectrophotometer at maximum reflectance wavelength of 774 nm. The reflectance response enhancement of the RNA-responsive G-quadruplex-based reflectometric biosensor was linearly proportional to the target oligo DENV2 RNA concentration in the range of 2 zM-2 μM, with a 0.447 zM limit of detection and a rapid response time of 30 min. Heightening in the reflectance signal based on structural transition of G-quadruplex in response to target RNA was successfully implemented in real-time DENV2 detection in non-invasive human fluid samples (i.e. saliva and urine) under informed consent.
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Affiliation(s)
- Nur Diyana Jamaluddin
- Southeast Asia Disaster Prevention Research Initiative (SEADPRI-UKM), Institute for Environment and Development (LESTARI), Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor Darul Ehsan, Malaysia
| | - Nur-Fadhilah Mazlan
- Southeast Asia Disaster Prevention Research Initiative (SEADPRI-UKM), Institute for Environment and Development (LESTARI), Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor Darul Ehsan, Malaysia
| | - Ling Ling Tan
- Southeast Asia Disaster Prevention Research Initiative (SEADPRI-UKM), Institute for Environment and Development (LESTARI), Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor Darul Ehsan, Malaysia.
| | - Nurul Yuziana Mohd Yusof
- Department of Earth Sciences and Environment, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor Darul Ehsan, Malaysia
| | - Bahariah Khalid
- Department of Medicine, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia; Hospital Serdang, Jalan Puchong, 43000 Kajang, Selangor Darul Ehsan, Malaysia.
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Lopes-Nunes J, Oliveira PA, Cruz C. G-Quadruplex-Based Drug Delivery Systems for Cancer Therapy. Pharmaceuticals (Basel) 2021; 14:671. [PMID: 34358097 PMCID: PMC8308530 DOI: 10.3390/ph14070671] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 07/10/2021] [Accepted: 07/12/2021] [Indexed: 12/15/2022] Open
Abstract
G-quadruplexes (G4s) are a class of nucleic acids (DNA and RNA) with single-stranded G-rich sequences. Owing to the selectivity of some G4s, they are emerging as targeting agents to overtake side effects of several potential anticancer drugs, and delivery systems of small molecules to malignant cells, through their high affinity or complementarity to specific targets. Moreover, different systems are being used to improve their potential, such as gold nano-particles or liposomes. Thus, the present review provides relevant data about the different studies with G4s as drug delivery systems and the challenges that must be overcome in the future research.
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Affiliation(s)
- Jéssica Lopes-Nunes
- CICS-UBI-Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal;
| | - Paula A. Oliveira
- Centre for Research and Technology of Agro-Environmental and Biological Sciences (CITAB), Inov4Agro, University of Trás-os-Montes and Alto Douro (UTAD), Quinta de Prados, 5000-801 Vila Real, 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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Pruška A, Marchand A, Zenobi R. Novel Insight into Proximal DNA Domain Interactions from Temperature-Controlled Electrospray Ionization Mass Spectrometry. Angew Chem Int Ed Engl 2021; 60:15390-15398. [PMID: 33822450 PMCID: PMC8251475 DOI: 10.1002/anie.202016757] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/07/2021] [Indexed: 01/05/2023]
Abstract
Quadruplexes are non-canonical nucleic acid structures essential for many cellular processes. Hybrid quadruplex-duplex oligonucleotide assemblies comprised of multiple domains are challenging to study with conventional biophysical methods due to their structural complexity. Here, we introduce a novel method based on native mass spectrometry (MS) coupled with a custom-built temperature-controlled nanoelectrospray ionization (TCnESI) source designed to investigate interactions between proximal DNA domains. Thermal denaturation experiments were aimed to study unfolding of multi-stranded oligonucleotide constructs derived from biologically relevant structures and to identify unfolding intermediates. Using the TCnESI MS, we observed changes in Tm and thermodynamic characteristics of proximal DNA domains depending on the number of domains, their position, and order in a single experiment.
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Affiliation(s)
- Adam Pruška
- Department of Chemistry and Applied BiosciencesETH ZurichVladimir-Prelog-Weg 38093ZurichSwitzerland
| | - Adrien Marchand
- Department of Chemistry and Applied BiosciencesETH ZurichVladimir-Prelog-Weg 38093ZurichSwitzerland
| | - Renato Zenobi
- Department of Chemistry and Applied BiosciencesETH ZurichVladimir-Prelog-Weg 38093ZurichSwitzerland
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Pruška A, Marchand A, Zenobi R. Novel Insight into Proximal DNA Domain Interactions from Temperature‐Controlled Electrospray Ionization Mass Spectrometry. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Adam Pruška
- Department of Chemistry and Applied Biosciences ETH Zurich Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Adrien Marchand
- Department of Chemistry and Applied Biosciences ETH Zurich Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences ETH Zurich Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
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Tan X, Jia F, Wang P, Zhang K. Nucleic acid-based drug delivery strategies. J Control Release 2020; 323:240-252. [PMID: 32272123 PMCID: PMC8079167 DOI: 10.1016/j.jconrel.2020.03.040] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 03/21/2020] [Accepted: 03/25/2020] [Indexed: 12/17/2022]
Abstract
Nucleic acids have not been widely considered as an optimal material for drug delivery. Indeed, unmodified nucleic acids are enzymatically unstable, too hydrophilic for cell uptake and payload encapsulation, and may cause unintended biological responses such as immune system activation and prolongation of the blood coagulation pathway. Recently, however, three major areas of development surrounding nucleic acids have made it worthwhile to reconsider their role for drug delivery. These areas include DNA/RNA nanotechnology, multivalent nucleic acid nanostructures, and nucleic acid aptamers, which, respectively, provide the ability to engineer nanostructures with unparalleled levels of structural control, completely reverse certain biological properties of linear/cyclic nucleic acids, and enable antibody-level targeting using an all-nucleic acid construct. These advances, together with nucleic acids' ability to respond to various stimuli (engineered or natural), have led to a rapidly increasing number of drug delivery systems with potential for spatiotemporally controlled drug release. In this review, we discuss recent progress in nucleic acid-based drug delivery strategies, their potential, unique use cases, and risks that must be overcome or avoided.
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Affiliation(s)
- Xuyu Tan
- Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave, Boston, MA 02115, USA
| | - Fei Jia
- Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave, Boston, MA 02115, USA
| | - Ping Wang
- College of Environmental Science and Engineering, Central South University of Forestry and Technology, Changsha 410007, China
| | - Ke Zhang
- College of Environmental Science and Engineering, Central South University of Forestry and Technology, Changsha 410007, China; Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave, Boston, MA 02115, USA.
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Largy E, Gabelica V. Native Hydrogen/Deuterium Exchange Mass Spectrometry of Structured DNA Oligonucleotides. Anal Chem 2020; 92:4402-4410. [PMID: 32039580 DOI: 10.1021/acs.analchem.9b05298] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Although solution hydrogen-deuterium exchange mass spectrometry (HDX/MS) is well-established for the analysis of the structure and dynamics of proteins, it is currently not exploited for nucleic acids. Here we used DNA G-quadruplex structures as model systems to demonstrate that DNA oligonucleotides are amenable to in-solution HDX/MS in native conditions. In trimethylammonium acetate solutions and in soft source conditions, the protonated phosphate groups are fully back-exchanged in the source, while the exchanged nucleobases remain labeled without detectable back-exchange. As a result, the exchange rates depend strongly on the secondary structure (hydrogen bonding status) of the oligonucleotides, but neither on their charge state nor on the presence of nonspecific adducts. We show that native mass spectrometry methods can measure these exchange rates on the second to the day time scale with high precision. Such combination of HDX with native MS opens promising avenues for the analysis of the structural and biophysical properties of oligonucleotides and their complexes.
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Affiliation(s)
- Eric Largy
- University of Bordeaux, INSERM and CNRS, Laboratoires Acides Nucléiques: Régulations Naturelle et Artificielle (ARNA, U1212, UMR5320), IECB, 2 rue Robert Escarpit, 33600 Pessac, France
| | - Valérie Gabelica
- University of Bordeaux, INSERM and CNRS, Laboratoires Acides Nucléiques: Régulations Naturelle et Artificielle (ARNA, U1212, UMR5320), IECB, 2 rue Robert Escarpit, 33600 Pessac, France
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Zhao H, Yuan X, Yu J, Huang Y, Shao C, Xiao F, Lin L, Li Y, Tian L. Magnesium-Stabilized Multifunctional DNA Nanoparticles for Tumor-Targeted and pH-Responsive Drug Delivery. ACS APPLIED MATERIALS & INTERFACES 2018; 10:15418-15427. [PMID: 29676144 DOI: 10.1021/acsami.8b01932] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Functional nucleic acids, which can target cancer cells and realize stimuli-responsive drug delivery in tumor microenvironment, have been widely applied for anticancer chemotherapy. At present, high cost, unsatisfactory biostability, and complicated fabrication process are the main limits for the development of DNA-based drug-delivery nanocarriers. Here, a doxorubicin (Dox)-delivery nanoparticle for tumor-targeting chemotherapy is developed taking advantage of rolling circle amplification (RCA) technique, by which a high quantity of functional DNAs can be efficiently collected. Furthermore, Mg2+, a major electrolyte in human body showing superior biocompatibility, can sufficiently condense the very long sequence of an RCA product and better preserve its functions. The resultant DNA nanoparticle exhibits a high biostability, making it a safe and ideal nanomaterial for in vivo application. Through cellular and in vivo experiments, we thoroughly demonstrate that this kind of Mg2+-stabilized multifunctional DNA nanoparticles can successfully realize tumor-targeted Dox delivery. Overall, exploiting RCA technique and Mg2+ condensation, this new strategy can fabricate nanoparticles with a nontoxic composition through a simple fabrication process and provides a good way to preserve and promote DNA functions, which will show a broad application potential in the biomedical field.
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Komiyama M, Yoshimoto K, Sisido M, Ariga K. Chemistry Can Make Strict and Fuzzy Controls for Bio-Systems: DNA Nanoarchitectonics and Cell-Macromolecular Nanoarchitectonics. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2017. [DOI: 10.1246/bcsj.20170156] [Citation(s) in RCA: 238] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Makoto Komiyama
- World Premier International (WPI) Research Centre for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki 305-0044
- Life Science Center of Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Ten-noudai, Tsukuba, Ibaraki 305-8577
| | - Keitaro Yoshimoto
- Department of Life Sciences, Graduate School of Arts and Science, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902
| | - Masahiko Sisido
- Professor Emeritus, Research Core for Interdisciplinary Sciences, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530
| | - Katsuhiko Ariga
- World Premier International (WPI) Research Centre for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki 305-0044
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-0827
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Bağda E, Bağda E, Yabaş E. Circular dichroism spectroscopic investigation of double-decker phthalocyanine with G-Quadruplex as promising telomerase inhibitor. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.07.093] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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