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Wang J, Qiao J, Zheng W, Lian H. Study on the Interaction of a Peptide Targeting Specific G-Quadruplex Structures Based on Chromatographic Retention Behavior. Int J Mol Sci 2023; 24:ijms24021438. [PMID: 36674950 PMCID: PMC9866954 DOI: 10.3390/ijms24021438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/01/2023] [Accepted: 01/09/2023] [Indexed: 01/12/2023] Open
Abstract
G-quadruplexes (G4s) are of vital biological significance and G4-specific ligands with conformational selectivity show great application potential in disease treatment and biosensing. RHAU, a RNA helicase associated with AU-rich element, exerts biological functions through the mediation of G4s and has been identified to be a G4 binder. Here, we investigated the interactions between the RHAU peptide and G4s with different secondary structures using size exclusion chromatography (SEC) in association with circular dichroism (CD), ultraviolet-visible (UV-Vis) absorption, and native polyacrylamide gel electrophoresis (Native-PAGE). Spectral results demonstrated that the RHAU peptide did not break the main structure of G4s, making it more reliable for G4 structural analysis. The RHAU peptide was found to display a structural selectivity for a preferential binding to parallel G4s as reflected by the distinct chromatographic retention behaviors. In addition, the RHAU peptide exhibited different interactions with intermolecular parallel G4s and intramolecular parallel G4s, providing a novel recognition approach to G4 structures. The findings of this study enriched the insight into the binding of RHAU to G4s with various conformations. It is noteworthy that SEC technology can be easy and reliable for elucidating G4-peptide interactions, especially for a multiple G4 coexisting system, which supplied an alternative strategy to screen novel specific ligands for G4s.
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Affiliation(s)
- Ju Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
| | - Junqin Qiao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
- Correspondence: (J.Q.); (H.L.)
| | - Weijuan Zheng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
| | - Hongzhen Lian
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering and Center of Materials Analysis, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
- Correspondence: (J.Q.); (H.L.)
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Zegers J, Peters M, Albada B. DNA G-quadruplex-stabilizing metal complexes as anticancer drugs. J Biol Inorg Chem 2023; 28:117-138. [PMID: 36456886 PMCID: PMC9981530 DOI: 10.1007/s00775-022-01973-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 11/17/2022] [Indexed: 12/04/2022]
Abstract
Guanine quadruplexes (G4s) are important targets for cancer treatments as their stabilization has been associated with a reduction of telomere ends or a lower oncogene expression. Although less abundant than purely organic ligands, metal complexes have shown remarkable abilities to stabilize G4s, and a wide variety of techniques have been used to characterize the interaction between ligands and G4s. However, improper alignment between the large variety of experimental techniques and biological activities can lead to improper identification of top candidates, which hampers progress of this important class of G4 stabilizers. To address this, we first review the different techniques for their strengths and weaknesses to determine the interaction of the complexes with G4s, and provide a checklist to guide future developments towards comparable data. Then, we surveyed 74 metal-based ligands for G4s that have been characterized to the in vitro level. Of these complexes, we assessed which methods were used to characterize their G4-stabilizing capacity, their selectivity for G4s over double-stranded DNA (dsDNA), and how this correlated to bioactivity data. For the biological activity data, we compared activities of the G4-stabilizing metal complexes with that of cisplatin. Lastly, we formulated guidelines for future studies on G4-stabilizing metal complexes to further enable maturation of this field.
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Affiliation(s)
- Jaccoline Zegers
- grid.4818.50000 0001 0791 5666Laboratory of Organic Chemistry, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Maartje Peters
- grid.4818.50000 0001 0791 5666Laboratory of Organic Chemistry, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Bauke Albada
- Laboratory of Organic Chemistry, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
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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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Santos T, Miranda A, Campello MPC, Paulo A, Salgado G, Cabrita EJ, Cruz C. Recognition of nucleolin through interaction with RNA G-quadruplex. Biochem Pharmacol 2021; 189:114208. [PMID: 32860827 DOI: 10.1016/j.bcp.2020.114208] [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: 05/20/2020] [Revised: 08/21/2020] [Accepted: 08/24/2020] [Indexed: 12/12/2022]
Abstract
The development of novel biomarkers for early-stage diagnosis of prostate cancer (PCa) has attracted the attention of researchers in the last decade. Nucleolin (NCL) has emerged as a possible biomarker of PCa due to its high expression levels in the surface of PCa cells and affinity towards parallel G4s since it contains four RNA-binding domains (RBDs). Herein, we developed a novel strategy based on a microfluidic platform for the detection of NCL in biological samples, such as human plasma. The RNA G4 (rG4) sequence found in human precursor microRNA 92b (pre-miR-92b) was used as a molecular recognition probe since it forms a single dominant parallel rG4 conformation in the presence of 0.1 mM K+ as confirmed by NMR spectroscopy. The additional stability of the rG4 structure was provided by the acridine orange derivative ligand C8, which stabilizes the pre-miR-92b rG4 structure, as denoted by an increase in more than 30 °C of its melting temperature. FRET-melting assay revealed a remarkable synergistic effect of NCL RBD1,2 and C8 on the stabilization of the pre-miR-92b rG4. The binding of pre-miR-92b to NCL RBD1,2 was determined by in silico studies, which revealed a binding pocket formed by a 12-residue linker between RBD1 and RBD2. Both, pre-miR-92b rG4 and pre-miR-92b rG4/C8 complex demonstrated high affinity towards NCL RBD1,2, as proved by fluorimetric titrations (KD range between 10-12 and 10-9 M). The stability and nuclease resistance of pre-miR-92b rG4 and pre-miR-92b rG4/C8 complex were evaluated as molecular recognition probes to capture and detect NCL. Finally, the microfluidic platform detects NCL in complex biological samples, such as human plasma. Overall, this work demonstrates the usefulness of the microfluidic platform based on the pre-miR-92b to detect NCL and the possibility to be used as a valuable biomedical tool in PCa diagnosis.
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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, Covilhã, Portugal
| | - André Miranda
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, Covilhã, Portugal
| | - Maria P C Campello
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10 (km 139,7), 2695-066 Bobadela LRS, Portugal
| | - António Paulo
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10 (km 139,7), 2695-066 Bobadela LRS, Portugal
| | - Gilmar Salgado
- Univ. Bordeaux, ARNA Laboratory, INSERM, U1212, CNRS UMR 5320, IECB, F-33600 Pessac, France
| | - Eurico J Cabrita
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica 2829-516, Portugal
| | - Carla Cruz
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, Covilhã, Portugal.
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Pont I, Martínez-Camarena Á, Galiana-Roselló C, Tejero R, Albelda MT, González-García J, Vilar R, García-España E. Development of Polyamine-Substituted Triphenylamine Ligands with High Affinity and Selectivity for G-Quadruplex DNA. Chembiochem 2020; 21:1167-1177. [PMID: 31701633 DOI: 10.1002/cbic.201900678] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Indexed: 01/01/2023]
Abstract
Currently, significant efforts are devoted to designing small molecules able to bind selectively to guanine quadruplexes (G4s). These noncanonical DNA structures are implicated in various important biological processes and have been identified as potential targets for drug development. Previously, a series of triphenylamine (TPA)-based compounds, including macrocyclic polyamines, that displayed high affinity towards G4 DNA were reported. Following this initial work, herein a series of second-generation compounds, in which the central TPA has been functionalised with flexible and adaptive linear polyamines, are presented with the aim of maximising the selectivity towards G4 DNA. The acid-base properties of the new derivatives have been studied by means of potentiometric titrations, UV/Vis and fluorescence emission spectroscopy. The interaction with G4s and duplex DNA has been explored by using FRET melting assays, fluorescence spectroscopy and circular dichroism. Compared with previous TPA derivatives with macrocyclic substituents, the new ligands reported herein retain the G4 affinity, but display two orders of magnitude higher selectivity for G4 versus duplex DNA; this is most likely due to the ability of the linear substituents to embrace the G4 structure.
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Affiliation(s)
- Isabel Pont
- Department of Inorganic Chemistry, Institute of Molecular Science, University of Valencia, Catedrático José Beltrán 2, 46980, Paterna, Spain.,Department of Chemistry, Imperial College London, White City Campus, London, W12 OBZ, UK
| | - Álvaro Martínez-Camarena
- Department of Inorganic Chemistry, Institute of Molecular Science, University of Valencia, Catedrático José Beltrán 2, 46980, Paterna, Spain
| | - Cristina Galiana-Roselló
- Department of Inorganic Chemistry, Institute of Molecular Science, University of Valencia, Catedrático José Beltrán 2, 46980, Paterna, Spain
| | - Roberto Tejero
- Department of Physical Chemistry, University of Valencia, Dr. Moliner s/n, 46100, Burjassot, Spain
| | - M Teresa Albelda
- Department of Inorganic Chemistry, Institute of Molecular Science, University of Valencia, Catedrático José Beltrán 2, 46980, Paterna, Spain
| | - Jorge González-García
- Department of Inorganic Chemistry, Institute of Molecular Science, University of Valencia, Catedrático José Beltrán 2, 46980, Paterna, Spain.,Department of Chemistry, Imperial College London, White City Campus, London, W12 OBZ, UK
| | - Ramón Vilar
- Department of Chemistry, Imperial College London, White City Campus, London, W12 OBZ, UK
| | - Enrique García-España
- Department of Inorganic Chemistry, Institute of Molecular Science, University of Valencia, Catedrático José Beltrán 2, 46980, Paterna, Spain
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