1
|
Zhan X, Deng L, Lian Y, Shu Z, Xu Y, Mai X, Krishna MS, Lu R, Wang A, Bai S, Zhou F, Xiong C, Xu Y, Ni J, Vandana JJ, Wang Z, Li Y, Sun D, Huang S, Liu J, Cheng GJ, Wu S, Chiang YC, Stjepanovic G, Jiang C, Shao Y, Chen G. Enhanced Recognition of a Herbal Compound Epiberberine by a DNA Quadruplex-Duplex Structure. Anal Chem 2024. [PMID: 39093925 DOI: 10.1021/acs.analchem.4c02054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
The small molecule epiberberine (EPI) is a natural alkaloid with versatile bioactivities against several diseases including cancer and bacterial infection. EPI can induce the formation of a unique binding pocket at the 5' side of a human telomeric G-quadruplex (HTG) sequence with four telomeric repeats (Q4), resulting in a nanomolar binding affinity (KD approximately 26 nM) with significant fluorescence enhancement upon binding. It is important to understand (1) how EPI binding affects HTG structural stability and (2) how enhanced EPI binding may be achieved through the engineering of the DNA binding pocket. In this work, the EPI-binding-induced HTG structure stabilization effect was probed by a peptide nucleic acid (PNA) invasion assay in combination with a series of biophysical techniques. We show that the PNA invasion-based method may be useful for the characterization of compounds binding to DNA (and RNA) structures under physiological conditions without the need to vary the solution temperature or buffer components, which are typically needed for structural stability characterization. Importantly, the combination of theoretical modeling and experimental quantification allows us to successfully engineer Q4 derivative Q4-ds-A by a simple extension of a duplex structure to Q4 at the 5' end. Q4-ds-A is an excellent EPI binder with a KD of 8 nM, with the binding enhancement achieved through the preformation of a binding pocket and a reduced dissociation rate. The tight binding of Q4 and Q4-ds-A with EPI allows us to develop a novel magnetic bead-based affinity purification system to effectively extract EPI from Rhizoma coptidis (Huang Lian) extracts.
Collapse
Affiliation(s)
- Xuan Zhan
- School of Medicine, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), Shenzhen 518172, Guangdong, P. R. China
| | - Liping Deng
- School of Medicine, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), Shenzhen 518172, Guangdong, P. R. China
| | - Yun Lian
- School of Medicine, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), Shenzhen 518172, Guangdong, P. R. China
| | - Zhiyu Shu
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore
| | - Yunong Xu
- School of Medicine, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), Shenzhen 518172, Guangdong, P. R. China
| | - Xinyi Mai
- School of Medicine, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), Shenzhen 518172, Guangdong, P. R. China
| | - Manchugondanahalli S Krishna
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore
| | - Rongguang Lu
- School of Medicine, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), Shenzhen 518172, Guangdong, P. R. China
| | - Anni Wang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), Shenzhen 518172, Guangdong, P. R. China
| | - Shiyao Bai
- School of Medicine, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), Shenzhen 518172, Guangdong, P. R. China
| | - Fangyu Zhou
- School of Medicine, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), Shenzhen 518172, Guangdong, P. R. China
| | - Chi Xiong
- MinJiang Collaborative Center for Theoretical Physics, College of Physics and Electronic Information Engineering, Minjiang University, Fuzhou 350108, Fujian, P. R. China
| | - Yingyi Xu
- LightEdge Technologies Ltd., Zhongshan 528400, Guangdong, P. R. China
| | - Jie Ni
- School of Medicine, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), Shenzhen 518172, Guangdong, P. R. China
| | - J Jeya Vandana
- Department of Surgery, Weill Cornell Medicine, New York, New York 10065, United States
- Tri-Institutional PhD Program in Chemical Biology, Weill Cornell Medicine, Memorial Sloan Kettering Cancer Center, The Rockefeller University, New York, New York 10065, United States
| | - Zi Wang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), Shenzhen 518172, Guangdong, P. R. China
| | - Yuqing Li
- Department of Urology, South China Hospital of Shenzhen University, Shenzhen 518111, Guangdong, P. R. China
| | - Dongmei Sun
- Guangdong Yifang Pharmaceutical, Foshan 528244, Guangdong, P. R. China
| | - Shaohui Huang
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 101499, P. R. China
| | - Jingyan Liu
- School of Medicine, The Second Affiliated Hospital, The Chinese University of Hong Kong, Shenzhen 518172, Guangdong, P. R. China
| | - Gui-Juan Cheng
- School of Medicine, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), Shenzhen 518172, Guangdong, P. R. China
| | - Song Wu
- Department of Urology, South China Hospital of Shenzhen University, Shenzhen 518111, Guangdong, P. R. China
| | - Ying-Chih Chiang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), Shenzhen 518172, Guangdong, P. R. China
| | - Goran Stjepanovic
- School of Medicine, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), Shenzhen 518172, Guangdong, P. R. China
| | - Cheng Jiang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), Shenzhen 518172, Guangdong, P. R. China
| | - Yong Shao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, Zhejiang Normal University, Jinhua 321004, Zhejiang, P. R. China
| | - Gang Chen
- School of Medicine, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), Shenzhen 518172, Guangdong, P. R. China
- Shenzhen Key Laboratory of Innovative Drug Synthesis, The Chinese University of Hong Kong, Shenzhen 518172, P. R. China
| |
Collapse
|
2
|
Han ZQ, Wen LN. Application of G-quadruplex targets in gastrointestinal cancers: Advancements, challenges and prospects. World J Gastrointest Oncol 2023; 15:1149-1173. [PMID: 37546556 PMCID: PMC10401460 DOI: 10.4251/wjgo.v15.i7.1149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 04/11/2023] [Accepted: 05/08/2023] [Indexed: 07/12/2023] Open
Abstract
Genomic instability and inflammation are considered to be two enabling characteristics that support cancer development and progression. G-quadruplex structure is a key element that contributes to genomic instability and inflammation. G-quadruplexes were once regarded as simply an obstacle that can block the transcription of oncogenes. A ligand targeting G-quadruplexes was found to have anticancer activity, making G-quadruplexes potential anticancer targets. However, further investigation has revealed that G-quadruplexes are widely distributed throughout the human genome and have many functions, such as regulating DNA replication, DNA repair, transcription, translation, epigenetics, and inflammatory response. G-quadruplexes play double regulatory roles in transcription and translation. In this review, we focus on G-quadruplexes as novel targets for the treatment of gastrointestinal cancers. We summarize the application basis of G-quadruplexes in gastrointestinal cancers, including their distribution sites, structural characteristics, and physiological functions. We describe the current status of applications for the treatment of esophageal cancer, pancreatic cancer, hepatocellular carcinoma, gastric cancer, colorectal cancer, and gastrointestinal stromal tumors, as well as the associated challenges. Finally, we review the prospective clinical applications of G-quadruplex targets, providing references for targeted treatment strategies in gastrointestinal cancers.
Collapse
Affiliation(s)
- Zong-Qiang Han
- Department of Laboratory Medicine, Beijing Xiaotangshan Hospital, Beijing 102211, China
| | - Li-Na Wen
- Department of Clinical Nutrition, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China
| |
Collapse
|
4
|
Ruiz N, Jarosova P, Taborsky P, Gargallo R. Study of the interaction of the palmatine alkaloid with hybrid G-quadruplex/duplex and i-motif/duplex DNA structures. Biophys Chem 2021; 281:106715. [PMID: 34784553 DOI: 10.1016/j.bpc.2021.106715] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/22/2021] [Accepted: 11/04/2021] [Indexed: 11/19/2022]
Abstract
There is an increasing interest in the study of guanine or cytosine-rich sequences that may fold into G-quadruplex (G4) or i-motif (iM) structures showing a short hairpin (or stem-loop) stabilized by Watson-Crick base pairs. These hybrid spatial arrangements may be target of ligands that have been shown to interact strongly with B-DNA. In this work, the interaction of the palmatine alkaloid with several sequences forming different G4s, iMs, and hybrid structures has been studied by means of spectroscopic and separation techniques, as well as multivariate data analysis methods. At the experimental conditions used in this work, the results have shown that this ligand strongly stabilizes parallel G4 structures, whereas a weaker interaction was observed with the antiparallel G4 adopted by the thrombin-binding aptamer or iMs. The presence of hairpins within the loops scarcely affects the affinity of this ligand for the hybrid G4/duplex or iM/duplex structures. Fluorescence measurements have provided evidence of a certain interaction with iMs at pH 5.1, despite the absence of thermal stabilization effects.
Collapse
Affiliation(s)
- Noelia Ruiz
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Martí I Franqués 1-11, E-08028 Barcelona, Spain
| | - Petra Jarosova
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Petr Taborsky
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic.
| | - Raimundo Gargallo
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Martí I Franqués 1-11, E-08028 Barcelona, Spain.
| |
Collapse
|
5
|
Figueiredo J, Santos T, Miranda A, Alexandre D, Teixeira B, Simões P, Lopes-Nunes J, Cruz C. Ligands as Stabilizers of G-Quadruplexes in Non-Coding RNAs. Molecules 2021; 26:6164. [PMID: 34684745 PMCID: PMC8540333 DOI: 10.3390/molecules26206164] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/03/2021] [Accepted: 10/06/2021] [Indexed: 11/16/2022] Open
Abstract
The non-coding RNAs (ncRNA) are RNA transcripts with different sizes, structures and biological functions that do not encode functional proteins. RNA G-quadruplexes (rG4s) have been found in small and long ncRNAs. The existence of an equilibrium between rG4 and stem-loop structures in ncRNAs and its effect on biological processes remains unexplored. For example, deviation from the stem-loop leads to deregulated mature miRNA levels, demonstrating that miRNA biogenesis can be modulated by ions or small molecules. In light of this, we report several examples of rG4s in certain types of ncRNAs, and the implications of G4 stabilization using small molecules, also known as G4 ligands, in the regulation of gene expression, miRNA biogenesis, and miRNA-mRNA interactions. Until now, different G4 ligands scaffolds were synthesized for these targets. The regulatory role of the above-mentioned rG4s in ncRNAs can be used as novel therapeutic approaches for adjusting miRNA levels.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Carla Cruz
- CICS-UBI—Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Hen-rique, 6200-506 Covilhã, Portugal; (J.F.); (T.S.); (A.M.); (D.A.); (B.T.); (P.S.); (J.L.-N.)
| |
Collapse
|