1
|
Gao C, Mohamed HI, Deng J, Umer M, Anwar N, Chen J, Wu Q, Wang Z, He Y. Effects of Molecular Crowding on the Structure, Stability, and Interaction with Ligands of G-quadruplexes. ACS OMEGA 2023; 8:14342-14348. [PMID: 37125118 PMCID: PMC10134454 DOI: 10.1021/acsomega.3c01169] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 04/03/2023] [Indexed: 05/03/2023]
Abstract
G-quadruplexes (G4s) are widely found in cells and have significant biological functions, which makes them a target for screening antitumor and antiviral drugs. Most of the previous research on G4s has been conducted mainly in diluted solutions. However, cells are filled with organelles and many biomolecules, resulting in a constant state of a crowded molecular environment. The conformation and stability of some G4s were found to change significantly in the molecularly crowded environment, and interactions with ligands were disturbed to some extent. The structure of the G4s and their biological functions are correlated, and the effect of the molecularly crowded environment on G4 conformational transitions and interactions with ligands should be considered in drug design targeting G4s. This review discusses the changes in the conformation and stability of G4s in a physiological environment. Moreover, the mechanism of action of the molecularly crowded environment affecting the G4 has been further reviewed based on previous studies. Furthermore, current challenges and future research directions are put forward. This review has implications for the design of drugs targeting G4s.
Collapse
Affiliation(s)
- Chao Gao
- National
R&D Center for Se-rich Agricultural Products Processing, Hubei
Engineering Research Center for Deep Processing of Green Se-rich Agricultural
Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Hany I. Mohamed
- Chemistry
Department, Faculty of Science, Benha University, Benha 13518, Egypt
| | - Jieya Deng
- National
R&D Center for Se-rich Agricultural Products Processing, Hubei
Engineering Research Center for Deep Processing of Green Se-rich Agricultural
Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Muhammad Umer
- Institute
for Forest Resources and Environment of Guizhou and Forestry College,
Research Center of Forest Ecology, Guizhou
University, Guiyang 550025, China
| | - Naureen Anwar
- Department
of Zoology, University of Narowal, Narowal, Punjab 51600, Pakistan
| | - Jixin Chen
- National
R&D Center for Se-rich Agricultural Products Processing, Hubei
Engineering Research Center for Deep Processing of Green Se-rich Agricultural
Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Qiao Wu
- Wuhan
Botanical Garden, Chinese Academy of Science, Wuhan 430074, China
| | - Zhangqian Wang
- National
R&D Center for Se-rich Agricultural Products Processing, Hubei
Engineering Research Center for Deep Processing of Green Se-rich Agricultural
Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Yi He
- National
R&D Center for Se-rich Agricultural Products Processing, Hubei
Engineering Research Center for Deep Processing of Green Se-rich Agricultural
Products, School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| |
Collapse
|
2
|
Telomerase: A prominent oncological target for development of chemotherapeutic agents. Eur J Med Chem 2023; 249:115121. [PMID: 36669398 DOI: 10.1016/j.ejmech.2023.115121] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/26/2022] [Accepted: 01/11/2023] [Indexed: 01/15/2023]
Abstract
Telomerase is a ribonucleoprotein (RNP) responsible for the maintenance of chromosomal integrity by stabilizing telomere length. Telomerase is a widely expressed hallmark responsible for replicative immortality in 80-90% of malignant tumors. Cancer cells produce telomerase which prevents telomere shortening by adding telomeres sequences beyond Hayflick's limit; which enables them to divide uncontrollably. The activity of telomerase is relatively low in somatic cells and absent in normal cells, but the re-activation of this RNP in normal cells suppresses p53 activity which leads to the avoidance of senescence causing malignancy. Here, we have focused explicitly on various anti-telomerase therapies and telomerase-inhibiting molecules for the treatment of cancer. We have covered molecules that are reported in developmental, preclinical, and clinical trial stages as potent telomerase inhibitors. Apart from chemotherapy, we have also included details of immunotherapy, gene therapy, G-quadruplex stabilizers, and HSP-90 inhibitors. The purpose of this work is to discuss the challenges behind the development of novel telomerase inhibitors and to identify various perspectives for designing anti-telomerase compounds.
Collapse
|
3
|
Pokhrel P, Wang J, Selvam S, Jonchhe S, Mandal S, Mao H. Ensemble Force Spectroscopy of a G-Quadruplex Cluster on a Single-Molecule Platform. Biomacromolecules 2022; 23:4795-4803. [PMID: 36322676 PMCID: PMC10347895 DOI: 10.1021/acs.biomac.2c00959] [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] [Indexed: 11/05/2022]
Abstract
Single-molecule methods offer high sensitivities with precisions superior to bulk assays. However, these methods are low in throughput and cannot repetitively interrogate the same cluster of molecular units. In this work, we investigate a tandem array of G-quadruplexes on a single-molecule DNA template with a throughput of at least two orders of magnitude higher than single-molecule force spectroscopy. During mechanical unfolding by optical tweezers, the array of G-quadruplexes experiences identical force, temperature, and ionic conditions, which not only reduce environmental noise but also render unfolding transitions indistinguishable among individual G-quadruplexes. The resultant ensemble behaviors are analyzed by scanning force diagrams, which reveals accurate F1/2 values, where 50% of G-quadruplexes are unfolded. Independent of the number of G-quadruplexes (n > 15) contained in a cluster, F1/2 can effectively evaluate G-quadruplex ligands in a new method called differential scanning forcemetry. When the same G-quadruplex cluster is subject to a series of constant forces in force-jump experiments, unfolding rate constants of G-quadruplexes can be effectively evaluated as a function of force. The high precision demonstrated in all of these measurements reflects the power of repetitive sampling on the same cluster of single-molecule entities under identical conditions. Since biomolecules such as DNA, RNA, and proteins can be conveniently incorporated in a tandem array, we anticipate that this ensemble assay on single-molecule entities (EASE) provides a generic means of ensemble force spectroscopy to amalgamate the accuracy of ensemble measurements with the precision of single-molecule methods.
Collapse
Affiliation(s)
| | | | - Sangeetha Selvam
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Sagun Jonchhe
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Shankar Mandal
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Hanbin Mao
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| |
Collapse
|
4
|
Pokhrel P, Sasaki S, Hu C, Karna D, Pandey S, Ma Y, Nagasawa K, Mao H. Single-molecule displacement assay reveals strong binding of polyvalent dendrimer ligands to telomeric G-quadruplex. Anal Biochem 2022; 649:114693. [PMID: 35500657 PMCID: PMC9133229 DOI: 10.1016/j.ab.2022.114693] [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: 02/22/2022] [Revised: 04/04/2022] [Accepted: 04/17/2022] [Indexed: 11/01/2022]
Abstract
Binding between a ligand and a receptor is a fundamental step in many natural or synthetic processes. In biosensing, a tight binding with a small dissociation constant (Kd) between the probe and analyte can lead to superior specificity and sensitivity. Owing to their capability of evaluating competitors, displacement assays have been used to estimate Kd at the ensemble average level. At the more sensitive single-molecule level, displacement assays are yet to be established. Here, we developed a single-molecule displacement assay (smDA) in an optical tweezers instrument and used this innovation to evaluate the binding of the L2H2-6OTD ligands to human telomeric DNA G-quadruplexes. After measuring Kd of linear and dendrimer L2H2-6OTD ligands, we found that dendrimer ligands have enhanced binding affinity to the G-quadruplexes due to their polyvalent geometry. This increased binding affinity enhanced inhibition of telomerase elongation on a telomere template in a Telomerase Repeated Amplification Protocol (TRAP). Our experiments demonstrate that the smDA approach can efficiently evaluate binding processes in chemical and biological processes.
Collapse
Affiliation(s)
- Pravin Pokhrel
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44242, USA
| | - Shogo Sasaki
- Department of Biotechnology and Life Science Faculty of Technology, Tokyo University of Agriculture and Technology (TUAT), 2-14-16 Naka-cho, Koganeishi, Tokyo, 184-8588, Japan
| | - Changpeng Hu
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44242, USA; Department of Pharmacy, The Second Affiliated Hospital, Army Medical University, Chongqing, 400037, China
| | - Deepak Karna
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44242, USA
| | - Shankar Pandey
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44242, USA
| | - Yue Ma
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology (TUAT), 2-14-16 Naka-cho, Koganeishi, Tokyo, 184-8588, Japan
| | - Kazuo Nagasawa
- Department of Biotechnology and Life Science Faculty of Technology, Tokyo University of Agriculture and Technology (TUAT), 2-14-16 Naka-cho, Koganeishi, Tokyo, 184-8588, Japan.
| | - Hanbin Mao
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44242, USA.
| |
Collapse
|
5
|
Largy E, König A, Ghosh A, Ghosh D, Benabou S, Rosu F, Gabelica V. Mass Spectrometry of Nucleic Acid Noncovalent Complexes. Chem Rev 2021; 122:7720-7839. [PMID: 34587741 DOI: 10.1021/acs.chemrev.1c00386] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to assess target structure as well as ligand binding stoichiometry, affinity, specificity, and binding modes are part of the drug development process. Mass spectrometry offers unique advantages as a biophysical method owing to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here, we review the fundamentals of mass spectrometry and all its particularities when studying noncovalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands.
Collapse
Affiliation(s)
- Eric Largy
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Alexander König
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Anirban Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Debasmita Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Sanae Benabou
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Frédéric Rosu
- Univ. Bordeaux, CNRS, INSERM, IECB, UMS 3033, F-33600 Pessac, France
| | - Valérie Gabelica
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| |
Collapse
|
6
|
Gao C, Liu Z, Hou H, Ding J, Chen X, Xie C, Song Z, Hu Z, Feng M, Mohamed HI, Xu S, Parkinson GN, Haider S, Wei D. BMPQ-1 binds selectively to (3+1) hybrid topologies in human telomeric G-quadruplex multimers. Nucleic Acids Res 2020; 48:11259-11269. [PMID: 33080032 PMCID: PMC7672424 DOI: 10.1093/nar/gkaa870] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 09/23/2020] [Accepted: 10/14/2020] [Indexed: 12/21/2022] Open
Abstract
A single G-quadruplex forming sequence from the human telomere can adopt six distinct topologies that are inter-convertible under physiological conditions. This presents challenges to design ligands that show selectivity and specificity towards a particular conformation. Additional complexity is introduced in differentiating multimeric G-quadruplexes over monomeric species, which would be able to form in the single-stranded 3′ ends of telomeres. A few ligands have been reported that bind to dimeric quadruplexes, but their preclinical pharmacological evaluation is limited. Using multidisciplinary approaches, we identified a novel quinoline core ligand, BMPQ-1, which bound to human telomeric G-quadruplex multimers over monomeric G-quadruplexes with high selectivity, and induced the formation of G-quadruplex DNA along with the related DNA damage response at the telomere. BMPQ-1 reduced tumor cell proliferation with an IC50 of ∼1.0 μM and decreased tumor growth rate in mouse by half. Biophysical analysis using smFRET identified a mixture of multiple conformations coexisting for dimeric G-quadruplexes in solution. Here, we showed that the titration of BMPQ-1 shifted the conformational ensemble of multimeric G-quadruplexes towards (3+1) hybrid-2 topology, which became more pronounced as further G-quadruplex units are added.
Collapse
Affiliation(s)
- Chao Gao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.,National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong AgriculturalUniversity, Wuhan, 430070, China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhu Liu
- National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Haitao Hou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.,Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Jieqin Ding
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.,Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Xin Chen
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Congbao Xie
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.,Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Zibing Song
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.,Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhe Hu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Mingqian Feng
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hany I Mohamed
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.,Chemistry Department, Faculty of Science, Benha University, Benha 13518, Egypt
| | - Shengzhen Xu
- Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Gary N Parkinson
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Shozeb Haider
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Dengguo Wei
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.,National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong AgriculturalUniversity, Wuhan, 430070, China
| |
Collapse
|
7
|
Zhao J, Zhai Q. Recent advances in the development of ligands specifically targeting telomeric multimeric G-quadruplexes. Bioorg Chem 2020; 103:104229. [DOI: 10.1016/j.bioorg.2020.104229] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 08/16/2020] [Accepted: 08/20/2020] [Indexed: 01/24/2023]
|
8
|
Maleki P, Mustafa G, Gyawali P, Budhathoki JB, Ma Y, Nagasawa K, Balci H. Quantifying the impact of small molecule ligands on G-quadruplex stability against Bloom helicase. Nucleic Acids Res 2020; 47:10744-10753. [PMID: 31544934 PMCID: PMC6847008 DOI: 10.1093/nar/gkz803] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 08/28/2019] [Accepted: 09/09/2019] [Indexed: 01/28/2023] Open
Abstract
G-quadruplex (GQ) stabilizing small molecule (SM) ligands have been used to stabilize human telomeric GQ (hGQ) to inhibit telomerase activity, or non-telomeric GQs to manipulate gene expression at transcription or translation level. GQs are known to inhibit DNA replication unless destabilized by helicases, such as Bloom helicase (BLM). Even though the impact of SM ligands on thermal stability of GQs is commonly used to characterize their efficacy, how these ligands influence helicase-mediated GQ unfolding is not well understood. Three prominent SM ligands (an oxazole telomestatin derivative, pyridostatin, and PhenDC3), which thermally stabilize hGQ at different levels, were utilized in this study. How these ligands influence BLM-mediated hGQ unfolding was investigated using two independent single-molecule approaches. While the frequency of dynamic hGQ unfolding events was used as the metric in the first approach, the second approach was based on quantifying the cumulative unfolding activity as a function of time. All three SM ligands inhibited BLM activity at similar levels, 2–3 fold, in both approaches. Our observations suggest that the impact of SM ligands on GQ thermal stability is not an ideal predictor for their inhibition of helicase-mediated unfolding, which is physiologically more relevant.
Collapse
Affiliation(s)
- Parastoo Maleki
- Department of Physics, Kent State University, Kent, OH 44242, USA
| | - Golam Mustafa
- Department of Physics, Kent State University, Kent, OH 44242, USA
| | - Prabesh Gyawali
- Department of Physics, Kent State University, Kent, OH 44242, USA
| | | | - Yue Ma
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Kazuo Nagasawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Hamza Balci
- Department of Physics, Kent State University, Kent, OH 44242, USA
| |
Collapse
|
9
|
Takeuchi R, Zou T, Wakahara D, Nakano Y, Sato S, Takenaka S. Cyclic Naphthalene Diimide Dimer with a Strengthened Ability to Stabilize Dimeric G-Quadruplex. Chemistry 2019; 25:8691-8695. [PMID: 31069868 DOI: 10.1002/chem.201901468] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/06/2019] [Indexed: 11/08/2022]
Abstract
A new type of dimeric cyclic naphthalene diimide derivatives (cNDI-dimers) carrying varied linker length were designed and synthesized to recognize dimeric G-quadruplex structures. All of the cNDI-dimers exhibited a high preference for recognizing G-quadruplex structures, and significantly enhanced the thermal stability of the dimeric G-quadruplex structure over the cNDI monomer by increasing the melting temperature by more than 23 °C, which indicated the strengthened ability of cNDI dimers for stabilizing dimeric G-quadruplex. cNDI dimers also showed a stronger ability to inhibit telomerase activity and stop telomere DNA elongation than cNDI monomer, which showed an improved anticancer potentiality for further therapeutic application.
Collapse
Affiliation(s)
- Ryusuke Takeuchi
- Department of Applied Chemistry, Kyushu Institute of Technology, Fukuoka, 804-8550, Japan
| | - Tingting Zou
- Department of Applied Chemistry, Kyushu Institute of Technology, Fukuoka, 804-8550, Japan.,Research Center for Bio-microsensing Technology, Kyushu Institute of Technology, Fukuoka, 804-8550, Japan
| | - Daiki Wakahara
- Department of Applied Chemistry, Kyushu Institute of Technology, Fukuoka, 804-8550, Japan
| | - Yoshifumi Nakano
- Department of Applied Chemistry, Kyushu Institute of Technology, Fukuoka, 804-8550, Japan
| | - Shinobu Sato
- Department of Applied Chemistry, Kyushu Institute of Technology, Fukuoka, 804-8550, Japan.,Research Center for Bio-microsensing Technology, Kyushu Institute of Technology, Fukuoka, 804-8550, Japan
| | - Shigeori Takenaka
- Department of Applied Chemistry, Kyushu Institute of Technology, Fukuoka, 804-8550, Japan.,Research Center for Bio-microsensing Technology, Kyushu Institute of Technology, Fukuoka, 804-8550, Japan
| |
Collapse
|
10
|
Gyawali P, Gc K, Ma Y, Abeysirigunawardena S, Nagasawa K, Balci H. Impact of Small Molecules on Intermolecular G-Quadruplex Formation. Molecules 2019; 24:molecules24081570. [PMID: 31010019 PMCID: PMC6514588 DOI: 10.3390/molecules24081570] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 04/18/2019] [Accepted: 04/19/2019] [Indexed: 11/24/2022] Open
Abstract
We performed single molecule studies to investigate the impact of several prominent small molecules (the oxazole telomestatin derivative L2H2-6OTD, pyridostatin, and Phen-DC3) on intermolecular G-quadruplex (i-GQ) formation between two guanine-rich DNA strands that had 3-GGG repeats in one strand and 1-GGG repeat in the other (3+1 GGG), or 2-GGG repeats in each strand (2+2 GGG). Such structures are not only physiologically significant but have recently found use in various biotechnology applications, ranging from DNA-based wires to chemical sensors. Understanding the extent of stability imparted by small molecules on i-GQ structures, has implications for these applications. The small molecules resulted in different levels of enhancement in i-GQ formation, depending on the small molecule and arrangement of GGG repeats. The largest enhancement we observed was in the 3+1 GGG arrangement, where i-GQ formation increased by an order of magnitude, in the presence of L2H2-6OTD. On the other hand, the enhancement was limited to three-fold with Pyridostatin (PDS) or less for the other small molecules in the 2+2 GGG repeat case. By demonstrating detection of i-GQ formation at the single molecule level, our studies illustrate the feasibility to develop more sensitive sensors that could operate with limited quantities of materials.
Collapse
Affiliation(s)
- Prabesh Gyawali
- Department of Physics, Kent State University, Kent, OH 44242, USA.
| | - Keshav Gc
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA.
| | - Yue Ma
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan.
| | | | - Kazuo Nagasawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan.
| | - Hamza Balci
- Department of Physics, Kent State University, Kent, OH 44242, USA.
| |
Collapse
|
11
|
A comparative study of assembly and disassembly process of dimeric and monomeric cyanine dyes with DNA templates. CHINESE CHEM LETT 2019. [DOI: 10.1016/j.cclet.2018.10.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
12
|
Saintomé C, Alberti P, Guinot N, Lejault P, Chatain J, Mailliet P, Riou JF, Bugaut A. Binding properties of mono- and dimeric pyridine dicarboxamide ligands to human telomeric higher-order G-quadruplex structures. Chem Commun (Camb) 2018; 54:1897-1900. [PMID: 29393312 DOI: 10.1039/c7cc07048a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Here, we report on the in vitro binding properties of the known pyridine dicarboxamide G-quadruplex ligand 360A and a new dimeric analogue (360A)2A to human telomeric DNA higher-order G-quadruplex (G4) structures. This study points to original binding features never reported for G4 ligands, and reveals a greater efficiency for the dimeric ligand to displace RPA (a ssDNA binding protein involved in telomere replication) from telomeric DNA.
Collapse
Affiliation(s)
- C Saintomé
- "Structure and Instability of Genomes" laboratory, Sorbonne Universités, Muséum National d'Histoire Naturelle (MNHN), Inserm U1154, CNRS UMR 7196, 75005 Paris, France.
| | | | | | | | | | | | | | | |
Collapse
|
13
|
Targeting glioma stem cells in vivo by a G-quadruplex-stabilizing synthetic macrocyclic hexaoxazole. Sci Rep 2017; 7:3605. [PMID: 28620243 PMCID: PMC5472576 DOI: 10.1038/s41598-017-03785-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 05/03/2017] [Indexed: 11/15/2022] Open
Abstract
G-quadruplex (G4) is a higher-order nucleic acid structure that is formed by guanine-rich sequences. G4 stabilization by small-molecule compounds called G4 ligands often causes cytotoxicity, although the potential medicinal impact of this effect has not been fully established. Here we demonstrate that a synthetic G4 ligand, Y2H2-6M(4)-oxazole telomestatin derivative (6OTD), limits the growth of intractable glioblastoma (grade IV glioma) and glioma stem cells (GSCs). Experiments involving a human cancer cell line panel and mouse xenografts revealed that 6OTD exhibits antitumor activity against glioblastoma. 6OTD inhibited the growth of GSCs more potently than it did the growth of differentiated non-stem glioma cells (NSGCs). 6OTD caused DNA damage, G1 cell cycle arrest, and apoptosis in GSCs but not in NSGCs. These DNA damage foci tended to colocalize with telomeres, which contain repetitive G4-forming sequences. Compared with temozolomide, a clinical DNA-alkylating agent against glioma, 6OTD required lower concentrations to exert anti-cancer effects and preferentially affected GSCs and telomeres. 6OTD suppressed the intracranial growth of GSC-derived tumors in a mouse xenograft model. These observations indicate that 6OTD targets GSCs through G4 stabilization and promotion of DNA damage responses. Therefore, G4s are promising therapeutic targets for glioblastoma.
Collapse
|
14
|
Abraham Punnoose J, Ma Y, Li Y, Sakuma M, Mandal S, Nagasawa K, Mao H. Adaptive and Specific Recognition of Telomeric G-Quadruplexes via Polyvalency Induced Unstacking of Binding Units. J Am Chem Soc 2017; 139:7476-7484. [PMID: 28505453 DOI: 10.1021/jacs.7b00607] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Targeting DNA G-quadruplexes using small-molecule ligands has shown to modulate biological functions mediated by G-quadruplexes inside cells. Given >716 000 G-quadruplex hosting sites in human genome, the specific binding of ligands to quadruplex becomes problematic. Here, we innovated a polyvalency based mechanism to specifically target multiple telomeric G-quadruplexes. We synthesized a tetrameric telomestatin derivative and evaluated its complex polyvalent binding with multiple G-quadruplexes by single-molecule mechanical unfolding in laser tweezers. We found telomestatin tetramer binds to multimeric telomeric G-quadruplexes >40 times stronger than monomeric quadruplexes, which can be ascribed to the polyvalency induced unstacking of binding units (or PIU binding) for G-quadruplexes. While stacking of telomestatin units in the tetramer imparts steric hindrance for the ligand to access stand-alone G-quadruplexes, the stacking disassembles to accommodate the potent polyvalent binding between the tetramer ligand and multimeric G-quadruplexes. We anticipate this adaptive PIU binding offers a generic mechanism to selectively target polymeric biomolecules prevalent inside cells.
Collapse
Affiliation(s)
- Jibin Abraham Punnoose
- Department of Chemistry and Biochemistry, Kent State University , Kent, Ohio 44242, United States
| | - Yue Ma
- Department of Biotechnology and Life Science Faculty of Technology, Tokyo University of Agriculture and Technology (TUAT) , 2-14-16 Naka-cho, Koganeishi, Tokyo 184-8588, Japan
| | - Yuanyuan Li
- Department of Chemistry and Biochemistry, Kent State University , Kent, Ohio 44242, United States
| | - Mai Sakuma
- Department of Biotechnology and Life Science Faculty of Technology, Tokyo University of Agriculture and Technology (TUAT) , 2-14-16 Naka-cho, Koganeishi, Tokyo 184-8588, Japan
| | - Shankar Mandal
- Department of Chemistry and Biochemistry, Kent State University , Kent, Ohio 44242, United States
| | - Kazuo Nagasawa
- Department of Biotechnology and Life Science Faculty of Technology, Tokyo University of Agriculture and Technology (TUAT) , 2-14-16 Naka-cho, Koganeishi, Tokyo 184-8588, Japan
| | - Hanbin Mao
- Department of Chemistry and Biochemistry, Kent State University , Kent, Ohio 44242, United States
| |
Collapse
|
15
|
Maleki P, Budhathoki JB, Roy WA, Balci H. A practical guide to studying G-quadruplex structures using single-molecule FRET. Mol Genet Genomics 2017; 292:483-498. [PMID: 28150040 DOI: 10.1007/s00438-017-1288-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 01/05/2017] [Indexed: 11/26/2022]
Abstract
In this article, we summarize the knowledge and best practices learned from bulk and single-molecule measurements to address some of the frequently experienced difficulties in single-molecule Förster resonance energy transfer (smFRET) measurements on G-quadruplex (GQ) structures. The number of studies that use smFRET to investigate the structure, function, dynamics, and interactions of GQ structures has grown significantly in the last few years, with new applications already in sight. However, a number of challenges need to be overcome before reliable and reproducible smFRET data can be obtained in measurements that include GQ. The annealing and storage conditions, the location of fluorophores on the DNA construct, and the ionic conditions of the experiment are some of the factors that are of critical importance for the outcome of measurements, and many of these manifest themselves in unique ways in smFRET assays. By reviewing these aspects and providing a summary of best practices, we aim to provide a practical guide that will help in successfully designing and performing smFRET studies on GQ structures.
Collapse
Affiliation(s)
- Parastoo Maleki
- Department of Physics, Kent State University, Kent, OH, 44242, USA
| | | | - William A Roy
- Department of Physics, Kent State University, Kent, OH, 44242, USA
| | - Hamza Balci
- Department of Physics, Kent State University, Kent, OH, 44242, USA.
| |
Collapse
|
16
|
Nagasawa K, Ma Y, Iida K, Nakamura T, Seimiya H, Ohtake T. Design, Synthesis and Evaluation of an L-Dopa-Derived Macrocyclic Hexaoxazole (6otd) as a G-Quadruplex-Selective Ligand. HETEROCYCLES 2016. [DOI: 10.3987/com-15-13383] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
17
|
Yu L, Yang Q, Xiang J, Sun H, Wang L, Li Q, Guan A, Tang Y. Targeting of parallel c-myc G-quadruplex by dimeric cyanine dye supramolecular assembly: dependence on the linker length. Analyst 2015; 140:1637-46. [DOI: 10.1039/c4an01912a] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The recognizing ability of parallel c-myc G-quadruplex by dimeric cyanine dyes depends on their linker length.
Collapse
Affiliation(s)
- Lijia Yu
- Beijing National Laboratory for Molecular Sciences
- Center for Molecular Science
- State Key Laboratory for Structural Chemistry for Unstable and Stable Species
- Institute of Chemistry
- Chinese Academy of Sciences (ICCAS)
| | - Qianfan Yang
- Beijing National Laboratory for Molecular Sciences
- Center for Molecular Science
- State Key Laboratory for Structural Chemistry for Unstable and Stable Species
- Institute of Chemistry
- Chinese Academy of Sciences (ICCAS)
| | - Junfeng Xiang
- Beijing National Laboratory for Molecular Sciences
- Center for Molecular Science
- State Key Laboratory for Structural Chemistry for Unstable and Stable Species
- Institute of Chemistry
- Chinese Academy of Sciences (ICCAS)
| | - Hongxia Sun
- Beijing National Laboratory for Molecular Sciences
- Center for Molecular Science
- State Key Laboratory for Structural Chemistry for Unstable and Stable Species
- Institute of Chemistry
- Chinese Academy of Sciences (ICCAS)
| | - Lixia Wang
- Beijing National Laboratory for Molecular Sciences
- Center for Molecular Science
- State Key Laboratory for Structural Chemistry for Unstable and Stable Species
- Institute of Chemistry
- Chinese Academy of Sciences (ICCAS)
| | - Qian Li
- Beijing National Laboratory for Molecular Sciences
- Center for Molecular Science
- State Key Laboratory for Structural Chemistry for Unstable and Stable Species
- Institute of Chemistry
- Chinese Academy of Sciences (ICCAS)
| | - Aijiao Guan
- Beijing National Laboratory for Molecular Sciences
- Center for Molecular Science
- State Key Laboratory for Structural Chemistry for Unstable and Stable Species
- Institute of Chemistry
- Chinese Academy of Sciences (ICCAS)
| | - Yalin Tang
- Beijing National Laboratory for Molecular Sciences
- Center for Molecular Science
- State Key Laboratory for Structural Chemistry for Unstable and Stable Species
- Institute of Chemistry
- Chinese Academy of Sciences (ICCAS)
| |
Collapse
|
18
|
Targeting G-quadruplex nucleic acids with heterocyclic alkaloids and their derivatives. Eur J Med Chem 2014; 97:538-51. [PMID: 25466923 DOI: 10.1016/j.ejmech.2014.11.021] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Revised: 11/05/2014] [Accepted: 11/11/2014] [Indexed: 01/25/2023]
Abstract
G-Quadruplex nucleic acids or G-quadruplexes (G4s) are four-stranded DNA or RNA secondary structures that are formed in guanine-rich sequences. They are widely distributed in functional regions of the human genome, such as telomeres, ribosomal DNA (rDNA), transcription start sites, promoter regions and untranslated regions of mRNA, suggesting that G-quadruplex structures may play a pivotal role in the control of a variety of cellular processes. G-Quadruplexes are viewed as valid therapeutic targets in human cancer diseases. Small molecules, from naturally occurring to synthetic, are exploited to specifically target G-quadruplexes and have proven to be a new class of anticancer agents. Notably, alkaloids are an important source of G-quadruplex ligands and have significant bioactivities in anticancer therapy. In this review, the authors provide a brief, up-to-date summary of heterocyclic alkaloids and their derivatives targeting G-quadruplexes.
Collapse
|
19
|
Ghimire C, Park S, Iida K, Yangyuoru P, Otomo H, Yu Z, Nagasawa K, Sugiyama H, Mao H. Direct quantification of loop interaction and π-π stacking for G-quadruplex stability at the submolecular level. J Am Chem Soc 2014; 136:15537-44. [PMID: 25296000 DOI: 10.1021/ja503585h] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The well-demonstrated biological functions of DNA G-quadruplex inside cells call for small molecules that can modulate these activities by interacting with G-quadruplexes. However, the paucity of the understanding of the G-quadruplex stability contributed from submolecular elements, such as loops and tetraguanine (G) planes (or G-quartets), has hindered the development of small-molecule binders. Assisted by click chemistry, herein, we attached pulling handles via two modified guanines in each of the three G-quartets in human telomeric G-quadruplex. Mechanical unfolding using these handles revealed that the loop interaction contributed more to the G-quadruplex stability than the stacking of G-quartets. This result was further confirmed by the binding of stacking ligands, such as telomestatin derivatives, which led to similar mechanical stability for all three G-quartets by significant reduction of loop interactions for the top and bottom G-quartets. The direct comparison of loop interaction and G-quartet stacking in G-quadruplex provides unprecedented insights for the design of more efficient G-quadruplex-interacting molecules. Compared to traditional experiments, in which mutations are employed to elucidate the roles of specific residues in a biological molecule, our submolecular dissection offers a complementary approach to evaluate individual domains inside a molecule with fewer disturbances to the native structure.
Collapse
Affiliation(s)
- Chiran Ghimire
- Department of Chemistry and Biochemistry and School of Biomedical Sciences, Kent State University , Kent, Ohio 44242, United States
| | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Zhang S, Wu Y, Zhang W. G-Quadruplex Structures and Their Interaction Diversity with Ligands. ChemMedChem 2014; 9:899-911. [DOI: 10.1002/cmdc.201300566] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Indexed: 12/22/2022]
|
21
|
Nagasawa K, Iida K, Tsubouchi G, Nakamura T. Synthesis of Macrocyclic Dimer of Cyclic Hexaoxazole and Examination of Its Interaction with Telomeric Oligonucleotide. HETEROCYCLES 2014. [DOI: 10.3987/com-13-s(s)97] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
22
|
Shibata K, Yoshida M, Takahashi T, Takagi M, Shin-ya K, Doi T. Synthesis of Heptaoxazole Macrocyclic Analogues of Telomestatin and Evaluation of Their Telomerase Inhibitory Activities. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2013. [DOI: 10.1246/bcsj.20130198] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Kazuaki Shibata
- Department of Applied Chemistry, Tokyo Institute of Technology
| | | | | | - Motoki Takagi
- Biomedicinal Information Research Center (BIRC), Japan Biological Informatics Consortium (JBIC)
| | - Kazuo Shin-ya
- National Institute of Advanced Industrial Science and Technology (AIST)
| | - Takayuki Doi
- Graduate School of Pharmaceutical Sciences, Tohoku University
| |
Collapse
|
23
|
The effect of pyridyl substituents on the thermodynamics of porphyrin binding to G-quadruplex DNA. Bioorg Med Chem 2013; 21:7515-22. [DOI: 10.1016/j.bmc.2013.09.036] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 09/07/2013] [Accepted: 09/14/2013] [Indexed: 11/22/2022]
|
24
|
Iida K, Nagasawa K. Macrocyclic Polyoxazoles as G-Quadruplex Ligands. CHEM REC 2013; 13:539-48. [DOI: 10.1002/tcr.201300015] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Indexed: 01/11/2023]
Affiliation(s)
- Keisuke Iida
- Tokyo University of Agriculture and Technology; 2-24-16 Naka-cho Koganei Tokyo 184-8588 Japan
| | - Kazuo Nagasawa
- Tokyo University of Agriculture and Technology; 2-24-16 Naka-cho Koganei Tokyo 184-8588 Japan
| |
Collapse
|
25
|
Iida K, Nakamura T, Yoshida W, Tera M, Nakabayashi K, Hata K, Ikebukuro K, Nagasawa K. Fluorescent-ligand-mediated screening of G-quadruplex structures using a DNA microarray. Angew Chem Int Ed Engl 2013; 52:12052-5. [PMID: 24150845 DOI: 10.1002/anie.201305366] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 09/10/2013] [Indexed: 01/13/2023]
Affiliation(s)
- Keisuke Iida
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei city, 184-8588 Tokyo (Japan)
| | | | | | | | | | | | | | | |
Collapse
|
26
|
Iida K, Nakamura T, Yoshida W, Tera M, Nakabayashi K, Hata K, Ikebukuro K, Nagasawa K. Fluorescent-Ligand-Mediated Screening of G-Quadruplex Structures Using a DNA Microarray. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201305366] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|