1
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Sun JW, Zou J, Zheng Y, Yuan H, Xie YZY, Wang XN, Ou TM. Design, synthesis, and evaluation of novel quindoline derivatives with fork-shaped side chains as RNA G-quadruplex stabilizers for repressing oncogene NRAS translation. Eur J Med Chem 2024; 271:116406. [PMID: 38688064 DOI: 10.1016/j.ejmech.2024.116406] [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: 02/03/2024] [Revised: 03/25/2024] [Accepted: 04/09/2024] [Indexed: 05/02/2024]
Abstract
NRAS mutation is the second most common oncogenic factor in cutaneous melanoma. Inhibiting NRAS translation by stabilizing the G-quadruplex (G4) structure with small molecules seems to be a potential strategy for cancer therapy due to the NRAS protein's lack of a druggable pocket. To enhance the effects of previously reported G4 stabilizers quindoline derivatives, we designed and synthesized a novel series of quindoline derivatives with fork-shaped side chains by introducing (alkylamino)alkoxy side chains. Panels of experimental results showed that introducing a fork-shaped (alkylamino)alkoxy side chain could enhance the stabilizing abilities of the ligands against NRAS RNA G-quadruplexes and their anti-melanoma activities. One of them, 10b, exhibited good antitumor activity in the NRAS-mutant melanoma xenograft mouse model, showing the therapeutic potential of this kind of compounds.
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Affiliation(s)
- Jia-Wei Sun
- School of Pharmaceutical Sciences, State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou, 510006, China
| | - Jing Zou
- School of Pharmaceutical Sciences, State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou, 510006, China
| | - Ying Zheng
- School of Pharmaceutical Sciences, State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou, 510006, China
| | - Hao Yuan
- School of Pharmaceutical Sciences, State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou, 510006, China
| | - Yuan-Ze-Yu Xie
- School of Pharmaceutical Sciences, State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou, 510006, China
| | - Xiao-Na Wang
- School of Pharmaceutical Sciences, State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou, 510006, China
| | - Tian-Miao Ou
- School of Pharmaceutical Sciences, State Key Laboratory of Oncology in South China, Sun Yat-sen University, Guangzhou, 510006, China.
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2
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M M, Patidar RK, Tiwari R, Srivastava N, Ranjan N. Nile Blue: A Red-Emissive Fluorescent Dye That Displays Differential Self-Assembly and Binding to G-Quadruplexes. J Phys Chem B 2023; 127:9915-9925. [PMID: 37956021 DOI: 10.1021/acs.jpcb.3c05084] [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: 11/15/2023]
Abstract
Nile Blue (NB) is a red-emissive dye that is well-known for imaging and staining applications. In this work, we describe the interaction of NB with various types of G-quadruplexes belonging to different topologies, molecularities, and conformations. Using spectroscopic techniques, we have determined the preferential binding of NB to c-Myc G-quadruplex and the other aspects of its binding. Concentration- and temperature-dependent studies showed that NB exists in a dynamic equilibrium between monomeric and H-aggregated states, which could be modulated by the addition of external agents such as anionic surfactants. NB displayed differential self-assembly with different types of G-quadruplex and duplex DNAs modulating its dynamic equilibrium between the monomeric and H-aggregated states. Fluorescence-based displacement studies revealed a 1:1 binding stoichiometry upon interaction with c-Myc G-quadruplex and an association constant of Kapp = 6.7 × 106 M-1. Circular dichroism studies indicated that NB does not cause changes in the overall conformation of either G-quadruplexes or duplexes; however, it does indicate nucleic acid-dependent self-assembly at higher concentrations. Heat capacity measurement showed a more negative change when compared to that in DNA duplex, indicating more burial of the polar surface area by NB to the G-quadruplex host.
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Affiliation(s)
- Midhun M
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Raebareli, New Transit Campus, Lucknow 226002, Uttar Pradesh, India
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research-Raebareli, New Transit Campus, Lucknow 226002, Uttar Pradesh, India
| | - Rajesh Kumar Patidar
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Raebareli, New Transit Campus, Lucknow 226002, Uttar Pradesh, India
| | - Ratnesh Tiwari
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Raebareli, New Transit Campus, Lucknow 226002, Uttar Pradesh, India
| | - Nidhi Srivastava
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research-Raebareli, New Transit Campus, Lucknow 226002, Uttar Pradesh, India
| | - Nihar Ranjan
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Raebareli, New Transit Campus, Lucknow 226002, Uttar Pradesh, India
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3
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Patidar RK, Tiwari K, Tiwari R, Ranjan N. Promoter G-Quadruplex Binding Styryl Benzothiazolium Derivative for Applications in Ligand Affinity Ranking and as Ethidium Bromide Substitute in Gel Staining. ACS APPLIED BIO MATERIALS 2023. [PMID: 37229607 DOI: 10.1021/acsabm.3c00060] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Fluorescent compounds that can preferentially interact with certain nucleic acids are of great importance in new drug discovery in a multitude of functions including fluorescence-based displacement assays and gel staining. Here, we report the discovery of an orange emissive styryl-benzothiazolium derivative (compound 4) which interacts preferentially with Pu22 G-quadruplex DNA among a pool of nucleic acid structures containing G-quadruplex, duplex, and single-stranded DNA structures as well as RNA structures. Fluorescence-based binding analysis revealed that compound 4 interacts with Pu22 G-quadruplex DNA in a 1:1 DNA to ligand binding stoichiometry. The association constant (Ka) for this interaction was found to be 1.12 (±0.15) × 106 M-1. Circular dichroism studies showed that the binding of the probe does not cause changes in the overall parallel G-quadruplex conformation; however, signs of higher-order complex formation were seen in the form of exciton splitting in the chromophore absorption region. UV-visible spectroscopy studies confirmed the stacking nature of the interaction of the fluorescent probe with the G-quadruplex which was further complemented by heat capacity measurement studies. Finally, we have shown that this fluorescent probe can be used toward G-quadruplex-based fluorescence displacement assays for ligand affinity ranking and as a substitute for ethidium bromide in gel staining.
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Affiliation(s)
- Rajesh Kumar Patidar
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Raebareli, New Transit Campus, Lucknow, Uttar Pradesh, India 226002
| | - Khushboo Tiwari
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Raebareli, New Transit Campus, Lucknow, Uttar Pradesh, India 226002
| | - Ratnesh Tiwari
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Raebareli, New Transit Campus, Lucknow, Uttar Pradesh, India 226002
| | - Nihar Ranjan
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Raebareli, New Transit Campus, Lucknow, Uttar Pradesh, India 226002
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4
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Vianney YM, Weisz K. High-affinity binding at quadruplex-duplex junctions: rather the rule than the exception. Nucleic Acids Res 2022; 50:11948-11964. [PMID: 36416262 PMCID: PMC9723630 DOI: 10.1093/nar/gkac1088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/19/2022] [Accepted: 10/26/2022] [Indexed: 11/24/2022] Open
Abstract
Quadruplex-duplex (Q-D) junctions constitute unique structural motifs in genomic sequences. Through comprehensive calorimetric as well as high-resolution NMR structural studies, Q-D junctions with a hairpin-type snapback loop coaxially stacked onto an outer G-tetrad were identified to be most effective binding sites for various polycyclic quadruplex ligands. The Q-D interface is readily recognized by intercalation of the ligand aromatic core structure between G-tetrad and the neighboring base pair. Based on the thermodynamic and structural data, guidelines for the design of ligands with enhanced selectivity towards a Q-D interface emerge. Whereas intercalation at Q-D junctions mostly outcompete stacking at the quadruplex free outer tetrad or intercalation between duplex base pairs to varying degrees, ligand side chains considerably contribute to the selectivity for a Q-D target over other binding sites. In contrast to common perceptions, an appended side chain that additionally interacts within the duplex minor groove may confer only poor selectivity. Rather, the Q-D selectivity is suggested to benefit from an extension of the side chain towards the exposed part of the G-tetrad at the junction. The presented results will support the design of selective high-affinity binding ligands for targeting Q-D interfaces in medicinal but also technological applications.
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Affiliation(s)
- Yoanes Maria Vianney
- Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff-Str. 4, D-17489 Greifswald, Germany
| | - Klaus Weisz
- To whom correspondence should be addressed. Tel: +49 3834 420 4426; Fax: +49 3834 420 4427;
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5
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Mendes E, Bahls B, Aljnadi IM, Paulo A. Indoloquinolines as scaffolds for the design of potent G-quadruplex ligands. Bioorg Med Chem Lett 2022; 72:128862. [PMID: 35716866 DOI: 10.1016/j.bmcl.2022.128862] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/09/2022] [Accepted: 06/13/2022] [Indexed: 11/19/2022]
Abstract
Indoloquinolines are natural alkaloids with known affinity to DNA and antiproliferative activity against bacteria, parasites, and cancer cells. Due to their non-chiral skeleton, their total synthesis is easy to achieve and throughout the years, many derivatives have been studied for their potential as drugs. Herein we review the indoloquinolines and bioisosters that have been designed, synthesised, and evaluated for their selective binding to G-quadruplex nucleic acid structures, as well as the reported effects in cancer cells. The data collected so far strongly suggest that indoloquinolines are good scaffolds for the development of drugs and probes targeting the G-quadruplex structures, but they also show that this scaffold is still underexplored.
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Affiliation(s)
- Eduarda Mendes
- Faculty of Pharmacy, Research Institute for Medicines (iMed.ULisboa), Universidade de Lisboa, Av. Prof. Gama Pinto, Lisbon 1649-003, Portugal
| | - Bárbara Bahls
- Faculty of Pharmacy, Research Institute for Medicines (iMed.ULisboa), Universidade de Lisboa, Av. Prof. Gama Pinto, Lisbon 1649-003, Portugal
| | - Israa M Aljnadi
- Faculty of Pharmacy, Research Institute for Medicines (iMed.ULisboa), Universidade de Lisboa, Av. Prof. Gama Pinto, Lisbon 1649-003, Portugal
| | - Alexandra Paulo
- Faculty of Pharmacy, Research Institute for Medicines (iMed.ULisboa), Universidade de Lisboa, Av. Prof. Gama Pinto, Lisbon 1649-003, Portugal.
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6
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Vianney YM, Weisz K. Indoloquinoline Ligands Favor Intercalation at Quadruplex-Duplex Interfaces. Chemistry 2021; 28:e202103718. [PMID: 34905232 PMCID: PMC9303235 DOI: 10.1002/chem.202103718] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Indexed: 11/30/2022]
Abstract
Quadruplex‐duplex (Q‐D) junctions are increasingly considered promising targets for medicinal and technological applications. Here, a Q‐D hybrid with a hairpin‐type snapback loop coaxially stacked onto the quadruplex 3’‐outer tetrad was designed and employed as a target structure for the indoloquinoline ligand SYUIQ‐5. NMR spectral analysis demonstrated high‐affinity binding of the ligand at the quadruplex‐duplex interface with association constants determined by isothermal titration calorimetry of about 107 M−1 and large exothermicities ΔH° of −14 kcal/mol in a 120 mM K+ buffer at 40 °C. Determination of the ligand‐bound hybrid structure revealed intercalation of SYUIQ‐5 between 3’‐outer tetrad and the neighboring CG base pair, maximizing π–π stacking as well as electrostatic interactions with guanine carbonyl groups in close vicinity to the positively charged protonated quinoline nitrogen of the tetracyclic indoloquinoline. Exhibiting considerable flexibility, the SYUIQ‐5 sidechain resides in the duplex minor groove. Based on comparative binding studies with the non‐substituted N5‐methylated indoloquinoline cryptolepine, the sidechain is suggested to confer additional affinity and to fix the alignment of the intercalated indoloquinoline aromatic core. However, selectivity for the Q‐D junction mostly relies on the geometry and charge distribution of the indoloquinoline ring system. The presented results are expected to provide valuable guidelines for the design of ligands specifically targeting Q‐D interfaces.
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Affiliation(s)
- Yoanes Maria Vianney
- Universität Greifswald Mathematisch-Naturwissenschaftliche Fakultät: Universitat Greifswald Mathematisch-Naturwissenschaftliche Fakultat, Institut für Biochemie, Felix-Hausdorff-Str. 4, 17489, Greifswald, GERMANY
| | - Klaus Weisz
- Universität Greifswald, Institut für Biochemie, Felix-Hausdorff-Str. 4, 17487, Greifswald, GERMANY
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7
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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.
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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
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8
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Dickerhoff J, Dai J, Yang D. Structural recognition of the MYC promoter G-quadruplex by a quinoline derivative: insights into molecular targeting of parallel G-quadruplexes. Nucleic Acids Res 2021; 49:5905-5915. [PMID: 33978746 PMCID: PMC8191789 DOI: 10.1093/nar/gkab330] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/11/2021] [Accepted: 04/22/2021] [Indexed: 01/21/2023] Open
Abstract
DNA G-Quadruplexes (G4s) formed in oncogene promoters regulate transcription. The oncogene MYC promoter G4 (MycG4) is the most prevalent G4 in human cancers. However, the most studied MycG4 sequence bears a mutated 3′-residue crucial for ligand recognition. Here, we report a new drug-like small molecule PEQ without a large aromatic moiety that specifically binds MycG4. We determined the NMR solution structures of the wild-type MycG4 and its 2:1 PEQ complex, as well as the structure of the 2:1 PEQ complex of the widely used mutant MycG4. Comparison of the two complex structures demonstrates specific molecular recognition of MycG4 and shows the clear effect of the critical 3′-mutation on the drug binding interface. We performed a systematic analysis of the four available complex structures involving the same mutant MycG4, which can be considered a model system for parallel G4s, and revealed for the first time that the flexible flanking residues are recruited in a conserved and sequence-specific way, as well as unused potential for selective ligand-G4 hydrogen-bond interactions. Our results provide the true molecular basis for MycG4-targeting drugs and new critical insights into future rational design of drugs targeting MycG4 and parallel G4s that are prevalent in promoter and RNA G4s.
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Affiliation(s)
- Jonathan Dickerhoff
- Purdue University, College of Pharmacy, Medicinal Chemistry and Molecular Pharmacology, 575 W Stadium Ave., West Lafayette, IN 47907, USA
| | - Jixun Dai
- College of Pharmacy, The University of Arizona, Tucson, AZ 85721, USA
| | - Danzhou Yang
- Purdue University, College of Pharmacy, Medicinal Chemistry and Molecular Pharmacology, 575 W Stadium Ave., West Lafayette, IN 47907, USA.,Purdue University Center for Cancer Research, 201 S University St, West Lafayette, IN 47906, USA.,Purdue University, Department of Chemistry, West Lafayette, IN, USA.,Purdue Institute for Drug Discovery, West Lafayette, IN, USA
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9
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Sanchez-Martin V, Soriano M, Garcia-Salcedo JA. Quadruplex Ligands in Cancer Therapy. Cancers (Basel) 2021; 13:3156. [PMID: 34202648 PMCID: PMC8267697 DOI: 10.3390/cancers13133156] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/18/2021] [Accepted: 06/20/2021] [Indexed: 02/07/2023] Open
Abstract
Nucleic acids can adopt alternative secondary conformations including four-stranded structures known as quadruplexes. To date, quadruplexes have been demonstrated to exist both in human chromatin DNA and RNA. In particular, quadruplexes are found in guanine-rich sequences constituting G-quadruplexes, and in cytosine-rich sequences forming i-Motifs as a counterpart. Quadruplexes are associated with key biological processes ranging from transcription and translation of several oncogenes and tumor suppressors to telomeres maintenance and genome instability. In this context, quadruplexes have prompted investigations on their possible role in cancer biology and the evaluation of small-molecule ligands as potential therapeutic agents. This review aims to provide an updated close-up view of the literature on quadruplex ligands in cancer therapy, by grouping together ligands for DNA and RNA G-quadruplexes and DNA i-Motifs.
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Affiliation(s)
- Victoria Sanchez-Martin
- Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain;
- Microbiology Unit, Biosanitary Research Institute IBS, University Hospital Virgen de las Nieves, 18014 Granada, Spain
- Department of Biochemistry, Molecular Biology III and Immunology, University of Granada, 18016 Granada, Spain
| | - Miguel Soriano
- Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain;
- Centre for Intensive Mediterranean Agrosystems and Agri-Food Biotechnology (CIAMBITAL), University of Almeria, 04001 Almeria, Spain
| | - Jose Antonio Garcia-Salcedo
- Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain;
- Microbiology Unit, Biosanitary Research Institute IBS, University Hospital Virgen de las Nieves, 18014 Granada, Spain
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10
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Wickhorst PJ, Ihmels H. Selective, pH-Dependent Colorimetric and Fluorimetric Detection of Quadruplex DNA with 4-Dimethylamino(phenyl)-Substituted Berberine Derivatives. Chemistry 2021; 27:8580-8589. [PMID: 33855748 PMCID: PMC8252107 DOI: 10.1002/chem.202100297] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Indexed: 12/20/2022]
Abstract
The 9- and 12-dimethylaminophenyl-substituted berberine derivatives 3 a and 3 b were readily synthesized by Suzuki-Miyaura reactions and shown to be useful fluorescent probes for the optical detection of quadruplex DNA (G4-DNA). Their association with the nucleic acids was investigated by spectrometric titrations, CD and LD spectroscopy, and with DNA-melting analysis. Both ligands bind to duplex DNA by intercalation and to G4-DNA by terminal π stacking. At neutral conditions, they bind with higher affinity (Kb =105 -106 M-1 ) to representative quadruplex forming oligonucleotides 22AG, c-myc, c-kit, and a2, than to duplex calf thymus (ct) DNA (Kb =5-7×104 M-1 ). At pH 5, however, the affinity of 3 a towards G4-DNA 22AG is higher (Kb =1.2×106 M-1 ), whereas the binding constant towards ct DNA is lower (Kb =3.9×103 M-1 ) than under neutral conditions. Notably, the association of the ligand with DNA results in characteristic changes of the absorption and emission properties under specific conditions, which may be used for optical DNA detection. Other than the parent berberine, the ligands do not show a noticeable increase of their very low intrinsic emission intensity upon association with DNA at neutral conditions. In contrast, a fluorescence light-up effect was observed upon association to duplex (Φfl =0.01) and quadruplex DNA (Φfl =0.04) at pH 5. This fluorimetric response to G4-DNA association in combination with the distinct, red-shifted absorption under these conditions provides a simple and conclusive optical detection of G4-DNA at lower pH.
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Affiliation(s)
- Peter Jonas Wickhorst
- Department of Chemistry – BiologyUniversity of Siegen, andCenter of Micro- and Nanochemistry and Engineering (Cμ)Adolf-Reichwein-Str. 257068SiegenGermany
| | - Heiko Ihmels
- Department of Chemistry – BiologyUniversity of Siegen, andCenter of Micro- and Nanochemistry and Engineering (Cμ)Adolf-Reichwein-Str. 257068SiegenGermany
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11
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Becher J, Berdnikova DV, Ihmels H, Stremmel C. Synthesis and investigation of quadruplex-DNA-binding, 9- O-substituted berberine derivatives. Beilstein J Org Chem 2020; 16:2795-2806. [PMID: 33281983 PMCID: PMC7684686 DOI: 10.3762/bjoc.16.230] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 11/02/2020] [Indexed: 12/20/2022] Open
Abstract
A small series of five novel berberine derivatives was synthesized by the Cu-catalyzed click reaction of 9-propargyladenine with 9-O-(azidoalkyl)berberine derivatives. The association of the resulting berberine-adenine conjugates with representative quadruplex-forming oligonucleotides 22AG dA(G3TTA)3G3 and a2 d(ACAG4TGTG4)2 was examined with photometric and fluorimetric titrations, thermal DNA denaturation analysis, and CD spectroscopy. The results from the spectrometric titrations indicated the formation of 2:1 or 1:1 complexes (ligand:G4-DNA) with log K b values of 10-11 (2:1) and 5-6 (1:1), which are typical for berberine derivatives. Notably, a clear relationship between the binding affinity of the ligands with the length of the alkyl linker chain, n, was not observed. However, depending on the structure, the ligands exhibited different effects when bound to the G4-DNA, such as fluorescent light-up effects and formation of ICD bands, which are mostly pronounced with a linker length of n = 4 (with a2) and n = 5 (with 22AG), thus indicating that each ligand-G4-DNA complex has a specific structure with respect to relative alignment and conformational flexibility of the ligand in the binding site. It was shown exemplarily with one representative ligand from the series that such berberine-adenine conjugates exhibit a selective binding, specifically a selectivity to quadruplex DNA in competition with duplex DNA, and a preferential thermal stabilization of the G4-DNA forms 22AG and KRAS. Notably, the experimental data do not provide evidence for a significant effect of the adenine unit on the binding affinity of the ligands, for example, by additional association with the loops, presumably because the adenine residue is sterically shielded by the neighboring triazole unit.
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Affiliation(s)
- Jonas Becher
- Department of Chemistry and Biology, University of Siegen and Center of Micro- and Nanochemistry and Engineering (Cμ); Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
| | - Daria V Berdnikova
- Department of Chemistry and Biology, University of Siegen and Center of Micro- and Nanochemistry and Engineering (Cμ); Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
| | - Heiko Ihmels
- Department of Chemistry and Biology, University of Siegen and Center of Micro- and Nanochemistry and Engineering (Cμ); Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
| | - Christopher Stremmel
- Department of Chemistry and Biology, University of Siegen and Center of Micro- and Nanochemistry and Engineering (Cμ); Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
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12
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Vianney YM, Preckwinkel P, Mohr S, Weisz K. Quadruplex-Duplex Junction: A High-Affinity Binding Site for Indoloquinoline Ligands. Chemistry 2020; 26:16910-16922. [PMID: 32975874 PMCID: PMC7756412 DOI: 10.1002/chem.202003540] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/21/2020] [Indexed: 12/23/2022]
Abstract
A parallel quadruplex derived from the Myc promoter sequence was extended by a stem-loop duplex at either its 5'- or 3'-terminus to mimic a quadruplex-duplex (Q-D) junction as a potential genomic target. High-resolution structures of the hybrids demonstrate continuous stacking of the duplex on the quadruplex core without significant perturbations. An indoloquinoline ligand carrying an aminoalkyl side chain was shown to bind the Q-D hybrids with a very high affinity in the order Ka ≈107 m-1 irrespective of the duplex location at the quadruplex 3'- or 5'-end. NMR chemical shift perturbations identified the tetrad face of the Q-D junction as specific binding site for the ligand. However, calorimetric analyses revealed significant differences in the thermodynamic profiles upon binding to hybrids with either a duplex extension at the quadruplex 3'- or 5'-terminus. A large enthalpic gain and considerable hydrophobic effects are accompanied by the binding of one ligand to the 3'-Q-D junction, whereas non-hydrophobic entropic contributions favor binding with formation of a 2:1 ligand-quadruplex complex in case of the 5'-Q-D hybrid.
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Affiliation(s)
- Yoanes Maria Vianney
- Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Pit Preckwinkel
- Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Swantje Mohr
- Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Klaus Weisz
- Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
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Singh M, Wang S, Joo H, Ye Z, Christison KM, Hekman R, Vierra C, Xue L. Use of neomycin as a structured amino-containing side chain motif for phenanthroline-based G-quadruplex ligands and telomerase inhibitors. Chem Biol Drug Des 2020; 96:1292-1304. [PMID: 32516846 DOI: 10.1111/cbdd.13741] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/05/2020] [Accepted: 05/31/2020] [Indexed: 01/05/2023]
Abstract
In this paper, we report the synthesis of a phenanthroline and neomycin conjugate (7). Compound 7 binds to a human telomeric G-quadruplex (G1) with a higher affinity compared with its parent compounds (phenanthroline and neomycin), which is determined by several biophysical studies. Compound 7 shows good selectivity for G-quadruplex (G4) DNA over duplex DNA. The binding of 7 with G1 is predominantly enthalpy-driven, and the binding stoichiometry of 7 with G1 is one for the tight-binding event as determined by ESI mass spectrometry. A plausible binding mode is a synergistic effect of end-stacking and groove interactions, as indicated by docking studies. Compound 7 can inhibit human telomerase activity at low micromolar concentrations, which is more potent than previously reported 5-substituted phenanthroline derivatives.
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Affiliation(s)
- Mandeep Singh
- Department of Chemistry, University of the Pacific, Stockton, CA, USA
| | - Siwen Wang
- Department of Chemistry, University of the Pacific, Stockton, CA, USA
| | - Hyun Joo
- Department of Chemistry, University of the Pacific, Stockton, CA, USA
| | - Zhihan Ye
- Department of Chemistry, University of the Pacific, Stockton, CA, USA
| | | | - Ryan Hekman
- Department of Biological Sciences, University of the Pacific, Stockton, CA, USA
| | - Craig Vierra
- Department of Biological Sciences, University of the Pacific, Stockton, CA, USA
| | - Liang Xue
- Department of Chemistry, University of the Pacific, Stockton, CA, USA
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