1
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Selective light-up of dimeric G-quadruplex forming aptamers for efficient VEGF165 detection. Int J Biol Macromol 2022; 224:344-357. [DOI: 10.1016/j.ijbiomac.2022.10.128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/08/2022] [Accepted: 10/13/2022] [Indexed: 11/05/2022]
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2
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Yan KKP, Obi I, Sabouri N. The RGG domain in the C-terminus of the DEAD box helicases Dbp2 and Ded1 is necessary for G-quadruplex destabilization. Nucleic Acids Res 2021; 49:8339-8354. [PMID: 34302476 PMCID: PMC8373067 DOI: 10.1093/nar/gkab620] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 07/02/2021] [Accepted: 07/07/2021] [Indexed: 12/31/2022] Open
Abstract
The identification of G-quadruplex (G4) binding proteins and insights into their mechanism of action are important for understanding the regulatory functions of G4 structures. Here, we performed an unbiased affinity-purification assay coupled with mass spectrometry and identified 30 putative G4 binding proteins from the fission yeast Schizosaccharomyces pombe. Gene ontology analysis of the molecular functions enriched in this pull-down assay included mRNA binding, RNA helicase activity, and translation regulator activity. We focused this study on three of the identified proteins that possessed putative arginine-glycine-glycine (RGG) domains, namely the Stm1 homolog Oga1 and the DEAD box RNA helicases Dbp2 and Ded1. We found that Oga1, Dbp2, and Ded1 bound to both DNA and RNA G4s in vitro. Both Dbp2 and Ded1 bound to G4 structures through the RGG domain located in the C-terminal region of the helicases, and point mutations in this domain weakened the G4 binding properties of the helicases. Dbp2 and Ded1 destabilized less thermostable G4 RNA and DNA structures, and this ability was independent of ATP but dependent on the RGG domain. Our study provides the first evidence that the RGG motifs in DEAD box helicases are necessary for both G4 binding and G4 destabilization.
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Affiliation(s)
- Kevin Kok-Phen Yan
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden
| | - Ikenna Obi
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden
| | - Nasim Sabouri
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden
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3
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Sutherland M, Li A, Kaghad A, Panagopoulos D, Li F, Szewczyk M, Smil D, Scholten C, Bouché L, Stellfeld T, Arrowsmith CH, Barsyte D, Vedadi M, Hartung IV, Steuber H, Britton R, Santhakumar V. Rational Design and Synthesis of Selective PRMT4 Inhibitors: A New Chemotype for Development of Cancer Therapeutics*. ChemMedChem 2021; 16:1116-1125. [PMID: 33513288 DOI: 10.1002/cmdc.202100018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Indexed: 11/07/2022]
Abstract
Protein arginine N-methyl transferase 4 (PRMT4) asymmetrically dimethylates the arginine residues of histone H3 and nonhistone proteins. The overexpression of PRMT4 in several cancers has stimulated interest in the discovery of inhibitors as biological tools and, potentially, therapeutics. Although several PRMT4 inhibitors have been reported, most display poor selectivity against other members of the PRMT family of methyl transferases. Herein, we report the structure-based design of a new class of alanine-containing 3-arylindoles as potent and selective PRMT4 inhibitors, and describe key structure-activity relationships for this class of compounds.
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Affiliation(s)
- Mathew Sutherland
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Alice Li
- Structural Genomics Consortium, University of Toronto, MaRS Centre, South Tower, Suite 700, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Anissa Kaghad
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Dimitrios Panagopoulos
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, MaRS Centre, South Tower, Suite 700, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Magdalena Szewczyk
- Structural Genomics Consortium, University of Toronto, MaRS Centre, South Tower, Suite 700, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - David Smil
- Structural Genomics Consortium, University of Toronto, MaRS Centre, South Tower, Suite 700, 101 College Street, Toronto, ON M5G 1L7, Canada.,Ontario Institute for Cancer Research, 661 University Ave, Toronto, ON M5G 0A3, Canada
| | - Cora Scholten
- Bayer A.G. Research and Development, Pharmaceuticals Muellerstr. 178, 13442, Berlin, Germany
| | - Léa Bouché
- Bayer A.G. Research and Development, Pharmaceuticals Muellerstr. 178, 13442, Berlin, Germany
| | - Timo Stellfeld
- Bayer A.G. Research and Development, Pharmaceuticals Muellerstr. 178, 13442, Berlin, Germany.,Innovation Campus Berlin, Nuvisan ICB GmbH, Müllerstraße 178, 13353, Berlin, Germany
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, MaRS Centre, South Tower, Suite 700, 101 College Street, Toronto, ON M5G 1L7, Canada.,Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, 610 University Ave, Toronto, ON M5G 2C1, Canada
| | - Dalia Barsyte
- Structural Genomics Consortium, University of Toronto, MaRS Centre, South Tower, Suite 700, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, MaRS Centre, South Tower, Suite 700, 101 College Street, Toronto, ON M5G 1L7, Canada.,Department of Pharmacology and Toxicology, University of Toronto, 1 King's College Cir, Toronto, ON M5S 1A8, Canada
| | - Ingo V Hartung
- Bayer A.G. Research and Development, Pharmaceuticals Muellerstr. 178, 13442, Berlin, Germany.,Merck Healthcare KGaA, Frankfurter Straße 250, 64293, Darmstadt, Germany
| | - Holger Steuber
- Bayer A.G. Research and Development, Pharmaceuticals Muellerstr. 178, 13442, Berlin, Germany.,Innovation Campus Berlin, Nuvisan ICB GmbH, Müllerstraße 178, 13353, Berlin, Germany
| | - Robert Britton
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Vijayaratnam Santhakumar
- Structural Genomics Consortium, University of Toronto, MaRS Centre, South Tower, Suite 700, 101 College Street, Toronto, ON M5G 1L7, Canada
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4
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Andreeva DV, Tikhomirov AS, Shchekotikhin AE. Ligands of G-quadruplex nucleic acids. RUSSIAN CHEMICAL REVIEWS 2021. [DOI: 10.1070/rcr4968] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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5
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Das RN, Andréasson M, Kumar R, Chorell E. Macrocyclization of bis-indole quinolines for selective stabilization of G-quadruplex DNA structures. Chem Sci 2020; 11:10529-10537. [PMID: 34094311 PMCID: PMC8162405 DOI: 10.1039/d0sc03519j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 09/15/2020] [Indexed: 11/21/2022] Open
Abstract
The recognition of G-quadruplex (G4) DNA structures as important regulatory elements in biological mechanisms, and the connection between G4s and the evolvement of different diseases, has sparked interest in developing small organic molecules targeting G4s. However, such compounds often lack drug-like properties and selectivity. Here, we describe the design and synthesis of a novel class of macrocyclic bis-indole quinolines based on their non-macrocyclic lead compounds. The effects of the macrocyclization on the ability to interact with G4 DNA structures were investigated using biophysical assays and molecular dynamic simulations. Overall, this revealed compounds with potent abilities to interact with and stabilize G4 structures and a clear selectivity for both G4 DNA over dsDNA and for parallel/hybrid G4 topologies, which could be attributed to the macrocyclic structure. Moreover, we obtained knowledge about the structure-activity relationship of importance for the macrocyclic design and how structural modifications could be made to construct improved macrocyclic compounds. Thus, the macrocyclization of G4 ligands can serve as a basis for the optimization of research tools to study G4 biology and potential therapeutics targeting G4-related diseases.
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Affiliation(s)
| | | | - Rajendra Kumar
- Department of Chemistry, Umeå University 90187 Umeå Sweden
| | - Erik Chorell
- Department of Chemistry, Umeå University 90187 Umeå Sweden
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6
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Prasad B, Das RN, Jamroskovic J, Kumar R, Hedenström M, Sabouri N, Chorell E. The Relation Between Position and Chemical Composition of Bis-Indole Substituents Determines Their Interactions with G-Quadruplex DNA. Chemistry 2020; 26:9561-9572. [PMID: 32187406 PMCID: PMC7497243 DOI: 10.1002/chem.202000579] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/16/2020] [Indexed: 01/20/2023]
Abstract
G-quadruplex (G4) DNA structures are linked to fundamental biological processes and human diseases, which has triggered the development of compounds that affect these DNA structures. However, more knowledge is needed about how small molecules interact with G4 DNA structures. This study describes the development of a new class of bis-indoles (3,3-diindolyl-methyl derivatives) and detailed studies of how they interact with G4 DNA using orthogonal assays, biophysical techniques, and computational studies. This revealed compounds that strongly bind and stabilize G4 DNA structures, and detailed binding interactions which for example, show that charge variance can play a key role in G4 DNA binding. Furthermore, the structure-activity relationships generated opened the possibilities to replace or introduce new substituents on the core structure, which is of key importance to optimize compound properties or introduce probes to further expand the possibilities of these compounds as tailored research tools to study G4 biology.
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Affiliation(s)
| | | | - Jan Jamroskovic
- Department of Medical Biochemistry and BiophysicsUmeå University90187UmeåSweden
| | | | | | - Nasim Sabouri
- Department of Medical Biochemistry and BiophysicsUmeå University90187UmeåSweden
| | - Erik Chorell
- Department of ChemistryUmeå University90187UmeåSweden
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7
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Kumar R, Chand K, Bhowmik S, Das RN, Bhattacharjee S, Hedenström M, Chorell E. Subtle structural alterations in G-quadruplex DNA regulate site specificity of fluorescence light-up probes. Nucleic Acids Res 2020; 48:1108-1119. [PMID: 31912160 PMCID: PMC7026600 DOI: 10.1093/nar/gkz1205] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 12/04/2019] [Accepted: 12/17/2019] [Indexed: 12/23/2022] Open
Abstract
G-quadruplex (G4) DNA structures are linked to key biological processes and human diseases. Small molecules that target specific G4 DNA structures and signal their presence would therefore be of great value as chemical research tools with potential to further advance towards diagnostic and therapeutic developments. However, the development of these types of specific compounds remain as a great challenge. In here, we have developed a compound with ability to specifically signal a certain c-MYC G4 DNA structure through a fluorescence light-up mechanism. Despite the compound's two binding sites on the G4 DNA structure, only one of them result in the fluorescence light-up effect. This G-tetrad selectivity proved to originate from a difference in flexibility that affected the binding affinity and tilt the compound out of the planar conformation required for the fluorescence light-up mechanism. The intertwined relation between the presented factors is likely the reason for the lack of examples using rational design to develop compounds with turn-on emission that specifically target certain G4 DNA structures. However, this study shows that it is indeed possible to develop such compounds and present insights into the molecular details of specific G4 DNA recognition and signaling to advance future studies of G4 biology.
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Affiliation(s)
- Rajendra Kumar
- Department of Chemistry, Umeå University, 90187 Umeå, Sweden
| | - Karam Chand
- Department of Chemistry, Umeå University, 90187 Umeå, Sweden
| | - Sudipta Bhowmik
- Department of Chemistry, Umeå University, 90187 Umeå, Sweden.,Department of Biophysics, Molecular Biology & Bioinformatics, University of Calcutta, 92, APC Road, Kolkata 700009, India
| | | | - Snehasish Bhattacharjee
- Department of Biophysics, Molecular Biology & Bioinformatics, University of Calcutta, 92, APC Road, Kolkata 700009, India
| | | | - Erik Chorell
- Department of Chemistry, Umeå University, 90187 Umeå, Sweden
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8
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Chen Y. Advances in the Synthesis of Methylated Products through Indirect Approaches. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201901240] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yantao Chen
- Medicinal Chemistry, Research and Early DevelopmentCardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca 43183 Gothenburg Sweden
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9
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Bhattacharjee S, Chakraborty S, Chorell E, Sengupta PK, Bhowmik S. Importance of the hydroxyl substituents in the B-ring of plant flavonols on their preferential binding interactions with VEGF G-quadruplex DNA: Multi-spectroscopic and molecular modeling studies. Int J Biol Macromol 2018; 118:629-639. [PMID: 29953891 DOI: 10.1016/j.ijbiomac.2018.06.115] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 06/22/2018] [Accepted: 06/23/2018] [Indexed: 10/28/2022]
Abstract
G-quadruplex (G4) structures are known to be promising anticancer drug targets and flavonols (an important class of flavonoids) are small molecules reported to possess several health-promoting properties including those of anticancer activities. In this work, we explored the interactions of the structurally related plant flavonols kaempferol (KAE; 3,5,7,4'OH flavone) and morin (MOR; 3,5,7,2',4'OH flavone) with various G4-DNA sequences along with duplex DNA using a combination of spectroscopic and molecular docking studies. Our results revealed that KAE shows preferential interaction with VEGF G4-DNA in comparison to the other G4 sequences and duplex DNA. Moreover, KAE enhances the thermal stability of VEGF G4-DNA. In contrast, MOR exhibits an appreciably weaker level of interaction with both duplex and various G4-DNAs, with no significant structural specificity. The contrasting DNA binding behaviors suggest a crucial role of the 2'OH substituent in the B-ring of flavonol moiety. While KAE is relatively planar, MOR adopts a significantly non-planar conformation attributable to steric hindrance from the additional 2'OH substituent. This small structural difference is apparently very important for the ability of KAE and MOR to interact with VEGF G4-DNA. Thus, KAE (but not MOR) appears to be an effective ligand for VEGF G4-DNA, opening up possibilities of its application for regulation of gene expression in cancer cells.
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Affiliation(s)
- Snehasish Bhattacharjee
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92 Acharya Prafulla Chandra Road, Kolkata 700009, India
| | - Sandipan Chakraborty
- Department of Microbiology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata 700019, India
| | - Erik Chorell
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
| | - Pradeep K Sengupta
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92 Acharya Prafulla Chandra Road, Kolkata 700009, India.
| | - Sudipta Bhowmik
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92 Acharya Prafulla Chandra Road, Kolkata 700009, India.
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10
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Prasad B, Jamroskovic J, Bhowmik S, Kumar R, Romell T, Sabouri N, Chorell E. Flexible Versus Rigid G-Quadruplex DNA Ligands: Synthesis of Two Series of Bis-indole Derivatives and Comparison of Their Interactions with G-Quadruplex DNA. Chemistry 2018; 24:7926-7938. [PMID: 29603472 DOI: 10.1002/chem.201800078] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Indexed: 12/30/2022]
Abstract
Small molecules that target G-quadruplex (G4) DNA structures are not only valuable to study G4 biology but also for their potential as therapeutics. This work centers around how different design features of small molecules can affect the interactions with G4 DNA structures, exemplified by the development of synthetic methods to bis-indole scaffolds. Our synthesized series of bis-indole scaffolds are structurally very similar but differ greatly in the flexibility of their core structures. The flexibility of the molecules proved to be an advantage compared to locking the compounds in the presumed bioactive G4 conformation. The flexible derivatives demonstrated similar or even improved G4 binding and stabilization in several orthogonal assays even though their entropic penalty of binding is higher. In addition, molecular dynamics simulations with the c-MYC G4 structure showed that the flexible compounds adapt better to the surrounding. This was reflected by an increased number of both stacking and polar interactions with both the residues in the G4 DNA structure and the DNA residues just upstream of the G4 structure.
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Affiliation(s)
- Bagineni Prasad
- Department of Chemistry, Umeå University, 901 87, Umeå, Sweden
| | - Jan Jamroskovic
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87, Umeå, Sweden
| | - Sudipta Bhowmik
- Department of Chemistry, Umeå University, 901 87, Umeå, Sweden.,Department of Biophysics, Molecular Biology & Bioinformatics, University of Calcutta, 700009, Kolkata, India
| | - Rajendra Kumar
- Department of Chemistry, Umeå University, 901 87, Umeå, Sweden
| | - Tajanena Romell
- Department of Chemistry, Umeå University, 901 87, Umeå, Sweden
| | - Nasim Sabouri
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87, Umeå, Sweden
| | - Erik Chorell
- Department of Chemistry, Umeå University, 901 87, Umeå, Sweden
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11
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Livendahl M, Jamroskovic J, Hedenström M, Görlich T, Sabouri N, Chorell E. Synthesis of phenanthridine spiropyrans and studies of their effects on G-quadruplex DNA. Org Biomol Chem 2017; 15:3265-3275. [DOI: 10.1039/c7ob00300e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Low molecular weight spirocycles efficiently stabilize G-quadruplex DNA without changing its structure by binding the top of the G-quadruplex structure.
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Affiliation(s)
- M. Livendahl
- Department of Chemistry
- Umeå University
- 901 87 Umeå
- Sweden
| | - J. Jamroskovic
- Department of Medical Biochemistry and Biophysics
- Umeå University
- 901 87 Umeå
- Sweden
| | - M. Hedenström
- Department of Chemistry
- Umeå University
- 901 87 Umeå
- Sweden
| | - T. Görlich
- Department of Chemistry
- Umeå University
- 901 87 Umeå
- Sweden
| | - N. Sabouri
- Department of Medical Biochemistry and Biophysics
- Umeå University
- 901 87 Umeå
- Sweden
| | - E. Chorell
- Department of Chemistry
- Umeå University
- 901 87 Umeå
- Sweden
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12
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Jamroskovic J, Livendahl M, Eriksson J, Chorell E, Sabouri N. Identification of Compounds that Selectively Stabilize Specific G-Quadruplex Structures by Using a Thioflavin T-Displacement Assay as a Tool. Chemistry 2016; 22:18932-18943. [DOI: 10.1002/chem.201603463] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Indexed: 12/13/2022]
Affiliation(s)
- Jan Jamroskovic
- Department of Medical Biochemistry and Biophysics; Umeå University; Umeå 901 87 Sweden
| | | | - Jonas Eriksson
- Laboratories for Chemical Biology Umeå; Chemical Biology Consortium Sweden; Department of Chemistry; Umeå University; Umeå 901 87 Sweden
| | - Erik Chorell
- Department of Chemistry; Umeå University; Umeå 901 87 Sweden
| | - Nasim Sabouri
- Department of Medical Biochemistry and Biophysics; Umeå University; Umeå 901 87 Sweden
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