1
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Yao XR, Jia MZ, Miao XL, Chen YR, Pan JQ, Zhang J. One-pot Tandem Synthesis and Spontaneous Product Separation of N-heterocycles based on Bifunctional Small-molecule Photocatalyst. CHEMSUSCHEM 2024; 17:e202301495. [PMID: 38086787 DOI: 10.1002/cssc.202301495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/28/2023] [Accepted: 12/11/2023] [Indexed: 02/07/2024]
Abstract
Homogeneous and heterogeneous reactions wherein the resulting products remain dissolved in solvents generally require complicated separation and purification process, despite the advantage of heterogeneous systems allowing retrieval of catalysts. Herein, we have developed an efficient approach for the one-pot tandem synthesis of quinazolines, quinazolinones and benzothiadiazine 1,1-dioxides from alcohols and amines utilizing a bifunctional bipyridinium photocatalyst with redox and Lewis acid sites using air as an oxidant. Through solvent-modulation strategy, the photocatalytic system exhibits high performance and enables most products to separate spontaneously. Consequently, the homogeneous catalyst can be reused by direct centrifugation isolation of the products. Notably, the method is also applicable to the less active substrates, such as heterocyclic alcohols and aliphatic alcohols, and thus provides an efficient and environmentally friendly photocatalytic route with spontaneous separation of N-heterocycles to reduce production costs and meet the needs of atomic economy and green chemistry.
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Affiliation(s)
- Xin-Rong Yao
- MOE Key Laboratory of Cluster Science, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488, P. R. China
| | - Meng-Ze Jia
- MOE Key Laboratory of Cluster Science, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488, P. R. China
| | - Xiao-Li Miao
- MOE Key Laboratory of Cluster Science, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488, P. R. China
| | - Yun-Rui Chen
- MOE Key Laboratory of Cluster Science, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488, P. R. China
| | - Jia-Qi Pan
- MOE Key Laboratory of Cluster Science, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488, P. R. China
| | - Jie Zhang
- MOE Key Laboratory of Cluster Science, Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 102488, P. R. China
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2
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Berner A, Das RN, Bhuma N, Golebiewska J, Abrahamsson A, Andréasson M, Chaudhari N, Doimo M, Bose PP, Chand K, Strömberg R, Wanrooij S, Chorell E. G4-Ligand-Conjugated Oligonucleotides Mediate Selective Binding and Stabilization of Individual G4 DNA Structures. J Am Chem Soc 2024; 146:6926-6935. [PMID: 38430200 PMCID: PMC10941181 DOI: 10.1021/jacs.3c14408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 03/03/2024]
Abstract
G-quadruplex (G4) DNA structures are prevalent secondary DNA structures implicated in fundamental cellular functions, such as replication and transcription. Furthermore, G4 structures are directly correlated to human diseases such as cancer and have been highlighted as promising therapeutic targets for their ability to regulate disease-causing genes, e.g., oncogenes. Small molecules that bind and stabilize these structures are thus valuable from a therapeutic perspective and helpful in studying the biological functions of the G4 structures. However, there are hundreds of thousands of G4 DNA motifs in the human genome, and a long-standing problem in the field is how to achieve specificity among these different G4 structures. Here, we developed a strategy to selectively target an individual G4 DNA structure. The strategy is based on a ligand that binds and stabilizes G4s without selectivity, conjugated to a guide oligonucleotide, that specifically directs the G4-Ligand-conjugated oligo (GL-O) to the single target G4 structure. By employing various biophysical and biochemical techniques, we show that the developed method enables the targeting of a unique, specific G4 structure without impacting other off-target G4 formations. Considering the vast amount of G4s in the human genome, this represents a promising strategy to study the presence and functions of individual G4s but may also hold potential as a future therapeutic modality.
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Affiliation(s)
- Andreas Berner
- Department
of Medical Biochemistry and Biophysics, Umeå University, Umeå 901 87, Sweden
| | | | - Naresh Bhuma
- Department
of Chemistry, Umeå University, Umeå 901 87, Sweden
| | | | | | - Måns Andréasson
- Department
of Chemistry, Umeå University, Umeå 901 87, Sweden
| | - Namrata Chaudhari
- Department
of Medical Biochemistry and Biophysics, Umeå University, Umeå 901 87, Sweden
| | - Mara Doimo
- Department
of Medical Biochemistry and Biophysics, Umeå University, Umeå 901 87, Sweden
| | - Partha Pratim Bose
- Department
of Biosciences and Nutrition, Karolinska
Institutet, Neo, Huddinge 141 57, Sweden
| | - Karam Chand
- Department
of Chemistry, Umeå University, Umeå 901 87, Sweden
| | - Roger Strömberg
- Department
of Biosciences and Nutrition, Karolinska
Institutet, Neo, Huddinge 141 57, Sweden
| | - Sjoerd Wanrooij
- Department
of Medical Biochemistry and Biophysics, Umeå University, Umeå 901 87, Sweden
| | - Erik Chorell
- Department
of Chemistry, Umeå University, Umeå 901 87, Sweden
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3
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Andreasson M, Donzel M, Abrahamsson A, Berner A, Doimo M, Quiroga A, Eriksson A, Chao YK, Overman J, Pemberton N, Wanrooij S, Chorell E. Exploring the Dispersion and Electrostatic Components in Arene-Arene Interactions between Ligands and G4 DNA to Develop G4-Ligands. J Med Chem 2024; 67:2202-2219. [PMID: 38241609 PMCID: PMC10860144 DOI: 10.1021/acs.jmedchem.3c02127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/14/2023] [Accepted: 01/08/2024] [Indexed: 01/21/2024]
Abstract
G-Quadruplex (G4) DNA structures are important regulatory elements in central biological processes. Small molecules that selectively bind and stabilize G4 structures have therapeutic potential, and there are currently >1000 known G4 ligands. Despite this, only two G4 ligands ever made it to clinical trials. In this work, we synthesized several heterocyclic G4 ligands and studied their interactions with G4s (e.g., G4s from the c-MYC, c-KIT, and BCL-2 promoters) using biochemical assays. We further studied the effect of selected compounds on cell viability, the effect on the number of G4s in cells, and their pharmacokinetic properties. This identified potent G4 ligands with suitable properties and further revealed that the dispersion component in arene-arene interactions in combination with electron-deficient electrostatics is central for the ligand to bind with the G4 efficiently. The presented design strategy can be applied in the further development of G4-ligands with suitable properties to explore G4s as therapeutic targets.
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Affiliation(s)
- Måns Andreasson
- Chemical
Biology Consortium Sweden, Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
| | - Maxime Donzel
- Chemical
Biology Consortium Sweden, Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
| | - Alva Abrahamsson
- Chemical
Biology Consortium Sweden, Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
| | - Andreas Berner
- Departments
of Medical Biochemistry and Biophysics, Umeå University, Umeå 90736, Sweden
| | - Mara Doimo
- Departments
of Medical Biochemistry and Biophysics, Umeå University, Umeå 90736, Sweden
- Clinical
Genetics Unit, Department of Women and Children’s Health, Padua University, 35128 Padua, Italy
| | - Anna Quiroga
- Departments
of Medical Biochemistry and Biophysics, Umeå University, Umeå 90736, Sweden
| | - Anna Eriksson
- Chemical
Biology Consortium Sweden, Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
| | - Yu-Kai Chao
- Mechanistic
and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K.
| | - Jeroen Overman
- Mechanistic
and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K.
| | - Nils Pemberton
- Medicinal
Chemistry, Research and Early Development, Respiratory and Immunology
(R&I), Bio Pharmaceuticals R&D, AstraZeneca, Gothenburg SE-43183, Sweden
| | - Sjoerd Wanrooij
- Departments
of Medical Biochemistry and Biophysics, Umeå University, Umeå 90736, Sweden
| | - Erik Chorell
- Chemical
Biology Consortium Sweden, Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
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4
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Gómez-Bra A, Gude L, Arias-Pérez MS. Synthesis, structural study and antitumor activity of novel alditol-based imidazophenanthrolines (aldo-IPs). Bioorg Med Chem 2024; 99:117563. [PMID: 38215623 DOI: 10.1016/j.bmc.2023.117563] [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: 07/05/2023] [Revised: 11/17/2023] [Accepted: 12/18/2023] [Indexed: 01/14/2024]
Abstract
A series of 1H-imidazo [4,5-f][1,10] phenanthroline derivatives functionalized at 2-position with chiral, and conformationally flexible polyhydroxy alkyl chains derived from carbohydrates (alditol-based imidazophenanthrolines, aldo-IPs) is presented herein. These novel glycomimetics showed relevant and differential cytotoxic activity against several cultured tumor cell lines (PC3, HeLa and HT-29), dependent on the nature and stereochemistry of the polyhydroxy alkyl chain. The mannose-based aldo-IP demonstrated the higher cytotoxicity in the series, substantially better than cisplatin metallo-drug in all cell lines tested, and better than G-quadruplex ligand 360A in HeLa and HT29 cells. Cell cycle experiments and Annexin V-PI assays revealed that aldo-IPs induce apoptosis in HeLa cells. Initial study of DNA interactions by DNA FRET melting assays proved that the aldo-IPs produce only a slight thermal stabilization of DNA secondary structures, more pronounced in the case of quadruplex DNA. Viscosity titrations with CT dsDNA suggest that the compounds behave as DNA groove binders, whereas equilibrium dialysis assays showed that the compounds bind CT with Ka values in the range 104-105 M-1. The aldo-IP derivatives were obtained with synthetically useful yields through a feasible one-pot multistep process, by aerobic oxidative cyclization of 1,10-phenanthroline-5,6-diamine with a selection of unprotected aldoses using (NH4)2SO4 as promoter.
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Affiliation(s)
- Ana Gómez-Bra
- Universidad de Alcalá, Departamento de Química Orgánica y Química Inorgánica, Instituto de Investigación Química "Andrés M. del Río" (IQAR), 28805-Alcalá de Henares, Madrid, Spain; Grupo DISCOBAC, Instituto de Investigación Sanitaria de Castilla-La Mancha (IDISCAM), Spain
| | - Lourdes Gude
- Universidad de Alcalá, Departamento de Química Orgánica y Química Inorgánica, Instituto de Investigación Química "Andrés M. del Río" (IQAR), 28805-Alcalá de Henares, Madrid, Spain; Grupo DISCOBAC, Instituto de Investigación Sanitaria de Castilla-La Mancha (IDISCAM), Spain.
| | - María-Selma Arias-Pérez
- Universidad de Alcalá, Departamento de Química Orgánica y Química Inorgánica, Instituto de Investigación Química "Andrés M. del Río" (IQAR), 28805-Alcalá de Henares, Madrid, Spain.
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5
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Elsebaie HA, El-Moselhy TF, El-Bastawissy EA, Elberembally KM, Badi RM, Elkaeed EB, Shaldam MA, Eldehna WM, Tawfik HO. Development of new thieno[2,3-d]pyrimidines as dual EGFR and STAT3 inhibitors endowed with anticancer and pro-apoptotic activities. Bioorg Chem 2024; 143:107101. [PMID: 38183682 DOI: 10.1016/j.bioorg.2024.107101] [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: 12/08/2023] [Revised: 12/20/2023] [Accepted: 01/03/2024] [Indexed: 01/08/2024]
Abstract
In part due to the resilience of cellular feedback pathways that develop therapeutic resistance to targeting the EGFR alone, using EGFR inhibitors alone was demonstrated to be unsuccessful in clinical trials. The over-activation of the signal transducer/activator of transcription 3 (STAT3) during the administration of an EGFR inhibitor is expected to play a substantial part in the failure and resistance of EGFR inhibitor treatment. Therein, we proposed a hypothesis that induced STAT3-mediated resistance to EGFR inhibition therapy could be addressed by a dual inhibition of EGFR and STAT3 method. To this end, we tried to discover new thieno[2,3-d]pyrimidine derivatives "5a-o". Results from the screening on A549 and MCF7 cancer cell lines revealed that compounds 5j and 5k showed two-digit nanomolar with appropriate safety towards the WI-38 cell line. The best molecules, 5j and 5k, were subjected to γ-radiation, and their cytotoxic efficacy didn't change after irradiation, demonstrating that not having to use it avoided its side effects. Compounds 5j and 5k demonstrated the highest inhibition when their potency was tested as dual inhibitors on EGFR 67 and 41 nM, respectively, and STAT3 5.52 and 3.34 nM, respectively, proved with in silico molecular docking and dynamic simulation. In light of the results presented above, the capacity of both powerful compounds to alter the cell cycle and initiate the apoptotic process in breast cancer MCF7 cells was investigated. Caspase-8, Bcl-2, Bax and Caspase-9 apoptotic indicators were studied.
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Affiliation(s)
- Heba A Elsebaie
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, Tanta 31527, Egypt.
| | - Tarek F El-Moselhy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, Tanta 31527, Egypt.
| | - Eman A El-Bastawissy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, Tanta 31527, Egypt
| | - Kamel M Elberembally
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, Tanta 31527, Egypt
| | - Rehab Mustafa Badi
- Department of Medical Physiology, College of Medicine, King Khalid University, Abha, Saudi Arabia.
| | - Eslam B Elkaeed
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City, Cairo, Egypt; Department of Pharmaceutical Sciences, College of Pharmacy, AlMaarefa University, Riyadh 13713, Saudi Arabia.
| | - Moataz A Shaldam
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh 33516, Egypt.
| | - Wagdy M Eldehna
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh 33516, Egypt.
| | - Haytham O Tawfik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, Tanta 31527, Egypt.
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6
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Saha A, Acharya BN, Parida M, Saxena N, Rajaiya J, Dash PK. Identification of 2,4-Diaminoquinazoline Derivative as a Potential Small-Molecule Inhibitor against Chikungunya and Ross River Viruses. Viruses 2023; 15:2194. [PMID: 38005871 PMCID: PMC10674894 DOI: 10.3390/v15112194] [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: 09/09/2023] [Revised: 10/20/2023] [Accepted: 10/22/2023] [Indexed: 11/26/2023] Open
Abstract
Alphaviruses are serious zoonotic threats responsible for significant morbidity, causing arthritis or encephalitis. So far, no licensed drugs or vaccines are available to combat alphaviral infections. About 300,000 chikungunya virus (CHIKV) infections have been reported in 2023, with more than 300 deaths, including reports of a few cases in the USA as well. The discovery and development of small-molecule drugs have been revolutionized over the last decade. Here, we employed a cell-based screening approach using a series of in-house small-molecule libraries to test for their ability to inhibit CHIKV replication. DCR 137, a quinazoline derivative, was found to be the most potent inhibitor of CHIKV replication in our screening assay. Both, the cytopathic effect, and immunofluorescence of infected cells were reduced in a dose-dependent manner with DCR 137 post-treatment. Most importantly, DCR 137 was more protective than the traditional ribavirin drug and reduced CHIKV plaque-forming units by several log units. CHIKV-E2 protein levels were also reduced in a dose-dependent manner. Further, DCR 137 was probed for its antiviral activity against another alphavirus, the Ross River virus, which revealed effective inhibition of viral replication. These results led to the identification of a potential quinazoline candidate for future optimization that might act as a pan-alphavirus inhibitor.
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Affiliation(s)
- Amrita Saha
- Virology Division, Defence Research & Development Establishment, Gwalior 474002, India; (A.S.); (M.P.)
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA;
| | - Badri Narayan Acharya
- Synthetic Chemistry Division, Defence Research & Development Establishment, Gwalior 474002, India;
| | - Manmohan Parida
- Virology Division, Defence Research & Development Establishment, Gwalior 474002, India; (A.S.); (M.P.)
| | - Nandita Saxena
- Pharmacology & Toxicology Division, Defence Research & Development Establishment, Gwalior 474002, India;
| | - Jaya Rajaiya
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA;
| | - Paban Kumar Dash
- Virology Division, Defence Research & Development Establishment, Gwalior 474002, India; (A.S.); (M.P.)
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7
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Doimo M, Chaudhari N, Abrahamsson S, L’Hôte V, Nguyen TH, Berner A, Ndi M, Abrahamsson A, Das R, Aasumets K, Goffart S, Pohjoismäki JLO, López MD, Chorell E, Wanrooij S. Enhanced mitochondrial G-quadruplex formation impedes replication fork progression leading to mtDNA loss in human cells. Nucleic Acids Res 2023; 51:7392-7408. [PMID: 37351621 PMCID: PMC10415151 DOI: 10.1093/nar/gkad535] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 06/09/2023] [Indexed: 06/24/2023] Open
Abstract
Mitochondrial DNA (mtDNA) replication stalling is considered an initial step in the formation of mtDNA deletions that associate with genetic inherited disorders and aging. However, the molecular details of how stalled replication forks lead to mtDNA deletions accumulation are still unclear. Mitochondrial DNA deletion breakpoints preferentially occur at sequence motifs predicted to form G-quadruplexes (G4s), four-stranded nucleic acid structures that can fold in guanine-rich regions. Whether mtDNA G4s form in vivo and their potential implication for mtDNA instability is still under debate. In here, we developed new tools to map G4s in the mtDNA of living cells. We engineered a G4-binding protein targeted to the mitochondrial matrix of a human cell line and established the mtG4-ChIP method, enabling the determination of mtDNA G4s under different cellular conditions. Our results are indicative of transient mtDNA G4 formation in human cells. We demonstrate that mtDNA-specific replication stalling increases formation of G4s, particularly in the major arc. Moreover, elevated levels of G4 block the progression of the mtDNA replication fork and cause mtDNA loss. We conclude that stalling of the mtDNA replisome enhances mtDNA G4 occurrence, and that G4s not resolved in a timely manner can have a negative impact on mtDNA integrity.
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Affiliation(s)
- Mara Doimo
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
- Department of Women and Children Health, University of Padova, 35128 Padova, Italy
| | - Namrata Chaudhari
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | - Sanna Abrahamsson
- Bioinformatics and Data Centre, Sahlgrenska Academy, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Valentin L’Hôte
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | - Tran V H Nguyen
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | - Andreas Berner
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | - Mama Ndi
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | | | | | - Koit Aasumets
- Department of Environmental and Biological Sciences, University of Eastern Finland, FI-80101 Joensuu, Finland
| | - Steffi Goffart
- Department of Environmental and Biological Sciences, University of Eastern Finland, FI-80101 Joensuu, Finland
| | - Jaakko L O Pohjoismäki
- Department of Environmental and Biological Sciences, University of Eastern Finland, FI-80101 Joensuu, Finland
| | - Marcela Dávila López
- Bioinformatics and Data Centre, Sahlgrenska Academy, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Erik Chorell
- Department of Chemistry, Umeå University, 90187 Umeå, Sweden
| | - Sjoerd Wanrooij
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
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8
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Deiana M, Andrés Castán J, Josse P, Kahsay A, Sánchez D, Morice K, Gillet N, Ravindranath R, Patel A, Sengupta P, Obi I, Rodriguez-Marquez E, Khrouz L, Dumont E, Abad Galán L, Allain M, Walker B, Ahn HS, Maury O, Blanchard P, Le Bahers T, Öhlund D, von Hofsten J, Monnereau C, Cabanetos C, Sabouri N. A new G-quadruplex-specific photosensitizer inducing genome instability in cancer cells by triggering oxidative DNA damage and impeding replication fork progression. Nucleic Acids Res 2023; 51:6264-6285. [PMID: 37191066 PMCID: PMC10325911 DOI: 10.1093/nar/gkad365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 03/31/2023] [Accepted: 04/26/2023] [Indexed: 05/17/2023] Open
Abstract
Photodynamic therapy (PDT) ideally relies on the administration, selective accumulation and photoactivation of a photosensitizer (PS) into diseased tissues. In this context, we report a new heavy-atom-free fluorescent G-quadruplex (G4) DNA-binding PS, named DBI. We reveal by fluorescence microscopy that DBI preferentially localizes in intraluminal vesicles (ILVs), precursors of exosomes, which are key components of cancer cell proliferation. Moreover, purified exosomal DNA was recognized by a G4-specific antibody, thus highlighting the presence of such G4-forming sequences in the vesicles. Despite the absence of fluorescence signal from DBI in nuclei, light-irradiated DBI-treated cells generated reactive oxygen species (ROS), triggering a 3-fold increase of nuclear G4 foci, slowing fork progression and elevated levels of both DNA base damage, 8-oxoguanine, and double-stranded DNA breaks. Consequently, DBI was found to exert significant phototoxic effects (at nanomolar scale) toward cancer cell lines and tumor organoids. Furthermore, in vivo testing reveals that photoactivation of DBI induces not only G4 formation and DNA damage but also apoptosis in zebrafish, specifically in the area where DBI had accumulated. Collectively, this approach shows significant promise for image-guided PDT.
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Affiliation(s)
- Marco Deiana
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87, Umeå, Sweden
| | | | - Pierre Josse
- Univ Angers, CNRS, MOLTECH-ANJOU, SFR MATRIX, F-49000 Angers, France
| | - Abraha Kahsay
- Department of Integrative Medical Biology, Umeå University, SE-901 87, Umeå, Sweden
| | | | - Korentin Morice
- Univ Angers, CNRS, MOLTECH-ANJOU, SFR MATRIX, F-49000 Angers, France
| | - Natacha Gillet
- ENS de Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, F-69342 Lyon, France
| | - Ranjitha Ravindranath
- ENS de Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, F-69342 Lyon, France
- Indian Institute for Science Education and Research (IISER), Tirupati-517507, India
| | - Ankit Kumar Patel
- Department of Radiation Sciences/Oncology, Umeå University, SE-901 87, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, SE-901 87, Umeå, Sweden
| | - Pallabi Sengupta
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87, Umeå, Sweden
| | - Ikenna Obi
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87, Umeå, Sweden
| | | | - Lhoussain Khrouz
- ENS de Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, F-69342 Lyon, France
| | - Elise Dumont
- ENS de Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, F-69342 Lyon, France
- Institut Universitaire de France, 5 rue Descartes, 75005 Paris, France
| | - Laura Abad Galán
- ENS de Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, F-69342 Lyon, France
| | - Magali Allain
- Univ Angers, CNRS, MOLTECH-ANJOU, SFR MATRIX, F-49000 Angers, France
| | - Bright Walker
- Department of Chemistry, Kyung Hee University, Seoul, 02447, South Korea
| | - Hyun Seo Ahn
- Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, South Korea
| | - Olivier Maury
- ENS de Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, F-69342 Lyon, France
| | | | - Tangui Le Bahers
- ENS de Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, F-69342 Lyon, France
- Institut Universitaire de France, 5 rue Descartes, 75005 Paris, France
| | - Daniel Öhlund
- Department of Radiation Sciences/Oncology, Umeå University, SE-901 87, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, SE-901 87, Umeå, Sweden
| | - Jonas von Hofsten
- Department of Integrative Medical Biology, Umeå University, SE-901 87, Umeå, Sweden
| | - Cyrille Monnereau
- ENS de Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, F-69342 Lyon, France
| | - Clément Cabanetos
- Univ Angers, CNRS, MOLTECH-ANJOU, SFR MATRIX, F-49000 Angers, France
- Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, South Korea
- Building Blocks for FUture Electronics Laboratory (2BFUEL), IRL CNRS 2002, Yonsei University, Seoul, South Korea
| | - Nasim Sabouri
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87, Umeå, Sweden
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9
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Deiana M, Chand K, Chorell E, Sabouri N. Parallel G-Quadruplex DNA Structures from Nuclear and Mitochondrial Genomes Trigger Emission Enhancement in a Nonfluorescent Nano-aggregated Fluorine-Boron-Based Dye. J Phys Chem Lett 2023; 14:1862-1869. [PMID: 36779779 PMCID: PMC9940295 DOI: 10.1021/acs.jpclett.2c03301] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 02/02/2023] [Indexed: 05/28/2023]
Abstract
Molecular self-assembly is a powerful tool for the development of functional nanostructures with adaptive optical properties. However, in aqueous solution, the hydrophobic effects in the monomeric units often afford supramolecular architectures with typical side-by-side π-stacking arrangement with compromised emissive properties. Here, we report on the role of parallel DNA guanine quadruplexes (G4s) as supramolecular disaggregating-capture systems capable of coordinating a zwitterionic fluorine-boron-based dye and promoting activation of its fluorescence signal. The dye's high binding affinity for parallel G4s compared to nonparallel topologies leads to a selective disassembly of the dye's supramolecular state upon contact with parallel G4s. This results in a strong and selective disaggregation-induced emission that signals the presence of parallel G4s observable by the naked eye and inside cells. The molecular recognition strategy reported here will be useful for a multitude of affinity-based applications with potential in sensing and imaging systems.
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Affiliation(s)
- Marco Deiana
- Department
of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | - Karam Chand
- Department
of Chemistry, Umeå University, 90187 Umeå, Sweden
| | - Erik Chorell
- Department
of Chemistry, Umeå University, 90187 Umeå, Sweden
| | - Nasim Sabouri
- Department
of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
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10
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The effect of side chain variations on quinazoline-pyrimidine G-quadruplex DNA ligands. Eur J Med Chem 2023; 248:115103. [PMID: 36645982 DOI: 10.1016/j.ejmech.2023.115103] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 01/05/2023] [Accepted: 01/06/2023] [Indexed: 01/09/2023]
Abstract
G-quadruplex (G4) DNA structures are involved in central biological processes such as DNA replication and transcription. These DNA structures are enriched in promotor regions of oncogenes and are thus promising as novel gene silencing therapeutic targets that can be used to regulate expression of oncoproteins and in particular those that has proven hard to drug with conventional strategies. G4 DNA structures in general have a well-defined and hydrophobic binding area that also is very flat and featureless and there are ample examples of G4 ligands but their further progression towards drug development is limited. In this study, we use synthetic organic chemistry to equip a drug-like and low molecular weight central fragment with different side chains and evaluate how this affect the compound's selectivity and ability to bind and stabilize G4 DNA. Furthermore, we study the binding interactions of the compounds and connect the experimental observations with the compound's structural conformations and electrostatic potentials to understand the basis for the observed improvements. Finally, we evaluate the top candidates' ability to selectively reduce cancer cell growth in a 3D co-culture model of pancreatic cancer which show that this is a powerful approach to generate highly active and selective low molecular weight G4 ligands with a promising therapeutic window.
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11
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Yu P, Cao W, Yang S, Wang Y, Xia A, Tan X, Wang L. Design, synthesis and antitumor evaluation of novel quinazoline analogs in hepatocellular carcinoma cell. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133718] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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12
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Su X, Tan Z, Wang G, Liu Z, Gan C, Yue L, Liu H, Xie Y, Yao Y, Ye T. Design, synthesis and biological evaluation of novel diarylacylhydrazones derivatives for the efficient treatment of idiopathic pulmonary fibrosis. Eur J Med Chem 2022; 245:114918. [DOI: 10.1016/j.ejmech.2022.114918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/27/2022] [Accepted: 11/05/2022] [Indexed: 11/13/2022]
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13
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Kumar R, Kumar V, Kamal R, Kumar A, Kaur S, Bansal A, Chetti P. 2,4‐Bis(2‐(
E
)‐arylidenehydrazinyl)quinazolines: Expeditious Synthesis, Characterization, Antiproliferative Effects against Breast Cancer Cell Line and Molecular Docking Studies. ChemistrySelect 2022. [DOI: 10.1002/slct.202202635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ravinder Kumar
- Department of Chemistry Kurukshetra University Kurukshetra, Kurukshetra 136119 Haryana INDIA
- Current Address: Department of Chemistry M. M. Engineering College Maharishi Markandeshwar (Deemed to be University) Mullana Ambala 133207 Haryana INDIA
| | - Vipan Kumar
- Department of Chemistry Kurukshetra University Kurukshetra, Kurukshetra 136119 Haryana INDIA
- Current Address: Department of Chemistry & MAP Section Department of Genetics and Plant Breeding CCS Haryana Agriculture University Hisar 125004 Haryana INDIA
| | - Raj Kamal
- Department of Chemistry Kurukshetra University Kurukshetra, Kurukshetra 136119 Haryana INDIA
| | - Ajay Kumar
- Department of Botanical & Environmental Sciences Guru Nanak Dev University Amritsar 143005 Punjab INDIA
| | - Satwinderjeet Kaur
- Department of Botanical & Environmental Sciences Guru Nanak Dev University Amritsar 143005 Punjab INDIA
| | - Arubhi Bansal
- Department of Chemistry National Institute of Technology (NIT) Kurukshetra 136119 Haryana INDIA
| | - Prabhakar Chetti
- Department of Chemistry National Institute of Technology (NIT) Kurukshetra 136119 Haryana INDIA
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14
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Liu S, Wang AJ, Li M, Zhang J, Yin GD, Shu WM, Yu WC. Rh(III)-Catalyzed Tandem Reaction Access to (Quinazolin-2-yl)methanone Derivatives from 2,1-Benzisoxazoles and α-Azido Ketones. J Org Chem 2022; 87:11253-11260. [PMID: 35938613 DOI: 10.1021/acs.joc.2c01214] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A Rh(III)-catalyzed tandem reaction for the synthesis of (quinazolin-2-yl)methanone derivatives has been explored from 2,1-benzisoxazoles and α-azido ketones. The transformation involves Rh(III)-catalyzed denitrogenation of α-azido ketones, aza-[4 + 2] cycloaddition, ring opening, and dehydration aromatization processes. Notably, the aza-[4 + 2] cycloaddition of an imine rhodium complex intermediate with 2,1-benzisoxazoles is the key to this reaction.
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Affiliation(s)
- Shan Liu
- College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou 434023, PR China
| | - An-Jing Wang
- College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou 434023, PR China
| | - Min Li
- College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou 434023, PR China
| | - Jing Zhang
- College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou 434023, PR China
| | - Guo-Dong Yin
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, Hubei Normal University, Huangshi 435002, PR China
| | - Wen-Ming Shu
- College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou 434023, PR China.,Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, Hubei Normal University, Huangshi 435002, PR China
| | - Wei-Chu Yu
- College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou 434023, PR China
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15
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Yang J, Wang L, Guan X, Qin JJ. Inhibiting STAT3 signaling pathway by natural products for cancer prevention and therapy: In vitro and in vivo activity and mechanisms of action. Pharmacol Res 2022; 182:106357. [PMID: 35868477 DOI: 10.1016/j.phrs.2022.106357] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/13/2022] [Accepted: 07/15/2022] [Indexed: 10/17/2022]
Abstract
Signal transducer and activator of transcription 3 (STAT3) plays a critical role in signal transmission from the plasma membrane to the nucleus, regulating the expression of genes involved in essential cell functions and controlling the processes of cell cycle progression and apoptosis. Thus, STAT3 has been elucidated as a promising target for developing anticancer drugs. Many natural products have been reported to inhibit the STAT3 signaling pathway during the past two decades and have exhibited significant anticancer activities in vitro and in vivo. However, there is no FDA-approved STAT3 inhibitor yet. The major mechanisms of these natural product inhibitors of the STAT3 signaling pathway include targeting the upstream regulators of STAT3, directly binding to the STAT3 SH2 domain and inhibiting its activation, inhibiting STAT3 phosphorylation and/or dimerization, and others. In the present review, we have systematically discussed the development of these natural product inhibitors of STAT3 signaling pathway as well as their in vitro and in vivo anticancer activity and mechanisms of action. Outlooks and perspectives on the associated challenges are provided as well.
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Affiliation(s)
- Jing Yang
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China; The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Lingling Wang
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China; School of Life Sciences, Tianjin University, Tianjin, China
| | - Xiaoqing Guan
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China; Key Laboratory of Prevention, Diagnosis and Therapy of Upper Gastrointestinal Cancer of Zhejiang Province, Hangzhou 310022, China.
| | - Jiang-Jiang Qin
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China; The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China; Key Laboratory of Prevention, Diagnosis and Therapy of Upper Gastrointestinal Cancer of Zhejiang Province, Hangzhou 310022, China.
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16
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Eugin Simon S, Ahmed U, Saad SM, Anwar A, Khan KM, Tan EW, Tan KO. New synthetic phenylquinazoline derivatives induce apoptosis by targeting the pro-survival members of the BCL-2 family. Bioorg Med Chem Lett 2022; 67:128731. [PMID: 35421577 DOI: 10.1016/j.bmcl.2022.128731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 04/05/2022] [Accepted: 04/08/2022] [Indexed: 11/02/2022]
Abstract
Chemo-resistant cancer cells acquire robust growth potential through cell signaling mechanisms such as the down-regulation of tumor suppressors and the up-regulation of pro-survival proteins, respectively. To overcome chemo-resistance of cancer, small molecule drugs that interact with the cell signaling proteins to enhance sensitization of cancer cells toward cancer therapies are likely to be effective for the treatment of chemo-drug resistant cancer. To identify high potency small molecules, a series of ten novel phenylquinazoline derivatives were synthesized to determine their cellular effects in MCF-7 and MCF-7- cisplatin-resistant (CR) human breast cancer cells which led to the identification of two bioactive compounds, SMS-IV-20 and SMS-IV-40, that exhibited an elevated level of cytotoxicity against the human breast cancer cells and spheroid cells. In addition, both compounds enhanced chemo-sensitization of the human breast cancer cells that were genetically engineered to express the tumor suppressor and pro-apoptotic proteins, MOAP-1, Bax, and RASSF1a (MBR), suggesting that the compounds interact with the MBR signaling pathway. Furthermore, when MCF-7-CR cells were treated with SMS-IV-20 and SMS-IV-40 in the presence of ABT-737, a BCL-XL and BCL-2 inhibitor, enhanced chemo-sensitization was observed, suggesting SMS-IV-20 and SMS-IV-40 exert antagonistic activity to regulate the functional activity of BCL-2 and BCL-XL. Western blot analysis showed that both SMS-IV-20 and SMS-IV-40 induced down-regulation of BCL-2 or both BCl-2 and BCL-XL expression, respectively while promoting the release of mitochondrial Cytochrome C. Taken together, the data showed that SMS-IV-20 and SMS-IV-40 are potent activators of apoptosis that enhance chemo-sensitization through their antagonistic actions on the pro-survival activity of the BCl-2 family in human cancer cells.
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Affiliation(s)
- Samson Eugin Simon
- Department of Biological Sciences, School of Medical and Life Sciences, Sunway University, No. 5 Jalan Universiti, Bandar Sunway, 47500, Selangor Darul Ehsan, Malaysia
| | - Usman Ahmed
- Department of Biological Sciences, School of Medical and Life Sciences, Sunway University, No. 5 Jalan Universiti, Bandar Sunway, 47500, Selangor Darul Ehsan, Malaysia
| | | | - Ayaz Anwar
- Department of Biological Sciences, School of Medical and Life Sciences, Sunway University, No. 5 Jalan Universiti, Bandar Sunway, 47500, Selangor Darul Ehsan, Malaysia
| | - Khalid Mohammed Khan
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan; Department of Clinical Pharmacy, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Ee Wern Tan
- Department of Biological Sciences, School of Medical and Life Sciences, Sunway University, No. 5 Jalan Universiti, Bandar Sunway, 47500, Selangor Darul Ehsan, Malaysia
| | - Kuan Onn Tan
- Department of Biological Sciences, School of Medical and Life Sciences, Sunway University, No. 5 Jalan Universiti, Bandar Sunway, 47500, Selangor Darul Ehsan, Malaysia.
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17
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Venkata Suseela Y, Sengupta P, Roychowdhury T, Panda S, Talukdar S, Chattopadhyay S, Chatterjee S, Govindaraju T. Targeting Oncogene Promoters and Ribosomal RNA Biogenesis by G-Quadruplex Binding Ligands Translate to Anticancer Activity. ACS BIO & MED CHEM AU 2022; 2:125-139. [PMID: 37101746 PMCID: PMC10114666 DOI: 10.1021/acsbiomedchemau.1c00039] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
G-Quadruplex (GQ) nucleic acids are promising therapeutic targets in anticancer research due to their structural robustness, polymorphism, and gene-regulatory functions. Here, we presented the structure-activity relationship of carbazole-based monocyanine ligands using region-specific functionalization with benzothiazole (TCA and TCZ), lepidine (LCA and LCZ), and quinaldine (QCA and QCZ) acceptor moieties and evaluated their binding profiles with different oncogenic GQs. Their differential turn-on fluorescence emission upon GQ binding confirmed the GQ-to-duplex selectivity of all carbazole ligands, while the isothermal titration calorimetry results showed selective interactions of TCZ and TCA to c-MYC and BCL-2 GQs, respectively. The aldehyde group in TCA favors stacking interactions with the tetrad of BCL-2 GQ, whereas TCZ provides selective groove interactions with c-MYC GQ. Dual-luciferase assay and chromatin immunoprecipitation (ChIP) showed that these molecules interfere with the recruitment of specific transcription factors at c-MYC and BCL-2 promoters and stabilize the promoter GQ structures to inhibit their constitutive transcription in cancer cells. Their intrinsic turn-on fluorescence response with longer lifetimes upon GQ binding allowed real-time visualization of GQ structures at subcellular compartments. Confocal microscopy revealed the uptake of these ligands in the nucleoli, resulting in nucleolar stress. ChIP studies further confirmed the inhibition of Nucleolin occupancy at multiple GQ-enriched regions of ribosomal DNA (rDNA) promoters, which arrested rRNA biogenesis. Therefore, carbazole ligands act as the "double-edged swords" to arrest c-MYC and BCL-2 overexpression as well as rRNA biogenesis, triggering synergistic inhibition of multiple oncogenic pathways and apoptosis in cancer cells.
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Affiliation(s)
- Yelisetty Venkata Suseela
- Bioorganic
Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, P.O., Bengaluru, Karnataka 560064, India
| | - Pallabi Sengupta
- Department
of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kankurgachi, Kolkata 700054, India
| | - Tanaya Roychowdhury
- Cancer
Biology and Inflammatory Disorder Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Suman Panda
- Department
of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kankurgachi, Kolkata 700054, India
| | - Sangita Talukdar
- Bioorganic
Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, P.O., Bengaluru, Karnataka 560064, India
| | - Samit Chattopadhyay
- Cancer
Biology and Inflammatory Disorder Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Subhrangsu Chatterjee
- Department
of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kankurgachi, Kolkata 700054, India
| | - Thimmaiah Govindaraju
- Bioorganic
Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, P.O., Bengaluru, Karnataka 560064, India
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18
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Jamroskovic J, Deiana M, Sabouri N. Probing the folding pathways of four-stranded intercalated cytosine-rich motifs at single base-pair resolution. Biochimie 2022; 199:81-91. [PMID: 35452743 DOI: 10.1016/j.biochi.2022.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 04/13/2022] [Accepted: 04/13/2022] [Indexed: 11/24/2022]
Abstract
Cytosine-rich DNA can fold into four-stranded intercalated structures called i-motifs (iMs) under acidic conditions through the formation of hemi-protonated C:C+ base pairs. However, the folding and stability of iMs rely on many other factors that are not yet fully understood. Here, we combined biochemical and biophysical approaches to determine the factors influencing iM stability under a wide range of experimental conditions. By using high-resolution primer extension assays, circular dichroism, and absorption spectroscopies, we demonstrate that the stabilities of three different biologically relevant iMs are not dependent on molecular crowding agents. Instead, some of the crowding agents affected overall DNA synthesis. We also tested a range of small molecules to determine their effect on iM stabilization at physiological temperature and demonstrated that the G-quadruplex-specific molecule CX-5461 is also a promising candidate for selective iM stabilization. This work provides important insights into the requirements needed for different assays to accurately study iM stabilization, which will serve as important tools for understanding the contribution of iMs in cell regulation and their potential as therapeutic targets.
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Affiliation(s)
- Jan Jamroskovic
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87, Umeå, Sweden.
| | - Marco Deiana
- 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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19
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Wang F, Cao XY, Lin GQ, Tian P, Gao D. Novel inhibitors of the STAT3 signaling pathway: an updated patent review (2014-present). Expert Opin Ther Pat 2022; 32:667-688. [PMID: 35313119 DOI: 10.1080/13543776.2022.2056013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION STAT3 is a critical transcription factor that transmits signals from the cell surface to the nucleus, thus influencing the transcriptional regulation of some oncogenes. The inhibition of the activation of STAT3 is considered a promising strategy for cancer therapy. Numerous STAT3 inhibitors bearing different scaffolds have been reported to date, with a few of them having been considered in clinical trials. AREAS COVERED This review summarizes the advances on STAT3 inhibitors with different structural skeletons, focusing on the structure-activity relationships in the related patent literature published from 2014 to date. EXPERT OPINION Since the X-ray crystal structure of STAT3β homo dimer bound to DNA was solved in 1998, the development of STAT3 inhibitors has gone through a boom in recent years. However, none of them have been approved for marketing, probably due to the complex biological functions of the STAT3 signaling pathway, including its character and the poor drug-like physicochemical properties of its inhibitors. Nonetheless, targeting STAT3 continues to be an exciting field for the development of anti-tumor agents along with the emergence of new STAT3 inhibitors with unique mechanisms of action.
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Affiliation(s)
- Feng Wang
- The Research Center of Chiral Drugs, Shanghai Frontiers Science Center for Traditional Chinese Medicine Chemical Biology and Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, Xuhui, China
| | - Xin-Yu Cao
- The Research Center of Chiral Drugs, Shanghai Frontiers Science Center for Traditional Chinese Medicine Chemical Biology and Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, Xuhui, China
| | - Guo-Qiang Lin
- The Research Center of Chiral Drugs, Shanghai Frontiers Science Center for Traditional Chinese Medicine Chemical Biology and Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, Xuhui, China
| | - Ping Tian
- The Research Center of Chiral Drugs, Shanghai Frontiers Science Center for Traditional Chinese Medicine Chemical Biology and Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, Xuhui, China
| | - Dingding Gao
- The Research Center of Chiral Drugs, Shanghai Frontiers Science Center for Traditional Chinese Medicine Chemical Biology and Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, Xuhui, China
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20
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Synthesis, structural characterization and biological properties of cyclometalated iridium(III) complexes containing 2-methyl-3-{(E)-[(quinolin-2-yl)methylidene]amino}quinazolin-4(3H)-one. Inorganica Chim Acta 2022. [DOI: 10.1016/j.ica.2021.120735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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21
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Niu K, Zhang X, Song Q, Feng Q. G-Quadruplex Regulation of VEGFA mRNA Translation by RBM4. Int J Mol Sci 2022; 23:ijms23020743. [PMID: 35054929 PMCID: PMC8776124 DOI: 10.3390/ijms23020743] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 02/01/2023] Open
Abstract
In eukaryotes, mRNAs translation is mainly mediated in a cap-dependent or cap-independent manner. The latter is primarily initiated at the internal ribosome entry site (IRES) in the 5'-UTR of mRNAs. It has been reported that the G-quadruplex structure (G4) in the IRES elements could regulate the IRES activity. We previously confirmed RBM4 (also known as LARK) as a G4-binding protein in human. In this study, to investigate whether RBM4 is involved in the regulation of the IRES activity by binding with the G4 structure within the IRES element, the IRES-A element in the 5'-UTR of vascular endothelial growth factor A (VEGFA) was constructed into a dicistronic reporter vector, psiCHECK2, and the effect of RBM4 on the IRES activity was tested in 293T cells. The results showed that the IRES insertion significantly increased the FLuc expression activity, indicating that this G4-containing IRES was active in 293T cells. When the G4 structure in the IRES was disrupted by base mutation, the IRES activity was significantly decreased. The IRES activity was notably increased when the cells were treated with G4 stabilizer PDS. EMSA results showed that RBM4 specifically bound the G4 structure in the IRES element. The knockdown of RBM4 substantially reduced the IRES activity, whereas over-expressing RBM4 increased the IRES activity. Taking all results together, we demonstrated that RBM4 promoted the mRNA translation of VEGFA gene by binding to the G4 structure in the IRES.
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Affiliation(s)
- Kangkang Niu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China; (K.N.); (X.Z.)
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Xiaojuan Zhang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China; (K.N.); (X.Z.)
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Qisheng Song
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA;
| | - Qili Feng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China; (K.N.); (X.Z.)
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
- Correspondence:
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22
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Huang X, He Z, Zhou K, Zhi H, Yang J. Fabrication of bifunctional G-quadruplex-hemin DNAzymes for colorimetric detection of apurinic/apyrimidinic endonuclease 1 and microRNA-21. Analyst 2021; 146:7379-7385. [PMID: 34816841 DOI: 10.1039/d1an01603b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
G-quadruplex-based complexes have been widely used in various analytical methods due to their outstanding capabilities of generating colorimetric, fluorescent or electrochemical signals. However, since loop sequences in traditional G-quadruplex structures are quite short, it is difficult to establish biosensors solely using G-quadruplex-based complexes. Herein, we attempted to lengthen the loop sequences of G-quadruplex structures and found that G-quadruplex-hemin DNAzymes (G-DNAzymes) with long loops (even 30 nucleotides) maintain high peroxidase activity. In addition, the peroxidase activity is not affected by the hybridization of the long loop with its complementary counterpart. Consequently, G-DNAzyme can be endowed with an additional function by taking the long loop as a recognition element, which may facilitate the construction of diverse colorimetric biosensors. Furthermore, by designing an apurinic/apyrimidinic site or a complementary sequence of microRNA-21 (miRNA-21) in long loops, bifunctional G-DNAzymes can be split in the presence of apurinic/apyrimidinic endonuclease 1 (APE1) or miRNA-21, decreasing their peroxidase activities. Accordingly, APE1 and miRNA-21 are quantified using 3,3',5,5'-tetramethylbenzidine as a chromophore. Using the G-DNAzyme, APE1 can be detected in a linear range from 2.5 to 22.5 U mL-1 with a LOD of 1.8 U mL-1. It is to be noted that benefitting from duplex-specific nuclease-induced signal amplification, the linear range of the miRNA-21 biosensor is broadened to 5 orders of magnitude, while the limit of detection is as low as 73 fM. This work demonstrates that G-DNAzymes with long loops can both generate signals and recognize targets, providing an alternative strategy to design G-quadruplex-based analytical methods.
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Affiliation(s)
- Xiaodong Huang
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials and Jiangsu Key Laboratory of Biofunctional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China.
| | - Zhenni He
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials and Jiangsu Key Laboratory of Biofunctional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China.
| | - Kejie Zhou
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials and Jiangsu Key Laboratory of Biofunctional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China.
| | - Huizhen Zhi
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials and Jiangsu Key Laboratory of Biofunctional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China.
| | - Jinfei Yang
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials and Jiangsu Key Laboratory of Biofunctional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China.
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23
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Dudek M, Deiana M, Szkaradek K, Janicki MJ, Pokładek Z, Góra RW, Matczyszyn K. Light-Induced Modulation of Chiral Functions in G-Quadruplex-Photochrome Systems. J Phys Chem Lett 2021; 12:9436-9441. [PMID: 34554762 PMCID: PMC8503878 DOI: 10.1021/acs.jpclett.1c02207] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 09/20/2021] [Indexed: 05/05/2023]
Abstract
The design of artificially engineered chiral structures has received much attention, but the implementation of dynamic functions to modulate the chiroptical response of the systems is less explored. Here, we present a light-responsive G-quadruplex (G4)-based assembly in which chirality enrichment is induced, tuned, and fueled by molecular switches. In particular, the mirror-image dependence on photoactivated azo molecules, undergoing trans-to-cis isomerization, shows chiral recognition effects on the inherent flexibility and conformational diversity of DNA G4s having distinct handedness (right- and left-handed). Through a detailed experimental and computational analysis, we bring compelling evidence on the binding mode of the photochromes on G4s, and we rationalize the origin of the chirality effect that is associated with the complexation event.
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Affiliation(s)
- Marta Dudek
- Advanced
Materials Engineering and Modelling Group, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Marco Deiana
- Department
of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | - Kinga Szkaradek
- Theoretical
Photochemistry and Photophysics Group, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Mikołaj J. Janicki
- Theoretical
Photochemistry and Photophysics Group, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Ziemowit Pokładek
- Advanced
Materials Engineering and Modelling Group, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Robert W. Góra
- Theoretical
Photochemistry and Photophysics Group, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Katarzyna Matczyszyn
- Advanced
Materials Engineering and Modelling Group, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
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24
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Deiana M, Mosser M, Le Bahers T, Dumont E, Dudek M, Denis-Quanquin S, Sabouri N, Andraud C, Matczyszyn K, Monnereau C, Guy L. Light-induced in situ chemical activation of a fluorescent probe for monitoring intracellular G-quadruplex structures. NANOSCALE 2021; 13:13795-13808. [PMID: 34477654 DOI: 10.1039/d1nr02855c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Light-activated functional materials capable of remote control over duplex and G-quadruplex (G4) nucleic acids formation at the cellular level are still very rare. Herein, we report on the photoinduced macrocyclisation of a helicenoid quinoline derivative of binaphthol that selectively provides easy access to an unprecedented class of extended heteroaromatic structures with remarkable photophysical and DNA/RNA binding properties. Thus, while the native bisquinoline precursor shows no DNA binding activity, the new in situ photochemically generated probe features high association constants to DNA and RNA G4s. The latter inhibits DNA synthesis by selectively stabilizing G4 structures associated with oncogenic promoters and telomere repeat units. Finally, the light sensitive compound is capable of in cellulo photoconversion, localizes primarily in the G4-rich sites of cancer cells, competes with a well-known G4 binder and shows a clear nuclear co-localization with the quadruplex specific antibody BG4. This work provides a benchmark for the future design and development of a brand-new generation of light-activated target-selective G4-binders.
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Affiliation(s)
- Marco Deiana
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden.
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25
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Deiana M, Obi I, Andreasson M, Tamilselvi S, Chand K, Chorell E, Sabouri N. A Minimalistic Coumarin Turn-On Probe for Selective Recognition of Parallel G-Quadruplex DNA Structures. ACS Chem Biol 2021; 16:1365-1376. [PMID: 34328300 PMCID: PMC8397291 DOI: 10.1021/acschembio.1c00134] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
![]()
G-quadruplex (G4)
DNA structures are widespread in the human genome
and are implicated in biologically important processes such as telomere
maintenance, gene regulation, and DNA replication. Guanine-rich sequences
with potential to form G4 structures are prevalent in the promoter
regions of oncogenes, and G4 sites are now considered as attractive
targets for anticancer therapies. However, there are very few reports
of small “druglike” optical G4 reporters that are easily
accessible through one-step synthesis and that are capable of discriminating
between different G4 topologies. Here, we present a small water-soluble
light-up fluorescent probe that features a minimalistic amidinocoumarin-based
molecular scaffold that selectively targets parallel G4 structures
over antiparallel and non-G4 structures. We showed that this biocompatible
ligand is able to selectively stabilize the G4 template resulting
in slower DNA synthesis. By tracking individual DNA molecules, we
demonstrated that the G4-stabilizing ligand perturbs DNA replication
in cancer cells, resulting in decreased cell viability. Moreover,
the fast-cellular entry of the probe enabled detection of nucleolar
G4 structures in living cells. Finally, insights gained from the structure–activity
relationships of the probe suggest the basis for the recognition of
parallel G4s, opening up new avenues for the design of new biocompatible
G4-specific small molecules for G4-driven theranostic applications.
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Affiliation(s)
- Marco Deiana
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | - Ikenna Obi
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | - Måns Andreasson
- Department of Chemistry, Umeå University, 90187 Umeå, Sweden
| | - Shanmugam Tamilselvi
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | - Karam Chand
- Department of Chemistry, Umeå University, 90187 Umeå, Sweden
| | - Erik Chorell
- Department of Chemistry, Umeå University, 90187 Umeå, Sweden
| | - Nasim Sabouri
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
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26
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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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27
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Dong J, Cheng XD, Zhang WD, Qin JJ. Recent Update on Development of Small-Molecule STAT3 Inhibitors for Cancer Therapy: From Phosphorylation Inhibition to Protein Degradation. J Med Chem 2021; 64:8884-8915. [PMID: 34170703 DOI: 10.1021/acs.jmedchem.1c00629] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Signal transducer and activator of transcription 3 (STAT3) is a transcription factor that regulates various biological processes, including proliferation, metastasis, angiogenesis, immune response, and chemoresistance. In normal cells, STAT3 is tightly regulated to maintain a transiently active state, while persistent STAT3 activation occurs frequently in cancers, associating with a poor prognosis and tumor progression. Targeting the STAT3 protein is a potentially promising therapeutic strategy for tumors. Although none of the STAT3 inhibitors has been marketed yet, a few of them have succeeded in entering clinical trials. This Review aims to systematically summarize the progress of the last 5 years in the discovery of directive STAT3 small-molecule inhibitors and degraders, focusing primarily on their structural features, design strategies, and bioactivities. We hope this Review will shed light on future drug design and inhibitor optimization to accelerate the discovery process of STAT3 inhibitors or degraders.
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Affiliation(s)
- Jinyun Dong
- Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang 310022, China.,Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310018, China
| | - Xiang-Dong Cheng
- Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang 310022, China.,Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310018, China
| | - Wei-Dong Zhang
- School of Pharmacy, Naval Medical University, Shanghai 200433, China
| | - Jiang-Jiang Qin
- Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang 310022, China.,Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310018, China
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28
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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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29
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Scognamiglio PL, Platella C, Napolitano E, Musumeci D, Roviello GN. From Prebiotic Chemistry to Supramolecular Biomedical Materials: Exploring the Properties of Self-Assembling Nucleobase-Containing Peptides. Molecules 2021; 26:3558. [PMID: 34200901 PMCID: PMC8230524 DOI: 10.3390/molecules26123558] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/24/2022] Open
Abstract
Peptides and their synthetic analogs are a class of molecules with enormous relevance as therapeutics for their ability to interact with biomacromolecules like nucleic acids and proteins, potentially interfering with biological pathways often involved in the onset and progression of pathologies of high social impact. Nucleobase-bearing peptides (nucleopeptides) and pseudopeptides (PNAs) offer further interesting possibilities related to their nucleobase-decorated nature for diagnostic and therapeutic applications, thanks to their reported ability to target complementary DNA and RNA strands. In addition, these chimeric compounds are endowed with intriguing self-assembling properties, which are at the heart of their investigation as self-replicating materials in prebiotic chemistry, as well as their application as constituents of innovative drug delivery systems and, more generally, as novel nanomaterials to be employed in biomedicine. Herein we describe the properties of nucleopeptides, PNAs and related supramolecular systems, and summarize some of the most relevant applications of these systems.
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Affiliation(s)
| | - Chiara Platella
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; (C.P.); (E.N.); (D.M.)
| | - Ettore Napolitano
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; (C.P.); (E.N.); (D.M.)
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy; (C.P.); (E.N.); (D.M.)
- Istituto di Biostrutture e Bioimmagini IBB-CNR, via Tommaso De Amicis 95, I-80145 Naples, Italy
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30
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Verma S, Ravichandiran V, Ranjan N. Beyond amyloid proteins: Thioflavin T in nucleic acid recognition. Biochimie 2021; 190:111-123. [PMID: 34118329 DOI: 10.1016/j.biochi.2021.06.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 05/25/2021] [Accepted: 06/04/2021] [Indexed: 01/01/2023]
Abstract
Thioflavin T (ThT) is a commercially available fluorescent dye that is commonly used in biomedical research for over five decades. It was first reported as an extrinsic fluorescent probe for the detection of amyloid fibrils and related processes and it has also been used extensively for assessing protein binding in fluorescence-based assays. Although the nucleic acid binding of ThT was reported half of a century ago in the 1970s, it was not widely explored until the start of this decade. In recent years, Thioflavin T has become a major tool in the recognition of many types of non-canonical nucleic acid conformations including duplexes, triplexes, and G-quadruplexes. The propensity of ThT binding is more towards base aberrations, bulges, and mismatches highlighting its importance in serving as a diagnostic tool in a variety of ailments/disease conditions. In this review, we cover major advancements in nucleic acid detection/binding by ThT to a variety of nucleic acid structures.
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Affiliation(s)
- Smita Verma
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER)-Raebareli, New Transit Campus, Lucknow, Uttar Pradesh, 226002, India; Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER)-Kolkata, Maniktala Main Road, Kolkata, 700054, India
| | - Velayutham Ravichandiran
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER)-Kolkata, Maniktala Main Road, Kolkata, 700054, India
| | - Nihar Ranjan
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER)-Raebareli, New Transit Campus, Lucknow, Uttar Pradesh, 226002, India.
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31
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Xu J, Jiang R, He H, Ma C, Tang Z. Recent advances on G-quadruplex for biosensing, bioimaging and cancer therapy. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116257] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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32
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Yu Z, Hendricks AL, Cowan JA. G-quadruplex targeting chemical nucleases as a nonperturbative tool for analysis of cellular G-quadruplex DNA. iScience 2021; 24:102661. [PMID: 34189433 PMCID: PMC8215219 DOI: 10.1016/j.isci.2021.102661] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 03/04/2021] [Accepted: 05/26/2021] [Indexed: 11/21/2022] Open
Abstract
G-quadruplex structures are associated with various biological activities, while in vivo evidence is essential to confirm the formation of G-quadruplexes inside cells. Most conventional agents that recognize G-quadruplex, including antibodies and small-molecule G-quadruplex ligands, either stabilize the G-quadruplex or prevent G-quadruplex unfolding by helicase, thereby artificially increasing the G-quadruplex levels in cells. Unambiguous study of G-quadruplexes at natural cellular levels requires agents that do not enhance the stability of G-quadruplex. Herein, we report the first example of nonperturbative chemical nucleases that do not influence the stability of G-quadruplex telomeric DNA but can selectively cleave G-quadruplex DNA over duplex DNA. These chemical nucleases can be readily taken up by cells and promote selective cleavage of telomeric DNA with low levels of nonselective DNA cleavage of other regions of the genome. The cleavage of G-quadruplex telomeric DNA by nonperturbative chemical nucleases confirms the formation of G-quadruplex telomeric DNA in live cells. Novel chemical nucleases exhibit no effect on G-quadruplex telomeric DNA stability Selective nucleases cleave G-quadruplex DNA over duplex DNA Cleavage of G-quadruplex telomeric DNA motifs confirms their existence in cells
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Affiliation(s)
- Zhen Yu
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, USA
| | - Amber L. Hendricks
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, USA
| | - James A. Cowan
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, USA
- Corresponding author
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33
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Müller D, Bessi I, Richter C, Schwalbe H. The Folding Landscapes of Human Telomeric RNA and DNA G-Quadruplexes are Markedly Different. Angew Chem Int Ed Engl 2021; 60:10895-10901. [PMID: 33539622 PMCID: PMC8252441 DOI: 10.1002/anie.202100280] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/04/2021] [Indexed: 01/23/2023]
Abstract
We investigated the folding kinetics of G‐quadruplex (G4) structures by comparing the K+‐induced folding of an RNA G4 derived from the human telomeric repeat‐containing RNA (TERRA25) with a sequence homologous DNA G4 (wtTel25) using CD spectroscopy and real‐time NMR spectroscopy. While DNA G4 folding is biphasic, reveals kinetic partitioning and involves kinetically favoured off‐pathway intermediates, RNA G4 folding is faster and monophasic. The differences in kinetics are correlated to the differences in the folded conformations of RNA vs. DNA G4s, in particular with regard to the conformation around the glycosidic torsion angle χ that uniformly adopts anti conformations for RNA G4s and both, syn and anti conformation for DNA G4s. Modified DNA G4s with 19F bound to C2′ in arabino configuration adopt exclusively anti conformations for χ. These fluoro‐modified DNA (antiTel25) reveal faster folding kinetics and monomorphic conformations similar to RNA G4s, suggesting the correlation between folding kinetics and pathways with differences in χ angle preferences in DNA and RNA, respectively.
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Affiliation(s)
- Diana Müller
- Goethe University Frankfurt/Centre for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Str. 7, 60438, Frankfurt am Main, Germany
| | - Irene Bessi
- Goethe University Frankfurt/Centre for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Str. 7, 60438, Frankfurt am Main, Germany.,Present address: Julius-Maximilians-University Würzburg, Institute of Organic Chemistry, Am Hubland 16, 97074, Würzburg, Germany
| | - Christian Richter
- Goethe University Frankfurt/Centre for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Str. 7, 60438, Frankfurt am Main, Germany
| | - Harald Schwalbe
- Goethe University Frankfurt/Centre for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Str. 7, 60438, Frankfurt am Main, Germany
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34
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Wang C, Rui X, Si D, Dai R, Zhu Y, Wen H, Li W, Liu J. Copper‐Catalyzed Three‐Component Cascade Reaction of Benzaldehyde with Benzylamine and Hydroxylamine or Aniline: Synthesis of 1,2,4‐Oxadiazoles and Quinazolines. Adv Synth Catal 2021. [DOI: 10.1002/adsc.202001535] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Chao Wang
- School of Pharmacy Nanjing University of Chinese Medicine Nanjing 210023 People's Republic of China
| | - Xiyan Rui
- School of Pharmacy Nanjing University of Chinese Medicine Nanjing 210023 People's Republic of China
| | - Dongjuan Si
- School of Pharmacy Nanjing University of Chinese Medicine Nanjing 210023 People's Republic of China
| | - Rupeng Dai
- School of Pharmacy Nanjing University of Chinese Medicine Nanjing 210023 People's Republic of China
| | - Yueyue Zhu
- School of Pharmacy Nanjing University of Chinese Medicine Nanjing 210023 People's Republic of China
| | - Hongmei Wen
- School of Pharmacy Nanjing University of Chinese Medicine Nanjing 210023 People's Republic of China
| | - Wei Li
- School of Pharmacy Nanjing University of Chinese Medicine Nanjing 210023 People's Republic of China
| | - Jian Liu
- School of Pharmacy Nanjing University of Chinese Medicine Nanjing 210023 People's Republic of China
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35
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The Folding Landscapes of Human Telomeric RNA and DNA G‐Quadruplexes are Markedly Different. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202100280] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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36
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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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37
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Obi I, Rentoft M, Singh V, Jamroskovic J, Chand K, Chorell E, Westerlund F, Sabouri N. Stabilization of G-quadruplex DNA structures in Schizosaccharomyces pombe causes single-strand DNA lesions and impedes DNA replication. Nucleic Acids Res 2020; 48:10998-11015. [PMID: 33045725 PMCID: PMC7641769 DOI: 10.1093/nar/gkaa820] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/09/2020] [Accepted: 09/17/2020] [Indexed: 12/30/2022] Open
Abstract
G-quadruplex (G4) structures are stable non-canonical DNA structures that are implicated in the regulation of many cellular pathways. We show here that the G4-stabilizing compound PhenDC3 causes growth defects in Schizosaccharomyces pombe cells, especially during S-phase in synchronized cultures. By visualizing individual DNA molecules, we observed shorter DNA fragments of newly replicated DNA in the PhenDC3-treated cells, suggesting that PhenDC3 impedes replication fork progression. Furthermore, a novel single DNA molecule damage assay revealed increased single-strand DNA lesions in the PhenDC3-treated cells. Moreover, chromatin immunoprecipitation showed enrichment of the leading-strand DNA polymerase at sites of predicted G4 structures, suggesting that these structures impede DNA replication. We tested a subset of these sites and showed that they form G4 structures, that they stall DNA synthesis in vitro and that they can be resolved by the breast cancer-associated Pif1 family helicases. Our results thus suggest that G4 structures occur in S. pombe and that stabilized/unresolved G4 structures are obstacles for the replication machinery. The increased levels of DNA damage might further highlight the association of the human Pif1 helicase with familial breast cancer and the onset of other human diseases connected to unresolved G4 structures.
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Affiliation(s)
- Ikenna Obi
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden
| | - Matilda Rentoft
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden
| | - Vandana Singh
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Jan Jamroskovic
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden
| | - Karam Chand
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
| | - Erik Chorell
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Nasim Sabouri
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden
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38
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Sullivan HJ, Chen B, Wu C. Molecular Dynamics Study on the Binding of an Anticancer DNA G-Quadruplex Stabilizer, CX-5461, to Human Telomeric, c-KIT1, and c-Myc G-Quadruplexes and a DNA Duplex. J Chem Inf Model 2020; 60:5203-5224. [PMID: 32820923 DOI: 10.1021/acs.jcim.0c00632] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
DNA G-quadruplex (G4) stabilizer, CX-5461, is in phase I/II clinical trials for advanced cancers with BRCA1/2 deficiencies. A FRET-melting temperature increase assay measured the stabilizing effects of CX-5461 to a DNA duplex (∼10 K), and three G4 forming sequences negatively implicated in the cancers upon its binding: human telomeric (∼30 K), c-KIT1 (∼27 K), and c-Myc (∼25 K). Without experimentally solved structures of these CX-5461-G4 complexes, CX-5461's interactions remain elusive. In this study, we performed a total of 73.5 μs free ligand molecular dynamics binding simulations of CX-5461 to the DNA duplex and three G4s. Three binding modes (top, bottom, and side) were identified for each system and their thermodynamic, kinetic, and structural nature were deciphered. The molecular mechanics/Poisson Boltzmann surface area binding energies of CX-5461 were calculated for the human telomeric (-28.6 kcal/mol), c-KIT1 (-23.9 kcal/mol), c-Myc (-22.0 kcal/mol) G4s, and DNA duplex (-15.0 kcal/mol) systems. These energetic differences coupled with structural differences at the 3' site explained the different melting temperatures between the G4s, while CX-5461's lack of intercalation to the duplex explained the difference between the G4s and duplex. Based on the interaction insight, CX-5461 derivatives were designed and docked, showing higher selectivity to the G4s over the duplex.
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Affiliation(s)
- Holli-Joi Sullivan
- College of Science and Mathematics, Rowan University, Glassboro, New Jersey 08028 USA
| | - Brian Chen
- College of Science and Mathematics, Rowan University, Glassboro, New Jersey 08028 USA
| | - Chun Wu
- College of Science and Mathematics, Rowan University, Glassboro, New Jersey 08028 USA
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39
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Gillard M, Weynand J, Bonnet H, Loiseau F, Decottignies A, Dejeu J, Defrancq E, Elias B. Flexible Ru
II
Schiff Base Complexes: G‐Quadruplex DNA Binding and Photo‐Induced Cancer Cell Death. Chemistry 2020; 26:13849-13860. [DOI: 10.1002/chem.202001409] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 05/28/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Martin Gillard
- Institut de la Matière Condensée et des Nanosciences (IMCN) Molecular Chemistry, Materials and Catalysis (MOST) Université catholique de Louvain (UCLouvain) Place Louis Pasteur 1, bte L4.01.02 1348 Louvain-la-Neuve Belgium
| | - Justin Weynand
- Institut de la Matière Condensée et des Nanosciences (IMCN) Molecular Chemistry, Materials and Catalysis (MOST) Université catholique de Louvain (UCLouvain) Place Louis Pasteur 1, bte L4.01.02 1348 Louvain-la-Neuve Belgium
- Département de Chimie Moléculaire UMR CNRS 5250 Université Grenoble Alpes (UGA) CS 40700-38058 Grenoble France
| | - Hugues Bonnet
- Département de Chimie Moléculaire UMR CNRS 5250 Université Grenoble Alpes (UGA) CS 40700-38058 Grenoble France
| | - Frédérique Loiseau
- Département de Chimie Moléculaire UMR CNRS 5250 Université Grenoble Alpes (UGA) CS 40700-38058 Grenoble France
| | - Anabelle Decottignies
- Université catholique de Louvain (UCLouvain) de Duve Institute Avenue Hippocrate 75 1200 Brussels Belgium
| | - Jérôme Dejeu
- Département de Chimie Moléculaire UMR CNRS 5250 Université Grenoble Alpes (UGA) CS 40700-38058 Grenoble France
| | - Eric Defrancq
- Département de Chimie Moléculaire UMR CNRS 5250 Université Grenoble Alpes (UGA) CS 40700-38058 Grenoble France
| | - Benjamin Elias
- Institut de la Matière Condensée et des Nanosciences (IMCN) Molecular Chemistry, Materials and Catalysis (MOST) Université catholique de Louvain (UCLouvain) Place Louis Pasteur 1, bte L4.01.02 1348 Louvain-la-Neuve Belgium
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40
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Altieri A, Dell’Aquila M, Pentimalli F, Giordano A, Alfano L. SMART (Single Molecule Analysis of Resection Tracks) Technique for Assessing DNA end-Resection in Response to DNA Damage. Bio Protoc 2020; 10:e3701. [PMID: 33659366 PMCID: PMC7842315 DOI: 10.21769/bioprotoc.3701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 05/28/2020] [Accepted: 06/17/2020] [Indexed: 11/02/2022] Open
Abstract
DNA double strand breaks (DSBs) are among the most toxic lesions affecting genome integrity. DSBs are mainly repaired through non-homologous end joining (NHEJ) and homologous recombination (HR). A crucial step of the HR process is the generation, through DNA end-resection, of a long 3' single-strand DNA stretch, necessary to prime DNA synthesis using a homologous region as a template, following DNA strand invasion. DNA end resection inhibits NHEJ and triggers homology-directed DSB repair, ultimately guaranteeing a faithful DNA repair. Established methods to evaluate the DNA end-resection process are the immunofluorescence analysis of the phospho-S4/8 RPA32 protein foci, a marker of DNA end-resection, or of the phospho-S4/8 RPA32 protein levels by Western blot. Recently, the Single Molecule Analysis of Resection Tracks (SMART) has been described as a reliable method to visualize, by immunofluorescence, the long 3' single-strand DNA tails generated upon cell treatment with a S-phase specific DNA damaging agent (such as camptothecin). Then, DNA tract lengths can be measured through an image analysis software (such as Photoshop), to evaluate the processivity of the DNA end-resection machinery. The preparation of DNA fibres is performed in non-denaturing conditions so that the immunofluorescence detects only the specific long 3' single-strand DNA tails, generated from DSB processing.
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Affiliation(s)
- Angela Altieri
- Department of Medicine, Surgery and Neuroscience, University of Siena and Istituto Toscana Tumori (ITT), Siena, Italy
| | - Milena Dell’Aquila
- Department of Medicine, Surgery and Neuroscience, University of Siena and Istituto Toscana Tumori (ITT), Siena, Italy
| | - Francesca Pentimalli
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori IRCCS, Fondazione G. Pascale, Naples, Italy
| | - Antonio Giordano
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori IRCCS, Fondazione G. Pascale, Naples, Italy
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Department of Biology, Temple University, Philadelphia PA, USA
| | - Luigi Alfano
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori IRCCS, Fondazione G. Pascale, Naples, Italy
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41
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Deiana M, Chand K, Jamroskovic J, Das RN, Obi I, Chorell E, Sabouri N. A site-specific self-assembled light-up rotor probe for selective recognition and stabilization of c-MYC G-quadruplex DNA. NANOSCALE 2020; 12:12950-12957. [PMID: 32525170 DOI: 10.1039/d0nr03404e] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Direct and unambiguous evidence of the formation of G-quadruplexes (G4s) in human cells have shown their implication in several key biological events and has emphasized their role as important targets for small-molecule cancer therapeutics. Here, we report on the first example of a self-assembled molecular-rotor G4-binder able to discriminate between an extensive panel of G4 and non-G4 structures and to selectively light-up (up to 64-fold), bind (nanomolar range), and stabilize the c-MYC promoter G4 DNA. In particular, association with the c-MYC G4 triggers the disassembly of its supramolecular state (disaggregation-induced emission, DIE) and induces geometrical restrictions (motion-induced change in emission, MICE) leading to a significant enhancement of its emission yield. Moreover, this optical reporter is able to selectively stabilize the c-MYC G4 and inhibit DNA synthesis. Finally, by using confocal laser-scanning microscopy (CLSM) we show the ability of this compound to localize primarily in the subnuclear G4-rich compartments of cancer cells. This work provides a benchmark for the future design and development of a new generation of smart sequence-selective supramolecular G4-binders that combine outstanding sensing and stability properties, to be utilized in anti-cancer therapy.
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Affiliation(s)
- Marco Deiana
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden.
| | - Karam Chand
- Department of Chemistry, Umeå University, 90187 Umeå, Sweden.
| | - Jan Jamroskovic
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden.
| | | | - Ikenna Obi
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden.
| | - Erik Chorell
- Department of Chemistry, Umeå University, 90187 Umeå, Sweden.
| | - Nasim Sabouri
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden.
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42
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Deiana M, Jamroskovic J, Obi I, Sabouri N. Unravelling the cellular emission fingerprint of the benchmark G-quadruplex-interactive compound Phen-DC3. Chem Commun (Camb) 2020; 56:14251-14254. [DOI: 10.1039/d0cc05483f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The G4-interactive binding interactions enable one to tune the optical properties of Phen-DC3, allowing the detection of G4 structures in cancer cells.
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Affiliation(s)
- Marco Deiana
- Department of Medical Biochemistry and Biophysics
- Umeå University
- Umeå 90187
- Sweden
| | - Jan Jamroskovic
- Department of Medical Biochemistry and Biophysics
- Umeå University
- Umeå 90187
- Sweden
| | - Ikenna Obi
- Department of Medical Biochemistry and Biophysics
- Umeå University
- Umeå 90187
- Sweden
| | - Nasim Sabouri
- Department of Medical Biochemistry and Biophysics
- Umeå University
- Umeå 90187
- Sweden
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