51
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Šmidlehner T, Košćak M, Božinović K, Majhen D, Schmuck C, Piantanida I. Fluorimetric and CD Recognition between Various ds-DNA/RNA Depends on a Cyanine Connectivity in Cyanine-guanidiniocarbonyl-pyrrole Conjugate. Molecules 2020; 25:molecules25194470. [PMID: 33003366 PMCID: PMC7583847 DOI: 10.3390/molecules25194470] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 09/25/2020] [Accepted: 09/27/2020] [Indexed: 11/16/2022] Open
Abstract
Two novel isosteric conjugates of guanidiniocarbonyl-pyrrole and 6-bromo-TO (thiazole orange) were prepared, differing only in linker connectivity to cyanine (benzothiazole nitrogen vs. quinoline nitrogen). The quinoline analog was significantly more susceptible to aggregation in an aqueous medium, which resulted in induced circular dichroism (ICD; λ = 450-550 nm) recognition between A-T(U) and G-C basepair containing polynucleotides. The benzothiazole-isostere showed pronounced (four-fold) fluorimetric selectivity toward ds-RNA in comparison to any ds-DNA, at variance to its quinoline-analogue fluorescence being weakly selective to GC-DNA. Preliminary screening on human tumor and normal lung cell lines showed that both dyes very efficiently enter living cells and accumulate in mitochondria, causing moderate cytotoxic effects, and thus could be considered as lead compounds toward novel theragnostic mitochondrial dyes.
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Affiliation(s)
- Tamara Šmidlehner
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (T.Š.); (M.K.)
| | - Marta Košćak
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (T.Š.); (M.K.)
| | - Ksenija Božinović
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; (K.B.); (D.M.)
| | - Dragomira Majhen
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; (K.B.); (D.M.)
| | - Carsten Schmuck
- Institute of Organic Chemistry, University of Duisburg-Essen, 45141 Essen, Germany;
| | - Ivo Piantanida
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (T.Š.); (M.K.)
- Correspondence: ; Tel.: +385-1-4571-326
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52
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Ganguly S, Ghosh D, Narayanaswamy N, Govindaraju T, Basu G. Dual DNA binding mode of a turn-on red fluorescent probe thiazole coumarin. PLoS One 2020; 15:e0239145. [PMID: 32941495 PMCID: PMC7497988 DOI: 10.1371/journal.pone.0239145] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 08/31/2020] [Indexed: 11/19/2022] Open
Abstract
Turn-on fluorescent probes show enhanced emission upon DNA binding, advocating their importance in imaging cellular DNA. We have probed the DNA binding mode of thiazole-coumarin (TC) conjugate, a recently reported hemicyanine-based turn-on red fluorescent probe, using a number of biophysical techniques and a series of short oligonucleotides. TC exhibited increased fluorescence anisotropy and decreased absorbance (~50%) at low [DNA]/[TC] ratio. Although the observed hypochromicity and the saturating value of [DNA base pair]:[TC] ratio is consistent with a previous study that suggested intercalation to be the DNA binding mode of TC, a distinctly different and previously unreported binding mode was observed at higher ratios of [DNA]:[TC]. With further addition of DNA, only oligonucleotides containing AnTn or (AT)n stretches showed further change-decreased hypochromicity, red shifted absorption peaks and concomitant fluorescence enhancement, saturating at about 1:1 [DNA]: [TC]. 1H-NMR chemical shift perturbation patterns and H1'-H6/H8 NOE cross-peaks of the 1:1 complex indicated minor groove binding by TC. ITC showed the 1:1 DNA binding event to be endothermic (ΔH° ~ 2 kcal/mol) and entropy driven (ΔS° ~ 32 cal/mol/K). Taken together, the experimental data suggest a dual DNA binding mode by TC. At low [DNA]/[TC] ratio, the dominant mode is intercalation. This switches to minor groove binding at higher [DNA]/[TC], only for sequences containing AnTn or (AT)n stretches. Turn-on fluorescence results only in the previously unreported minor groove bound state. Our results allow a better understanding of DNA-ligand interaction for the newly reported turn-on probe TC.
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Affiliation(s)
| | - Debasis Ghosh
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Nagarjun Narayanaswamy
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - T. Govindaraju
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Gautam Basu
- Department of Biophysics, Bose Institute, Kolkata, India
- * E-mail: ,
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53
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Tumir LM, Zonjić I, Žuna K, Brkanac SR, Jukić M, Huđek A, Durgo K, Crnolatac I, Glavaš-Obrovac L, Cardullo N, Pulvirenti L, Muccilli V, Tringali C, Stojković MR. Synthesis, DNA/RNA-interaction and biological activity of benzo[k,l]xanthene lignans. Bioorg Chem 2020; 104:104190. [PMID: 32919130 DOI: 10.1016/j.bioorg.2020.104190] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/30/2020] [Accepted: 08/05/2020] [Indexed: 12/20/2022]
Abstract
Interactions of two newly synthesized and six previously reported benzoxanthene lignans (BXLs), analogues of rare natural products, with DNA/RNA, G-quadruplex and HSA were evaluated by a set of spectrophotometric methods. Presence/absence of methoxy and hydroxy groups on the benzoxanthene core and minor modifications at C-1/C-2 side pendants - presence/absence of phenyl ring and presence/absence of methoxy and hydroxy groups on phenyl ring - influenced the fluorescence changes and the binding strength to double-stranded (ds-) and G-quadruplex structures. In general, compounds without phenyl ring showed stronger fluorescence changes upon binding than phenyl-substituted BXLs. On the other hand, BXLs with an unsubstituted phenyl ring showed the best stabilization effects of G-quadruplex. Circular dichroism spectroscopy results suggest mixed binding mode, groove binding and partial intercalation, to ds-DNA/RNA and end-stacking to top or bottom G-tetrads as the main binding modes of BXLs to those targets. All compounds exhibited micromolar binding affinities toward HSA and an increased protein thermal stability. Moderate to strong antiradical scavenging activity was observed for all BXLs with hydroxy groups at C-6, C-9 and C-10 positions of the benzoxanthene core, except for derivative bearing methoxy groups at these positions. BXLs with unsubstituted or low-substituted phenyl ring and one derivative without phenyl ring showed strong growth inhibition of Gram-positive Staphylococcus aureus. All compounds showed moderate to strong tumor cell growth-inhibitory activity and cytotoxicity.
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Affiliation(s)
- Lidija-Marija Tumir
- Ruđer Bošković Institute, Division of Organic Chemistry and Biochemistry, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Iva Zonjić
- Ruđer Bošković Institute, Division of Organic Chemistry and Biochemistry, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Kristina Žuna
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierrotijeva 6, 10000 Zagreb, Croatia
| | - Sandra Radić Brkanac
- University of Zagreb, Faculty of Science, Department of Biology, Rooseveltov trg 6/III, HR-10 000 Zagreb, Croatia
| | - Marijana Jukić
- Department of Medicinal Chemistry, Biochemistry and Laboratory Medicine, Faculty of Medicine Osijek, Josip Juraj Strossmayer University of Osijek, Huttlerova 4, HR-31000 Osijek, Croatia
| | - Ana Huđek
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierrotijeva 6, 10000 Zagreb, Croatia
| | - Ksenija Durgo
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierrotijeva 6, 10000 Zagreb, Croatia
| | - Ivo Crnolatac
- Ruđer Bošković Institute, Division of Organic Chemistry and Biochemistry, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Ljubica Glavaš-Obrovac
- Department of Medicinal Chemistry, Biochemistry and Laboratory Medicine, Faculty of Medicine Osijek, Josip Juraj Strossmayer University of Osijek, Huttlerova 4, HR-31000 Osijek, Croatia
| | - Nunzio Cardullo
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, I-95125 Catania, Italy
| | - Luana Pulvirenti
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, I-95125 Catania, Italy
| | - Vera Muccilli
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, I-95125 Catania, Italy
| | - Corrado Tringali
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, I-95125 Catania, Italy
| | - Marijana Radić Stojković
- Ruđer Bošković Institute, Division of Organic Chemistry and Biochemistry, Bijenička cesta 54, 10000 Zagreb, Croatia.
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54
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Rafique J, Farias G, Saba S, Zapp E, Bellettini IC, Momoli Salla CA, Bechtold IH, Scheide MR, Santos Neto JS, Monteiro de Souza Junior D, de Campos Braga H, Ribeiro LFB, Gastaldon F, Pich CT, Frizon TEA. Selenylated-oxadiazoles as promising DNA intercalators: Synthesis, electronic structure, DNA interaction and cleavage. DYES AND PIGMENTS : AN INTERNATIONAL JOURNAL 2020; 180:108519. [PMID: 32382200 PMCID: PMC7204724 DOI: 10.1016/j.dyepig.2020.108519] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/04/2020] [Accepted: 05/04/2020] [Indexed: 05/09/2023]
Abstract
A series of selenylated-oxadiazoles were prepared and their interaction with DNA was investigated. The photophysical studies showed that all the selenylated compounds presented absorption between 270 and 329 nm, assigned to combined n→π* and π→π* transitions, and an intense blue emission (325-380 nm) with quantum yield in the range of Φ F = 0.1-0.4. DFT and TD-DFT calculations were also performed to study the likely geometry and the excited state of these compounds. Electrochemical studies revealed the ionization potential energies (-5.13 to -6.01 eV) and electron affinity energies (-2.25 to -2.83 eV), depending directly on the electronic effect (electron-donating or electron-withdrawing) of the substituent attached to the product. Finally, the UV-Vis DNA interaction experiments indicated that the compounds can interact with the DNA molecule due to intercalation, except for 3g (which interacted via electrostatic interaction). Plasmid cleavage assay presented positive results only for 3f that presented the strongest interaction results. These results made the tested selenylated-oxadiazoles as suitable structures for the development of drugs and the design of structurally-related therapeutics.
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Affiliation(s)
- Jamal Rafique
- Institute of Chemistry, Federal University of Mato Grosso do Sul, Campo Grande, MS, Brazil
- Corresponding author.;
| | - Giliandro Farias
- Chemistry Department, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Sumbal Saba
- Center for Natural and Human Sciences-CCNH, Federal University of ABC, Santo André, SP, Brazil
- Corresponding author.;
| | - Eduardo Zapp
- Department of Exact Sciences and Education, Federal University of Santa Catarina, Blumenau, SC, Brazil
| | | | | | | | | | | | | | - Hugo de Campos Braga
- Institute of Science and Technology, Federal University of São Paulo, São José dos Campos, SP, Brazil
| | | | - Francine Gastaldon
- Department of Energy and Sustainability, Federal University of Santa Catarina, Araranguá, SC, Brazil
| | - Claus Tröger Pich
- Department of Energy and Sustainability, Federal University of Santa Catarina, Araranguá, SC, Brazil
| | - Tiago Elias Allievi Frizon
- Department of Energy and Sustainability, Federal University of Santa Catarina, Araranguá, SC, Brazil
- Corresponding author.
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55
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Weißenstein A, Vysotsky MO, Piantanida I, Würthner F. Naphthalene diimide–amino acid conjugates as novel fluorimetric and CD probes for differentiation between ds-DNA and ds-RNA. Beilstein J Org Chem 2020; 16:2032-2045. [PMID: 32874350 PMCID: PMC7445415 DOI: 10.3762/bjoc.16.170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 08/04/2020] [Indexed: 11/23/2022] Open
Abstract
Two novel unnatural amino acids, prepared by linking a dicationic purple-coloured and fluorescent naphthalene diimide (NDI) at core position to amino acid side chains of variable length, strongly interacted with ds-DNA/RNA by threading intercalation. Different from a reference NDI dye with identical visible range absorbance (520–540 nm) and Stokes shifts in emission (+60 nm, quantum yield > 0.2), only these amino acid–NDI conjugates showed selective fluorimetric response for GC-DNA in respect to AT(U)-polynucleotides. The DNA/RNA binding-induced circular dichroism (ICD) response of NDI at 450–550 nm strongly depended on the length and rigidity of the linker to the amino acid unit, which controls the orientation of the NDI unit inside within the intercalative binding site. The ICD selectivity also depends on the type of polynucleotide, thus the studied NDI dyes act as dual fluorimetric/ICD probes for sensing the difference between here used GC-DNA, AT-DNA and AU-RNA.
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Affiliation(s)
- Annike Weißenstein
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Myroslav O Vysotsky
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Ivo Piantanida
- Division of Organic Chemistry & Biochemistry, Ruđer Bošković Institute, PO Box 180, 10002 Zagreb, Croatia
| | - Frank Würthner
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
- Center for Nanosystems Chemistry (CNC), Universität Würzburg, Theodor-Boveri-Weg, 97074 Würzburg, Germany
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56
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Rubim de Santana PI, Ferreira Neto DC, Goncalves ADS, Almeida JSFDD, França TCC, Figueroa-Villar JD. Complete chemical shift assignment and molecular modeling studies of two chromene derivatives as potential leads for new anticancer drugs. J Biomol Struct Dyn 2020; 39:5498-5508. [PMID: 32657645 DOI: 10.1080/07391102.2020.1790419] [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] [Indexed: 01/05/2023]
Abstract
The compounds 7-chloro-9-(2-hydroxy-4,4-dimethyl-6-oxocyclohex-1-en-1-yl)-3,3-dimethyl-2,3,4,9-tetrahydro-1H-xanthen-1-one (5) and 5-[-7-chloro-2,4-dioxo-1H, 2H, 3H, 4H, 5H-chromeno[2,3-d]pyrimidin-5-yl)]-1,3-diazinane-2,4,6-trione (7), were synthesized from dimedone and barbituric acid and had their three-dimensional structures and precise chemical shifts assignments obtained by Nuclear Magnetic Resonance (NMR) from 1H, 13C, APT, COSY, HSQC, and HMBC spectra. Additional HOMO-LUMO DFT calculations corroborated the NMR results and pointed to the most stable stereoisomers of each compound. Besides, further docking and molecular dynamic studies suggest that the stereoisomers (9S)-7-chloro-9-(2-hydroxy-4,4-dimethyl-6-oxocyclohex-1-en-1-yl)-3,3-dimethyl-2,3,4,9-tetrahydro-1H-xanthen-1-one, and 5-[(5S)-7-chloro-2,4-dioxo-1H, 2H, 3H, 4H, 5H-chromeno[2,3-d]pyrimidin-5-yl)]-1,3-diazinane-2,4,6-trione of these compounds may act as DNA intercalators and qualify as potential leads for the development of new anticancer drugs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Priscila Ivo Rubim de Santana
- Medicinal Chemistry Group, Chemical Engineering Department, Military Institute of Engineering, Rio de Janeiro, Brazil
| | - Denise Cristian Ferreira Neto
- Medicinal Chemistry Group, Chemical Engineering Department, Military Institute of Engineering, Rio de Janeiro, Brazil
| | - Arlan da Silva Goncalves
- Laboratory of Molecular Modeling Applied to the Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Rio de Janeiro, Brazil.,Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | | | - Tanos Celmar Costa França
- Laboratory of Molecular Modeling Applied to the Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Rio de Janeiro, Brazil.,Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - José Daniel Figueroa-Villar
- Medicinal Chemistry Group, Chemical Engineering Department, Military Institute of Engineering, Rio de Janeiro, Brazil
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57
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Berdnikova DV, Heider J, Ihmels H, Sewald N, Pithan PM. Photoinduced Release of DNA‐Binding Ligands from the [4+4] Dimers of Benzo[ b]quinolizinium and Anthracene Derivatives. CHEMPHOTOCHEM 2020. [DOI: 10.1002/cptc.202000015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Daria V. Berdnikova
- Department of Chemistry-BiologyUniversity of Siegen Adolf-Reichwein-Str. 2 57068 Siegen Germany
| | - Josef Heider
- Department of Chemistry-BiologyUniversity of Siegen Adolf-Reichwein-Str. 2 57068 Siegen Germany
| | - Heiko Ihmels
- Department of Chemistry-BiologyUniversity of Siegen Adolf-Reichwein-Str. 2 57068 Siegen Germany
| | - Norbert Sewald
- Department of Chemistry, Organic and Bioorganic ChemistryBielefeld University PO Box 100121 33501 Bielefeld Germany
| | - Phil M. Pithan
- Department of Chemistry-BiologyUniversity of Siegen Adolf-Reichwein-Str. 2 57068 Siegen Germany
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58
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Kolchina N, Khavinson V, Linkova N, Yakimov A, Baitin D, Afanasyeva A, Petukhov M. Systematic search for structural motifs of peptide binding to double-stranded DNA. Nucleic Acids Res 2020; 47:10553-10563. [PMID: 31598715 PMCID: PMC6847403 DOI: 10.1093/nar/gkz850] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 09/17/2019] [Accepted: 09/29/2019] [Indexed: 01/06/2023] Open
Abstract
A large variety of short biologically active peptides possesses antioxidant, antibacterial, antitumour, anti-ageing and anti-inflammatory activity, involved in the regulation of neuro-immuno-endocrine system functions, cell apoptosis, proliferation and differentiation. Therefore, the mechanisms of their biological activity are attracting increasing attention not only in modern molecular biology, biochemistry and biophysics, but also in pharmacology and medicine. In this work, we systematically analysed the ability of dipeptides (all possible combinations of the 20 standard amino acids) to bind all possible combinations of tetra-nucleotides in the central part of dsDNA in the classic B-form using molecular docking and molecular dynamics. The vast majority of the dipeptides were found to be unable to bind dsDNA. However, we were able to identify 57 low-energy dipeptide complexes with peptide-dsDNA possessing high selectivity for DNA binding. The analysis of the dsDNA complexes with dipeptides with free and blocked N- and C-terminus showed that selective peptide binding to dsDNA can increase dramatically with the peptide length.
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Affiliation(s)
- Nina Kolchina
- Petersburg Nuclear Physics Institute named after B.P. Konstantinov, NRC "Kurchatov Institute", Gatchina, Russia.,Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia.,Russian Scientific Center of Radiology and Surgical Technologies named after A.M. Granov, St. Petersburg, Russia
| | - Vladimir Khavinson
- Saint Petersburg Institute of Bioregulation and Gerontology, St. Petersburg, Russia.,Pavlov Institute of Physiology of RAS, St. Petersburg, Russia.,North-Western State Medical University named after I.I. Mechnikov, St. Petersburg, Russia
| | - Natalia Linkova
- Saint Petersburg Institute of Bioregulation and Gerontology, St. Petersburg, Russia.,Academy of postgraduate education under FSBU FSCC of FMBA of Russia, Moscow, Russia
| | - Alexander Yakimov
- Petersburg Nuclear Physics Institute named after B.P. Konstantinov, NRC "Kurchatov Institute", Gatchina, Russia.,Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| | - Dmitry Baitin
- Petersburg Nuclear Physics Institute named after B.P. Konstantinov, NRC "Kurchatov Institute", Gatchina, Russia
| | - Arina Afanasyeva
- Petersburg Nuclear Physics Institute named after B.P. Konstantinov, NRC "Kurchatov Institute", Gatchina, Russia.,Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia.,National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Michael Petukhov
- Petersburg Nuclear Physics Institute named after B.P. Konstantinov, NRC "Kurchatov Institute", Gatchina, Russia.,Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia.,Russian Scientific Center of Radiology and Surgical Technologies named after A.M. Granov, St. Petersburg, Russia
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59
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Guo P, Farahat AA, Paul A, Kumar A, Boykin DW, Wilson WD. Extending the σ-Hole Motif for Sequence-Specific Recognition of the DNA Minor Groove. Biochemistry 2020; 59:1756-1768. [PMID: 32293884 DOI: 10.1021/acs.biochem.0c00090] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The majority of current drugs against diseases, such as cancer, can bind to one or more sites in a protein and inhibit its activity. There are, however, well-known limits on the number of druggable proteins, and complementary current drugs with compounds that could selectively target DNA or RNA would greatly enhance the availability of cellular probes and therapeutic progress. We are focusing on the design of sequence-specific DNA minor groove binders that, for example, target the promoter sites of transcription factors involved in a disease. We have started with AT-specific minor groove binders that are known to enter human cells and have entered clinical trials. To broaden the sequence-specific recognition of these compounds, several modules that have H-bond acceptors that strongly and specifically recognize G·C base pairs were identified. A lead module is a thiophene-N-alkyl-benzimidazole σ-hole-based system with terminal phenyl-amidines that have excellent affinity and selectivity for a G·C base pair in the minor groove. Efforts are now focused on optimizing this module. In this work, we are evaluating modifications to the compound aromatic system with the goal of improving GC selectivity and affinity. The lead compounds retain the thiophene-N-alkyl-BI module but have halogen substituents adjacent to an amidine group on the terminal phenyl-amidine. The optimum compounds must have strong affinity and specificity with a residence time of at least 100 s.
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Affiliation(s)
- Pu Guo
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, 50 Decatur Street Southeast, Atlanta, Georgia 30303, United States
| | - Abdelbasset A Farahat
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, 50 Decatur Street Southeast, Atlanta, Georgia 30303, United States.,Master of Pharmaceutical Sciences Program, California Northstate University, 9700 West Taron Drive, Elk Grove, California 95757, United States
| | - Ananya Paul
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, 50 Decatur Street Southeast, Atlanta, Georgia 30303, United States
| | - Arvind Kumar
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, 50 Decatur Street Southeast, Atlanta, Georgia 30303, United States
| | - David W Boykin
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, 50 Decatur Street Southeast, Atlanta, Georgia 30303, United States
| | - W David Wilson
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, 50 Decatur Street Southeast, Atlanta, Georgia 30303, United States
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60
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Farahat AA, Guo P, Shoeib H, Paul A, Boykin DW, Wilson WD. Small Sequence-Sensitive Compounds for Specific Recognition of the G⋅C Base Pair in DNA Minor Groove. Chemistry 2020; 26:4539-4551. [PMID: 31884714 PMCID: PMC7265973 DOI: 10.1002/chem.201904396] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/10/2019] [Indexed: 12/24/2022]
Abstract
A series of small diamidines with thiophene and modified N-alkylbenzimidazole σ-hole module represent specific binding to single G⋅C base pair (bp) DNA sequence. The variation of N-alkyl or aromatic rings were sensitive to microstructures of the DNA minor groove. Thirteen new compounds were synthesized to test their binding affinity and selectivity. The dicyanobenzimidazoles needed to synthesize the target diamidines were made via condensation/cyclization reactions of different aldehydes with different 3-amino-4-(alkyl- or phenyl-amino) benzonitriles. The final diamidines were synthesized using lithium bis-trimethylsilylamide (LiN[Si(CH3 )3 ]2 ) or Pinner methods. The newly synthesized compounds showed strong binding and selectivity to AAAGTTT compared to similar sequences AAATTT and AAAGCTTT investigated by several biophysical methods including biosensor-SPR, fluorescence spectroscopy, DNA thermal melting, ESI-MS spectrometry, circular dichroism, and molecular dynamics. The binding affinity results determined by fluorescence spectroscopy are in accordance with those obtained by biosensor-SPR. These small size single G⋅C bp highly specific binders extend the compound database for future biological applications.
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Affiliation(s)
- Abdelbasset A. Farahat
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St SE, Atlanta, GA 30303, USA
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Pu Guo
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St SE, Atlanta, GA 30303, USA
| | - Hadir Shoeib
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St SE, Atlanta, GA 30303, USA
| | - Ananya Paul
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St SE, Atlanta, GA 30303, USA
| | - David W. Boykin
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St SE, Atlanta, GA 30303, USA
| | - W. David Wilson
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St SE, Atlanta, GA 30303, USA
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61
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Ban Ž, Griesbeck S, Tomić S, Nitsch J, Marder TB, Piantanida I. A Quadrupolar Bis-Triarylborane Chromophore as a Fluorimetric and Chirooptic Probe for Simultaneous and Selective Sensing of DNA, RNA and Proteins. Chemistry 2020; 26:2195-2203. [PMID: 31756013 PMCID: PMC7065195 DOI: 10.1002/chem.201903936] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 11/21/2019] [Indexed: 12/29/2022]
Abstract
A water-soluble tetracationic quadrupolar bis-triarylborane chromophore showed strong binding to ds-DNA, ds-RNA, ss-RNA, as well as to the naturally most abundant protein, BSA. The novel dye can distinguish between DNA/RNA and BSA by fluorescence emission separated by Δ ν ˜ =3600 cm-1 , allowing for the simultaneous quantification of DNA/RNA and protein (BSA) in a mixture. The applicability of such fluorimetric differentiation in vitro was demonstrated, strongly supporting a protein-like target as a dominant binding site of 1 in cells. Moreover, our dye also bound strongly to ss-RNA, with the unusual rod-like structure of the dye, decorated by four positive charges at its termini and having a hydrophobic core, acting as a spindle for wrapping A, C and U ss-RNAs, but not poly G, the latter preserving its secondary structure. To the best of our knowledge, such unmatched, multifaceted binding activity of a small molecule toward DNA, RNA, and proteins and the selectivity of its fluorimetric and chirooptic response makes the quadrupolar bis-triarylborane a novel chromophore/fluorophore moiety for biochemical applications.
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Affiliation(s)
- Željka Ban
- Division of Organic Chemistry and BiochemistryRuder Boškovic InstituteZagrebCroatia
| | - Stefanie Griesbeck
- Institut für Anorganische Chemie andInstitute for Sustainable Chemistry & Catalysis with BoronJulius-Maximilians-Universität Würzburg97074WürzburgGermany
| | - Sanja Tomić
- Division of Organic Chemistry and BiochemistryRuder Boškovic InstituteZagrebCroatia
| | - Jörn Nitsch
- Institut für Anorganische Chemie andInstitute for Sustainable Chemistry & Catalysis with BoronJulius-Maximilians-Universität Würzburg97074WürzburgGermany
| | - Todd B. Marder
- Institut für Anorganische Chemie andInstitute for Sustainable Chemistry & Catalysis with BoronJulius-Maximilians-Universität Würzburg97074WürzburgGermany
| | - Ivo Piantanida
- Division of Organic Chemistry and BiochemistryRuder Boškovic InstituteZagrebCroatia
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Koulenti D, Xu E, Song A, Sum Mok IY, Karageorgopoulos DE, Armaganidis A, Tsiodras S, Lipman J. Emerging Treatment Options for Infections by Multidrug-Resistant Gram-Positive Microorganisms. Microorganisms 2020; 8:E191. [PMID: 32019171 PMCID: PMC7074912 DOI: 10.3390/microorganisms8020191] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 01/26/2020] [Accepted: 01/28/2020] [Indexed: 12/22/2022] Open
Abstract
Antimicrobial agents are currently the mainstay of treatment for bacterial infections worldwide. However, due to the increased use of antimicrobials in both human and animal medicine, pathogens have now evolved to possess high levels of multi-drug resistance, leading to the persistence and spread of difficult-to-treat infections. Several current antibacterial agents active against Gram-positive bacteria will be rendered useless in the face of increasing resistance rates. There are several emerging antibiotics under development, some of which have been shown to be more effective with an improved safety profile than current treatment regimens against Gram-positive bacteria. We will extensively discuss these antibiotics under clinical development (phase I-III clinical trials) to combat Gram-positive bacteria, such as Staphylococcus aureus, Enterococcus faecium and Streptococcus pneumoniae. We will delve into the mechanism of actions, microbiological spectrum, and, where available, the pharmacokinetics, safety profile, and efficacy of these drugs, aiming to provide a comprehensive review to the involved stakeholders.
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Affiliation(s)
- Despoina Koulenti
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4072, Australia; (E.X.); (A.S.); (I.Y.S.M.); (J.L.)
- 2nd Critical Care Department, Attikon University Hospital, 12462 Athens, Greece;
| | - Elena Xu
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4072, Australia; (E.X.); (A.S.); (I.Y.S.M.); (J.L.)
| | - Andrew Song
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4072, Australia; (E.X.); (A.S.); (I.Y.S.M.); (J.L.)
| | - Isaac Yin Sum Mok
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4072, Australia; (E.X.); (A.S.); (I.Y.S.M.); (J.L.)
| | - Drosos E. Karageorgopoulos
- 4th Department of Internal Medicine, Attikon University Hospital, 12462 Athens, Greece; (D.E.K.); (S.T.)
| | | | - Sotirios Tsiodras
- 4th Department of Internal Medicine, Attikon University Hospital, 12462 Athens, Greece; (D.E.K.); (S.T.)
| | - Jeffrey Lipman
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4072, Australia; (E.X.); (A.S.); (I.Y.S.M.); (J.L.)
- Department of Intensive Care Medicine, Royal Brisbane and Women’s Hospital, Brisbane, QLD 4029, Australia
- Anesthesiology and Critical Care, Centre Hospitalier Universitaire De Nîmes (CHU), University of Montpellier, 30029 Nîmes, France
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Kölsch S, Ihmels H, Mattay J, Sewald N, Patrick BO. Reversible photoswitching of the DNA-binding properties of styrylquinolizinium derivatives through photochromic [2 + 2] cycloaddition and cycloreversion. Beilstein J Org Chem 2020; 16:111-124. [PMID: 32082430 PMCID: PMC7006495 DOI: 10.3762/bjoc.16.13] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 01/08/2020] [Indexed: 12/17/2022] Open
Abstract
It was demonstrated that styrylquinolizinium derivatives may be applied as photoswitchable DNA ligands. At lower ligand:DNA ratios (≤1.5), these compounds bind to duplex DNA by intercalation, with binding constants ranging from K b = 4.1 × 104 M to 2.6 × 105 M (four examples), as shown by photometric and fluorimetric titrations as well as by CD and LD spectroscopic analyses. Upon irradiation at 450 nm, the methoxy-substituted styrylquinolizinium derivatives form the corresponding syn head-to-tail cyclobutanes in a selective [2 + 2] photocycloaddition, as revealed by X-ray diffraction analysis of the reaction products. These photodimers bind to DNA only weakly by outside-edge association, but they release the intercalating monomers upon irradiation at 315 nm in the presence of DNA. As a result, it is possible to switch between these two ligands and likewise between two different binding modes by irradiation with different excitation wavelengths.
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Affiliation(s)
- Sarah Kölsch
- Department of Chemistry and Biology, Organic Chemistry II, University of Siegen, Adolf-Reichwein-Str. 2, D-57068 Siegen, Germany
| | - Heiko Ihmels
- Department of Chemistry and Biology, Organic Chemistry II, University of Siegen, Adolf-Reichwein-Str. 2, D-57068 Siegen, Germany
| | - Jochen Mattay
- Department of Chemistry, Organic and Bioorganic Chemistry, Bielefeld University, PO Box 100121, D-33501 Bielefeld, Germany
| | - Norbert Sewald
- Department of Chemistry, Organic and Bioorganic Chemistry, Bielefeld University, PO Box 100121, D-33501 Bielefeld, Germany
| | - Brian O Patrick
- Department of Chemistry, Structural Chemistry Facility, The University of British Columbia, 2036 Main Mall, V6T 1Z1, Vancouver, BC, Canada
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64
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Müller S, Paulus J, Mattay J, Ihmels H, Dodero VI, Sewald N. Photocontrolled DNA minor groove interactions of imidazole/pyrrole polyamides. Beilstein J Org Chem 2020; 16:60-70. [PMID: 31976017 PMCID: PMC6964667 DOI: 10.3762/bjoc.16.8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 12/20/2019] [Indexed: 12/21/2022] Open
Abstract
Azobenzenes are photoswitchable molecules capable of generating significant structural changes upon E-to-Z photoisomerization in peptides or small molecules, thereby controlling geometry and functionality. E-to-Z photoisomerization usually is achieved upon irradiation at 350 nm (π–π* transition), while the Z-to-E isomerization proceeds photochemically upon irradiation at >400 nm (n–π* transition) or thermally. Photoswitchable compounds have frequently been employed as modules, e.g., to control protein–DNA interactions. However, their use in conjunction with minor groove-binding imidazole/pyrrole (Im/Py) polyamides is yet unprecedented. Dervan-type Im/Py polyamides were equipped with an azobenzene unit, i.e., 3-(3-(aminomethyl)phenyl)azophenylacetic acid, as the linker between two Im/Py polyamide strands. Only the (Z)-azobenzene-containing polyamides bound to the minor groove of double-stranded DNA hairpins. Photoisomerization was exemplarily evaluated by 1H NMR experiments, while minor groove binding of the (Z)-azobenzene derivatives was proven by CD titration experiments. The resulting induced circular dichroism (ICD) bands of the bound ligands, together with the photometric determination of the dsDNA melting temperature, revealed a significant stabilization of the DNA upon association with the ligand. The (Z)-azobenzene acted as a building block inducing a reverse turn, which favored hydrogen bonds between the pyrrole/imidazole amide and the DNA bases. In contrast, the E-configured polyamides did not induce any ICD characteristic for minor groove binding. The incorporation of the photoswitchable azobenzene unit is a promising strategy to obtain photoswitchable Im/Py hairpin polyamides capable of interacting with the dsDNA minor groove only in the Z-configuration.
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Affiliation(s)
- Sabrina Müller
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, PO Box 100131, D-33501 Bielefeld, Germany
| | - Jannik Paulus
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, PO Box 100131, D-33501 Bielefeld, Germany
| | - Jochen Mattay
- Organic Chemistry I, Department of Chemistry, Bielefeld University, PO Box 100131, D-33501 Bielefeld, Germany
| | - Heiko Ihmels
- Organic Chemistry II, Department Chemistry - Biology, Siegen University, Adolf-Reichwein-Str. 2, D-57068 Siegen, Germany
| | - Veronica I Dodero
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, PO Box 100131, D-33501 Bielefeld, Germany
| | - Norbert Sewald
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, PO Box 100131, D-33501 Bielefeld, Germany
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65
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Bucevičius J, Gilat T, Lukinavičius G. Far-red switching DNA probes for live cell nanoscopy. Chem Commun (Camb) 2020; 56:14797-14800. [DOI: 10.1039/d0cc06759h] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Blinking far-red hydroxymethyl silicon-rhodamine and Hoechst conjugates for chromatin nanoscopy in live cells.
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Affiliation(s)
- Jonas Bucevičius
- Chromatin Labeling and Imaging Group
- Department of NanoBiophotonics
- Max Planck Institute for Biophysical Chemistry
- 37077 Göttingen
- Germany
| | - Tanja Gilat
- Chromatin Labeling and Imaging Group
- Department of NanoBiophotonics
- Max Planck Institute for Biophysical Chemistry
- 37077 Göttingen
- Germany
| | - Gražvydas Lukinavičius
- Chromatin Labeling and Imaging Group
- Department of NanoBiophotonics
- Max Planck Institute for Biophysical Chemistry
- 37077 Göttingen
- Germany
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66
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Đud M, Glasovac Z, Margetić D, Piantanida I. Guanidino-aryl derivatives: protonation and structure tuning for spectrophotometric recognition of ds-DNA and ds-RNA. NEW J CHEM 2020. [DOI: 10.1039/d0nj01879a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fine interplay between protonation of guanidine and size of Aryl controls DNA/RNA recognition and fluorimetric or CD response.
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Affiliation(s)
- Mateja Đud
- Laboratory for Physical Organic Chemistry
- Division of Organic Chemistry & Biochemistry
- Ruđer Bošković Institute
- HR 10002 Zagreb
- Croatia
| | - Zoran Glasovac
- Laboratory for Physical Organic Chemistry
- Division of Organic Chemistry & Biochemistry
- Ruđer Bošković Institute
- HR 10002 Zagreb
- Croatia
| | - Davor Margetić
- Laboratory for Physical Organic Chemistry
- Division of Organic Chemistry & Biochemistry
- Ruđer Bošković Institute
- HR 10002 Zagreb
- Croatia
| | - Ivo Piantanida
- Laboratory for Biomolecular Interactions and Spectroscopy
- Division of Organic Chemistry & Biochemistry, Ruđer Bošković Institute
- HR 10002 Zagreb
- Croatia
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67
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Saha U, Dolai M, Konar S, Das A, Butcher RJ, Kumar GS, Mukhopadhyay S. Design and synthesis of a sulphur containing Schiff base drug: DNA binding studies and theoretical calculations. J Biomol Struct Dyn 2019; 39:263-271. [PMID: 31870222 DOI: 10.1080/07391102.2019.1708799] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The Schiff base compound MTA ((E)-5-methyl-N'-((5-methylthiophen-2-yl)methylene)-1H-pyrazole-3-carbohydrazide) derived from 2-thiophenecarboxaldehyde and 5-methylpyrazole-3-carbohydrazide has been designed to develop new sulphur containing DNA targeted molecule. The MTA has been characterized by elemental analyses, 1H-NMR, single crystal X-ray diffraction studies as well as by geometry optimization of using DFT/B3LYP. The interaction of MTA with Calf thymus DNA (CT-DNA) was studied by spectroscopic and calorimetric techniques. The synthesized compound was found to bind with CT-DNA through groove binding mode, and the binding constant was estimated to be (4.15 ± 0.08) × 104 M-1. The negative ΔG0 and positive ΔS0 values obtained from the calorimetric technique confirmed the spontaneity of the binding of MTA with DNA.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Urmila Saha
- Biophysical Chemistry Laboratory, Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Malay Dolai
- Department of Chemistry, Prabhat Kumar College, Contai, India
| | - Saugata Konar
- Department of Chemistry, The Bhawanipur Education Society College, Kolkata, India
| | - Amit Das
- Department of Chemistry, Ramsaday College, Howrah, India
| | - Ray J Butcher
- Department of Chemistry, Howard University, Washington, DC, USA
| | - Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory, Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
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68
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Cartuche L, Reyes-Batlle M, Sifaoui I, Arberas-Jiménez I, Piñero JE, Fernández JJ, Lorenzo-Morales J, Díaz-Marrero AR. Antiamoebic Activities of Indolocarbazole Metabolites Isolated from Streptomyces sanyensis Cultures. Mar Drugs 2019; 17:md17100588. [PMID: 31627366 PMCID: PMC6836125 DOI: 10.3390/md17100588] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/11/2019] [Accepted: 10/15/2019] [Indexed: 12/19/2022] Open
Abstract
Indolocarbazoles are a family of natural alkaloids characterized by their potent protein kinase and topoisomerase I inhibitory activity. Among them, staurosporine (1) has exhibited promising inhibitory activity against parasites. Based on new insights on the activity and mechanism of action of STS in Acanthamoeba parasites, this work reports the isolation, identification, and the anti-Acanthamoeba activity of the minor metabolites 7-oxostaurosporine (2), 4′-demethylamino-4′-oxostaurosporine (3), and streptocarbazole B (4), isolated from cultures of the mangrove strain Streptomyces sanyensis. A clear correlation between the antiparasitic activities and the structural elements and conformations of the indolocarbazoles 1–4 was observed. Also, the study reveals that 7-oxostaurosporine (2) affects membrane permeability and causes mitochondrial damages on trophozoites of A. castellanii Neff.
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Affiliation(s)
- Luis Cartuche
- Instituto Universitario de Bio-Orgánica Antonio González (IUBO AG), Centro de Investigaciones Biomédicas de Canarias (CIBICAN), Universidad de La Laguna (ULL), Avda. Astrofísico F. Sánchez 2, 38206 La Laguna, Tenerife, Spain.
- Departamento de Química y Ciencias Exactas, Sección Química Básica y Aplicada, Universidad Técnica Particular de Loja (UTPL), San Cayetano alto s/n, A.P. 1101608 Loja, Ecuador.
| | - María Reyes-Batlle
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Islas Canarias, Departamento de Obstetricia y Ginecología, Pediatría, Medicina Preventiva y Salud Pública, Toxicología, Medicina Legal y Forense y Parasitología, Universidad de La Laguna, Avda. Astrofísico F. Sánchez s/n, 38206 La Laguna, Tenerife, Spain.
| | - Ines Sifaoui
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Islas Canarias, Departamento de Obstetricia y Ginecología, Pediatría, Medicina Preventiva y Salud Pública, Toxicología, Medicina Legal y Forense y Parasitología, Universidad de La Laguna, Avda. Astrofísico F. Sánchez s/n, 38206 La Laguna, Tenerife, Spain.
| | - Iñigo Arberas-Jiménez
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Islas Canarias, Departamento de Obstetricia y Ginecología, Pediatría, Medicina Preventiva y Salud Pública, Toxicología, Medicina Legal y Forense y Parasitología, Universidad de La Laguna, Avda. Astrofísico F. Sánchez s/n, 38206 La Laguna, Tenerife, Spain.
| | - José E Piñero
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Islas Canarias, Departamento de Obstetricia y Ginecología, Pediatría, Medicina Preventiva y Salud Pública, Toxicología, Medicina Legal y Forense y Parasitología, Universidad de La Laguna, Avda. Astrofísico F. Sánchez s/n, 38206 La Laguna, Tenerife, Spain.
| | - José J Fernández
- Instituto Universitario de Bio-Orgánica Antonio González (IUBO AG), Centro de Investigaciones Biomédicas de Canarias (CIBICAN), Universidad de La Laguna (ULL), Avda. Astrofísico F. Sánchez 2, 38206 La Laguna, Tenerife, Spain.
- Departamento de Química Orgánica, Universidad de La Laguna (ULL), Avda. Astrofísico F. Sánchez, 2, 38206 La Laguna, Tenerife, Spain.
| | - Jacob Lorenzo-Morales
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Islas Canarias, Departamento de Obstetricia y Ginecología, Pediatría, Medicina Preventiva y Salud Pública, Toxicología, Medicina Legal y Forense y Parasitología, Universidad de La Laguna, Avda. Astrofísico F. Sánchez s/n, 38206 La Laguna, Tenerife, Spain.
| | - Ana R Díaz-Marrero
- Instituto Universitario de Bio-Orgánica Antonio González (IUBO AG), Centro de Investigaciones Biomédicas de Canarias (CIBICAN), Universidad de La Laguna (ULL), Avda. Astrofísico F. Sánchez 2, 38206 La Laguna, Tenerife, Spain.
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69
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Mahalakshmi G, Vennila KN, Selvakumar B, Rao PL, Malwade R, Deval S, Madhuri S, Seenivasaperumal M, Elango KP. Spectroscopic investigations on DNA binding profile of two new naphthyridine carboxamides and their application as turn-on fluorescent DNA staining probes. J Biomol Struct Dyn 2019; 38:3443-3451. [PMID: 31422749 DOI: 10.1080/07391102.2019.1657501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Two new 10-methoxydibenzo[b,h][1,6]naphthyridine-2-carboxamide derivatives (R1 and R2) have been synthesized and characterized using different spectral techniques. The binding of these probes with DNA was investigated using spectral (Electronic, fluorescence, 1H NMR and circular dichroism) and molecular docking studies. These probes exhibited a strong fluorescence around 440 nm upon excitation around 380 nm. Electronic and competitive fluorescence titration studies, in HEPES [(4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid)] buffer/dimethyl sulfoxide (pH 7.4) medium, suggest that these probes bind strongly to DNA, which is substantiated by 1H NMR study. The binding constants are calculated to be 5.3 × 107 and 6.8 × 106 M-1 for R1 and R2, respectively. From the results of spectral studies, it is proposed that the mechanism of binding of these probes with DNA is through minor groove binding mode, which is further confirmed by circular dichroism and molecular docking studies. Initial cell viability screening using MTT (3-[4,5-methylthiazol-2-yl]-2,5-diphenyl-tetrazolium bromide) assay shows that normal Vero cells are viable towards these probes at nano molar concentration, which is the concentration range employed in the present study for DNA staining (IC50 in the order of 0.023 mM). The enhancement in fluorescence intensity of these probes upon binding with DNA enables the staining of DNA in agarose gel in gel electrophoresis experiment. The sensitivity of these probes is comparable with that of ethidium bromide and DNA amounts as low as 4 nano gram are detectable.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- G Mahalakshmi
- Department of Chemistry, Gandhigram Rural Institute (Deemed to be University), Gandhigram, India
| | - K N Vennila
- Department of Chemistry, Gandhigram Rural Institute (Deemed to be University), Gandhigram, India
| | | | - P Lakshmana Rao
- National Institute of Animal Biotechnology, Hyderabad, India
| | - Ruchi Malwade
- National Institute of Animal Biotechnology, Hyderabad, India
| | - Sunny Deval
- National Institute of Animal Biotechnology, Hyderabad, India
| | - S Madhuri
- National Institute of Animal Biotechnology, Hyderabad, India
| | - M Seenivasaperumal
- Department of Chemistry, Gandhigram Rural Institute (Deemed to be University), Gandhigram, India
| | - Kuppanagounder P Elango
- Department of Chemistry, Gandhigram Rural Institute (Deemed to be University), Gandhigram, India
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70
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A fluorescent aminosugar to rapidly screen and study RNA binders. Methods Enzymol 2019. [PMID: 31239051 DOI: 10.1016/bs.mie.2019.05.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
RNA targeted high-throughput assays that allow for rapid detection of high affinity binding ligands are important in RNA recognition studies. A number for fluorescent dyes have been reported that can assist in rapidly identifying nucleic acid (RNA) binding elements without the need for immobilization of RNA or the ligand. A number of these dyes are planar aromatic molecules that bind non-specifically to nucleic acids and often distort their parent nucleic acid structures leading to ambiguity in the interpretation of results. In this light, we report here, the use of an aminoglycoside (neomycin) based fluorescent probe (F-Neo) which can reversibly bind to different RNA motifs and help identify ligands with needed affinity and selectivity, without any immobilization of the probe or the target. In this chapter, we provide the details of the assay development, experimental considerations and data analysis to use the probe and identify novel ligands. We then provide a brief introduction to calorimetry (ITC) and circular dichroism (CD) spectroscopy based methods in validating the binding of such identified compounds.
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71
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Ihmels H, Karbasiyoun M, Löhl K, Stremmel C. Structural flexibility versus rigidity of the aromatic unit of DNA ligands: binding of aza- and azoniastilbene derivatives to duplex and quadruplex DNA. Org Biomol Chem 2019; 17:6404-6413. [PMID: 31225566 DOI: 10.1039/c9ob00809h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The known azastilbene (E)-1,2-di(quinolin-3-yl)ethane (2a) and the novel azoniastilbene derivatives (E)-2-(2-(naphthalen-2-yl)vinyl)quinolizinium (2b) and (E)-3,3'-(ethane-1,2-diyl)bis(1-methylquinolinin-1-ium) (2c) were synthesized. Their interactions with duplex and quadruplex DNA (G4-DNA) were studied by photometric, fluorimetric, polarimetric and flow-LD analysis, and by thermal DNA denaturation studies, as well as by 1H-NMR spectroscopy. The main goal of this study was a comparison of these conformationally flexible compounds with the known G4-DNA-binding diazoniadibenzo[b,k]chrysenes, that have a comparable π-system extent, but a rigid structure. We have observed that the aza- and azoniastilbene derivatives 2a-c, i.e. compounds with almost the same spatial dimensions and steric demand, bind to DNA with an affinity and selectivity that depends significantly on the number of positive charges. Whereas the charge neutral derivative 2a binds unspecifically to the DNA backbone of duplex DNA, the ionic compounds 2b and 2c are typical DNA intercalators. Notably, the bis-quinolinium derivative 2c binds to G4-DNA with moderate affinity (Kb = 4.8 × 105 M-1) and also stabilizes the G4-DNA towards thermal denaturation (ΔTm = 11 °C at ligand-DNA ratio = 5.0). Strikingly, the corresponding rigid counterpart, 4a,12a-diazonia-8,16-dimethyldibenzo[b,k]chrysene, stabilizes the G4-DNA to an even greater extent under identical conditions (ΔTm = 27 °C). These results indicate that the increased flexibility of a G4-DNA ligand does not necessarily lead to stronger interactions with the G4-DNA as compared with rigid ligands that have essentially the same size and π system extent.
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Affiliation(s)
- H Ihmels
- Department of Chemistry and Biology, University of Siegen, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany.
| | - M Karbasiyoun
- Department of Chemistry and Biology, University of Siegen, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany.
| | - K Löhl
- Department of Chemistry and Biology, University of Siegen, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany.
| | - C Stremmel
- Department of Chemistry and Biology, University of Siegen, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany.
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72
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Targeting the NFAT:AP-1 transcriptional complex on DNA with a small-molecule inhibitor. Proc Natl Acad Sci U S A 2019; 116:9959-9968. [PMID: 31019078 DOI: 10.1073/pnas.1820604116] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The transcription factor nuclear factor of activated T cells (NFAT) has a key role in both T cell activation and tolerance and has emerged as an important target of immune modulation. NFAT directs the effector arm of the immune response in the presence of activator protein-1 (AP-1), and T cell anergy/exhaustion in the absence of AP-1. Envisioning a strategy for selective modulation of the immune response, we designed a FRET-based high-throughput screen to identify compounds that disrupt the NFAT:AP-1:DNA complex. We screened ∼202,000 small organic compounds and identified 337 candidate inhibitors. We focus here on one compound, N-(3-acetamidophenyl)-2-[5-(1H-benzimidazol-2-yl)pyridin-2-yl]sulfanylacetamide (Compound 10), which disrupts the NFAT:AP-1 interaction at the composite antigen-receptor response element-2 site without affecting the binding of NFAT or AP-1 alone to DNA. Compound 10 binds to DNA in a sequence-selective manner and inhibits the transcription of the Il2 gene and several other cyclosporin A-sensitive cytokine genes important for the effector immune response. This study provides proof-of-concept that small molecules can inhibit the assembly of specific DNA-protein complexes, and opens a potential new approach to treat human diseases where known transcription factors are deregulated.
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A New Generation of Minor-Groove-Binding-Heterocyclic Diamidines That Recognize G·C Base Pairs in an AT Sequence Context. Molecules 2019; 24:molecules24050946. [PMID: 30866557 PMCID: PMC6429135 DOI: 10.3390/molecules24050946] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 02/28/2019] [Accepted: 03/01/2019] [Indexed: 12/17/2022] Open
Abstract
We review the preparation of new compounds with good solution and cell uptake properties that can selectively recognize mixed A·T and G·C bp sequences of DNA. Our underlying aim is to show that these new compounds provide important new biotechnology reagents as well as a new class of therapeutic candidates with better properties and development potential than other currently available agents. In this review, entirely different ways to recognize mixed sequences of DNA by modifying AT selective heterocyclic cations are described. To selectively recognize a G·C base pair an H-bond acceptor must be incorporated with AT recognizing groups as with netropsin. We have used pyridine, azabenzimidazole and thiophene-N-methylbenzimidazole GC recognition units in modules crafted with both rational design and empirical optimization. These modules can selectively and strongly recognize a single G·C base pair in an AT sequence context. In some cases, a relatively simple change in substituents can convert a heterocyclic module from AT to GC recognition selectivity. Synthesis and DNA interaction results for initial example lead modules are described for single G·C base pair recognition compounds. The review concludes with a description of the initial efforts to prepare larger compounds to recognize sequences of DNA with more than one G·C base pairs. The challenges and initial successes are described along with future directions.
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