1
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Matić J, Piotrowski P, Vrban L, Kobetić R, Vianello R, Jurić I, Fabijanić I, Pernar Kovač M, Brozovic A, Piantanida I, Schmuck C, Radić Stojković M. Distinctive Nucleic Acid Recognition by Lysine-Embedded Phenanthridine Peptides. Int J Mol Sci 2024; 25:4866. [PMID: 38732083 PMCID: PMC11084427 DOI: 10.3390/ijms25094866] [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: 03/28/2024] [Revised: 04/25/2024] [Accepted: 04/27/2024] [Indexed: 05/13/2024] Open
Abstract
Three new phenanthridine peptide derivatives (19, 22, and 23) were synthesized to explore their potential as spectrophotometric probes for DNA and RNA. UV/Vis and circular dichroism (CD) spectra, mass spectroscopy, and computational analysis confirmed the presence of intramolecular interactions in all three compounds. Computational analysis revealed that compounds alternate between bent and open conformations, highlighting the latter's crucial influence on successful polynucleotide recognition. Substituting one glycine with lysine in two regioisomers (22, 23) resulted in stronger binding interactions with DNA and RNA than for a compound containing two glycines (19), thus emphasizing the importance of lysine. The regioisomer with lysine closer to the phenanthridine ring (23) exhibited a dual and selective fluorimetric response with non-alternating AT and ATT polynucleotides and induction of triplex formation from the AT duplex. The best binding constant (K) with a value of 2.5 × 107 M-1 was obtained for the interaction with AT and ATT polynucleotides. Furthermore, apart from distinguishing between different types of ds-DNA and ds-RNA, the same compound could recognize GC-rich DNA through distinct induced CD signals.
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Affiliation(s)
- Josipa Matić
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (J.M.); (R.K.); (I.J.); (I.F.); (I.P.)
| | - Patryciusz Piotrowski
- Institute for Organic Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany; (P.P.)
| | - Lucija Vrban
- Laboratory for the Computational Design and Synthesis of Functional Materials, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (L.V.); (R.V.)
| | - Renata Kobetić
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (J.M.); (R.K.); (I.J.); (I.F.); (I.P.)
| | - Robert Vianello
- Laboratory for the Computational Design and Synthesis of Functional Materials, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (L.V.); (R.V.)
| | - Ivona Jurić
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (J.M.); (R.K.); (I.J.); (I.F.); (I.P.)
| | - Ivana Fabijanić
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (J.M.); (R.K.); (I.J.); (I.F.); (I.P.)
| | - Margareta Pernar Kovač
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (M.P.K.); (A.B.)
| | - Anamaria Brozovic
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (M.P.K.); (A.B.)
| | - Ivo Piantanida
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (J.M.); (R.K.); (I.J.); (I.F.); (I.P.)
| | - Carsten Schmuck
- Institute for Organic Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany; (P.P.)
| | - Marijana Radić Stojković
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (J.M.); (R.K.); (I.J.); (I.F.); (I.P.)
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2
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Sviben I, Glavaš M, Erben A, Bachelart T, Pavlović Saftić D, Piantanida I, Basarić N. Dipeptides Containing Pyrene and Modified Photochemically Reactive Tyrosine: Noncovalent and Covalent Binding to Polynucleotides. Molecules 2023; 28:7533. [PMID: 38005255 PMCID: PMC10672942 DOI: 10.3390/molecules28227533] [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: 10/05/2023] [Revised: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
Dipeptides 1 and 2 were synthesized from unnatural amino acids containing pyrene as a fluorescent label and polynucleotide binding unit, and modified tyrosine as a photochemically reactive unit. Photophysical properties of the peptides were investigated by steady-state and time-resolved fluorescence. Both peptides are fluorescent (Φf = 0.3-0.4) and do not show a tendency to form pyrene excimers in the concentration range < 10-5 M, which is important for their application in the fluorescent labeling of polynucleotides. Furthermore, both peptides are photochemically reactive and undergo deamination delivering quinone methides (QMs) (ΦR = 0.01-0.02), as indicated from the preparative photomethanolysis study of the corresponding N-Boc protected derivatives 7 and 8. Both peptides form stable complexes with polynucleotides (log Ka > 6) by noncovalent interactions and similar affinities, binding to minor grooves, preferably to the AT reach regions. Peptide 2 with a longer spacer between the fluorophore and the photo-activable unit undergoes a more efficient deamination reaction, based on the comparison with the N-Boc protected derivatives. Upon light excitation of the complex 2·oligoAT10, the photo-generation of QM initiates the alkylation, which results in the fluorescent labeling of the oligonucleotide. This study demonstrated, as a proof of principle, that small molecules can combine dual forms of fluorescent labeling of polynucleotides, whereby initial addition of the dye rapidly forms a reversible high-affinity noncovalent complex with ds-DNA/RNA, which can be, upon irradiation by light, converted to the irreversible (covalent) form. Such a dual labeling ability of a dye could have many applications in biomedicinal sciences.
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Affiliation(s)
| | | | | | | | | | - Ivo Piantanida
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; (I.S.); (M.G.); (A.E.); (T.B.); (D.P.S.)
| | - Nikola Basarić
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; (I.S.); (M.G.); (A.E.); (T.B.); (D.P.S.)
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3
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Huang W, Feng S, Liu J, Liang B, Zhou Y, Yu M, Liang J, Huang J, Lü X, Huang W. Configuration-Induced Multichromism of Phenanthridine Derivatives: A Type of Versatile Fluorescent Probe for Microenvironmental Monitoring. Angew Chem Int Ed Engl 2023; 62:e202219337. [PMID: 36602266 DOI: 10.1002/anie.202219337] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 01/06/2023]
Abstract
Fluorescent probes are attractive in diagnosis and sensing. However, most reported fluorophores can only detect one or few analytes/parameters, notably limiting their applications. Here we have designed three phenanthridine-based fluorophores (i.e., B1, F1, and T1 with 1D, 2D, and 3D molecular configuration, respectively) capable of monitoring various microenvironments. In rigidifying media, all fluorophores show bathochromic emissions but with different wavelength and intensity changes. Under compression, F1 shows a bathochromic emission of over 163 nm, which results in organic fluorophore-based full-color piezochromism. Moreover, both B1 and F1 exhibit an aggregation-caused quenching (ACQ) behavior, while T1 is an aggregation-induced emission (AIE) fluorophore. Further, F1 and T1 selectively concentrate in cell nucleus, whereas B1 mainly stains the cytoplasm in live cell imaging. This work provides a general design strategy of versatile fluorophores for microenvironmental monitoring.
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Affiliation(s)
- Wei Huang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, 155 Yangqiao West Road, Fuzhou, Fujian 350002, P. R. China
| | - Shiyu Feng
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, 155 Yangqiao West Road, Fuzhou, Fujian 350002, P. R. China.,Fujian Science & Technology Innovation Laboratory for Optoelectronic Information of China, Fuzhou, Fujian 350108, P. R. China.,University of Chinese Academy of Sciences, 19 A Yuquan Road, Beijing, 100049, P. R. China
| | - Jie Liu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, 155 Yangqiao West Road, Fuzhou, Fujian 350002, P. R. China
| | - Baoshuai Liang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, 155 Yangqiao West Road, Fuzhou, Fujian 350002, P. R. China.,University of Chinese Academy of Sciences, 19 A Yuquan Road, Beijing, 100049, P. R. China
| | - Ya Zhou
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P. R. China
| | - Mengya Yu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P. R. China
| | - Jiayuan Liang
- Center for High Pressure Science and Technology Advanced Research (HPSTAR), Shanghai, 201203, P. R. China
| | - Jiaguo Huang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, P. R. China
| | - Xujie Lü
- Center for High Pressure Science and Technology Advanced Research (HPSTAR), Shanghai, 201203, P. R. China
| | - Weiguo Huang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, 155 Yangqiao West Road, Fuzhou, Fujian 350002, P. R. China.,Fujian Science & Technology Innovation Laboratory for Optoelectronic Information of China, Fuzhou, Fujian 350108, P. R. China.,University of Chinese Academy of Sciences, 19 A Yuquan Road, Beijing, 100049, P. R. China
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4
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Matić J, Tandarić T, Radić Stojković M, Šupljika F, Karačić Z, Tomašić Paić A, Horvat L, Vianello R, Tumir LM. Phenanthridine-pyrene conjugates as fluorescent probes for DNA/RNA and an inactive mutant of dipeptidyl peptidase enzyme. Beilstein J Org Chem 2023; 19:550-565. [PMID: 37153642 PMCID: PMC10155618 DOI: 10.3762/bjoc.19.40] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 04/14/2023] [Indexed: 05/10/2023] Open
Abstract
Two novel conjugate molecules were designed: pyrene and phenanthridine-amino acid units with a different linker length between the aromatic fragments. Molecular modelling combined with spectrophotometric experiments revealed that in neutral and acidic buffered water solutions conjugates predominantly exist in intramolecularly stacked conformations because of the π-π stacking interaction between pyrene and phenanthridine moieties. The investigated systems exhibited a pH-dependent excimer formation that is significantly red-shifted relative to the pyrene and phenanthridine fluorescence. While the conjugate with a short linker showed negligible spectrophotometric changes due to the polynucleotide addition, the conjugate with a longer and more flexible linker exhibited a micromolar and submicromolar binding affinity for ds-polynucleotides and inactivated a mutant of dipeptidyl peptidase enzyme E451A. Confocal microscopy revealed that the conjugate with the longer linker entered the HeLa cell membranes and blue fluorescence was visualized as the dye accumulated in the cell membrane.
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Affiliation(s)
- Josipa Matić
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Tana Tandarić
- Laboratory for the Computational Design and Synthesis of Functional Materials, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Marijana Radić Stojković
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Filip Šupljika
- Laboratory for Physical Chemistry and Corrosion, Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Croatia
| | - Zrinka Karačić
- Laboratory for Protein Biochemistry and Molecular Modelling, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Ana Tomašić Paić
- Laboratory for Protein Biochemistry and Molecular Modelling, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Lucija Horvat
- Laboratory for Molecular Plant Biology and Biotechnology, Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Robert Vianello
- Laboratory for the Computational Design and Synthesis of Functional Materials, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Lidija-Marija Tumir
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
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5
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Aschmann D, Vallet C, Tripathi SK, Ruiz‐Blanco YB, Brabender M, Schmuck C, Sanchez‐Garcia E, Knauer SK, Giese M. Selective Disruption of Survivin's Protein‐Protein Interactions: A Supramolecular Approach Based on Guanidiniocarbonylpyrrole. Chembiochem 2022; 23:e202100618. [PMID: 35043526 PMCID: PMC9303230 DOI: 10.1002/cbic.202100618] [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: 11/09/2021] [Revised: 12/09/2021] [Indexed: 11/20/2022]
Abstract
Targeting specific protein binding sites to interfere with protein‐protein interactions (PPIs) is crucial for the rational modulation of biologically relevant processes. Survivin, which is highly overexpressed in most cancer cells and considered to be a key player of carcinogenesis, features two functionally relevant binding sites. Here, we demonstrate selective disruption of the Survivin/Histone H3 or the Survivin/Crm1 interaction using a supramolecular approach. By rational design we identified two structurally related ligands (LNES and LHIS), capable of selectively inhibiting these PPIs, leading to a reduction in cancer cell proliferation.
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Affiliation(s)
- Dennis Aschmann
- Department of Organic Chemistry University of Duisburg-Essen Universitätsstr. 7 45141 Essen Germany
| | - Cecilia Vallet
- Department of Molecular Biology II University of Duisburg-Essen Universitätsstr. 5 45141 Essen Germany
| | - Sunil K. Tripathi
- Computational Biochemistry University of Duisburg-Essen Universitätsstr. 2 45117 Essen Germany
| | - Yasser B. Ruiz‐Blanco
- Computational Biochemistry University of Duisburg-Essen Universitätsstr. 2 45117 Essen Germany
| | - Max Brabender
- Department of Molecular Biology II University of Duisburg-Essen Universitätsstr. 5 45141 Essen Germany
| | - Carsten Schmuck
- Department of Organic Chemistry University of Duisburg-Essen Universitätsstr. 7 45141 Essen Germany
| | - Elsa Sanchez‐Garcia
- Computational Biochemistry University of Duisburg-Essen Universitätsstr. 2 45117 Essen Germany
| | - Shirley K. Knauer
- Department of Molecular Biology II University of Duisburg-Essen Universitätsstr. 5 45141 Essen Germany
| | - Michael Giese
- Department of Organic Chemistry University of Duisburg-Essen Universitätsstr. 7 45141 Essen Germany
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6
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Asadi S, Masoodi HR, Mehrabi H. Theoretical insights of solvent effect on tautomerism, stability, and electronic properties of 6‐ketomethylphenanthridine. J PHYS ORG CHEM 2021. [DOI: 10.1002/poc.4294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Sara Asadi
- Department of Chemistry, Faculty of Science Vali‐e‐Asr University of Rafsanjan Rafsanjan Iran
| | - Hamid Reza Masoodi
- Department of Chemistry, Faculty of Science Vali‐e‐Asr University of Rafsanjan Rafsanjan Iran
| | - Hossein Mehrabi
- Department of Chemistry, Faculty of Science Vali‐e‐Asr University of Rafsanjan Rafsanjan Iran
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7
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Erben A, Sviben I, Mihaljević B, Piantanida I, Basarić N. Non-Covalent Binding of Tripeptides-Containing Tryptophan to Polynucleotides and Photochemical Deamination of Modified Tyrosine to Quinone Methide Leading to Covalent Attachment. Molecules 2021; 26:molecules26144315. [PMID: 34299591 PMCID: PMC8306964 DOI: 10.3390/molecules26144315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/09/2021] [Accepted: 07/13/2021] [Indexed: 12/01/2022] Open
Abstract
A series of tripeptides TrpTrpPhe (1), TrpTrpTyr (2), and TrpTrpTyr[CH2N(CH3)2] (3) were synthesized, and their photophysical properties and non-covalent binding to polynucleotides were investigated. Fluorescent Trp residues (quantum yield in aqueous solvent ΦF = 0.03–0.06), allowed for the fluorometric study of non-covalent binding to DNA and RNA. Moreover, high and similar affinities of 2×HCl and 3×HCl to all studied double stranded (ds)-polynucleotides were found (logKa = 6.0–6.8). However, the fluorescence spectral responses were strongly dependent on base pair composition: the GC-containing polynucleotides efficiently quenched Trp emission, at variance to AT- or AU-polynucleotides, which induced bisignate response. Namely, addition of AT(U) polynucleotides at excess over studied peptide induced the quenching (attributed to aggregation in the grooves of polynucleotides), whereas at excess of DNA/RNA over peptide the fluorescence increase of Trp was observed. The thermal denaturation and circular dichroism (CD) experiments supported peptides binding within the grooves of polynucleotides. The photogenerated quinone methide (QM) reacts with nucleophiles giving adducts, as demonstrated by the photomethanolysis (quantum yield ΦR = 0.11–0.13). Furthermore, we have demonstrated photoalkylation of AT oligonucleotides by QM, at variance to previous reports describing the highest reactivity of QMs with the GC reach regions of polynucleotides. Our investigations show a proof of principle that QM precursor can be imbedded into a peptide and used as a photochemical switch to enable alkylation of polynucleotides, enabling further applications in chemistry and biology.
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Affiliation(s)
- Antonija Erben
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia; (A.E.); (I.S.); (I.P.)
| | - Igor Sviben
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia; (A.E.); (I.S.); (I.P.)
| | - Branka Mihaljević
- Department of Material Chemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia;
| | - Ivo Piantanida
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia; (A.E.); (I.S.); (I.P.)
| | - Nikola Basarić
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia; (A.E.); (I.S.); (I.P.)
- Correspondence:
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8
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Pasch P, Killa M, Junghans HL, Schmidt M, Schmidt S, Voskuhl J, Hartmann L. Take your Positions and Shine: Effects of Positioning Aggregation-Induced Emission Luminophores within Sequence-Defined Macromolecules. Chemistry 2021; 27:10186-10192. [PMID: 33876476 PMCID: PMC8362002 DOI: 10.1002/chem.202101086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Indexed: 12/17/2022]
Abstract
A luminophore with aggregation‐induced emission (AIE) is employed for the conjugation onto supramolecular ligands to allow for detection of ligand binding. Supramolecular ligands are based on the combination of sequence‐defined oligo(amidoamine) scaffolds and guanidiniocarbonyl‐pyrrole (GCP) as binding motif. We hypothesize that AIE properties are strongly affected by positioning of the luminophore within the ligand scaffold. Therefore, we systematically investigate the effects placing the AIE luminophore at different positions within the overall construct, for example, in the main or side chain of the olig(amidoamine). Indeed, we can show that the position within the ligand structure strongly affects AIE, both for the ligand itself as well as when applying the ligand for the detection of different biological and synthetic polyanions.
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Affiliation(s)
- Peter Pasch
- Department for Organic Chemistry and Macromolecular Chemistry, Heinrich Heine University Duesseldorf, Universitätsstraße 1, Düsseldorf, 40225, Germany
| | - Matthias Killa
- Faculty of chemistry (Organic chemistry) and CENIDE, University of Duisburg Essen, Universitätsstrasse 7, 45141, Essen, Germany
| | - Hauke Lukas Junghans
- Department for Organic Chemistry and Macromolecular Chemistry, Heinrich Heine University Duesseldorf, Universitätsstraße 1, Düsseldorf, 40225, Germany
| | - Melanie Schmidt
- Department for Organic Chemistry and Macromolecular Chemistry, Heinrich Heine University Duesseldorf, Universitätsstraße 1, Düsseldorf, 40225, Germany
| | - Stephan Schmidt
- Department for Organic Chemistry and Macromolecular Chemistry, Heinrich Heine University Duesseldorf, Universitätsstraße 1, Düsseldorf, 40225, Germany
| | - Jens Voskuhl
- Faculty of chemistry (Organic chemistry) and CENIDE, University of Duisburg Essen, Universitätsstrasse 7, 45141, Essen, Germany
| | - Laura Hartmann
- Department for Organic Chemistry and Macromolecular Chemistry, Heinrich Heine University Duesseldorf, Universitätsstraße 1, Düsseldorf, 40225, Germany
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9
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Pasch P, Höing A, Ueclue S, Killa M, Voskuhl J, Knauer SK, Hartmann L. PEGylated sequence-controlled macromolecules using supramolecular binding to target the Taspase1/Importin α interaction. Chem Commun (Camb) 2021; 57:3091-3094. [PMID: 33625405 DOI: 10.1039/d0cc07139k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A novel strategy to inhibit the oncologically relevant protease Taspase1 is explored by developing PEGylated macromolecular ligands presenting the supramolecular binding motif guanidiniocarbonylpyrrole (GCP). Taspase1 requires interaction of its nuclear localization signal (NLS) with import receptor Importin α. We show the synthesis and effective interference of PEGylated multivalent macromolecular ligands with Taspase1-Importin α-complex formation.
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Affiliation(s)
- Peter Pasch
- Department for Organic Chemistry and Macromolecular Chemistry, Heinrich Heine University Düsseldorf, Universitätsstraße 1, Düsseldorf 40225, Germany.
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10
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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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11
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Novel Harmicines with Improved Potency against Plasmodium. Molecules 2020; 25:molecules25194376. [PMID: 32977642 PMCID: PMC7583898 DOI: 10.3390/molecules25194376] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 09/17/2020] [Accepted: 09/22/2020] [Indexed: 12/31/2022] Open
Abstract
Harmicines represent hybrid compounds composed of β-carboline alkaloid harmine and cinnamic acid derivatives (CADs). In this paper we report the synthesis of amide-type harmicines and the evaluation of their biological activity. N-harmicines 5a–f and O-harmicines 6a–h were prepared by a straightforward synthetic procedure, from harmine-based amines and CADs using standard coupling conditions, 1-[bis(dimethylamino)methylene]-1H-1,2,3-triazolo [4,5-b]pyridinium 3-oxid hexafluorophosphate (HATU) and N,N-diisopropylethylamine (DIEA). Amide-type harmicines exerted remarkable activity against the erythrocytic stage of P. falciparum, in low submicromolar concentrations, which was significantly more pronounced compared to their antiplasmodial activity against the hepatic stages of P. berghei. Furthermore, a cytotoxicity assay against the human liver hepatocellular carcinoma cell line (HepG2) revealed favorable selectivity indices of the most active harmicines. Molecular dynamics simulations demonstrated the binding of ligands within the ATP binding site of PfHsp90, while the calculated binding free energies confirmed higher activity of N-harmicines 5 over their O-substituted analogues 6. Amino acids predominantly affecting the binding were identified, which provided guidelines for the further derivatization of the harmine framework towards more efficient agents.
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12
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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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Pantalon Juraj N, Krklec M, Novosel T, Perić B, Vianello R, Raić-Malić S, Kirin SI. Copper(ii) and zinc(ii) complexes of mono- and bis-1,2,3-triazole-substituted heterocyclic ligands. Dalton Trans 2020; 49:9002-9015. [PMID: 32558875 DOI: 10.1039/d0dt01244k] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Chelating 1,4-disubstituted mono- (8a-8d) and bis-1,2,3-triazole-based (9a-11a) ligands were prepared by regioselective copper(i)-catalysed 1,3-dipolar cycloaddition of terminal alkynes with aromatic azides, together with bioconjugate 13a synthesized by amide coupling of l-phenylalanine methyl ester to 11a. Cu(ii) and Zn(ii) complexes were prepared and single crystal structures were determined for complexes 8aCu, 8dCu, 9cCu and 10cCu, as well as the free ligands 10a and 10c. The in situ prepared Zn(ii) complexes were studied by NMR spectroscopy, while the stoichiometry of the Cu(ii) complexes in solution was determined by UV-Vis titrations and confirmed by the electronic structure DFT calculations at the (SMD)/M05-2X/6-31+G(d)/LanL2DZ+ECP level of theory.
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14
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Vallet C, Aschmann D, Beuck C, Killa M, Meiners A, Mertel M, Ehlers M, Bayer P, Schmuck C, Giese M, Knauer SK. Functional Disruption of the Cancer-Relevant Interaction between Survivin and Histone H3 with a Guanidiniocarbonyl Pyrrole Ligand. Angew Chem Int Ed Engl 2020; 59:5567-5571. [PMID: 31916356 PMCID: PMC7155087 DOI: 10.1002/anie.201915400] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Indexed: 12/21/2022]
Abstract
The protein Survivin is highly upregulated in most cancers and considered to be a key player in carcinogenesis. We explored a supramolecular approach to address Survivin as a drug target by inhibiting the protein-protein interaction of Survivin and its functionally relevant binding partner Histone H3. Ligand L1 is based on the guanidiniocarbonyl pyrrole cation and serves as a highly specific anion binder in order to target the interaction between Survivin and Histone H3. NMR titration confirmed binding of L1 to Survivin's Histone H3 binding site. The inhibition of the Survivin-Histone H3 interaction and consequently a reduction of cancer cell proliferation were demonstrated by microscopic and cellular assays.
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Affiliation(s)
- Cecilia Vallet
- Department of Molecular Biology IIUniversity of Duisburg-EssenUniversitätsstraße 545141EssenGermany
| | - Dennis Aschmann
- Institute for Organic ChemistryUniversity of Duisburg-EssenGermany
| | - Christine Beuck
- Department of Structural and Medicinal BiochemistryUniversity of Duisburg-EssenGermany
| | - Matthias Killa
- Institute for Organic ChemistryUniversity of Duisburg-EssenGermany
| | - Annika Meiners
- Department of Molecular Biology IIUniversity of Duisburg-EssenUniversitätsstraße 545141EssenGermany
| | - Marcel Mertel
- Institute for Organic ChemistryUniversity of Duisburg-EssenGermany
| | - Martin Ehlers
- Institute for Organic ChemistryUniversity of Duisburg-EssenGermany
| | - Peter Bayer
- Department of Structural and Medicinal BiochemistryUniversity of Duisburg-EssenGermany
| | - Carsten Schmuck
- Institute for Organic ChemistryUniversity of Duisburg-EssenGermany
| | - Michael Giese
- Institute for Organic ChemistryUniversity of Duisburg-EssenGermany
| | - Shirley K. Knauer
- Department of Molecular Biology IIUniversity of Duisburg-EssenUniversitätsstraße 545141EssenGermany
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15
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Vallet C, Aschmann D, Beuck C, Killa M, Meiners A, Mertel M, Ehlers M, Bayer P, Schmuck C, Giese M, Knauer SK. Funktionelle Inhibition der krebsrelevanten Interaktion von Survivin und Histon H3 mit einem Guanidiniumcarbonylpyrrol‐Liganden. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915400] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Cecilia Vallet
- Lehrstuhl für Molekularbiologie II Universität Duisburg-Essen Universitätsstraße 5 45141 Essen Deutschland
| | - Dennis Aschmann
- Institut für organische Chemie Universität Duisburg-Essen Deutschland
| | - Christine Beuck
- Lehrstuhl für strukturelle und medizinische Biochemie Universität Duisburg-Essen Deutschland
| | - Matthias Killa
- Institut für organische Chemie Universität Duisburg-Essen Deutschland
| | - Annika Meiners
- Lehrstuhl für Molekularbiologie II Universität Duisburg-Essen Universitätsstraße 5 45141 Essen Deutschland
| | - Marcel Mertel
- Institut für organische Chemie Universität Duisburg-Essen Deutschland
| | - Martin Ehlers
- Institut für organische Chemie Universität Duisburg-Essen Deutschland
| | - Peter Bayer
- Lehrstuhl für strukturelle und medizinische Biochemie Universität Duisburg-Essen Deutschland
| | - Carsten Schmuck
- Institut für organische Chemie Universität Duisburg-Essen Deutschland
| | - Michael Giese
- Institut für organische Chemie Universität Duisburg-Essen Deutschland
| | - Shirley K. Knauer
- Lehrstuhl für Molekularbiologie II Universität Duisburg-Essen Universitätsstraße 5 45141 Essen Deutschland
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16
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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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17
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Pantalon Juraj N, Miletić GI, Perić B, Popović Z, Smrečki N, Vianello R, Kirin SI. Stereochemistry of Hexacoordinated Zn(II), Cu(II), Ni(II), and Co(II) Complexes with Iminodiacetamide Ligands. Inorg Chem 2019; 58:16445-16457. [PMID: 31774277 DOI: 10.1021/acs.inorgchem.9b02200] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Metal complexes of iminodiacetamide (imda) ligands and metal ions Zn(II), Cu(II), Ni(II), and Co(II) were prepared using eight imda ligands (L1-L8) substituted with groups of different steric and electronic properties on the central amine N atom (H atom, methyl, isopropyl, and benzyl) and the para position of the phenyl rings (nitro and dimethylamino). The effect of these substituents on the stoichiometry (ML and ML2), geometry, and stereochemistry (mer, trans-fac, cis-fac) of the complexes was studied in the solid state, in solution, and by density functional theory calculations. Single-crystal and powder X-ray diffraction, thermogravimetry, and IR spectroscopy showed that in the solid state imda ligands preferentially form trans-fac ML2 complexes, with the exception of the cis-fac complex 7Zn. NMR spectroscopy of diamagnetic Zn(II) and paramagnetic Co(II) complexes revealed the formation of both ML and ML2 complexes in solution, which was also confirmed by UV-vis titrations. Variable-temperature NMR was used to study the effect of the substituent on the central amine N atom on the Zn-N bond strength and nitrogen inversion. The relative stabilities of the isomers were rationalized by computations and the optimized structures used for geometry analysis.
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Affiliation(s)
| | - Goran I Miletić
- Ruđer Bošković Institute , Bijenička c. 54 , HR-10000 Zagreb , Croatia
| | - Berislav Perić
- Ruđer Bošković Institute , Bijenička c. 54 , HR-10000 Zagreb , Croatia
| | - Zora Popović
- Department of Chemistry, Faculty of Science , University of Zagreb , Horvatovac 102a , HR-10000 Zagreb , Croatia
| | - Neven Smrečki
- Department of Chemistry, Faculty of Science , University of Zagreb , Horvatovac 102a , HR-10000 Zagreb , Croatia
| | - Robert Vianello
- Ruđer Bošković Institute , Bijenička c. 54 , HR-10000 Zagreb , Croatia
| | - Srećko I Kirin
- Ruđer Bošković Institute , Bijenička c. 54 , HR-10000 Zagreb , Croatia
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