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Szánti-Pintér E, Jirkalová L, Pohl R, Bednárová L, Kudova E. Stereoselective Reduction of Steroidal 4-Ene-3-ketones in the Presence of Biomass-Derived Ionic Liquids Leading to Biologically Important 5β-Steroids. ACS Omega 2024; 9:7043-7052. [PMID: 38371788 PMCID: PMC10870401 DOI: 10.1021/acsomega.3c08963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/19/2023] [Accepted: 01/23/2024] [Indexed: 02/20/2024]
Abstract
The stereoselective reduction of the steroidal 4-ene-3-ketone moiety (enone) affords the 5β-steroid backbone that is a key structural element of biologically important neuroactive steroids. Neurosteroids have been currently studied as novel and potent central nervous system drug-like compounds for the treatment of, e.g., postpartum depression. As a green methodology, we studied the palladium-catalyzed hydrogenation of steroidal 4-ene-3-ketones in the presence of ionic liquids derived from natural carboxylic acids. The hydrogenation proceeds with improved 5β-selectivity in the presence of tetrabutylammonium carboxylates as additives compared to the exclusive use of an organic solvent. Under optimal conditions, using tetrabutylammonium d-mandelate, the reduction of testosterone led to 5β-dihydrotestosterone in high yield and stereoselectivity and no byproduct formation was observed. Moreover, the catalyst could be recycled. The presence of additional substituents on the steroid backbone showed a significant effect on the 5β-selectivity.
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Affiliation(s)
- Eszter Szánti-Pintér
- Institute of Organic Chemistry
and Biochemistry of the Czech Academy of Sciences, Prague 166 10, Czech Republic
| | - Lada Jirkalová
- Institute of Organic Chemistry
and Biochemistry of the Czech Academy of Sciences, Prague 166 10, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry
and Biochemistry of the Czech Academy of Sciences, Prague 166 10, Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry
and Biochemistry of the Czech Academy of Sciences, Prague 166 10, Czech Republic
| | - Eva Kudova
- Institute of Organic Chemistry
and Biochemistry of the Czech Academy of Sciences, Prague 166 10, Czech Republic
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2
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Osifová Z, Kalvoda T, Galgonek J, Culka M, Vondrášek J, Bouř P, Bednárová L, Andrushchenko V, Dračínský M, Rulíšek L. What are the minimal folding seeds in proteins? Experimental and theoretical assessment of secondary structure propensities of small peptide fragments. Chem Sci 2024; 15:594-608. [PMID: 38179543 PMCID: PMC10763034 DOI: 10.1039/d3sc04960d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 11/22/2023] [Indexed: 01/06/2024] Open
Abstract
Certain peptide sequences, some of them as short as amino acid triplets, are significantly overpopulated in specific secondary structure motifs in folded protein structures. For example, 74% of the EAM triplet is found in α-helices, and only 3% occurs in the extended parts of proteins (typically β-sheets). In contrast, other triplets (such as VIV and IYI) appear almost exclusively in extended parts (79% and 69%, respectively). In order to determine whether such preferences are structurally encoded in a particular peptide fragment or appear only at the level of a complex protein structure, NMR, VCD, and ECD experiments were carried out on selected tripeptides: EAM (denoted as pro-'α-helical' in proteins), KAM(α), ALA(α), DIC(α), EKF(α), IYI(pro-β-sheet or more generally, pro-extended), and VIV(β), and the reference α-helical CATWEAMEKCK undecapeptide. The experimental data were in very good agreement with extensive quantum mechanical conformational sampling. Altogether, we clearly showed that the pro-helical vs. pro-extended propensities start to emerge already at the level of tripeptides and can be fully developed at longer sequences. We postulate that certain short peptide sequences can be considered minimal "folding seeds". Admittedly, the inherent secondary structure propensity can be overruled by the large intramolecular interaction energies within the folded and compact protein structures. Still, the correlation of experimental and computational data presented herein suggests that the secondary structure propensity should be considered as one of the key factors that may lead to understanding the underlying physico-chemical principles of protein structure and folding from the first principles.
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Affiliation(s)
- Zuzana Osifová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2, 160 00, Praha 6 Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University Hlavova 2030 Prague 128 00 Czech Republic
| | - Tadeáš Kalvoda
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2, 160 00, Praha 6 Czech Republic
| | - Jakub Galgonek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2, 160 00, Praha 6 Czech Republic
| | - Martin Culka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2, 160 00, Praha 6 Czech Republic
| | - Jiří Vondrášek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2, 160 00, Praha 6 Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2, 160 00, Praha 6 Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2, 160 00, Praha 6 Czech Republic
| | - Valery Andrushchenko
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2, 160 00, Praha 6 Czech Republic
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2, 160 00, Praha 6 Czech Republic
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2, 160 00, Praha 6 Czech Republic
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Kuprikova N, Ondruš M, Bednárová L, Riopedre-Fernandez M, Slavětínská L, Sýkorová V, Hocek M. Superanionic DNA: enzymatic synthesis of hypermodified DNA bearing four different anionic substituents at all four nucleobases. Nucleic Acids Res 2023; 51:11428-11438. [PMID: 37870471 PMCID: PMC10681718 DOI: 10.1093/nar/gkad893] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 09/06/2023] [Accepted: 10/04/2023] [Indexed: 10/24/2023] Open
Abstract
We designed and synthesized a set of four 2'-deoxyribonucleoside 5'-O-triphosphates (dNTPs) derived from 5-substituted pyrimidines and 7-substituted 7-deazapurines bearing anionic substituents (carboxylate, sulfonate, phosphonate, and phosphate). The anion-linked dNTPs were used for enzymatic synthesis of modified and hypermodified DNA using KOD XL DNA polymerase containing one, two, three, or four modified nucleotides. The polymerase was able to synthesize even long sequences of >100 modified nucleotides in a row by primer extension (PEX). We also successfully combined two anionic and two hydrophobic dNTPs bearing phenyl and indole moieties. In PCR, the combinations of one or two modified dNTPs gave exponential amplification, while most of the combinations of three or four modified dNTPs gave only linear amplification in asymmetric PCR. The hypermodified ONs were successfully re-PCRed and sequenced by Sanger sequencing. Biophysical studies including hybridization, denaturation, CD spectroscopy and molecular modelling and dynamics suggest that the presence of anionic modifications in one strand decreases the stability of duplexes while still preserving the B-DNA conformation, whilst the DNA hypermodified in both strands adopts a different secondary structure.
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Affiliation(s)
- Natalia Kuprikova
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843 Prague 2, Czech Republic
| | - Marek Ondruš
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Miguel Riopedre-Fernandez
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Lenka Poštová Slavětínská
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Veronika Sýkorová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843 Prague 2, Czech Republic
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Inniss NL, Kozic J, Li F, Rosas-Lemus M, Minasov G, Rybáček J, Zhu Y, Pohl R, Shuvalova L, Rulíšek L, Brunzelle JS, Bednárová L, Štefek M, Kormaník JM, Andris E, Šebestík J, Li ASM, Brown PJ, Schmitz U, Saikatendu K, Chang E, Nencka R, Vedadi M, Satchell KJ. Discovery of a Druggable, Cryptic Pocket in SARS-CoV-2 nsp16 Using Allosteric Inhibitors. ACS Infect Dis 2023; 9:1918-1931. [PMID: 37728236 PMCID: PMC10961098 DOI: 10.1021/acsinfecdis.3c00203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023]
Abstract
A collaborative, open-science team undertook discovery of novel small molecule inhibitors of the SARS-CoV-2 nsp16-nsp10 2'-O-methyltransferase using a high throughput screening approach with the potential to reveal new inhibition strategies. This screen yielded compound 5a, a ligand possessing an electron-deficient double bond, as an inhibitor of SARS-CoV-2 nsp16 activity. Surprisingly, X-ray crystal structures revealed that 5a covalently binds within a previously unrecognized cryptic pocket near the S-adenosylmethionine binding cleft in a manner that prevents occupation by S-adenosylmethionine. Using a multidisciplinary approach, we examined the mechanism of binding of compound 5a to the nsp16 cryptic pocket and developed 5a derivatives that inhibited nsp16 activity and murine hepatitis virus replication in rat lung epithelial cells but proved cytotoxic to cell lines canonically used to examine SARS-CoV-2 infection. Our study reveals the druggability of this newly discovered SARS-CoV-2 nsp16 cryptic pocket, provides novel tool compounds to explore the site, and suggests a new approach for discovery of nsp16 inhibition-based pan-coronavirus therapeutics through structure-guided drug design.
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Affiliation(s)
- Nicole L. Inniss
- Department of Microbiology-Immunology and Center for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, 60611, United States
| | - Ján Kozic
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Monica Rosas-Lemus
- Department of Microbiology-Immunology and Center for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, 60611, United States
| | - George Minasov
- Department of Microbiology-Immunology and Center for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, 60611, United States
| | - Jiří Rybáček
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Yingjie Zhu
- WuXi AppTec Co., Ltd, China (Shanghai) Pilot Free Trade Zone, Shanghai, 201308, China
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Ludmilla Shuvalova
- Department of Pharmacology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, 60611, United States
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Joseph S. Brunzelle
- Northwestern Synchrotron Research Center, Life Sciences Collaborative Access Team, Northwestern University, Argonne, IL, 60439, United States
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Milan Štefek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Ján Michael Kormaník
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Erik Andris
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Jaroslav Šebestík
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Alice Shi Ming Li
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada, and Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Peter J. Brown
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Uli Schmitz
- Structural Chemistry, Gilead Pharmaceuticals, San Mateo, CA, 94404, United States
| | - Kumar Saikatendu
- Takeda Development Center Americas, Inc., San Diego, CA, 92121, United States
| | - Edcon Chang
- Takeda Development Center Americas, Inc., San Diego, CA, 92121, United States
| | - Radim Nencka
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Masoud Vedadi
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada, and Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Karla J.F. Satchell
- Department of Microbiology-Immunology and Center for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, 60611, United States
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Kaleta J, Dudič M, Ludvíková L, Liška A, Zaykov A, Rončević I, Mašát M, Bednárová L, Dron PI, Teat SJ, Michl J. Phenyl-Substituted Cibalackrot Derivatives: Synthesis, Structure, and Solution Photophysics. J Org Chem 2023. [PMID: 37219972 DOI: 10.1021/acs.joc.2c02706] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Three symmetrically and three unsymmetrically substituted cibalackrot (7,14-diphenyldiindolo[3,2,1-de:3',2',1'-ij][1,5]naphthyridine-6,13-dione, 1) dyes carrying two derivatized phenyl rings have been synthesized as candidates for molecular electronics and especially for singlet fission, a process of interest for solar energy conversion. Solution measurements provided singlet and triplet excitation energies and fluorescence yields and lifetimes; conformational properties were analyzed computationally. The molecular properties are close to ideal for singlet fission. However, crystal structures, obtained by single-crystal X-ray diffraction (XRD), are rather similar to those of the polymorphs of solid 1, in which the formation of a charge-separated state followed by intersystem crossing, complemented with excimer formation, outcompetes singlet fission. Results of calculations by the approximate SIMPLE method suggest which ones among the solid derivatives are the best candidates for singlet fission, but it appears difficult to change the crystal packing in a desirable direction. We also describe the preparation of three specifically deuteriated versions of 1, expected to help sort out the mechanism of fast intersystem crossing in its charge-separated state.
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Affiliation(s)
- Jiří Kaleta
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague, Czech Republic
| | - Miroslav Dudič
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague, Czech Republic
| | - Lucie Ludvíková
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague, Czech Republic
| | - Alan Liška
- J. Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague 8, Czech Republic
| | - Alexandr Zaykov
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague, Czech Republic
- University of Chemistry and Technology, Technicka 5, 16000 Prague 6, Czech Republic
| | - Igor Rončević
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague, Czech Republic
| | - Milan Mašát
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague, Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague, Czech Republic
| | - Paul I Dron
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague, Czech Republic
| | - Simon J Teat
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720-1460, United States
| | - Josef Michl
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague, Czech Republic
- Department of Chemistry, University of Colorado, Boulder, Colorado 80309-0215, United States
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6
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Izquierdo-García P, Fernández-García JM, Medina Rivero S, Šámal M, Rybáček J, Bednárová L, Ramírez-Barroso S, Ramírez FJ, Rodríguez R, Perles J, García-Fresnadillo D, Crassous J, Casado J, Stará IG, Martín N. Helical Bilayer Nanographenes: Impact of the Helicene Length on the Structural, Electrochemical, Photophysical, and Chiroptical Properties. J Am Chem Soc 2023; 145:11599-11610. [PMID: 37129470 DOI: 10.1021/jacs.3c01088] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Helical bilayer nanographenes (HBNGs) are chiral π-extended aromatic compounds consisting of two π-π stacked hexabenzocoronenes (HBCs) joined by a helicene, thus resembling van der Waals layered 2D materials. Herein, we compare [9]HBNG, [10]HBNG, and [11]HBNG helical bilayers endowed with [9], [10], and [11]helicenes embedded in their structure, respectively. Interestingly, the helicene length defines the overlapping degree between the two HBCs (number of benzene rings involved in π-π interactions between the two layers), being 26, 14, and 10 benzene rings, respectively, according to the X-ray analysis. Unexpectedly, the electrochemical study shows that the lesser π-extended system [9]HBNG shows the strongest electron donor character, in part by interlayer exchange resonance, and more red-shifted values of emission. Furthermore, [9]HBNG also shows exceptional chiroptical properties with the biggest values of gabs and glum (3.6 × 10-2) when compared to [10]HBNG and [11]HBNG owing to the fine alignment in the configuration of [9]HBNG between its electric and magnetic dipole transition moments. Furthermore, spectroelectrochemical studies as well as the fluorescence spectroscopy support the aforementioned experimental findings, thus confirming the strong impact of the helicene length on the properties of this new family of bilayer nanographenes.
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Affiliation(s)
- Patricia Izquierdo-García
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Jesús M Fernández-García
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Samara Medina Rivero
- Departament of Physical Chemistry, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain
- Department of Physics & Astronomy, University of Sheffield, S3 7RH Sheffield, U.K
| | - Michal Šámal
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Jiří Rybáček
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Sergio Ramírez-Barroso
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Francisco J Ramírez
- Departament of Physical Chemistry, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain
| | - Rafael Rodríguez
- Institut des Sciences Chimiques de Rennes (ISCR), UMR 6226 CNRS─Univ Rennes, 35000 Rennes, France
| | - Josefina Perles
- Laboratorio DRX Monocristal, SIdI, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - David García-Fresnadillo
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Jeanne Crassous
- Institut des Sciences Chimiques de Rennes (ISCR), UMR 6226 CNRS─Univ Rennes, 35000 Rennes, France
| | - Juan Casado
- Departament of Physical Chemistry, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain
| | - Irena G Stará
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Nazario Martín
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
- IMDEA-Nanociencia, C/Faraday, 9, Campus de Cantoblanco, 28049 Madrid, Spain
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Houska V, Ukraintsev E, Vacek J, Rybáček J, Bednárová L, Pohl R, Stará IG, Rezek B, Starý I. Helicene-based π-conjugated macrocycles: their synthesis, properties, chirality and self-assembly into molecular stripes on a graphite surface. Nanoscale 2023; 15:1542-1553. [PMID: 36383069 DOI: 10.1039/d2nr04209f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Fully aromatic helicenes are attractive building blocks for the construction of inherently chiral π-conjugated macrocyclic nanocarbons. These hitherto rare molecular architectures are envisaged to exhibit remarkable (chir)optical properties, self-assembly, charge/spin transport, induced ring current or a fascinating Möbius topology. Here the synthesis of helically chiral macrocycles that combine angular dibenzo[5]helicene units as corners and linear trans-stilbene-4,4'-diyl linkers as edges is reported. By subjecting a racemic or enantiopure divinyl derivative of dibenzo[5]helicene to olefin metathesis, which was catalysed by a 2nd generation Piers catalyst under kinetic control, a π-conjugated helicene cyclic trimer (33%) and a tetramer (22%) were obtained, which were separated by GPC. Combining racemic/asymmetric synthesis with the resolution of enantiomers/diastereomers by SFC/HPLC on a chiral column, both homochiral (+)-(M,M,M)/(-)-(P,P,P) and heterochiral (+)-(M,M,P)/(-)-(M,P,P) stereoisomers of the helicene cyclic trimer could be obtained in an enantio- and diastereomerically enriched form. The complete energy profile of their interconversion was compiled on the basis of kinetic measurements and numerical solution of the proposed kinetic model. In equilibrium, the heterochiral diastereomer predominates over the homochiral one (ca. 75 : 25 at 76 °C). π-Conjugation along a large, twisted circuit in the helicene cyclic trimer is rather disrupted, stabilising this formally antiaromatic molecule. Using an optimised PeakForce mode of ambient AFM, the self-assembly of otherwise highly mobile stereoisomers of the helicene cyclic trimer on the HOPG surface could be studied. Irrespective of the stereochemistry, strong preferences for the edge-to-edge interaction of these macrocycles were found to form very long parallel 1D molecular stripes in ordered 2D nanocrystals, a result also supported by molecular dynamics simulations. Six trityl groups, initially introduced to the macrocycle to enhance solubility, serve as a key "molecular Velcro" system in the self-assembly of macrocycles to maximise their mutual van der Waals interactions.
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Affiliation(s)
- Václav Houska
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 128 43 Prague 2, Czech Republic.
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic.
| | - Egor Ukraintsev
- Institute of Physics, Czech Academy of Sciences, Cukrovarnická 10, 162 00 Prague 6, Czech Republic
- Department of Physics, Faculty of Electrical Engineering, CTU in Prague, Technická 2, 166 27 Prague 6, Czech Republic
| | - Jaroslav Vacek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic.
| | - Jiří Rybáček
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic.
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic.
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic.
| | - Irena G Stará
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic.
| | - Bohuslav Rezek
- Department of Physics, Faculty of Electrical Engineering, CTU in Prague, Technická 2, 166 27 Prague 6, Czech Republic
| | - Ivo Starý
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic.
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8
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Sakamoto D, Gay Sánchez I, Rybáček J, Vacek J, Bednárová L, Pazderková M, Pohl R, Císařová I, Stará IG, Starý I. Cycloiridated Helicenes as Chiral Catalysts in the Asymmetric Transfer Hydrogenation of Imines. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Daisuke Sakamoto
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 542/2, Prague 166 10, Czech Republic
| | - Isabel Gay Sánchez
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 542/2, Prague 166 10, Czech Republic
| | - Jiří Rybáček
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 542/2, Prague 166 10, Czech Republic
| | - Jaroslav Vacek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 542/2, Prague 166 10, Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 542/2, Prague 166 10, Czech Republic
| | - Markéta Pazderková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 542/2, Prague 166 10, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 542/2, Prague 166 10, Czech Republic
| | - Ivana Císařová
- Department of Inorganic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030/8, Prague 128 43, Czech Republic
| | - Irena G. Stará
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 542/2, Prague 166 10, Czech Republic
| | - Ivo Starý
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 542/2, Prague 166 10, Czech Republic
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9
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Tichotová M, Ešnerová A, Tučková L, Bednárová L, Císařová I, Baszczyňski O, Procházková E. 31P NMR parameters may facilitate the stereochemical analysis of phosphorus-containing compounds. J Magn Reson 2022; 336:107149. [PMID: 35121491 DOI: 10.1016/j.jmr.2022.107149] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/19/2022] [Accepted: 01/19/2022] [Indexed: 06/14/2023]
Abstract
Conventional Nuclear Magnetic Resonance (NMR) analysis relies on H-H/C-H interactions. However, these interactions are sometimes insufficient for an accurate and precise NMR analysis. In this study, we show that 31P NMR parameters can provide critical structural insights into the stereochemistry of phosphorus-containing compounds. For this purpose, we prepared a set of model phosphorus-based proline derivatives, separated diastereoisomers, and determined their absolute configuration by single-crystal X-ray diffraction. After supplementing these results by electronic circular dichroism (ECD) spectroscopy, we combined experimental data and DFT calculations from our model compounds to perform a detailed conformational analysis, thereby determining their relative configuration. Overall, our findings establish an experimental paradigm for combining 31P NMR spectroscopy with other optical methods to facilitate the stereochemical analysis of phosphorus-containing compounds.
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Affiliation(s)
- Markéta Tichotová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 160 00 Prague, Czech Republic; Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, 116 28 Prague, Czech Republic
| | - Aneta Ešnerová
- Department of Organic Chemistry, Faculty of Science, Charles University, 116 28 Prague, Czech Republic
| | - Lucie Tučková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 160 00 Prague, Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 160 00 Prague, Czech Republic
| | - Ivana Císařová
- Department of Inorganic Chemistry, Faculty of Science, Charles University, 116 28 Prague, Czech Republic
| | - Ondřej Baszczyňski
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 160 00 Prague, Czech Republic; Department of Organic Chemistry, Faculty of Science, Charles University, 116 28 Prague, Czech Republic
| | - Eliška Procházková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 160 00 Prague, Czech Republic.
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10
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Giacobelli VG, Fujishima K, Lepšík M, Tretyachenko V, Kadavá T, Makarov M, Bednárová L, Novák P, Hlouchová K. In vitro evolution reveals non-cationic protein-RNA interaction mediated by metal ions. Mol Biol Evol 2022; 39:6524634. [PMID: 35137196 PMCID: PMC8892947 DOI: 10.1093/molbev/msac032] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
RNA–peptide/protein interactions have been of utmost importance to life since its earliest forms, reaching even before the last universal common ancestor (LUCA). However, the ancient molecular mechanisms behind this key biological interaction remain enigmatic because extant RNA–protein interactions rely heavily on positively charged and aromatic amino acids that were absent (or heavily under-represented) in the early pre-LUCA evolutionary period. Here, an RNA-binding variant of the ribosomal uL11 C-terminal domain was selected from an approximately 1010 library of partially randomized sequences, all composed of ten prebiotically plausible canonical amino acids. The selected variant binds to the cognate RNA with a similar overall affinity although it is less structured in the unbound form than the wild-type protein domain. The variant complex association and dissociation are both slower than for the wild-type, implying different mechanistic processes involved. The profile of the wild-type and mutant complex stabilities along with molecular dynamics simulations uncovers qualitative differences in the interaction modes. In the absence of positively charged and aromatic residues, the mutant uL11 domain uses ion bridging (K+/Mg2+) interactions between the RNA sugar-phosphate backbone and glutamic acid residues as an alternative source of stabilization. This study presents experimental support to provide a new perspective on how early protein–RNA interactions evolved, where the lack of aromatic/basic residues may have been compensated by acidic residues plus metal ions.
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Affiliation(s)
- Valerio G Giacobelli
- Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Prague, 12800, Czech Republic
| | - Kosuke Fujishima
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, 1528550, Japan.,Graduate School of Media and Governance, Keio University, Fujisawa, 2520882, Japan
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, 16610, Czech Republic
| | - Vyacheslav Tretyachenko
- Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Prague, 12800, Czech Republic
| | - Tereza Kadavá
- Department of Biochemistry, Faculty of Science, Charles University, Prague, 12800, Czech Republic
| | - Mikhail Makarov
- Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Prague, 12800, Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, 16610, Czech Republic
| | - Petr Novák
- Institute of Microbiology, The Czech Academy of Sciences, Vestec, 25250, Czech Republic
| | - Klára Hlouchová
- Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Prague, 12800, Czech Republic.,Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, 16610, Czech Republic
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11
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Stary I, Palata O, Andronova A, Šámal M, Nejedlý J, Rybáček J, Buděšínský M, Bednárová L, Pospíšil L, Císařová I, Stará IG. Synthesis of (Di)thiahelicenes and Dithiophenohelicenes by [2+2+2] Cycloisomerisation of Alkynes. Helv Chim Acta 2022. [DOI: 10.1002/hlca.202100225] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Ivo Stary
- Institute of Organic Chemistry and Biochemistry Organic Chemistry Flemingovo n. 2 166 10 Prague 6 CZECH REPUBLIC
| | - Ondřej Palata
- Ústav organické chemie a biochemie Akademie věd České republiky: Ustav organicke chemie a biochemie Akademie ved Ceske republiky Chemistry CZECH REPUBLIC
| | - Angelina Andronova
- Ústav organické chemie a biochemie Akademie věd České republiky: Ustav organicke chemie a biochemie Akademie ved Ceske republiky Chemistry CZECH REPUBLIC
| | - Michal Šámal
- Ústav organické chemie a biochemie Akademie věd České republiky: Ustav organicke chemie a biochemie Akademie ved Ceske republiky Chemistry CZECH REPUBLIC
| | - Jindřich Nejedlý
- Ústav organické chemie a biochemie Akademie věd České republiky: Ustav organicke chemie a biochemie Akademie ved Ceske republiky Chemistry CZECH REPUBLIC
| | - Jiří Rybáček
- Ústav organické chemie a biochemie Akademie věd České republiky: Ustav organicke chemie a biochemie Akademie ved Ceske republiky Chemistry CZECH REPUBLIC
| | - Miloš Buděšínský
- Ústav organické chemie a biochemie Akademie věd České republiky: Ustav organicke chemie a biochemie Akademie ved Ceske republiky Chemistry CZECH REPUBLIC
| | - Lucie Bednárová
- Ústav organické chemie a biochemie Akademie věd České republiky: Ustav organicke chemie a biochemie Akademie ved Ceske republiky Chemistry CZECH REPUBLIC
| | - Lubomír Pospíšil
- Ústav organické chemie a biochemie Akademie věd České republiky: Ustav organicke chemie a biochemie Akademie ved Ceske republiky Chemistry CZECH REPUBLIC
| | - Ivana Císařová
- Charles University Faculty of Science: Univerzita Karlova Prirodovedecka fakulta Inorganic chemistry CZECH REPUBLIC
| | - Irena G. Stará
- Ústav organické chemie a biochemie Akademie věd České republiky: Ustav organicke chemie a biochemie Akademie ved Ceske republiky Chemistry CZECH REPUBLIC
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12
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Šámal M, Rybáček J, Holec J, Hanus J, Vacek J, Buděšínský M, Bednárová L, Fiedler P, Slušná MŠ, Stará IG, Starý I. Push–pull amino-nitro helicenes: synthesis, (chir)optical properties and self-assembly into thin films. Chem Commun (Camb) 2022; 58:12732-12735. [DOI: 10.1039/d2cc03892g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of regioisomeric push–pull amino-nitro [6]helicenes and a related [7]helicene derivative were prepared and their racemates resolved into enantiomers.
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Affiliation(s)
- Michal Šámal
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Jiří Rybáček
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Jan Holec
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Jan Hanus
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Jaroslav Vacek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Miloš Buděšínský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Pavel Fiedler
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Michaela Šrámová Slušná
- Institute of Inorganic Chemistry, Czech Academy of Sciences, Husinec-Řež 1001, 250 68 Řež, Czech Republic
| | - Irena G. Stará
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Ivo Starý
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
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13
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Cadart T, Nečas D, Kaiser RP, Favereau L, Císařová I, Gyepes R, Hodačová J, Kalíková K, Bednárová L, Crassous J, Kotora M. Cover Feature: Rhodium‐Catalyzed Enantioselective Synthesis of Highly Fluorescent and CPL‐Active Dispiroindeno[2,1‐
c
]fluorenes (Chem. Eur. J. 44/2021). Chemistry 2021. [DOI: 10.1002/chem.202102392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Timothée Cadart
- Department of Organic Chemistry Faculty of Science Charles University Hlavova 8 128 43 Praha 2 Czech Republic
| | - David Nečas
- Department of Organic Chemistry Faculty of Science Charles University Hlavova 8 128 43 Praha 2 Czech Republic
| | - Reinhard P. Kaiser
- Department of Organic Chemistry Faculty of Science Charles University Hlavova 8 128 43 Praha 2 Czech Republic
| | | | - Ivana Císařová
- Department of Inorganic Chemistry Faculty of Science Charles University Hlavova 8 128 43 Praha 2 Czech Republic
| | - Róbert Gyepes
- Academy of Sciences of the Czech Republic J. Heyrovský Institute of Physical Chemistry, v.v.i. Dolejškova 2155/3 182 23 Praha 8 Czech Republic
| | - Jana Hodačová
- Department of Organic Chemistry University of Chemistry and Technology Technická 5 166 28 Praha 6 Czech Republic
| | - Květa Kalíková
- Department of Physical and Macromolecular Chemistry Faculty of Science Charles University Hlavova 8 128 43 Praha 2 Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 166 10 Prague 6 Czech Republic
| | - Jeanne Crassous
- Université de Rennes CNRS, ISCR-UMR 6226 35000 Rennes France
| | - Martin Kotora
- Department of Organic Chemistry Faculty of Science Charles University Hlavova 8 128 43 Praha 2 Czech Republic
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14
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Cadart T, Nečas D, Kaiser RP, Favereau L, Císařová I, Gyepes R, Hodačová J, Kalíková K, Bednárová L, Crassous J, Kotora M. Rhodium-Catalyzed Enantioselective Synthesis of Highly Fluorescent and CPL-Active Dispiroindeno[2,1-c]fluorenes. Chemistry 2021; 27:11279-11284. [PMID: 33830567 DOI: 10.1002/chem.202100759] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Indexed: 12/12/2022]
Abstract
The enantioselective synthesis of chiral [7]-helical dispirodihydro[2,1-c]indenofluorenes (DSF-IFs) was achieved for the first time in good yields with high er values (er up to 99 : 1). The crucial step of the whole reaction sequence was the enantioselective intramolecular [2+2+2] cycloaddition of tethered triynediols to indenofluorenediols, which was catalyzed by a Rh/SEGPHOS® complex. Further transformations led to the corresponding DSF-IFs. The prepared helically chiral DSF-IFs combine circularly polarized luminescence (CPL) activity (glum =∼10-3 ) with exceptionally high fluorescence quantum yields (up to Φlum =0.97).
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Affiliation(s)
- Timothée Cadart
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, 128 43, Praha 2, Czech Republic
| | - David Nečas
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, 128 43, Praha 2, Czech Republic
| | - Reinhard P Kaiser
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, 128 43, Praha 2, Czech Republic
| | - Ludovic Favereau
- Université de Rennes, CNRS, ISCR-UMR 6226, 35000, Rennes, France
| | - Ivana Císařová
- Department of Inorganic Chemistry, Faculty of Science, Charles University, Hlavova 8, 128 43, Praha 2, Czech Republic
| | - Róbert Gyepes
- Academy of Sciences of the Czech Republic, J. Heyrovský Institute of Physical Chemistry, v.v.i., Dolejškova 2155/3, 182 23, Praha 8, Czech Republic
| | - Jana Hodačová
- Department of Organic Chemistry, University of Chemistry and Technology, Technická 5, 166 28, Praha 6, Czech Republic
| | - Květa Kalíková
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Hlavova 8, 128 43, Praha 2, Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 166 10, Prague 6, Czech Republic
| | - Jeanne Crassous
- Université de Rennes, CNRS, ISCR-UMR 6226, 35000, Rennes, France
| | - Martin Kotora
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, 128 43, Praha 2, Czech Republic
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15
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Makarov M, Meng J, Tretyachenko V, Srb P, Březinová A, Giacobelli VG, Bednárová L, Vondrášek J, Dunker AK, Hlouchová K. Enzyme catalysis prior to aromatic residues: Reverse engineering of a dephospho-CoA kinase. Protein Sci 2021; 30:1022-1034. [PMID: 33739538 PMCID: PMC8040869 DOI: 10.1002/pro.4068] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 03/12/2021] [Accepted: 03/13/2021] [Indexed: 11/07/2022]
Abstract
The wide variety of protein structures and functions results from the diverse properties of the 20 canonical amino acids. The generally accepted hypothesis is that early protein evolution was associated with enrichment of a primordial alphabet, thereby enabling increased protein catalytic efficiencies and functional diversification. Aromatic amino acids were likely among the last additions to genetic code. The main objective of this study was to test whether enzyme catalysis can occur without the aromatic residues (aromatics) by studying the structure and function of dephospho-CoA kinase (DPCK) following aromatic residue depletion. We designed two variants of a putative DPCK from Aquifex aeolicus by substituting (a) Tyr, Phe and Trp or (b) all aromatics (including His). Their structural characterization indicates that substituting the aromatics does not markedly alter their secondary structures but does significantly loosen their side chain packing and increase their sizes. Both variants still possess ATPase activity, although with 150-300 times lower efficiency in comparison with the wild-type phosphotransferase activity. The transfer of the phosphate group to the dephospho-CoA substrate becomes heavily uncoupled and only the His-containing variant is still able to perform the phosphotransferase reaction. These data support the hypothesis that proteins in the early stages of life could support catalytic activities, albeit with low efficiencies. An observed significant contraction upon ligand binding is likely important for appropriate organization of the active site. Formation of firm hydrophobic cores, which enable the assembly of stably structured active sites, is suggested to provide a selective advantage for adding the aromatic residues.
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Affiliation(s)
- Mikhail Makarov
- Department of Cell Biology, Faculty of ScienceCharles University, BIOCEVPragueCzech Republic
- Department of Biochemistry, Faculty of ScienceCharles UniversityPragueCzech Republic
| | - Jingwei Meng
- Department of Biochemistry and Molecular Biology, Center for Computational Biology and BioinformaticsIndiana University School of MedicineIndianapolisIndianaUSA
| | - Vyacheslav Tretyachenko
- Department of Cell Biology, Faculty of ScienceCharles University, BIOCEVPragueCzech Republic
- Department of Biochemistry, Faculty of ScienceCharles UniversityPragueCzech Republic
| | - Pavel Srb
- Institute of Organic Chemistry and Biochemistry, IOCB Research Centre & Gilead Sciences, Academy of Sciences of the Czech RepublicPragueCzech Republic
| | - Anna Březinová
- Proteomics Core Facility, BIOCEV, Faculty of Science, Charles UniversityPragueCzech Republic
| | | | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry, IOCB Research Centre & Gilead Sciences, Academy of Sciences of the Czech RepublicPragueCzech Republic
| | - Jiří Vondrášek
- Institute of Organic Chemistry and Biochemistry, IOCB Research Centre & Gilead Sciences, Academy of Sciences of the Czech RepublicPragueCzech Republic
| | - A. Keith Dunker
- Department of Biochemistry and Molecular Biology, Center for Computational Biology and BioinformaticsIndiana University School of MedicineIndianapolisIndianaUSA
| | - Klára Hlouchová
- Department of Cell Biology, Faculty of ScienceCharles University, BIOCEVPragueCzech Republic
- Institute of Organic Chemistry and Biochemistry, IOCB Research Centre & Gilead Sciences, Academy of Sciences of the Czech RepublicPragueCzech Republic
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16
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Özdemir Z, Šaman D, Bertula K, Lahtinen M, Bednárová L, Pazderková M, Rárová L, Wimmer Z. Rapid Self-Healing and Thixotropic Organogelation of Amphiphilic Oleanolic Acid-Spermine Conjugates. Langmuir 2021; 37:2693-2706. [PMID: 33595317 DOI: 10.1021/acs.langmuir.0c03335] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Natural and abundant plant triterpenoids are attractive starting materials for the synthesis of conformationally rigid and chiral building blocks for functional soft materials. Here, we report the rational design of three oleanolic acid-triazole-spermine conjugates, containing either one or two spermine units in the target molecules, using the Cu(I)-catalyzed Huisgen 1,3-dipolar cycloaddition reaction. The resulting amphiphile-like molecules 2 and 3, bearing just one spermine unit in the respective molecules, self-assemble into highly entangled fibrous networks leading to gelation at a concentration as low as 0.5% in alcoholic solvents. Using step-strain rheological measurements, we show rapid self-recovery (up to 96% of the initial storage modulus) and sol ⇔ gel transition under several cycles. Interestingly, rheological flow curves reveal the thixotropic behavior of the gels. To the best of our knowledge, this kind of behavior was not shown in the literature before, neither for a triterpenoid nor for its derivatives. Conjugate 4, having a bolaamphiphile-like structure, was found to be a nongelator. Our results indicate that the position and number of spermine units alter the gelation properties, gel strength, and their self-assembly behavior. Preliminary cytotoxicity studies of the target compounds 2-4 in four human cancer cell lines suggest that the position and number of spermine units affect the biological activity. Our results also encourage exploring other triterpenoids and their derivatives as sustainable, renewable, and biologically active building blocks for multifunctional soft organic nanomaterials.
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Affiliation(s)
- Zulal Özdemir
- Department of Chemistry of Natural Compounds, University of Chemistry and Technology in Prague, Technická 5, 16028 Prague 6, Czech Republic
- Isotope Laboratory, Institute of Experimental Botany of the Czech Academy of Sciences, Vídeňská 1083, 14220 Prague 4, Czech Republic
| | - David Šaman
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 16610 Prague 6, Czech Republic
| | - Kia Bertula
- Department of Applied Physics, Aalto University, Puumiehenkuja 2, FI-02150 Espoo, Finland
| | - Manu Lahtinen
- Department of Chemistry, University of Jyväskylä, P.O. Box 35, FI-40014 Jyväskylä, Finland
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 16610 Prague 6, Czech Republic
| | - Markéta Pazderková
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 16610 Prague 6, Czech Republic
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, 12116 Prague 2, Czech Republic
| | - Lucie Rárová
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences, and Faculty of Science, Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic
| | - Zdeněk Wimmer
- Department of Chemistry of Natural Compounds, University of Chemistry and Technology in Prague, Technická 5, 16028 Prague 6, Czech Republic
- Isotope Laboratory, Institute of Experimental Botany of the Czech Academy of Sciences, Vídeňská 1083, 14220 Prague 4, Czech Republic
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17
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Ondruš M, Sýkorová V, Bednárová L, Pohl R, Hocek M. Enzymatic synthesis of hypermodified DNA polymers for sequence-specific display of four different hydrophobic groups. Nucleic Acids Res 2020; 48:11982-11993. [PMID: 33152081 PMCID: PMC7708046 DOI: 10.1093/nar/gkaa999] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/08/2020] [Accepted: 10/13/2020] [Indexed: 12/13/2022] Open
Abstract
A set of modified 2′-deoxyribonucleoside triphosphates (dNTPs) bearing a linear or branched alkane, indole or phenyl group linked through ethynyl or alkyl spacer were synthesized and used as substrates for polymerase synthesis of hypermodified DNA by primer extension (PEX). Using the alkyl-linked dNTPs, the polymerase synthesized up to 22-mer fully modified oligonucleotide (ON), whereas using the ethynyl-linked dNTPs, the enzyme was able to synthesize even long sequences of >100 modified nucleotides in a row. In PCR, the combinations of all four modified dNTPs showed only linear amplification. Asymmetric PCR or PEX with separation or digestion of the template strand can be used for synthesis of hypermodified single-stranded ONs, which are monodispersed polymers displaying four different substituents on DNA backbone in sequence-specific manner. The fully modified ONs hybridized with complementary strands and modified DNA duplexes were found to exist in B-type conformation (B- or C-DNA) according to CD spectral analysis. The modified DNA can be replicated with high fidelity to natural DNA through PCR and sequenced. Therefore, this approach has a promising potential in generation and selection of hypermodified aptamers and other functional polymers.
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Affiliation(s)
- Marek Ondruš
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843 Prague 2, Czech Republic
| | - Veronika Sýkorová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843 Prague 2, Czech Republic
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18
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Sundar MS, Klepetářová B, Bednárová L, Muller G. Synthesis, Chiral Resolution, and Optical Properties of 2,18‐Dihydoxy‐5,10,15‐trioxa[9]helicene. European J Org Chem 2020. [DOI: 10.1002/ejoc.202001177] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- M. Shyam Sundar
- The Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
| | - Blanka Klepetářová
- The Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
| | - Lucie Bednárová
- The Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
| | - Gilles Muller
- Department of Chemistry San José State University One Washington Square San José, California 95192-0101 USA
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19
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Kaufman F, Dostálková A, Pekárek L, Thanh TD, Kapisheva M, Hadravová R, Bednárová L, Novotný R, Křížová I, Černý J, Grubhoffer L, Ruml T, Hrabal R, Rumlová M. Characterization and in vitro assembly of tick-borne encephalitis virus C protein. FEBS Lett 2020; 594:1989-2004. [PMID: 32510601 DOI: 10.1002/1873-3468.13857] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/12/2020] [Accepted: 05/17/2020] [Indexed: 01/10/2023]
Abstract
Tick-borne encephalitis virus (TBEV), a member of flaviviruses, represents a serious health threat by causing human encephalitis mainly in central and eastern Europe, Russia, and northeastern Asia. As no specific therapy is available, there is an urgent need to understand all steps of the TBEV replication cycle at the molecular level. One of the critical events is the packaging of flaviviral genomic RNA by TBEV C protein to form a nucleocapsid. We purified recombinant TBEV C protein and used a combination of physical-chemical approaches, such as size-exclusion chromatography, circular dichroism, NMR spectroscopies, and transmission electron microscopy, to analyze its structural stability and its ability to dimerize/oligomerize. We compared the ability of TBEV C protein to assemble in vitro into a nucleocapsid-like structure with that of dengue C protein.
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Affiliation(s)
- Filip Kaufman
- Department of Biotechnology, University of Chemistry and Technology, Prague, Prague, Czech Republic
| | - Alžběta Dostálková
- Department of Biotechnology, University of Chemistry and Technology, Prague, Prague, Czech Republic
| | - Lukáš Pekárek
- Department of Biotechnology, University of Chemistry and Technology, Prague, Prague, Czech Republic
| | - Tung Dinh Thanh
- Department of Biotechnology, University of Chemistry and Technology, Prague, Prague, Czech Republic
| | - Marina Kapisheva
- Department of Biotechnology, University of Chemistry and Technology, Prague, Prague, Czech Republic
| | - Romana Hadravová
- Department of Biotechnology, University of Chemistry and Technology, Prague, Prague, Czech Republic.,Institute of Organic Chemistry and Biochemistry (IOCB) Research Centre & Gilead Sciences, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry (IOCB) Research Centre & Gilead Sciences, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Radim Novotný
- Department of Biotechnology, University of Chemistry and Technology, Prague, Prague, Czech Republic.,NMR Laboratory, University of Chemistry and Technology, Prague, Prague, Czech Republic
| | - Ivana Křížová
- Department of Biotechnology, University of Chemistry and Technology, Prague, Prague, Czech Republic
| | - Jiří Černý
- Faculty of Tropical AgriSciences, Czech University of Life Sciences, Prague, Prague, Czech Republic
| | - Libor Grubhoffer
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Tomáš Ruml
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Prague, Czech Republic
| | - Richard Hrabal
- NMR Laboratory, University of Chemistry and Technology, Prague, Prague, Czech Republic
| | - Michaela Rumlová
- Department of Biotechnology, University of Chemistry and Technology, Prague, Prague, Czech Republic
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20
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Nejedlý J, Šámal M, Rybáček J, Sánchez IG, Houska V, Warzecha T, Vacek J, Sieger L, Buděšínský M, Bednárová L, Fiedler P, Císařová I, Starý I, Stará IG. Synthesis of Racemic, Diastereopure, and Enantiopure Carba- or Oxa[5]-, [6]-, [7]-, and -[19]helicene (Di)thiol Derivatives. J Org Chem 2020; 85:248-276. [PMID: 31808692 DOI: 10.1021/acs.joc.9b02965] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A series of carba- or oxa[5]-, [6]-, [7]-, and -[19]helicene (di)thiols was prepared. The Miyazaki-Newman-Kwart rearrangement of (dimethylcarbamothioyl)oxy (oxa)helicenes in a flow reactor or nucleophilic substitution of dichloro (oxa)helicenes with alkanethiolates were used in the sulfanylation step. Despite the high temperatures employed in this key step, no conformational scrambling was observed during the asymmetric synthesis of the diastereo- and enantiopure oxahelicenes. Single-molecule conductivity of the longest oxa[19]helicene dithiol derivative was studied by the scanning tunneling microscopy break-junction method.
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Affiliation(s)
- Jindřich Nejedlý
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences , Flemingovo nám. 2 , 166 10 Prague 6 , Czech Republic.,Department of Organic Chemistry, Faculty of Science , Charles University in Prague , Hlavova 2030/8 , 128 43 Prague 2 , Czech Republic
| | - Michal Šámal
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences , Flemingovo nám. 2 , 166 10 Prague 6 , Czech Republic
| | - Jiří Rybáček
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences , Flemingovo nám. 2 , 166 10 Prague 6 , Czech Republic
| | - Isabel Gay Sánchez
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences , Flemingovo nám. 2 , 166 10 Prague 6 , Czech Republic.,Department of Organic Chemistry, Faculty of Science , Charles University in Prague , Hlavova 2030/8 , 128 43 Prague 2 , Czech Republic
| | - Václav Houska
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences , Flemingovo nám. 2 , 166 10 Prague 6 , Czech Republic.,Department of Physical and Macromolecular Chemistry, Faculty of Science , Charles University in Prague , Hlavova 2030/8 , 128 43 Prague 2 , Czech Republic
| | - Tomáš Warzecha
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences , Flemingovo nám. 2 , 166 10 Prague 6 , Czech Republic
| | - Jaroslav Vacek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences , Flemingovo nám. 2 , 166 10 Prague 6 , Czech Republic
| | - Ladislav Sieger
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences , Flemingovo nám. 2 , 166 10 Prague 6 , Czech Republic.,Department of Physics, Faculty of Electrical Engineering , CTU in Prague , Technická 2 , 166 27 Prague 6 , Czech Republic
| | - Miloš Buděšínský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences , Flemingovo nám. 2 , 166 10 Prague 6 , Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences , Flemingovo nám. 2 , 166 10 Prague 6 , Czech Republic
| | - Pavel Fiedler
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences , Flemingovo nám. 2 , 166 10 Prague 6 , Czech Republic
| | - Ivana Císařová
- Department of Inorganic Chemistry, Faculty of Science , Charles University in Prague , Hlavova 2030/8 , 128 43 Prague 2 , Czech Republic
| | - Ivo Starý
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences , Flemingovo nám. 2 , 166 10 Prague 6 , Czech Republic
| | - Irena G Stará
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences , Flemingovo nám. 2 , 166 10 Prague 6 , Czech Republic
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21
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Holec J, Rybáček J, Vacek J, Karras M, Bednárová L, Buděšínský M, Slušná M, Holý P, Schmidt B, Stará IG, Starý I. Chirality‐Controlled Self‐Assembly of Amphiphilic Dibenzo[6]helicenes into Langmuir–Blodgett Thin Films. Chemistry 2019. [DOI: 10.1002/chem.201903286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jan Holec
- Institute of Organic Chemistry and BiochemistryCzech Academy of Sciences Flemingovo nám. 2 166 10 Prague 6 Czech Republic
- Department of Organic ChemistryUniversity of Chemistry and Technology, Prague Technická 5 166 28 Prague 6 Czech Republic
| | - Jiří Rybáček
- Institute of Organic Chemistry and BiochemistryCzech Academy of Sciences Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Jaroslav Vacek
- Institute of Organic Chemistry and BiochemistryCzech Academy of Sciences Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Manfred Karras
- Institute of Organic Chemistry and BiochemistryCzech Academy of Sciences Flemingovo nám. 2 166 10 Prague 6 Czech Republic
- Institut für ChemieUniversitaet Potsdam Karl-Liebknecht-Straße 24–25 14476 Potsdam-Golm Germany
| | - Lucie Bednárová
- Institute of Organic Chemistry and BiochemistryCzech Academy of Sciences Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Miloš Buděšínský
- Institute of Organic Chemistry and BiochemistryCzech Academy of Sciences Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Michaela Slušná
- Institute of Inorganic ChemistryCzech Academy of Sciences Husinec-Řež 1001 250 68 Řež Czech Republic
| | - Petr Holý
- Institute of Organic Chemistry and BiochemistryCzech Academy of Sciences Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Bernd Schmidt
- Institut für ChemieUniversitaet Potsdam Karl-Liebknecht-Straße 24–25 14476 Potsdam-Golm Germany
| | - Irena G. Stará
- Institute of Organic Chemistry and BiochemistryCzech Academy of Sciences Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Ivo Starý
- Institute of Organic Chemistry and BiochemistryCzech Academy of Sciences Flemingovo nám. 2 166 10 Prague 6 Czech Republic
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22
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Holec J, Rybáček J, Vacek J, Karras M, Bednárová L, Buděšínský M, Slušná M, Holý P, Schmidt B, Stará IG, Starý I. Front Cover: Chirality‐Controlled Self‐Assembly of Amphiphilic Dibenzo[6]helicenes into Langmuir–Blodgett Thin Films (Chem. Eur. J. 49/2019). Chemistry 2019. [DOI: 10.1002/chem.201903285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jan Holec
- Institute of Organic Chemistry and BiochemistryCzech Academy of Sciences Flemingovo nám. 2 166 10 Prague 6 Czech Republic
- Department of Organic ChemistryUniversity of Chemistry and Technology, Prague Technická 5 166 28 Prague 6 Czech Republic
| | - Jiří Rybáček
- Institute of Organic Chemistry and BiochemistryCzech Academy of Sciences Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Jaroslav Vacek
- Institute of Organic Chemistry and BiochemistryCzech Academy of Sciences Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Manfred Karras
- Institute of Organic Chemistry and BiochemistryCzech Academy of Sciences Flemingovo nám. 2 166 10 Prague 6 Czech Republic
- Institut für ChemieUniversitaet Potsdam Karl-Liebknecht-Straße 24–25 14476 Potsdam-Golm Germany
| | - Lucie Bednárová
- Institute of Organic Chemistry and BiochemistryCzech Academy of Sciences Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Miloš Buděšínský
- Institute of Organic Chemistry and BiochemistryCzech Academy of Sciences Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Michaela Slušná
- Institute of Inorganic ChemistryCzech Academy of Sciences Husinec-Řež 1001 250 68 Řež Czech Republic
| | - Petr Holý
- Institute of Organic Chemistry and BiochemistryCzech Academy of Sciences Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Bernd Schmidt
- Institut für ChemieUniversitaet Potsdam Karl-Liebknecht-Straße 24–25 14476 Potsdam-Golm Germany
| | - Irena G. Stará
- Institute of Organic Chemistry and BiochemistryCzech Academy of Sciences Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Ivo Starý
- Institute of Organic Chemistry and BiochemistryCzech Academy of Sciences Flemingovo nám. 2 166 10 Prague 6 Czech Republic
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23
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Novotná V, Hamplová V, Lejček L, Pociecha D, Cigl M, Fekete L, Glogarová M, Bednárová L, Majewski PW, Gorecka E. Organic nanotubes created from mesogenic derivatives. Nanoscale Adv 2019; 1:2835-2839. [PMID: 36133609 PMCID: PMC9418705 DOI: 10.1039/c9na00175a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 06/15/2019] [Indexed: 06/16/2023]
Abstract
A facile route to prepare nanotubes from rod-like mesogens dissolved in typical organic solvents is reported. For selected types of chiral rod-like molecules, nanotubes were formed from both enantiomers and racemic mixtures by slow evaporation from solution, regardless of the solvent, concentration or deposition type. The obtained supramolecular assemblies were studied using AFM, TEM and SEM techniques, and other experimental techniques (IR, UV-Vis spectroscopy and X-ray diffraction) were also applied. The difference in the surface tension at opposite crystallite surfaces is suggested as a possible mechanism for nanotube nucleation. We propose a quite new rolling-up mechanism related to the surface tension difference at opposite crystallite surfaces.
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Affiliation(s)
- Vladimíra Novotná
- Institute of Physics of the Czech Academy of Sciences Na Slovance 2 CZ-182 21 Prague 8 Czech Republic +420286890527 +420266053111
| | - Věra Hamplová
- Institute of Physics of the Czech Academy of Sciences Na Slovance 2 CZ-182 21 Prague 8 Czech Republic +420286890527 +420266053111
| | - Lubor Lejček
- Institute of Physics of the Czech Academy of Sciences Na Slovance 2 CZ-182 21 Prague 8 Czech Republic +420286890527 +420266053111
| | - Damian Pociecha
- Faculty of Chemistry, University of Warsaw ul. Zwirki i Wigury 101 02-089 Warsaw Poland +48228221075
| | - Martin Cigl
- Institute of Physics of the Czech Academy of Sciences Na Slovance 2 CZ-182 21 Prague 8 Czech Republic +420286890527 +420266053111
| | - Ladislav Fekete
- Institute of Physics of the Czech Academy of Sciences Na Slovance 2 CZ-182 21 Prague 8 Czech Republic +420286890527 +420266053111
| | - Milada Glogarová
- Institute of Physics of the Czech Academy of Sciences Na Slovance 2 CZ-182 21 Prague 8 Czech Republic +420286890527 +420266053111
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry of the CAS Flemingovo n. 2,166 10 Prague 6 CZ-182 21 Prague 6 Czech Republic
| | - Pawel W Majewski
- Faculty of Chemistry, University of Warsaw ul. Zwirki i Wigury 101 02-089 Warsaw Poland +48228221075
| | - Ewa Gorecka
- Faculty of Chemistry, University of Warsaw ul. Zwirki i Wigury 101 02-089 Warsaw Poland +48228221075
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24
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Holec J, Rybáček J, Vacek J, Karras M, Bednárová L, Buděšínský M, Slušná M, Holý P, Schmidt B, Stará IG, Starý I. Chirality‐Controlled Self‐Assembly of Amphiphilic Dibenzo[6]helicenes into Langmuir–Blodgett Thin Films. Chemistry 2019; 25:11494-11502. [DOI: 10.1002/chem.201901695] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Indexed: 02/01/2023]
Affiliation(s)
- Jan Holec
- Institute of Organic Chemistry and BiochemistryCzech Academy of Sciences Flemingovo nám. 2 166 10 Prague 6 Czech Republic
- Department of Organic ChemistryUniversity of Chemistry and Technology, Prague Technická 5 166 28 Prague 6 Czech Republic
| | - Jiří Rybáček
- Institute of Organic Chemistry and BiochemistryCzech Academy of Sciences Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Jaroslav Vacek
- Institute of Organic Chemistry and BiochemistryCzech Academy of Sciences Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Manfred Karras
- Institute of Organic Chemistry and BiochemistryCzech Academy of Sciences Flemingovo nám. 2 166 10 Prague 6 Czech Republic
- Institut für ChemieUniversitaet Potsdam Karl-Liebknecht-Straße 24–25 14476 Potsdam-Golm Germany
| | - Lucie Bednárová
- Institute of Organic Chemistry and BiochemistryCzech Academy of Sciences Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Miloš Buděšínský
- Institute of Organic Chemistry and BiochemistryCzech Academy of Sciences Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Michaela Slušná
- Institute of Inorganic ChemistryCzech Academy of Sciences Husinec-Řež 1001 250 68 Řež Czech Republic
| | - Petr Holý
- Institute of Organic Chemistry and BiochemistryCzech Academy of Sciences Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Bernd Schmidt
- Institut für ChemieUniversitaet Potsdam Karl-Liebknecht-Straße 24–25 14476 Potsdam-Golm Germany
| | - Irena G. Stará
- Institute of Organic Chemistry and BiochemistryCzech Academy of Sciences Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Ivo Starý
- Institute of Organic Chemistry and BiochemistryCzech Academy of Sciences Flemingovo nám. 2 166 10 Prague 6 Czech Republic
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25
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Rončević I, Jirásek M, Severa L, Reyes‐Gutierrez PE, Teplý F, Bednárová L, Hromadová M, Pospíšil L. Front Cover: Chiroptical Redox Switching of Tetra‐Cationic Derivatives of Azoniahelicenes (ChemElectroChem 12/2019). ChemElectroChem 2019. [DOI: 10.1002/celc.201900762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Igor Rončević
- Department of Organic SynthesisInstitute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nám. 2 Prague 6 Czech Rep
| | - Michael Jirásek
- Department of Organic SynthesisInstitute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nám. 2 Prague 6 Czech Rep
| | - Lukáš Severa
- Department of Organic SynthesisInstitute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nám. 2 Prague 6 Czech Rep
| | - Paul Eduardo Reyes‐Gutierrez
- Department of Organic SynthesisInstitute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nám. 2 Prague 6 Czech Rep
| | - Filip Teplý
- Department of Organic SynthesisInstitute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nám. 2 Prague 6 Czech Rep
| | - Lucie Bednárová
- Department of Organic SynthesisInstitute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nám. 2 Prague 6 Czech Rep
| | - Magdaléna Hromadová
- Department of Electrochemistry at NanoscaleJ. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Dolejškova 3 18223 Prague Czech Rep
| | - Lubomír Pospíšil
- Department of Organic SynthesisInstitute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nám. 2 Prague 6 Czech Rep
- Department of Electrochemistry at NanoscaleJ. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Dolejškova 3 18223 Prague Czech Rep
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26
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Rončević I, Jirásek M, Severa L, Reyes‐Gutierrez PE, Teplý F, Bednárová L, Hromadová M, Pospíšil L. Chiroptical Redox Switching of Tetra‐Cationic Derivatives of Azoniahelicenes. ChemElectroChem 2019. [DOI: 10.1002/celc.201900761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Igor Rončević
- Department of Organic SynthesisInstitute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nám. 2 Prague 6 Czech Rep
| | - Michael Jirásek
- Department of Organic SynthesisInstitute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nám. 2 Prague 6 Czech Rep
| | - Lukáš Severa
- Department of Organic SynthesisInstitute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nám. 2 Prague 6 Czech Rep
| | - Paul E. Reyes‐Gutierrez
- Department of Organic SynthesisInstitute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nám. 2 Prague 6 Czech Rep
| | - Filip Teplý
- Department of Organic SynthesisInstitute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nám. 2 Prague 6 Czech Rep
| | - Lucie Bednárová
- Department of Organic SynthesisInstitute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nám. 2 Prague 6 Czech Rep
| | - Magdaléna Hromadová
- Department of Electrochemistry at NanoscaleJ. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Dolejškova 3 18223 Prague Czech Rep
| | - Lubomír Pospíšil
- Department of Organic SynthesisInstitute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nám. 2 Prague 6 Czech Rep
- Department of Electrochemistry at NanoscaleJ. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Dolejškova 3 18223 Prague Czech Rep
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27
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Volejníková A, Melicherčík P, Nešuta O, Vaňková E, Bednárová L, Rybáček J, Čeřovský V. Antimicrobial peptides prevent bacterial biofilm formation on the surface of polymethylmethacrylate bone cement. J Med Microbiol 2019; 68:961-972. [PMID: 31107198 DOI: 10.1099/jmm.0.001000] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
PURPOSE Antibiotic-loaded polymethylmethacrylate-based bone cement has been implemented in orthopaedics to cope with implant-related infections associated with the formation of bacterial biofilms. In the context of emerging bacterial resistance to current antibiotics, we examined the efficacy of short antimicrobial peptide-loaded bone cement in inhibiting bacterial adhesion and consequent biofilm formation on its surface. METHODOLOGY The ability of α-helical antimicrobial peptides composed of 12 amino acid residues to prevent bacterial biofilm [methicillin-resistant Staphylococcus aureus (MRSA), Staphylococcus epidermidis, Pseudomonas aeruginosa and Escherichia coli] formation on the surface of model implants made from polymethylmethacrylate-based bone cement was evaluated by colony-forming unit (c.f.u.) counting of bacteria released by sonication from the biofilms formed on their surfaces. The biofilms on model implant surfaces were also visualized by light microscopy after staining with tetrazolium dye (MTT) and by scanning electron microscopy. RESULTS When incorporated in the implants, these peptides caused a mean reduction in the number of bacterial cells attached to implants' surfaces (by five orders of magnitude), and 88 % of these implants showed no bacterial adhesion after being exposed to growth media containing various bacteria. CONCLUSION The results showed that the antibiofilm activity of these peptides was comparable to that of the antibiotics, but the peptides exhibited broader specificity than the antibiotics. Given the rapid development of antibiotic resistance, antimicrobial peptides show promise as a substitute for antibiotics for loading into bone cements.
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Affiliation(s)
- Andrea Volejníková
- 1 Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Pavel Melicherčík
- 2 Department of Orthopaedics, First Faculty of Medicine, Charles University in Prague and Motol University Hospital, V Úvalu 84, 150 06 Prague 5, Czech Republic
| | - Ondřej Nešuta
- 1 Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Eva Vaňková
- 1 Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Lucie Bednárová
- 1 Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Jiří Rybáček
- 1 Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Václav Čeřovský
- 1 Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
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28
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Rončević I, Jirásek M, Severa L, Reyes‐Gutierrez PE, Teplý F, Bednárová L, Hromadová M, Pospíšil L. Chiroptical Redox Switching of Tetra‐Cationic Derivatives of Azoniahelicenes. ChemElectroChem 2019. [DOI: 10.1002/celc.201900204] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Igor Rončević
- Department of Organic SynthesisInstitute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nám. 2 Prague 6 Czech Rep
| | - Michael Jirásek
- Department of Organic SynthesisInstitute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nám. 2 Prague 6 Czech Rep
| | - Lukáš Severa
- Department of Organic SynthesisInstitute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nám. 2 Prague 6 Czech Rep
| | - Paul Eduardo Reyes‐Gutierrez
- Department of Organic SynthesisInstitute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nám. 2 Prague 6 Czech Rep
| | - Filip Teplý
- Department of Organic SynthesisInstitute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nám. 2 Prague 6 Czech Rep
| | - Lucie Bednárová
- Department of Organic SynthesisInstitute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nám. 2 Prague 6 Czech Rep
| | - Magdaléna Hromadová
- Department of Electrochemistry at NanoscaleJ. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Dolejškova 3 18223 Prague Czech Rep
| | - Lubomír Pospíšil
- Department of Organic SynthesisInstitute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo nám. 2 Prague 6 Czech Rep
- Department of Electrochemistry at NanoscaleJ. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Dolejškova 3 18223 Prague Czech Rep
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Machara A, Křivánek J, Dolejšová K, Havlíčková J, Bednárová L, Hanus R, Majer P, Kyjaková P. Identification and Enantiodivergent Synthesis of (5 Z,9 S)-Tetradec-5-en-9-olide, a Queen-Specific Volatile of the Termite Silvestritermes minutus. J Nat Prod 2018; 81:2266-2274. [PMID: 30299957 DOI: 10.1021/acs.jnatprod.8b00632] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The queens of social insects differ from sterile colony members in many aspects of their physiology. Besides adaptations linked with their specialization for reproduction and extended lifespan, the queens also invest in the maintenance of their reproductive dominance by producing exocrine chemicals signaling their presence to the nestmates. The knowledge of the chemistry of queen-specific cues in termites is scarce. In addition to the contact recognition based on cuticular hydrocarbons, long-range signals mediated by volatiles are expected to participate in queen signaling, especially in populous colonies of higher termites (Termitidae). In queens of the higher termite Silvestritermes minutus (Syntermitinae), we have detected a previously undescribed volatile. It is present in important quantities on the body surface and in the headspace, ovaries, and body cavity. MS and GC-FTIR data analyses led us to propose the structure of the compound to be a macrolide 10-pentyl-3,4,5,8,9,10-hexahydro-2 H-oxecin-2-one. We performed enantiodivergent syntheses of two possible enantiomers starting from enantiopure ( S)-glycidyl tosylate. The synthetic sequence involved macrolide-closing metathesis quenched with a ruthenium scavenging agent. The absolute and relative configuration of the compound was assigned to be (5 Z,9 S)-tetradec-5-en-9-olide. Identification and preparation of the compound allow for investigation of its biological significance.
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Affiliation(s)
- Aleš Machara
- Institute of Organic Chemistry and Biochemistry of the CAS , Flemingovo n. 542/2 , 166 10 , Prague 6 , Czech Republic
| | - Jan Křivánek
- Institute of Organic Chemistry and Biochemistry of the CAS , Flemingovo n. 542/2 , 166 10 , Prague 6 , Czech Republic
| | - Klára Dolejšová
- Institute of Organic Chemistry and Biochemistry of the CAS , Flemingovo n. 542/2 , 166 10 , Prague 6 , Czech Republic
| | - Jana Havlíčková
- Institute of Organic Chemistry and Biochemistry of the CAS , Flemingovo n. 542/2 , 166 10 , Prague 6 , Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry of the CAS , Flemingovo n. 542/2 , 166 10 , Prague 6 , Czech Republic
| | - Robert Hanus
- Institute of Organic Chemistry and Biochemistry of the CAS , Flemingovo n. 542/2 , 166 10 , Prague 6 , Czech Republic
| | - Pavel Majer
- Institute of Organic Chemistry and Biochemistry of the CAS , Flemingovo n. 542/2 , 166 10 , Prague 6 , Czech Republic
| | - Pavlína Kyjaková
- Institute of Organic Chemistry and Biochemistry of the CAS , Flemingovo n. 542/2 , 166 10 , Prague 6 , Czech Republic
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30
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Klívar J, Šámal M, Jančařík A, Vacek J, Bednárová L, Buděšínský M, Fiedler P, Starý I, Stará IG. Asymmetric Synthesis of Diastereo- and Enantiopure Bioxahelicene 2,2′-Bipyridines. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800541] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Jiří Klívar
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Michal Šámal
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Andrej Jančařík
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Jaroslav Vacek
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Miloš Buděšínský
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Pavel Fiedler
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Ivo Starý
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Irena G. Stará
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nám. 2 166 10 Prague 6 Czech Republic
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31
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Karras M, Dąbrowski M, Pohl R, Rybáček J, Vacek J, Bednárová L, Grela K, Starý I, Stará IG, Schmidt B. Helicenes as Chirality-Inducing Groups in Transition-Metal Catalysis: The First Helically Chiral Olefin Metathesis Catalyst. Chemistry 2018; 24:10994-10998. [DOI: 10.1002/chem.201802786] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 06/18/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Manfred Karras
- Institut für Chemie; Universität Potsdam; Karl-Liebknecht-Str. 24-25 14476 Potsdam Germany
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo n. 2 166 10 Prague 6 Czech Republic
| | - Michał Dąbrowski
- Faculty of Chemistry, Biological and Chemical Research Center; University of Warsaw; Żwirki i Wigury 101 02-089 Warsaw Poland
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo n. 2 166 10 Prague 6 Czech Republic
| | - Jiří Rybáček
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo n. 2 166 10 Prague 6 Czech Republic
| | - Jaroslav Vacek
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo n. 2 166 10 Prague 6 Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo n. 2 166 10 Prague 6 Czech Republic
| | - Karol Grela
- Faculty of Chemistry, Biological and Chemical Research Center; University of Warsaw; Żwirki i Wigury 101 02-089 Warsaw Poland
| | - Ivo Starý
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo n. 2 166 10 Prague 6 Czech Republic
| | - Irena G. Stará
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo n. 2 166 10 Prague 6 Czech Republic
| | - Bernd Schmidt
- Institut für Chemie; Universität Potsdam; Karl-Liebknecht-Str. 24-25 14476 Potsdam Germany
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32
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Abstract
G-Quadruplexes are four-stranded nucleic acid structures typically stabilized by GGGG tetrads. These structures are intrinsically fluorescent, which expands the known scope of nucleic acid function and raises the possibility that they could eventually be used as signaling components in label-free sensors constructed from DNA or RNA. In this study, we systematically investigated the effects of mutations in tetrads, loops, and overhanging nucleotides on the fluorescence intensity and maximum emission wavelength of >500 sequence variants of a reference DNA G-quadruplex. Some of these mutations modestly increased the fluorescence intensity of this G-quadruplex, while others shifted its maximum emission wavelength. Mutations that increased the fluorescence intensity were distinct from those that increased the maximum emission wavelength, suggesting a trade-off between these two biochemical properties. The fluorescence intensity and maximum emission wavelength were also correlated with multimeric state: the most fluorescent G-quadruplexes were monomers, while those with the highest maximum emission wavelengths typically formed dimeric structures. Oligonucleotides containing multiple G-quadruplexes were in some cases more fluorescent than those containing a single G-quadruplex, although this depended on the length and sequence of the spacer linking the G-quadruplexes. These experiments provide new insights into the properties of fluorescent G-quadruplexes and should aid in the development of improved label-free nucleic acid sensors.
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Affiliation(s)
- Tat'ána Majerová
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Prague 166 10 , Czech Republic
| | - Tereza Streckerová
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Prague 166 10 , Czech Republic.,Department of Biochemistry and Microbiology , University of Chemistry and Technology , Prague 166 10 , Czech Republic
| | - Lucie Bednárová
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Prague 166 10 , Czech Republic
| | - Edward A Curtis
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Prague 166 10 , Czech Republic
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33
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Dorčák V, Novák D, Kabeláč M, Kroutil O, Bednárová L, Veverka V, Vacek J. Structural Stability of Peptidic His-Containing Proton Wire in Solution and in the Adsorbed State. Langmuir 2018; 34:6997-7005. [PMID: 29763545 DOI: 10.1021/acs.langmuir.7b04139] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Molecular wires are functional molecules applicable in the field of transfer processes in technological and biochemical applications. Besides molecular wires with the ability to transfer electrons, research is currently focused on molecular wires with high proton affinity and proton transfer ability. Recently, proposed peptidic proton wires (H wires) are one example. Their ability to mediate the transport of protons from aqueous solutions onto the surface of a Hg electrode in a catalytic hydrogen evolution reaction was investigated by constant-current chronopotentiometric stripping. However, elucidating the structure of H wires and rationalizing their stability are key requirements for their further research and application. In this article, we focus on the His (H) and Ala (A)-containing peptidic H wire A3-(H-A2)6 in solution and after its immobilization onto the electrode surface in the presence of the secondary structure stabilizer 2,2,2-trifluoroethanol (TFE). We found that the solvent containing more than 25% of TFE stabilizes the helical structure of A3-(H-A2)6 not only in solution but also in the adsorbed state. The TFE efficacy to stabilize α-helical structure was confirmed using high-resolution nuclear magnetic resonance, circular dichroism, and molecular dynamics simulation. Experimental and theoretical results indicated A3-(H-A2)6 to be a high proton-affinity peptidic H wire with an α-helical structure stabilized by TFE, which was confirmed in a comparative study with hexahistidine as an example of a peptide with a definitely disordered and random coil structure. The results presented here could be used for further investigation of the peptidic H wires and for the application of electrochemical methods in the research of proton transfer phenomena in general.
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Affiliation(s)
- Vlastimil Dorčák
- The Czech Academy of Sciences , Institute of Biophysics , Kralovopolska 135 , 612 65 Brno , Czech Republic
| | - David Novák
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry , Palacky University , Hnevotinska 3 , 775 15 Olomouc , Czech Republic
| | - Martin Kabeláč
- Department of Chemistry, Faculty of Science , University of South Bohemia , Branisovska 31 , 370 05 Ceske Budejovice , Czech Republic
| | - Ondřej Kroutil
- Institute of Physics and Biophysics, Faculty of Science , University of South Bohemia , Branisovska 1760 , 370 05 Ceske Budejovice , Czech Republic
| | - Lucie Bednárová
- The Czech Academy of Sciences , Institute of Organic Chemistry and Biochemistry , Flemingovo nam. 2 , 160 00 Prague , Czech Republic
| | - Václav Veverka
- The Czech Academy of Sciences , Institute of Organic Chemistry and Biochemistry , Flemingovo nam. 2 , 160 00 Prague , Czech Republic
| | - Jan Vacek
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry , Palacky University , Hnevotinska 3 , 775 15 Olomouc , Czech Republic
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34
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Talele HR, Koval D, Severa L, Reyes-Gutiérrez PE, Císařová I, Sázelová P, Šaman D, Bednárová L, Kašička V, Teplý F. Diquats with Robust Chirality: Facile Resolution, Synthesis of Chiral Dyes, and Application as Selectors in Chiral Analysis. Chemistry 2018; 24:7601-7604. [PMID: 29575285 DOI: 10.1002/chem.201800369] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Indexed: 12/25/2022]
Abstract
Diquats with extremely high racemization barriers with ΔG≠theor of 233 kJ mol-1 at 180 °C are described. Reported configurational robustness is due to a combination of two structural features: the rigid o-xylylene tether connecting the nitrogen atoms and the presence of two substituents in the bay region of the bipyridinium scaffold. The straightforward synthesis of diquats, plus facile resolution and derivatization make them attractive for chiral application studies. This is demonstrated by: 1) synthesis of the first non-racemic diquat dyes with pronounced chiroptical properties, and 2) capability of diquats to interact stereospecifically with chiral molecules. This suggests potential for diquat derivatives to be used as chiral selectors in separation methods.
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Affiliation(s)
- Harish R Talele
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 542/2, 166 10, Prague 6, Czech Republic
| | - Dušan Koval
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 542/2, 166 10, Prague 6, Czech Republic
| | - Lukáš Severa
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 542/2, 166 10, Prague 6, Czech Republic
| | - Paul E Reyes-Gutiérrez
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 542/2, 166 10, Prague 6, Czech Republic
| | - Ivana Císařová
- Department of Inorganic Chemistry, Charles University, Hlavova 2030/8, 128 43, Prague 2, Czech Republic
| | - Petra Sázelová
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 542/2, 166 10, Prague 6, Czech Republic
| | - David Šaman
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 542/2, 166 10, Prague 6, Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 542/2, 166 10, Prague 6, Czech Republic
| | - Václav Kašička
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 542/2, 166 10, Prague 6, Czech Republic
| | - Filip Teplý
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nam. 542/2, 166 10, Prague 6, Czech Republic
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35
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Karras M, Holec J, Bednárová L, Pohl R, Schmidt B, Stará IG, Starý I. Asymmetric Synthesis of Nonracemic 2-Amino[6]helicenes and Their Self-Assembly into Langmuir Films. J Org Chem 2018; 83:5523-5538. [DOI: 10.1021/acs.joc.8b00538] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Manfred Karras
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 166 10 Prague 6, Czech Republic
- Universitaet Potsdam, Institut fuer Chemie, Karl-Liebknecht-Straße 24-25, D-14476 Potsdam-Golm, Germany
| | - Jan Holec
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 166 10 Prague 6, Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 166 10 Prague 6, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 166 10 Prague 6, Czech Republic
| | - Bernd Schmidt
- Universitaet Potsdam, Institut fuer Chemie, Karl-Liebknecht-Straße 24-25, D-14476 Potsdam-Golm, Germany
| | - Irena G. Stará
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 166 10 Prague 6, Czech Republic
| | - Ivo Starý
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 166 10 Prague 6, Czech Republic
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36
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Brandt JR, Pospíšil L, Bednárová L, da Costa RC, White AJP, Mori T, Teplý F, Fuchter MJ. Intense redox-driven chiroptical switching with a 580 mV hysteresis actuated through reversible dimerization of an azoniahelicene. Chem Commun (Camb) 2018; 53:9059-9062. [PMID: 28737778 DOI: 10.1039/c7cc04903j] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Electrochemical reduction of an azoniahelicene affords a dimer, accompanied by a strong change in the electronic circular dichroism. The fast dimerisation event leads to a >500 mV shift of the oxidation potential, affording a large area of bistability, where the chiroptical signal only depends on the redox history.
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Affiliation(s)
- Jochen R Brandt
- Department of Chemistry, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.
| | - Lubomír Pospíšil
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, 16610 Prague, Czech Republic and J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences, 18223 Prague, Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, 16610 Prague, Czech Republic
| | | | - Andrew J P White
- Department of Chemistry, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.
| | - Tadashi Mori
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Filip Teplý
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, 16610 Prague, Czech Republic
| | - Matthew J Fuchter
- Department of Chemistry, Imperial College London, South Kensington Campus, London SW7 2AZ, UK. and Centre for Plastic Electronics, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
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37
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Kolesnikova S, Hubálek M, Bednárová L, Cvacka J, Curtis EA. Multimerization rules for G-quadruplexes. Nucleic Acids Res 2017; 45:8684-8696. [PMID: 28911118 PMCID: PMC5587800 DOI: 10.1093/nar/gkx637] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 07/20/2017] [Indexed: 01/05/2023] Open
Abstract
G-quadruplexes can multimerize under certain conditions, but the sequence requirements of such structures are not well understood. In this study, we investigated the ability of all possible variants of the central tetrad in a monomeric, parallel-strand G-quadruplex to form higher-order structures. Although most of these 256 variants existed primarily as monomers under the conditions of our screen, ∼10% formed dimers or tetramers. These structures could form in a wide range of monovalent and divalent metal ions, and folding was highly cooperative in both KCl and MgCl2. As was previously shown for G-quadruplexes that bind GTP and promote peroxidase reactions, G-quadruplexes that form dimers and tetramers have distinct sequence requirements. Some mutants could also form heteromultimers, and a second screen was performed to characterize the sequence requirements of these structures. Taken together, these experiments provide new insights into the sequence requirements and structures of both homomultimeric and heteromultimeric G-quadruplexes.
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Affiliation(s)
- Sofia Kolesnikova
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 166 10, Czech Republic.,Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague 166 28, Czech Republic
| | - Martin Hubálek
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 166 10, Czech Republic
| | - Lucie Bednárová
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 166 10, Czech Republic
| | - Josef Cvacka
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 166 10, Czech Republic
| | - Edward A Curtis
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 166 10, Czech Republic
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38
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Kaleta J, Bednárová L, Čížková M, Wen J, Kaletová E, Michl J. IR Spectra of n-Bu 4M (M = Si, Ge, Sn, Pb), n-BuAuPPh 3-d 15, and "n-Bu" on a Gold Surface. J Phys Chem A 2017; 121:4619-4625. [PMID: 28497963 DOI: 10.1021/acs.jpca.7b03404] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Observed and DFT-calculated IR spectra of n-Bu4M (M = Si, Ge, Sn, Pb), (CH3CH2CH213CD2)4Sn, and n-BuAuPPh3-d15 are reported and assigned. The asymmetric CH stretching vibration of the CH2 group adjacent to the metal atom appears as a distinct shoulder at ∼2934 cm-1, whereas for other CH2 groups it is located at ∼2922 cm-1. The characteristic peak at ∼2899 cm-1 is attributed to an overtone of a symmetric CH2 bend at ∼1445 cm-1. In n-BuAuPPh3-d15, the CH stretching vibrations of the butyl group are shifted to lower frequencies by ∼10 cm-1, and two possible rationalizations are offered.
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Affiliation(s)
- Jiří Kaleta
- Institute of Organic Chemistry and Biochemistry AS CR , Flemingovo nám. 2, 166 10 Praha 6, Czech Republic.,Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80309-0215, United States
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry AS CR , Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
| | - Martina Čížková
- Institute of Organic Chemistry and Biochemistry AS CR , Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
| | - Jin Wen
- Institute of Organic Chemistry and Biochemistry AS CR , Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
| | - Eva Kaletová
- Institute of Organic Chemistry and Biochemistry AS CR , Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
| | - Josef Michl
- Institute of Organic Chemistry and Biochemistry AS CR , Flemingovo nám. 2, 166 10 Praha 6, Czech Republic.,Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80309-0215, United States
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39
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Nejedlý J, Šámal M, Rybáček J, Tobrmanová M, Szydlo F, Coudret C, Neumeier M, Vacek J, Vacek Chocholoušová J, Buděšínský M, Šaman D, Bednárová L, Sieger L, Stará IG, Starý I. Synthesis of Long Oxahelicenes by Polycyclization in a Flow Reactor. Angew Chem Int Ed Engl 2017; 56:5839-5843. [DOI: 10.1002/anie.201700341] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Jindřich Nejedlý
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nám. 2 16610 Prague 6 Czech Republic
| | - Michal Šámal
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nám. 2 16610 Prague 6 Czech Republic
| | - Jiří Rybáček
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nám. 2 16610 Prague 6 Czech Republic
| | - Miroslava Tobrmanová
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nám. 2 16610 Prague 6 Czech Republic
| | - Florence Szydlo
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nám. 2 16610 Prague 6 Czech Republic
| | - Christophe Coudret
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nám. 2 16610 Prague 6 Czech Republic
| | - Maria Neumeier
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nám. 2 16610 Prague 6 Czech Republic
| | - Jaroslav Vacek
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nám. 2 16610 Prague 6 Czech Republic
| | - Jana Vacek Chocholoušová
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nám. 2 16610 Prague 6 Czech Republic
| | - Miloš Buděšínský
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nám. 2 16610 Prague 6 Czech Republic
| | - David Šaman
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nám. 2 16610 Prague 6 Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nám. 2 16610 Prague 6 Czech Republic
| | - Ladislav Sieger
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nám. 2 16610 Prague 6 Czech Republic
- Department of Physics; CTU in Prague; Faculty of Electrical Engineering; Technická 2 16627 Prague 6 Czech Republic
| | - Irena G. Stará
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nám. 2 16610 Prague 6 Czech Republic
| | - Ivo Starý
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nám. 2 16610 Prague 6 Czech Republic
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40
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Machová I, Hubálek M, Lepšík M, Bednárová L, Pazderková M, Kopecký V, Snášel J, Dostál J, Pichová I. The Role of Cysteine Residues in Catalysis of Phosphoenolpyruvate Carboxykinase from Mycobacterium tuberculosis. PLoS One 2017; 12:e0170373. [PMID: 28135343 PMCID: PMC5279734 DOI: 10.1371/journal.pone.0170373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 01/04/2017] [Indexed: 11/25/2022] Open
Abstract
Mycobacterium tuberculosis (MTb), the causative agent of tuberculosis, can persist in macrophages for decades, maintaining its basic metabolic activities. Phosphoenolpyruvate carboxykinase (Pck; EC 4.1.1.32) is a key player in central carbon metabolism regulation. In replicating MTb, Pck is associated with gluconeogenesis, but in non-replicating MTb, it also catalyzes the reverse anaplerotic reaction. Here, we explored the role of selected cysteine residues in function of MTb Pck under different redox conditions. Using mass spectrometry analysis we confirmed formation of S–S bridge between cysteines C391 and C397 localized in the C-terminal subdomain. Molecular dynamics simulations of C391-C397 bridged model indicated local conformation changes needed for formation of the disulfide. Further, we used circular dichroism and Raman spectroscopy to analyze the influence of C391 and C397 mutations on Pck secondary and tertiary structures, and on enzyme activity and specificity. We demonstrate the regulatory role of C391 and C397 that form the S–S bridge and in the reduced form stabilize Pck tertiary structure and conformation for gluconeogenic and anaplerotic reactions.
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Affiliation(s)
- Iva Machová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Martin Hubálek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Markéta Pazderková
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
- Institute of Physics, Faculty of Mathematics and Physics, Charles University in Prague, Prague, Czech Republic
| | - Vladimír Kopecký
- Institute of Physics, Faculty of Mathematics and Physics, Charles University in Prague, Prague, Czech Republic
| | - Jan Snášel
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jiří Dostál
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Iva Pichová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
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41
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Tichá A, Stanchev S, Škerle J, Began J, Ingr M, Švehlová K, Polovinkin L, Růžička M, Bednárová L, Hadravová R, Poláchová E, Rampírová P, Březinová J, Kašička V, Majer P, Strisovsky K. Sensitive Versatile Fluorogenic Transmembrane Peptide Substrates for Rhomboid Intramembrane Proteases. J Biol Chem 2017; 292:2703-2713. [PMID: 28069810 DOI: 10.1074/jbc.m116.762849] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 01/05/2017] [Indexed: 11/06/2022] Open
Abstract
Rhomboid proteases are increasingly being explored as potential drug targets, but their potent and specific inhibitors are not available, and strategies for inhibitor development are hampered by the lack of widely usable and easily modifiable in vitro activity assays. Here we address this bottleneck and report on the development of new fluorogenic transmembrane peptide substrates, which are cleaved by several unrelated rhomboid proteases, can be used both in detergent micelles and in liposomes, and contain red-shifted fluorophores that are suitable for high-throughput screening of compound libraries. We show that nearly the entire transmembrane domain of the substrate is important for efficient cleavage, implying that it extensively interacts with the enzyme. Importantly, we demonstrate that in the detergent micelle system, commonly used for the enzymatic analyses of intramembrane proteolysis, the cleavage rate strongly depends on detergent concentration, because the reaction proceeds only in the micelles. Furthermore, we show that the catalytic efficiency and selectivity toward a rhomboid substrate can be dramatically improved by targeted modification of the sequence of its P5 to P1 region. The fluorogenic substrates that we describe and their sequence variants should find wide use in the detection of activity and development of inhibitors of rhomboid proteases.
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Affiliation(s)
- Anežka Tichá
- From the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague 166 10.,the First Faculty of Medicine, Charles University, Kateřinská 32, Prague 121 08, and
| | - Stancho Stanchev
- From the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague 166 10
| | - Jan Škerle
- From the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague 166 10.,the Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, Prague 128 43
| | - Jakub Began
- From the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague 166 10.,the Department of Genetics and Microbiology, Faculty of Science, Charles University, Viničná 5, Prague 128 44
| | - Marek Ingr
- the Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, Prague 128 43.,the Department of Physics and Materials Engineering, Tomas Bata University in Zlín, Faculty of Technology, nám. T.G. Masaryka 5555, 76001, Zlín, Czech Republic
| | - Kateřina Švehlová
- From the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague 166 10
| | - Lucie Polovinkin
- From the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague 166 10.,the Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, Prague 128 43
| | - Martin Růžička
- From the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague 166 10.,the Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, Prague 128 43
| | - Lucie Bednárová
- From the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague 166 10
| | - Romana Hadravová
- From the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague 166 10
| | - Edita Poláchová
- From the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague 166 10
| | - Petra Rampírová
- From the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague 166 10
| | - Jana Březinová
- From the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague 166 10
| | - Václav Kašička
- From the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague 166 10
| | - Pavel Majer
- From the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague 166 10
| | - Kvido Strisovsky
- From the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo n. 2, Prague 166 10,
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42
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Sánchez IG, Šámal M, Nejedlý J, Karras M, Klívar J, Rybáček J, Buděšínský M, Bednárová L, Seidlerová B, Stará IG, Starý I. Oxahelicene NHC ligands in the asymmetric synthesis of nonracemic helicenes. Chem Commun (Camb) 2017; 53:4370-4373. [DOI: 10.1039/c7cc00781g] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Oxahelicene NHC ligands were used in Ni-catalysed enantioselective cycloisomerisation of alkynes to obtain helicenes in up to 86% ee.
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Affiliation(s)
- Isabel Gay Sánchez
- Institute of Organic Chemistry and Biochemistry
- Czech Academy of Sciences
- 166 10 Prague 6
- Czech Republic
| | - Michal Šámal
- Institute of Organic Chemistry and Biochemistry
- Czech Academy of Sciences
- 166 10 Prague 6
- Czech Republic
| | - Jindřich Nejedlý
- Institute of Organic Chemistry and Biochemistry
- Czech Academy of Sciences
- 166 10 Prague 6
- Czech Republic
| | - Manfred Karras
- Institute of Organic Chemistry and Biochemistry
- Czech Academy of Sciences
- 166 10 Prague 6
- Czech Republic
| | - Jiří Klívar
- Institute of Organic Chemistry and Biochemistry
- Czech Academy of Sciences
- 166 10 Prague 6
- Czech Republic
| | - Jiří Rybáček
- Institute of Organic Chemistry and Biochemistry
- Czech Academy of Sciences
- 166 10 Prague 6
- Czech Republic
| | - Miloš Buděšínský
- Institute of Organic Chemistry and Biochemistry
- Czech Academy of Sciences
- 166 10 Prague 6
- Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry
- Czech Academy of Sciences
- 166 10 Prague 6
- Czech Republic
| | - Beata Seidlerová
- Institute of Organic Chemistry and Biochemistry
- Czech Academy of Sciences
- 166 10 Prague 6
- Czech Republic
| | - Irena G. Stará
- Institute of Organic Chemistry and Biochemistry
- Czech Academy of Sciences
- 166 10 Prague 6
- Czech Republic
| | - Ivo Starý
- Institute of Organic Chemistry and Biochemistry
- Czech Academy of Sciences
- 166 10 Prague 6
- Czech Republic
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43
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Biedermann D, Buchta M, Holečková V, Sedlák D, Valentová K, Cvačka J, Bednárová L, Křenková A, Kuzma M, Škuta C, Peikerová Ž, Bartůněk P, Křen V. Silychristin: Skeletal Alterations and Biological Activities. J Nat Prod 2016; 79:3086-3092. [PMID: 28006905 DOI: 10.1021/acs.jnatprod.6b00750] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Silychristin is the second most abundant flavonolignan (after silybin) present in the fruits of Silybum marianum. A group of compounds containing silychristin (3) and its derivatives such as 2,3-dehydrosilychristin (4), 2,3-dehydroanhydrosilychristin (5), anhydrosilychristin (6), silyhermin (7), and isosilychristin (8) were studied. Physicochemical data of these compounds acquired at high resolution were compared. The absolute configuration of silyhermin (7) was proposed to be identical to silychristin A (3a) in ring D (10R,11S). The preparation of 2,3-dehydrosilychristin (4) was optimized. The Folin-Ciocalteau reduction and DPPH and ABTS radical scavenging assays revealed silychristin and its analogues to be powerful antioxidants, which were found to be more potent than silybin and 2,3-dehydrosilybin. Compounds 4-6 exhibited inhibition of microsomal lipoperoxidation (IC50 4-6 μM). Moreover, compounds 4-8 were found to be almost noncytotoxic for 10 human cell lines of different histogenetic origins. On the basis of these results, compounds 3-6 are likely responsible for most of the antioxidant properties of silymarin attributed traditionally to silybin (silibinin).
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Affiliation(s)
- David Biedermann
- Institute of Microbiology, Laboratory of Biotransformation, Czech Academy of Sciences , Vídeňská 1083, CZ 142 20 Prague, Czech Republic
| | - Martin Buchta
- Stolařská 601/4 , CZ 747 14 Ludgeřovice, Czech Republic
| | - Veronika Holečková
- Institute of Microbiology, Laboratory of Biotransformation, Czech Academy of Sciences , Vídeňská 1083, CZ 142 20 Prague, Czech Republic
| | - David Sedlák
- CZ-OPENSCREEN: National Infrastructure for Chemical Biology, Institute of Molecular Genetics, Czech Academy of Sciences , Vídeňská 1083, CZ 142 20 Praha 4, Czech Republic
| | - Kateřina Valentová
- Institute of Microbiology, Laboratory of Biotransformation, Czech Academy of Sciences , Vídeňská 1083, CZ 142 20 Prague, Czech Republic
| | - Josef Cvačka
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences , Flemingovo náměstí 2, CZ 166 10 Prague, Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences , Flemingovo náměstí 2, CZ 166 10 Prague, Czech Republic
| | - Alena Křenková
- Institute of Microbiology, Laboratory of Biotransformation, Czech Academy of Sciences , Vídeňská 1083, CZ 142 20 Prague, Czech Republic
| | - Marek Kuzma
- Institute of Microbiology, Laboratory of Biotransformation, Czech Academy of Sciences , Vídeňská 1083, CZ 142 20 Prague, Czech Republic
| | - Ctibor Škuta
- CZ-OPENSCREEN: National Infrastructure for Chemical Biology, Institute of Molecular Genetics, Czech Academy of Sciences , Vídeňská 1083, CZ 142 20 Praha 4, Czech Republic
| | - Žaneta Peikerová
- CZ-OPENSCREEN: National Infrastructure for Chemical Biology, Institute of Molecular Genetics, Czech Academy of Sciences , Vídeňská 1083, CZ 142 20 Praha 4, Czech Republic
| | - Petr Bartůněk
- CZ-OPENSCREEN: National Infrastructure for Chemical Biology, Institute of Molecular Genetics, Czech Academy of Sciences , Vídeňská 1083, CZ 142 20 Praha 4, Czech Republic
| | - Vladimír Křen
- Institute of Microbiology, Laboratory of Biotransformation, Czech Academy of Sciences , Vídeňská 1083, CZ 142 20 Prague, Czech Republic
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44
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Švehlová K, Lawrence MS, Bednárová L, Curtis EA. Altered biochemical specificity of G-quadruplexes with mutated tetrads. Nucleic Acids Res 2016; 44:10789-10803. [PMID: 27789695 PMCID: PMC5159562 DOI: 10.1093/nar/gkw987] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 10/07/2016] [Accepted: 10/24/2016] [Indexed: 01/09/2023] Open
Abstract
A fundamental motif in canonical nucleic acid structure is the base pair. Mutations that disrupt base pairs are typically destabilizing, but stability can often be restored by a second mutation that replaces the original base pair with an isosteric variant. Such concerted changes are a way to identify helical regions in secondary structures and to identify new functional motifs in sequenced genomes. In principle, such analysis can be extended to non-canonical nucleic acid structures, but this approach has not been utilized because the sequence requirements of such structures are not well understood. Here we investigate the sequence requirements of a G-quadruplex that can both bind GTP and promote peroxidase reactions. Characterization of all 256 variants of the central tetrad in this structure indicates that certain mutations can compensate for canonical G-G-G-G tetrads in the context of both GTP-binding and peroxidase activity. Furthermore, the sequence requirements of these two motifs are significantly different, indicating that tetrad sequence plays a role in determining the biochemical specificity of G-quadruplex activity. Our results provide insight into the sequence requirements of G-quadruplexes, and should facilitate the analysis of such motifs in sequenced genomes.
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Affiliation(s)
- Kateřina Švehlová
- Institute of Organic Chemistry and Biochemistry ASCR, Prague 166 10, Czech Republic
- Charles University in Prague, Faculty of Science, Prague 128 44, Czech Republic
| | - Michael S Lawrence
- Cancer Center and Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry ASCR, Prague 166 10, Czech Republic
| | - Edward A Curtis
- Institute of Organic Chemistry and Biochemistry ASCR, Prague 166 10, Czech Republic
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45
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Klívar J, Jančařík A, Šaman D, Pohl R, Fiedler P, Bednárová L, Starý I, Stará IG. [2+2+2] Cycloisomerisation of Aromatic Cyanodiynes in the Synthesis of Pyridohelicenes and Their Analogues. Chemistry 2016; 22:14401-5. [DOI: 10.1002/chem.201602747] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Jiří Klívar
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Andrej Jančařík
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - David Šaman
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Pavel Fiedler
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Ivo Starý
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Irena G. Stará
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nám. 2 166 10 Prague 6 Czech Republic
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46
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Doležal M, Hadravová R, Kožíšek M, Bednárová L, Langerová H, Ruml T, Rumlová M. Functional and Structural Characterization of Novel Type of Linker Connecting Capsid and Nucleocapsid Protein Domains in Murine Leukemia Virus. J Biol Chem 2016; 291:20630-42. [PMID: 27514744 DOI: 10.1074/jbc.m116.746461] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Indexed: 12/24/2022] Open
Abstract
The assembly of immature retroviral particles is initiated in the cytoplasm by the binding of the structural polyprotein precursor Gag with viral genomic RNA. The protein interactions necessary for assembly are mediated predominantly by the capsid (CA) and nucleocapsid (NC) domains, which have conserved structures. In contrast, the structural arrangement of the CA-NC connecting region differs between retroviral species. In HIV-1 and Rous sarcoma virus, this region forms a rod-like structure that separates the CA and NC domains, whereas in Mason-Pfizer monkey virus, this region is densely packed, thus holding the CA and NC domains in close proximity. Interestingly, the sequence connecting the CA and NC domains in gammaretroviruses, such as murine leukemia virus (MLV), is unique. The sequence is called a charged assembly helix (CAH) due to a high number of positively and negatively charged residues. Although both computational and deletion analyses suggested that the MLV CAH forms a helical conformation, no structural or biochemical data supporting this hypothesis have been published. Using an in vitro assembly assay, alanine scanning mutagenesis, and biophysical techniques (circular dichroism, NMR, microcalorimetry, and electrophoretic mobility shift assay), we have characterized the structure and function of the MLV CAH. We provide experimental evidence that the MLV CAH belongs to a group of charged, E(R/K)-rich, single α-helices. This is the first single α-helix motif identified in viral proteins.
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Affiliation(s)
- Michal Doležal
- From the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 16610 Prague 6
| | - Romana Hadravová
- From the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 16610 Prague 6
| | - Milan Kožíšek
- From the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 16610 Prague 6
| | - Lucie Bednárová
- From the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 16610 Prague 6
| | - Hana Langerová
- the Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague 6, Technická 3, 166 28 Prague, and
| | - Tomáš Ruml
- the Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague 6, Technická 3, 166 28 Prague, and
| | - Michaela Rumlová
- From the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 16610 Prague 6, the Department of Biotechnology, University of Chemistry and Technology, Technická 5, 166 28 Prague, Czech Republic
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47
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Nešuta O, Hexnerová R, Buděšínský M, Slaninová J, Bednárová L, Hadravová R, Straka J, Veverka V, Čeřovský V. Antimicrobial Peptide from the Wild Bee Hylaeus signatus Venom and Its Analogues: Structure-Activity Study and Synergistic Effect with Antibiotics. J Nat Prod 2016; 79:1073-1083. [PMID: 26998557 DOI: 10.1021/acs.jnatprod.5b01129] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Venoms of hymenopteran insects have attracted considerable interest as a source of cationic antimicrobial peptides (AMPs). In the venom of the solitary bee Hylaeus signatus (Hymenoptera: Colletidae), we identified a new hexadecapeptide of sequence Gly-Ile-Met-Ser-Ser-Leu-Met-Lys-Lys-Leu-Ala-Ala-His-Ile-Ala-Lys-NH2. Named HYL, it belongs to the category of α-helical amphipathic AMPs. HYL exhibited weak antimicrobial activity against several strains of pathogenic bacteria and moderate activity against Candida albicans, but its hemolytic activity against human red blood cells was low. We prepared a set of HYL analogues to evaluate the effects of structural modifications on its biological activity and to increase its potency against pathogenic bacteria. This produced several analogues exhibiting significantly greater activity compared to HYL against strains of both Staphylococcus aureus and Pseudomonas aeruginosa even as their hemolytic activity remained low. Studying synergism of HYL peptides and conventional antibiotics showed the peptides act synergistically and preferentially in combination with rifampicin. Fluorescent dye propidium iodide uptake showed the tested peptides were able to facilitate entrance of antibiotics into the cytoplasm by permeabilization of the outer and inner bacterial cell membrane of P. aeruginosa. Transmission electron microscopy revealed that treatment of P. aeruginosa with one of the HYL analogues caused total disintegration of bacterial cells. NMR spectroscopy was used to elucidate the structure-activity relationship for the effect of amino acid residue substitution in HYL.
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Affiliation(s)
- Ondřej Nešuta
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic
- Faculty of Food and Biochemical Technology, University of Chemistry and Technology Prague , Technická 5, 166 28 Prague 6, Czech Republic
| | - Rozálie Hexnerová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic
| | - Miloš Buděšínský
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic
| | - Jiřina Slaninová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic
| | - Romana Hadravová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic
| | - Jakub Straka
- Department of Zoology, Faculty of Science, Charles University in Prague , Viničná 7, 12843 Prague 2, Czech Republic
| | - Václav Veverka
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic
| | - Václav Čeřovský
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic
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48
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Vymětal J, Bednárová L, Vondrášek J. Effect of TFE on the Helical Content of AK17 and HAL-1 Peptides: Theoretical Insights into the Mechanism of Helix Stabilization. J Phys Chem B 2016; 120:1048-59. [DOI: 10.1021/acs.jpcb.5b11228] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jiří Vymětal
- Institute of Organic Chemistry and Biochemistry, AS CR, Flemingovo náměsti 2, 166 10 Prague 6, Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry, AS CR, Flemingovo náměsti 2, 166 10 Prague 6, Czech Republic
| | - Jiří Vondrášek
- Institute of Organic Chemistry and Biochemistry, AS CR, Flemingovo náměsti 2, 166 10 Prague 6, Czech Republic
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49
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Mikulášková B, Zemenová J, Pirník Z, Pražienková V, Bednárová L, Železná B, Maletínská L, Kuneš J. Effect of palmitoylated prolactin-releasing peptide on food intake and neural activation after different routes of peripheral administration in rats. Peptides 2016; 75:109-17. [PMID: 26643957 DOI: 10.1016/j.peptides.2015.11.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 11/23/2015] [Accepted: 11/24/2015] [Indexed: 01/08/2023]
Abstract
Obesity is an escalating epidemic, but an effective non-invasive therapy is still scarce. For obesity treatment, anorexigenic neuropeptides are promising tools, but their delivery from the periphery to the brain is complicated by their peptide character. In order to overcome this unfavorable fact, we have applied the lipidization of neuropeptide prolactin-releasing peptide (PrRP), whose strong anorexigenic effect was demonstrated. A palmitoylated analog of human PrRP (h palm-PrRP31) was injected in free-fed Wistar rats by three routes: subcutaneous (s.c.), intraperitoneal (i.p) (both 5 mg/kg) and intravenous (i.v.) (from 0.01 to 0.5 mg/kg). We found a circulating compound in the blood after all three applications with the highest concentration after i.v. administration. This corresponds to the effect on food intake, which was also strongest after i.v. injection. Moreover, this is in agreement with the fact that the expression of c-Fos in specific brain regions involved in food intake regulation was also highest after intravenous application. Pharmacokinetic data are further supported by results obtained from dynamic light scattering and CD spectroscopy. Human palm-PrRP31 analog showed a strong tendency to micellize, and formation of aggregates suggested lower availability after i.p. or s.c. application. We have demonstrated that palm-PrRP influenced food intake even in free fed rats. Not surprisingly, the maximal effect was achieved after the intravenous application even though two orders of magnitude lower dose was used compared to both two other applications. We believe that palm-PrRP could have a potential as an antiobesity drug when its s.c. application would be improved.
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Affiliation(s)
- Barbora Mikulášková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Czech Republic; Institute of Physiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Jana Zemenová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Czech Republic; University of Chemistry and Technology, Department of Analytical Chemistry, Prague, Czech Republic
| | - Zdenko Pirník
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Czech Republic; Laboratory of Functional Neuromorphology, Institute of Experimental Endocrinology, SAS, Bratislava, Slovak Republic; Department of Human and Clinical Pharmacology, University of Veterinary Medicine, Košice, Slovak Republic
| | - Veronika Pražienková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Czech Republic
| | - Blanka Železná
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Czech Republic
| | - Lenka Maletínská
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Czech Republic
| | - Jaroslav Kuneš
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Czech Republic; Institute of Physiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
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50
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Vimberg V, Kuzma M, Stodůlková E, Novák P, Bednárová L, Šulc M, Gažák R. Hydnocarpin-Type Flavonolignans: Semisynthesis and Inhibitory Effects on Staphylococcus aureus Biofilm Formation. J Nat Prod 2015; 78:2095-103. [PMID: 26273725 DOI: 10.1021/acs.jnatprod.5b00430] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A new, efficient, and general semisynthesis of hydnocarpin-type flavonolignans was developed and optimized, enabling gram-scale production of hydnocarpin D (2). Moreover, the syntheses of optically pure hydnocarpin isomers [(10R,11R)-hydnocarpin (1a), (10R,11R)-hydnocarpin D (2a), and (10S,11S)-hydnocarpin D (2b)], as well as the synthesis of isohydnocarpin (8), were achieved for the first time utilizing this new method. The synthesis is based on the two-step transformation of the readily available flavonolignans from milk thistle (Silybum marianum), accessible by isolation from the commercial extract silymarin. The first step relies on the regioselective formylation of the C-3 hydroxy group of the dihydroflavonol-type precursor using the Vilsmeier-Haack reagent, followed by formic acid elimination by triethylamine in the second step. The synthesized compounds were effective inhibitors of Staphylococcus aureus biofilm formation, with (10S,11S)-hydnocarpin D (2b) being the most potent inhibitor. Furthermore, the effect of glucose on biofilm formation was tested, and glucose decreased the biofilm inhibitory activity of 2b. Moreover, 2b increased the susceptibility of Staph. aureus to enrofloxacin.
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Affiliation(s)
- Vladimir Vimberg
- Institute of Microbiology of the Academy of Sciences of the Czech Republic , v.v.i., Vídeňská 1083, Prague 4, CZ 142 20, Czech Republic
| | - Marek Kuzma
- Institute of Microbiology of the Academy of Sciences of the Czech Republic , v.v.i., Vídeňská 1083, Prague 4, CZ 142 20, Czech Republic
| | - Eva Stodůlková
- Institute of Microbiology of the Academy of Sciences of the Czech Republic , v.v.i., Vídeňská 1083, Prague 4, CZ 142 20, Czech Republic
| | - Petr Novák
- Institute of Microbiology of the Academy of Sciences of the Czech Republic , v.v.i., Vídeňská 1083, Prague 4, CZ 142 20, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University in Prague , Hlavova 8, Prague 2, CZ 128 40, Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry of the AS CR , v.v.i., Flemingovo náměstí 2, Prague 6, CZ 166 10, Czech Republic
| | - Miroslav Šulc
- Institute of Microbiology of the Academy of Sciences of the Czech Republic , v.v.i., Vídeňská 1083, Prague 4, CZ 142 20, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University in Prague , Hlavova 8, Prague 2, CZ 128 40, Czech Republic
| | - Radek Gažák
- Institute of Microbiology of the Academy of Sciences of the Czech Republic , v.v.i., Vídeňská 1083, Prague 4, CZ 142 20, Czech Republic
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