1
|
Photonics of Trimethine Cyanine Dyes as Probes for Biomolecules. Molecules 2022; 27:molecules27196367. [PMID: 36234904 PMCID: PMC9573451 DOI: 10.3390/molecules27196367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 09/16/2022] [Accepted: 09/22/2022] [Indexed: 11/29/2022] Open
Abstract
Cyanine dyes are widely used as fluorescent probes in biophysics and medical biochemistry due to their unique photophysical and photochemical properties (their photonics). This review is focused on a subclass of the most widespread and studied cyanine dyes—trimethine cyanines, which can serve as potential probes for biomolecules. The works devoted to the study of the noncovalent interaction of trimethine cyanine dyes with biomolecules and changing the properties of these dyes upon the interaction are reviewed. In addition to the spectral-fluorescent properties, elementary photochemical properties of trimethine cyanines are considered, including: photoisomerization and back isomerization of the photoisomer, generation and decay of the triplet state, and its quenching by oxygen and other quenchers. The influence of DNA and other nucleic acids, proteins, and other biomolecules on these properties is covered. The interaction of a monomer dye molecule with a biomolecule usually leads to a fluorescence growth, damping of photoisomerization (if any), and an increase in intersystem crossing to the triplet state. Sometimes aggregation of dye molecules on biomolecules is observed. Quenching of the dye triplet state in a complex with biomolecules by molecular oxygen usually occurs with a rate constant much lower than the diffusion limit with allowance for the spin-statistical factor 1/9. The practical application of trimethine cyanines in biophysics and (medical) biochemistry is also considered. In conclusion, the prospects for further studies on the cyanine dye–biomolecule system and the development of new effective dye probes (including probes of a new type) for biomolecules are discussed.
Collapse
|
2
|
Chernii S, Gerasymchuk Y, Losytskyy M, Szymański D, Tretyakova I, Łukowiak A, Pekhnyo V, Yarmoluk S, Chernii V, Kovalska V. Modification of insulin amyloid aggregation by Zr phthalocyanines functionalized with dehydroacetic acid derivatives. PLoS One 2021; 16:e0243904. [PMID: 33411832 PMCID: PMC7790233 DOI: 10.1371/journal.pone.0243904] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 12/01/2020] [Indexed: 02/06/2023] Open
Abstract
Amyloid fibrils are widely studied both as target in conformational disorders and as basis for the development of protein-based functional materials. The three Zr phthalocyanines bearing dehydroacetic acid residue (PcZr(L1)2) and its condensed derivatives (PcZr(L2)2 and PcZr(L3)2) as out-of-plane ligands were synthesized and their influence on insulin fibril formation was studied by amyloid-sensitive fluorescent dye based assay, scanning electron microscopy, fluorescent and absorption spectroscopies. The presence of Zr phthalocyanines was shown to modify the fibril formation. The morphology of fibrils formed in the presence of the Zr phthalocyanines differs from that of free insulin and depends on the structure of out-of-plane ligands. It is shown that free insulin mostly forms fibril clusters with the length of about 0.3-2.1 μm. The presence of Zr phthalocyanines leads to the formation of individual 0.4-2.8 μm-long fibrils with a reduced tendency to lateral aggregation and cluster formation (PcZr(L1)2), shorter 0.2-1.5 μm-long fibrils with the tendency to lateral aggregation without clusters (PcZr(L2)2), and fibril-like 0.2-1.0 μm-long structures (PcZr(L3)2). The strongest influence on fibrils morphology made by PcZr(L3)2 could be explained by the additional stacking of phenyl moiety of the ligand with aromatic amino acids in protein. The evidences of binding of studied Zr phthalocyanines to mature fibrils were shown by absorption spectroscopy (for PcZr(L1)2 and PcZr(L2)2) and fluorescent spectroscopy (for PcZr(L3)2). These complexes could be potentially used as external tools allowing the development of functional materials on protein fibrils basis.
Collapse
Affiliation(s)
- Svitlana Chernii
- Institute of Molecular Biology and Genetics, NASU, Kyiv, Ukraine
| | - Yuriy Gerasymchuk
- Institute of Low Temperature and Structure Research, PAS, Wroclaw, Poland
| | | | - Damian Szymański
- Institute of Low Temperature and Structure Research, PAS, Wroclaw, Poland
| | - Iryna Tretyakova
- Institute of General and Inorganic Chemistry, NASU, Kyiv, Ukraine
| | - Anna Łukowiak
- Institute of Low Temperature and Structure Research, PAS, Wroclaw, Poland
| | - Vasyl Pekhnyo
- Institute of General and Inorganic Chemistry, NASU, Kyiv, Ukraine
| | - Sergiy Yarmoluk
- Institute of Molecular Biology and Genetics, NASU, Kyiv, Ukraine
| | - Viktor Chernii
- Institute of General and Inorganic Chemistry, NASU, Kyiv, Ukraine
| | | |
Collapse
|
3
|
|
4
|
Chernii S, Losytskyy M, Kelm A, Gorski A, Tretyakova I, Yarmoluk S, Chernii V, Kovalska V. Study of tetraphenylporphyrins as modifiers of insulin amyloid aggregation. J Mol Recognit 2019; 33:e2811. [PMID: 31497916 DOI: 10.1002/jmr.2811] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Revised: 08/09/2019] [Accepted: 08/16/2019] [Indexed: 11/07/2022]
Abstract
Amyloid fibrils are rigid β-pleated protein aggregates that are connected with series of harmful diseases and at the same time are promising as base for novel nanomaterials. Thus, design of compounds able to inhibit or redirect those aggregates formation is important both for the biomedical aims and for nanotechnology applications. Here, we studied the effect of tetraphenylporphyrins (metal free, their Cu and Pd complexes, and those functionalized by carboxy and amino groups on periphery) on insulin amyloid self-assembling. The strongest impact on insulin aggregation was demonstrated by a metal-free porphyrin bearing four carboxy groups. This compound strongly suppresses insulin aggregation (about 88% reduction in amyloid-sensitive probe emission) inducing formation of fibrils with the length close to this of free insulin (1.7 ± 0.6 μm as compared with 1.4 ± 0.4 μm, respectively) with an essentially reduced tendency to lateral aggregation. Contrarily, the presence of tetraphenylporphyrin containing four amino groups only slightly affects fibrils' morphology and makes weaker impact on insulin aggregation yield (about 44% reduction). This is explained by the ability of aromatic carboxy groups of 5,10,15,20-(tetra-4-carboxyphenyl)porphyrin to interact with complementary protein-binding groups and thus stabilize the supramolecular complex. For 5,10,15,20-(tetra-4-aminophenyl)porphyrin, full protonation takes place in acidic medium of protein aggregation reaction; this results in the high positive charge of TPPN4 (equal or close to +6) and hence higher contribution of coulombic repulsion to interaction of TPPN4 with insulin. One more possible mechanism of the lower inhibition effect of TPPN4 as compared with TPPC4 could be the more restricted possibility of the former as compared with the latter to form H bonds with insulin groups. It was also shown that metal-free, Pd-containing, and Cu-containing tetraphenylporphyrins without peripheral substituents make almost the same impact on the protein self-assembling. We suppose this to be due to coordination saturation of these metal atoms.
Collapse
Affiliation(s)
- Svitlana Chernii
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Mykhaylo Losytskyy
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Anna Kelm
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Alexandr Gorski
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Iryna Tretyakova
- V.I. Vernadsky Institute of General and Inorganic Chemistry, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Sergiy Yarmoluk
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Victor Chernii
- V.I. Vernadsky Institute of General and Inorganic Chemistry, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Vladyslava Kovalska
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| |
Collapse
|
5
|
Vus K, Girych M, Trusova V, Gorbenko G, Kurutos A, Vasilev A, Gadjev N, Deligeorgiev T. Cyanine dyes derived inhibition of insulin fibrillization. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2018.11.149] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
6
|
Kovalska V, Chernii S, Losytskyy M, Ostapko J, Tretyakova I, Gorski A, Chernii V, Yarmoluk S. Activity of Zn and Mg phthalocyanines and porphyrazines in amyloid aggregation of insulin. J Mol Recognit 2017; 31. [PMID: 28856782 PMCID: PMC6175167 DOI: 10.1002/jmr.2660] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 07/04/2017] [Accepted: 08/07/2017] [Indexed: 11/22/2022]
Abstract
Formation of the deposits of protein aggregates—amyloid fibrils in an intracellular and intercellular space—is common to a large group of amyloid‐associated disorders. Among the approaches to develop of therapy of such disorders is the use of agents preventing protein fibrillization. Polyaromatic complexes—porphyrins and phthalocyanines—are known as compounds possessing anti‐fibrillogenic activity. Here, we explore the impact of related macrocyclic complexes—phthalocyanines (Pc) and octaphenyl porphyrazines (Pz) of Mg and Zn—on aggregation of amyloidogenic protein insulin. Pz complexes are firstly reported as compounds able to affect protein fibrillization. The effect of Pc and Pz complexes on the kinetics and intensity of insulin aggregation was studied by the fluorescent assay using amyloid sensitive cyanine dye. This has shown the impact of metal ion on the anti‐fibrillogenic properties of macrocyclic complexes—the effect on the fibrillization kinetics of Mg‐containing compounds is much more pronounced comparing to that of Zn analogues. Scanning electron microscopy experiments have demonstrated that filamentous fibrils are the main product of aggregation both for free insulin and in the presence of macrocyclic complexes. However, those fibrils are distinct by their length and proneness to lateral aggregation. The Pc complexes cause the increase in variation of fibrils length 0.9 to 2.7 nm in opposite to 1.4 to 2.0 nm for free insulin, whereas Pz complexes cause certain shortening of the fibrils to 0.8 to 1.6 nm. The averaged size of the fibrils population was estimated by dynamic light scattering; it correlates with the size of single fibrils detected by scanning electron microscopy.
Collapse
Affiliation(s)
- V Kovalska
- Institute of Molecular Biology and Genetics NASU, Kyiv, Ukraine
| | - S Chernii
- Institute of Molecular Biology and Genetics NASU, Kyiv, Ukraine.,V.I. Vernadskii Institute of General and Inorganic Chemistry NASU, Kyiv, Ukraine
| | - M Losytskyy
- Institute of Molecular Biology and Genetics NASU, Kyiv, Ukraine.,V.I. Vernadskii Institute of General and Inorganic Chemistry NASU, Kyiv, Ukraine
| | - J Ostapko
- Institute of Physical Chemistry PAS, Warsaw, Poland
| | - I Tretyakova
- V.I. Vernadskii Institute of General and Inorganic Chemistry NASU, Kyiv, Ukraine
| | - A Gorski
- Institute of Physical Chemistry PAS, Warsaw, Poland
| | - V Chernii
- V.I. Vernadskii Institute of General and Inorganic Chemistry NASU, Kyiv, Ukraine
| | - S Yarmoluk
- Institute of Molecular Biology and Genetics NASU, Kyiv, Ukraine
| |
Collapse
|
7
|
Kovalska V, Chernii S, Cherepanov V, Losytskyy M, Chernii V, Varzatskii O, Naumovets A, Yarmoluk S. The impact of binding of macrocyclic metal complexes on amyloid fibrillization of insulin and lysozyme. J Mol Recognit 2017; 30. [DOI: 10.1002/jmr.2622] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 02/01/2017] [Accepted: 02/10/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Vladyslava Kovalska
- Institute of Molecular Biology and Genetics; National Academy of Sciences of Ukraine; Kyiv Ukraine
| | - Svitlana Chernii
- Institute of Molecular Biology and Genetics; National Academy of Sciences of Ukraine; Kyiv Ukraine
| | | | - Mykhaylo Losytskyy
- Institute of Molecular Biology and Genetics; National Academy of Sciences of Ukraine; Kyiv Ukraine
| | - Victor Chernii
- V.I. Vernadsky Institute of General and Inorganic Chemistry; National Academy of Sciences of Ukraine; Kyiv Ukraine
| | - Oleg Varzatskii
- V.I. Vernadsky Institute of General and Inorganic Chemistry; National Academy of Sciences of Ukraine; Kyiv Ukraine
| | - Anton Naumovets
- Institute of Physics; National Academy of Sciences of Ukraine; Kyiv Ukraine
| | - Sergiy Yarmoluk
- Institute of Molecular Biology and Genetics; National Academy of Sciences of Ukraine; Kyiv Ukraine
| |
Collapse
|
8
|
Vus K, Tarabara U, Kurutos A, Ryzhova O, Gorbenko G, Trusova V, Gadjev N, Deligeorgiev T. Aggregation behavior of novel heptamethine cyanine dyes upon their binding to native and fibrillar lysozyme. MOLECULAR BIOSYSTEMS 2017; 13:970-980. [DOI: 10.1039/c7mb00185a] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Novel cyanine dyes can be used for amyloid fibril detection.
Collapse
Affiliation(s)
- Kateryna Vus
- Department of Nuclear and Medical Physics
- V.N. Karazin Kharkiv National University
- Kharkiv
- Ukraine
| | - Ulyana Tarabara
- Department of Nuclear and Medical Physics
- V.N. Karazin Kharkiv National University
- Kharkiv
- Ukraine
| | - Atanas Kurutos
- Faculty of Chemistry and Pharmacy
- Sofia University
- Sofia
- Bulgaria
| | - Olga Ryzhova
- Department of Nuclear and Medical Physics
- V.N. Karazin Kharkiv National University
- Kharkiv
- Ukraine
| | - Galyna Gorbenko
- Department of Nuclear and Medical Physics
- V.N. Karazin Kharkiv National University
- Kharkiv
- Ukraine
| | - Valeriya Trusova
- Department of Nuclear and Medical Physics
- V.N. Karazin Kharkiv National University
- Kharkiv
- Ukraine
| | - Nikolai Gadjev
- Faculty of Chemistry and Pharmacy
- Sofia University
- Sofia
- Bulgaria
| | | |
Collapse
|
9
|
Kuperman MV, Chernii SV, Losytskyy MY, Kryvorotenko DV, Derevyanko NO, Slominskii YL, Kovalska VB, Yarmoluk SM. Trimethine cyanine dyes as fluorescent probes for amyloid fibrils: The effect of N,N′-substituents. Anal Biochem 2015; 484:9-17. [DOI: 10.1016/j.ab.2015.04.038] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 04/29/2015] [Accepted: 04/30/2015] [Indexed: 11/25/2022]
|
10
|
Study of anti-fibrillogenic activity of iron(II) clathrochelates. Bioorg Med Chem 2014; 22:1883-8. [PMID: 24565971 DOI: 10.1016/j.bmc.2014.01.048] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 01/23/2014] [Accepted: 01/27/2014] [Indexed: 01/19/2023]
Abstract
The macrocyclic compounds mono- and bis-iron(II) clathrochelates were firstly studied as potential anti-fibrillogenic agents using fluorescent inhibitory assay, atomic force microscopy and flow cytometry. It is shown that presence of the clathrochelates leads to the change in kinetics of insulin fibrillization reaction and reduces the amount of formed fibrils (up to 70%). The nature of ribbed substituent could determine the activity of clathrochelates-the higher inhibitory effect is observed for compounds containing carboxybenzenesulfide groups, while the inhibitory properties only slightly depend on the size of complex species. The mono- and bis-clathrochelate derivatives of meta-mercaptobenzoic acid have close values of IC₅₀ namely 16 ± 2 and 24 ± 5 μM, respectively. The presence of clathrochelates decreases the fibril diameter from 5-12 nm for free insulin fibrils to 3-8 nm for these formed in the clathrochelate presence, it also prevents the lateral aggregation of mature fibrils and formation of superfibrillar clusters. However the addition of clathrochelate results in more heterogeneous (both by size and structure) insulin aggregates population as compared to the free insulin. This way, cage complexes-iron(II) clathrochelates are proposed as efficient agents able to suppress the protein aggregation processes.
Collapse
|
11
|
Kovalska VB, Losytskyy MY, Chernii SV, Chernii VY, Tretyakova IM, Yarmoluk SM, Volkov SV. Towards the anti-fibrillogenic activity of phthalocyanines with out-of-plane ligands: correlation with self-association proneness. ACTA ACUST UNITED AC 2013. [DOI: 10.7124/bc.00083c] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- V. B. Kovalska
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
| | - M. Yu. Losytskyy
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
| | - S. V. Chernii
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
| | - V. Ya. Chernii
- Vernadsky Institute of general and inorganic chemistry, National Academy of Sciences of Ukraine
| | - I. M. Tretyakova
- Vernadsky Institute of general and inorganic chemistry, National Academy of Sciences of Ukraine
| | - S. M. Yarmoluk
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
| | - S. V. Volkov
- Vernadsky Institute of general and inorganic chemistry, National Academy of Sciences of Ukraine
| |
Collapse
|
12
|
Inshyn DI, Kovalska VB, Losytskyy MY, Slominskii YL, Tolmachev OI, Yarmoluk SM. Development of a quantitative structure activity relations (QSAR) model to guide the design of fluorescent dyes for detecting amyloid fibrils. Biotech Histochem 2013; 89:1-7. [DOI: 10.3109/10520295.2013.785593] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
13
|
Common benzothiazole and benzoxazole fluorescent DNA intercalators for studying Alzheimer Aβ1-42 and prion amyloid peptides. Biotechniques 2012; 52:000113873. [DOI: 10.2144/000113873] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 05/04/2012] [Indexed: 11/23/2022] Open
Abstract
Amyloids are fibrillar protein aggregates associated with a number of neurodegenerative pathologies including Alzheimer and Creutzfeldt—Jakob disease. The study of amyloids is usually based on fluorescence with the dye thioflavin-T. Although a number of amyloid binding compounds have been synthesized, many are nonfluorescent or not readily available for research use. Here we report on a class of commercial benzothiazole/benzoxazole containing fluorescent DNA intercalators from Invitrogen that possess the ability to bind amyloid Aβ1-42 peptide and hamster prion. These dyes fluoresce from 500–750 nm and are available as dimers or monomers. We demonstrate that these dyes can be used as acceptors for thioflavin-T fluorescence resonance energy transfer as well as reporter groups for binding studies with Congo red and chrysamine G. As more potential therapeutic compounds for these diseases are generated, there is a need for simple and inexpensive methods to monitor their interactions with amyloids. The fluorescent dyes reported here are readily available and can be used as tools for biochemical studies of amyloid structures and in vitro screening of potential therapeutics.
Collapse
|
14
|
Kovalska V, Losytskyy M, Chernii V, Volkova K, Tretyakova I, Cherepanov V, Yarmoluk S, Volkov S. Studies of anti-fibrillogenic activity of phthalocyanines of zirconium containing out-of-plane ligands. Bioorg Med Chem 2012; 20:330-4. [DOI: 10.1016/j.bmc.2011.10.083] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Revised: 10/28/2011] [Accepted: 10/29/2011] [Indexed: 10/15/2022]
|
15
|
Brandenburg E, Berlepsch HV, Koksch B. Specific in situ discrimination of amyloid fibrilsversus α-helical fibres by the fluorophore NIAD-4. ACTA ACUST UNITED AC 2012; 8:557-64. [DOI: 10.1039/c1mb05370a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|