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Binacchi F, Giorgi E, Salvadori G, Cirri D, Stifano M, Donati A, Garzella L, Busto N, Garcia B, Pratesi A, Biver T. Exploring the interaction between a fluorescent Ag(I)-biscarbene complex and non-canonical DNA structures: a multi-technique investigation. Dalton Trans 2024; 53:9700-9714. [PMID: 38775704 DOI: 10.1039/d4dt00851k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Silver compounds are mainly studied as antimicrobial agents, but they also have anticancer properties, with the latter, in some cases, being better than their gold counterparts. Herein, we analyse the first example of a new Ag(I)-biscarbene that can bind non-canonical structures of DNA, more precisely G-quadruplexes (G4), with different binding signatures depending on the type of G4. Moreover, we show that this Ag-based carbene binds the i-motif DNA structure. Alternatively, its Au(I) counterpart, which was investigated for comparison, stabilises mitochondrial G4. Theoretical in silico studies elucidated the details of different binding modes depending on the geometry of G4. The two complexes showed increased cytotoxic activity compared to cisplatin, overcoming its resistance in ovarian cancer. The binding of these new drug candidates with other relevant biosubstrates was studied to afford a more complete picture of their possible targets. In particular, the Ag(I) complex preferentially binds DNA structures over RNA structures, with higher binding constants for the non-canonical nucleic acids with respect to natural calf thymus DNA. Regarding possible protein targets, its interaction with the albumin model protein BSA was also tested.
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Affiliation(s)
- Francesca Binacchi
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy.
| | - Ester Giorgi
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy.
| | - Giacomo Salvadori
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy.
| | - Damiano Cirri
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy.
| | - Mariassunta Stifano
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy.
| | - Aurora Donati
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy.
| | - Linda Garzella
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy.
| | - Natalia Busto
- Departamento de Ciencias de la Salud, Universidad de Burgos, Paseo de los Comendadores s/n, 09001 Burgos, Spain
| | - Begona Garcia
- Departamento de Química, Universidad de Burgos, Plaza Misael Bañuelos s/n, 09001 Burgos, Spain
| | - Alessandro Pratesi
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy.
| | - Tarita Biver
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy.
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Kashapov R, Razuvayeva Y, Kashapova N, Ziganshina A, Salnikov V, Sapunova A, Voloshina A, Zakharova L. Emergence of Nanoscale Drug Carriers through Supramolecular Self-Assembly of RNA with Calixarene. Int J Mol Sci 2023; 24:ijms24097911. [PMID: 37175618 PMCID: PMC10178118 DOI: 10.3390/ijms24097911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/15/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
Supramolecular self-assembly is a powerful tool for the development of polymolecular assemblies that can form the basis of useful nanomaterials. Given the increasing popularity of RNA therapy, the extension of this concept of self-assembly to RNA is limited. Herein, a simple method for the creation of nanosized particles through the supramolecular self-assembly of RNA with a three-dimensional macrocycle from the calixarene family was reported for the first time. This self-assembly into nanoparticles was realized using cooperative supramolecular interactions under mild conditions. The obtained nanoparticles are able to bind various hydrophobic (quercetin, oleic acid) and hydrophilic (doxorubicin) drugs, as a result of which their cytotoxic properties are enhanced. This work demonstrates that intermolecular interactions between flexible RNA and rigid calixarene is a promising route to bottom-up assembly of novel supramolecular soft matter, expanding the design possibilities of nanoscale drug carriers.
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Affiliation(s)
- Ruslan Kashapov
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, 8 Arbuzov Str., 420088 Kazan, Russia
| | - Yuliya Razuvayeva
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, 8 Arbuzov Str., 420088 Kazan, Russia
| | - Nadezda Kashapova
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, 8 Arbuzov Str., 420088 Kazan, Russia
| | - Albina Ziganshina
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, 8 Arbuzov Str., 420088 Kazan, Russia
| | - Vadim Salnikov
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, 2/31 Lobachevsky Str., 420111 Kazan, Russia
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 18, Kremlyovskaya Str., 420008 Kazan, Russia
| | - Anastasiia Sapunova
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, 8 Arbuzov Str., 420088 Kazan, Russia
| | - Alexandra Voloshina
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, 8 Arbuzov Str., 420088 Kazan, Russia
| | - Lucia Zakharova
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center of RAS, 8 Arbuzov Str., 420088 Kazan, Russia
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On the Different Mode of Action of Au(I)/Ag(I)-NHC Bis-Anthracenyl Complexes Towards Selected Target Biomolecules. Molecules 2020; 25:molecules25225446. [PMID: 33233711 PMCID: PMC7699860 DOI: 10.3390/molecules25225446] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/14/2020] [Accepted: 11/16/2020] [Indexed: 12/20/2022] Open
Abstract
Gold and silver N-heterocyclic carbenes (NHCs) are emerging for therapeutic applications. Multiple techniques are here used to unveil the mechanistic details of the binding to different biosubstrates of bis(1-(anthracen-9-ylmethyl)-3-ethylimidazol-2-ylidene) silver chloride [Ag(EIA)2]Cl and bis(1-(anthracen-9-ylmethyl)-3-ethylimidazol-2-ylidene) gold chloride [Au(EIA)2]Cl. As the biosubstrates, we tested natural double-stranded DNA, synthetic RNA polynucleotides (single-poly(A), double-poly(A)poly(U) and triple-stranded poly(A)2poly(U)), DNA G-quadruplex structures (G4s), and bovine serum albumin (BSA) protein. Absorbance and fluorescence titrations, mass spectrometry together with melting and viscometry tests show significant differences in the binding features between silver and gold compounds. [Au(EIA)2]Cl covalently binds BSA. It is here evidenced that the selectivity is high: low affinity and external binding for all polynucleotides and G4s are found. Conversely, in the case of [Ag(EIA)2]Cl, the binding to BSA is weak and relies on electrostatic interactions. [Ag(EIA)2]Cl strongly/selectively interacts only with double strands by a mechanism where intercalation plays the major role, but groove binding is also operative. The absence of an interaction with triplexes indicates the major role played by the geometrical constraints to drive the binding mode.
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Dong Z, Liu X, Tan L. Biophysical insights into the interaction of two enantiomers of Ru(II) complex [Ru(bpy) 2(7-CH 3-dppz)] 2+ with the RNA poly(U-A⁎U) triplex. J Biol Inorg Chem 2020; 25:1085-1095. [PMID: 33040210 DOI: 10.1007/s00775-020-01825-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 09/28/2020] [Indexed: 01/14/2023]
Abstract
To determine the factors affecting the stabilization of RNA triple-stranded structure by chiral Ru(II) polypyridyl complexes, a new pair of enantiomers, ∆-[Ru(bpy)2(7-CH3-dppz)]2+ (∆-1; bpy = 2,2'-bipyridine, 7-CH3-dppz = 7-methyl-dipyrido[3,2-a,2',3'-c]phenazine) and Λ-[Ru(bpy)2(7-CH3-dppz)]2+ (Λ-1), have been synthesized and characterized in this work. Binding properties of the two enantiomers with the RNA poly(U-A⁎U) triplex (where "-" denotes the Watson - Crick base pairing and "⁎" denotes the Hoogsteen base pairing) have been studied by spectroscopy and hydrodynamics methods. Under the conditions used in this study, changes in absorption spectra of the two enantiomers are not very different from each other when bound to the triplex, although the binding affinity of ∆-1 is higher than that of Λ-1. Fluorescence titrations and viscosity experiments give convincing evidence for a true intercalative binding of enantiomers with the triplex. However, melting experiments indicated that the two enantiomers selectively stabilized the triplex. The enantiomer ∆-1 stabilize the template duplex and third-strand of the triplex, while it's more effective for stabilization of the template duplex. In stark contrast to ∆-1, Λ-1 stabilizes the triplex without any effect on the third-strand stabilization, suggesting this one extremely prefers to stabilize the template duplex rather than third-strand. Besides, the triplex stabilization effect of ∆-1 is more marked in comparison with that of Λ-1. The obtained results suggest that substituent effects and chiralities of Ru(II) polypyridyl complexes play important roles in the triplex stabilization. Complexes Λ/Δ-[Ru(bpy)2(7-CH3-dppz)]2+ (Λ/Δ-1; bpy = 2,2'-bipyridine, 7-CH3-dppz = 7-methyl-dipyrido[3,2-a,2',3'-c]phenazine) were prepared as stabilizers for poly(U-A ∗ U) triplex. Results suggest the triplex stabilization depends the chiral structures of Λ/Δ-1, indicating that [Ru(bpy)2(7-CH3-dppz)]2+ is a non-specific intercalator for poly(U-A ∗ U) investigated in this work.
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Affiliation(s)
- Zhan Dong
- College of Chemistry, Xiangtan University, Xiangtan, 411105, People's Republic of China
| | - Xiaohua Liu
- Academic Affairs Office, Xiangtan University, Xiangtan, 411105, People's Republic of China
| | - Lifeng Tan
- Key Lab of Environment-Friendly Chemistry and Application in Ministry of Education, Xiangtan University, Xiangtan, 411105, People's Republic of China. .,Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Xiangtan University, Xiangtan, 411105, People's Republic of China.
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5
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Jawad B, Poudel L, Podgornik R, Ching WY. Thermodynamic Dissection of the Intercalation Binding Process of Doxorubicin to dsDNA with Implications of Ionic and Solvent Effects. J Phys Chem B 2020; 124:7803-7818. [PMID: 32786213 DOI: 10.1021/acs.jpcb.0c05840] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Doxorubicin (DOX) is a cancer drug that binds to dsDNA through intercalation. A comprehensive microsecond timescale molecular dynamics study is performed for DOX with 16 tetradecamer dsDNA sequences in explicit aqueous solvent, in order to investigate the intercalation process at both binding stages (conformational change and insertion binding stages). The molecular mechanics generalized Born surface area (MM-GBSA) method is adapted to quantify and break down the binding free energy (BFE) into its thermodynamic components, for a variety of different solution conditions as well as different DNA sequences. Our results show that the van der Waals interaction provides the largest contribution to the BFE at each stage of binding. The sequence selectivity depends mainly on the base pairs located downstream from the DOX intercalation site, with a preference for (AT)2 or (TA)2 driven by the favorable electrostatic and/or van der Waals interactions. Invoking the quartet sequence model proved to be most successful to predict the sequence selectivity. Our findings also indicate that the aqueous bathing solution (i.e., water and ions) opposes the formation of the DOX-DNA complex at every binding stage, thus implying that the complexation process preferably occurs at low ionic strength and is crucially dependent on solvent effects.
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Affiliation(s)
- Bahaa Jawad
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City 64110, Missouri, United States.,Department of Applied Sciences, University of Technology, Baghdad 10066, Iraq
| | - Lokendra Poudel
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Rudolf Podgornik
- School of Physical Sciences and Kavli Institute of Theoretical Science, University of Chinese Academy of Sciences, Beijing 100049, China.,CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100090, China.,Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Wai-Yim Ching
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City 64110, Missouri, United States
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Zhou Y, Bielec K, Pasitsuparoad P, Hołyst R. Single-molecule brightness analysis for the determination of anticancer drug interactions with DNA. Analyst 2020; 145:6600-6606. [PMID: 32785299 DOI: 10.1039/d0an01108h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Anthracyclines are one of the most studied anticancer drugs approved for medical treatment. The equilibrium constant (K) of the reaction between these drugs with DNA in both in vitro and in vivo experiments lacks consensus. The K values vary from 104 up to 108 M-1, which suggest a 1000-fold error in determining the effective concentration needed to form the drug-DNA complex. Until 2014, only one study by García [J. Phys. Chem. B, 2014, 118, 1288-1295] showed that the binding of anthracycline representative doxorubicin occurs in two reactions. We support this result by brightness analysis at a single molecular level for the four most common anthracyclines: doxorubicin, daunorubicin, epirubicin, and idarubicin.
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Affiliation(s)
- Ying Zhou
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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7
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Wang F, Sun Y, Liu X, Li Y, Tan L. Third-strand stabilizing effects of the RNA poly(U)·poly(A)*poly(U) triplex by a ruthenium(II) polypyridine complex and its hexaarginine peptide conjugate. Int J Biol Macromol 2019; 135:1134-1141. [PMID: 31176864 DOI: 10.1016/j.ijbiomac.2019.06.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 05/28/2019] [Accepted: 06/04/2019] [Indexed: 01/14/2023]
Abstract
In this work, a Ru(II) complex [Ru(bpy)2(pip-CO2H)]2+ (Ru1) and its hexaarginine peptide conjugate [Ru(bpy)2(pic-Arg6)]8+ (Ru2) have been synthesized and characterized. The binding of Ru1 and Ru2 with poly(U)•poly(A)*poly(U) triplex has been studied. Results suggest that Ru1 binds in the surface of the minor groove while Ru2 binds to the minor groove of the triplex. Consequently, the triplex stabilization is barely affected by Ru1, while with Ru2 the triplex stabilizing effect is so strong that that dissociation of the triplex shows an overlapping of both melting processes with the melting temperature increased to a maximum of 56.1 °C at the CRu2/CUAU ratio of 0.05, where ΔTm1 and ΔTm2 are 19.6 and 10.1 °C, respectively. Furthermore, the effect of Ru2 stabilizing the third strand at such a low binding ratio of 0.05 is more marked than what obsereved for flavone luteolin and [Ru(bpy)2(mdpz)]2+, which are so far the strongest triplex stabilizers in the reported organic small molecules and metal complexes, respectively. Considering the structure natures of Ru2, conceivably except for electrostatic interaction, the forces stabilizing the triplex should also involve hydrophobic interaction and hydrogen bingding. To our knowledge, this work represents a first example of improving the triplex stabilization by a metallopeptide.
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Affiliation(s)
- Fangfang Wang
- College of Chemistry, Xiangtan University, Xiangtan 411105, PR China
| | - Yanmei Sun
- College of Chemistry, Xiangtan University, Xiangtan 411105, PR China
| | - Xiaohua Liu
- Academic Affairs Office, Xiangtan University, Xiangtan 411105, PR China
| | - Yi Li
- Key Laboratory of Theoretical Organic Chemistry and Function Molecule, Ministry of Education, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, PR China
| | - Lifeng Tan
- Key Lab of Environment-friendly Chemistry and Application in Ministry of Education, Xiangtan University, Xiangtan 411105, PR China; Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Xiangtan University, Xiangtan 411105, PR China.
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8
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Zhang X, Poniewierski A, Sozański K, Zhou Y, Brzozowska-Elliott A, Holyst R. Fluorescence correlation spectroscopy for multiple-site equilibrium binding: a case of doxorubicin–DNA interaction. Phys Chem Chem Phys 2019; 21:1572-1577. [DOI: 10.1039/c8cp06752j] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Quantification of multiple equilibrium binding on the example of doxorubicin–DNA interaction using fluorescence correlation spectroscopy.
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Affiliation(s)
- Xuzhu Zhang
- Department of Soft Condensed Matter
- Institute of Physical Chemistry
- Polish Academy of Sciences
- Warsaw
- Poland
| | - Andrzej Poniewierski
- Department of Soft Condensed Matter
- Institute of Physical Chemistry
- Polish Academy of Sciences
- Warsaw
- Poland
| | - Krzysztof Sozański
- Department of Soft Condensed Matter
- Institute of Physical Chemistry
- Polish Academy of Sciences
- Warsaw
- Poland
| | - Ying Zhou
- Department of Soft Condensed Matter
- Institute of Physical Chemistry
- Polish Academy of Sciences
- Warsaw
- Poland
| | - Anna Brzozowska-Elliott
- Department of Soft Condensed Matter
- Institute of Physical Chemistry
- Polish Academy of Sciences
- Warsaw
- Poland
| | - Robert Holyst
- Department of Soft Condensed Matter
- Institute of Physical Chemistry
- Polish Academy of Sciences
- Warsaw
- Poland
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