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Buchelnikov AS, Evstigneev VP, Evstigneev MP. Hetero-association models of non-covalent molecular complexation. Phys Chem Chem Phys 2019; 21:7717-7731. [PMID: 30931443 DOI: 10.1039/c8cp03183e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The present review discusses the current state-of-the-art in building models enabling the description of non-covalent equilibrium complexation of different types of molecules in solution, which results in the formation of supramolecular structures different in length and composition (hetero-association or supramolecular multicomponent co-polymerisation). The description is focused on standard physical and chemical quantities such as experimental observables and equilibrium parameters of interaction (equilibrium constants and concentrations). The major partial cases of the hetero-association models, such as finite and indefinite isodesmic and cooperative complexations, and Benesi-Hildebrand and Langmuir adsorption models are considered. Future challenges in the development of the hetero-association models are provided.
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General statistical-thermodynamical treatment of one-dimensional multicomponent molecular hetero-assembly in solution. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.06.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Evstigneev MP, Buchelnikov AS, Kostjukov VV, Pashkova IS, Evstigneev VP. Indistinguishability of the models of molecular self-assembly. Supramol Chem 2012. [DOI: 10.1080/10610278.2012.752090] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Maxim P. Evstigneev
- a Department of Physics , Sevastopol National Technical University , Universitetskaya str. 33, Sevastopol , 99053 , Ukraine
| | - Anatoly S. Buchelnikov
- a Department of Physics , Sevastopol National Technical University , Universitetskaya str. 33, Sevastopol , 99053 , Ukraine
| | - Viktor V. Kostjukov
- a Department of Physics , Sevastopol National Technical University , Universitetskaya str. 33, Sevastopol , 99053 , Ukraine
| | - Irina S. Pashkova
- a Department of Physics , Sevastopol National Technical University , Universitetskaya str. 33, Sevastopol , 99053 , Ukraine
| | - Vladyslav P. Evstigneev
- a Department of Physics , Sevastopol National Technical University , Universitetskaya str. 33, Sevastopol , 99053 , Ukraine
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Quantification of the interceptor action of caffeine on the in vitro biological effect of the anti-tumour agent topotecan. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2011; 40:969-80. [PMID: 21674180 DOI: 10.1007/s00249-011-0712-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Revised: 05/01/2011] [Accepted: 05/16/2011] [Indexed: 10/18/2022]
Abstract
Using published in vitro data on the dependence of the percentage of apoptosis induced by the anti-cancer drug topotecan in a leukaemia cell line on the concentration of added caffeine, and a general model of competitive binding in a system containing two aromatic drugs and DNA, it has been shown to be possible to quantify the relative change in the biological effect just using a set of component concentrations and equilibrium constants of the complexation of the drugs. It is also proposed that a general model of competitive binding and parameterization of that model may potentially be applied to any system of DNA-targeting aromatic drugs under in vitro conditions. The main reasons underpinning the proposal are the general feature of the complexation of aromatic drugs with DNA and their interaction in physiological media via hetero-association.
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Evstigneev VP, Mosunov AA, Buchelnikov AS, Hernandez Santiago AA, Evstigneev MP. Complete solution of the problem of one-dimensional non-covalent non-cooperative self-assembly in two-component systems. J Chem Phys 2011; 134:194902. [DOI: 10.1063/1.3589899] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Beshnova DA, Bereznyak EG, Shestopalova AV, Evstigneev MP. A novel computational approach “BP-STOCH” to study ligand binding to finite lattice. Biopolymers 2010; 95:208-16. [DOI: 10.1002/bip.21562] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Santiago AH, Rosas Castilla S, Morales Rodriguez A, Aleskerova E, Lantushenko A, Kostjukov V, Davies D, Evstigneev M. Relation between structure and enthalpy for stacking interactions of aromatic molecules. Mol Phys 2010. [DOI: 10.1080/00268976.2010.498389] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Complexation of biologically active aromatic compounds with DNA in the presence of theophylline. J Biol Phys 2009; 35:115-26. [PMID: 19669556 DOI: 10.1007/s10867-008-9124-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2008] [Accepted: 11/26/2008] [Indexed: 10/21/2022] Open
Abstract
(1)H NMR measurements (500 MHz) have been used to determine the equilibrium hetero-association constants of theophylline (THP) with various biologically active aromatic compounds (daunomycin, novantrone, ethidium bromide, proflavine, norfloxacin) and the complexation constants of THP with both single- and double-stranded oligonucleotides in solution. The results provide a quantitative estimation of the effect of THP on the binding of aromatic ligands with DNA, and a determination of the fraction of aromatic ligand removed from DNA on addition of THP.
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Quantitation of the molecular mechanisms of biological synergism in a mixture of DNA-acting aromatic drugs. Biophys Chem 2008; 132:148-58. [DOI: 10.1016/j.bpc.2007.11.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2007] [Revised: 11/04/2007] [Accepted: 11/05/2007] [Indexed: 01/01/2023]
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Odille FGJ, Jónsson S, Stjernqvist S, Rydén T, Wärnmark K. On the Characterization of Dynamic Supramolecular Systems: A General Mathematical Association Model for Linear Supramolecular Copolymers and Application on a Complex Two-Component Hydrogen-Bonding System. Chemistry 2007; 13:9617-36. [PMID: 17868169 DOI: 10.1002/chem.200700032] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A general mathematical model for the characterization of the dynamic (kinetically labile) association of supramolecular assemblies in solution is presented. It is an extension of the equal K (EK) model by the stringent use of linear algebra to allow for the simultaneous presence of an unlimited number of different units in the resulting assemblies. It allows for the analysis of highly complex dynamic equilibrium systems in solution, including both supramolecular homo- and copolymers without the recourse to extensive approximations, in a field in which other analytical methods are difficult. The derived mathematical methodology makes it possible to analyze dynamic systems such as supramolecular copolymers regarding for instance the degree of polymerization, the distribution of a given monomer in different copolymers as well as its position in an aggregate. It is to date the only general means to characterize weak supramolecular systems. The model was fitted to NMR dilution titration data by using the program Matlab, and a detailed algorithm for the optimization of the different parameters has been developed. The methodology is applied to a case study, a hydrogen-bonded supramolecular system, salen 4+porphyrin 5. The system is formally a two-component system but in reality a three-component system. This results in a complex dynamic system in which all monomers are associated to each other by hydrogen bonding with different association constants, resulting in homo- and copolymers 4n5m as well as cyclic structures 6 and 7, in addition to free 4 and 5. The system was analyzed by extensive NMR dilution titrations at variable temperatures. All chemical shifts observed at different temperatures were used in the fitting to obtain the DeltaH degrees and DeltaS degrees values producing the best global fit. From the derived general mathematical expressions, system 4+5 could be characterized with respect to above-mentioned parameters.
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Affiliation(s)
- Fabrice G J Odille
- Organic Chemistry, Department of Chemistry, Lund University, P.O. Box 124, 221 00 Lund, Sweden
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Evstigneev MP, Evstigneev VP, Davies DB. A method for analysis of multicomponent systems of interacting aromatic molecules in solution. J Chem Phys 2007; 127:154511. [DOI: 10.1063/1.2785182] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Evstigneev MP, Rybakova KA, Davies DB. Formation of complexes of antimicrobial agent norfloxacin with antitumor antibiotics of anthracycline series. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2007. [DOI: 10.1134/s0036024407050275] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Evstigneev MP, Khomich VV, Davies DB. Complexation of anthracycline drugs with DNA in the presence of caffeine. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2006; 36:1-11. [PMID: 17061089 DOI: 10.1007/s00249-006-0071-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2006] [Revised: 03/22/2006] [Accepted: 04/24/2006] [Indexed: 10/24/2022]
Abstract
The competitive binding of anthracycline antitumour drugs, [daunomycin (DAU), doxorubicin (DOX) or nogalamycin (NOG)], with caffeine (CAF) to a model DNA oligomer has been investigated by 500 MHz 1H NMR spectroscopy under physiological solution conditions. The method depends on the stepwise analysis of one-component (self-association), two-component (hetero-association and DNA complexation) and three-component interactions, in order to de-convolute the overall binding of the anthracycline antibiotic and CAF to DNA into two competing processes, viz. hetero-association of the antibiotic-CAF ('interceptor' action of CAF) and CAF-DNA complexation ('protector' action of CAF). It is found that the complexation of DAU with DNA in the presence of CAF is mainly affected by the CAF-DNA complexation, whereas the binding of either DOX or NOG to DNA is affected approximately equally by both the CAF-DNA complexation and CAF-antibiotic hetero-association. Quantitative evaluation of the three-component mixture of drug-CAF-DNA has enabled the proportion of the antibiotic displaced from DNA on addition of CAF to be calculated over a large range of CAF concentration, which may provide a quantitative basis for the change in anthracycline-related toxicity on addition of CAF.
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Affiliation(s)
- M P Evstigneev
- Department of Physics, Sevastopol National Technical University, Sevastopol 99053, Crimea, Ukraine.
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Evstigneev MP, Rybakova KA, Davies DB. Heteroassociation of antibiotic norfloxacin with aromatic vitamins in aqueous solution. Biophysics (Nagoya-shi) 2006. [DOI: 10.1134/s0006350906040129] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Evstigneev MP, Rybakova KA, Davies DB. Complexation of norfloxacin with DNA in the presence of caffeine. Biophys Chem 2006; 121:84-95. [PMID: 16455179 DOI: 10.1016/j.bpc.2005.12.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2005] [Revised: 12/05/2005] [Accepted: 12/07/2005] [Indexed: 10/25/2022]
Abstract
(1)H NMR spectroscopy (500 MHz) has been used to quantify the complexation of the antibacterial antibiotic Norfloxacin (NOR) with DNA in the presence of Caffeine (CAF). Separate studies have been made for the self-association of NOR, its hetero-association with CAF and complexation with a model self-complementary DNA tetramer, 5'-d(TpGpCpA), in order to determine the equilibrium parameters (induced chemical shifts, association constants, enthalpy and entropy) of the two-component mixtures to aid the analysis of the three-component systems. Investigations of the self-association of NOR and its hetero-association with CAF show that the aggregation of NOR molecules and association with CAF in solution are driven by the stacking of aromatic chromophores. The complexation of NOR with d(TGCA) has been analysed in terms of intercalation with the double-stranded form and non-intercalative binding with the single-stranded form of DNA. Investigations of the competitive binding of NOR and CAF with DNA show that at physiological concentrations of NOR (muM) and CAF (mM) the dominant mechanism influencing the affinity of NOR with DNA is the displacement of bound NOR molecules from DNA due to CAF-DNA complexation (i.e. the protector action of Caffeine).
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Affiliation(s)
- M P Evstigneev
- Department of Physics, Sevastopol National Technical University, Studgorodok, Sevastopol, 99053, Crimea, Ukraine.
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Rozvadovskaya AO, Evstigneev VP, Davies DB, Evstigneev MP. Interaction between aromatic antibiotics and vitamins: 1H NMR study of heteroassociation of nicotinamide and anthracycline antitumor antibiotics. Biophysics (Nagoya-shi) 2006. [DOI: 10.1134/s0006350906020047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Evstigneev MP, Mukhina YV, Davies DB. 1H NMR study of the hetero-association of flavin-mononucleotide with mutagenic dyes: ethidium bromide and proflavine. Mol Phys 2006. [DOI: 10.1080/00268970500512323] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Evstigneev MP, Evstigneev VP, Santiago AAH, Davies DB. Effect of a mixture of caffeine and nicotinamide on the solubility of vitamin (B2) in aqueous solution. Eur J Pharm Sci 2006; 28:59-66. [PMID: 16483751 DOI: 10.1016/j.ejps.2005.12.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2005] [Revised: 12/22/2005] [Accepted: 12/30/2005] [Indexed: 11/20/2022]
Abstract
The effect of caffeine (CAF) and nicotinamide (NMD) on the solubility of a vitamin B2 derivative (FMN) has been evaluated for mixtures containing either a single hydrotrope (CAF or NMD) or the two hydrotropes simultaneously. A model for analysis of ternary systems, which takes into account all possible complexes between the molecules, has been developed and tested with experimental NMR data on the three-component mixture FMN-CAF-NMD. The results indicate that special attention should be given to the concentration of a hydrotropic agent used to enhance the solubility of a particular drug. A decrease in the efficacy of solubility of the vitamin on addition of large amounts of hydrotropic agent is expected in the two-component systems due to the increased proportion of self-association of the hydrotrope. It is found that a mixture of two hydrotropic agents leads to an increase in the solubility of the vitamin in three-component compared to the two-component system. Rather than using just one hydrotropic agent, it is proposed that a strategy for optimising the solubility of aromatic drugs is to use a mixture of hydrotropic agents.
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Affiliation(s)
- M P Evstigneev
- Department of Physics, Sevastopol National Technical University, Studgorodok, Sevastopol, 99053 Crimea, Ukraine.
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Ulanowska K, Piosik J, Gwizdek-Wiśniewska A, We Grzyn G. Formation of stacking complexes between caffeine (1,2,3-trimethylxanthine) and 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine may attenuate biological effects of this neurotoxin. Bioorg Chem 2006; 33:402-13. [PMID: 16165186 DOI: 10.1016/j.bioorg.2005.07.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2005] [Revised: 07/17/2005] [Accepted: 07/27/2005] [Indexed: 11/26/2022]
Abstract
1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) is a neurotoxin causing symptoms that may resemble those observed in patients suffering from Parkinson's disease. Therefore, MPTP-treated laboratory animals are currently the most favored models to study therapeutic intervention strategies in this disease. It was demonstrated recently that caffeine (1,2,3-trimethylxanthine) intake decreases the risk of Parkinson's disease in various human populations and attenuates MPTP-induced neurological effects in animal models. Since the effects of caffeine on MPTP-treated animals were mimicked by several antagonists of the adenosine A(2A) receptor, it was suggested that caffeine attenuates MPTP toxicity by blocking this receptor. Here, using microcalorimetry and molecular modeling, we demonstrate that caffeine can form stacking (pi-pi) complexes with MPTP. We found that a biological activity of MPTP (induction of mutations in a microbiological mutagenicity assay), which is completely independent on the A(2A) receptor blockade, is significantly reduced by caffeine. Therefore, we suggest that caffeine may attenuate neurotoxicity of MPTP (and possibly other polycyclic aromatic toxins) and reveal its protective effects on the risk of Parkinson's disease not only by blocking the A(2A) receptor but also by sequestering neurotoxin molecules in mixed complexes, especially in stomach.
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Affiliation(s)
- Katarzyna Ulanowska
- Department of Molecular Biology, University of Gdańsk, Kładki 24, 80-822 Gdansk, Poland
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Evstigneev MP, Davies DB, Veselkov AN. Stochastic models (cooperative and non-cooperative) for NMR analysis of the hetero-association of aromatic molecules in aqueous solution. Chem Phys 2006. [DOI: 10.1016/j.chemphys.2005.07.030] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Analysis by Means of 1H NMR Spectroscopy of Heteroassociaion in Water Solution of Antitumor Antibiotics Daunomycin and Actinomycin D. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2005. [DOI: 10.1007/s11178-005-0308-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Zhao J, Xia S, Gao H. Investigation of Interaction of Proflavine and Naphthol Red in Nucleic Acids by Light‐Absorption Spectrometry. JOURNAL OF MACROMOLECULAR SCIENCE PART A-PURE AND APPLIED CHEMISTRY 2004. [DOI: 10.1081/ma-120027177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Veselkov A, Evstigneev M, Rozvadovskaya A, Hernandez Santiago A, Zubchenok O, Djimant L, Davies D. 1H NMR structural and thermodynamical analysis of the hetero-association of daunomycin and novatrone in aqueous solution. J Mol Struct 2004. [DOI: 10.1016/j.molstruc.2004.05.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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