1
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Mikaelian G, Megariotis G, Theodorou DN. Interactions of a Novel Anthracycline with Oligonucleotide DNA and Cyclodextrins in an Aqueous Environment. J Phys Chem B 2024; 128:6291-6307. [PMID: 38899795 PMCID: PMC11228990 DOI: 10.1021/acs.jpcb.4c02213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 06/07/2024] [Accepted: 06/11/2024] [Indexed: 06/21/2024]
Abstract
Berubicin, a chemotherapy medication belonging to the class of anthracyclines, is simulated in double-stranded DNA sequences and cyclodextrins in an aqueous environment via full-atom molecular dynamics simulations on the time scale of microseconds. The drug is studied in both the neutral and protonated states so as to better comprehend the role of its charge in the formed complexes. The noncovalent berubicin-DNA and berubicin-cyclodextrin complexes are investigated in detail, paying special attention to their thermodynamic description by employing the double decoupling method, the solvent balance method, the weighted solvent accessible surface model, and the linear interaction energy method. A novel approach for extracting the desolvation thermodynamics of the binding process is also presented. Both the binding and desolvation Gibbs energies are decomposed into entropic and enthalpic contributions so as to elucidate the nature of complexation and its driving forces. Selected structural and geometrical properties of all the complexes, which are all stable, are analyzed. Both cyclodextrins under consideration are widely utilized for drug delivery purposes, and a comparative investigation between their bound states with berubicin is carried out.
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Affiliation(s)
- Georgios Mikaelian
- School
of Chemical Engineering, National Technical
University of Athens (NTUA), 9 Heroon Polytechniou Street, Zografou Campus, 15780 Athens, GR ,Greece
| | - Grigorios Megariotis
- School
of Chemical Engineering, National Technical
University of Athens (NTUA), 9 Heroon Polytechniou Street, Zografou Campus, 15780 Athens, GR ,Greece
- School
of Engineering, Department of Mineral Resources Engineering, University of Western Macedonia, 50100 Kozani, Greece
| | - Doros N. Theodorou
- School
of Chemical Engineering, National Technical
University of Athens (NTUA), 9 Heroon Polytechniou Street, Zografou Campus, 15780 Athens, GR ,Greece
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2
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Schönbeck C, Kari J, Westh P. ITC analysis of polydisperse systems: Unravelling the impact of sample heterogeneity. Anal Biochem 2024; 687:115446. [PMID: 38147946 DOI: 10.1016/j.ab.2023.115446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/13/2023] [Accepted: 12/20/2023] [Indexed: 12/28/2023]
Abstract
Binding interactions often involve heterogeneous samples displaying a distribution of binding sites that vary in affinity and binding enthalpy. Examples include biological samples like proteins and chemically produced samples like modified cyclodextrins. Experimental studies often ignore sample heterogeneity and treat the system as an interaction of two homogeneous species, i.e. a chemically well-defined ligand binding to one type of site. The present study explores, by simulations and experiments, the impact of heterogeneity in isothermal titration calorimetry (ITC) setups where one of the binding components is heterogeneous. It is found that the standard single-site model, based on the assumption of two homogeneous binding components, provides excellent fits to simulated ITC data when the binding free energy is normally distributed and all sites have similar binding enthalpies. In such cases, heterogeneity can easily go undetected but leads to underestimated binding constants. Heterogeneity in the binding enthalpy is a bigger problem and may result in enthalpograms of increased complexity that are likely to be misinterpreted as two-site binding or other complex binding models. Finally, it is shown that heterogeneity can account for previously observed experimental anomalies. All simulations are accessible in Google Colab for readers to experiment with the simulation parameters.
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Affiliation(s)
| | - Jeppe Kari
- Department of Science and Environment, Roskilde University, Denmark
| | - Peter Westh
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Denmark
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3
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Grimm LM, Setiadi J, Tkachenko B, Schreiner PR, Gilson MK, Biedermann F. The temperature-dependence of host-guest binding thermodynamics: experimental and simulation studies. Chem Sci 2023; 14:11818-11829. [PMID: 37920355 PMCID: PMC10619620 DOI: 10.1039/d3sc01975f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 09/24/2023] [Indexed: 11/04/2023] Open
Abstract
The thermodynamic parameters of host-guest binding can be used to describe, understand, and predict molecular recognition events in aqueous systems. However, interpreting binding thermodynamics remains challenging, even for these relatively simple molecules, as they are determined by both direct and solvent-mediated host-guest interactions. In this contribution, we focus on the contributions of water to binding by studying binding thermodynamics, both experimentally and computationally, for a series of nearly rigid, electrically neutral host-guest systems and report the temperature-dependent thermodynamic binding contributions ΔGb(T), ΔHb(T), ΔSb(T), and ΔCp,b. Combining isothermal titration calorimetry (ITC) measurements with molecular dynamics (MD) simulations, we provide insight into the binding forces at play for the macrocyclic hosts cucurbit[n]uril (CBn, n = 7-8) and β-cyclodextrin (β-CD) with a range of guest molecules. We find consistently negative changes in heat capacity on binding (ΔCp,b) for all systems studied herein - as well as for literature host-guest systems - indicating increased enthalpic driving forces for binding at higher temperatures. We ascribe these trends to solvation effects, as the solvent properties of water deteriorate as temperature rises. Unlike the entropic and enthalpic contributions to binding, with their differing signs and magnitudes for the classical and non-classical hydrophobic effect, heat capacity changes appear to be a unifying and more general feature of host-guest complex formation in water. This work has implications for understanding protein-ligand interactions and other complex systems in aqueous environments.
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Affiliation(s)
- Laura M Grimm
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz Platz 1 76344 Eggenstein-Leopoldshafen Germany
| | - Jeffry Setiadi
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego 9255 Pharmacy Lane La Jolla CA 92093 USA
| | - Boryslav Tkachenko
- Institute of Organic Chemistry, Justus Liebig University Giessen Heinrich-Buff-Ring 17 35392 Giessen Germany
| | - Peter R Schreiner
- Institute of Organic Chemistry, Justus Liebig University Giessen Heinrich-Buff-Ring 17 35392 Giessen Germany
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego 9255 Pharmacy Lane La Jolla CA 92093 USA
| | - Frank Biedermann
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz Platz 1 76344 Eggenstein-Leopoldshafen Germany
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4
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Çınaroğlu SS, Biggin PC. The role of loop dynamics in the prediction of ligand-protein binding enthalpy. Chem Sci 2023; 14:6792-6805. [PMID: 37350814 PMCID: PMC10284145 DOI: 10.1039/d2sc06471e] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 05/31/2023] [Indexed: 06/24/2023] Open
Abstract
The enthalpic and entropic components of ligand-protein binding free energy reflect the interactions and dynamics between ligand and protein. Despite decades of study, our understanding and hence our ability to predict these individual components remains poor. In recent years, there has been substantial effort and success in the prediction of relative and absolute binding free energies, but the prediction of the enthalpic (and entropic) contributions in biomolecular systems remains challenging. Indeed, it is not even clear what kind of performance in terms of accuracy could currently be obtained for such systems. It is, however, relatively straight-forward to compute the enthalpy of binding. We thus evaluated the performance of absolute enthalpy of binding calculations using molecular dynamics simulation for ten inhibitors against a member of the bromodomain family, BRD4-1, against isothermal titration calorimetry data. Initial calculations, with the AMBER force-field showed good agreement with experiment (R2 = 0.60) and surprisingly good accuracy with an average of root-mean-square error (RMSE) = 2.49 kcal mol-1. Of the ten predictions, three were obvious outliers that were all over-predicted compared to experiment. Analysis of various simulation factors, including parameterization, buffer concentration and conformational dynamics, revealed that the behaviour of a loop (the ZA loop on the periphery of the binding site) strongly dictates the enthalpic prediction. Consistent with previous observations, the loop exists in two distinct conformational states and by considering one or the other or both states, the prediction for the three outliers can be improved dramatically to the point where the R2 = 0.95 and the accuracy in terms of RMSE improves to 0.90 kcal mol-1. However, performance across force-fields is not consistent: if OPLS and CHARMM are used, different outliers are observed and the correlation with the ZA loop behaviour is not recapitulated, likely reflecting parameterization as a confounding problem. The results provide a benchmark standard for future study and comparison.
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Affiliation(s)
- Süleyman Selim Çınaroğlu
- Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford South Parks Road Oxford OX1 3QU UK +44 (0)1865 613238 +44 (0)1865 613305
| | - Philip C Biggin
- Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford South Parks Road Oxford OX1 3QU UK +44 (0)1865 613238 +44 (0)1865 613305
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5
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dos Santos Ferreira CI, Gonzales AP, Mazzobre MF, Ulrih NP, Buera MDP. Solubility, sorption isotherms and thermodynamic parameters of β-cyclodextrin complexes with poplar propolis components: Practical implicances. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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6
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Del Regno R, Santonoceta GDG, Della Sala P, De Rosa M, Soriente A, Talotta C, Spinella A, Neri P, Sgarlata C, Gaeta C. Molecular Recognition in an Aqueous Medium Using Water-Soluble Prismarene Hosts. Org Lett 2022; 24:2711-2715. [PMID: 35389649 PMCID: PMC9016763 DOI: 10.1021/acs.orglett.2c00819] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
![]()
The synthesis of
water-soluble prism[n]arenes
(n = 5 and 6) bearing anionic carboxylato groups
on the rims is described. The binding properties of this novel class
of water-soluble hosts are studied by nuclear magnetic resonance and
calorimetry. The complexation of singly and doubly charged ammonium
guests with the more rigid pentamer is enthalpically driven by secondary
interactions, while the thermodynamic fingerprint for the larger hexamer
reveals driving forces that strongly depend on the guest charge and/or
size.
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Affiliation(s)
- Rocco Del Regno
- Dipartimento di Chimica e Biologia "A. Zambelli", Università di Salerno, Via Giovanni Paolo II 132, I-84084 Fisciano, Salerno, Italy
| | - Giuseppina D G Santonoceta
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, I-95125 Catania, Italy
| | - Paolo Della Sala
- Dipartimento di Chimica e Biologia "A. Zambelli", Università di Salerno, Via Giovanni Paolo II 132, I-84084 Fisciano, Salerno, Italy
| | - Margherita De Rosa
- Dipartimento di Chimica e Biologia "A. Zambelli", Università di Salerno, Via Giovanni Paolo II 132, I-84084 Fisciano, Salerno, Italy
| | - Annunziata Soriente
- Dipartimento di Chimica e Biologia "A. Zambelli", Università di Salerno, Via Giovanni Paolo II 132, I-84084 Fisciano, Salerno, Italy
| | - Carmen Talotta
- Dipartimento di Chimica e Biologia "A. Zambelli", Università di Salerno, Via Giovanni Paolo II 132, I-84084 Fisciano, Salerno, Italy
| | - Aldo Spinella
- Dipartimento di Chimica e Biologia "A. Zambelli", Università di Salerno, Via Giovanni Paolo II 132, I-84084 Fisciano, Salerno, Italy
| | - Placido Neri
- Dipartimento di Chimica e Biologia "A. Zambelli", Università di Salerno, Via Giovanni Paolo II 132, I-84084 Fisciano, Salerno, Italy
| | - Carmelo Sgarlata
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6, I-95125 Catania, Italy
| | - Carmine Gaeta
- Dipartimento di Chimica e Biologia "A. Zambelli", Università di Salerno, Via Giovanni Paolo II 132, I-84084 Fisciano, Salerno, Italy
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7
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Lachance-Brais C, Hennecker CD, Alenaizan A, Luo X, Toader V, Taing M, Sherrill CD, Mittermaier AK, Sleiman HF. Tuning DNA Supramolecular Polymers by the Addition of Small, Functionalized Nucleobase Mimics. J Am Chem Soc 2021; 143:19824-19833. [PMID: 34783562 DOI: 10.1021/jacs.1c08972] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nucleobase mimicking small molecules able to reconfigure DNA are a recently discovered strategy that promises to extend the structural and functional diversity of nucleic acids. However, only simple, unfunctionalized molecules such as cyanuric acid and melamine have so far been used in this approach. In this work, we show that the addition of substituted cyanuric acid molecules can successfully program polyadenine strands to assemble into supramolecular fibers. Unlike conventional DNA nanostructure functionalization, which typically end-labels DNA strands, our approach incorporates functional groups into DNA with high density using small molecules and results in new DNA triple helices coated with alkylamine or alcohol units that grow into micrometer-long fibers. We find that small changes in the small molecule functional group can result in large structural and energetic variation in the overall assembly. A combination of circular dichroism, atomic force microscopy, molecular dynamics simulations, and a new thermodynamic method, transient equilibrium mapping, elucidated the molecular factors behind these large changes. In particular, we identify substantial DNA sugar and phosphate group deformations to accommodate a hydrogen bond between the phosphate and the small-molecule functional groups, as well as a critical chain length of the functional group which switches this interaction from intra- to interfiber. These parameters allow the controlled formation of hierarchical, hybrid DNA assemblies simply through the addition and variation of small, functionalized molecules.
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Affiliation(s)
| | - Christopher D Hennecker
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, QC H3A0B8, Canada
| | - Asem Alenaizan
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332-0400, United States
| | - Xin Luo
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, QC H3A0B8, Canada
| | - Violeta Toader
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, QC H3A0B8, Canada
| | - Monica Taing
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, QC H3A0B8, Canada
| | - C David Sherrill
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332-0400, United States
| | - Anthony K Mittermaier
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, QC H3A0B8, Canada
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, QC H3A0B8, Canada
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8
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Belica-Pacha S, Daśko M, Buko V, Zavodnik I, Miłowska K, Bryszewska M. Thermodynamic Studies of Interactions between Sertraline Hydrochloride and Randomly Methylated β-Cyclodextrin Molecules Supported by Circular Dichroism Spectroscopy and Molecular Docking Results. Int J Mol Sci 2021; 22:12357. [PMID: 34830239 PMCID: PMC8620473 DOI: 10.3390/ijms222212357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 11/12/2021] [Accepted: 11/13/2021] [Indexed: 12/20/2022] Open
Abstract
The interaction between sertraline hydrochloride (SRT) and randomly methylated β-cyclodextrin (RMβCD) molecules have been investigated at 298.15 K under atmospheric pressure. The method used-Isothermal Titration Calorimetry (ITC) enabled to determine values of the thermodynamic functions like the enthalpy (ΔH), the entropy (ΔS) and the Gibbs free energy (ΔG) of binding for the examined system. Moreover, the stoichiometry coefficient of binding (n) and binding/association constant (K) value have been calculated from the experimental results. The obtained outcome was compared with the data from the literature for other non-ionic βCD derivatives interacting with SRT and the enthalpy-entropy compensation were observed and interpreted. Furthermore, the connection of RMβCD with SRT was characterized by circular dichroism spectroscopy (CD) and complexes of βCD derivatives with SRT were characterized through the computational studies with the use of molecular docking (MD).
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Affiliation(s)
- Sylwia Belica-Pacha
- Unit of Biophysical Chemistry, Department of Physical Chemistry, Faculty of Chemistry, University of Lodz, Pomorska 165, 90-236 Lodz, Poland
| | - Mateusz Daśko
- Department of Inorganic Chemistry, Faculty of Chemistry, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdansk, Poland;
| | - Vyacheslav Buko
- Division of Biochemical Pharmacology, Institute of Biochemistry of Biologically Active Compounds, National Academy of Sciences, BLK-50, 230030 Grodno, Belarus; (V.B.); (I.Z.)
- Department of Biotechnology, School of Medical Sciences, Krakowska 9, 15-875 Bialystok, Poland
| | - Ilya Zavodnik
- Division of Biochemical Pharmacology, Institute of Biochemistry of Biologically Active Compounds, National Academy of Sciences, BLK-50, 230030 Grodno, Belarus; (V.B.); (I.Z.)
- Department of Biochemistry, Yanka Kupala Grodno State University, BLK-50, 230030 Grodno, Belarus
| | - Katarzyna Miłowska
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland; (K.M.); (M.B.)
| | - Maria Bryszewska
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland; (K.M.); (M.B.)
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9
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Rigaud S, Mathiron D, Moufawad T, Landy D, Djedaini-Pilard F, Marçon F. Cyclodextrin Complexation as a Way of Increasing the Aqueous Solubility and Stability of Carvedilol. Pharmaceutics 2021; 13:1746. [PMID: 34834163 PMCID: PMC8620534 DOI: 10.3390/pharmaceutics13111746] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/13/2021] [Accepted: 10/15/2021] [Indexed: 11/24/2022] Open
Abstract
We studied the effect of several CDs on carvedilol's solubility and chemical stability in various aqueous media. Our present results show that it is possible to achieve a carvedilol concentration of 5 mg/mL (12.3 mM) in the presence of 5 eq of γCD or RAMEB in an aqueous medium with an acceptable acid pH (between 3.5 and 4.7). Carvedilol formed 1:1 inclusion complexes but those with RAMEB appear to be stronger (K = 317 M-1 at 298 K) than that with γCD (K = 225 M-1 at 298 K). The complexation of carvedilol by RAMEB significantly increased the drug's photochemical stability in aqueous solution. These results might constitute a first step towards the development of a novel oral formulation of carvedilol.
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Affiliation(s)
- Sébastien Rigaud
- Laboratoire de Glycochimie des Antimicrobiens et des Agroressources UMR 7378 CNRS, Université de Picardie Jules Verne, 33 Rue Saint-Leu, F-80039 Amiens, France;
| | - David Mathiron
- Plateforme-Analytique, Université de Picardie Jules Verne, 33 Rue Saint-Leu, F-80039 Amiens, France;
| | - Tarek Moufawad
- Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV, UR 4492), ULCO, F-59140 Dunkerque, France; (T.M.); (D.L.)
| | - David Landy
- Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV, UR 4492), ULCO, F-59140 Dunkerque, France; (T.M.); (D.L.)
| | - Florence Djedaini-Pilard
- Laboratoire de Glycochimie des Antimicrobiens et des Agroressources UMR 7378 CNRS, Université de Picardie Jules Verne, 33 Rue Saint-Leu, F-80039 Amiens, France;
| | - Frédéric Marçon
- Laboratoire AGIR UR4294, Université de Picardie Jules Verne, 1 Rue des Louvels, F-80039 Amiens, France;
- Pharmacie à Usage Intérieur, Centre Hospitalier Universitaire d’Amiens-Picardie, 1 Rue du Professeur Christian Cabrol, F-80054 Amiens, France
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10
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Walkowiak JJ, Ballauff M. Interaction of Polyelectrolytes with Proteins: Quantifying the Role of Water. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2100661. [PMID: 34194953 PMCID: PMC8224434 DOI: 10.1002/advs.202100661] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/29/2021] [Indexed: 05/11/2023]
Abstract
A theoretical model is presented for the free energy ΔGb of complex formation between a highly charged polyelectrolyte and a protein. The model introduced here comprises both the effect of released counterions and the uptake or release of water molecules during complex formation. The resulting expression for ΔGb is hence capable of describing the dependence of ΔGb on temperature as well as on the concentration of salt in the system: An increase of the salt concentration in the solution increases the activity of the ions and counterion release becomes less effective for binding. On the other hand, an increased salt concentration leads to the decrease of the activity of water in bulk. Hence, release of water molecules during complex formation will be more advantageous and lead to an increase of the magnitude of ΔGb and the binding constant. It is furthermore demonstrated that the release or uptake of water molecules is the origin of the marked enthalpy-entropy cancellation observed during complex formation of polyelectrolytes with proteins. The comparison with experimental data on complex formation between a synthetic (sulfated dendritic polyglycerol) and natural polyelectrolytes (DNA; heparin) with proteins shows full agreement with theory.
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Affiliation(s)
- Jacek J. Walkowiak
- Institut für Chemie und BiochemieFreie Universität BerlinTaktstraße 3Berlin14195Germany
- Aachen‐Maastricht Institute for Biobased MaterialsMaastricht UniversityBrightlands Chemelot Campus, Urmonderbaan 22Geleen6167 RDThe Netherlands
| | - Matthias Ballauff
- Institut für Chemie und BiochemieFreie Universität BerlinTaktstraße 3Berlin14195Germany
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11
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Falconer RJ, Schuur B, Mittermaier AK. Applications of isothermal titration calorimetry in pure and applied research from 2016 to 2020. J Mol Recognit 2021; 34:e2901. [PMID: 33975380 DOI: 10.1002/jmr.2901] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/02/2021] [Accepted: 04/26/2021] [Indexed: 02/06/2023]
Abstract
The last 5 years have seen a series of advances in the application of isothermal titration microcalorimetry (ITC) and interpretation of ITC data. ITC has played an invaluable role in understanding multiprotein complex formation including proteolysis-targeting chimeras (PROTACS), and mitochondrial autophagy receptor Nix interaction with LC3 and GABARAP. It has also helped elucidate complex allosteric communication in protein complexes like trp RNA-binding attenuation protein (TRAP) complex. Advances in kinetics analysis have enabled the calculation of kinetic rate constants from pre-existing ITC data sets. Diverse strategies have also been developed to study enzyme kinetics and enzyme-inhibitor interactions. ITC has also been applied to study small molecule solvent and solute interactions involved in extraction, separation, and purification applications including liquid-liquid separation and extractive distillation. Diverse applications of ITC have been developed from the analysis of protein instability at different temperatures, determination of enzyme kinetics in suspensions of living cells to the adsorption of uremic toxins from aqueous streams.
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Affiliation(s)
- Robert J Falconer
- School of Chemical Engineering & Advanced Materials, University of Adelaide, Adelaide, South Australia, Australia
| | - Boelo Schuur
- Faculty of Science and Technology, University of Twente, Enschede, Netherlands
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12
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Matencio A, Caldera F, Rubin Pedrazzo A, Khazaei Monfared Y, K Dhakar N, Trotta F. A physicochemical, thermodynamical, structural and computational evaluation of kynurenic acid/cyclodextrin complexes. Food Chem 2021; 356:129639. [PMID: 33819789 DOI: 10.1016/j.foodchem.2021.129639] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 03/03/2021] [Accepted: 03/15/2021] [Indexed: 12/28/2022]
Abstract
In this work, the interaction between Kynurenic acid (KYNA) and several natural and modified cyclodextrins (CDs) is carried out. Among all the CD tested, HPβ-CD showed the strongest complexation constant (KF), with a value of 270.94 ± 29.80 M-1. Between natural (α- and β-) CDs, the complex of KYNA with β-CD was the most efficient. The inclusion complex of KYNA with CDs showed a strong influence of pH and temperature. The KF value decreased at high pH values, when the pKa was passed. Moreover, an increase of the temperature caused a decrease in the KF values. The thermodynamic parameters of the complexation (ΔH°, ΔS° and ΔG°) were studied with negative entropy, enthalpy and spontaneity of the process at 25 °C. Moreover, the inclusion complex was also characterized using FTIR and TGA. Finally, molecular docking calculations provided different interactions and their influence in the complexation constant.
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Affiliation(s)
- Adrián Matencio
- Dip. Di Chimica, Università di Torino, via P. Giuria 7, 10125 Torino, Italy.
| | - Fabrizio Caldera
- Dip. Di Chimica, Università di Torino, via P. Giuria 7, 10125 Torino, Italy
| | | | | | - Nilesh K Dhakar
- Dip. Di Chimica, Università di Torino, via P. Giuria 7, 10125 Torino, Italy
| | - Francesco Trotta
- Dip. Di Chimica, Università di Torino, via P. Giuria 7, 10125 Torino, Italy
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13
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Achazi K, Haag R, Ballauff M, Dernedde J, Kizhakkedathu JN, Maysinger D, Multhaup G. Understanding the Interaction of Polyelectrolyte Architectures with Proteins and Biosystems. Angew Chem Int Ed Engl 2021; 60:3882-3904. [PMID: 32589355 PMCID: PMC7894192 DOI: 10.1002/anie.202006457] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Indexed: 02/06/2023]
Abstract
The counterions neutralizing the charges on polyelectrolytes such as DNA or heparin may dissociate in water and greatly influence the interaction of such polyelectrolytes with biomolecules, particularly proteins. In this Review we give an overview of studies on the interaction of proteins with polyelectrolytes and how this knowledge can be used for medical applications. Counterion release was identified as the main driving force for the binding of proteins to polyelectrolytes: Patches of positive charge become multivalent counterions of the polyelectrolyte and lead to the release of counterions from the polyelectrolyte and a concomitant increase in entropy. This is shown from investigations on the interaction of proteins with natural and synthetic polyelectrolytes. Special emphasis is paid to sulfated dendritic polyglycerols (dPGS). The Review demonstrates that we are moving to a better understanding of charge-charge interactions in systems of biological relevance. Research along these lines will aid and promote the design of synthetic polyelectrolytes for medical applications.
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Affiliation(s)
- Katharina Achazi
- Institut für Chemie und BiochemieFreie Universität BerlinTakustrasse 314195BerlinGermany
| | - Rainer Haag
- Institut für Chemie und BiochemieFreie Universität BerlinTakustrasse 314195BerlinGermany
| | - Matthias Ballauff
- Institut für Chemie und BiochemieFreie Universität BerlinTakustrasse 314195BerlinGermany
- IRIS AdlershofHumboldt Universität zu BerlinZum Grossen Windkanal 612489BerlinGermany
| | - Jens Dernedde
- Charité-Universitätsmedizin BerlinInstitute of Laboratory MedicineClinical Chemistry, and PathobiochemistryCVK Augustenburger Platz 113353BerlinGermany
| | - Jayachandran N. Kizhakkedathu
- Centre for Blood ResearchDepartment of Pathology and Laboratory MedicineLife Science InstituteDepartment of ChemistrySchool of Biomedical EngineeringUniversity of British ColumbiaVancouverV6T 1Z3Canada
| | - Dusica Maysinger
- Department of Pharmacology and TherapeuticsMcGill UniversityMontrealH3G 1Y6Canada
| | - Gerd Multhaup
- Department of Pharmacology and TherapeuticsMcGill UniversityMontrealH3G 1Y6Canada
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Çınaroğlu SS, Biggin PC. Evaluating the Performance of Water Models with Host-Guest Force Fields in Binding Enthalpy Calculations for Cucurbit[7]uril-Guest Systems. J Phys Chem B 2021; 125:1558-1567. [PMID: 33538161 DOI: 10.1021/acs.jpcb.0c11383] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Computational prediction of thermodynamic components with computational methods has become increasingly routine in computer-aided drug design. Although there has been significant recent effort and improvements in the calculation of free energy, the prediction of enthalpy (and entropy) remains underexplored. Furthermore, there has been relatively little work reported so far that attempts to comparatively assess how well different force fields and water models perform in conjunction with each other. Here, we report a comprehensive assessment of force fields and water models using host-guest systems that mimic many features of protein-ligand systems. These systems are computationally inexpensive, possibly because of their small size compared to protein-ligand systems. We present absolute enthalpy calculations using the multibox approach on a set of 25 cucurbit[7]uril-guest pairs. Eight water models were considered (TIP3P, TIP4P, TIP4P-Ew, SPC, SPC/E, OPC, TIP5P, Bind3P), along with five force fields commonly used in the literature (GAFFv1, GAFFv2, CGenFF, Parsley, and SwissParam). We observe that host-guest binding enthalpies are strongly sensitive to the selection of force field and water model. In terms of water models, we find that TIP3P and its derivative Bind3P are the best performing models for this particular host-guest system. The performance is generally better for aliphatic compounds than for aromatic ones, suggesting that aromaticity remains a difficult property to include accurately in these simple force fields.
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Affiliation(s)
| | - Philip C Biggin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K
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15
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Van Guyse JFR, Bera D, Hoogenboom R. Adamantane Functionalized Poly(2-oxazoline)s with Broadly Tunable LCST-Behavior by Molecular Recognition. Polymers (Basel) 2021; 13:374. [PMID: 33530443 PMCID: PMC7865518 DOI: 10.3390/polym13030374] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 01/27/2023] Open
Abstract
Smart or adaptive materials often utilize stimuli-responsive polymers, which undergo a phase transition in response to a given stimulus. So far, various stimuli have been used to enable the modulation of drug release profiles, cell-interactive behavior, and optical and mechanical properties. In this respect, molecular recognition is a powerful tool to fine-tune the stimuli-responsive behavior due to its high specificity. Within this contribution, a poly(2-oxazoline) copolymer bearing adamantane side chains was synthesized via triazabicyclodecene-catalyzed amidation of the ester side chains of a poly(2-ethyl-2-oxazoline-stat-2-methoxycarbonylpropyl-2-oxazoline) statistical copolymer. Subsequent complexation of the pendant adamantane groups with sub-stoichiometric amounts (0-1 equivalents) of hydroxypropyl β-cyclodextrin or β-cyclodextrin enabled accurate tuning of its lower critical solution temperature (LCST) over an exceptionally wide temperature range, spanning from 30 °C to 56 °C. Furthermore, the sharp thermal transitions display minimal hysteresis, suggesting a reversible phase transition of the complexed polymer chains (i.e., the β-cyclodextrin host collapses together with the polymers) and a minimal influence by the temperature on the supramolecular association. Analysis of the association constant of the polymer with hydroxypropyl β-cyclodextrin via 1H NMR spectroscopy suggests that the selection of the macrocyclic host and rational polymer design can have a profound influence on the observed thermal transitions.
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Affiliation(s)
| | | | - Richard Hoogenboom
- Supramolecular Chemistry Group, Centre of Macromolecular Chemistry (CMaC), Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-S4, B-9000 Ghent, Belgium; (J.F.R.V.G.); (D.B.)
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16
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Kang J, Kang AM. Comment on "Physicochemical stimuli as tuning parameters to modulate the structure and stability of nanostructured lipid carriers and release kinetics of encapsulated antileprosy drugs" by R. Kanwar, M. Gradzielski, S. Prevost, G. Kaur, M. S. Appavou and S. K. Mehta, J. Mater. Chem. B, 2019, 7, 6539. J Mater Chem B 2020; 8:10205-10208. [PMID: 33125021 DOI: 10.1039/d0tb01160f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In a recent article [R. Kanwar et al., J. Mater. Chem. B, 2019, 7(42), 6539-6555], the authors characterized the interactions between drug-loaded nanostructured lipid carriers and bovine serum albumin using thermodynamics. They found that the interactions are spontaneous and driven by entropy. In this present paper, we report our analysis of these results in terms of equilibrium thermodynamics to show that the binding reactions exhibit enthalpy-entropy compensation. Our findings may prove useful for designing nanostructured lipid carriers.
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Affiliation(s)
- Jonghoon Kang
- Department of Biology, Valdosta State University, Valdosta, Georgia, USA.
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17
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Certain carboxylic acid buffers can destabilize β-cyclodextrin complexes by competitive interaction. Int J Pharm 2020; 589:119774. [DOI: 10.1016/j.ijpharm.2020.119774] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/11/2020] [Accepted: 08/13/2020] [Indexed: 11/22/2022]
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18
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Achazi K, Haag R, Ballauff M, Dernedde J, Kizhakkedathu JN, Maysinger D, Multhaup G. Wechselwirkung von Polyelektrolyt‐Architekturen mit Proteinen und Biosystemen. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006457] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Katharina Achazi
- Institut für Chemie und Biochemie Freie Universität Berlin Takustraße 3 14195 Berlin Deutschland
| | - Rainer Haag
- Institut für Chemie und Biochemie Freie Universität Berlin Takustraße 3 14195 Berlin Deutschland
| | - Matthias Ballauff
- Institut für Chemie und Biochemie Freie Universität Berlin Takustraße 3 14195 Berlin Deutschland
- IRIS Adlershof Humboldt-Universität zu Berlin Zum Großen Windkanal 6 12489 Berlin Deutschland
| | - Jens Dernedde
- Charité-Universitätsmedizin Berlin Institut für Laboratoriumsmedizin Klinische Chemie und Pathobiochemie CVK Augustenburger Platz 1 13353 Berlin Deutschland
| | - Jayachandran N. Kizhakkedathu
- Centre for Blood Research Department of Pathology and Laboratory Medicine Life Science Institute Department of Chemistry School of Biomedical Engineering University of British Columbia Vancouver V6T 1Z3 Kanada
| | - Dusica Maysinger
- Department of Pharmacology and Therapeutics McGill University Montreal H3G 1Y6 Kanada
| | - Gerd Multhaup
- Department of Pharmacology and Therapeutics McGill University Montreal H3G 1Y6 Kanada
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19
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Tosstorff A, Cole JC, Taylor R, Harris SF, Kuhn B. Identification of Noncompetitive Protein–Ligand Interactions for Structural Optimization. J Chem Inf Model 2020; 60:6595-6611. [DOI: 10.1021/acs.jcim.0c00858] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Andreas Tosstorff
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, U.K
| | - Jason C. Cole
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, U.K
| | - Robin Taylor
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, U.K
| | - Seth F. Harris
- Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Bernd Kuhn
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
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Matencio A, Navarro-Orcajada S, García-Carmona F, López-Nicolás JM. Applications of cyclodextrins in food science. A review. Trends Food Sci Technol 2020. [DOI: 10.1016/j.tifs.2020.08.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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21
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Thermodynamic Analysis of Etoricoxib in Amphiprotic and Amphiprotic: Aprotic Solvent Mixtures at Several Temperatures. J SOLUTION CHEM 2020. [DOI: 10.1007/s10953-020-00953-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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22
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Xu X, Ballauff M. Interaction of Lysozyme with a Dendritic Polyelectrolyte: Quantitative Analysis of the Free Energy of Binding and Comparison to Molecular Dynamics Simulations. J Phys Chem B 2019; 123:8222-8231. [DOI: 10.1021/acs.jpcb.9b07448] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Xiao Xu
- School of Chemical Engineering, Nanjing University of Science and Technology, 200 Xiao Ling Wei, 210094 Nanjing, P. R. China
| | - Matthias Ballauff
- Soft Matter and Functional Materials, Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, 14109 Berlin, Germany
- Institut für Physik, Humboldt-Universität zu Berlin, 12489 Berlin, Germany
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