1
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Raghunathan S. Solvent accessible surface area-assessed molecular basis of osmolyte-induced protein stability. RSC Adv 2024; 14:25031-25041. [PMID: 39131493 PMCID: PMC11310836 DOI: 10.1039/d4ra02576h] [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: 04/05/2024] [Accepted: 07/05/2024] [Indexed: 08/13/2024] Open
Abstract
In solvent-modulated protein folding, under certain physiological conditions, an equilibrium exists between the unfolded and folded states of the protein without any need to break or make a covalent bond. In this process, interactions between various protein groups (peptides) and solvent molecules are known to play a major role in determining the directionality of the chemical reaction. However, an understanding of the mechanism of action of the co(solvent) by a generic theoretical underpinning is lacking. In this study, a generic solvation model is developed based on statistical mechanics and the thermodynamic transfer free energy model by considering the microenvironment polarity of the interacting co(solvent)-protein system. According to this model, polarity and the fractional solvent-accessible surface areas contribute to the interaction energies. The present model includes various orientations of participating interactant solvent surfaces of suitable areas. As model systems, besides the backbone we consider naturally occurring amino acid residues solvated in ten different osmolytes, small organic compounds known to modulate protein stability. The present model is able to predict the correct trend of the osmolyte-peptide interactions ranging from stabilizing to destabilizing not only for the backbone but also for side chains. Our model predicts Asn, Gln, Asp, Glu, Arg and Pro to be highly stable in most of the protecting osmolytes while Ala, Val, Ile, Leu, Thr, Met, Lys, Phe, Trp and Tyr are predicted to be moderately stable, and Ser, Cys and Histidine are predicted to be least stable. However, in denaturing solvents, both backbone and side chain models show similar stabilities in urea and guanidine. One of the important aspects of this model is that it is essentially parameter-free and consistent with the electrostatics of the interaction partners that make this model suitable for estimating any solute-solvent interaction energies.
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Affiliation(s)
- Shampa Raghunathan
- École Centrale School of Engineering, Mahindra University Hyderabad 500043 India
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2
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Chialvo AA. Preferential Solvation Phenomena as Solute-Induced Structure-Making/Breaking Processes: Linking Thermodynamic Preferential Interaction Parameters to Fundamental Structure Making/Breaking Functions. J Phys Chem B 2024; 128:5228-5245. [PMID: 38754065 DOI: 10.1021/acs.jpcb.4c00385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
In this work, we identify the explicit macroscopic-to-microscopic rigorous links between existing thermodynamic preferential interaction parameters Γ Q α Q β ( χ i ) and microstructural descriptors based on total correlation function integrals, leading to their unambiguous characterization in terms of fundamental structure making/breaking functions S α β . First, we provide the statistics mechanical framework to identify a universal molecular-based signature for the preferential solvation P S phenomenon involving solutes at infinite dilution in mixed-solvent environments and discuss its fundamental properties. Then, we characterize the S α β functions relevant to the P S process, identify the microscopic markers for the existing preferential interaction parameters Γ Q α Q β ( χ i ) in terms of the S α β functions, and test their compliance with a pair of essential microstructural constraints linked to the properties of the universal P S signature. Moreover, we illustrate the analysis by probing the behavior of a representative ternary system comprising the solubility of methane in aqueous 1,4-dioxane mixed-solvent environments under ambient conditions. Finally, we discuss some relevant issues surrounding the statistical mechanical (microstructural) interpretation of the thermodynamic (macroscopic) preferential interaction parameters, review some pitfalls in their evaluation from molecular simulation, and provide an outlook.
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Affiliation(s)
- Ariel A Chialvo
- Retired Scientist, Knoxville, Tennessee 37922-3108, United States
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3
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Olgenblum GI, Carmon N, Harries D. Not Always Sticky: Specificity of Protein Stabilization by Sugars Is Conferred by Protein-Water Hydrogen Bonds. J Am Chem Soc 2023; 145:23308-23320. [PMID: 37845197 PMCID: PMC10603812 DOI: 10.1021/jacs.3c08702] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
Solutes added to buffered solutions directly impact protein folding. Protein stabilization by cosolutes or crowders has been shown to be largely driven by protein-cosolute volume exclusion complemented by chemical and soft interactions. By contrast to previous studies that indicate the invariably destabilizing role of soft protein-sugar attractions, we show here that soft interactions with sugar cosolutes are protein-specific and can be stabilizing or destabilizing. We experimentally follow the folding of two model miniproteins that are only marginally stable but in the presence of sugars and polyols fold into representative and distinct secondary structures: β-hairpin or α-helix. Our mean-field model reveals that while protein-sugar excluded volume interactions have a similar stabilizing effect on both proteins, the soft interactions add a destabilizing contribution to one miniprotein but further stabilize the other. Using molecular dynamics simulations, we link the soft protein-cosolute interactions to the weakening of direct protein-water hydrogen bonding due to the presence of sugars. Although these weakened hydrogen bonds destabilize both the native and denatured states of the two proteins, the resulting contribution to the folding free energy can be positive or negative depending on the amino acid sequence. This study indicates that the significant variation between proteins in their soft interactions with sugar determines the specific response of different proteins, even to the same sugar.
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Affiliation(s)
- Gil I Olgenblum
- The Fritz Haber Research Center, and the Harvey M. Kruger Center for Nanoscience & Nanotechnology, Institute of Chemistry, The Hebrew University, Jerusalem 9190401, Israel
| | - Neta Carmon
- The Fritz Haber Research Center, and the Harvey M. Kruger Center for Nanoscience & Nanotechnology, Institute of Chemistry, The Hebrew University, Jerusalem 9190401, Israel
| | - Daniel Harries
- The Fritz Haber Research Center, and the Harvey M. Kruger Center for Nanoscience & Nanotechnology, Institute of Chemistry, The Hebrew University, Jerusalem 9190401, Israel
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4
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Ko SK, Björkengren G, Berner C, Winter G, Harris P, Peters GHJ. Combining Molecular Dynamics Simulations and Biophysical Characterization to Investigate Protein-Specific Excipient Effects on Reteplase during Freeze Drying. Pharmaceutics 2023; 15:1854. [PMID: 37514040 PMCID: PMC10384596 DOI: 10.3390/pharmaceutics15071854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/24/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
We performed molecular dynamics simulations of Reteplase in the presence of different excipients to study the stabilizing mechanisms and to identify the role of excipients during freeze drying. To simulate the freeze-drying process, we divided the process into five distinct steps: (i) protein-excipient formulations at room temperature, (ii) the ice-growth process, (iii)-(iv) the partially solvated and fully dried formulations, and (v) the reconstitution. Furthermore, coarse-grained (CG) simulations were employed to explore the protein-aggregation process in the presence of arginine. By using a coarse-grained representation, we could observe the collective behavior and interactions between protein molecules during the aggregation process. The CG simulations revealed that the presence of arginine prevented intermolecular interactions of the catalytic domain of Reteplase, thus reducing the aggregation propensity. This suggests that arginine played a stabilizing role by interacting with protein-specific regions. From the freeze-drying simulations, we could identify several protein-specific events: (i) collapse of the domain structure, (ii) recovery of the drying-induced damages during reconstitution, and (iii) stabilization of the local aggregation-prone region via direct interactions with excipients. Complementary to the simulations, we employed nanoDSF, size-exclusion chromatography, and CD spectroscopy to investigate the effect of the freeze-drying process on the protein structure and stability.
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Affiliation(s)
- Suk Kyu Ko
- Department of Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Gabriella Björkengren
- Department of Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Carolin Berner
- Department of Pharmacy, Ludwig Maximilian University of Munich, 81377 Munich, Germany
| | - Gerhard Winter
- Department of Pharmacy, Ludwig Maximilian University of Munich, 81377 Munich, Germany
| | - Pernille Harris
- Department of Chemistry, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Günther H J Peters
- Department of Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
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5
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Abstract
Glycoscience assembles all the scientific disciplines involved in studying various molecules and macromolecules containing carbohydrates and complex glycans. Such an ensemble involves one of the most extensive sets of molecules in quantity and occurrence since they occur in all microorganisms and higher organisms. Once the compositions and sequences of these molecules are established, the determination of their three-dimensional structural and dynamical features is a step toward understanding the molecular basis underlying their properties and functions. The range of the relevant computational methods capable of addressing such issues is anchored by the specificity of stereoelectronic effects from quantum chemistry to mesoscale modeling throughout molecular dynamics and mechanics and coarse-grained and docking calculations. The Review leads the reader through the detailed presentations of the applications of computational modeling. The illustrations cover carbohydrate-carbohydrate interactions, glycolipids, and N- and O-linked glycans, emphasizing their role in SARS-CoV-2. The presentation continues with the structure of polysaccharides in solution and solid-state and lipopolysaccharides in membranes. The full range of protein-carbohydrate interactions is presented, as exemplified by carbohydrate-active enzymes, transporters, lectins, antibodies, and glycosaminoglycan binding proteins. A final section features a list of 150 tools and databases to help address the many issues of structural glycobioinformatics.
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Affiliation(s)
- Serge Perez
- Centre de Recherche sur les Macromolecules Vegetales, University of Grenoble-Alpes, Centre National de la Recherche Scientifique, Grenoble F-38041, France
| | - Olga Makshakova
- FRC Kazan Scientific Center of Russian Academy of Sciences, Kazan Institute of Biochemistry and Biophysics, Kazan 420111, Russia
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6
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Arsiccio A, Ganguly P, Shea JE. A Transfer Free Energy Based Implicit Solvent Model for Protein Simulations in Solvent Mixtures: Urea-Induced Denaturation as a Case Study. J Phys Chem B 2022; 126:4472-4482. [PMID: 35679169 DOI: 10.1021/acs.jpcb.2c00889] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We developed a method for implicit solvent molecular dynamics simulations of proteins in solvent mixtures (model with implicit solvation thermodynamics, MIST). The MIST method introduces experimental group transfer free energies to the generalized Born formulation for generating molecular trajectories without the need for developing rigorous explicit-solvent force fields for multicomponent solutions. As a test case, we studied the urea-induced denaturation of the Trp-cage miniprotein in water. We demonstrate that our method allows efficient exploration of the conformational space of the protein in only a few hundreds of nanoseconds of all-atom unbiased simulations. Furthermore, selective implementation of the transfer free energies of specific peptide groups, backbone, and side chains enables us to decouple their specific energetic contributions to the conformational changes of the protein. The approach herein developed can readily be extended to the investigation of complex matrices as well as to the characterization of protein aggregation. The MIST method is implemented in Plumed (ver. 2.8) as a separate module called SASA.
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Affiliation(s)
- Andrea Arsiccio
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Pritam Ganguly
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, United States.,Department of Physics, University of California, Santa Barbara, Santa Barbara, California 93106, United States
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7
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Dyrda-Terniuk T, Sugajski M, Pryshchepa O, Śliwiak J, Buszewska-Forajta M, Pomastowski P, Buszewski B. The Study of Protein-Cyclitol Interactions. Int J Mol Sci 2022; 23:2940. [PMID: 35328362 PMCID: PMC8952220 DOI: 10.3390/ijms23062940] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/02/2022] [Accepted: 03/05/2022] [Indexed: 11/17/2022] Open
Abstract
Investigation of interactions between the target protein molecule and ligand allows for an understanding of the nature of the molecular recognition, functions, and biological activity of protein-ligand complexation. In the present work, non-specific interactions between a model protein (Bovine Serum Albumin) and four cyclitols were investigated. D-sorbitol and adonitol represent the group of linear-structure cyclitols, while shikimic acid and D-(-)-quinic acid have cyclic-structure molecules. Various analytical methods, including chromatographic analysis (HPLC-MS/MS), electrophoretic analysis (SDS-PAGE), spectroscopic analysis (spectrofluorimetry, Fourier transform infrared spectroscopy, and Raman spectroscopy), and isothermal titration calorimetry (ITC), were applied for the description of protein-cyclitol interactions. Additionally, computational calculations were performed to predict the possible binding places. Kinetic studies allowed us to clarify interaction mechanisms that may take place during BSA and cyclitol interaction. The results allow us, among other things, to evaluate the impact of the cyclitol's structure on the character of its interactions with the protein.
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Affiliation(s)
- Tetiana Dyrda-Terniuk
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarina 7, 87-100 Toruń, Poland; (T.D.-T.); (M.S.); (O.P.); (B.B.)
- Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4, 87-100 Toruń, Poland
| | - Mateusz Sugajski
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarina 7, 87-100 Toruń, Poland; (T.D.-T.); (M.S.); (O.P.); (B.B.)
- Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4, 87-100 Toruń, Poland
| | - Oleksandra Pryshchepa
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarina 7, 87-100 Toruń, Poland; (T.D.-T.); (M.S.); (O.P.); (B.B.)
- Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4, 87-100 Toruń, Poland
| | - Joanna Śliwiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland;
| | - Magdalena Buszewska-Forajta
- Institute of Veterinary Medicine, Nicolaus Copernicus University in Toruń, Gagarina 7, 87-100 Toruń, Poland;
| | - Paweł Pomastowski
- Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4, 87-100 Toruń, Poland
| | - Bogusław Buszewski
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarina 7, 87-100 Toruń, Poland; (T.D.-T.); (M.S.); (O.P.); (B.B.)
- Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4, 87-100 Toruń, Poland
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8
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Martínez L. ComplexMixtures.jl: Investigating the structure of solutions of complex-shaped molecules from a solvent-shell perspective. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.117945] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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9
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Arsiccio A, Rospiccio M, Shea JE, Pisano R. Force Field Parameterization for the Description of the Interactions between Hydroxypropyl-β-Cyclodextrin and Proteins. J Phys Chem B 2021; 125:7397-7405. [PMID: 34210121 PMCID: PMC8287564 DOI: 10.1021/acs.jpcb.1c04033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cyclodextrins are cyclic oligosaccharides, widely used as drug carriers, solubilizers, and excipients. Among cyclodextrins, the functionalized derivative known as hydroxypropyl-β-cyclodextrin (HPβCD) offers several advantages due to its unique structural features. Its optimal use in pharmaceutical and medical applications would benefit from a molecular-level understanding of its behavior, as can be offered by molecular dynamics simulations. Here, we propose a set of parameters for all-atom simulations of HPβCD, based on the ADD force field for sugars developed in our group, and compare it to the original CHARMM36 description. Using Kirkwood-Buff integrals of binary HPβCD-water mixtures as target experimental data, we show that the ADD-based description results in a considerably improved prediction of HPβCD self-association and interaction with water. We then use the new set of parameters to characterize the behavior of HPβCD toward the different amino acids. We observe pronounced interactions of HPβCD with both polar and nonpolar moieties, with a special preference for the aromatic rings of tyrosine, phenylalanine, and tryptophan. Interestingly, our simulations further highlight a preferential orientation of HPβCD's hydrophobic cavity toward the backbone atoms of amino acids, which, coupled with a favorable interaction of HPβCD with the peptide backbone, suggest a propensity for HPβCD to denature proteins.
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Affiliation(s)
- Andrea Arsiccio
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Marcello Rospiccio
- Molecular Engineering Laboratory, Department of Applied Science and Technology, Politecnico di Torino, 24 corso Duca degli Abruzzi, Torino 10129, Italy
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States.,Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - Roberto Pisano
- Molecular Engineering Laboratory, Department of Applied Science and Technology, Politecnico di Torino, 24 corso Duca degli Abruzzi, Torino 10129, Italy
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10
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Ploetz EA, Karunaweera S, Bentenitis N, Chen F, Dai S, Gee MB, Jiao Y, Kang M, Kariyawasam NL, Naleem N, Weerasinghe S, Smith PE. Kirkwood-Buff-Derived Force Field for Peptides and Proteins: Philosophy and Development of KBFF20. J Chem Theory Comput 2021; 17:2964-2990. [PMID: 33878263 DOI: 10.1021/acs.jctc.1c00075] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A new classical nonpolarizable force field, KBFF20, for the simulation of peptides and proteins is presented. The force field relies heavily on the use of Kirkwood-Buff theory to provide a comparison of simulated and experimental Kirkwood-Buff integrals for solutes containing the functional groups common in proteins, thus ensuring intermolecular interactions that provide a good balance between the peptide-peptide, peptide-solvent, and solvent-solvent distributions observed in solution mixtures. In this way, it differs significantly from other biomolecular force fields. Further development and testing of the intermolecular potentials are presented here. Subsequently, rotational potentials for the ϕ/ψ and χ dihedral degrees of freedom are obtained by analysis of the Protein Data Bank, followed by small modifications to provide a reasonable balance between simulated and observed α and β percentages for small peptides. This, the first of two articles, describes in detail the philosophy and development behind KBFF20.
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Affiliation(s)
- Elizabeth A Ploetz
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Sadish Karunaweera
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Nikolaos Bentenitis
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Feng Chen
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Shu Dai
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Moon B Gee
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Yuanfang Jiao
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Myungshim Kang
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Nilusha L Kariyawasam
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Nawavi Naleem
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | | | - Paul E Smith
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
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11
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Scherbinina SI, Toukach PV. Three-Dimensional Structures of Carbohydrates and Where to Find Them. Int J Mol Sci 2020; 21:E7702. [PMID: 33081008 PMCID: PMC7593929 DOI: 10.3390/ijms21207702] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 02/06/2023] Open
Abstract
Analysis and systematization of accumulated data on carbohydrate structural diversity is a subject of great interest for structural glycobiology. Despite being a challenging task, development of computational methods for efficient treatment and management of spatial (3D) structural features of carbohydrates breaks new ground in modern glycoscience. This review is dedicated to approaches of chemo- and glyco-informatics towards 3D structural data generation, deposition and processing in regard to carbohydrates and their derivatives. Databases, molecular modeling and experimental data validation services, and structure visualization facilities developed for last five years are reviewed.
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Affiliation(s)
- Sofya I. Scherbinina
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky prospect 47, 119991 Moscow, Russia
- Higher Chemical College, D. Mendeleev University of Chemical Technology of Russia, Miusskaya Square 9, 125047 Moscow, Russia
| | - Philip V. Toukach
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky prospect 47, 119991 Moscow, Russia
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12
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Loftsson T. Cyclodextrins in Parenteral Formulations. J Pharm Sci 2020; 110:654-664. [PMID: 33069709 DOI: 10.1016/j.xphs.2020.10.026] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/14/2020] [Accepted: 10/14/2020] [Indexed: 12/26/2022]
Abstract
Most drugs have very limited solubility in water and some can be extremely difficult to formulate as parenteral solutions where the dose should preferably be dissolved in couple of ml of aqueous media without use of organic solvents and surface active agents, or application of somewhat extreme techniques such as prodrug formation. Thus, pharmaceutical formulators are constantly looking for new, biologically acceptable, and low-cost armamentarium for parenteral formulation development. Cyclodextrins (CDs) are enabling pharmaceutical excipients that can temporarily camouflage undesirable physiochemical drug properties such as low aqueous solubility through formation of drug/CD inclusion complexes. CDs are cyclic oligosaccharides that have similar physiological and biological properties like linear saccharides of comparable molecular weight. Due to their very favorable toxicological and pharmacokinetic profiles their usage in parenteral drug formulations is frequently preferred over other solubilizing techniques. Here the physiochemical and biological properties of CDs are reviewed as well as their pharmacokinetics after intravenous administration. Their regulatory status is briefly reviewed and their tendency to self-assemble to form clusters or aggregates discussed. Finally, some examples are given of how CDs are applied in aqueous parenteral formulations, how their solubilizing effect has been enhanced and how their target concentration is determined.
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Affiliation(s)
- Thorsteinn Loftsson
- Faculty of Pharmaceutical Sciences, University of Iceland, Hofsvallagata 53, IS-107 Reykjavik, Iceland.
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13
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Arsiccio A, Ganguly P, La Cortiglia L, Shea JE, Pisano R. ADD Force Field for Sugars and Polyols: Predicting the Additivity of Protein-Osmolyte Interaction. J Phys Chem B 2020; 124:7779-7790. [PMID: 32790371 PMCID: PMC7901642 DOI: 10.1021/acs.jpcb.0c05345] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
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The protein–osmolyte interaction has been shown experimentally to follow an
additive construct, where the individual osmolyte–backbone and
osmolyte–side-chain interactions contribute to the overall conformational
stability of proteins. Here, we computationally reconstruct this additive relation using
molecular dynamics simulations, focusing on sugars and polyols, including sucrose and
sorbitol, as model osmolytes. A new set of parameters (ADD) is developed for this
purpose, using the individual Kirkwood–Buff integrals for sugar–backbone
and sugar–side-chain interactions as target experimental data. We show that the
ADD parameters can reproduce the additivity of protein–sugar interactions and
correctly predict sucrose and sorbitol self-association and their interaction with
water. The accurate description of the separate osmolyte–backbone and
osmolyte–side-chain contributions also automatically translates into a good
prediction of preferential exclusion from the surface of ribonuclease A and
α-chymotrypsinogen A. The description of sugar polarity is improved compared to
previous force fields, resulting in closer agreement with the experimental data and
better compatibility with charged groups, such as the guanidinium moiety. The ADD
parameters are developed in combination with the CHARMM36m force field for proteins, but
good compatibility is also observed with the AMBER 99SB-ILDN and the OPLS-AA force
fields. Overall, exploiting the additivity of protein–osmolyte interactions is a
promising approach for the development of new force fields.
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Affiliation(s)
- Andrea Arsiccio
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Pritam Ganguly
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Lorenzo La Cortiglia
- Department of Applied Science and Technology, Politecnico di Torino, 24 Corso Duca Degli Abruzzi, Torino 10129, Italy
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, United States.,Department of Physics, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Roberto Pisano
- Department of Applied Science and Technology, Politecnico di Torino, 24 Corso Duca Degli Abruzzi, Torino 10129, Italy
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14
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Cloutier TK, Sudrik C, Mody N, Sathish HA, Trout BL. Machine Learning Models of Antibody–Excipient Preferential Interactions for Use in Computational Formulation Design. Mol Pharm 2020; 17:3589-3599. [DOI: 10.1021/acs.molpharmaceut.0c00629] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Theresa K. Cloutier
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Chaitanya Sudrik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Neil Mody
- Dosage Form Design and Development, AstraZeneca, Gaithersburg, Maryland 20878, United States
| | - Hasige A. Sathish
- Dosage Form Design and Development, AstraZeneca, Gaithersburg, Maryland 20878, United States
| | - Bernhardt L. Trout
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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15
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Olgenblum GI, Sapir L, Harries D. Properties of Aqueous Trehalose Mixtures: Glass Transition and Hydrogen Bonding. J Chem Theory Comput 2020; 16:1249-1262. [PMID: 31917927 PMCID: PMC7467637 DOI: 10.1021/acs.jctc.9b01071] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Trehalose is a naturally occurring disaccharide known to remarkably stabilize biomacromolecules in the biologically active state. The stabilizing effect is typically observed over a large concentration range and affects many macromolecules including proteins, lipids, and DNA. Of special interest is the transition from aqueous solution to the dense and highly concentrated glassy state of trehalose that has been implicated in bioadaptation of different organisms toward desiccation stress. Although several mechanisms have been suggested to link the structure of the low water content glass with its action as an exceptional stabilizer, studies are ongoing to resolve which are most pertinent. Specifically, the role that hydrogen bonding plays in the formation of the glass is not well resolved. Here we model aqueous trehalose mixtures over a wide concentration range, using molecular dynamics simulations with two available force fields. Both force fields indicate glass transition temperatures and osmotic pressures that are close to experimental values, particularly at high trehalose contents. We develop and employ a methodology that allows us to analyze the thermodynamics of hydrogen bonds in simulations at different water contents and temperatures. Remarkably, this analysis is able to link the liquid to glass transition with changes in hydrogen bond characteristics. Most notably, the onset of the glassy state can be quantitatively related to the transition from weakly to strongly correlated hydrogen bonds. Our findings should help resolve the properties of the glass and the mechanisms of its formation in the presence of added macromolecules.
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Affiliation(s)
- Gil I Olgenblum
- Institute of Chemistry, the Fritz Haber Research Center, and the Harvey M. Kruger Center for Nanoscience & Nanotechnology , The Hebrew University , Jerusalem 9190401 , Israel
| | - Liel Sapir
- Department of Mechanical Engineering and Materials Science , Duke University , Durham , North Carolina 27708 , United States
| | - Daniel Harries
- Institute of Chemistry, the Fritz Haber Research Center, and the Harvey M. Kruger Center for Nanoscience & Nanotechnology , The Hebrew University , Jerusalem 9190401 , Israel
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16
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Cloutier T, Sudrik C, Mody N, Sathish HA, Trout BL. Molecular Computations of Preferential Interaction Coefficients of IgG1 Monoclonal Antibodies with Sorbitol, Sucrose, and Trehalose and the Impact of These Excipients on Aggregation and Viscosity. Mol Pharm 2019; 16:3657-3664. [PMID: 31276620 DOI: 10.1021/acs.molpharmaceut.9b00545] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Preferential interactions of formulation excipients govern their overall interactions with protein molecules, and molecular dynamics simulations allow for the examination of the interactions at the molecular level. We used molecular dynamics simulations to examine the interactions of sorbitol, sucrose, and trehalose with three different IgG1 antibodies to gain insight into how these excipients impact aggregation and viscosity. We found that sucrose and trehalose reduce aggregation more than sorbitol because of their larger size and their stronger interactions with high-spatial aggregation propensity residues compared to sorbitol. Two of the antibodies had high viscosity in sodium acetate buffer, and for these, we found that sucrose and trehalose tended to have opposite effects on viscosity. The data presented here provide further insight into the mechanisms of interactions of these three carbohydrate excipients with the antibody surface and thus their impact on excipient stabilization of antibody formulations.
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Affiliation(s)
- Theresa Cloutier
- Chemical Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Chaitanya Sudrik
- Chemical Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Neil Mody
- Dosage Form Design and Development, AstraZeneca , Gaithersburg , Maryland 20878 , United States
| | - Hasige A Sathish
- Dosage Form Design and Development, AstraZeneca , Gaithersburg , Maryland 20878 , United States
| | - Bernhardt L Trout
- Chemical Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
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Loftsson T, Saokham P, Sá Couto AR. Self-association of cyclodextrins and cyclodextrin complexes in aqueous solutions. Int J Pharm 2019; 560:228-234. [PMID: 30771468 DOI: 10.1016/j.ijpharm.2019.02.004] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/07/2019] [Accepted: 02/09/2019] [Indexed: 12/23/2022]
Abstract
Cyclodextrins (CDs) are oligosaccharides that self-assemble in aqueous solutions to form transient clusters, nanoparticles and small microparticles. The critical aggregation concentration (cac) of the natural αCD, βCD and γCD in pure aqueous solutions was estimated to be 25, 8 and 9 mg/ml, respectively. The cac of 2-hydroxypropyl-β-cyclodextrin (HPβCD), that consists of mixture of isomers, was estimated to be significantly higher or 118 mg/ml. Addition of chaotropic agents (i.e. that disrupts non-covalent bonds such as hydrogen bonds) to the aqueous media increases the cac. Formation of drug/CD complexes can increase or decrease the cac. Due to the transient nature of the CD clusters and nanoparticles they can be difficult to detect and their presence is frequently ignored. However, they have profound effect on the physiochemical properties of CDs and their pharmaceutical applications. For example, the values of stability constants of drug/CD complexes can be both concentration dependent and method dependent. Like in the case of micelles water-soluble polymers can enhance the solubilizing effect of CDs. Also, formation of drug/CD complex nanoparticles appears to increase the ability of CDs to enhance drug delivery through some mucosal membranes.
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Affiliation(s)
- Thorsteinn Loftsson
- Faculty of Pharmaceutical Sciences, University of Iceland, Hofsvallagata 53, IS-107 Reykjavík, Iceland.
| | - Phennapha Saokham
- College of Pharmacy, Rangsit University, Pathum Thani 12000, Thailand.
| | - André Rodrigues Sá Couto
- Faculty of Pharmaceutical Sciences, University of Iceland, Hofsvallagata 53, IS-107 Reykjavík, Iceland.
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