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1.
Agglomeration of celecoxib by quasi-emulsion solvent diffusion method without stabilizer: effect of good solvent.
Maghsoodi, M, Nokhodchi, A
Pharmaceutical development and technology. 2018;(10):1037-1046
Abstract
AIM: The aim of the present research is to investigate the feasibility of agglomeration of crystals by the quasi-emulsion solvent diffusion method without using a stabilizer. METHOD Two solvent systems comprising a solvent and an antisolvent (water) were used to prepare celecoxib agglomerates. To this end, seven solvents including propanol, methyl acetate, methyl ethyl ketone, butanol, ethyl acetate, isopropyl acetate, and pentanol were examined. The agglomerates were evaluated by micromeritic properties (e.g., size, density, flowability), yield, drug physical state, friability, and dissolution behavior. RESULTS In the present study the clear trend was observed experimentally in the agglomerate properties as a function of physical properties of the solvent such as miscibility with water. Solvents with high water miscibility (25% v/v) resulted in sticky and hollow particles, while solvents with low water miscibility (3%v/v) led to the formation of agglomerates with low strength. However, the agglomerates made from the solvents with intermediate water miscibility (10% v/v), may reflect a greater integrity of the agglomerates regarding yield and strength. CONCLUSION Results of this study offer a useful starting point for a conceptual framework to guide the selection of solvent systems for the quasi-emulsion solvent diffusion method without using a stabilizer.
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2.
Effect of Atomic Charges on Octanol-Water Partition Coefficient Using Alchemical Free Energy Calculation.
Ogata, K, Hatakeyama, M, Nakamura, S
Molecules (Basel, Switzerland). 2018;(2)
Abstract
The octanol-water partition coefficient (logPow) is an important index for measuring solubility, membrane permeability, and bioavailability in the drug discovery field. In this paper, the logPow values of 58 compounds were predicted by alchemical free energy calculation using molecular dynamics simulation. In free energy calculations, the atomic charges of the compounds are always fixed. However, they must be recalculated for each solvent. Therefore, three different sets of atomic charges were tested using quantum chemical calculations, taking into account vacuum, octanol, and water environments. The calculated atomic charges in the different environments do not necessarily influence the correlation between calculated and experimentally measured ∆Gwater values. The largest correlation coefficient values of the solvation free energy in water and octanol were 0.93 and 0.90, respectively. On the other hand, the correlation coefficient of logPow values calculated from free energies, the largest of which was 0.92, was sensitive to the combination of the solvation free energies calculated from the calculated atomic charges. These results reveal that the solvent assumed in the atomic charge calculation is an important factor determining the accuracy of predicted logPow values.
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3.
Quantifying the Effects of Hydrogen Bonding on Nitrile Frequencies in GFP: Beyond Solvent Exposure.
First, JT, Slocum, JD, Webb, LJ
The journal of physical chemistry. B. 2018;(26):6733-6743
Abstract
Vibrational spectroscopy is a powerful tool for characterizing the complex noncovalent interactions that arise in biological systems. The nitrile stretching frequency has proven to be a particularly convenient biological probe, but the interpretation of nitrile spectroscopy is complicated by its sensitivity to local hydrogen bonding interactions. This often inhibits the straightforward interpretation of nitrile spectra by requiring knowledge of the molecular-level details of the local environment surrounding the probe. While the effect of hydrogen bonds on nitrile frequencies has been well-documented for small molecules in solution, there have been relatively few studies of these effects in a complex protein system. To address this, we introduced a nitrile probe at nine locations throughout green fluorescent protein (GFP) and compared the mean vibrational frequency of each probe to the specific hydrogen bonding geometries observed in molecular dynamics (MD) simulations. We show that a continuum of hydrogen bonding angles is found depending on the particular location of each nitrile, and that the differences in these angles account for the differences in the measured nitrile frequency. We further observed that the temperature dependence of the nitrile frequencies (measured as a frequency-temperature line slope, FTLS) was a good indicator of the hydrogen bonding interactions of the probe, even in scenarios where the nitrile was involved in complex and restricted hydrogen bonds, both from protein and from water. While constant offsets to the nitrile frequency to all hydrogen bonding environments have been applied before to interpret shifts in nitrile frequency, we show that this is insufficient in systems where the hydrogen bonds may be restricted by the surrounding medium. However, the strength of the observed correlation between nitrile frequency and hydrogen bonding angle suggests that it may be possible to disentangle electrostatic effects and effects of the orientation of hydrogen bonding on the nitrile stretching frequency. Meanwhile, the experimental measurement of the FTLS of the nitrile is an excellent tool to identify changes in the hydrogen bonding interactions for a particular probe.
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4.
The solvent side of proteinaceous membrane-less organelles in light of aqueous two-phase systems.
Zaslavsky, BY, Ferreira, LA, Darling, AL, Uversky, VN
International journal of biological macromolecules. 2018;:1224-1251
Abstract
Water represents a common denominator for liquid-liquid phase transitions leading to the formation of the polymer-based aqueous two-phase systems (ATPSs) and a set of the proteinaceous membrane-less organelles (PMLOs). ATPSs have a broad range of biotechnological applications, whereas PMLOs play a number of crucial roles in cellular compartmentalization and often represent a cellular response to the stress. Since ATPSs and PMLOs contain high concentrations of polymers (such as polyethylene glycol (PEG), polypropylene glycol (PPG), Ucon, and polyvinylpyrrolidone (PVP), Dextran, or Ficoll) or biopolymers (peptides, proteins and nucleic acids), it is expected that the separated phases of these systems are characterized by the noticeable changes in the solvent properties of water. These changes in solvent properties can drive partitioning of various compounds (proteins, nucleic acids, organic low-molecular weight molecules, metal ions, etc.) between the phases of ATPSs or between the PMLOs and their surroundings. Although there is a sizable literature on the properties of the ATPS phases, much less is currently known about PMLOs. In this perspective article, we first represent liquid-liquid phase transitions in water, discuss different types of biphasic (or multiphasic) systems in water, and introduce various PMLOs and some of their properties. Then, some basic characteristics of polymer-based ATPSs are presented, with the major focus being on the current understanding of various properties of ATPS phases and solvent properties of water inside them. Finally, similarities and differences between the polymer-based ATPSs and biological PMLOs are discussed.
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5.
Solvent Networks Tune Thermodynamics of Oligosaccharide Complex Formation in an Extended Protein Binding Site.
Kunstmann, S, Gohlke, U, Broeker, NK, Roske, Y, Heinemann, U, Santer, M, Barbirz, S
Journal of the American Chemical Society. 2018;(33):10447-10455
Abstract
The principles of protein-glycan binding are still not well understood on a molecular level. Attempts to link affinity and specificity of glycan recognition to structure suffer from the general lack of model systems for experimental studies and the difficulty to describe the influence of solvent. We have experimentally and computationally addressed energetic contributions of solvent in protein-glycan complex formation in the tailspike protein (TSP) of E. coli bacteriophage HK620. HK620TSP is a 230 kDa native trimer of right-handed, parallel beta-helices that provide extended, rigid binding sites for bacterial cell surface O-antigen polysaccharides. A set of high-affinity mutants bound hexa- or pentasaccharide O-antigen fragments with very similar affinities even though hexasaccharides introduce an additional glucose branch into an occluded protein surface cavity. Remarkably different thermodynamic binding signatures were found for different mutants; however, crystal structure analyses indicated that no major oligosaccharide or protein topology changes had occurred upon complex formation. This pointed to a solvent effect. Molecular dynamics simulations using a mobility-based approach revealed an extended network of solvent positions distributed over the entire oligosaccharide binding site. However, free energy calculations showed that a small water network inside the glucose-binding cavity had the most notable influence on the thermodynamic signature. The energy needed to displace water from the glucose binding pocket depended on the amino acid at the entrance, in agreement with the different amounts of enthalpy-entropy compensation found for introducing glucose into the pocket in the different mutants. Studies with small molecule drugs have shown before that a few active water molecules can control protein complex formation. HK620TSP oligosaccharide binding shows that similar fundamental principles also apply for glycans, where a small number of water molecules can dominate the thermodynamic signature in an extended binding site.
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6.
Influence of Solvent on the Drug-Loading Process of Amphiphilic Nanogel Star Polymers.
Carr, AC, Piunova, VA, Maarof, H, Rice, JE, Swope, WC
The journal of physical chemistry. B. 2018;(21):5356-5367
Abstract
We present an all-atom molecular dynamics study of the effect of a range of organic solvents (dichloromethane, diethyl ether, toluene, methanol, dimethyl sulfoxide, and tetrahydrofuran) on the conformations of a nanogel star polymeric nanoparticle with solvophobic and solvophilic structural elements. These nanoparticles are of particular interest for drug delivery applications. As drug loading generally takes place in an organic solvent, this work serves to provide insight into the factors controlling the early steps of that process. Our work suggests that nanoparticle conformational structure is highly sensitive to the choice of solvent, providing avenues for further study as well as predictions for both computational and experimental explorations of the drug-loading process. Our findings suggest that when used in the drug-loading process, dichloromethane, tetrahydrofuran, and toluene allow for a more extensive and increased drug-loading into the interior of nanogel star polymers of the composition studied here. In contrast, methanol is more likely to support shallow or surface loading and, consequently, faster drug release rates. Finally, diethyl ether should not work in a formulation process since none of the regions of the nanogel star polymer appear to be sufficiently solvated by it.
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7.
Large scale analysis of protein conformational transitions from aqueous to non-aqueous media.
Rueda, AJV, Monzon, AM, Ardanaz, SM, Iglesias, LE, Parisi, G
BMC bioinformatics. 2018;(1):27
Abstract
BACKGROUND Biocatalysis in organic solvents is nowadays a common practice with a large potential in Biotechnology. Several studies report that proteins which are co-crystallized or soaked in organic solvents preserve their fold integrity showing almost identical arrangements when compared to their aqueous forms. However, it is well established that the catalytic activity of proteins in organic solvents is much lower than in water. In order to explain this diminished activity and to further characterize the behaviour of proteins in non-aqueous environments, we performed a large-scale analysis (1737 proteins) of the conformational diversity of proteins crystallized in aqueous and co-crystallized or soaked in non-aqueous media. RESULTS Using proteins' experimentally determined conformational diversity taken from CoDNaS database, we found that proteins in non-aqueous media display much lower conformational diversity when compared to the corresponding conformers obtained in water. When conformational diversity is compared between conformers obtained in different non-aqueous media, their structural differences are larger and mostly independent of the presence of cognate ligands. We also found that conformers corresponding to non-aqueous media have larger but less flexible cavities, lower number of disordered regions and lower active-site residue mobility. CONCLUSIONS Our results show that non-aqueous media conformers have specific structural features and that they do not adopt extreme conformations found in aqueous media. This makes them clearly different from their corresponding aqueous conformers.
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8.
Probing selectivity of mixed-mode reversed-phase/weak-anion-exchange liquid chromatography to advance method development.
Dores-Sousa, JL, De Vos, J, Kok, WT, Eeltink, S
Journal of chromatography. A. 2018;:75-81
Abstract
The current study comprises a systematic investigation to assess retention properties and selectivity of a mixed-mode reversed-phase/weak-anion-exchange (RP/WAX) stationary phase to aid method development. Retention was investigated for different compound classes which vary in hydrophobicity, van der Waals surface area, and charge as function of organic content, pH, and ionic strength of the mobile phase. The linear-solvent-strength model was successfully applied for aromatic hydrocarbons to obtain retention-time predictions based on log P values and van der Waals surface area values. For phenols, predictions were based on log P values and data from a single scouting run performed in isocratic mode to estimate the S parameter; the deviations between experimental and predicted retention times were smaller than 6%. To describe the mixed-mode (RP/WAX) retention behavior of singly and doubly negatively-charged aromatic acids, a novel model combining the linear-solvent-strength and the empirical stoichiometric-displacement-net-charge models is proposed and validated. Using combinations of three scouting runs that are not linearly dependent, the maximum prediction error was 11% and changes in selectivity were correctly forecasted when altering the mobile-phase composition, i.e., either organic modifier content or ionic strength. When using nine scouting runs in combination with a least-squares regression approach to determine the model parameters, the maximum prediction error was 6%.
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9.
Effects of different force fields on the structural character of α synuclein β-hairpin peptide (35-56) in aqueous environment.
Kundu, S
Journal of biomolecular structure & dynamics. 2018;(2):302-317
Abstract
The hallmark of Parkinson's disease (PD) is the intracellular protein aggregation forming Lewy Bodies (LB) and Lewy neuritis which comprise mostly of a protein, alpha synuclein (α-syn). Molecular dynamics (MD) simulation methods can augment experimental techniques to understand misfolding and aggregation pathways with atomistic resolution. The quality of MD simulations for proteins and peptides depends greatly on the accuracy of empirical force fields. The aim of this work is to investigate the effects of different force fields on the structural character of β hairpin fragment of α-syn (residues 35-56) peptide in aqueous solution. Six independent MD simulations are done in explicit solvent using, AMBER03, AMBER99SB, GROMOS96 43A1, GROMOS96 53A6, OPLS-AA, and CHARMM27 force fields with CMAP corrections. The performance of each force field is assessed from several structural parameters such as root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), solvent accessible surface area (SASA), formation of β-turn, the stability of folded β-hairpin structure, and the favourable conformations obtained for different force fields. In this study, CMAP correction of CHARMM27 force field is found to overestimate the helical conformation, while GROMOS96 53A6 is found to most successfully capture the conformational dynamics of α-syn β-hairpin fragment as elicited from NMR.
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10.
Explicit treatment of active-site waters enhances quantum mechanical/implicit solvent scoring: Inhibition of CDK2 by new pyrazolo[1,5-a]pyrimidines.
Hylsová, M, Carbain, B, Fanfrlík, J, Musilová, L, Haldar, S, Köprülüoğlu, C, Ajani, H, Brahmkshatriya, PS, Jorda, R, Kryštof, V, et al
European journal of medicinal chemistry. 2017;:1118-1128
Abstract
We present comprehensive testing of solvent representation in quantum mechanics (QM)-based scoring of protein-ligand affinities. To this aim, we prepared 21 new inhibitors of cyclin-dependent kinase 2 (CDK2) with the pyrazolo[1,5-a]pyrimidine core, whose activities spanned three orders of magnitude. The crystal structure of a potent inhibitor bound to the active CDK2/cyclin A complex revealed that the biphenyl substituent at position 5 of the pyrazolo[1,5-a]pyrimidine scaffold was located in a previously unexplored pocket and that six water molecules resided in the active site. Using molecular dynamics, protein-ligand interactions and active-site water H-bond networks as well as thermodynamics were probed. Thereafter, all the inhibitors were scored by the QM approach utilizing the COSMO implicit solvent model. Such a standard treatment failed to produce a correlation with the experiment (R2 = 0.49). However, the addition of the active-site waters resulted in significant improvement (R2 = 0.68). The activities of the compounds could thus be interpreted by taking into account their specific noncovalent interactions with CDK2 and the active-site waters. In summary, using a combination of several experimental and theoretical approaches we demonstrate that the inclusion of explicit solvent effects enhance QM/COSMO scoring to produce a reliable structure-activity relationship with physical insights. More generally, this approach is envisioned to contribute to increased accuracy of the computational design of novel inhibitors.