Small Molecules In Solution Research Articles

Essential ingredients for rational drug design.

This short review focuses on three aspects of rational drug design that we consider of utmost importance: the conformation of small molecules in solid form, the conformation of small molecules in solution and lesser studied interactions in protein-ligand complexes. Using examples from recent literature, we will illustrate these different aspects and how they have contributed to the discovery of potent modulators.

The Effect of Bulky Substituents on Two π-Conjugated Mesogenic Fluorophores. Their Organic Polymers and Zinc-Bridged Luminescent Networks.

From a dicyano-phenylenevinylene (PV) and an azobenzene (AB) skeleton, two new symmetrical salen dyes were obtained. Terminal bulky substituents able to reduce intermolecular interactions and flexible tails to guarantee solubility were added to the fluorogenic cores. Photochemical performances were investigated on the small molecules in solution, as neat crystals and as dopants in polymeric matrixes. High fluorescence quantum yield in the orange-red region was observed for the brightest emissive films (88% yield). The spectra of absorption and fluorescence were predicted by Density Functional Theory (DFT) calculations. The predicted energy levels of the frontier orbitals are in good agreement with voltammetry and molecular spectroscopy measures. Employing the two dyes as dopants of a nematic polymer led to remarkable orange or yellow luminescence, which dramatically decreases in on-off switch mode after liquid crystal (LC) order was lost. The fluorogenic cores were also embedded in organic polymers and self-assembly zinc coordination networks to transfer the emission properties to a macro-system. The final polymers emit from red to yellow both in solution and in the solid state and their photoluminescence (PL) performance are, in some cases, enhanced when compared to the fluorogenic cores.

Detection of Macromolecular Content in a Mixed Solution of Protein Macromolecules and Small Molecules Using a Weak Measurement Linear Differential System.

In this paper, we propose a linear differential detection system based on a frequency domain weak measurement. The system can be used for detecting optical substances. Moreover, we completed an experiment to detect himan serum albumin (HSA) content in a mixture of human serum albumin and l-proline via dialysis. This work also proves the differential function of the system. This experiment can be further extended to detecting protein content in a mixed solution that contains protein macromolecules and various small molecules. It is very important for detecting molecules without photomarking in solutions of complex biological samples. In this paper, the system has an optical resolution of 1.39 × 10-5, and resolution of 4.06 × 10-8 mol/L for himan serum protein solution.

Brillouin spectroscopy of biorelevant fluids in relation to viscosity and solute concentration.

The measurement of intracellular viscoelastic properties by Brillouin scattering is a rapidly developing field in biophysics and medicine. Here, the Brillouin spectroscopy is applied for a number of aqueous solutions of biorelevant molecules to reveal relations between the Brillouin line parameters (frequency and width) and viscosity or solute concentration. It is found that for the majority of the studied biorelevant molecules the solute concentration governs the Brillouin frequency in a universal manner. On the other hand, the relations between the macroscopic viscosity and Brillouin peak parameters are different for different solutes. We conclude that for biological fluids the viscosity evaluation from Brillouin data needs prior knowledge about the chemical composition. This result challenges the fidelity of the indirect experimental determinations of the cellular viscosity, when small molecule solutions are used for the calibration.

Budding and Fission of Vesicles Induced by Small Solute Molecules

Budding and Fission of Vesicles Induced by Small Solute Molecules

Covalent capture of supramolecular species in an aqueous solution of water-miscible small organic molecules.

Since an early report in the 1970s, the mesoscale inhomogeneities formed in an aqueous solution of water-miscible small organic molecules have been debated for over forty years with a variety of explanations. Although it was recently established that these inhomogeneities are supramolecular species caused by trace impurities, the structure of the supramolecular species and the mechanism behind their formation are not yet clear. By means of covalent capture, we herein disclose that the formation mechanism of the supramolecular species consists of a two-step self-assembly process: the small molecules first assemble into primary micelles with a trace amount of impurity, and the formed dynamic ultra-small micelles aggregate further through hydrogen bonding to achieve a buildup of thermodynamic mesoscale inhomogeneities. Based on this finding, supramolecular species have been used as elements for pH-responsive size-changeable drug carriers, which respond to the acidic tumour extracellular milieu and decompose into small particles for deep tumour penetration and effective distribution.

Surface-enhanced infrared attenuated total reflection spectroscopy via carbon nanodots for small molecules in aqueous solution.

In this study, carbon nanodots (CNDs) with excellent aqueous dispersibility, narrow size distribution, and oxygen-rich functional groups have been prepared via a green electrochemical method. Graphite electrodes were directly electrolyzed at ambient temperatures to form uniform CNDs in deionized water, which is free from additional oxidant/reductant. As-synthesized CNDs have been applied to coat an attenuated total reflection (ATR) waveguide enabling surface-enhanced infrared absorption (SEIRA) spectroscopic studies for detecting a variety of analytes in aqueous phase with remarkably enhanced IR band intensities. Finally, the proposed ATR-SEIRA strategy enabled quantitatively analyzing adenine in aqueous solution after optimizing the amount of CNDs, the solution pH, and potential CND aggregation. Graphical abstract.

The effects of NaCl on enzyme encapsulation by zeolitic imidazolate frameworks-8

Metal-organic framework (MOF) has generated a lot of research interests for it can be employed as immobilization material for enzyme. There are many small molecules in enzyme solution during the extraction process, such as NaCl. It is important to study the effects of the small molecules on MOFs. Here we report a facile and efficient method to encapsulate (R)-1-phenylethanol dehydrogenase ((R)-PEDH) into zeolitic imidazolate framework-8 (ZIF-8). In this work, the effects of NaCl on shape of ZIF-8 and enzyme encapsulation have been investigated. The scanning electron microscope (SEM) results showed that 0.1 M NaCl affect the morphology of ZIF-8 while the crystal structure was not changed analyzed by X-ray diffraction (XRD), and 0.1 M NaCl consisted in the encapsulation system of (R)-PEDH@ZIF-8 enhanced the activity up to 2.5 folds than no NaCl consisted during prepared (R)-PEDH@ZIF-8. The (R)-PEDH@ZIF-8 (prepared with 0.1 M NaCl) enhanced the storage stability and resist ability against trypsin, and the (R)-PEDH@ZIF-8 has been successfully reused.

Photoinduced disinfection in sunlit natural waters: Measurement of the second order inactivation rate constants between E. coli and photogenerated transient species

This work uncovers the implications of the estimation of exogenous inactivation rates for E. coli after the initial lag phase, and presents a strategy for the determination of the second-order inactivation rate constants (k2nd) of these bacteria with relevant transient species promoted by solar light in natural waters. For this purpose, specific precursors were considered (nitrate ion, rose bengal, anthraquinone-2-sulfonate) as well as the respective photo-generated transient species (i.e., hydroxyl radical (•OH), singlet oxygen (1O2) and triplet excited states). Under these conditions and by using suitable reference compounds (acesulfame K and 2,4,6-trimethylphenol in different series of experiments), the k2nd values were obtained after developing a proper competition kinetics methodology. The k2nd values were (2.5 ± 0.9) × 1011, (3.8 ± 1.6) × 107 and (1.8 ± 0.7) × 1010 M−1 s−1 for the inactivation of E. coli by •OH, 1O2 and the triplet state of anthraquinone-2-sulfonate (3AQ2S*), respectively. The measurement of a reaction rate constant that is higher than the diffusion-control limit for small molecules in aqueous solution implies that bacteria behave differently from molecules, e.g., because of the large size difference between bacteria and the transients. The obtained k2nd values were used for the modeling of the bacteria inactivation kinetics in outdoor systems (both water bodies and SODIS bottles), limited to the exponential decay phase that follows the initial lag time. Afterwards, the role of dissolved organic matter (DOM) as precursor of transient species for bacterial elimination was systematically studied. The interaction of different sunlight wavelength regions (UVB, UV-A, blue, green and yellow light) with Suwannee river (SW) and Nordic Lake organic matter (ND) was tested, and the photoinduced disinfection exerted by DOM isolates (SW DOM, Suwannee River Humic Acid, Suwannee River Fulvic Acid or Pony Lake Fulvic Acid) was compared. It was not possible to achieve a complete differentiation of the individual contributions of DOM triplet states (3DOM*) and 1O2 to bacterial inactivation. However, the application of competition kinetics to E. coli under solar irradiation in the presence of SW led to a k2nd value of (2.17 ± 0.40) × 1010 M−1 s−1, which is very near the value for inactivation by 3AQ2S* and suggests that the latter behaved very similar to SW-3DOM* and was a good 3DOM* proxy in the present case. The determination of the second-order inactivation rate constants of E. coli with •OH, 3DOM* and 1O2 represents a significant progress in the understanding of the external inactivation pathways of bacteria. It also allows predicting that, after the lag phase, 1O2 would contribute to photoinactivation to a far lesser extent than •OH and 3DOM*.

Diffusion Behavior of Water Molecules in Hydrogels with Controlled Network Structure

Hydrogels have attracted attention as biomaterials because of the similar property to biological soft tissues. One of the applications of hydrogels for biomaterials is drug release carrier. For the application, it is important to understand and to control the diffusion behavior of molecules in hydrogels. There are three major models describing diffusion behavior of small molecules in the polymer solution. First is the Ogston model, in which polymer network is considered to behave as an obstacle preventing the diffusion of particles. Second is the hydrodynamic model, in which the existence of polymer increases the effective viscosity and decreases diffusion speed of particles. Third is the free volume model, in which particles diffuse passing through free volume of solvent and polymer. Although the validity of these models has been investigated by many researchers, there is no clear experimental evidence to support any models. Thus, even now, many models are left without validation. The muddling of models was assisted by the heterogeneity in conventional hydrogels. To understand the diffusion behavior of small molecules in a hydrogel, the validation of these models using a homogeneous hydrogel is necessary. Recently, we have developed a homogeneous hydrogel, Tetra-PEG gel, by combining two kinds of tetra-armed pre-polymers. It has been revealed that Tetra-PEG gel has an extremely homogeneous network structure, and network structure parameters (polymer volume fraction : φ 0, molecular weight between crosslinks : M w, binding ratio : p) of Tetra-PEG gel can be controlled independently. In this study, we investigated the effect of network structures on the self-diffusion coefficient of water molecules (D) in Tetra-PEG gels and in pure water (D 0) by Pulsed field-gradient spin-echo Nuclear Magnetic Resonance (PGSE-NMR). The values of D/D 0 decreased as an exponential function with an increase in φ 0 (0 - 0.15), and was independent of M w (10k, 20k g/mol) (Figure 1). This result well agreed with three models, and the difference among three models was negligible. On the other hand, D/D 0 decreased with a decrease in p (0 - 1) (Figure 1). This result was not reproduced by any three models, suggesting these models were not valid to describe diffusion behavior of small molecules in a hydrogel. Here, we tested another model proposed by M. Tokita et al. In the model, the diffusion of probe molecules is mainly determined by the correlation length of the polymer network (blob size : ξ) and the hydrodynamic radius of the probe molecules (R h) as, D/D 0 = exp(-R h/ξ). In Figure 2, D/D 0 in Tetra-PEG gels were plotted against 1/ξ. The values of xwere estimated by our previous small angle neutron scattering experiment. As shown in the figure, all the data including p-tune results fall onto a guide showing D/D 0 = 0.97exp(-2.8/ξ). The experimental values of the front coefficient (0.97) and R h (2.8Å) were close to the theoretical value (1.0) and the hydrodynamic radius of a water molecule (3.0Å), respectively. These results suggest that Tokita’s model is the correct model to describe the diffusion behavior of small molecules in a hydrogel. Figure 1

Quantifying the Effects of Hydrogen Bonding on Nitrile Frequencies in GFP: Beyond Solvent Exposure.

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.

Scalable Directed Assembly of Highly Crystalline 2,7-Dioctyl[1]benzothieno[3,2- b][1]benzothiophene (C8-BTBT) Films.

Assembly of organic semiconductors with ordered crystal structure has been actively pursued for electronics applications such as organic field-effect transistors (OFETs). Among various film deposition methods, solution-based film growth from small molecule semiconductors is preferable because of its low material and energy consumption, low cost, and scalability. Here, we show scalable and controllable directed assembly of highly crystalline 2,7-dioctyl[1]benzothieno[3,2- b][1]benzothiophene (C8-BTBT) films via a dip-coating process. Self-aligned stripe patterns with tunable thickness and morphology over a centimeter scale are obtained by adjusting two governing parameters: the pulling speed of a substrate and the solution concentration. OFETs are fabricated using the C8-BTBT films assembled at various conditions. A field-effect hole mobility up to 3.99 cm2 V-1 s-1 is obtained. Owing to the highly scalable crystalline film formation, the dip-coating directed assembly process could be a great candidate for manufacturing next-generation electronics. Meanwhile, the film formation mechanism discussed in this paper could provide a general guideline to prepare other organic semiconducting films from small molecule solutions.

On demand manufacturing of patient-specific liquid capsules via co-ordinated 3D printing and liquid dispensing

A method for the production of liquid capsules with the potential of modifying drug dose and release is presented. For the first time, the co-ordinated use of fused deposition modelling (FDM), 3D printing and liquid dispensing to fabricate individualised dosage form on demand in a fully automated fashion has been demonstrated. Polymethacrylate shells (Eudragit EPO and RL) for immediate and extended release were fabricated using FDM 3D printing and simultaneously filled using a computer-controlled liquid dispenser loaded with model drug solution (theophylline) or suspension (dipyridamole). The impact of printing modes: simultaneous shell printing and filling (single-phase) or sequential 3D printing of shell bottom, filling and shell cap (multi-phase), nozzle size, syringe volume, and shell structure has been reported. The use of shell thickness of 1.6 mm, and concentric architecture allowed successful containment of liquid core whilst maintaining the release properties of the 3D printed liquid capsule. The linear relationship between the theoretical and the actual volumes from the dispenser reflected its potential for accurate dosing (R2 = 0.9985). Modifying the shell thickness of Eudragit RL capsule allowed a controlled extended drug release without the need for formulation change. Owing to its low cost and versatility, this approach can be adapted to wide spectrum of liquid formulations such as small and large molecule solutions and obviate the need for compatibility with the high temperature of FDM 3D printing process. In a clinical setting, health care staff will be able to instantly manufacture in small volumes liquid capsules with individualised dose contents and release pattern in response to specific patient's needs.

Lennard–Jones Lecture 2017*

ABSTRACTSome examples of the use of molecular dynamics simulation to study solutions of small molecules in ionic liquids are discussed. It is shown that electrostatic forces, while not the dominant solute–solvent interaction, determine the local solute environment. The solubility of aromatics and the changes in the spectra of low-frequency intermolecular vibrations in two related ionic liquids (one dicationic and one monocationic) are compared with experimental results and related to the local environment.

A Capture-SELEX Strategy for Multiplexed Selection of RNA Aptamers Against Small Molecules.

In vitro selection of aptamers that recognize small organic molecules has proven difficult, in part due to the challenge of immobilizing small molecules on solid supports for SELEX (Systematic Evolution of Ligands by Exponential Enrichment). This study describes the implementation of RNA Capture-SELEX, a selection strategy that uses an RNA library to yield ligand-responsive RNA aptamers targeting small organic molecules in solution. To demonstrate the power of this method we selected several aptamers with specificity towards either the natural sweetener rebaudioside A or the food-coloring agent carminic acid. In addition, Bio-layer interferometry is used to screen clonal libraries of aptamer candidates and is used to interrogate aptamer affinity. The RNA-based Capture-SELEX strategy described here simplifies selection of RNA aptamers against small molecules by avoiding ligand immobilization, while also allowing selection against multiple candidate targets in a single experiment. This makes RNA Capture-SELEX particularly attractive for accelerated development of RNA aptamers targeting small metabolites for incorporation into synthetic riboswitches and for analytical biosensors.

Application of reference-modified density functional theory: Temperature and pressure dependences of solvation free energy.

Recently, we proposed a reference-modified density functional theory (RMDFT) to calculate solvation free energy (SFE), in which a hard-sphere fluid was introduced as the reference system instead of an ideal molecular gas. Through the RMDFT, using an optimal diameter for the hard-sphere reference system, the values of the SFE calculated at room temperature and normal pressure were in good agreement with those for more than 500 small organic molecules in water as determined by experiments. In this study, we present an application of the RMDFT for calculating the temperature and pressure dependences of the SFE for solute molecules in water. We demonstrate that the RMDFT has high predictive ability for the temperature and pressure dependences of the SFE for small solute molecules in water when the optimal reference hard-sphere diameter determined for each thermodynamic condition is used. We also apply the RMDFT to investigate the temperature and pressure dependences of the thermodynamic stability of an artificial small protein, chignolin, and discuss the mechanism of high-temperature and high-pressure unfolding of the protein. © 2017 Wiley Periodicals, Inc.

Semisynthetic Bioluminescent Sensor Proteins for Direct Detection of Antibodies and Small Molecules in Solution.

Single-step immunoassays that can be performed directly in solution are ideally suited for point-of-care diagnostics. Our group recently developed a new platform of bioluminescent sensor proteins (LUMABS; LUMinescent AntiBody Sensor) that allow antibody detection in blood plasma. Thus far, LUMABS has been limited to the detection of antibodies recognizing natural peptide epitopes. Here, we report the development of semisynthetic LUMABS sensors that recognize nonpeptide epitopes. The non-natural amino acid para-azidophenylalanine was introduced at the position of the original antibody-recognition sites as a chemical handle to enable site-specific conjugation of synthetic epitope molecules coupled to a dibenzocylcooctyne moiety via strain-promoted click chemistry. The approach was successfully demonstrated by developing semisynthetic LUMABS sensors for antibodies targeting the small molecules dinitrophenol and creatinine (DNP-LUMABS and CR-LUMABS) with affinities of 5.8 pM and 1.3 nM, respectively. An important application of these semisynthetic LUMABS is the detection of small molecules using a competitive assay format, which is demonstrated here for the detection of creatinine. Using a preassembled complex of CR-LUMABS and an anti-creatinine antibody, the detection of high micromolar concentrations of creatinine was possible both in buffer and in 1:1 diluted blood plasma. The use of semisynthetic LUMABS sensors significantly expands the range of antibody targets and enables the application of LUMABS sensors for the ratiometric bioluminescent detection of small molecules using a competitive immunoassay format.

A new polymethylmetacrylate membrane improves the membrane adhesion of blood components and clinical efficacy

BackgroundHemodialysis with polymethylmetacrylate (PMMA) membrane dialyzers allows unique protein adsorption. New PMMA dialyzers should demonstrate equivalent protein adsorption, but improved hemocompatibility.MethodsPlatelet adhesion and activation and protein adsorption were determined for the new PMMA membrane dialyzer Filtryzer® NF (NF) and conventional Filtryzer® BG (BG) in vitro. In clinical study, six subjects were treated with NF and BG for 3 months each in a crossover design. Three months after the use of each dialyzer, solute removal, hemocompatibility, peripheral circulation by skin perfusion pressure (SPP), and other dialysis-related side effects were also compared.ResultsProtein adsorption pattern was similar on NF and BG, but platelet adhesion and activation were much lower on NF in vitro. Clinically, NF and BG removed equivalent amounts of small molecule solutes and low-molecular-weight proteins. The platelet count and peripheral circulation were stable during dialysis with NF, whereas both were decreased during dialysis with BG. The percent changes in SPP were significantly smaller with NF compared with BG. Data on the dialysis-related side effects were no significant differences in any individual items or in the mean total score for the two groups, but the mean score of the seven items tended to be lower with NF. Protein adsorption by the membranes is considered one factor associated with clinically improvements. But activated platelets induce the aggregation of platelets, leukocytes, and erythrocytes, which can interfere with peripheral circulation during dialysis. Decreased peripheral circulation causes dialysis-related side effects. Therefore reduced platelet activation during dialysis by NF may be significant in improving the prognosis of patients, as well as reducing the frequency of side effects.ConclusionsThe new PMMA membrane dialyzer NF shows substantially improved hemocompatibility. We expect this product will improve the condition of chronic dialysis patients.Trial registrationUMIN000024955

Suppression of Hydrogen Evolution by Oxygen Reduction in Nanoporous Electrocatalysts.

Electroreduction of small molecules in aqueous solution often competes with the hydrogen evolution reaction (HER), especially if the reaction is driven even moderately hard using a large overpotential. Here, the oxygen reduction reaction (ORR) was studied under proton diffusion-limited conditions in slightly acidic electrolytes: a model system to study the relative transport kinetics of protons and reactants to an electrocatalyst and the relationship between transport and catalytic performance. Using dealloyed nanoporous nickel-platinum (np-NiPt) electrodes, we find the hydrogen evolution reaction can be completely suppressed even at high overpotentials (-400 mV vs RHE). In addition, the mechanism of oxygen reduction can be changed by using buffered versus unbuffered solutions, suggesting the reaction selectivity is associated with a transient rise (or lack thereof) in the interface pH at the np-NiPt surface. Independently controlling reactant transport to electrocatalyst surfaces at high overpotentials exhibited a surprisingly rich phenomenology that may offer a generalizable strategy to increase activity and selectivity during electroreduction reactions.

Averaged Condensed Phase Model for Simulating Molecules in Complex Environments.

The need for configurational sampling dramatically increases the cost of combined quantum mechanics/molecular mechanics (QM/MM) simulations of chemical processes in solution. We developed an averaged condensed phase environment (ACPE) model that constructs an effective polarizable environment directly from explicitly sampled molecular dynamics configurations via the K-means++ algorithm and a mathematically rigorous translation of the molecular mechanics parameters. The model captures detailed heterogeneous features in the environment that may be difficult to describe using a conventional polarizable continuum model. Instead of performing repeated QM/MM calculations for each new configuration of the environment, the ACPE approach allows one to perform a single QM calculation on an averaged configuration. Here, we demonstrate the model by computing electronic excitation energies for several small molecules in solution. The ACPE model predicts the excitation energies in excellent agreement with conventional configurational averaging yet with orders of magnitude of reduction in the computational cost.