Internal standard capillary electrophoresis as a high-throughput method for pKa determination in drug discovery and development

Acidity constants and protonation sites of cyclic dinucleotides determined by capillary electrophoresis, quantum chemical calculations, and NMR spectroscopy

Cyclic dinucleotides (CDNs) are important second messengers in bacteria and eukaryotes. Detailed characterization of their physicochemical properties is a prerequisite for understanding their biological functions. Herein, we examine acid-base and electromigration properties of selected CDNs employing capillary electrophoresis (CE), density functional theory (DFT), and nuclear magnetic resonance (NMR) spectroscopy to provide benchmark pKa values, as well as to unambiguously determine the protonation sites. Acidity constants (pKa) of the NH+ moieties of adenine and guanine bases and actual and limiting ionic mobilities of CDNs were determined by nonlinear regression analysis of the pH dependence of their effective electrophoretic mobilities measured by CE in aqueous background electrolytes in a wide pH range (0.98-11.48), at constant temperature (25°C), and constant ionic strength (25 mM). The thermodynamic pKa values were found to be in the range 3.31-4.56 for adenine and 2.28-3.61 for guanine bases, whereas the pKa of enol group of guanine base was in the range 10.21-10.40. Except for systematic shifts of ∼2 pKa, the pKa values calculated by the DFT-D3//COSMO-RS composite protocol that included large-scale conformational sampling and "cross-morphing" were in a relatively good agreement with the pKas determined by CE and predict N1 atom of adenine and N7 atom of guanine as the protonation sites. The protonation of the N1 atom of adenine and N7 atom of guanine in acidic background electrolytes (BGEs) and the dissociation of the enol group of guanine in alkaline BGEs was confirmed also by NMR spectroscopy.

Determination of acidity constants of pyridines, imidazoles, and oximes by capillary electrophoresis

The acidity constant in the form of pKa is one of the most important physicochemical quantities. There are prediction tools available for calculating the pKa , but they only deliver precise calculated values for a relatively small set of chemicals. For complex structures with multiple functional groups in particular, the error in the predicted pKa is high due to the application domain of the corresponding models. Thus, we aim to enlarge the dataset of experimentally determined pKa values using capillary electrophoresis. We, therefore, selected various pyridines, imidazoles, and oximes to determine the pKa values using the internal standard approach and the classical method. Especially oximes were not investigated in the past, and predictions for them include larger errors. Thus, our experimentally determined values could contribute to an improved understanding of various functional groups impacting the pKa values and serve as additional datasets to develop improved pKa prediction tools.

Voltammetric Sensor Based on the Poly(p-aminobenzoic Acid) for the Simultaneous Quantification of Aromatic Aldehydes as Markers of Cognac and Brandy Quality

Cognac and brandy quality control is an actual topic in food analysis. Aromatic aldehydes, particularly syringaldehyde and vanillin, are one of the markers used for these purposes. Therefore, simple and express methods for their simultaneous determination are required. The voltammetric sensor based on the layer-by-layer combination of multi-walled carbon nanotubes (MWCNTs) and electropolymerized p-aminobenzoic acid (p-ABA) provides full resolution of the syringaldehyde and vanillin oxidation peaks. Optimized conditions of p-ABA electropolymerization (100 µM monomer in Britton-Robinson buffer pH 2.0, twenty cycles in the polarization window of -0.5 to 2.0 V with a potential scan rate of 100 mV·s^-1) were found. The poly(p-ABA)-based electrode was characterized by scanning electron microscopy (SEM), cyclic voltammetry, and electrochemical impedance spectroscopy (EIS). Electrooxidation of syringaldehyde and vanillin is an irreversible two-electron diffusion-controlled process. In the differential pulse mode, the sensor allows quantification of aromatic aldehydes in the ranges of 0.075-7.5 and 7.5-100 µM for syringaldehyde and 0.50-7.5 and 7.5-100 µM for vanillin with the detection limits of 0.018 and 0.19 µM, respectively. The sensor was applied to cognac and brandy samples and compared to chromatography.

Extension of the Internal Standard Method for Determination of Thermodynamic Acidity Constants of Compounds Sparingly Soluble in Water by Capillary Zone Electrophoresis

The paper extends applicability of the internal standard method published in 2009 (Fuguet E. et al., J. Chromatogr. A 2009, 1216(17), 3646). Although the original capillary zone electrophoresis method was suggested to determine thermodynamic acidity constants of compounds sparingly soluble in aqueous solutions by carrying out only runs at two different pH values (i.e., without the need to perform many experiments over the appropriate pH range including the form of a low-ionized analyte), we proved that the approach also virtually overcomes any interactions of the analyte in mixed solvents, so that the experiments can be carried out in a methanol-water buffer where the solubility is much better. Applicability of the extended method is illustrated on six selected β-blockers.

Determination of the aqueous pKa of very insoluble drugs by capillary electrophoresis: Internal standards for methanol-water extrapolation

A fast determination of acidity constants (pK_a) of very insoluble drugs has become a necessity in drug discovery process because it often produces molecules that are highly lipophilic and sparingly soluble in water. In this work the high throughput internal standard capillary electrophoresis (IS-CE) method has been adapted to the determination of pK_a of water insoluble compounds by measurement in methanol/aqueous buffer mixtures. For this purpose, the reference pK_a values for a set of 46 acid-base compounds of varied structure (internal standards) have been established in methanol-water mixtures at several solvent composition levels (with a maximum of 40% methanol). The IS-CE method has been successfully applied to seven test drugs of different chemical nature with intrinsic solubilities lower than 10^-6 M. pK_a values have been determined at different methanol/aqueous buffer compositions and afterwards Yasuda-Shedlovsky extrapolation method has been applied to obtain the aqueous pK_a. The obtained results have successfully been compared to literature ones obtained by other methods. It is concluded that the IS-CE method allows the determination of aqueous pK_a values using low proportions of methanol, becoming then more accurate in the extrapolation procedure than other reference methods.

Determination of acidity constants, ionic mobilities, and hydrodynamic radii of carborane-based inhibitors of carbonic anhydrases by capillary electrophoresis

Capillary electrophoresis (CE) has been applied for determination of the thermodynamic acidity constants (pK_a ) of the sulfamidoalkyl and sulfonamidoalkyl groups, the actual and limiting ionic mobilities and hydrodynamic radii of important compounds, eight carborane-based inhibitors of carbonic anhydrases, which are potential new anticancer drugs. Two types of carboranes were investigated, (i) icosahedral cobalt bis(dicarbollide)(1-) ion with sulfamidoalkyl moieties, and (ii) 7,8-nido-dicarbaundecaborate with sulfonamidoalkyl side chains. First, the mixed acidity constants, pK_a ^mix , of the sulfamidoalkyl and sulfonamidoalkyl groups of the above carboranes and their actual ionic mobilities were determined by nonlinear regression analysis of the pH dependences of their effective electrophoretic mobility measured by capillary electrophoresis in the pH range 8.00-12.25, at constant ionic strength (25 mM), and constant temperature (25°C). Second, the pK_a ^mix were recalculated to the thermodynamic pK_a s using the Debye-Hückel theory. The sulfamidoalkyl and sulfonamidoalkyl groups were found to be very weakly acidic with the pK_a s in the range 10.78-11.45 depending on the type of carborane cluster and on the position and length of the alkyl chain on the carborane scaffold. These pK_a s were in a good agreement with the pK_a s (10.67-11.27) obtained by new program AnglerFish (freeware at https://echmet.natur.cuni.cz), which provides thermodynamic pK_a s and limiting ionic mobilities directly from the raw CE data. The absolute values of the limiting ionic mobilities of univalent and divalent carborane anions were in the range 18.3-27.8 TU (Tiselius unit, 1 × 10^-9 m² /Vs), and 36.4-45.9 TU, respectively. The Stokes hydrodynamic radii of univalent and divalent carborane anions varied in the range 0.34-0.52 and 0.42-0.52 nm, respectively.

Determination of acidity constants at 37 °C through the internal standard capillary electrophoresis (IS-CE) method: internal standards and application to polyprotic drugs

This work provides the pKa at the biorelevant temperature of 37 °C for a set of compounds proposed as internal standards for the internal standard capillary electrophoresis (IS-CE) method. This is a high throughput method that allows the determination of the acidity constants of compounds in a short time, avoiding the exact measurement of the pH of the buffers used. pH electrode calibration at 37 °C can be avoided too. In order to anchor the pKa values obtained through the IS-CE method in the pH scale, the acidity constant at 37 °C of some of the standards has been determined also by the reference potentiometric method. In general, a decrease in the pKa value is observed when changing the temperature from 25 to 37 °C, and the magnitude of the change depends on the nature of the compounds. Once the pKa values at 37 °C of the internal standards have been established, the method is applied to the determination of the acidity constants of seven polyprotic (5 diprotic and 2 triprotic) drugs. The obtained mobility-pH profiles show well-defined curves, and the fits provide precise pKa values. Due to the lack of reference data at 37 °C only the pKa values of labetalol can be compared to values from the literature, and a very good agreement is observed.

Competing pathways for photoremovable protecting groups: the effects of solvent, oxygen and encapsulation

Photolysis of p-hydroxyphenacyloxy arenes releases free phenols in good yields governed by their pK_a. At high pK_a, new byproducts (Bvs. A) reveal a change in reaction mechanism.

Determining molecular properties with differential mobility spectrometry and machine learning

The fast and accurate determination of molecular properties is highly desirable for many facets of chemical research, particularly in drug discovery where pre-clinical assays play an important role in paring down large sets of drug candidates. Here, we present the use of supervised machine learning to treat differential mobility spectrometry - mass spectrometry data for ten topological classes of drug candidates. We demonstrate that the gas-phase clustering behavior probed in our experiments can be used to predict the candidates' condensed phase molecular properties, such as cell permeability, solubility, polar surface area, and water/octanol distribution coefficient. All of these measurements are performed in minutes and require mere nanograms of each drug examined. Moreover, by tuning gas temperature within the differential mobility spectrometer, one can fine tune the extent of ion-solvent clustering to separate subtly different molecular geometries and to discriminate molecules of very similar physicochemical properties.

Automated techniques in pKa determination: Low, medium and high-throughput screening methods

Drug discovery programs that generate hundreds of new molecular entities need efficient methodologies for physicochemical profiling. Several high-throughput methods for pK_a screening have been developed in the last 15 years to determine this key physicochemical parameter. Separation techniques such as HPLC-MS or capillary electrophoresis are particularly well-suited due to their high throughput and capacity to deal with impure or complex samples. In addition, potentiometric and (mostly) UV-metric-based methods (plate-based and automated systems), find their place as very precise methodologies for pK_a determination despite of somewhat lower throughput. Finally, pK_a prediction software packages are useful estimator tools but, to date, they cannot replace experimental measurements when accurate pK_a values are required.

The Utility of Calculated Proton Affinities in Drug Design: A DFT Study

Computer-aided drug design comprises several predictive tools, which can calculate various properties of the candidates under development. Proton affinity (PA) is related to pKa (the negative log of the acid dissociation constant (Ka)) one of the fundamental physical properties of drug candidates, determining their water solubility and thus their pharmacokinetic profile. The following questions therefore emerged: to what extent are PA predictions useful in drug design, and can they be reliably used to derive pKa values? Using density functional theory (DFT), it was established that for violuric acid, with three ionisation groups, the PAs correlate well with the measured pKas (R2 = 0.990). Furthermore, an excellent correlation within the amiloride compound family was achieved (R2 = 0.922). In order to obtain correlations for larger compound collections (n = 210), division into chemical families was necessary: carboxylic acids (R2 = 0.665), phenols (R2 = 0.871), and nitrogen-containing molecules (R2 = 0.742). These linear relationships were used to predict pKa values of 90 drug molecules with known pKas. A total of 48 % of the calculated values were within 1 logarithmic unit of the experimental number, but mainstream empirically based methods easily outperform this approach. The conclusion can therefore be reached that PA values cannot be reliably used for predicting pKa values globally but are useful within chemical families and in the event where a specific tautomer of a drug needs to be identified.

Assessing Physicochemical Properties of Drug Molecules via Microsolvation Measurements with Differential Mobility Spectrometry

The microsolvated state of a molecule, represented by its interactions with only a small number of solvent molecules, can play a key role in determining the observable bulk properties of the molecule. This is especially true in cases where strong local hydrogen bonding exists between the molecule and the solvent. One method that can probe the microsolvated states of charged molecules is differential mobility spectrometry (DMS), which rapidly interrogates an ion's transitions between a solvated and desolvated state in the gas phase (i.e., few solvent molecules present). However, can the results of DMS analyses of a class of molecules reveal information about the bulk physicochemical properties of those species? Our findings presented here show that DMS behaviors correlate strongly with the measured solution phase pK_a and pK_b values, and cell permeabilities of a set of structurally related drug molecules, even yielding high-resolution discrimination between isomeric forms of these drugs. This is due to DMS's ability to separate species based upon only subtle (yet predictable) changes in structure: the same subtle changes that can influence isomers' different bulk properties. Using 2-methylquinolin-8-ol as the core structure, we demonstrate how DMS shows promise for rapidly and sensitively probing the physicochemical properties of molecules, with particular attention paid to drug candidates at the early stage of drug development. This study serves as a foundation upon which future drug molecules of different structural classes could be examined.

Equilibrium acidities of cinchona alkaloid organocatalysts bearing 6′-hydrogen bonding donors in DMSO

The pK_a values of 18 cinchona alkaloid based organocatalysts bearing 6′-hydrogen bonding donors were determined by the overlapping indicator method in DMSO via UV spectrophotometric titrations. The pK_a values are in the range of 6.76–20.24.

Novel Instrument for Automated pK(a) Determination by Internal Standard Capillary Electrophoresis

The internal standard capillary electrophoresis method (IS-CE) has been implemented in a novel sequential injection-capillary electrophoresis instrument for the high-throughput determination of acidity constants (pK(a)) regardless of aqueous solubility, number of pK(a) values, or structure. This instrument comprises a buffer creation system that automatically mixes within a few seconds four reagents for in situ creation of the separation electrolyte with a pH range of 2-13, ionic strength of 10-100 mM and organic solvent content from 0% to 40%. Combined with 1.2 kV/cm and a short effective length (15 cm to the UV detector) fast 20 s electrophoretic separations can be obtained. The low standard deviation of the replicates and the low variation compared to reference values show that this system can accurately determine acidity constants of drugs by IS-CE. A single pK(a) can be determined in 2 min and a set of 20 measurements in half an hour, allowing rapid, simple, and flexible determination of pK(a) values of pharmaceutical targets.

Application of capillary electrophoresis in determination of acid dissociation constant values

The chemical groups undergoing protonation or deprotonation in solution are described by the acid dissociation constant value, the key parameter for physicochemical characterization of biologically- and pharmacologically-important compounds. Capillary electrophoresis (CE) proved to be suitable technique for its determination: it enables automated and accurate measurements even for minute amount of sample, does not require the information about concentration, and handle both the impure and complex samples. In this review, a number of contributions reporting on the application of CE in pKa prediction has been summarized and critically discussed. The reader will find herein the brief introduction of theory, summary of all works published in the last decade, considerations on the most important innovations and achievements, and the discussion of pKa-related issues as e.g. the role of pKa-shifts in the chiral separation mechanism or the elucidation of migration order reversals observed during CE-mediated separations.