Hydrophobicity estimations by reversed-phase liquid chromatography. Implications for biological partitioning processes

An Automated, Open-Source Workflow for the Generation of (3D) Fragment Libraries

The recent success of fragment-based drug discovery (FBDD) is inextricably linked to adequate library design. To guide the design of our fragment libraries, we have constructed an automated workflow in the open-source KNIME software. The workflow considers chemical diversity and novelty of the fragments, and can also take into account the three-dimensional (3D) character. This design tool can be used to create large and diverse libraries but also to select a small number of representative compounds as a focused set of unique screening compounds to enrich existing fragment libraries. To illustrate the procedures, the design and synthesis of a 10-membered focused library is reported based on the cyclopropane scaffold, which is underrepresented in our existing fragment screening library. Analysis of the focused compound set indicates significant shape diversity and a favorable overall physicochemical profile. By virtue of its modular setup, the workflow can be readily adjusted to design libraries that focus on properties other than 3D shape.

Effect of regio- and stereoisomerism on antifouling 2,5-diketopiperazines

Marine biofouling is a problem that plagues all maritime industries at vast economic and environmental cost. Previous and current methods to prevent biofouling have employed the use of heavy metals and other toxic or highly persistent chemicals, and these methods are now coming under immense regulatory pressure. Recent studies have illustrated the potential of nature-inspired tetrasubstituted 2,5-diketopiperazines (2,5-DKPs) as eco-friendly marine biocides for biofouling control. These highly active symmetrically substituted 2,5-DKPs can be generated by combining structural motifs from cationic innate defence peptides and natural marine antifoulants. A balance between a threshold hydrophobic contribution and sufficient cationic charge has been established as key for bioactivity, and our current study further increases understanding of the antifouling mechanism by investigating the effect of both regio- and stereochemistry. Novel synthetic routes for the generation of unsymmetrical 2,5-DKPs were developed and a library of nine compounds was prepared. The compounds were screened against a series of four model macrofouling organisms (Ciona savignyi, Mytilus galloprovincialis, Spirobranchus cariniferus, and Undaria pinnatifida). Several of the evaluated compounds displayed inhibitory activity at sub-micromolar concentrations. The structural contributions to antifouling bioactivity were studied using NMR spectroscopy and molecular modelling, revealing a strong dependence on a stable amphiphilic solution structure regardless of substitution pattern.

Modeling of Anticancer Sulfonamide Derivatives Lipophilicity by Chemometric and Quantitative Structure-Retention Relationships Approaches

Sulfonamides are a classic group of chemotherapeutic drugs with a broad spectrum of pharmacological action, including anticancer activity. In this work, reversed-phase high-performance liquid chromatography and biomimetic chromatography were applied to characterize the lipophilicity of sulfonamide derivatives with proven anticancer activities against human colon cancer. Chromatographically determined lipophilicity parameters were compared with obtained logP, employing various computational approaches. Similarities and dissimilarities between experimental and computational logP were studied using principal component analysis, cluster analysis, and the sum of ranking differences. Furthermore, quantitative structure–retention relationship modeling was applied to understand the influences of sulfonamide’s molecular properties on lipophilicity and affinity to phospholipids.

Towards eco-friendly marine antifouling biocides - Nature inspired tetrasubstituted 2,5-diketopiperazines

Marine biofouling plagues all maritime industries at vast economic and environmental cost. Previous and most current methods to control biofouling have employed highly persistent toxins and heavy metals, including tin, copper, and zinc. These toxic methods are resulting in unacceptable environmental harm and are coming under immense regulatory pressure. Eco-friendly alternatives are urgently required to effectively mitigate the negative consequence of biofouling without causing collateral harm. Amphiphilic micropeptides have recently been shown to exhibit excellent broad-spectrum antifouling activity, with a non-toxic mode of action and innate biodegradability. The present work focused on incorporating the pharmacophore derived from amphiphilic micropeptides into a 2,5-diketopiperazine (DKP) scaffold. This privileged structure is present in a vast number of natural products, including marine natural product antifoulants, and provides advantages of synthetic accessibility and adaptability. A novel route to symmetrical tetrasubstituted DKPs was developed and a library of amphiphilic 2,5-DKPs were subsequently synthesised. These biodegradable compounds were demonstrated to be potent marine antifoulants displaying broad-spectrum activity in the low micromolar range against a range of common marine fouling organisms. The outcome of planned coating and field trials will dictate the future development of the lead compounds.

Teicoplanin-Modified HPLC Column as a Source of Experimental Parameters for Prediction of the Anticonvulsant Activity of 1,2,4-Triazole-3-Thiones by the Regression Models

The cell membrane is a complex system that consists of lipids, proteins, polysaccharides, and amphiphilic phospholipids. It plays an important role in ADME processes that are responsible for the final pharmaceutical effects of xenobiotics (bioavailability, activity). To study drug-membrane interaction at the molecular level, several high-performance liquid chromatography (HPLC) membrane model systems have been proposed which are mimicking mainly its lipid character. The aim of this work was to study interactions of new synthesized antiepileptic compounds of 4-alkyl-5-(3-chlorophenyl)-2,4-dihydro-3H-1,2,4-triazole-3-thione derivatives with Chirobiotic column containing glycoprotein ligand attached to the silica matrix. The affinity of the analytes to immobilized glycoprotein ligand was examined chromatographically in reversed-phase mode. The thermodynamics of interactions between bioactive compounds and teicoplanin was studied in terms of the van't Hoff linear relationship ln k vs. 1/T in the range of 5-45 °C. Change in enthalpy (ΔH°), change in entropy (ΔS°) and change in Gibbs free energy (ΔG°) were estimated utilizing graphical extrapolation and interpolation methods. The density functional theory (DFT) approach and docking simulations were used to get the molecular interpretation and prove the obtained experimental results. Cross-correlations of chromatographic and thermodynamic parameters with non-empirical topological and quantum chemical indices suggest that the polarizability of analytes appears to be responsible for the interactions of the tested molecules with teicoplanin and, ultimately, their retention on the column. Experimental and theoretical parameters were subjected to statistical analysis using regression models. Partial least squares (PLS) regression model showed the usefulness of the experimentally measured parameter φ0 (MeOH) to discriminate between anticonvulsant active and inactive 1,2,4-triazole-3-thione derivatives. Obtained results point out the usefulness of interaction of potential anticonvulsants with glycoprotein class of compounds to anticipate their activity.

Substituted sulfonamide bioisosteres of 8-hydroxyquinoline as zinc-dependent antibacterial compounds

A series of substituted sulfonamide bioisosteres of 8-hydroxyquinoline were evaluated for their antibacterial activity against the common mastitis causative pathogens Streptococcus uberis, Staphylococcus aureus and Escherichia coli, both in the presence and absence of supplementary zinc. Compounds 9a-e, 10a-c, 11a-e, 12 and 13 were demonstrated to have MICs of 0.0625 µg/mL against S. uberis in the presence of 50 µM ZnSO₄. Against S. aureus compounds 9g (MIC 4 µg/mL) and 11d (MIC 8 µg/mL) showed the greatest activity, whereas all compounds were found to be inactive against E. coli (MIC > 256 µg/mL); again in the presence of 50 µM ZnSO₄. All compounds were demonstrated to be significantly less active in the absence of supplementary zinc. Compound 9g was subsequently confirmed to be bactericidal, with an MBC (≥3log₁₀ cfu/mL reduction) of 0.125 µg/mL against S. uberis in the presence of 50 µM ZnSO₄. To validate the sanitising activity of compound 9g in the presence of supplementary zinc, a quantitative suspension disinfection (sanitizer) test was performed. In this preliminary test, sanitizing activity (>5log₁₀ reduction of CFU/mL in 5 min) was observed against S. uberis for compound 9g at concentrations as low as 1 mg/mL, validating the potential of this compound to function as a topical sanitizer against the major environmental mastitis-causing microorganism S. uberis.

One pot solvothermal synthesis of novel fluorescent phloem-mobile phenylpyrazole amide pesticides fused olefin moieties to enhance insecticidal bioactivities and photodegradation properties

In order to find a novel type of fluorescent phloem-mobile insecticides, a facile one-pot solvothermal strategy via fipronil addition-elimination substitution reaction with the corresponding acyl chloride derivatives has been employed to construct series of phenylpyrazole amide derivatives (PAs) fused olefin moieties in high yields. The investigation for insecticidal bioactivities of PAs against 3rd instar larvae of Plutella xylostella exhibited better activities than that of fipronil, which can be elucidated by enhanced phloem mobility and calcium ions' coordination with amide N-C=O, CC double bonds and chloride ions, extended conjugate moieties and decreasing steric hindrance of the stereoscopic structure. The introduction of amide units conferred phloem mobility to PAs, which was evaluated by the hydrophobic parameters determined with reversed-phase HPLC through the chromatographic capacity factor. By introducing conjugate moieties and organic chromophore into phenylpyrazole parent structure to increase their conjugation degree and light absorption abilities, PAs exhibited good photodegradation properties. The relationships between extended conjugate moieties of parent structure, electronegativity of substituted groups and photodegradation properties have been discussed. The olefin units connected to PAs caused electronic absorption and fluorescent wavelengths bathochromic shifted. Under simulated solar irradiation, PAs can be reconverted into fipronil parent fragments by photodegradation, thereby enhancing their insecticidal activity. The fluorescent quantum yields of PAs were almost 4 times that of fipronil, which also laid a foundation for the natural degradation and fluorescence detection of insecticide residues.

Reversed phase HPLC with high temperature ethanol/water mobile phases as a green alternative method for the estimation of octanol/water partition coefficients

High temperature ethanol/water was explored as a green eluent in the reversed-phase liquid chromatographic approximation of pure water retention (log k_w) and subsequent estimation of the octanol/water partition coefficient (log P) via the Collander equation and the Leave-One-Out method. As part of this work, linear solvation energy relationships were employed to compare the log k_w extrapolated systems based on high temperature ethanol/water, ambient acetonitrile/water, and ambient methanol/water mobile phases. Based on the comparisons of the three organic modifiers, high temperature ethanol/water mobile phases were observed to provide the best estimation of log P. This conclusion is based on a high log P correlation of 0.968 R² and a near unity cos θ value of 0.997 between LSER coefficient vectors of ethanol/water estimated log P and octanol/water log P systems. The method employed in this work, further, provided high correlation for the hydrogen-bonding basicity term between the two systems.

QSAR characterization of new synthesized hydantoins with antiproliferative activity

Hydantois have been identified as constituents of a number of pharmacologically active molecules. In the present study, we have examined in vitro antiproliferative activity against human colon cancer cell lines HCT-116 of three series of 3-(4-substituted benzyl)-hydantoins with various substituent attached in position 5 of the hydantoin ring. Since the investigated compounds have recently been synthesized and show antiproliferative activity, a good understanding of the properties of the potential drug responsible for their pharmacokinetics is an important goal for their further development. One of the important properties is lipophilicity. Lipophilicity has been assessed by reversed-phase liquid chromatography (high-performance thin-layer chromatography and high-pressure liquid chromatography) by means of direct and indirect (using calibration curve) methods. Chromatographic lipophilicity indices in addition to calculated logP values were compared by hierarchical cluster analysis. The linear solvation energy relationship approach was used to understand and compare the types and relative strength of the molecular interactions that occur in the chromatographic as well as in the n-octanol-water partitioning systems. Finally, correlation between in silico pharmacokinetic predictors and antiproliferative activity was examined. Preliminary quantitative structure-activity relationship modeling indicates that pharmacokinetic predictors capture only one-quarter of all chemical features that are important for antiproliferative activity itself. Among selected descriptors are chromatographic lipophilicity indices.

Repeatability of n-octanol/water partition coefficient values between liquid chromatography measurement methods

The n-octanol/water partition coefficient (K_OW) is a physical/chemical property that is extensively used for regulatory and environmental risk and exposure assessments. The K_OW value can estimate various chemical properties such as water solubility, bioavailability, and toxicity using quantitative structure-activity relationships which demands an accurate knowledge of this property. The present investigation aims to compare outcomes of three commonly cited methods of K_OW measurement in the literature for six hydrophobic chemicals with insecticidal functions as well as highly volatile petroleum constituents. This measurement has been difficult to obtain for the selected pyrethroid insecticides, cypermethrin, and bifenthrin and is a novel measurement for the latter: polycyclic aromatic sulfur heterocycles, dibenzothiophene (DBT), and three of its alkyl derivatives except for DBT. The K_OW values were obtained using two liquid chromatographic methods with isocratic and gradient programming, and the slow-stirring method following OECD 117 and 123 guidelines, respectively. The mean log K_OW values of bifenthrin, cypermethrin, DBT, methyl-DBT, dimethyl-DBT, and diethyl-DBT were 8.4 ± 0.1, 6.0 ± 0.3, 4.8 ± 0.0, 5.4 ± 0.1, 6.0 ± 0.1, and 6.8 ± 0.0 using the HPLC method with gradient programing. The K_OW values were significantly reproducible within a method, however, not between the methods. Results suggest assessing a chemical's property and environmental risk and exposure solely based on the K_OW value should be practiced with caution.

The Impact of Lipophilicity in Drug Discovery: Rapid Measurements by Means of Reversed-Phase HPLC

Lipophilicity constitutes a vital physicochemical property in drug design as it is connected with pharmacodynamic and pharmacokinetic properties as well as toxicological aspects of candidate drugs. Traditional partitioning experiments to determine n-octanol-water coefficients are laborious and time-consuming, while they cannot be reliably performed for highly lipophilic or compounds undergoing degradation. Alternatively, lipophilicity of candidate drugs can be accurately and reproducibly determined using reversed-phase liquid chromatography. In this chapter, the details of protocols for lipophilicity assessment using reversed-phase HPLC, under conditions which provide the best simulation of n-octanol-water partition coefficients, are described.

Lipophilicity and biomimetic properties measured by HPLC to support drug discovery

HPLC methods that use chromatographic retention times for gaining information about the properties of compounds for the purpose of designing drug molecules are reviewed. Properties, such as lipophilicity, protein binding, phospholipid binding, and acid/base character can be incorporated in the design of molecules with the right biological distribution and pharmacokinetic profile to become an effective drug. Standardization of various methodologies is suggested in order to obtain data suitable for inter-laboratory comparison. The published HPLC methods for lipophilicity, acid/base character, protein and phospholipid binding are critically reviewed and compared with each other using the solvation equation approach. One of the most important discussion points is how these data can be used in models and how they can influence the drug discovery process. Therefore, the published models for volume of distribution, unbound volume of distribution and drug efficiency are also discussed. The general relationships between the chemical structure and biomimetic HPLC properties are described in view of ranking and selecting putative drug molecules.

Structure-retention behaviour of biologically active fused 1,2,4-triazinones--correlation with in silico molecular properties

The chromatographic behaviour and significant lipophilicity/hydrophobicity indices (log k(w), S, φ(0)) are presented for 21 biologically active fused 1,2,4-triazinones based on the linear relationship: log k = log k(w)-Sφ established for the retention on LC-18 HPLC column, using as mobile phases mixtures of three organic modifiers with water. The effect of these mobile phase modifiers on the chromatographic behaviour of solutes was established and the organic modifier of choice is suggested. The complex correlation of slopes versus intercepts obtained for acetonitrile, contrary to linear ones obtained for methanol and dioxane are disclosed. The observed difference in retention mechanism for acetonitrile compared to methanol and dioxane is explained by intermolecular interactions encoded in lipophilicity. Linear correlations with statistically significant levels between log kw values determined from three different chromatographic systems were obtained. The relationships between log k(w) constants (derived from the linear model for methanol-water mobile phases) and predicted log P and log S values by the use of various computational methods were investigated and these were established with high correlation coefficients. The predicted log P values plotted against φ(0 (MeOH)) indices showed the best fit. Principal component analysis was used to compare various lipophilicity parameters of the solutes and their in silico biological descriptors relevant to optimal pharmacokinetics profile. The similarities and dissimilarities between all the variables and molecular structures of solutes are presented. Statistically significant correlations were found between the chromatographic lipophilicity indices and the calculated pharmacokinetic descriptors: fraction unbound in brain (f(u, brain)), oral bioavailability (%F), permeability and intestinal absorption in jejunum (Caco-2), skin permeation (log K(p)) and blood/brain concentration (log BB).

Microwave-assisted preparation, structural characterization, lipophilicity, and anti-cancer assay of some hydroxycoumarin derivatives

ABSTRACT

A new series of hydroxycoumarin derivatives has been synthesized using conventional synthesis. The syntheses were accelerated by microwave assistance. Yields in both cases were comparable (59-69 %). The structures were established by 1H and 13C NMR spectroscopy and high-resolution mass spectrometry. Five compounds (5-hydroxy-4,7-dimethylcoumarin, 6-acetyl-5-hydroxy-4,7-dimethylcoumarin, 4-(cyanomethoxy)chromen-2-one, 5-(cyanomethoxy)-4,7-dimethylchromen-2-one, and 6-acetyl-5-(cyanomethoxy)-4,7-dimethylchromen-2-one) were assayed for anti-cancer activity. For all presented coumarin derivatives, lipophilicity was measured using reversed-phase TLC in different eluent systems with standardization. In addition, the crystal structure of 6-acetyl-5-hydroxy-4,7-dimethylcoumarin has been solved by X-ray structure analysis of single crystals.

GRAPHICAL ABSTRACT

Quantitative retention-structure and retention-activity relationship studies of local anesthetics by micellar liquid chromatography

The retention of compounds in micellar liquid chromatography (MLC) is governed by hydrophobic and electrostatic forces. For ionic compounds, both interactions should be considered. The present report offers a novel retention model that includes the hydrophobicity of compounds and the molar fraction of the charged form of compounds and compares it with other previously reported models. High correlations between the logarithm of capacity factors and these structural parameters were obtained for local anesthetics with different degrees of ionization using a nonionic surfactant solution as mobile phase. Modeling the retention of compounds as a function of physicochemical parameters and experimental variables is established by means of multiple linear regression. In addition, a predictive model for estimating the hydrophobicity of local anesthetics is proposed. Finally, quantitative and qualitative retention-activity relationships in MLC are also investigated for these compounds. An excellent correlation between the capacity factors in MLC and the anesthetic potency of local anesthetics was obtained.

Critical evaluation of screening techniques for emerging environmental contaminants based on accurate mass measurements with time-of-flight mass spectrometry

Emerging contaminants from wastewater effluent samples were analysed, using posttarget and nontarget analysis techniques. The samples were analysed with an ultra performance liquid chromatograph-time-of-flight mass spectrometer (UPLC-TOF-MS), and the resulting data were processed with commercial deconvolution software. The method works well for posttarget analysis with prior information about the retention times of the compounds of interest. With positive polarity, 63 of 66 compounds and with negative polarity, 18 of 20 compounds were correctly identified in a spiked sample, while two compounds of a total of 88 fell out of the mass range. Furthermore, a four-stage process for identification was developed for the posttarget analysis lacking the retention time data. In the process, the number of candidate compounds was reduced by using the accurate mass of selected compounds in two steps (stages 1 and 2), structure-property relationships (stage 3) and isotope patterns of the analytes (stage 4). The process developed was validated by analysing wastewater samples spiked with 88 compounds. This procedure can be used to gain a preliminary indication of the presence of certain analytes in the samples. Nontarget analysis was tested by applying a theoretical mass spectra library for a wastewater sample spiked with six pharmaceuticals. The results showed a high number of false identifications. In addition, manual processing of the data was considered laborious and ineffective. Finally, the posttarget analysis was applied to a real wastewater sample. The analysis revealed the presence of six compounds that were afterwards confirmed with standard compounds as being correct. Three psycholeptics (nordiazepam, oxazepam and temazepam) could be tentatively identified, using the identification process developed. Posttarget analysis with UPLC-TOF-MS proved to be a promising method for analysing wastewater samples, while we concluded that the software for nontarget analysis will need improvement before it can be used in environmental analytical work with LC-TOF-MS systems.

Revisiting thin-layer chromatography as a lipophilicity determination tool--a comparative study on several techniques with a model solute set

The lipophilicity of a compound is a fundamental property related to pharmaceutical and biomedical activity. As many approaches are mixed together in every-day published studies, the subject needs some standardization. The paper presents a comparative study on several approaches of TLC lipophilicity determination: a single TLC run, extrapolation of a retention, principal component analysis of a retention matrix, PARAFAC on a three-way array and a PLS regression. All techniques were applied to 35 model solutes with simple molecules, using nine concentrations of six modifiers: acetonitrile, acetone, dioxane, propan-2-ol, methanol and tetrahydrofurane. The elaborated comparative analysis formed several general recommendations. Methanol and dioxane were the best modifiers, while acetonitrile gave the worst and inacceptable correlation of retention with lipophilicity. Surprisingly, good correlations were obtained for the single TLC runs and this method is underestimated in the literature. The advanced chemometric processing proposed recently, such as PCA, PARAFAC and PLS did not show a visible advantage comparing to classical methods. A need to use a robust regression and robust correlation measures, due to presence of significant outliers, was also noticed and studied.

Cellular transport of anti-inflammatory pro-drugs originated from a herbal formulation of Zingiber cassumunar and Nigella sativa

Background

The rhizome of Zingiber cassumunar and the seed of Nigella sativa are two ingredients in Thai traditional medicine to relieve dysmenorrhea and adjust the menstrual cycle. Mixture of these two herbs produces three esters, namely (E)-4-(3,4-dimethoxyphenyl)but-3-en-1-yl linoleate (1), (E)-4-(3,4-dimethoxyphenyl)but-3-en-1-yl oleate (2) and (E)-4-(3,4-dimethoxyphenyl)but-3-en-1-yl palmitate (3). The aim of this study is to examine in vitro absorption of these esters and evaluate their transport across the membrane.

Methods

In vitro transport of these three esters was observed in Caco-2 cell monolayers. The ester compounds 1, 2 and 3 at a concentration of 10 μM were hydrolyzed by porcine liver esterase.

Results

All esters transported across the Caco-2 cell without enzymatic hydrolysis. The apparent permeability coefficients P_app of compound 1 at 53 μM and 106 μM were 13.94 (0.60) × 10^-6 and 14.33 (0.17) × 10^-6cm/s respectively, while those of compound 2 were 9.45 (0.29) × 10^-6 and 10.08 (0.32) × 10^-6cm/s, respectively. P_app values of compound 3 were 7.48 (0.31) × 10^-6cm/s at 53 μM and 8.60 (0.55) × 10^-6cm/s at 106 μM. P_app values of the parent compound (compound D), i.e. (E)-4-(3,4-dimethoxyphenyl)but-3-en-1-ol were 8.53 (0.83) × 10^-6cm/s at 53 μM and 16.38 (0.61) × 10^-6cm/s at 106 μM. The ester hydrolysis of compounds 1, 2 and 3 by porcine liver esterase was monitored by HPLC and the hydrolysis reactions were completed within 10 minutes.

Conclusion

Using the Caco-2 cell monolayer model, the present study finds that compounds (E)-4-(3,4-dimethoxyphenyl)but-3-en-1-yl linoleate (1), (E)-4-(3,4-dimethoxyphenyl)but-3-en-1-yl oleate (2) and (E)-4-(3,4-dimethoxyphenyl)but-3-en-1-yl palmitate (3) originated from Prasaplai preparation (a Thai herbal formula) may be transported through a facilitated mechanism and serve as pro-drugs to increase the compound D level in the blood.

Alternative measures of lipophilicity: from octanol-water partitioning to IAM retention

This review describes lipophilicity parameters currently used in drug design and QSAR studies. After a short historical overview, the complex nature of lipophilicity as the outcome of polar/nonpolar inter- and intramolecular interactions is analysed and considered as the background for the discussion of the different lipophilicity descriptors. The first part focuses on octanol-water partitioning of neutral and ionisable compounds, evaluates the efficiency of predictions and provides a short description of the experimental methods for the determination of distribution coefficients. A next part is dedicated to reversed-phase chromatographic techniques, HPLC and TLC in lipophilicity assessment. The two methods are evaluated for their efficiency to simulate octanol-water and the progress achieved in the refinement of suitable chromatographic conditions, in particular in the field of HPLC, is outlined. Liposomes as direct models of biological membranes are examined and phospolipophilicity is compared to the traditional lipophilicity concept. Difficulties associated with liposome-water partitioning are discussed. The last part focuses on Immobilised Artificial Membrane (IAM) chromatography as an alternative which combines membrane simulation with rapid measurements. IAM chromatographic retention is compared to octanol-water and liposome-water partitioning as well as to reversed-phase retention and its potential to predict biopartitioning and biological activities is discussed.