In recent years biologically active compounds isolated from insects call special interest of drug... more In recent years biologically active compounds isolated from insects call special interest of drug researchers. According to some Polish etnopharmacological observations, secretion from the grasshopper's abdomen (Orthoptera family) is believed to speed up the process of wound healing. In the present work we focused on determination of main components of the lipid fraction of material from grasshopper abdomen using GC-MS/MS. Samples were qualitatively analyzed using gas chromatography coupled with mass spectrometry. Both liquid-liquid extraction and solid-phase extraction pretreatment methods were used to concentrate and fractionate the compounds from the insect. In the derivatized fractions ca. 350 compounds were identified, including substances of known biological activity. The potential agents affecting wound healing have been indicated. A set of compounds characteristic for all the studied Chorthippus spp., have been identified. Data analysis revealed different lipidomic profiles of grasshoppers depending on the insects origin and collection area.
Journal of Pharmaceutical and Biomedical Analysis, 2005
A combined pH/organic solvent linear gradient mode in high performance liquid chromatography (HPL... more A combined pH/organic solvent linear gradient mode in high performance liquid chromatography (HPLC) is presented as a new approach to determination of low concentrations of ionogenic analytes in biological material. The approach consists in simultaneous development of linear gradients of pH and organic modifier in the mobile phase. Advantages of the method are illustrated in postmortem analysis of opipramol in material from suicide victims. Very narrow peaks without tailing were obtained and several times lower limits of analyte quantitation were achieved using ultraviolet detection as compared to a standard isocratic method. The double gradient HPLC method seems to be especially valuable in case of ionogenic analytes dispersed in complex biological matrices. That is due to a high selectivity of the double gradient method and the lack of peak tailing, which is commonly observed for basic analytes chromatographed at isocratic conditions.
Combinatorial Chemistry & High Throughput Screening, 2004
Artificial neural networks (ANNs) have been applied for the quantitative structure-activity relat... more Artificial neural networks (ANNs) have been applied for the quantitative structure-activity relationships (QSAR) studies of antibacterial activity against Escherichia coli, Serratia marcescens, Proteus vulgaris, Klebsiella pneumoniae and Pseudomonas aeruginosa of a large series of new imidazole derivatives. Antibacterial activity against individual bacteria, expressed as logarithm of reciprocal of the minimal inhibitory concentrations, log 1/MIC, has been related to a number of physicochemical and structural parameters of the imidazole derivatives investigated. Molecular descriptors of agents were obtained by quantum-chemical calculations combined with molecular modelling and from respective structure fragment reference data (e.g., log P). A high correlation resulted between the predicted from ANN model antibacterial activity, log 1/MIC(ANN), and that from biological experiments, log 1/MIC(exp), both for the data used in learning and in the testing sets of imidazoles. Correlation coefficient, R, depending on the type of bacteria and structural subset of analysed imidazole compounds, varies from 0.875 to 0.969. The applicability of ANNs has been demonstrated for the prediction of pharmacological potency of new imidazole derivatives based on their structural descriptors generated exclusively by calculation chemistry.
A new reversed-phase high-performance liquid chromatographic (RP HPLC) procedure has been theoret... more A new reversed-phase high-performance liquid chromatographic (RP HPLC) procedure has been theoretically and experimentally established. The approach consists of the simultaneous development of a gradient of pH and of the organic modifier in the mobile phase. The proposed theoretical model of the pH/organic solvent doublegradient RP HPLC allows determination of both pK a and the lipophilicity parameter of the ionized and the nonionized form of the analyte and prediction of the retention times at specific separation conditions as well as bandwidth for all analytes. The model provides a rational basis for optimization of separation of ionizable analytes at any given chromatographic mode and analysis conditions. In addition, in the case of pH/organic solvent doublegradient RP HPLC, a compression of analyte peak and its reduced tailing can be expected.
The aim of this work was to develop a nonlinear mixed-effect chromatographic model able to descri... more The aim of this work was to develop a nonlinear mixed-effect chromatographic model able to describe the retention times of weak acids and bases in all possible combinations of organic modifier content and mobile-phase pH. Further, we aimed to identify the influence of basic covariates, like lipophilicity (log P), dissociation constant (pKa), and polar surface area (PSA), on the intercompound variability of chromatographic parameters. Lastly, we aimed to propose the optimal limited experimental design to the estimation process of parameters through a maximum a posteriori (MAP) Bayesian method to facilitate the method development process. The data set comprised retention times for two series of organic modifier content collected at different pH for a large series of acids and bases. The obtained typical parameters and their distribution were subsequently used as priors to improve the estimation process from reduced design with a variable number of preliminary experiments. The MAP Baye...
The aim of this study was to develop a population pharmacokinetic model of sufentanil and to asse... more The aim of this study was to develop a population pharmacokinetic model of sufentanil and to assess the influence of covariates in critically ill children admitted to pediatric intensive care unit (PICU). After institutional approval 41 children were enrolled into the study. Blood samples for PK assessment were collected from routinely placed arterial catheters, during and after discontinuation of infusion. Population nonlinear mixed-effect modeling was performed using NONMEM. A two-compartment model described sufentanil PK sufficiently. Typical values of the central and peripheral volume of distribution, and the metabolic and inter-compartmental clearance for a theoretical patient of 70 kg weight were VC = 7.90 l, VT = 481 l, Cl = 45.3 l/hr, and Q = 38.3 l/hr. High inter-individual variability of all PK parameters was noted. Allometric/isometric principles to scale sufentanil PK revealed that to achieve the same steady-state sufentanil concentrations in plasma for pediatric patie...
Recent reports from our laboratory presented a comprehensive theory and demonstrated feasibility ... more Recent reports from our laboratory presented a comprehensive theory and demonstrated feasibility of reversed-phase liquid chromatography (RP-LC) employing the programmed gradient of pH of the mobile phase. The aim of that work was to explore the usefulness of the pH gradient-based approach in fractionation of peptides. The experiments were performed on a series of peptides separated at various LC conditions.
Evaluation of a generalized use of the log Sum(k+1) AA descriptor in a QSRR model to predict pept... more Evaluation of a generalized use of the log Sum(k+1) AA descriptor in a QSRR model to predict peptide retention on RPLC systems At the current state of knowledge, the rational optimization of the chromatographic separation of peptides, as well as the identification of proteins in proteomics are challenges for analytical chemists. In this paper the generalized applicability of a recently derived descriptor log Sum(k+1) AA in a QSRR equation to model peptide retention in RP-LC systems was evaluated. For that purpose, two sets of peptides analyzed on dissimilar RP-LC systems were considered. A first set of 28 peptides was measured on 17 columns/systems, while a second of 70 peptides was eluted on four. The aim of this work was to confirm the usefulness of the partly experimental log Sum(k+1) AA descriptor for the prediction of peptides retention compared to the initially applied, fully experimental log Sum AA descriptor. The verification of the predictive abilities of both QSRR models, applying either the initial or the alternative descriptor, was done by using the leave-one-out and leave-three-out cross-validation procedures. The results seem to demonstrate that the QSRR model with log Sum(k+1) AA , for which the retention measurement of only seven out of 20 existing amino acids is necessary, possesses similar or in some cases even better predictive abilities than that containing log Sum AA .
Journal of Biochemical and Biophysical Methods, 2001
Affinity chromatography (AC) followed by quantitative structure/retention relationships (QSRR) an... more Affinity chromatography (AC) followed by quantitative structure/retention relationships (QSRR) analysis provides information on both the analytes and the macromolecules forming the stationary phases. QSRR equations derived for test series of analytes (often drugs) are interpreted in terms of structural requirements of the specific binding sites on macromolecules. Chromatographically demonstrated differences in analyte/macromolecule interactions may be relevant to molecular pharmacology and
One of the initial steps of proteomic analysis is peptide separation. However, little information... more One of the initial steps of proteomic analysis is peptide separation. However, little information from RP-HPLC, employed for peptides separation, is utilized in proteomics. Meanwhile, prediction of the retention time for a given peptide, combined with routine MS/MS data analysis, could help to improve the confidence of peptide identifications. Recently, a number of models has been proposed to characterize quantitatively the structure of a peptide and to predict its gradient RP-HPLC retention at given separation conditions. The chromatographic behavior of peptides has usually been related to their amino acid composition. However, different values of retention coefficients of the same amino acid in different peptides at different neighborhoods were commonly observed. Therefore, specific retention coefficients were derived by regression analysis or by artificial neural networks (ANNs) with the use of a set of peptides retention. In the review, various approaches for peptide elution time prediction in RP-HPLC are presented and critically discussed. The contribution of sequence dependent parameters (e.g., amphipathicity or peptide sequence) and peptide physicochemical descriptors (e.g., hydrophobicity or peptide length) that have been shown to affect the peptide retention time in LC are considered and analyzed. The predictive capability of the retention time prediction models based on quantitative structure-retention relationships (QSRRs) are discussed in details. Advantages and limitations of various retention prediction strategies are identified. It is concluded that proper processing of chromatographic data by statistical learning techniques can result in information of direct use for proteomics, which is otherwise wasted.
Journal of Pharmaceutical and Biomedical Analysis, 2009
The use of the experimental molecular descriptor logSumAA and some possible alternatives were eva... more The use of the experimental molecular descriptor logSumAA and some possible alternatives were evaluated in the QSRR analysis of peptides. To quantitatively characterize the structure of analytes in a previously proposed QSRR the following three structural descriptors were applied: the logarithm of the sum of gradient retention times of the amino acids composing the individual peptide, logSumAA; the logarithm of
Recently, increasing attention has been paid to the use of ionic liquids for high-performance liq... more Recently, increasing attention has been paid to the use of ionic liquids for high-performance liquid chromatography (HPLC) and capillary electrophoresis. In the present study, the silanol-suppressing potency of ionic liquids was evaluated by HPLC using the two-retention site model proposed previously by Nahum and Horváth (J. Chromatogr. 1981, 203, 53-63). The binding constant, KA, in that approach has been demonstrated to reliably reflect the ability of the ionic liquids to block the silanols of the silica support material of the stationary phase. The determinations were carried out for ionic liquids of the 1-alkyl-3-methylimidazolium group with the use of a series of basic drugs as the test analytes. Comparison of ionic liquids with standard mobile phase additives such as triethylamine showed the former to possess advantages as silanol suppressors in HPLC. The main advantage of the method is that it provides a simple and fast determination of the silanol complex stability, which allowed comparison of the suppressing efficiency of several ionic liquids.
Previous studies have shown that four experimental runs, where both temperature T and gradient ti... more Previous studies have shown that four experimental runs, where both temperature T and gradient time tG are varied, can be used for the reliable prediction of separation as a function of these two variables (two-dimensional optimization). Computer simulation (e.g., DryLab) can then be used to predict “optimized” conditions for maximum sample resolution using either isocratic or gradient elution. Samples that
Statistical evaluation of linear and quadratic models of chromatographic retention was performed.... more Statistical evaluation of linear and quadratic models of chromatographic retention was performed. The relationships describing retention were derived for a set of 23 carefully selected test analytes chromatographed on 18 HPLC columns using methanol-water or acetonitrile-water solutions as mobile phase. It was ascertained whether the square term in the quadratic model improves the description of chromatographic retention in a statistically significant manner. It was also checked whether the retention data extrapolated to a hypothetical neat water eluent (log k w ) obtained with the two models and the two organic modifiers are equivalent or should be considered different. The research proved that both models yield similar results and the extrapolated log k w values do not differ statistically significantly in the case of methanol-containing mobile phases. In the case of acetonitrile-water systems the log k w values obtained with linear and quadratic models are normally statistically different. Correlation analysis for log k w vs. log P parameters was performed for data determined on six columns. The best correlations were achieved employing log k w data derived with the linear model for methanol/ water systems.
We aimed at evaluation the potential diagnostic role of urinary nucleosides in urogenital tract c... more We aimed at evaluation the potential diagnostic role of urinary nucleosides in urogenital tract cancer. Concentrations of 12 nucleosides determined by LC-MS/MS were subjected to correlation, association and interaction analyses. We identified six pairs of nucleosides differently correlated in the group of patients and controls (p < 0.05). N-2-methylguanosine (odds ratio: 4.82; 95% CI: 1.78-12.93; p = 0.002) and N,N-dimethylguanosine (odds ratio: 5.45; 95% CI: 1.78-16.44; p = 0.003), were significantly associated with the disease risk (p-corrected = 0.004). Interaction between N-2-methylguanosine and adenosine (p-interaction = 0.019) suggested their multiplicative effect on the outcome. Urinary nucleosides, namely N,N-dimethylguanosine and N-2-methylguanosine may have the potential to serve as prognostic biomarkers. Gender-specific differences in urogenital tract cancer are likely to occur.
Propofol is a commonly used agent in total intravenous anesthesia (TIVA). However, the link betwe... more Propofol is a commonly used agent in total intravenous anesthesia (TIVA). However, the link between its pharmacokinetics and pharmacodynamics has not been fully characterized in children yet. Our aim was to determine the quantitative relationship between the venous plasma concentration and bispectral index (BIS) effect in a heterogeneous group of pediatric patients undergoing various surgical procedures (ASA status I-III). Nine male and nine female patients were anesthetized with propofol-fentanyl TIVA. Sparse venous samples for propofol concentrations assay and dense BIS measurements were collected during and after the end of infusion. Nonlinear mixed-effect modeling in NONMEM was used for data analysis. A three-compartment model was linked with a classical Emax model through a biophase compartment to describe the available data. All clearance and volume terms were allometrically scaled to account for the body mass difference among the patients under study. A typical patient had th...
The retention characteristics of a newly synthesized stationary phase were determined for reverse... more The retention characteristics of a newly synthesized stationary phase were determined for reversed-phase high-performance liquid chromatography obtained by chemical immobilization of cholesterol on spherical silica gel. For a designed series of analytes the retention factors, log k, were determined at several compositions of the methanol-water mobile phase. Logarithms of retention factor corresponding to a hypothetical pure water eluent, log k w , were calculated by extrapolation of the linear relationships of individual log k data versus volume percent of methanol. The series of 24 test analytes were characterized structurally by means of the logarithms of n-octanol -water partition coefficients, log P, by a set of the linear solvation energy relationship (LSER)-based descriptors of the polarity and bulkiness of the analytes and by structural descriptors of analyte size and polarity acquired by molecular modelling. Quantitative structure-retention relationships (QSRR) were derived by multiple regression analysis using the three groups of structural descriptors of analytes and the log k w data determined on the new stationary phase. For the sake of comparison the corresponding QSRR equations were also derived for retention parameters determined on a standard octadecylsilica and on the so-called immobilized artificial membrane (IAM) stationary phase. The QSRR analysis clearly proved distinctive retention properties of the new cholesterol -silica stationary phase. It has been concluded that the new phase may possess valuable analytical specificity. Its application for modelling penetration of xenobiotics through biological membranes appears rather unlikely.
Journal of chromatography. B, Analytical technologies in the biomedical and life sciences, Jan 25, 2002
In this report the affinity high-performance liquid chromatography data, which were determined on... more In this report the affinity high-performance liquid chromatography data, which were determined on silica-based human serum albumin, alpha1-acid glycoprotein, keratin, collagen, melanin, amylose tris(3,5-dimethylphenylcarbamate), and basic fatty acid binding protein columns, are discussed. Using a quantitative structure-retention relationship (QSRR) approach the affinity data were interpreted in terms of structural requirements of specific binding sites on biomacromolecules. The unique chromatographic properties of immobilized artificial membrane and cholesterol stationary phases were also analyzed from the point of view of mimicking biological processes. It has been demonstrated that chemometric processing of appropriately designed sets of chromatographic data derived in systems comprising biomolecules provides information of relevance for molecular pharmacology and rational drug design.
The study was aimed at quantitative comparison of retention properties of modern stationary phase... more The study was aimed at quantitative comparison of retention properties of modern stationary phases for reversed-phase HPLC. Three approaches, the calculated logarithm of octanol/water partition coefficient (clogP)-based model, the molecular modeling descriptors-based model and the hydrophobic-subtraction model, were compared and discussed. Gradient retention time, t R , of a series of test analytes was a dependent variable in the quantitative structure-retention relationship (QSRR) equations describing retention in terms of analytes' structure descriptors. The QSRRs derived were used to characterize in quantitative manner the specific retention properties of nine representative reversed-phase HPLC. Either the theoretically calculated logarithm of octanol/water partition coefficient, or the structural descriptors from molecular modeling were employed to quantitatively characterize the structure of the analytes. The three molecular modeling-derived structural descriptors considered were: the total dipole moment, the electron excess charge of the most negatively charged atom and the water-accessible molecular surface area. In addition to the above standard QSRR approaches, a recently developed parameterization of reversed-phase column selectivity based on the hydrophobic-subtraction model of Snyder et al. [L.R. Snyder, J.W. Dolan, J.W. Carr, The hydrophobic-subtraction model of reversed-phase column selectivity, J. Chromatogr. A 1060 77] was considered. According to the hydrophobic-subtraction model, reversed-phase columns are characterized by five selectivity parameters derived from the linear solvation energy relationships (LSER) theory. Values of these parameters are available for more than 300 different columns. It has been demonstrated that the clogP-based model, the molecular modeling descriptors-based model and the hydrophobic-subtraction model provide generally similar classification of the HPLC columns studied. Some differences in column classification by the three approaches considered are discussed in terms of specific properties of individual stationary phases. All the approaches allow a quantitative, although multidimensional, characteristic of HPLC columns, however, the nonempirical QSRR-based approach is simpler and require less labor.
A suppression of silanophilic interactions by the selected ionic liquids added to the mobile phas... more A suppression of silanophilic interactions by the selected ionic liquids added to the mobile phase in thin-layer chromatography (TLC) and high-performance liquid chromatography (HPLC) is reported. Acetonitrile was used as the eluent, alone or with various concentrations of water and phosphoric buffer pH 3. Selectivity of the normal (NP) and the reversed (RP) stationary phase material was examined using a series of proton-acceptor basic drugs analytes. The ionic liquids studied appeared to significantly affect analyte retention in NP-TLC, RP-TLC and RP-HPLC systems tested. Consequently, the increased separation selectivity was attained. Due to ionic liquid additives to eluent even analytes could be chromatographed, which were not eluted from the silica-based stationary phase materials with 100% of acetonitrile in the mobile phase. Addition of ionic liquid already in very small concentration (0.5%, v/v) could reduce the amount of acetonitrile used during the optimization of basic analytes separations in TLC and HPLC systems. Moreover, the influence of temperature on the separation of basic analytes was demonstrated and considered in practical HPLC method development.
In recent years biologically active compounds isolated from insects call special interest of drug... more In recent years biologically active compounds isolated from insects call special interest of drug researchers. According to some Polish etnopharmacological observations, secretion from the grasshopper's abdomen (Orthoptera family) is believed to speed up the process of wound healing. In the present work we focused on determination of main components of the lipid fraction of material from grasshopper abdomen using GC-MS/MS. Samples were qualitatively analyzed using gas chromatography coupled with mass spectrometry. Both liquid-liquid extraction and solid-phase extraction pretreatment methods were used to concentrate and fractionate the compounds from the insect. In the derivatized fractions ca. 350 compounds were identified, including substances of known biological activity. The potential agents affecting wound healing have been indicated. A set of compounds characteristic for all the studied Chorthippus spp., have been identified. Data analysis revealed different lipidomic profiles of grasshoppers depending on the insects origin and collection area.
Journal of Pharmaceutical and Biomedical Analysis, 2005
A combined pH/organic solvent linear gradient mode in high performance liquid chromatography (HPL... more A combined pH/organic solvent linear gradient mode in high performance liquid chromatography (HPLC) is presented as a new approach to determination of low concentrations of ionogenic analytes in biological material. The approach consists in simultaneous development of linear gradients of pH and organic modifier in the mobile phase. Advantages of the method are illustrated in postmortem analysis of opipramol in material from suicide victims. Very narrow peaks without tailing were obtained and several times lower limits of analyte quantitation were achieved using ultraviolet detection as compared to a standard isocratic method. The double gradient HPLC method seems to be especially valuable in case of ionogenic analytes dispersed in complex biological matrices. That is due to a high selectivity of the double gradient method and the lack of peak tailing, which is commonly observed for basic analytes chromatographed at isocratic conditions.
Combinatorial Chemistry & High Throughput Screening, 2004
Artificial neural networks (ANNs) have been applied for the quantitative structure-activity relat... more Artificial neural networks (ANNs) have been applied for the quantitative structure-activity relationships (QSAR) studies of antibacterial activity against Escherichia coli, Serratia marcescens, Proteus vulgaris, Klebsiella pneumoniae and Pseudomonas aeruginosa of a large series of new imidazole derivatives. Antibacterial activity against individual bacteria, expressed as logarithm of reciprocal of the minimal inhibitory concentrations, log 1/MIC, has been related to a number of physicochemical and structural parameters of the imidazole derivatives investigated. Molecular descriptors of agents were obtained by quantum-chemical calculations combined with molecular modelling and from respective structure fragment reference data (e.g., log P). A high correlation resulted between the predicted from ANN model antibacterial activity, log 1/MIC(ANN), and that from biological experiments, log 1/MIC(exp), both for the data used in learning and in the testing sets of imidazoles. Correlation coefficient, R, depending on the type of bacteria and structural subset of analysed imidazole compounds, varies from 0.875 to 0.969. The applicability of ANNs has been demonstrated for the prediction of pharmacological potency of new imidazole derivatives based on their structural descriptors generated exclusively by calculation chemistry.
A new reversed-phase high-performance liquid chromatographic (RP HPLC) procedure has been theoret... more A new reversed-phase high-performance liquid chromatographic (RP HPLC) procedure has been theoretically and experimentally established. The approach consists of the simultaneous development of a gradient of pH and of the organic modifier in the mobile phase. The proposed theoretical model of the pH/organic solvent doublegradient RP HPLC allows determination of both pK a and the lipophilicity parameter of the ionized and the nonionized form of the analyte and prediction of the retention times at specific separation conditions as well as bandwidth for all analytes. The model provides a rational basis for optimization of separation of ionizable analytes at any given chromatographic mode and analysis conditions. In addition, in the case of pH/organic solvent doublegradient RP HPLC, a compression of analyte peak and its reduced tailing can be expected.
The aim of this work was to develop a nonlinear mixed-effect chromatographic model able to descri... more The aim of this work was to develop a nonlinear mixed-effect chromatographic model able to describe the retention times of weak acids and bases in all possible combinations of organic modifier content and mobile-phase pH. Further, we aimed to identify the influence of basic covariates, like lipophilicity (log P), dissociation constant (pKa), and polar surface area (PSA), on the intercompound variability of chromatographic parameters. Lastly, we aimed to propose the optimal limited experimental design to the estimation process of parameters through a maximum a posteriori (MAP) Bayesian method to facilitate the method development process. The data set comprised retention times for two series of organic modifier content collected at different pH for a large series of acids and bases. The obtained typical parameters and their distribution were subsequently used as priors to improve the estimation process from reduced design with a variable number of preliminary experiments. The MAP Baye...
The aim of this study was to develop a population pharmacokinetic model of sufentanil and to asse... more The aim of this study was to develop a population pharmacokinetic model of sufentanil and to assess the influence of covariates in critically ill children admitted to pediatric intensive care unit (PICU). After institutional approval 41 children were enrolled into the study. Blood samples for PK assessment were collected from routinely placed arterial catheters, during and after discontinuation of infusion. Population nonlinear mixed-effect modeling was performed using NONMEM. A two-compartment model described sufentanil PK sufficiently. Typical values of the central and peripheral volume of distribution, and the metabolic and inter-compartmental clearance for a theoretical patient of 70 kg weight were VC = 7.90 l, VT = 481 l, Cl = 45.3 l/hr, and Q = 38.3 l/hr. High inter-individual variability of all PK parameters was noted. Allometric/isometric principles to scale sufentanil PK revealed that to achieve the same steady-state sufentanil concentrations in plasma for pediatric patie...
Recent reports from our laboratory presented a comprehensive theory and demonstrated feasibility ... more Recent reports from our laboratory presented a comprehensive theory and demonstrated feasibility of reversed-phase liquid chromatography (RP-LC) employing the programmed gradient of pH of the mobile phase. The aim of that work was to explore the usefulness of the pH gradient-based approach in fractionation of peptides. The experiments were performed on a series of peptides separated at various LC conditions.
Evaluation of a generalized use of the log Sum(k+1) AA descriptor in a QSRR model to predict pept... more Evaluation of a generalized use of the log Sum(k+1) AA descriptor in a QSRR model to predict peptide retention on RPLC systems At the current state of knowledge, the rational optimization of the chromatographic separation of peptides, as well as the identification of proteins in proteomics are challenges for analytical chemists. In this paper the generalized applicability of a recently derived descriptor log Sum(k+1) AA in a QSRR equation to model peptide retention in RP-LC systems was evaluated. For that purpose, two sets of peptides analyzed on dissimilar RP-LC systems were considered. A first set of 28 peptides was measured on 17 columns/systems, while a second of 70 peptides was eluted on four. The aim of this work was to confirm the usefulness of the partly experimental log Sum(k+1) AA descriptor for the prediction of peptides retention compared to the initially applied, fully experimental log Sum AA descriptor. The verification of the predictive abilities of both QSRR models, applying either the initial or the alternative descriptor, was done by using the leave-one-out and leave-three-out cross-validation procedures. The results seem to demonstrate that the QSRR model with log Sum(k+1) AA , for which the retention measurement of only seven out of 20 existing amino acids is necessary, possesses similar or in some cases even better predictive abilities than that containing log Sum AA .
Journal of Biochemical and Biophysical Methods, 2001
Affinity chromatography (AC) followed by quantitative structure/retention relationships (QSRR) an... more Affinity chromatography (AC) followed by quantitative structure/retention relationships (QSRR) analysis provides information on both the analytes and the macromolecules forming the stationary phases. QSRR equations derived for test series of analytes (often drugs) are interpreted in terms of structural requirements of the specific binding sites on macromolecules. Chromatographically demonstrated differences in analyte/macromolecule interactions may be relevant to molecular pharmacology and
One of the initial steps of proteomic analysis is peptide separation. However, little information... more One of the initial steps of proteomic analysis is peptide separation. However, little information from RP-HPLC, employed for peptides separation, is utilized in proteomics. Meanwhile, prediction of the retention time for a given peptide, combined with routine MS/MS data analysis, could help to improve the confidence of peptide identifications. Recently, a number of models has been proposed to characterize quantitatively the structure of a peptide and to predict its gradient RP-HPLC retention at given separation conditions. The chromatographic behavior of peptides has usually been related to their amino acid composition. However, different values of retention coefficients of the same amino acid in different peptides at different neighborhoods were commonly observed. Therefore, specific retention coefficients were derived by regression analysis or by artificial neural networks (ANNs) with the use of a set of peptides retention. In the review, various approaches for peptide elution time prediction in RP-HPLC are presented and critically discussed. The contribution of sequence dependent parameters (e.g., amphipathicity or peptide sequence) and peptide physicochemical descriptors (e.g., hydrophobicity or peptide length) that have been shown to affect the peptide retention time in LC are considered and analyzed. The predictive capability of the retention time prediction models based on quantitative structure-retention relationships (QSRRs) are discussed in details. Advantages and limitations of various retention prediction strategies are identified. It is concluded that proper processing of chromatographic data by statistical learning techniques can result in information of direct use for proteomics, which is otherwise wasted.
Journal of Pharmaceutical and Biomedical Analysis, 2009
The use of the experimental molecular descriptor logSumAA and some possible alternatives were eva... more The use of the experimental molecular descriptor logSumAA and some possible alternatives were evaluated in the QSRR analysis of peptides. To quantitatively characterize the structure of analytes in a previously proposed QSRR the following three structural descriptors were applied: the logarithm of the sum of gradient retention times of the amino acids composing the individual peptide, logSumAA; the logarithm of
Recently, increasing attention has been paid to the use of ionic liquids for high-performance liq... more Recently, increasing attention has been paid to the use of ionic liquids for high-performance liquid chromatography (HPLC) and capillary electrophoresis. In the present study, the silanol-suppressing potency of ionic liquids was evaluated by HPLC using the two-retention site model proposed previously by Nahum and Horváth (J. Chromatogr. 1981, 203, 53-63). The binding constant, KA, in that approach has been demonstrated to reliably reflect the ability of the ionic liquids to block the silanols of the silica support material of the stationary phase. The determinations were carried out for ionic liquids of the 1-alkyl-3-methylimidazolium group with the use of a series of basic drugs as the test analytes. Comparison of ionic liquids with standard mobile phase additives such as triethylamine showed the former to possess advantages as silanol suppressors in HPLC. The main advantage of the method is that it provides a simple and fast determination of the silanol complex stability, which allowed comparison of the suppressing efficiency of several ionic liquids.
Previous studies have shown that four experimental runs, where both temperature T and gradient ti... more Previous studies have shown that four experimental runs, where both temperature T and gradient time tG are varied, can be used for the reliable prediction of separation as a function of these two variables (two-dimensional optimization). Computer simulation (e.g., DryLab) can then be used to predict “optimized” conditions for maximum sample resolution using either isocratic or gradient elution. Samples that
Statistical evaluation of linear and quadratic models of chromatographic retention was performed.... more Statistical evaluation of linear and quadratic models of chromatographic retention was performed. The relationships describing retention were derived for a set of 23 carefully selected test analytes chromatographed on 18 HPLC columns using methanol-water or acetonitrile-water solutions as mobile phase. It was ascertained whether the square term in the quadratic model improves the description of chromatographic retention in a statistically significant manner. It was also checked whether the retention data extrapolated to a hypothetical neat water eluent (log k w ) obtained with the two models and the two organic modifiers are equivalent or should be considered different. The research proved that both models yield similar results and the extrapolated log k w values do not differ statistically significantly in the case of methanol-containing mobile phases. In the case of acetonitrile-water systems the log k w values obtained with linear and quadratic models are normally statistically different. Correlation analysis for log k w vs. log P parameters was performed for data determined on six columns. The best correlations were achieved employing log k w data derived with the linear model for methanol/ water systems.
We aimed at evaluation the potential diagnostic role of urinary nucleosides in urogenital tract c... more We aimed at evaluation the potential diagnostic role of urinary nucleosides in urogenital tract cancer. Concentrations of 12 nucleosides determined by LC-MS/MS were subjected to correlation, association and interaction analyses. We identified six pairs of nucleosides differently correlated in the group of patients and controls (p < 0.05). N-2-methylguanosine (odds ratio: 4.82; 95% CI: 1.78-12.93; p = 0.002) and N,N-dimethylguanosine (odds ratio: 5.45; 95% CI: 1.78-16.44; p = 0.003), were significantly associated with the disease risk (p-corrected = 0.004). Interaction between N-2-methylguanosine and adenosine (p-interaction = 0.019) suggested their multiplicative effect on the outcome. Urinary nucleosides, namely N,N-dimethylguanosine and N-2-methylguanosine may have the potential to serve as prognostic biomarkers. Gender-specific differences in urogenital tract cancer are likely to occur.
Propofol is a commonly used agent in total intravenous anesthesia (TIVA). However, the link betwe... more Propofol is a commonly used agent in total intravenous anesthesia (TIVA). However, the link between its pharmacokinetics and pharmacodynamics has not been fully characterized in children yet. Our aim was to determine the quantitative relationship between the venous plasma concentration and bispectral index (BIS) effect in a heterogeneous group of pediatric patients undergoing various surgical procedures (ASA status I-III). Nine male and nine female patients were anesthetized with propofol-fentanyl TIVA. Sparse venous samples for propofol concentrations assay and dense BIS measurements were collected during and after the end of infusion. Nonlinear mixed-effect modeling in NONMEM was used for data analysis. A three-compartment model was linked with a classical Emax model through a biophase compartment to describe the available data. All clearance and volume terms were allometrically scaled to account for the body mass difference among the patients under study. A typical patient had th...
The retention characteristics of a newly synthesized stationary phase were determined for reverse... more The retention characteristics of a newly synthesized stationary phase were determined for reversed-phase high-performance liquid chromatography obtained by chemical immobilization of cholesterol on spherical silica gel. For a designed series of analytes the retention factors, log k, were determined at several compositions of the methanol-water mobile phase. Logarithms of retention factor corresponding to a hypothetical pure water eluent, log k w , were calculated by extrapolation of the linear relationships of individual log k data versus volume percent of methanol. The series of 24 test analytes were characterized structurally by means of the logarithms of n-octanol -water partition coefficients, log P, by a set of the linear solvation energy relationship (LSER)-based descriptors of the polarity and bulkiness of the analytes and by structural descriptors of analyte size and polarity acquired by molecular modelling. Quantitative structure-retention relationships (QSRR) were derived by multiple regression analysis using the three groups of structural descriptors of analytes and the log k w data determined on the new stationary phase. For the sake of comparison the corresponding QSRR equations were also derived for retention parameters determined on a standard octadecylsilica and on the so-called immobilized artificial membrane (IAM) stationary phase. The QSRR analysis clearly proved distinctive retention properties of the new cholesterol -silica stationary phase. It has been concluded that the new phase may possess valuable analytical specificity. Its application for modelling penetration of xenobiotics through biological membranes appears rather unlikely.
Journal of chromatography. B, Analytical technologies in the biomedical and life sciences, Jan 25, 2002
In this report the affinity high-performance liquid chromatography data, which were determined on... more In this report the affinity high-performance liquid chromatography data, which were determined on silica-based human serum albumin, alpha1-acid glycoprotein, keratin, collagen, melanin, amylose tris(3,5-dimethylphenylcarbamate), and basic fatty acid binding protein columns, are discussed. Using a quantitative structure-retention relationship (QSRR) approach the affinity data were interpreted in terms of structural requirements of specific binding sites on biomacromolecules. The unique chromatographic properties of immobilized artificial membrane and cholesterol stationary phases were also analyzed from the point of view of mimicking biological processes. It has been demonstrated that chemometric processing of appropriately designed sets of chromatographic data derived in systems comprising biomolecules provides information of relevance for molecular pharmacology and rational drug design.
The study was aimed at quantitative comparison of retention properties of modern stationary phase... more The study was aimed at quantitative comparison of retention properties of modern stationary phases for reversed-phase HPLC. Three approaches, the calculated logarithm of octanol/water partition coefficient (clogP)-based model, the molecular modeling descriptors-based model and the hydrophobic-subtraction model, were compared and discussed. Gradient retention time, t R , of a series of test analytes was a dependent variable in the quantitative structure-retention relationship (QSRR) equations describing retention in terms of analytes' structure descriptors. The QSRRs derived were used to characterize in quantitative manner the specific retention properties of nine representative reversed-phase HPLC. Either the theoretically calculated logarithm of octanol/water partition coefficient, or the structural descriptors from molecular modeling were employed to quantitatively characterize the structure of the analytes. The three molecular modeling-derived structural descriptors considered were: the total dipole moment, the electron excess charge of the most negatively charged atom and the water-accessible molecular surface area. In addition to the above standard QSRR approaches, a recently developed parameterization of reversed-phase column selectivity based on the hydrophobic-subtraction model of Snyder et al. [L.R. Snyder, J.W. Dolan, J.W. Carr, The hydrophobic-subtraction model of reversed-phase column selectivity, J. Chromatogr. A 1060 77] was considered. According to the hydrophobic-subtraction model, reversed-phase columns are characterized by five selectivity parameters derived from the linear solvation energy relationships (LSER) theory. Values of these parameters are available for more than 300 different columns. It has been demonstrated that the clogP-based model, the molecular modeling descriptors-based model and the hydrophobic-subtraction model provide generally similar classification of the HPLC columns studied. Some differences in column classification by the three approaches considered are discussed in terms of specific properties of individual stationary phases. All the approaches allow a quantitative, although multidimensional, characteristic of HPLC columns, however, the nonempirical QSRR-based approach is simpler and require less labor.
A suppression of silanophilic interactions by the selected ionic liquids added to the mobile phas... more A suppression of silanophilic interactions by the selected ionic liquids added to the mobile phase in thin-layer chromatography (TLC) and high-performance liquid chromatography (HPLC) is reported. Acetonitrile was used as the eluent, alone or with various concentrations of water and phosphoric buffer pH 3. Selectivity of the normal (NP) and the reversed (RP) stationary phase material was examined using a series of proton-acceptor basic drugs analytes. The ionic liquids studied appeared to significantly affect analyte retention in NP-TLC, RP-TLC and RP-HPLC systems tested. Consequently, the increased separation selectivity was attained. Due to ionic liquid additives to eluent even analytes could be chromatographed, which were not eluted from the silica-based stationary phase materials with 100% of acetonitrile in the mobile phase. Addition of ionic liquid already in very small concentration (0.5%, v/v) could reduce the amount of acetonitrile used during the optimization of basic analytes separations in TLC and HPLC systems. Moreover, the influence of temperature on the separation of basic analytes was demonstrated and considered in practical HPLC method development.
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