Reliability of logP predictions based on calculated molecular descriptors: a critical review.

Correct QSAR analysis requires reliable measured or calculated logP values, being logP the most frequently utilized and most important physico-chemical parameter in such studies. Since the publication of theoretical fundamentals of logP prediction, many commercial software solutions are available. These programs are all based on experimental data of huge databases therefore the predicted logP values are mostly acceptable - especially for known structures and their derivatives. In this study we critically reviewed the published methods and compared the predictive power of commercial softwares (CLOGP, KOWWIN, SciLogP/ULTRA) to each other and to our recently developed automatic QS(P)AR program. We have selected a very diverse set of 625 known drugs (98%) and drug-like molecules with experimentally validated logP values. We have collected 78 reported "outliers" as well, which could not be predicted by the "traditional" methods. We used these data in the model building and validation. Finally, we used an external validation set of compounds missing from public databases. We emphasized the importance of data quality, descriptor calculation and selection, and presented a general, reliable descriptor selection and validation technique for such kind of studies. Our method is based on the strictest mathematical and statistical rules, fully automatic and after the initial settings there is no option for user intervention. Three approaches were applied: multiple linear regression, partial least squares analysis and artificial neural network. LogP predictions with a multiple linear regression model showed acceptable accuracy for new compounds therefore it can be used for "in-silico-screening" and/or planning virtual/combinatorial libraries.

Quinazolone-alkyl-carboxylic acid derivatives inhibit transmembrane Ca(2+) ion flux to (+)-(S)-alpha-amino-3-hydroxy-5-methylisoxazole-4-propionic acid.

Comparison of the kinetics of the inward Ca(2+) ion flux to (S)-alpha-Amino-3-hydroxy-5-methylisoxazole-4-propionic acid [(S)-AMPA] in cerebrocortical homogenates and that of the previously reported transmembrane Na(+) ion influx mediated by an AMPA receptor in hippocampal homogenates established that the agonist-induced opening of the AMPA receptor channels occurs in two kinetically distinguishable phases. Here we report that the 2-methyl-4-oxo-3H-quinazoline-3-acetic acid (Q1) inhibits the major slow-phase response specifically, whereas the acetyl piperidine derivative (Q5) is a more potent inhibitor of the fast-phase response. Both the quinazolone-3-propionic acid (Q2) and the quinazolone-3-acetic acid methyl ester (Q3) enhanced the slow-phase response to (S)-AMPA. The information provided by docking different Q1, Q2, and Q5 models at the ligand-binding core of iGluRs were used to define agonistic and antagonistic modes of interactions. Based on the effects of quinazolone-3-alkyl-carboxylic acid derivatives on specific [(3)H]Glu binding and kinetically distinguishable Ca(2+) ion permeability responses to (S)-AMPA and molecular modeling, the fast- and the slow-phase (S)-AMPA-elicited Ca(2+) ion fluxes were corresponded to different subunit compositions and degrees of S1S2 bridging interaction relative to substitution of kainate thereupon. Substitutions of agonists and antagonists into the iGluR2 S1S2 ligand binding core induced different modes of domain-domain bridging.

Multiwavelength spectrophotometric determination of acid dissociation constants part V: microconstants and tautomeric ratios of diprotic amphoteric drugs.

The acid-base equilibria of several diprotic amphoteric drugs, namely, niflumic acid, norfloxacin, piroxicam, pyridoxine and 2-methyl-4-oxo-3H-quinazoline-3-acetic acid have been characterized in terms of microconstants and tautomeric ratios. A multiwavelength spectrophotometric (WApH) titration method for determination of acid dissociation constants (pKa values) of ionizable compounds developed previously was applied for this purpose. Microspeciation was investigated by three approaches: (1) selective monitoring of ionizable group by spectrophotometry, (2) deductive method and (3) k(z) method for determination of tautomeric ratio from co-solvent mixtures. The formulation for (3) has been derived and found to invoke fewer assumptions than a reported procedure (K. Takács-Novák, A. Avdeef, K.J Box, B. Podányi, G. Szász, J. Pharm. Biomed. Anal., 12 (1994) 1369-1377). It has been shown that the WApH technique, for such types of ampholytes, is able to deduce the microconstants and tautomeric ratios which are in good agreement with literature data.

Ion-pair partition of quarternary ammonium drugs: the influence of counter ions of different lipophilicity, size, and flexibility.

PURPOSE: The ion-pair partition of quaternary ammonium (QA) pharmacons with organic counter ions of different lipophilicity, size, shape and flexibility was studied to elucidate relationships between ion-pair formation and chemical structure. METHODS: The apparent partition coefficient (P') of 4 QAs was measured in octanol/pH 7.4 phosphate buffer system by the shake-flask method as a function of molar excess of ten counter ions (Y), namely: mesylate (MES), acetate (AC), pyruvate (PYRU), nicotinate (NIC), hydrogenfumarate (HFUM), hydrogenmaleate (HMAL), p-toluenesulfonate (PTS), caproate (CPR), deoxycholate (DOC) and prostaglandin E1 anion (PGE1). RESULTS: Based on 118 of highly precise logP' values (SD< 0.05), the intrinsic lipophilicity (without external counter ions) and the ion-pair partition of QAs (with different counter ions) were characterized. Linear correlation was found between the logP' of ion-pairs and the size of the counter ions described by the solvent accessible surface area (SASA). The lipophilicity increasing effect of the counter ions were quantified and the following order was established: DOC approximate to PGE1 >> CPR approximate to PTS >> NIC approximate to HMAL >> PYRU approximate to AC approximate to MES approximate to HFUM. Analyzing the lipophilicity/molar ratio (QA:Y) profile, the differences in the ion-pair formation were shown and attributed to the differences in the flexibility/rigidity and size both of QA and Y. CONCLUSIONS: Since the largest (in average, 300 X) lipophilicity enhancement was found by the influence of DOC and PGE1 and considerable (on average 40 X) increase was observed by CPR and PTS, it was concluded that bile acids and prostaglandin anions may play a significant role in the ion-pair transport of quaternary ammonium drugs and caproic acid and p-toluenesulfonic acid may be useful salt forming agents to improve the pharmacokinetics of hydrophilic drugs.

Multiwavelength spectrophotometric determination of acid dissociation constants: Part II. First derivative vs. target factor analysis.

PURPOSE: Acid dissociation constants (pKa values) denote the extent of ionization of drug molecules at different pH values, which is important in understanding their penetration through biological membranes and their interaction with the receptors. However, many drug molecules are sparingly soluble in water or contain ionization centres with overlapping pKa values, making precise pKa determination difficult using conventional spectrophotometric titration. In this work, we investigate a multiwavelength spectrophotometric titration (WApH) method for the determination of pKa values. METHODS: Spectral changes which arise during pH-metric titrations of substances with concentration of about 10(-5) M were captured by means of an optical system developed in this study. All experiments were carried out in 0.15 M KCI solution at 25 +/- 0.5 degrees C. Mathematical treatments based on the first derivative spectrophotometry procedure and the target factor analysis method were applied to calculate the pKa values from the multiwavelength absorption titration data. RESULTS: pKa values were determined by the WApH technique for six ionizable substances, namely, benzoic acid, phenol, phthalic acid, nicotinic acid, p-aminosalicylic acid and phenolphthalein. CONCLUSIONS: The pKa values measured using the WApH technique are in excellent agreement with those measured pH-metrically. We have demonstrated that the first derivative spectrophometry procedure provides a relatively simple way to visualize the pKa values which are consistent with those determined using the target factor analysis method. However, for ionization systems with insufficient spectral data obtained around the sought pKa values or with closely overlapping pKa values, the target factor analysis method outperforms the first derivative procedure in terms of obtaining the results. Using the target factor analysis method, it has been shown that the two-step ionization of phenolphthalein involves a colorless anion intermediate and a red colored di-anion.

Characterization of potential NMDA and cholecystokinin antagonists I. acid-base properties of 2-methyl-4-oxo-3H-quinazoline-3-alkyl-carboxylic acids at the molecular and submolecular levels.

The protonation macroconstants (log K) of 4(3H)-quinazolone (1) and two 2-methyl-4-oxo-3H-alkyl-quinazoline-3-carboxylic acid derivatives (2,3) were determined by pH-potentiometry. The acid-base chemistry of compounds 2 and 3, where proton-bindings take place in an overlapping fashion, was described in terms of protonation microconstants as well. Microspeciation was carried out by two means: UV-pH titration (selective, pH-dependent monitoring of the N1-binding site), and deductively (using a derivative compound as covalently fixed model of one of the protonation isomers). The microconstant values obtained by the two different methods are in agreement within 0.05 log K units. Microspeciation revealed remarkable differences between the two homologue compounds (2 and 3). The microconstant values show that insertion of a second methylene moiety into the aliphatic acid side-chain (1) increases the electron-density and most basicity parameters of both functional groups; (2) significantly modifies the extent of site-site interactions in the molecule; (3) opens new conformational preferences by N1 ring nitrogen-carboxylic group intramolecular hydrogen bond formation and (4) reverses the predominantly zwitterion-involved protonation pathway into a neutral form-involved pathway. These molecules exemplify that microconstant values allow the comparative prediction and quantitative evaluation of pharmacokinetic behaviour, and signify the fact that microspeciation is a powerful tool in the process of drug development.

Characterization of potential NMDA and cholecystokinin antagonists. II. Lipophilicity studies on 2-methyl-4-oxo-3H-quinazoline-3-alkyl-carboxylic acid derivatives.

The lipophilicity of 17 newly synthesized potential NMDA and cholecystokinin antagonist 2-methyl-4-oxo-3H-quinazoline-3-alkyl-carboxylic acid derivatives has been investigated. The apparent partition coefficients of two amphoteric compounds of overlapping protonation (Q1 and Q2) were determined by shake-flask method and converted into true log P values using the protonation microconstants. The difference between their lipophilicity expressed with the true partition coefficients was less, than it could be expected from the 2D structures and was explained with conformational preferences and formation of intramolecular interactions. Out of the other 15 monoprotic quinazolone compounds the lipophilicity of ten molecules (Q8-Q17, experimental set) was determined by TLC method with the help of a calibration set consisting of 12 standard molecules, five quinazolones (Q3-Q7) and seven pyrido[1,2-a]pyrimidines (PP1-PP7). In order to justify the suitability of pyrido-pyrimidines as standards for the chromatographic log P determination of quinazolones, first Q3-Q7 were examined by TLC and HPLC using PP1-PP7 for calibration. Data showed good agreement of results obtained by shake-flask and two different chromatographic methods indicating the similar chromatographic behavior of the two bicyclic systems and the relevance of PP1-PP7 to extend the calibration set of quinazolones. The obtained log P values proved mostly the expected structure-activity relationships. Some findings, however, have revealed specific partition behavior of the compounds providing useful information in the estimation of their pharmacokinetics, and these are discussed in the paper.

On the partition of ampholytes: application to blood-brain distribution.

Partition coefficients in the water-octanol, -cyclohexane, and -dichloromethane systems were determined as a function of pH for three non-zwitterionic ampholytes (nitrazepam, albendazole sulfoxide, and sulfadimidine) and three zwitterionic ampholytes (morphine, difloxacin, and niflumic acid). From known macro- and microprotonation constants in water, the concentration of cation, anion, neutral form, and zwitterion can be found, and partition coefficients can then be calculated for the partition of the neutral form in water to the neutral form in the organic solvent for all six compounds. These micropartition coefficients were then used to obtain descriptors for the neutral form in the general linear free energy (LFER) equation of Abraham. Knowledge of the descriptors enables a number of physicochemical and biochemical properties of the neutral form to be estimated; a detailed analysis is given of the estimation of the blood-brain distribution ratio for the process of going from the neutral form in blood to the neutral form in brain. A related procedure leads to an estimation of the distribution ratio for the process of going from the zwitterion in blood to the neutral form in brain.

Interlaboratory study of log P determination by shake-flask and potentiometric methods.

The pKa and log P values of 23 structurally diverse compounds, including well known drugs and two pharmacons under development, were determined by potentiometry. Also, the log P data were measured by the shake-flask method. Many of the samples were investigated at both of the participating laboratories in order to evaluate the reproducibility of the pH-metric log P technique. The interlaboratory evaluation of pKa and log P data obtained by potentiometry showed excellent agreement (average delta pKa = +/-0.02 and delta log P = +/-0.07). The log P values obtained by the two different methods, ranging from -1.84 to 5.80 (nearly eight orders of magnitude), were in very good concordance, as shown by the linear regression analysis: log PpH-metric = 0.9794 log Pshake-flask -0.0397 (r = 0.9987, s = +/-0.091, F = 8153). The advantages of potentiometric log P determination are discussed.

pH-metric log P. 6. Effects of sodium, potassium, and N-CH3-D-glucamine on the octanol-water partitioning of prostaglandins E1 and E2.

The pH-dependent octanol-water partition behavior of prostaglandins (Pg) E1 and E2 was studied by an automated potentiometric titration method. In 0.15 M KCl at 25 degrees C, the log P values of PgE1 and PgE2 are 3.20 +/- 0.02 and 2.90 +/- 0.02, respectively. The partition parameter also was determined in 0.15 M NaCl, 0.10 M NaCl, and 0.0003 M KCl for PgE1; no ionic strength dependence was observed. In contrast, the Pg anion partitioning, described by the extraction constant, log Ke (= [X+Pg-]OCT/[X+]AQ[Pg-]AQ, where X = Na or K), showed dependence on the nature and concentration of the background salt. For PgE1, the log Ke values are 0.50 +/- 0.08 (0.15 M KCl), 0.18 +/- 0.16 (0.15 M NaCl), 0.86 +/- 0.08 (0.10 M NaCl), and 1.80 +/- 0.09 (0.0003 M KCl); for PgE2, the log Ke value is 0.20 +/- 0.29. The extraction of the Pg anion into octanol by N-methyl-D-glucamine (glucamine) was also studied. In 0.15 M KCl, the log Ke value is 1.82 +/- 0.07. The extraction of the prostaglandin-glucamine complex into octanol maximizes at about pH 8.8. Due to the low aqueous solubility of the prostaglandins, the aqueous pKa values were determined by extrapolation from methanol-water solutions by the Yasuda-Shedlovsky technique. The Debye-Hückel theory was applied to predict the ionic strength dependence of the octanol-water ion-pair extraction constants (log Ke).

Acid-base properties of terbutaline in terms of protonation macro- and microconstants.

The acid/base chemistry of terbutaline was characterized at the molecular level in terms of protonation macroconstants and microconstants. The macroconstants were measured by potentiometry and calculated by standard evaluation methods. The stepwise macroconstant values were log K1 = 11.01, log K2 = 9.89, and log K3 = 8.57 at 25.0 degrees C and 0.2 M ionic strength. The microconstants were deduced using the relationships between macro- and microconstants and an appropriate data set of model compounds (resorcinol and phenylephrine). The molecule of terbutaline contains three ionizable functional groups. In the unprotonated form of the molecule, the two identical phenolate groups are slightly more basic than the secondary amino group, whereas the amino basicity significantly exceeds that of the phenolate site, when the other phenol is protonated. This is due to the large phenolate-phenolate intramolecular interaction. The phenolate-phenolate and the phenolate-amino interactivity parameters were found to be -1.21 and -0.41 log E units, respectively.

Determination of protonation macro- and microconstants and octanol/water partition coefficient of the antiinflammatory drug niflumic acid.

The drug niflumic acid is an amphoteric substance with overlapping pKa values. The acid-base chemistry of the molecule has been characterized in terms of protonation macroconstants (with reference to stoichiometric ionizations) and microconstants (with reference to ionizations of individual species). The proton-binding sites were assigned using 1H and 13C NMR spectroscopy. Due to the very poor water solubility of niflumic acid, the aqueous pKa values were determined from the apparent ionization constants in methanol-water solutions of various proportions by extrapolation to zero co-solvent using the Yasuda-Shedlovsky procedure. The kz tautomerization microconstant of the equilibrium unionized form<-->zwitterionic form was determined from mixtures of organic solvent (dioxane or methanol) with aqueous buffer (at the pH of isoelectric point) by UV spectroscopy, and used for calculation of the other protonation microconstants. The zwitterionic form of the molecule predominates over the uncharged form, the concentration being maximal at the isoelectric pH. The apparent partition coefficients (Papp) of niflumic acid were measured in octanol/water solution by the shake-flask method over a wide pH range. The lipophilicity profile (logPapp vs pH) shows a parabolic shape near its maximum at the isoelectric point. A relationship derived between Papp, PXH0(micropartition coefficient of the uncharged microspecies) and PX-(partition coefficient of the anion) is valid for amphoteric drugs, in cases where the partition of the unionized form and the ion-pair partition of anion can be confirmed. The logP values of microspecies indicate the high lipophilicity of niflumic acid, which is consistent with its good skin penetration and absorption.

Partitioning behaviour of local anesthetic fomocaine derivatives.

The octanol/water partitioning behaviour of local anesthetic fomocaine derivatives has been investigated. The true partition coefficients obtained from log P(app) values reflect well the high lipophilicity of these aminoalkylaryl-ether type compounds. A consequence of this is that the partitioning of the protonated form is not negligible as was proved by the log P(i) values of the ionized molecule measured at pH 4.0. The effect of ionization on partitioning was studied and characterized by the pQ values. This ionization influence on lipophilicity was found quite constant (pQ approximately 4) among the hydroxypiperidine analogs. A parabolic relationship was obtained between the acute toxicity and the log P values of several of the examined compounds.

Relationship between partitioning properties and (calculated) molecular surface. SPR investigation of imidazoquinazolone derivatives.

Structure-property relationship (SPR) investigations have been carried out for a series of N-bridged compounds synthetized recently as potential antithrombotic agents. The octanol/water partition coefficient and reversed phase HPLC retention (log k') were determined experimentally for ten imidazoquinazolone derivatives. Calculations including total geometry optimization and surface area have been carried out. The isotropic surface area (ISA) of supermolecules were obtained. The good correlations were found between log P, log k' and ISA values, provide simple and reliable means by using a single structural parameter for the log P prediction of polycyclic N-bridged compounds.

Protonation equilibria of quinolone antibacterials.

The acid-base properties of seven antibacterial 7-piperazinyl fluoroquinolone derivatives were studied by potentiometry and UV and NMR spectroscopy. These molecules contain two proton-binding sites of similar basicity, namely, the piperazine amino and the carboxylate groups, as proven by 1H NMR spectroscopy. The basicities are quantitated at the molecular level in terms of macroconstants, and also at the submolecular level in terms of microconstants. The microconstants are then used to calculate the concentration of the positive, zwitterionic, neutral, and negatively charged species (microspeciation). The zwitterionic forms always predominate over their neutral protonation isomers, but the zwitterionic:neutral concentration ratio is considerably different for the examined fluoroquinolone derivatives.