Superdelocalizability and charge density. A correlation with partition coefficients

Lipophilicity in drug design: an overview of lipophilicity descriptors in 3D-QSAR studies

The pharmacophore concept is a fundamental cornerstone in drug discovery, playing a critical role in determining the success of in silico techniques, such as virtual screening and 3D-QSAR studies. The reliability of these approaches is influenced by the quality of the physicochemical descriptors used to characterize the chemical entities. In this context, a pivotal role is exerted by lipophilicity, which is a major contribution to host-guest interaction and ligand binding affinity. Several approaches have been undertaken to account for the descriptive and predictive capabilities of lipophilicity in 3D-QSAR modeling. Recent efforts encode the use of quantum mechanical-based descriptors derived from continuum solvation models, which open novel avenues for gaining insight into structure-activity relationships studies.

Comparative Aroma Extract Dilution Analysis (cAEDA) of Fat from Tainted Boars, Castrated Male Pigs, and Female Pigs

The aroma profile of porcine fat from tainted boars, female pigs, and castrated male pigs was investigated by application of comparative aroma extract dilution analysis (cAEDA) on a SAFE distillate of volatiles prepared from porcine back fat samples. The AEDA resulted in a total of 16 aroma active compounds for boar fat with flavor dilution (FD) factors ranging from 2 to 2048, whereas 12 aroma active compounds were found in fat of female pigs and 14 in fat of castrated male pigs, both with FD factors ranging from 2 to 32. Odor activity values (OAVs) of key components for each fat were identified: In boar fat androstenone, skatole, indole, and 2-aminoacetophenone showed highest OAVs, whereas 2,5-dimethylpyrazine, 2,4-decadienal, and δ-decalactone showed highest OAVs in fat of female pigs. Fat of castrated male pigs showed highest OAVs for skatole, indole, 1-octen-3-ol and methional. Finally, the off-flavor attributes of boar fat were successfully simulated by a recombinant of all odorants at their natural concentration level in deodorized sunflower oil.

2-Aminoacetophenone Is the Main Volatile Phase I Skatole Metabolite in Pietrain × Baden-Württemberg Hybrid Type Boars

Skatole metabolites have been considered as putative contributors to boar taint. Recently, 2-aminoacetophenone, a volatile phase I skatole metabolite, was identified in back fat samples from boars of Pietrain × Baden-Württemberg hybrid type. This paper addresses the question of the physiological origin of the observed 2-aminoacetophenone in these pigs. Microsomal fractions from nine boars were isolated, and formation of skatole metabolites was subsequently analyzed by stable-isotope dilution analysis (SIDA) using headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME/GC-MS). Significant breed-related differences in phase I skatole metabolism were observed, explaining the high levels of 2-aminoacetophenone in Pietrain × Baden-Württemberg hybrid type boars.

Determination of n-octanol/water partition coefficients of weak ionizable solutes by RP-HPLC with neutral model compounds

The utilization of neutral compounds as model compounds is put forward for determination of the n-octanol/water partition coefficient (K(ow)) of highly hydrophobic, weak acidic compounds by reversed-phase high performance liquid chromatography (RP-HPLC). It is based on a linear relationship between the logarithm of apparent n-octanol/water partition coefficient (log K(ow)″), expressing hydrophobicity of acidic solutes more accurately, and the logarithm of RP-HPLC retention factor of the solutes corresponding to the neat aqueous fraction of mobile phase (log k(w)). The availability of neutral model compounds was theoretically tested for this novel protocol. Moreover, a high consistency of linear log K(ow)″-log k(w) correlations was demonstrated between a mixed training set of neutral and acidic model compounds, and a training set of neutral model compounds. It is proved in theory that for a certain set of compounds investigated, all derived linear relationships between log K(ow)″ and log k(w) have a unit slope and the same intercept, regardless of mobile phase pH. This model was applied to measure log K(ow) of lipophilic aristolochic acid I (AA I) and aristolochic acid II (AA II). Log K(ow) values for AA I and AA II are 4.45±0.07 and 3.99±0.06, respectively. To the best of our knowledge, this is the first report on experimental log K(ow) data for AAs. The proposed strategy solves the problem of lacking suitable acidic model compounds with reliable experimental K(ow) in determining K(ow) of lipophilic acidic solutes by RP-HPLC.

Determination of n-octanol/water partition coefficient for DDT-related compounds by RP-HPLC with a novel dual-point retention time correction

n-Octanol/water partition coefficients (P) for DDTs and dicofol were determined by reversed-phase high performance liquid chromatography (RP-HPLC) on a C(18) column using methanol-water mixture as mobile phase. A dual-point retention time correction (DP-RTC) was proposed to rectify chromatographic retention time (t(R)) shift resulted from stationary phase aging. Based on this correction, the relationship between logP and logk(w), the logarithm of the retention factor extrapolated to pure water, was investigated for a set of 12 benzene homologues and DDT-related compounds with reliable experimental P as model compounds. A linear regression logP=(1.10±0.04) logk(w) - (0.60±0.17) was established with correlation coefficient R(2) of 0.988, cross-validated correlation coefficient R(cv)(2) of 0.983 and standard deviation (SD) of 0.156. This model was further validated using four verification compounds, naphthalene, biphenyl, 2,2-bis(4-chlorophenyl)-1,1-dichloroethane (p,p'-DDD) and 2,2-bis(4-chlorophenyl)-1,1-dichloroethene (p,p'-DDE) with similar structure to DDT. The RP-HPLC-determined P values showed good consistency with shake-flask (SFM) or slow-stirring (SSM) results, especially for highly hydrophobic compounds with logP in the range of 4-7. Then, the P values for five DDT-related compounds, 2-(2-chlorophenyl)-2-(4-chlorophenyl)-1,1,1-trichloroethane (o,p'-DDT), 2-(2-chlorophenyl)-2-(4-chlorophenyl)-1,1-dichloroethane (o,p'-DDD), 2-(2-chlorophenyl)-2-(4-chlorophenyl)-1,1-dichloroethene (o,p'-DDE), and 2,2,2-trichloro-1,1-bis(4-chlorophenyl)ethanol (dicofol) and its main degradation product 4,4'-dichlorobenzophenone (p,p'-DBP) were evaluated by the improved RP-HPLC method for the first time. The excellent precision with SD less than 0.03 proved that the novel DP-RTC protocol can significantly increases the determination accuracy and reliability of P by RP-HPLC.

ERβ ligands. Part 4: Synthesis and structure–activity relationships of a series of 2-phenylquinoline derivatives

A new class of estrogen receptor beta (ERbeta) ligands based on the 2-phenylquinoline scaffold was prepared. Several analogues with C4 substitution displayed high affinity (3-5 nM) and significant selectivity (up to 83-fold) for ERbeta. The best compound, 13b, was profiled as a selective partial agonist for ERbeta at 1 muM in a cell-based transcriptional assay. Uterine weight bioassay of 13b indicated no activation of ERalpha in vivo.

Environmental swap energy and role of configurational entropy in transfer of small molecules from water into alkanes

We studied the effect of segmented solvent molecules on the free energy of transfer of small molecules from water into alkanes (hexane, heptane, octane, decane, dodecane, tetradecane, and hexadecane). For these alkanes we measured partition coefficients of benzene, 3-methylindole (3MI), 2,3,4,6-tetrachlorophenol (TeCP), and 2,4,6-tribromophenol (TriBP) at 3, 11, 20, 33 [corrected], and 47 degrees C. For 3MI, TeCP, and TriBP the dependence of free energy of transfer on length of alkane chains was found to be very different from that for benzene. In contrast to benzene, the energy of transfer for 3MI, TeCP, and TriBP was independent of the number of carbons in alkanes. To interpret data, we used the classic Flory-Huggins (FH) theory of concentrated polymer solutions for the alkane phase. For benzene, the measured dependence of energy of transfer on the number of carbons in alkanes agreed well with predictions based on FH model in which the size of alkane segments was obtained from the ratio of molar volumes of alkanes and the solute. We show that for benzene, the energy of transfer can be divided into two components, one called environmental swap energy (ESE), and one representing the contribution of configurational entropy of alkane chains. For 3MI, TeCP, and TriBP the contribution of configurational entropy was not measurable even though the magnitude of the effect predicted from the FH model for short chain alkanes was as much as 20 times greater than experimental uncertainties. From the temperature dependence of ESE we obtained enthalpy and entropy of transfer for benzene, 3MI, TeCP, and TriBP. Experimental results are discussed in terms of a thermodynamic cycle considering creation of cavity, insertion of solute, and activation of solute-medium attractive interactions. Our results suggest that correcting experimental free energy of transfer by Flory-Huggins configurational entropy term is not generally appropriate and cannot be applied indiscriminately.

Markovian chemicals "in silico" design (MARCH-INSIDE), a promising approach for computer-aided molecular design I: discovery of anticancer compounds

A simple stochastic approach, designed to model the movement of electrons throughout chemical bonds, is introduced. This model makes use of a Markov matrix to codify useful structural information in QSAR. The self-return probabilities of this matrix throughout time ((SR)pi(k)) are then used as molecular descriptors. Firstly, a calculation of (SR)pi(k) is made for a large series of anticancer and non-anticancer chemicals. Then, k-Means Cluster Analysis allows us to split the data series into clusters and ensure a representative design of training and predicting series. Next, we develop a classification function through Linear Discriminant Analysis (LDA). This QSAR discriminates between anticancer compounds and non-active compounds with a correct global classification of 90.5% in the training series. The model also correctly classified 86.07% of the compounds in the predicting series. This classification function is then used to perform a virtual screening of a combinatorial library of coumarins. In this connection, the biological assay of some furocoumarins, selected by virtual screening using the present model, gives good results. In particular, a tetracyclic derivative of 5-methoxypsoralen (5-MOP) has an IC50 against HL-60 tumoral line around 6 to 10 times lower than those for 8-MOP and 5-MOP (reference drugs), respectively. Finally, application of Iso-contribution Zone Analysis (IZA) provides structural interpretation of the biological activity predicted with this QSAR.

Substructure and whole molecule approaches for calculating log P

Lipophilicity is a major determinant of pharmacokinetic and pharmacodynamic properties of drug molecules. Correspondingly, there is great interest in medicinal chemistry in developing methods of deriving the quantitative descriptor of lipophilicity, the partition coefficient P, from molecular structure. Roughly, methods for calculating log P can be divided into two major classes: Substructure approaches have in common that molecules are cut into atoms (atom contribution methods) or groups (fragmental methods); summing the single-atom or fragmental contributions (supplemented by applying correction rules in the latter case) results in the final log P. Whole molecule approaches inspect the entire molecule; they use for instance molecular lipophilicity potentials (MLP), topological indices or molecular properties to quantify log P. In this review, representative members of substructure and whole molecule approaches for calculating log P are described; their advantages and shortcomings are discussed. Finally, the predictive power of some calculation methods is compared and a scheme for classifying calculation methods is proposed.

Molecular orbital-generated QSARs in a homologous series of alkoxyresorufins and studies of their interactive docking with P450s

1. Molecular and electronic structural parameters have been determined, by molecular orbital (MO) calculations, for a homologous series of 8 alkoxyresorufins (methoxy- to octoxy-). 2. Quantitative structure-activity relationships (QSARs) between these structural parameters and the rates of metabolism of the alkoxyresorufins in hepatic microsomes from the 3-methylcholanthrene (MC)-, and phenobarbital (PB)-pretreated mouse, and the beta-naphthoflavone (beta NF)-pretreated rat have been established. 3. The most significant single relationship is between beta NF-induction of cytochrome P4501 (CYP1A) and the total nucleophilic superdelocalizability (sigma SN) for the eight compounds in the series. 4. For double regressions, the electronic charge on the alkoxy oxygen, Q(O), or alpha-carbon Q(C), is important when combined with the hydrophobic substituent constant (pi). 5. These findings indicate that the rates of metabolism of these alkoxyresorufins are dependent upon their ability to cross cellular membranes, to fit the relevant CYP1A binding site, and on their ability to accept electrons from a donor nucleophilic species. 6. A different set of parameters correlated with CYP2B activity, namely, parameters of overall shape, which indicates that the way in which the alkoxyresorufins fit the CYP2B site, determines their differences in specificity. 7. Computer graphic interactive docking studies of the alkoxyresorufins with their affinity-specific cytochromes P450, namely, methoxy- with CYP1A2; ethoxy- with CYP1A1; pentoxy- with CYP2B1; and benzyloxy- with CYP3A, have also been undertaken to show the specific interactions of the alkoxyresorufins with the binding sites of the individual P450s.

Relationship between translobular migration in perfused rat liver and hydrophobicity of dialkyl dithiolanylidenemalonates and related compounds

The translobular migration of five dialkyl dithiolanylidenemalonates and five related compounds in perfused rat liver was determined and related with the hydrophobicity, log P. In the elution profile from the perfused rat liver, the peak position (elution volume) varied from 1.5 ml for dimethyl dithiolanylidenemalonate to 186 ml for the dibutyl analogue, dependent on the length of the alcoholic alkyl groups or the hydrophobicity of the compounds. An excellent correlation exists between--log (elution volume) and log P. The hydrophobic interaction with sinusoidal components seems to retard the compound migration from the periportal zone to the hepatic vein. Addition of rat blood (5% v/v) to the perfusion Tyrode solution accelerated the migration of hydrophobic compounds resulting in a gentler slope of the correlation plot. A similar correlation with log P was observed for translobular migrations of other xenobiotics such as naphthalene, nitroanisole, dichlorobenzenes and parathion in rat liver perfused with autologous blood.

Comparative study of lipophilicity versus topological molecular descriptors in biological correlations

This paper analyzes the relative efficacies of lipophilicity vis-à-vis topological indices in the correlation of the biological properties of four groups of bioactive molecules: alcohols, barbiturates, triazinones , and ketobemidones . Wiener number (W), information-theoretic topological parameters (IC, SIC, CIC, IWD , and IWD ), and molecular connectivity indices (1 chi, 1 chi V) were used as the molecular descriptors. Results show that theoretical indices are comparable or superior to log P in biological correlations.

Molecular topology and aqueous solubility of aliphatic alcohols

A physically based method for arriving at topological indexes is described. The derived indexes correlate with molecular surface areas and with the molecular connectivity index. The newly derived index seems to account better for the expected distinctions among primary, secondary, and tertiary alcohol aqueous solubilities. This study suggests that the Del Re method for calculating molecular charges and dipole moments also may be used, without appreciable change, to provide estimates of molecular refraction.