A new approach to predict the biological activity of molecules based on similarity of their interaction fields and the logP and logD values: application to auxins

The activity of a biological compound is dependent both on specific binding to a target receptor and its ADME (Absorption, Distribution, Metabolism, Excretion) properties. A challenge to predict biological activity is to consider both contributions simultaneously in deriving quantitative models. We present a novel approach to derive QSAR models combining similarity analysis of molecular interaction fields (MIFs) with prediction of logP and/or logD. This new classification method is applied to a set of about 100 compounds related to the auxin plant hormone. The classification based on similarity of their interaction fields is more successful for the indole than the phenoxy compounds. The classification of the phenoxy compounds is however improved by taking into account the influence of the logP and/or the logD values on biological activity. With the new combined method, the majority (8 out of 10) of the previously misclassified derivatives of phenoxy acetic acid are classified in accord with their bioassays. The recently determined crystal structure of the auxin-binding protein 1 (ABP1) enabled validation of our approach. The results of docking a few auxin related compounds with different biological activity to ABP1 correlate well with the classification based on similarity of MIFs only. Biological activity is, however, better predicted by a combined similarity of MIFs + logP/logD approach.     

Antioxidant activity of novel indole derivatives and protection of the myocardial damage in rabbits

Novel indole derivatives containing a triazole moiety (1a-d, 2a-c) were synthesized as lead compounds with interesting pharmacological profiles. Their antioxidant activity was investigated on in vitro non-enzymatic rat hepatic microsomal lipid peroxidation. All compounds showed significant effect in the above assay. The effect depended mainly on the attachment position of the triazole moiety on the indole nucleus. The most potent antioxidant derivatives la, 1c and 1d were tested for their protective ability against the oxidative damage of the myocardium after ischemia-reperfusion, in male rabbits which were subjected to 30 min regional ischemia followed by reperfusion. The tested antioxidant compounds 1a, 1c and 1d were continuously infused for 30 min starting at 10th min of ischemia and lasted at 10th min of reperfusion. The concentration of malondialdehyde (MDA, a marker of lipid peroxidation) and hemodynamic parameters (blood pressure and heart rate) were measured in the baseline, at 20th min of the sustained ischemia, 1st and 20th min of reperfusion. It was found that the examined compounds la, 1c and 1d reduced significantly the level of MDA in rabbits under ischemia-reperfusion and proved to be promising substances for further evaluation of anti-ischemic properties.     

Quantitative Structure–Retention Relationships as Useful Tool to Characterize Chromatographic Systems and Their Potential to Simulate Biological Processes

Quantitative structure–retention relationships (QSRR) date back to the 1970s and are associated with the evolution of modern Chromatography, while in conjunction with quantitative structure–property relationships (QSPR), they make part of the QSAR discipline. The present review offers a survey of QSRR from a medicinal chemistry point of view, highlighting the merits of this approach in exploiting the friendly chromatographic techniques for the establishment of the physico chemical profiling of drug and drug candidates. It starts with a short overview on QSRR methodology concerning molecular representation, statistical tools and model validation. It continues focusing on the major recent achievements of QSRR with regard to the characterization of chromatographic systems and thereupon to the improvement of stationary phases and to experimental design, while emphasizing their application in drug design. The inter-relation of retention with lipophilicity, a property of paramount interest in drug action and the merit of biomimetic chromatography and of MEEKC systems to simulate essential pharmacokinetic properties are commented under the insights offered by QSRR, in conjunction with QSPR. Characteristic examples are discussed.     

Study of the lipophilicity of selenium species

In this work the lipophilicity of different selenium species occurring in environmental matrices and food, Se(IV), Se(VI), selenomethionine (Se-Met), selenocystamine (Se-CM), selenocystine (Se-Cyst), and dimethyl diselenide (CH₃)₂Se₂, was investigated in the octanol–water system, using the shaking flask method and detection with inductively coupled plasma–atomic emission spectrometry (ICP–AES), in order to assess their environmental fate and tendency to bioaccumulate. Polarography was also used for the electrochemically active Se species, Se(IV), Se-Cyst, Se-CM and (CH₃)₂Se₂, and the results were compared with those measured by ICP–AES. Furthermore, the influence of pH was studied by determining the logarithm of the distribution coefficient, log D, at three pH values, 5, 7, and 9, as was the impact of the marine environment on the lipophilicity profile of the six investigated Se species. The results were compared with those estimated approximately by use of PrologD software, based on the Ghose-Crippen log P (P: partition coefficient) calculation system, the only system which incorporates values—even though approximate—for the atom type of Se. Finally, from our experimental data an indicative value of the Se–Se fragment for log P prediction, for use in drug design, was estimated.     

Fraction Lipophilicity Index (FLI). A drug-like metric for orally administered ionizable drugs

ABSTRACT

Fraction Lipophilicity Index (FLI) was developed as a metric for assessing drug likeness of ionizable oral drugs. Considering that both log P and log D have distinct roles in drug action, the metric FLI allocates lipophilicity to a pH dependent neutral fraction of the molecule and is a weighted combination of log P and log D. It is expressed by equation: FLI = 2 x log P–│log D│. A dataset of 368 basic and acidic drugs was analyzed. Based on available % absorption data, drugs were classified into class 1 (268 drugs) and class 2 (100 drugs). The freeware MedChem Designer was used for log P and log D calculations at pH 7.4 and pH 5.5 for acids. Based on class 1, a drug-like FLI range 0–8 was defined. FLI distribution for class 2 is shifted towards significantly lower values. Comparison of FLI with rule of 5 (Ro5) shows that it leads to fewer values outside the established range than the corresponding log P violations for class 1. For class 2 it gives more alerts than Ro5 and can be considered complementary to Ro5, while it also sets lower limits to discriminate drugs with poor absorption.     

Reactions of indole derivatives with cardioprotective activity with reactive oxygen species. Comparison with melatonin

We have previously reported on the synthesis of novel indole derivatives containing an amine-triazole moiety (1a-d, 2a-c), and their antioxidant activity on in vitro non-enzymatic rat hepatic microsomal lipid peroxidation. Some of the compounds showed protective activity against oxidative injury of ischemic myocardium. In the present paper we investigated the interactions of these derivatives with reactive oxygen species, in order to find a mechanism of their antioxidant capacity and to identify structural characteristics responsible for these properties. These interactions were compared with melatonin, which is also an indole derivative. The antioxidant profiles of the compounds were established by different in vitro protocols as follows: 1) by the interaction of the compounds with the 1,1-diphenyl-2-picrylhydrazyl (DPPH) stable free radical, 2) their scavenging effects on superoxide anions using an enzymic system of xanthine-xanthine oxidase, 3) their inhibitory effects on xanthine oxidase and 4) their ability to scavenge hydroxyl radicals by comparison with dimethyl sulfoxide (DMSO) for *OH. All compounds were found to interact with DPPH, most of them to be superoxide anion scavengers and to be strong hydroxyl radical scavengers. Derivatives 1a and 1d substituted on the nitrogen of the indolic nucleus were found to have better antioxidant properties than the reference compounds used and melatonin.     

Electrostatic interactions and ionization effect in immobilized artificial membrane retention. A comparative study with octanol-water partitioning

The present study is a continuation of our efforts to investigate the effect of electrostatic interactions and ionization on immobilized artificial membrane (IAM) retention. The previous set of neutral and basic drugs was extended to include acids and ampholytes and analogous buffer conditions in the mobile phase were used, namely morpholinepropanesulfonic acid and phosphate buffer saline, adjusted at pH 7.4. The important contribution of electrostatic forces in IAM retention of positively charged species was further justified by the results of the present study, while analogous electrostatic interactions for ionized acidic drugs were not found to affect significantly the affinity for the IAM stationary phase. The critical role of shielding or exposure of the charged centers on the IAM surface, as a result of the effect of the aqueous component of the mobile phase, was evaluated by the use of water instead of buffer for a number of drugs. Measurements at pH 5.0 demonstrated the effect of ionization in IAM retention despite the partial compensation by electrostatic interactions in the case of protonated basic drugs. Silanophilic interactions were also found to play a potential role as secondary interactions in IAM retention. IAM chromatographic indices were compared to octanol-water distribution coefficients and the corresponding relationships established. Finally, solvation analysis was applied in the aim to gain insight in the balance of forces between IAM retention and octanol-water partitioning. The results showed that apart from electrostatic interactions, there is no significant differentiation between the two systems.     

Electrochemical study of some non-steroidal anti-inflammatory drugs: solvent effect and antioxidant activity

The electrochemical behavior of 12 non-steroidal anti-inflammatory drugs (NSAIDs) was studied by means of cyclic voltammetry at a glassy carbon electrode. The underlying solvent had a considerable effect to the oxidation potentials of the investigated NSAIDs due to the alteration of their polar intermediates’ solvation. Oxicams were more capable of electrochemical oxidation, and the influence of both specific and non-specific solute–solvent interactions in their reactivity was confirmed by means of Kamlet–Taft’s analysis. Oxicams were further studied by chronoamperometry at the potentials of 300, 500, and 800 mV. The results obtained by the employed electroanalytical techniques were compared with the reactivity of oxicams towards 1,1- diphenyl-2-dipicrylhydrazyl (DPPH). The study showed a correlation of oxicams’ amperometric signal at 800 mV with their absolute reaction rate, z with DPPH.     

Exploring the elution mechanism of selenium species on liquid chromatography

In the present work, the chromatographic behavior of eight selenium species, namely selenites (Se(IV)), selenates (Se(VI)), seleno‐DL ‐methionine (Se‐Met), selenocystine (Se‐Cyst), selenocystamine (Se‐CM), selenourea (Se‐U), dimethylselenide ((CH₃)₂Se) and dimethyldiselenide ((CH₃)₂Se₂), was investigated under different stationary and mobile phase conditions, in an effort to unravel secondary interferences in their underlying elution mechanism. For this purpose, two end‐capped and a polar‐embedded reversed‐phase stationary phases were employed using different mobile phase conditions. Retention factors (log k_w) were compared with octanol–water distribution coefficients (log D) as well as with log k_w values on two immobilized artificial membrane (IAM) columns and two immobilized artificial plasma proteins stationary phases, obtained in our previous work. The role of electrostatic interactions was confirmed by introducing the net charge of the investigated Se species as an additional term in the log k_w/log D interrelation, which in most cases proved to be statistically significant. Principal component analysis of retention factors on all stationary phases and octanol–water log D values, however, showed that the elution of the investigated selenium species is mainly governed by partitioning mechanism under all different chromatographic conditions, while the pH of the mobile phase and the special column characteristics have only a minor effect.     

Retention of structurally diverse drugs in human serum albumin chromatography and its potential to simulate plasma protein binding

The retention behavior of 39 structurally diverse neutral, basic and acidic drugs was investigated on an HSA stationary phase using PBS buffer (pH 7.0) and acetonitrile or 2-propanol as organic modifiers. Extrapolated or directly measured log k_w values as well as isocratic retention factors were correlated with plasma protein binding data taken from the literature. Retention factors determined in the presence of 10% acetonitrile led to high quality 1:1 correlation with apparent log K_HSA values. The derived reference equation was successfully validated using a secondary set of 24 drugs. Further analysis of HSA retention into more fundamental properties revealed the involvement of anionic species in solute-stationary phase interactions, expressed by the negatively charged fraction, besides the partitioning mechanism which was reflected by lipophilicity. Protonation of basic drugs, although less important, may also influence retention, leading to reduced partitioning into the HSA surface as a net effect, while it seems to have no effect on HSA binding. The above results were further confirmed by linear solvation energy relationships (LSER).