Quantitative relationship between rat intestinal absorption and Abraham descriptors

Computational pharmacology and computational chemistry of 4-hydroxyisoleucine: Physicochemical, pharmacokinetic, and DFT-based approaches

Computational pharmacology and chemistry of drug-like properties along with pharmacokinetic studies have made it more amenable to decide or predict a potential drug candidate. 4-Hydroxyisoleucine is a pharmacologically active natural product with prominent antidiabetic properties. In this study, ADMETLab 2.0 was used to determine its important drug-related properties. 4-Hydroxyisoleucine is compliant with important drug-like physicochemical properties and pharma giants' drug-ability rules like Lipinski's, Pfizer, and GlaxoSmithKline (GSK) rules. Pharmacokinetically, it has been predicted to have satisfactory cell permeability. Blood-brain barrier permeation may add central nervous system (CNS) effects, while a very slight probability of being CYP2C9 substrate exists. None of the well-known toxicities were predicted in silico, being congruent with wet lab results, except for a "very slight risk" for respiratory toxicity predicted. The molecule is non ecotoxic as analyzed with common indicators such as bioconcentration and LC₅₀ for fathead minnow and daphnia magna. The toxicity parameters identified 4-hydroxyisoleucine as non-toxic to androgen receptors, PPAR-γ, mitochondrial membrane receptor, heat shock element, and p53. However, out of seven parameters, not even a single toxicophore was found. The density functional theory (DFT) study provided support to the findings obtained from drug-like property predictions. Hence, it is a very logical approach to proceed further with a detailed pharmacokinetics and drug development process for 4-hydroxyisoleucine.

Theoretical consideration on the prediction of in vivo toxicity from in vitro toxicity: Effect of bio-uptake equilibrium, kinetics and mode of action

Although in vitro assay is an ideal alternative method for the in vivo toxicity prediction, different in vivo-in vitro correlations have been observed for the toxicity endpoints obtained from different levels of species. In this paper, theoretical in vivo-in vitro toxicity correlations have been developed for cytotoxicity versus human, mammalian and fish toxicity, respectively. These theoretical models were then used to investigate the correlations and the influencing factors between in vivo and in vitro toxicity. Bio-uptake equilibrium theory can well explain why there is a significant correlation between fish and cell toxicity (R² = 0.70); why human toxicity is very close to fish toxicity; and why hydrophobic compounds exhibit relatively greater toxicity than reactive or specifically-acting compounds to human and fish as compared to cells. The kinetic theory can well explain why there is a very poor relationship between mammal and cell toxicity (R² = 0.44). This paper reveals that polar and ionized compounds can more easily pass through cell membrane and have greater bioconcentration potential. Increasing of hydrophobicity and ionization can increase the cytotoxicity. Inclusion of descriptors representing hydrophobicity, ionization, acidity and absorption into the correlation equations can significantly improve the correlations of cytotoxicity with human and fish toxicity (R² > 0.8), but not with mammal toxicity (R² = 0.49). These descriptors reflect the differences of the toxicodynamics and toxicokinetics between cells and organisms.

Investigation on modes of toxic action to rats based on aliphatic and aromatic compounds and comparison with fish toxicity based on exposure routes

The modes of toxic action (MOAs) play an important role in the assessment of the ecotoxicity of organic pollutants. However, few studies have been reported on the MOAs in rat toxicity. In this paper, the toxic contributions of functional groups in 1255 aromatic compounds were calculated from regression and were then compared with the toxic contributions in aliphatic compounds. The results show that some functional groups have same toxic contributions both in aromatic and aliphatic compounds, but some have not. To investigate the MOAs in rat toxicity, the distribution of toxic ratio (TR) was examined for well-known baseline and less inert compounds and thresholds of log TR=0.3 and 0.5 were used to classify baseline, less inert and reactive compounds. The results showed that some compounds identified as baseline compounds in fish toxicity were also classified as baseline compounds in rat toxicity. Except for phenols and anilines which were identified as less inert compounds in fish toxicity, aromatic compounds with functional groups such as ether, nitrile, nitrophenol, isocyanatoe and chloro were identified as less inert chemicals in rat toxicity. Reactive compounds identified in fish toxicity exhibit greater toxicity to rats. These compounds can undergo nucleophilic substitution, acylation and Schiff base formation with biological macromolecules. The critical body residues (CBRs) calculated from absorption and bioconcentration show that log 1/CBRs in rat toxicity are not equal to that in fish for some compounds. It suggests that the exposure route can affect the identification of MOAs between these two species for these compounds.

Structure-property relationship for cellular accumulation of macrolones in human polymorphonuclear leukocytes (PMNs)

Macrolones are a new class of antimicrobial compounds consisting of a macrolide scaffold linked to a 4-quinolone-3-carboxylic acid moiety via C(4″) position of a macrolide. As macrolides are known to possess favorable pharmacokinetic properties by accumulating in inflammatory cells, in this study we determined the intensity of accumulation in human polymorphonuclear leukocytes (PMNs) of 57 compounds of the macrolone class and analyzed the relationship between the molecular structure and this cellular pharmacokinetic property. Accumulation of macrolones ranged from 0 to 5.5-fold higher than the standard macrolide azithromycin. Distinct structural features in all three considered molecule parts: the macrolide scaffold, quinolone moiety and the linker, affect cellular accumulation. Interestingly, while the parent macrolide, azithromycin, accumulates approximately 3-fold more than clarithromycin, among macrolones all clarithromycin derivatives accumulated in PMNs significantly more than their azithromycin counterparts. Modeling cellular accumulation of macrolones with simple molecular descriptors, as well as with the measured octanol-water distribution coefficient, revealed that the number of hydrogen bond donors and secondary amide groups negatively contribute to macrolone accumulation, while lipophilicity makes a positive contribution.

Linear Solvation Energy Relationships in the Determination of Specificity and Selectivity of Stationary Phases

The retention of fifty structurally different compounds has been studied using linear solvation energy relationships. Investigations were performed with the use of six various stationary phases with two mobile phases (50/50 % v/v methanol/water and 50/50 % v/v acetonitrile/water). Packing materials were home-made and functionalized with octadecyl, alkylamide, cholesterol, alkyl-phosphate and phenyl molecules. This is the first attempt to compare all of these stationary phases synthesized on the same silica gel batch. Therefore, all of them may be compared in more complex and believable way, than it was performed earlier in former investigations. The phase properties (based on Abraham model) were used to the classification of stationary phases according to their interaction properties. The hydrophilic system properties s, a, b indicate stronger interactions between solute and mobile phase for most of the columns. Both e and v cause greater retention as a consequence of preferable interactions with stationary phase by electron pairs and cavity formation as well as hydrophobic bonds. However, alkyl-phosphate phase has different retention properties, as it was expressed by positive sign of s coefficient. It may be concluded that most important parameters influencing the retention of compounds are volume and hydrogen bond acceptor basicity. The LSER coefficients showed also the dependency on the type of organic modifier used as a mobile phase component.

Solvent effects on the structure-property relationship of anticonvulsant hydantoin derivatives: A solvatochromic analysis

Considering the pharmaceutical importance of hydantoins, a set of 25 derivatives of phenytoin, nirvanol and 5-methyl-5-phenylhydantoin, the lipophilicities of which were gradually increased by the introduction of different alkyl, cycloalkyl and alkenyl groups in position N3, was synthesized. Their properties under consideration were either estimated empirically, by UV/Vis spectroscopy, or calculated using established medicinal chemistry software. The UV absorption spectra of the investigated compounds were recorded in the region from 200 to 400 nm, in selected solvents of different polarities. The effects of solvent dipolarity/polarizability and solvent-solute hydrogen bonding interactions were analyzed by means of the linear solvation energy relationship (LSER) concept proposed by Kamlet and Taft. Furthermore, the relationships between solvent-solute interactions and selected structural features of the solutes, which are believed to markedly affect the processes of absorption, distribution, metabolism, excretion and toxicity (ADMETox), were discussed. Satisfactory correlations were found between hydrogen bonding properties and solute size and the in silico calculated bioactivity descriptors, in particular %Abs. (human intestinal absorption), log BB (blood-brain barrier permeation) and log k_A (protein binding affinities) parameters. In view of the results of this study, the investigated hydantoin derivatives met the pharmacokinetic criteria for pre-selection as drug candidates and qualified them for the pharmacodynamic phase of antiepileptic drug development.

Ionization-specific analysis of human intestinal absorption

This study presents a mechanistic QSAR analysis of human intestinal absorption of drugs and drug-like compounds using a data set of 567 %HIA values. Experimental data represent passive diffusion across intestinal membranes, and are considered to be reasonably free of carrier-mediated transport or other unwanted effects. A nonlinear model was developed relating %HIA to physicochemical properties of drugs (lipophilicity, ionization, hydrogen bonding, and molecular size). The model describes ion-specific intestinal permeability of drugs by both transcellular and paracellular routes, and also accounts for unstirred water layer effects. The obtained model was validated on two external data sets consisting of in vivo human jejunal permeability coefficients (P(eff)) and absorption rate constants (K(a)). Validation results demonstrate good predictive power of the model (RMSE = 0.35-0.45 log units for log K(a) and log P(eff)). High prediction accuracy together with clear physicochemical interpretation (log P, pK(a)) makes this model particularly suitable for use in property-based drug design.

Characterization of microemulsion liquid chromatography systems by solvation parameter model and comparison with other physicochemical and biological processes

The solvation parameter model has been applied to characterize four microemulsion liquid chromatography (MELC) systems and two micellar liquid chromatography (MLC) systems, and utilized to compare the above systems with other physicochemical and biological processes in this study. The microemulsion mobile phases were composed of sodium dodecyl sulfate (SDS), polyoxyethylene (23) lauryl ether (Brij 35), butanol, heptane and phosphate buffer (pH 7.0) at the designated ratios. The results showed the main difference between the concerned MELC and MLC systems was the decrease of hydrogen-bond basicity of stationary phase with the addition of heptane in microemulsion. Principal component analysis with normalized coefficients can provide consistent results involving the similarities among various systems with that obtained by distance parameter d. Except for some proven similarities of chromatographic systems to octanol-water partition coefficients (logP) and human skin permeation (logK(p)), a microemulsion HPLC system, the mobile phase being 3.3% SDS-6.6% butanol-1.6% heptane-88.5% buffer, was found very similar to drug penetration across blood-brain barrier and its predictive capability for this biological process was originally evaluated in this study.

Quantitative structure-retention relationship studies using immobilized artificial membrane chromatography I: Amended linear solvation energy relationships with the introduction of a molecular electronic factor

Linear solvation energy relationships (LSERs) amended by the introduction of a molecular electronic factor were employed to establish quantitative structure-retention relationships using immobilized artificial membrane (IAM) chromatography, in particular ionizable solutes. The chromatographic indices, log k(IAM), were determined by HPLC on an IAM.PC.DD2 column for 53 structurally diverse compounds, including neutral, acidic and basic compounds. Unlike neutral compounds, the IAM chromatographic retention of ionizable compounds was affected by their molecular charge state. When the mean net charge per molecule (delta) was introduced into the amended LSER as the sixth variable, the LSER regression coefficient was significantly improved for the test set including ionizable solutes. The delta coefficients of acidic and basic compounds were quite different indicating that the molecular electronic factor had a markedly different impact on the retention of acidic and basic compounds on IAM column. Ionization of acidic compounds containing a carboxylic group tended to impair their retention on IAM, while the ionization of basic compounds did not have such a marked effect. In addition, the extra-interaction with the polar head of phospholipids might cause a certain change in the retention of basic compounds. A comparison of calculated and experimental retention indices suggested that the semi-empirical LSER amended by the addition of a molecular electronic factor was able to reproduce adequately the experimental retention factors of the structurally diverse solutes investigated.

Predicting MDCK cell permeation coefficients of organic molecules using membrane-interaction QSAR analysis

AIM

To use membrane-interaction quantitative structure-activity relationship analysis (MI-QSAR) to develop predictive models of partitioning of organic compounds in gastrointestinal cells.

METHODS

A training set of 22 structurally diverse compounds, whose apparent permeability across cellular membranes of Madin-Darby canine kidney (MDCK) cells were measured, were used to construct MI-QSAR models. Molecular dynamic simulations were used to determine the explicit interaction of each test compound (solute) with a dimyristoyl-phosphatidyl-choline monolayer membrane model. An additional set of intramolecular solute descriptors were computed and considered in the trial pool of descriptors for building MI-QSAR models. The QSAR models were optimized using multidimensional linear regression fitting and the stepwise method. A test set of 8 compounds were evaluated using the MI-QSAR models as part of a validation process.

RESULTS

MI-QSAR models of the gastrointestinal absorption process were constructed. The descriptors found in the best MI-QSAR models are as follows: 1) ClogP (the logarithm of the 1-octanol/water partition coefficient); 2) E(HOMO) (the highest occupied molecular orbital energy); 3) E(s) (stretch energy); 4) PM(Y) (the principal moment of inertia Y, the inertia along the y axis in the rectangular coordinates; 5) C(t) (total connectivity); and 6) E(nb) (the energy of interactions between all of the non-bonded atoms). The most important descriptor in the models is ClogP.

CONCLUSION

Permeability is not only determined by the properties of drug molecules, but is also very much influenced by the molecule-membrane interaction process.

Capter 11 Filtering in Drug Discovery

This chapter discusses the concept of filtering in drug discovery. Multiple filters may be incorporated into a definition of drug-likeness and this leads to tradeoffs among compound properties in compounds intended for screening. The optimization of compound properties may require some type of multiparameter optimization scheme in library design. Fingerprint algorithms can be used to guide diversity. Filters also need to be employed in the chemistry synthesis planning process so that good quality compounds are made. Differences in property ranges between oral and injectable drugs are summarized in the chapter. Oral drugs are lower in MWT and have fewer H-bond donors, acceptors, and rotatable bonds. A scheme for separating central nervous system (CNS)- from non-CNS-active drugs in the WDI allowed the discovery of simple parameters relating to passive blood brain barrier (BBB) permeability and the prediction of p-glycoprotein (PGP) affinity. The PGP transporter is a major barrier to the entry of compounds to the CNS. Appropriately determined PGP efflux ratios can be used as a measure of compound affinity to PGP.