Discovery of Novel, Potent, and Specific Cell-Death Inducers in the Jurkat Acute Lymphoblastic Leukemia Cell Line

The limited clinical efficacy of many cancer therapeutics has initiated intense research efforts toward the discovery of novel chemical entities in this field. In this study, 31 hit candidates were selected from nearly 800,000 database compounds in a ligand-based virtual screening campaign. In turn, three of these hits were found to have (sub)micromolar potencies in proliferation assays with the Jurkat acute lymphatic leukemic cell line. In this assay, the three hits were found to exhibit higher potency than clinically tested cell-death inducers (GDC-0152, AT-406, and birinapant). Importantly, antiproliferative activity toward non-cancer peripheral blood mononuclear cells (PBMCs) was found to be marginal. Further biological characterization demonstrated the cell-death-inducing properties of these compounds. Biological testing of hit congeners excluded a nonspecific, toxic effect of the novel structures. Altogether, these findings may have profound relevance for the development of clinical candidates in tumor therapy.

Large, chemically diverse dataset of logP measurements for benchmarking studies

Lipophilicity is a crucial parameter in drug development since it impacts both ADME properties and target affinity of drug candidates. In early drug discovery stage, accurate tools for logP prediction are highly desired. Many calculation methods were developed to aid pharmaceutical scientists in drug research; however almost all suffer from insufficient accuracy and variation of performance in several regions of the chemical space associated with new chemical entities. The low predictive power of existing software packages can be explained by limited availability and/or variable quality of experimental logP values associated with training set used, which stem from various protocols and poorly cover chemical space. In this study, a dataset of 1000 diverse test compounds out of 4.5 million was generated; logP values of 759 purchasable compounds (46% non-ionizable, 30% basic, 17% acidic, 0.5% zwitterionic and 6.5% ampholytes) from this selected set were experimentally determined by UHPLC followed by UV detection or MS detection when necessary. Finally, a data collection of 707 validated logP values ranging from 0.30 to 7.50 is now available for benchmarking of existing and development of new approaches to predict octanol/water partition coefficients of chemical compounds.

QSAR modeling and data mining link Torsades de Pointes risk to the interplay of extent of metabolism, active transport, and HERG liability

We collected 1173 hERG patch clamp (PC) data (IC50) from the literature to derive twelve classification models for hERG inhibition, covering a large variety of chemical descriptors and classification algorithms. Models were generated using 545 molecules and validated through 258 external molecules tested in PC experiments. We also evaluated the suitability of the best models to predict the activity of 26 proprietary compounds tested in radioligand binding displacement (RBD). Results proved the necessity to use multiple validation sets for a true estimation of model accuracy and demonstrated that using various descriptors and algorithms improves the performance of ligand-based models. Intriguingly, one of the most accurate models uncovered an unexpected link between extent of metabolism and hERG liability. This hypothesis was fairly reinforced by using the Biopharmaceutics Drug Disposition Classification System (BDDCS) that recognized 94% of the hERG inhibitors as extensively metabolized in vivo. Data mining suggested that high Torsades de Pointes (TdP) risk results from an interplay of hERG inhibition, extent of metabolism, active transport, and possibly solubility. Overall, these new findings might improve both the decision making skills of pharmaceutical scientists to mitigate hERG liability during the drug discovery process and the TdP risk assessment during drug development.

Large-scale evaluation of log P predictors: local corrections may compensate insufficient accuracy and need of experimentally testing every other compound

A large variety of log P calculation methods failed to produce sufficient accuracy in log P prediction for two in-house datasets of more than 96000 compounds contrary to their significantly better performances on public datasets. The minimum Root Mean Squared Error (RMSE) of 1.02 and 0.65 were calculated for the Pfizer and Nycomed datasets, respectively, in the 'out-of-box' implementation. Importantly, the use of local corrections (LC) implemented in the ALOGPS program based on experimental in-house log P data significantly reduced the RMSE to 0.59 and 0.48 for the Pfizer and Nycomed datasets, respectively, instantly without retraining the model. Moreover, more than 60% of molecules predicted with the highest confidence in each set had a mean absolute error (MAE) less than 0.33 log units that is only ca. 10% higher than the estimated variation in experimental log P measurements for the Pfizer dataset. Therefore, following this retrospective analysis, we suggest that the use of the predicted log P values with high confidence may eliminate the need of experimentally testing every other compound. This strategy could reduce the cost of measurements for pharmaceutical companies by a factor of 2, increase the confidence in prediction at the analog design stage of drug discovery programs, and could be extended to other ADMET properties.

IAP antagonists: promising candidates for cancer therapy

A promising strategy in cancer therapy aims to promote apoptosis in cancer cells. Targeting inhibitor of apoptosis proteins (IAPs) with small-molecule inhibitors has attracted increasing interest in triggering cancer cell death. It is considered to have great potential for cancer drug discovery because IAPs block apoptosis at the core of the apoptotic machinery and are aberrantly expressed in various tumors. This review focuses on the current development of small-molecule IAP antagonists for cancer therapy.

Thermodynamics of organic chemical hydration: QSPR models using physicochemical HYBOT descriptors

Stable and predictive quantitative structure-property relationship (QSPR) models of thermodynamics of chemical hydration (changes in Gibbs energy, DeltaG(air/water), enthalpy, DeltaH(air/water) and entropy DeltaS(air/water)) were obtained on the basis of physicochemical descriptors calculated by the HYBOT program. The structurally diverse training set (n = 151) and test set (n = 37) included 13 mono-functional chemical classes. The applied HYBOT descriptors comprise molecular polarizability alpha (as a volume-related term), the sum of partial negative charges on all atoms in a molecule SigmaQ(-) (as an electrostatic term) and the sum of H-bond acceptor and donor factors SigmaC(a) and SigmaC(d) (as H-bond terms). Final equations for changes in Gibbs energy and enthalpy provided good statistical criteria and standard deviations on the level of errors of experimental determinations. All four above-mentioned terms essentially contribute to hydration enthalpy and each of them increases negative values of enthalpy. Hydration Gibbs energy predominantly depends on hydrogen bonding between solute and water molecules. Steric and electrostatic terms act in opposite directions and partly compensate each other. Changes in entropy correlate with increasing H-bond acceptor ability, whereas the other three descriptors exhibit inverse correlations.

Novel TOPP descriptors in 3D-QSAR analysis of apoptosis inducing 4-aryl-4H-chromenes: comparison versus other 2D- and 3D-descriptors

Novel 3D-descriptors using Triplets Of Pharmacophoric Points (TOPP) were evaluated in QSAR-studies on 80 apoptosis-inducing 4-aryl-4H-chromenes. A predictive QSAR model was obtained using PLS, confirmed by means of internal and external validations. Performance of the TOPP approach was compared with that of other 2D- and 3D-descriptors; statistical analysis indicates that TOPP descriptors perform best. A ranking of TOPP>GRIND>BCI 4096=ECFP>FCFP>GRID-GOLPE>>DRAGON>>>MDL 166 was achieved. Finally, in a 'consensus' analysis predictions obtained using the single methods were compared with an average approach using six out of eight methods. The use of the average is statistically superior to the single methods. Beyond it, the use of several methods can help to easily investigate the presence/absence of outliers according to the 'consensus' of the predicted values: agreement among all the methods indicates a precise prediction, whereas large differences between predicted values (for the same compounds by different methods) would demand caution when using such predictions.

Virtual Screening for Novel Openers of Pancreatic KATPChannels

Ligand-based virtual screening approaches were applied to search for new chemotype KCOs activating Kir6.2/SUR1 KATP channels. A total of 65 208 commercially available compounds, extracted from the ZINC archive, served as database for screening. In a first step, pharmacokinetic filtering via VolSurf reduced the initial database to 1913 compounds. Afterward, six molecules were selected as templates for similarity searches: similarity scores, obtained toward these templates, were calculated with the GRIND, FLAP, and TOPP approaches, which differently encode structural information into potential pharmacophores. In this way, we obtained 32 hit candidates, 16 via GRIND and eight each via FLAP and TOPP. For biological testing of the hit candidates, their effects on membrane potentials in HEK 293 cells expressing Kir6.2/SUR1 were studied. GRIND, FLAP, and TOPP all yielded hits, but no method top-ranked all the actives. Thus, parallel application of different approaches probably improves hit detection.

Structure-activity relationships of K(ATP) channel openers

Given their many physiological functions, K(ATP) channels represent promising drug targets. Sulfonylureas like glibenclamide block K(ATP) channels; they are used in the therapy of type 2 diabetes. Openers of K(ATP) channels (KCOs) e.g. relax smooth muscle and induce hypotension. KCOs are chemically heterogeneous and include as different classes as the benzopyrans, cyanoguanidines, thioformamides, thiadiazines and pyridyl nitrates. Examples for new chemical entities more recently developed as KCOs include cyclobutenediones, dihydropyridine related structures, and tertiary carbinols. Structure-activity relationships of the main chemical classes of KCOs are discussed.

Second-generation K(ATP) channel openers

This review discusses structural aspects of second-generation K(ATP) channel openers (KCOs), which exhibit improved tissue-selectivity. Their therapeutic profile is debated with main focus on cardiac ischemia, asthma, and urinary incontinence.

Binding studies and GRIND/ALMOND-based 3D QSAR analysis of benzothiazine type K(ATP)-channel openers

For seventeen 1,4-benzothiazine potassium channel openers, we performed binding studies in rat aortic smooth muscle cells and cardiomyocytes, compared their binding affinities with published relaxation data, and derived 3D-QSAR models using GRIND/ALMOND descriptors. Binding affinities in smooth muscle cells range from a pK(D) of 4.76 for compound 3e to 9.10 for compound 4c. Comparison of data for smooth muscle relaxation and binding shows preferentially higher pEC(50)s for the former. In cardiomyocytes, pK(D) values range from 4.21 for 3e to 8.16 for 4c. 3D-QSAR analysis resulted in PLS models of two latent variables for all three activities with determination coefficients of 0.97 (smooth muscle relaxation) and 0.94 (smooth muscle cells- and cardiomyocytes-binding). Internal validation yielded q(2) values of 0.69, 0.66, and 0.64. The carbonyl on the N-4 substituent, the hydrogen bond acceptor at C-6, the five-membered ring at N-4, and the gem-dimethyls mainly guide strong binding and strong smooth muscle relaxation.

log P Estimation of 1,2-Dithiole-3-thiones and 1,2-Dithiole-3-ones: A Comparison of Experimental and Calculative Approaches

PURPOSE

To estimate experimental log P values of formerly described 5-formyl- and 5-acyl-dithiole-3-thiones (DTT) and -dithiole-3-ones (DTO) and to check the validity of five log P calculation programs via experimental log P for a database of 68 DTT and DTO.

METHODS

Experimental log P values were measured by means of octanol/water partitioning; for determining solute concentrations in water, RP-HPLC with spectrophotometric detection was used. For calculating log P, the fragmental methods ACD/log P, CLOGP, and KOWWIN, the atom-based approach XLOGP, and the whole-molecule approach QLOGP were applied.

RESULTS

Quality of calculations significantly differs depending on the subset under consideration. For database compounds 01-48, comprising alkyl and aryl substitution in 4- and 5-position, the fragmental methods ACD/log P, CLOGP, and KOWWIN perform significantly better than the atom-based approach XLOGP and the whole-molecule method QLOGP. For database compounds 49-68, comprising formyl and acyl substitution in 4- and 5-position, superiority of the whole-molecule method QLOGP over the substructure-based approaches is observed. The strong underestimation of log P for compounds 49-68 probably indicates hidden physicochemical phenomena resulting from the juxtaposition of the acyl and dithiole moieties.

CONCLUSIONS

All calculation methods included in this study need a thorough refinement to adequately cope with particular solvation behavior suspected to prevail in formyl- or acyl-DTT and DTO, which represent a chemical class of high pharmacological interest.

Pharmacophore, Drug Metabolism, and Pharmacokinetics Models on Non-Peptide AT1, AT2, and AT1/AT2Angiotensin II Receptor Antagonists

About 20 non-peptide angiotensin II receptor antagonists are in various stages of clinical development. Different modeling approaches were used to predict the pharmacophoric requirements for AT(1) (angiotensin II receptor subtype 1) affinity. However, to our knowledge, none was used to predict both the selectivity toward AT(1) and AT(2) (angiotensin II receptor subtype 2) receptor subtypes. In this paper, partial least squares discriminant analysis is applied to derive the chemical features guiding AT(1) and AT(2) selectivity or mixed AT(1)/AT(2) receptor binding. The method can be used to modulate AT(1) versus AT(2) selectivity. Concerns that unopposed stimulation of the AT(2) receptor might produce adverse effects initiated a search for new balanced antagonists. Moreover, it can serve as a fast filtering procedure in database searches. Finally, some relevant pharmacokinetics and metabolic properties of the database of 53 compounds are calculated using the VolSurf and MetaSite software to allow the simultaneous characterization of pharmacodynamic and pharmacokinetics properties of the chemical space of angiotensin II receptor antagonists.

Comparison of Ligand-Based and Structure-Based 3D-QSAR Approaches: A Case Study on (Aryl-)Bridged 2-Aminobenzonitriles Inhibiting HIV-1 Reverse Transcriptase

Ligand- (GRIND) and structure-based (GLUE/GRIND) 3D-QSAR approaches were compared for 55 (aryl-)bridged 2-aminobenzonitriles inhibiting HIV-1 reverse transcriptase (HIV-1 RT). The ligand-based model was built from conformers selected by in vacuo minimization. The available X-ray structure of 3v in complex with HIV-1 RT allowed comparative structure-based calculations using the new docking software GLUE for conformer selection. Both models were validated via statistics and via virtual receptor sites (VRS) considering pharmacophoric regions and mutual distances, which were also compared with experimental evidence. The statistics show slight superiority of the structure-based approach in terms of fitting and prediction. By encoding relevant molecular interaction fields (MIF) into pharmacophoric regions, 10 such regions were derived from both models; they all fit the real receptor except HBD2. Also mutual distances highly agree between the real site and both VRS. Although distances from the structure-based approach are closer to the real receptor, present data prove the validity of the ligand-based GRIND approach.

The Impact of Lipophilicity in Drug Research: A Case Report on ß-Blockers

The key importance of lipophilicity in bio-studies is discussed for beta-blockers. Examples of their lipophilicity-dependent pharmacological properties including pharmacokinetic, pharmacodynamic and clinical aspects are reviewed. Comprehensive lipophilicity compilations of beta-blockers are lacking so far. LogP calculations with 10 programs for 30 clinically relevant beta-blockers are presented for the first time in this review.

GRIND/ALMOND investigations on CysLT1 receptor antagonists of the quinolinyl(bridged)aryl type

One of the current routes in developing antiasthmatics is CysLT(1) receptor antagonism. For a training set of 54 CysLT(1) receptor antagonists of the quinolinyl(bridged)aryl type we developed chemometric QSAR models applying GRID independent descriptors (=GRIND). PLS analysis resulted in a two-component model explaining 67% of the variance for CysLT(1) receptor binding (r2=0.67, SDEC = 0.47, q2=0.54). GRIND variables 11-50 and 22-55 are responsible for high-affinity binding; variable 11-62 is detrimental. The predictivity of the above chemometric model is tested with a set of 69 CysLT(1) receptor antagonists, exhibiting varying chemical similarity to the training set. Nearly 50% of the test set are quite well predicted. The quality of prediction coincides in part with chemical subclassification: phenylene bridged compounds are quite well predicted; for structures with bridging heterocycles predictions are rather poor. For explaining the outlier behavior, a PLS discriminant analysis including the training set and the strongest outliers of the test set was performed. The scores plot of discriminant PLS shows an almost complete separation between the two subsets. A PLS coefficients plot explains which GRIND variables are important for the discrimination between the training set and the outliers of the test set.

KATP channel openers: structure-activity relationships and therapeutic potential

ATP-sensitive potassium channels (K(ATP) channels) are heteromeric complexes of pore-forming inwardly rectifying potassium channel subunits and regulatory sulfonylurea receptor subunits. K(ATP) channels were identified in a variety of tissues including muscle cells, pancreatic beta-cells, and various neurons. They are regulated by the intracellular ATP/ADP ratio; ATP induces channel inhibition and MgADP induces channel opening. Functionally, K(ATP) channels provide a means of linking the electrical activity of a cell to its metabolic state. Shortening of the cardiac action potential, smooth muscle relaxation, inhibition of both insulin secretion, and neurotransmitter release are mediated via K(ATP) channels. Given their many physiological functions, K(ATP) channels represent promising drug targets. Sulfonylureas like glibenclamide block K(ATP) channels; they are used in the therapy of type 2 diabetes. Openers of K(ATP) channels (KCOs), for example, relax smooth muscle and induce hypotension. KCOs are chemically heterogeneous and include as different classes as the benzopyrans, cyanoguanidines, thioformamides, thiadiazines, and pyridyl nitrates. Examples for new chemical entities more recently developed as KCOs include cyclobutenediones, dihydropyridine related structures, and tertiary carbinols.

Chemometric Studies on the Bactericidal Activity of Quinolones via an Extended VolSurf Approach

An extended VolSurf approach, that additionally includes SHAPE descriptors, was applied to a dataset of 55 quinolones. Bactericidal activity was measured at Bayer AG, Germany, for Gram-negative (Escherichia coli and Pseudomonas aeruginosa) and Gram-positive bacteria (Staphylococcus aureus and Enterococcus faecalis). Chemometric analysis was first approached via a classical VolSurf approach. The following descriptors were found most important: bactericidal activity particularly increases with high values of the best volume (BV11(OH2)) and the minimum energy (Emin1(OH2)) of the water probe, high values of the integy moment (ID(DRY)) of the lipophilic probe, and high values of the hydrophilic region (W(O)) of the hydrogen bond acceptor probe. Best volume (BV31(OH2)) of the water probe and best volume (BV12(DRY)) and lipophilic regions (D(DRY)) of the lipophilic probe as well as H-bonding capacity derived with the CO probe (HB(O)) are inversely related to activity. PLS analysis yields a five-component model with an r(2) of 0.83 and a q(2) of 0.43 after variable selection via fractional factorial design (FFD). Chemometric modeling could be improved by including newly derived SHAPE descriptors, which were merged with the VolSurf descriptors and subjected to PLS analysis. The global model of this extended VolSurf approach is optimal with two components and exhibits a significantly improved statistical quality; a marginally reduced r(2) (0.75 versus 0.83) is more than compensated by a highly improved predictivity with a q(2) of 0.63 versus 0.43. To prove model quality, external prediction of seven test set quinolones was performed. The precise prediction of all test set molecules nicely demonstrates the robustness and statistical significance of the obtained chemometric model using the extended VolSurf approach.

Molecular modeling and QSAR studies on K(ATP) channel openers of the benzopyran type

The present paper describes our molecular modeling and quantitative structure-activity relationships (QSARs) studies on K(ATP) channel openers (KCOs) of the benzopyran type. In the first part we performed molecular modeling investigations with seven benzopyrans, varied at the C3- and C4-positions, in order to understand which molecular features at these positions are essentially effecting the biological activity. The impact of C6-substitution on biological activity was studied in the second part via HANSCH analysis. For this purpose physicochemical properties (charge distributions, lowest unoccupied molecular orbital (LUMO) energies, desolvation energies, volumes and dipole moments) were calculated for a set of 50 C6-varied benzopyrans. A QSAR equation was developed showing a relationship between the vasodilator activity and the direction of the dipole vector of the ligands. The conclusion can be drawn that a direct interaction between the C6-substituents and the receptor structure is not of primary importance. However, the substitutents influence the orientation of the whole ligand approaching the binding site. An unfavorably oriented ligand cannot bind to the binding site, thus exhibiting weak activity.

Suitability of molecular descriptors for database mining. A comparative analysis

Database mining methods rely on the molecular descriptors used to characterize a structural database. In the present investigation, five different types of descriptors (log P, UNITY fingerprints, ISIS keys, VolSurf, and GRIND) are applied to characterize various databases (n = 1007, 100, and 229) comprising drugs almost exclusively. The validity of the descriptors is comparatively analyzed via principal component analysis and its hierarchical variant, consensus principal component analysis. Both pharmacodynamic and pharmacokinetic aspects of database mining are treated. For pharmacodynamic aspects, clustering behavior achieved with the different descriptors is tested on the chemically homogeneous beta-blockers, benzodiazepines, and penicillins and on the chemically more diverse class I antiarrhythmics. The following ranking is observed: UNITY fingerprints > ISIS keys and GRIND > VolSurf > log P. Regarding information content, the CPCA superweight plot indicates similarity between fingerprints and ISIS keys as well as between VolSurf and log P, while GRIND differs from all the remaining descriptors. Solubility data and blood/brain barrier penetrating behavior serve as test cases for pharmacokinetic aspects. Comparison of the descriptors applied to these data reveals that VolSurf has the most realistic and consistent behavior, GRIND shows intermediate behavior, while UNITY fingerprints and ISIS keys are not well suited for pharmacokinetic profiling. From this comparative analysis, we conclude that VolSurf descriptors exhibit particular advantages in treating pharmacokinetic aspects; UNITY fingerprints, ISIS keys, and GRIND descriptors are of special value for tackling pharmacodynamic aspects of database mining. The parameter log P is of limited applicability in database mining because of rather poor reliability and lack of completeness of data.

GBR compounds and mepyramines as cocaine abuse therapeutics: chemometric studies on selectivity using grid independent descriptors (GRIND)

Cocaine is one of the most widely abused drugs in the industrial world. Substantial evidence has accumulated that the dopamine transporter (DAT) is a key target for cocaine regarding its reinforcing effects. This work describes the application of chemometric methods to a data set of 54 N(1)-benzhydryl-oxy-alkyl-N(4)-phenyl-alk(en)yl-piperazines (GBR compounds) and chemically related mepyramines as putative candidates in cocaine abuse therapy. The aim of the study is to gain insight into the structural requirements that determine the affinity of the data set molecules to the DAT and the serotonin transporter (SERT) as well as their inhibitory potency on dopamine uptake. The compounds in the dataset are described using the recently developed GRID independent descriptors (GRIND), which allow one to obtain fast three-dimensional quantitative structure-activity relationship models without the need of aligning and superimposing the structures; the results are interpreted in a convenient pharmacophoric-like fashion. In the first part of the work, the selectivity of the database molecules for DAT binding vs dopamine reuptake inhibition is investigated. In the second part, the selectivity of the compounds for DAT binding vs SERT binding is studied. In both cases, significant models are obtained, which define the structural features responsible for the respective selectivity profiles. Moreover, the information has potential interest for the design of new derivatives with improved selectivity.

6-Sulfonylchromenes as highly potent K(ATP)-channel openers

We synthesized K(ATP)-channel openers (KCOs) composed of the 4-pyridonechromene moiety of bimakalim (1) and a variety of sulfonyl-containing 6-substituents 4-29. Dilator potencies were measured in rat aorta and trachea. In both test systems the KCOs exhibit potency ranges of roughly 3 log units. The 6-N-phenyl-N-methylsulfonamido derivative 24 shows the highest potency. In rat aorta the potency spectrum ranges from a pEC(50) value of 8.76 to 5.68; in rat trachea it ranges from 8.01 to 4.99. On average, the dilator activity is about 0.8 log units stronger in the aorta. Aortic relaxation by chromene 13 is markedly retarded, the clinical relevance of which (e.g., preventing tachycardia) remains to be clarified. Binding affinities were determined in myocardial membranes and aortic smooth muscle cells of the rat. The affinity spectrum in myocardial membranes ranges from a pK(D) of 7.83 to 5.18; the highest affinity in aortic smooth muscle cells is measured for compound 28 (pK(D) = 8.55), whereas the lowest affinity is measured for 4 (pK(D) = 4.51). Significant selectivities discriminating between K(ATP)-channels of different organs could not be detected. PLS analysis yielded no significant correlation between vasodilator activity in aorta and chemical descriptors (GRIND). Compounds 13, 24, and 28 represent the most potent KCOs of the 4-pyridonechromene type published so far. Their 6-substituents exhibit a phenyl ring with a congruent conformational orientation in relation to the sulfonylchromene. From SAR data and conformational analysis we postulate that these new 6-substituents extend the binding site for chromene KCOs. Correspondingly, we assume that the receptor area exhibits two separate interaction sites with the capacity to bind 6-substituents: (a) one site interacting with negatively polarized partial structures (e.g., CN, NO(2), SO(2)) and (b) one spatially restricted site enabling favorable pi-interactions.

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.

Synthesis, in vitro skin permeation studies, and PLS-analysis of new naproxen derivatives

PURPOSE

To synthesize new naproxen (01) derivatives with amide or ester structures or with a combination of the two (02-15). To compare their physicochemical properties with naproxen esters (16-22) and their respective skin permeation behavior. To study structure-permeation relationships via partial least squares (PLS)-analysis.

METHODS

Stability, aqueous, and octanol solubility were determined. Lipophilicity and further 53 chemical descriptors were computed. A suitable in-vitro skin permeation model was developed to compare maximal flux (Jmax) of derivatives. Based on these flux data, PLS-analysis was performed to derive structure-permeation relationships.

RESULTS

None of the new derivatives showed an improved flux in comparison to naproxen. This result can be explained by PLS-analysis: skin permeation increases with the solubility both in water and in octanol. For a good permeation, an optimized molecule should exhibit a small volume with a spherical shape. The surface area should be large in relation to volume, as indicated by the rugosity parameter. A clear separation between the hydrophobic and the hydrophilic domain (= high amphiphilic moment) is favorable. Lipophilicity is inversely correlated with skin permeation.

CONCLUSIONS

PLS-analysis is a valuable tool to derive significant, internally predictive quantitative models for structure-permeation relationships of naproxen derivatives in the above described skin permeation assay.

Relaxant activity in rat aorta and trachea, conversion to a muscarinic receptor antagonist and structure-activity relationships of new K(ATP) activating 6-varied benzopyrans

To characterize ATP-sensitive channels (K(ATP) channels) benzopyrans with different substituents at position 6 were synthesized as new K(ATP)-activators. Their relaxant potencies were determined in rat aorta and trachea. In aorta, pEC50-values (-log, M) ranged from 7.37 to 5.43; in trachea, pEC50-values were 0.3 to 0.8 log units lower. Functional data were compared with binding data obtained in calf tracheal cells using the cyanoguanidine [3H]P1075 (N-cyano-N'-1,1-dimethyl[2,3(n)-3H]propyl)-N11-(3-pyridinyl)guanidine) as radioligand. A high correlation (r = 0.96) between pEC50- and pKD-values indicated that tracheal relaxation produced by benzopyrans is mediated via K(ATP) channels without signal amplification. The permanently charged trimethylammonium derivative designed as a probe for the membrane site of action completely lost its affinity for K(ATP) channels, but converted to an antagonist for muscarinic acetylcholine receptors (pK(B) = 6.12+/-0.10), as confirmed in radioligand binding studies (pK(D) = 5.77+/-0.04). Structure-activity analyses revealed that the 6-substituent influences biological activity by a direct receptor interaction of its own and not indirectly by withdrawing electrons from the benzopyran nucleus. The variance of the biological activity is primarily determined by electrostatic properties, but desolvation energies additionally contribute.

6-Substituted benzopyrans as potassium channel activators: synthesis, vasodilator properties, and multivariate analysis

During the last 10 years compounds have been discovered which can activate or block KATP channels. In particular, K channel activators (KCA) have been found to be smooth muscle relaxants with their main utility in hypertension and bronchodilation. In this paper we describe the synthesis of new KCA of the benzopyran type with a fixed 4-substituent and a systematic variation in the 6-position. The relaxant potency in rat aorta and trachea was used for biological characterization of the benzopyrans. In both biological test systems, they exhibit potency ranges of more than 3 log units. Structure-activity relationships are investigated by principal component analysis (PCA) and partial least-squares (PLS) analysis. Most striking outliers in an initial PLS analysis of the entire database were the unsubstituted 6-H compound 13 as well as 34 and 35. For the remaining set of 31 compounds, a 3-component PLS model explains the variance in biological activity to 81% in the aortic and to 82% in the tracheal test system. 6-Substituents influence affinity by a direct (presumably dipolar) interaction with the receptor site. According to the 2D-plot of the partial PLS weights, a strong electronegativity as well as high values for the integy moment and for the heat of formation in water dominate the first component; low values for substituent size (as defined by globularity or surface) are in addition favorable for high potency. High lipophilicity and low minimum energies of interaction dominate the second component. Chemical descriptors for the biological potency of the test set in rat aorta and rat trachea are very similar according to the almost identical projection of the Y-variables onto the X-component space.

Multivariate analysis of experimental and computational descriptors of molecular lipophilicity

Two experimental (log P, R(Mw)) and 17 calculation descriptors for molecular lipophilicity (fragmental, atom-based or based on molecular properties) were investigated by multvariate analysis for a database of 159 compounds including both simple structures as well as more complex drug molecules. Principal component analysis (PCA) of the entire database exhibits a clustering of chemical groups; preciseness of clustering corresponds to chemical similarity. Thus, diversity searching in databases might effectively be performed by PCA on the basis of calculated log P. The comparative validity check of experimental and computational procedures by regression analysis and PCA was performed with a chemically balanced, reduced data set (n = 55) representing 11 chemical groups with 5 members each. Regression of experimental descriptors (log Poct versus RMW) proves that chromatographic data, obtained under well-defined experimental conditions, can be used as valid substitutes for log P. Regression of calculated versus experimental lipophilicity data shows a superiority of fragmental over atom-based methods and approaches based on molecular properties, as indicated by correlation coefficients, slopes and intercepts. In addition, PCA revealed that fragmental methods (Rekker-type, KOWWIN, KLOGP) sense the compound ranking in log P data to almost the same extent as experimental approaches. For atom-based procedures and CLOGP, both the comparability of absolute values and the sensing of the compound ranking in the database are slightly less. This trend is more pronounced for the methods based on molecular properties, with the exception of BLOGP.

In vitro and in vivo characterization of a calcium modulator of the diphenylalkylamine type with selective coronary dilatory properties

VUF 8929 (N-¿2-[bis(p-fluorophenyl)methoxy]ethyl¿-(2-phenyl)ethylamine maleate, CAS 140890-71-7) is a diphenylalkylamine derivative structurally related to prenylamine. The calcium antagonistic properties of this compound have been studied in in vitro and in vivo systems. VUF 8929 has affinity for the voltage-operated calcium channel. Its pKD for the displacement of [3H]nitrendipine bound to cerebral rat cortex is 6.27 (+/- 0.17). The compound influences the [3H]nitrendipine binding through an allosteric interaction with a site adjacent to the dihydropyridine binding site. Competitive experiments with the additional presence of the phenylalkylamine gallopamil showed that this allosteric site is a property common to diphenyl- and phenylalkylamines. It was further observed that VUF 8929 has a high affinity for calmodulin as it shows high potency in inhibiting the calmodulin mediated activation of PDE. The inhibition of K+ (IC50 0.5 mumol/l)- and noradrenaline (IC50 1.3 mumol/l)-induced contractions of rabbit aorta rings was in the same concentration range as found for the calmodulin inhibitory activity. In vitro platelet aggregation was also inhibited in the same concentration range when washed platelets were used. Thus calmodulin antagonism may contribute to the observed effects on aorta ring contractions and platelets aggregation. Platelet aggregation, however, in media in which albumin was added or in platelet rich plasma was not affected. It is assumed that due to the high lipophilicity, common to many diphenylalkylamines, VUF 8929 has a strong binding to plasma proteins. This may also explain why orally administered VUF 8929 did not affect the alpha 2-induced pressor response in pithed rats and the ex vivo collagen induced aggregation response. The haemodynamic profile in anaesthetized dogs showed that intravenous injected VUF 8929 reduced the workload of the heart while coronary blood flow increases at a dose of 0.3 mg/kg. Reversible occlusion of the coronary artery, which leads to S-T segment elevation and local venous acidosis, were reduced by VUF 8929 indicating that the compound has anti-ischaemic properties.

IN CONCLUSION

VUF 8929 is a calcium antagonist which has anti-ischaemic properties, reduces the workload of the heart and increases coronary flow. Due to these properties VUF 8929 is a potential cardioprotective agent.

Comparative evaluation of the predictive power of calculation procedures for molecular lipophilicity

The predictive power of four calculation procedures for molecular lipophilicity is checked by comparing with experimental data (log P and chromatographical RMw) taken from the literature. Two sets of test compounds are used: the first comprises simple organic molecules and the second consists of more complicated drug molecules. Our comparative evaluation leads us to conclude that the predictive power is significantly better for not too complicated organic molecules than for drugs with complicated structural pattern. The four investigated calculation procedures should be arranged in two groups with significantly differing predictive power: (a) Rekker and Hansch/Leo and (b) Ghose/Crippen and Suzuki/Kudo. This conclusion is based on a statistical control using log P and RMw as the independent parameters. Correlations have in common: (1) slopes in correlations with calculated data based on fragmental methods are not significantly different from 1; calculations with data from atom-based procedures show up in most cases with slopes below 1. (2) The accompanying overall statistics underline the superiority of the fragmental methods. We think that all four tested calculation procedures have their own restrictions; for future development we would advise a thorough reconsideration of structural effects not fully (or even not at all) incorporated in the data sets. Special attention will have to be paid to the conformational aspects of lipophilic behavior.

Structural dependence of the allosteric interaction of semi-rigid verapamil analogues with dihydropyridine-binding in kitten heart

Structural determinants of the allosteric interaction of semi-rigid verapamil analogues with dihydropyridine binding were investigated in kitten heart using [3H](+)-isradipine as radioligand. Chemical variations were performed in the alkyl chain of verapamil and include introduction of unsaturation (double or triple bonds) or the insertion of cyclohexyl moieties. Introduction of unsaturation generally reduces the allosteric interaction in the case of 'double bond'-and abolishes it in the case of 'triple bond'-derivatives. Also the introduction of cyclohexyl moieties diminishes the potency of allosteric interaction: derivatives with the phenylethylamino side chain in an equatorial position exhibit the allosteric interaction, while it is lacking in derivatives with the basic side chain in axial position. Thus, the reduced conformational flexibility of the new verapamil congeners reduces or abolishes their ability to allosterically interfere with dihydropyridine binding. A molecular interpretation was approached by molecular modelling studies. The strategy was to find low energy conformations common to the active congeners, but not shared by the inactive ones. Structural features discriminating allosterically active and inactive congeners comprise: 1) the position of the nitrogen, 2) the volume occupied by the N-methyl groups, 3) the direction of the N-H bond and 4) the position of the phenyl ring in the basic side chain.

Semi-rigid analogues of the calcium antagonist verapamil: a molecular modelling study

In this work the rigid-analogue approach has been used to obtain information on the active conformation(s) of the calcium antagonist verapamil. A series of semi-rigid analogues of verapamil were synthesized and their biological activities evaluated on guinea-pig heart and aorta. These molecules were analysed by means of molecular modelling techniques. On the basis of the pharmacological profile and conformational analysis of these compounds, two different models for negative inotropic and negative chronotropic activity are proposed. The two actions seem to be due to conformations of the molecules which differ in the orientation of their phenylethylamino groups.