Open PHACTS computational protocols for in silico target validation of cellular phenotypic screens: knowing the knowns.

Phenotypic screening is in a renaissance phase and is expected by many academic and industry leaders to accelerate the discovery of new drugs for new biology. Given that phenotypic screening is per definition target agnostic, the emphasis of in silico and in vitro follow-up work is on the exploration of possible molecular mechanisms and efficacy targets underlying the biological processes interrogated by the phenotypic screening experiments. Herein, we present six exemplar computational protocols for the interpretation of cellular phenotypic screens based on the integration of compound, target, pathway, and disease data established by the IMI Open PHACTS project. The protocols annotate phenotypic hit lists and allow follow-up experiments and mechanistic conclusions. The annotations included are from ChEMBL, ChEBI, GO, WikiPathways and DisGeNET. Also provided are protocols which select from the IUPHAR/BPS Guide to PHARMACOLOGY interaction file selective compounds to probe potential targets and a correlation robot which systematically aims to identify an overlap of active compounds in both the phenotypic as well as any kinase assay. The protocols are applied to a phenotypic pre-lamin A/C splicing assay selected from the ChEMBL database to illustrate the process. The computational protocols make use of the Open PHACTS API and data and are built within the Pipeline Pilot and KNIME workflow tools.

Valerenic acid derivatives as novel subunit-selective GABAA receptor ligands - in vitro and in vivo characterization.

BACKGROUND AND PURPOSE: Subunit-specific modulators of gamma-aminobutyric acid (GABA) type A (GABA(A)) receptors can help to assess the physiological function of receptors with different subunit composition and also provide the basis for the development of new drugs. Valerenic acid (VA) was recently identified as a beta(2/3) subunit-specific modulator of GABA(A) receptors with anxiolytic potential. The aim of the present study was to generate VA derivatives as novel GABA(A) receptor modulators and to gain insight into the structure-activity relation of this molecule. EXPERIMENTAL APPROACH: The carboxyl group of VA was substituted by an uncharged amide or amides with different chain length. Modulation of GABA(A) receptors composed of different subunit compositions by the VA derivatives was studied in Xenopus oocytes by means of the two-microelectrode voltage-clamp technique. Half-maximal stimulation of GABA-induced chloride currents (I(GABA)) through GABA(A) receptors (EC(50)) and efficacies (maximal stimulation of I(GABA)) were estimated. Anxiolytic activity of the VA derivatives was studied in mice, applying the elevated plus maze test. KEY RESULTS: Valerenic acid amide (VA-A) displayed the highest efficacy (more than twofold greater I(GABA) enhancement than VA) and highest potency (EC(50)= 13.7 +/- 2.3 microM) on alpha(1)beta(3) receptors. Higher efficacy and potency of VA-A were also observed on alpha(1)beta(2)gamma(2s) and alpha(3)beta(3)gamma(2s) receptors. Anxiolytic effects were most pronounced for VA-A. CONCLUSIONS AND IMPLICATIONS: Valerenic acid derivatives with higher efficacy and affinity can be generated. Greater in vitro action of the amide derivative correlated with a more pronounced anxiolytic effect in vivo. The data give further confidence in targeting beta(3) subunit containing GABA(A) receptors for development of anxiolytics.

Pharmacoinformatic approaches to design natural product type ligands of ABC-transporters.

ABC-transporter have been recognized as being responsible for multiple drug resistance in tumor therapy, for decreased brain uptake and low oral bioavailability of drug candidates, and for drug-drug interactions and drug induced cholestasis. P-glycoprotein (ABCB1), the paradigm protein in the field, is mainly effluxing natural product toxins and shows very broad substrate specificity. Within this article we will highlight SAR and QSAR approaches for designing natural product type inhibitors of ABCB1 and related proteins as well as in silico strategies to predict ABCB1 substrates and inhibitors in order to design out undesirable drug/protein interaction.

An updated unified pharmacophore model of the benzodiazepine binding site on gamma-aminobutyric acid(a) receptors: correlation with comparative models.

A successful unified pharmacophore/receptor model which has guided the synthesis of subtype selective compounds is reviewed in light of recent developments both in ligand synthesis and structural studies of the binding site itself. The evaluation of experimental data in combination with a comparative model of the alpha1beta2gamma2 GABA(A) receptor leads to an orientation of the pharmacophore model within the Bz BS. Results not only are important for the rational design of selective ligands, but also for the identification and evaluation of possible roles which specific residues may have within the benzodiazepine binding pocket.

Future directions for drug transporter modelling.

Since the late 1980s computational methods such as quantitative structure-activity relationship (QSAR) and pharmacophore approaches have become more widely applied to assess interactions between drug-like molecules and transporters, starting with P-glycoprotein (P-gp). Identifying molecules that interact with P-gp and other transporters is important for drug discovery, but it is normally ascertained using laborious in vitro and in vivo studies. Computational QSAR and pharmacophore models can be used to screen commercial databases of molecules rapidly and suggest those likely to bind as substrates or inhibitors for transporters. These predictions can then be readily verified in vitro, thus representing a more efficient route to screening. Recently, the application of this approach has seen the identification of new substrates and inhibitors for several transporters. The successful application of computational models and pharmacophore models in particular to predict transporter binding accurately represents a way to anticipate drug-drug interactions of novel molecules from molecular structure. These models may also see incorporation in future pharmacokinetic-pharmacodynamic models to improve predictions of in vivo drug effects in patients. The implications of early assessment of transporter activity, current advances in QSAR, and other computational methods for future development of these and systems-based approaches will be discussed.

Interaction field based and hologram based QSAR analysis of propafenone-type modulators of multidrug resistance.

Overexpression of membrane bound, ATP-dependent transport proteins is one of the predominant mechanisms leading to multiple drug resistance in tumor therapy as well as in the treatment of bacterial and fungal infections. In tumor therapy, P-glycoprotein (P-gp, ABCB1) is responsible for transport of a wide variety of natural product toxins out of tumor cells leading to decreased accumulation of cytotoxic drugs within the cells. Inhibition of P-gp thus gives rise to a resensitization of multidrug resistant tumor cells and represents a versatile approach for modulation of multidrug resistance. Within this paper, a set of propafenone-type inhibitors of P-gp were analyzed using both interaction field based methods such as CoMFA and CoMSIA and Hologram QSAR. With both methods, highly predictive models with q2-values>0.65 were obtained. Models using logP as additional descriptor generally yielded higher predictive power. On basis of unfavorable steric and favorable electrostatic and hydrophobic interaction fields, these models were able to explain all outlayers identified in previous Hansch-analyses. For HQSAR analysis, models with q2-values up to 0.72 were obtained. Positive influences were found for electron donating groups on the aromatic systems. Highly negative influences were found for diphenylalkylamine substituents, which is a further hint for steric hindrance. The models with highest predictive power were used for screening of a small virtual library. Synthesis and pharmacological testing of a sub set of this library showed that the external predictivity of the HQSAR models generally is lower than the internal one.

Isospin violation in epsilon'.

On the basis of a next-to-leading-order calculation in chiral perturbation theory, the first complete analysis of isospin breaking for direct CP violation in K0-->2 pi decays is performed. We find a destructive interference between three different sources of isospin violation in the CP violation parameter epsilon'. Within the uncertainties of large-N(c) estimates for the low-energy constants, the isospin violating correction for epsilon' is below 15%.

Prediction of the aroma quality and the threshold values of some pyrazines using artificial neural networks.

An artificial neural network is used to predict both the classification of aroma compounds and their flavor impression threshold values for a series of pyrazines. The classification set consists of 98 compounds (32 green, 43 bell-pepper, and 23 nutty smelling pyrazines), and the regression sets consist of 24 green and 37 bell-pepper odorous pyrazines. The best classification of the three aroma impressions (93.7%) is obtained by using a multilayer perceptron network architecture. To predict the threshold values of bell-pepper fragrance, a standard Pearson R correlation coefficient of 0.936 for the training set, 0.912 for the verification set, and 0.926 for the test set is received with two hidden layers consisting of two and one neurons. The network for the threshold prediction of the class of green-smelling pyrazines with one hidden layer containing three neurons turns out to be the best with a standard Pearson R correlation coefficient of 0.859 for the training, 0.918 for the verification, and 0.948 for the test set. These good correlations show that artificial neural networks are versatile tools for the classification of aroma compounds.

Heat storage in horses during submaximal exercise before and after humid heat acclimation.

The effect of humid heat acclimation on thermoregulatory responses to humid and dry exercise-heat stress was studied in six exercise-trained Thoroughbred horses. Horses were heat acclimated by performing moderate-intensity exercise for 21 days in heat and humidity (HH) [34.2-35.7 degrees C; 84-86% relative humidity (RH); wet bulb globe temperature (WBGT) index approximately 32 degrees C]. Horses completed exercise tests at 50% of peak O(2) uptake until a pulmonary arterial temperature (T(pa)) of 41.5 degrees C was attained in cool dry (CD) (20-21.5 degrees C; 45-50% RH; WBGT approximately 16 degrees C), hot dry (HD 0) [32-34 degrees C room temperature (RT); 45-55% RH; WBGT approximately 25 degrees C], and HH conditions (HH 0), and during the second hour of HH on days 3, 7, 14, and 21, and in HD on the 18th day (HD 18) of heat acclimation. The ratios of required evaporative capacity to maximal evaporative capacity of the environment (E(req)/E(max)) for CD, HD, and HH were approximately 1.2, 1.6, and 2.5, respectively. Preexercise T(pa) and rectal temperature were approximately 0.5 degrees C lower (P < 0. 05) on days 7, 14, and 21 compared with day 0. With exercise in HH, there was no effect of heat acclimation on the rate of rise in T(pa) (and therefore exercise duration) nor the rate of heat storage. In contrast, exercise duration was longer, rate of rise in T(pa) was significantly slower, and rate of heat storage was decreased on HD 18 compared with HD 0. It was concluded that, during uncompensable heat stress in horses, heat acclimation provided modest heat strain advantages when E(req)/E(max) was approximately 1.6, but at higher E(req)/E(max) no advantages were observed.

Total body water and ECFV measured using bioelectrical impedance analysis and indicator dilution in horses.

The purposes of this study were 1) to determine the compartmentation of body water in horses by using indicator dilution techniques and 2) to simultaneously measure bioelectrical impedance to current flow at impulse current frequencies of 5 and 200 kHz to formulate predictive equations that could be used to estimate total body water (TBW), extracellular fluid volume (ECFV), and intracellular fluid volume (ICFV). Eight horses and ponies weighing from 214 to 636 kg had catheters placed into the left and right jugular veins. Deuterium oxide, sodium thiocyanate, and Evans blue were infused for the measurement of TBW, ECFV, and plasma volume (PV), respectively. Bioelectrical impedance was measured by using a tetrapolar electrode configuration, with electrode pairs secured above the knee and hock. Measured TBW, ECFV, and PV were 0.677 +/- 0.022, 0.253 +/- 0.006, and 0.040 +/- 0.002 l/kg body mass, respectively. Strong linear correlations were determined among measured variables that allowed for the prediction of TBW, ECFV, ICFV, and PV from measures of horse length or height and impedance. It is concluded that bioelectrical impedance analysis (BIA) can be used to improve the predictive accuracy of noninvasive estimates of ECFV and PV in euhydrated horses at rest.

Heat acclimation improves regulation of plasma volume and plasma Na(+) content during exercise in horses.

This study determined the plasma volume (PV) and ion responses to heat acclimation and exercise in six trained Thoroughbred horses during 21 days of exposure to heat and humidity (33 degrees C, 83% relative humidity) for 4 h/day. During the 2nd h on days 0, 3, 7, 14, and 21, horses performed a standardized treadmill test, running at 50% of peak O(2) uptake until pulmonary artery temperature reached 41.5 degrees C. Heat acclimation resulted in an increase in PV from 21.3 +/- 1.1 liters on day 0 to 24.3 +/- 1.0 liters on day 14, returning to 22.6 +/- 0.9 liters on day 21. The corresponding total plasma protein contents were 1,273 +/- 53, 1,455 +/- 81, and 1,377 +/- 57 g, respectively, and increases in total plasma Na(+) plus Cl(-) content were 5,145 +/- 126, 5,749 +/- 146, and 5,394 +/- 114 mmol, respectively. Thus changes in PV were accompanied by direct changes in plasma protein and osmolyte contents. With exercise on day 0, PV decreased by 7.1 +/- 0.7% at 5 min of exercise and remained decreased (-6.7 +/- 1.3%) at 5 min of recovery. By day 21, PV decreased significantly less than on day 0 (by 5.2 +/- 0.9% at 5 min of exercise), was decreased by only 2.0 +/- 1.6% at 5 min of recovery, and was fully restored at 15 min of recovery. Plasma Na(+) concentration increased 3 meq/l during the first 5 min of exercise and was normalized by 5 min of recovery on day 0 and by end exercise on day 21. It is concluded that improved ability to regulate PV during exercise in response to heat acclimatization is associated with an increased PV and an improved conservation of Na(+).

Equine sweating responses to submaximal exercise during 21 days of heat acclimation.

This study examined sweating responses in six exercise-trained horses during 21 consecutive days (4 h/day) of exposure to, and daily exercise in, hot humid conditions (32-34 degrees C, 80-85% relative humidity). On days 0, 3, 7, 14, and 21, horses completed a standardized exercise test on a treadmill (6 degrees incline) at a speed eliciting 50% of maximal O(2) uptake until a pulmonary artery temperature of 41.5 degrees C was attained. Sweat was collected at rest, every 5 min during exercise, and during 1 h of standing recovery for measurement of ion composition (Na(+), K(+), and Cl(-)) and sweating rate (SR). There was no change in the mean time to reach a pulmonary artery temperature of 41.5 degrees C (range 19.09 +/- 1.41 min on day 0 to 20.92 +/- 1.98 min on day 3). Peak SR during exercise (ml. m(-2). min(-1)) increased on day 7 (57.5 +/- 5. 0) but was not different on day 21 (48.0 +/- 4.7) compared with day 0 (52.0 +/- 3.4). Heat acclimation resulted in a 17% decline in SR during recovery and decreases in body mass and sweat fluid losses during the standardized exercise test of 25 and 22%, respectively, by day 21. By day 21, there was also a 10% decrease in mean sweat Na(+) concentration for a given SR during exercise and recovery; this contributed to an approximately 26% decrease in calculated total sweat ion losses (3,112 +/- 114 mmol on day 0 vs. 2,295 +/- 107 mmol on day 21). By day 21, there was a decrease in sweating threshold ( approximately 1 degrees C) but no change in sweat sensitivity. It is concluded that horses responded to 21 days of acclimation to, and exercise in, hot humid conditions with a reduction in sweat ion losses attributed to decreases in sweat Na(+) concentration and SR during recovery.

Structure-activity relationship studies of propafenone analogs based on P-glycoprotein ATPase activity measurements.

Propafenone analogs (PAs) were previously identified as potent inhibitors of P-glycoprotein (Pgp)-mediated toxin efflux. For this as well as other classes of Pgp inhibitors, lipophilicity as well as hydrogen bond acceptor strength are important determinants of biological activity. The question as to whether a direct interaction between PA-type modulators and Pgp takes place was addressed by means of Pgp ATPase measurements and transport studies. Propafenone-type modulators stimulated ATPase activity up to 2-fold over basal activity in a concentration-dependent biphasic manner. Within a series of structural homologs, Ka values of ATPase stimulation strongly correlated with lipophilicity. Analogs containing a quaternary nitrogen stimulated Pgp ATPase activity with lesser efficacy, while Ka values were somewhat higher when compared to corresponding tertiary analogs. Transport studies performed in inside-out plasma membrane (I/O) vesicles demonstrated that analogs containing a tertiary nitrogen rapidly associated with the biomembrane. Quaternary analogs, which are restricted by a permanent positive charge in transiting the plasma membrane by diffusion, accumulated in Pgp containing I/O vesicles in an ATP-dependent and cyclosporin A-inhibitable manner, which identified them as Pgp substrates. Identical structure-activity relationships were found in either Pgp ATPase stimulation experiments in I/O vesicles or in toxin efflux inhibition studies using intact cells. Therefore, differences in membrane transit are not responsible for the observed structure-activity relationships.

The importance of a nitrogen atom in modulators of multidrug resistance.

The presence of a nitrogen atom, charged at physiological pH, has frequently been considered to be a hallmark of P-glycoprotein (PGP) inhibitors, although certain steroids, such as progesterone, lack a nitrogen atom and still are active modulators of PGP. The present study was aimed at investigating the role the nitrogen atom plays in the activity of PGP inhibitors. Propafenone-related amines, anilines, and amides that cover a broad range of pK(a) values, as well as an ester, were synthesized and tested for multidrug resistance-reverting activity. The sum of the hydrogen bond acceptor strengths was calculated and correlated with EC(50) values for PGP inhibition. For the complete set of 12 compounds, an excellent correlation between these two parameters was found; this included the ester GP570, which lacks a nitrogen atom but contains the strong hydrogen bond-accepting ester unit. The interaction of the nitrogen atom with PGP therefore is nonional and is determined by the sum of the hydrogen acceptor strengths of the region. The high predictivity of the obtained model is demonstrated in a leave-one-out cross-validation procedure.

Artificial neural networks as versatile tools for prediction of MDR-modulatory activity.

Following our ongoing studies on structure-activity relationship studies of propafenone-type modulators of multidrug resistance, we performed both a Free-Wilson analysis and a combined Hansch/Free-Wilson analysis on a set of 48 compounds using artificial neural networks (ANN). In comparison to classical multiple linear regression (MLR) analysis, the ANN showed equal or even slightly better predictive power in leave one out cross validation procedures and was remarkably superior when performing a leave 8 out cross validation. Additionally, it was possible to train a network using only 14 compounds and to properly predict the MDR-modulating activity of the remaining 34 compounds. In this case, the MLR analysis completely failed due to insufficient number of cases. Attempts to extract informations on which input descriptors are important using a genetic input selection algorithm failed. Best results were obtained using those descriptors which showed highest statistical significance in MLR analyses.

Synthesis and in vitro multidrug resistance modulating activity of a series of dihydrobenzopyrans and tetrahydroquinolines.

A series of dihydrobenzopyrans and tetrahydroquinolines was synthesized and pharmacologically tested for their ability to inhibit P-glycoprotein mediated daunomycin efflux in multidrug resistant CCRF-CEM vcr1000 cells. Several compounds exhibit activities in the range of the reference compounds verapamil and propafenone. Preliminary structure-activity relationship studies propose the importance of high molar refractivity values of the compounds and the presence of an additional basic nitrogen atom.

Substituted 4-acylpyrazoles and 4-acylpyrazolones: synthesis and multidrug resistance-modulating activity.

A series of 4-acyl-3-pyrazolone derivatives with a 3-substituted 2-hydroxy-3-aminopropyl chain attached to pyrazole N-1 (7-20) as well as isomeric 4-acyl-5-(3-substituted 3-amino-2-hydroxypropoxy)pyrazole derivatives (5, 6) were synthesized, and their multidrug resistance (MDR)-modulating activity was measured using the daunomycin efflux assay. Reaction of N1-substituted 4-acyl-3-pyrazolones (tautomer to 4-acyl-5-hydroxypyrazoles) with excessive epichlorohydrin and successive treatment with an appropriate amine resulted in N-alkylation and thus afforded the target pyrazolone derivatives 7-20. In contrast, O-alkylation occurred upon reaction with 1 equiv of epichlorohydrin and subsequent treatment with amine leading to the corresponding 4-acyl-5-pyrazolyl ethers 5 and 6. QSAR studies showed a good correlation of MDR-modulating activity with lipophilicity of the compounds. Inclusion of hydrogen bond acceptor strength and steric parameters as descriptors led to a QSAR equation with remarkably increased predictive power (r2cv = 0.92). Additionally, ortho substitution of the propanolamine side chain and the acyl moiety is favorable. Detailed NMR spectroscopic investigations were carried out with the title compounds.