Benchmark Compounds Research Articles

Cross-conjugation and quantum interference: a general correlation?

We discuss the relationship between the π-conjugation pattern, molecular length, and charge transport properties of molecular wires, both from an experimental and a theoretical viewpoint. Specifically, we focus on the role of quantum interference in the conductance properties of cross-conjugated molecules. For this, we compare experiments on two series of dithiolated wires. The first set we synthesized consists of three dithiolated oligo(phenylene ethynylene) (OPE) benchmark compounds with increasing length. The second series synthesized comprises three molecules with different π-conjugation patterns, but identical lengths, i.e. an anthracene (linear conjugation), an anthraquinone (cross-conjugation), and a dihydroanthracene (broken conjugation) derivative. To benchmark reliable trends, conductance experiments on these series have been performed by various techniques. Here, we compare data obtained by conductive-probe atomic force microscopy (CP-AFM) for self-assembled monolayers (SAMs) with single-molecule break junction and multi-molecule EGaIn data from other groups. For the benchmark OPE-series, we consistently find an exponential decay of the conductance with molecular length characterized by β = 0.37 ± 0.03 Å(-1) (CP-AFM). Remarkably, for the second series, we do not only find that the linearly conjugated anthracene-containing wire is the most conductive, but also that the cross-conjugated anthraquinone-containing wire is less conductive than the broken-conjugated derivative. We attribute the low conductance values for the cross-conjugated species to quantum interference effects. Moreover, by theoretical modeling, we show that destructive quantum interference is a robust feature for cross-conjugated structures and that the energy at which complete destructive interference occurs can be tuned by the choice of side group. The latter provides an outlook for future devices in this fascinating field connecting chemistry and physics.

Multiparametric One-Color Assays for Functional Assessment of Cardiomyocytes

Heart-related health problems remain a leading cause of mortality in developed countries. To efficiently fight these problems, cardiology needs an information-rich screening for new drug candidates. Recent achievements in stem cell research provide a long-awaited solution by producing human stem-cell derived cardiomyocytes and, thus, providing various disease-in-a-dish models of cardiac disorders.Two biologically distinct parameters are required to efficiently characterize the cardiomyocytes function: changes in cell membrane potential and distribution of intracellular calcium ions. Unfortunately, due to experimental limitations and lack of appropriate fluorescent indicators, the traditional approach to perform such an assessment is to record one signal at a time.Here we present novel approach to perform multi-parametric assessment of cardiomyocytes while using two functionally different fluorescent indicators excited by the same wavelength of light. Specifically, using the IC200 HCS screening system (Vala Sciences), we performed a functional assessment of stem cell-derived cardiomyocytes by parallel optical recording of two physiologically distinct signals in real time: dynamic changes in cell membrane voltage as well as redistribution of calcium ions in cells. To do that, in addition to a calcium indicator Fluo4, we used a novel highly efficient voltage-sensitive fluorescent dye (VF 2.1) to detect voltage changes in cardiomyocytes.To perform data analysis, we have developed a dedicated software program that by creating spatially distinct subsets of masks is separating calcium and voltage signals. Using our multiparametric assay, we have performed several screening campaigns using benchmark compounds such as modulators of ion channels involved in generation of cardiac action potential (hERG channels, sodium and calcium voltage-gated ion channels), as well as drugs that affect the intracellular calcium handling. In summary, we have developed a multi-parametric approach for comprehensive screening of a human stem cell-derived cardiomyocytes for drug discovery and cardiotoxicity purposes.

Effective visualization of integrated knowledge and data to enable informed decisions in drug development and translational medicine

Integrative understanding of preclinical and clinical data is imperative to enable informed decisions and reduce the attrition rate during drug development. The volume and variety of data generated during drug development have increased tremendously. A new information model and visualization tool was developed to effectively utilize all available data and current knowledge. The Knowledge Plot integrates preclinical, clinical, efficacy and safety data by adding two concepts: knowledge from the different disciplines and protein binding.Internal and public available data were gathered and processed to allow flexible and interactive visualizations. The exposure was expressed as the unbound concentration of the compound and the treatment effect was normalized and scaled by including expert opinion on what a biologically meaningful treatment effect would be.The Knowledge Plot has been applied both retrospectively and prospectively in project teams in a number of different therapeutic areas, resulting in closer collaboration between multiple disciplines discussing both preclinical and clinical data. The Plot allows head to head comparisons of compounds and was used to support Candidate Drug selections and differentiation from comparators and competitors, back translation of clinical data, understanding the predictability of preclinical models and assays, reviewing drift in primary endpoints over the years, and evaluate or benchmark compounds in due diligence comparing multiple attributes.The Knowledge Plot concept allows flexible integration and visualization of relevant data for interpretation in order to enable scientific and informed decision-making in various stages of drug development. The concept can be used for communication, decision-making, knowledge management, and as a forward and back translational tool, that will result in an improved understanding of the competitive edge for a particular project or disease area portfolio. In addition, it also builds up a knowledge and translational continuum, which in turn will reduce the attrition rate and costs of clinical development by identifying poor candidates early.

In vitro and in vivo characterization of a novel hedgehog signaling antagonist in human glioblastoma cell lines

Glioblastoma multiforme (GBM) is composed of heterogeneous and genetically different cells, which are highly invasive and motile. The standard chemotherapeutic agent, temozolomide, affects GBM cell proliferation but is generally unable to prevent tumor recurrence. Hedgehog pathway activation has been reported to be relevant in GBM and different pharmacological pathway modulators have been identified. We report that by growing a commercially available recurrent GBM cell line (DBTRG-05MG) without serum and in the presence of defined growth factors; we obtained a less differentiated cell population, growing in suspension as neurospheres, in which the Hedgehog pathway is activated. Furthermore, the expression profile of Hedgehog pathway components found in DBTRG-05MG neurospheres is similar to primary stem-like cells derived from recurrent GBM patients. We report the effect of our novel specific Smoothened receptor antagonist (SEN450) on neurosphere growing cells and compared its effect to that of well known benchmark compounds. Finally, we showed that SEN450 is both antiproliferative on its own and further reduces tumor volume after temozolomide pretreatment in a mouse xenograft model using DBTRG-05MG neurosphere cells. Altogether our data indicate that the Hedgehog pathway is not irreversibly switched off in adherent cells but can be reactivated when exposed to well-defined culture conditions, thus restoring the condition observed in primary tumor-derived material, and that pharmacological modulation of this pathway can have profound influences on tumor proliferation. Therefore, pharmacological inhibition of the Hedgehog pathway is a potentially useful therapeutic approach in GBM.

Interference with Bile Salt Export Pump Function Is a Susceptibility Factor for Human Liver Injury in Drug Development

The bile salt export pump (BSEP) is an efflux transporter, driving the elimination of endobiotic and xenobiotic substrates from hepatocytes into the bile. More specifically, it is responsible for the elimination of monovalent, conjugated bile salts, with little or no assistance from other apical transporters. Disruption of BSEP activity through genetic disorders is known to manifest in clinical liver injury such as progressive familial intrahepatic cholestasis type 2. Drug-induced disruption of BSEP is hypothesized to play a role in the development of liver injury for several marketed or withdrawn therapeutics. Unfortunately, preclinical animal models have been poor predictors of the liver injury associated with BSEP interference observed for humans, possibly because of interspecies differences in bile acid composition, differences in hepatobiliary transporter modulation or constitutive expression, as well as other mechanisms. Thus, a BSEP-mediated liver liability may go undetected until the later stages of drug development, such as during clinical trials or even postlicensing. In the absence of a relevant preclinical test system for BSEP-mediated liver injury, the toxicological relevance of available in vitro models to human health rely on the use of benchmark compounds with known clinical outcomes, such as marketed or withdrawn drugs. In this study, membrane vesicles harvested from BSEP-transfected insect cells were used to assess the activity of more than 200 benchmark compounds to thoroughly investigate the relationship between interference with BSEP function and liver injury. The data suggest a relatively strong association between the pharmacological interference with BSEP function and human hepatotoxicity. Although the most accurate translation of risk would incorporate pharmacological potency, pharmacokinetics, clearance mechanisms, tissue distribution, physicochemical properties, indication, and other drug attributes, the additional understanding of a compound's potency for BSEP interference should help to limit or avoid BSEP-related liver liabilities in humans that are not often detected by standard preclinical animal models.

Boryltrihydroborate: Synthesis, Structure, and Reactivity as a Reductant in Ionic, Organometallic, and Radical Reactions

Reaction of lithium 1,3-bis(2,6-diisopropylphenyl)-2,3-dihydro-1H-1,3,2-diazaborol-2-ide with borane.THF provides the first boryl-substituted borohydride: lithium [1,3-bis(2,6-diisopropylphenyl)-2,3-dihydro-1H-1,3,2-diazaborol-2-yl]trihydroborate. The compound is fully characterized by (11)B, (1)H, and (7)Li NMR spectra and other means, and these data are compared to neutral and anionic benchmark compounds. The compound crystallizes as a dimer complexed to four THF molecules. The dimer lacks the bridging B-H bonds seen in neutral boranes and is instead held together by ionic Li---HB interactions. A preliminary scan of reactions with several iodides shows that the compound participates in an ionic reduction (with a primary-alkyl iodide), an organometallic reduction (Pd-catalyzed with an aryl iodide), and a radical reduction (AIBN-initiated with a sugar-derived iodide). Accordingly the new borylborohydride class may share properties of both traditional borohydrides and isoelectronic N-heterocyclic carbene boranes.

Structural studies of sparsely substituted synthetic chlorins and phorbines establish benchmarks for changes in the ligand core and framework of chlorophyll macrocycles

Understanding the changes in molecular structure of tetrapyrrole macrocycles upon derivatization of the organic framework is essential for diverse studies ranging from metal complexation to formation of supramolecular assemblies. New, sparsely substituted free base chlorin, 17-oxochlorin, phorbine and 13 1-oxophorbine macrocycles provide benchmarks for naturally occurring hydroporphyrins and have been examined here by X-ray crystallography, resonance Raman spectroscopy, and density functional theoretical (DFT) calculations. The macrocycles contain no substituents other than a geminal-dimethyl group attached to the reduced, pyrroline ring. The X-ray studies indicate that the benchmark compounds exhibit only slight distortion from planarity, which increases along the series porphine < chlorin < oxochlorin < phorbine < oxophorbine. The elongated C β C β bond distance due to sp 3 versus sp 2 hybridization in the pyrroline ring (ring D) of the (oxo)chlorins and (oxo)phorbines (1.52–1.54 Å) versus that of porphine (1.35 Å) is accompanied by altered bond angles in ring D. Introduction of ring E (exocyclic ring) in a chlorin to give the phorbine or oxophorbine causes alteration of the bond angles at many sites in the framework of the macrocycle; for example, the bond angles of N3 C14 C15 in the (oxo)phorbine are widened by ∼11° compared to those of porphine or the analogous sparsely substituted chlorin. As a result, the shape of the macrocycle core changes along the series of porphine (nearly square), (oxo)chlorin (kite-shaped), and (oxo)phorbine (right-angled trapezoid), and the core size increases in the order porphine < phorbine ∼ oxophorbine < oxochlorin ∼ chlorin. Comparison of the bond distances and angles in ring E of the phorbine versus oxophorbine indicates that the shortening of the C13 C13 1 bond owing to the presence of the oxo-group is quite small, only 0.024 Å; thus, the unsymmetrical structure of ring E does not appear to be due to conjugation with the C13 1 O group but may be a characteristic feature of the (oxo)phorbine framework. The X-ray data further indicate that the lengths of the oxochlorin C17 O and oxophorbine C13 1 O groups are essentially identical, a result also predicted by DFT calculations. Regardless, the observed frequencies for the stretching vibrations of the C17 O (1721 cm −1) and C13 1 O (1701 cm −1) groups are different and suggest that conjugation of the latter group with the π-system of the macrocycle is greater than that of the former group. Collectively, the studies provide new insights into the individual factors that give rise to the overall structural characteristics of various macrocycles.

Organic Super‐Acceptors with Efficient Intramolecular Charge‐Transfer Interactions by [2+2] Cycloadditions of TCNE, TCNQ, and F4‐TCNQ to Donor‐Substituted Cyanoalkynes

Rivaling the best one: Thermal [2+2] cycloadditions of TCNE, TCNQ, and F(4)-TCNQ to N,N-dimethylanilino-substituted cyanoalkynes afforded a new class of organic super-acceptors featuring efficient intramolecular charge-transfer interactions. These acceptors rival the acceptor F(4)-TCNQ in the propensity for reversible electron uptake as well as in electron affinity (see figure), which makes them interesting as p-type dopants for potential application in optoelectronic devices.Thermal [2+2] cycloadditions of tetracyanoethene (TCNE), 7,7,8,8-tetracyanoquinodimethane (TCNQ), and 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane (F(4)-TCNQ) to N,N-dimethylanilino-substituted (DMA-substituted) alkynes bearing either nitrile, dicyanovinyl (DCV; -CH==C(CN)(2)), or tricyanovinyl (TCV; -C(CN)==C(CN)(2)) functionalities, followed by retro-electrocyclization, afforded a new class of stable organic super-acceptors. Despite the nonplanarity of these acceptors, as revealed by X-ray crystallographic analysis and theoretical calculations, efficient intramolecular charge-transfer (CT) interactions between the DMA donors and the CN-containing acceptor moieties are established. The corresponding CT bands appear strongly bathochromically shifted with maxima up to 1120 nm (1.11 eV) accompanied by an end-absorption in the near infrared around 1600 nm (0.78 eV) for F(4)-TCNQ adducts. Electronic absorption spectra of selected acceptors were nicely reproduced by applying the spectroscopy oriented configuration interaction (SORCI) procedure. The electrochemical investigations of these acceptors by cyclic voltammetry (CV) and rotating disc voltammetry (RDV) in CH(2)Cl(2) identified their remarkable propensity for reversible electron uptake rivaling the benchmark compounds TCNQ (E(red,1)=-0.25 V in CH(2)Cl(2) vs. Fc(+)/Fc) and F(4)-TCNQ (E(red,1)=+0.16 V in CH(2)Cl(2) vs. Fc(+)/Fc). Furthermore, the electron-accepting power of these new compounds expressed as adiabatic electron affinity (EA) has been estimated by theoretical calculations and compared to the reference acceptor F(4)-TCNQ, which is used as a p-type dopant in the fabrication of organic light-emitting diodes (OLEDs) and solar cells. A good linear correlation exists between the calculated EAs and the first reduction potentials E(red,1). Despite the substitution with strong DMA donors, the predicted EAs reach the value calculated for F(4)-TCNQ (4.96 eV) in many cases, which makes the new acceptors interesting for potential applications as dopants in organic optoelectronic devices. The first example of a charge-transfer salt between the DMA-substituted TCNQ adduct (E(red,1)=-0.27 V vs. Fc(+)/Fc) and the strong electron donor decamethylferrocene ([FeCp*(2)]; Cp*=pentamethylcyclopentadienide; E(ox,1)=-0.59 V vs. Fc(+)/Fc) is described. Interestingly, the X-ray crystal structure showed that in the solid state the TCNQ moiety in the acceptor underwent reductive sigma-dimerization upon reaction with the donor.

Discovery of potent furan piperazine sodium channel blockers for treatment of neuropathic pain

The synthesis and pharmacological characterization of a novel furan-based class of voltage-gated sodium channel blockers is reported. Compounds were evaluated for their ability to block the tetrodotoxin-resistant sodium channel Na v1.8 (PN3) as well as the Na v1.2 and Na v1.5 subtypes. Benchmark compounds from this series possessed enhanced potency, oral bioavailability, and robust efficacy in a rodent model of neuropathic pain, together with improved CNS and cardiovascular safety profiles compared to the clinically used sodium channel blockers mexiletine and lamotrigine.

A novel radioligand for glycine transporter 1: characterization and use in autoradiographic and in vivo brain occupancy studies

In an effort to develop agents to test the NMDA hypofunction hypothesis of schizophrenia, benchmark compounds from a program to discover potent, selective, competitive glycine transporter 1 (GlyT1) inhibitors were radiolabeled in order to further study the detailed pharmacology of these inhibitors and the distribution of GlyT1 in brain. We here report the in vitro characterization of [35S](S)-2-amino-4-chloro-N-(1-(4-phenyl-1-(propylsulfonyl)piperidin-4-yl)ethyl)benzamide ([35S]ACPPB), a radiotracer developed from a potent and selective non-sarcosine-derived GlyT1 inhibitor, its use in autoradiographic studies to localize (S)-2-amino-6-chloro-N-(1-(4-phenyl-1-(propylsulfonyl)piperidin-4-yl)ethyl)benzamide (ACPPB) binding sites in rat and rhesus brain and for in vivo occupancy assays of competitive GlyT1 inhibitors. Functional potencies of unlabeled compounds were characterized by [14C]glycine uptake into JAR (human placental choriocarcinoma) cells and synaptosomes. Radioligand binding studies were performed with tissue homogenates. Autoradiographic studies were performed on tissue slices. ACPPB is a potent (Kd=1.9 nM), selective, GlyT1 inhibitor that, when radiolabeled with [35S], is a well-behaved radioligand with low nondisplaceable binding. Autoradiographic studies of rat and rhesus brain slices with this ligand showed that specific binding sites were plentiful and nonhomogeneously distributed, with high levels of binding in the brainstem, cerebellar white matter, thalamus, cortical white matter and spinal cord gray matter. In vivo studies demonstrate displaceable binding of [35S]ACPPB in rat brain tissues following iv administration of this radioligand. This is the first report of detailed anatomical localization of GlyT1 using direct radioligand binding, and the first demonstration that an in vivo occupancy assay is feasible, suggesting that it may also be feasible to develop positron emission tomography tracers for GlyT1.

P38 MAP kinase inhibitors. Part 6: 2-Arylpyridazin-3-ones as templates for inhibitor design

p38 inhibitors based on 3,4-dihydropyrido[4,3- d]pyrimidazin-2-one template were synthesized and their SAR explored. Benchmark compounds 30, 35, and 36 were found to be potent against the enzyme. Crystal structure of p38 in complex with 30 indicated a key π-stacking interaction with the pendant tyrosine residue-35 in the glycine-rich loop.

Gene expression profiling reveals multiple toxicity endpoints induced by hepatotoxicants

Microarray technology continues to gain increased acceptance in the drug development process, particularly at the stage of toxicology and safety assessment. In the current study, microarrays were used to investigate gene expression changes associated with hepatotoxicity, the most commonly reported clinical liability with pharmaceutical agents. Acetaminophen, methotrexate, methapyrilene, furan and phenytoin were used as benchmark compounds capable of inducing specific but different types of hepatotoxicity. The goal of the work was to define gene expression profiles capable of distinguishing the different subtypes of hepatotoxicity. Sprague–Dawley rats were orally dosed with acetaminophen (single dose, 4500 mg/kg for 6, 24 and 72 h), methotrexate (1 mg/kg per day for 1, 7 and 14 days), methapyrilene (100 mg/kg per day for 3 and 7 days), furan (40 mg/kg per day for 1, 3, 7 and 14 days) or phenytoin (300 mg/kg per day for 14 days). Hepatic gene expression was assessed using toxicology-specific gene arrays containing 684 target genes or expressed sequence tags (ESTs). Principal component analysis (PCA) of gene expression data was able to provide a clear distinction of each compound, suggesting that gene expression data can be used to discern different hepatotoxic agents and toxicity endpoints. Gene expression data were applied to the multiplicity-adjusted permutation test and significantly changed genes were categorized and correlated to hepatotoxic endpoints. Repression of enzymes involved in lipid oxidation (acyl-CoA dehydrogenase, medium chain, enoyl CoA hydratase, very long-chain acyl-CoA synthetase) were associated with microvesicular lipidosis. Likewise, subsets of genes associated with hepatotocellular necrosis, inflammation, hepatitis, bile duct hyperplasia and fibrosis have been identified. The current study illustrates that expression profiling can be used to: (1) distinguish different hepatotoxic endpoints; (2) predict the development of toxic endpoints; and (3) develop hypotheses regarding mechanisms of toxicity.

Effects of Membrane Partitioning and Other Physical Chemical Properties on the Apparent Potency of “Membrane Active” Compounds Evaluated Using Red Blood Cell Lysis Assays

The membrane-destabilizing properties of Amphotericin B and Zwittergent were used as benchmark compounds for examining in detail their membrane-altering effects in a series of human red blood cell lysis assays. The procedures included examining dose responses and the effects of different cell concentrations on potency in rbc lysis assays. In order to enhance detection of subtle membrane effects, we also used a range of NaCl concentrations to osmotically stress the rbc's. Using the benchmark compounds, a set of conditions was developed for examination of subtle membrane effects that may be applied to series of compounds with suspected membrane-perturbation activity. A group of experiments was defined that allow detection of the most important membrane-modifying behaviors among a diverse group of compounds. From an initial screen of bacterial growth inhibition over 150 compounds were examined for membrane-altering properties using the limited experimental protocols developed from the benchmark compounds. Several dose-response patterns were observed as useful for classifying compounds based on their tendency to alter membrane integrity and to partition into the lipids of membranes, as well as their propensity to form aggregates or precipitates. The methods may prove generally useful for distinguishing compounds whose primary activity is membrane destabilization from more interesting and useful pharmacological mechanisms of action.

Benchmark compounds. Structures of cobalt(II) complexes of triphenylphosphine- and triphenylarsine oxides

The structures of the Co(OPPh3)2Cl2, Co(OPPh3)2Br2, Co(OPPh3)2I2, Co(OAsPh3)2Br2 and Co(OAsPh3)2(NO3)2 complexes have been determined by X-ray diffraction methods; all have pseudo-tetrahedral co-ordination for cobalt.

An analysis of electrical resistivity of compositions within the Mo–Si–B ternary system part II: Multi-phase composites

The temperature dependence of electrical resistivity between 25 and 1500°C was determined for several multiphase composites within the Mo–Si–B system. The electrical behavior of these composites is determined by that of the single phase components and can be characterized as representative of semimetallic behavior. A predictive model for the resistivity of composites based on the properties of the single phase benchmark compounds was developed based on a logarithmic rule-of-mixture relationship. Error values for the model were calculated based on experimental error in the determination of volume fraction, porosity, and resistivity of each phase as a function of temperature. Experimental resistivity values for multiphase compositions within the Mo 5Si 3–MoSi 2, Mo 5Si 3B x (T1)–MoB–MoSi 2, and Mo 5Si 3B x –Mo 5SiB 2 (T2)–Mo 3Si phase fields are shown to be in good agreement with the model to within one standard deviation.

Liquid-crystalline reference compounds

Abstract A polar (PCH-5) and a non-polar (152) compound are introduced as liquid-crystalline bench-mark compounds. The materials chosen are affordable, stable, easy to handle and possess nematic mesophases between 30–54·9 and 24–103·4°C. All relevant macroscopic physical properties, such as refractive indices n o n e, dielectric permittivities ∥⊊, elastic constants K 11, K 22 and K 33, and bulk and rotational viscosities are given as a function of temperature, wavelength and frequency, when applicable. The reference compounds are available from E. Merck, Darmstadt.