Inactive Compounds Research Articles

G protein-coupled estrogen receptor (GPER) deficiency induces cardiac remodeling through oxidative stress

Oxidative stress has been implicated in the unfavorable changes in cardiac function and remodeling that occur after ovarian estrogen loss. Using ovariectomized rat models, we previously reported that the cardioprotective actions of estrogen are mediated by the G protein-coupled estrogen receptor (GPER). Here, in 9-month-old, female cardiomyocyte-specific GPER knockout (KO) mice vs sex- and age-matched wild-type (WT) mice, we found increased cardiac oxidative stress and oxidant damage, measured as a decreased ratio of reduced glutathione to oxidized glutathione, increased 4-hydroxynonenal and 8-hydroxy-2'-deoxyguanosine (8-oxo-DG) staining, and increased expression of oxidative stress-related genes. GPER KO mice also displayed increased heart weight, cardiac collagen deposition, and Doppler-derived filling pressure, and decreased percent fractional shortening and early mitral annular velocity compared with WT controls. Treatment of GPER KO mice for 8 weeks with phosphonium [10-(4,5-dimethoxy-2-methyl 3,6-dioxo-1,4-cyclohexadien-1-yl)decyl] triphenyl-,mesylate (MitoQ), a mitochondria-targeted antioxidant, significantly attenuated these measures of cardiac dysfunction, and MitoQ decreased 8-oxo-DG intensity compared with treatment with an inactive comparator compound, (1-decyl)triphenylphosphonium bromide (P <0.05). A real-time polymerase chain reaction array analysis of 84 oxidative stress and antioxidant defense genes revealed that MitoQ attenuates the increase in NADPH oxidase 4 and prostaglandin-endoperoxide synthase 2 and the decrease in uncoupling protein 3 and glutathione S-transferase kappa 1 seen in GPER KO mice. Our findings suggest that the cardioprotective effects of GPER include an antioxidant role and that targeted strategies to limit oxidative stress after early noncancerous surgical extirpation of ovaries or menopause may help limit alterations in cardiac structure and function related to estrogen loss.

Ameliorative impact of mycophenolate mofetil on diabetic kidney disease; a review on current knowledge

Diabetic kidney disease as a common problem of diabetes can be the main cause of renal insufficiency in severe and untreated cases. Various aspects play a role in the progress of diabetic nephropathy, including gradual accumulation of AGEs (advanced glycation end-products), advancement in the pathway of polyol, oxidative stress, high filtration in glomeruli and increase in TGF-β (transforming growth factor-β) expression. Inflammatory process is known as a definite factor in the development of diabetic nephropathy. Increased molecules that cause inflammation comprise chemokines, cytokines, C-reactive protein (CRP), and adhesion molecules. Since pathogenesis of diabetic nephropathy basically is due to inflammatory procedure, therefore, the first therapeutic goal is to relieve inflammation. Numerous studies on animals have shown that anti-inflammatory effects of drugs are beneficial in treating nephropathy related to diabetes, but protective effects of these drugs have not been recognized in humans. Some substances involved in renal protective and anti-inflammatory in diabetic animals comprise; thiazolidinedione, statins, spironolactone, immunosuppressant, GLP-1 receptor agonist, angiotensin II receptor antagonist (ARB), cholecystokinin, and glucagon-like peptide-1. Mycophenolate mofetil (MMF) is a biologically inactive compound that belongs to a group of drugs that acts to suppress or restrain immune system. Therefore, mycophenolate, by weakening the immune system, prevents rejecting transplanted organ in the body. Here are some studies on the effect of MMF on inflammation as a significant factor in the development of diabetic problems.

The Mu.Ta.Lig. Chemotheca: A Community-Populated Molecular Database for Multi-Target Ligands Identification and Compound-Repurposing.

For every lead compound developed in medicinal chemistry research, numerous other inactive or less active candidates are synthetized/isolated and tested. The majority of these compounds will not be selected for further development due to a sub-optimal pharmacological profile. However, some poorly active or even inactive compounds could live a second life if tested against other targets. Thus, new therapeutic opportunities could emerge and synergistic activities could be identified and exploited for existing compounds by sharing information between researchers who are working on different targets. The Mu.Ta.Lig (Multi-Target Ligand) Chemotheca database aims to offer such opportunities by facilitating information exchange among researchers worldwide. After a preliminary registration, users can (a) virtually upload structures and activity data for their compounds with corresponding, and eventually known activity data, and (b) search for other available compounds uploaded by the users community. Each piece of information about given compounds is owned by the user who initially uploaded it and multiple ownership is possible (this occurs if different users uploaded the same compounds or information pertaining to the same compounds). A web-based graphical user interface has been developed to assist compound uploading, compounds searching and data retrieval. Physico-chemical and ADME properties as well as substructure-based PAINS evaluations are computed on the fly for each uploaded compound. Samples of compounds that match a set of search criteria and additional data on these compounds could be requested directly from their owners with no mediation by the Mu.Ta.Lig Chemotheca team. Guest access provides a simplified search interface to retrieve only basic information such as compound IDs and related 2D or 3D chemical structures. Moreover, some compounds can be hidden to Guest users according to an owner's decision. In contrast, registered users have full access to all of the Chemotheca data including the permission to upload new compounds and/or update experimental/theoretical data (e.g., activities against new targets tested) related to already stored compounds. In order to facilitate scientific collaborations, all available data are connected to the corresponding owner's email address (available for registered users only). The Chemotheca web site is accessible at http://chemotheca.unicz.it.

A Permselective Graphene Oxide/Polyvinyl Alcohol Composite Membrane for Rechargeable Alkaline Zinc Manganese Dioxide Batteries

Rechargeable alkaline Zn/MnO2 batteries are currently attractive candidates for grid-scale energy storage due to its low cost, safety characteristics, and high gravimetric capacity of MnO2 (308 mAh/g per electron). However, commercialization of this battery has not achieved big success due to its limited cycle life and restricted depth of discharge (DOD). Accessing higher DOD results in higher energy densities, but leads to detrimental characteristics like phase transformation of MnO2 and the zinc redistribution. Recently, a class of Bi-birnessite (a layered MnO2 structure with bismuth oxide) material intercalated with Cu2+ has been reported as being able to stabilize the MnO2 structure and deliver near-full two-electron capacity for more than 6,000 cycles in the absence of zinc [1]. However, when a zinc anode is used, the most detrimental effect arises from zincate ions ([Zn(OH)4]2-) that traverse to the cathode side and react to form a spinel phase ZnMn2O4, a highly resistive and electrochemically inactive compound, leading to rapid energy density loss and battery failure [2]. Therefore, inhibiting ZnMn2O4 formation remains a major challenge for the long-term cycling of an energy dense secondary Zn/MnO2 battery. Previously, we reported the use of a zincate-absorbing interlayer fabricated of calcium hydroxide, which successfully prevents ZnMn2O4 formation [3]. In this presentation, we report the strategy of developing a separator featuring selective transport of OH- and [Zn(OH)4]2- ions. We fabricate a graphene oxide-poly(vinyl alcohol) (GO-PVA) composite membrane with a layered structure. The GO membrane, which is composed of stacked and overlapped GO monolayers with a narrow interlayer spacing (~13.5Å for GO laminates swelled in water), has been demonstrated to be excellent filters for gases and liquids. The nanocapillaries formed within the membranes as well as the oxygen functional groups which repel the bulky [Zn(OH)4]2- anions are responsible for its ion sieving properties. PVA is impregnated to provide a conductive pathway for OH- ions and to improve the mechanical stability. We successfully demonstrate the superiority of the GO/PVA composite membrane in suppressing zincate ion crossover (Fig.1(a)), while minimally impairing OH- conduction. Its application in primary batteries significantly increases the energy density by obtaining capacity of more than 1.5 e- per Mn atom above 0.9V (Fig.1(b)). In rechargeable batteries, it slows down the capacity fade of a conventional zinc/electrolytic γ-MnO2 (Zn/EMD) battery during deep cycling within the 1st electron capacity (Fig.1(c)), while it helps to achieve more than 200 cycles with full 2-electron capacity retained in a zinc/birnessite battery (Fig.1(d)).

Hydrolysis-Kinetic Study of AEBSF, a Protease Inhibitor Used during Cell-Culture Processing of the HIV-1 Broadly Neutralizing Antibody CAP256-VRC25.26.

One approach to mitigate product clipping during HIV mAb CAP256-VRC26.25 cell-culture development is the addition of the protease inhibitor 4-(2-aminoethyl) benzenesulfonyl fluoride (AEBSF) to the cell-culture media. AEBSF can undergo hydrolysis to form an inactive compound, 4-(2-aminoethyl) benzenesulfonic acid. Using mass-spectrometry detection, a kinetic profile of AEBSF hydrolysis was generated for conditions simulating those of cell culture at pH 7.0 and 37 °C. It was found that increasing the pH or the temperature could accelerate AEBSF hydrolysis. The kinetic-study results in this report provide an analytical characterization and guidance when optimizing an AEBSF-addition strategy for product-clipping control during cell-culture development and offer an alternative approach for AEBSF-related clearance studies post protein production.

Discovery of Novel Adenosine Receptor Antagonists through a Combined Structure- and Ligand-Based Approach Followed by Molecular Dynamics Investigation of Ligand Binding Mode.

An intense effort is made by pharmaceutical and academic research laboratories to identify and develop selective antagonists for each adenosine receptor (AR) subtype as potential clinical candidates for "soft" treatment of various diseases. Crystal structures of subtypes A2A and A1ARs offer exciting opportunities for structure-based drug design. In the first part of the present work, Maybridge HitFinder library of 14400 compounds was utilized to apply a combination of structure-based against the crystal structure of A2AAR and ligand-based methodologies. The docking poses were rescored by CHARMM energy minimization and calculation of the desolvation energy using Poisson-Boltzmann equation electrostatics. Out of the eight selected and tested compounds, five were found positive hits (63% success). Although the project was initially focused on targeting A2AAR, the identified antagonists exhibited low micromolar or micromolar affinity against A2A/A3, ARs, or A3AR, respectively. Based on these results, 19 compounds characterized by novel chemotypes were purchased and tested. Sixteen of them were identified as AR antagonists with affinity toward combinations of the AR family isoforms (A2A/A3, A1/A3, A1/A2A/A3, and A3). The second part of this work involves the performance of hundreds of molecular dynamics (MD) simulations of complexes between the ARs and a total of 27 ligands to resolve the binding interactions of the active compounds, which were not achieved by docking calculations alone. This computational work allowed the prediction of stable and unstable complexes which agree with the experimental results of potent and inactive compounds, respectively. Of particular interest is that the 2-amino-thiophene-3-carboxamides, 3-acylamino-5-aryl-thiophene-2-carboxamides, and carbonyloxycarboximidamide derivatives were found to be selective and possess a micromolar to low micromolar affinity for the A3 receptor.

Characterization and performance of common alkali metals and alkaline earth metals loaded Mn/TiO2 catalysts for NOx removal with NH3

The influence of four common alkali metals and alkaline earth metals (Na, K, Mg and Ca) on Mn/TiO2 catalysts for selective catalytic reduction of NOx with NH3 was investigated. K, Na and Ca deactivated the catalysts and the deactivation effects were shown in sequence as K > Na > Ca, while Mg improved the capability of the catalysts. Furthermore, physical and chemical properties of catalysts were characterized by XRD, H2-TPR, NH3-TPD, BET, FESEM, XPS, TG and in situ DRIFTS analyses. Characterization results suggested that the obvious decrease of NH3 adsorption and surface redox ability and the formation of inactive compounds could take credit for the deactivation caused by alkali metals and alkaline earth metals except Mg. The atomic concentrations of Mn3+ and relative concentration ratios of Oα/(Oα+Oβ) on the surfaces were also important factors for SCR activities of Mn/TiO2 catalysts doped with the main group IA elements (Na and K). The in situ DRIFTS tests further confirmed that the alkaline size resulted in the considerable changes in the desorption strength of ammonia which was in accordance with the NH3-TPD results. Meanwhile, the slight decrease of NH3 adsorption and surface redox ability and the formation of MgMn2O4 appeared to be directly correlated with the better SCR performance of the catalysts doped with Mg. Moreover, acid site and redox site played important roles in the catalytic cycle for Mn/TiO2 catalysts during the NH3-SCR reaction.

Identification of Estrogen Receptor α Antagonists from Natural Products via In Vitro and In Silico Approaches.

Estrogen receptor α (ERα) is a successful target for ER-positive breast cancer and also reported to be relevant in many other diseases. Selective estrogen receptor modulators (SERMs) make a good therapeutic effect in clinic. Because of the drug resistance and side effects of current SERMs, the discovery of new SERMs is given more and more attention. Virtual screening is a validated method to high effectively to identify novel bioactive small molecules. Ligand-based machine learning methods and structure-based molecular docking were first performed for identification of ERα antagonist from in-house natural product library. Naive Bayesian and recursive partitioning models with two kinds of descriptors were built and validated based on training set, test set, and external test set and then were utilized for distinction of active and inactive compounds. Totally, 162 compounds were predicted as ER antagonists and were further evaluated by molecular docking. According to docking score, we selected 8 representative compounds for both ERα competitor assay and luciferase reporter gene assay. Genistein, daidzein, phloretin, ellagic acid, ursolic acid, (−)-epigallocatechin-3-gallate, kaempferol, and naringenin exhibited different levels for antagonistic activity against ERα. These studies validated the feasibility of machine learning methods for predicting bioactivities of ligands and provided better insight into the natural products acting as estrogen receptor modulator, which are important lead compounds for future new drug design.

Two-color, one-photon uncaging of glutamate and GABA.

Neuronal cells receive a variety of excitatory and inhibitory signals which they process to generate an output signal. In order to study the interaction between excitatory and inhibitory receptors with exogenously applied transmitters in the same preparation, two caging chromophores attached to glutamate and GABA were developed that were selectively photolyzed by different wavelengths of light. This technique has the advantage that the biologically inactive caged compound can be applied at equilibrium prior to the near instantaneous release of the transmitters. This method therefore mimics the kinetics of endogenously released transmitters that is otherwise not possible in brain slice preparations. Repeated photolysis with either of the two wavelengths resulted in GABA- or glutamate-induced activation of both ionotropic and metabotropic receptors to evoke reproducible currents. With these compounds, the interaction between inhibitory and excitatory receptors was examined using whole field photolysis.

ProSelection: A Novel Algorithm to Select Proper Protein Structure Subsets for in Silico Target Identification and Drug Discovery Research.

Molecular docking is widely applied to computer-aided drug design and has become relatively mature in the recent decades. Application of docking in modeling varies from single lead compound optimization to large-scale virtual screening. The performance of molecular docking is highly dependent on the protein structures selected. It is especially challenging for large-scale target prediction research when multiple structures are available for a single target. Therefore, we have established ProSelection, a docking preferred-protein selection algorithm, in order to generate the proper structure subset(s). By the ProSelection algorithm, protein structures of "weak selectors" are filtered out whereas structures of "strong selectors" are kept. Specifically, the structure which has a good statistical performance of distinguishing active ligands from inactive ligands is defined as a strong selector. In this study, 249 protein structures of 14 autophagy-related targets are investigated. Surflex-dock was used as the docking engine to distinguish active and inactive compounds against these protein structures. Both t test and Mann-Whitney U test were used to distinguish the strong from the weak selectors based on the normality of the docking score distribution. The suggested docking score threshold for active ligands (SDA) was generated for each strong selector structure according to the receiver operating characteristic (ROC) curve. The performance of ProSelection was further validated by predicting the potential off-targets of 43 U.S. Federal Drug Administration approved small molecule antineoplastic drugs. Overall, ProSelection will accelerate the computational work in protein structure selection and could be a useful tool for molecular docking, target prediction, and protein-chemical database establishment research.

Utility of bis(methylthio)methylene malononitrile as a synthon in the synthesis of new poly-functionalized cyanoiminopyrimidines

A new series of 4-(alkyl/arylamino)-6-amino-5-cyano-2-cyanoimino-1H-pyrimidine was obtained via one-pot three-component reaction of bis(methylthio)methylene malononitrile, primary amines, and cyanoguanidine using sodium ethoxide as basic catalyst. The same new products were prepared by classical route via reaction of (alkyl/arylamino)(methylthio)methylene malononitrile with cyanoguanidine in presence of sodium ethoxide. In absence of amines, bis(methylthio)methylene malononitrile reacts directly with cyanoguanidine in presence of sodium ethoxide to give 4-ethoxy-2-cyanoimino-1H-pyrimidine. On the other hand, multicomponents reaction of bis(methylthio)methylene malononitrile with cyanoguanidine and binucleophilic β-hydroxyamines and/or ortho-phenylenediamine gave perspective 4-methyl- and/or 5-methyl-1,3-oxazolidin-2-ylidenemalononitrile and 1,3-dihydro-2H-benzimidazol-2-ylidenemalononitrile, which are inactive compounds toward reaction with cyanoguanidine to give the expected 4-(alkyl/arylamino)-2-cyanoimino-1H-pyrimidines.

Molecular Connectivity Predefines Polypharmacology: Aliphatic Rings, Chirality, and sp3 Centers Enhance Target Selectivity.

Dark chemical matter compounds are small molecules that have been recently identified as highly potent and selective hits. For this reason, they constitute a promising class of possible candidates in the process of drug discovery and raise the interest of the scientific community. To this purpose, Wassermann et al. (2015) have described the application of 2D descriptors to characterize dark chemical matter. However, their definition was based on the number of reported positive assays rather than the number of known targets. As there might be multiple assays for one single target, the number of assays does not fully describe target selectivity. Here, we propose an alternative classification of active molecules that is based on the number of known targets. We cluster molecules in four classes: black, gray, and white compounds are active on one, two to four, and more than four targets respectively, whilst inactive compounds are found to be inactive in the considered assays. In this study, black and inactive compounds are found to have not only higher solubility, but also a higher number of chiral centers, sp3 carbon atoms and aliphatic rings. On the contrary, white compounds contain a higher number of double bonds and fused aromatic rings. Therefore, the design of a screening compound library should consider these molecular properties in order to achieve target selectivity or polypharmacology. Furthermore, analysis of four main target classes (GPCRs, kinases, proteases, and ion channels) shows that GPCR ligands are more selective than the other classes, as the number of black compounds is higher in this target superfamily. On the other side, ligands that hit kinases, proteases, and ion channels bind to GPCRs more likely than to other target classes. Consequently, depending on the target protein family, appropriate screening libraries can be designed in order to minimize the likelihood of unwanted side effects early in the drug discovery process. Additionally, synergistic effects may be obtained by library design toward polypharmacology.

Structural studies and biological activity evaluation of Pd(II), Pt(II) and Ru(II) complexes containing N‐phenyl, N`‐(3‐triazolyl)thiourea

[MCl(H2L)(OH2)]·1.5H2O (M = Pd(II) (1) and Pt(II) (2)) and [Ru(H2L)2(OH2)2]·3H2O (3) (H3L: N‐phenyl, N`‐(3‐triazolyl)thiourea) were synthesized, characterized and tested for their antibacterial activities against Staphylococcus aureus and Escherichia coli bacteria. The thiourea derivative is coordinated to Mn+ ions as a mono‐negatively N,S‐bidentate ligand via the enolization of C = S group and triazole N center. The density functional theory calculations reveal that presence of a water molecule in a trans position to triazole ring increased the stability of d8 metal ions complexes via the formation of strong Cl…NH intramolecular H‐bond. The cis‐Ru(II)‐isomer with two isoenergetically H2L− molecules are more stable than the trans‐analog. Coordination of H3L to Ru(II) ion did not alter the toxicity of the free ligand, while the interaction with the d8 metal ions gave rise to inactive compounds.

Pellitorine, an extract of Tetradium daniellii, is an antagonist of the ion channel TRPV1

BackgroundTransient Receptor Potential Vanilloid 1 (TRPV1) confers noxious heat and inflammatory pain signals in the peripheral nervous system. Clinical trial of resiniferatoxin from Euphorbia species is successfully aimed at TRPV1 in cancer pain management and heading toward new selective painkiller status that further validates this target for drug discovery efforts. Evodia species, used in traditional medicine for hundreds of years, are a recognised source of different TRPV1 agonists, but no antagonist has yet been reported. Hypothesis/PurposeIn a search for painkiller leads, we noted for the first time a TRPV1 antagonist activity in the fresh fruits of Tetradium daniellii (Benn.) T.G. Hartley (syn. Evodia hupehensis Dode). MethodsThrough a combination of extraction and purification methods with functional TRPV1-specific Ca2+ uptake assays (bioactivity-guided fractionation/isolation/purification); we isolated a new painkiller candidate that is a distant structural homologue of capsiate exovanilloids and endovanilloids such as anandamide, but a putative competitive inhibitor of the TRPV1. Four additional inactive compounds (N-isobutyl-4,5-epoxy-2E-decadienamide, geranylpsoralen, 8-(7′,8′-epoxygeranyloxy)psoralen, and xanthotoxol) were also co-purified with pellitorine. Their structures were established by extensive 1D- and 2D-NMR spectroscopic analysis. Results1H- and 13C NMR determination of the chemical structure revealed it to be pellitorine, (2E,4E)-N-(2-methylpropyl)deca-2,4-dienamide, which can compete structurally with algesics released in inflammation. In contrast to previous isolates from Evodia species, pellitorine blocked capsaicin-evoked Ca2+ uptake with an IC50 of 154 µg/ml (0.69 mM/l). N-Isobutyl-4,5-epoxy-2E-decadienamide and geranylpsoralen, 8-(7′,8′-epoxygeranyloxy)psoralen, and xanthotoxol did not affect the TRPV1. ConclusionThis is the first evidence that pellitorine, an aliphatic alkylamide analogue of capsaicin, can serve as an antagonist of the TRPV1 and may inhibit exovanilloid-induced pain.

Abstract 5084: Potent and isoform-selective ATAD2 bromodomain inhibitor with unprecedented chemical structure and mode of action

Abstract ATAD2 (ATPase family AAA-domain containing protein 2, also called ANCCA) is an epigenetic regulator that binds to chromatin through its bromodomain (BD), a motif specialized for acetyl-lysine recognition. ATAD2 directly associates with multiple transcription factors such as ERα, AR, E2F, and Myc; hence, ATAD2 has been proposed to act as a co-factor for oncogenic transcription factors. Furthermore, we have recently reported a novel role for ATAD2 during DNA replication, uncovering interactions between ATAD2 and histone acetylation marks on newly synthesized histone H4. High expression of ATAD2 strongly correlates with poor patient prognosis in multiple tumor types, including gastric, endometrial, hepatocellular, ovarian, breast and lung cancers. However, the exact function of ATAD2 in these tumor types remains unclear. A more thorough validation of ATAD2 as a therapeutic target is hampered by the lack of isoform-selective, potent and cellularly active ATAD2 inhibitors. A systematic assessment of crystal structures of BD-containing protein family predicted that development of selective inhibitors of ATAD2 would be challenging. In line with this prediction, only limited progress in developing lead compounds targeting ATAD2 has been reported so far. A few notable exceptions relied on fragments as starting points, however, their weak potency, insufficient selectivity against other BDs, permeability limitations or modest cellular activity have curbed their further development towards drug candidates. Here we embarked on a novel strategy to identify ATAD2 inhibitors: 11 different DNA-encoded libraries adding up to 67 billion unique encoded compounds were combined and incubated with ATAD2 BD followed by two rounds of affinity-mediated selection. This approach provided with several series of binders, for which specific target engagement of their SMOL moiety upon off-DNA synthesis was confirmed in biochemical and biophysical assays. Several rounds of potency optimization led to the identification of BAY-850, a highly potent and ATAD2 (isoform A) mono-selective inhibitor, which holds an amine substituted 3-(2-furyl)benzamide core. This compound shows - as revealed by size exclusion chromatography and native mass spectrometry - a novel mode of action for a BD inhibitor based on specific target dimerization. In a cellular fluorescence recovery after photobleaching (FRAP) assay BAY-850 displaced wild-type ATAD2 from the chromatin to the same extent as the genetic mutagenesis of ATAD2 BD. In contrast, chemically very similar inactive control compounds showed no major effects on ATAD2 association with the chromatin. These results qualify BAY-850 as the first biologically active ATAD2 isoform A-specific chemical probe, which will enable further elucidation of the cancer biology of this intriguing protein. Citation Format: Amaury E. Fernández-Montalván, Markus Berger, Benno Kuropka, Seong Joo Koo, Volker Badock, Joerg Weiske, Simon J. Holton, Apirat Chaikuad, Laura Díaz-Sáez, James Bennett, Oleg Federov, Kilian Huber, Paolo Centrella, Matthew A. Clark, Christoph E. Dumelin, Eric A. Sigel, Holly S. Soutter, Dawn M. Troast, Ying Zhang, John W. Cuozzo, Anthony D. Keefe, Didier Roche, Vincent Rodeschini, Jan Hübner, Hilmar Weinmann, Ingo V. Hartung, Matyas Gorjanacz. Potent and isoform-selective ATAD2 bromodomain inhibitor with unprecedented chemical structure and mode of action [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5084. doi:10.1158/1538-7445.AM2017-5084

Multi-structure docking analysis of BACE1 crystal structures and non-peptidic ligands

In order to design novel non-peptidic inhibitors of BACE1, many research groups have attempted using computational studies including docking analyses. Since there are too many 3D structures for BACE1 in the protein database, the selection of suitable crystal structures is a key prerequisite for the successful application of molecular docking. We employed a multi-structure docking protocol. In which 615 ligands’ structures were docked into 150 BACE1 structures. The large number of the resultant docking scores were post-processed by different data analysis methods including exploratory data analysis, regression analysis and discriminant analysis. It was found that using one crystal structure for docking did not result in high accuracy for predicting activity of the BACE1 inhibitors. Instead, using of the multi-structural docking scores, post-processed by chemometrics methods arrived to highly accurate predictive models. In this regards, the PDB accession codes of 4B70, 4DVF and 2WEZ could discriminate between active and inactive compounds, with higher accuracy. Clustering of the BACE1 structures based on principal component analysis of the crystallographic structures the revealed that the discriminant structures are in the center of the clusters. Thus, these structures can be selected as predominant crystal structures for docking studies of non-peptidic BACE1 inhibitors.

Qualitative and quantitative simulation of androgen receptor antagonists: A case study of polybrominated diphenyl ethers

Recently, great attention has been paid to the identification and prediction of the androgen disrupting potencies of polybrominated diphenyl ethers (PBDEs). However, few existing models can discriminate active and inactive compounds, which make the quantitative prediction process including the quantitative structure-activity relationship (QSAR) technique unreliable. In this study, different grouping methods were investigated and compared for qualitative identification, including molecular docking and molecular dynamics simulations (MD). The results showed that qualitative identification based on MD, which is lab-independent, accurate and closer to the real transcriptional activation process, could separate 90.5% of active and inactive chemicals and was preferred. The 3D-QSAR models built as the quantitative simulation method showed r2 and q2 values of 0.513 and 0.980, respectively. Together, a novel workflow combining qualitative identification and quantitative simulations was generated with processes including activeness discrimination and activity prediction. This workflow, for analyzing the antagonism of androgen receptor (AR) of PBDEs is not only allowing researchers to reduce their intense laboratory experiments but also assisting them in inspecting and adjusting their laboratory systems and results.

Synthesis, ADMET Properties, and Biological Evaluation of Benzothiazole Compounds Targeting Chemokine Receptor 2 (CXCR2).

Herein we describe the synthesis and biological evaluation of a series of novel benzothiazoles based on a diaryl urea scaffold previously reported in some allosteric chemokine receptor 2 (CXCR2) inhibitors. From a library of 41 new compounds, 17 showed significant inhibition of CXCR2, with IC50 values less than 10 μm and selectivity over CXCR4. Our ADMET simulations suggest favorable drug-like properties for the active compounds. Importantly, we developed a predictive model that can distinguish active from inactive compounds; this will serve as a valuable tool to guide the design of optimized compounds to be evaluated in preclinical models.

A Novel Anti-Hepatitis C Virus and Antiproliferative Agent Alters Metabolic Networks in HepG2 and Hep3B Cells.

A series of novel diflunisal hydrazide-hydrazones has been reported together with their anti-hepatitis C virus and antiproliferative activities in a number of human hepatoma cell lines. However, the mechanisms underlying the efficacy of these agents remain unclear. It was chosen to investigate the lead diflunisal hydrazide-hydrazone, 2′,4′-difluoro-4-hydroxy-N′- [(pyridin-2-yl)methylidene]biphenyl-3-carbohydrazide (compound 3b), in two cultured human hepatoma cell lines—HepG2 and Hep3B—using a metabolomic protocol aimed at uncovering any effects of this agent on cellular metabolism. One sub-therapeutic concentration (2.5 μM) and one close to the IC50 for antimitotic effect (10 μM), after 72 h in cell culture, were chosen for both compound 3b and its inactive parent compound diflusinal as a control. A GCMS-based metabolomic investigation was performed on cell lysates after culture for 24 h. The intracellular levels of a total of 42 metabolites were found to be statistically significantly altered in either HepG2 or Hep3B cells, only eight of which were affected in both cell lines. It was concluded that compound 3b affected the following pathways—purine and pyrimidine catabolism, the glutathione cycle, and energy metabolism through glycolysis and the pentose phosphate pathway. Although the metabolomic findings occurred after 24 h in culture, significant cytotoxicity of compound 3b to both HepG2 and Hep3B cells at 10 μM were reported not to occur until 72 h in culture. These observations show that metabolomics can provide mechanistic insights into the efficacy of novel drug candidates prior to the appearance of their pharmacological effect.

How Frequently Are Pan-Assay Interference Compounds Active? Large-Scale Analysis of Screening Data Reveals Diverse Activity Profiles, Low Global Hit Frequency, and Many Consistently Inactive Compounds.

Undetected pan-assay interference compounds (PAINS) with false-positive activities in assays often propagate through medicinal chemistry programs and compromise their outcomes. Although a large number of PAINS have been classified, often on the basis of individual studies or chemical experience, little has been done so far to systematically assess their activity profiles. Herein we report a large-scale analysis of the behavior of PAINS in biological screening assays. More than 23 000 extensively tested compounds containing PAINS substructures were detected, and their hit rates were determined. Many consistently inactive compounds were identified. The hit frequency was low overall, with median values of two to five hits for PAINS tested in hundreds of assays. Only confined subsets of PAINS produced abundant hits. The same PAINS substructure was often found in consistently inactive and frequently active compounds, indicating that the structural context in which PAINS occur modulates their effects.