Identification of novel PI3Kδ inhibitors by docking,ADMET prediction and molecular dynamics simulations

BackgroundPhosphoinositide-3-kinase Delta (PI3Kδ) plays a key role in B-cell signal transduction and inhibition of PI3Kδ is confirmed to have clinical benefit in certain types of activation of B-cell malignancies. Virtual screening techniques have been used to discover new molecules for developing novel PI3Kδ inhibitors with little side effects.MethodComputer aided drug design method were used to rapidly screen optimal PI3Kδ inhibitors from the Asinex database. Virtual screening based molecular docking was performed to find novel and potential lead compound targeting PI3Kδ, at first. Subsequently, drug likeness studies were carried out on the retrieved hits to evaluate and analyze their drug like properties such as absorption, distribution, metabolism, excretion, and toxicity (ADMET) for toxicity prediction. Three least toxic compounds were selected for the molecular dynamics (MD) simulations for 30 ns in order to validate its stability inside the active site of PI3Kδ receptor.ResultsBased on the present in silico analysis, two molecules have been identified which occupied the same binding pocket confirming the selection of active site. ASN 16296138 (Glide score: −12.175 kcal/mol, cdocker binding energy: −42.975 kcal/mol and ΔG_bind value: −90.457 kcal/mol) and BAS 00227397 (Glide score: −10.988 kcal/mol, cdocker binding energy: −39.3376 kcal/mol and ΔG_bind value: −81.953 kcal/mol) showed docking affinities comparatively much stronger than those of already reported known inhibitors against PI3Kδ. These two ligand’s behaviors also showed consistency during the simulation of protein-ligand complexes for 30000 ps respectively, which is indicative of its stability in the receptor pocket.ConclusionCompound ASN 16296138 and BAS 00227397 are potential candidates for experimental validation of biological activity against PI3Kδ in future drug discovery studies. This study smoothes the path for the development of novel leads with improved binding properties, high drug likeness, and low toxicity to humans for the treatment of cancer.     

Inhibition of NF-κB prevents high glucose-induced proliferation and plasminogen activator inhibitor-1 expression in vascular smooth muscle cells

Recent epidemiologic studies clearly showed that early intensive glucose control has a legacy effect for preventing diabetic macrovascular complications. However, the cellular and molecular processes by which high glucose leads to macrovascular complications are poorly understood. Vascular smooth muscle cell (VSMC) dysfunction due to high glucose is a characteristic of diabetic vascular complications. Activation of nuclear factor-κB (NF-κB) may play a key role in the regulation of inflammation and proliferation of VSMCs. We examined whether VSMC proliferation and plasminogen activator inhibitor-1 (PAI-1) expression induced by high glucose were mediated by NF-κB activation. Also, we determined whether selective inhibition of NF-κB would inhibit proliferation and PAI-1 expression in VSMCs. VSMCs of the aorta of male SD rats were treated with various concentrations of glucose (5.6, 11.1, 16.7, and 22.2 mM) with or without an inhibitor of NF-κB or expression of a recombinant adenovirus vector encoding an IκB-α mutant (Ad-IκBαM). VSMC proliferation was examined using an MTT assay. PAI-1 expression was assayed by real-time PCR and PAI-1 protein in the media was measured by ELISA. NF-κB activation was determined by immunohistochemical staining, NF-κB reporter assay, and immunoblotting. We found that glucose stimulated VSMC proliferation and PAI-1 expression in a dose-dependent manner up to 22.2 mM. High glucose (22.2 mM) alone induced an increase in NF-κB activity. Treatment with inhibitors of NF-κB such as MG132, PDTC or expression of Ad-IκB-αM in VSMCs prevented VSMC proliferation and PAI-1 expression induced by high glucose. In conclusion, inhibition of NF-κB activity prevented high glucose-induced VSMC proliferation and PAI-1 expression.     

Anti-Neuroinflammatory Effects of Vanillin Through the Regulation of Inflammatory Factors and NF-κB Signaling in LPS-Stimulated Microglia

Applied Biochemistry and Biotechnology - Microglia, resident macrophages of the central nervous system (CNS), is responsible for immune responses and homeostasis of the CNS. Microglia plays a...     

Honokiol ameliorates endothelial dysfunction through suppression of PTX3 expression,a key mediator of IKK/IκB/NF-κB,in atherosclerotic cell model

Pentraxin 3 (PTX3) was identified as a marker of the inflammatory response and overexpressed in various tissues and cells related to cardiovascular disease. Honokiol, an active component isolated from the Chinese medicinal herb Magnolia officinalis, was shown to have a variety of pharmacological activities. In the present study, we aimed to investigate the effects of honokiol on palmitic acid (PA)-induced dysfunction of human umbilical vein endothelial cells (HUVECs) and to elucidate potential regulatory mechanisms in this atherosclerotic cell model. Our results showed that PA significantly accelerated the expression of PTX3 in HUVECs through the IκB kinase (IKK)/IκB/nuclear factor-κB (NF-κB) pathway, reduced cell viability, induced cell apoptosis and triggered the inflammatory response. Knockdown of PTX3 supported cell growth and prevented apoptosis by blocking PA-inducted nitric oxide (NO) overproduction. Honokiol significantly suppressed the overexpression of PTX3 in PA-inducted HUVECs by inhibiting IκB phosphorylation and the expression of two NF-κB subunits (p50 and p65) in the IKK/IκB/NF-κB signaling pathway. Furthermore, honokiol reduced endothelial cell injury and apoptosis by regulating the expression of inducible NO synthase and endothelial NO synthase, as well as the generation of NO. Honokiol showed an anti-inflammatory effect in PA-inducted HUVECs by significantly inhibiting the generation of interleukin-6 (IL-6), IL-8 and monocyte chemoattractant protein-1. In summary, honokiol repaired endothelial dysfunction by suppressing PTX3 overexpression in an atherosclerotic cell model. PTX3 may be a potential therapeutic target for atherosclerosis.     

Structural Aspect of a Thermal Activation Effect in the MnO x /γ-Al2O3 System

Solid-phase reactions in the aluminum–manganese oxide system, including the structural mechanism of the thermal activation of catalysts, were studied at temperatures up to 1100°C. It was found that the solid-phase reaction at 900–1000°C occurred via two pathways because of the diffusion of manganese ions to aluminum oxide and aluminum ions to manganese oxide. Nanoheterogeneous state of the active component, which was observed in the range 25–600°C, is the product of incomplete decomposition of the high-temperature aluminum–manganese phase Mn_{2.1 – x} Al_{0.9 + x} O₄ (0 x 0.6) with a cubic spinel structure; this phase was equilibrium at the synthesis temperature but metastable below 650°C.     

Synthesis and biological evaluation of 3-(piperidin-4-yl)isoxazolo[4,5-d]pyrimidine derivatives as novel PI3Kδ inhibitors

An efficient synthesis of novel 3-(piperidin-4-yl)isoxazolo[4, 5-d]pyrimidine scaffold has been designed and deveopled. A series of 5-phenylurea derivatives was synthesized using this method. Their cytotoxic activities against breast cancer cell line BT-474 were evaluated by CCK-8 assay. Most of them showed potent anti-proliferative activities, of which compound 20 and 21 exhibited IC₅₀s of 1.565 μmol/L and 1.311 μmol/L, respectively. Furthermore, compound 20 and 21 also showed potent inhibitory activities against PI3Kδ with IC₅₀s of 0.286 μmol/L and 0.452 μmol/L, respectively. These results indicate that these 3-(piperidin-4-yl)isoxazolo[4, 5-d] pyrimidine derivatives are novel antitumor agents through the inhibition of PI3Kδ.     

Effect of La_2O_3/γAl_2O_3 Catalyst on the Activation of CH_4 and CO_2 to C_02 Hydrocarbons under Non-equilibrium Plasma

The oxidative coupling of methane (OCM) to C2 hydrocarbons using carbon dioxide as oxidant is an attractive process from environmental point of view. Only a few research papers reported for it1-3. In general, the yield of C2 hydrocarbons was about 6%. This indicated that the method of catalytic activation was unfavorable to the reaction. It is necessary for us to find a new method in order to activate reaction and improve C2 hydrocarbon yield. Non-equilibrium plasma is a cold plasma in…     

Structure of x-ray photoelectron 2p and 1s spectra and x-ray Kα emission line of copper in YBa2Cu3O7−δ and CuO,on the basis of SCF-Xα-SW calculations

Conclusions Through an analysis of the electronic structure of the ground state and 2p and 1s hole states of the CuO₄ ^6– cluster, modeling the immediate environment of a copper atom (one of the two types) in YBa₂Cu₃O_7– and the immediate environment of the copper atom in CuO, it has been shown that upon ionization of core levels of copper, there is a radical reconstruction of the valence band of the cluster with a change in character of the chemical bond from covalent to ionic. Along with this, charge is transferred from the copper-oxygen bond to the central atom. Ionization of core levels leads to intense excitation of electrons into the upper semifilled valence level of the cluster 3b_1g, and also leads to the appearance in the x-ray photoelectron and x-ray spectra (K spectra, for example) of intense satellite lines with strong multiplet splitting (with the exception of the satellite of the x-ray photoelectron 1s spectrum). We have confirmed the interpretation of the x-ray photoelectron 2p_3/2 (2p_1/2) spectrum and have predicted the form of the x-ray photoelectron 1s spectrum of copper(II). On the basis of the same approach, a complex structure has been predicted for the x-ray K emission line and it has been confirmed that the shift of this line in compounds of copper(II) must be made with some caution, as the shift may be due (for example) to a change in relative intensities of the main and satellite lines, which are located relative to each other at a distance of 0.4 eV.Institute of Inorganic Chemistry, Siberian Branch, Russian Academy of Sciences. Translated from Zhurnal Strukturnoi Khimii, Vol. 33, No. 4, pp. 14–22, July–August, 1992.     

Experimental comparison of the relative yield of 3γ/2γ positron annihilation using semiconductor and scintillation detectors

The yield of three photon positron annihilation is measured using semiconductor and scintillation detectors in a comparison for applications in positron emission tomography, particularly in the exploitation of three photon positron annihilation imaging where good energy resolution and good efficiency are required. In this experimental study four detectors, High-purity Germanium (HPGe), Sodium Iodide (NaI(Tl)), Lanthanum Chloride (LaCl₃:10%Ce³⁺) and Lanthanum Bromide (LaBr₃:5%Ce³⁺) were used. The peak-to-peak method was used with a ²²Na source to determine these yields. Aluminium was employed as a reference material as its high electron density reduces positronium formation and lifetimes. Teflon was also used in order to enhance the formation of ortho-positronium, since quenching is low, leading to increased three photon positron annihilation. The relative 3γ/2γ yields obtained were (3.04±0.11)·10⁻², (2.17±0.11)·10⁻², (3.26±0.10)·10⁻² and (2.03±0.11)·10⁻² for LaBr₃:Ce, LaCl₃:Ce, NaI(Tl) and HPGe detectors, respectively. Among these detectors LaBr₃:Ce proved to be the detector of choice for three photon imaging applications as it has both good energy resolution and efficiency.     

Formation of the active centers of mixed palladium/γ-Al2O3 catalysts for oxidative purification of gases and their role in the adsorption and activation of carbon monoxide and oxygen

Physicochemical methods (ESR, ESDO, IR spectroscopy, photoluminescence, XRDA, TPD, TPV, etc.) were used to study the status of supported elements in modified Pd/-Al₂O₃ catalysts. The nature of the active centers of adsorption of O₂ and CO was determined. THe laws of the formation of the catalysts and changes of state of supported elements under the effects of environment and temperature wer identified.D. V. Sokolskii Institute of Organic Catalysis and Electrochemistry, Kazakh Academy of Sciences Alma-Ata. Translated from Teoreticheskaya i Eksperimental'naya Khimiya, Vo. 27, No. 6, pp. 646–653, November–December, 1991. Original article submitted September 5, 1991.     

Chemoenzymatic synthesis of (2S,3S,4S)-form, the physiologically active stereoisomer of dehydroxymethylepoxyquinomicin (DHMEQ), a potent inhibitor on NF-κB

A new route for (2S,3S,4S)-form, the physiologically active stereoisomer of dehydroxymethylepoxyquinomicin (DHMEQ), a potent NF-κB inhibitor, was established by chemoenzymatic approach. Elaboration on the asymmetric epoxidation of a p-benzoquinone monoketal with benzylcinchonidinium tert-butylhydroperoxide yielded an epoxyenone, in 79.8% ee and 57% yield in reproducible manner. By way of the transformation of this key intermediate to enantiomerically pure (2S,3S,4S)-DHMEQ, the contaminating undesired enantiomer could be effectively removed by applying Burkholderia cepacia lipase-catalyzed hydrolysis of diacylated precursor. The above integrated combination of chemical asymmetric synthesis and enzyme-catalyzed kinetic resolution enabled us to prepare active DHMEQ in a large-scale.     

Role of support nature （γ-Al2O3 and SiO2-Al2O3） on the performances of rhenium oxide catalysts in the metathesis of ethylene and 2-pentene

The metathesis of ethylene and 2-pentene was studied as an alternative route for propylene production over Re2O7/γ-Al2O3 and Re2O7/SiO2-Al2O3 catalysts. Both NH3 temperature-programmed desorption (NH3-TPD) and H2 temperature-programmed reduction (H2-TPR) results showed that Re2O7/SiO2-Al2O3 exhibited stronger acidity and weaker metal-support interaction than Re2O7/γ-Al2O3. At 35 60℃, isomerization free metathesis was observed only over Re2O7/γ-Al2O3, suggesting that the formation of metal-carbene metathesis active sites required only weak acidity. Our results suggest that on the Re2O7/SiO2-Al2O3, hydrido-rhenium species ([Re]-H) were formed in addition to the metathesis active sites, resulting in the isomerization of the initial 1-butene product into 2-butenes. A subsequent secondary metathesis reaction between these 2-butenes and the excess ethylene could explain the enhanced yields of propylene observed. The results demonstrate the potential for high yield of propylene from alternative feedstocks.     

An LC/ESI–MS/MS method to quantify the PI3K inhibitor GDC-0084 in human plasma and cerebrospinal fluid: Validation and clinical application

A liquid chromatography electrospray ionization tandem mass spectrometry (LC/ESI–MS/MS) method was developed and validated to measure GDC-0084 in human plasma and cerebrospinal fluid (CSF). Reverse-phase chromatography with gradient elution was performed using a C₁₈ column (50 × 2.0 mm, 3 μm). Solid-phase extraction of plasma and CSF was employed to give excellent recovery. MS detection was performed with positive ion screening in multiple reaction monitoring mode. The precursor to the product ions (Q1 → Q3) selected for GDC-0084 and GDC-0084-d₆ were 383.2 → 353.2 and 389.2 → 353.2, respectively. A separate calibration curve was established for human plasma and CSF. Both calibration curves, ranging from 0.2 to 200 ng/mL, were linear and had acceptable intra- and inter-day precision and accuracy. The lower limit of quantitation and limit of detection for GDC-0084 in human plasma were 0.2 ng/mL (signal/noise ≥47) and 0.005 ng/mL (signal/noise ≥3.5), respectively, and for GDC-0084 in human CSF were 0.2 ng/mL (signal/noise ≥19.7) and 0.04 ng/mL (signal/noise ≥7.2). This method was successfully applied to analyze serial plasma samples obtained from children with diffuse intrinsic pontine gliomas and other midline gliomas who participated in pharmacokinetic studies as part of a phase I clinical trial of GDC-0084.     

Effects of calcination and reduction temperature on the performance of Co-Pt-ZrO2/γ-A12O3 catalysts for Fischer-Tropsch synthesis

采用浸渍法制备了Co-Pt-ZrO2/γ-Al2O3催化剂,对其进行了BET、XRD和TPR等表征,并在浆态床反应器上考察了焙烧温度和还原温度对催化剂费托合成反应性能的影响.结果表明,焙烧温度过高,容易造成Co物种和载体间的相互作用增强,使部分氧化钻颗粒聚集或烧结,导致催化剂的F-T合成反应活性和C5+烃选择性降低.还原温度较低时,钴物种不能充分还原,CO加氢活性低,甲烷选择性高,重质烃选择性低;还原温度过高,则可能造成活性物种的烧结,反而降低了催化剂的活性和重质烃选择性.在原料气n(H2)/n( CO)=2.0、483 K、2.4 MPa和空速3.6 L/( gcat·h)的条件下,31.08％ Co～0.11％Pt ～ 7.16％ ZrO2/Al2O3催化剂在673 K焙烧.纯H2下653 K还原后,其费托性能最佳;CO转化率为27.0％,C5+的选择性为83.0％.     

Effect of La2O3／γ—Al2O3 Catalyst on the Activation of CH4 and CO2 to C2 Hydrocarbons under Non—equilibrium Plasma

In the reaction of methane and carbon dioxide to C2 hydrocabons under non-equilibrium plasma, methane conversion was decreased,but selectivity of C2 hydroxarbons was increased when using La2O3/γ-Al2O3 as catalyst. So the yield of C2 hydrocarbons was higher than using plasma alone. The synergism of La2O3/γ-Al2O3 and plasma gave methane conversion of 24.9% and C2 yield of 18.1%. The distribution of C2 hydrocarbons changed when Pd-La2O3/γ-Al2O3 was used as catalyst,the major C2 product was ethylene.