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Discovery of A-1331852, a First-in-Class, Potent, and Orally-Bioavailable BCL-X L Inhibitor
Abstract not provided
ABT-199, a potent and selective BCL-2 inhibitor, achieves antitumor activity while sparing platelets
Abstract not provided
BCL Gem [SWR 21-64]
This repository contains all the methods to build, test, and release the gem available as rake tasks via bundler/gem_tasks.
CASP11 – An Evaluation of a Modular BCL::Fold-Based Protein Structure Prediction Pipeline
In silico prediction of a protein’s tertiary structure remains an unsolved problem. The community-wide Critical Assessment of Protein Structure Prediction (CASP) experiment provides a double-blind study to evaluate improvements in protein structure prediction algorithms. We developed a protein structure prediction pipeline employing a three-stage approach, consisting of low-resolution topology search, high-resolution refinement, and molecular dynamics simulation to predict the tertiary structure of proteins from the primary structure alone or including distance restraints either from predicted residue-residue contacts, nuclear magnetic resonance (NMR) nuclear overhauser effect (NOE) experiments, or mass spectroscopy (MS) cross-linking (XL) data. The protein structure prediction pipeline was evaluated in the CASP11 experiment on twenty regular protein targets as well as thirty-three ‘assisted’ protein targets, which also had distance restraints available. Although the low-resolution topology search module was able to sample models with a global distance test total score (GDT_TS) value greater than 30% for twelve out of twenty proteins, frequently it was not possible to select the most accurate models for refinement, resulting in a general decay of model quality over the course of the prediction pipeline. In this study, we provide a detailed overall analysis, study one target protein in more detail as it travels through the protein structure prediction pipeline, and evaluate the impact of limited experimental data.
Characterization of BCL strain gages for use to 1366 K (2000 F)
Strain gage behavior under static and transient heating conditions at various strain rates and high temperatures (1366 K(2000 F) was studied. Optimum time-temperature parameters were developed for preconditioning (prestabilizing) the gages. A limited study was carried out to determine the extent of spalling of platinum cladding during fabrication of platinum-clad wire strain gages. Further verification was also carried out on the convergence and repeatability of the apparent strain characteristics of the gage under heating and cooling cycles. The significance of these characteristics from the standpoint of enhancing measurement accuracy is also discussed. It was concluded that the gage should perform satisfactorily to temperatures approaching 1366 K (2000 F).
Short-chain C6 ceramide sensitizes AT406-induced anti-pancreatic cancer cell activity
Our previous study has shown that AT406, a first-in-class small molecular antagonist of IAPs (inhibitor of apoptosis proteins), inhibits pancreatic cancer cell proliferation in vitro and in vivo. The aim of this research is to increase AT406's sensitivity by adding short-chain C6 ceramide. We show that co-treatment of C6 ceramide dramatically potentiated AT406-induced caspase/apoptosis activation and cytotoxicity in established (Panc-1 and Mia-PaCa-2 lines) and primary human pancreatic cancer cells. Reversely, caspase inhibitors largely attenuated C6 ceramide plus AT406-induced above cancer cell death. Molecularly, C6 ceramide downregulated Bcl-2 to increase AT406's sensitivity in pancreatic cancer cells. Intriguingly, C6 ceramide-mediated AT406 sensitization was nullified with Bcl-2 shRNA knockdown or pretreatment of the Bcl-2 inhibitor ABT-737. In vivo, liposomal C6 ceramide plus AT406 co-administration dramatically inhibited Panc-1 xenograft tumor growth in severe combined immunodeficient (SCID) mice. The combined anti-tumor activity was significantly more potent than either single treatment. Expressions of IAPs (cIAP1/XIAP) and Bcl-2 were downregulated in Panc-1 xenografts with the co-administration. Together, we demonstrate that C6 ceramide sensitizes AT406-mediated anti-pancreatic cancer cell activity possibly via downregulating Bcl-2. - Highlights: • C6 ceramide dramatically potentiates AT406-induced pancreatic cancer cell death. • C6 ceramide facilitates AT406-induced pancreatic cancer cell apoptosis. • C6 ceramide downregulates Bcl-2 to increase AT406's sensitivity in pancreatic cancer cells. • Liposomal C6 ceramide enhances AT406-induced anti-pancreatic cancer activity in vivo.
Heterolysis of H 2 Across a Classical Lewis Pair, 2,6-Lutidine∙BCl3: Synthesis, Characterization, and Mechanism
In this study, we report that 2,6-lutidine∙trichloroborane (Lut∙BCl 3 ) reacts with H 2 in toluene, bromobenzene, dichloromethane, and Lut solvents producing the neutral hydride, Lut∙BHCl 2 . The mechanism was modeled with density functional theory, and energies of stationary states were calculated at the G3(MP2)B3 level of theory. Lut∙BCl 3 was calculated to react with H 2 and form the ion pair, [LutH + ][HBCl 3 – ], with a barrier of ΔH ≠ =24.7 kcal mol –1 (ΔG ≠ =29.8 kcal mol –1 ). Metathesis with a second molecule of Lut∙BCl 3 produced Lut∙BHCl 2 and [LutH + ][BCl 4 – ]. The overall reaction is exothermic by 6.0 kcal mol –1 (Δ r G°=–1.1). Alternate pathways were explored involving the borenium cation (LutBCl 2 + ) and the four-membered boracycle [(CH 2 {NC 5 H 3 Me})BCl 2 ]. Barriers for addition of H 2 across the Lut/LutBCl 2 + pair and the boracycle B—C bond are substantially higher (ΔG ≠ =42.1 and 49.4 kcal mol –1 , respectively), such that these pathways are excluded. The barrier for addition of H 2 to the boracycle B—N bond is comparable (ΔH ≠ =28.5 and ΔG ≠ =32 kcal mol –1 ). Conversion of the intermediate 2-(BHCl 2 CH 2 )-6-Me(C 5 H 3 NH) to Lut∙BHCl 2 may occur by intermolecular steps involving proton/hydride transfers to Lut/BCl 3 . Intramolecular protodeboronation, which could form Lut∙BHCl 2 directly, is prohibited by a high barrier (ΔH ≠ =52, ΔG ≠ =51 kcal mol –1 ).
Angelica sinensis polysaccharides promotes apoptosis in human breast cancer cells via CREB-regulated caspase-3 activation
Angelica sinensis polysaccharide (ASP) is purified from the fresh roots of Angelica sinensis (AS). This traditional Chinese medicine has been used for thousands of years for treating gynecological diseases and used in functional foods for the prevention and treatment of various diseases, such as inflammation and cancer. The antitumor activity of ASP is related to its biological activities, because it suppresses a variety of pro-proliferative or anti-apoptotic factors that are dramatically expressed in cancer cells of given types. In this study, we show that angelica sinensis polysaccharide induced apoptosis in breast cancer cells of T47D over-expressing the Cyclic AMP response element binding protein (CREB), inducing apoptosis-related signaling pathway activity. The result also found that ASP caused cell death was linked to caspase activity, accompanied by the loss of mitochondrial membrane potential, cytochrome c release, and Bax translocation from the cytosol to the mitochondria. We found that ASP significantly affected the poly-ADP-ribose polymerase (PARP), Bcl-2 Associated X Protein (Bax), Bcl-2, Bcl-xL and apoptotic protease activating facter-1 (Apaf1) protein expression in a dose- and time-dependent manner. DAPI staining and Flow cytometry were used to analyze apoptosis. The nude mice xenograft model was used to evaluate the antitumor effect of ASP in vivo. ASP has profound antitumor effect on T47D cells, probably by inducing apoptosis through CREB signaling pathway. Thus, these results suggest that ASP would be a promising therapeutic agent for breast cancer. - Highlights: • CREB and Caspase-3 signaling pathways are involved in the ASP induced breast cancer cells apoptosis. • ROCK1/Mlc signaling pathway plays a critical role in this ASP-mediated apoptosis. • Angelica sinensis polysaccharide (ASP) affected the PARP, Bax, Bcl-2, Bcl-xL and Apaf1 protein expression. • The activation of CREB and ROCK1 promotes caspase-3 activation and apoptosis induced by ASP.
Peptide design by optimization on a data-parameterized protein interaction landscape
Many applications in protein engineering require optimizing multiple protein properties simultaneously, such as binding one target but not others or binding a target while maintaining stability. Such multistate design problems require navigating a high-dimensional space to find proteins with desired characteristics. A model that relates protein sequence to functional attributes can guide design to solutions that would be hard to discover via screening. In this work, we measured thousands of protein–peptide binding affinities with the high-throughput interaction assay amped SORTCERY and used the data to parameterize a model of the alpha-helical peptide-binding landscape for three members of the Bcl-2 family of proteins: Bcl-x L , Mcl-1, and Bfl-1. We applied optimization protocols to explore extremes in this landscape to discover peptides with desired interaction profiles. Computational design generated 36 peptides, all of which bound with high affinity and specificity to just one of Bcl-x L , Mcl-1, or Bfl-1, as intended. We designed additional peptides that bound selectively to two out of three of these proteins. The designed peptides were dissimilar to known Bcl-2–binding peptides, and high-resolution crystal structures confirmed that they engaged their targets as expected. Excellent results on this challenging problem demonstrate the power of a landscape modeling approach, and the designed peptides have potential uses as diagnostic tools or cancer therapeutics.
Activation of Wnt3α/β-catenin signal pathway attenuates apoptosis of the cerebral microvascular endothelial cells induced by oxygen-glucose deprivation
Brain microvascular endothelial cells (BMECs) play vital roles in cerebral ischemia, during which many signal pathways mediate BMECs apoptosis. In this study, we explored the potential role of Wnt3α/β-catenin signal in BMECs apoptosis induced by ischemia. Here, we found that oxygen-glucose deprivation (OGD) could induce apoptosis of BMECs with Wnt3a mRNA expression decrease. Meanwhile, activation Wnt3a/β-catenin signal with exogenous Wnt3α protein (100 ng/ml) or Lithium Chloride (LiCl, 4 mM) decreased significantly apoptosis of BMECs induced by OGD with increasing expression of Bcl-2 in the whole cell and β-catenin in the nucleus. But, inhibition Wnt3a/β-catenin signal with DKK1 (100 ng/ml) or 2.4-diamino quinazoline (DQ, 0.2 μM) increased apoptosis of BMECs with decreasing expression of Bcl-2. These results suggest that activation Wnt3α/β-catenin signal attenuate apoptosis of BMECs induced by ischemia. - Highlights: • OGD induced BMECs apoptosis with Wnt3a mRNA expression decrease. • Activation Wnt signal reduced BMECs apoptosis with increasing Bcl-2 and β-catenin. • Inhibition Wnt signal increased BMECs apoptosis with decreasing Bcl-2. • Wnt3α/β-catenin signal attenuates apoptosis of BMECs induced by ischemia.
Low expression level of HMBOX1 in high-grade serous ovarian cancer accelerates cell proliferation by inhibiting cell apoptosis
Highlights: • HMBOX1 was significantly downregulated in HGSOC tissues and ovarian cancer cell lines. • There was a negative correlation between the expression of HMBOX1 and cell proliferation of ovarian cancer cell lines. • HMBOX1 inhibited the cell proliferation and promoted the cell apoptosis. • HMBOX1 downregulated the expression of Bcl-2, Bcl-xL and upregulated that of Bad, Bax and Caspase3. Homeobox-containing 1 (HMBOX1) has been described as a transcription factor involved in the occurrence of some tumors, but its roles in ovarian cancer have never been reported. Here we aimed to investigate the roles of HMBOX1 on high-grade serous ovarian carcinoma (HGSOC). In this present study, HMBOX1 expression was decreased in HGSOC tissues and ovarian cancer cell lines (HO8910 and A2780) compared with ovarian surface epithelial tissues or normal human ovarian surface epithelial cell line (HOSEpiC). The cell proliferation of HOSEpiC was weaker than ovarian cancer cell lines. By altering the expression of HMBOX1 in A2780 and HOSEpiC, we demonstrated that HMBOX1 inhibited the cell proliferation and promoted the cell apoptosis. Furthermore, our study revealed that HMBOX1 downregulated the expression of anti-apoptotic proteins (Bcl-2, Bcl-xL), raised the expression of pro-apoptotic-regulated proteins (Bad, Bax), apoptotic executionior (Caspase3), and P53. In conclusion, HMBOX1 played important roles in occurrence of HGSOC through regulation of proliferation and apoptosis, which implied that HMBOX1 might serve as a new therapeutic target for HGSOC.
MicroRNA-133b inhibits hepatocellular carcinoma cell progression by targeting Sirt1
MicroRNAs (miRNAs) are a class of small non-coding RNAs that function as critical gene regulators by targeting mRNAs for translational repression or degradation. In this study, we showed that the expression level of miR-133b was decreased, while Sirt1 mRNA expression levels were increased in hepatocellular carcinoma (HCC) and cell lines, and we identified Sirt1 as a novel direct target of miR-133b. The over-expression of miR-133b suppressed Sirt1 expression. In addition, miR-133b over-expression resulted in attenuating HCC cell proliferation and invasion together with apoptosis increase in vitro. HepG2 cell transplantation revealed that up-regulation of miR-133b could inhibit HCC tumor genesis in vivo. Forced expression of Sirt1 partly rescued the effect of miR-133b in vitro. Furthermore, our study showed that miR-133b over-expression or Sirt1 down-regulation elevated E-cadherin expression, and repressed glypican-3 (GPC3) and the anti-apoptotic proteins (Bcl-2, Bcl-xL, and Mcl-1) expression. The inhibition of GPC3 expression repressed Bcl-2, Bcl-xL, and Mcl-1 expression, and elevated E-cadherin expression. Moreover, the Sirt1 up-regulation resulted in increases in HCC cell proliferation and invasion together with decreases apoptosis, and increases in the cytosolic accumulation and nuclear translocation of the transcription factor β-catenin in vitro. But the effect of Sirt1 up-regulation was partly reversed by GPC3 down-regulation in vitro. Taken together, these findings provide insight into the role and mechanism of miR-133b in regulating HCC cell proliferation, invasion and apoptosis via the miR-133b/Sirt1/GPC3/Wnt β-catenin axis, and miR-133b may serve as a potential therapeutic target in HCC in the future. - Highlights: • Sirt1 is a direct target of miR-133b in HCC. • miR-133b over-expression suppresses HCC progression in vitro and in vivo. • Sirt1 restoration reverses the effect of miR-133b over-expression on HCC cells. • GPC3 down-regulation reverses the effect of Sirt1 up-regulation on HCC cells. • Sirt1 activates Wnt β-catenin signaling by GPC3 in vitro.
Exogenous hydrogen sulfide protects from endothelial cell damage, platelet activation, and neutrophils extracellular traps formation in hyperhomocysteinemia rats
Highlights: • NaHS protects from ECs damage, platelet activation and NETs formation. • NaHS regulates platelets activation concern the phosphor-p38 MAPK pathway. • The inhibition of NaHS on platelets activation which prevents the NETs formation. Hydrogen sulfide (H{sub 2}S) prevents endothelial cells damage and P-selectin of platelets promotes neutrophils extracellular traps (NETs) formation. However, how sodium hydrosulfide (NaHS), a donor that produces H{sub 2}S regulates the activation of platelets and whether H{sub 2}S inhibits the formation of neutrophils extracellular traps in hyperhomocysteinemia rats have not been previously investigated. The morphological and ultrastructural alterations of endothelial cells (ECs) and platelets were tested by transmission electron microscopy. The expressions of P-selectin of platelets were determined by flow cytometry. Additionally, the cellular ROS and the H{sub 2}S level were detected by DCFH-DA staining and H{sub 2}S probe, the expressions of Bax and Bcl-2 in arteries and cultured ECs from rat thoracic aortas and the phosphor-p38 mitogen-activated protein kinase (MAPK), CSE and CBS of platelets were measured by western blotting. The NETs formations, the concentration of DNA in serum and supernatant of cultured neutrophils stimulated with platelet-rich plasma (PRP) were tested by Sytox Green and PicoGreen commercial Kits. The vascular ECs damaged, the expression of P-selectin of platelets and NETs formation increased; the concentration of DNA in serum and supernatant of cultured neutrophils stimulated with PRP also increased; the expression of Bax increased while Bcl-2 decreased in arteries, the phosphor-p38 MAPK of platelets increased while CSE and CBS have no statistically significant changes in the HHcy group compared to the control group. In the cultured ECs, the ROS level increased while the H{sub 2}S level decreased after 48 and 72 h treatment by HHcy; the expression of Bcl-2 decreased while Bax increased after 72 h treatment by HHcy. NaHS significantly inhibited the ECs injured, cellular ROS production, platelet activation and NETs formation, reversed the expressions of Bax, Bcl-2, phosphor-p38 MAPK, P-selectin and the increased concentration of DNA in serum and supernatant of cultured neutrophils which caused by high homocysteine. Our results demonstrate that the donor of H{sub 2}S inhibits the platelets activation and NETs formation, which concerts the protection of ECs in hyperhomocysteinemia.
Bicircular Light Floquet Engineering of Magnetic Symmetry and Topology and Its Application to the Dirac Semimetal Cd 3 As 2
Here, we show that bicircular light (BCL) is a versatile way to control magnetic symmetries and topology in materials. The electric field of BCL, which is a superposition of two circularly polarized light waves with frequencies that are integer multiples of each other, traces out a rose pattern in the polarization plane that can be chosen to break selective symmetries, including spatial inversion. Using a realistic low-energy model, we theoretically demonstrate that the three-dimensional Dirac semimetal Cd 3 As 2 is a promising platform for BCL Floquet engineering. Without strain, BCL irradiation induces a transition to a noncentrosymmetric magnetic Weyl semimetal phase with tunable energy separation between the Weyl nodes. In the presence of strain, we predict the emergence of a magnetic topological crystalline insulator with exotic unpinned surface Dirac states that are protected by a combination of twofold rotation and time reversal (2') and can be controlled by light.
Assessment of Existing OpenStudio Measures: Reviews, Interviews, and Future Developments
OpenStudio Measure development is continuously in progress and greatly propelled by the collaborative efforts within the building energy modeling community. To ensure the widespread adoption and benefit of OpenStudio Measures, developers must understand the current status of Measure development and the needs of OpenStudio Measure users. The first step involves a comprehensive review of existing content to prevent redundancy and gain insights into how OpenStudio Measures are used in the building energy modeling community. This knowledge can then be integrated into the Measure development process, and the expertise of practitioners and OpenStudio Measure users can be leveraged to shape future Measures. Numerous OpenStudio Measures have been created and shared on the Building Component Library (BCL). The BCL is an open-source repository housing various OpenStudio-related resources, including building component blocks, descriptive metadata, and Measures describing modifications to building energy models. The OpenStudio Measures in BCL encompass a wide range of energy conservation Measures from basic lighting power reduction to complex HVAC model transformation. They also enable users to generate customized reports and facilitate the integration of energy simulation with other analytical processes. This report presents review of 272 currently available OpenStudio Measures in BCL. The OpenStudio Measures were reviewed by category and subcategory. These Measures are summarized by their functionalities and keywords. To gain insights into how OpenStudio Measures are used in building energy modeling community, interviews were conducted. A total of 12 interview responses were collected from 6 individuals in the industry and 6 individuals in academia. The knowledge acquired from reviewing the existing Measures and interview results will be integrated into the Measure development process, and the expertise of practitioners and OpenStudio Measure users will be leveraged to shape future Measures.
Identification of a Covalent Molecular Inhibitor of Anti-apoptotic BFL-1 by Disulfide Tethering
The BCL-2 family is composed of anti- and pro-apoptotic members that respectively protect or disrupt mitochondrial integrity. Anti-apoptotic overexpression can promote oncogenesis by trapping the BCL-2 homology 3 (BH3) “killer domains” of pro-apoptotic proteins in a surface groove, blocking apoptosis. Groove inhibitors, such as the relatively large BCL-2 drug venetoclax (868 Da), have emerged as cancer therapies. BFL-1 remains an undrugged oncogenic protein and can cause venetoclax resistance. Having identified a unique C55 residue in the BFL-1 groove, we performed a disulfide tethering screen to determine if C55 reactivity could enable smaller molecules to block BFL-1's BH3-binding functionality. We found that a disulfide-bearing N-acetyltryptophan analog (304 Da adduct) effectively targeted BFL-1 C55 and reversed BFL-1-mediated suppression of mitochondrial apoptosis. Structural analyses implicated the conserved leucine-binding pocket of BFL-1 as the interaction site, resulting in conformational remodeling. Thus, therapeutic targeting of BFL-1 may be achievable through the design of small, cysteine-reactive drugs.