Discovery of novel FGFR4 inhibitors through a build-up fragment strategy.

Hepatocellular carcinoma (HCC) is a leading cause of cancer-related death. FGFR4 has been implicated in HCC progression, making it a promising therapeutic target. We introduce an approach for identifying novel FGFR4 inhibitors by sequentially adding fragments to a common warhead unit. This strategy resulted in the discovery of a potent inhibitor, 4c, with an IC50 of 33 nM and high selectivity among members of the FGFR family. Although further optimisation is required, our approach demonstrated the potential for discovering potent FGFR4 inhibitors for HCC treatment, and provides a useful method for obtaining hit compounds from small fragments.

Precursor deconvolution error estimation: The missing puzzle piece in false discovery rate in top-down proteomics.

Top-down proteomics (TDP) directly analyzes intact proteins and thus provides more comprehensive qualitative and quantitative proteoform-level information than conventional bottom-up proteomics (BUP) that relies on digested peptides and protein inference. While significant advancements have been made in TDP in sample preparation, separation, instrumentation, and data analysis, reliable and reproducible data analysis still remains one of the major bottlenecks in TDP. A key step for robust data analysis is the establishment of an objective estimation of proteoform-level false discovery rate (FDR) in proteoform identification. The most widely used FDR estimation scheme is based on the target-decoy approach (TDA), which has primarily been established for BUP. We present evidence that the TDA-based FDR estimation may not work at the proteoform-level due to an overlooked factor, namely the erroneous deconvolution of precursor masses, which leads to incorrect FDR estimation. We argue that the conventional TDA-based FDR in proteoform identification is in fact protein-level FDR rather than proteoform-level FDR unless precursor deconvolution error rate is taken into account. To address this issue, we propose a formula to correct for proteoform-level FDR bias by combining TDA-based FDR and precursor deconvolution error rate.

The comparison of the accuracy of temporary crowns fabricated with several 3D printers and a milling machine.

PURPOSE: The purpose of this in vitro study was to compare the accuracy of various 3D printers and a milling machine. MATERIALS AND METHODS: The die model was designed using CAD (Autodesk Inventor 2018 sp3). The 30 µm cement space was given to the die and the ideal crown of the mandibular left first molar was designed using CAD (ExoCAD). The crowns were produced using the milling machine (Imes-icore 250i) and the 3D printers (Zenith U, Zenith D, W11) and they were divided into four groups. In all groups, the interior of each crown was scanned (Identica blue) and superimposed (Geomagic Control X) with the previously designed die. The difference between the die and the actual crown was measured at specific points. The Kruskal-Wallis test, the Mann-Whitney test, and Bonferroni's method were performed with a statistical analysis software (P < .008 in inter-group comparison P < .001 in intra-group comparison). RESULTS: In all groups, the center of the occlusal area and the anti-rotational dimple area showed significantly greater difference and the marginal area showed the smallest difference comparatively. The mean value of the difference in each area and the sum of the differences were higher in order of W11, Imes-icore 250i, Zenith D, and Zenith U. CONCLUSION: The digital light processing (DLP) method shows higher accuracy compared to the sereolithography (SLA) method using the same resin material.

Ferroelectric synaptic devices based on CMOS-compatible HfAlOx for neuromorphic and reservoir computing applications.

The hafnium oxide-based ferroelectric tunnel junction (FTJ) has been actively researched because of desirable advantages such as low power and CMOS compatibility to operate as a memristor. In the case of HfAlOx (HAO), the remanent polarization (Pr) value is high and the atomic radius of Al is smaller than that of Hf; therefore, ferroelectricity can be better induced without mechanical force. In this paper, we propose an FTJ using HAO as a ferroelectric layer through electrical analysis and experiments; further, we experimentally demonstrate its capability as a synaptic device. Moreover, we evaluate the maximum 2Pr and TER value of the device according to the difference in conditions of thickness and cell area. The optimized device conditions are analyzed, and a large value of 2Pr (>∼43 µC cm-2) is obtained. Furthermore, we show that paired-pulse facilitation, paired-pulse depression, and spike-timing-dependent plasticity can be utilized in HAO-based FTJs. In addition, this study demonstrates the use of an FTJ device as a physical reservoir to implement reservoir computing. Through a series of processes, the synaptic properties of FTJs are verified for the feasibility of their implementation as an artificial synaptic device.

Suboptimal Mitochondrial Activity Facilitates Nuclear Heat Shock Responses for Proteostasis and Genome Stability.

Thermal stress induces dynamic changes in nuclear proteins and relevant physiology as a part of the heat shock response (HSR). However, how the nuclear HSR is fine-tuned for cellular homeostasis remains elusive. Here, we show that mitochondrial activity plays an important role in nuclear proteostasis and genome stability through two distinct HSR pathways. Mitochondrial ribosomal protein (MRP) depletion enhanced the nucleolar granule formation of HSP70 and ubiquitin during HSR while facilitating the recovery of damaged nuclear proteins and impaired nucleocytoplasmic transport. Treatment of the mitochondrial proton gradient uncoupler masked MRP-depletion effects, implicating oxidative phosphorylation in these nuclear HSRs. On the other hand, MRP depletion and a reactive oxygen species (ROS) scavenger non-additively decreased mitochondrial ROS generation during HSR, thereby protecting the nuclear genome from DNA damage. These results suggest that suboptimal mitochondrial activity sustains nuclear homeostasis under cellular stress, providing plausible evidence for optimal endosymbiotic evolution via mitochondria-to-nuclear communication.

Analog Resistive Switching and Artificial Synaptic Behavior of ITO/WOX/TaN Memristors.

In this work, we fabricated an ITO/WOX/TaN memristor device by reactive sputtering to investigate resistive switching and conduct analog resistive switching to implement artificial synaptic devices. The device showed good pulse endurance (104 cycles), a high on/off ratio (>10), and long retention (>104 s) at room temperature. The conduction mechanism could be explained by Schottky emission conduction. Further, the resistive switching characteristics were performed by additional pulse-signal-based experiments for more practical operation. Lastly, the potentiation/depression characteristics were examined for 10 cycles. The results thus indicate that the WOX-based devices are appropriate candidates for synaptic devices as well as next-generation nonvolatile memory.

Impact of annealing temperature on the remanent polarization and tunneling electro-resistance of ferroelectric Al-doped HfOx tunnel junction memory.

The ferroelectric characteristics of a metal-ferroelectric-metal (MFM) ferroelectric tunneling junction (FTJ) capacitor device are investigated herein. The device consists of an aluminum-doped hafnium oxide (HAO) insulator sandwiched between tungsten (W) and titanium nitride (TiN) metal electrodes. Rapid thermal annealing (RTA) is performed for 20 s under a nitrogen atmosphere at temperatures of 750 °C, 800 °C, and 850 °C to find that ferroelectricity with a large remanent polarization (Pr) of 41.28 µC cm-2 can be obtained at the optimum annealing temperature of 800 °C. The presence of ferroelectricity is confirmed by polarization-switching positive-up-negative-down (PUND) measurements and by the hysteric polarization-voltage (P-V) loop. All devices exhibit excellent reliability, with an endurance of up to ∼106 cycles and long retention characteristics. In addition, the interfacial paraelectric capacitance (Ci) values of the three HAO FTJs are investigated via pulse-switching measurements. The results indicate that the HAO film annealed at 800 °C for 20 s exhibits an excellent tunneling electro-resistance (TER) ratio of 186% and this is attributed to the extra paraelectric layer formed between the ferroelectric layer and the bottom electrode. The detailed findings of this study are expected to assist in the development of hafnium oxide-based ferroelectric non-volatile memory applications.

Enhancement of Resistive and Synaptic Characteristics in Tantalum Oxide-Based RRAM by Nitrogen Doping.

Resistive random-access memory (RRAM) for neuromorphic systems has received significant attention because of its advantages, such as low power consumption, high-density structure, and high-speed switching. However, variability occurs because of the stochastic nature of conductive filaments (CFs), producing inaccurate results in neuromorphic systems. In this article, we fabricated nitrogen-doped tantalum oxide (TaOx:N)-based resistive switching (RS) memory. The TaOx:N-based device significantly enhanced the RS characteristics compared with a TaOx-based device in terms of resistance variability. It achieved lower device-to-device variability in both low-resistance state (LRS) and high-resistance state (HRS), 8.7% and 48.3% rather than undoped device of 35% and 60.7%. Furthermore, the N-doped device showed a centralized set distribution with a 9.4% variability, while the undoped device exhibited a wider distribution with a 17.2% variability. Concerning pulse endurance, nitrogen doping prevented durability from being degraded. Finally, for synaptic properties, the potentiation and depression of the TaOx:N-based device exhibited a more stable cycle-to-cycle variability of 4.9%, compared with only 13.7% for the TaOx-based device. The proposed nitrogen-doped device is more suitable for neuromorphic systems because, unlike the undoped device, uniformity of conductance can be obtained.

Bipolar Switching Characteristics of Transparent WOX-Based RRAM for Synaptic Application and Neuromorphic Engineering.

In this work, we evaluate the resistive switching (RS) and synaptic characteristics of a fully transparent resistive random-access memory (T-RRAM) device based on indium-tin-oxide (ITO) electrodes. Here, we fabricated ITO/WOX/ITO capacitor structure and incorporated DC-sputtered WOX as the switching layer between the two ITO electrodes. The device shows approximately 77% (including the glass substrate) of optical transmittance in visible light and exhibits reliable bipolar switching behavior. The current-voltage (I-V) curve is divided into two types: partial and full curves affected by the magnitude of the positive voltage during the reset process. In the partial curve, we confirmed that the retention could be maintained for more than 104 s and the endurance for more than 300 cycles could be stably secured. The switching mechanism based on the formation/rupture of the filament is further explained through the extra oxygen vacancies provided by the ITO electrodes. Finally, we examined the responsive potentiation and depression to check the synaptic characteristics of the device. We believe that the transparent WOX-based RRAM could be a milestone for neuromorphic devices as well as future non-volatile transparent memory.

Prolongation of Fate of Bacteriophages In Vivo by Polylactic-Co-Glycolic-Acid/Alginate-Composite Encapsulation.

With concern growing over antibiotics resistance, the use of bacteriophages to combat resistant bacteria has been suggested as an alternative strategy with which to enable the selective control of targeted pathogens. One major challenge that restrains the therapeutic application of bacteriophages as antibacterial agents is their short lifespan, which limits their antibacterial effect in vivo. Here, we developed a polylactic-co-glycolic acid (PLGA)/alginate-composite microsphere for increasing the lifespan of bacteriophages in vivo. The alginate matrix in PLGA microspheres encapsulated the bacteriophages and protected them against destabilization by an organic solvent. Encapsulated bacteriophages were detected in the tissue for 28 days post-administration, while the bacteriophages administered without advanced encapsulation survived in vivo for only 3-5 days. The bacteriophages with extended fate showed prophylaxis against the bacterial pathogens for 28 days post-administration. This enhanced prophylaxis is presumed to have originated from the diminished immune response against these encapsulated bacteriophages because of their controlled release. Collectively, composite encapsulation has prophylactic potential against bacterial pathogens that threaten food safety and public health.

FLASHIda enables intelligent data acquisition for top-down proteomics to boost proteoform identification counts.

The detailed analysis and structural characterization of proteoforms by top-down proteomics (TDP) has gained a lot of interest in biomedical research. Data-dependent acquisition (DDA) of intact proteins is non-trivial due to the diversity and complexity of proteoforms. Dedicated acquisition methods thus have the potential to greatly improve TDP. Here, we present FLASHIda, an intelligent online data acquisition algorithm for TDP that ensures the real-time selection of high-quality precursors of diverse proteoforms. FLASHIda combines fast charge deconvolution algorithms and machine learning-based quality assessment for optimal precursor selection. In an analysis of E. coli lysate, FLASHIda increases the number of unique proteoform level identifications from 800 to 1500 or generates a near-identical number of identifications in one third of the instrument time when compared to standard DDA mode. Furthermore, FLASHIda enables sensitive mapping of post-translational modifications and detection of chemical adducts. As a software extension module to the instrument, FLASHIda can be readily adopted for TDP studies of complex samples to enhance proteoform identification rates.

Mass Deconvolution of Top-Down Mass Spectrometry Datasets by FLASHDeconv.

Mass deconvolution, the determination of proteoform precursor and fragment masses, is crucial for top-down proteomics data analysis. Here we describe the detailed procedure to run FLASHDeconv, an ultrafast, high-quality mass deconvolution tool. Both spectrum- and feature-level deconvolution results are obtainable in various output formats by FLASHDeconv. FLASHDeconv is runnable in different environments such as the command line and OpenMS workflows.

Structure-activity relationships of novel quinazoline derivatives with high selectivity for HER2 over EGFR.

The gene amplification of human epidermal growth factor receptor 2 (HER2) plays an essential role in the proliferation and progression of several cancers. However, HER2 inhibitors such as lapatinib strongly suppress wild-type EGFR, resulting in severe adverse effects. Therefore, there is an unmet need for highly selective HER2 inhibitors. In this study, we describe the design and synthesis of novel quinazoline derivatives that exhibit enhanced selectivity for HER2 over wild-type EGFR. Structure-activity relationship analysis indicated that the selectivity for HER2 over EGFR depends on the aniline moiety at C-4 and the substituents at C-6 in the quinazoline derivatives. Compound 7c with an IC50 of 8 nM for HER2 exhibited significantly higher selectivity for HER2 over EGFR, with a 240-fold improvement over lapatinib. In addition, the synthesized compounds exhibited anti-proliferative activity in the nanomolar range against SKBR3, a human breast cancer cell line that overexpresses HER2.

Clinical Efficacy of Sealer-based Obturation Using Calcium Silicate Sealers: A Randomized Clinical Trial.

INTRODUCTION: This randomized controlled clinical trial compared the clinical efficacy and outcome of a sealer-based obturation technique (SBO) with calcium silicate sealers and a continuous wave of condensation technique (CWC) with a resin-based sealer. METHODS: Root canals were prepared using rotary instruments and 2.5% sodium hypochlorite. At the next visit, patients were enrolled and randomly assigned into 2 groups on the basis of the obturation protocol: CWC with AH Plus sealer and SBO with Endoseal TCS. Patients were assessed for the level of postoperative pain using a numeric rating scale. The quality of root canal obturation was evaluated in terms of the sealer extrusion, root-filling voids, and level of root filling. The participants were recalled after at least 6 months. Healing of the teeth was determined as a decrease in Periapical Index score and resolution of symptoms. The results were statistically compared by using the χ2 test or Fisher exact test, followed by multivariate analysis with logistic regression. RESULTS: A total of 74 teeth were included in the analysis (79% recalls), and the mean follow-up period was 17 months (6-29 months). Two groups expressed identical distribution of postoperative pain (P = .973) and similar quality of root canal obturation. The total success rates were 93.2% (CWC 92.3%, SBO 94.3%) by loose criteria and 60.8% (CWC 51.3%, SBO 71.4%) by strict criteria, with no significant differences between the 2 groups. The success rate by loose criteria in teeth with sealer extrusion was significantly lower than those in teeth without sealer extrusion (P = .049). CONCLUSIONS: SBO using an Endoseal TCS could be a possible alternative to CWC using AH Plus. Sealer extrusion and postoperative pain were found to negatively impact prognosis of the endodontic treatment.

Metabolic flux from the Krebs cycle to glutamate transmission tunes a neural brake on seizure onset.

Kohlschütter-Tönz syndrome (KTS) manifests as neurological dysfunctions, including early-onset seizures. Mutations in the citrate transporter SLC13A5 are associated with KTS, yet their underlying mechanisms remain elusive. Here, we report that a Drosophila SLC13A5 homolog, I'm not dead yet (Indy), constitutes a neurometabolic pathway that suppresses seizure. Loss of Indy function in glutamatergic neurons caused "bang-induced" seizure-like behaviors. In fact, glutamate biosynthesis from the citric acid cycle was limiting in Indy mutants for seizure-suppressing glutamate transmission. Oral administration of the rate-limiting α-ketoglutarate in the metabolic pathway rescued low glutamate levels in Indy mutants and ameliorated their seizure-like behaviors. This metabolic control of the seizure susceptibility was mapped to a pair of glutamatergic neurons, reversible by optogenetic controls of their activity, and further relayed onto fan-shaped body neurons via the ionotropic glutamate receptors. Accordingly, our findings reveal a micro-circuit that links neural metabolism to seizure, providing important clues to KTS-associated neurodevelopmental deficits.

ZNF598 co-translationally titrates poly(GR) protein implicated in the pathogenesis of C9ORF72-associated ALS/FTD.

C9ORF72-derived dipeptide repeat proteins have emerged as the pathogenic cause of neurodegeneration in amyotrophic lateral sclerosis and frontotemporal dementia (C9-ALS/FTD). However, the mechanisms underlying their expression are not fully understood. Here, we demonstrate that ZNF598, the rate-limiting factor for ribosome-associated quality control (RQC), co-translationally titrates the expression of C9ORF72-derived poly(GR) protein. A Drosophila genetic screen identified key RQC factors as potent modifiers of poly(GR)-induced neurodegeneration. ZNF598 overexpression in human neuroblastoma cells inhibited the nuclear accumulation of poly(GR) protein and decreased its cytotoxicity, whereas ZNF598 deletion had opposing effects. Poly(GR)-encoding sequences in the reporter RNAs caused translational stalling and generated ribosome-associated translation products, sharing molecular signatures with canonical RQC substrates. Furthermore, ZNF598 and listerin 1, the RQC E3 ubiquitin-protein ligase, promoted poly(GR) degradation via the ubiquitin-proteasome pathway. An ALS-relevant ZNF598R69C mutant displayed loss-of-function effects on poly(GR) expression, as well as on general RQC. Moreover, RQC function was impaired in C9-ALS patient-derived neurons, whereas lentiviral overexpression of ZNF598 lowered their poly(GR) expression and suppressed proapoptotic caspase-3 activation. Taken together, we propose that an adaptive nature of the RQC-relevant ZNF598 activity allows the co-translational surveillance to cope with the atypical expression of pathogenic poly(GR) protein, thereby acquiring a neuroprotective function in C9-ALS/FTD.

Discovery of potent colony-stimulating factor 1 receptor inhibitors by replacement of hinge-binder moieties.

Tumor-associated macrophages (TAMs) are predominantly associated with tumor growth. Colony-stimulating factor 1 receptor (CSF1R) acts as a key regulator of TAM survival and differentiation and is a molecular target for cancer therapies. Herein, novel CSF1R inhibitors were identified through a replacement strategy for the hinge-binding moiety. The introduction of imidazo[1,2-a]pyridine (49) or pyrazolo[1,5-a]pyridine (50) as hinge binders led to 87% and 82% inhibition at 10 nM for CSF1R in the enzymatic assay, with IC50 values of 25 nM and 27 nM in MNFS60 cells, respectively. These derivatives significantly inhibited CSF1R phosphorylation in cells. Our approach could be utilized as a strategy to discover novel kinase inhibitors.

Succinate-treated macrophages attenuate dextran sodium sulfate colitis in mice.

BACKGROUND/AIMS: The safety and effectiveness of adalimumab was demonstrated in a phase 3 trial in Japanese patients with intestinal Behçet's disease. The aim of this study was to evaluate the long-term safety and effectiveness of adalimumab in Japanese patients with intestinal Behçet's disease.

LSM12-EPAC1 defines a neuroprotective pathway that sustains the nucleocytoplasmic RAN gradient.

Nucleocytoplasmic transport (NCT) defects have been implicated in neurodegenerative diseases such as C9ORF72-associated amyotrophic lateral sclerosis and frontotemporal dementia (C9-ALS/FTD). Here, we identify a neuroprotective pathway of like-Sm protein 12 (LSM12) and exchange protein directly activated by cyclic AMP 1 (EPAC1) that sustains the nucleocytoplasmic RAN gradient and thereby suppresses NCT dysfunction by the C9ORF72-derived poly(glycine-arginine) protein. LSM12 depletion in human neuroblastoma cells aggravated poly(GR)-induced impairment of NCT and nuclear integrity while promoting the nuclear accumulation of poly(GR) granules. In fact, LSM12 posttranscriptionally up-regulated EPAC1 expression, whereas EPAC1 overexpression rescued the RAN gradient and NCT defects in LSM12-deleted cells. C9-ALS patient-derived neurons differentiated from induced pluripotent stem cells (C9-ALS iPSNs) displayed low expression of LSM12 and EPAC1. Lentiviral overexpression of LSM12 or EPAC1 indeed restored the RAN gradient, mitigated the pathogenic mislocalization of TDP-43, and suppressed caspase-3 activation for apoptosis in C9-ALS iPSNs. EPAC1 depletion biochemically dissociated RAN-importin ß1 from the cytoplasmic nuclear pore complex, thereby dissipating the nucleocytoplasmic RAN gradient essential for NCT. These findings define the LSM12-EPAC1 pathway as an important suppressor of the NCT-related pathologies in C9-ALS/FTD.