Discovery of novel imidazo[1,2-b]pyridazine derivatives as potent covalent inhibitors of CDK12/13.

Triple-negative breast cancer (TNBC) is widely recognized as the most aggressive subtype of breast cancer, and treatment options for patients with TNBC remain highly limited. Recently, cyclin-dependent kinases 12/13 (CDK12/13) have been identified as promising therapeutic targets for TNBC. In our study, we report the design and synthesis of novel imidazo[1,2-b]pyrazine-based covalent inhibitors of CDK12/13, which exhibit potent inhibitory activity against TNBC cells.

A Medicinal Chemistry Perspective on Protein Tyrosine Phosphatase Nonreceptor Type 2 in Tumor Immunology.

PTPN2 (protein tyrosine phosphatase nonreceptor type 2) is an important member of the protein tyrosine phosphatase (PTP) family. It plays a crucial role in dephosphorylating tyrosine-phosphorylated proteins and modulating critical signaling pathways associated with T-cell receptors, IL-2, IFNγ, and various cytokines. In recent years, the PTPN2's biological role has been clarified, particularly since its association with tumor immunology was gradually revealed in 2017, making it a star target for cancer immunotherapy.

Optical metabolic imaging identifies metabolic shifts and mitochondria heterogeneity in POLG mutator macrophages.

The polymerase gamma (POLG) gene mutation is associated with mitochondria and metabolism disorders, resulting in heterogeneous responses to immunological activation and posing challenges for mitochondrial disease therapy. Optical metabolic imaging captures the autofluorescent signal of two coenzymes, NADH and FAD, and offers a label-free approach to detect cellular metabolic phenotypes, track mitochondria morphology, and quantify metabolic heterogeneity. In this study, fluorescence lifetime imaging (FLIM) of NAD(P)H and FAD revealed that POLG mutator macrophages exhibit a decreased NAD(P)H lifetime, and optical redox ratio compared to the wild-type macrophages, indicating an increased dependence on glycolysis.

Label-free Detection and Characterization of Metabolism in Fresh and Cryopreserved Macrophages.

Cryopreservation is a widely used technique to preserve biological samples for extended periods of time at low temperatures. Even though it is known to have significant effects on cell viability, its effect on their metabolism remains unexplored. Studying how cryopreservation influences the metabolism of cells is important to guarantee the reliability of samples transported between sites for analysis.

Discovery of SET domain-binding primary alkylamine-tethered degraders for the simultaneous degradation of NSD2-long and RE-IIBP isoforms.

Nuclear receptor binding SET domain protein 2 (NSD2) is involved in various pathologic processes and is considered as an important target for cancer therapy. Due to alternative splicing, NSD2 has 3 isoforms: long, short and RE-IIBP. Although previous studies reported the degradation of PWWP1 domain-containing NSD2-long and short isoforms through PWWP1-binding molecules, the degradation of RE-IIBP which does not contain PWWP1 has been neglected to date.

Discovery of CLPP-1071 as an Exceptionally Potent and Orally Efficacious Human ClpP Activator with Strong In Vivo Antitumor Activity.

caseinolytic protease P (ClpP) is essential for maintaining mitochondrial proteome homeostasis, and its activation is increasingly recognized as a promising cancer therapy strategy. Herein, based on structure-guided drug design, we discovered a series of potent ClpP activators by introducing a methyl group to the imipridone scaffold of the ClpP activator in Phase III clinical trials. Through structural optimization of the lead compound, the most optimal compound, , exhibited exceptionally potent ClpP agonistic activity (EC = 23.

Discovery of KW0113 as a First and Effective PROTAC Degrader of DNMT1 Protein.

DNA methyltransferase 1 (DNMT1) is an attractive therapeutic target for acute myelocytic leukemia (AML) and other malignancies. It has been reported that the genetic depletion of DNMT1 inhibited AML cell proliferation through reversing DNA methylation abnormalities. However, no DNMT1-targeted PROTAC degraders have been reported yet.

Evaluation of Cellpose segmentation with sequential thresholding for instance segmentation of cytoplasms within autofluorescence images.

Background: Autofluorescence imaging of the coenzyme, reduced nicotinamide adenine dinucleotide (phosphate) (NAD(P)H), provides a label-free technique to assess cellular metabolism. Because NAD(P)H is localized in the cytosol and mitochondria, instance segmentation of cell cytoplasms from NAD(P)H images allows quantification of metabolism with cellular resolution. However, accurate cytoplasmic segmentation of autofluorescence images is difficult due to irregular cell shapes and cell clusters.

Discovery of a Covalent Inhibitor Selectively Targeting the Autophosphorylation Site of c-Src Kinase.

Nonreceptor tyrosine kinase c-Src plays a crucial role in cell signaling and contributes to tumor progression. However, the development of selective c-Src inhibitors turns out to be challenging. In our previous study, we performed posttranslational modification-inspired drug design (PTMI-DD) to provide a plausible way for designing selective kinase inhibitors.

3D convolutional neural networks predict cellular metabolic pathway use from fluorescence lifetime decay data.

Fluorescence lifetime imaging of the co-enzyme reduced nicotinamide adenine dinucleotide (NADH) offers a label-free approach for detecting cellular metabolic perturbations. However, the relationships between variations in NADH lifetime and metabolic pathway changes are complex, preventing robust interpretation of NADH lifetime data relative to metabolic phenotypes. Here, a three-dimensional convolutional neural network (3D CNN) trained at the cell level with 3D NAD(P)H lifetime decay images (two spatial dimensions and one time dimension) was developed to identify metabolic pathway usage by cancer cells.

Label-free spatially maintained measurements of metabolic phenotypes in cells.

Metabolic reprogramming at a cellular level contributes to many diseases including cancer, yet few assays are capable of measuring metabolic pathway usage by individual cells within living samples. Here, autofluorescence lifetime imaging is combined with single-cell segmentation and machine-learning models to predict the metabolic pathway usage of cancer cells. The metabolic activities of MCF7 breast cancer cells and HepG2 liver cancer cells were controlled by growing the cells in culture media with specific substrates and metabolic inhibitors.

Discovery of PVD-06 as a Subtype-Selective and Efficient PTPN2 Degrader.

Protein tyrosine phosphatase nonreceptor Type 2 (PTPN2) is an attractive target for cancer immunotherapy. PTPN2 and another subtype of PTP1B are highly similar in structure, but their biological functions are distinct. Therefore, subtype-selective targeting of PTPN2 remains a challenge for researchers.

Perfusability and immunogenicity of implantable pre-vascularized tissues recapitulating features of native capillary network.

Vascularization is a key pre-requisite to engineered anatomical scale three dimensional (3-D) constructs to ensure their nutrient and oxygen supply upon implantation. Presently, engineered pre-vascularized 3-D tissues are limited to only micro-scale hydrogels, which meet neither the anatomical scale needs nor the complexity of natural extracellular matrix (ECM) environments. Anatomical scale perfusable constructs are critically needed for translational applications.

Comparison of phasor analysis and biexponential decay curve fitting of autofluorescence lifetime imaging data for machine learning prediction of cellular phenotypes.

Autofluorescence imaging of the coenzymes reduced nicotinamide (phosphate) dinucleotide (NAD(P)H) and oxidized flavin adenine dinucleotide (FAD) provides a label-free method to detect cellular metabolism and phenotypes. Time-domain fluorescence lifetime data can be analyzed by exponential decay fitting to extract fluorescence lifetimes or by a fit-free phasor transformation to compute phasor coordinates. Here, fluorescence lifetime data analysis by biexponential decay curve fitting is compared with phasor coordinate analysis as input data to machine learning models to predict cell phenotypes.

POSEA: A novel algorithm to evaluate the performance of multi-object instance image segmentation.

Many techniques and software packages have been developed to segment individual cells within microscopy images, necessitating a robust method to evaluate images segmented into a large number of unique objects. Currently, segmented images are often compared with ground-truth images at a pixel level; however, this standard pixel-level approach fails to compute errors due to pixels incorrectly assigned to adjacent objects. Here, we define a per-object segmentation evaluation algorithm (POSEA) that calculates segmentation accuracy metrics for each segmented object relative to a ground truth segmented image.

Label-free optical imaging of cell function and collagen structure for cell-based therapies.

Cell-based therapies harness functional cells or tissues to mediate healing and treat disease. Assessment of cellular therapeutics requires methods that are non-destructive to ensure therapies remain viable and uncontaminated for use in patients. Optical imaging of endogenous collagen, by second-harmonic generation, and the metabolic coenzymes NADH and FAD, by autofluorescence microscopy, provides tissue structure and cellular information.

Osr1 Regulates Macrophage-mediated Liver Inflammation in Nonalcoholic Fatty Liver Disease Progression.

Background & Aims: Liver macrophage-mediated inflammation contributes to the pathogenesis of the nonalcoholic fatty liver disease (NAFLD) and nonalcoholic steatohepatitis (NASH). Odd skipped-related 1 (Osr1) is a putative transcription factor previously reported to be involved in NASH progression; however, the underlying mechanisms remain unknown. The current study focused on the role of Osr1 in macrophage polarization and metabolism and its associated functions in the inflammation-induced pathogenesis of NASH.

Metal-free photo-induced sulfidation of aryl iodide and other chalcogenation.

A photo-induced C-S radical cross-coupling of aryl iodides and disulfides under transition-metal and external photosensitizer free conditions for the synthesis of aryl sulfides at room temperature has been presented, which features mild reaction conditions, broad substrate scope, high efficiency, and good functional group compatibility. The developed methodology could be readily applied to forge C-S bond in the field of pharmaceutical and material science.

Autochthonous Probiotics Alleviate the Adverse Effects of Dietary Histamine in Juvenile Grouper ().

High dose (0.3%) of dietary histamine can cause adverse effects on growth performance, innate immunity, and gut health in juvenile grouper (). In the present study, three autochthonous probiotics ( SE5, sp.

Autofluorescence Imaging to Evaluate Cellular Metabolism.

Cellular metabolism is the process by which cells generate energy, and many diseases, including cancer, are characterized by abnormal metabolism. Reduced nicotinamide adenine (phosphate) dinucleotide (NAD(P)H) and oxidized flavin adenine dinucleotide (FAD) are coenzymes of metabolic reactions. NAD(P)H and FAD exhibit autofluorescence and can be spectrally isolated by excitation and emission wavelengths.

Fluorescence intensity and lifetime redox ratios detect metabolic perturbations in T cells.

The auto-fluorescent coenzymes reduced nicotinamide dinucleotide (NADH) and oxidized flavin adenine dinucleotide (FAD) allow label-free detection of cellular metabolism. The optical redox ratio, which is traditionally computed as the ratio of NADH and FAD intensities, allows quantification of cell redox state. In addition to multiple formulations of the optical redox ratio from NADH and FAD intensity measurements, a fluorescence lifetime redox ratio (FLIRR) based on the fractions of protein-bound NADH and FAD was developed to overcome the limitations of experimental factors that influence fluorescence intensity measurements.

Repurposing antimycotic ciclopirox olamine as a promising anti-ischemic stroke agent.

Ischemic stroke is a severe disorder resulting from acute cerebral thrombosis. Here we demonstrated that post-ischemic treatment with ciclopirox olamine (CPX), a potent antifungal clinical drug, alleviated brain infarction, neurological deficits and brain edema in a classic rat model of ischemic stroke. Single dose post-ischemic administration of CPX provided a long-lasting neuroprotective effect, which can be further enhanced by multiple doses administration of CPX.

Development of Novel -hydroxypyridone Derivatives as Potential Anti-Ischemic Stroke Agents.

Our previous study had identified ciclopirox (CPX) as a promising lead compound for treatment of ischemic stroke. To find better neuroprotective agents, a series of -hydroxypyridone derivatives based on CPX were designed, synthesized, and evaluated in this study. Among these derivatives, compound exhibits significant neuroprotection against oxygen glucose deprivation and oxidative stress-induced injuries in neuronal cells.

Pepper fragrant essential oil (PFEO) and functionalized MCM-41 nanoparticles: formation, characterization, and bactericidal activity.

Background: It is well known that plant essential oils have good antimicrobial activity. However, their strong volatility and intense odor limit their application. Mesoporous silica (MCM-41), a non-toxic mesoporous material with excellent loading capability, is a promising delivery system for different types of food ingredients in the food industry.