Enhancing Chemical Reaction Monitoring with a Deep Learning Model for NMR Spectra Image Matching to Target Compounds.

In the synthetic laboratory, researchers typically rely on nuclear magnetic resonance (NMR) spectra to elucidate structures of synthesized products and confirm whether they match the desired target compounds. As chemical synthesis technology evolves toward intelligence and continuity, efficient computer-assisted structure elucidation (CASE) techniques are required to replace time-consuming manual analysis and provide the necessary speed. However, current CASE methods typically aim to derive precise chemical structures from spectroscopic data, yet they suffer from drawbacks such as low accuracy, high computational cost, and reliance on chemical libraries. In meticulously designed chemical synthesis reactions, researchers prioritize confirming the attainment of the target product based on NMR spectra, rather than focusing on identifying the specific product obtained. For this purpose, we innovatively developed a binary classification model, termed as MatCS, to directly predict the relationship between NMR spectra image (including 1H NMR and 13C NMR) and the molecular structure of the target compound. After evaluating various feature extraction methods, MatCS employs a combination of the Graph Attention Networks and Graph Convolutional Networks to learn the structural features of molecular graphs and the pretrained ResNet101 network with a Convolutional Block Attention Module to extract features from NMR spectra images. The results show that on a challenging Testsim data set, which poses difficulty in distinguishing spectra of similar molecular structures, MatCS achieves comprehensive evaluation metrics with an F1-score of 0.81 and an AUC value of 0.87. Simultaneously, it exhibited commendable performance on an external SDBS data set containing experimental NMR spectra, showcasing substantial potential for structural verification tasks in real automated chemical synthesis.

Identification and biological evaluation of fused tetrahydroisoquinoline derivatives as Wnt/ß-catenin signaling inhibitors to suppress colorectal cancer.

Colorectal cancer (CRC) has been becoming one of the most common causes of cancer mortality worldwide. Accumulating studies suggest that the progressive up-regulation of Wnt/ß-catenin signaling is a crucial hallmark of CRC, and suppressing it is a promising strategy to treat CRC. Herein, we reported our latest efforts in the discovery of novel fused tetrahydroisoquinoline derivatives with good anti-CRC activities by screening our in-house berberine-like library and further structure-activity relationship (SAR) studies, in which we identified compound 10 is a potent lead compound with significant antiproliferation potencies. By the biotinylated probe and LC-MS/MS study, Hsp90 was identified as its molecular target, which is a fully different mechanism of action from what we reported before. Further studies showed compound 10 directly engaged the N-terminal site of Hsp90 and promoted the degradation of ß-catenin, thereby suppressing the Wnt/ß-catenin signaling. More importantly, compound 10 exhibits favorable pharmacokinetic parameters and significant anti-tumor efficacies in the HCT116 xenograft model. Taken together, this study furnished the discovery of candidate drug compound 10 possessing a novel fused tetrahydroisoquinoline scaffold with excellent in vitro and in vivo anti-CRC activities by targeting Hsp90 to disturb Wnt/ß-catenin signaling pathway, which lay a foundation for discovering more effective CRC-targeted therapies.

Discovery and Optimization of Tetrahydroisoquinoline Derivatives To Enhance Lysosome Biogenesis as Preclinical Candidates for the Treatment of Alzheimer's Disease.

More than 55 million individuals are suffering from Alzheimer's disease (AD), while the effective therapeutic strategies remain elusive. Our previous study identified a lysosome-enhancing lead compound LH2-051 with a tetrahydroisoquinoline scaffold through a novel dopamine transporter-cyclin-dependent kinase 9-transcription factor EB (DAT-CDK9-TFEB) regulation mechanism to promote TFEB activation and lysosome biogenesis. Here, we launched a comprehensive structure-activity relationship study for LH2-051, and 47 new derivatives were designed and synthesized, in which several compounds exhibited remarkable lysosome-enhancing activities. Notably, compounds 37 and 45 exhibited more favorable TFEB activation and lysosome biogenesis capabilities, good safety profiles, and excellent pharmacokinetic profiles with high brain penetration. Further investigations demonstrated that both compounds significantly enhance the clearance of Aß aggregates and ameliorate the impairment of learning, memory, and cognition in APP/PS1 mice. Overall, these results indicated that compounds 37 and 45 are promising preclinical drug candidates for the treatment of AD.

Innovative Diagnosis and Therapeutic Modalities: Engineered Exosomes in Autoimmune Disease.

Autoimmune diseases refer to a group of conditions where the immune system produces an immune response against self-antigens, resulting in tissue damage. These diseases have profound impacts on the health of patients. In recent years, with the rapid development in the field of biomedicine, engineered exosomes have emerged as a noteworthy class of biogenic nanoparticles. By precisely manipulating the cargo and surface markers of exosomes, engineered exosomes have gained enhanced anti-inflammatory, immunomodulatory, and tissue reparative abilities, providing new prospects for the treatment of autoimmune diseases. Engineered exosomes not only facilitate the efficient delivery of bioactive molecules including nucleic acids, proteins, and cytokines, but also possess the capability to modulate immune cell functions, suppress inflammation, and restore immune homeostasis. This review mainly focuses on the applications of engineered exosomes in several typical autoimmune diseases. Additionally, this article comprehensively summarizes the current approaches for modification and engineering of exosomes and outlines their prospects in clinical applications. In conclusion, engineered exosomes, as an innovative therapeutic approach, hold promise for the management of autoimmune diseases. However, while significant progress has been made, further rigorous research is still needed to address the challenges that engineered exosomes may encounter in the therapeutic intervention process, in order to facilitate their successful translation into clinical practice and ultimately benefit a broader population of patients.

Highly efficient ion-transport "polymer-in-ceramic" electrolytes boost stable all-solid-state Li metal batteries.

"Polymer-in-ceramic" (PIC) electrolytes are widely investigated for all-solid-state batteries (ASSBs) due to their good thermal stability and mechanical performance. However, achieving fast and diversified lithium-ion transport inside the PIC electrolyte and uniform Li+ deposition at the electrolyte/Li anode interface simultaneously remains a challenge. Besides, the effect of ceramic particle size on Li+ transport and Li anodic compatibility is still unclear, which is essential for revealing the enhanced mechanism of the performance for PIC electrolytes. Herein, PIC with moderate ceramic size and contents are prepared and studied to strike a balance between ionic conductivity and anodic compatibility. Through moderate filler-filler interfacial impedance and appropriate surface roughness, a particle size of 17 µm is optimized to facilitate homogeneous Li+ flux on anode and enhance Li+ conductivity of the electrolyte. The PIC electrolyte with ceramic particle size of 17 µm achieves a high lithium ion transference number (0.74) and an ionic conductivity of 4.11 × 10-4 S cm-1 at 60 °C. The Li/PIC/Li symmetric cell can stably cycle for 2800 h at 0.2 mA cm-2 with 0.2 mAh cm-2. Additionally, the Li/PIC/LiFePO4 cell also delivers a superior cycling performance at 0.5C, a high capacity retention of 93.28% after 100 cycles and 83.17% after 200 cycles, respectively.

Effects of Aerobic Exercise on Executive and Memory Functions in Patients With Alzheimer's Disease: A Systematic Review.

BACKGROUND: Alzheimer's disease threatens the health of older adults, particularly by disrupting executive and memory functions, and many studies have shown that aerobic exercise prevents and improves the symptoms associated with the disease. OBJECTIVE: The objective was to systematically review the effects of aerobic exercise on executive and memory functions in patients with Alzheimer's disease and to determine the effect factors and mechanisms of the design of aerobic exercise intervention programs. METHOD: Relevant literature was searched in three databases (PubMed, Web of Science, and EBSCO) from January 1, 2014 to March 1, 2023, using a subject-word search method. Data on 10 items, including author and country, were extracted from the literature after screening. The quality of the literature was evaluated using the Physiotherapy Evidence Database scale, and a systematic review was performed. RESULTS: Twelve papers from seven countries were ultimately included, embodying 11 randomized controlled trials and one study with a repeated-measures design. The overall quality of the studies was good as 657 study participants, aged 45 years and older who had varying degrees of Alzheimer's disease and significant symptoms, were included. Aerobic exercise was found to have a significant positive impact on executive and memory functions in people with Alzheimer's disease. CONCLUSION: The effects of aerobic exercise on aspects of executive function were mainly characterized by improvements in inhibitory control, working memory, and cognitive flexibility, whereas the effects on aspects of memory function were mainly characterized by improvements in logical memory, situational memory, and short-term memory.

Establishment of a hydrodynamic delivery system in ducks.

Chronic hepatitis B virus (HBV) poses a significant global health challenge as it can lead to acute or chronic liver disease and hepatocellular carcinoma (HCC). To establish a safety experimental model, a homolog of HBV-duck HBV (DHBV) is often used for HBV research. Hydrodynamic-based gene delivery (HGD) is an efficient method to introduce exogenous genes into the liver, making it suitable for basic research. In this study, a duck HGD system was first constructed by injecting the reporter plasmid pLIVE-SEAP via the ankle vein. The highest expression of SEAP occurred when ducks were injected with 5 µg/mL plasmid pLIVE-SEAP in 10% bodyweight volume of physiological saline for 6 s. To verify the distribution and expression of exogenous genes in multiple tissues, the relative level of foreign gene DNA and ß-galactosidase staining of LacZ were evaluated, which showed the plasmids and their products were located mainly in the liver. Additionally, ß-galactosidase staining and fluorescence imaging indicated the delivered exogenous genes could be expressed in a short time. Further, the application of the duck HGD model on DHBV treatment was investigated by transferring representative anti-HBV genes IFNα and IFNγ into DHBV-infected ducks. Delivery of plasmids expressing IFNα and IFNγ inhibited DHBV infection and we established a novel efficient HGD method in ducks, which could be useful for drug screening of new genes, mRNAs and proteins for anti-HBV treatment.

Preparation of a Key Intermediate En Route to the Anti-HIV Drug Lenacapavir.

A very efficient four-step synthesis of the main fragment of Gilead's anti-HIV drug lenacapavir is described. The route showcases a 1,2-addition to an intermediate aldehyde using an organozinc halide derived from a commercially available difluorobenzyl Grignard reagent. This sets the stage for the oxidation of the resulting secondary alcohol to the desired ketone, which relies solely on catalytic amounts of TEMPO together with NaClO as the terminal oxidant, affording the targeted ketone in 67% overall yield.

Nanoparticles as Heterogeneous Catalysts for ppm Pd-Catalyzed Aminations in Water.

A general protocol employing heterogeneous catalysis has been developed that enables ppm of Pd-catalyzed C-N cross-coupling reactions under aqueous micellar catalysis. A new nanoparticle catalyst containing specifically ligated Pd, in combination with nanoreactors composed of the designer surfactant Savie, a biodegradable amphiphile, catalyzes C-N bond formations in recyclable water. A variety of coupling partners, ranging from highly functionalized pharmaceutically relevant APIs to educts from the Merck Informer Library, readily participate under these environmentally responsible, sustainable reaction conditions. Other key features associated with this report include the low levels of residual Pd found in the products, the recyclability of the aqueous reaction medium, the use of ocean water as an alternative source of reaction medium, options for the use of pseudohalides as alternative reaction partners, and associated low E factors. In addition, an unprecedented 5-step, one-pot sequence is presented, featuring several of the most widely used transformations in the pharmaceutical industry, suggesting potential industrial applications.

Comprehensive Analysis of the Expression of Cell Adhesion Molecules Genes in Hepatocellular Carcinoma and their Prognosis, and Biological Significance.

BACKGROUND: Collagen-related cell adhesion molecules (CAMs) are a major component of the extracellular matrix (ECM) and often accumulate in the liver during chronic liver disease or hepatocellular carcinoma (HCC). In this study we identified several promising collagens related to CAMs that may be of clinical use for the diagnosis and prognosis of HCC. METHODS: We obtained multi-omics data including RNA sequencing (RNA-Seq) data, microarray data, proteomic data from the TCGA, GEO databases, GTEx, and NODE. Bioinformatics analyses were then performed to investigate correlations between the expression patterns of significant genes and HCC. Tumor tissue and para-cancerous tissue samples from HCC patients were also used to validate the results using RT-PCR. RESULTS: A literature research and LASSO-COX analysis identified three significant collagen-related CAM genes: SERPINH1, DCN, and ITGB1. Immunohistochemistry images in the Human Protein Atlas Project database showed that SERPINH1 and ITGB1 proteins were moderately or highly expressed in HCC tumor tissues compared to para-cancerous tissue, whereas DCN expression was lower in HCC tumor tissue. These results were validated by RT-PCR. Low- and high-risk groups of HCC patients were distinguished by the logistic panel in the TCGA database. These showed significantly different prognosis, clinicopathological features, and immune cell infiltration. Logistic regression was used to construct predictive models based on the individual expression levels of DCN, SERPINH1, and ITGB1. These showed highly accurate diagnostic ability (AUC = 0.987). CONCLUSIONS: The current findings suggest that the collagen-related CAMs DCN, SERPINH1, and ITGB1 may be potential therapeutic targets in HCC. Logistic panels of DCN, SERPINH1 and ITGB1 could serve as non-invasive and effective diagnostic biomarkers for HCC. CLINICAL TRIAL REGISTRATION: Identifier: NCT03189992. Registered on June 4, 2017. Retrospectively registered (https://clinicaltrials.gov/).

Downregulation of peripheral luteinizing hormone rescues ovariectomy-associated cognitive deficits in APP/PS1 mice.

Alzheimer's disease (AD) is more prevalent in women than men, supposing due to the decline of estrogens in menopause, accompanied by increased gonadotropins such as luteinizing hormone (LH). We and others found that the transcription factor early growth response-1 (EGR1) regulates cholinergic function including the expression of acetylcholinesterase (AChE) and plays a significant role in cognitive decline of AD. Here we investigated in APP/PS1 mice by ovariectomy (OVX) and estradiol (E2) supplementation or inhibition of LH the effect on hippocampus-related cognition and related molecular changes. We found that OVX-associated cognitive impairment was accompanied by increased dorsal hippocampal EGR1 expression, which was rescued by downregulating peripheral LH rather than by supplementing E2. We also found in postmortem AD brains a higher expression of pituitary LH-mRNA and higher EGR1 expression in the posterior hippocampus. Both, in human and mice, there was a significant positive correlation between respectively posterior/dorsal hippocampal EGR1 and peripheral LH expression. We conclude that peripheral increased LH and increased posterior hippocampal EGR1 plays a significant role in AD pathology.

Phased genome assemblies reveal haplotype-specific genetic load in the critically endangered Chinese Bahaba (Teleostei, Sciaenidae).

While haplotype-specific genetic load shapes the evolutionary trajectory of natural and captive populations, mixed-haplotype assembly and genotyping hindered its characterization in diploids. Herein, we produced two phased genome assemblies of the critically endangered fish Chinese Bahaba (Bahaba taipingensis, Sciaenidae, Teleostei) and resequenced 20 whole genomes to quantify population genetic load at a haplotype level. We identified frame-shifting variants as the most deleterious type, followed by mutations in the 5'-UTR, 3'-UTR and missense mutations at conserved amino acids. Phased haplotypes revealed gene deletions and high-impact deleterious variants. We estimated ~1.12% of genes missing or interrupted per haplotype, with a significant overlap of disrupted genes (30.35%) between haplotype sets. Relative proportions of deleterious variant categories differed significantly between haplotypes. Simulations suggested that purifying selection struggled to purge slightly deleterious genetic load in captive breeding compared to genotyping interventions, and that higher inter-haplotypic variance of genetic load predicted more efficient purging by artificial selection. Combining the knowledge of haplotype-resolved genetic load with predictive modelling will be immensely useful for understanding the evolution of deleterious variants and guiding conservation planning.

Impact of Nonionic Surfactants on Reactions of IREDs. Applications to Tandem Chemoenzymatic Sequences in Water.

The influence of added surfactant to aqueous reaction mixtures containing various IREDs has been determined. Just the presence of a nonionic surfactant tends to increase both rates and extent of conversion to the targeted amines. The latter can be as much as >40% relative to buffer alone. Several tandem sequences featuring several steps that combine use of an IRED together with various types of chemocatalysis are also presented, highlighting the opportunities for utilizing chemoenzymatic catalysis, all in water.

Modifying the amino acids in conformational motion pathway of the α-amylase of Geobacillus stearothermophilus improved its activity and stability.

Amino acids along the conformational motion pathway of the enzyme molecule correlated to its flexibility and rigidity. To enhance the enzyme activity and thermal stability, the motion pathway of Geobacillus stearothermophilus α-amylase has been identified and molecularly modified by using the neural relational inference model and deep learning tool. The significant differences in substrate specificity, enzymatic kinetics, optimal temperature, and thermal stability were observed among the mutants with modified amino acids along the pathway. Mutants especially the P44E demonstrated enhanced hydrolytic activity and catalytic efficiency (kcat/KM) than the wild-type enzyme to 95.0% and 93.8% respectively, with the optimum temperature increased to 90°C. This mutation from proline to glutamic acid has increased the number and the radius of the bottleneck of the channels, which might facilitate transporting large starch substrates into the enzyme. The mutation could also optimize the hydrogen bonding network of the catalytic center, and diminish the spatial hindering to the substrate entry and exit from the catalytic center.

Circular RNA from Tyrosylprotein Sulfotransferase 2 Gene Inhibits Cisplatin Sensitivity in Head and Neck Squamous Cell Carcinoma by Sponging miR-770-5p and Interacting with Nucleolin.

Chemoresistance poses a significant challenge in the treatment of advanced head and neck squamous cell cancer (HNSCC). The role and mechanism of circular RNAs (circRNAs) in HNSCC chemoresistance remain understudied. We conducted circRNA microarray analysis to identify differentially expressed circRNAs in HNSCC. The expression of circRNAs from the tyrosylprotein sulfotransferase 2 (TPST2) gene and miRNAs was evaluated through qPCR, while the circular structure of circTPST2 was verified using Sanger sequencing and RNase R. Through Western blotting, biotin-labeled RNA pulldown, RNA immunoprecipitation, mass spectrometry, and rescue experiments, we discovered miR-770-5p and nucleolin as downstream targets of circTPST2. Functional tests, including CCK8 assays and flow cytometry, assessed the chemoresistance ability of circTPST2, miR-770-5p, and Nucleolin. Additionally, FISH assays determined the subcellular localization of circTPST2, miR-770-5p, and Nucleolin. IHC staining was employed to detect circTPST2 and Nucleolin expression in HNSCC patients. circTPST2 expression was inversely correlated with cisplatin sensitivity in HNSCC cell lines. Remarkably, high circTPST2 expression correlated with lower overall survival rates in chemotherapeutic HNSCC patients. Mechanistically, circTPST2 reduced chemosensitivity through sponge-like adsorption of miR-770-5p and upregulation of the downstream protein Nucleolin in HNSCC cells. The TCGA database revealed improved prognosis for patients with low circTPST2 expression after chemotherapy. Moreover, analysis of HNSCC cohorts demonstrated better prognosis for patients with low Nucleolin protein expression after chemotherapy. We unveil circTPST2 as a circRNA associated with chemoresistance in HNSCC, suggesting its potential as a marker for selecting chemotherapy regimens in HNSCC patients. Further exploration of the downstream targets of circTPST2 advanced our understanding and improved treatment strategies for HNSCC.

A case-control study and systematic review of the association between glutathione S-transferase genes and chronic kidney disease.

Background: GSTM1 deletion was reported to be associated with CKD progression in cohort studies. However, the results of case‒control studies were conflicting. The association between GST genes and CKD progression needs to be studied in China. Therefore, we conducted this case‒control study and systematic review for Southwest China to outline the association between GST genes and CKD. Methods: CKD patients and healthy controls were enrolled from June 1, 2022 to 1 August 2022. Reported case‒control studies were identified by searching databases until 1 September 2022 for meta-analysis. Results: Significant associations were found between deletions of GSTM1 and GSTT1 and CKD risk (all P < 0.01) but not in GSTP1 rs1695 (all P > 0.05) in Southwest China. Then, we conducted a meta-analysis on 30 studies and found positive associations between deletions of GSTM1 and GSTT1 and CKD risk (all P < 0.01) but failed to find associations in GSTP1 rs1695 (all P > 0.05). Stratification analysis for ethnicity only showed a significant association in Southern Asia (P < 0.05) but not in Eastern Asia or other populations. This was different from our case‒control results. The current evidence was influenced by study quality and PCR method but not by control selection. Given the different stages of CKD patients, a subanalysis of disease stages was performed, and the results remained positive. Interestingly, we found no significant associations between DM-CKD and GST genes, which should be interpreted with caution. Conclusion: We found that GSTM1 and GSTT1 null genotypes were risk factors for CKD in China. The results of the meta-analysis were somewhat different from our results. We considered that antioxidant therapy might be useful for the treatment of these patients.