Comprehensive analysis of peroxisome proliferator-activated receptors to predict the drug resistance, immune microenvironment, and prognosis in stomach adenocarcinomas.

Background: Peroxisome proliferator-activated receptors (PPARs) exert multiple functions in the initiation and progression of stomach adenocarcinomas (STAD). This study analyzed the relationship between PPARs and the immune status, molecular mutations, and drug therapy in STAD. Methods: The expression profiles of three PPAR genes (PPARA, PPARD and PPARG) were downloaded from The Cancer Genome Atlas (TCGA) dataset to analyze their expression patterns across pan-cancer. The associations between PPARs and clinicopathologic features, prognosis, tumor microenvironment, genome mutation and drug sensitivity were also explored. Co-expression between two PPAR genes was calculated using Pearson analysis. Regulatory pathways of PPARs were scored using gene set variation analysis (GSVA) package. Quantitative real-time polymerase chain reaction (qRT-PCR), Western blot, Cell Counting Kit-8 (CCK-8) assay and transwell assay were conducted to analyze the expression and function of the PPAR genes in STAD cell lines (AGS and SGC7901 cells). Results: PPARA, PPARD and PPARG were more abnormally expressed in STAD samples and cell lines when compared to most of 32 type cancers in TCGA. In STAD, the expression of PPARD was higher in Grade 3+4 and male patients, while that of PPARG was higher in patient with Grade 3+4 and age > 60. Patients in high-PPARA expression group tended to have longer survival time. Co-expression analysis revealed 6 genes significantly correlated with the three PPAR genes in STAD. Single-sample GSEA (ssGSEA) showed that the three PPAR genes were enriched in 23 pathways, including MITOTIC_SPINDLE, MYC_TARGETS_V1, E2F_TARGETS and were closely correlated with immune cells, including NK_cells_resting, T_cells_CD4_memory_resting, and macrophages_M0. Immune checkpoint genes (CD274, SIGLEC15) were abnormally expressed between high-PPAR expression and low-PPAR expression groups. TTN, MUC16, FAT2 and ANK3 genes had a high mutation frequency in both high-PPARA/PPARG and low-PPARA/PPARG expression group. Fourteen and two PPARA/PPARD drugs were identified to be able to effectively treat patients in high-PPARA/PPARG and low-PPARA/PPARG expression groups, respectively. We also found that the chemotherapy drug Vinorelbine was positively correlated with the three PPAR genes, showing the potential of Vinorelbine to serve as a treatment drug for STAD. Furthermore, cell experiments demonstrated that PPARG had higher expression in AGS and SGC7901 cells, and that inhibiting PPARG suppressed the viability, migration and invasion of AGS and SGC7901 cells. Conclusions: The current results confirmed that the three PPAR genes (PPARA, PPARD and PPARG) affected STAD development through mediating immune microenvironment and genome mutation.

Development and validation of an LC-MS/MS method for quantifying NAD+ and related metabolites in mice sciatic nerves and its application to a nerve injury animal model.

Recent studies highlight the pivotal roles of Nicotinamide adenine dinucleotide (NAD+) and its metabolites in aging and neurodegeneration. Accurate quantification of NAD+ and its metabolite levels in cells or tissues is crucial for advancing biochemical research and interventions targeting aging and neurodegenerative diseases. This study presents an accurate, precise, and rapid LC-MS/MS method using a surrogate matrix to quantify endogenous substances NAD+, nicotinamide mononucleotide (NMN), nicotinamide (NAM), adenosine diphosphate ribose (ADPR), and cyclic adenosine diphosphate ribose (cADPR) concentrations in mice sciatic nerves. Considering the properties of the phosphate groups in the analytes, the column and mobile phase were systematically optimized. These five polar analytes exhibited excellent analytical performance and baseline separation within 5 min on an Atlantis Premier BEH C18 AX column, with methylene phosphonic acid as a mobile phase additive. Enhanced sensitivity addressed the challenges posed by the small sample size of mice sciatic nerve and low NMN and cADPR detection. The method was fully validated, with linear correlation coefficients exceeding 0.992, precision (%relative standard deviation, RSD) values within 8.8%, and accuracy values between 92.2% and 107.3%, suggesting good reproducibility. Analytical recoveries in spiked and diluted matrix ranged from 87.8% to 104.7%, indicating the suitability of water as a surrogate matrix. Application of the method to quantify NAD+ and its metabolite levels in normal and injured mice sciatic nerve identified cADPR as a sensitive biomarker in the nerve injury model. This method is anticipated to deepen our understanding of the connections between NAD+ and its metabolites in health and disease, potentially improving diagnoses of various neurological disorders and aiding drug development for aging and neurodegenerative diseases.

Accurate prediction of Kp,uu,brain based on experimental measurement of Kp,brain and computed physicochemical properties of candidate compounds in CNS drug discovery.

A mathematical equation model was developed by building the relationship between the fu,b/fu,p ratio and the computed physicochemical properties of candidate compounds, thereby predicting Kp,uu,brain based on a single experimentally measured Kp,brain value. A total of 256 compounds and 36 marketed published drugs including acidic, basic, neutral, zwitterionic, CNS-penetrant, and non-CNS penetrant compounds with diverse structures and physicochemical properties were involved in this study. A strong correlation was demonstrated between the fu,b/fu,p ratio and physicochemical parameters (CLogP and ionized fraction). The model showed good performance in both internal and external validations. The percentages of compounds with Kp,uu,brain predictions within 2-fold variability were 80.0 %-83.3 %, and more than 90 % were within a 3-fold variability. Meanwhile, "black box" QSAR models constructed by machine learning approaches for predicting fu,b/fu,p ratio based on the chemical descriptors are also presented, and the ANN model displayed the highest accuracy with an RMSE value of 0.27 and 86.7 % of the test set drugs fell within a 2-fold window of linear regression. These models demonstrated strong predictive power and could be helpful tools for evaluating the Kp,uu,brain by a single measurement parameter of Kp,brain during lead optimization for CNS penetration evaluation and ranking CNS drug candidate molecules in the early stages of CNS drug discovery.

High-throughput screening of LogD by using a sample pooling approach based on the traditional shake flask method.

A new approach for screening LogD is presented. The method is based on the shake flask method combined with rapid generic LC-MS/MS bioanalysis by using a sample pooling approach that enables high-throughput screening of LogD or LogP in the drug discovery stage. The method is evaluated by a comparison of measured LogD between single and pooled compounds for a test set of structurally diverse compounds with a wide range of LogD values (from -0.04 to 6.01). Test compounds include 10 commercially available drug standards along with 27 new chemical entities. A good correlation (RMSE = 0.21, R2 = 0.9879) of LogD between the single and pooled compounds was obtained, suggesting that at least 37 compounds can be simultaneously measured with acceptable accuracy. The sample pooling method significantly reduced the number of bioanalysis samples as compared to the single compound measurement by the conventional shake flask method. The impact of DMSO content on LogD measurement was also investigated and the result demonstrated that at least 0.5% DMSO was tolerated in this method. The current new development will facilitate the drug discovery process by more rapidly assessing the LogD or LogP of drug candidates.

A small molecule protects mitochondrial integrity by inhibiting mTOR activity.

Apoptosis activation by cytochrome c release from mitochondria to cytosol is a normal cellular response to mitochondrial damage. Using cellular apoptosis assay, we have found small-molecule apoptosis inhibitors that protect cells from mitochondrial damage. Previously, we reported the discovery of a small molecule, Compound A, which blocks dopaminergic neuron death in a rat model of Parkinson's disease through targeting succinate dehydrogenase subunit B (SDHB) of complex II to protect the integrity of the mitochondrial respiratory chain. Here, we report a small molecule, Compound R6, which saves cells from apoptosis via mammalian target of rapamycin (mTOR)-mediated induction of autophagy. Additionally, we show that Compound R6 protects mitochondrial integrity and respiration after induction of the intrinsic apoptosis pathway. Encouragingly, and supporting the potential further application of Compound R6 as a tool for basic and medicinal research, a pharmacokinetics (PK) profiling study showed that Compound R6 is metabolically stable and can pass the blood-brain barrier. Moreover, Compound R6 accumulates in the brain of test animals via intravenous and intraperitoneal administration. Finally, we found that Compound R6 confers significant neuroprotective effects on a rat cerebral ischemia/reperfusion model, demonstrating its potential as a promising drug candidate for neurodegenerative diseases.

Identification and Optimization of Novel Cathepsin C Inhibitors Derived from EGFR Inhibitors.

In the course of developing the biochemistry to chemistry activity-based protein profiling (BTC-ABPP) method, we herein unexpectedly discovered that the epidermal growth factor receptor irreversible inhibitor WZ4002 also functioned as a low micromolar inhibitor of cathepsin C (CatC), a promising target for the treatment of numerous inflammatory and autoimmune diseases. Building on from this discovery, and following structure-activity relationship investigations guided by computational modeling, a novel series of pyridine scaffold compounds were developed as irreversible CatC inhibitors, further culminated in identifying a highly potent and selective inhibitor 22, which displays good metabolic stability and oral bioavailability. In vivo studies revealed that compound 22 clearly displays the ability to inhibit CatC, consequently leading to efficient inhibition of downstream neutrophil serine proteases in both bone marrow and blood. The overall excellent profile of compound 22 made it an interesting candidate for further preclinical investigation.

Identification of entacapone as a chemical inhibitor of FTO mediating metabolic regulation through FOXO1.

Recent studies have established the involvement of the fat mass and obesity-associated gene (FTO) in metabolic disorders such as obesity and diabetes. However, the precise molecular mechanism by which FTO regulates metabolism remains unknown. Here, we used a structure-based virtual screening of U.S. Food and Drug Administration-approved drugs to identify entacapone as a potential FTO inhibitor. Using structural and biochemical studies, we showed that entacapone directly bound to FTO and inhibited FTO activity in vitro. Furthermore, entacapone administration reduced body weight and lowered fasting blood glucose concentrations in diet-induced obese mice. We identified the transcription factor forkhead box protein O1 (FOXO1) mRNA as a direct substrate of FTO, and demonstrated that entacapone elicited its effects on gluconeogenesis in the liver and thermogenesis in adipose tissues in mice by acting on an FTO-FOXO1 regulatory axis.

Novel quinazoline derivatives bearing various 6-benzamide moieties as highly selective and potent EGFR inhibitors.

A series of novel quinazoline derivatives bearing various C-6 benzamide substituents were synthesized and evaluated as EGFR inhibitors, and most showed significant inhibitory potency against EGFR kinase. In particular, compound 6g possessed potent inhibitory activity against EGFR wild-type (IC50 = 5 nM), and strong antiproliferative activity against HCC827 and Ba/F3 (L858R) cell lines. Kinase profiling against a panel of 365 kinases showed that 6g was highly selective for EGFR. Furthermore, 6g showed desirable properties in assays of liver microsome metabolic stability and cytochromes P450 inhibition and preliminary pharmacokinetic study. The overall attractive profile of 6g made it an interesting compound for further development.

Discovery of a Highly Potent, Selective, and Metabolically Stable Inhibitor of Receptor-Interacting Protein 1 (RIP1) for the Treatment of Systemic Inflammatory Response Syndrome.

On the basis of its essential role in driving inflammation and disease pathology, cell necrosis has gradually been verified as a promising therapeutic target for treating atherosclerosis, systemic inflammatory response syndrome (SIRS), and ischemia injury, among other diseases. Most necrosis inhibitors targeting receptor-interacting protein 1 (RIP1) still require further optimization because of weak potency or poor metabolic stability. We conducted a phenotypic screen and identified a micromolar hit with novel amide structure. Medicinal chemistry efforts yielded a highly potent, selective, and metabolically stable drug candidate, compound 56 (RIPA-56). Biochemical studies and molecular docking revealed that RIP1 is the direct target of this new series of type III kinase inhibitors. In the SIRS mice disease model, 56 efficiently reduced tumor necrosis factor alpha (TNFα)-induced mortality and multiorgan damage. Compared to known RIP1 inhibitors, 56 is potent in both human and murine cells, is much more stable in vivo, and is efficacious in animal model studies.

Focusing on probe-modified peptides: a quick and effective method for target identification.

A new and efficient method focusing on probe-modified peptides was developed to identify the target protein and modification site of a hit compound or a drug. This method exhibited high click conjugation efficiency and few false-positive results. The modification site further facilitated target validation, biological mechanism study and new indications exploration.

Function of high-resolution manometry in the analysis of peroral endoscopic myotomy for achalasia.

BACKGROUND: Peroral endoscopic myotomy (POEM) was introduced as a new effective therapeutic option for esophageal achalasia. METHOD: A total of 112 achalasia patients categorized into three subtypes by HRM who underwent POEM were enrolled in our study. Eckardt score and HRM were performed preoperation, 6 months, and 1 year after POEM to evaluate the effectiveness, safety, and feasibility of POEM and to investigate the treatment response to POEM for the three subtypes of achalasia, classified by high-resolution manometry (HRM). RESULTS: POEM was successfully performed in all patients. Compared with pre-POEM scores, the Eckardt scores were significantly reduced from 7.3 ± 1.4 to 1.0 ± 0.8 6 months after POEM and to 1.2 ± 0.6 1 year after POEM (p < 0.05). The LESP before treatment was 41.8 ± 15.3 mmHg, compared with a LESP of 18.4 ± 7.1 mmHg 6 months after POEM and 20.7 ± 7.5 mmHg 1 year after POEM (p < 0.05). In addition, POEM decreased the 4-s IRP from 33.4 ± 9.0 to 14.6 ± 3.8 mmHg 6 months after POEM and to 16.4 ± 3.9 mmHg 1 year after POEM (p < 0.05). The 4-s IRP was reduced to <15 mmHg in 64 of 112 patients. Type II had the best response to POEM, while type III exhibited the worst response. CONCLUSIONS: POEM appears to be an effective and less invasive treatment for achalasia. HRM can be useful in the classification of achalasia, while these subclassifications help to predict the responsiveness to POEM.

O-GlcNAc-modification of SNAP-29 regulates autophagosome maturation.

The mechanism by which nutrient status regulates the fusion of autophagosomes with endosomes/lysosomes is poorly understood. Here, we report that O-linked ß-N-acetylglucosamine (O-GlcNAc) transferase (OGT) mediates O-GlcNAcylation of the SNARE protein SNAP-29 and regulates autophagy in a nutrient-dependent manner. In mammalian cells, OGT knockdown, or mutating the O-GlcNAc sites in SNAP-29, promotes the formation of a SNAP-29-containing SNARE complex, increases fusion between autophagosomes and endosomes/lysosomes, and promotes autophagic flux. In Caenorhabditis elegans, depletion of ogt-1 has a similar effect on autophagy; moreover, expression of an O-GlcNAc-defective SNAP-29 mutant facilitates autophagic degradation of protein aggregates. O-GlcNAcylated SNAP-29 levels are reduced during starvation in mammalian cells and in C. elegans. Our study reveals a mechanism by which O-GlcNAc-modification integrates nutrient status with autophagosome maturation.

LC-MS determination and pharmacokinetic study of six phenolic components in rat plasma after taking traditional Chinese medicinal-preparation: Guanxinning lyophilized powder for injection.

A traditional Chinese medicinal preparation (TCMP) named Guanxinning lyophilized powder for injection composed of Salvia miltiorrhiza Bge. (SMB) and Ligusticum chuanxiong Hort. (LCH) was studied. In order to learn the kinetic behaviors of the lyophilized powder and provide proofs for rational administration, we have developed a sensitive and reproducible method for determination and pharmacokinetic study of six main phenolic components {danshensu (DSS), protocatechuic acid (PAC), protocatechuic aldehyde (PAL), chlorogenic acid (CHA), caffeic acid (CAA) and salvianolic acid B (SAB)} of Guanxinning in rat plasma using liquid chromatography-mass spectrometric (LC-MS) method. Sample preparations were carried out by protein precipitation with the addition of methanol followed by liquid-liquid extraction with ethyl acetate-ethyl ether (3:1, v/v) after internal standard (IS, galic acid) spiked. After evaporation to dryness, the resultant residue was reconstituted in methanol and injected onto a Kromasil C(18) column (150 mm x 4.6 mm i.d. with 5 microm particle size). The analytes were analyzed by using negative electrospray ionization (ESI) mass spectrometry in selected ion monitoring (SIM) mode. The method was with good linearity in the range 0.342-85.0 microgmL(-1) for DSS, 0.0647-12.9 microgmL(-1) for PAC, 0.0933-18.7 microgmL(-1) for PAL, 0.0085-3.40 microgmL(-1) for CHA, 0.0138-2.75 microgmL(-1) for CAA and 0.0272-810 microgmL(-1) for SAB (r>0.99). The average extract recoveries of the six analytes from rat plasma were all no less than 75%, the precision and accuracy determined were all within the required limits. This LC-MS method was successfully applied to pharmacokinetic study of the six phenolic components of Guanxinning lyophilized powder for injection in rats.