From Hit to Lead: Structure-Based Optimization of Novel Selective Inhibitors of Receptor-Interacting Protein Kinase 1 (RIPK1) for the Treatment of Inflammatory Diseases.

Receptor-interacting protein kinase 1 (RIPK1) is a key regulator of cellular necroptosis, which is considered as an important therapeutic target for necroptosis-related indications. Herein, we report the structural optimization and structure-activity relationship investigations of a series of eutectic 5-substituted-indole-3-carboxamide derivatives. The prioritized compound 10b exhibited low nanomolar IC50 values against RIPK1 and showed good kinase selectivity. Based on its eutectic structure, 10b occupied both the allosteric and ATP binding pockets of RIPK1, making it a potent dual-mode inhibitor of RIPK1. In vitro, 10b had a potent protective effect against necroptosis in cells. Compound 10b also provided robust protection in a TNFα-induced systemic inflammatory response syndrome (SIRS) model and imiquimod (IMQ)-induced psoriasis model. It also showed good pharmacokinetic properties and low toxicity. Overall, 10b is a promising lead compound for drug discovery targeting RIPK1 and warrants further study.

Single-cell RNA sequencing reveals the lineage of malignant epithelial cells and upregulation of TAGLN2 promotes peritoneal metastasis in gastric cancer

Background Peritoneal metastasis (PM) is an important factor contributing to poor prognosis in patients with gastric cancer (GC). Transcriptomic sequencing has been used to explore the molecular changes in metastatic cancers, but comparing the bulk RNA-sequencing data between primary tumors and metastases in PM studies is unreasonable due to the small proportion of tumor cells in PM tissues. Methods We performed single-cell RNA-sequencing analysis on four gastric adenocarcinoma specimens, including one primary tumor sample (PT), one adjacent nontumoral sample (PN), one peritoneal metastatic sample (MT) and one normal peritoneum sample (MN), from the same patient. Pseudotime trajectory analysis was used to display the process by which nonmalignant epithelial cells transform into tumor cells and then metastasize to the peritoneum. Finally, in vitro and in vivo assays were used to validate one of the selected genes that promote peritoneal metastasis. Results Single-cell RNA sequencing showed that a development curve was found from normal mucosa to tumor tissues and then into metastatic sites on peritoneum. TAGLN2 was found to trigger this metastasis process. The migration and invasion capability of GC cells were changed by downregulating and upregulating TAGLN2 expression. Mechanistically, TAGLN2 might modulate tumor metastasis via alterations in cell morphology and several signaling pathways, thus promoting epithelial–mesenchymal transition (EMT). Conclusions In summary, we identified and validated TAGLN2 as a novel gene involved in GC peritoneal metastasis. This study provided valuable insight into the mechanisms of GC metastasis and developed a potential therapeutic target to prevent GC cell dissemination (AU)

Study of the Effect of Intestinal Microbes on Obesity: A Bibliometric Analysis.

Obesity is a serious public health problem. According to statistics, there are millions of obese people worldwide. Research studies have discovered a complex and intricate relationship between the gut microbiota and obesity. Probing and summarizing the relationship between intestinal microbes and obesity has important guiding significance for the accurate control of the research direction and expanding the choice of obesity treatment methods. We used bibliometric analysis to analyze the published literature with the intention to reveal the research hotspots and development trends on the effects of intestinal microbes on obesity from a visualization perspective, both qualitatively and quantitatively. The results showed that current research is focusing on related mechanisms of the effects of intestinal microbes on obesity and therapeutic methods for obesity. Several noteworthy hotspots within this field have garnered considerable attention and are expected to remain the focal points of future research. Of particular interest are the mechanisms by which intestinal microbes potentially regulate obesity through metabolite interactions, as well as the role of microbiomes as metabolic markers of obesity. These findings strongly suggest that gut microbes continue to be a key target in the quest for effective obesity treatments. Co-operation and communication between countries and institutions should be strengthened to promote development in this field to benefit more patients with obesity.

Discovery of 5-((1H-indazol-3-yl) methylene)-2-thioxoimidazolidin-4-one derivatives as a new class of AHR agonists with anti-psoriasis activity in a mouse model.

Aryl hydrocarbon receptor (AHR) is a ligand dependent transcription factor and participates in the regulation of the immune balance of Th17/22 and Treg cells. It has been found to be widely expressed in the skin, and involved in the pathology of psoriasis. Therefore, AHR is thought as a potential intervention target for psoriasis. Here, we report the discovery of 5-((1H-indazol-3-yl) methylene)-2-thioxoimidazolidin-4-one derivatives as a new class of AHR agonists. Structure-activity relationship analyses led to the identification of the most active compound, 5- ((1H-indazol-3-yl)methylene) -3- (prop-2-yn-1-yl) -2-thiooimidazolidin-4-one (24e), which exhibited an EC50 value of 0.015 µM against AHR. Mechanism of action studies showed that 24e regulated the expression of CYP1A1 by activating the AHR pathway. Topical administration of 24e substantially alleviated imiquimod (IMQ)-induced psoriasis-like skin lesion. Overall, compound 24e could be a good lead compound for drug discovery against psoriasis, and hence deserving further in-depth studies.

Single-cell RNA sequencing reveals the lineage of malignant epithelial cells and upregulation of TAGLN2 promotes peritoneal metastasis in gastric cancer.

BACKGROUND: Peritoneal metastasis (PM) is an important factor contributing to poor prognosis in patients with gastric cancer (GC). Transcriptomic sequencing has been used to explore the molecular changes in metastatic cancers, but comparing the bulk RNA-sequencing data between primary tumors and metastases in PM studies is unreasonable due to the small proportion of tumor cells in PM tissues. METHODS: We performed single-cell RNA-sequencing analysis on four gastric adenocarcinoma specimens, including one primary tumor sample (PT), one adjacent nontumoral sample (PN), one peritoneal metastatic sample (MT) and one normal peritoneum sample (MN), from the same patient. Pseudotime trajectory analysis was used to display the process by which nonmalignant epithelial cells transform into tumor cells and then metastasize to the peritoneum. Finally, in vitro and in vivo assays were used to validate one of the selected genes that promote peritoneal metastasis. RESULTS: Single-cell RNA sequencing showed that a development curve was found from normal mucosa to tumor tissues and then into metastatic sites on peritoneum. TAGLN2 was found to trigger this metastasis process. The migration and invasion capability of GC cells were changed by downregulating and upregulating TAGLN2 expression. Mechanistically, TAGLN2 might modulate tumor metastasis via alterations in cell morphology and several signaling pathways, thus promoting epithelial-mesenchymal transition (EMT). CONCLUSIONS: In summary, we identified and validated TAGLN2 as a novel gene involved in GC peritoneal metastasis. This study provided valuable insight into the mechanisms of GC metastasis and developed a potential therapeutic target to prevent GC cell dissemination.

Intraoperative Pathological Evaluation of Suspicious Peritoneal Nodules for Surgical Decision-making in Gastric Cancer.

BACKGROUND: When frozen pathological results of suspicious peritoneal nodules found in gastric cancer (GC) patients are negative or indeterminant, whether to perform gastrectomy will always be a dilemma for surgeons. This study aimed to facilitate intraoperative surgical decision-making based on frozen section (FS) results and clinicopathological characteristics. METHODS: From January 2015 to July 2021, 318 GC patients were enrolled retrospectively. The correlations between frozen and paraffin pathology of peritoneal nodules were examined. Then, predictive factors of positive paraffin section (PS) results were identified, and a nomogram was constructed. The survival significance of gastrectomy was also explored. RESULTS: Of 70 FS-negative patients, 59 (84.3%) had concordant negative PS results, while the PS results of 11 (15.7%) were positive. Forty-six (93.9%) and 3 (6.1%) of 49 patients with indeterminant FS results had positive and negative PS results, respectively. The PS results of 95 FS-positive patients were all positive. A nomogram for predicting positive PS results was developed based on Lauren type, nodule distribution, and CA125. Gastrectomy for FS-negative patients improved survival compared to no gastrectomy (HR 0.26, 95% CI 0.11-0.62; P = 0.0012). Survival benefits for gastrectomy vs. no gastrectomy were not demonstrated in patients with indeterminant (HR 0.74, 95% CI 0.27-2.01; P = 0.53) and positive (HR 0.87, 95% CI 0.43-1.74; P = 0.69) FS results. CONCLUSIONS: Gastrectomy can be justified for the treatment of operable GC patients with negative frozen pathological results of peritoneal nodules. For patients with positive and indeterminant frozen pathological results, gastrectomy is not recommended unless it is performed as palliative surgery.

Association of systemic inflammatory markers and tertiary lymphoid structure with pathological complete response in gastric cancer patients receiving preoperative treatment: a retrospective cohort study.

BACKGROUND: Assessment of systemic and local immune responses is crucial in determining the efficacy of cancer interventions. The identification of specific factors that correlate with pathological complete response (pCR) is essential for optimizing treatment decisions. METHODS: In this retrospective study, a total of 521 patients diagnosed with gastric adenocarcinoma who underwent curative gastrectomy following preoperative treatment were reviewed. Of these patients, 463 did not achieve pCR (non-pCR) and 58 achieved pCR. Clinicopathological factors were evaluated to identify predictors for pCR using a logistic regression model. Additionally, a smaller cohort (n=76) was derived using propensity score matching to investigate local immune response, specifically the features of tertiary lymphoid structure (TLS) using H&E staining, immunohistochemistry, and multiplex immunofluorescence. RESULTS: The multivariate regression analysis demonstrated a significant association between low systemic inflammatory status and pCR, as evidenced by reduced levels of the combined systemic immune-inflammation index (SII) and neutrophil-to-lymphocyte ratio (NLR) (SII+NLR) (odds ratio: 3.33, 95% CI: 1.79-6.17, P<0.001). In the smaller cohort analysis, distinct TLS characteristics were correlated with the presence of pCR. Specifically, a higher density of TLS and a lower proportion of PD1+ cells and CD8+ cells within TLS in the tumor bed were strongly associated with pCR. CONCLUSION: Both systemic and local immune profile were associated with pCR. A low level of SII+NLR served as an independent predictor of pCR, while distinct TLS features were associated with the presence of pCR. Focusing on the immune profile was crucial for optimal management of gastric cancer patients receiving preoperative treatment.

Identification of metabolism-related genes for predicting peritoneal metastasis in patients with gastric cancer.

OBJECTIVE: The reprogramming of metabolism is an important factor in the metastatic process of cancer. In our study, we intended to investigate the predictive value of metabolism-related genes (MRGs) in recurrent gastric cancer (GC) patients with peritoneal metastasis. METHODS: The sequencing data of mRNA of GC patients were obtained from Asian Cancer Research Group (ACRG) and the GEO databases (GSE53276). The differentially expressed MRGs (DE-MRGs) between a cell line without peritoneal metastasis (HSC60) and one with peritoneal metastasis (60As6) were analyzed with the Limma package. According to the LASSO regression, eight MRGs were identified as crucially related to peritoneal seeding recurrence in patients. Then, disease free survival related genes were screened using Cox regression, and a promising prognostic model was constructed based on 8 MRGs. We trained and verified it in two independent cohort. RESULTS: We confirmed 713 DE-MRGs and the enriched pathways. Pathway analysis found that the MRG-related pathways were related to tumor metabolism development. With the help of Kaplan-Meier analysis, we found that the group with higher risk scores had worse rates of peritoneal seeding recurrence than the group with lower scores in the cohorts. CONCLUSIONS: This study developed an eight-gene signature correlated with metabolism that could predict peritoneal seeding recurrence for GC patients. This signature could be a promising prognostic model, providing better strategy in treatment.

Non-classical ferroptosis inhibition by a small molecule targeting PHB2.

Ferroptosis is a new type of programmed cell death characterized by iron-dependent lipid peroxidation. Ferroptosis inhibition is thought as a promising therapeutic strategy for a variety of diseases. Currently, a majority of known ferroptosis inhibitors belong to either antioxidants or iron-chelators. Here we report a new ferroptosis inhibitor, termed YL-939, which is neither an antioxidant nor an iron-chelator. Chemical proteomics revealed the biological target of YL-939 to be prohibitin 2 (PHB2). Mechanistically, YL-939 binding to PHB2 promotes the expression of the iron storage protein ferritin, hence reduces the iron content, thereby decreasing the susceptibility to ferroptosis. We further showed that YL-939 could substantially ameliorate liver damage in a ferroptosis-related acute liver injury model by targeting the PHB2/ferritin/iron axis. Overall, we identified a non-classical ferroptosis inhibitor and revealed a new regulation mechanism of ferroptosis. These findings may present an attractive intervention strategy for ferroptosis-related diseases.

Generative deep learning enables the discovery of a potent and selective RIPK1 inhibitor.

The retrieval of hit/lead compounds with novel scaffolds during early drug development is an important but challenging task. Various generative models have been proposed to create drug-like molecules. However, the capacity of these generative models to design wet-lab-validated and target-specific molecules with novel scaffolds has hardly been verified. We herein propose a generative deep learning (GDL) model, a distribution-learning conditional recurrent neural network (cRNN), to generate tailor-made virtual compound libraries for given biological targets. The GDL model is then applied to RIPK1. Virtual screening against the generated tailor-made compound library and subsequent bioactivity evaluation lead to the discovery of a potent and selective RIPK1 inhibitor with a previously unreported scaffold, RI-962. This compound displays potent in vitro activity in protecting cells from necroptosis, and good in vivo efficacy in two inflammatory models. Collectively, the findings prove the capacity of our GDL model in generating hit/lead compounds with unreported scaffolds, highlighting a great potential of deep learning in drug discovery.

Tertiary lymphoid structure patterns predicted anti-PD1 therapeutic responses in gastric cancer.

Objective: Recent studies have highlighted the distinct value of tertiary lymphoid structure (TLS) for immunotherapeutic response prediction. However, it remains unclear whether TLS could play such roles in gastric cancer (GC). Methods: In this study, tumor tissue slices from 292 GC patients from Zhongshan Hospital were firstly reviewed to explore the correlation between TLS and clinical characteristics. Subsequently, we curated 38 reported genes that may function as triggers of TLS and performed consensus molecular subtyping in public RNA-seq datasets to determine TLS patterns in GC. Based on the differentially expressed genes acquired from two TLS patterns, we quantified TLS-related genes on the principal component analysis (PCA) algorithm to develop TLS score. A Zhongshan immunotherapy cohort including 13 patients who received programmed cell death 1 (PD1) blockade therapy was established to conduct RNA sequencing analysis and multiplex immunohistochemistry (mIHC) tests using formalin-fixed and paraffin-embedded (FFPE) tissues. The corresponding TLS score and immune cell counts were further compared based on therapeutic response variations. Results: Mature TLS was revealed as an independent prognostic factor in 292 GC patients. Patients with higher TLS score was characterized by prolonged survival time and superior response to immunotherapy. TLS score was correlated with immunotherapy-related characters, such as microsatellite instability (MSI) and tumor mutation burden (TMB). In addition, RNA-seq data analysis in the Zhongshan immunotherapy cohort indicated that a higher TLS score was correlated with a superior response to PD1 blockade therapy. mIHC tests also revealed that PD1+CD8+ T cell counts were significantly increased in the high-TLS score group. Conclusions: This study highlighted that TLS was significantly associated with immune landscape diversity and complexity. Quantitatively evaluating TLS patterns of individual tumor will strengthen our understanding of TME characteristics and promote more effective immunotherapy strategies.

A combination of eye-gaze and head-gaze interactions improves efficiency and user experience in an object positioning task in virtual environments.

Eye-gaze and head-gaze are two hands-free interaction modes in virtual reality, each of which has demonstrated different strengths. Selecting suitable interaction modes in different scenarios is important to achieve efficient interaction in virtual scenes. This study compared the movement time in an object positioning task by examining eye-gaze interaction and head-gaze interaction in various conditions. In turn, it identified the superior zones for each mode, respectively. Based on this information, we designed a combination mode - utilizing eye-gaze interaction at the acceleration phase and deceleration phase and head-gaze interaction at the correction phase - to achieve the optimal interaction mode, which has allowed us to obtain higher efficiency and subjective satisfaction. This study provides a comprehensive analysis of the characteristics of the eye-gaze and head-gaze interaction modes and provides valuable insights into selecting the appropriate interaction modes for virtual reality applications.

An orally available Mpro inhibitor is effective against wild-type SARS-CoV-2 and variants including Omicron.

Emerging SARS-CoV-2 variants continue to cause waves of new infections globally. Developing effective antivirals against SARS-CoV-2 and its variants is an urgent task. The main protease (Mpro) of SARS-CoV-2 is an attractive drug target because of its central role in viral replication and its conservation among variants. We herein report a series of potent α-ketoamide-containing Mpro inhibitors obtained using the Ugi four-component reaction. The prioritized compound, Y180, showed an IC50 of 8.1 nM against SARS-CoV-2 Mpro and had oral bioavailability of 92.9%, 31.9% and 85.7% in mice, rats and dogs, respectively. Y180 protected against wild-type SARS-CoV-2, B.1.1.7 (Alpha), B.1.617.1 (Kappa) and P.3 (Theta), with EC50 of 11.4, 20.3, 34.4 and 23.7 nM, respectively. Oral treatment with Y180 displayed a remarkable antiviral potency and substantially ameliorated the virus-induced tissue damage in both nasal turbinate and lung of B.1.1.7-infected K18-human ACE2 (K18-hACE2) transgenic mice. Therapeutic treatment with Y180 improved the survival of mice from 0 to 44.4% (P = 0.0086) upon B.1.617.1 infection in the lethal infection model. Importantly, Y180 was also highly effective against the B.1.1.529 (Omicron) variant both in vitro and in vivo. Overall, our study provides a promising lead compound for oral drug development against SARS-CoV-2.

Identification of triazolopyridine derivatives as a new class of AhR agonists and evaluation of anti-psoriasis effect in a mouse model.

The aryl hydrocarbon receptor (AhR), a ligand-dependent transcription factor, can regulate the immune balance of Th17/22 and Treg cells, which plays an important role in the development and maintenance of the skin barrier. We herein report the discovery of triazolopyridine derivatives as a new class of AhR agonists. Structure-activity relationship analyses led to the identification of the most active compound, 6-bromo-2-(4-bromophenyl)-[1,2,4]triazolo[1,5-a]pyridine (12a), with an EC50 (50% effective concentration) value of 0.03 nM. Compound 12a could induce rapid nuclear enrichment of AhR, trigger the transcription of downstream genes and promote skin barrier repair. Topical or oral administration of 12a could significantly alleviate imiquimod (IMQ)-induced psoriasis-like skin lesion. Considering the excellent in vivo anti-psoriasis activity as well as good pharmacokinetic properties, 12a could be a promising lead compound for drug discovery against psoriasis, and deserving further investigation.

Discovery of 3,4-Dihydrobenzo[f][1,4]oxazepin-5(2H)-one Derivatives as a New Class of Selective TNIK Inhibitors and Evaluation of Their Anti-Colorectal Cancer Effects.

The Traf2- and Nck-interacting protein kinase (TNIK) is a downstream signal protein of the Wnt/ß-catenin pathway and has been thought of as a potential target for the treatment of colorectal cancer (CRC) that is often associated with dysregulation of Wnt/ß-catenin signaling pathway. Herein, we report the discovery of a series of 3,4-dihydrobenzo[f][1,4]oxazepin-5(2H)-one derivatives as a new class of TNIK inhibitors. Structure-activity relationship (SAR) analyses led to the identification of a number of potent TNIK inhibitors with compound 21k being the most active one (IC50: 0.026 ± 0.008 µM). This compound also displayed excellent selectivity for TNIK against 406 other kinases. Compound 21k could efficiently suppress CRC cell proliferation and migration in in vitro assays and exhibited considerable antitumor activity in the HCT116 xenograft mouse model. It also showed favorable pharmacokinetic properties. Overall, 21k could be a promising lead compound for drug discovery targeting TNIK and deserves further studies.

Structural Optimization and Structure-Activity Relationship Studies of 6,6-Dimethyl-4-(phenylamino)-6H-pyrimido[5,4-b][1,4]oxazin-7(8H)-one Derivatives as A New Class of Potent Inhibitors of Pan-Trk and Their Drug-Resistant Mutants.

Tropomyosin receptor kinases (TrkA, TrkB, and TrkC) are attractive therapeutic targets for multiple cancers. Two first-generation small-molecule Trks inhibitors, larotrectinib and entrectinib, have just been approved to use clinically. However, the drug-resistance mutations of Trks have already emerged, which calls for new-generation Trks inhibitors. Herein, we report the structural optimization and structure-activity relationship studies of 6,6-dimethyl-4-(phenylamino)-6H-pyrimido[5,4-b][1,4]oxazin-7(8H)-one derivatives as a new class of pan-Trk inhibitors. The prioritized compound 11g exhibited low nanomolar IC50 values against TrkA, TrkB, and TrkC and various drug-resistant mutants. It also showed good kinase selectivity. 11g displayed excellent in vitro antitumor activity and strongly suppressed Trk-mediated signaling pathways in intact cells. In in vivo studies, compound 11g exhibited good antitumor activity in BaF3-TEL-TrkA and BaF3-TEL-TrkCG623R allograft mouse models without exhibiting apparent toxicity. Collectively, 11g could be a promising lead compound for drug discovery targeting Trks and deserves further investigation.

Demethylation of the SFRP4 Promoter Drives Gastric Cancer Progression via the Wnt Pathway.

Wnt signaling is believed to be an important contributor to tumor development and has been reported to be modulated by secreted frizzled-related proteins (SFRP). Nevertheless, the role of secreted frizzled-related protein 4 (SFRP4) in tumorigenesis remains controversial. We aim to explore its biological function in gastric cancer. Genomes analysis based on the Gene Expression Omnibus (GEO) dataset was used to find the differential gene expression between different tumor-node-metastasis (TNM) stages of gastric cancer. IHC was used to determine the relationship between SFRP4 expression and clinicopathologic characteristics in patients with gastric cancer. The influence of SFRP4 on tumor progression was evaluated by CCK-8, colony formation, cell apoptosis, and cell cycle in vitro, as well as xenograft model in vivo. The methylation status of SFRPs was examined in gastric cancer specimens by quantitative methylation analysis. SFRP4 was most upregulated in advanced gastric cancer. High intratumoral SFRP4 expression, which was associated with tumor invasion and metastasis, was also a poor prognostic indicator for patients with gastric cancer. In vitro and in vivo studies revealed that SFRP4 could promote tumor growth; however, IWR-1 could suppress tumor growth mediated by SFRP4 overexpression. Mechanistic exploration found that SFRP4 was overexpressed by the decrease of promoter methylation and thus could competitively antagonize the inhibitory effect of SFRP1 on Wnt pathway activation and tumor progression in gastric cancer. IMPLICATIONS: In gastric cancer, the expression of SFRP4 was upregulated by decreased methylation. High intratumoral SFRP4 expression could activate the Wnt pathway to promote tumor progression and predict poor survival of patients with gastric cancer.

Small molecules in targeted cancer therapy: advances, challenges, and future perspectives.

Due to the advantages in efficacy and safety compared with traditional chemotherapy drugs, targeted therapeutic drugs have become mainstream cancer treatments. Since the first tyrosine kinase inhibitor imatinib was approved to enter the market by the US Food and Drug Administration (FDA) in 2001, an increasing number of small-molecule targeted drugs have been developed for the treatment of malignancies. By December 2020, 89 small-molecule targeted antitumor drugs have been approved by the US FDA and the National Medical Products Administration (NMPA) of China. Despite great progress, small-molecule targeted anti-cancer drugs still face many challenges, such as a low response rate and drug resistance. To better promote the development of targeted anti-cancer drugs, we conducted a comprehensive review of small-molecule targeted anti-cancer drugs according to the target classification. We present all the approved drugs as well as important drug candidates in clinical trials for each target, discuss the current challenges, and provide insights and perspectives for the research and development of anti-cancer drugs.