DOTAD: A Database of Therapeutic Antibody Developability.

The development of therapeutic antibodies is an important aspect of new drug discovery pipelines. The assessment of an antibody's developability-its suitability for large-scale production and therapeutic use-is a particularly important step in this process. Given that experimental assays to assess antibody developability in large scale are expensive and time-consuming, computational methods have been a more efficient alternative. However, the antibody research community faces significant challenges due to the scarcity of readily accessible data on antibody developability, which is essential for training and validating computational models. To address this gap, DOTAD (Database Of Therapeutic Antibody Developability) has been built as the first database dedicated exclusively to the curation of therapeutic antibody developability information. DOTAD aggregates all available therapeutic antibody sequence data along with various developability metrics from the scientific literature, offering researchers a robust platform for data storage, retrieval, exploration, and downloading. In addition to serving as a comprehensive repository, DOTAD enhances its utility by integrating a web-based interface that features state-of-the-art tools for the assessment of antibody developability. This ensures that users not only have access to critical data but also have the convenience of analyzing and interpreting this information. The DOTAD database represents a valuable resource for the scientific community, facilitating the advancement of therapeutic antibody research. It is freely accessible at http://i.uestc.edu.cn/DOTAD/ , providing an open data platform that supports the continuous growth and evolution of computational methods in the field of antibody development.

Risk Prediction Models for Invasive Mechanical Ventilation in Patients with Autoimmune Encephalitis: A Retrospective Cohort Study.

Methods: A multivariate predictive nomogram model was developed using the risk factors identified by LASSO regression and assessed by receiver operator characteristics (ROC) curve, calibration curve, and decision curve analysis. Results: The risk factors predictive of severe respiratory failure were male gender, impaired hepatic function, elevated intracranial pressure, and higher neuron-specific enolase. The final nomogram achieved an AUC of 0.770. After validation by bootstrapping, a concordance index of 0.748 was achieved. Conclusions: Our nomogram accurately predicted the risk of developing respiratory failure needing IMV in AE patients and provide clinicians with a simple and effective tool to guide treatment interventions in the AE patients.

[Effect of astragaloside â £ on angiotensin â ¡-induced inflammatory response of vascular endothelial cells and mechanism].

This study was designed to determine the inhibitory effect of astragaloside Ⅳ(AS-Ⅳ), a principal bioactive component extracted from the Chinese medicinal Astragali Radix, on the inflammatory response of vascular endothelial cells induced by angiotensin Ⅱ(Ang Ⅱ), the most major pathogenic factor for cardiovascular diseases, and to clarify the role of calcium(Ca~(2+))/phosphatidylinosi-tol-3-kinase(PI3K)/protein kinase B(Akt)/endothelial nitric oxide synthase(eNOS)/nitric oxide(NO) pathway in the process. To be specific, human umbilical vein endothelial cells(HUVECs) were cultured in the presence of AS-Ⅳ with or without the specific inhibitor of NO synthase(NG-monomethyl-L-arginine, L-NMMA), inhibitor of PI3K/Akt signaling pathway(LY294002), or Ca~(2+)-chelating agent(ethylene glycol tetraacetic acid, EGTA) prior to Ang Ⅱ stimulation. The inhibitory effect of AS-Ⅳ on Ang Ⅱ-induced inflammatory response and the involved mechanism was determined with enzyme-linked immunosorbent assay(ELISA), cell-based ELISA assay, Western blot, and monocyte adhesion assay which determined the fluorescently labeled human monocytic cell line(THP-1) adhered to Ang Ⅱ-stimulated endothelial cells. AS-Ⅳ increased the production of NO by HUVECs in a dose-and time-dependent manner(P<0.05) and raised the level of phosphorylated eNOS(P<0.05). The above AS-Ⅳ-induced changes were abolished by pretreatment with L-NMMA, LY294002, or EGTA. Compared with the control group, Ang Ⅱ obviously enhanced the production and release of cytokines(tumor necrosis factor-α, interleukin-6), chemokines(monocyte chemoattractant protein-1) and adhesion molecules(intercellular adhesion molecule-1, vascular cellular adhesion molecule-1), and the number of monocytes adhered to HUVECs(P<0.05), which were accompanied by the enhanced levels of phosphorylated inhibitor of nuclear factor-κBα protein and activities of nuclear factor-κB(NF-κB)(P<0.05). This study also demonstrated that Ang Ⅱ-induced inflammatory response was inhibited by pretreatment with AS-Ⅳ(P<0.05). In addition, the inhibitory effect of AS-Ⅳ was abrogated by pretreatment with L-NMMA, LY294002, or EGTA(P<0.05). This study provides a direct link between AS-Ⅳ and Ca~(2+)/PI3K/Akt/eNOS/NO pathway in AS-Ⅳ-mediated anti-inflammatory actions in endothelial cells exposed to Ang Ⅱ. The results indicate that AS-Ⅳ attenuates endothelial cell-mediated inflammatory response induced by Ang Ⅱ via the activation of Ca~(2+)/PI3K/Akt/eNOS/NO signaling pathway.

The mechanism of Renshen-Fuzi herb pair for treating heart failure-Integrating a cardiovascular pharmacological assessment with serum metabolomics.

Background: Renshen-Fuzi herb pair (RS-FZ) is often used in the clinical treatment of heart failure (HF) and has a remarkable therapeutic effect. However, the mechanism of RS-FZ for treating HF remains unclear. In our study, we explored the mechanism of RS-FZ for treating HF. Methods: Evaluation of RS-FZ efficacy by cardiovascular pharmacology. Moreover, Global metabolomics profiling of the serum was detected by UPLC-QTOF/MS. Multivariate statistics analyzed the specific serum metabolites and corresponding metabolic pathways. Combining serum metabolomics with network pharmacology, animal experiments screened and validated the critical targets of RS-FZ intervention in HF. Results: RS-FZ significantly ameliorated myocardial fibrosis, enhanced cardiac function, and reduced the serum HF marker (brain natriuretic peptide) level in rats with HF. Through topological analysis of the "Metabolite-Target-Component" interaction network, we found that 79 compounds of RS-FZ directly regulated the downstream specific serum metabolites by acting on four critical target proteins (CYP2D6, EPHX2, MAOB, and ENPP2). The immunohistochemistry results showed that RS-FZ observably improved the expression of CYP2D6 and ENPP2 proteins while decreasing the expression of EPHX2 and MAOB proteins dramatically. Conclusion: The integrated cardiovascular pharmacological assessment with serum metabolomics revealed that RS-FZ plays a crucial role in the treatment of HF by intervening in CYP2D6, EPHX2, MAOB, and ENPP2 target proteins. It provides a theoretical basis for RS-FZ for treating HF.

Identification of potential biomarkers of inflammation-related genes for ischemic cardiomyopathy.

Objective: Inflammation plays an important role in the pathophysiology of ischemic cardiomyopathy (ICM). We aimed to identify potential biomarkers of inflammation-related genes for ICM and build a model based on the potential biomarkers for the diagnosis of ICM. Materials and methods: The microarray datasets and RNA-Sequencing datasets of human ICM were downloaded from the Gene Expression Omnibus database. We integrated 8 microarray datasets via the SVA package to screen the differentially expressed genes (DEGs) between ICM and non-failing control samples, then the differentially expressed inflammation-related genes (DEIRGs) were identified. The least absolute shrinkage and selection operator, support vector machine recursive feature elimination, and random forest were utilized to screen the potential diagnostic biomarkers from the DEIRGs. The potential biomarkers were validated in the RNA-Sequencing datasets and the functional experiment of the ICM rat, respectively. A nomogram was established based on the potential biomarkers and evaluated via the area under the receiver operating characteristic curve (AUC), calibration curve, decision curve analysis (DCA), and Clinical impact curve (CIC). Results: 64 DEGs and 19 DEIRGs were identified, respectively. 5 potential biomarkers (SERPINA3, FCN3, PTN, CD163, and SCUBE2) were ultimately selected. The validation results showed that each of these five potential biomarkers showed good discriminant power for ICM, and their expression trends were consistent with the bioinformatics results. The results of AUC, calibration curve, DCA, and CIC showed that the nomogram demonstrated good performance, calibration, and clinical utility. Conclusion: SERPINA3, FCN3, PTN, CD163, and SCUBE2 were identified as potential biomarkers associated with the inflammatory response to ICM. The proposed nomogram could potentially provide clinicians with a helpful tool to the diagnosis and treatment of ICM from an inflammatory perspective.

Triptolide Alleviates Oxidized LDL-Induced Endothelial Inflammation by Attenuating the Oxidative Stress-Mediated Nuclear Factor-Kappa B Pathway.

Background: Endothelial inflammation triggered by oxidized LDL (ox-LDL) is a crucial mechanism involved in atherosclerosis. Triptolide (TP), a primary active ingredient of the traditional Chinese medicine Tripterygium wilfordii Hook F, possesses antioxidant and anti-inflammatory properties in vivo. However, limited information is available regarding these effects on endothelial inflammation occurring in atherosclerosis. Objectives: This study investigated the effects and possible mechanisms of action of TP on ox-LDL-induced inflammatory responses in human umbilical vein endothelial cells. Methods: Human umbilical vein endothelial cells were preincubated with TP at the indicated concentrations for 1 hour and then incubated with ox-LDL (50 µg/mL) for the indicated times. Results: Preincubation of cultured human umbilical vein endothelial cells with TP inhibited ox-LDL-induced cytokine and chemokine production, adhesion molecule expression, and monocyte adhesion in a concentration-dependent manner. The concentrations of 8-isoprostane, malondialdehyde, and superoxide increased after human umbilical vein endothelial cells were exposed to ox-LDL, which were associated with decreased activities of total superoxide dismutase and its isoenzyme (ie, CuZn- superoxide dismutase). Preincubation with TP reversed ox-LDL-induced effects in all events. Moreover, preincubation with TP also attenuated ox-LDL-induced nuclear factor-kappa B transcriptional activation in a concentration-dependent manner, via the suppression of inhibitor of kappa Balpha (IκBα) phosphorylation and subsequent nuclear factor-kappa B DNA binding. Conclusions: These data indicate that TP inhibits ox-LDL-induced endothelial inflammation, possibly via suppression of the oxidative stress-dependent activation of the nuclear factor-kappa B signaling pathway.

SSH2.0: A Better Tool for Predicting the Hydrophobic Interaction Risk of Monoclonal Antibody.

Therapeutic antibodies play a crucial role in the treatment of various diseases. However, the success rate of antibody drug development is low partially because of unfavourable biophysical properties of antibody drug candidates such as the high aggregation tendency, which is mainly driven by hydrophobic interactions of antibody molecules. Therefore, early screening of the risk of hydrophobic interaction of antibody drug candidates is crucial. Experimental screening is laborious, time-consuming, and costly, warranting the development of efficient and high-throughput computational tools for prediction of hydrophobic interactions of therapeutic antibodies. In the present study, 131 antibodies with hydrophobic interaction experiment data were used to train a new support vector machine-based ensemble model, termed SSH2.0, to predict the hydrophobic interactions of antibodies. Feature selection was performed against CKSAAGP by using the graph-based algorithm MRMD2.0. Based on the antibody sequence, SSH2.0 achieved the sensitivity and accuracy of 100.00 and 83.97%, respectively. This approach eliminates the need of three-dimensional structure of antibodies and enables rapid screening of therapeutic antibody candidates in the early developmental stage, thereby saving time and cost. In addition, a web server was constructed that is freely available at http://i.uestc.edu.cn/SSH2/.

A novel m6A-related prognostic signature for predicting the overall survival of hepatocellular carcinoma patients.

Liver hepatocellular carcinoma (LIHC) comprises most cases of liver cancer with a poor prognosis. N6 -methyladenosine (m6A) plays important biological functions in cancers. Thus, the present research was aimed to determine biomarkers of m6A regulators that could effectively predict the prognosis of LIHC patients. Based on the data collected from the Cancer Genome Atlas (TCGA) database, the correlation between the mRNA expression levels and copy number variation (CNV) patterns were determined. Higher mRNA expression resulted from the increasing number of 9 genes. Using the univariate Cox regression analysis, 11 m6A regulators that had close correlations with the LIHC prognosis were identified. In addition, under the support of the multivariate Cox regression models and the least absolute shrinkage and selection operator, a 4-gene (YTHDF2, IGF2BP3, KIAA1429, and ALKBH5) signature of m6A regulators was constructed. This signature was expected to present a prognostic value in LIHC (log-rank test p value < 0.0001). The GSE76427 (n = 94) and ICGC-LIRI-JP (n = 212) datasets were used to validate the prognostic signature, suggesting strong power to predict patients' prognosis for LIHC. To sum up, genetic alterations in m6A regulatory genes were identified as reliable and effective biomarkers for predicting the prognosis of LIHC patients.

Protective Effects of Shenfuyixin Granule on H2O2-Induced Apoptosis in Neonatal Rat Cardiomyocytes.

Shenfuyixin granule (SFYXG, i.e., Xinshuaikang granule) is a prescription, commonly used in the clinical experience, which plays a significant role in the treatment of heart failure. The purpose of this present research was to investigate the protective effect of SFYXG, and the mechanism about anti-H2O2-induced oxidative stress and apoptosis in the neonatal rat cardiomyocytes. Myocardial cells, as is well known, were divided into 4 groups: normal, model, SFYXG, and coenzyme Q10 group, respectively. Cells viability was determined by MTT assay. Flow cytometry and AO/EB staining were implemented to test the apoptosis rate and intracellular reactive oxygen species (ROS) level. Mitochondrion membrane potential (MMP) was evaluated by JC-1 fluorescence probe method. The myocardial ultrastructure of mitochondrion was measured by electron microscope. The related mRNA expression levels of Bax, Bcl-2, Caspase-3, caspase-8, and caspase-9 were detected by real-time polymerase chain reaction (PCR). Also, the expression levels of Bax and Bcl-2 protein were detected by Western blot, and the expression levels of caspase-3, caspase-8, and caspase-9 protein were tested by caspase-Glo®3 Assay, caspase-Glo®8 Assay, and caspase-Glo®9 Assay, respectively. GAPDH was used as the internal reference gene/protein. The results revealed that SFYXG (0.5 mg/ml) raised the viability of myocardial cell, weakened the apoptosis rate and ROS level, corrected the mitochondrion membrane potential stability, and improved cell morphology and ultrastructure of myocardial mitochondrion. Furthermore, SFYXG upregulated the antiapoptosis gene of Bcl-2, but downregulated the proapoptosis genes of Bax, caspase-3, and caspase-9. In conclusion, SFYXG could appear to attenuate myocardial injury by its antioxidative and antiapoptosis effect.

Triptolide attenuates renal damage by limiting inflammatory responses in DOCA-salt hypertension.

BACKGROUND: Triptolide (TP), a principal bioactive component of traditional Chinese medicine Tripterygium wilfordii Hook. F., has been shown to have immunosuppressive/anti-inflammatory actions in vitro. Moreover, it is well established that inflammatory mechanisms contribute to the progression of hypertension-induced renal injury. Therefore, this study was performed to determine the protective effects of TP on renal injury in salt-sensitive hypertension and to identify the possible mechanisms for TP-induced protection. METHODS: Ten-week-old male C57BL/6 mice were subjected to uninephrectomy and deoxycorticosterone acetate (DOCA)-salt treatment with or without intraperitoneal administration of various concentrations of TP. RESULTS: Five weeks after the treatment, systolic blood pressure measured by tail-cuff plethysmography increased in DOCA-salt-treated mice, but no difference was found between DOCA-salt-treated mice with or without TP treatment. Treatment with TP dose-dependently attenuated increments in urinary albumin and 8-isoprostane excretion, and glomerulosclerosis and tubulointerstitial injury and fibrosis in DOCA-salt-treated mice. Moreover, our data showed that treatment with TP dose-dependently inhibited DOCA-salt-induced interstitial monocyte/macrophage infiltration associated with decreases in renal levels of proinflammatory cytokine/chemokine and adhesion molecule, as well as renal activated NF-κB concentrations. Our results also demonstrated that suppression of inflammatory responses with dexamethasone, an immunosuppressive agent, alleviated DOCA-salt hypertension-induced renal injury. CONCLUSIONS: TP treatment induced renal protection associated with inhibition of monocyte/macrophage-mediated inflammatory responses without lowering blood pressure. Thus, our data for the first time indicate that TP treatment ameliorates renal injury possibly via attenuating inflammatory responses in salt-sensitive hypertension.

RKIP reduction enhances radioresistance by activating the Shh signaling pathway in non-small-cell lung cancer.

Non-small-cell lung cancer (NSCLC) is exceptionally deadly because the tumors lack sensitive early-stage diagnostic biomarkers and are resistant to radiation and chemotherapy. Here, we investigated the role and mechanism of Raf kinase inhibitory protein (RKIP) in NSCLC radioresistance. The clinical data showed that the RKIP expression level was generally lower in radioresistant NSCLC tissues than in radiosensitive tissues. Reduced RKIP expression was related to NSCLC radioresistance and poor prognosis. In vitro experiments showed that RKIP knockdown increased radioresistance and metastatic ability in NSCLC cell lines. Mechanistically, RKIP reduction activated the Shh signaling pathway by derepressing Smoothened (Smo) and initiating glioma-associated oncogene-1 (Gli1)-mediated transcription in NSCLC. In addition, the inappropriately activated Shh-Gli1 signaling pathway then enhanced cancer stem cell (CSC) expression in the cell lines. The increasing quantity of CSCs in the tumor ultimately promotes the radiation resistance of NSCLC. Together, these results suggest that RKIP plays a vital role in radiation response and metastasis in NSCLC. RKIP reduction enhances radioresistance by activating the Shh signaling pathway and initiating functional CSCs. This role makes it a promising therapeutic target for improving the efficacy of NSCLC radiation treatment.

Jia-Shen decoction-medicated serum inhibits angiotensin-II induced cardiac fibroblast proliferation via the TGF-ß1/Smad signaling pathway.

Jia-Shen decoction (JSD) is a traditional Chinese medicine, which is used widely to treat chronic heart failure. However, the underlying mechanism remains to be elucidated. The present study aimed to investigate the mechanism underlying the effects of JSD on cardiac fibroblast (CF) proliferation and differentiation. The CFs were obtained from the hearts of neonatal (1­3­day old) Sprague­Dawley rats and treated with JSD-medicated serum (JSDS) with or without angiotensin II (Ang II). Cell proliferation was assessed using Cell Counting Kit­8 reagent. In addition, the mRNA expression levels of transforming growth factor­ß1 (TGF­ß1) and phosphorylated small mothers against decapentaplegic (p­Smad)2/3 and their protein expression levels were analyzed. CF proliferation was significantly increased in the Ang II­treated group, compared with the control group (P<0.05). The expression levels of collagen, α­smooth muscle actin, TGF­ß1 and p­Smad2/3 were also increased in the Ang II­treated group (P<0.05). Following JSDS treatment, the increased levels of collagen and cell proliferation were inhibited, and the increased expression levels of p­Smad2 and p­Smad3 were also inhibited (P<0.05). These data suggested that JSDS may inhibit CF proliferation via attenuating the TGF­ß1/Smad signaling pathway.

Protective effects of Jiashen Prescription () on myocardial infarction in rats.

OBJECTIVE: To evaluate the effects of Jiashen Prescription (, JSP) on myocardial infarction (MI) size and cardiac function at the early stage of MI in rats. METHODS: One hundred male Sprague-Dawley rats were subjected to sham-operation or MI induced by ligating the left anterior descending coronary artery. The rats with MI were treated with vehicle, JSP 3 and 6 g/(kg·d), or losartan 10 mg/(kg·d) for 1 week. RESULTS: Compared with the vehicle-treated MI rats, 6 g/(kg·d) JSP reduced MI size 3 days after MI (P<0.05), and attenuated the MI-induced increases in left ventricular end-diastolic and end-systolic dimension and decreases in fractional shortening and ejection fraction 1 week after MI (P<0.05). In addition, 6 g/(kg·d) JSP and losartan were equally effective in reducing MI size and enhancing cardiac functional recovery. CONCLUSION: JSP reduces MI size and improves cardiac function after MI, suggesting that JSP has potential as a therapy for MI.