SOJNMF: Identifying Multidimensional Molecular Regulatory Modules by Sparse Orthogonality-Regularized Joint Non-Negative Matrix Factorization Algorithm.

Cancer is not only a very aggressive but also a very diverse disease. Recent advances in high-throughput omics technologies of cancer have enabled biomedical researchers to have more opportunities for studying its multi-level biological regulatory mechanism. However, there are few methods to explore the underlying mechanism of cancer by identifying its multidimensional molecular regulatory modules from the multidimensional omics data of cancer. In this paper, we propose a sparse orthogonality-regularized joint non-negative matrix factorization (SOJNMF) algorithm which can integratively analyze multidimensional omics data. This method can not only identify multidimensional molecular regulatory modules, but reduce the overlap rate of features among the multidimensional modules while ensuring the sparsity of the coefficient matrix after decomposition. Gene expression data, miRNA expression data and gene methylation data of liver cancer are integratively analyzed based on SOJNMF algorithm. Then, we obtain 238 multidimensional molecular regulatory modules. The results of permutation test indicate that different omics features within these modules are significantly correlated in statistics. Meanwhile, the results of functional enrichment analysis show that these multidimensional modules are significantly related to the underlying mechanism of the occurrence and development of liver cancer.

Discovery of hydrazide-containing oseltamivir analogues as potent inhibitors of influenza A neuraminidase.

Neuraminidase (NA) inhibitors play a prime role in treating influenza. However, a variety of viruses containing mutant NAs have developed severe drug resistance towards NA inhibitors, so it is of crucial significance to solve this problem. Encouraged by urea-containing compound 12 disclosed by our lab, we designed a series of oseltamivir derivatives bearing hydrazide fragment for targeting the 150 cavity. Among the synthesized compounds, compound 17a showed 8.77-fold, 4.12-fold, 203-fold and 6.23-fold more potent activity than oseltamivir carboxylate against NAs from H5N1, H1N1, H5N1-H274Y, H1N1-H274Y, respectively. Meanwhile, the best compound 17a exhibited satisfactory metabolic stability in vitro. This study offers an important reference for the structural optimization of oseltamivir aiming at potent inhibition against H274Y mutant of NAs.

Hypoxia preconditioning improves structure and function of astrocytes mitochondria via PGC-1α/HIF signal.

The protective effect of astrocytes on nerves was demonstrated by mitochondrial transfer. The neuroprotective effect of hypoxic pretreatment is widely accepted. The aim of this research is to investigate the role of hypoxic preconditioning on astrocytes mitochondria. Rat neuronal cells and astrocytes were isolated and cultured. A hypoxic preconditioned astrocyte and oxygen glucose deprivation (OGD) neuronal cell co-culture experiment was used to detect the effect of hypoxic preconditioning (HP) on nerve damage. The silencing of proliferatoractivated receptor γ coactivator-1α (PGC-1α) with siRNA was used to explore the role of HP in the repair of nerve damage and biogenesis of mitochondria. HP increased astrocyte viability and promoted neuroprotective factor secretion. The expression levels of antioxidant enzymes, PGC-1α and uncoupling protein2 (UCP2) were up-regulated by HP. In addition, HP improved mitochondrial function and reduced oxidative stress induced by OGD. It was found that HP astrocytes had a greater neuroprotective effect than normal astrocytes cells. Neuronal apoptosis and reactive oxygen species levels were down-regulated by cell co-culture. The PGC-1α siRNA experiment showed that hypoxia treatment promotes mitochondrial biogenesis and plays a neuroprotective role. HP significantly enhanced the efficacy of astrocytes in the treatment of neuronal injury.

Discovery of a non-zwitterionic oseltamivir analogue as a potent influenza a neuraminidase inhibitor.

The most of potent neuraminidase inhibitors as zwitterions with poor lipophilicity suffered from the poor oral bioavailability. Herein, we describe a rational journey to discover a non-zwitterionic neuraminidase inhibitor 24a containing urea. It showed potent inhibitions against neuraminidases from group 1(H5N1 and H1N1) and group 2 (H3N2) subtypes and exhibited more strong inhibitory activities against neuraminidases from H274Y mutants than oseltamivir carboxylate. Whether administrated by orally or intravenous injection, the pharmacokinetic profile of compound 24a in SD rats were improved compared to oseltamivir carboxylate.

[Identifying critical state of breast cancer cell differentiation based on landscape dynamic network biomarkers].

Breast cancer is a malignant tumor with the highest morbidity and mortality in female in recent years, and it is a complex disease that affects human health. Studies have shown that dynamic network biomarkers (DNB) can effectively identify critical states at which complex diseases such as breast cancer change from a normal state to a disease state. However, the traditional DNB method requires data from multiple samples in the same disease state, which is usually unachievable in clinical diagnosis. This paper quantitatively analyzes the time series data of MCF-7 breast cancer cells and finds the DNB module of a single sample in the time series based on landscape DNB (L-DNB) method. Then, a comprehensive index is constructed to detect its early warning signals to determine the critical state of breast cancer cell differentiation. The results of this study may be of great significance for the prevention and early diagnosis of breast cancer. It is expected that this paper can provide references for the related research of breast cancer.

Application of carbamyl in structural optimization.

Carbamyl is considered a privileged structure in medicinal chemistry. It has a wide range of biological activities such as antimicrobial, anticancer, anti-epilepsy, for which the best evidence is a number of marketed carbamyl-containing drugs. Carbamyl is formed of primary amine and carbonyl moieties that act as hydrogen bond donors and hydrogen acceptors with residues of targets respectively, which are benefit for improving pharmacological activities. In other cases, the introduced carbamyl improves drug-like properties including oral bioavailability. In this review, we introduce the carbamyl-containing drugs and the application of carbamyl in structural optimization as a result of enhancing activities or/and drug-like properties.

Identifying Dysregulated lncRNA-Associated ceRNA Network Biomarkers in CML Based on Dynamical Network Biomarkers.

The incidence of chronic myeloid leukemia (CML) is increasing year by year, which is a serious threat to human health. Early diagnosis can reduce mortality and improve prognosis. LncRNAs have been shown to be effective biomarkers for a variety of diseases and can act as competitive endogenous RNA (ceRNA). In this study, the dysregulated lncRNA-associated ceRNA networks (DLCN) of the chronic phase (CP), accelerated phase (AP), and blastic crisis (BC) for CML are constructed. Then, based on dynamic network biomarkers (DNB), some dysregulated lncRNA-associated ceRNA network biomarkers of CP, AP, and BC for CML are identified according to DNB criteria. Thus, a lncRNA (SNHG5) is identified from DLCN_CP, a lncRNA (DLEU2) is identified from DLCN_AP, and two lncRNAs (SNHG3, SNHG5) are identified from DLCN_BC. In addition, the critical index (CI) used to detect disease outbreaks shows that CML occurs in CP, which is consistent with clinical medicine. By analyzing the functions of the identified ceRNA network biomarkers, it has been found that they are effective lncRNA biomarkers directly or indirectly related to CML. The result of this study will help deepen the understanding of CML pathology from the perspective of ceRNA and help discover the effective biomarkers of CP, AP, and BC for CML in the future, so as to help patients get timely treatment and reduce the mortality of CML.

Identifying critical states of hepatocellular carcinoma based on landscape dynamic network biomarkers.

Hepatocellular carcinoma (HCC) is the major histological form of primary liver cancer. It has usually reached the disease state once the patient is diagnosed since there are no specific symptoms in the early stages of HCC. This fact increases the difficulty of curing HCC. Recently, quantities of evidence have shown that many mathematical methods (such as dynamic network biomarkers, DNB) can be used to detect critical states or tipping points of complex diseases. However, it is difficult to apply the DNB theory to the clinic since multiple samples are generally unavailable for individual patient. This paper constructs a novel method based on landscape dynamic network biomarkers (L-DNB), which aims to detect early warning signals from cirrhosis state to very advanced HCC state in individual patient. The selected dataset contains multiple samples for each HCC state. A score that indicates the disease characteristics is calculated for each sample by RNA-seq data, and several scores constitute a distribution in the same state. Quantifying the statistical characteristics of these distributions and determining that low-grade dysplastic and high-grade dysplastic are the critical states of HCC. These results can provide scientific advice for early warning indicators and optimal treatment time for HCC.

Design, synthesis and biological evaluation of oseltamivir derivatives containing pyridyl group as potent inhibitors of neuraminidase for influenza A.

Influenza A neuraminidase plays an indispensable role in the process of replication and transmission of influenza, so the neuraminidase inhibition can prevent the reproduction of the viruses therefore achieve the effect of treatment of influenza. However, drug resistance of neuraminidase inhibitors such as oseltamivir highlights the need to develop novel structural neuraminidase inhibitors. Here we explored a series of oseltamivir derivatives bearing pyridyl group. Among them, compound 23b exhibiting potent inhibitory activity against neuraminidase from H5N1 subtype was comparable to oseltamivir carboxylate. Cytopathic effect inhibition assay in MDCK cells indicated that compound 23b exerted powerful inhibitions on influenza viruses. And compound 23b were nontoxic to MDCK cells. Meanwhile, compound 23b showed high stability towards rat liver microsomes, human liver microsomes and human plasma. This research enriched the structural type of neuraminidase inhibitors.

Synthesis and Biological Evaluation of NH2-Sulfonyl Oseltamivir Analogues as Influenza Neuraminidase Inhibitors.

A series of NH2-sulfonyl oseltamivir analogues were designed, synthesized, and their inhibitory activities against neuraminidase from H5N1 subtype evaluated. The results indicated that the IC50 value of compound 4a, an oseltamivir analogue via methyl sulfonylation of C5-NH2, was 3.50 µM. Molecular docking simulations suggested that 4a retained most of the interactions formed by oseltamivir carboxylate moieties and formed an additional hydrogen bond with the methylsulfonyl group. Meanwhile, 4a showed high stability towards human liver microsomes. More importantly, 4a without basic moieties is not a zwitterion as reported on the general structure of neuraminidase inhibitors. This research will provide valuable reference for the research of new types of neuraminidase inhibitors.

Acetaminophen Responsive miR-19b Modulates SIRT1/Nrf2 Signaling Pathway in Drug-Induced Hepatotoxicity.

Previous studies suggest that activation of SIRT1 protects liver from acetaminophen (APAP)-induced injury; however, the detailed mechanism of SIRT1 modulation in this process is still incomplete. Therefore, this study was to investigate the pathophysiological role of SIRT1 in APAP-mediated hepatotoxicity. We found that SIRT1 mRNA and protein were markedly upregulated in human LO2 cells and mouse liver upon APAP exposure. In vitro, the specific knockdown of SIRT1 expression ultimately aggravated APAP-evoked cellular antioxidant defense in LO2 cells. Moreover, lentivirus-mediated knockdown of hepatic SIRT1 expression exacerbated APAP-induced oxidative stress and liver injury, especially reduction of Nrf2 and subsequent downregulation of several antioxidant genes. Intriguingly, 30 mg/kg SRT1720, the specific SIRT1 activator, which greatly enhanced Nrf2 expression and antioxidant defense, and then eventually reversed APAP-induced hepatic liver injury in mice. Furthermore, APAP responsive miR-19b played an important role in regulating SIRT1 expression, whereas overexpression miR-19b largely abolished the induction of SIRT1 by APAP in vitro and in vivo. Specific SIRT1 3'-UTR mutation, which disrupted the interaction of miRNA-3'UTR, and successfully abrogated the modulation by miR-19b. Notably, hepatic miR-19b overexpression worsened the APAP-induced hepatotoxicity. In general, our results support the notion that the strong elevation of SIRT1 by APAP responsive miR-19b may represent a compensatory mechanism to protect liver against the drug-induced damage, at least in part by enhancing Nrf2-mediated antioxidant capacity in the liver.

Genistein Ameliorates Ischemia/Reperfusion-Induced Renal Injury in a SIRT1-Dependent Manner.

Renal ischemia/reperfusion (I/R) injury continues to be a complicated situation in clinical practice. Genistein, the main isoflavone found in soy products, is known to possess a wide spectrum of biochemical and pharmacological activities. However, the protective effect of genistein on renal I/R injury has not been well investigated. In the current study, we explore whether genistein exhibits its renal-protective effects through SIRT1 (Sirtuin 1) in I/R-induced mice model. We found the treatment of genistein significantly reduced renal I/R-induced cell death, simultaneously stimulating renal cell proliferation. Meanwhile, SIRT1 expression was up-regulated following the administration of genistein in renal region. Furthermore, pharmacological inhibition or shRNA-mediated depletion of SIRT1 significantly reversed the protective effect of genistein on renal dysfunction, cellular damage, apoptosis, and proliferation following I/R injury, suggesting an indispensible role of the increased SIRT1 expression and activity in this process. Meanwhile, the reduced p53 and p21 expression and increased PCNA (Proliferating Cell Nuclear Antigen) expression were blocked after the depletion of SIRT1 compared with the genistein treatment group in the renal I/R process. Hence, our results provided further experimental basis for the potential use of genistein for the treatment of kidney disease with deficiency of SIRT1 activity.

Formononetin protects against acetaminophen-induced hepatotoxicity through enhanced NRF2 activity.

To examine the effects of formononetin (FMN) on Acetaminophen (APAP)-induced liver injury in vitro and in vivo. Human non-tumor hepatic cells LO2 were pretreated with either vehicle or FMN (20, 40 µM), for 6 h, followed by incubation with or without APAP (10 mM) for 24 h. In an in vivo assay, male BALB/c mice were randomly divided into four groups: (1) control group; (2) APAP group; (3) APAP + FMN (50 mg/Kg); (4) APAP + FMN (100 mg/Kg). The mice in the control and APAP groups were pre-treated with vehicle; the other two groups were pretreated daily with FMN (50, 100 mg/Kg) orally for 7 consecutive days. After the final treatment, acute liver injury was induced in all groups, except the control group, by intraperitoneal (i.p.) injection of 300 mg/Kg APAP. In LO2 cells, APAP exposure decreased the cell viability and glutathione (GSH) content, which were both greatly restored by FMN pretreatment. Overdose of APAP increased hepatic malondialdehyde (MDA) content, serum alanine aminotransferase (ALT), and aspartate aminotransferase (AST) activity in experimental mice. Supplementation with 100 mg/Kg FMN significantly reduced APAP-induced elevated levels of MDA (1.97 ± 0.27 vs 0.55 ± 0.14 nmol/mg protein, p < 0.001), ALT (955.80 ± 209.40 vs 46.90 ± 20.40 IU/L, p < 0.001) and AST (1533.80 ± 244.80 vs 56.70 ± 28.80 IU/L, p < 0.001), and hepatic GSH level (5.54 ± 0.93 vs 8.91 ± 1.11 µmol/mg protein, p < 0.001) was significantly increased. These results were further validated by histopathology and TdT-mediated biotin-dUTP nick-endlabeling (TUNEL) staining, pretreatment with 100 mg/Kg FMN significant decreased APAP-induced hepatocellular damage and cell apoptosis (36.55 ± 3.82 vs 2.58 ± 1.80%, p < 0.001). Concomitantly, FMN stimulated the expression of Nrf2 and antioxidant gene expression in the presence of APAP. These data provide an experimental basis for the use of FMN in the treatment of patients with APAP-induced hepatotoxicity.