Systematic Characterization of Active Antitumor Constituents from the Shaggy Bracket Medicinal Mushroom Inonotus hispidus (Agaricomycetes) by UPLC-Q-TOF/MS and Network Pharmacology.

Inonotus hispidus is a well-known medicinal fungus and has been used in the treatment of cancer in China, but the material basis and potential mechanisms are still limited. The present study aimed to use in vitro experiments, UPLC-Q-TOF/MS and network pharmacology to predict active compounds and possible mechanisms of cultivated and wild I. hispidus. The cytotoxicity results in vitro showed that the extracts of cultivated and wild fruit bodies exhibited the highest inhibitory effects against MDA-MB-231 cells, and the 50% inhibition concentration, (IC50) values were 59.82 and 92.09 µg/mL, respectively. Of the two extracts, a total of 30 possible chemical components, including 21 polyphenols and nine fatty acids, were identified. Network pharmacology showed that five active polyphenols (osmundacetone, isohispidin, inotilone, hispolon, and inonotusin A) and 11 potential targets (HSP90AA1, AKT1, STAT3, EGFR, ESR1, PIK3CA, HIF1A, ERBB2, TERT, EP300 and HSP90AB1) were found to be closely associated with antitumor activity. Furthermore, 18 antitumor-related pathways were identified using the compound-target-pathway network. The molecular docking revealed that the active polyphenols had a good binding ability to the core targets, and the results were consistent with those of network pharmacology. Based on these findings, we speculate that I. hispidus can exert its antitumor activity through multicomponent, multitarget, and multichannel mechanisms of action.

Cadmium stress interacts with nutrient availability and light condition to affect the growth of Hydrocotyle vulgaris.

Heavy metal pollution is becoming a serious problem in wetland and often co-occurs with nutrient availability and light conditions variation. We hypothesized that nutrient availability and light condition can affect the growth of wetland plants under heavy metal stress. To test this hypothesis, single ramets of a common, clonal wetland plant Hydrocotyle vulgaris were grown for four weeks at three levels of cadmium with three levels of nutrient availability under 30% or 100% light conditions. High level of nutrient availability and high light condition overall promoted growth of H. vulgaris under Cd stress. Under the two light conditions, responses of H. vulgaris to Cd treatments differed among three nutrient levels. Under 30% light condition, 2 mg L-1 Cd2+ treatment decreased total mass at the low nutrient level and decreased ramet number at the medium nutrient level; 0.5 and 2 mg L-1 Cd2+ treatments decreased leaf mass ratio at the low and the medium nutrient levels. Under 100% light condition, 2 mg L-1 Cd2+ treatments significantly decreased total mass at the high level of nutrients; 2 mg L-1 Cd2+ treatment decreased ramet number at the medium and the high nutrient levels and decreased leaf mass ratio at the medium nutrient levels. Our results suggested that Cd stress can interact with nutrient availability and light condition to affect the performance of wetland plants such as H. vulgaris.

Detection of differential selection pressure and functional-specific sites in subunits of vertebrate neuronal nicotinic acetylcholine receptors.

The nicotinic acetylcholine receptors (nAChR) are made of subunits evolved from a common ancestor. Despite the similarity in their sequences and structures, the properties of these subunits vary significantly. Thus, identifying the evolution features and function-related sites specific to each subunit is essential for understanding the characteristics of the subunits and the receptors assembled by them. In this study, we examined the sequence features of the nine neuronal nAChRs subunits from representative vertebrate species. Analysis revealed that all the subunits were subject to strong purifying selection in evolution, and each was under a unique pattern of selection pressures. At the same time, the functional constraints were not uniform within each subunit, with different domains in the molecule being subject to different selection pressures. We also detected potential positive selection events in the subunits or subunit clusters, and identified the sites might be associated with the function specificity of each subunit. Furthermore, positive selection at some domains might contribute to the diversity of subunit function; for example, the ß9 strand might be related to the agonist specificity of α subunit in heteromeric receptor and ß4-ß5 linker could be involved in Ca2+ permeability. Subunits α7, α4 and ß2 subunits possess a strong adaptability in vertebrates. Our results highlighted the importance of tracking functional differentiation in protein sequence underlying functional properties of nAChRs. In summary, our work may provide clues on understanding the diversity and the function specificity of the nAChR subunits, as well as the receptors co-assembled by them.Communicated by Ramaswamy H. Sarma.

Screening novel drug candidates for Alzheimer's disease by an integrated network and transcriptome analysis.

MOTIVATION: Alzheimer's disease (AD) is a serious degenerative brain disease and the most common cause of dementia. The current available drugs for AD provide symptomatic benefit, but there is no effective drug to cure the disease. The emergence of large-scale genomic, pharmacological data provides new opportunities for drug discovery and drug repositioning as a promising strategy in searching novel drug for AD. RESULTS: In this study, we took advantage of our increasing understanding based on systems biology approaches on the pathway and network levels and perturbation datasets from the Library of Integrated Network-Based Cellular Signatures to introduce a systematic computational process to discover new drugs implicated in AD. First, we collected 561 genes that have reported to be risk genes of AD, and applied functional enrichment analysis on these genes. Then, by quantifying proximity between 5595 molecule drugs and AD based on human interactome, we filtered out 1092 drugs that were proximal to the disease. We further performed an Inverted Gene Set Enrichment analysis on these drug candidates, which allowed us to estimate effect of perturbations on gene expression and identify 24 potential drug candidates for AD treatment. Results from this study also provided insights for understanding the molecular mechanisms underlying AD. As a useful systematic method, our approach can also be used to identify efficacious therapies for other complex diseases. AVAILABILITY AND IMPLEMENTATION: The source code is available at https://github.com/zer0o0/drug-repo.git. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Analysis of the Deleterious Single-Nucleotide Polymorphisms Associated With Antidepressant Efficacy in Major Depressive Disorder.

Major depressive disorder (MDD) is a serious mental disease with negative effects on both mental and physical health of the patient. Currently, antidepressants are among the major ways to ease or treat MDD. However, the existing antidepressants have limited efficacy in treating MDD, with a large fraction of patients either responding inadequately or differently to antidepressants during the treatment. Pharmacogenetics studies have found that the genetic features of some genes are associated with the antidepressant efficacy. In order to obtain a better understanding on the relationship between the genetic factors and antidepressant treatment response, we compiled a list of 233 single-nucleotide polymorphisms (SNPs) significantly associated with the antidepressant efficacy in treating MDD. Of the 13 non-synonymous SNPs in the list, three (rs1065852, rs3810651, and rs117986340) may influence the structures and function of the corresponding proteins. Besides, the influence of rs1065852 on the structure of CYP2D6 was further investigated via molecular dynamics simulations. Our results showed that compared to the native CYP2D6 the flexibility of the F-G loop was reduced in the mutant. As a portion of the substrate access channel, the lower flexibility of F-G loop may reduce the ability of the substrates to enter the channel, which may be the reason for the lower enzyme activity of mutant. This study may help us to understand the impact of genetic variation on antidepressant efficacy and provide clues for developing new antidepressants.

Analyzing the genes and pathways related to major depressive disorder via a systems biology approach.

INTRODUCTION: Major depressive disorder (MDD) is a mental disorder caused by the combination of genetic, environmental, and psychological factors. Over the years, a number of genes potentially associated with MDD have been identified. However, in many cases, the role of these genes and their relationship in the etiology and development of MDD remains unclear. Under such situation, a systems biology approach focusing on the function correlation and interaction of the candidate genes in the context of MDD will provide useful information on exploring the molecular mechanisms underlying the disease. METHODS: We collected genes potentially related to MDD by screening the human genetic studies deposited in PubMed (https://www.ncbi.nlm.nih.gov/pubmed). The main biological themes within the genes were explored by function and pathway enrichment analysis. Then, the interaction of genes was analyzed in the context of protein-protein interaction network and a MDD-specific network was built by Steiner minimal tree algorithm. RESULTS: We collected 255 candidate genes reported to be associated with MDD from available publications. Functional analysis revealed that biological processes and biochemical pathways related to neuronal development, endocrine, cell growth and/or survivals, and immunology were enriched in these genes. The pathways could be largely grouped into three modules involved in biological procedures related to nervous system, the immune system, and the endocrine system, respectively. From the MDD-specific network, 35 novel genes potentially associated with the disease were identified. CONCLUSION: By means of network- and pathway-based methods, we explored the molecular mechanism underlying the pathogenesis of MDD at a systems biology level. Results from our work could provide valuable clues for understanding the molecular features of MDD.

Identification of functional divergence sites in dopamine receptors of vertebrates.

Dopamine is one of the major neurotransmitters in the brain and body, and regulates a wide variety of functions via its binding with dopamine receptors. Abnormalities in dopamine receptors have also been found to be related to various neurological disorders. For such reason, dopamine receptors are among the key components to understanding the molecular mechanisms of many diseases, they are also the potential drug targets for the treatment of many diseases. Till now, five different dopamine receptors (D1-D5) have been identified in mammals, which are assumed to be evolved from a common ancestor after multiple gene duplication events and functional divergence. Thus, identifying the specific features of each dopamine receptor, will not only provide clues for understanding the functional differences between the receptors, but also help us to design drugs specific for a certain subtype of receptor. In this study, we investigated the functional divergence in dopamine receptors in representative vertebrate species by analyzing their molecular evolution features. Our results showed that the coefficients for type I functional divergence (θI) were significantly greater than 0 for all the pairwise comparisons between the five dopamine receptors, suggesting that type I functional divergence, i.e., altered functional constraints or different evolutionary rates, may have taken place at some amino acids in the receptors. We further identified 84 potential type I functional divergence peptide sites for the pairwise comparisons between the D1-like and D2-like are identified in total. When these sites were mapped to the 3D structure of dopamine receptors, most of them were included in ICL3, M6 and M7 domains. Especially, sixteen of these sites may be the major sites associated with the changes of properties between D1-like and D2-like receptors. These sites provide molecular basis for further studies such as dopamine receptor function exploration and subtype specific drug design and screening.

Analyzing the genes related to Alzheimer's disease via a network and pathway-based approach.

BACKGROUND: Our understanding of the molecular mechanisms underlying Alzheimer's disease (AD) remains incomplete. Previous studies have revealed that genetic factors provide a significant contribution to the pathogenesis and development of AD. In the past years, numerous genes implicated in this disease have been identified via genetic association studies on candidate genes or at the genome-wide level. However, in many cases, the roles of these genes and their interactions in AD are still unclear. A comprehensive and systematic analysis focusing on the biological function and interactions of these genes in the context of AD will therefore provide valuable insights to understand the molecular features of the disease. METHOD: In this study, we collected genes potentially associated with AD by screening publications on genetic association studies deposited in PubMed. The major biological themes linked with these genes were then revealed by function and biochemical pathway enrichment analysis, and the relation between the pathways was explored by pathway crosstalk analysis. Furthermore, the network features of these AD-related genes were analyzed in the context of human interactome and an AD-specific network was inferred using the Steiner minimal tree algorithm. RESULTS: We compiled 430 human genes reported to be associated with AD from 823 publications. Biological theme analysis indicated that the biological processes and biochemical pathways related to neurodevelopment, metabolism, cell growth and/or survival, and immunology were enriched in these genes. Pathway crosstalk analysis then revealed that the significantly enriched pathways could be grouped into three interlinked modules-neuronal and metabolic module, cell growth/survival and neuroendocrine pathway module, and immune response-related module-indicating an AD-specific immune-endocrine-neuronal regulatory network. Furthermore, an AD-specific protein network was inferred and novel genes potentially associated with AD were identified. CONCLUSION: By means of network and pathway-based methodology, we explored the pathogenetic mechanism underlying AD at a systems biology level. Results from our work could provide valuable clues for understanding the molecular mechanism underlying AD. In addition, the framework proposed in this study could be used to investigate the pathological molecular network and genes relevant to other complex diseases or phenotypes.