Predicting the points of interaction of small molecules in the NF-κB pathway

<p>Abstract</p> <p>Background</p> <p>The similarity property principle has been used extensively in drug discovery to identify small compounds that interact with specific drug targets. Here we show it can be applied to identify the interactions of small molecules within the NF-κB signalling pathway.</p> <p>Results</p> <p>Clusters that contain compounds with a predominant interaction within the pathway were created, which were then used to predict the interaction of compounds not included in the clustering analysis.</p> <p>Conclusions</p> <p>The technique successfully predicted the points of interactions of compounds that are known to interact with the NF-κB pathway. The method was also shown to be successful when compounds for which the interaction points were unknown were included in the clustering analysis.</p

Advocating the need of a systems biology approach for personalised prognosis and treatment of B-CLL patients

The clinical course of B-CLL is heterogeneous. This heterogeneity leads to a clinical dilemma: can we identify those patients who will benefit from early treatment and predict the survival? In recent years, mathematical modelling has contributed significantly in understanding the complexity of diseases. In order to build a mathematical model for determining prognosis of B-CLL one has to identify, characterise and quantify key molecules involved in the disease. Here we discuss the need and role of mathematical modelling in predicting B-CLL disease pathogenesis and suggest a new systems biology approach for a personalised therapy of B-CLL patients

Novel 1,3,4-oxadiazole induces anticancer activity by targeting NF-κB in hepatocellular carcinoma cells

Aberrant activation of NF-κB is linked with the progression of human malignancies including hepatocellular carcinoma (HCC), and blockade of NF-κB signaling could be a potential target in the treatment of several cancers. Therefore, designing of novel small molecule inhibitors that target NF-κB activation is of prime importance in the treatment of several cancers. In the present work, we report the synthesis of series of 1,3,4-oxadiazoles, investigated their anticancer potential against HCC cells, and identified 2-(3-chlorobenzo[b]thiophen-2-yl)-5-(3-methoxyphenyl)-1,3,4-oxadiazole (CMO) as the lead compound. Further, we examined the effect of CMO on cell cycle distribution (flow cytometry), apoptosis (annexin V-propidium iodide-FITC staining), and phosphorylation of NF-κB signaling pathway proteins (IκB and p65) in HCC cells. We found that CMO induced antiproliferative effect in dose- and time-dependent manner. Also, CMO significantly increased the percentage of sub-G1 cell population and induced apoptosis. Furthermore, CMO found to decrease the phosphorylation of IκB (Ser 32) in the cytoplasmic extract and p65 (Ser 536) in the nuclear extract of HCC cells. It also abrogated the DNA binding ability and transcriptional activity of NF-κB. CMO induced the cleavage of PARP and caspase-3 in a time-dependent manner. In addition, transfection with p65 small interfering RNA blocks CMO-induced caspase-3/7 activation. Molecular docking analysis revealed that CMO interacts with the hydrophobic region of p65 protein. Thus, we are reporting CMO as an inhibitor of NF-κB signaling pathway

Identification of a prognostic signature for old-age mortality by integrating genome-wide transcriptomic data with the conventional predictors: the Vitality 90+ Study

Background Prediction models for old-age mortality have generally relied upon conventional markers such as plasma-based factors and biophysiological characteristics. However, it is unknown whether the existing markers are able to provide the most relevant information in terms of old-age survival or whether predictions could be improved through the integration of whole-genome expression profiles. Methods We assessed the predictive abilities of survival models containing only conventional markers, only gene expression data or both types of data together in a Vitality 90+ study cohort consisting of n = 151 nonagenarians. The all-cause death rate was 32.5% (49 of 151 individuals), and the median follow-up time was 2.55 years. Results Three different feature selection models, the penalized Lasso and Ridge regressions and the C-index boosting algorithm, were used to test the genomic data. The Ridge regression model incorporating both the conventional markers and transcripts outperformed the other models. The multivariate Cox regression model was used to adjust for the conventional mortality prediction markers, i.e., the body mass index, frailty index and cell-free DNA level, revealing that 331 transcripts were independently associated with survival. The final mortality-predicting transcriptomic signature derived from the Ridge regression model was mapped to a network that identified nuclear factor kappa beta (NF-κB) as a central node. Conclusions Together with the loss of physiological reserves, the transcriptomic predictors centered around NF-κB underscored the role of immunoinflammatory signaling, the control of the DNA damage response and cell cycle, and mitochondrial functions as the key determinants of old-age mortality.BioMed Central open acces

The expression and signalling patterns of CD180 toll like receptor in Chronic Lymphocytic Leukaemia (CLL)

Chronic lymphocytic leukaemia (CLL) is characterised by a progressive accumulation of mature CD5+CD20+CD23+ lymphocytes. Despite the remarkable progress in our understanding of the immunobiology of CLL, the aetiology of the disease remains unknown. The consensus is that CLL cells are driven by (auto)antigen(s) through the B cell receptor (BCR) and are regulated by a variety of signals received from the microenvironment, including toll-like receptors (TLR).Our group has previously shown that engagement of the CD180 orphan TLR expressed by approximately 60% of CLL cells, can re-wire the sIgM-mediated signalling from a pro-survival pathway, involving phosphatidylinositol-4,5-bisphosphate3-kinase (PI3K) and protein kinase B (AKT) to the potentially pro-apoptotic pathway through mitogen-activated protein kinase (p38MAPK). However, little is known about the function of the other BCR - sIgD in CLL and its possible interaction with CD180. Here we studied intracellular signalling and apoptosis of CLL cells following sole or sequential ligation of CD180 and sIgD. Our data indicated that following sequential ligation of CD180 and sIgD, CLL samples demonstrated enhanced p38MAPK phosphorylation leading to increased apoptosis of CLL cells indicating synergistic relationship between CD180 and sIgD. To better understand the prognostic importance of CD180 expression we sought to determine whether CD180 and other prognostic markers such as CD38 and ZAP70 displayed any correlation with the known cytogenetic aberrations:TP53 and DLEU1. Our results suggested that CLL cells with DLEU1 deletion are characterised by the negative expression of both, CD180 and CD38, and this might have a significance for CLL prognosis. To explain this correlation, we hypothesised that interaction of CLL cells with their microenvironment through TLRs leads to the expansion of leukaemic clones, in vivo, in lymph nodes. Our results indicated that CD180 is heterogeneously expressed in the paraffin tissue sections of the lymph nodes of CLL patients and its expression positively correlates with the expression of Ki-67. Our data demonstrated, that although CD180 expression and signaling might have negative prognostic importance in CLL due to the enhanced proliferation of leukaemic cells, its interaction with sIgD would re-direct leukaemic cells towards apoptosis thus opening new opportunities for the disease immunotherapy

Molecular Science for Drug Development and Biomedicine

With the avalanche of biological sequences generated in the postgenomic age, molecular science is facing an unprecedented challenge, i.e., how to timely utilize the huge amount of data to benefit human beings. Stimulated by such a challenge, a rapid development has taken place in molecular science, particularly in the areas associated with drug development and biomedicine, both experimental and theoretical. The current thematic issue was launched with the focus on the topic of “Molecular Science for Drug Development and Biomedicine”, in hopes to further stimulate more useful techniques and findings from various approaches of molecular science for drug development and biomedicine

Tumor-induced senescent T cells promote the secretion of pro-inflammatory cytokines and angiogenic factors by human monocytes/macrophages through a mechanism that involves Tim-3 and CD40L

Solid tumors are infiltrated by immune cells where macrophages and senescent T cells are highly represented. Within the tumor microenvironment, a cross-talk between the infiltrating cells may occur conditioning the characteristic of the in situ immune response. Our previous work showed that tumors induce senescence of T cells, which are powerful suppressors of lympho-proliferation. In this study, we report that Tumor-Induced Senescent (TIS)-T cells may also modulate monocyte activation. To gain insight into this interaction, CD4+ or CD8+TIS-T or control-T cells were co-incubated with autologous monocytes under inflammatory conditions. After co-culture with CD4+ or CD8+TIS-T cells, CD14+ monocytes/macrophages (Mo/Ma) exhibit a higher expression of CD16+ cells and a reduced expression of CD206. These Mo/Ma produce nitric oxide and reactive oxygen species; however, TIS-T cells do not modify phagocyte capacity of Mo/Ma. TIS-T modulated-Mo/Ma show a higher production of pro-inflammatory cytokines (TNF, IL-1β and IL-6) and angiogenic factors (MMP-9, VEGF-A and IL-8) and a lower IL-10 and IP-10 secretion than monocytes co-cultured with controls. The mediator(s) present in the supernatant of TIS-T cell/monocyte-macrophage co-cultures promote(s) tubulogenesis and tumor-cell survival. Monocyte-modulation induced by TIS-T cells requires cell-to-cell contact. Although CD4+ shows different behavior from CD8+TIS-T cells, blocking mAbs against T-cell immunoglobulin and mucin protein 3 and CD40 ligand reduce pro-inflammatory cytokines and angiogenic factors production, indicating that these molecules are involved in monocyte/macrophage modulation by TIS-T cells. Our results revealed a novel role for TIS-T cells in human monocyte/macrophage modulation, which may have deleterious consequences for tumor progression. This modulation should be considered to best tailor the immunotherapy against cancer.Fil: Ramello, María Cecilia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Córdoba. Centro de Investigaciones en Bioquímica Clínica e Inmunología; ArgentinaFil: Tosello Boari, Jimena. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Córdoba. Centro de Investigaciones en Bioquímica Clínica e Inmunología; ArgentinaFil: Canale, Fernando Pablo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Córdoba. Centro de Investigaciones en Bioquímica Clínica e Inmunología; ArgentinaFil: Mena, Hebe Agustina. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Medicina Experimental. Academia Nacional de Medicina de Buenos Aires. Instituto de Medicina Experimental; ArgentinaFil: Negrotto, Soledad. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Medicina Experimental. Academia Nacional de Medicina de Buenos Aires. Instituto de Medicina Experimental; ArgentinaFil: Gastman, B. Cleveland Clinic; Estados UnidosFil: Gruppi, Adriana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Córdoba. Centro de Investigaciones en Bioquímica Clínica e Inmunología; ArgentinaFil: Acosta Rodriguez, Eva Virginia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Córdoba. Centro de Investigaciones en Bioquímica Clínica e Inmunología; ArgentinaFil: Montes, Carolina Lucia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Córdoba. Centro de Investigaciones en Bioquímica Clínica e Inmunología; Argentin

Prediction of the anti-inflammatory effects of bioactive components of a Hippocampus species-based TCM formulation on chronic kidney disease using network pharmacology

Purpose: To systematically study and predict the therapeutic targets and signaling pathways of Hippocampus (HPC) against chronic kidney disease (CKD) using network pharmacology.Methods: By combining database mining, literature searching, screening of disease targets, and network construction, the effects of various components of HPC on several proteins related to CKD were predicted and the active compounds were screened. Genes related to the selected compounds were linked using the SEA database. The correlation between CKD and genes was determined using OMIM, DisGenNet, and GeneCards databases. Pathway-enrichment analyses of overlapping genes were undertaken using online databases.Results: A total of 144 compounds in HPC were identified. Analyses of clusters suggest that the active components of HPC and the target genes against the inflammation caused by CKD were due to 10 compounds and 25 genes. Metascape results showed that these HPC targets are related to CKD inflammation.Conclusion: The active components of HPC and the target genes against CKD inflammation are involved in multiple signaling pathways, such as AGE-RAGE, TLR, TNF, and NF-κB. This work provides scientific evidence to support the clinical use of HPC against CKD

Control of Inflammation Using Drug Delivery Strategies in in vitro Models

Regulation of inflammation is a crucial component of the immune system in response to injury and infection. In otherwise healthy individuals, an initial acute inflammatory response will subside once the injury or infection is eradicated. However, in certain disease states including autoimmune disease and persistent infection, miscommunication between cells of the immune system leads to a chronic inflammatory response, contributing to disease pathology and exacerbating symptoms. A major regulator of inflammation communication at the cellular level is transcription factor (TF) NF-κB. Under normal conditions, NF-κB is bound to an inhibitor in the cytoplasm. In a chronic disease state, NF-κB is overactive and found in the unbound form, resulting in increased production of inflammatory signals. Transcription factor decoys (TFD) are small nucleic acid sequences (~20 base pairs) that mimic the binding site for the TF on the native DNA, but do not encode for any proteins. By binding to the TF in the cytoplasm, TFD have potential to limit excessive immune signaling and inflammatory protein production. Unfortunately, clinical success of TFD has been hampered by a lack of an effective delivery method. Lack of stability and ease of degradation of the TFD require a protective carrier for delivery; however many synthetic carrier systems induce toxicity or an enhanced inflammatory response. In disease states characterized by excessive inflammation, treatment-induced toxicity or immune response is highly undesirable. The Bader lab has previously reported a nanoparticle carrier system based on natural polysaccharides, designed specifically for the treatment of rheumatoid arthritis. The materials used in this system have properties that can be exploited for the additional application of DNA delivery. This thesis will detail the adaptation of polysialic acid-N-trimethyl chitosan nanoparticles to be used as delivery vehicles for an NF-κB TFD treatment in in vitro models of rheumatoid arthritis and cystic fibrosis