Corynebacterium diphtheriae (Cd) is a Gram-positive human pathogen responsible for diphtheria infection and once regarded for high mortalities worldwide. The fatality gradually decreased with ...improved living standards and further alleviated when many immunization programs were introduced. However, numerous drug-resistant strains emerged recently that consequently decreased the efficacy of current therapeutics and vaccines, thereby obliging the scientific community to start investigating new therapeutic targets in pathogenic microorganisms. In this study, our contributions include the prediction of modelome of 13 C. diphtheriae strains, using the MHOLline workflow. A set of 463 conserved proteins were identified by combining the results of pangenomics based core-genome and core-modelome analyses. Further, using subtractive proteomics and modelomics approaches for target identification, a set of 23 proteins was selected as essential for the bacteria. Considering human as a host, eight of these proteins (glpX, nusB, rpsH, hisE, smpB, bioB, DIP1084, and DIP0983) were considered as essential and non-host homologs, and have been subjected to virtual screening using four different compound libraries (extracted from the ZINC database, plant-derived natural compounds and Di-terpenoid Iso-steviol derivatives). The proposed ligand molecules showed favorable interactions, lowered energy values and high complementarity with the predicted targets. Our proposed approach expedites the selection of C. diphtheriae putative proteins for broad-spectrum development of novel drugs and vaccines, owing to the fact that some of these targets have already been identified and validated in other organisms.
Schistosomiasis remains a serious health issue nowadays for an estimated one billion people in 79 countries around the world. Great efforts have been made to identify good vaccine candidates during ...the last decades, but only three molecules reached clinical trials so far. The reverse vaccinology approach has become an attractive option for vaccine design, especially regarding parasites like
spp. that present limitations for culture maintenance. This strategy also has prompted the construction of multi-epitope based vaccines, with great immunological foreseen properties as well as being less prone to contamination, autoimmunity, and allergenic responses. Therefore, in this study we applied a robust immunoinformatics approach, targeting
transmembrane proteins, in order to construct a chimeric antigen. Initially, the search for all hypothetical transmembrane proteins in GeneDB provided a total of 584 sequences. Using the PSORT II and CCTOP servers we reduced this to 37 plasma membrane proteins, from which extracellular domains were used for epitope prediction. Nineteen common MHC-I and MHC-II binding epitopes, from eight proteins, comprised the final multi-epitope construct, along with suitable adjuvants. The final chimeric multi-epitope vaccine was predicted as prone to induce B-cell and IFN-γ based immunity, as well as presented itself as stable and non-allergenic molecule. Finally, molecular docking and molecular dynamics foresee stable interactions between the putative antigen and the immune receptor TLR 4. Our results indicate that the multi-epitope vaccine might stimulate humoral and cellular immune responses and could be a potential vaccine candidate against schistosomiasis.
and its supernatant showed protective effects in different chemically-induced colitis models in mice. Recently, we described 7 peptides found in the
supernatant, all belonging to a protein called ...Microbial Anti-inflammatory Molecule (MAM). These peptides were able to inhibit NF-κB pathway
and showed anti-inflammatory properties
in a DiNitroBenzene Sulfate (DNBS)-induced colitis model. In this current proof we tested MAM effect on NF-κB pathway
, using a transgenic model of mice producing luciferase under the control of NF-κB promoter. Moreover, we tested this protein on Dextran Sodium Sulfate (DSS)-induced colitis in mice. To study the effect of MAM we orally administered to the mice a
strain carrying a plasmid containing the cDNA of MAM under the control of a eukaryotic promoter.
delivered plasmids in epithelial cells of the intestinal membrane allowing thus the production of MAM directly by host. We showed that MAM administration inhibits NF-κB pathway
. We confirmed the anti-inflammatory properties of MAM in DNBS-induced colitis but also in DSS model. In DSS model MAM was able to inhibit Th1 and Th17 immune response while in DNBS model MAM reduced Th1, Th2, and Th17 immune response and increased TGFβ production.
Cardiac glycosides (CGs) have a long history of treating cardiac diseases. However, recent reports have suggested that CGs also possess anticancer and antiviral activities. The primary mechanism of ...action of these anticancer agents is by suppressing the Na
/k
-ATPase by decreasing the intracellular K
and increasing the Na
and Ca
. Additionally, CGs were known to act as inhibitors of IL8 production, DNA topoisomerase I and II, anoikis prevention and suppression of several target genes responsible for the inhibition of cancer cell proliferation. Moreover, CGs were reported to be effective against several DNA and RNA viral species such as influenza, human cytomegalovirus, herpes simplex virus, coronavirus, tick-borne encephalitis (TBE) virus and Ebola virus. CGs were reported to suppress the HIV-1 gene expression, viral protein translation and alters viral pre-mRNA splicing to inhibit the viral replication. To date, four CGs (Anvirzel, UNBS1450, PBI05204 and digoxin) were in clinical trials for their anticancer activity. This review encapsulates the current knowledge about CGs as anticancer and antiviral drugs in isolation and in combination with some other drugs to enhance their efficiency. Further studies of this class of biomolecules are necessary to determine their possible inhibitory role in cancer and viral diseases.
Metabolic disorders are an increasing concern in the industrialized world. Current research has shown a direct link between the composition of the gut microbiota and the pathogenesis of obesity and ...diabetes. In only a few weeks, an obesity-inducing diet can lead to increased gut permeability and microbial dysbiosis, which contributes to chronic inflammation in the gut and adipose tissues, and to the development of insulin resistance. In this review, we examine the interplay between gut inflammation, insulin resistance, and the gut microbiota, and discuss how some probiotic species can be used to modulate gut homeostasis. We focus primarily on
, a highly abundant butyrate-producing bacterium that has been proposed both as a biomarker for the development of different gut pathologies and as a potential treatment due to its production of anti-inflammatory metabolites.
This review gathers recent information about genomic and transcriptomic studies in the
genus, exploring, for example, prediction of pathogenicity islands and stress response in different pathogenic ...and non-pathogenic species. In addition, is described several phylogeny studies to
, exploring since the identification of species until biological speciation in one species belonging to the genus
. Important concepts associated with virulence highlighting the role of Pld protein and Tox gene. The adhesion, characteristic of virulence factor, was described using the sortase mechanism that is associated to anchorage to the cell wall. In addition, survival inside the host cell and some diseases, were too addressed for pathogenic corynebacteria, while important biochemical pathways and biotechnological applications retain the focus of this review for non-pathogenic corynebacteria. Concluding, this review broadly explores characteristics in genus
showing to have strong relevance inside the medical, veterinary, and biotechnology field.
SARS-CoV-2 has ushered a global pandemic with no effective drug being available at present. Although several FDA-approved drugs are currently under clinical trials for drug repositioning, there is an ...on-going global effort for new drug identification. In this paper, using multi-omics (interactome, proteome, transcriptome, and bibliome) data and subsequent integrated analysis, we present the biological events associated with SARS-CoV-2 infection and identify several candidate drugs against this viral disease. We found that: (i) Interactome-based infection pathways differ from the other three omics-based profiles. (ii) Viral process, mRNA splicing, cytokine and interferon signaling, and ubiquitin mediated proteolysis are important pathways in SARS-CoV-2 infection. (iii) SARS-CoV-2 infection also shares pathways with Influenza A, Epstein-Barr virus, HTLV-I, Measles, and Hepatitis virus. (iv) Further, bacterial, parasitic, and protozoan infection pathways such as Tuberculosis, Malaria, and Leishmaniasis are also shared by this virus. (v) A total of 50 candidate drugs, including the prophylaxis agents and pathway specific inhibitors are identified against COVID-19. (vi) Betamethasone, Estrogen, Simvastatin, Hydrocortisone, Tositumomab, Cyclosporin A etc. are among the important drugs. (vii) Ozone, Nitric oxide, plasma components, and photosensitizer drugs are also identified as possible therapeutic candidates. (viii) Curcumin, Retinoic acids, Vitamin D, Arsenic, Copper, and Zinc may be the candidate prophylaxis agents. Nearly 70% of our identified agents are previously suggested to have anti-COVID-19 effects or under clinical trials. Among our identified drugs, the ones that are not yet tested, need validation with caution while an appropriate drug combination from these candidate drugs along with a SARS-CoV-2 specific antiviral agent is needed for effective COVID-19 management.
Display omitted
•SARS-CoV-2 shares Influenza, EBV, HTLV-I, Measles, and Hepatitis virus infection pathways.•SARS-CoV-2 also shares Tuberculosis, Malaria, and Leishmaniasis infection pathways.•mRNA splicing, cytokine and IFN signaling, and ubiquitin are important pathways.•Betamethasone, Estrogen, Statin, Tositumomab, Cyclosporin A are top candidate drugs.•Ozone, Nitric oxide, plasma components, and photosensitizer drugs are also important against COVID-19.•Curcumin, Retinoic acids, Vitamin D, Arsenic, Copper, and Zinc are candidate prophylaxis agents.
Psychological stress predisposes our body to several disorders. Understanding the cellular and molecular mechanisms involved in the physiological responses to psychological stress is essential for ...the success of therapeutic applications. New studies show, by using in vivo inducible Cre/loxP-mediated approaches in combination with pharmacological blockage, that sympathetic nerves, activated by psychological stress, induce brown adipocytes to produce IL-6. Strikingly, this cytokine promotes gluconeogenesis in hepatocytes, that results in the decline of tolerance to inflammatory organ damage. The comprehension arising from this research will be crucial for the handling of many inflammatory diseases. Here, we review recent advances in our comprehension of the sympathetic nerve-adipocyte axis in the tissue microenvironment.
The COVID-19 pandemic has infected millions worldwide, leaving a global burden for long-term care of COVID-19 survivors. It is thus imperative to study post-COVID (i.e., short-term) and long-COVID ...(i.e., long-term) effects, specifically as local and systemic pathophysiological outcomes of other coronavirus-related diseases (such as Middle East Respiratory Syndrome (MERS) and Severe Acute Respiratory Syndrome (SARS)) were well-cataloged. We conducted a comprehensive review of adverse post-COVID health outcomes and potential long-COVID effects. We observed that such adverse outcomes were not localized. Rather, they affected different human systems, including: (i) immune system (e.g., Guillain-Barré syndrome, rheumatoid arthritis, pediatric inflammatory multisystem syndromes such as Kawasaki disease), (ii) hematological system (vascular hemostasis, blood coagulation), (iii) pulmonary system (respiratory failure, pulmonary thromboembolism, pulmonary embolism, pneumonia, pulmonary vascular damage, pulmonary fibrosis), (iv) cardiovascular system (myocardial hypertrophy, coronary artery atherosclerosis, focal myocardial fibrosis, acute myocardial infarction, cardiac hypertrophy), (v) gastrointestinal, hepatic, and renal systems (diarrhea, nausea/vomiting, abdominal pain, anorexia, acid reflux, gastrointestinal hemorrhage, lack of appetite/constipation), (vi) skeletomuscular system (immune-mediated skin diseases, psoriasis, lupus), (vii) nervous system (loss of taste/smell/hearing, headaches, spasms, convulsions, confusion, visual impairment, nerve pain, dizziness, impaired consciousness, nausea/vomiting, hemiplegia, ataxia, stroke, cerebral hemorrhage), (viii) mental health (stress, depression and anxiety). We additionally hypothesized mechanisms of action by investigating possible molecular mechanisms associated with these disease outcomes/symptoms. Overall, the COVID-19 pathology is still characterized by cytokine storm that results to endothelial inflammation, microvascular thrombosis, and multiple organ failures.
Fungi play a key role in several important ecological functions, ranging from organic matter decomposition to symbiotic associations with plants. Moreover, fungi naturally inhabit the human body and ...can be beneficial when administered as probiotics. In mycology, the internal transcribed spacer (ITS) region was adopted as the universal marker for classifying fungi. Hence, an accurate and robust method for ITS classification is not only desired for the purpose of better diversity estimation, but it can also help us gain a deeper insight into the dynamics of environmental communities and ultimately comprehend whether the abundance of certain species correlate with health and disease. Although many methods have been proposed for taxonomic classification, to the best of our knowledge, none of them fully explore the taxonomic tree hierarchy when building their models. This in turn, leads to lower generalization power and higher risk of committing classification errors. Here we introduce HiTaC, a robust hierarchical machine learning model for accurate ITS classification, which requires a small amount of data for training and can handle imbalanced datasets. HiTaC was thoroughly evaluated with the established TAXXI benchmark and could correctly classify fungal ITS sequences of varying lengths and a range of identity differences between the training and test data. HiTaC outperforms state-of-the-art methods when trained over noisy data, consistently achieving higher F1-score and sensitivity across different taxonomic ranks, improving sensitivity by 6.9 percentage points over top methods in the most noisy dataset available on TAXXI. HiTaC is publicly available at the Python package index, BIOCONDA and Docker Hub. It is released under the new BSD license, allowing free use in academia and industry. Source code and documentation, which includes installation and usage instructions, are available at https://gitlab.com/dacs-hpi/hitac.
PDF
