Rescuing the Host Immune System by Targeting the Immune Evasion Complex ORF8-IRF3 in SARS-CoV-2 Infection with Natural Products Using Molecular Modeling Approaches

The perennial emergence of SARS-CoV-2 and its new variants causing upper respiratory complexities since December 2019 has aggravated the pandemic situation around the world. SARS-CoV-2 encodes several proteins among which ORF8 is a novel factor that is unique to SARS-CoV-2 only and is reported to help the virus in disease severity and immune evasion. ORF8-IRF3 complex induces endoplasmic reticulum stress, thus helps in the evasion of immune response. Consequently, targeting the ORF8-IRF3 complex is considered as a prime target for the discovery of novel drugs against SARS-CoV-2. In this regard, computational methods are of great interest to fast track the identification and development of novel drugs. Virtual screening of South African Natural Compounds Database (SANCDB), followed by docking and molecular dynamics (MD) simulation analysis, were performed to determine novel natural compounds. Computational molecular search and rescoring of the SANCDB database followed by induced-fit docking (IFD) protocol identified Quercetin 3-O-(6″-galloyl)-beta-D-galactopyranoside (SANC00850), Tribuloside (SANC01050), and Rutin (SANC00867) are the best scoring compounds. Structural-dynamic properties assessment revealed that these three compounds have stable dynamics, compactness, and a higher number of hydrogen bonds. For validation, we used MM/GBSA, in silico bioactivity estimation and dissociation constant (KD) approaches, which revealed that these compounds are the more potent inhibitors of the ORF8-IRF3 complex and would rescue the host immune system potentially. These compounds need further in vitro and in vivo validations to be used as therapeutics against SARS-CoV-2 to rescue the host immune system during COVID-19 infection.

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Schistosomes alter expression of immunomodulatory gene products following in vivo praziquantel exposure

10.1101/2020.01.22.915710 ◽

2020 ◽

Author(s):

Paul McCusker ◽

Claudia M. Rohr ◽

John D. Chan

Keyword(s):

Immune System ◽

Immune Evasion ◽

Host Immune System ◽

Gene Products ◽

Response To Chemotherapy ◽

Kunitz Type ◽

Insight Into ◽

Immunomodulatory Gene

AbstractControl of the neglected tropical disease schistosomiasis relies almost entirely on praziquantel (PZQ) monotherapy. How PZQ clears parasite infections remains poorly understood. Many studies have examined the effects of PZQ on worms cultured in vitro, observing outcomes such as muscle contraction. However, conditions worms are exposed to in vivo may vary considerably from in vitro experiments given the short half-life of PZQ and the importance of host immune system engagement for drug efficacy in animal models. Here, we investigated the effects of in vivo PZQ exposure on Schistosoma mansoni. Measurement of pro-apoptotic caspase activation revealed that worm death occurs only after parasites shift from the mesenteric vasculature to the liver, peaking 24 hours after drug treatment. This indicates that PZQ is not directly schistocidal, since the drug’s half-life is ∼2 hours, and focuses attention on parasite interactions with the host immune system following the shift of worms to the liver. RNA-Seq of worms harvested from mouse livers following sub-lethal PZQ treatment revealed drug-evoked changes in the expression of putative immunomodulatory and anticoagulant gene products. Several of these gene products localized to the schistosome esophagus and may be secreted into the host circulation. These include several Kunitz-type protease inhibitors, which are also found in the secretomes of other blood feeding animals. These transcriptional changes may reflect mechanisms of parasite immune-evasion in response to chemotherapy, given the role of complement-mediated attack and the host innate / humoral immune response in parasite elimination. One of these isoforms, SmKI-1, has been shown to exhibit immunomodulatory and anti-coagulant properties. These data provide insight into the effect of in vivo PZQ exposure on S. mansoni, and the transcriptional response of parasites to the stress of chemotherapy.Author SummaryThe disease schistosomiasis is caused by parasitic worms that live within the circulatory system. While this disease infects over 200 million people worldwide, treatment relies almost entirely on one drug, praziquantel, whose mechanism is poorly understood. In this study, we analyzed the effects of praziquantel treatment on the gene expression of parasites harvested from mice treated with praziquantel chemotherapy. Despite the rapid action of the drug on worms in vitro, we found that key outcomes in vivo (measurement of cell death and changes in gene expression) occurred relatively late (12+ hours after drug administration). We found that worms increased the expression of immunomodulatory gene products in response to praziquantel, including a Kunitz-type protease inhibitor that localized to the worm esophagus and may be secreted to the external host environment. These are an intriguing class of proteins, because they display anti-coagulant and immunomodulatory properties. Up-regulation of these gene products may reflect a parasite mechanism of immune-evasion in response to chemotherapy. This research provides insight into the mechanism of praziquantel by observing the effect of this drug on worms within the context of the host immune system.

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Biofilm formation in the lung contributes to virulence and drug tolerance of Mycobacterium tuberculosis

Nature Communications ◽

10.1038/s41467-021-21748-6 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Poushali Chakraborty ◽

Sapna Bajeli ◽

Deepak Kaushal ◽

Bishan Dass Radotra ◽

Ashwani Kumar

Keyword(s):

Mycobacterium Tuberculosis ◽

Immune System ◽

Biofilm Formation ◽

Antimycobacterial Activity ◽

Drug Tolerance ◽

Host Immune System ◽

Tissue Sections ◽

Slow Growing

AbstractTuberculosis is a chronic disease that displays several features commonly associated with biofilm-associated infections: immune system evasion, antibiotic treatment failures, and recurrence of infection. However, although Mycobacterium tuberculosis (Mtb) can form cellulose-containing biofilms in vitro, it remains unclear whether biofilms are formed during infection in vivo. Here, we demonstrate the formation of Mtb biofilms in animal models of infection and in patients, and that biofilm formation can contribute to drug tolerance. First, we show that cellulose is also a structural component of the extracellular matrix of in vitro biofilms of fast and slow-growing nontuberculous mycobacteria. Then, we use cellulose as a biomarker to detect Mtb biofilms in the lungs of experimentally infected mice and non-human primates, as well as in lung tissue sections obtained from patients with tuberculosis. Mtb strains defective in biofilm formation are attenuated for survival in mice, suggesting that biofilms protect bacilli from the host immune system. Furthermore, the administration of nebulized cellulase enhances the antimycobacterial activity of isoniazid and rifampicin in infected mice, supporting a role for biofilms in phenotypic drug tolerance. Our findings thus indicate that Mtb biofilms are relevant to human tuberculosis.

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Antitumor and immunomodulatory activity of Inonotus obliquus

Herba Polonica ◽

10.1515/hepo-2017-0013 ◽

2017 ◽

Vol 63 (2) ◽

pp. 48-58 ◽

Cited By ~ 6

Author(s):

Justyna Staniszewska ◽

Marcin Szymański ◽

Ewa Ignatowicz

Keyword(s):

Immune System ◽

Tumor Cells ◽

Good Alternative ◽

Immunomodulatory Activity ◽

Host Immune System ◽

Protein Synthesis Inhibition ◽

Inonotus Obliquus ◽

Different Types

SummaryThe article presents the antitumor and immunomodulatory activity of compounds and extracts fromInonotus obliquus.Polysaccharides isolated from sclerotium have a direct antitumor effect due to protein synthesis inhibition in tumor cells. Polysaccharides derived from the mycelium function by activating the immune system. Due to the limited toxicity of these substances, both extracts as well as isolated and purified chemicals may be a good alternative to current chemotherapy and play a role in cancer prevention.In vitroexperiments have shown the inhibition of inflammation with the influence of action ofI. obliquusextracts; however,in vivoexperiments on animals implanted with tumor cells of different types have shown the activation of the host immune system. This led to decrease in tumor mass and prolonged survival. The immunomodulatory mechanism of action is complex and it seems that stimulation of macrophages and induction of apoptosis in cancer cells is of great importance.

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Multiparameter Optimization of Trypanocidal Cruzain Inhibitors With In Vivo Activity and Favorable Pharmacokinetics

Frontiers in Pharmacology ◽

10.3389/fphar.2021.774069 ◽

2022 ◽

Vol 12 ◽

Author(s):

Ivani Pauli ◽

Celso de O. Rezende Jr. ◽

Brian W. Slafer ◽

Marco A. Dessoy ◽

Mariana L. de Souza ◽

...

Keyword(s):

Parasite Burden ◽

Host Cells ◽

Benzimidazole Derivatives ◽

Pharmacokinetic Studies ◽

Host Immune System ◽

Novel Drugs ◽

Main Metabolic Pathway ◽

Multiparameter Optimization

Cruzain, the main cysteine protease of Trypanosoma cruzi, plays key roles in all stages of the parasite’s life cycle, including nutrition acquisition, differentiation, evasion of the host immune system, and invasion of host cells. Thus, inhibition of this validated target may lead to the development of novel drugs for the treatment of Chagas disease. In this study, a multiparameter optimization (MPO) approach, molecular modeling, and structure-activity relationships (SARs) were employed for the identification of new benzimidazole derivatives as potent competitive inhibitors of cruzain with trypanocidal activity and suitable pharmacokinetics. Extensive pharmacokinetic studies enabled the identification of metabolically stable and permeable compounds with high selectivity indices. CYP3A4 was found to be involved in the main metabolic pathway, and the identification of metabolic soft spots provided insights into molecular optimization. Compound 28, which showed a promising trade-off between pharmacodynamics and pharmacokinetics, caused no acute toxicity and reduced parasite burden both in vitro and in vivo.

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Analysis of the intestinal microbiota in COVID-19 patients and its correlation with the inflammatory factor IL-18 and SARS-CoV-2-specific IgA

10.1101/2020.08.12.20173781 ◽

2020 ◽

Cited By ~ 1

Author(s):

Wanyin Tao ◽

Shu Zhu ◽

Guorong Zhang ◽

Xiaofang Wang ◽

Meng Guo ◽

...

Keyword(s):

Immune System ◽

Gastrointestinal Tract ◽

Gut Microbiota ◽

Disease Severity ◽

Specific Cell ◽

Host Immune System ◽

Inflammatory Factor ◽

Cytokine Storm

The current global COVID-19 pandemic is caused by beta coronavirus Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), which already infected over 10 million and caused 500 thousand deaths by June 2020. Overproduction of cytokines triggered by COVID-19 infection, known as "cytokine storm", is a highly risk factor associated with disease severity. However, how COVID-19 infection induce cytokine storm is still largely unknown. Accumulating in vitro and in vivo evidence suggests that gut is also susceptible to COVID19 infection: Human intestinal organoids, an in vitro model which mimic the specific cell type and spatial structure of the intestine, were susceptible to SARS-CoV2 infection; A significant fraction of patients reported gut symptoms; Viral RNA may persist for more than 30 days and infectious virus could be isolated in fecal samples. The gastrointestinal tract is the primary site of interaction between the host immune system with symbiotic and pathogenic microorganisms. The bacteria resident in our gastrointestinal tract, known as gut microbiota, is important to maintain the homeostasis of our immune system. While imbalance of gut microbiota, or dysbiosis, is associated with multiple inflammation diseases5. It's possible that SARS-CoV-2 infection may lead to alternation of gut microbiota thus worsen the host symptom. IL-18 is a proinflammatory cytokine produced multiple enteric cells, including intestinal epithelial cells (IECs), immune cells as well as enteric nervous system, and was shown to increase in the serum of COVID-19 patients. Immunoglobin A (IgA) is mainly produced in the mucosal surfaces, in humans 40-60mg kg-1 day-1 than all other immunoglobulin isotypes combined, and at least 80% of all plasma cells are located in the intestinal lamina propria. Recent study showed that SARS-CoV-2 specific IgA in the serum is positively correlate with the disease severity in COVID-19 patients11. Here we investigated the alterations of microbiota in COVID-19 patients, and its correlation with inflammatory factor IL-18 and SARS-CoV2 specific IgA.

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MTS1338, a smallMycobacterium tuberculosisRNA, regulates transcriptional shifts consistent with bacterial adaptation for entering into dormancy and survival within host macrophages

10.1101/474304 ◽

2018 ◽

Author(s):

Elena G. Salina ◽

Artem Grigorov ◽

Yulia Skvortsova ◽

Konstantin Majorov ◽

Oksana Bychenko ◽

...

Keyword(s):

Immune System ◽

Ex Vivo ◽

Host Immune System ◽

Rna Seq ◽

Bacterial Adaptation ◽

Translational Activity ◽

Non Coding Rna ◽

Constitutive Overexpression

AbstractSmall non-coding RNAs play a significant role in bacterial adaptation to changing environmental conditions. We investigated the dynamics of expression of MTS1338, a small non-coding RNA ofMycobacterium tuberculosis, in the mouse modelin vivo, regulation of its expression in theex vivoinfected macrophages, and the consequences of its overexpression in bacterial cultures. Here we demonstrate that MTS1338 significantly contributes to host-pathogen interactions. Activation of the host immune system triggered NO-inducible up-regulation of MTS1338 in macrophage-engulfed mycobacteria. Constitutive overexpression of MTS1338 in cultured mycobacteria improved their survivalin vitrounder low pH conditions. MTS1338 up-regulation launched a spectrum of shifts in the transcriptome profile similar to those reported forM. tuberculosisadaptation to hostile intra-macrophage environment. Using the RNA-seq approach, we demonstrate that gene expression changes accompanying MTS1338 overexpression indicate reduction in translational activity and bacterial growth, which is consistent with entering the dormant state. Taken together, our results suggest a direct involvement on this sRNA in the interplay between mycobacteria and the host immune system during infectious process.

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Gut mélange à trois: fluctuating selection modulated by microbiota, host immune system, and antibiotics

10.1101/2021.12.30.474527 ◽

2021 ◽

Author(s):

Hugo Condessa Barreto ◽

Beatriz Abreu ◽

Isabel Gordo

Keyword(s):

Immune System ◽

Iron Homeostasis ◽

Host Immune System ◽

Iron Availability ◽

Lipocalin 2 ◽

Fluctuating Selection ◽

Microbe Interactions ◽

Host Microbe Interactions

Iron is critical in host-microbe interactions, and its availability is under tight regulation in the mammalian gut. Antibiotics and inflammation are known to perturb iron availability in the gut, which could subsequently alter host-microbe interactions. Here, we show that an adaptive allele of iscR, encoding a major regulator of iron homeostasis of Escherichia coli, is under fluctuating selection in the mouse gut. In vivo competitions in immune-competent, immune-compromised, and germ-free mice reveal that the selective pressure on an iscR mutant E. coli is modulated by the presence of antibiotics, other members of the microbiota, and the immune system. In vitro assays show that iron availability is an important mediator of the iscR allele fitness benefits or costs. We identify Lipocalin-2, a host's innate immune system protein that prevents bacterial iron acquisition, as a major host mechanism underlying fluctuating selection of the iscR allele. Our results provide a remarkable example of strong fluctuating selection acting on bacterial iron regulation in the mammalian gut.

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CandidaBiofilms and the Host: Models and New Concepts for Eradication

International Journal of Microbiology ◽

10.1155/2012/845352 ◽

2012 ◽

Vol 2012 ◽

pp. 1-16 ◽

Cited By ~ 44

Author(s):

Hélène Tournu ◽

Patrick Van Dijck

Keyword(s):

Immune System ◽

High Throughput ◽

Biofilm Formation ◽

Host Immune System ◽

Alternative Strategies ◽

New Concepts ◽

Potential Applications ◽

Lock Therapy

Biofilms define mono- or multispecies communities embedded in a self-produced protective matrix, which is strongly attached to surfaces. They often are considered a general threat not only in industry but also in medicine. They constitute a permanent source of contamination, and they can disturb the proper usage of the material onto which they develop. This paper relates to some of the most recent approaches that have been elaborated to eradicateCandidabiofilms, based on the vast effort put in ever-improving models of biofilm formationin vitroandin vivo, including novel flow systems, high-throughput techniques and mucosal models. Mixed biofilms, sustaining antagonist or beneficial cooperation between species, and their interplay with the host immune system are also prevalent topics. Alternative strategies against biofilms include the lock therapy and immunotherapy approaches, and material coating and improvements. The host-biofilm interactions are also discussed, together with their potential applications inCandidabiofilm elimination.

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Studies on phospholipid turnover argue against sloughing of tegumental membranes in adult Schistosoma mansoni

Parasitology ◽

10.1017/s0031182099004679 ◽

1999 ◽

Vol 119 (3) ◽

pp. 287-294 ◽

Cited By ~ 25

Author(s):

J. F. H. M. BROUWERS ◽

P. J. SKELLY ◽

L. M. G. VAN GOLDE ◽

A. G. M. TIELENS

Keyword(s):

Fatty Acid ◽

Immune System ◽

Schistosoma Mansoni ◽

Immune Evasion ◽

Crucial Role ◽

Host Immune System ◽

Pulse Labelling ◽

High Turnover ◽

Membrane Complex

The tegumental membrane complex of Schistosoma mansoni is the site of interaction between the parasite and the host. The tegument is involved in uptake of many nutrients, but also plays a crucial role in the evasion of the actions of the host immune system. Essential for the success of this evasion is maintaining the integrity of the tegumental membranes. The rate of turnover of phospholipids was investigated by pulse-labelling worms cultured in vitro, followed by additional incubation in the presence of unlabelled substrates. Tegumental membranes were isolated, characterized using antibodies against specific tegumental proteins, and analysed. It was demonstrated that the most prominent fatty acid found in tegumental phospholipids, palmitate, incorporated rapidly into the phospholipid fraction during a 30 min pulse labelling. In a subsequent 20 h chase with unlabelled substrates, the incorporated radioactivity was lost again from the tegumental membrane complex. This high turnover of palmitate was found to be limited to phosphatidylcholine (PC) only. The turnover was due to deacylation/reacylation, and not to the sloughing of membranes as is the case in schistosomula. It is speculated that this rapid turnover of PC in the tegument of adult schistosomes plays a new and important role in the immune evasion by the parasite.

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Nippocystatin, a Cysteine Protease Inhibitor fromNippostrongylus brasiliensis, Inhibits Antigen Processing and Modulates Antigen-Specific Immune Response

Infection and Immunity ◽

10.1128/iai.69.12.7380-7386.2001 ◽

2001 ◽

Vol 69 (12) ◽

pp. 7380-7386 ◽

Cited By ~ 78

Author(s):

Teruki Dainichi ◽

Yoichi Maekawa ◽

Kazunari Ishii ◽

Tianqian Zhang ◽

Baher Fawzy Nashed ◽

...

Keyword(s):

Immune System ◽

Protease Inhibitor ◽

Cysteine Protease ◽

Antigen Processing ◽

Cysteine Proteases ◽

Cysteine Protease Inhibitor ◽

Host Immune System ◽

Nippostrongylus Brasiliensis

ABSTRACT During infection, parasites evade the host immune system by modulating or exploiting the immune system; e.g., they suppress expression of major histocompatibility complex class II molecules or secrete cytokine-like molecules. However, it is not clear whether helminths disturb the immune responses of their hosts by controlling the antigen-processing pathways of the hosts. In this study, we identified a new cysteine protease inhibitor, nippocystatin, derived from excretory-secretory (ES) products of an intestinal nematode,Nippostrongylus brasiliensis. Nippocystatin, which belongs to cystatin family 2, consists of 144 amino acids and is secreted as a 14-kDa mature form. In vivo treatment of ovalbumin (OVA)-immunized mice with recombinant nippocystatin (rNbCys) profoundly suppressed OVA-specific proliferation of splenocytes but not non-antigen-specific proliferation of splenocytes. OVA-specific cytokine production was also greatly suppressed in rNbCys-treated mice. Although the serum levels of both OVA-specific immunoglobulin G1 (IgG1) and IgG2a were not affected by rNbCys treatment, OVA-specific IgE was preferentially downregulated in rNbCys-treated mice. In vitro rNbCys inhibited processing of OVA by lysosomal cysteine proteases from the spleens of mice. Mice with anti-nippocystatin antibodies became partially resistant to infection with N. brasiliensis. Based on these findings, N. brasiliensis appears to skillfully evade host immune systems by secreting nippocystatin, which modulates antigen processing in antigen-presenting cells of hosts.

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