Your browser doesn't support javascript.
Show: 20 | 50 | 100
Results 1 - 20 de 23
Filter
1.
Biomolecules ; 13(4)2023 04 18.
Article in English | MEDLINE | ID: covidwho-2299784

ABSTRACT

In humans, the cytosolic glutathione S-transferase (GST) family of proteins is encoded by 16 genes presented in seven different classes. GSTs exhibit remarkable structural similarity with some overlapping functionalities. As a primary function, GSTs play a putative role in Phase II metabolism by protecting living cells against a wide variety of toxic molecules by conjugating them with the tripeptide glutathione. This conjugation reaction is extended to forming redox sensitive post-translational modifications on proteins: S-glutathionylation. Apart from these catalytic functions, specific GSTs are involved in the regulation of stress-induced signaling pathways that govern cell proliferation and apoptosis. Recently, studies on the effects of GST genetic polymorphisms on COVID-19 disease development revealed that the individuals with higher numbers of risk-associated genotypes showed higher risk of COVID-19 prevalence and severity. Furthermore, overexpression of GSTs in many tumors is frequently associated with drug resistance phenotypes. These functional properties make these proteins promising targets for therapeutics, and a number of GST inhibitors have progressed in clinical trials for the treatment of cancer and other diseases.


Subject(s)
COVID-19 , Neoplasms , Humans , COVID-19/genetics , Proteins , Glutathione Transferase/metabolism , Enzyme Inhibitors/pharmacology , Neoplasms/genetics , Neoplasms/drug therapy , Glutathione/metabolism
2.
Toxicol In Vitro ; 83: 105394, 2022 Sep.
Article in English | MEDLINE | ID: covidwho-2115544

ABSTRACT

We previously reported that delivery of nickel nanoparticles (NiNPs) and bacterial lipopolysaccharide (LPS) into the lungs of mice synergistically increased IL-6 production and inflammation, and male mice were more susceptible than female mice. The primary goal of this study was to utilize an in vitro human lung epithelial cell model (BEAS-2B) to investigate the intracellular signaling mechanisms that mediate IL-6 production by LPS and NiNPs. We also investigated the effect of sex hormones on NiNP and LPS-induced IL-6 production in vitro. LPS and NiNPs synergistically induced IL-6 mRNA and protein in BEAS-2B cells. TPCA-1, a dual inhibitor of IKK-2 and STAT3, blocked the synergistic increase in IL-6 caused by LPS and NiNPs, abolished STAT3 activation, and reduced C/EBPß. Conversely, SC144, an inhibitor of the gp130 component of the IL-6 receptor, enhanced IL-6 production induced by LPS and NiNPs. Treatment of BEAS-2B cells with sex hormones (17ß-estradiol, progesterone, or testosterone) or the anti-oxidant NAC, had no effect on IL-6 induction by LPS and NiNPs. These data suggest that LPS and NiNPs induce IL-6 via STAT3 and C/EBPß in BEAS-2B cells. While BEAS-2B cells are a suitable model to study mechanisms of IL-6 production, they do not appear to be suitable for studying the effect of sex hormones.


Subject(s)
Lipopolysaccharides , Nanoparticles , Animals , CCAAT-Enhancer-Binding Protein-beta/metabolism , Cell Line , Epithelial Cells , Female , Humans , Interleukin-6/genetics , Interleukin-6/metabolism , Lipopolysaccharides/pharmacology , Male , Mice , Nickel , STAT3 Transcription Factor/metabolism
3.
Int J Mol Sci ; 23(15)2022 Jul 29.
Article in English | MEDLINE | ID: covidwho-1994080

ABSTRACT

Landmark discoveries in molecular oncology have provided a wide-angle overview of the heterogenous and therapeutically challenging nature of cancer. The power of modern 'omics' technologies has enabled researchers to deeply and comprehensively characterize molecular mechanisms underlying cellular functions. Interestingly, high-throughput technologies have opened new horizons for the design and scientific fool-proof evaluation of the pharmacological properties of targeted chemical compounds to tactfully control the activities of the oncogenic protein networks. Groundbreaking discoveries have galvanized the expansion of the repertoire of available pharmacopoeia to therapeutically target a myriad of deregulated oncogenic pathways. Natural product research has undergone substantial broadening, and many of the drugs which constitute the backbone of modern pharmaceuticals have been derived from the natural cornucopia. Baicalein has gradually gained attention because of its unique ability to target different oncogenic signal transduction cascades in various cancers. We have partitioned this review into different sub-sections to provide a broader snapshot of the oncogenic pathways regulated by baicalein. In this review, we summarize baicalein-mediated targeting of WNT/ß-catenin, AKT/mTOR, JAK/STAT, MAPK, and NOTCH pathways. We also critically analyze how baicalein regulates non-coding RNAs (microRNAs and long non-coding RNAs) in different cancers. Finally, we conceptually interpret baicalein-mediated inhibition of primary and secondary growths in xenografted mice.


Subject(s)
Flavanones , MicroRNAs , Neoplasms , Animals , Carcinogenesis , Flavanones/pharmacology , Flavanones/therapeutic use , Mice , MicroRNAs/metabolism , Neoplasms/drug therapy , Neoplasms/genetics , Neoplasms/metabolism , Signal Transduction
4.
World J Hepatol ; 14(6): 1131-1141, 2022 Jun 27.
Article in English | MEDLINE | ID: covidwho-1979514

ABSTRACT

BACKGROUND: Coronavirus disease 19 (COVID-19) has not only been shown to affect the respiratory system, but has also demonstrated variable clinical presentations including gastrointestinal tract disorders. In addition, abnormalities in liver enzymes have been reported indicating hepatic injury. It is known that severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) might infect cells via the viral receptor angiotensin-converting enzyme 2 (ACE2) which is expressed in several organs including the liver. The viral Spike glycoprotein binds to ACE2 and must be cleaved by Furin and Type 2 Serine Protease to enter the cells. After that, the Akt/mTOR signaling pathway is activated and several COVID-19 changes are triggered. AIM: To analyze liver and gastrointestinal symptoms and cell signaling pathways triggered by SARS-CoV-2 infection due to virus-liver interactions in silico. METHODS: In this in silico study, the three-dimensional structures of the Akt, mTORC1 and Furin (receptors) were selected from the Protein Data Bank (PDB) and the structures of inhibitors (ligands) MK-2206, CC-223 and Naphthofluorescein were selected from PubChem and ZINC databases. Ligand files were downloaded as 2D structures and converted to optimized 3D structures using ViewerLite 4.2 software. Marvin Sketch® software was used to calculate prediction of the protonated form of inhibitors in a physiological environment (pH 7.4). AutoDock Tools (ADT) software was used to calculate and delimit the Grid box used in the molecular docking of each structure selected in the PDB. In addition, protonated ligands were prepared for molecular docking using ADT software. Molecular docking was performed using ADT software tools connected to Vina software. Analysis of the amino acid residues involved in ligand interactions, as well as ligand twists, the atoms involved in interactions, bond type and strength of interactions were performed using PyMol® and Discovery Studio® (BIOVIA) software. RESULTS: Molecular docking analysis showed that the mTORC1/CC-223 complex had affinity energy between the receptor and ligand of -7.7 kcal/moL with interactions ranging from 2.7 to 4.99 Å. There were four significant chemical bonds which involved two of five polypeptide chains that formed the FKBP12-Rapamycin-Binding (FRB) domain. The strongest was a hydrogen bond, the only polar interaction, and Van der Waals interactions shown to be present in 12 residues of mTORC1's FRB domain. With regard to the Akt/MK-2206 complex there were three Van der Waals interactions and 12 chemical bonds in which seven residues of Akt were involved with all five rings of the MK-2206 structure. In this way, both ASP 388 and GLN 391 bind to the same MK-2206 ring, the smaller one. However, LYS 386 had four chemical bonds with the inhibitor, one with each structure ring, while LYS 387 binds two distinct rings. One of the MK-2206 inhibitor's rings which binds to LYS 387 also binds simultaneously to ILE 367 and LEU 385 residues, and the fifth ring of the structure was involved in a bond with the ALA 382 residue. The hydrogen bonds were the shortest bonds in the complex (2.61 and 3.08 Å) and all interactions had an affinity energy of -8.8 kcal/moL. The affinity energy in the Furin/Naphhofluorescein complex was -9.8 kcal/moL and involved six interactions ranging from 2.57 to 4.98 Å. Among them, two were polar and the others were non-polar, in addition to twelve more Van der Waals interactions. Two distinct hydrogen bonds were formed between Furin and its inhibitor involving GLN 388 and ALA 532 residues. ALA 532 also binds to two distinct rings of Naphthofluorescein, while TRP 531 residue has two simultaneous bonds with the inhibitor. CONCLUSION: Liver infection and signaling pathways altered by SARS-CoV-2 can be modulated by inhibitors that demonstrate significant interaction affinity with human proteins, which could prevent the development of infection and symptoms.

5.
12th International Conference on Biomedical Engineering and Technology, ICBET 2022 ; : 156-160, 2022.
Article in English | Scopus | ID: covidwho-1962431

ABSTRACT

The serine/threonine p21-activating PAK kinases which act as important mediators of the Rho family of GTPases (Rho GTPases) Cdc42ĝ€¢GTP and Racĝ€¢GTP. PAK1 is one of the key molecules in the regulation of cytoskeletal actin assembly, phenotypic signaling, gene expression, and directly affects many cellular processes such as cell motility, invasion, metastasis, cell growth, angiogenesis, cell cycle progression. To date, several sulphated steroidal saponins have been reported to block the PAK1-dependent growth of A549 lung cancer. In this study, we investigated molecular interactions of N-triterpene saponins and PAK1 in silico molecular docking, and further evaluated the binding affinities. Molecular docking simulation was performed through AutoDock 4.2.2. an automated docking tool. We found that N-triterpene saponin 2 had the higher binding affinity towards PAK1 targeted protein. To the best of our knowledge, no report on N-triterpene saponins as a PAK1 inhibitor. © 2022 ACM.

6.
Immunity ; 55(7): 1284-1298.e3, 2022 07 12.
Article in English | MEDLINE | ID: covidwho-1945246

ABSTRACT

While studies have elucidated many pathophysiological elements of COVID-19, little is known about immunological changes during COVID-19 resolution. We analyzed immune cells and phosphorylated signaling states at single-cell resolution from longitudinal blood samples of patients hospitalized with COVID-19, pneumonia and/or sepsis, and healthy individuals by mass cytometry. COVID-19 patients showed distinct immune compositions and an early, coordinated, and elevated immune cell signaling profile associated with early hospital discharge. Intra-patient longitudinal analysis revealed changes in myeloid and T cell frequencies and a reduction in immune cell signaling across cell types that accompanied disease resolution and discharge. These changes, together with increases in regulatory T cells and reduced signaling in basophils, also accompanied recovery from respiratory failure and were associated with better outcomes at time of admission. Therefore, although patients have heterogeneous immunological baselines and highly variable disease courses, a core immunological trajectory exists that defines recovery from severe SARS-CoV-2 infection.


Subject(s)
COVID-19 , Pneumonia , Disease Progression , Humans , SARS-CoV-2
8.
Cell ; 185(8): 1414-1430.e19, 2022 04 14.
Article in English | MEDLINE | ID: covidwho-1757193

ABSTRACT

Cytokines are powerful immune modulators that initiate signaling through receptor dimerization, but natural cytokines have structural limitations as therapeutics. We present a strategy to discover cytokine surrogate agonists by using modular ligands that exploit induced proximity and receptor dimer geometry as pharmacological metrics amenable to high-throughput screening. Using VHH and scFv to human interleukin-2/15, type-I interferon, and interleukin-10 receptors, we generated combinatorial matrices of single-chain bispecific ligands that exhibited diverse spectrums of functional activities, including potent inhibition of SARS-CoV-2 by surrogate interferons. Crystal structures of IL-2R:VHH complexes revealed that variation in receptor dimer geometries resulted in functionally diverse signaling outputs. This modular platform enabled engineering of surrogate ligands that compelled assembly of an IL-2R/IL-10R heterodimer, which does not naturally exist, that signaled through pSTAT5 on T and natural killer (NK) cells. This "cytokine med-chem" approach, rooted in principles of induced proximity, is generalizable for discovery of diversified agonists for many ligand-receptor systems.


Subject(s)
COVID-19 , Cytokines , Humans , Interleukin-2/pharmacology , Killer Cells, Natural , Ligands , Receptors, Interleukin-10 , SARS-CoV-2
9.
Int J Mol Sci ; 23(4)2022 Feb 11.
Article in English | MEDLINE | ID: covidwho-1686818

ABSTRACT

The annual meeting "Signal Transduction-Receptors, Mediators and Genes" of the Signal Transduction Society (STS) is an interdisciplinary conference which is open to all scientists sharing a common interest in the elucidation of the signaling pathways mediating physiological or pathological processes in the health and disease of humans, animals, plants, fungi, prokaryotes, and protists. The 24th meeting on signal transduction was held from 15 to 17 November 2021 in Weimar, Germany. As usual, keynote presentations by invited scientists introduced the respective workshops, and were followed by speakers chosen from the submitted abstracts. A special workshop focused on "Target Identification and Interaction". Ample time was reserved for the discussion of the presented data during the workshops. Unfortunately, due to restrictions owing to the SARS-CoV-2 pandemic, the poster sessions-and thus intensive scientific discussions at the posters-were not possible. In this report, we provide a concise summary of the various workshops and further aspects of the scientific program.


Subject(s)
Signal Transduction/physiology , Biomedical Research , Germany , Societies, Scientific
10.
J Virol ; 96(2): e0167821, 2022 01 26.
Article in English | MEDLINE | ID: covidwho-1511415

ABSTRACT

The positive-sense, single-stranded RNA genome SARS-CoV-2 harbors functionally important cis-acting elements governing critical aspects of viral gene expression. However, insights on how these elements sense various signals from the host cell and regulate viral protein synthesis are lacking. Here, we identified two novel cis-regulatory elements in SARS-CoV-2 ORF1a and S RNAs and describe their role in translational control of SARS-CoV-2. These elements are sequence-unrelated but form conserved hairpin structures (validated by NMR) resembling gamma activated inhibitor of translation (GAIT) elements that are found in a cohort of human mRNAs directing translational suppression in myeloid cells in response to IFN-γ. Our studies show that treatment of human lung cells with receptor-binding S1 subunit, S protein pseudotyped lentivirus, and S protein-containing virus-like particles triggers a signaling pathway involving DAP-kinase1 that leads to phosphorylation and release of the ribosomal protein L13a from the large ribosomal subunit. Released L13a forms a virus activated inhibitor of translation (VAIT) complex that binds to ORF1a and S VAIT elements, causing translational silencing. Translational silencing requires extracellular S protein (and its interaction with host ACE2 receptor), but not its intracellular synthesis. RNA-protein interaction analyses and in vitro translation experiments showed that GAIT and VAIT elements do not compete with each other, highlighting differences between the two pathways. Sequence alignments of SARS-CoV-2 genomes showed a high level of conservation of VAIT elements, suggesting their functional importance. This VAIT-mediated translational control mechanism of SARS-CoV-2 may provide novel targets for small molecule intervention and/or facilitate development of more effective mRNA vaccines. IMPORTANCE Specific RNA elements in the genomes of RNA viruses play important roles in host-virus interaction. For SARS-CoV-2, the mechanistic insights on how these RNA elements could sense the signals from the host cell are lacking. Here we report a novel relationship between the GAIT-like SARS-CoV-2 RNA element (called VAITs) and the signal generated from the host cell. We show that for SARS-CoV-2, the interaction of spike protein with ACE2 not only serves the purpose for viral entry into the host cell, but also transduces signals that culminate into the phosphorylation and the release of L13a from the large ribosomal subunit. We also show that this event leads to the translational arrest of ORF1a and S mRNAs in a manner dependent on the structure of the RNA elements. Translational control of viral mRNA by a host-cell generated signal triggered by viral protein is a new paradigm in the host-virus relationship.


Subject(s)
COVID-19 , Host Microbial Interactions , RNA, Viral/immunology , SARS-CoV-2 , A549 Cells , COVID-19/immunology , COVID-19/virology , Host Microbial Interactions/genetics , Host Microbial Interactions/immunology , Humans , Protein Binding , SARS-CoV-2/genetics , SARS-CoV-2/immunology , Virus Internalization
11.
J Photochem Photobiol B ; 226: 112357, 2022 Jan.
Article in English | MEDLINE | ID: covidwho-1510060

ABSTRACT

Mitochondrial antiviral signaling (MAVS) protein mediates innate antiviral responses, including responses to certain coronaviruses such as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). We have previously shown that ultraviolet-A (UVA) therapy can prevent virus-induced cell death in human ciliated tracheal epithelial cells (HTEpC) infected with coronavirus-229E (CoV-229E), and results in increased intracellular levels of MAVS. In this study, we explored the mechanisms by which UVA light can activate MAVS, and whether local UVA light application can activate MAVS at locations distant from the light source (e.g. via cell-to-cell communication). MAVS levels were compared in HTEpC exposed to 2 mW/cm2 narrow band (NB)-UVA for 20 min and in unexposed controls at 30-40% and at 100% confluency, and in unexposed HTEpC treated with supernatants or lysates from UVA-exposed cells or from unexposed controls. MAVS was also assessed in different sections of confluent monolayer plates where only one section was exposed to NB-UVA. Our results showed that UVA increases the expression of MAVS protein. Further, cells in a confluent monolayer exposed to UVA conferred an elevation in MAVS in cells adjacent to the exposed section, and also in cells in the most distant sections which were not exposed to UVA. In this study, human ciliated tracheal epithelial cells exposed to UVA demonstrate increased MAVS protein, and also appear to transmit this influence to confluent cells not exposed to UVA, likely via cell-cell signaling.


Subject(s)
Adaptor Proteins, Signal Transducing/metabolism , Adaptor Proteins, Signal Transducing/radiation effects , Ultraviolet Rays , Adaptor Proteins, Signal Transducing/immunology , COVID-19/immunology , COVID-19/radiotherapy , COVID-19/virology , Cell Communication/immunology , Cell Communication/radiation effects , Cells, Cultured , Epithelial Cells/immunology , Epithelial Cells/radiation effects , Host Microbial Interactions/immunology , Host Microbial Interactions/radiation effects , Humans , Immunity, Innate/radiation effects , Photobiology , SARS-CoV-2/immunology , SARS-CoV-2/pathogenicity , Signal Transduction/immunology , Signal Transduction/radiation effects , Trachea/cytology , Ultraviolet Therapy
12.
Molecules ; 26(20)2021 Oct 14.
Article in English | MEDLINE | ID: covidwho-1470935

ABSTRACT

Excessive host inflammation following infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is associated with severity and mortality in coronavirus disease 2019 (COVID-19). We recently reported that the SARS-CoV-2 spike protein S1 subunit (S1) induces pro-inflammatory responses by activating toll-like receptor 4 (TLR4) signaling in macrophages. A standardized extract of Asparagus officinalis stem (EAS) is a unique functional food that elicits anti-photoaging effects by suppressing pro-inflammatory signaling in hydrogen peroxide and ultraviolet B-exposed skin fibroblasts. To elucidate its potential in preventing excessive inflammation in COVID-19, we examined the effects of EAS on pro-inflammatory responses in S1-stimulated macrophages. Murine peritoneal exudate macrophages were co-treated with EAS and S1. Concentrations and mRNA levels of pro-inflammatory cytokines were assessed using enzyme-linked immunosorbent assay and reverse transcription and real-time polymerase chain reaction, respectively. Expression and phosphorylation levels of signaling proteins were analyzed using western blotting and fluorescence immunomicroscopy. EAS significantly attenuated S1-induced secretion of interleukin (IL)-6 in a concentration-dependent manner without reducing cell viability. EAS also markedly suppressed the S1-induced transcription of IL-6 and IL-1ß. However, among the TLR4 signaling proteins, EAS did not affect the degradation of inhibitor κBα, nuclear translocation of nuclear factor-κB p65 subunit, and phosphorylation of c-Jun N-terminal kinase p54 subunit after S1 exposure. In contrast, EAS significantly suppressed S1-induced phosphorylation of p44/42 mitogen-activated protein kinase (MAPK) and Akt. Attenuation of S1-induced transcription of IL-6 and IL-1ß by the MAPK kinase inhibitor U0126 was greater than that by the Akt inhibitor perifosine, and the effects were potentiated by simultaneous treatment with both inhibitors. These results suggest that EAS attenuates S1-induced IL-6 and IL-1ß production by suppressing p44/42 MAPK and Akt signaling in macrophages. Therefore, EAS may be beneficial in regulating excessive inflammation in patients with COVID-19.


Subject(s)
Asparagus Plant/chemistry , Interleukin-1beta/metabolism , Interleukin-6/metabolism , Macrophages/drug effects , Plant Extracts/pharmacology , Signal Transduction/drug effects , Animals , Asparagus Plant/metabolism , Butadienes/pharmacology , Cell Survival/drug effects , Interleukin-1beta/genetics , Interleukin-6/genetics , Macrophages/cytology , Macrophages/metabolism , Male , Mice , Mice, Inbred C57BL , Mitogen-Activated Protein Kinase 1/antagonists & inhibitors , Mitogen-Activated Protein Kinase 1/metabolism , Mitogen-Activated Protein Kinase 3/antagonists & inhibitors , Mitogen-Activated Protein Kinase 3/metabolism , Nitriles/pharmacology , Phosphorylation/drug effects , Plant Extracts/chemistry , Plant Stems/chemistry , Plant Stems/metabolism , Proto-Oncogene Proteins c-akt/antagonists & inhibitors , Proto-Oncogene Proteins c-akt/metabolism , Spike Glycoprotein, Coronavirus/pharmacology , Toll-Like Receptor 4/metabolism , Transcription, Genetic/drug effects
13.
Pharmacol Res ; 172: 105784, 2021 10.
Article in English | MEDLINE | ID: covidwho-1322310

ABSTRACT

It is becoming progressively more understandable that pharmaceutical targeting of drug-resistant cancers is challenging because of intra- and inter-tumor heterogeneity. Interestingly, naturally derived bioactive compounds have unique ability to modulate wide-ranging deregulated oncogenic cell signaling pathways. In this review, we have focused on the available evidence related to regulation of PI3K/AKT/mTOR, Wnt/ß-catenin, NF-κB and TRAIL/TRAIL-R by fisetin in different cancers. Fisetin has also been shown to inhibit the metastatic spread of cancer cells in tumor-bearing mice. We have also summarized how fisetin regulated autophagy in different cancers. In addition, this review also covers fisetin-mediated regulation of VEGF/VEGFR, EGFR, necroptosis and Hippo pathway. Fisetin has entered into clinical trials particularly in context of COVID19-associated inflammations. Furthermore, fisetin mediated effects are also being tested in clinical trials with reference to osteoarthritis and senescence. These developments will surely pave the way for full-fledge and well-designed clinical trials of fisetin in different cancers. However, we still have to comprehensively analyze and fully unlock pharmacological potential of fisetin against different oncogenic signaling cascades and non-coding RNAs. Fisetin has remarkable potential as chemopreventive agent and future studies must converge on the identification of additional regulatory roles of fisetin for inhibition and prevention of cancers.


Subject(s)
Antineoplastic Agents, Phytogenic/administration & dosage , Flavonols/administration & dosage , Nanostructures/administration & dosage , Neoplasms/drug therapy , Animals , Chemoprevention , Humans , Intercellular Signaling Peptides and Proteins/metabolism , NF-kappa B/metabolism , Neoplasms/metabolism , Neoplasms/prevention & control , Receptors, Vascular Endothelial Growth Factor/metabolism , Signal Transduction/drug effects , TOR Serine-Threonine Kinases/metabolism , beta Catenin/metabolism
14.
Curr Pharm Biotechnol ; 22(10): 1315-1324, 2021.
Article in English | MEDLINE | ID: covidwho-1290817

ABSTRACT

BACKGROUND: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is the causative agent of the current pandemic of Coronavirus Disease-2019 (COVID-19). The progression of COVID-19 is related to an excessive host inflammatory immune response to SARS-CoV-2 infection, which is considered a major cause of disease severity and death. Dysregulated immune response produces huge amounts of pro-inflammatory cytokines and chemokines called "cytokine storm". Moreover, the activation of microthrombi formation plays an important role in multiple organ failure. METHODS: Keeping into consideration the potent anti-inflammatory activity of black seed and its major constituent Thymoquinone (TQ), we hypothesize their potential implication in the treatment of COVID-19 patients. A literature search was performed in PubMed, ScienceDirect, Google Scholar and Scopus electronic databases using the terms, including black seed, N. sativa, thymoquinone, SARSCoV- 2, COVID-19 and inflammatory immune response. RESULTS: Various studies confirmed that Black seed and TQ reduced the thrombus formation, the expression of tissue factor and the immune activation. Furthermore, TQ demonstrated the broad-spectrum antimicrobial activity that may be effective in controlling the secondary infections in COVID-19 patients. CONCLUSION: Keeping into consideration the multi-targeting nature of the black seed and TQ, they may be used as a potential therapeutic formulation or as an adjunct therapy in the treatment of COVID-19 patients.


Subject(s)
COVID-19 , Benzoquinones , Cytokines , Humans , SARS-CoV-2 , Seeds
15.
J Biomed Inform ; 118: 103801, 2021 06.
Article in English | MEDLINE | ID: covidwho-1219153

ABSTRACT

Understanding the molecular mechanism of COVID-19 pathogenesis helps in the rapid therapeutic target identification. Usually, viral protein targets host proteins in an organized fashion. The expression of any viral gene depends mostly on the host translational machinery. Recent studies report the great significance of codon usage biases in establishing host-viral protein-protein interactions (PPI). Exploring the codon usage patterns between a pair of co-evolved host and viral proteins may present novel insight into the host-viral protein interactomes during disease pathogenesis. Leveraging the similarity in codon usage patterns, we propose a computational scheme to recreate the host-viral protein-protein interaction network. We use host proteins from seventeen (17) essential signaling pathways for our current work towards understanding the possible targeting mechanism of SARS-CoV-2 proteins. We infer both negatively and positively interacting edges in the network. Further, extensive analysis is performed to understand the host PPI network topologically and the attacking behavior of the viral proteins. Our study reveals that viral proteins mostly utilize codons, rare in the targeted host proteins (negatively correlated interaction). Among them, non-structural proteins, NSP3 and structural protein, Spike (S), are the most influential proteins in interacting with multiple host proteins. While ranking the most affected pathways, MAPK pathways observe to be the worst affected during the SARS-CoV-2 infection. Several proteins participating in multiple pathways are highly central in host PPI and mostly targeted by multiple viral proteins. We observe many potential targets (host proteins) from the affected pathways associated with the various drug molecules, including Arsenic trioxide, Dexamethasone, Hydroxychloroquine, Ritonavir, and Interferon beta, which are either under clinical trial or in use during COVID-19.


Subject(s)
COVID-19 , Codon Usage , Host-Pathogen Interactions , Protein Interaction Maps , Signal Transduction , COVID-19/diagnosis , COVID-19/therapy , Humans
16.
Front Cell Dev Biol ; 9: 626821, 2021.
Article in English | MEDLINE | ID: covidwho-1175535

ABSTRACT

Deciphering the functional impact of genetic variation is required to understand phenotypic diversity and the molecular mechanisms of inherited disease and cancer. While millions of genetic variants are now mapped in genome sequencing projects, distinguishing functional variants remains a major challenge. Protein-coding variation can be interpreted using post-translational modification (PTM) sites that are core components of cellular signaling networks controlling molecular processes and pathways. ActiveDriverDB is an interactive proteo-genomics database that uses more than 260,000 experimentally detected PTM sites to predict the functional impact of genetic variation in disease, cancer and the human population. Using machine learning tools, we prioritize proteins and pathways with enriched PTM-specific amino acid substitutions that potentially rewire signaling networks via induced or disrupted short linear motifs of kinase binding. We then map these effects to site-specific protein interaction networks and drug targets. In the 2021 update, we increased the PTM datasets by nearly 50%, included glycosylation, sumoylation and succinylation as new types of PTMs, and updated the workflows to interpret inherited disease mutations. We added a recent phosphoproteomics dataset reflecting the cellular response to SARS-CoV-2 to predict the impact of human genetic variation on COVID-19 infection and disease course. Overall, we estimate that 16-21% of known amino acid substitutions affect PTM sites among pathogenic disease mutations, somatic mutations in cancer genomes and germline variants in the human population. These data underline the potential of interpreting genetic variation through the lens of PTMs and signaling networks. The open-source database is freely available at www.ActiveDriverDB.org.

17.
J Biol Chem ; 296: 100449, 2021.
Article in English | MEDLINE | ID: covidwho-1091794

ABSTRACT

Hck, a Src family nonreceptor tyrosine kinase (SFK), has recently been established as an attractive pharmacological target to improve pulmonary function in COVID-19 patients. Hck inhibitors are also well known for their regulatory role in various malignancies and autoimmune diseases. Curcumin has been previously identified as an excellent DYRK-2 inhibitor, but curcumin's fate is tainted by its instability in the cellular environment. Besides, small molecules targeting the inactive states of a kinase are desirable to reduce promiscuity. Here, we show that functionalization of the 4-arylidene position of the fluorescent curcumin scaffold with an aryl nitrogen mustard provides a stable Hck inhibitor (Kd = 50 ± 10 nM). The mustard curcumin derivative preferentially interacts with the inactive conformation of Hck, similar to type-II kinase inhibitors that are less promiscuous. Moreover, the lead compound showed no inhibitory effect on three other kinases (DYRK2, Src, and Abl). We demonstrate that the cytotoxicity may be mediated via inhibition of the SFK signaling pathway in triple-negative breast cancer and murine macrophage cells. Our data suggest that curcumin is a modifiable fluorescent scaffold to develop selective kinase inhibitors by remodeling its target affinity and cellular stability.


Subject(s)
Curcumin/pharmacology , Drug Design , Epithelial Cells/drug effects , Protein Kinase Inhibitors/pharmacology , Proto-Oncogene Proteins c-hck/antagonists & inhibitors , Animals , Cell Line, Tumor , Cloning, Molecular , Curcumin/analogs & derivatives , Curcumin/chemical synthesis , Drug Stability , Epithelial Cells/enzymology , Epithelial Cells/pathology , Escherichia coli/genetics , Escherichia coli/metabolism , Gene Expression , Gene Expression Regulation , Genetic Vectors/chemistry , Genetic Vectors/metabolism , HEK293 Cells , HT29 Cells , Humans , Mice , Mitogen-Activated Protein Kinase 1/genetics , Mitogen-Activated Protein Kinase 1/metabolism , Mitogen-Activated Protein Kinase 3/genetics , Mitogen-Activated Protein Kinase 3/metabolism , Protein Kinase Inhibitors/chemical synthesis , Protein Serine-Threonine Kinases/genetics , Protein Serine-Threonine Kinases/metabolism , Protein-Tyrosine Kinases/genetics , Protein-Tyrosine Kinases/metabolism , Proto-Oncogene Proteins c-abl/genetics , Proto-Oncogene Proteins c-abl/metabolism , Proto-Oncogene Proteins c-hck/chemistry , Proto-Oncogene Proteins c-hck/genetics , Proto-Oncogene Proteins c-hck/metabolism , RAW 264.7 Cells , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Structure-Activity Relationship , src-Family Kinases/genetics , src-Family Kinases/metabolism
18.
Hum Cell ; 34(2): 698-699, 2021 Mar.
Article in English | MEDLINE | ID: covidwho-1060392

ABSTRACT

The current COVID-19 is one of the deadliest pandemics in recent decades. In the lack of a specific treatment for this novel infection, knowing the role of cell signaling pathways in the pathogenesis of this infection could be useful in finding effective drugs against this disease. The mammalian or mechanistic target of rapamycin (mTOR) is an important cell signaling pathway that has important role in the regulation of cell growth, protein synthesis, and metabolism in reactance to upstream signals in both pathological and normal physiological conditions. Recently, some researchers have suggested the therapeutic potential of mTOR inhibitors such as rapamycin against COVID-19. However, it is important to consider the role of activation of this pathway in controlling immune system response against viral activity in drug repositioning of rapamycin and other mTOR inhibitors in SARS-CoV-2 infection.


Subject(s)
COVID-19 Drug Treatment , Drug Repositioning , Immune System/immunology , Signal Transduction/genetics , Sirolimus/pharmacology , Sirolimus/therapeutic use , TOR Serine-Threonine Kinases/antagonists & inhibitors , TOR Serine-Threonine Kinases/physiology , COVID-19/immunology , Humans , Signal Transduction/physiology
19.
Vaccines (Basel) ; 9(1)2021 Jan 11.
Article in English | MEDLINE | ID: covidwho-1022026

ABSTRACT

The world is suffering from the coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). SARS-CoV-2 uses its spike protein to enter the host cells. Vaccines that introduce the spike protein into our body to elicit virus-neutralizing antibodies are currently being developed. In this article, we note that human host cells sensitively respond to the spike protein to elicit cell signaling. Thus, it is important to be aware that the spike protein produced by the new COVID-19 vaccines may also affect the host cells. We should monitor the long-term consequences of these vaccines carefully, especially when they are administered to otherwise healthy individuals. Further investigations on the effects of the SARS-CoV-2 spike protein on human cells and appropriate experimental animal models are warranted.

20.
Trends Microbiol ; 29(3): 224-237, 2021 03.
Article in English | MEDLINE | ID: covidwho-989295

ABSTRACT

Pathogens usurp host pathways to generate a permissive environment for their propagation. The current spread of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection presents the urgent need to understand the complex pathogen-host interplay for effective control of the virus. SARS-CoV-2 reorganizes the host cytoskeleton for efficient cell entry and controls host transcriptional processes to support viral protein translation. The virus also dysregulates innate cellular defenses using various structural and nonstructural proteins. This results in substantial but delayed hyperinflammation alongside a weakened interferon (IFN) response. We provide an overview of SARS-CoV-2 and its uniquely aggressive life cycle and discuss the interactions of various viral proteins with host signaling pathways. We also address the functional changes in SARS-CoV-2 proteins, relative to SARS-CoV. Our comprehensive assessment of host signaling in SARS-CoV-2 pathogenesis provides some complex yet important strategic clues for the development of novel therapeutics against this rapidly emerging worldwide crisis.


Subject(s)
COVID-19/virology , SARS-CoV-2/pathogenicity , COVID-19/metabolism , Humans , Immunity/physiology , Life Cycle Stages , Signal Transduction/physiology , Viral Proteins/genetics , Viral Proteins/metabolism
SELECTION OF CITATIONS
SEARCH DETAIL