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1.
Molecules ; 27(6)2022 Mar 14.
Article in English | MEDLINE | ID: covidwho-1742556

ABSTRACT

Nafamostat, a synthetic serine protease inhibitor, has been used for the treatment of inflammatory diseases such as pancreatitis. Recently, an increasing number of studies have shown the promising antiviral effects of nafamostat for the treatment of coronavirus disease-19 (COVID-19). This study aimed to develop a novel liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis and to characterize the pharmacokinetics of nafamostat in rats. Nafamostat in the rat plasma was extracted by solid phase extraction, and 13C6-nafamostat was used as an internal standard. The quantification limit of nafamostat in the rat plasma was 0.5 ng/mL. The LC-MS/MS method was fully validated and applied to characterize the pharmacokinetics of nafamostat in rats. Following intravenous injection (2 mg/kg), nafamostat in the plasma showed a multiexponential decline with an average elimination half-life (t1/2) of 1.39 h. Following oral administration of nafamostat solutions (20 mg/kg) in 10% dimethyl sulfoxide (DMSO) and in 10% DMSO with 10% Tween 80, nafamostat was rapidly absorbed, and the average oral bioavailability was 0.95% and 1.59%, respectively. The LC-MS/MS method and the pharmacokinetic information of nafamostat could be helpful for the further preclinical and clinical studies of nafamostat.


Subject(s)
COVID-19 , Tandem Mass Spectrometry , Animals , Benzamidines , Chromatography, Liquid/methods , Guanidines , Rats , Rats, Sprague-Dawley , Serine Proteinase Inhibitors/pharmacology , Tandem Mass Spectrometry/methods
2.
J Ethnopharmacol ; 291: 115038, 2022 Jun 12.
Article in English | MEDLINE | ID: covidwho-1739924

ABSTRACT

ETHNOPHARMACOLOGICAL RELEVANCE: Red sage (Lantana camara L.) (Verbenaceae) is a widely spread plant that was traditionally used in Brazil, India, Kenya, Thailand, Mexico, Nigeria, Australia and Southeast Asia for treating several ailments including rheumatism and leprosy. Despite its historical role in relieving respiratory diseases, limited studies progressed to the plant's probable inhibition to respiratory viruses especially after the striking spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections. AIM OF THE STUDY: This study aimed to investigate the inhibitory activity of different L. camara cultivars to SARS-CoV-2, that was not previously inspected, and clarify their mechanisms of action in the metabolomics viewpoint, and to determine the biomarkers that are related to such activity using UPLC-MS/MS coupled to in vitro-studies and chemometric analysis. MATERIALS AND METHODS: Chemical profiling of different cultivars was accomplished via UPLC-MS/MS. Principle component analysis (PCA) and orthogonal projection to latent structures (OPLS) models were built using SIMCA® (multivariate data analysis software). Cytotoxicity and COVID-19 inhibitory activity testing were done followed by TaqMan Real-time RT-PCR (Reverse transcription polymerase chain reaction) assay that aimed to study extracts' effects on RNA-dependent RNA polymerase (RdRp) and E-genes expression levels. Detected biomarkers from OPLS analysis were docked into potential targets pockets to investigate their possible interaction patterns using Schrodinger® suite. RESULTS: UPLC-MS/MS analysis of different cultivars yielded 47 metabolites, most of them are triterpenoids and flavonoids. PCA plots revealed that inter-cultivar factor has no pronounced effect on the chemical profiles of extracts except for L. camara, cultivar Drap d'or flowers and leaves extracts as well as for L. camara cv Chelsea gem leaves extract. Among the tested extracts, flowers and leaves extracts of L. camara cv Chelsea gem, flowers extracts of L. camara cv Spreading sunset and L. camara cv Drap d'or showed the highest selectivity indices scoring 12.3, 10.1, 8.6 and 7.8, respectively, indicating their relative high safety and efficacy. Leaves and flowers extracts of L. camara cv Chelsea gem, flowers extracts of L. camara cv Spreading sunset and L. camara cv Drap d'or were the most promising inhibitors to viral plaques exhibiting IC50 values of 3.18, 3.67, 4.18 and 5.01 µg/mL, respectively. This was incremented by OPLS analysis that related their promising COVID-19 inhibitory activities to the presence of twelve biomarkers. Inhibiting the expression of RdRp gene is the major mechanism behind the antiviral activity of most extracts at almost all concentration levels. Molecular docking of the active biomarkers against RdRp revealed that isoverbascoside, luteolin-7,4'-O-diglucoside, camarolic acid and lantoic acid exhibited higher docking scores of -11.378, -10.64, -6.72 and -6.07 kcal/mol, respectively, when compared to remdesivir (-5.75 kcal/mol), thus these four compounds can serve as promising anti-COVID-19 candidates. CONCLUSION: Flowers and leaves extracts of four L. camara cultivars were recognized as rich sources of phytoconstituents possessing anti-COVID-19 activity. Combination of UPLC-MS/MS and chemometrics is a promising approach to detect chemical composition differences among the cultivars and correlate them to COVID-19 inhibitory activities allowing to pinpoint possible biomarkers. Further in-vitro and in-vivo studies are required to verify their activity.


Subject(s)
COVID-19 , Lantana , Biomarkers/analysis , COVID-19/drug therapy , Chromatography, High Pressure Liquid , Chromatography, Liquid , Lantana/chemistry , Molecular Docking Simulation , Plant Extracts/analysis , Plant Extracts/pharmacology , Plant Leaves/chemistry , SARS-CoV-2 , Tandem Mass Spectrometry
3.
Anal Chim Acta ; 1203: 339650, 2022 Apr 22.
Article in English | MEDLINE | ID: covidwho-1729460

ABSTRACT

Because of the coronavirus pandemic, hydroalcoholic gels have become essential products to prevent the spread of COVID-19. This research aims to develop a simple, fast and sustainable microextraction methodology followed by gas chromatography tandem mass spectrometry (GC-MS/MS) to analyze simultaneously 60 personal care products (PCPs) including fragrances allergens, synthetic musks, preservatives and plasticizers in hand sanitizers. Micro-matrix-solid-phase dispersion (µMSPD) and solid-phase microextraction (SPME) were compared with the aim of obtaining high sensitivity and sample throughput. SPME demonstrated higher efficiency being selected as sample treatment. Different dilutions of the sample in ultrapure water were assessed to achieve high sensitivity but, at the same time, to avoid or minimize matrix effect. The most critical parameters affecting SPME (fibre coating, extraction mode and temperature) were optimized by design of experiments (DOE). The method was successfully validated in terms of linearity, precision and accuracy, obtaining recovery values between 80 and 112% for most compounds with relative standard deviation (RSD) values lower than 10%. External calibration using standards prepared in ultrapure water demonstrated suitability due to the absence of matrix effect. Finally, the simple, fast and high throughput method was applied to the analysis of real hydroalcoholic gel samples. Among the 60 target compounds, 39 of them were found, highlighting the high number of fragrance allergens, at concentrations ranging between 0.01 and 217 µg g-1. Most of the samples were not correctly labelled attending cosmetic Regulation (EU) No 1223/2009, and none of them followed the World Health Organization (WHO) recommendation for hand sanitizers formulation.


Subject(s)
COVID-19 , Cosmetics , Hand Sanitizers , Cosmetics/analysis , Gas Chromatography-Mass Spectrometry/methods , Gels , Hand Sanitizers/analysis , Humans , Pandemics , Solid Phase Microextraction/methods , Tandem Mass Spectrometry/methods
5.
Anal Chem ; 94(10): 4426-4436, 2022 03 15.
Article in English | MEDLINE | ID: covidwho-1713091

ABSTRACT

SARS-CoV-2 infection causes a significant reduction in lipoprotein-bound serum phospholipids give rise to supramolecular phospholipid composite (SPC) signals observed in diffusion and relaxation edited 1H NMR spectra. To characterize the chemical structural components and compartmental location of SPC and to understand further its possible diagnostic properties, we applied a Statistical HeterospectroscopY in n-dimensions (SHY-n) approach. This involved statistically linking a series of orthogonal measurements made on the same samples, using independent analytical techniques and instruments, to identify the major individual phospholipid components giving rise to the SPC signals. Thus, an integrated model for SARS-CoV-2 positive and control adults is presented that relates three identified diagnostic subregions of the SPC signal envelope (SPC1, SPC2, and SPC3) generated using diffusion and relaxation edited (DIRE) NMR spectroscopy to lipoprotein and lipid measurements obtained by in vitro diagnostic NMR spectroscopy and ultrahigh-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS). The SPC signals were then correlated sequentially with (a) total phospholipids in lipoprotein subfractions; (b) apolipoproteins B100, A1, and A2 in different lipoproteins and subcompartments; and (c) MS-measured total serum phosphatidylcholines present in the NMR detection range (i.e., PCs: 16.0,18.2; 18.0,18.1; 18.2,18.2; 16.0,18.1; 16.0,20.4; 18.0,18.2; 18.1,18.2), lysophosphatidylcholines (LPCs: 16.0 and 18.2), and sphingomyelin (SM 22.1). The SPC3/SPC2 ratio correlated strongly (r = 0.86) with the apolipoprotein B100/A1 ratio, a well-established marker of cardiovascular disease risk that is markedly elevated during acute SARS-CoV-2 infection. These data indicate the considerable potential of using a serum SPC measurement as a metric of cardiovascular risk based on a single NMR experiment. This is of specific interest in relation to understanding the potential for increased cardiovascular risk in COVID-19 patients and risk persistence in post-acute COVID-19 syndrome (PACS).


Subject(s)
COVID-19 , Cardiovascular Diseases , Adult , Biomarkers , COVID-19/complications , COVID-19/diagnosis , Cardiovascular Diseases/diagnosis , Humans , Lipoproteins , Phospholipids , Risk Factors , SARS-CoV-2 , Tandem Mass Spectrometry/methods
6.
J Photochem Photobiol B ; 229: 112415, 2022 Apr.
Article in English | MEDLINE | ID: covidwho-1712830

ABSTRACT

Noscapine (NSC) is a benzyl-isoquinoline alkaloid discovered in 1930 as an antitussive agent. Recently, NSC has also been reported to exhibit antitumor activity and, according to computational studies, it is able to attack the protease enzyme of Coronavirus (COVID-19) and thus could be used as antiviral for COVID-19 pandemic. Therefore, an increasing use of this drug could be envisaged in the coming years. NSC is readily metabolized with a half-life of 4.5 h giving rise to cotarnine, hydrocotarnine, and meconine, arising from the oxidative breaking of the CC bond between isoquinoline and phthalide moieties. Because of its potentially increasing use, high concentrations of NSC but also its metabolites will be delivered in the environment and potentially affect natural ecosystems. Thus, the aim of this work is to investigate the degradation of NSC in the presence of naturally occurring photocatalysts. As a matter of fact, the present contribution has demonstrated that NSC can be efficiently degraded in the presence of a derivative of the natural organic dye Riboflavin (RFTA) upon exposure to visible light. Indeed, a detailed study of the mechanism involved in the photodegradation revealed the similarities between the biomimetic and the photocatalyzed processes. In fact, the main photoproducts of NSC were identified as cotarnine and opianic acid based on a careful UPLC-MS2 analysis compared to the independently synthesized standards. The former is coincident with one of the main metabolites obtained in humans, whereas the latter is related to meconine, a second major metabolite of NSC. Photophysical experiments demonstrated that the observed oxidative cleavage is mediated mainly by singlet oxygen in a medium in which the lifetime of 1O2 is long enough, or by electron transfer to the triplet excited state of RFTA if the photodegradation occurs in aqueous media, where the 1O2 lifetime is very short.


Subject(s)
COVID-19 , Environmental Restoration and Remediation , Noscapine , Biomimetics , Chromatography, Liquid , Coloring Agents , Ecosystem , Humans , Light , Pandemics , Photolysis , Riboflavin/chemistry , Tandem Mass Spectrometry , Water/chemistry
7.
Int J Mol Sci ; 23(5)2022 Feb 22.
Article in English | MEDLINE | ID: covidwho-1707649

ABSTRACT

Omics-based technologies have been largely adopted during this unprecedented global COVID-19 pandemic, allowing the scientific community to perform research on a large scale to understand the pathobiology of the SARS-CoV-2 infection and its replication into human cells. The application of omics techniques has been addressed to every level of application, from the detection of mutations, methods of diagnosis or monitoring, drug target discovery, and vaccine generation, to the basic definition of the pathophysiological processes and the biochemical mechanisms behind the infection and spread of SARS-CoV-2. Thus, the term COVIDomics wants to include those efforts provided by omics-scale investigations with application to the current COVID-19 research. This review summarizes the diverse pieces of knowledge acquired with the application of COVIDomics techniques, with the main focus on proteomics and metabolomics studies, in order to capture a common signature in terms of proteins, metabolites, and pathways dysregulated in COVID-19 disease. Exploring the multiomics perspective and the concurrent data integration may provide new suitable therapeutic solutions to combat the COVID-19 pandemic.


Subject(s)
COVID-19/metabolism , Metabolomics/methods , Proteome/metabolism , Proteomics/methods , COVID-19/epidemiology , COVID-19/virology , Chromatography, Liquid/methods , Host-Pathogen Interactions , Humans , Pandemics , SARS-CoV-2/physiology , Tandem Mass Spectrometry/methods
8.
Int J Mol Sci ; 23(4)2022 Feb 16.
Article in English | MEDLINE | ID: covidwho-1704472

ABSTRACT

Rapid and precise diagnostic methods are required to control emerging infectious diseases effectively. Human body fluids are attractive clinical samples for discovering diagnostic targets because they reflect the clinical statuses of patients and most of them can be obtained with minimally invasive sampling processes. Body fluids are good reservoirs for infectious parasites, bacteria, and viruses. Therefore, recent clinical proteomics methods have focused on body fluids when aiming to discover human- or pathogen-originated diagnostic markers. Cutting-edge liquid chromatography-mass spectrometry (LC-MS)-based proteomics has been applied in this regard; it is considered one of the most sensitive and specific proteomics approaches. Here, the clinical characteristics of each body fluid, recent tandem mass spectroscopy (MS/MS) data-acquisition methods, and applications of body fluids for proteomics regarding infectious diseases (including the coronavirus disease of 2019 [COVID-19]), are summarized and discussed.


Subject(s)
Chromatography, Liquid/methods , Communicable Diseases/diagnosis , Mass Spectrometry/methods , Microbiological Techniques/methods , Proteomics/methods , Body Fluids , COVID-19 Testing/methods , Humans , Tandem Mass Spectrometry
9.
J Pharm Biomed Anal ; 212: 114646, 2022 Apr 01.
Article in English | MEDLINE | ID: covidwho-1699455

ABSTRACT

SBECD (Captisol®) with an average degree of substitution of 6.5 sulfobutylether functional groups (SBE = 6.5), is a solubility enhancer for remdesivir (RDV) and a major component in Veklury, which was approved by FDA for the treatment of patients with COVID-19 over 12 years old and weighing over 40 kg who require hospitalization. SBECD is cleared mainly by renal filtration, thus, potential accumulation of SBECD in the human body is a concern for patients dosed with Veklury with compromised renal function. An LC-MS/MS method was developed and validated for specific, accurate, and precise determination of SBECD concentrations in human plasma. In this method, the hexa-substituted species, SBE6, was selected for SBECD quantification, and the mass transition from its dicharged molecular ion [(M-2H)/2]2-, Molecular (parent) Ion (Q1)/Molecular (parent) Ion (Q3) of m/z 974.7/974.7, was selected for quantitative analysis of SBECD. Captisol-G (SBE-γ-CD, SBE = 3) was chosen as the internal standard. With 25 µL of formic-acid-treated sample and with a calibration range of 10.0-1000 µg/mL, the method was validated with respect to pre-established criteria based on regulatory guidelines and was applied to determine SBECD levels in plasma samples collected from pediatric patients during RDV clinical studies.


Subject(s)
COVID-19 , beta-Cyclodextrins , Adenosine Monophosphate/analogs & derivatives , Alanine/analogs & derivatives , COVID-19/drug therapy , Child , Chromatography, Liquid , Humans , SARS-CoV-2 , Sodium , Tandem Mass Spectrometry/methods
10.
Metabolomics ; 18(1): 6, 2021 12 20.
Article in English | MEDLINE | ID: covidwho-1669925

ABSTRACT

INTRODUCTION: The diagnosis of COVID-19 is normally based on the qualitative detection of viral nucleic acid sequences. Properties of the host response are not measured but are key in determining outcome. Although metabolic profiles are well suited to capture host state, most metabolomics studies are either underpowered, measure only a restricted subset of metabolites, compare infected individuals against uninfected control cohorts that are not suitably matched, or do not provide a compact predictive model. OBJECTIVES: Here we provide a well-powered, untargeted metabolomics assessment of 120 COVID-19 patient samples acquired at hospital admission. The study aims to predict the patient's infection severity (i.e., mild or severe) and potential outcome (i.e., discharged or deceased). METHODS: High resolution untargeted UHPLC-MS/MS analysis was performed on patient serum using both positive and negative ionization modes. A subset of 20 intermediary metabolites predictive of severity or outcome were selected based on univariate statistical significance and a multiple predictor Bayesian logistic regression model was created. RESULTS: The predictors were selected for their relevant biological function and include deoxycytidine and ureidopropionate (indirectly reflecting viral load), kynurenine (reflecting host inflammatory response), and multiple short chain acylcarnitines (energy metabolism) among others. Currently, this approach predicts outcome and severity with a Monte Carlo cross validated area under the ROC curve of 0.792 (SD 0.09) and 0.793 (SD 0.08), respectively. A blind validation study on an additional 90 patients predicted outcome and severity at ROC AUC of 0.83 (CI 0.74-0.91) and 0.76 (CI 0.67-0.86). CONCLUSION: Prognostic tests based on the markers discussed in this paper could allow improvement in the planning of COVID-19 patient treatment.


Subject(s)
COVID-19/blood , Chromatography, Liquid/methods , Metabolomics/methods , Tandem Mass Spectrometry/methods , Aged , Biomarkers/blood , Female , Humans , Male , Middle Aged , Prognosis , SARS-CoV-2 , Severity of Illness Index
11.
STAR Protoc ; 3(1): 101177, 2022 03 18.
Article in English | MEDLINE | ID: covidwho-1665545

ABSTRACT

With new emerging SARS-CoV-2 strains and their increased pathogenicity, diagnosis has become more challenging. Molecular diagnosis often involves the use of nasopharyngeal swabs and subsequent real-time PCR-based tests. Although this test is the gold standard, it has several limitations; therefore, more complementary assays are required. This protocol describes how to identify SARS-CoV-2 protein from patients' nasopharyngeal swab samples. We first introduce the approach of label-free quantitative proteomics. We then detail target verification by triple quadrupole mass spectrometry (MS)-based targeted proteomics. For complete details on the use and execution of this profile, please refer to Bankar et al. (2021).


Subject(s)
COVID-19/metabolism , Nasopharynx/metabolism , Proteomics , SARS-CoV-2/metabolism , Specimen Handling , Tandem Mass Spectrometry , Viral Proteins/metabolism , Female , Humans , Male , Nasopharynx/virology
12.
J Proteomics ; 255: 104501, 2022 03 20.
Article in English | MEDLINE | ID: covidwho-1654819

ABSTRACT

Phosphorylation of viral proteins serves as a regulatory mechanism during the intracellular life cycle of infected viruses. There is therefore a pressing need to develop a method to efficiently purify and enrich phosphopeptides derived from viral particles in biological samples. In this study, we utilized Phos-tag technology to analyze the functional phosphorylation of the nucleocapsid protein (N protein; NP) of severe respiratory syndrome coronavirus 2 (SARS-CoV-2). Viral particles were collected from culture supernatants of SARS-CoV-2-infected VeroE6/TMPRSS2 cells by ultracentrifugation, and phosphopeptides were purified by Phos-tag magnetic beads for LC-MS/MS analysis. Analysis revealed that NP was reproducibly phosphorylated at serine 79 (Ser79). Multiple sequence alignment and phylogenetic analysis showed that the Ser79 was a distinct phospho-acceptor site in SARS-CoV-2 but not in other beta-coronaviruses. We also found that the prolyl-isomerase Pin1 bound to the phosphorylated Ser79 in NP and positively regulated the production of viral particles. These results suggest that SARS-CoV-2 may have acquired the potent virus-host interaction during its evolution mediated by viral protein phosphorylation. Moreover, Phos-tag technology can provide a useful means for analyzing the functional phosphorylation of viral proteins. SIGNIFICANCE: In this study, we aimed to investigate the functional phosphorylation of SARS-CoV-2 NP. For this purpose, we used Phos-tag technology to purify and enrich virus-derived phosphopeptides with high selectivity and reproducibility. This method can be particularly useful in analyzing viral phosphopeptides from cell culture supernatants that often contain high concentrations of fetal bovine serum and supplements. We newly identified an NP phosphorylation site at Ser79, which is important for Pin1 binding. Furthermore, we showed that the interaction between Pin1 and phosphorylated NP could enhance viral replication in a cell culture model.


Subject(s)
Nucleocapsid Proteins , Phosphopeptides , Chromatography, Liquid , Coronavirus Nucleocapsid Proteins , Humans , NIMA-Interacting Peptidylprolyl Isomerase/metabolism , Nucleocapsid Proteins/chemistry , Phosphopeptides/chemistry , Phosphoproteins , Phosphorylation , Phylogeny , Pyridines , Reproducibility of Results , SARS-CoV-2 , Tandem Mass Spectrometry
13.
Anal Chim Acta ; 1196: 339405, 2022 Mar 01.
Article in English | MEDLINE | ID: covidwho-1632732

ABSTRACT

Metabolomics (both targeted and untargeted) has become the gold standard in biomarker discovery. Whereas targeted approaches only provide information for the selected markers, thus hampering the determination of out-of-the-box markers, the common bottleneck of untargeted metabolomics is the identification of detected biomarkers. In this study, we developed a strategy based on derivatization and LC-MS/MS detection in a precursor ion scan for the untargeted determination of a specific part of the metabolome (carbonyl-containing metabolites). The usefulness of this guided metabolomics approach has been demonstrated by elucidating carbonyl-containing biomarkers of COVID-19 severity. First, the LC-MS/MS behavior of 63 model compounds after O-benzylhydroxylamine derivatization was studied. A precursor ion scan of m/z 91 was selected as a suitable approach for the untargeted detection of carbonyl-containing metabolites. The method was able to detect ≈300 potential carbonyl-containing molecules in plasma, including mono-/di-/tricarbonylic compounds with satisfactory intra-day and inter-day repeatability and RSDs commonly <15%. Additionally, the semiquantitative nature of the precursor ion scan method was confirmed by comparison with a fully validated targeted method. The application of the guided metabolomics method to COVID-19 plasma samples revealed the presence of four potential COVID-19 severity biomarkers. Based on their LC-MS/MS behavior, these biomarkers were elucidated as 2-hydroxybutyrate, 2,3-dihydroxybutyrate, 2-oxobutyrate and 2-hydroxy-3-methylbutyrate. Their structures were confirmed by comparison with reference materials. The alterations of these biomarkers with COVID-19 severity were confirmed by a target analysis of a larger set of samples. Our results confirm that guided metabolomics is an alternative approach for the untargeted detection of selected families of metabolites; this approach can accelerate their elucidation and provide new perspectives for the establishment of health/disease biomarkers.


Subject(s)
COVID-19 , Tandem Mass Spectrometry , Biomarkers , Chromatography, Liquid , Humans , Metabolome , Metabolomics , SARS-CoV-2
14.
Anal Bioanal Chem ; 414(5): 1949-1962, 2022 Feb.
Article in English | MEDLINE | ID: covidwho-1607761

ABSTRACT

Recently, numerous diagnostic approaches from different disciplines have been developed for SARS-CoV-2 diagnosis to monitor and control the COVID-19 pandemic. These include MS-based assays, which provide analytical information on viral proteins. However, their sensitivity is limited, estimated to be 5 × 104 PFU/ml in clinical samples. Here, we present a reliable, specific, and rapid method for the identification of SARS-CoV-2 from nasopharyngeal (NP) specimens, which combines virus capture followed by LC-MS/MS(MRM) analysis of unique peptide markers. The capture of SARS-CoV-2 from the challenging matrix, prior to its tryptic digestion, was accomplished by magnetic beads coated with polyclonal IgG-α-SARS-CoV-2 antibodies, enabling sample concentration while significantly reducing background noise interrupting with LC-MS analysis. A sensitive and specific LC-MS/MS(MRM) analysis method was developed for the identification of selected tryptic peptide markers. The combined assay, which resulted in S/N ratio enhancement, achieved an improved sensitivity of more than 10-fold compared with previously described MS methods. The assay was validated in 29 naive NP specimens, 19 samples were spiked with SARS-CoV-2 and 10 were used as negative controls. Finally, the assay was successfully applied to clinical NP samples (n = 26) pre-determined as either positive or negative by RT-qPCR. This work describes for the first time a combined approach for immuno-magnetic viral isolation coupled with MS analysis. This method is highly reliable, specific, and sensitive; thus, it may potentially serve as a complementary assay to RT-qPCR, the gold standard test. This methodology can be applied to other viruses as well.


Subject(s)
COVID-19 Testing/methods , COVID-19/diagnosis , Chromatography, Liquid/methods , Immunomagnetic Separation/methods , SARS-CoV-2/genetics , Tandem Mass Spectrometry/methods , Amino Acid Sequence , Antibodies, Viral/chemistry , Biomarkers/chemistry , COVID-19/immunology , COVID-19/virology , COVID-19 Testing/instrumentation , COVID-19 Testing/standards , Chromatography, Liquid/instrumentation , Chromatography, Liquid/standards , Humans , Immunomagnetic Separation/instrumentation , Immunomagnetic Separation/standards , Nasopharynx/virology , Peptides/chemistry , Peptides/immunology , SARS-CoV-2/immunology , Sensitivity and Specificity , Tandem Mass Spectrometry/instrumentation , Tandem Mass Spectrometry/standards
15.
Biomed Pharmacother ; 146: 112513, 2022 Feb.
Article in English | MEDLINE | ID: covidwho-1575252

ABSTRACT

The interactions of four sulfonylated Phe(3-Am)-derived inhibitors (MI-432, MI-463, MI-482 and MI-1900) of type II transmembrane serine proteases (TTSP) such as transmembrane protease serine 2 (TMPRSS2) were examined with serum albumin and cytochrome P450 (CYP) isoenzymes. Complex formation with albumin was investigated using fluorescence spectroscopy. Furthermore, microsomal hepatic CYP1A2, 2C9, 2C19 and 3A4 activities in presence of these inhibitors were determined using fluorometric assays. The inhibitory effects of these compounds on human recombinant CYP3A4 enzyme were also examined. In addition, microsomal stability assays (60-min long) were performed using an UPLC-MS/MS method to determine depletion percentage values of each compound. The inhibitors showed no or only weak interactions with albumin, and did not inhibit CYP1A2, 2C9 and 2C19. However, the compounds tested proved to be potent inhibitors of CYP3A4 in both assays performed. Within one hour, 20%, 12%, 14% and 25% of inhibitors MI-432, MI-463, MI-482 and MI-1900, respectively, were degraded. As essential host cell factor for the replication of the pandemic SARS-CoV-2, the TTSP TMPRSS2 emerged as an important target in drug design. Our study provides further preclinical data on the characterization of this type of inhibitors for numerous trypsin-like serine proteases.


Subject(s)
Antiviral Agents/metabolism , Cytochrome P-450 Enzyme System/metabolism , Protease Inhibitors/metabolism , Serine Endopeptidases/metabolism , Serum Albumin, Human/metabolism , Antiviral Agents/analysis , Antiviral Agents/pharmacology , Dose-Response Relationship, Drug , Humans , Isoenzymes/metabolism , Microsomes, Liver/drug effects , Microsomes, Liver/metabolism , Protease Inhibitors/analysis , Protease Inhibitors/pharmacology , Protein Binding/physiology , Serine Endopeptidases/analysis , Spectrometry, Fluorescence/methods , Tandem Mass Spectrometry/methods
16.
Phytomedicine ; 96: 153888, 2022 Feb.
Article in English | MEDLINE | ID: covidwho-1560803

ABSTRACT

BACKGROUND: Traditional Chinese medicine (TCM) is regarded as a large database containing hundreds to thousands of chemical constituents that can be further developed as clinical drugs, such as artemisinin in Artemisia annua. However, effectively exploring novel candidates is still a challenge faced by researchers. PURPOSE: In this work, an integrated strategy combining chemical profiling, molecular networking, chemical isolation, and activity evaluation (CMCA strategy) was proposed and applied to systematically characterize and screen novel candidates, and Forsythiae fructus (FF) was used as an example. STUDY DESIGN: It contained four parts. First, the chemical compounds in FF were detected by ultra-high-performance liquid chromatography-mass spectrometry (UPLC/Q-TOF MS) with data-dependent acquisition, and further, the targeted compounds were screened out based on an in-house database. In the meantime, the representative MS/MS fragmentation behaviors of different chemical structure types were summarized. Second, homologous constituents were grouped and organized based on feature-guided molecular networking, and the nontargeted components with homologous mass fragmentation behaviors were characterized. Third, the novel compounds were isolated and unambiguously identified by nuclear magnetic resonance (NMR). Finally, the anti-angiotensin-converting enzyme 2 (ACE2) activities of isolated chemical constituents were further evaluated by in vitro experiments. RESULTS: A total of 278 compounds were profiled in FF, including 151 targeted compounds and 127 nontargeted compounds. Among them, 16 were unambitiously identified by comparison with reference standards. Moreover, 25 were classified into potential novel compounds. Two novel compounds were unambiguously identified by using conventional chromatographic methods, and they were named phillyrigeninside D (peak 254) and forsythenside O (peak 155). Furthermore, the ACE2 activity of the compounds in FF was evaluated by modern pharmacological methods, and among them, suspensaside A was confirmed to present obvious anti-ACE2 activity. CONCLUSION: Our work provides meaningful information for revealing potential FF candidates for the treatment of COVID-19, along with new insight for exploring novel candidates from complex systems.


Subject(s)
COVID-19 , Drugs, Chinese Herbal , Angiotensin-Converting Enzyme 2 , Chromatography, High Pressure Liquid , Humans , Plant Extracts , SARS-CoV-2 , Tandem Mass Spectrometry
17.
STAR Protoc ; 3(1): 101045, 2022 03 18.
Article in English | MEDLINE | ID: covidwho-1537118

ABSTRACT

In this protocol, we describe global proteome profiling for the respiratory specimen of COVID-19 patients, patients suspected with COVID-19, and H1N1 patients. In this protocol, details for identifying host, viral, or bacterial proteome (Meta-proteome) are provided. Major steps of the protocol include virus inactivation, protein quantification and digestion, desalting of peptides, high-resolution mass spectrometry (HRMS)-based analysis, and downstream bioinformatics analysis. For complete details on the use and execution of this profile, please refer to Maras et al. (2021).


Subject(s)
COVID-19/diagnosis , Genomics/methods , Proteomics/methods , COVID-19/metabolism , Chromatography, Liquid/methods , Computational Biology , Diagnostic Tests, Routine , Gene Expression Profiling , Genetic Techniques , Genome, Viral/genetics , Humans , Influenza A Virus, H1N1 Subtype/metabolism , Influenza A Virus, H1N1 Subtype/pathogenicity , Peptides , Proteome , SARS-CoV-2/metabolism , SARS-CoV-2/pathogenicity , Specimen Handling/methods , Tandem Mass Spectrometry/methods , Virome/genetics , Virome/physiology
18.
Int J Environ Res Public Health ; 18(22)2021 11 22.
Article in English | MEDLINE | ID: covidwho-1534066

ABSTRACT

This study aimed to analyse the association between endogenous hair steroid hormones as reliable biological indicators of an individual's stress level and the social environmental factors experienced during military training that are manifested at the beginning of compulsory military service. Hair steroid hormone concentrations-cortisol, cortisone, dehydroepiandrosterone (DHEA), and testosterone-in a group of 185 conscripts were measured using the ultra-high performance liquid chromatography-tandem mass spectrometry method. Six subjective social environmental factors in the military-attitude towards the military and military service, adaptation to the military environment, team, task, and norm cohesion, as well as psychological (un)safety in the group-were evaluated using military-specific research questionnaires. Weak but significant negative correlations were identified between cortisol and adaptation (r = -0.176, p < 0.05), attitude (r = -0.147, p < 0.05) as well as between testosterone and task cohesion (r = -0.230, p < 0.01) levels. Additionally, a multiple forward stepwise regression analysis highlighted that cortisone variation might be partially explained by task cohesion; the DHEA-determined by psychological (un)safety in the group, attitude towards the military and military service, and norm cohesion; and the testosterone-determined by task cohesion and adaptation to the new military environment. The results of this study suggest that subjective measures of social factors can be used to predict hair steroid hormone levels as objective measures of the chronic stress perceived by conscripts during their basic military training.


Subject(s)
Military Personnel , Tandem Mass Spectrometry , Hair , Humans , Hydrocortisone , Steroids
19.
Eur Rev Med Pharmacol Sci ; 25(21): 6782-6796, 2021 Nov.
Article in English | MEDLINE | ID: covidwho-1524866

ABSTRACT

OBJECTIVE: This study aimed to evaluate the eicosanoid and pro resolutive parameters in SARS COVID-19 patients with the severe acute respiratory syndrome. PATIENTS AND METHODS: Fourteen male patients with an acute respiratory syndrome caused by SARS COVID-19 and four healthy controls were evaluated by measuring the following parameters in plasma: Polyunsaturated fatty acids: EPA, DHA, ARA, and DPA. Specialized Pro-resolving mediators (SPMs) (including monohydroxy-containing precursors 17-HDHA, 18-HEPE, 14-HDHA) resolvins, maresins, protectins, and lipoxins. The eicosanoids group included prostaglandins, thromboxanes, and leukotrienes. RESULTS: Plasma from COVID-19 patients presented higher amounts of pro-inflammatory and pro-thrombotic lipid mediators as compared to healthy subjects (65.7 pg/ml vs. 10.2 pg/ml), including thromboxane (2142.6 pg/ml vs. 10.4 pg/ml), and the ratio between total plasma pro-inflammatory mediators versus total SPM's was 13.2 to 0,4, respectively. CONCLUSIONS: A clear disbalance favoring the pro-inflammatory axis is described, showing the need to perform future clinical interventions in these patients using SPM's or monohydroxylated lipid mediators derivates from fatty acids.


Subject(s)
COVID-19/diagnosis , Eicosanoids/blood , Inflammation Mediators/blood , Acute Disease , Adult , COVID-19/pathology , COVID-19/virology , Case-Control Studies , Chromatography, High Pressure Liquid , Fatty Acids, Unsaturated/blood , Humans , Male , SARS-CoV-2/isolation & purification , Severity of Illness Index , Tandem Mass Spectrometry , Thromboxanes/blood
20.
Phytomedicine ; 95: 153784, 2022 Jan.
Article in English | MEDLINE | ID: covidwho-1521466

ABSTRACT

BACKGROUND: Coronavirus disease 2019 (COVID-19) is a pandemic that has caused a high number of deaths worldwide. Inflammatory factors may play important roles in COVID-19 progression. Yindan Jiedu granules (YDJDG) can inhibit the progression of COVID-19, but the associated mechanism is unclear. PURPOSE: To evaluate the therapeutic effects of YDJDG on COVID-19 and explore its underlying mechanism. METHODS: We recruited 262 participants and randomly assigned 97 patients each to the YDJDG and control groups using one-to-one propensity score matching (PSM). Clinical effects were observed and serum inflammatory and immune indicators were measured. The target network model of YDJDG was established by predicting and determining the targets of identified compounds. The main constituents of the YDJDG extracts were identified and evaluated using high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) and molecular docking. Besides, the anti-inflammatory effects of YDJDG and its specific biological mechanism of action were studied. RESULTS: After PSM, the results showed that compared with the control group, the YDJDG group had a shorter time of dissipation of acute pulmonary exudative lesions (p < 0.0001), shorter time to negative conversion of viral nucleic acid (p < 0.01), more rapid decrease in serum amyloid A level and erythrocyte sedimentation rate (p < 0.0001), and a higher rate of increase in CD4+T cell count (p = 0.0155). By overlapping the genes of YDJDG and COVID-19, 213 co-targeted genes were identified. Metascape enrichment analysis showed that 25 genes were significantly enriched in the NF-κB pathway, which were mainly targets of luteolin, quercetin, and kaempferol as confirmed by MS analysis. Molecular docking revealed that the ligands of three compounds had strong interaction with NF-κB p65 and IκBα. In vivo, YDJDG significantly protected animals from lipopolysaccharide (LPS)-induced acute lung injury (ALI), decreasing the lung wet/dry weight ratio, ALI score, and lung histological damage. In LPS-treated RAW264.7 cells, YDJDG suppressed nuclear translocation of NF-κB p65. In vivo and in vitro, YDJDG exerted anti-inflammatory effects by inhibiting the production of inflammatory cytokines (IL-6, IL-1ß, and TNF-α). These effects were accompanied by the inhibition of NF-ĸB activation and IκBα phosphorylation. CONCLUSION: YDJDG may shorten the COVID-19 course and delay its progression by suppressing inflammation via targeting the NF-κB pathway.


Subject(s)
COVID-19 , NF-kappa B , Animals , Anti-Inflammatory Agents/pharmacology , Cytokines , Humans , Lipopolysaccharides/pharmacology , Molecular Docking Simulation , NF-kappa B/metabolism , SARS-CoV-2 , Signal Transduction , Tandem Mass Spectrometry
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