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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.
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
3.
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
4.
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
5.
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
6.
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
7.
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
8.
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
9.
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
10.
J Am Soc Mass Spectrom ; 32(4): 1116-1125, 2021 Apr 07.
Article in English | MEDLINE | ID: covidwho-1397839

ABSTRACT

The metabolism of vitamin D3 includes a parallel C-3 epimerization pathway-in addition to the standard metabolic processes for vitamin D3-reversing the stereochemical configuration of the -OH group at carbon-3 (ß→α). While the biological function of the 3α epimer has not been elucidated yet, the additional species cannot be neglected in the analytical determination of vitamin D3, as it has the potential to introduce analytical errors if not properly accounted for. Recently, some inconsistent mass spectral behavior was seen for the 25-hydroxyvitamin D3 (25(OH)D3) epimers during quantification using electrospray LC-MS/MS. The present work extends that of Flynn et al. ( Ann. Clin. Biochem. 2014, 51, 352-559) and van den Ouweland et al. ( J. Chromatogr. B 2014, 967, 195-202), who reported larger electrospray ionization response factors for the 3α epimer of 25(OH)D3 in human serum samples as compared to the regular 3ß variant. The present work was concerned with the mechanistic reasons for these differences. We used a combination of electrospray ionization, atmospheric pressure chemical ionization, and density functional theory calculations to uncover structural dissimilarities between the epimers. A plausible mechanism is described based on intramolecular hydrogen bonding in the gas phase, which creates a small difference of proton affinities between the epimers. More importantly, this mechanism allows the explanation of the different ionization efficiencies of the epimers based on kinetic control of the ionization process, where ionization initially takes place at the hydroxyl group with subsequent proton transfer to a basic carbon atom. The barrier for this transfer differs between the epimers and is in direct competition with H2O elimination from the protonated hydroxyl group. The "hidden" site of high gas phase basicity was revealed through computational calculations and appears to be inaccessible via direct protonation.


Subject(s)
Calcifediol/blood , Chromatography, Liquid/methods , Tandem Mass Spectrometry/methods , Calcifediol/chemistry , Density Functional Theory , Gases , Molecular Structure , Protons , Solvents , Stereoisomerism
11.
Proteomics ; 21(7-8): e2000226, 2021 04.
Article in English | MEDLINE | ID: covidwho-1384280

ABSTRACT

A major part of the analysis of parallel reaction monitoring (PRM) data is the comparison of observed fragment ion intensities to a library spectrum. Classically, these libraries are generated by data-dependent acquisition (DDA). Here, we test Prosit, a published deep neural network algorithm, for its applicability in predicting spectral libraries for PRM. For this purpose, we targeted 1529 precursors derived from synthetic viral peptides and analyzed the data with Prosit and DDA-derived libraries. Viral peptides were chosen as an example, because virology is an area where in silico library generation could significantly improve PRM assay design. With both libraries a total of 1174 precursors were identified. Notably, compared to the DDA-derived library, we could identify 101 more precursors by using the Prosit-derived library. Additionally, we show that Prosit can be applied to predict tandem mass spectra of synthetic viral peptides with different collision energies. Finally, we used a spectral library predicted by Prosit and a DDA library to identify SARS-CoV-2 peptides from a simulated oropharyngeal swab demonstrating that both libraries are suited for peptide identification by PRM. Summarized, Prosit-derived viral spectral libraries predicted in silico can be used for PRM data analysis, making DDA analysis for library generation partially redundant in the future.


Subject(s)
COVID-19/virology , Proteomics/methods , SARS-CoV-2/chemistry , Viral Proteins/analysis , Amino Acid Sequence , Humans , Neural Networks, Computer , Peptide Library , Peptides/analysis , Tandem Mass Spectrometry/methods
12.
Anal Bioanal Chem ; 413(29): 7215-7227, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1375628

ABSTRACT

Glycosylation analysis of viral glycoproteins contributes significantly to vaccine design and development. Among other benefits, glycosylation analysis allows vaccine developers to assess the impact of construct design or producer cell line choices for vaccine production, and it is a key measure by which glycoproteins that are produced for use in vaccination can be compared to their native viral forms. Because many viral glycoproteins are multiply glycosylated, glycopeptide analysis is a preferrable approach for mapping the glycans, yet the analysis of glycopeptide data can be cumbersome and requires the expertise of an experienced analyst. In recent years, a commercial software product, Byonic, has been implemented in several instances to facilitate glycopeptide analysis on viral glycoproteins and other glycoproteomics data sets, and the purpose of the study herein is to determine the strengths and limitations of using this software, particularly in cases relevant to vaccine development. The glycopeptides from a recombinantly expressed trimeric S glycoprotein of the SARS-CoV-2 virus were first analyzed using an expert-based analysis strategy; subsequently, analysis of the same data set was completed using Byonic. Careful assessment of instances where the two methods produced different results revealed that the glycopeptide assignments from Byonic contained more false positives than true positives, even when the data were assessed using a 1% false discovery rate. The work herein provides a roadmap for removing the spurious assignments that Byonic generates, and it provides an assessment of the opportunity cost for relying on automated assignments for glycopeptide data sets from viral glycoproteins.


Subject(s)
Glycopeptides/metabolism , Spike Glycoprotein, Coronavirus/metabolism , Algorithms , Amino Acid Sequence , Chromatography, Liquid/methods , Spike Glycoprotein, Coronavirus/chemistry , Tandem Mass Spectrometry/methods
13.
Anal Bioanal Chem ; 413(26): 6503-6511, 2021 Nov.
Article in English | MEDLINE | ID: covidwho-1370381

ABSTRACT

We describe a rapid liquid chromatography/tandem mass spectrometry (LC-MS/MS) method for the direct detection and quantitation of SARS-CoV-2 nucleoprotein in gargle solutions and saliva. The method is based on a multiple-reaction monitoring (MRM) mass spectrometry approach with a total cycle time of 5 min per analysis and allows the detection and accurate quantitation of SARS-CoV-2 nucleoprotein as low as 500 amol/µL. We improved the sample preparation protocol of our recent piloting SARS-CoV-2 LC-MS study regarding sensitivity, reproducibility, and compatibility with a complementary reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) analysis of the same sample. The aim of this work is to promote diagnostic tools that allow identifying and monitoring SARS-CoV-2 infections by LC-MS/MS methods in a routine clinical environment.


Subject(s)
COVID-19 Testing/methods , COVID-19/diagnosis , SARS-CoV-2/isolation & purification , Saliva/virology , Tandem Mass Spectrometry/methods , COVID-19 Testing/economics , Chromatography, Liquid/economics , Chromatography, Liquid/methods , Coronavirus Nucleocapsid Proteins/analysis , Coronavirus Nucleocapsid Proteins/isolation & purification , Humans , Limit of Detection , Phosphoproteins/analysis , Phosphoproteins/isolation & purification , Reproducibility of Results , Specimen Handling , Tandem Mass Spectrometry/economics , Time Factors
14.
Int J Mol Sci ; 22(16)2021 Aug 17.
Article in English | MEDLINE | ID: covidwho-1367845

ABSTRACT

The specificity of a diagnostic assay depends upon the purity of the biomolecules used as a probe. To get specific and accurate information of a disease, the use of synthetic peptides in diagnostics have increased in the last few decades, because of their high purity profile and ability to get modified chemically. The discovered peptide probes are used either in imaging diagnostics or in non-imaging diagnostics. In non-imaging diagnostics, techniques such as Enzyme-Linked Immunosorbent Assay (ELISA), lateral flow devices (i.e., point-of-care testing), or microarray or LC-MS/MS are used for direct analysis of biofluids. Among all, peptide-based ELISA is considered to be the most preferred technology platform. Similarly, peptides can also be used as probes for imaging techniques, such as single-photon emission computed tomography (SPECT) and positron emission tomography (PET). The role of radiolabeled peptides, such as somatostatin receptors, interleukin 2 receptor, prostate specific membrane antigen, αß3 integrin receptor, gastrin-releasing peptide, chemokine receptor 4, and urokinase-type plasminogen receptor, are well established tools for targeted molecular imaging ortumor receptor imaging. Low molecular weight peptides allow a rapid clearance from the blood and result in favorable target-to-non-target ratios. It also displays a good tissue penetration and non-immunogenicity. The only drawback of using peptides is their potential low metabolic stability. In this review article, we have discussed and evaluated the role of peptides in imaging and non-imaging diagnostics. The most popular non-imaging and imaging diagnostic platforms are discussed, categorized, and ranked, as per their scientific contribution on PUBMED. Moreover, the applicability of peptide-based diagnostics in deadly diseases, mainly COVID-19 and cancer, is also discussed in detail.


Subject(s)
COVID-19 Testing/methods , COVID-19/diagnosis , Peptides/analysis , COVID-19/virology , Databases, Factual , Enzyme-Linked Immunosorbent Assay/methods , Humans , Positron-Emission Tomography/methods , Receptors, Somatostatin , SARS-CoV-2/isolation & purification , Tandem Mass Spectrometry/methods , Tomography, Emission-Computed, Single-Photon/methods
15.
J Chromatogr B Analyt Technol Biomed Life Sci ; 1181: 122884, 2021 Sep 01.
Article in English | MEDLINE | ID: covidwho-1364212

ABSTRACT

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) vaccines are the most promising approach to control the COVID-19 pandemic. There are eminent needs to develop robust analytical methods to ensure quality control, as well as to evaluate the long-term efficacy and safety of vaccine. Although in vivo animal tests, such as serum-based ELISA, have been commonly used for quality control of vaccines, these methods have poor precision, are labor intensive, and require the availability of expensive, specific antibodies. Thus, there is growing interest to develop robust bioanalytical assays as alternatives for qualitative and quantitative evaluation of complex vaccine antigens. In this study, a liquid chromatography tandem mass spectrometry method was developed using optimized unique peptides for simultaneous determination of spike (S) and nucleocapsid (N) protein. Method sensitivity, linearity, repeatability, selectivity, and recovery were evaluated. The amount of S and N proteins in 9 batches of inactivated COVID-19 vaccines were quantified, and their compositions relative to total protein content were consistent. We believe this method can be applied for quality evaluation of other S and/or N protein based COVID-19 vaccine, and could be extended to other viral vector, and protein subunit-based vaccines.


Subject(s)
COVID-19 Vaccines/analysis , Chromatography, Liquid/methods , Coronavirus Nucleocapsid Proteins/analysis , SARS-CoV-2/chemistry , Spike Glycoprotein, Coronavirus/analysis , Tandem Mass Spectrometry/methods , COVID-19/virology , Humans , Quality Control , Vaccines, Inactivated/analysis
16.
Molecules ; 26(16)2021 Aug 06.
Article in English | MEDLINE | ID: covidwho-1362397

ABSTRACT

Protein glycosylation that mediates interactions among viral proteins, host receptors, and immune molecules is an important consideration for predicting viral antigenicity. Viral spike proteins, the proteins responsible for host cell invasion, are especially important to be examined. However, there is a lack of consensus within the field of glycoproteomics regarding identification strategy and false discovery rate (FDR) calculation that impedes our examinations. As a case study in the overlap between software, here as a case study, we examine recently published SARS-CoV-2 glycoprotein datasets with four glycoproteomics identification software with their recommended protocols: GlycReSoft, Byonic, pGlyco2, and MSFragger-Glyco. These software use different Target-Decoy Analysis (TDA) forms to estimate FDR and have different database-oriented search methods with varying degrees of quantification capabilities. Instead of an ideal overlap between software, we observed different sets of identifications with the intersection. When clustering by glycopeptide identifications, we see higher degrees of relatedness within software than within glycosites. Taking the consensus between results yields a conservative and non-informative conclusion as we lose identifications in the desire for caution; these non-consensus identifications are often lower abundance and, therefore, more susceptible to nuanced changes. We conclude that present glycoproteomics softwares are not directly comparable, and that methods are needed to assess their overall results and FDR estimation performance. Once such tools are developed, it will be possible to improve FDR methods and quantify complex glycoproteomes with acceptable confidence, rather than potentially misleading broad strokes.


Subject(s)
Algorithms , Glycopeptides/analysis , Glycoproteins/analysis , COVID-19/metabolism , Databases, Protein , Glycopeptides/chemistry , Glycoproteins/chemistry , Glycosylation , Humans , Proteomics/methods , Proteomics/standards , SARS-CoV-2/metabolism , Software , Spike Glycoprotein, Coronavirus/analysis , Spike Glycoprotein, Coronavirus/chemistry , Tandem Mass Spectrometry/methods , Viral Fusion Proteins/analysis , Viral Fusion Proteins/chemistry
17.
J Am Chem Soc ; 143(31): 12014-12024, 2021 08 11.
Article in English | MEDLINE | ID: covidwho-1333882

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) utilizes an extensively glycosylated surface spike (S) protein to mediate host cell entry, and the S protein glycosylation plays key roles in altering the viral binding/function and infectivity. However, the molecular structures and glycan heterogeneity of the new O-glycans found on the S protein regional-binding domain (S-RBD) remain cryptic because of the challenges in intact glycoform analysis by conventional bottom-up glycoproteomic approaches. Here, we report the complete structural elucidation of intact O-glycan proteoforms through a hybrid native and denaturing top-down mass spectrometry (MS) approach employing both trapped ion mobility spectrometry (TIMS) quadrupole time-of-flight and ultrahigh-resolution Fourier transform ion cyclotron resonance (FTICR)-MS. Native top-down TIMS-MS/MS separates the protein conformers of the S-RBD to reveal their gas-phase structural heterogeneity, and top-down FTICR-MS/MS provides in-depth glycoform analysis for unambiguous identification of the glycan structures and their glycosites. A total of eight O-glycoforms and their relative molecular abundance are structurally elucidated for the first time. These findings demonstrate that this hybrid top-down MS approach can provide a high-resolution proteoform-resolved mapping of diverse O-glycoforms of the S glycoprotein, which lays a strong molecular foundation to uncover the functional roles of their O-glycans. This proteoform-resolved approach can be applied to reveal the structural O-glycoform heterogeneity of emergent SARS-CoV-2 S-RBD variants as well as other O-glycoproteins in general.


Subject(s)
Polysaccharides/analysis , SARS-CoV-2/chemistry , Spike Glycoprotein, Coronavirus/chemistry , Carbohydrate Sequence , Polysaccharides/chemistry , Protein Domains , Tandem Mass Spectrometry/methods
18.
Anal Bioanal Chem ; 413(23): 5811-5820, 2021 Sep.
Article in English | MEDLINE | ID: covidwho-1321733

ABSTRACT

Remdesivir is a nucleotide analog prodrug that has received much attention since the outbreak of the COVID-19 pandemic in December 2019. GS-441524 (Nuc) is the active metabolite of remdesivir and plays a pivotal role in the clinical treatment of COVID-19. Here, a robust HPLC-MS/MS method was developed to determine Nuc concentrations in rat plasma samples after a one-step protein precipitation process. Chromatographic separation was accomplished on Waters XBrige C18 column (50 × 2.1 mm, 3.5 µm) under gradient elution conditions. Multiple reaction monitoring transitions in electrospray positive ion mode were m/z 292.2 → 163.2 for Nuc and 237.1 → 194.1 for the internal standard (carbamazepine). The quantitative analysis method was fully validated in line with the United States Food and Drug Administration guidelines. The linearity, accuracy and precision, matrix effect, recovery, and stability results met the requirements of the guidelines. Uncertainty of measurement and incurred sample reanalysis were analyzed to further ensure the robustness and reproducibility of the method. This optimized method was successfully applied in a rat pharmacokinetics study of remdesivir (intravenously administration, 5 mg kg-1). The method can act as a basis for further pharmacokinetic and clinical efficacy investigations in patients with COVID-19. Graphical abstract.


Subject(s)
Adenosine Monophosphate/analogs & derivatives , Adenosine/analogs & derivatives , Alanine/analogs & derivatives , Antiviral Agents/blood , Chromatography, High Pressure Liquid/methods , Tandem Mass Spectrometry/methods , Adenosine/blood , Adenosine/pharmacokinetics , Adenosine/standards , Adenosine Monophosphate/blood , Adenosine Monophosphate/pharmacokinetics , Adenosine Monophosphate/standards , Alanine/blood , Alanine/pharmacokinetics , Alanine/standards , Animals , Antiviral Agents/pharmacokinetics , Antiviral Agents/standards , Limit of Detection , Male , Quality Control , Rats , Rats, Sprague-Dawley , Reference Standards , Reproducibility of Results
19.
J Chromatogr B Analyt Technol Biomed Life Sci ; 1179: 122862, 2021 Aug 01.
Article in English | MEDLINE | ID: covidwho-1313204

ABSTRACT

Niclosamide, which is an anti-tapeworm drug, was developed in 1958. However, recent studies have demonstrated the antiviral effects of niclosamide against the SARS-CoV-2 virus, which causes COVID-19. In this study, we developed and validated a quantitative analysis method for the determination of niclosamide in rat and dog plasma using liquid chromatography-tandem mass spectrometry (LC-MS/MS), and used this method for pharmacokinetic studies. Biological samples were prepared using the protein precipitation method with acetonitrile. Ibuprofen was used as an internal standard. The mobile phase used to quantify niclosamide in rat or dog plasma consisted of 10 mM ammonium formate in distilled water-acetonitrile (30:70, v/v) or 5 mM ammonium acetate-methanol (30:70, v/v). An XDB-phenyl column (5 µm, 2.1 × 50 mm) and a Kinetex® C18 column (5 µm, 2.1 × 500 mm) were used as reverse-phase liquid chromatography columns for rat and dog plasma analyses, respectively. Niclosamide and ibuprofen were detected under multiple reaction monitoring conditions using the electrospray ionization interface running in the negative ionization mode. Niclosamide presented linearity in the concentration ranges of 1-3000 ng/mL (r = 0.9967) and 1-1000 ng/mL (r = 0.9941) in rat and dog plasma, respectively. The intra- and inter-day precision values were < 7.40% and < 6.35%, respectively, for rat plasma, and < 3.95% and < 4.01%, respectively, for dog plasma. The intra- and inter-day accuracy values were < 4.59% and < 6.63%, respectively, for rat plasma, and < 12.1% and < 10.9%, respectively, for dog plasma. In addition, the recoveries of niclosamide ranged between 87.8 and 99.6% and 102-104% for rat and dog plasma, respectively. Niclosamide was stable during storage under various conditions (three freeze-thaw cycles, 6 h at room temperature, long-term, and processed samples). A reliable LC-MS/MS method for niclosamide detection was successfully used to perform pharmacokinetic studies in rats and dogs. Niclosamide presented dose-independent pharmacokinetics in the dose range of 0.3-3 mg/kg after intravenous administration, and drug exposure in rats and dogs after oral administration was very low. Additionally, niclosamide presented high plasma protein binding (>99.8%) and low metabolic stability. These results can be helpful for further developing and understanding the pharmacokinetic characteristics of niclosamide to expand its clinical use.


Subject(s)
Chromatography, High Pressure Liquid/methods , Niclosamide/blood , Tandem Mass Spectrometry/methods , Animals , Dogs , Humans , Male , Rats , Rats, Sprague-Dawley
20.
Ther Drug Monit ; 43(4): 570-576, 2021 08 01.
Article in English | MEDLINE | ID: covidwho-1305442

ABSTRACT

ABSTRACT: Therapeutic drug monitoring of hydroxychloroquine (HCQ) has been recommended to optimize the treatment of patients with COVID-19. The authors describe an ultrahigh-performance liquid chromatography tandem spectrometry method developed in a context of emergency, to analyze HCQ in both human plasma and blood samples. After adding the labeled internal standard and simple protein precipitation, plasma samples were analyzed using a C18 column. Blood samples required evaporation before analysis. The total chromatographic run time was 4 minutes (including 1.5 minutes of column equilibration). The assay was linear over the calibration range (r2 > 0.99) and up to 1.50 mcg/mL for the plasma samples (5.00 mcg/mL for the blood matrix). The limit of quantification was 0.0150 mcg/mL for plasma samples (0.05 mcg/mL blood matrix) with accuracy and precision ranging from 91.1% to 112% and from 0.750% to 11.1%, respectively. Intraday and interday precision and accuracy values were within 15.0%. No significant matrix effect was observed in the plasma or blood samples. This method was successfully applied to patients treated for COVID-19 infection. A simple and rapid ultrahigh-performance liquid chromatography tandem spectrometry method adapted to HCQ therapeutic drug monitoring in the context of SARS-CoV-2 infection was successfully developed and validated.


Subject(s)
COVID-19/drug therapy , Drug Monitoring/standards , Emergency Medical Services/standards , Hydroxychloroquine/blood , Tandem Mass Spectrometry/standards , Antirheumatic Agents/blood , Antirheumatic Agents/therapeutic use , COVID-19/blood , Chromatography, High Pressure Liquid/methods , Chromatography, High Pressure Liquid/standards , Chromatography, Liquid/methods , Chromatography, Liquid/standards , Drug Monitoring/methods , Emergency Medical Services/methods , Humans , Hydroxychloroquine/therapeutic use , Pandemics , Tandem Mass Spectrometry/methods
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