key: cord-345929-z7yfegr5 authors: Thakur, Suman S. title: Proteomics and Its Application in Pandemic Diseases date: 2020-11-06 journal: J Proteome Res DOI: 10.1021/acs.jproteome.0c00824 sha: doc_id: 345929 cord_uid: z7yfegr5 nan Using in silico studies, Barros et al. found that the antimalarial drug metaquine and anti-HIV antiretroviral saquinavir interact with four SARS-CoV-2 receptors, including Nsp9 replicase, main protease (Mpro), NSP15 endoribonuclease, and spike protein (S protein), interacting with human ACE2; therefore, they may be repurposed for COVID-19 treatment. The bioinformatics analysis of BCG antigens by Glisic et al. suggested that four bacterial proteins, Rv0934, Rv3763, Rv3875, and Rv2997, have similar properties as the S1 protein of SARS-CoV-2; therefore, they might be effective against SARS-CoV-2. A molecular docking and dynamics simulation analysis suggested that noscapine binds with the main protease of SARS-CoV-2 and produces conformational changes (Kumar et al.) . Furthermore, Maffucci and Contini used an in silico approach to find drug candidates against the main proteinase and spike protein of SARS-CoV-2. This led to the finding that indinavir, polymyxin B, daptomycin, terlipressin, and thymopentin can be repurposed against the SARS-CoV-2 infection. Interestingly, the studies by Stamatakis et al. suggested that the antigenic peptides generated from the S1 spike glycoprotein of SARS-CoV-2 using aminopeptidases ERAP1, ERAP2, and IRAP might be helpful in selecting better epitopes for immunogenic studies and the design of a vaccine for COVID-19. Metabolites in SARS-CoV-2 patients were analyzed by NMR and mass spectrometry with the observations of an increase in the α-1-acid glycoprotein, an increased kynurenine/tryptophan ratio, low total and HDL apolipoprotein A1, low HDL triglycerides, high LDL and VLDL triglycerides, elevated glutamine/glutamate, and Fischer's ratios that are consistent with diabetes, coronary artery disease, and liver dysfunction risk (Kimhofer et al.) . By using NMR spectroscopy, Loo et al. reported that inactivation by heat causes the degradation of lipoproteins and changes in various metabolic information in SARS-CoV-2-infected plasma samples. Saunders et al. described the coronavirus-specific web portal (https:// metatryp-coronavirus.whoi.edu/) in METATRY V2.0 that can be used for coronavirus proteomics research. This web portal is helpful for finding peptide biomarkers and specific taxonomic groups. Published: November 6, 2020 Rosa-Fernandes et al. reported a method to study the ocular surface proteome, especially for infants exposed to the Zika virus during the gestation period without early clinical symptoms, and named it the cellular imprinting proteomic assay (CImPA). In the conjunctival epithelium of infants exposed to the Zika virus, neutrophil, eosinophil infiltration, and degranulation were detected by this proteomic assay. Furthermore, virus-like particles (VLPs) have been applied in vaccine therapies. Lavado-Garcı́a et al. used quantitative proteomics to identify the changes in the secretome of VLPs and the coproduction of extracellular vesicles (EVs) under different conditions, including nontransfected and transfected with and without plasmid coding for HIV-1 Gag polyprotein. Interestingly, a computational method was used to find an allosteric site on the SARS-CoV-2 spike protein by Di Paola et al., as its detection would weaken the spike−ACE2 interaction and thereby reduce the viral infection. Another study by Verkhivker suggests that the spike protein of SARS-CoV-2 may function as an allosteric regulatory engine fluctuating between dynamic functional states. Hadi-Alijanvand and Rouhani reported the higher binding affinity of the closed state of ACE2 for the S1 protein of SARS-CoV-2 compared with the open state of ACE2 by using a computational approach. Furthermore, Nadeau et al. used a computational approach to study the SARS-CoV-2-interacting human proteins using the GoNet algorithm. Using a ferret model for the H1N1 2009 pandemic influenza A virus, Chen et al. reported the host glycomic response and its age-dependent severity. They suggested that a high level of mannose may be related to the severity of the influenza A virus due to the overactive innate immune system. In the case of the Ebola virus, Banerjee and Mitra proposed the tetrameric assembly model to the VP35 protein and suggested that the Cterminal of VP35 interacts with human protein kinase R to stop its autophosphorylation. This Special Issue provides a platform to understand pandemic diseases. Here several topics have been encouraged that connect proteomics and pandemic diseases, including proteomic technologies, biomarker discovery, pathogenesis, mechanistic details of proteins, protein−protein interactions, signaling pathways, post-translational modifications, computational proteomics, prevention and vaccination, drug repurposing, and therapeutic agents and their mode of action. It will be thrilling to find the bridge between proteomics and pandemic diseases, especially for COVID-19. Proteomics and Informatics for Understanding Phases and Identifying Biomarkers in COVID-19 Disease Computational Immune Proteomics Approach to Target COVID-19 Techniques and Strategies for Potential Protein Target Discovery and Active Pharmaceutical Molecule Screening in a Pandemic Utility of Proteomics in Emerging and Re-Emerging Infectious Diseases Caused by RNA Viruses SARS-CoV-2-Encoded Proteome and Human Genetics: From Interaction-Based to Ribosomal Biology Impact on Disease and Risk Processes Molecular Basis of SARS-CoV-2 Infection and Rational Design of Potential Antiviral Agents: Modeling and Simulation Approaches Targeting Proteases for Treating COVID-19 A Chain Only as Strong as Its Weakest Link": An Up-to-Date Literature Review on the Bidirectional Interaction of Pulmonary Fibrosis and COVID-19 Rapid Response to Pandemic Threats: Immunogenic Epitope Detection of Pandemic Pathogens for Diagnostics and Vaccine Development Using Peptide Microarrays A Novel Strategy for the Development of Vaccines for SARS-CoV-2 (COVID-19) and Other Viruses Using AI and Viral Shell Disorder The COVID-19 Pandemic from a Human Genetic Perspective Perspective on Proteomics for Virus Detection in Clinical Samples Mass-Spectrometric Detection of SARS-CoV-2 Virus in Scrapings of the Epithelium of the Nasopharynx of Infected Patients via Nucleocapsid N Serum Proteomics in COVID-19 Patients: Altered Coagulation and Complement Status as a Function of IL-6 Level Quantitative In-Vitro Diagnostic NMR Spectroscopy for Lipoprotein and Metabolite Measurements in Plasma and Serum: Recommendations for Analytical Artefact Minimization with Special Reference to COVID-19/SARS-CoV-2 Samples Evidence of Structural Protein Damage and Membrane Lipid Remodeling in Red Blood Cells from COVID-19 Patients Quantitative Proteomic Analysis of Porcine Intestinal Epithelial Cells Infected with Porcine Deltacoronavirus Using iTRAQ-Coupled LC-MS/MS Age-Dependent Glycomic Response to the 2009 Pandemic H1N1 Influenza Virus and Its Association with Disease Severity Cellular Imprinting Proteomics Assay: A Novel Method for Detection of Neural and Ocular Disorders Applied to Congenital Zika Virus Syndrome Ebola Virus VP35 Protein: Modeling of the Tetrameric Structure and an Analysis of Its Interaction with Human PKR Shell Disorder Analysis Suggests That Pangolins Offered a Window for a Silent Spread of an Attenuated SARS-CoV-2 Precursor among Humans Computational Identification of Human Biological Processes and Protein Sequence Motifs Putatively Targeted by SARS-CoV-2 Proteins Using Protein−Protein Interaction Networks Interaction of Drug Candidates with Various SARS-CoV-2 Receptors: An in Silico Study to Combat COVID-19 The Discovery of a Putative Allosteric Site in the SARS-CoV-2 Spike Protein Using an Integrated Structural/ Dynamic Approach Molecular Simulations and Network Modeling Reveal an Allosteric Signaling in the SARS-CoV-2 Studying the Effects of ACE2 Mutations on the Stability, Dynamics, and Dissociation Process of SARS-CoV-2 S1/hACE2 Complexes Maffucci, I.; Contini, A. In Silico Drug Repurposing for SARS-CoV-2 Main Proteinase and Spike Proteins Biological Rationale for the Repurposing of BCG Vaccine against SARS-CoV-2 Deciphering the Structural Enigma of HLA Class-II Binding Peptides for Enhanced Immunoinformatics-based Prediction of Vaccine Epitopes Repurposing of FDA-Approved Toremifene to Treat COVID-19 by Blocking the Spike Glycoprotein and NSP14 of SARS-CoV-2 Molecular Binding Mechanism and Pharmacology Comparative Analysis of Noscapine for Repurposing against SARS-CoV-2 Protease Nucleotide Analogues as Inhibitors of SARS-CoV-2 Polymerase, a Key Drug Target for COVID-19 Structural Insights into the Binding Modes of Viral RNA-Dependent RNA Polymerases Using a Function-Site Interaction Fingerprint Method for RNA Virus Drug Discovery Integrative Modeling of Quantitative Plasma Lipoprotein, Metabolic, and Amino Acid Data Reveals a Multiorgan Pathological Signature of SARS-CoV-2 Infection Theoretical Insights into the Anti-SARS-CoV-2 Activity of Chloroquine and Its Analogs and In Silico Screening of Main Protease Inhibitors METATRYP v 2.0: Metaproteomic Least Common Ancestor Analysis for Taxonomic Inference Using Specialized Sequence Assemblies−Standalone Software and Web Servers for Marine Microorganisms and Coronaviruses