Interaction of Drug Candidates with Various SARS-CoV-2 Receptors: An in Silico Study to Combat COVID-19.

Abstract:

:The world is currently facing the COVID-19 pandemic caused by the SARS-CoV-2 virus. The pandemic is causing the death of people around the world, and public and social health measures to slow or prevent the spread of COVID-19 are being implemented with the involvement of all members of society. Research institutions are accelerating the discovery of vaccines and therapies for COVID-19. In this work, molecular docking was used to study (in silico) the interaction of 24 ligands, divided into four groups, with four SARS-CoV-2 receptors, Nsp9 replicase, main protease (Mpro), NSP15 endoribonuclease, and spike protein (S-protein) interacting with human ACE2. The results showed that the antimalarial drug Metaquine and anti-HIV antiretroviral Saquinavir interacted with all the studied receptors, indicating that they are potential candidates for multitarget drugs for COVID-19.

journal_name

J Proteome Res

authors

Barros RO,Junior FLCC,Pereira WS,Oliveira NMN,Ramos RM

doi

10.1021/acs.jproteome.0c00327

subject

Has Abstract

pub_date

2020-11-06 00:00:00

pages

4567-4575

issue

11

eissn

1535-3893

issn

1535-3907

journal_volume

19

pub_type

杂志文章
  • Nationwide Health Data Management System: a novel approach for integrating biomarker measurements with comprehensive health records in large populations studies.

    abstract::The nation-wide electronic health record database acts as an interoperable repository of health data obtained throughout citizen contacts with health care providers. This system improves accessibility for citizens and researchers to health data with the ability to assign context to disease development. In that system,...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr1007784

    authors: Sepper R,Ross P,Tiik M

    更新日期:2011-01-07 00:00:00

  • Quantitative profiling of the detergent-resistant membrane proteome of iota-b toxin induced vero cells.

    abstract::Enzyme-mediated 18O/16O differential labeling of proteome samples often suffers from incomplete exchange of the carboxy-terminus oxygen atoms, resulting in ambiguity in the measurable abundance differences. In this study, an 18O/16O labeling strategy was optimized for and applied to the solution-based comparative anal...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr049790s

    authors: Blonder J,Hale ML,Chan KC,Yu LR,Lucas DA,Conrads TP,Zhou M,Popoff MR,Issaq HJ,Stiles BG,Veenstra TD

    更新日期:2005-03-01 00:00:00

  • Fecal Metabolomics as a Novel Noninvasive Method for Short-Term Stress Monitoring in Beef Cattle.

    abstract::Traditional measures of short-term stress response such as fecal glucocorticoid metabolites (FGM) are widely used in controlled settings to quantify the intensity of stimulation to which cattle are exposed. However, FGMs present several methodological and interpretation pitfalls when applied on animals in free-ranging...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.9b00655

    authors: Valerio A,Casadei L,Giuliani A,Valerio M

    更新日期:2020-02-07 00:00:00

  • Phylomat: an automated protein motif analysis tool for phylogenomics.

    abstract::Recent progress in genomics, proteomics, and bioinformatics enables unprecedented opportunities to examine the evolutionary history of molecular, cellular, and developmental pathways through phylogenomics. Accordingly, we have developed a motif analysis tool for phylogenomics (Phylomat, http://alg.ncsa.uiuc.edu/pmat) ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr0499040

    authors: Graham WV,Tcheng DK,Shirk AL,Attene-Ramos MS,Welge ME,Gaskins HR

    更新日期:2004-11-01 00:00:00

  • Deuterium-Free, Three-Plexed Peptide Diethylation for Highly Accurate Quantitative Proteomics.

    abstract::The deuterium, a frequently used stable isotope in isotopic labeling for quantitative proteomics, could deteriorate the accuracy and precision of proteome quantification owing to the retention time shift of deuterated peptides from the hydrogenated counterpart. We introduce a novel three-plexed peptide "diethylation" ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.8b00775

    authors: Jung J,Jeong K,Choi Y,Kim SA,Kim H,Lee JW,Kim VN,Kim KP,Kim JS

    更新日期:2019-03-01 00:00:00

  • Thyroid-state influence on protein-expression profile of rat skeletal muscle.

    abstract::We analyzed the whole-cell protein content of gastrocnemius muscles from rats in different thyroid states. Twenty differentially expressed proteins were unambiguously identified. They were involved in substrates and energy metabolism, stress response, cell structure, and gene expression. This study represents the firs...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr0701299

    authors: Silvestri E,Burrone L,de Lange P,Lombardi A,Farina P,Chambery A,Parente A,Lanni A,Goglia F,Moreno M

    更新日期:2007-08-01 00:00:00

  • Quantitative Proteomics Reveals Potential Crosstalk between a Small RNA CoaR and a Two-Component Regulator Slr1037 in Synechocystis sp. PCC6803.

    abstract::Bacterial small RNAs (sRNAs) and two-component systems (TCSs) were two vital regulatory mechanisms employed by microorganisms to respond to environmental changes and stresses. As a promising "autotrophic cell factory", photosynthetic cyanobacteria have attracted a lot of attention these years. Although most studies fo...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.7b00243

    authors: Sun T,Chen L,Zhang W

    更新日期:2017-08-04 00:00:00

  • Proteomic analysis of lipid microdomains from lipopolysaccharide-activated human endothelial cells.

    abstract::The endothelium plays a critical role in orchestrating the inflammatory response seen during sepsis. Many of the inflammatory effects of Gram-negative sepsis are elicited by lipopolysaccharide (LPS), a glycolipid component of bacterial cell walls. Lipid-rich microdomains have been shown to concentrate components of th...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr049824w

    authors: Karsan A,Blonder J,Law J,Yaquian E,Lucas DA,Conrads TP,Veenstra T

    更新日期:2005-03-01 00:00:00

  • Contribution of proteomics to the study of plant pathogenic fungi.

    abstract::Phytopathogenic fungi are one of the most damaging plant parasitic organisms, and can cause serious diseases and important yield losses in crops. The study of the biology of these microorganisms and the interaction with their hosts has experienced great advances in recent years due to the development of moderm, holist...

    journal_title:Journal of proteome research

    pub_type: 杂志文章,评审

    doi:10.1021/pr200873p

    authors: Gonzalez-Fernandez R,Jorrin-Novo JV

    更新日期:2012-01-01 00:00:00

  • Proteomics reveals that redox regulation is disrupted in patients with ethylmalonic encephalopathy.

    abstract::Deficiency of the sulfide metabolizing protein ETHE1 is the cause of ethylmalonic encephalopathy (EE), an inherited and severe metabolic disorder. To study the molecular effects of EE, we performed a proteomics study on mitochondria from cultured patient fibroblast cells. Samples from six patients were analyzed and re...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr101218d

    authors: Palmfeldt J,Vang S,Stenbroen V,Pavlou E,Baycheva M,Buchal G,Monavari AA,Augoustides-Savvopoulou P,Mandel H,Gregersen N

    更新日期:2011-05-06 00:00:00

  • Poly(glycidyl methacrylate/divinylbenzene)-IDA-FeIII in phosphoproteomics.

    abstract::The study of protein phosphorylation has grown exponentially in recent years, as it became evident that important cellular functions are regulated by phosphorylation and dephosphorylation of proteins on serine, threonine and tyrosine residues. The use of immobilized metal affinity chromatography (IMAC) to enrich phosp...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr050224m

    authors: Aprilita NH,Huck CW,Bakry R,Feuerstein I,Stecher G,Morandell S,Huang HL,Stasyk T,Huber LA,Bonn GK

    更新日期:2005-11-01 00:00:00

  • Comparison of GC-MS and NMR for metabolite profiling of rice subjected to submergence stress.

    abstract::Natural disasters such as drought, extreme temperatures, and flooding can severely impact crop production. Understanding the metabolic response of crops threatened with these disasters provides insights into biological response mechanisms that can influence survival. In this study, a comparative analysis of GC-MS and ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr300953k

    authors: Barding GA Jr,Béni S,Fukao T,Bailey-Serres J,Larive CK

    更新日期:2013-02-01 00:00:00

  • Proteomic analysis of oxidative stress-responsive proteins in human pneumocytes: insight into the regulation of DJ-1 expression.

    abstract::Oxidative injury is believed to play an important role in the pathogenesis of lung diseases such as emphysema and lung cancer. We examined the effects of a classic reactive oxygen species, H 2O 2, on the hydrogen peroxide response proteins (HPRP) in human pneumocytes using comparative two-dimensional gel electrophores...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr800295j

    authors: Duan X,Kelsen SG,Merali S

    更新日期:2008-11-01 00:00:00

  • Self-assembling protein arrays using electronic semiconductor microchips and in vitro translation.

    abstract::Protein arrays will greatly accelerate research and development in medical and biological sciences. We have used cell-free protein biosynthesis and a parallel immobilization strategy for producing protein biochips. We demonstrate a model two-protein microarray using luciferase and green fluorescent protein, both expre...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr0300011

    authors: Oleinikov AV,Gray MD,Zhao J,Montgomery DD,Ghindilis AL,Dill K

    更新日期:2003-05-01 00:00:00

  • Time Course of Molecular and Metabolic Events in the Development of Insulin Resistance in Fructose-Fed Rats.

    abstract::We aimed to determine the time-course of metabolic changes related to the early onset of insulin resistance (IR), trying to evidence breaking points preceding the appearance of the clinical IR phenotype. The model chosen was the fructose (FRU)-fed rat compared to controls fed with starch. We focused on the hepatic met...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.6b00043

    authors: Polakof S,Dardevet D,Lyan B,Mosoni L,Gatineau E,Martin JF,Pujos-Guillot E,Mazur A,Comte B

    更新日期:2016-06-03 00:00:00

  • Mass spectrometric characterization of the surface-associated 42 kDa lipoprotein JlpA as a glycosylated antigen in strains of Campylobacter jejuni.

    abstract::Campylobacter jejuni is the most common cause of bacterial gastroenteritis in the developed world. Immunoproteomics highlighted a 42-45 kDa antigen that comigrated on two-dimensional (2-DE) gels with the C. jejuni major outer membrane protein (MOMP). Predictive analysis revealed two candidates for the identity of the ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr900544x

    authors: Scott NE,Bogema DR,Connolly AM,Falconer L,Djordjevic SP,Cordwell SJ

    更新日期:2009-10-01 00:00:00

  • Protein expression in sputum of smokers and chronic obstructive pulmonary disease patients: a pilot study by CapLC-ESI-Q-TOF.

    abstract::The current report describes the use of CapLC-ESI-Q/TOF-MS for investigating the proteome profiles of hypertonic saline-induced sputum samples from 56 smokers. The severity of their lung disease ranged from normal (healthy smokers) to chronic bronchitis, chronic obstructive pulmonary disease (COPD), and COPD with emph...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr070440q

    authors: Casado B,Iadarola P,Pannell LK,Luisetti M,Corsico A,Ansaldo E,Ferrarotti I,Boschetto P,Baraniuk JN

    更新日期:2007-12-01 00:00:00

  • Characterization of tau in cerebrospinal fluid using mass spectrometry.

    abstract::The neurodegenerative disorder Alzheimer's disease (AD) is the most common cause of dementia in the elderly. The presence of neurofibrillary tangles, consisting of hyperphosphorylated tau protein, is one of the major neuropathologic characteristics of the disease, making this protein an attractive biomarker for AD and...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr7008669

    authors: Portelius E,Hansson SF,Tran AJ,Zetterberg H,Grognet P,Vanmechelen E,Höglund K,Brinkmalm G,Westman-Brinkmalm A,Nordhoff E,Blennow K,Gobom J

    更新日期:2008-05-01 00:00:00

  • Quantitative Proteomic Approaches for Analysis of Protein S-Nitrosylation.

    abstract::S-Nitrosylation is a redox-based post-translational modification of a protein in response to nitric oxide (NO) signaling, and it participates in a variety of processes in diverse biological systems. The significance of this type of protein modification in health and diseases is increasingly recognized. In the central ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章,评审

    doi:10.1021/acs.jproteome.5b00857

    authors: Qu Z,Greenlief CM,Gu Z

    更新日期:2016-01-04 00:00:00

  • Phosphoproteomic analysis of human mesenchymal stromal cells during osteogenic differentiation.

    abstract::Human mesenchymal stromal cells (hMSCs) are promising candidates for cell therapy and tissue regeneration. Knowledge of the molecular mechanisms governing hMSC commitment into osteoblasts is critical to the development of therapeutic applications for human bone diseases. Because protein phosphorylation plays a critica...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr200868p

    authors: Lo T,Tsai CF,Shih YR,Wang YT,Lu SC,Sung TY,Hsu WL,Chen YJ,Lee OK

    更新日期:2012-02-03 00:00:00

  • Replaceable cross-linked polyacrylamide for high performance separation of proteins.

    abstract::An alternative sieving matrix, replaceable cross-linked polyacrylamide (rCPA), was developed for sodium dodecyl sulfate capillary gel electrophoresis (SDS-CGE) separation of proteins. This rCPA could be conveniently pressurized into separation capillaries under a pressure of 80 psi. SDS-CGE separations using this matr...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr0500206

    authors: Lu JJ,Liu S,Pu Q

    更新日期:2005-05-01 00:00:00

  • Systematic analyses of the transcriptome, translatome, and proteome provide a global view and potential strategy for the C-HPP.

    abstract::To estimate the potential of the state-of-the-art proteomics technologies on full coverage of the encoding gene products, the Chinese Human Chromosome Proteome Consortium (CCPC) applied a multiomics strategy to systematically analyze the transciptome, translatome, and proteome of the same cultured hepatoma cells with ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr4009018

    authors: Chang C,Li L,Zhang C,Wu S,Guo K,Zi J,Chen Z,Jiang J,Ma J,Yu Q,Fan F,Qin P,Han M,Su N,Chen T,Wang K,Zhai L,Zhang T,Ying W,Xu Z,Zhang Y,Liu Y,Liu X,Zhong F,Shen H,Wang Q,Hou G,Zhao H,Li G,Liu S,G

    更新日期:2014-01-03 00:00:00

  • Glycomic analyses of glycoproteins in bile and serum during rat hepatocarcinogenesis.

    abstract::Fucosylated alpha-fetoprotein (AFP) is a specific tumor marker for hepatocellular carcinomas (HCC). However, the mechanisms underlying the increase in fucosylated AFP in serum of patients with HCC are largely unknown. Recently, we reported that fucosylation is a possible signal for the secretion of glycoproteins into ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr100414r

    authors: Nakagawa T,Takeishi S,Kameyama A,Yagi H,Yoshioka T,Moriwaki K,Masuda T,Matsumoto H,Kato K,Narimatsu H,Taniguchi N,Miyoshi E

    更新日期:2010-10-01 00:00:00

  • Large-scale quantitative assessment of different in-solution protein digestion protocols reveals superior cleavage efficiency of tandem Lys-C/trypsin proteolysis over trypsin digestion.

    abstract::The complete and specific proteolytic cleavage of protein samples into peptides is crucial for the success of every shotgun LC-MS/MS experiment. In particular, popular peptide-based label-free and targeted mass spectrometry approaches rely on efficient generation of fully cleaved peptides to ensure accurate and sensit...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr300273g

    authors: Glatter T,Ludwig C,Ahrné E,Aebersold R,Heck AJ,Schmidt A

    更新日期:2012-11-02 00:00:00

  • MPK4 Phosphorylation Dynamics and Interacting Proteins in Plant Immunity.

    abstract::Arabidopsis MAP kinase 4 (MPK4) has been proposed to be a negative player in plant immunity, and it is also activated by pathogen-associated molecular patterns (PAMPs), such as flg22. The molecular mechanisms by which MPK4 is activated and regulates plant defense remain elusive. In this study, we investigated Arabidop...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.8b00345

    authors: Zhang T,Schneider JD,Lin C,Geng S,Ma T,Lawrence SR,Dufresne CP,Harmon AC,Chen S

    更新日期:2019-03-01 00:00:00

  • Distinguishing between Spectral Clustering and Cluster Analysis of Mass Spectra.

    abstract::The term "spectral clustering" is sometimes used to refer to the clustering of mass spectrometry data. However, it also classically refers to a family of popular clustering algorithms. To avoid confusion, a more specific term could advantageously be coined. ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.8b00516

    authors: Borges H,Guibert R,Permiakova O,Burger T

    更新日期:2019-01-04 00:00:00

  • On-line concentration of microheterogeneous proteins by capillary electrophoresis using SDS and PEO as additives.

    abstract::In this paper, we describe a method for analyzing large-volume protein samples using capillary electrophoresis in conjunction with laser-induced fluorescence detection (CE-LIF). To improve the stacking and separation efficiencies of proteins, we added either 0.01% sodium dodecyl sulfate (SDS) or 0.01% poly(ethylene ox...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr050298y

    authors: Huang YF,Hsieh MM,Tseng WL,Chang HT

    更新日期:2006-02-01 00:00:00

  • Ferritin heavy chain is the host factor responsible for HCV-induced inhibition of apoB-100 production and is required for efficient viral infection.

    abstract::Hepatic fat export occurs by apolipoprotein B-100-containing lipoprotein production, whereas impaired production leads to liver steatosis. Hepatitis C virus (HCV) infection is associated to dysregulation of apoB-100 secretion and steatosis; however, the molecular mechanism by which HCV affects the apoB-100 secretion i...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr201128s

    authors: Mancone C,Montaldo C,Santangelo L,Di Giacomo C,Costa V,Amicone L,Ippolito G,Pucillo LP,Alonzi T,Tripodi M

    更新日期:2012-05-04 00:00:00

  • Purification and identification of O-GlcNAc-modified peptides using phosphate-based alkyne CLICK chemistry in combination with titanium dioxide chromatography and mass spectrometry.

    abstract::A selective method for the enrichment of O-GlcNAcylated peptides using a novel CLICK chemistry reagent is described. Peptides modified by O-GlcNAc were enzymatically labeled with N-azidoacetylgalactosamine. The azide was then reacted with a phospho-alkyne using CLICK chemistry and O-GlcNAcGalNAzPO(4)-containing peptid...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr100565j

    authors: Parker BL,Gupta P,Cordwell SJ,Larsen MR,Palmisano G

    更新日期:2011-04-01 00:00:00

  • Mycobacterium tuberculosis-specific phagosome proteome and underlying signaling pathways.

    abstract::The phagosome is very important to host immunity and tissue homeostasis maintenance. The destiny of the phagosome is closely associated with the outcome of the pathogen within. Most pathogens are successfully delivered to the lysosome and destroyed via the fusion of the phagosome with the lysosome. Mycobacterium tube...

    journal_title:Journal of proteome research

    pub_type: 杂志文章,评审

    doi:10.1021/pr300125t

    authors: He Y,Li W,Liao G,Xie J

    更新日期:2012-05-04 00:00:00