scholarly journals Molecular characterization of ebselen binding activity to SARS-CoV-2 main protease

2020 ◽  
Vol 6 (37) ◽  
pp. eabd0345 ◽  
Author(s):  
Cintia A. Menéndez ◽  
Fabian Byléhn ◽  
Gustavo R. Perez-Lemus ◽  
Walter Alvarado ◽  
Juan J. de Pablo
Keyword(s):  
Molecular Level ◽  
Protein A ◽  
Strain Analysis ◽  
Binding Activity ◽  
Allosteric Effect ◽  
Surface Loop ◽  
Main Protease ◽  
Site Access ◽  
A Site

There is an urgent need to repurpose drugs against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Recent computational-experimental screenings have identified several existing drugs that could serve as effective inhibitors of the virus’ main protease, Mpro, which is involved in gene expression and replication. Among these, ebselen (2-phenyl-1,2-benzoselenazol-3-one) appears to be particularly promising. Here, we examine, at a molecular level, the potential of ebselen to decrease Mpro activity. We find that it exhibits a distinct affinity for the catalytic region. Our results reveal a higher-affinity, previously unknown binding site localized between the II and III domains of the protein. A detailed strain analysis indicates that, on such a site, ebselen exerts a pronounced allosteric effect that regulates catalytic site access through surface-loop interactions, thereby inducing a reconfiguration of water hotspots. Together, these findings highlight the promise of ebselen as a repurposed drug against SARS-CoV-2.

scholarly journals Biochemical Characterization of Streptococcus pneumoniae Penicillin-Binding Protein 2b and Its Implication in β-Lactam Resistance

2004 ◽  
Vol 48 (5) ◽  
pp. 1848-1855 ◽  
Author(s):  
Estelle Pagliero ◽  
Laurent Chesnel ◽  
Julie Hopkins ◽  
Jacques Croizé ◽  
Otto Dideberg ◽  
...  
Keyword(s):  
Streptococcus Pneumoniae ◽  
Biochemical Characterization ◽  
Protein A ◽  
Strain Analysis ◽  
Penicillin G ◽  
Penicillin Binding Protein ◽  
Class B ◽  
Selection Of

ABSTRACT Extensive use of β-lactam antibiotics has led to the selection of pathogenic streptococci resistant to β-lactams due to modifications of the penicillin-binding proteins (PBPs). PBP2b from Streptococcus pneumoniae is a monofunctional (class B) high-molecular-weight PBP catalyzing the transpeptidation between adjacent stem peptides of peptidoglycan. The transpeptidase domain of PBP2b isolated from seven clinical resistant (CR) strains contains 7 to 44 amino acid changes over the sequence of PBP2b from the R6 β-lactam-sensitive strain. We show that the extracellular soluble domains of recombinant PBP2b proteins (PBP2b*) originating from these CR strains have an in vitro affinity for penicillin G that is reduced by up to 99% from that of the R6 strain. The Thr446Ala mutation is always observed in CR strains and is close to the key conserved motif (S443SN). The Thr446Ala mutation in R6 PBP2b* displays a 60% reduction in penicillin G affinity in vitro compared to that for the wild-type protein. A recombinant R6 strain expressing the R6 PBP2b Thr446Ala mutation is twofold less sensitive to piperacillin than the parental S. pneumoniae strain. Analysis of the Thr446Ala mutation in the context of the PBP2b CR sequences revealed that its influence depends upon the presence of other unidentified mutations.

scholarly journals Purification and partial characterization of four proteins from human parotid saliva

1971 ◽  
Vol 123 (3) ◽  
pp. 455-464 ◽  
Author(s):  
Anders Bennick ◽  
George E. Connell
Keyword(s):  
Serum Proteins ◽  
Protein A ◽  
Gel Filtration ◽  
Binding Activity ◽  
Significant Activity ◽  
Parotid Saliva ◽  
Polyacrylamide Electrophoresis ◽  
Ph Range ◽  
Human Parotid Saliva

Four proteins, which have been designated A, B, C and D, have been purified from human parotid saliva. These proteins are the major constituents of parotid saliva which migrate rapidly to the anode in polyacrylamide electrophoresis at pH9.5. Gel filtration and polyacrylamide electrophoresis were employed in the purification procedures. After purification all four preparations were tested for homogeneity by electrophoresis at pH2.8 and 9.5, by isoelectric focusing in the pH range 3–10, by immunodiffusion, and by sedimentation in the analytical ultracentrifuge. None of the proteins showed significant activity in assays for amylase, acid and alkaline phosphatase, protease, lysozyme, ribonuclease, peroxidase, β-glucuronidase, β-galactosidase, iron-binding activity and esterase. No cross-reactions were detected with antisera specific for lactoferrin and 15 serum proteins. All four proteins were rich in glutamic acid, proline and glycine and were lacking completely the sulphur-containing amino acids. Proteins A and C contained no threonine or tyrosine. Carbohydrate could be demonstrated only in protein A at a concentration of 4% of the total protein.

scholarly journals Analysis of the Mechanism by Which Glucose Inhibits Maltose Induction of MAL Gene Expression in Saccharomyces

Genetics ◽  
2000 ◽  
Vol 154 (1) ◽  
pp. 121-132
Author(s):  
Zhen Hu ◽  
Yingzi Yue ◽  
Hua Jiang ◽  
Bin Zhang ◽  
Peter W Sherwood ◽  
...  
Keyword(s):  
Gene Expression ◽  
Glucose Repression ◽  
Protein A ◽  
The Other ◽  
Maltose Permease ◽  
Inducer Exclusion ◽  
Glucose Inhibition ◽  
Independent Mechanism ◽  
Mal Genes

Abstract Expression of the MAL genes required for maltose fermentation in Saccharomyces cerevisiae is induced by maltose and repressed by glucose. Maltose-inducible regulation requires maltose permease and the MAL-activator protein, a DNA-binding transcription factor encoded by MAL63 and its homologues at the other MAL loci. Previously, we showed that the Mig1 repressor mediates glucose repression of MAL gene expression. Glucose also blocks MAL-activator-mediated maltose induction through a Mig1p-independent mechanism that we refer to as glucose inhibition. Here we report the characterization of this process. Our results indicate that glucose inhibition is also Mig2p independent. Moreover, we show that neither overexpression of the MAL-activator nor elimination of inducer exclusion is sufficient to relieve glucose inhibition, suggesting that glucose acts to inhibit induction by affecting maltose sensing and/or signaling. The glucose inhibition pathway requires HXK2, REG1, and GSF1 and appears to overlap upstream with the glucose repression pathway. The likely target of glucose inhibition is Snf1 protein kinase. Evidence is presented indicating that, in addition to its role in the inactivation of Mig1p, Snf1p is required post-transcriptionally for the synthesis of maltose permease whose function is essential for maltose induction.

scholarly journals In silico characterization of masitinib interaction with SARS‐CoV‐2 main protease

ChemMedChem ◽  
2021 ◽  
Author(s):  
Ulises Martínez-Ortega ◽  
Diego I. Figueroa-Figueroa ◽  
Francisco Hernández-Luis ◽  
Rodrigo Aguayo-Ortiz
Keyword(s):  
In Silico ◽  
Main Protease ◽  
In Silico Characterization

scholarly journals Synthesis and Characterization of a Fullerenol Derivative for Potential Biological Applications

2020 ◽  
Vol 4 (1) ◽  
pp. 15
Author(s):  
Eduardo Ravelo-Nieto ◽  
Alvaro Duarte-Ruiz ◽  
Luis H. Reyes ◽  
Juan C. Cruz
Keyword(s):  
Phase Transfer ◽  
Protein A ◽  
Structural Features ◽  
Cellular Level ◽  
Cellulose Membrane ◽  
Cell Penetration ◽  
Covalent Functionalization ◽  
Dialysis Tubing ◽  
Surface Functionality

Several biological barriers are generally responsible for the limited delivery of cargoes at the cellular level. Fullerenols have unique structural features and possess suitable properties for interaction with the cells. This study aimed to synthesize and characterize a fullerenol derivative with desirable characteristics (size, charge, functionality) to develop cell penetration vehicles. Fullerenol was synthesized from fullerene (C60) solubilized in toluene, followed by hydroxylation with hydrogen peroxide and tetra-n-butylammonium hydroxide (TBAH) as a phase transfer catalyst. The obtained product was purified by a Florisil chromatography column (water as the eluent), followed by dialysis (cellulose membrane dialysis tubing) and freeze-drying (yield 66%). Subsequently, a silane coupling agent was conjugated on the fullerenol surface to render free amine functional groups for further covalent functionalization with other molecules. Characterization via UV–VIS, FTIR-ATR, Raman, DLS, and SEM techniques was conducted to evaluate the composition, size, morphology, surface functionality, and structural properties. We are currently working on the conjugation of the potent cell-penetrating agents Buforin II (BUFII) and the Outer Membrane Protein A (OmpA) on the surface of the fullerenol to estimate whether cell penetration and endosome escape are improved concerning conventional polymeric vehicles and our previous developments with iron oxide nanoparticles.

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