Journal: Molecular Informatics

Article Title: Screening of Clinically Approved and Investigation Drugs as Potential Inhibitors of SARS‐CoV‐2: A Combined in silico and in vitro Study

doi: 10.1002/minf.202100062

Figure Lengend Snippet: Box and Whisker plot representation of MM/GBSA scores of selected hit compounds at the SARS‐CoV‐2 Main Protease target. In the plots, central line in box represents median, bottom line of box is first quartile (25 %), top line of box is third quartile (75 %), bottom of whiskers is first quarter minus 1.5× interquartile range, top of whiskers is third quarter plus 1.5× interquartile range, and dots are outliers.

Article Snippet: Two different inhibitor screening assay kits against Spike protein were used as ACE2:SARS‐CoV‐2 Spike S1 (#79945) and SARS‐CoV‐2 Spike:ACE2 (Cat. #79931), (BPS Bioscience).

Techniques: Whisker Assay

Journal: Molecular Informatics

Article Title: Screening of Clinically Approved and Investigation Drugs as Potential Inhibitors of SARS‐CoV‐2: A Combined in silico and in vitro Study

doi: 10.1002/minf.202100062

Figure Lengend Snippet: Box and Whisker plot representation of MM/GBSA scores of selected hit compounds at the SARS‐CoV‐2 Spike/ACE2 target. In the plots, central line in box represrents median, bottom line of box is first quartile (25 %), top line of box is third quartile (75 %), bottom of whiskers is first quarter minus 1.5× interquartile range, top of whiskers is third quarter plus 1.5× interquartile range, and dots are outliers.

Article Snippet: Two different inhibitor screening assay kits against Spike protein were used as ACE2:SARS‐CoV‐2 Spike S1 (#79945) and SARS‐CoV‐2 Spike:ACE2 (Cat. #79931), (BPS Bioscience).

Techniques: Whisker Assay

Journal: Molecular Informatics

Article Title: Screening of Clinically Approved and Investigation Drugs as Potential Inhibitors of SARS‐CoV‐2: A Combined in silico and in vitro Study

doi: 10.1002/minf.202100062

Figure Lengend Snippet: Change in SARS‐CoV‐2 Spike/ACE2 binding with different inhibitor concentrations. The compound was tested at least with four replicates. Mean and standard deviation results were provided at the figure.

Article Snippet: Two different inhibitor screening assay kits against Spike protein were used as ACE2:SARS‐CoV‐2 Spike S1 (#79945) and SARS‐CoV‐2 Spike:ACE2 (Cat. #79931), (BPS Bioscience).

Techniques: Binding Assay, Standard Deviation

Journal: Bioorganic Chemistry

Article Title: Synthesis of novel calcium channel blockers with ACE2 inhibition and dual antihypertensive/anti-inflammatory effects: A possible therapeutic tool for COVID-19

doi: 10.1016/j.bioorg.2021.105272

Figure Lengend Snippet: Effect of synthetized derivatives on ACE2:SARS-CoV-2 Spike (RBD) inhibition.

Article Snippet: In order to measure Angiotensin-Converting Enzyme 2 (ACE2) receptor inhibition activity, the ACE2:SARS-CoV-2 Spike (RBD) Inhibitor Screening Colorimetric Assay Kit # 78031 (Bps Bioscience, Cornerstone Court W, Ste B San Diego, CA 92121) was used.

Techniques: Inhibition

Journal: Bioorganic Chemistry

Article Title: Synthesis of novel calcium channel blockers with ACE2 inhibition and dual antihypertensive/anti-inflammatory effects: A possible therapeutic tool for COVID-19

doi: 10.1016/j.bioorg.2021.105272

Figure Lengend Snippet: SAR for the most potent compounds. DHPMs: Dihydropyrimidines, CCBs: calcium channel blockers, ACE2: Angiotensin-converting enzyme 2, THP-1: Human monocytic cell line, IL-6: Interleukine-6, LPS: Lipopolysaccharide, CRP: C-Reactive Protein.

Article Snippet: In order to measure Angiotensin-Converting Enzyme 2 (ACE2) receptor inhibition activity, the ACE2:SARS-CoV-2 Spike (RBD) Inhibitor Screening Colorimetric Assay Kit # 78031 (Bps Bioscience, Cornerstone Court W, Ste B San Diego, CA 92121) was used.

Techniques:

Journal: Life

Article Title: 1,2,3-Triazole-Benzofused Molecular Conjugates as Potential Antiviral Agents against SARS-CoV-2 Virus Variants

doi: 10.3390/life12091341

Figure Lengend Snippet: Three-dimensional binding mode of compound 9 (green) at the binding interface between the SARS-CoV-2 S-RBD (red) and human ACE2 (blue).

Article Snippet: SARS-CoV-2 assay kit (SARS-CoV-2 Assay Kit, Biosource, Muskego, WI, USA) and the Omicron variant Spike RBD inhibitor screening kits (B.1.1.529 BA.1, Omicron Variant Assay Kit, BPS Bioscience, San Diego, CA, USA) were used to evaluate the anti-SARS-CoV-2 activity in vitro.

Techniques: Binding Assay

Journal: Vaccines

Article Title: In Silico and In Vitro Evaluation of the Molecular Mimicry of the SARS-CoV-2 Spike Protein by Common Short Constituent Sequences (cSCSs) in the Human Proteome: Toward Safer Epitope Design for Vaccine Development

doi: 10.3390/vaccines12050539

Figure Lengend Snippet: Overview of the present study. Common short constituent sequences (cSCSs) between the SARS-CoV-2 spike protein and the human proteome were identified informatically. Based on these cSCSs, anti-cSCS (spike) antibodies were developed against synthetic cSCS peptides. Anti-cSCS (spike) antibodies were tested by ELISA and Western blot analyses. This figure was created with BioRender.com and Adobe Photoshop Elements Version 14.

Article Snippet: To test the ability of antibodies to inhibit the spike-ACE2 interaction (i.e., to test the neutralizing ability of antibodies), we used the SARS-CoV-2 Spike S1/ACE2 Binding Inhibitor Screening Kit (Catalog Number COV-K01; Cosmo Bio, Tokyo, Japan) according to the manufacturer’s instructions.

Techniques: Enzyme-linked Immunosorbent Assay, Western Blot

Journal: Vaccines

Article Title: In Silico and In Vitro Evaluation of the Molecular Mimicry of the SARS-CoV-2 Spike Protein by Common Short Constituent Sequences (cSCSs) in the Human Proteome: Toward Safer Epitope Design for Vaccine Development

doi: 10.3390/vaccines12050539

Figure Lengend Snippet: Three-dimensional structures of the cSCS regions of the SARS-CoV-2 spike protein ( left ) and human proteins ( right ). The cSCSs in the spike protein are shown in red, and those in human proteins are shown in light green (arrows).

Article Snippet: To test the ability of antibodies to inhibit the spike-ACE2 interaction (i.e., to test the neutralizing ability of antibodies), we used the SARS-CoV-2 Spike S1/ACE2 Binding Inhibitor Screening Kit (Catalog Number COV-K01; Cosmo Bio, Tokyo, Japan) according to the manufacturer’s instructions.

Techniques:

Journal: Vaccines

Article Title: In Silico and In Vitro Evaluation of the Molecular Mimicry of the SARS-CoV-2 Spike Protein by Common Short Constituent Sequences (cSCSs) in the Human Proteome: Toward Safer Epitope Design for Vaccine Development

doi: 10.3390/vaccines12050539

Figure Lengend Snippet: Complete amino acid sequence of the SARS-CoV-2 spike protein showing cSCSs and peptide epitopes for anti-cSCS (spike) antibodies. The entire sequence was obtained from NC_045512.2 (RefSeq). Amino acid residues in blue indicate the S1 domain. cSCSs are shown in bold and highlighted in yellow with the names of their corresponding human proteins. Peptides 1, 2, and 3 are boxed and shown in red. The receptor-binding domain (RBD) is enclosed in red lines, with the receptor-binding motif (RBM) shaded in pink. N-linked glycosylation sites are located at 603, 616, 657, 709, 717, 801, 1074, 1098, 1134, 1158, 1173, and 1194.

Article Snippet: To test the ability of antibodies to inhibit the spike-ACE2 interaction (i.e., to test the neutralizing ability of antibodies), we used the SARS-CoV-2 Spike S1/ACE2 Binding Inhibitor Screening Kit (Catalog Number COV-K01; Cosmo Bio, Tokyo, Japan) according to the manufacturer’s instructions.

Techniques: Sequencing, Binding Assay

Journal: Vaccines

Article Title: In Silico and In Vitro Evaluation of the Molecular Mimicry of the SARS-CoV-2 Spike Protein by Common Short Constituent Sequences (cSCSs) in the Human Proteome: Toward Safer Epitope Design for Vaccine Development

doi: 10.3390/vaccines12050539

Figure Lengend Snippet: Inhibitory assay for the spike-ACE2 interaction (ELISA #2 in ). The indicated p -values were obtained by two-sided unpaired Student’s t tests between the samples with the least dilution factor and the samples with “no addition” of a potential inhibitor (control). The error bars indicate the standard deviation. Asterisks indicate statistical significance (***: p < 0.001). ( a ) Inhibitor control (ε-poly-L-lysine). ( b ) Anti-Peptide 1 antibody. ( c ) Anti-Peptide 2 antibody. ( d ) Anti-Peptide 3 antibody. ( e ) Anti-spike antibody (commercial). ( f ) Anti-IL-7 antibody.

Article Snippet: To test the ability of antibodies to inhibit the spike-ACE2 interaction (i.e., to test the neutralizing ability of antibodies), we used the SARS-CoV-2 Spike S1/ACE2 Binding Inhibitor Screening Kit (Catalog Number COV-K01; Cosmo Bio, Tokyo, Japan) according to the manufacturer’s instructions.

Techniques: Enzyme-linked Immunosorbent Assay, Standard Deviation