| Literature DB >> 35251340 |
Man Hagiyama1, Fuka Takeuchi1, Aki Sugano2, Azusa Yoneshige1, Takao Inoue1, Akihiro Wada1, Hiroshi Kajiyama1, Yutaka Takaoka3,4, Kenroh Sasaki5, Akihiko Ito1.
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uses its S1 spike protein to bind to angiotensin-converting enzyme 2 (ACE2) on human cells in the first step of cell entry. Tryptanthrin, extracted from leaves of the indigo plant, Polygonum tinctorium, using d-limonene (17.3 µg/ml), is considered to inhibit ACE2-mediated cell entry of another type of coronavirus, HCoV-NL63. The current study examined whether this extract could inhibit the binding of the SARS-CoV-2 spike protein to ACE2. Binding was quantified as cell-bound fluorescence intensity in live cell cultures in which canine kidney MDCK cells overexpressing ACE2 were incubated with fluorescein-labeled S1 spike protein. When indigo extract, together with S1 protein, was added at 8,650x and 17,300x dilutions, fluorescence intensity decreased in a dose- and S1 extract-dependent manner, without affecting cell viability. When 4.0-nM tryptanthrin was added instead of the indigo extract, fluorescence intensity also decreased, but to a lesser degree than with indigo extract. Docking simulation analyses revealed that tryptanthrin readily bound to the receptor-binding domain of the S1 protein, and identified 2- and 7-amino acid sequences as the preferred binding sites. The indigo extract appeared to inhibit S1-ACE2 binding at high dilutions, and evidently contained other inhibitory elements as well as tryptanthrin. This extract may be useful for the prevention or treatment of SARS-CoV-2 infection. Copyright: © Hagiyama et al.Entities:
Keywords: coronavirus disease 2019 prevention; d-limonene; docking simulation; indigo plant; natural product; severe acute respiratory syndrome coronavirus 2 spike protein; tryptanthrin
Year: 2022 PMID: 35251340 PMCID: PMC8892618 DOI: 10.3892/etm.2022.11200
Source DB: PubMed Journal: Exp Ther Med ISSN: 1792-0981 Impact factor: 2.447
Figure 1high performance liquid chromatography analysis of indigo extract. (A) Tryptanthrin standard (10.0 µg/ml). (B) Indigo extract (tryptanthrin content, 17.3 µg/ml).
Figure 2Expression of ACE2 in MDCK cells. (A) Immunofluorescence of untransfected MDCK, MDCK-vector and MDCK-ACE2 cells using an anti-ACE2 antibody (green; upper). In the lower panels, MDCK-ACE2 cells were incubated with indigo extract, tryptanthrin or d-limonene at indicated dilutions or concentrations, together with S1-Fc-fluorescein. Cell nuclei were labeled with DAPI (blue). Merged images of green and blue fluorescent signals are presented (scale bars=50 µm). (B) Western blot analyses of various types of MDCK cells using an anti-ACE2 antibody. An arrowhead indicates ACE2-specific bands. The blot was re-probed with an anti-β-actin antibody to determine the amount of protein loading per lane. (C) WST-8 assays of MDCK cellsin the presence of serially diluted indigo extract. Viability percentages are line-plotted by dots with bars indicating the mean and standard deviation from triplicate wells, respectively. P-values from one-way ANOVA are shown above the graph. aP=0.0168 and bP<0.001 vs. X=0 (absence of extract). ACE2, angiotensin-converting enzyme 2; dil, dilution; MDCK, Madin-Darby canine kidney.
Figure 3Quantification of S1 proteins bound to ACE2 on MDCK cells. (A) MDCK, MDCK-ACE2 and MDCK-vector cells were incubated with S1-Fc-fluorescein (3 µg/ml). In some MDCK-ACE2 cell cultures, either indigo extract or tryptanthrin was also added at indicated dilution rates or concentrations. After one day of incubation and wash, fluorescent intensity of fluorescein remaining on the cells was measured using a confocal laser microscopy system. Representative photomicrographs are presented. Below each image, the mean and standard deviation of the intensity (arbitrary unit) are presented for the corresponding experimental group. aP=1.20x10-13, bP=0.0033 and cP>0.999 vs. MDCK-ACE2 cell intensity; dP=0.0027 vs. tryptanthrin treatment (scale bars=50 µm). (B) In MDCK-ACE2 cell cultures, various ratios of concentrations of indigo extract and S1-Fc-fluorescein were used. The ratio was expressed as 1 under the conditions in A (indigo extract, 17,300-fold dilution; S1-Fc-fluorescein, 3 µg/ml). The ratio (logarithmic in X-axis) and fluorescent intensity (linear in Y-axis) are presented in a scatter plot (n=5 for each ratio group). The dot distribution approximates a linear function (dotted lines). Correlations and statistical significance were analyzed using Spearman's rank test. R2 and P-values are presented. aP=3x10-4 as indicated. ACE2, angiotensin-converting enzyme 2; MDCK, Madin-Darby canine kidney.
Docking results of tryptanthrin-S1 spike protein docking run per 100 times.
| Docking score | |||
|---|---|---|---|
| No. of correct binding models | Mean ± SD | Most stable | Score rankinga |
| 58 | -5.88±0.10 | -6.02 | 26 |
aRank of the most stable docking score.
Docking results of the same binding mode in 58 correct tryptanthrin-S1 spike protein bindings.
| No. of the same binding mode | Amino acids targeted | Docking score (mean ± SD) |
|---|---|---|
| 45 | 455-456 and 488-494 | -5.88±0.02 |
Figure 4Same binding mode of tryptanthrin-S1 docking. Magenta, receptor binding domain; yellow, reported residues contacting to ACE2; blue, amino acids targeted in the same binding mode
Amino acid residues of SARS-CoV-2 S1 spike protein that are involved in binding to ACE2 or tryptanthrin.
| ACE2 amino acids | Tryptanthrin (45 poses) amino acids |
|---|---|
| K417, G446, Y449, Y453, L455a, F456a, A475, F486, N487, Y489a, Q493a, G496, Q498, T500, N501, G502 and Y505 | L455a, F456a E484, G485, C488, Y489a, F490, L492 and Q493a |
aFour residues are common to S1-ACE2 and S1-tryptanthrin binding. For tryptanthrin-S1 docking, the same binding mode was repeated 45 times in 58 correct binding runs (presented in Table I). Binding was defined by proximity of 4 Å between S1 and ACE2 or S1 and tryptanthrin. ACE2, angiotensin-converting enzyme 2.