Table 1.
Molecular docking results and thermodynamic parameters of the natural products binding to the S1 domain of SARS-CoV-2 spike protein.
| Compound | The binding energy (kcal/mol) of Molecular docking calculation |
The thermodynamic parameters of ITC binding assaya |
|||||||
|---|---|---|---|---|---|---|---|---|---|
| ACE2-free spike protein | spike-ACE2 complex protein |
ΔS (J/mol·K) | -TΔS (kJ/mol) | ΔH (kJ/mol) | ΔG (kJ/mol) | n | c | Kd (μM) | |
| Dioscin (TDEC2019CA001572) | −8.8 | −8.9 | 110.6 | −32.98 | −3.153 | −36.13 | 5.488 | 117.3 | 0.468 |
| Cephalinone D (TDEC2020CN000221) | −8.1 | −8.7 | 33.45 | −9.972 | −20.62 | −30.59 | 0.333 | 0.8 | 4.371 |
| Celastrol (TDEC2019CA001707) | −8.9 | −8.3 | 667.9 | −199.1 | 166.2 | −32.92 | 1.409 | 8.2 | 1.712 |
| Saikosaponin C (TDEC2019CA001664) | −8.6 | −9.1 | 476.6 | −142.1 | 112.5 | −29.55 | 2.802 | 4.2 | 6.65 |
| Epimedin C (TDEC2019CA001733) | −8.2 | −8.1 | 379.0 | −113.0 | 81.37 | −31.64 | 2.967 | 10.4 | 2.86 |
| Epimedin C (TDEC2019CA001733) | −8.2 | −8.1 | 383.30 | −114.30 | 82.65 | −31.62 | 2.965 | 10.2 | 2.908 |
| Candidine (TDEC2020CN000246) | −9.0 | −9.8 | −243.4 | 72.58 | −100 | −27.42 | 0.115 | 0.1 | 15.7 |
| Torvoside K (TDEC2019CN000617) | −8.8 | −8.3 | −130.8 | 39.01 | −69.97 | −30.96 | 2.823 | 7.5 | 3.761 |
| Amentoflavone (TDEC2019CA001644) | −8.5 | −9.1 | −172.7 | 51.48 | −82.13 | −30.65 | 2.731 | 6.4 | 4.27 |
a
1 kcal = 4.1868 kj.