Table 1.
Binding phenomenological coefficients and Gibbs energies of binding of various SARS-CoV-2 strains. The reference column gives references from which the values of on-rate constant, kon, off-rate constant, koff, dissociation constant, KD, and temperature T were taken. In all the references, KD was calculated from kon and koff, using the equation KD = koff /kon. The data reported by Laffeber et al., (2021) and Augusto et al., (2021) were collected at 25 °C, while the data from Barton et al., (2021) were collected at 37 °C. These data were used to calculate the binding phenomenological coefficients, LB, binding constant, KB, and standard Gibbs energy of binding, ΔBG⁰, using equations (16), (17), (18), respectively. The LB values have been multiplied by 1018, to make comparison easier. Zhang et al., (2021) reported the dissociation equilibrium constant of the Omicron strain to be 8.85 nM. Based on this value, equation (17) was used to determine the binding constant, KB, which was found to be 1.13 ∙ 10+8 M−1. The binding constant was used to find standard Gibbs energy of binding, ΔBG⁰, which was found to be −45.96 kJ/mol for the Omicron strain. Moreover, ΔBG⁰ values of all the strains are more negative at 25 °C than at 37 °C. This is in good agreement with the negative standard entropies of binding in Table 2, Table 3, which give the temperature dependence of ΔBG⁰, according to the equation (∂G/∂T)p = - S (Atkins and de Paula, 2011, 2014).
| Mutations | kon (M−1s−1) | koff (s−1) | KD (M) | T (°C) | Reference | LB ∙ 1018 (mol2 K /J s dm³) | KB (M−1) | ΔBG⁰ (kJ/mol) |
|---|---|---|---|---|---|---|---|---|
| Wild type (Hu-1) | 4.50E+05 | 7.80E-03 | 1.70E-08 | 25 | Laffeber et al., 2021 | 16.05 | 5.88E+07 | −44.35 |
| N501Y | 5.70E+05 | 1.30E-03 | 2.40E-09 | 25 | Laffeber et al., 2021 | 2.87 | 4.17E+08 | −49.20 |
| E484K | 8.90E+05 | 1.10E-02 | 1.30E-08 | 25 | Laffeber et al., 2021 | 24.27 | 7.69E+07 | −45.01 |
| K417 N | 3.50E+05 | 2.40E-02 | 7.50E-08 | 25 | Laffeber et al., 2021 | 55.07 | 1.33E+07 | −40.67 |
| E484K/N501Y | 1.10E+06 | 1.50E-03 | 1.40E-09 | 25 | Laffeber et al., 2021 | 3.23 | 7.14E+08 | −50.54 |
| K417 N/E484K/N501Y | 7.60E+05 | 4.30E-03 | 5.80E-09 | 25 | Laffeber et al., 2021 | 9.25 | 1.72E+08 | −47.01 |
| Wild type (Hu-1) | 1.50E+05 | 3.20E-03 | 2.13E-08 | 25 | Augusto et al. (2021) | 6.70 | 4.69E+07 | −43.79 |
| E484K | 1.60E+05 | 3.10E-03 | 1.97E-08 | 25 | Augusto et al. (2021) | 6.61 | 5.08E+07 | −43.98 |
| L452R/E484Q | 7.20E+05 | 3.30E-03 | 4.60E-09 | 25 | Augusto et al. (2021) | 6.95 | 2.17E+08 | −47.59 |
| N440K | 3.10E+05 | 3.10E-03 | 9.90E-09 | 25 | Augusto et al. (2021) | 6.44 | 1.01E+08 | −45.69 |
| Wild type (Hu-1) | 9.00E+05 | 6.68E-02 | 6.26E-08 | 37 | Barton et al. (2021) | 118.20 | 1.60E+07 | −42.77 |
| K417 N | 4.90E+05 | 1.77E-01 | 3.49E-07 | 37 | Barton et al. (2021) | 358.76 | 2.87E+06 | −38.34 |
| K417T | 5.50E+05 | 1.26E-01 | 2.26E-07 | 37 | Barton et al. (2021) | 260.77 | 4.42E+06 | −39.46 |
| S477 N | 8.10E+05 | 3.48E-02 | 4.26E-08 | 37 | Barton et al. (2021) | 72.39 | 2.35E+07 | −43.76 |
| E484K | 1.54E+06 | 8.18E-02 | 5.26E-08 | 37 | Barton et al. (2021) | 169.94 | 1.90E+07 | −43.22 |
| N501Y (Alpha) | 1.59E+06 | 1.11E-02 | 5.50E-09 | 37 | Barton et al. (2021) | 18.35 | 1.82E+08 | −49.04 |
| K417 N/E484K | 1.02E+06 | 2.51E-01 | 2.51E-07 | 37 | Barton et al. (2021) | 537.10 | 3.98E+06 | −39.19 |
| K417T/E484K | 1.10E+06 | 1.68E-01 | 1.47E-07 | 37 | Barton et al. (2021) | 339.23 | 6.80E+06 | −40.57 |
| E484K/N501Y (UK2) | 2.33E+06 | 1.18E-02 | 3.70E-09 | 37 | Barton et al. (2021) | 18.09 | 2.70E+08 | −50.06 |
| K417 N/E484K/N501Y (Beta) | 1.46E+06 | 2.91E-02 | 1.74E-08 | 37 | Barton et al. (2021) | 53.29 | 5.75E+07 | −46.07 |
| K417T/E484K/N501Y (Gamma) | 1.56E+06 | 2.11E-02 | 1.22E-08 | 37 | Barton et al. (2021) | 39.93 | 8.20E+07 | −46.99 |