Table 2:

Calculated binding free energy of notable miniprotein therapeutic candidates with wild-type and N501Y spike proteins.

Protein	LCB1	LCB3	CTC-445.2
Experimental $K_{\text{d}}\left(\text{WT}\right)\left(\text{nM}\right)$	0.50a	0.82a	21b
${\Delta \text{G}}_{\text{PB}}\left(\text{WT}\right)(\text{kcal}/\text{mol})$ c	−83.0	−85.6	−75.3
${\Delta \text{G}}_{\text{PB}}\left(\text{N}501\text{Y}\right)(\text{kcal}/\text{mol})$ d	−58.9	−58.7	−63.2
$\Delta \Delta {\text{G}}_{\text{PB}}(\text{kcal}/\text{mol})$ e	−24.0	−26.9	−12.0
${\Delta \text{G}}_{\exp }\left(\text{WT}\right)(\text{kcal}/\text{mol})$ f	−12.8	−12.5	−10.5
${\Delta \text{G}}_{\text{corr}}\left(\text{WT}\right)(\text{kcal}/\text{mol})$ g	−12.3	−13.0	−10.2
${\Delta \text{G}}_{\text{corr}}\left(\text{N}501\text{Y}\right)(\text{kcal}/\text{mol})$ h	−5.9	−5.9	−7.1
$\Delta \Delta {\text{G}}_{\text{corr}}(\text{kcal}/\text{mol})$ i	6.4	7.1	3.2
Predicted fold Change of $K_{\text{d}}$j	43,000	154,000	200
Predicted $K_{\text{d}}\left(\text{N}501\text{Y}\right)\left(\mu \text{M}\right)$k	21	126	4.2

^aEstimated $K_{\text{d}}$ values for miniproteins obtained from Cao et al. BLI experiments.⁷

^bReported $K_{\text{d}}$ value against wild-type spike protein.⁵⁰

^cDirectly calculated binding free energy of system with the given protein and the wild-type spike protein without empirical correction.

^dDirectly calculated binding free energy of system with the given protein and the N501Y spike protein without empirical correction.

^eDifference between wild-type and N501Y spike binding affinities for given protein.

^fExperimental binding affinity converted to Gibbs binding free energy: $\Delta {\text{G}}_{\exp }=-\text{RT}ln\left(K_{\text{d}}\right)$.

^gCalculated binding free energy of the protein/wild-type spike system (corrected from the directly calculated binding free energy ${\Delta \text{G}}_{\text{PB}}$) using Eq. (1).

^hCalculated binding free energy of the protein/N501Y spike system (corrected from the directly calculated binding free energy ${\Delta \text{G}}_{\text{PB}}$) using Eq. (1).

ⁱDifference between wild-type and N501Y spike corrected binding affinities for given protein: $\Delta \Delta {\text{G}}_{\text{corr}}=\Delta {\text{G}}_{\text{corr}}\left(\text{N}501\text{Y}\right)-\Delta {\text{G}}_{\text{corr}}\left(\text{WT}\right)$.

^jPredicted fold change of K_d (from the binding affinity of given protein with wild-type spike to that with the N501Y mutant) converted from $\Delta \Delta {\text{G}}_{\text{corr}}$.

^kPredicted $K_{\text{d}}$ for given protein binding with the N501Y spike using the original $K_{\text{d}}$ for wild-type spike and the predicted fold change.