Comparison of computed relative MM interaction energies of known inhibitors to the SARS-CoV-2 M^pro deriving from crystal structures 6Y2F and 6LU7 (ref. 12 and 14).

Inhibitor	Formula: P5–P4–P3–P2–P1–P1′	ΔΔEint,MMa [kcal mol−1]	M w b [g mol−1]	IC50expc SARS-CoV (2003) Mpro [μM]	IC50expd SARS-CoV-2 (2019/20) Mpro [μM]
13ae,f		4.4	583.7	—	2.39
13bf		0.0i	591.7	0.90	0.67
N3g		−4.1	680.8	—	—
11nh		7.6	532.6	0.33	—
11rf,h		5.6	572.7	0.71	0.18

^aRelative interaction energy taken with respect to the reference inhibitor 13b was calculated by molecular mechanics (MM-OPLS3e) in solution: ΔΔE_int,MM = ΔE_int,MM(I_x) − ΔE_int,MM(13b) = [E_tot,MM{M^pro–I_x}_aq − E_tot,MM{M^pro}_aq − E_tot,MM{I_x}_aq] − ΔE_int,MM(13b), where E_tot,MM is total energy of solvated enzyme-inhibitor complex {M^pro–I_x}_aq, solvated enzyme {M^pro}_aq, or solvated inhibitor {I_x}_aq.^35–38 The relative interaction energy ΔΔE_int,MM describes changes in bonding and non-bonding components of potential energy of the enzyme and inhibitor upon the enzyme-inhibitor complex formation.

^bMolar mass.

^cHalf-maximal inhibitory concentration determined in enzyme-inhibition assay for the M^pro of SARS-CoV from the 2003 outbreak.^14,23

^dHalf-maximal inhibitory concentration determined in enzyme-inhibition assay for the M^pro of SARS-CoV-2 from the 2019/20 outbreak.¹²

^eInteraction energy of irreversible Michael acceptor or α-ketoamide inhibitors was computed after breaking the covalent bond of the P1 residue to the catalytic Cys145.

^fTaken from ref. 12.

^gTaken from ref. 14.

^hTaken from ref. 23.

ⁱThe 13b was used as the reference inhibitor in all calculations of the relative interaction energy ΔΔE_int,MM.