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. 2022 Jan 20;12(5):2741–2750. doi: 10.1039/d1ra07447d

The interactions that were established upon docking the guanosine triphosphate and its derivatives into the SARS-CoV-2 RdRp active site. Docking scores are calculated using AutoDock Vina software, while PLIP is used to get the interactions established. The interactions of positive (sofosbuvir, remdesivir, and ribavirin) and negative (cinnamaldehyde and thymoquinone) control compounds are listed as well in the table.

Compound AutoDock score (kcal mol−1) H-Bonding/salt bridges Hydrophobic interaction
No. Amino acids involved No. Amino acids involved
GTP −8 16 Y619, D623, N691, S759(2), D760(2), D761(2), A762, V763, W800, E811(2), C813, S814 2 D760, D761
Sofosbuvir −7.5 7 R555, D618, C622, D761, E811, C813, S814 1 K621
Remdesivir −7.5 12 T246(3), T248, R249, T462(2), M463, D760, N790, N791(2) 3 T246, M463(2)
Ribavirin −7.3 10 R555(2), W617, D618, D761(2), A762, W800, C813, S814 0 —
10 phenyl −7.7 11 D760, D761(4), W800, E811(2), C813, S814(2) 0 —
C12 −7.8 16 R555, C622, D623, S682(2), A685, T687, A688, N691, S759, D760, D761(2), E811, C813, S814 1 A688
graphic file with name d1ra07447d-t1.jpg −7.9 12 D623, N691, S759, D760(5), D761, W800, H810, E811 2 L758(2)
graphic file with name d1ra07447d-t2.jpg −8 6 W617, Y619, D623, S682, N691, A762 3 Y619, D623, N691
C15 −7.7 10 D618, K621, D623, R624, R624, Y680(2), D760(2), D761 1 E811
C16 −7.9 6 R555, W617, D760, E811, S814(2) 2 Y619, D760
C17 −7.8 9 R555(3), D618, K621(2), R624, T680, D760 0 —
C18 −8.1 7 R555, 617W, 621K, 623D(2), D761 0 —
C19 −7.9 12 K621, C622, D623(2), D761(2), W800, E811(2), C813, S814(2) 2 Y619, D760
C30 −7.8 8 R553, W617(2), Y619, D761(2), A762, W800 1 D760
C31 −7.8 5 D623, D760, E811(2), C813 1 D761
C32 −7.9 10 Y619, K621, R624(2), S682, N691, S759(2), D760, D761 1 R555
C33 −7.6 8 K551, R555, D618, D760, W800, H810(2), E811 2 D760, D761
C34 −7.9 6 D760(2), D761(2), K798, S814 4 Inline graphic, D761, K798, E811
C35 −7.8 7 D761, A762, W800, H810, E811(3) 2 D760, D761
C36 −7.9 11 D618, K621, C622, D623, S682(2), N691, S759, D761(3) 4 I589(2), L758(2)
C37 −7.9 8 R555(2), R624, T680, S681, S682, D760(2) 2 N691, D760
C38 −7.9 11 W617, Y619(2), D760, D761(3), A762, W800, E811(2) 1 D760
C39 −7.7 7 R555, R624, Y680(2), S682, S759, D760 5 Y619, D623(2), N691, D760
Cinnamaldehyde −5 3 C813, S814(2) 3 D761, V763, F812
Thymoquinone −5.3 2 C813, S814 2 V763, E811