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Table 3 Effects of epitopic missense variants on TNFA-certolizumab pegol interaction

From: Missense variants in the TNFA epitopes and their effects on interaction with therapeutic antibodies—in silico analysis

SNP_ID Amino acid positiona Amino acid change ∆∆G (Kcal/mol)b Antibody chains MutaBindb PPcheck
mCSM-PPI2 SAAMBE-3D MutaBind ∆∆G (kcal/mol) Total stabilizing energy (kJ/mol)
WT H − 269.69
L − 152.18
rs1298153213 45 D>N − 0.619 0.95 0.61 H 0.98 − 277.93
L 0.46 − 152.11
rs373646181 85 V>F − 1.58 0.01 0.7 H 0.97 − 271.68
L 0.54 − 152.18
rs778731236 85 V>G 0.416 1.55 0.99 H 1.08 − 266.54
L 0.47 − 152.18
rs373646181 85 V>I 0.339 0.53 0.79 H 1.01 − 274.09
L 0.48 − 152.17
rs376368223 131 R>Q − 0.078 0.94 2.31 H 2.52 − 236.86
L 0.57 − 152.06
rs777545571 135 E>G 0.784 0.67 2.25 H 1.03 − 269.49
L 1.98 − 145.12
rs758189183 135 E>K 1.119 0.67 1.86 H 0.92 − 279.21
L 1.74 − 157.25
rs770509340 138 R>Q 0.026 2.25 1.77 H 0.41 − 269.36
L 1.96 − 120.82
rs141307820 138 R>W 0.652 1.53 2.19 H 0.51 − 269.49
L 2.42 − 142.18
rs370893734 140 D>N 0.64 0.75 0.64 H 0.42 − 269.56
L 0.88 − 147.77
rs370893734 140 D>Y − 0.122 0.25 0.92 H 0.74 − 269.58
L 1.21 − 149.7
  1. aAmino acid positions were calculated excluding the signal peptide (76 amino acids)
  2. bPositive values of ∆∆G indicate decreasing affinity