Identification of new bioactive molecules by computational methods (Appendices)

Appendices Appendix A. Table 1. clogD7.4, pka values and percentage of ionic forms at pH 7.2. Compd clog D7.4 pKa Prevalent Ionic Form (%) 1a-1d 0.02 2.0 ± 0.4 9.3 ± 0.4 ZW(100) 2a-2d 0.04 7.2 ± 0.4 N(49) P(51) 3a-3d 1.41 7.3 ± 0.4 N(47) P(53) 4a-4d 0.76 7.4 ± 0.4 12.1 ± 1.0 N (39) P(61) Table 2. ΔEGM values (kcal/mol) and torsional angle values (degrees) of 1a considering MM conformers within 5 kcal/mol from the global minimum. NH3 O NO Br O abc d e f t1 t2 Frame ΔEGM (kcal/mol) Torsional Angles (°) τ1a τ2b 1 0 80 2 2 0.41 176 -8 3 1.51 -62 2 aτ1: abcd; bτ2: dcef Table 3. ΔEGM values (kcal/mol) and torsional angle values (degrees) of 1b considering MM conformers within 5 kcal/mol from the global minimum. NH3 O NO Br O abc d e f t1 t2 Frame ΔEGM (kcal/mol) Torsional Angles (°) τ1a τ2b 1 0 72 -5 2 1.92 -173 5 3 4.13 -53 3 aτ1: abcd; bτ2: dcef Table 4. ΔEGM values (kcal/mol) and torsional angle values (degrees) of 1c considering MM conformers within 5 kcal/mol from the global minimum. NH3 O NO Br O abc d e f t1 t2 Frame ΔEGM (kcal/mol) Torsional Angles (°) τ1a τ2b 1 0 -72 4 11 1.92 173 -4 23 4.13 53 -3 aτ1: abcd; bτ2: dcef Table 5. ΔEGM values (kcal/mol) and torsional angle values (degrees) of 1d considering MM conformers within 5 kcal/mol from the global minimum. NH3 O NO Br O abc d e f t1 t2 Frame ΔEGM (kcal/mol) Torsional Angles (°) τ1a τ2b 1 0 -80 -2 13 0.41 - 176 10 25 1.51 62 -2 aτ1: abcd; bτ2: dcef Table 6. ΔEGM values (kcal/mol) and torsional angle values (degrees) of 2b considering MM conformers within 5 kcal/mol from the global minimum. NH3 O NO Br O abc d e f gh t1 t2 t3 Frame ΔEGM (kcal/mol) Torsional Angles (°) τ1a τ2b τ3c 1 0 -62 -90 -1 2 0.26 -176 -96 -1 3 0.76 62 -95 -1 4 0.79 -63 95 1 5 1.53 -178 84 1 6 1.99 63 99 1 aτ1: abcd; bτ2: dcef; cτ3: fegh Table 7. ΔEGM values (kcal/mol) and torsional angle values (degrees) of 2c considering MM conformers within 5 kcal/mol from the global minimum. NH3 O NO Br O abc d e f gh t1 t2 t3 Frame ΔEGM (kcal/mol) Torsional Angles (°) τ1a τ2b τ3c 1 0 62 90 1 2 0.26 176 96 1 3 0.76 -62 95 1 4 0.79 63 -95 -1 5 1.53 178 -84 -1 6 1.99 -63 -99 -1 aτ1: abcd; bτ2: dcef; cτ3: fegh Table 8. ΔEGM values (kcal/mol) and torsional angle values (degrees) of 2d considering MM conformers within 5 kcal/mol from the global minimum. NH3 O NO Br O abc d e f gh t1 t2 t3 Frame ΔEGM (kcal/mol) Torsional Angles (°) τ1a τ2b τ3c 1 0 -179 89 1 2 0.16 -66 89 1 3 0.94 -178 -96 -1 4 1.09 -65 -97 -2 5 1.26 61 95 1 6 2.41 62 -94 -1 aτ1: abcd; bτ2: dcef; cτ3: fegh Table 9. ΔEGM values (kcal/mol) and torsional angle values (degrees) of 3b considering MM conformers within 5 kcal/mol from the global minimum. NH3 O NO Br O abc d e f ghj k t1 t2 t3 t4 t5 Frame ΔEGM (kcal/mol) Torsional Angles (°) τ1a τ2b τ3c τ4d τ5e 1 0 -178 82 3 171 -88 2 0.22 -62 -89 -1 -179 -90 3 0.48 -63 -86 -3 -82 106 4 0.48 -176 -96 -1 -179 90 5 0.67 -64 94 2 176 93 6 0.80 -62 -90 -1 85 -105 7 0.81 -179 100 7 96 -91 8 0.83 -64 96 4 84 75 9 0.86 -176 -92 -2 -82 -74 10 0.98 -176 -97 0 84 -106 11 1.02 62 -95 -1 -179 90 12 1.14 -174 -54 -8 -76 -71 13 1.50 -63 95 1 -86 -75 14 1.54 62 -95 0 84 75 15 1.58 62 -93 -1 -84 -75 16 1.77 63 99 2 177 -87 17 1.90 -177 78 0 -89 103 18 2.33 64 106 4 85 73 19 2.65 62 98 1 -86 105 aτ1: abcd; bτ2: dcef; cτ3: fegh; dτ4: eghj; eτ5: ghjk Table 10. ΔEGM values (kcal/mol) and torsional angle values (degrees) of 3c considering MM conformers within 5 kcal/mol from the global minimum. NH3 O NO Br O abc d e f ghj k t1 t2 t3 t4 t5 Frame ΔEGM (kcal/mol) Torsional Angles (°) τ1a τ2b τ3c τ4d τ5e 1 0 178 -82 -3 -171 -91 2 0.22 62 89 1 179 -90 3 0.48 63 86 3 82 74 4 0.48 176 96 1 179 -90 5 0.67 64 -94 -2 -176 -93 6 0.80 62 90 1 -85 105 7 0.81 179 -100 -7 -96 91 8 0.83 64 -96 -4 -84 -75 9 0.86 176 92 2 82 74 10 0.98 176 97 0 -84 106 11 1.02 -62 95 1 179 -90 12 1.14 174 54 8 76 71 13 1.50 63 -95 -1 86 -105 14 1.54 -62 95 0 -85 105 15 1.58 -62 93 1 84 75 16 1.77 -63 -100 -2 -178 -93 17 1.90 177 -78 0 89 76 18 2.33 -64 -106 -4 -85 -73 19 2.65 -62 -98 -1 86 -105 aτ1: abcd; bτ2: dcef; cτ3: fegh; dτ4: eghj; eτ5: ghjk Table 11. ΔEGM values (kcal/mol) and torsional angle values (degrees) of 3d considering MM conformers within 5 kcal/mol from the global minimum. NH3 O NO Br O abc d e f ghj k t1 t2 t3 t4 t5 Frame ΔEGM (kcal/mol) Torsional Angles (°) τ1a τ2b τ3c τ4d τ5e 1 0 -66 -104 -5 -93 95 2 0.08 -64 -91 -4 -168 88 3 0.26 -67 71 6 77 71 4 0.37 -179 89 1 179 -90 5 0.51 -66 89 1 179 -90 6 0.80 -179 87 2 83 74 7 0.93 -179 89 1 -85 -75 8 0.98 -178 -94 -2 -177 -93 9 1.03 -66 90 1 -84 106 10 1.27 -177 -97 -5 -83 -72 11 1.65 61 95 1 179 90 12 1.76 -64 -94 -2 87 -105 13 1.78 -178 -95 -1 86 75 14 2.17 61 95 0 -84 -74 15 2.21 61 93 1 84 75 16 2.22 62 -95 -2 -178 87 17 2.90 62 -100 -3 -86 -75 18 3.16 62 -92 0 86 75 aτ1: abcd; bτ2: dcef; cτ3: fegh; dτ4: eghj; eτ5: ghjk Table 12. ΔEGM values (kcal/mol) and torsional angle values (degrees) of 4b considering MM conformers within 5 kcal/mol from the global minimum. NH3 N H NO Br O abc d e f ghj k t1 t2 t3 t4 t5 Frame ΔEGM (kcal/mol) Torsional Angles (°) τ1a τ2b τ3c τ4d τ5e 1 0 -66 -88 0 -179 -90 2 0.62 61 -90 -1 179 -90 3 0.87 178 -93 -1 179 90 4 1.02 177 87 2 165 95 5 1.65 -66 98 0 174 93 6 1.85 63 100 1 178 -87 7 2.20 -178 -45 -6 -95 -92 aτ1: abcd; bτ2: dcef; cτ3: fegh; dτ4: eghj; eτ5: ghjk Table 13. ΔEGM values (kcal/mol) and torsional angle values (degrees) of 4c considering MM conformers within 5 kcal/mol from the global minimum. NH3 N H NO Br O abc d e f ghj k t1 t2 t3 t4 t5 Frame ΔEGM (kcal/mol) Torsional Angles (°) τ1a τ2b τ3c τ4d τ5e 1 0 66 88 0 179 90 2 0.62 -61 90 1 -179 90 3 0.87 -178 93 1 -179 -90 4 1.02 -177 -87 -2 -165 -95 5 1.65 66 -98 0 -174 -93 6 1.85 -63 -100 -1 -178 87 7 2.20 178 45 6 95 92 aτ1: abcd; bτ2: dcef; cτ3: fegh; dτ4: eghj; eτ5: ghjk Table 14. ΔEGM values (kcal/mol) and torsional angle values (degrees) of 4d considering MM conformers within 5 kcal/mol from the global minimum. Table 22. Non-bond interaction energies (kcal/mol), Cα RMSD (Å) of C153 and H180 calculated with respect to the starting position. χ1 torsion angle of C153 (degrees) and angle values of the hydrogen bond between C153 and H180 (degrees) of the 2d/PfGAPDH complexes obtained by Monte Carlo/Minimization procedure. Complex Binding approach Nonbond interaction energies (kcal/mol) RMSD (C153) RMSD (H180) χ1 (C153) Angle value of the hydrogen bond between C153 and H180 DHAa XDAa 1b BA1 -4.669 0.25 0.49 -59.01 112.63 140.69 2 BA1 6.707 0.43 0.57 -52.56 138.01 103.76 3 BA1 -3.328 0.55 0.53 -68.38 146.55 87.23 4 BA1 -1.624 0.42 0.52 -64.00 139.37 95.65 5 BA1 1.640 0.73 0.48 -90.42 145.59 75.79 6 BA1 27.515 4.85 0.95 73.94 134.68 66.24 7 BA1 26.893 5.09 1.09 68.07 138.51 66.86 8b BA2 -4.486 0.18 0.47 -61.75 110.95 136.36 9 BA2 31.233 0.80 0.44 -84.66 162.98 95.30 10 BA2 1.998 0.44 0.45 -67.82 121.66 134.07 11 BA2 -2.483 0.92 0.79 -73.33 157.78 101.95 12 BA2 6.849 1.54 1.10 -54.08 109.08 88.33 13 BA2 48.071 5.45 1.49 95.08 102.02 78.27 14 BA2 11.591 5.37 1.53 88.93 81.57 89.24 15 BA2 5.159 5.39 1.56 87.53 84.45 97.62 a D: Sγ of C153; A: Nτ of H180; H: Hγ of C153; X: Cβ of C153. bSelected complex. Table 23. Non-bond interaction energies (kcal/mol), Cα RMSD (Å) of C153 and H180 calculated with respect to the starting position. χ1 torsion angle of C153 (degrees) and angle values of the hydrogen bond between C153 and H180 (degrees) of the 3a/PfGAPDH complexes obtained by Monte Carlo/Minimization procedure. Complex Binding approach Nonbond interaction energies (kcal/mol) RMSD (C153) RMSD (H180) χ1 (C153) Angle value of the hydrogen bond between C153 and H180 DHAa XDAa 1 b BA1 -7.548 0.29 0.50 -67.97 114.51 132.53 2 BA1 -1.630 0.38 0.54 -64.30 102.85 102.43 3 BA1 8.123 1.05 0.59 -62.61 124.13 77.21 4 BA1 -0.096 3.27 0.57 -57.42 132.03 67.75 5 BA1 3.763 2.94 0.52 -59.42 130.96 70.23 6 BA1 43.707 5.51 0.95 69.97 143.27 66.76 7b BA2 -8.943 0.15 0.55 -61.13 110.89 131.72 8 BA2 -3.476 0.85 0.54 -95.77 127.36 91.87 9 BA2 -2.418 1.07 0.53 -80.34 121.48 84.06 10 BA2 21.830 2.04 0.40 -49.19 132.99 64.39 11 BA2 20.578 1.91 0.58 -25.09 159.16 86.19 12 BA2 65.453 5.00 1.13 62.44 124.73 59.36 13 BA2 57.282 5.61 1.80 59.74 142.64 91.85 14 BA2 -4.548 5.65 1.98 75.59 146.11 91.45 a D: Sγ of C153; A: Nτ of H180; H: Hγ of C153; X: Cβ of C153. bSelected complex. Table 24. Non-bond interaction energies (kcal/mol), Cα RMSD (Å) of C153 and H180 calculated with respect to the starting position. χ1 torsion angle of C153 (degrees) and angle values of the hydrogen bond between C153 and H180 (degrees) of the 3b/PfGAPDH complexes obtained by Monte Carlo/Minimization procedure. Complex Binding approach Nonbond interaction energies (kcal/mol) RMSD (C153) RMSD (H180) χ1 (C153) Angle value of the hydrogen bond between C153 and H180 DHAa XDAa 1 b BA1 -8.083 0.24 0.52 -60.68 111.09 133.00 2 BA1 -0.558 0.63 0.47 -68.85 140.51 71.77 3 BA1 -0.526 0.88 0.47 -70.07 128.52 71.76 4 BA1 0.225 1.10 0.45 -85.75 133.74 66.31 5 BA1 1.173 1.30 0.41 -90.55 133.66 66.61 6 BA1 29.900 4.59 0.90 78.83 129.83 65.49 7 BA1 36.515 5.56 1.25 70.78 148.90 68.16 8 b BA2 -6.955 0.13 0.48 -62.85 113.08 132.95 9 BA2 0.974 0.37 0.49 -69.05 139.27 86.60 10 BA2 1.253 1.52 0.38 -111.84 132.92 66.31 11 BA2 1.591 1.90 0.38 -81.44 133.04 64.63 12 BA2 1.498 1.89 0.37 -72.64 135.22 66.03 13 BA2 62.130 4.94 0.89 26.06 136.89 61.01 a D: Sγ of C153; A: Nτ of H180; H: Hγ of C153; X: Cβ of C153. bSelected complex. Table 25. Non-bond interaction energies (kcal/mol), Cα RMSD (Å) of C153 and H180 calculated with respect to the starting position. χ1 torsion angle of C153 (degrees) and angle values of the hydrogen bond between C153 and H180 (degrees) of the 3c/PfGAPDH complexes obtained by Monte Carlo/Minimization procedure. Complex Binding approach Nonbond interaction energies (kcal/mol) RMSD (C153) RMSD (H180) χ1 (C153) Angle value of the hydrogen bond between C153 and H180 DHAa XDAa 1b BA1 -11.956 0.24 0.46 -66.78 103.72 136.77 2 BA1 0.996 1.39 0.41 -85.51 129.86 70.54 3 BA1 -3.224 1.51 0.41 -71.88 132.36 63.85 4 BA1 29.703 1.51 0.47 -56.12 135.55 74.01 5 BA1 38.053 1.29 0.57 -38.40 117.06 89.62 6 BA1 30.459 5.13 1.31 98.11 74.23 82.45 7 BA1 53.717 5.86 1.74 112.96 80.81 73.87 8 BA1 65.850 6.00 1.63 102.52 77.31 77.33 9 b BA2 -10.615 0.24 0.58 -60.98 111.57 134.81 10 BA2 5.234 0.89 1.05 -98.93 135.11 79.96 11 BA2 23.086 0.33 0.82 -80.92 127.01 106.79 12 BA2 10.481 0.42 0.89 -56.38 111.45 109.75 13 BA2 22.524 0.49 0.80 -83.60 132.03 114.42 14 BA2 17.192 5.31 1.17 87.69 110.85 69.75 15 BA2 19.364 5.63 1.28 74.89 109.19 67.83 16 BA2 13.948 5.90 1.39 69.12 134.83 63.66 a D: Sγ of C153; A: Nτ of H180; H: Hγ of C153; X: Cβ of C153. bSelected complex. Table 26. Non-bond interaction energies (kcal/mol), Cα RMSD (Å) of C153 and H180 calculated with respect to the starting position. χ1 torsion angle of C153 (degrees) and angle values of the hydrogen bond between C153 and H180 (degrees) of the 3d/PfGAPDH complexes obtained by Monte Carlo/Minimization procedure. Complex Binding approach Nonbond interaction energies (kcal/mol) RMSD (C153) RMSD (H180) χ1 (C153) Angle value of the hydrogen bond between C153 and H180 DHAa XDAa 1b BA1 -9.268 0.15 0.61 -62.84 115.65 139.87 2 BA1 -1.073 0.21 0.58 -75.02 123.19 96.00 3 BA1 -6.940 1.36 0.52 -69.37 122.49 78.16 4 BA1 21.722 3.31 0.63 -77.28 149.44 74.05 5 BA1 8.731 3.11 0.60 -72.15 142.00 69.76 6 BA1 39.745 5.13 0.97 74.02 131.98 90.36 7 BA1 3.301 4.44 0.78 57.21 124.20 113.72 8 BA1 38.717 5.11 1.32 64.48 128.34 139.87 9 b BA2 -7.732 0.27 0.47 -60.21 110.37 126.20 10 BA2 -2.542 0.44 0.43 -96.65 132.75 112.43 11 BA2 -4.840 1.06 0.44 -68.46 118.23 76.28 12 BA2 9.679 1.48 0.46 -67.88 122.01 72.56 13 BA2 -0.422 1.29 0.46 -64.36 130.04 74.71 14 BA2 30.203 7.06 1.06 -38.67 88.26 65.49 15 BA2 54.048 6.67 0.97 -56.33 85.89 79.58 a D: Sγ of C153; A: Nτ of H180; H: Hγ of C153; X: Cβ of C153. bSelected complex. Table 27. Non-bond interaction energies (kcal/mol), Cα RMSD (Å) of C153 and H180 calculated with respect to the starting position. χ1 torsion angle of C153 (degrees) and angle values of the hydrogen bond between C153 and H180 (degrees) of the 4a/PfGAPDH complexes obtained by Monte Carlo/Minimization procedure. Complex Binding approach Nonbond interaction energies (kcal/mol) RMSD (C153) RMSD (H180) χ1 (C153) Angle value of the hydrogen bond between C153 and H180 DHAa XDAa 1 b BA1 -7.193 0.30 0.49 -67.75 118.81 133.97 2 BA1 -1.133 0.19 0.50 -63.78 110.87 123.77 3 BA1 7.825 1.32 0.45 -150.23 137.88 65.33 4 BA1 11.784 1.92 0.48 -88.28 136.90 65.28 5 BA1 0.382 2.19 0.42 -57.18 115.90 70.80 6 BA1 31.489 5.98 2.40 66.50 132.38 120.08 7 BA1 27.649 6.21 2.27 87.23 147.46 112.23 8b BA2 -8.592 0.15 0.55 -61.44 111.23 131.51 9 BA2 -1.674 0.80 0.40 -83.05 138.26 73.16 10 BA2 -2.000 0.71 0.38 -69.12 123.52 77.95 11 BA2 8.792 1.06 0.40 -96.26 125.25 76.87 12 BA2 0.468 2.32 0.41 -79.71 139.48 69.07 13 BA2 33.031 5.01 0.78 75.50 135.61 68.07 14 BA2 12.445 5.07 0.93 72.85 142.57 72.40 15 BA2 8.165 5.23 0.73 79.85 137.32 71.91 a D: Sγ of C153; A: Nτ of H180; H: Hγ of C153; X: Cβ of C153. bSelected complex. Table 28. Non-bond interaction energies (kcal/mol), Cα RMSD (Å) of C153 and H180 calculated with respect to the starting position. χ1 torsion angle of C153 (degrees) and angle values of the hydrogen bond between C153 and H180 (degrees) of the 4b/PfGAPDH complexes obtained by Monte Carlo/Minimization procedure. Complex Binding approach Nonbond interaction energies (kcal/mol) RMSD (C153) RMSD (H180) χ1 (C153) Angle value of the hydrogen bond between C153 and H180 DHAa XDAa 1 b BA1 -9.210 0.24 0.52 -60.716 109.973 133.558 2 BA1 1.238 0.32 0.51 -59.441 117.474 133.722 3 BA1 2.808 0.44 0.48 -71.937 130.285 86.974 4 BA1 -1.802 1.22 0.45 -70.121 132.247 71.701 5 BA1 -1.053 2.42 0.43 -68.219 126.322 74.058 6 BA1 54.368 5.89 1.54 42.036 129.141 54.820 7 b BA2 -8.829 0.15 0.48 -61.117 113.253 134.609 8 BA2 6.424 0.21 0.63 -50.689 96.497 140.972 9 BA2 -5.552 1.12 0.58 -70.661 121.288 75.045 10 BA2 14.907 1.98 0.54 -65.283 102.210 85.612 11 BA2 12.699 2.63 0.36 -171.189 134.414 66.610 a D: Sγ of C153; A: Nτ of H180; H: Hγ of C153; X: Cβ of C153. bSelected complex. Table 29. Non-bond interaction energies (kcal/mol), Cα RMSD (Å) of C153 and H180 calculated with respect to the starting position. χ1 torsion angle of C153 (degrees) and angle values of the hydrogen bond between C153 and H180 (degrees) of the 4c/PfGAPDH complexes obtained by Monte Carlo/Minimization procedure. Complex Binding approach Nonbond interaction energies (kcal/mol) RMSD (C153) RMSD (H180) χ1 (C153) Angle value of the hydrogen bond between C153 and H180 DHAa XDAa 1b BA1 -11.308 0.24 0.46 -68.298 106.515 135.050 2 BA1 6.045 0.73 0.47 -79.674 134.533 83.225 3 BA1 -7.754 0.79 0.46 -83.562 145.409 80.635 4 BA1 43.389 2.16 0.42 -91.101 129.520 78.582 5 BA1 -7.423 2.78 0.41 -64.444 122.684 75.675 6 b BA2 -10.031 0.23 0.58 -60.636 111.693 135.004 7 BA2 6.583 1.62 0.51 -84.190 129.563 65.748 8 BA2 33.100 1.16 0.55 -67.865 144.767 84.095 9 BA2 -2.830 3.18 0.55 -66.556 142.478 71.062 10 BA2 12.445 2.98 0.63 -51.666 90.754 100.242 11 BA2 39.554 5.15 1.12 72.671 141.922 68.779 12 BA2 39.481 6.02 1.30 68.903 136.415 68.834 13 BA2 26.735 6.25 1.29 66.143 124.229 66.560 a D: Sγ of C153; A: Nτ of H180; H: Hγ of C153; X: Cβ of C153. bSelected complex. Table 30. Non-bond interaction energies (kcal/mol), Cα RMSD (Å) of C153 and H180 calculated with respect to the starting position. χ1 torsion angle of C153 (degrees) and angle values of the hydrogen bond between C153 and H180 (degrees) of the 4d/PfGAPDH complexes obtained by Monte Carlo/Minimization procedure. Complex Binding approach Nonbond interaction energies (kcal/mol) RMSD (C153) RMSD (H180) χ1 (C153) Angle value of the hydrogen bond between C153 and H180 DHAa XDAa 1b BA1 -10.135 0.15 0.62 -62.88 114.49 127.58 2 BA1 -3.974 0.59 0.48 -75.60 128.80 85.74 3 BA1 1.163 1.65 0.40 -71.08 135.36 66.17 4 BA1 0.991 1.89 0.42 -68.27 135.55 66.47 5 BA1 3.749 3.41 1.04 -58.46 138.77 67.58 6 BA1 51.161 5.17 1.01 68.45 145.98 71.16 7 BA1 55.187 5.39 1.02 63.48 149.66 74.46 8 BA1 35.102 4.90 1.02 63.19 154.24 78.57 9 b BA2 -8.962 0.22 0.48 -60.42 110.96 137.97 10 BA2 14.339 1.15 0.51 -77.00 104.35 89.18 11 BA2 -5.076 0.55 0.53 -65.64 106.85 108.32 12 BA2 -0.527 1.10 0.49 -66.78 130.14 72.22 13 BA2 -2.602 2.15 0.71 -166.12 132.32 61.09 14 BA2 35.708 5.18 0.97 72.35 101.84 77.96 15 BA2 -3.830 5.31 1.50 60.05 133.06 82.38 16 BA2 26.130 5.82 0.95 69.20 111.57 83.88 a D: Sγ of C153; A: Nτ of H180; H: Hγ of C153; X: Cβ of C153. bSelected complex. Table 31. Non-bond interaction energies (kcal/mol), Cα RMSD (Å) of C153 and H180 calculated with respect to the starting position, χ1 torsion angle of C153(degrees), and angles of the hydrogen bond between C153 and H180 (degrees) of the best docked complexes after unrestrained structure optimization. Lig. Binding approach Nonbond interaction energies (kcal/mol) RMSD (C153) RMSD (H180) χ1 (C153) Angle DHAa Angle XDAa 1a BA1 -22.590 0.52 0.74 -73.73 124.17 129.23 BA2 -13.343 0.62 0.65 -68.64 115.89 125.47 1b BA1 -17.717 0.47 0.86 -70.70 115.94 135.20 BA2 -16.548 0.65 0.79 -74.40 116.61 131.37 1c BA1 -19.845 0.51 0.66 -73.77 113.02 133.38 BA2 -16.387 0.52 0.71 -73.81 117.95 130.53 1d BA1 -18.308 0.16 0.18 -72.34 120.56 131.82 BA2 -16.774 0.61 0.78 -75.43 119.16 131.23 2a BA1 -17.205 0.37 0.81 -70.65 125.10 133.32 BA2 -11.536 0.53 0.24 -71.44 113.63 128.58 2b BA1 -17.427 0.66 0.79 -72.33 104.17 130.40 BA2 -13.269 0.76 0.60 -76.07 118.43 127.47 2c BA1 -13.921 0.56 0.95 -66.98 128.46 132.79 BA2 -10.281 0.49 0.46 -68.15 128.04 129.50 2d BA1 -14.750 0.46 0.76 -67.34 109.79 129.42 BA2 -6.510 0.67 0.85 -69.67 117.43 133.81 3a BA1 -18.374 0.48 0.76 -71.37 122.78 130.26 BA2 -16.607 0.65 0.54 -72.08 116.39 130.52 3b BA1 -19.049 0.41 0.67 -65.87 116.90 137.39 BA2 -14.111 0.55 0.42 -74.55 120.22 128.86 3c BA1 -21.182 0.53 0.96 -64.38 121.32 130.60 BA2 -13.996 0.60 0.67 -69.63 123.43 129.39 3d BA1 -24.553 0.51 1.06 -69.32 119.37 131.37 BA2 -11.600 0.47 0.72 -70.48 124.35 131.32 4a BA1 -22.191 0.48 0.83 -71.71 122.05 134.89 BA2 -17.572 0.43 0.56 -72.41 119.55 130.34 4b BA1 -23.495 0.30 0.51 -66.11 111.60 133.22 BA2 -17.404 0.55 0.53 -71.56 121.53 124.83 4c BA1 -22.441 0.40 0.92 -65.50 125.77 129.05 BA2 -14.363 0.70 0.49 -69.16 121.15 130.51 4d BA1 -24.176 0.31 0.76 -70.83 116.59 133.40 BA2 -11.351 0.51 0.67 -71.98 120.05 131.71 Table 32. Summary of Procheck results obtained for the selected docked complexes. Structure Binding Approach Residues favored regions (%) Residues allowed regions (%) Residues generously allowed regions (%) Residues disallowed regions (%) Poor rotamer (%) 1YWG - 85.2 14.0 0.8 0.0 1.1 1a/PfGAPDH BA1 83.1 15.7 0.7 0.5 0.9 1a/PfGAPDH BA2 83.3 15.4 0.9 0.4 0.9 1b/PfGAPDH BA1 83.1 15.6 0.9 0.4 0.9 1b/PfGAPDH BA2 82.9 16.3 0.6 0.3 1.5 1c/PfGAPDH BA1 83.0 15.7 0.9 0.4 0.9 1c/PfGAPDH BA2 81.9 17.1 0.6 0.3 0.9 1d/PfGAPDH BA1 83.2 15.6 0.7 0.5 0.9 1d/PfGAPDH BA2 82.3 16.8 0.7 0.3 1.2 2a/PfGAPDH BA1 83.2 15.3 0.9 0.5 0.9 2a/PfGAPDH BA2 83.3 15.4 0.9 0.4 0.9 2b/PfGAPDH BA1 83.0 15.8 0.8 0.4 0.9 2b/PfGAPDH BA2 83.1 15.6 0.9 0.4 0.9 2c/PfGAPDH BA1 82.9 15.9 0.7 0.5 0.9 2c/PfGAPDH BA2 83.1 15.6 0.9 0.4 0.9 2d/PfGAPDH BA1 83.3 15.3 0.9 0.4 0.9 2d/PfGAPDH BA2 83.1 15.5 1.0 0.3 0.9 3a/PfGAPDH BA1 83.4 15.2 0.9 0.4 0.9 3a/PfGAPDH BA2 83.4 15.2 0.9 0.5 0.9 3b/PfGAPDH BA1 83.0 15.8 0.7 0.5 0.9 3b/PfGAPDH BA2 82.3 16.7 0.8 0.3 1.1 3c/PfGAPDH BA1 83.3 15.3 0.9 0.4 0.9 3c/PfGAPDH BA2 83.2 15.4 0.9 0.5 0.9 3d/PfGAPDH BA1 83.1 15.6 0.8 0.5 0.9 3d/PfGAPDH BA2 83.4 15.3 0.9 0.4 0.9 4a/PfGAPDH BA1 83.4 15.3 0.8 0.5 0.9 4a/PfGAPDH BA2 83.3 15.2 1.1 0.4 0.9 4b/PfGAPDH BA1 83.1 15.6 0.8 0.5 0.9 4b/PfGAPDH BA2 83.3 15.4 0.8 0.5 0.9 4c/PfGAPDH BA1 83.6 15.0 0.9 0.5 0.9 4c/PfGAPDH BA2 83.0 15.7 0.9 0.4 0.9 4d/PfGAPDH BA1 83.0 15.7 0.9 0.4 0.9 4d/PfGAPDH BA2 83.5 15.2 0.8 0.6 0.9 Table 33. Calculated RMSD (Å) of the ligand conformation in the docked complexes with respect to the conformers obtained by the conformational analysis. The energy difference (ΔE) from the global minimum energy conformer (GM) is also reported. Compound Binding Approach RMSD (Ǻ) ΔEGM (kcal/mol) 1a BA1 0.52 0 1a BA2 0.45 0 1b BA1 0.36 1.92 1b BA2 0.39 1.92 1c BA1 0.48 1.92 1c BA2 0.49 1.92 1d BA1 0.19 1.51 1d BA2 0.68 0 2a BA1 0.16 1.09 2a BA2 0.30 1.09 2b BA1 0.18 1.53 2b BA2 0.70 0.26 2c BA1 0.49 1.53 2c BA2 0.28 1.53 2d BA1 0.47 1.25 2d BA2 0.30 1.09 3a BA1 0.28 0.08 3a BA2 0.39 0.51 3b BA1 0.48 1.77 3b BA2 0.68 0.86 3c BA1 0.29 0.81 Table 3. ΔEGM values (kcal/mol), torsional angle values (degrees) and occurrence rates (%) of conformational families of 9a considering MM conformers within 5 kcal/mol from the global minimum. d cb a e fg hN O Cl O H N H3C 1 2 3Cl Family ΔEGMa (kcal/mol) Torsional Angles (°) Occurrence Rate (%) τ1b τ2c τ3d TTC 0.00-4.88 ~180 ~180 ~0.00 23 TTT 0.34-4.96 ~180 ~180 ~180 25 TCT 1.96-4.89 ~180 ~0.00 ~180 29 TCC 2.37-4.92 ~180 ~0.00 ~0.00 23 aThe values reported refer to the lowest and the highest energy conformers of the family. b τ1 torsional angle is calculated considering the amide bond atoms. c τ2: a, b, c, and d atoms. d τ3: e, f, g, and h atoms. Table 4. ΔEGM values (kcal/mol), torsional angle values (degrees) and occurrence rates (%) of conformational families of 9b considering MM conformers within 5 kcal/mol from the global minimum. d cb a e f g hN O MeO O H N H3C 1 2 3Cl Family ΔEGMa (kcal/mol) Torsional Angles (°) Occurrence Rate (%) τ1b τ2c τ3d TTC 0.00-4.98 ~180 ~180 ~0.00 23 TTT 0.45-4.98 ~180 ~180 ~180 18 TCC 1.96-4.97 ~180 ~0.00 ~0.00 34 TCT 2.18-4.77 ~180 ~0.00 ~180 25 aThe values reported refer to the lowest and the highest energy conformers of the family. b τ1 torsional angle is calculated considering the amide bond atoms. c τ2: a, b, c, and d atoms. d τ3: e, f, g, and h atoms. Table 5. ΔEGM values (kcal/mol), torsional angle values (degrees) and occurrence rates (%) of conformational families of 9c considering MM conformers within 5 kcal/mol from the global minimum. d cb a e f g hN O F O HN H3C 1 2 3 Cl Family ΔEGMa (kcal/mol) Torsional Angles (°) Occurrence Rate (%) τ1b τ2c τ3d TTC 0.00-4.99 ~180 ~180 ~0.00 28 TTT 0.38-4.97 ~180 ~180 ~180 21 TCT 1.84-4.20 ~180 ~0.00 ~180 22 TCC 1.89-4.68 ~180 ~0.00 ~0.00 29 aThe values reported refer to the lowest and the highest energy conformers of the family. b τ1 torsional angle is calculated considering the amide bond atoms. c τ2: a, b, c, and d atoms. d τ3: e, f, g, and h atoms. Table 6. ΔEGM values (kcal/mol), torsional angle values (degrees) and occurrence rates (%) of conformational families of 9d considering MM conformers within 5 kcal/mol from the global minimum. d cb a e f g hN O Me O H N H3C 1 2 3 Cl Torsional Angles (°) Occurrence Rate Family ΔEGMa (kcal/mol) τ1b τ2c τ3d (%) TTC 0.00-4.94 ~180 ~180 ~0.00 26 TTT 0.05-4.72 ~180 ~180 ~180 24 TCT 1.92-4.86 ~180 ~0.00 ~180 22 TCC 2.02-4.58 ~180 ~0.00 ~0.00 28 aThe values reported refer to the lowest and the highest energy conformers of the family. b τ1 torsional angle is calculated considering the amide bond atoms. c τ2: a, b, c, and d atoms. d τ3: e, f, g, and h atoms. Table 7. ΔEGM values (kcal/mol), torsional angle values (degrees) and occurrence rates (%) of conformational families of 9e considering MM conformers within 5 kcal/mol from the global minimum. d cb a e f g hN O Cl O H N H3C 1 2 3 Cl Family ΔEGMa (kcal/mol) Torsional Angles (°) Occurrence Rate (%) τ1b τ2c τ3d TTT 0.00-4.82 ~180 ~180 ~180 26 TTC 0.05-4.99 ~180 ~180 ~0.00 22 TCC 1.64-4.58 ~180 ~0.00 ~0.00 27 TCT 1.74-4.76 ~180 ~0.00 ~180 25 aThe values reported refer to the lowest and the highest energy conformers of the family. b τ1 torsional angle is calculated considering the amide bond atoms. c τ2: a, b, c, and d atoms. d τ3: e, f, g, and h atoms. Table 8. ΔEGM values (kcal/mol), torsional angle values (degrees) and occurrence rates (%) of conformational families of 9f considering MM conformers within 5 kcal/mol from the global minimum. d cb a e f g hN O O H N H3C1 2 3CF3 Family ΔEGMa (kcal/mol) Torsional Angles (°) Occurrence Rate (%) τ1b τ2c τ3d TTT 0.00-4.98 ~180 ~180 ~180 22 TTC 0.33-4.99 ~180 ~180 ~0.00 26 TCT 1.95-4.98 ~180 ~0.00 ~180 24 TCC 2.37-4.90 ~180 ~0.00 ~0.00 28 aThe values reported refer to the lowest and the highest energy conformers of the family. b τ1 torsional angle is calculated considering the amide bond atoms. c τ2: a, b, c, and d atoms. d τ3: e, f, g, and h atoms. Table 9. ΔEGM values (kcal/mol), torsional angle values (degrees) and occurrence rates (%) of conformational families of 9g considering MM conformers within 5 kcal/mol from the global minimum. d cb a e fg hN O O H N 1 2 3Br Family ΔEGMa (kcal/mol) Torsional Angles (°) Occurrence Rate (%) τ1b τ2c τ3d TTC 0.00-4.98 ~180 ~180 ~0.00 20 TTT 0.32-4.99 ~180 ~180 ~180 24 TCC 2.57-4.99 ~180 ~0.00 ~0.00 27 TCT 2.63-4.98 ~180 ~0.00 ~180 29 aThe values reported refer to the lowest and the highest energy conformers of the family. b τ1 torsional angle is calculated considering the amide bond atoms. c τ2: a, b, c, and d atoms. Table 10. ΔEGM values (kcal/mol), torsional angle values (degrees) and occurrence rates (%) of conformational families of 9h considering MM conformers within 5 kcal/mol from the global minimum. d cb a e f g hN O Me O H N H3C 1 2 3Cl Me Family ΔEGMa (kcal/mol) Torsional Angles (°) Occurrence Rate (%) τ1b τ2c τ3d TTT 0.00-4.99 ~180 ~180 ~180 25 TTC 0.05-4.94 ~180 ~180 ~0.00 23 TCC 2.02-4.91 ~180 ~0.00 ~0.00 29 TCT 2.19-4.92 ~180 ~0.00 ~180 23 aThe values reported refer to the lowest and the highest energy conformers of the family. b τ1 torsional angle is calculated considering the amide bond atoms. c τ2: a, b, c, and d atoms. d τ3: e, f, g, and h atoms. Table 11. ΔEGM values (kcal/mol), torsional angle values (degrees) and occurrence rates (%) of conformational families of 9i considering MM conformers within 5 kcal/mol from the global minimum. d cb a e fg hN O Me O H N H3C 1 2 3Cl MeO Family ΔEGMa (kcal/mol) Torsional Angles (°) Occurrence Rate (%) τ1b τ2c τ3d TTC 0.00-4.94 ~180 ~180 ~0.00 25 TTT 0.15-4.98 ~180 ~180 ~180 20 TCT 2.19-4.99 ~180 ~0.00 ~180 26 TCC 2.38-4.87 ~180 ~0.00 ~0.00 29 aThe values reported refer to the lowest and the highest energy conformers of the family. b τ1 torsional angle is calculated considering the amide bond atoms. c τ2: a, b, c, and d atoms. d τ3: e, f, g, and h atoms. Table 12. ΔEGM values (kcal/mol), torsional angle values (degrees) and occurrence rates (%) of conformational families of (R)-10b considering MM conformers within 5 kcal/mol from the global minimum. d cb a N OH O H N H3C 1 2 Cl 3 e fg h Family ΔEGMa (kcal/mol) Torsional Angles (°) Occurrence Rate (%) τ1b τ2c τ3d TTA0.00-4.80 ~180 ~180 ~-120 19 TTT 0.07-4.80 ~180 ~180 ~180 21 TCT 1.76-4.96 ~180 ~0.00 ~180 27.5 TTG+ 2.16-4.77 ~180 ~180 ~60 12 TCA2.75-4.37 ~180 ~0.00 ~-120 19 TTG3.36-3.66 ~180 ~180 ~-60 1 TCG4.88 ~180 ~0.00 ~-60 0.5 aThe values reported refer to the lowest and the highest energy conformers of the family. b τ1 torsional angle is calculated considering the amide bond atoms. c τ2: a, b, c, and d atoms. d τ2: e, f, g, and d htoms. Table 13. Conformational energy, structural classification, and intramolecular distances (Å) of calculated DFT conformers of 1. d cb N O O H N H3C Cl i j kl m Y X Z 4 5 3 1 2 e fg h a Familya Sub-family ΔEGM (kcal/mol) Distances (Å) Torsional Angles (°)b-f d1 (X-Y) d2 (X-Z) d3 (Y-Z) τ1 τ2 τ3 τ4 τ5 TCC I 0.00 7.1 8.7 9.2 -173 25 -21 94 -111 TCC II 0.57 6.1 9.3 10.1 -174 26 22 84 -84 TCT I 1.66 7.5 7.2 11.0 -174 26 -148 101 -113 TCT I 1.66 9.4 7.3 10.6 172 -24 -149 111 -124 a The data reported are referred to the enantiomer E1, the other enantiomer presents the same conformational energy, the same pharmacophore distances, and the same absolute torsion angle values but with opposite sign. bτ1 torsional angle is calculated considering the amide bond atoms. cτ2: a, b, c, and d atoms. dτ3: e, f, g, and h atoms. eτ4: c, d, i, and j atoms. fτ5: b, k, l, and m atoms. Table 20. Conformational energy, structural classification, and intramolecular distances (Å) of calculated DFT conformers of 9h. d cb N O O H N H3C Cl i j kl m Y X Z 4 5 3 1 2 e fg h a Me Me Familya Sub-family ΔEGM (kcal/mol) Distances (Å) Torsional Angles (°)b-f d1 (X-Y) d2 (X-Z) d3 (Y-Z) τ1 τ2 τ3 τ4 τ5 TCC I 0.00 7.3 9.2 9.8 -173 27 24 99 -110 TCC II 0.40 6.2 9.3 10.1 -174 26 23 84 -84 TCT I 1.40 7.2 7.3 10.9 -172 27 -145 100 -105 TCT I 1.44 9.3 7.3 10.6 173 -23 -147 110 -122 a The data reported are referred to the enantiomer E1, the other enantiomer presents the same conformational energy, the same pharmacophore distances, and the same absolute torsion angle values but with opposite sign. bτ1 torsional angle is calculated considering the amide bond atoms. cτ2: a, b, c, and d atoms. dτ3: e, f, g, and h atoms. eτ4: c, d, i, and j atoms. fτ5: b, k, l, and m atoms. Table 21. Conformational energy, structural classification, and intramolecular distances (Å) of calculated DFT conformers of 9i. d cb N O O H N H3C Cl i j klm Y X Z 4 5 3 1 2 e fg h a Me MeO Familya Sub-family ΔEGM (kcal/mol) Distances (Å) Torsional Angles (°)b-f d1 (X-Y) d2 (X-Z) d3 (Y-Z) τ1 τ2 τ3 τ4 τ5 TCC I 0.00 7.4 9.2 9.8 -174 26 26 98 -114 TCC II 0.23 6.1 9.3 10.2 -174 26 26 84 -84 TCT I 1.21 7.4 7.2 10.9 -174 26 -143 100 -112 TCT I 1.30 9.4 7.3 10.5 172 -24 -145 110 -125 a The data reported are referred to the enantiomer E1, the other enantiomer presents the same conformational energy, the same pharmacophore distances, and the same absolute torsion angle values but with opposite sign. bτ1 torsional angle is calculated considering the amide bond atoms. cτ2: a, b, c, and d atoms. dτ3: e, f, g, and h atoms. eτ4: c, d, i, and j atoms. fτ5: b, k, l, and m atoms. Table 22. TSP conformers grouped according to the intramolecular distances between the X, Y, and Z rings. Group Conformer Compounds Distances (Å)a Pharmacophoreb d1 (X-Y) d2 (X-Z) d3 (Y-Z) A TCC I 1, 9a-f, 9h-i and 10a 7.0 9.1 9.6 1 B TCC II 1, 9a-f, 9h-i and 10a 6.2 9.3 10.1 - C TCT I 1, 9a-f, 9h-i and 10a 7.3 7.2 10.9 2 C TCA- (±)-10b 7.0 7.1 9.5 2 C TCG+ (±)-10b 7.3 7.0 10.3 2 D TCT I 1, 9d, 9h, 9i 9.3 7.3 10.5 - E TCT III 9a-c, 9e-f and 10a 9.7 7.3 10.8 - F TCC I 9g 6.1 5.6 10.4 3 G TTC IV 9g 4.5 5.4 9.2 - H TCG- (±)-10b 9.6 8.3 7.9 4 aAverage values. b Conformers matching similarity criteria with the intra-molecular distances of the hot spot residues of hydrophobic PPI motifs. Table 23. cLogD7.4 of compounds 1, 9a-i, and 10a-b. Cpd clog D7.4 1 5.03 9a 5.63 9b 5.29 9c 4.65 9d 4.97 9e 5.29 9f 4.78 9g 5.29 9h 5.98 9i 4.77 10a 4.07 (±) 10b 5.31 Nut-3a 5.00 aACD/Percepta 2017 software. Appendix C Table 1. Calculated ionic interactions between 20S (positive) and PA28(negative) obtained using the X-ray complexes of human 20S proteasome with human PA28 (PDB IDs: 7NAO and 7NAP). human 20S proteasome (positive) Groove human PA28α (negative) R21 (α1) α1-α2 E133(subunit α1-α2) K30 (α1) α1-α2 E233 (subunit α1-α2) K18 (α2) α2-α3 E143 subunit α2-α3 K64 (α3) α2-α3 Y249 C-term (subunit α2-α3) R4 (α3) α3-α4 D137 (subunit α3-α4) R17 (α3) α3-α4 E133 (subunit α3-α4) K27 (α4) α3-α4 E233 (subunit α3-α4) K48 (α4) α3-α4 Y239 C-term (subunit α3-α4) K61 (α4) α3-α4 Y239 C-term (subunit α3-α4) K166 (α4) α4-α5 E233 (subunit α4-α5) K166 (α4) α4-α5 E234 (subunit α4-α5) K66 (α5) α4-α5 Y239 C-term (subunit α4-α5) R20 (α5) α5-α6 E143 (subunit α5-α6) R20 (α5) α5-α6 D144 (subunit α5-α6) K32 (α5) α5-α6 E243 (subunit α5-α6) R51 (α6) α5-α6 Y249 C-term (subunit α5-α6) M1 (α5) - E215 (subunit α6-α7) R18 (α6) α6-α7 E133 (subunit α6-α7) R18 (α6) α6-α7 D134 (subunit α6-α7) R169 (α6) α6-α7 E233 (subunit α6-α7) R66 (α7) α6-α7 Y239 C-term (subunit α6-α7) R20 (α7) α7-α1 E143 (subunit α7-α1) K206 (α7) α7-α1 E235 (subunit α7-α1) Table 2. Calculated ionic interactions between 20S (positive) and PA200(negative) obtained using the X-ray complexes of human 20S proteasome with human PA200 (PDB IDs: 6KWY and 6REY). human 20S proteasome (positive) human PA200 (negative) R21 (α1) E579 K181 (α1) D670 E672 K184 (α1) D666 D670 K186 (α1) D661 K51 (α2) E667 K53 (α2) E571 E568 K64 (α2) E569 K165 (α2) E573 K176 (α2) D885 E884 R177 (α2) D885 E884 K176 (α3) E1329 D1330 K195 (α3) D1196 K199 (α3) D1196 E1164 K205 (α3) E1068 K210 (α3) E1068 K52 (α4) E1329 K166 (α4) E1617 R53 (α5) D1616 M1 N-term (α6) D1815 R51 (α6) A1843 C-term K62 (α6) A1843 C-term R164 (α6) D1834 M1 N-term (α7) E445 Table 3. Ionic interactions between human 20S (positive) and 19S (negative) in the SA/EA1-2 state (PDB IDs: 5T0G; 6MSB; 6MSD). human 20S proteasome (positive) human 19S (negative) Rpt R21 (α1) E415 Rpt3 (groove α1-α2) K55 (α1) D337 Rpt3 (groove α1-α2) K181 (α1) E400 Rpt3 (groove α1-α2) K53 (α2) D410 E413 K418 C-term Rpt3 (groove α1-α2) Rpt3 (groove α1-α2) Rpt3 (groove α1-α2) K64 (α2) K418 C-term Rpt3 (groove α1-α2) R176 (α2) D162 Rpn (PSMD11) K199 (α3) E424 Rpt2 (groove α3-α4) K166 (α4) E411 Rpt1 (groove α4-α5) R18 (α6) D390 Rpt5 (groove α5-α6) R51 (α6) A439 C-term Rpt5 (groove α5-α6) K62 (α6) A439 C-term Rpt5 (groove α5-α6) K179 (α7) E365 Rpt4 (groove α6-α7) K206 (α7) E359 Rpt4 (groove α6-α7) K208 (α7) E360 Rpt4 (groove α6-α7) Table 4. Ionic interactions between human 20S (positive) and 19S (negative) in the SB/EB state (PDB IDs: 5T0H; 6MSE). human 20S proteasome (positive) human 19S (negative) Rpt K165 (α2) E415 Rpt3 (groove α1-α2) K199 (α3) E424 Rpt2 (groove α3-α4) R18 (α6) D390 Rpt5 (groove α5-α6) R174 (α6) E383 Rpt5 (groove α5-α6) K206 (α7) E359 Rpt5 (groove α5-α6) K208 (α7) E360 Rpt5 (groove α5-α6) Table 5. Ionic interactions between human 20S (positive) and 19S (negative) in the SC/EC1-2 state (PDB IDs: 5T0I; 6MSG; 6MSH). human 20S proteasome (positive) human 19S (negative) Rpt K30 (α1) D410 Rpt3 (groove α1-α2) K53 (α2) K418 C-term Rpt3 (groove α1-α2) K64 (α2) K418 C-term Rpt3 (groove α1-α2) K165 (α2) E413 Rpt3 (groove α1-α2) K64 (α3) K406 C-term Rpt6 (groove α2-α3) K251 (α3) E417 Rpt2 (groove α3-α4) R51(α6) A439 C-term Rpt5 (groove α5-α6) K62(α6) A439 C-term Rpt5 (groove α5-α6) R174 (α6) E382 Rpt5 (groove α5-α6) Table 6. Ionic interactions between human 20S (positive) and the RP protein complex 19S (negative) in the SD/ED1-2 state (PDB IDs: 5T0J; 6MSJ; 6MSK). human 20S proteasome (positive) human 19S (negative) Rpt K53 (α2) E413 Rpt3 (groove α1-α2) K165 (α2) K418 C-term Rpt3 (groove α1-α2) R50 (α3) K406 C-term Rpt6 (groove α2-α3) K64 (α3) K406 C-term Rpt6 (groove α2-α3) K61 (α4) L440 C-term Rpt2 (groove α3-α4) R163 (α4) D389 Rpt2 (groove α3-α4) K66 (α5) N433C-term Rpt1 (groove α4-α5) R18 (α6) D389 D390 Rpt5 (groove α5-α6) Rpt5 (groove α5-α6) R51 (α6) A439 C-term Rpt5 (groove α5-α6) K62 (α6) A439 C-term Rpt5 (groove α5-α6) R164 (α6) E418 E422 Rpt5 (groove α5-α6) Rpt5 (groove α5-α6) R174 (α6) D378 Rpt5 (groove α5-α6) Table 7. Ligand-residue non-bond interaction energies (kcal/mol) of the H2TTPS/h20S complex obtained by Monte Carlo and SA calculations using as starting binding site the α1-α2 groove of 20S in the closed conformation. The residues involved in the interaction with the RPs or the small activator molecule ZYA (PDB:8F7K) are noted and the corresponding RPs are reported. h20S amino acids Subunit Non-bond interaction Energy (kcal/mol) RPsa and ZYA Tot vdW Coulomb M1 α1 -6.61 -3.94 -2.67 S2 α1 -2.98 -3.00 0.02 R3 α1 -9.20 -3.97 -5.23 R11 α1 -6.33 -0.68 -5.66 G20b α1 -3.81 -2.62 -1.19 19S (SA/EA1-2); ZYA R21b,c,d α1 -10.35 -5.67 -4.68 19S (SA/EA1-2; SC/EC1-2; SD/ED1-2) PA28 and PA200 L22b α1 -4.36 -4.47 0.12 19S (SA/EA1-2; SC/EC1-2) V25b α1 -4.49 -4.12 -0.37 19S (SA/EA1-2; SB/EB); ZYA E26b α1 -0.91 -4.98 4.07 19S (SA/EA1-2; SB/ECB1-2; SC/EC1-2) F29b α1 -3.00 -3.82 0.82 19S (SB/ECB1-2; SC/EC1-2) K30c α1 -10.30 -4.33 -5.97 19S (SC/EC1-2) and PA28 N33 α1 -0.94 -1.19 0.25 A157b α1 -0.87 -0.39 -0.48 19S (SA/EA1-2; SB/ECB1-2; SC/EC1-2; SD/ED1-2); ZYA Y159 α1 -3.84 -3.82 -0.01 K171 α1 -9.28 -2.28 -7.00 Q172 α1 -3.42 -1.73 -1.69 T173 α1 -7.24 -2.19 -5.05 A27 α2 -2.08 -2.00 -0.08 A28b α2 -0.22 -1.18 0.96 ZYA K50 α2 -5.19 -0.62 -4.57 K51c α2 -7.07 -4.19 -2.88 PA200 N52 α2 -1.41 -1.38 -0.03 K53c α2 -8.86 -5.10 -3.76 19S (SA/EA1-2; SC/EC1-2; SD/ED1-2) PA200 I55 α2 -1.43 -1.02 -0.41 K64c α2 -21.59 -1.26 -20.33 19S (SA/EA1-2; SC/EC1-2); ZYA M79b α2 -4.13 -3.38 -0.76 19S (SA/EA1-2; SC/EC1-2; SD/ED1-2); ZYA G80b α2 -1.77 -1.62 -0.15 19S (SA/EA1-2; SC/EC1-2); ZYA P81b α2 -0.79 -0.70 -0.09 19S (SA/EA1-2; SC/EC1-2; SD/ED1-2) H20 - -1.14 -0.76 -0.38 a In the case of 19S, the corresponding 26S functional states are specified in brackets:. b Residues involved in the interaction with the HbYX motif present at the C-terminal tails of Rpt3 (α1/α2) (19S) and with ZYA. c Positively charged residues involved in ionic interaction with RPs (i.e., PA28, PA200 and 19S). dResidues involved in the interaction with PA28 activation loop. Table 8. Ligand-residue non-bond interaction energies (kcal/mol) of the H2TTPS/h20S complex obtained by Monte Carlo and SA calculations using as starting binding site the α3-α4 groove of 20S in the open conformation. The residues involved in the interaction with the RPs or the small activator molecule ZYA (PDB:8F7K) are noted and the corresponding RPs are reported. h20S amino acids Subunit Non-bond interaction Energy (kcal/mol) RPsa and ZYA Tot vdW Coulomb R17b,c,d α3 -7.93 -2.02 -5.91 19S (SB/EB) PA28 L18b α3 -3.29 -3.18 -0.10 19S (SB/EB ; SC/EC1-2) V21b α3 -4.47 -4.06 -0.41 19S (SD/ED1-2); ZYA E22 α3 -0.20 -5.34 5.14 Y23d α3 -0.32 -0.35 0.03 PA28 A24 α3 -0.16 -0.25 0.09 M25 α3 -2.79 -2.19 -0.59 H30 α3 -3.88 -1.42 -2.46 Q149 α3 -1.37 -0.98 -0.40 P152 α3 -3.29 -3.10 -0.18 W159 α3 -4.31 -2.15 -2.15 K160 α3 -11.25 -2.24 -9.01 A161 α3 -2.77 -1.44 -1.33 Table 5. ΔEGM values (kcal/mol) and torsional angle values (degrees) of MM and DFT conformers of THIA-5. N S N O O t1 a b c d t2 e hg fO tOMe i jk l Conf Starting conformer (MM) DFT conformer ΔEGM (kcal/mol) τ1a τ2b τOMe ΔEGM (kcal/mol) τ1a τ2b τOMe 1A 0 9° -32° 0° 0.00 90° 90° 0° 1B 0 -9° 32° 0° 0.00 90° 90° 180° 1A 0.05 -9° 32° 180° 0.00 90° 90° 0° 1B 0.05 -9° -32° 180° 0.00 90° 90° 180° aThe values reported refer to the lowest and highest energy conformer of the family. τ1a: abcd; τ2b: efgh; τOMe: ijkl. Table 6. ΔEGM values (kcal/mol) and torsional angle values (degrees) of MM and DFT conformers of THIA-6. N S N O O t1 a b c d t2 e hg fO O tOMe i jk l m n o p tOMe2 Conf Starting conformer (MM) DFT conformer ΔEGM (kcal/mol) τ1a τ2b τOMe τOMe2 ΔEGM (kcal/mol) τ1a τ2b τOMe τOMe2 1A 0.00 9 -32 0 0 0.00 90° 90° 0° 0° 1B 0.00 -9 32 0 0 0.00 90° 90° 180° 180° 2A 0.00 9 -32 0 180° 0.23 90° 90° 0° 180° 2B 0.00 -9 32 0 180° 0.23 90° 90° 180° 0° 1A 0.05 -9 32 180° 180° 0.00 90° 90° 0° 0° 1B 0.05 9 -32 180° 180° 0.00 90° 90° 180° 180° 2A 0.05 9 -32 180° 0 0.23 90° 90° 180° 0° 2B 0.05 -9 32 180° 0 0.23 90° 90° 0° 180° aThe values reported refer to the lowest and highest energy conformer of the family. τ1a: abcd; τ2b: efgh; τOMe: ijkl; τOMe2: mnop Table 7. ΔEGM values (kcal/mol) and torsional angle values (degrees) of MM and DFT conformers of THIA-7. N S N O O t1 a b c d t2 e hg fO tOMe i k j l Cl Conf Starting conformer (MM) DFT conformer ΔEGM (kcal/mol) τ1a τ2b τOMe ΔEGM (kcal/mol) τ1a τ2b τOMe 1A 0 8° -33° 0° 0.00 90° 90° 0 1B 0 -8° 33° 0° 0.00 90° 90° 180° 1A 0.05 -8° 33° 180° 0.00 90° 90° 0 1B 0.05 8° -33° 180° 0.00 90° 90° 180° aThe values reported refer to the lowest and highest energy conformer of the family. τ1a: abcd; τ2b: efgh; τOMe: ijkl. Table 8. ΔEGM values (kcal/mol) and torsional angle values (degrees) of MM and DFT conformers of THIA-8. N S N O O t1 a bc d t2 e h g fO tOMe i k j l H Conf Starting conformer (MM) DFT conformer ΔEGM (kcal/mol) τ1a τ2b τOMe ΔEGM (kcal/mol) τ1a τ2b τOMe 1A 0.33 0° 180° 0° 0.00 90° 180° 0° 1B 0.38 0° 180° 180° 0.00 90° 180° 180° 2A 0.05 0° 0° 0° 0.72 90° 0° 0° 2B 0 0° 0° 180° 0.72 90° 0° 180° aThe values reported refer to the lowest and highest energy conformer of the family. τ1a: abcd; τ2b: efgh; τOMe: ijkl. Table 9. ΔEGM values (kcal/mol) and torsional angle values (degrees) of MM and DFT conformers of THIA-9. N S N O O t1 a b c d t2 e g f h Conf Starting conformer (MM) DFT conformer ΔEGM (kcal/mol) τ1a τ2b ΔEGM (kcal/mol) τ1a τ2b 1A 0 7° 148° 0.00 90° 90° 1A 0 -7° -148 0.00 90° 90° a The values reported refer to the lowest and highest energy conformer of the family. τ1a: abcd; τ2b: efgh. Table 10. ΔEGM values (kcal/mol) and torsional angle values (degrees) of MM and DFT conformers of THIA-10. N S N O O t1 a b c d t2 e g fF h Conf Starting conformer (MM) DFT conformer ΔEGM (kcal/mol) τ1a τ2b ΔEGM (kcal/mol) τ1a τ2b 1A 0 -10° +32° 0.00 90° 90° 1A 0 +10° -32° 0.00 90° 90° aThe values reported refer to the lowest and highest energy conformer of the family. τ1a: abcd; τ2b: efgh. Table 11. Selected 3CLpro and THIA-2 docked complexes: ligand conformer, binding mode, ligand-protein non-bond interaction energies (kcal/mol), and distance (Å) between THIA S1 and Cys145 sulfur atom. Complex Binding Mode Nonbonded interaction energies (kcal/mol) Vdw Coulomb Dist S1-SCys DFT conformer 1 II -38.5438 -35.2715 -3.27229 3.87211 2B 2 II -38.2819 -34.8204 -3.46146 3.76548 2B 3 I -37.7726 -37.227 -0.545614 3.43123 1B 4 II -37.7694 -35.0276 -2.74181 3.58838 1B 5 I -37.7428 -37.2461 -0.496678 3.4514 1B 6 IV -37.1403 -38.606 1.46566 3.34761 1A 7 IV -37.0753 -38.5347 1.45946 3.36116 1A 8 II -36.0199 -33.8959 -2.12396 3.77912 1B 9 II -35.0494 -31.1844 -3.865 3.55714 2A 10 I -33.483 -34.685 1.20209 3.15277 2B 11 I -32.504 -33.538 1.03398 3.62471 2B 12 I -32.4709 -34.1964 1.72557 3.38585 2B 13 I -31.9036 -33.1339 1.23033 3.93662 2A 14 I -31.8383 -33.0723 1.23407 3.93439 2A 15 III -30.6344 -28.6518 -1.98257 3.89249 1A 16 III -29.2721 -27.744 -1.52814 3.50433 2B Table 12. DFT conformer, binding mode, ligand-protein non-bond interaction energies (kcal/mol), distance (Å) between the THIA sulfur atom S1 and Cys145 sulfur atom of the selected 3CLpro and THIA-4 docked complexes. Complex Binding Mode Nonbonded interaction energies (kcal/mol) Vdw Coulomb Dist S1-SCys DFT conformer 1 II -36.5098 -33.8092 -2.70059 3.59471 1B 2 II -34.7952 -32.6152 -2.17998 3.65672 1A 3 I -30.0629 -32.5601 2.49718 3.39406 1B Table 13. DFT conformer, binding mode, ligand-protein non-bond interaction energies (kcal/mol), distance (Å) between the THIA sulfur atom S1 and Cys145 sulfur atom of the selected 3CLpro and THIA-7 docked complexes. Complex Binding Mode Nonbonded interaction energies (kcal/mol) Vdw Coulomb Dist S1-SCys DFT conformer 1 II -37.7838 -34.8061 -2.97769 3.50877 1B 2 I -31.0708 -33.0867 2.01594 3.33871 1B 3 I -30.988 -33.0236 2.0356 3.3533 1B 4 II -30.3905 -28.8106 -1.57994 3.61521 1A 5 III -29.5137 -26.6137 -2.90002 3.34087 1B 6 I -23.5017 -24.0366 0.53488 3.91534 1A Table 14. DFT conformer, binding mode, ligand-protein non-bond interaction energies (kcal/mol), distance (Å) between the THIA sulfur atom S1 and Cys145 sulfur atom of the selected 3CLpro and THIA-8 docked complexes. Complex Binding Mode Nonbonded interaction energies (kcal/mol) Vdw Coulomb Dist S1-SCys DFT conformer 1 IV -37.5685 -38.4296 0.861123 3.2873 2A 2 II -36.0927 -33.9649 -2.12779 3.6883 1B 3 II -35.8822 -33.8225 -2.05961 3.72721 1B 4 I -33.276 -33.6347 0.358675 3.18869 2B 5 III -32.2539 -30.81 -1.44392 3.27606 1B 6 I -32.2437 -33.2754 1.03164 3.45885 1B 7 I -31.2258 -32.4789 1.25307 3.28696 2B 8 III -27.8867 -25.7594 -2.1273 3.82194 2A 9 I -27.4426 -28.4937 1.05114 3.88072 2B 10 III -26.5165 -24.409 -2.1075 3.79432 2B 7BQ7 SARS-CoV-2 Crystal structure of 2019-nCoV nsp16-nsp10 complex 2.37 7DIY SARS-CoV-2 Crystal structure of SARS-CoV-2 nsp10 bound to nsp14ExoN domain reveals an exoribonuclease with both structural and functional integrity. 2.69 6W61 SARS-CoV-2 Crystal Structure of the methyltransferase-stimulatory factor complex of NSP16 and NSP10 from SARS CoV-2. 2 7C2I SARS-CoV-2 Crystal structure of SARS-CoV-2 nsp10/nsp16 2'-Omethylase and its implication on antiviral drug design. 2.5 7C2J SARS-CoV-2 Crystal structure of SARS-CoV-2 nsp10/nsp16 2'-Omethylase and its implication on antiviral drug design. 2.8 6YZ1 SARS-CoV-2 Structural analysis of the SARS-CoV-2 methyltransferase complex involved in RNA cap creation bound to sinefungin. 2.4 6W4H SARS-CoV-2 High-resolution structures of the SARS-CoV-2 2'- O - methyltransferase reveal strategies for structure-based inhibitor design. 1.8 6W75 SARS-CoV-2 High-resolution structures of the SARS-CoV-2 2'- O - methyltransferase reveal strategies for structure-based inhibitor design. 1.95 6WKQ SARS-CoV-2 High-resolution structures of the SARS-CoV-2 2'- O - methyltransferase reveal strategies for structure-based inhibitor design. 1.98 6WVN SARS-CoV-2 High-resolution structures of the SARS-CoV-2 2'- O - methyltransferase reveal strategies for structure-based inhibitor design. 2 7JYY SARS-CoV-2 Mn2+ coordinates Cap-0-RNA to align substrates for efficient 2'- O -methyl transfer by SARS-CoV-2 nsp16. 2.05 7JZ0 SARS-CoV-2 High-resolution structures of the SARS-CoV-2 2'- O - methyltransferase reveal strategies for structure-based inhibitor design. 2.15 7L6T SARS-CoV-2 Mn2+ coordinates Cap-0-RNA to align substrates for efficient 2'- O -methyl transfer by SARS-CoV-2 nsp16. 1.78 7L6R SARS-CoV-2 Mn2+ coordinates Cap-0-RNA to align substrates for efficient 2'- O -methyl transfer by SARS-CoV-2 nsp16. 1.98 7ULT SARS-CoV-2 Crystal Structure of SARS-CoV-2 nsp16/10 Heterodimer Apo-Form. 1.9 6WRZ SARS-CoV-2 High-resolution structures of the SARS-CoV-2 2'- O - methyltransferase reveal strategies for structure-based inhibitor design. 2.25 6WQ3 SARS-CoV-2 High-resolution structures of the SARS-CoV-2 2'- O - methyltransferase reveal strategies for structure-based inhibitor design. 2.1 7EGQ SARS-CoV-2 Coupling of N7-methyltransferase and 3'-5' exoribonuclease with SARS-CoV-2 polymerase reveals mechanisms for capping and proofreading. 3.35 7MC5 SARS-CoV-2 Crystal structure of the SARS-CoV-2 ExoN-nsp10 complex 1.64 7MC6 SARS-CoV-2 Crystal structure of the SARS-CoV-2 ExoN-nsp10 complex containing Mg2+ ion 2.10 7N0B SARS-CoV-2 Cryo-EM structure of SARS-CoV-2 nsp10-nsp14 (WT)- RNA complex 3.90 7N0C SARS-CoV-2 Cryo-EM structure of the monomeric form of SARS-CoV-2 nsp10-nsp14 (E191A)-RNA complex 3.40 7N0D SARS-CoV-2 Cryo-EM structure of the tetrameric form of SARS-CoV-2 nsp10-nsp14 (E191A)-RNA complex 2.50 7EIZ SARS-CoV-2 Coupling of N7-methyltransferase and 3'-5' exoribonuclease with SARS-CoV-2 polymerase reveals mechanisms for capping and proofreading 3.78 6XKM SARS-CoV-2 Room Temperature Structure of SARS-CoV-2 NSP10/NSP16 Methyltransferase in a Complex with SAM Determined by Fixed-Target Serial Crystallography 2.25 8BSD SARS-CoV-2 SARS-CoV-2 nsp10-16 methyltransferase in complex with tubercidin 1.95 8C5M SARS-CoV-2 SARS-CoV-2 nsp10-16 methyltransferase in complex with MTA 1.9 8OT0 SARS-CoV-2 SARS-CoV-2 nsp10-16 methyltransferase in complex with MTA and glycine 2.21 8OTO SARS-CoV-2 SARS-CoV-2 nsp10-16 methyltransferase in complex with AMP 1.8 8OV2 SARS-CoV-2 SARS-CoV-2 nsp10-16 methyltransferase in complex with Sangivamycin 1.86 8OV3 SARS-CoV-2 SARS-CoV-2 nsp10-16 methyltransferase in complex with 5-Iodotubercidin 1.82 8OV4 SARS-CoV-2 SARS-CoV-2 nsp10-16 methyltransferase in complex with Toyocamycin 1.93 8A23 SARS-CoV-2 Crystal structure of SARS-CoV-2 nsp10/nsp16 methyltransferase in complex with TO383 2.8 8F4S SARS-CoV-2 Crystal Structure of the SARS-CoV-2 2'-OMethyltransferase with Compound 5a bound to the Cryptic Pocket of nsp16 2.15 8F4Y SARS-CoV-2 Crystal Structure of SARS-CoV-2 2'-O-Methyltransferase in Complex with Compound 5a covalently bound to nsp16 and nsp10 2.13 7KOA SARS-CoV-2 Room Temperature Structure of SARS-CoV-2 nsp10/16 Methyltransferase in a Complex with Cap-0 and SAM Determined by Pink-Beam Serial Crystallography 2.40 6WKS SARS-CoV-2 Structure of SARS-CoV-2 nsp16/nsp10 in complex with RNA cap analogue (m7GpppA) and S-adenosylmethionine 1.8 7JPE SARS-CoV-2 Room Temperature Structure of SARS-CoV-2 Nsp10/Nsp16 Methyltransferase in a Complex with m7GpppA Cap-0 and SAM Determined by Fixed-Target Serial Crystallography 2.18 6WJT SARS-CoV-2 2.0 Angstrom Resolution Crystal Structure of nsp16-nsp10 Heterodimer from SARS-CoV-2 in Complex with S-AdenosylL-Homocysteine 2 7LW3 SARS-CoV-2 Structure of SARS-CoV-2 nsp16/nsp10 complex in presence of Cap-1 analog (m7GpppAmU) and SAH 2.3 7LW4 SARS-CoV-2 Structure of SARS-CoV-2 nsp16/nsp10 complex in presence of S-adenosyl-L-homocysteine (SAH) 2.5 7JHE SARS-CoV-2 Room Temperature Structure of SARS-CoV-2 nsp10/nsp16 Methyltransferase in a Complex with 2'-O-methylated 2.25 m7GpppA Cap-1 and SAH Determined by Fixed-Target Serial Crystallography Table 2. RMSF values (Å) for each residue of nsp10. RESIDUE RMSF RESIDUE RMSF RESIDUE RMSF Phe19 5,8201 Val57 0,536104 Lys95 0,549715 Ala20 3,50823 Thr58 0,618234 Tyr96 0,602921 Val21 1,5828 Pro59 0,37405 Val97 0,427929 Asp22 0,777806 Glu60 0,613266 Gln98 0,341622 Ala23 0,528362 Ala61 0,460623 Ile99 0,309611 Ala24 0,497857 Asn62 0,566037 Pro100 0,350423 Lys25 0,916308 Met63 1,11727 Thr101 0,578022 Ala26 0,461762 Asp64 0,607824 Thr102 0,485959 Tyr27 0,401876 Gln65 0,437603 Cys103 0,487528 Lys28 0,788167 Glu66 0,641971 Ala104 0,44258 Asp29 0,549919 Ser67 0,337974 Asn105 0,603582 Tyr30 0,768581 Phe68 0,376283 Asp106 0,314811 Leu31 0,532326 Gly69 0,314291 Pro107 0,30884 Ala32 0,591376 Gly70 0,364311 Val108 0,367631 Ser33 0,826151 Ala71 0,375075 Gly109 0,316099 Gly34 0,815863 Ser72 0,459513 Phe110 0,611959 Gly35 0,58484 Cys73 0,444282 Thr111 0,368274 Gln36 1,14311 Cys74 0,424957 Leu112 0,665826 Pro37 0,429392 Leu75 0,328316 Lys113 0,491701 Ile38 0,421764 Tyr76 0,469555 Asn114 0,429153 Thr39 0,666665 Cys77 0,474664 Thr115 0,692179 Asn40 0,661094 Arg78 0,438985 Val116 0,505459 Cys41 0,475023 Cys79 0,465674 Cys117 0,432967 Val42 0,525008 His80 0,850719 Thr118 0,774298 Lys43 0,571997 Ile81 0,602414 Val119 0,753032 Met44 0,428732 Asp82 0,689313 Cys120 0,630145 Leu45 0,717999 His83 0,531023 Gly121 0,368122 Cys46 0,544911 Pro84 0,680804 Met122 0,587032 Thr47 0,66467 Asn85 1,42938 Trp123 0,338881 His48 0,598463 Pro86 1,63621 Lys124 0,772571 Thr49 0,674142 Lys87 1,62468 Gly125 0,500507 Gly50 0,541001 Gly88 0,727877 Tyr126 0,803357 Thr51 0,724646 Phe89 1,50918 Gly127 0,660837 Gly52 0,495726 Cys90 0,477689 Cys128 0,712272 Gln53 0,587994 Asp91 0,927401 Ser129 1,06329 Ala54 0,554959 Leu92 0,435975 Cys130 1,15043 Ile55 0,569861 Lys93 0,57331 Thr56 0,418209 Gly94 0,325941 . Table 3. Substructures of nsp14. Residues Secondary structurea 26-28 η1 31-33 η2 34-35 β1 38-39 β2 53-55 β3 76-81 α1 83-85 η3 86-96 β4 104-111 β5 116-118 β6 122-126 β7 131-135 β8 138-139 β9 144-149 η4 151-154 η5 159-174 α2 182-185 β10 189-195 α3 199-200 β11 216-218 β12 223-225 β13 235-237 β14 240-243 β15 244-247 η6 253-257 α4 270-286 α5 302-320 α1’ 328-332 β1’ 248-251 β2’ 368-376 αA 381-385 β3’ 396-400 β4’ 433-437 αB 446-448 βA 473-475 βB 476-479 αC 485-502 α2’ 505-511 β5’ 516-520 α3’ Table 4. RMSF values (Å) for each residue of nsp14. RESIDUE RMSF RESIDUE RMSF RESIDUE RMSF Thr25 17,3786 Pro70 1,91258 Val115 0,897473 His26 17,0232 Asn71 1,21821 Asn116 0,848561 Leu27 14,7702 Met72 0,907916 Leu117 0,916107 Ser28 15,0218 Phe73 0,794768 Val118 1,04801 Val29 14,6737 Ile74 0,586242 Ala119 1,05831 Asp30 16,4586 Thr75 0,972264 Val120 1,29646 Thr31 17,573 Arg76 1,05206 Pro121 1,85414 Lys32 18,3122 Glu77 1,35763 Thr122 2,87111 Phe33 17,0806 Glu78 0,848642 Lys155 2,60102 Lys34 16,3096 Ala79 0,549549 Gly156 1,29453 Thr35 16,2939 Ile80 0,741134 Leu157 1,1537 Glu36 17,2954 Arg81 1,15876 Pro158 0,904313 Gly37 16,1635 His82 0,766142 Trp159 0,99008 Leu38 15,936 Val83 0,934459 Asn160 0,964433 Cys39 15,708 Arg84 0,630847 Val161 0,971099 Val40 17,7498 Ala85 0,403569 Val162 0,883655 Asp41 17,9983 Trp86 0,439482 Arg163 0,980364 Ile42 16,1629 Ile87 0,453582 Ile164 0,936769 Pro43 17,0909 Gly88 0,511434 Lys165 1,38632 Gly44 16,4962 Phe89 0,681106 Ile166 0,710038 Ile45 15,5016 Asp90 0,786387 Val167 0,845289 Pro46 16,4856 Val91 0,701118 Gln168 1,57969 Lys47 17,8057 Glu92 1,2472 Met169 0,781426 Asp48 17,0547 Gly93 1,13971 Leu170 0,873684 Met49 17,0669 Cys94 3,09272 Ser171 1,0556 Thr50 17,3559 His95 4,30977 Asp172 0,96103 Tyr51 15,6198 Ala96 4,00124 Thr173 0,829656 Arg52 14,7028 Thr97 4,49171 Leu174 0,760095 Arg53 10,9953 Arg98 7,44022 Lys175 1,02637 Leu54 9,40089 Glu99 6,41445 Asn176 1,07162 Ile55 8,21741 Ala100 4,8725 Leu177 0,949635 Ser56 5,95449 Val101 4,75873 Ser178 0,780219 Met57 3,92795 Gly102 3,54184 Asp179 1,13021 Met58 4,33177 Thr103 3,35345 Arg180 0,766528 Gly59 4,46968 Asn104 3,69241 Val181 0,518621 Phe60 3,66988 Leu105 2,33218 Val182 0,685801 Lys61 6,0921 Pro106 2,83172 Phe183 0,491341 Met62 3,96094 Leu107 1,9276 Val184 0,574136 Asn63 5,98618 Gln108 0,860218 Leu185 0,685508 Tyr64 4,29688 Leu109 0,664363 Trp186 0,649552 Gln65 3,90611 Gly110 0,534024 Ala187 1,28685 Val66 3,0944 Phe111 0,758057 His188 3,72208 Asn67 3,1851 Ser112 0,60396 Gly189 1,15117 Gly68 2,65784 Thr113 0,99233 Phe190 1,43941 Tyr69 2,97106 Gly114 0,799761 Glu191 1,39225 RESIDUE RMSF RESIDUE RMSF RESIDUE RMSF Leu192 1,24472 Tyr237 1,0878 Val282 0,467251 Thr193 1,0951 Asn238 0,784993 His283 0,757473 Ser194 1,07939 Pro239 0,658069 Glu284 0,805336 Met195 0,93347 Phe240 0,785859 Cys285 0,647048 Lys196 1,30751 Met241 0,693947 Phe286 0,730958 Tyr197 1,15776 Ile242 0,97821 Val287 0,988542 Phe198 1,1792 Asp243 1,01963 Lys288 2,01921 Val199 1,02174 Val244 0,683028 Arg289 3,38837 Lys200 1,57732 Gln245 0,931015 Val290 1,90386 Ile201 1,19703 Gln246 1,02856 Asp291 1,29665 Gly202 1,07897 Trp247 0,745689 Trp292 1,68058 Pro203 1,18352 Gly248 1,03333 Thr293 0,642726 Glu204 1,20063 Phe249 0,772476 Ile294 0,639476 Arg205 1,48631 Thr250 1,06825 Glu295 1,2614 Thr206 1,28641 Gly251 0,776032 Tyr296 0,732151 Cys207 1,20386 Asn252 0,934638 Pro297 0,646457 Cys208 1,40642 Leu253 0,7344 Ile298 0,827817 Leu209 1,68184 Gln254 0,828349 Ile299 1,20346 Cys210 1,3278 Ser255 0,797356 Gly300 0,875663 Asp211 1,26794 Asn256 0,725103 Asp301 1,32799 Arg212 1,20071 His257 0,753416 Glu302 1,28527 Arg213 1,02284 Asp258 1,01099 Leu303 0,971096 Ala214 0,957458 Leu259 0,917873 Lys304 1,0088 Thr215 1,15145 Tyr260 1,59262 Ile305 0,678945 Cys216 1,01061 Cys261 0,682321 Asn306 0,931877 Phe217 1,2508 Gln262 1,24644 Ala307 0,67795 Ser218 1,36281 Val263 0,894738 Ala308 0,601972 Thr219 1,49239 His264 0,786709 Cys309 0,695183 Ala220 1,78597 Gly265 0,938588 Arg310 1,4989 Ser221 1,74534 Asn266 2,06174 Lys311 0,806393 Asp222 1,49744 Ala267 2,5253 Val312 0,669873 Thr223 1,24042 His268 2,77839 Gln313 0,765923 Tyr224 1,19207 Val269 1,16994 His314 0,786049 Ala225 0,950998 Ala270 0,728756 Met315 0,911266 Cys226 0,948632 Ser271 0,688342 Val316 0,859231 Trp227 0,941191 Cys272 0,69211 Val317 0,881648 His228 0,997772 Asp273 0,562596 Lys318 1,09833 His229 1,21908 Ala274 0,463624 Ala319 0,843686 Ser230 1,096 Ile275 0,598585 Ala320 0,909746 Ile231 1,46232 Met276 0,568924 Leu321 1,11043 Gly232 1,23055 Thr277 0,388412 Leu322 1,34716 Phe233 1,32455 Arg278 0,427679 Ala323 1,0562 Asp234 1,02863 Cys279 0,451699 Asp324 1,2926 Tyr235 1,07422 Leu280 0,487897 Lys325 1,27305 Val236 0,7692 Ala281 0,44646 Phe326 1,20409 RESIDUE RMSF RESIDUE RMSF RESIDUE RMSF Pro327 1,22612 Thr372 5,79603 Gly417 0,775858 Val328 1,15237 His373 4,37319 Ser418 0,773129 Leu329 1,13523 Ser374 5,3534 Leu419 0,733186 His330 1,21734 Asp375 3,84268 Tyr420 0,849805 Asp331 1,11603 Lys376 3,24447 Val421 0,768454 Ile332 1,16233 Phe377 1,60826 Asn422 1,05362 Gly333 1,2419 Thr378 1,39515 Lys423 1,05777 Asn334 1,57256 Asp379 2,27187 His424 0,735054 Pro335 1,51378 Gly380 1,20953 Ala425 0,555272 Lys336 1,76934 Val381 0,879683 Phe426 0,903176 Ala337 1,70162 Cys382 1,00776 His427 0,793835 Ile338 1,37585 Leu383 0,899019 Thr428 0,963809 Lys339 1,30048 Phe384 1,00928 Pro429 0,902941 Cys340 0,914219 Trp385 0,711127 Ala430 0,999832 Val341 1,07626 Asn386 0,821109 Phe431 1,21045 Pro342 1,33877 Cys387 0,936039 Asp432 1,27879 Gln343 1,6884 Asn388 1,2317 Lys433 1,44553 Ala344 1,15784 Val389 1,07325 Ser434 0,930248 Asp345 1,76662 Asp390 1,39996 Ala435 0,869475 Val346 1,35904 Arg391 1,2935 Phe436 0,818381 Glu347 1,9057 Tyr392 1,00339 Val437 0,976947 Trp348 1,27439 Pro393 0,978239 Asn438 0,824232 Lys349 1,72953 Ala394 0,9401 Leu439 0,793817 Phe350 1,26836 Asn395 1,13061 Lys440 0,728196 Tyr351 1,39807 Ser396 0,83125 Gln441 1,06817 Asp352 1,81069 Ile397 0,731675 Leu442 0,821816 Ala353 2,07642 Val398 0,79956 Pro443 0,713645 Gln354 2,72604 Cys399 0,660064 Phe444 0,854212 Pro355 4,2759 Arg400 0,913415 Phe445 0,968268 Cys356 5,53015 Phe401 0,949784 Tyr446 1,07532 Ser357 7,33495 Asp402 0,964296 Tyr447 0,986592 Asp358 9,28995 Thr403 1,09375 Ser448 1,09469 Lys359 10,253 Arg404 1,16259 Asp449 1,44155 Ala360 9,20341 Val405 1,23224 Ser450 1,29927 Tyr361 8,15214 Leu406 2,13895 Pro451 1,38341 Lys362 8,78697 Ser407 1,07906 Cys452 1,76624 Ile363 6,50535 Asn408 1,0893 Glu453 2,69811 Glu364 5,94953 Leu409 1,05698 Ser454 3,36002 Glu365 4,21334 Asn410 1,1256 His455 5,82245 Leu366 2,24336 Leu411 0,627392 Gly456 6,89349 Phe367 3,75751 Pro412 0,631364 Lys457 8,98888 Tyr368 3,1232 Gly413 0,644577 Gln458 10,7161 Ser369 4,14811 Cys414 0,743976 Val459 12,3266 Tyr370 6,19649 Asp415 1,08308 Val460 12,7987 Ala371 5,87416 Gly416 0,886046 Ser461 11,3752 RESIDUE RMSF RESIDUE RMSF Asp462 10,7658 Ser507 0,691864 Ile463 9,3659 Leu508 0,716797 Asp464 6,4498 Trp509 0,680597 Tyr465 5,43109 Val510 0,858315 Val466 3,36542 Tyr511 1,01375 Pro467 1,89106 Lys512 1,09149 Leu468 2,38112 Gln513 1,29802 Lys469 2,32109 Phe514 0,926341 Ser470 1,60347 Asp515 1,32143 Ala471 1,39625 Thr516 1,45509 Thr472 1,24406 Tyr517 1,99968 Cys473 1,1217 Asn518 1,4656 Ile474 1,1565 Leu519 1,27455 Thr475 1,21139 Trp520 1,29413 Arg476 2,77147 Asn521 1,64872 Cys477 1,68278 Thr522 1,67599 Asn478 1,45928 Phe523 1,65963 Leu479 2,70399 Gly480 2,90282 Gly481 2,399 Ala482 2,04647 Val483 1,91636 Cys484 1,60441 Arg485 2,35788 His486 1,49256 His487 1,19769 Ala488 1,14685 Asn489 1,56516 Glu490 1,23263 Tyr491 1,03505 Arg492 1,82474 Leu493 1,21268 Tyr494 0,898709 Leu495 0,88376 Asp496 1,00966 Ala497 0,807312 Tyr498 0,78406 Asn499 0,907818 Met500 0,962664 Met501 0,83259 Ile502 1,19219 Ser503 0,996275 Ala504 0,864594 Gly505 0,851752 Phe506 0,850529 Table 4. RMSF values (Å) for each residue of nsp16. RESIDUE RMSF RESIDUE RMSF RESIDUE RMSF Ser2 1,00909 Thr48 0,241996 Leu94 0,723127 Gln3 0,710154 Gln49 0,231127 Leu95 0,360856 Ala4 0,390086 Leu50 0,186607 Val96 0,374815 Trp5 0,948751 Cys51 0,196594 Asp97 0,588954 Gln6 0,852605 Gln52 0,232731 Ser98 0,400799 Pro7 0,286983 Tyr53 0,195304 Asp99 0,517581 Gly8 0,234549 Leu54 0,202803 Leu100 0,678662 Val9 0,220359 Asn55 0,24972 Asn101 0,614397 Ala10 0,256059 Thr56 0,25547 Asp102 0,655466 Met11 0,336806 Leu57 0,278686 Phe103 0,479479 Pro12 0,325901 Thr58 0,293127 Val104 0,71338 Asn13 0,445763 Leu59 0,435495 Ser105 0,454735 Leu14 0,69797 Ala60 0,343058 Asp106 0,473504 Tyr15 0,602084 Val61 0,372537 Ala107 0,43339 Lys16 0,524373 Pro62 0,42615 Asp108 0,45432 Met17 0,567593 Tyr63 0,661058 Ser109 0,541459 Gln18 0,552156 Asn64 0,820551 Thr110 0,450107 Arg19 1,26485 Met65 0,410748 Leu111 0,578284 Met20 0,57724 Arg66 0,43521 Ile112 0,463678 Leu21 0,673525 Val67 0,309705 Gly113 0,455799 Leu22 0,477764 Ile68 0,297567 Asp114 0,774286 Glu23 0,906344 His69 0,265853 Cys115 0,926738 Lys24 0,801615 Phe70 0,379866 Ala116 0,933159 Cys25 0,458623 Gly71 0,302585 Thr117 0,692837 Asp26 0,667393 Ala72 0,320941 Val118 0,724343 Leu27 0,438936 Gly73 0,394663 His119 0,759203 Gln28 0,739728 Ser74 0,504158 Thr120 0,74724 Asn29 1,05031 Asp75 0,649272 Ala121 0,773192 Tyr30 1,0932 Lys76 1,21771 Asn122 0,850836 Gly31 1,38306 Gly77 0,448801 Lys123 0,501722 Asp32 1,04637 Val78 0,428892 Trp124 0,356238 Ser33 0,952597 Ala79 0,383661 Asp125 0,385392 Ala34 0,730261 Pro80 0,348047 Leu126 0,242399 Thr35 0,850932 Gly81 0,310539 Ile127 0,24819 Leu36 0,521219 Thr82 0,365559 Ile128 0,208493 Pro37 0,543788 Ala83 0,327374 Ser129 0,232782 Lys38 0,68911 Val84 0,303381 Asp130 0,318688 Gly39 0,491333 Leu85 0,300692 Met131 0,481017 Ile40 0,45301 Arg86 0,672852 Tyr132 0,681915 Met41 0,581845 Gln87 0,349024 Asp133 0,960581 Met42 0,458915 Trp88 0,301663 Pro134 1,67864 Asn43 0,571522 Leu89 0,369465 Lys135 2,07142 Val44 0,314295 Pro90 0,398464 Thr136 1,7612 Ala45 0,277477 Thr91 0,620053 Lys137 3,43119 Lys46 0,242192 Gly92 0,623066 Asn138 3,65722 Tyr47 0,235829 Thr93 0,486433 Val139 3,96853 RESIDUE RMSF RESIDUE RMSF RESIDUE RMSF Thr140 2,90973 Phe187 0,327544 Thr234 0,4277 Lys141 2,37052 Ala188 0,255656 Asn235 0,687517 Glu142 1,28291 Trp189 0,313699 Pro236 0,432782 Asn143 0,469469 Trp190 0,235639 Ile237 0,398273 Asp144 0,69052 Thr191 0,176448 Gln238 0,841395 Ser145 0,402165 Ala192 0,145225 Leu239 0,548386 Lys146 0,570827 Phe193 0,152324 Ser240 0,393325 Glu147 0,97932 Val194 0,160184 Ser241 0,447384 Gly148 0,439833 Thr195 0,22014 Tyr242 0,758258 Phe149 0,356878 Asn196 0,272782 Ser243 0,384069 Phe150 0,327693 Val197 0,461425 Leu244 0,389902 Thr151 0,584571 Asn198 0,48783 Phe245 0,575529 Tyr152 1,06058 Ala199 0,317816 Asp246 0,522897 Ile153 0,416106 Ser200 0,321647 Met247 0,414358 Cys154 0,294478 Ser201 0,285759 Ser248 0,469632 Gly155 0,304047 Ser202 0,25135 Lys249 0,828547 Phe156 0,551654 Glu203 0,270322 Phe250 0,332408 Ile157 0,371855 Ala204 0,156746 Pro251 0,351813 Gln158 0,541086 Phe205 0,50676 Leu252 0,366358 Gln159 0,644612 Leu206 0,308289 Lys253 1,28403 Lys160 0,506617 Ile207 0,129528 Leu254 0,924934 Leu161 0,330971 Gly208 0,175682 Arg255 1,15519 Ala162 0,316712 Cys209 0,248314 Gly256 0,504304 Leu163 0,373873 Asn210 0,305108 Thr257 0,48098 Gly164 0,302165 Tyr211 0,324232 Ala258 0,461456 Gly165 0,236746 Leu212 0,376452 Val259 0,503844 Ser166 0,201091 Gly213 0,414089 Met260 0,729275 Val167 0,242361 Lys214 0,559587 Ser261 0,717336 Ala168 0,157063 Pro215 0,452518 Leu262 0,712876 Ile169 0,16798 Arg216 0,775405 Lys263 1,48867 Lys170 0,278019 Glu217 0,917411 Glu264 1,48382 Ile171 0,196708 Gln218 0,838245 Gly265 0,774606 Thr172 0,236062 Ile219 0,40042 Gln266 0,855728 Glu173 0,35712 Asp220 0,418707 Ile267 0,838403 His174 0,580737 Gly221 0,372379 Asn268 0,747503 Ser175 0,312063 Tyr222 0,902203 Asp269 0,698581 Trp176 0,300117 Val223 0,371621 Met270 0,822446 Asn177 0,286661 Met224 0,331642 Ile271 0,565215 Ala178 0,290296 His225 0,34051 Leu272 0,610294 Asp179 0,375653 Ala226 0,325287 Ser273 0,549848 Leu180 0,306272 Asn227 0,341725 Leu274 0,488303 Tyr181 0,253746 Tyr228 0,279755 Leu275 0,437814 Lys182 0,529374 Ile229 0,356234 Ser276 0,453147 Leu183 0,595239 Phe230 0,456486 Lys277 0,583203 Met184 0,274125 Trp231 0,343455 Gly278 0,451009 Gly185 0,275854 Arg232 0,379084 Arg279 1,05557 His186 0,404593 Asn233 0,411247 Leu280 0,432172 Table 5. SARS-CoV-2 Nsp14 regions exhibiting changes in secondary structure. Residues Secondary Structure (%) α-helix β-sheet Coil His26-Ser28 31 0 69 Lys32-Phe33 0 15 85 Glu36-Leu38 15 0 85 Met49-Thr50 0 15 85 Tyr51-Met58 31 61 8 Gln65-Asp67 15 0 85 Arg76-Arg81 85 0 15 Val83-Ala85 46 0 54 Ala100-Gly102 8 0 92 Gly156-Pro158 0 31 69 Val199-Lys200 0 31 69 Cys216-Ser218 0 92 8 Thr223-Ala225 0 92 8 Trp227-His229 15 0 85 Tyr235-Tyr237 0 77 23 Val244-Trp247 77 0 23 Leu253-Tyr260 92 8 0 Ser357-Lys359 8 0 92 Ala360-Lys362 8 0 92 Ile363-Phe367 15 85 0 Tyr370-Asp375 46 0 54 Asn410-Pro412 0 92 8 Cys414-Gly416 8 0 92 Lys433-Phe436 85 0 15 Leu439-Gln441 0 92 8 Tyr446-Ser448 0 85 15 Asp462-Tyr465 8 0 92 Cys473-Thr475 0 85 15 Arg476-Leu479 61 0 39 Thr516-Phe523 85 0 15 Table 6. RMSF values (Å) for each residue of nsp16. RESIDUE RMSF RESIDUE RMSF RESIDUE RMSF Ser2 1,00909 Thr48 0,241996 Leu94 0,723127 Gln3 0,710154 Gln49 0,231127 Leu95 0,360856 Ala4 0,390086 Leu50 0,186607 Val96 0,374815 Trp5 0,948751 Cys51 0,196594 Asp97 0,588954 Gln6 0,852605 Gln52 0,232731 Ser98 0,400799 Pro7 0,286983 Tyr53 0,195304 Asp99 0,517581 Gly8 0,234549 Leu54 0,202803 Leu100 0,678662 Val9 0,220359 Asn55 0,24972 Asn101 0,614397 Ala10 0,256059 Thr56 0,25547 Asp102 0,655466 Met11 0,336806 Leu57 0,278686 Phe103 0,479479 Pro12 0,325901 Thr58 0,293127 Val104 0,71338 Asn13 0,445763 Leu59 0,435495 Ser105 0,454735 Leu14 0,69797 Ala60 0,343058 Asp106 0,473504 Tyr15 0,602084 Val61 0,372537 Ala107 0,43339 Lys16 0,524373 Pro62 0,42615 Asp108 0,45432 Met17 0,567593 Tyr63 0,661058 Ser109 0,541459 Gln18 0,552156 Asn64 0,820551 Thr110 0,450107 Arg19 1,26485 Met65 0,410748 Leu111 0,578284 Met20 0,57724 Arg66 0,43521 Ile112 0,463678 Leu21 0,673525 Val67 0,309705 Gly113 0,455799 Leu22 0,477764 Ile68 0,297567 Asp114 0,774286 Glu23 0,906344 His69 0,265853 Cys115 0,926738 Lys24 0,801615 Phe70 0,379866 Ala116 0,933159 Cys25 0,458623 Gly71 0,302585 Thr117 0,692837 Asp26 0,667393 Ala72 0,320941 Val118 0,724343 Leu27 0,438936 Gly73 0,394663 His119 0,759203 Gln28 0,739728 Ser74 0,504158 Thr120 0,74724 Asn29 1,05031 Asp75 0,649272 Ala121 0,773192 Tyr30 1,0932 Lys76 1,21771 Asn122 0,850836 Gly31 1,38306 Gly77 0,448801 Lys123 0,501722 Asp32 1,04637 Val78 0,428892 Trp124 0,356238 Ser33 0,952597 Ala79 0,383661 Asp125 0,385392 Ala34 0,730261 Pro80 0,348047 Leu126 0,242399 Thr35 0,850932 Gly81 0,310539 Ile127 0,24819 Leu36 0,521219 Thr82 0,365559 Ile128 0,208493 Pro37 0,543788 Ala83 0,327374 Ser129 0,232782 Lys38 0,68911 Val84 0,303381 Asp130 0,318688 Gly39 0,491333 Leu85 0,300692 Met131 0,481017 Ile40 0,45301 Arg86 0,672852 Tyr132 0,681915 Met41 0,581845 Gln87 0,349024 Asp133 0,960581 Met42 0,458915 Trp88 0,301663 Pro134 1,67864 Asn43 0,571522 Leu89 0,369465 Lys135 2,07142 Val44 0,314295 Pro90 0,398464 Thr136 1,7612 Table 10. Interactions of Leu45 from Nsp10 of Nsp10-Nsp14 complex for every PDB considered and divided by energy of mutation. AA Medium Low LEU45 PDB Structure ΔΔG Interactions PDB Structure ΔΔG Interactions 7MC5 1,01 HB(bb): CYS39 Alkyl: LEU38 7EGQ_HK 0,69 HB(bb): CYS39 Alkyl: VAL40 7MC6 1,03 HB(bb): CYS39 Alkyl: LEU38 VAL40 7EIZ 0,57 HB(bb): CYS39 Alkyl: LEU38 VAL40 Table 11. Interactions of Lys93 from Nsp10 of Nsp10-Nsp16 complex for every PDB considered and divided by energy of mutation. AA Medium Low PDB Structure ΔΔG Interactions PDB Structure ΔΔG Interactions LYS93 7ULT 1.05 HB: ALA6905 CH: SER6903 6W4H 0.7 HB: SER6903 6WKQ 1.02 HB: SER6903 6W61 0.57 HB: SER6903 6WVN 1.21 HB: SER6903 6W75 0.81 HB: SER6903 7JYY 1.08 HB: ALA6905 CH: SER6903 6WJT 0.83 HB: SER6903 CH: ALA6905 7L6R 1.29 HB: ALA6905, SER6903 CH: SER6903 7JZ0 0.89 HB: ALA6905, SER6903 CH: SER6903 6WQ3 1.47 HB: ALA6905, SER6903 CH: SER6903 7L6T 0.99 HB: SER6903 CH: ALA6905 6WRZ 1.49 HB: ALA6905 8BSD 0.63 HB: SER6903 CH: ASP6904 8OT0 1 HB: SER6903 8BZV 0.81 HB: SER6903 CH: ASP6904 8OV2 1.27 HB: ALA6905, SER6903 CH: SER6903 8C5M 0.96 HB: SER6903 8OTO 1.17 HB: ALA6905, SER6903 CH: SER6903 8OV3 0.72 HB: SER6903 CH: SER6903 6wks 1.21 HB: ALA6905(107), SER6903(105) 8OV4 0.57 HB: SER6903 CH: ALA6905, SER6903 7JHE 1.14 HB: ALA6905(107), SER6903(105) CH: SER6903(105) 8F4S 0.85 HB: SER6903 ALA6905 7LW3 1 HB: SER6903(105) CH: SER6903(105) 8F4Y_cov 0.81 HB: SER6903 7LW4 1.34 HB: SER6903(105) 8F4Y_nocov 0.82 HB: SER6903 7R1U 1.22 HB: ALA6905(107), SER6903(105) CH: ASP6904(106) 7KOA 0.93 HB: SER6903(105) CH: ASP6904(106) 8A23 1.76 HB: 6XKM 0.94 HB: ALA6905(107), SER6903(105) SER6903(105) 6YZ1 0.9 HB: SER6903(105) CH: ALA6905(107) 7BQ7 0.97 HB: ALA6905(107) CH: SER6903(105) , ALA6905(107) 7C2I 0.77 HB: SER6903(105) 7C2J 0.84 HB: SER6903(105) CH: ASP6904(106) 7JPE 0.53 HB: SER6903(105) Table 12. Interactions of Lys93 from Nsp10 of Nsp10-Nsp14 complex for every PDB considered and divided by energy of mutation. AA High Medium Low LYS4346/93 PDB Structure ΔΔG Interactions PDB Structure ΔΔG Interactions PDB Structure ΔΔG Interactions 7DIY 2,33 HB: TYR51 THR127 Ionic: ASP126 CHO: GLN22 7EGQ_UX 1,22 HB: TYR51 7MC5 2,05 HB: TYR51 THR127 CHO: GLN22 7EGQ_HK 1,96 HB: THR127 Ionic: ASP126 7MC6 2,31 HB: THR127 Ionic: ASP126 CHO: GLN22 7N0B 2,65 Ionic: ASP126 7N0C 3,69 HB: TYR51 Ionic: ASP126 7N0D 2,38 HB: THR127 Ionic: ASP126 7EIZ 2,62 HB: ASN130 THR127 Ionic: ASP126 Table 13. Interactions of Val21 of Nsp10 from Nsp10-Nsp14 complex for every PDB considered and divided by energy of mutation. AA Medium Low PHE 4272/19 PDB Structure ΔΔG Interactions PDB Structure ΔΔG Interactions 7MC5 1,04 Alkyl: LYS200 Pi-alkyl: TYR237 Pi-sigma: PHE217 HB(bb): ILE201 7DIY 0,92 Alkyl: LYS200 Pi-sigma: PHE217 HB(bb): ILE201 7N0B 1,44 Alkyl: LYS200 Pi-sigma: PHE217 HB(bb): ILE201 7MC6 0,82 Alkyl: LYS200 Pi-alkyl: PHE217 HB(bb): ILE201 7N0D 1,16 Alkyl: LYS200 Pi-alkyl: TYR237 Pi-sigma: PHE217 HB(bb): ILE201 7N0C 0,96 Alkyl: LYS200 Pi-alkyl: TYR237 Pi-sigma: PHE217 HB(bb): ILE201 7EGQ_UX 1,24 Alkyl: LYS200 Pi-alkyl: PHE217 HB(bb): ILE201 7EGQ_HK 0,72 Alkyl: LYS200 Pi-alkyl: PHE217 HB(bb): ILE201 Table 6. Interactions of Phe 8 of Nsp14 from Nsp10-Nsp14 complex for every PDB considered and divided by energy of mutation. Medium Low PHE8 PDB Structure ΔΔG Interactions PDB Structure ΔΔG Interactions 7DIY 1,8 Pi-alkyl: LEU14 Pi-cation: HIS80 7MC5 0,55 Pi-alkyl: LEU14 Pi-cation: HIS80 Pi-Sulfur: MET57 HB(bb): THR5 7N0B 1,74 Pi-alkyl: LEU14 CHO: HIS80 7MC6 0,61 Pi-alkyl: LEU14 Pi-cation: HIS80 Pi-Sulfur: MET57 HB(bb): THR5 7N0C 1,49 Pi-alkyl: LEU14 CHO: HIS80 7N0D 0,83 Pi-alkyl: LEU14 Pi-Sulfur: MET57 CHO: HIS80 7EGQ_UX 1,4 Pi-alkyl: LEU14 Pi-Pi stacked: HIS80 7EGQ_HK 1,43 Pi-alkyl: LEU14 HB(bb): THR5 7EIZ 1,54 Pi-alkyl: LEU14 Pi-Pi T-shaped: HIS80 HB(bb): THR5 Table 14. Interactions of Val 66 of Nsp14 from Nsp10-Nsp14 complex for every PDB considered and divided by energy of mutation. AA Medium Low VAL66 PDB Structure ΔΔG Interactions PDB Structure ΔΔG Interactions 7DIY 1,48 Pi-alkyl: PHE16 7MC5 1,61 Pi-alkyl: PHE16 7MC6 1,63 Pi-alkyl: PHE16 7N0B 1,87 Pi-alkyl: PHE16 7N0C 1,76 Pi-alkyl: PHE16 7N0D 1,45 Pi-alkyl: PHE16 7EGQ_UX 1,43 Pi-alkyl: PHE16 7EGQ_HK 1,45 Pi-alkyl: PHE16 Table 15. Interactions of Asn130 of Nsp14 from Nsp10-Nsp14 complex for every PDB considered and divided by energy of mutation. AA Medium Low ASN130 PDB Structure ΔΔG Interactions PDB Structure ΔΔG Interactions 7EIZ 1 HB(bb): LYS93 7MC5 0,52 HB: Asp82, HIS83 HB(bb): GLY88 Table 16. Interactions of Lys196 of Nsp14 from Nsp10-Nsp14 complex for every PDB considered and divided by energy of mutation. AA Medium Low LYS196 PDB Structure ΔΔG Interactions PDB Structure ΔΔG Interactions 7N0B 1,47 Pi-alkyl: PHE19 7DIY 0,82 Pi-alkyl: PHE19 CH-O: ALA18 7N0C 1,28 Pi-alkyl: PHE19 Alkyl: ALA18 7N0D 0,76 Pi-alkyl: PHE19 7EIZ 1,29 Pi-alkyl: PHE19 Alkyl: ALA18 7EGQ_UX 0,55 Pi-alkyl: PHE19 HB: ALA18 Table 17. Interactions of Lys200 of Nsp14 from Nsp10-Nsp14 complex for every PDB considered and divided by energy of mutation. AA High Medium Low LYS20 0 PDB Structur e ΔΔ G Interaction s PDB Structur e ΔΔ G Interaction s PDB Structure ΔΔ G Interaction s 7EIZ 2,21 Ionic: ASP82 HB: ALA18 and ALA20 7N0B 1,31 HB: ALA20 Alkyl: VAL21 7DIY 0,56 HB: ALA20 Alkyl: VAL21 Alkyl: VAL21 7N0D 1,13 Alkyl: VAL21 7MC6 0,54 Alkyl: VAL21 7N0C 0,91 Alkyl: VAL21 7EGQ_U X 0,59 Alkyl: VAL21 CHO: PHE19 7EGQ_H K 0,63 Alkyl: VAL21 Table 18. Interactions of Ile201 of Nsp14 from Nsp10-Nsp14 complex for every PDB considered and divided by energy of mutation. AA Medium Low ILE201 PDB Structure ΔΔG Interactions PDB Structure ΔΔG Interactions 7DIY 1,21 HB: VAL21, PHE19 7N0D 0,96 HB: VAL21, PHE19 Alkyl: ALA20 7MC5 1,35 HB: VAL21, PHE19 7EGQ_UX 0,61 HB: VAL21, PHE19 CHO: ALA20 7MC6 1,3 HB: VAL21, PHE19 Alkyl: ALA20 7EGQ_HK 1,53 HB: VAL21, PHE19 7EIZ 1,08 HB: VAL21, PHE19 Alkyl: ALA20 Table 19. Interactions of Val42 of Nsp16 from Nsp10-Nsp16 complex for every PDB considered and divided by energy of mutation. AA Medium Low PDB Structure ΔΔG Interactions PDB Structure ΔΔG Interactions VAL44(6842) 7ULT 1.04 No interaction 6W4H 0.95 No interaction 8BSD 1.01 No interaction 6W61 0.94 No interaction 8BZV 1.04 No interaction 6W75 0.94 No interaction 8OT0 1.06 No interaction 6WJT 0.88 No interaction 8OV2 1 No interaction 6WKQ 0.83 No interaction 8OV3 1.02 No interaction 6WVN 0.81 No interaction 8F4S 1.15 No interaction 7JYY 0.9 No interaction 8F4Y_cov 1.03 No interaction 7JZ0 0.9 No interaction 8F4Y_nocov 1.02 No interaction 7L6R 0.72 No interaction 7BQ7 1 No interaction 7L6T 0.77 No interaction 8A23 1.1 No interaction 8C5M 0.96 No interaction 6WQ3 0.77 No interaction 8OV4 0.92 No interaction 8OTO 0.97 No interaction 6wks 0.92 No interaction 7KOA 0.89 No interaction 6XKM 0.91 No interaction 6YZ1 0.93 No interaction 7C2I 0.93 No interaction 7C2J 0.69 No interaction 7JHE 0.86 No interaction 7JPE 0.92 No interaction 7LW3 0.88 No interaction 7LW4 0.71 No interaction 7R1U 0.87 No interaction 7JPE_B Nsp10 bound to nsp16, SAM and Cap-0 7KOA_B Nsp10 bound to nsp16, SAM and Cap-0 8BSD_B Nsp10 bound to nsp16 and the inhibitors analogues of SAM/SAH 8BZV_B Nsp10 bound to nsp16 and the inhibitors analogues of SAM/SAH 8C5M_B Nsp10 bound to nsp16 and the inhibitors analogues of SAM/SAH 8OT0_B Nsp10 bound to nsp16 and the inhibitors analogues of SAM/SAH 8OTO_B Nsp10 bound to nsp16 and the inhibitors analogues of SAM/SAH 8OV2_B Nsp10 bound to nsp16 and the inhibitors analogues of SAM/SAH 8OV3_B Nsp10 bound to nsp16 and the inhibitors analogues of SAM/SAH 8OV4_B Nsp10 bound to nsp16 and the inhibitors analogues of SAM/SAH 8A23_B Nsp10 bound to nsp16 and the inhibitors analogues of SAM/SAH 10 5YN5_B MERS-CoV Nsp10 bound to nsp16 without cofactor and substrate 5YN6_B Nsp10 bound to nsp16 and the cofactor SAM 5YN8_B Nsp10 bound to nsp16 and the cofactor SAH 5YNB_B Nsp10 bound to nsp16 and the inhibitors analogues of SAM/SAH 5YNF_B Nsp10 bound to nsp16 and cap-0 5YNI_B Nsp10 bound to nsp16, SAM and Cap-0 5YNJ_B Nsp10 bound to nsp16 and Cap-0 5YNM_B Nsp10 bound to nsp16, SAM and Cap-0 5YNO_B Nsp10 bound to nsp16, SAH and Cap-0 5YNP_B Nsp10 bound to nsp16 and the inhibitors analogues of SAM/SAH and Cap-0 5YNQ_B Nsp10 bound to nsp16, SAH and Cap-0 11 7LW3_B SARS-CoV-2 Nsp10 bound to nsp16, SAH and Cap-1 12 7LW4_B SARS-CoV-2 Nsp10 bound to nsp16 and the cofactor SAH 13 7EIZ_H SARS-CoV-2 Nsp10 in monomeric form of the SARS-CoV2 replication-transcription complex Table 26. Nsp14 structural clusters Cluster PDB ID+chain Species Functional State 1 7EGQ_K SARS-CoV-2 Nsp14 in dimeric form of the SARSCoV-2 replication-transcription complex 7EGQ_X 7QGI_D SARS-CoV-2 Nsp14 APO form 2 7QIF_D Nsp14 bound to Cap-0 7R2V_A Nsp14 APO form bound to SAH 7R2V_B 7DIY_B SARS-CoV-2 7MC5_A Nsp14-exoribonuclease domain bound to nsp10 7MC6_A 5C8S_D SARS-CoV Nsp14 bound to nsp10, RNA and SAH 3 5C8T_D Nsp14 bound to nsp10 and the cofactor SAH 5C8U_D Nsp14 bound to nsp10 5NFY_A 5NFY_B 5NFY_C 5NFY_D 5C8S_B SARS-CoV Nsp14 bound to nsp10 and the cofactor SAH 4 5C8T_B Nsp14 bound to nsp10 and the cofactor SAH 5C8U_B Nsp14 bound to nsp10 7N0B_B SARS-CoV-2 Nsp14 bound to nsp10 and RNA 7N0C_B 7N0D_B 5 7N0D_D 7N0D_F 7N0D_H 6 7EIZ SARS-CoV-2 Nsp14 in monomeric form of the SARS-CoV-2 replication-transcription complex Table 20. Nsp16 structural clusters. Cluster PDB ID+chain Species Functional State 7R1U_A Nsp16 bound to nsp10, SAM and Cap-0 6W4H_A Nsp16 bound to nsp10 and the cofactor SAM 7BQ7_A Nsp16 bound to nsp10 and the cofactor SAM 6YZ1_A Nsp16 bound to nsp10 and the inhibitors analogues of SAM/SAH 6W61_A Nsp16 bound to nsp10 and the cofactor SAM 7C2I_A Nsp16 bound to nsp10 and the cofactor SAM 7C2J_A Nsp16 bound to nsp10 and the cofactor SAM 6WKQ_A Nsp16 bound to nsp10 and the inhibitors analogues of SAM/SAH 6WKQ_C Nsp16 bound to nsp10 and the inhibitors analogues of SAM/SAH 6WJT_A Nsp16 bound to nsp10 and the cofactor SAH 6WJT_C Nsp16 bound to nsp10 and the cofactor SAH 6WVN_A Nsp16 bound to nsp10, SAM and Cap-0 6W75_A Nsp16 bound to nsp10 and the cofactor SAM 6W75_C Nsp16 bound to nsp10 and the cofactor SAM 1 7JZ0_A SARS-CoV-2 Nsp16 bound to nsp10, SAH and Cap-1 7JZ0_C Nsp16 bound to nsp10, SAH and Cap-1 6WRZ_A Nsp16 bound to nsp10, SAH and Cap-0 6WQ3_A Nsp16 bound to nsp10, SAH and Cap-0 7JYY_A Nsp16 bound to nsp10, SAM and Cap-0 7JYY_C Nsp16 bound to nsp10, SAM and Cap-0 7L6R_A Nsp16 bound to nsp10, SAH and Cap-1 7L6T_A Nsp16 bound to nsp10, SAH and Cap-1 7ULT_A Nsp16 bound to nsp10 without cofactor and substrate 7ULT_C Nsp16 bound to nsp10 without cofactor and substrate 6WKS_A Nsp16 bound to nsp10, SAM and Cap-0 6XKM_A Nsp16 bound to nsp10 and the cofactor SAM 7JHE_A Nsp16 bound to nsp10, SAH and Cap-1 7JPE_A Nsp16 bound to nsp10, SAM and Cap-0 7KOA_A Nsp16 bound to nsp10, SAM and Cap-0 8BSD_A Nsp16 bound to nsp10 and the inhibitors analogues of SAM/SAH 8BZV_A Nsp16 bound to nsp10 and the inhibitors analogues of SAM/SAH 8C5M_A Nsp16 bound to nsp10 and the inhibitors analogues of SAM/SAH 8OT0_A Nsp16 bound to nsp10 and the inhibitors analogues of SAM/SAH 8OTO_A Nsp16 bound to nsp10 and the inhibitors analogues of SAM/SAH 8OV2_A Nsp16 bound to nsp10 and the inhibitors analogues of SAM/SAH 8OV3_A Nsp16 bound to nsp10 and the inhibitors analogues of SAM/SAH 8OV4_A Nsp16 bound to nsp10 and the inhibitors analogues of SAM/SAH 8A23_A Nsp16 bound to nsp10 and the inhibitors analogues of SAM/SAH 8F4S_A Nsp16 bound to nsp10 and allosteric inhibitors 8F4Y_A Nsp16 bound to nsp10 and allosteric inhibitors 5YN5_A Nsp16 bound to nsp10 without cofactor and substrate 5YN6_A Nsp16 bound to nsp10 and the cofactor SAM 5YNB_A Nsp16 bound to nsp10 and the inhibitors analogues of SAM/SAH 5YNF_A Nsp16 bound to nsp10 and cap-0 5YNI_A Nsp16 bound to nsp10, SAM and Cap-0 5YNJ_A Nsp16 bound to nsp10 and Cap-0 5YNM_A MERS-CoV Nsp16 bound to nsp10, SAM and Cap-0 5YNO_A Nsp16 bound to nsp10, SAH and Cap-0 5YNP_A Nsp16 bound to nsp10 and the inhibitors analogues of SAM/SAH and Cap-0 5YNQ_A Nsp16 bound to nsp10, SAH and Cap-0 2XYQ_A Nsp16 bound to nsp10 and the cofactor SAH 2XYR_A Nsp16 bound to nsp10 and the inhibitors analogues of SAM/SAH 2XYV_A SARS-CoV Nsp16 bound to nsp10 and the cofactor SAH 3R24_A Nsp16 bound to nsp10 and the cofactor SAM 5YN8_A Nsp16 bound to nsp10 and the cofactor SAH 2 7LW3_A SARS-CoV-2 Nsp16 bound to nsp10, SAH and Cap-1 3 7LW4_A SARS-CoV-2 Nsp16 bound to nsp10 and the cofactor SAH Appendix F Table 1. Ligand-protein nonbonded interaction energies (kcal/mol) of the minimized hCav 3.1-DM1 docked complexes. Cluster Ligand Conformer Starting Binding area Pose Nonbonded interaction energies (kcal/mol) vdW interaction energies (kcal/mol) Electrostatic Interaction Energy (kcal/mol) 1 1B BS1 119 -45.8919 -32.1119 -13.78 2 1B BS1 101 -45.8601 -33.0348 -12.8253 3 1A BS1 64 -44.1931 -32.5893 -11.6037 4 1B BS1 112 -41.2559 -29.0154 -12.2405 5 1B BS1 55 -41.1739 -28.6655 -12.5084 6 1A BS1 63 -39.4157 -28.4242 -10.9915 7 1A BS1 72 -38.0692 -32.7384 -5.33079 8 1A BS2 224 -37.689 -21.9423 -15.7467 9 1B BS1 83 -36.2362 -31.3223 -4.91388 10 1B BS1 151 -36.0604 -23.5273 -12.5332 11 1B BS2 45 -35.6707 -23.0986 -12.5721 12 1A BS1 89 -35.3076 -30.4899 -4.81769 13 1A BS1 60 -35.2537 -30.1083 -5.14541 14 1A BS2 210 -34.9317 -24.4629 -10.4687 15 1A BS1 71 -34.059 -26.0283 -8.03075 16 1A BS1 199 -34.0138 -26.6948 -7.31903 17 1A BS1 104 -33.7124 -30.8277 -2.88469 18 1B BS2 9 -33.534 -22.7951 -10.739 19 1B BS1 240 -33.1051 -29.4344 -3.67071 20 1B BS1 80 -33.098 -28.5088 -4.58916 21 1B BS2 1 -31.2629 -20.4711 -10.7918 22 1A BS2 77 -31.0412 -20.5125 -10.5287 23 1A BS2 67 -30.6331 -19.1556 -11.4775 24 1A BS2 223 -27.7984 -24.6815 -3.11695 25 1A BS2 18 -26.8243 -18.5289 -8.29533 26 1B BS2 149 -26.7283 -16.4883 -10.24 27 1B BS2 109 -26.4708 -14.3109 -12.1599 28 1B BS2 205 -24.3211 -21.6161 -2.70508 29 1B BS2 133 -24.0073 -22.6183 -1.38904 30 1B BS2 219 -22.3782 -21.6773 -0.70093 31 1B BS2 8 -21.7828 -18.6248 -3.15805 32 1A BS2 53 -21.1178 -17.9474 -3.1704 33 1A BS2 118 -20.8806 -19.1276 -1.75302 Table 2. Ligand-protein nonbonded interaction energies (kcal/mol) of the minimized hCav 3.1-DM2 docked complexes. Cluster Ligand Conforme r Startin g Binding area Pos e Nonbonde d interaction energies (kcal/mol) vdW interactio n energies (kcal/mol) Electrostati c Interaction Energy (kcal/mol) 1 2B BS1 32 -47.5358 -33.5137 -14.0221 2 1A BS1 175 -46.5379 -34.8788 -11.6591 3 2A BS1 5 -45.6616 -31.4881 -14.1735 4 1B BS1 67 -45.6162 -31.8135 -13.8026 5 2B BS2 27 -44.9982 -28.5799 -16.4184 6 2B BS1 39 -44.3626 -31.6753 -12.6874 7 1A BS1 189 -42.4087 -30.4685 -11.9403 8 1A BS1 60 -42.1887 -29.4221 -12.7665 9 1B BS1 158 -41.8783 -30.3017 -11.5766 10 1B BS1 25 -41.5111 -29.4197 -12.0914 11 1B BS1 84 -41.0219 -29.9985 -11.0234 12 2A BS2 211 -40.8569 -30.7761 -10.0809 13 2B BS1 200 -40.4729 -27.896 -12.577 14 1A BS2 37 -40.4145 -25.3688 -15.0458 15 2B BS1 199 -40.0603 -28.7809 -11.2794 16 2A BS1 195 -40.0112 -30.7039 -9.30726 17 2B BS1 231 -39.5073 -28.6337 -10.8736 18 1A BS1 156 -39.3753 -35.7746 -3.60079 19 2B BS2 218 -38.9917 -24.7643 -14.2275 20 2A BS2 89 -38.8676 -27.4474 -11.4203 21 2B BS2 92 -38.6237 -23.8817 -14.742 22 2B BS1 103 -38.1719 -27.0776 -11.0943 23 2A BS1 216 -38.0995 -28.8873 -9.21217 24 1A BS1 144 -38.0364 -27.1862 -10.8502 25 2A BS1 48 -37.4763 -33.1075 -4.36877 26 1B BS1 60 -37.1665 -28.5742 -8.59232 27 1B BS1 19 -36.8732 -33.5594 -3.31388 28 2B BS2 28 -36.8335 -24.8097 -12.0238 29 2A BS1 138 -36.6241 -26.46 -10.164 30 1B BS1 227 -36.5407 -24.8497 -11.691 31 1A BS1 70 -36.5176 -26.7135 -9.80411 32 1B BS1 207 -36.3178 -23.7947 -12.523 33 1A BS1 110 -36.0331 -31.7609 -4.27228 34 1A BS1 138 -35.8619 -26.4948 -9.36705 35 1A BS1 184 -35.7636 -31.805 -3.95857 36 2A BS2 86 -35.7551 -22.4635 -13.2916 37 1B BS1 47 -34.9076 -28.6944 -6.21322 38 2A BS2 45 -34.8813 -23.0829 -11.7984 39 1A BS2 216 -34.8348 -22.947 -11.8877 40 2B BS2 215 -34.7853 -22.9669 -11.8184 41 2B BS2 69 -34.3784 -26.6052 -7.77322 42 1B BS1 55 -33.5875 -29.4212 -4.16635 43 2B BS2 2 -33.5082 -21.2678 -12.2405 44 2B BS2 63 -32.7222 -21.6184 -11.1038 45 2A BS1 242 -32.7056 -30.7857 -1.91985 46 2B BS2 1 -32.3099 -20.0688 -12.2411 47 1B BS1 102 -32.1687 -28.0426 -4.12618 48 1B BS2 21 -32.0081 -19.7671 -12.241 49 1A BS1 124 -31.9762 -22.8632 -9.11304 50 1A BS1 101 -31.7537 -28.6325 -3.12125 51 1A BS1 68 -31.2976 -23.3981 -7.89955 52 1B BS2 147 -30.8627 -19.6809 -11.1818 53 2A BS2 70 -30.7758 -21.7481 -9.02773 54 1B BS2 138 -30.0629 -19.3483 -10.7146 55 1A BS2 138 -29.7321 -24.6138 -5.11827 56 2A BS2 52 -29.2948 -17.0967 -12.1981 57 1B BS2 44 -28.8918 -16.4962 -12.3956 58 2A BS2 41 -28.5653 -18.1339 -10.4314 59 1A BS2 35 -27.8308 -19.2208 -8.60999 60 1A BS2 12 -27.1165 -16.0319 -11.0847 61 2A BS2 121 -27.0708 -27.5568 0.485971 62 2A BS2 53 -26.803 -18.1664 -8.63653 63 2B BS2 135 -26.6127 -24.1801 -2.43251 64 1B BS2 116 -26.073 -17.2846 -8.78839 65 2B BS2 8 -24.9721 -21.4888 -3.48328 66 1A BS2 33 -24.1568 -22.9569 -1.19997 67 2A BS2 74 -22.9666 -19.8069 -3.15973 68 2A BS2 19 -22.9216 -23.2694 0.347813 69 1B BS2 137 -22.6699 -20.5448 -2.12511 70 2B BS2 223 -22.0706 -21.4248 -0.64582 71 1B BS2 173 -21.3497 -17.1822 -4.16753 72 1B BS2 211 -19.1409 -17.3759 -1.76494 73 1A BS2 53 -18.7877 -17.3223 -1.46545 74 1A BS2 141 -18.5515 -17.506 -1.04546 75 1A BS2 181 -18.2426 -16.2046 -2.03801 Table 2. Ligand-residue nonbonded interaction energies (kcal/mol) of hCav3.1/DM1 best docked complex (Binding Mode I; residues within 5 Å from any ligand atom). Residue Interaction Energy (kcal/mol) VDW Interaction Energy (kcal/mol) Electrostatic Interaction Energy (kcal/mol) L872 -1.288515 -1.303090 0.014575 F875 -0.221154 -0.167896 -0.053258 I876 -0.717273 -0.708119 -0.009154 F917 -2.219640 -2.502266 0.282626 L920 -4.384540 -4.433690 0.049151 T921 -7.301880 -5.249785 -2.052095 Q922 -3.665305 -3.430976 -0.234329 G951 -0.919295 -0.767102 -0.152194 N952 -2.401039 -2.279716 -0.121324 Y953 -0.368932 -0.296900 -0.072032 L955 -0.187378 -0.219766 0.032387 F956 -3.290110 -3.289534 -0.000576 S1461 -0.075968 -0.097531 0.021563 K1462 -14.514602 -2.827102 -11.687500 L1498 -0.686451 -0.913878 0.227427 L1499 -0.714450 -0.821870 0.107420 A1502 -1.015302 -0.657345 -0.357958