Table 8. Prime MMGBSA Binding Energy (kcal/mol) Estimations for Compounds with the Voltage-Dependent L-type Calcium Channel Alpha-1C Subunit (CAC1C_ HUMAN)a.
| ligand-residue
interactions with distance (Å) |
|||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| sr. no. | compound | docking score | ΔGbinding | glide energy | log Ki (μM) | ΔGsolv GB | ΔGHbond | ΔGvdW | ΔGcoulomb | ΔGlipophilic | ΔGcovalent | hydrogen bond | electrostatic/ hydrophobic |
| 1 | (methylsulfanyl) butyl glucosinolate | −6.93 | −41.93 | −46.79 | −14.98 | 22.75 | −4.10 | −37.55 | −16.54 | −9.05 | 2.56 | salt bridge: LYS676 (2.23); conventional hydrogen bond: TYR144 (2.13), TYR144 (2.51), GLN671 (2.34), ASP150 (1.80), PHE147 (1.97) | attractive charge: LYS676 (2.23); alkyl: PRO146 (5.37) |
| 2 | epsilon-viniferin | −5.13 | −40.01 | −53.47 | −14.15 | 40.63 | −3.08 | −36.93 | −34.94 | −12.19 | 8.59 | conventional hydrogen bond: GLU149 (1.59), GLN671 (1.65), PRO148 (1.92), ASN156 (1.80); carbon hydrogen bond: GLY674 (2.45) | pi-cation: LYS676 (4.29); pi-anion: GLU149 (3.84); pi-pi stacked: TYR144 (5.44); pi-alkyl: LYS234 (4.20) |
| 3 | eugenol | −5.12 | −30.79 | −22.58 | −10.14 | 10.31 | −0.55 | −19.94 | −6.20 | −19.46 | 6.11 | conventional hydrogen bond: TYR144 (1.59); carbon hydrogen bond: GLN671 (2.93), GLN671 (2.79) | pi-pi T-shaped: TYR144 (4.82); alkyl: LEU141 (3.83), ARG240 (4.48), VAL241 (4.45); pi-alkyl: TYR144 (5.18), MET670 (4.27) |
| 4 | scoparone | −4.87 | −33.21 | −25.93 | −11.20 | 12.36 | −0.67 | −27.89 | −4.38 | −11.65 | 0.75 | conventional hydrogen bond: ASP150 (1.91); carbon hydrogen bond: ASP150 (2.97), GLY674 (2.61), MET670 (2.55), GLN671 (2.97), PHE673 (2.47), PHE673 (2.84); pi-donor hydrogen bond: PHE147 (2.92) | alkyl: PRO146 (4.43), MET670 (4.57); pi-alkyl: TYR144 (5.30), PRO146 (5.27) |
| 5 | sinapic acid | −4.77 | −12.86 | −22.70 | −2.36 | 5.19 | −2.23 | −23.53 | 12.35 | −7.45 | 3.21 | salt bridge: ARG237 (1.81), ARG237 (3.17); conventional hydrogen bond: ASP150 (1.88); carbon hydrogen bond: GLU149 (2.98), ASP150 (2.40), ASP151 (2.40) | attractive charge: ARG237 (1.81), ARG237 (3.17), ARG240 (5.30); pi-anion: ASP150 (3.54); alkyl: LYS234 (4.47); Pi-alkyl: PHE147 (4.66) |
| 6 | 2-coumaric acid | −4.01 | −14.20 | −14.61 | −2.94 | −5.19 | −1.56 | −14.72 | 18.22 | −12.94 | 3.74 | conventional hydrogen bond: TYR144 (1.87), GLN671 (2.21), GLN671 (1.85); carbon hydrogen bond: ARG237 (2.87) | attractive charge: ARG240 (5.52); pi-sulfur: MET670 (5.40) |
| 7 | dehydrosalsolidine | −4.01 | −30.50 | −28.29 | −10.02 | 15.30 | −1.14 | −25.55 | −11.31 | −9.65 | 1.89 | conventional hydrogen bond: ASP150 (2.22), GLN671 (1.94); carbon hydrogen bond: ASN156 (2.68), ASP150 (2.59), GLU149 (2.56) | alkyl: PRO146 (5.34); pi-alkyl: PHE147 (5.22) |
| 8 | verapamil | −3.84 | −37.17 | −45.42 | −12.91 | 35.19 | −1.50 | −40.25 | −19.05 | −14.41 | 3.89 | salt bridge: GLU149 (1.76); conventional hydrogen bond: PHE147 (2.14), PHE147 (2.83); carbon hydrogen bond: PRO146 (2.74), GLU149 (2.26), PHE147 (2.63), ILE145 (2.46), ASN156 (2.57), ASN156 (2.63) | attractive charge: GLU149 (1.76), ASP150 (5.51); pi-cation: LYS676 (4.37); pi-pi T-shaped: TYR719 (5.73); alkyl: LEU728 (5.24), VAL729 (4.83), PRO146 (4.92); pi-alkyl: TYR144 (4.17), TYR719 (4.73) |
ΔG Binding: binding free energy; pKi: logarithmic of inhibition constant Ki; ΔG bind solv GB: generalized born electrostatic solvation energy; ΔG bind H bond: hydrogen bonding energy; ΔG bind vdW: van der Waals forces energy; ΔG bind coulomb: coulomb binding energy; ΔG bind lipophilic: lipophilic binding energy; ΔG bind covalent: covalent binding energy; These energies all contribute to ΔG binding, the free energy of binding.