Table 3 Amino acids of Chain a of NLRP3 protein involved in interactions with selected alkaloids with their binding affinity.
Compounds | Interaction Type | Binding affinity | Interacting amino acid residues | Inhibition constant | Ligand Efficiency |
|---|---|---|---|---|---|
Oxyacanthine | Pi-cation, Charge-charge Positive-Positive | -15.2 | GLU 375, HIS 724, ARG 172 | 0.1679 | -5.06 |
Neferine | Pi-alkyl, alkyl, Conventional, Pi-stacked, Pi-Pi Donor, Pi cation, Carbon hydrogen, Charge-Charge | -10.4 | ASP 662, ASN 656, GLU 629, VAL 353, PRO 352, | 2.289 | -2.08 |
Magnoflorine | Pi-Pi cation, Conventional, Positive-Positive | -11.3 | ARG 378, ARG 172, PHE 210 | 1.004 | -3.76 |
Corynoline | Pi-Pi cation, Conventional, Positive-Positive | -11.8 | TRP 416, GLY 509, ARG 167 | 0.586 | -3.93 |
Columbamine | Conventional, Positive-Positive | -10.4 | ARG 167, SER 658 | 2.289 | -5.2 |
Berberine | Carbon hydrogen, Pi-Pi cation, Positive-Positive | -10.4 | THR 169, ARG 167, TRP 416 | 2.289 | -3.46 |
Berbamine | Carbon hydrogen, Pi-Pi cation, Positive-Positive | -13.9 | ARG 167, TRP 416, ILE 521 | 0.122 | -4.63 |
Palmatine | Carbon hydrogen, Positive-Positive | -10.8 | ARG 167 | 0.975 | -10.8 |
Tranilast (Synthetic Positive Control) | Carbon hydrogen, Positive-Positive, Pi-Pi cation | -10.3 | TRP 416 THR 169 ARG 167 | 1.881 | -3.43 |
Oridonin (Natural Positive Control) | Conventional hydrogen, Carbon hydrogen, Bump Conventional hydrogen bond | -11.6 | ARG 167 | 0.300 | -5.8 |
