Fig 1.
(A) The 3D structure of SI (PDB code 3LPO). (B) the disaccharide base of kotalanol. (C) The disaccharide base of acarbose. (D) The disaccharide base of HA.
Fig 2.
(A) The docking pose of SI-acarbose. (B) The docking pose of SI-kotalanol. (C) The docking pose of SI-HA.
Fig 3.
(A) The RMSD plot during MD simulations. (B) The Rg plot during MD simulations. (C) The SASA score.
Table 1.
The number of atoms in different systems.
Fig 4.
(A) RMSF plot during MD simulations. (B) the active residues for inhibitors binding.
Fig 5.
Differences in the secondary structures of residues Gly530 to Glu580 of (A) SI. (B) SI-kotalanol. (C) SI-HA. (D) SI-acarbose.
Table 2.
The probability (%) for alpha (residue 530–580) of the four systems during MD simulations.
Fig 6.
(A) RMSD plot of residue 530–580 between free SI and SI-kotalanol. (B) the relative frequency of RMSD plot of residue 530–580 between free SI and SI- kotalanol. (C) RMSD plot of residue 530–580 of free SI and SI-HA. (D) the relative frequency of RMSD plot of residue 530–580 between free SI and SI- HA. (E) RMSD plot of residue 530–580 between free SI and SI-acarbose. (F) the relative frequency of RMSD plot of residue 530–580 between free SI and SI-acarbose.
Fig 7.
(A) The distance between Asn572H and the O atom of Gly570. (B) The relative frequency of distance between Asn572H and the O atom of Gly570 of the four complexes. (C) The hydrogen bond between Asn572H and the O atom of Gly570.
Fig 8.
Free energy landscape (FEL) and structures of the two most stable structures of the four systems.
The α helix in residue 530–580 (A) ADA. (B) ADA-FR0 complex. (C) ADA-FR2 complex. (D) ADA-PRH complex.
Table 3.
The probability(%) for corresponding most stable structures and substable structures.
Fig 9.
Subnetwork analysis of the protein−ligand interaction.
(A) The subnetwork of SI-kotalanol. (B) The subnetwork of SI-HA. (C) The subnetwork of SI-acarbose.
Table 4.
The MM-PBSA score for three complexes (kcal /mol).