2.2 Virtual Screening and Docking
The crystal structures of TP53, CASP1 and HSP90AB1 proteins were
obtained from RCSB Protein Data Bank20 (PDB ID:
2Z2121,1RWX22 ,5FWK23, respectively). The
sequences of four protein were obtained from Uniprot
Knowledgebase24 (Identifier: NLRP3-Q96P20,
TP53-P04637, CASP1-P29466 and HSP90AB1-P08238). With I-TASSER242526
(https://zhanglab.ccmb.med.umich.edu/I-TASSER/)25-27, the crystal structures of NLRP3 was constructed complete protein
structure. The complete protein structure contained ligands for
predicting binding sites and the highest confidence model was chosen.
Ramachandran plot validation of our modeling structure was shown in
Figure 4 and the 3D-profilevalidation of modeling structure was shown in
Figure 5. It can help us to find whether the structure is reliable. We
used ‘Prepared protein’ module in Accelrys Discovery Studio (DS)
software to prepare the proteins in order to make the result more
credible. 18776 TCM compounds from TCM Database @ Taiwan
(http://tcm.cmu.edu.tw) 8 which were filtered by
Linpinski’s Rule of Five, were applied to dock into NLRP3, TP53, 1RWX
and 5FWK protein structures by using LigandFit
module28 in DS. To minimized docking poses between
ligands and proteins, Chemistry at HARvard Molecular Mechanics (CHARMm)
force field 29,30 were used. During the docking
process, the DREIDING force field containing Gasteiger charges was chosen
to calculate the interaction energy for each ligand. The ADMET
Descriptors module in DS was used to calculate absorption, distribution,
metabolism, excretion, toxicity (ADMET) properties such as solubility,
blood-brain barrier (BBB) penetration, hepatotoxicity, cytochrome P450
2D6 (CYP2D6) inhibition, plasma protein binding (PPB) level and
absorption. Results of the docking studied were ranked according to Dock
Score which was calculated mainly based on the interaction energy
between ligand and protein.