Preparation of compound and proteins
Compound preparation; The 2D structure of the compound was drawn in Marvin Sketch software, and the 2D structure was transformed into the 3D structure. Save the treated compound in *.mol2 format. Import the *.Mol2 file of the compound into the Ligprep module in the Schrodinger package for ligand preparation, that is, ionization (pH: 7.0+/-2.0), desalination, generation of tautomers, etc. The ligand was optimized using the same force field (OPLSˍ2005) as in the receptor optimization process. Other parameters were software default values.
Protein preparation; according to the target information obtained by virtual screening, the protein structures were downloaded from the PDB protein database (https://www.rcsb.org/)) for molecular docking.
Target screening of compound
Target screening using the PASS server; The PASS (http://www.pharmaexpert.ru/passonline/) server can predict the potential targets of drug-like compounds based on small molecular active fragments12. We used the PASS online server to predict the different biological activities of the compound according to the compound’s structure. When the constructed compound 2D mol format is entered into PASS's SAR training set database, the server will automatically represent the structure in the form of MNA (Multilevel Neighborhoods of Atoms) descriptors. The prediction program will match the compound with the training set to get a list of biological activities. The target with prediction accuracy Pa > 0.9 was selected as the possible active target of the compound.13 All parameters in the calculation process are set by system default.
Target prediction in the PharmMapper database; The PharmMapper (http://59.78.96.61/pharmmapper/submit_file.php) server was used to predict the target of the compound13. The server can predict the target in a few minutes to tens of minutes. When the mol format file of the compound is uploaded to the PharmMapper web server, the server can automatically find the pharmacophore that best matches the molecular conformation of the query, and sort it according to its matching program14. The server can provide protein targets of the top 300 points. The score represents the degree of agreement between the small molecule and the pharmacophore model. The higher the score, the more likely it is to be a target protein for drug molecules. We determine the potential targets of the compound based on the Normalized Fit Score.
Target prediction in the PDB database; the PDB protein database (http://www.rcsb.org/pdb/ligand/chemAdvSearch.do), which provides a lot of information about proteins and ligands, is the most important database for collecting biological macromolecular structures. The target of the compound can be predicted by searching for ligands with a similar structure of the compound.
Target prediction using ROCS; ROCS (http://targetfishing.molcalx.com.cn/) is a program developed by OpenEye to compare the shape and pharmacophore similarity of compounds15. ROCS can be used to predict the multi-classification targets of compounds16. It has been proved that ROCS can be successfully used for target prediction17, 18. We use ROCS to search the database of known active compounds to predict the targets of the compound in Alzheimer's disease, cancer, diabetes, and, inflammation. The ShapeTanimoto value was used to evaluate the screened targets.
Molecular docking and Pharmacophore model construction
Molecular docking; iGEMDOCK (http://gemdock.life.nctu.edu.tw/dock/igemdock.php) is an open-source molecular docking software that can dock compound molecules to the receptor protein binding pocket19. To investigate the binding activity of the compound to the target protein, the molecular docking of the compound was studied by using the computer-aided drug design software package iGEMDOCK. The crystal structure of the target protein for molecular docking was downloaded by searching the protein target library. In the study, the original ligand in the receptor was used as the positive control (reference compound). The active sites are determined by the coordinates of the co-crystalline compounds of each protein. In molecular docking, the groups on the protein can bind to the compound molecule through van der Waals force, hydrogen bond, and electrostatic interaction to match the binding site with the lowest energy. The binding degree of the target protein and the compound is judged by the binding energy. When the binding conception of the compound and the receptor is stable, the energy is lower, and the greater the possibility of interaction is.
Pharmacophore model construction;The pharmacophore model can be constructed according to the receptor-ligand interaction model by LigandScout software20. Based on the results of molecular docking calculation, the action mode of the compound was analyzed by the Ligandscout program to determine whether the target compound matched the pharmacophore characteristics of the target protein.