Chembiodraw ultra 14

Molecular docking studies were performed to investigate the binding mode of compound 17 to SDH using Autodock vina 1.1.2 (Scripps Research, San Diego, CA, USA) The three-dimensional (3D) structures of compound 17 were drawn by ChemBioDraw Ultra 14.0 (PerkinElmer, Waltham, MA, USA) and ChemBio3D Ultra 14.0 softwares (PerkinElmer, Waltham, MA, USA) The AutoDock Tools 1.5.6 package (http://mgltools.scripps.edu) was employed to generate the docking input files. The search grid of SDH was identified as center_x: 86.459, center_y: 65.6, and center_z: 85.537 with dimensions size_x: 15, size_y: 15, and size_z: 15. The value of exhaustiveness was set to 20. For Vina docking, the default parameters were used if it was not mentioned. The best-scoring pose, as judged by the Vina docking score, was chosen and visually analyzed using PyMOL1.7.6 software (http://www.pymol.org/).

HJ's chemical constituents were obtained from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (http://tcmspw.com/tcmsp.php) and published studies [15 (link)–18 ]. The structural formulas were formed using ChemBioDraw Ultra 14.0 (PerkinElmer, USA) and exported in the format as SYBYL2 (^∗.mol 2).

Initial structures of the Na⁺/K⁺-ATPase complexed with CGs were obtained from the Protein Data Bank (PDB; PDB ID: 4HYT, 4RES, 4RET) (Laursen et al., 2013 (link), 2015 (link)) and coordinates for GEV were generated using ChemBioDraw Ultra 14.0 (PerkinElmer, Waltham, MA, USA). After removing ligands in the original data, we performed computational docking using the Autodock Vina program (Trott and Olson, 2010 (link)) with the protein and the compound as receptor and ligand, respectively. Structural superposition of 4HYT, 4RES, and 4RET coordinates was performed using WinCoot (Emsley et al., 2010 (link)). Structural representation of docking results was done with PyMOL (The PyMOL Molecular Graphics System, Version 1.8 Schrödinger, LLC., New York, NY, USA).

Analysis of the RIF binding site of RpoB was achieved by characterizing the pocket binding surface. The ‘Surface and Maps’ features of MOE were used to create the visualization of the binding site according to its lipophilicity. The cyclic hexapeptide sequences were determined from the binding pocket characteristics and resulted in 7500 sequences from amino acid combination. The ChemBioDraw Ultra 14.0 (PerkinElmer, Waltham, MA, USA) software was used to generate all cyclic peptide structures with the ‘Biopolymer’ feature, and the 2D structures were then saved in .cdx and .mol formats. To construct the database, all structures were then imported to a .mdb database file and the 3D structures was generated through several preparation steps according to our previous study [32 (link)]. Ligands were subjected to a ‘Wash’ protocol to retrieve the protonated states of the compounds, followed by fixing the partial charges and adjustment of the hydrogens and lone pairs for the minimization steps.

Autodock Vina 1.1.2 software was used to analyze the binding of GA‐D and human 14‐3‐3ε. The three‐dimensional structure (PDB ID: 2BR9) of human 14‐3‐3ε was obtained from the protein database (http://www.rcsb.org/pdb/home/home.do). ChemBioDraw Ultra 14.0 and ChemBio3D Ultra 14.0 software from CambridgeSoft Corp (PerkinElmer) were used to draw the three‐dimensional structure of GA‐D. Autodock tools were used to convert the structures of small molecules and proteins into pdbqt files with central coordinates (center_x:‐18.1999, center_YRV 3.771, center_z:15.771), and the search space was as follows: size_x: 50; size_y: 50; and size_z: 50. PyMoL 2.3.0 and Ligplotv 2.2.0 were used to analyze the interaction mode of the best scoring posture, as judged using the Vina docking score.

The X-ray crystallographic structure of GOx (PDB code: 3QVR) was obtained from the Protein Data Bank. DSPE, DOPC, DPPG, FOP, and cholesterol were preprocessed using ChemBio3D Ultra 14.0 (PerkinElmer, Waltham, MA, USA) and ChemBioDraw Ultra 14.0 (PerkinElmer, Waltham, MA, USA). The interactions between GOx and membrane materials were performed using AutoDock Tools 1.5.6 (Scripps Research Institute, San Diego, CA, USA) and AutoDock Vina (Scripps Research Institute, San Diego, CA, USA). The docking results were analyzed using PyMOL (Schrodinger, New York, NY, USA) [35 (link)]. Hydrogen bonds and docking diagram between GOx and membrane materials were recorded to analyze the interaction between GOx and the MVL membrane.