Sybyl x 2

All the calculations were carried out on a Lenovo PC with Windows 8.1 system using Tripos Sybyl-X 2.1 (TriposInc, St Louis, MO, USA) molecular modelling package. The crystal structural data of EGFR kinase domain complexed with lapatinib (PDB code: 1xkk) was obtained from RCSB Protein Data Bank²³ (link). The procedure of molecular docking was carried out according to our previous reported¹⁶ (link).

All performances of computational works were carried out on the Tripos Sybyl-X 2.1 (Tripos Inc, St Louis, MO, USA) molecular modeling package.

Computational docking of HVH-2930 onto the C-terminal domain of hHSP90α homology model was conducted as described previously 28 (link), 29 (link). The docking was performed using Tripos Sybyl-X 2.1 in the Windows 7 operating system. All ligands were prepared in mol2 format using the sketch module and minimized. Tripos force field and Gasteiger-Hückel charge; conjugate-gradient method with convergence criterion of 0.001 kcal mol-1.Å-1 and max iteration to 10000 for energy minimization were used. Our previously reported homology model of hHSP90:ATP complex was used as a receptor for docking 29 (link). The protomol was defined with twenty amino acid residues adjacent to the ATP binding pocket and the binding cavity of the hHSP90 homodimer. The threshold parameter was set to 0.50 with a bloat parameter of 5 Å. Docking was conducted using the default settings of Surflex-Dock GeomX, generating 50 maximum poses per ligand and performing CScore (consensus score) calculations 30 (link). The binding conformation of HVH-2930 was selected by considering the Surflex-Dock score, CScore, and visual inspection. Visualization and rendering of docking models were performed on a Maestro graphic user interface in Schrödinger 2020-1 and Benchware 3D explorer program.

All the procedures for docking modeling were carried out using the Tripos Sybyl-X 2.1.1 (Tripos Inc, St Louis, MO, USA) molecular modeling package with a Windows 7 professional K operating system. The structure of compound 9 was sketched and saved in the MOL2 format. Sequentially, Gasteiger–Hückel charges were assigned to all the atoms. To optimize the structure, energy minimization was conducted under a standard tripos force field with convergence to maximum derivatives of 0.001 kcal mol⁻¹.Å⁻¹. As a target receptor for 9, the X-ray structure of murine iNOS in complex with the inhibitor AR-C124355 (PDB id: 3E6O) was downloaded at a resolution of 2.6 Å from Protein Data Bank (https://www.rcsb.org). To prepare the receptor, all the water molecules and duplicated chains were deleted, hydrogen atoms were attached, and Amber 7 FF99 charges were assigned using the biopolymer module in the Sybyl program.

All docking modeling procedures were performed using the Tripos Sybyl-X 2.1.1 (Tripos Inc., St Louis, MO, USA) molecular modeling package with a Windows 7 professional K operating system. First, compounds 3h and 3K were prepared with the sketch module and saved as mol2 format; we then assigned all atoms Gasteiger-Hückel charges. Before performing molecular docking, in order to obtain a stable conformation that converged to the maximum derivatives of 0.001 kcal mol−1.Å−1, we performed an energy minimization of ligands. The crystal structure of PKM2 in complex with phenylalanine (Protein Data Bank [PDB]:4FXJ) used in the experiment was downloaded from PDB. To prepare the receptor, the ligand phenylalanine was extracted, and all water molecules were deleted from the complex structure. The structure was then prepared with the protein preparation module of Sybyl-X 2.1.1 using the default parameters.

As previously described [30 (link)], a virtual molecular docking analysis was conducted to determine how PF interacts with the LuxS protein. The chemical structure of PF was downloaded from PubChem, while the three-dimensional structure of LuxS protein of S. suis HA9801 was previously reported by our group. The LuxS protein model was pre-processed with the SYBYL-X 2.1 software (Triops, USA), including hydrogenation, side-chain repair, and deletion of water molecules. Finally, the AMBER force field was used to minimize the energy of the protein. PF was operated by adding hydrogen atoms and Gasteiger-Hückel charge, and optimized with the Tripos force field of SYBYL-X 2.1 software (convergence criterion: 0.005 kcal/(Å mol)), and saved in MOL2 format.

All simulations and calculations were performed using SYBYL-X 2.1 software (Tripos Inc., St. Louis, MO, USA) running on Windows 10 workstations. The three-dimensional structures of these PAMs were drawn using the SKETCH module and were then optimized with the Tripos force field and Gasteiger–Hückel charges. The Ki values of all molecules were converted into pKi by the following formula: pKi = −logKi. The minimization parameters were set with an energy gradient of 0.005 kcal/(mol·Å) and a maximum iteration of 1000 by the Powell method, and the other parameters were set as defaults [40 (link)].