Glide 6.9 module

Molecular docking studies were performed to examine the interactions of each ligand with the NS5 protein via the Glide 6.9 module in the Schrödinger suite of programs.^{24,25 (link)} The crystal structure of the NS5 protein (PDB ID: 6kr2) was used for the ligand docking studies.^{26 (link)} The protein structure was prepared and minimized through Protein Preparation Wizard in Maestro Schrödinger 10.4. The OPLS4e force field was used to assign the missing partial charges, as well as missing protons.^{27,28 (link)} The prime module was used to fill the missing loops, and to produce zero order bonds to metal ions. PROPKA was used to predict the pKa of the proteins. Using the OPLS4e force field, the complex was subjected to restricted minimization for optimizing the heavy atoms and hydrogens to ease steric hinderance.^{29 (link)} The LigPrep tool (Schrödinger) was used to prepare the ligands by altering their torsions, and assigning them suitable protonation states. The tautomeric and ionization states were generated for each ligand through Epik (Schrödinger (2015c) Prime. The Glide_XP dock tool was used for docking, and the results were analyzed for the best docked pose.

To get structural insights into ligand-protein complex, the co-crystal structure of USP7-CD with non-covalent inhibitor FT671 (PDB ID: 5NGE) was used for the in silico studies [14 ,15 (link)] using the Glide 6.9 module of the Schrödinger suite of programs, version 2020-2 [[16] , [17] , [18] , [19] (link), [20] (link), [21] , [22] (link), [23] (link), [24] (link), [25] ]. The protein preparation wizard tool and OPLS3 force field were employed for protein preparation, minimization, and optimization. The ligand molecules were prepared using Schrödinger's LIGPREP module, which generates the correct protonation and possible ionization states. A receptor grid was generated around the centroid of the co-crystalized ligand (FT671) with a grid box of 10 × 10 × 10 Å. The Glide XP module was used to dock the ligands, and results were analyzed for the best-docked poses [18 ,19 (link)]. Molecular mechanics with generalized Born and surface area solvation (MMGBSA) was used to further validate the docked poses by evaluating the binding free energies of the ligand-receptor complex. For this, the Prime module from the Schrödinger suite was used with default settings.