The ligands: geldanamycin (GDA) and ursolic acid acetate (UAA), were downloaded from PubChem (https:// pubch em. ncbi. nlm. nih. gov) in structure data file (sdf) format, and isomukaadial acetate was drawn using 2D sketcher in Maestro v12.8 (Schrödinger 2019) . Each ligand (2D structure) was converted to its lowest energy 3D conformation using the LigPrep module of Maestro v12.8 in Schrödinger 2021-2 (Schrödinger 2019) . In brief, the geometries of the ligands were optimized by assigning them appropriate protonation states (Shelley et al. 2007 ). The ligands were then optimized using OPLS4 force field, generating possible ionization states at a target pH of 7.4 +/-2.0 using EPIK. Stereoisomers were computed to retain specified chiralities at most generating 32 per ligand Schrödinger (2021) .
Maestro v12
Manufactured by Schrödinger
Sourced in United States
Maestro v12.8 is a computational chemistry software package developed by Schrödinger. It provides a comprehensive set of tools for molecular modeling, simulation, and analysis. The software enables users to perform a wide range of calculations, including quantum mechanical, molecular mechanics, and hybrid methods, to study the properties and behaviors of chemical compounds and biological systems.
Automatically generated - may contain errors
24 protocols using maestro v12
1
Optimizing Ligand Conformations for Docking
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Cathepsin C Binding Pocket Docking
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Three-dimensional structure of cathepsin C (PDB ID: 3PDF) [18] (link) was retrieved from the Protein Data Bank (http://www.rcsb.org ), and ligand (DAB1) three-dimensional structure was designed in the academic version of Maestro v12.3 (Schrödinger Release 2020–1:Maestro, Schrödinger, LLC, New York, NY, 2020). The co-crystallized cyanamide-based inhibitor compound 17 binding region [18] (link) was selected as an active pocket in the cathepsin crystal structure for the molecular docking simulation with DAB1 compound.
3
Molecular Docking of Cathepsin C and DAB1
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The molecular docking simulation for cathepsin C and compound DAB1 was performed using Chimera-AutoDock Vina plugin setup [19] (link). Briefly, both receptor and ligand structures were prepared, including addition of polar hydrogen and charges to each structure, for docking using Dock prep tool in Chimera-1.14 [20] (link). The selected receptor protein (cathepsin C) was the monomer unit consisting of a single heavy chain, light chain and the exclusion unit. The docking was conducted under default parameters in the selected active pocket of receptor covered by docking grid box of size 17.07 × 14.29 × 17.68 Å along the x, y, and z axes and center at 31.05, 26.05, and 18.57 Å region using AutoDock Vina [21] (link), as a plugin in USCF Chimera-1.14. Finally, docked conformations were selected based on the highest docking score with the least root mean square deviation (RMSD) values and further analyzed for intermolecular interaction profile using Maestro v12.3 (Schrödinger). The docking studies were performed was performed on the active site of monomer
4
Crystallographic Structure Preparation of M^pro
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The crystallographic structure of Mpro (PDB Code: 6LU7) was retrieved from the Protein Data Bank and prepared using the protein preparation wizard available in the Maestro v12.3 Schrödinger, LLC, 2020.1 (https://www.schrodinger.com/downloads/releases accessed on 6 June 2022) software package. All missing residues were added, and all ligands, except cofactors and crystallographic water molecules, were removed. H-bonds were adjusted at variable pH, assigned bond order, and the structures protonated according to a pH of 7.0. The protonated structures were minimized using an Optimized Potentials for Liquid Simulations (OPLS) force field.
5
Molecular Modelling and Simulation Tools
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AMBER and AmberTools19, University of California, San Francisco, USA; AutoDock4.2 software, The Scripps Research Insitute, San Deigo, USA; Discovery Studio 2016, Dassault Systemes BIOVIA, San Deigo, USA; GaussView 5.0.9, Carnegie Mellon University Gaussian, Conneticut, USA; GROMACS v2018.2, University of Groningen, Uppsala Sweden; R v3.6.1, R Core Team, Vienna, Austria; Maestro v12.5, Schrödinger, New York, USA; MD-TASK v1.0.1, Research Unit in Bioinformatics (RUBi), Rhodes University, Makhanda, South Africa; PyMOL Molecular Graphics System; v1.7.2.1 Schrödinger, New York, USA.
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Structural Preparation of Human MCM7 Protein
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The crystal structure of human MCM7 protein (PDB code: 6XTY) was downloaded from RCSB Protein Data Bank (PDB)47 (link). MCM7 protein was co-crystalized with the MCM protein family, therefore the target MCM7 protein was separated and removed the water, metal ions, cofactors, other molecules, and other proteins by the Maestro v-12.5 of Schrödinger Suite 2020-348 . The MCM7 protein was initially processed and prepared by the protein preparation wizard (Prep Wizard) of Schrödinger Suite 2020-349 (link). The prepared protein has been further utilized for molecular docking and other experiments.
7
Visualizing Protein Secondary Structures
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The PDB structures were visualized using PyMOL 2.4.1 (35 ) and the academic version of Schrodinger Maestro v12.5 (36 ). Specifically, aligned PDB structures were visualized using PyMOL, and reassigned secondary structures were visualized using Maestro v12.5. κ-helices and 310-helices were represented as ribbons and tubes, respectively. Ribbons were drawn passing through alpha carbons.
8
Maestro and Desmond Molecular Dynamics
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All computational studies were carried out using Maestro v 12.8 of the Schrodinger suite and academic Desmond v6.5 by D.E. Shaw Research for molecular dynamics. The workflow of this study is summarized in Figure 1 .![]()
Study workflow.
9
Molecular Docking of Drug Compound
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Molecular docking studies were validated to confirm the selected drug to study the interaction of drug with the protein. For docking investigations, the 3D structures of the target proteins (PBD ID-6VVO) was acquired from the Protein Data Bank (PDB) at (https://www.rcsb.org/ )73 (link). Compound (ID: PA16471233) (CHEMBL ID 430483) identified from webGestalt was downloaded from the PubChem databases (https://pubchem.ncbi.nlm.nih.gov/ )74 (link). The molecular docking software, maestro v12.8 (Schrödinger), was used to perform molecular docking and visualize interactions75 .
10
In silico Molecular Modeling Workflow
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All the in silico studies were carried out by Maestro v 12.8 (Schrodinger 2020) as depicted in Fig. 1 .Fig. 1 ![]()
Study workflow.
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