Crystal structures of RegX3 (PDB Id 2OQR) and MtrA (PDB Id 2GWR) were obtained from PDB and energy minimised using the OPLS 2005 forcefield in Schrodinger suite version 9.3. A homology model of MprA was developed using Prime and the crystal structures of PrrA and PhoP (PDB Ids 3ROJ, 1YS7, 1YS6, 1KGS, 3F6P, 2ZWM and 1NXO) as templates. The model was energy minimised using the OPLS 2005 forcefield in Schrodinger suite version 9.3. Active site prediction was done using the Sitemap module while grid generation was done using the Glide module of Schrodinger LLC version 3.5. 2500 compounds in the BITS database were then docked against the generated sitemaps and grids by high throughput virtual screening (HTVS). Shortlisted compounds were used for further studies. Detailed methods have been provided in the supplemental section .
Opls 2005 force field
Manufactured by Schrödinger
Sourced in United States
The OPLS-2005 force field is a molecular mechanics force field developed by Schrödinger. It is designed to model the interactions between atoms in molecular systems. The OPLS-2005 force field provides a set of parameters that describe the potential energy functions for different types of atoms and their interactions, enabling accurate simulation of molecular structures and dynamics.
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Lab products found in correlation
Protein preparation wizard panel, by Schrödinger (3 mentions)
Receptor grid generation, by Schrödinger (2 mentions)
Protein preparation wizard tool, by Schrödinger (1 mentions)
Protein preparation tool, by Schrödinger (1 mentions)
Protein preparation wizard in maestro v9, by Schrödinger (1 mentions)
Sitemap module, by Schrödinger (1 mentions)
Glide module, by Schrödinger (1 mentions)
Schrodinger suite, by Schrödinger (1 mentions)
Maestro program, by Schrödinger (1 mentions)
Ligprep, by Schrödinger (1 mentions)
14 protocols using opls 2005 force field
1
Structural Modeling and Virtual Screening of MprA
2
Structural Preparation of MASTL Kinase
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The crystal structure of kinase domain of MASTL (PDB ID: 5LOH)24 was retrieved from Protein Data Bank (http://www.rcsb.org/pdb/home/home.do )45 . Staurosporine was removed from the active site for docking various compounds of interest. The optimization and minimization of protein was then carried out using Protein Preparation Wizard tool in Schrodinger46 (link) and OPLS-2005 force field47 (link). The tool fixes the protein and makes it suitable for molecular docking. It corrects the incorrect bond orders, charge states, orientations of different amide, hydroxyl and aromatic groups within a protein structure, which cannot be determined by the X-ray structure due to limited resolution. To minimize the strains and steric collisions in protein, energy minimization was done by molecular mechanics calculation using OPLS-2005 force field47 (link) available in the Protein Preparation tool46 (link).
The missing disordered C-helix (activation loop) of the kinase from the X-ray structure was modeled using Schrodinger as well as online I- TASSER webserver48 (link).
The missing disordered C-helix (activation loop) of the kinase from the X-ray structure was modeled using Schrodinger as well as online I- TASSER webserver48 (link).
3
Structural Preparation of FAAH Protein
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The three-dimensional (3D) X-ray crystallized structure of FAAH (PDB ID: 2VYA) was retrieved from RSCB Protein Data Bank (http://www.rscb.org/ ), and prepared in Protein Preparation Wizard using OPLS 2005 force-field (Schrödinger LLC). The structure was pre-processed to assign bond orders, add hydrogens and disulfide bridges, create zero-order bonds to metals, remove water molecules beyond 5Å of heteroatom (HET) groups, and generate HET states using Epik at pH 7.0 ± 2.0. Protein structure was refined to optimize the H-bond assignment by sampling water orientations with PROPKA at pH 7.0 as well as processed for restrained minimization to converge heavy atoms to 0.30 Å RMSD [71 (link)].
4
Virtual Screening of VEEV NLS Inhibitors
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Virtual screening was carried out on the IMPα:VEEV NLS crystal structure [PDB:3VE6, 2.83 Å resolution]. To prepare the protein structure for docking, all solvent molecules were deleted and bond orders for the ligand and the protein were adjusted. The missing H-atoms were added, and side chains then energy-minimised using the OPLS-2005 force field (Maestro software Schrodinger). The ligand-binding site was defined using Receptor Grid generation (Schrodinger) centred on the Min-NLS within PDB 3VE6; default settings were used for all other parameters.
5
Anthocyanin Compounds Preparation and Docking
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The LigPrep tool was used to prepare the bioactive Anthocyanin compounds used in molecular docking. At pH = 7.2 ± 0.2, their ionization states and tautomers were generated, followed by optimization using the OPLS 2005 force field (Schrodinger release 2017).
6
HDAC2 Binding Analysis with Metavert
7
Protein-Ligand Docking for Receptor Binding
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Docking was carried out on the PR with bound ulipristal acetate and a peptide from the corepressor SMRT crystal structure [PDB:4OAR, 2.41 Å resolution]. To prepare the protein structure for docking, all solvent molecules were deleted and bond orders for the ligand and the protein were adjusted. The missing H-atoms were added, and side chains then energy-minimised using the OPLS-2005 force field (Maestro, Schrodinger). The ligand-binding site was defined using Receptor Grid generation (Schrodinger) centered on the bound ligand Ulipristal acetate within PDB 4OAR; default settings were used for all other parameters.
The 1NHZ structure was prepared for docking in the same manner, except that the ligand-binding site used was defined by allowing SiteMap to identify top ranked binding sites and select the one that best fit the pose of the ligand from the 1NHZ crystal structure for the Receptor Grid generation; default settings were used for all other parameters.
The 1NHZ structure was prepared for docking in the same manner, except that the ligand-binding site used was defined by allowing SiteMap to identify top ranked binding sites and select the one that best fit the pose of the ligand from the 1NHZ crystal structure for the Receptor Grid generation; default settings were used for all other parameters.
8
Structural Analysis of COVID-19 Protease
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To combat the current situation of COVID-19 protein structure of COVID-19 main protease with co-crystallized structure (PDB IDs: 5R7Y, 5R7Z, 5R80, 5R81, 5R82, having resolution <2 Å, R-Value Free <0.30, R-Value Work <0.25) were selected and obtained from Protein Data Bank (http://www.rscb.org ) with good resolutions [[15] (link), [16] (link), [17] (link), [18] (link), [19] (link)]. Protein structure was prepared using protein preparation wizard in Maestro panel. During preparation of protein bond orders were assigned and hydrogen atoms were added as well. Water molecules were removed within 3 Ǻ of het groups [20 (link)]. Finally, OPLS-2005 force field was applied to minimize the structure of protein (Schrodinger, LLC, NY, USA, 2009) [21 (link)]. Further receptor grid boxes were generated using “Glide's Receptor Grid Generation” module at the active site (with the radius of 20 Å around the crystal structure) of co-crystallized ligand with the computing cubic box of 10 Ǻ × 10 Ǻ × 10 Ǻ [22 (link)].
9
Homology Modeling and Evaluation of PfPAP2
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The 3D structure for PfPAP2 is homology modeled using Phyre2 V 2.0 (Protein Homology/analogy Recognition Engine) server available online20 (link). The models were screened for unfavorable steric contacts and remodeled using either a rotamer library database of SCHRODINGER.3 Explicit hydrogens were added to the protein and were subjected to energy minimization using OPLS2005 force field in SCHRODINGER. Energy minimization and relaxation of the loop regions was performed using 500 iterations in a simple minimization method. The 3D energy minimized model evaluation was performed in PROCHECK33 . The quality of modeled structure was validated by Ramachandran plot.
10
Structural Modeling of Sfh5 with PtdIns
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Protein models were prepared using the Protein Preparation Wizard panel in the Schrödinger suite (2018–1, Schrodinger, LLC, Mew York, NY, 2018). The Sfh5 structure was optimized with the OPLS_2005 forcefield in the Schrödinger suite to relieve all atom and bond strains found after adding all missing side chains and/or atoms. The Sfh5::PtdIns model was generated by structural overlay of Sfh1::PtdIns complex (PDB ID 3B7N; Schaaf et al., 2008 (link)) on Sfh5 monomer. The heme group of Sfh5 was replaced by PtdIns, which was extracted from Sfh1. The Sfh5::PtdIns complex was energy minimized to relieve Sfh5 and PtdIns atoms of any van der Waal steric clashes and complex was optimized for electrostatic interactions. Molecular graphics and analyses were performed with UCSF Chimera and Schrödinger’s Maestro program.
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