The PDB files for the crystal structures of Bcl-2, NF-κB/p65, and p38 were obtained using the protein data bank codes 1YSW, 1MY5, and 4FA2, respectively. The molecular docking procedure was performed under the C-DOCKER protocol of Accelry’s Discovery Studio 2017R2 software. For ligand preparation, the structure of BAP 16 was constructed using ChemDraw Professional 17.0 software, saved in SDF file format and minimised using Accelry’s Discovery Studio 2017R2 software. The protein structures were cleaned and inspected for errors, hydrogens were added, and the water molecules were deleted. For Bcl-2 protein as a receptor, the centroid of the binding site was defined based on the ligand in the cocrystal structure. Then removed the original ligand and placed the molecule of BAP 16 in the sphere position to carry out molecular docking. Subsequently, p65 and P38 proteins were defined as receptors and docked in a similar process. For energy minimisation, the CHARMM force field was utilised within Accelry’s Discovery Studio 2017R2 software. Finally, types of interactions between the docked proteins and BAP 16 were analysed.
Discovery studio 2017 r2
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Discovery Studio 2017 R2 is a comprehensive software package for molecular modeling, simulation, and analysis. It provides tools for visualizing and analyzing molecular structures, predicting protein-ligand interactions, and designing new compounds. The software is designed to support research in areas such as drug discovery, materials science, and structural biology.
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26 protocols using discovery studio 2017 r2
1
Molecular Docking of BAP 16 with Proteins
2
In Silico Evaluation of Rosemary Compounds
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In our study, RA, CA and UA were tested for their interaction with BACE1, AChE, synapsin I, II and III. The 3D structures of BACE1 (PDB ID: 2WJO), ACHE (PDB ID: 4PQE) and synapsin III (PDB ID: 2P0A) were acquired from the RCSB Protein data bank (PDB) (https://www.rcsb.org/ ) accessed on 15 February 2022 [75 (link)]. Synapsin I and II structures were generated through AlphaFold (https://alphafold.ebi.ac.uk/ ) accessed on 15 February 2022 [76 (link)]. The 3D structures of RA, CA and UA were constructed using ArgusLab (http://www.arguslab.com/arguslab.com/ArgusLab.html ) accessed on 18 February 2022 [77 ]. AutoDOCK Vina [49 (link)] was employed to assess the structure of the receptor–ligand complex and to ascertain the feasibility of the structural topographies necessary for the interaction of the compounds derived from R. officinalis with AD target proteins. It allows for the exploration of possible key active site residues involved in the intermolecular interactions with the ligand. The automated docking models generated were visualized using BIOVIA Discovery Studio 2017 R2 [78 ]. The best pose was chosen based on the highest scoring from the top 10 poses of ligand binding sites.
3
Molecular Modeling of rePON1 Carbamate Interactions
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The three-dimensional structure of rePON1 PDB code 1V04 [14 (link)] was used for molecular modelling. Carbamate structures were modelled and minimized using the MMFF94 force field implemented in ChemBio3D Ultra 12.0 (PerkinElmer, Inc., Waltham, MA, USA). Discovery Studio 2017 R2, with the CDOCKER docking protocol, using a CHARMM force field (BioVia, San Diego, CA, USA), generated 20 docking poses for each carbamate in the active site gorge of rePON1, as described earlier [53 (link)]. Poses were scored and ranked according to the calculated CDOCKER energy for interactions between carbamate and rePON1 active site residues (i.e., hydrogen bonds, π–π interactions, cation–π interactions and electrostatic interactions).
4
Molecular Docking for Protein-Peptide Interactions
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BIOVIA Discovery Studio 2017 R2 (Biovia, San Diego, CA, USA) was used to carry out the molecular docking simulation. ZDOCK of Discovery Studio with ZRANK (ranks docked poses) was used by the following parameters: Angular step size as 15; RMSD cutoff as 6.0; interface cutoff as 9.0; the maximum number of clusters as 60, then RDOCK procedure was used to refine the docked poses by using the Chemistry at Harvard Macromolecular Mechanics (CHARMM) force field [14] (link), [21] (link). In addition to Discovery Studio, other docking methods, HPEPDOCK, AutoDock Vina, and ZDOCK were tried, but the peptide was docked with either unfolded conformation or docked with too low-affinity binding poses.
5
Structural Analysis of α-Synuclein Mutants
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Several structures of α-synuclein have been determined using X-ray, NMR and electron microscopy techniques, yet most of the structures are available for small fragments of α-synuclein (http://www.rcsb.org/ ). Merely, three NMR structures exist for full-length α-synuclein. Out of these, Protein Data Bank (PDB) codes 1XQ843 (link) and 2KKW44 (link) are micelle-bound α-synuclein structures. Recently, third NMR structure (PDB 2N0A)45 (link) was reported for a pathogenic fibril of full-length human α-synuclein. We have used chain A of PDBs 2N0A and 2KKW for our study. Structures for the mutants were generated by computationally mutating the corresponding amino acid residue in the wild type NMR structure (PDB 2N0A)45 (link). Mutagenesis Wizard of PyMOL (The PyMOL Molecular Graphics System, Schrödinger, LLC) was used for creating the point mutation. The resulting mutant structure was energy-minimized prior to MD simulation. Residue Ser-129 was phosphorylated using “Build and Edit Protein” module of the Discovery Studio 2017 R2 (BIOVIA, San Diego: Dassault Systèmes).
6
Structural Modeling of Amino Acids
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The 3D structures of 20 amino acids (Supplementary Figure S2 ) were built and the charge states were assigned by Discovery Studio 2017 R2 (BIOVIA, San Diego, CA, USA). In the case of His, both tautomeric structures namely Hsd (protonated at delta N) and Hse (protonated at epsilon N) were created. A previous study reported that capping of the termini of the amino acids ensured that the dynamics of the φ and ψ torsion angles were analogues to the dynamics within a peptide chain [32 (link)]. Accordingly, N and C termini of each amino acid were capped with acetyl (ACE) and N-methyl amide (NME) groups, respectively (Figure 5 ), for removing charge effects and imitating the peptide bond. The 3D structure of each amino acid was verified by a comparison with the energy minimized structure.
7
CD81 Protein Crystal Structure Docking
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The three-dimensional
(3D) X-ray crystal structure of CD81 was retrieved from the Protein
Data Bank (PDB code: 5M3T).41 (link) The chemical structures of6 , 7 , and 8 were drawn using sketch
molecules module of BIOVIA Discovery Studio 2017R2.42 Initially, hydrogen atoms were incorporated to optimize
the geometry of ligands via molecular mechanics (MM) employing universal
force fields and steepest descent algorithm implemented in Avogadro
tools.43 (link) The docking study was conducted
to know the bioactive conformation and the binding affinity of compounds6 , 7 , and 8 toward CD81. The compounds 6 –8 were docked by defining the grid box
with a 1 Å spacing and size of 30 × 30 × 30 pointing
in x, y, and z directions
around the binding site of CD81 following the standard protocols of
AutoDock44 (link) and AutoDock Vina45 (link) tools. The Lamarckian genetic algorithm was
employed as the search algorithm with default values.46 (link) The most appropriate conformation of the docked complex
was taken for further computational analysis. The complete protocol
of the docking study was explained in our earlier communication.47 (link) PyMol,48 (link) Discovery
Studio Visualizer,42 and LigPlot+49 (link) were deployed for the 3D visualization
and subsequent inspection of the docked complexes.
(3D) X-ray crystal structure of CD81 was retrieved from the Protein
Data Bank (PDB code: 5M3T).41 (link) The chemical structures of
molecules module of BIOVIA Discovery Studio 2017R2.42 Initially, hydrogen atoms were incorporated to optimize
the geometry of ligands via molecular mechanics (MM) employing universal
force fields and steepest descent algorithm implemented in Avogadro
tools.43 (link) The docking study was conducted
to know the bioactive conformation and the binding affinity of compounds
with a 1 Å spacing and size of 30 × 30 × 30 pointing
in x, y, and z directions
around the binding site of CD81 following the standard protocols of
AutoDock44 (link) and AutoDock Vina45 (link) tools. The Lamarckian genetic algorithm was
employed as the search algorithm with default values.46 (link) The most appropriate conformation of the docked complex
was taken for further computational analysis. The complete protocol
of the docking study was explained in our earlier communication.47 (link) PyMol,48 (link) Discovery
Studio Visualizer,42 and LigPlot+49 (link) were deployed for the 3D visualization
and subsequent inspection of the docked complexes.
8
Molecular Docking of Kinase Structures
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Crystal structures of IRAK4, ASK1, ITK, and LYN, with codes 2NRU [37 (link)], 3VW6 [21 (link)], 1SM2 [38 (link)], and 3A4O [39 (link)], respectively, were obtained from PDB [26 (link)]. Human PDBs were selected, considering the resolution and no missing residues. Subsequently, protein preparation was carried out as described above. Molecular docking studies were performed with the LigandFit module [40 (link)] of Discovery Studio 2017 R2 (BIOVIA, San Diego, CA, USA). The ligand molecules were built and optimized using the Prepare Ligand protocol. Partial charges were applied onto the proteins, as well as ligands using the Momany and Rone method of partial charge estimation. Energy was minimized using the CHARMm forcefield. The binding site of each protein was defined on the basis of the co-crystallized ligand. One hundred docked poses were generated for each ligand, and scored using the Ligscore 1, Ligscore 2, Piecewise linear potential 1 (PLP1), Piecewise linear potential 2 (PLP2), Jain, and Potential of mean force (PMF) scoring functions. The binding modes of the ligands were carefully chosen on the basis of protein-ligand interactions.
9
Ebselen Docked into 6PGD Crystal
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The study was performed based on the crystal structure of 6PGD (PDB code: 5UQ9). Ebselen was initially positioned into the NADP+ binding site and then docked by CDOCKER in BIOVIA Discovery Studio 2017 R2 (DS) software. Docking results showed that there are van der Waals interaction, electrostatic interaction, and hydrogen bond interaction when the ligand binds to the receptor.
10
Protein Kinase Structure Retrieval
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Crystal structures of various protein kinases were retrieved from the RCSB Protein Data Bank (PDB) [26 (link)]. All ligands and water molecules were removed from the original PDBs. Structures were examined for missing residues, and no such residues were found. Furthermore, bond orders and charges were inspected using the prepare protein protocol of Discovery Studio 2017 R2 (BIOVIA, San Diego, CA, USA).
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