Docking study was conducted in the extra precision (XP) mode of the Schrödinger 2019-3 suite. The target protein receptor grid was generated by using the Maestro tool of Schrödinger suite 2019-3. The grid box was generated based on the presence of an internal ligand in that particular receptor (Friesner et al., 2006 (link)). The active site of NS5 (4K6M) was generated using an internal ligand whereas site mapping was done for NS3 helicase (2Z83) and NS3 protease (4R8T). The prepared phytoconstituents were docked against specified protein targets of JEV such as NS3 helicase ((PDB ID: 2Z83 ), NS5 (PDB ID: 4K6M ), and NS3 protease (PDB ID: 4R8T ). The OPLS3e force field was used and possible stable configuration of ligands in the active site of targets is selected based on doc scores. The interactions between the ligand and protein were characterized through the formation of hydrogen bonding, π- π, van der Waals, and hydrophobic interactions (Friesner et al., 2006 (link); Gálvez et al., 2018 (link)).
Maestro tool
Manufactured by Schrödinger
Maestro is a computational chemistry software tool developed by Schrödinger. It serves as an integrated platform for performing molecular modeling and simulations. The core function of Maestro is to provide a graphical user interface for accessing and utilizing Schrödinger's suite of computational chemistry applications.
Automatically generated - may contain errors
8 protocols using maestro tool
1
Molecular Docking of Phytoconstituents Against JEV Targets
2
Emodin-RSV-F Protein Docking Protocol
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The structure files of Emodin (PubChem CID: 3220) and RSV-F (HRSVgp08, PDBID: 4CCF) protein were obtained from PubChem and Protein Date Bank (PDB). The RSV-F protein underwent structural preparation via the Maestro tool within the Schrodinger suite, entailing the excision of water molecules, the annexation of hydrogen atoms, and the amendment of structural aberrations. Subsequently, the entirety of the RSV-F protein was designated as the docking target. Energy minimization of the Emodin molecule was executed to secure its lowest energy conformation. The Ligand Docking approach was employed for molecular docking, accentuating the ligand’s interactions with the target protein. Post-docking, the outcomes were archived in the mdb file format, discovery and PyMOL was utilized for the visual dissection of the results.
3
Structural Analysis of Drug Crystals
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
A dataset of crystal structures
for 10 drugs and clinical candidates was assembled (Figure 1 ). It is composed of five macrocyclic
erythronolides (erythromycin, clarithromycin, azithromycin, roxithromycin,
and telithromycin) and five HCV NS3 protease inhibitors, three of
which are macrocyclic (danoprevir, vaniprevir, and grazoprevir) and
two are non-macrocyclic drugs (asunaprevir and telaprevir). All crystal
structures of these 10 compounds were retrieved from the PDB (www.rcsb.org/pdb )58 (link) and CSD (www.ccdc.cam.ac.uk )59 (link) using searches
by common name, synonyms, and chemical structure.
From the PDB,
only crystal structures with a resolution <3 Å were included
in the dataset, except for one structure for each of roxithromycin
(1JZZ: 3.8 Å)
and telithromycin (1P9X: 3.4 Å) in which the structures showed interesting conformations
(seeResults and Discussion ). All structures
found in the CSD for the 10 compounds were included in the dataset.
The structures were imported and analyzed with the Maestro tool from
the Schrödinger Suite.37 Hydrogen
atoms were added according to the ionization state at pH 7.4 using
the Epik tool.60 No further structural
refinements were carried out.
for 10 drugs and clinical candidates was assembled (
erythronolides (erythromycin, clarithromycin, azithromycin, roxithromycin,
and telithromycin) and five HCV NS3 protease inhibitors, three of
which are macrocyclic (danoprevir, vaniprevir, and grazoprevir) and
two are non-macrocyclic drugs (asunaprevir and telaprevir). All crystal
structures of these 10 compounds were retrieved from the PDB (
by common name, synonyms, and chemical structure.
From the PDB,
only crystal structures with a resolution <3 Å were included
in the dataset, except for one structure for each of roxithromycin
(1JZZ: 3.8 Å)
and telithromycin (1P9X: 3.4 Å) in which the structures showed interesting conformations
(see
found in the CSD for the 10 compounds were included in the dataset.
The structures were imported and analyzed with the Maestro tool from
the Schrödinger Suite.37 Hydrogen
atoms were added according to the ionization state at pH 7.4 using
the Epik tool.60 No further structural
refinements were carried out.
4
Molecular Docking of Ganoderma Triterpenoids against DENV Protease
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The various triterpenoids of G. lucidum that have been reported in anti-viral studies36 (link),45 (link),47 (link), were searched and retrieved from the PubChem database (https://pubchem.ncbi.nlm.nih.gov )48 (link), and considered for screening with DENV protease. Also, the known DENV protease inhibitor 1,8-Dihydroxy-4,5-dinitroanthraquinone was downloaded and used as positive control in the molecular docking analysis49 (link). The three-dimensional (3D) structure at fine resolution of 1.5 Å for the viral protein “NS2B-NS3 protease” was collected using PDB ID: 2FOM from the RCSB PDB (http://www.rcsb.org/pdb/home/home.do )40 (link). The NS3pro domain in Chain B of the protease was selected for screening with selected triterpenoids. Visualization of the molecular structure of ligand and protein was performed using the Maestro tool of the Schrödinger software modules suite50 (link). All other molecular docking and molecular dynamics simulations below were also carried out using Schrödinger software modules.
5
Triazole-Bridged N-Glycosides Docking
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The docking studies were carried out using various derived triazole bridged N-glycosides of pyrazolo[1,5-a]pyrimidinone with proposed binding pocket of X-ray crystallographic structure (Protein Data Bank ID: 1A52, resolution: 2.6 Å). Docking was performed using Autodock Vina 4.0, and the interaction between the ligands and protein after docking was visualized and analyzed using PyMol software. The Biovia Discovery Studio Visualizer v20.1.0.19295 was used for 2D visualization and detailed ligand interaction visualization. The Schrödinger Maestro tool was utilized for QSAR and SAR studies.
6
Molecular Docking with Maestro
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Maestro (Schrödinger Release 2021-2: Maestro, Schrödinger, LLC, New York, NY, USA, 2020-3.) was applied to XP program (extra precision) site-specific super molecular docking. After the completion of XP (extra precision), molecular docking by Maestro Tool (https://www.schrodinger.com/products/maestro , accessed on 26 July 2022) of Schrödinger Suite Software (https://www.schrodinger.com/ , accessed on 26 July 2022), every protein–ligand complex structure in PDB format was taken from the docked post-viewing file for post-docking visualization, investigation of non-bond interactions, and evaluation of hydrophobicity and bioactivity.
7
Triazole-linked Pyrazolo[1,5-a]Pyrimidine Glycohybrids
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
The docking studies were carried out using various derived triazole-linked pyrazolo[1,5-a]pyrimidine-based glycohybrids with proposed binding pocket of X-ray crystallographic structure (Protein Data Bank ID: 3PP0 , resolution: 2.4 Å). Docking was performed using Autodock Vina 4.0, and the interaction between the ligands and protein after docking was visualized and analyzed using PyMol software. The Biovia Discovery Studio Visualizer v20.1.0.19295 was used for 2D visualization and detailed ligand interaction visualization. The Schrödinger Maestro tool was utilized for QSAR and SAR studies.
8
Structural Analysis of PGAM1 Protein
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Human PGAM1 structure (PDB-ID: 5Y2I) was retrieved from protein data bank (https://www.rcsb.org/ ) (Berman, Henrick & Nakamura, 2003 (link)). The crystal structure of PGAM1 in complex with ligand PGMI-004A was in dimeric form consisting of two chains (Chain A and B). Protein preparation wizard embedded in Schrödinger’s Maestro tool (Sastry et al., 2013 (link)) was used for preprocessing of structure. All water molecules and other co-crystal ligands were removed and structure was minimized using OPLS2005 forcefield to remove all steric clashes. Similarly, for molecular docking studies compounds were prepared using Ligprep tool embedded in Schrodinger software (Guasch et al., 2013 (link)). Different ionization states and tautomeric forms were generated at pH 7.0 (Li, Robertson & Jensen, 2005 (link)).
About PubCompare
Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.
We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.
However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.
Ready to get started?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!