The structures of flavonoids and their derivatives were built by using builder panel in Maestro. The flavonoids were taken for ligand preparation by LigPrep 2.3 module (Schrödinger, USA) which performs addition of hydrogens, 2D to 3D conversion, realistic bond lengths and bond angles, low energy structure with correct chiralities, ionization states, tautomers, stereochemistries and ring conformations. The homology model of human P-gp in apo state was kindly provided by Dr. Stephen Aller (The University of Alabama at Birmingham, Birmingham, AL).
Ligprep 2.3 module
Manufactured by Schrödinger
Sourced in United States
LigPrep 2.3 is a module within the Schrödinger software suite. It is designed to prepare ligand structures for use in computational chemistry and drug discovery workflows. The core function of LigPrep 2.3 is to generate high-quality 3D molecular structures from 1D or 2D representations of chemical compounds.
Automatically generated - may contain errors
14 protocols using ligprep 2.3 module
1
Flavonoid Docking on Human P-gp
2
3D Structure Generation and Conformer Analysis of HVS-16
3
Meleagrin 3D Structure Generation
4
3D Ligand Structure Optimization
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The Lig Prep 2.3 module (Lig Prep, version 2.3, 2015, Schrödinger, USA) was used to construct the 3D structure for each compound and look for alternative conformers. The OPLS force field (OPLS 3, Schrödinger, USA) was used to geometrically optimize each ligand structure and to compute the partial atomic charges. Finally, 32 poses with distinct steric characteristics for each ligand were created for subsequent docking investigations.
5
Phytochemical Analysis of Egyptian Propolis
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Based on a focused literature review targeting the chemical profile of Egyptian propolis, one hundred and fifty phytochemicals were retrieved for the generation of an in-house dataset of the most frequently occurring compounds in Egyptian propolis (Table S1† ). The two-dimensional structures of most compounds along with those for the two reference drugs; febuxostat (CID 134018) and allopurinol (CID 2094) were obtained from PubChem database (https://pubchem.ncbi.nlm.nih.gov/ ) of the National Centre for Biotechnology Information in sdf file format. Unavailable structures in the PubChem database were searched in different literature and drawn using ChemDraw software (CambridgeSoft Corporation, Cambridge, USA) and saved as (.sdf) files.
After the dataset generation, the chemical structure of each compound was imported into the Maestro 11.8 panel interface (Maestro, version 11.8, 2018, Schrödinger, USA). The LigPrep 2.3 module (LigPrep, version 2.3, 2018, Schrödinger, USA) was implemented to generate the 3D structure and to search for different conformers. The OPLS (OPLS 2005, Schrödinger, USA) force field was implemented to geometrically optimize each ligand structure and compute partial atomic charges. Finally, since the chirality center of each ligand was not specified, 32 poses per ligand were generated with different steric features for subsequent docking studies.
After the dataset generation, the chemical structure of each compound was imported into the Maestro 11.8 panel interface (Maestro, version 11.8, 2018, Schrödinger, USA). The LigPrep 2.3 module (LigPrep, version 2.3, 2018, Schrödinger, USA) was implemented to generate the 3D structure and to search for different conformers. The OPLS (OPLS 2005, Schrödinger, USA) force field was implemented to geometrically optimize each ligand structure and compute partial atomic charges. Finally, since the chirality center of each ligand was not specified, 32 poses per ligand were generated with different steric features for subsequent docking studies.
6
Ligand Structure Optimization for Docking
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The structures of all compounds used in the docking studies were 2D sketched using the Maestro 9.3 panel (Maestro, version 9.3, 2012, Schrödinger, New York, NY, USA). The LigPrep 2.3 module (LigPrep, version 2.3, 2012, Schrödinger, New York, NY, USA) of the Schrödinger suite was utilized to generate the 3D structures and to search different conformers. The Optimized Potentials for Liquid Simulation (OPLS_2005, Schrödinger, New York, NY, USA) force field was applied to geometrically optimize the ligands and compute partial atomic charges. Finally, at most, 32 poses per ligand were generated with different steric features for the subsequent docking studies.
7
Structural Optimization and Conformer Generation
8
Molecular Docking of Isolated Compounds
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The nine isolated compounds were further promoted to molecular docking study to investigate their molecular binding mechanism with the target enzyme. The SDF format of the structure was imported to Schrödinger Maestro 10.2 software package (LLC, New York, NY, USA). To construct the 3D structure and search for alternative conformers, the Lig Prep 2.3 module (Lig Prep, version 2.3, 2015, Schrödinger, Cambridge, MA, USA) was used to perform energy minimization of ligand structures. In order to geometrically optimize each ligand structure and generate tautomers, the OPLS (OPLS 3, Schrödinger, New York, NY, USA) force field was used. Epik was utilized to produce all of the ionization states.
9
3D Structure Generation and Optimization
10
Isolation and Characterization of Cleistanthins A and B
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The natural compounds of cleistanthins A and B were isolated and purified from the leaves of Cleistanthus collinus using column chromatographic method and the structures were determined.[4 (link)] These structures [Figure 1 ] were built using builder panel in Maestro and ligand preparation was carried out for these compounds by Ligprep 2.3 module (Schrödinger, USA, 2009). Ligprep performs addition of hydrogens, 2D to 3D conversion, realistic bond lengths and bond angles, low energy structure with correct chiralities, ionization states, tautomers, stereochemistries and ring conformations. The energy minimized compounds were subjected to biological activity prediction based on their structural orientation using PASS (Prediction of Activity Spectra for Substances) tool.[6 (link)]
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