Moe 2014

Molecular docking studies were performed using Molecular Operating Environment (MOE) 2014.09 software (Chemical Computing Group, Montreal, QC, Canada) to predict the poses and orientation of L-arginine on the surface of curcumin. The 3D structure of curcumin was built using the builder interface and the energy was reduced to a root mean square deviation (RMSD) gradient of 0.01 kcal/mol using the QuickPrep tool of the MOE software. Moreover, the 3D structures of L-arginine and curcumin were built using MOE Builder and their energy was minimized. L-arginine was docked into the surface of curcumin using an induced-fit docking protocol with the Triangle Matcher method and dG scoring system for pose ranking. Free energy values were elected and reported after a visual assessment of the resultant docking poses with the highest stability and lowest binding.

Molecular Operating Environment (MOE) 2014.09 software (Chemical Computing Group, Montreal, QC, Canada) was used to execute molecular docking investigations to anticipate both the stability and potential orientation of curcumin inside the cavity and/or rim of various cyclodextrins; β-CD, HE β-CD, HP β-CD, and SBE β-CD (Captisol). The 3D structure of β-CD was downloaded from the Protein Data Bank (PDB) at https://www.rcsb.org (accessed on 1 March 2022) as the PDB file code: 5E6Z [20 (link)]. The 3D structure of HE β-CD, HP β-CD, and SBE β-CD were built using the builder interface of MOE software via substituting the hydroxyl group with ethyl, isopropyl, and sulfobuteryl radicals, respectively [21 (link)]. Hydrogens were added, and the energy of the CD structures was minimized to an RMSD (root mean square deviation) gradient of 0.01 kcal/mol using the QuickPrep tool of the MOE software. The compounds’ 3D structures were also built using a MOE builder. Curcumin was docked into the inclusion cavity of the various CDs using an induced-fit docking protocol, the Triangle Matcher method, and the dG scoring system for pose ranking. Following visual assessment of the resultant docking poses, poses with the highest stability and lowest binding free energy value were elected and reported.

Molecular Operating Environment (MOE) 2014.09 software (Chemical Computing Group, Montreal, QC, Canada) was used to investigate the docking, energy scores and potential orientation of imipenem within the cavity and/or rim of β-CD and HP β-CD. The 3D structure of β-CD was downloaded from Protein Data Bank (PDB) at https://www.rcsb.org (1 June 2022) as PDB file code: 5E6Z [21 (link)]. The 3D structure of HP β-CD was designed using the builder interface of MOE software via substituting the hydroxyl group with isopropyl radicals [22 (link)]. Compounds were docked into the cavity of the CDs using an induced-fit docking protocol using the Triangle Matcher method and dG scoring system for pose ranking.

In order to predict the orientation within the cavity and/or rim and gain more insights into the stability/binding constants of Diclo with α-CD, β-CD, γ-CD, and HP-β-CD, molecular docking studies were performed using Molecular Operating Environment (MOE) 2014.09 software (Chemical Computing Group, Montreal, QC, Canada). The crystal structures of CDs were extracted from Protein Data Bank (PDB): α-CD (PDB code: 5E6Y), β-CD (PDB code: 5E6Z), and γ-CD (PDB code: 5E70) [19 (link)]. Since no crystal structure is available for HP-β-CD, the crystal structure of β-CD (PDB code: 5E6Z) was used as a template to build the 3D structure of HP-β-CD by substituting four primary hydroxyl groups with 2-hydroxypropyl radical, as described elsewhere [20 (link)]. The 3D crystal structure of Diclo was retrieved from crystallographic data available in the Cambridge structural database (Ref. Code: LIQFUN) [21 (link)]. The docking simulations were performed using the induced fit docking protocol. All other parameters were used with the default molecular operating environment (MOE) settings. The resulting docking poses were visually inspected, and the best energy pose for each type of the four Diclo-CD complexes was selected.

Molecular docking studies were performed with the Molecular Operating Environment (MOE) 2014.09 software (Chemical Computing Group, Montreal, QC, Canada) to predict the stability and possible orientation of various bases on the surface of ketoprofen. The 3D structure of ketoprofen was constructed using the builder interface, and its energy was minimized to an RMSD (root mean square deviation) gradient of 0.01 kcal/mol using the QuickPrep tool in the MOE software. Similarly, the 3D structures of arginine, lysine, and tromethamine were built using the MOE builder, and their energies were minimized. The three bases were docked onto the surface of ketoprofen using an induced-fit docking protocol with the Tri-angle Matcher method and dG scoring system for pose ranking. After a visual assessment of the resultant docking poses, those with the highest stability and lowest binding free energy values were selected and reported.

Molecular docking studies were carried out using Molecular Operating Environment (MOE 2014.0901) software, Chemical Computing Group, Montreal, Canada, following the docking protocol [36 (link)]. The X-ray crystal structure of the TGF-β (PDB ID: 1VJY) active site was downloaded from the RCSB Protein Date Bank website [37 (link)]. The validity of the used docking protocol was confirmed when the root-mean-square deviation (RMSD) score was less than 1.5 or 2 Å [38 (link)].