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Moe version 2014

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MOE version 2014.0901 is a software tool for computational chemistry and drug discovery. It provides functionality for molecular modeling, structure-based drug design, and molecular property prediction. The software is used by researchers and scientists in the field of chemistry and pharmaceutical development.

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Mmff94x force field, by Chemical Computing Group (1 mentions)

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MOE 2014.09

13 protocols using moe version 2014

1

Molecular Docking of Potential Compounds

Cited 3 times
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The software builder of MOE® version 2014.0901 (Chemical Computing group Inc., Montreal, QC, Canada) was used to generate the 3-D structure of the investigated molecules. MMFF94x forcefield was utilized to minimize the energy of the molecules and to obtain the corresponding mdb file needed for docking [33 (link)]. The bond length was adjusted in the constructed structures using Avogadro software which was also used to calculate the Marsilli–Gastiger partial charges.
MOE® version 2014.0901 (Chemical Computing group Inc., Montreal, QC, Canada) docking software was used for this task. First, locating possible target positions in the carrier was performed using the MOE’s site finder tool. After, dummy atoms were added [34 (link)]. Each of the investigated molecules was placed at these locations utilizing the triangle matcher placement method. Flexible docking was conducted adopting the ASE scoring function. A mean value of the top five poses binding energies and their SD were calculated [32 (link),35 (link),36 (link)].
Sokol M.B., Chirkina M.V., Yabbarov N.G., Mollaeva M.R., Podrugina T.A., Pavlova A.S., Temnov V.V., Hathout R.M., Metwally A.A, & Nikolskaya E.D. (2022). Structural Optimization of Platinum Drugs to Improve the Drug-Loading and Antitumor Efficacy of PLGA Nanoparticles. Pharmaceutics, 14(11), 2333.
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2

Phylogenetic Analysis and 3D Docking of BmDXR

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The amino acid sequence of BmDXR was aligned with the selected amino acid sequences from other organisms by MAFFT online1, then edited by BioEdit v7.25, and phylogenetically analyzed by using the Maximum Likelihood method in MEGA 7 (Kumar et al., 2016 (link)). The structure of BmDXR was predicted by SWISS-MODEL2 (Guex et al., 2009 (link); Bienert et al., 2017 (link); Waterhouse et al., 2018 (link)). The 3D structure of BmDXR was virtually docked with FSM through Molecular Operating Environment (MOE) version 2014.09 (Chemical Computing Group).
Wang S., Li M., Luo X., Yu L., Nie Z., Liu Q., An X., Ao Y., Liu Q., Chen J., Tian Y., Zhao J, & He L. (2020). Inhibitory Effects of Fosmidomycin Against Babesia microti in vitro. Frontiers in Cell and Developmental Biology, 8, 247.
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3

Molecular Docking Simulation of Inhibitors against AGS and BGUS

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Inhibitors with significant potency were subjected to docking simulation, with the aim of revealing the probable molecular determinants underlying the inhibitory activity against AGS or BGUS. The X-ray crystal structure of BGUS (PDB ID: 3LPF) was obtained from the Protein Data Bank (PDB) database. Since the X-ray crystal structure of AGS of Saccharomyces cerevisiae has not been reported, a homology model of the enzyme was constructed by employing the crystal structure of isomaltase as a template (PDB ID: 3AJ7) on the SWISS MODEL webserver [46 (link)]. Then, the X-ray crystal structure of AGS built by homology modeling or BGUS was prepared using MOE (Version 2014. 09, Chemical Computing Group Inc., Montreal, Canada). The target compounds were docked into the active sites of AGS or BGUS using the Triangular Matching docking method. A total of 30 conformations for each ligand–protein complex were generated. Finally, the 2D and 3D plots were depicted for analysis of the interactions among inhibitors and the amino acid residues in the binding pocket.
Rao G., Yu H., Zhang M., Cheng Y., Ran K., Wang J., Wei B., Li M., Shan W., Zhan Z, & Ying Y. (2022). α-Glucosidase and Bacterial β-Glucuronidase Inhibitors from the Stems of Schisandra sphaerandra Staph. Pharmaceuticals, 15(3), 329.
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4

Carbohydrate Recognition Domain Structure Analysis

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The crystal structure
of the carbohydrate recognition domain of the H1 subunit of the ASGPR
was obtained from the RCSB protein data bank (https://www.rcsb.org/) with a code
of 1DV8. The
isomeric SMILES corresponding to the chemical structure of the studied
ligand (carbohydrate); glycyrrhetinic acid was obtained using PubChem.
The corresponding 3D chemical structures were generated using the
builder function of MOE version 2014.0901 (Chemical Computing Group
Inc., Montreal, Canada). Further, energy minimization was performed
using MMFF94x forcefield of the same software.34 (link)−36 The docking
analysis was employed using MOE version 2014.0901 (Chemical Computing
Group Inc., Montreal, Canada). The pdb file of the protein nanoparticle
matrix was imported to MOE where the identification of the binding
sites was performed using the MOE’s “Site finder”
tool37 (link) to be ready for docking using the
“triangle matcher” as a placement method. This software
creates dummy atoms around the docking target atoms. These dummy atoms
are considered the docking positions. The software-integrated London
score was utilized for calculating the binding energy scoring value.38 (link)−41 (link)
Ossama M., Hathout R.M., Attia D.A, & Mortada N.D. (2019). Enhanced Allicin Cytotoxicity on HEPG-2 Cells Using Glycyrrhetinic Acid Surface-Decorated Gelatin Nanoparticles. ACS Omega, 4(6), 11293-11300.
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5

Antimalarial Drug Structure Optimization

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The isomeric SMILES corresponding to the chemical structures of the studied antimalarial drugs; CQ and HCQ were obtained using PubChem®. The corresponding 3D chemical structures were generated using the builder function of MOE® version 2014.0901 (Chemical Computing Group Inc., Montreal, Canada). Further, energy minimization was carried out for all the investigated molecules using MMFF94x forcefield of the same software [21 (link)].
Hathout R.M., Abdelhamid S.G, & Metwally A.A. (2020). Chloroquine and hydroxychloroquine for combating COVID-19: Investigating efficacy and hypothesizing new formulations using Bio/chemoinformatics tools. Informatics in Medicine Unlocked, 21, 100446.
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6

Structural Analysis of Delivery and Target Receptors

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The crystal structure of the relevant delivery and the related receptor targets were obtained from the protein data bank (http://www.rcsb.org). The codes 2ACM corresponded to Mucin. The codes 6m17, 3zyk corresponded to the ACE-2 and PICALM, respectively. The polar hydrogens were added to the obtained pdb files using MOE® version 2014.0901 (Chemical Computing Group Inc., Montreal, Canada).
Hathout R.M., Abdelhamid S.G, & Metwally A.A. (2020). Chloroquine and hydroxychloroquine for combating COVID-19: Investigating efficacy and hypothesizing new formulations using Bio/chemoinformatics tools. Informatics in Medicine Unlocked, 21, 100446.
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7

Molecular Descriptors in Drug Docking

Cited 3 times
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In order to explain the differences in docking scores observed for the studied drugs, some crucial constitutional, electronic, and topological descriptors were calculated. The selected descriptors were the molecular weight, LogP (o/w), total polar surface area, number of H-atom donors and acceptors, and molecular globularity and molecular flexibility [37 (link)]. The descriptors were calculated using MOE® version 2014.0901 (Chemical Computing group Inc., Montreal, QC, Canada) utilizing the molecules’ mdb files generated using the same software [38 (link),39 (link)].
Sokol M.B., Chirkina M.V., Yabbarov N.G., Mollaeva M.R., Podrugina T.A., Pavlova A.S., Temnov V.V., Hathout R.M., Metwally A.A, & Nikolskaya E.D. (2022). Structural Optimization of Platinum Drugs to Improve the Drug-Loading and Antitumor Efficacy of PLGA Nanoparticles. Pharmaceutics, 14(11), 2333.
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8

Antibiotics Structural Optimization

Cited 1 time
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The isomeric SMILES corresponding to the chemical structures of the studied antibiotics; cefotaxime and ceftriaxone were obtained using PubChem. The corresponding 3D chemical structures were generated using the builder function of MOE version 2014.0901 (Chemical Computing Group Inc., Montreal, Canada). Further, energy minimization was carried out for all the investigated molecules using MMFF94x forcefield of the same software28 (link),29 .
Hathout R.M., Abdelhamid S.G., El-Housseiny G.S, & Metwally A.A. (2020). Comparing cefotaxime and ceftriaxone in combating meningitis through nose-to-brain delivery using bio/chemoinformatics tools. Scientific Reports, 10, 21250.
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9

Physicochemical Profiling of Tobramycin and AOT

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The physical descriptors (constitutional and electronic) of tobramycin and its AOT-complex were calculated. The selected descriptors were the total polar surface area, number of hydrogen bond donors, number of hydrogen bond acceptors, molecular globularity, molecular flexibility, LogP (O/W) and the molecular weight. The descriptors were calculated using MOE version 2014.0901 (Chemical Computing Group Inc., Montreal, Canada) after constructing the two investigated drugs utilising the builder tool in the same software to generate the 3D structures of the investigated drugs from their isomeric SMILES obtained from The PubChem Project® [48 (link),49 (link)].
Hill M., Cunningham R.N., Hathout R.M., Johnston C., Hardy J.G, & Migaud M.E. (2019). Formulation of Antimicrobial Tobramycin Loaded PLGA Nanoparticles via Complexation with AOT. Journal of Functional Biomaterials, 10(2), 26.
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10

Structural Analysis of Nose-Brain Receptors

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The crystal structure of the relevant nose-to-brain delivery and the therapeutic targets related to the bacterial cell wall receptors were obtained from the protein data bank (http://www.rcsb.org). The following codes: 2ACM and 3G6I corresponded to Mucin and P-gp efflux-pump receptors, respectively. 26CW and 2WAD corresponded to the protein binding proteins 1A and 2B, respectively. The polar hydrogens were added to the obtained pdb files using MOE version 2014.0901 (Chemical Computing Group Inc., Montreal, Canada).
Hathout R.M., Abdelhamid S.G., El-Housseiny G.S, & Metwally A.A. (2020). Comparing cefotaxime and ceftriaxone in combating meningitis through nose-to-brain delivery using bio/chemoinformatics tools. Scientific Reports, 10, 21250.
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