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Moe 2020

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MOE 2020.09 is a software suite developed by Chemical Computing Group for molecular modeling and drug discovery. It provides a wide range of tools for visualization, analysis, and manipulation of chemical structures and biological data. The core function of MOE 2020.09 is to enable researchers and scientists to explore and understand the properties and behaviors of molecules and their interactions.

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Marvinsketch v21, by ChemAxon (2 mentions)

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MOE) software 2020.0901 MOE, Version 2020-09

15 protocols using moe 2020

1

Structural Optimization and Docking of Mn2+ Complex

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Firstly, the structure of the Mn 2+ -complex was drawn in Marvinsketch v21.11 (Chemaxon Ltd; https://chemaxon.com) enabling correct assignment of coordinate bonding. The resulting structure was 'cleaned' in 3D and saved in .gjf format for input into the Gaussian 16 revC.01 package (Gaussian Inc.
340 Quinnipiac st., Bldg. 40, Wallingford CT 06492, USA). The molecular structure of the Mn 2+ -complex was subsequently optimized in water as a solvent via the hybrid B3LYP (Becke-3 Parameter-Lee-Yang-Parr) [35] (link) DFT (Density Functional Theory) method in GEN mode to enable assignment in the calculation of the 6-31G** and LANL2DZ basis sets, to atoms H, O, C, N and Mn respectively. Gaussview 6 (Gaussian Inc. 340 Quinnipiac st., Bldg. 40, Wallingford CT 06492, USA) was next used to examine the structures of all converged structures and the nal optimized structure was exported in .pdb le format.
The Mn 2+ -complex was subsequently imported into MOE 2020.09 (Chemical Computing Group ULC; https://www.chemcomp.com/) and docked to PDB entry 1XQ8 with triangle matching placement and scoring with the London dG scoring function. Subsequent re nement of all docked poses using the GBVI/WSA dG scoring function with induced t was undertaken. Finally, the top docked pose was manipulated and visualized also using MOE 2020.09 (Chemical Computing Group ULC; https://www.chemcomp.com/).
Queiroz D.D., Ribeiro T.P., Gonçalves J.M., Mattos L.M.M., Gerhardt E., Freitas J., Palhano F.L., Frases S., Pinheiro A.S., McCann M., Knox A., Devereux M., Outeiro T.F, & Pereira M.D. (2022). A water-soluble manganese(II) octanediaoate/phenanthroline complex acts as an antioxidant and attenuates alpha-synuclein toxicity. Biochimica et biophysica acta. Molecular basis of disease, 1868(10).
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2

Structural Optimization and Docking of Mn2+ Complex

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Firstly, the structure of the Mn 2+ -complex was drawn in Marvinsketch v21.11 (Chemaxon Ltd; https://chemaxon.com) enabling correct assignment of coordinate bonding. The resulting structure was 'cleaned' in 3D and saved in .gjf format for input into the Gaussian 16 revC.01 package (Gaussian Inc.
340 Quinnipiac st., Bldg. 40, Wallingford CT 06492, USA). The molecular structure of the Mn 2+ -complex was subsequently optimized in water as a solvent via the hybrid B3LYP (Becke-3 Parameter-Lee-Yang-Parr) [35] (link) DFT (Density Functional Theory) method in GEN mode to enable assignment in the calculation of the 6-31G** and LANL2DZ basis sets, to atoms H, O, C, N and Mn respectively. Gaussview 6 (Gaussian Inc. 340 Quinnipiac st., Bldg. 40, Wallingford CT 06492, USA) was next used to examine the structures of all converged structures and the nal optimized structure was exported in .pdb le format.
The Mn 2+ -complex was subsequently imported into MOE 2020.09 (Chemical Computing Group ULC; https://www.chemcomp.com/) and docked to PDB entry 1XQ8 with triangle matching placement and scoring with the London dG scoring function. Subsequent re nement of all docked poses using the GBVI/WSA dG scoring function with induced t was undertaken. Finally, the top docked pose was manipulated and visualized also using MOE 2020.09 (Chemical Computing Group ULC; https://www.chemcomp.com/).
Queiroz D.D., Ribeiro T.d.P., Gonçalves J.M., Mattos L.M.M., Gerhardt E., Freitas J.A.d., Palhano F.L., Frasés S., Pinheiro A.S., McCann M., Knox A.J.S., Devereux M., Outeiro T.F., & Pereira M.D. (2021). A Water-Soluble Manganese(II) Octanediaoate/Phenanthroline Complex Acts as an Antioxidant and Attenuates Alpha-Synuclein Toxicity.
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3

Molecular Docking Protocol for Protein-Ligand Binding

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PDB structures were prepared for molecular docking experiments using the protein structural preparation tool followed by Protonate3D, as implemented in the Molecular Operating Environment (MOE) 2020.09 (Chemical Computing Group, Inc., Montreal, Quebec, Canada, http://www.chemcomp.com). Ligand structures were built with MOE and minimized using the MM-FF94x force field until a root-mean-square deviation (RMSD) gradient of 0.05 kcal/(mol Å) was reached. In the first step for protein preparation, we preprocessed the structure using the standard protocol, which included the assigning of bond orders, the adding of hydrogens, the creating of disulfide bonds, and the prediction of the structural protonation state at a physiological pH of 7.4. The structure was subjected to a short energy minimization routine to relax it using the Amber 99 force field as implemented in MOE. The following standard parameters were selected: receptor van der Waals scaling, 0.50; ligand van der Waals scaling, 0.50; and a maximum of 20 poses per ligand. The best docking pose for 14 was selected based on the lowest RMSD value, which was 1.7 Å.
Cioffi C.L., Raja A., Muthuraman P., Jayaraman A., Jayakumar S., Varadi A., Racz B, & Petrukhin K. (2021). Identification of Transthyretin Tetramer Kinetic Stabilizers That Are Capable of Inhibiting the Retinol-Dependent Retinol Binding Protein 4-Transthyretin Interaction: Potential Novel Therapeutics for Macular Degeneration, Transthyretin Amyloidosis, and Their Common Age-Related Comorbidities. Journal of medicinal chemistry, 64(13), 9010-9041.
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4

Determining Optimal VHH Linker Length

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Following domain binning and HDX epitope mapping, the approximate epitope and binding location of many monomeric VHHs against the spike protein were determined. To calculate the length of the desired linker between two VHHs, the distance between the center of the known epitope was measured in both the open and closed state of the spike protein in MOE 2020.09 (Chemical Computing Group). To account for cases where the shortest distance between two sites would result in a clash and to account for the unknown binding orientation of the VHH in relation to the spike protein (where the terminus would be located), an additional buffer distance was added to the initial measurement. Given that an amino acid can cover 3.5–4.0 angstroms in an extended conformation, the measured distance was then converted to a minimum number of amino acids that would be required to bridge such a distance. The resulting number of amino acids was then further converted to the minimum number of linker subunits that could connect the two sites.
Hollingsworth S.A., Noland C.L., Vroom K., Saha A., Sam M., Gao Q., Zhou H., Grandy D.U., Singh S., Wen Z., Warren C., Ma X.S., Malashock D., Galli J., Go G., Eddins M., Mayhood T., Sathiyamoorthy K., Fridman A., Raoufi F., Gomez-Llorente Y., Patridge A., Tang Y., Chen S.J., Bailly M., Ji C., Kingsley L.J., Cheng A.C., Geierstanger B.H., Gorman D.M., Zhang L, & Pande K. (2023). Discovery and multimerization of cross-reactive single-domain antibodies against SARS-like viruses to enhance potency and address emerging SARS-CoV-2 variants. Scientific Reports, 13, 13668.
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5

Molecular Docking of CRG Tetrasaccharides with HSV-1 gD

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The structures of kappa-, beta-, iota- and lambda-CRG tetrasacharides were obtained using the molecular editor of the MOE 2020.0901 program [Molecular Operating Environment (MOE), 2020.09; Chemical Computing Group ULC, 1010 Sherbrooke St. West, Suite #910, Montreal, QC, Canada, H3A 2R7, 2020]. For molecular docking, CRG tetrasacharides structures were used, which were solvated in the aqueous phase and optimised with the forcefield Amber10:EHT. The crystal structures of the complexes of the HSV-1 gD glycoprotein with the HSEA/M receptor (PDB ID 1JMA) were used as a target protein. The calculation of the electrostatic potential of the molecular surface of glycoprotein gD was carried out using the MOE 2019.01 program. Molecular docking of glycoprotein gD with the CRG tetrasacharides was performed using the Dock module of the MOE 2020.09 software. The structures of 30 complexes were calculated with Score London dG, and the 5 most energetically advantageous complexes were optimised with Score GBVI/WSA dG. Contact analysis was carried out using the Ligand Interaction module of the MOE program.
Krylova N.V., Kravchenko A.O., Iunikhina O.V., Pott A.B., Likhatskaya G.N., Volod’ko A.V., Zaporozhets T.S., Shchelkanov M.Y, & Yermak I.M. (2022). Influence of the Structural Features of Carrageenans from Red Algae of the Far Eastern Seas on Their Antiviral Properties. Marine Drugs, 20(1), 60.
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6

Structural Analysis of Glucosidase and Amylase

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The X-ray structure of the α-glucosidase enzyme (PDB: 2QMJ) and α-amylase (PDB: 1XCW) were downloaded from the protein databank (PDB) website (https://www.rcsb.org/), at a resolution of 1.90 Å and 2.00 Å respectively. All the molecular modeling and docking studies were carried out using MOE 2020.09 (Chemical Computing Group, Canada) as the computational software. First, all the hydrogen atoms were added using the Protonate 3D algorithm where the protonation states of the amino acid residues were assigned, and the partial charges of atoms were added. In addition, the compounds were drawn using the builder tool and energy was minimized using the MMFF94× force field. MOE induced-fit Dock tool used to dock the synthesized compounds into the active site. The selection of the final docked ligand–enzyme poses was according to the criteria of binding energy score and combined with ligand–receptor interactions.
Ayoup M.S., Khaled N., Abdel-Hamid H., Ghareeb D.A., Nasr S.A., Omer A., Sonousi A., Kassab A.E, & Eltaweil A.S. (2024). Novel sulfonamide derivatives as multitarget antidiabetic agents: design, synthesis, and biological evaluation. RSC Advances, 14(11), 7664-7675.
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7

In silico Molecular Modeling Protocol

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In silico calculations were performed in Molecular Operating Environment (MOE), 2020.09 (Chemical Computing Group ULC, Montreal, QC, Canada). A full description of the methodology used can be found in Supplementary Material S3.
Bouz G., Bouz S., Janďourek O., Konečná K., Bárta P., Vinšová J., Doležal M, & Zitko J. (2021). Synthesis, Biological Evaluation, and In Silico Modeling of N-Substituted Quinoxaline-2-Carboxamides. Pharmaceuticals, 14(8), 768.
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8

Molecular Docking and MD Simulations

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Inputs for molecular docking and MD were prepared in Molecular Operating Environment (MOE), 2020.09 (Chemical Computing Group ULC, Montreal, QC, Canada). The docking was run in MOE. MD simulations were run in NAMD2 [44 (link)] (version GIT20190909) and analysed in VMD version (1.9.4a51) [45 (link)]. For experimental details, see the Supplementary Material.
Pang L., Weeks S.D., Juhás M., Strelkov S.V., Zitko J, & Van Aerschot A. (2021). Towards Novel 3-Aminopyrazinamide-Based Prolyl-tRNA Synthetase Inhibitors: In Silico Modelling, Thermal Shift Assay and Structural Studies. International Journal of Molecular Sciences, 22(15), 7793.
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9

Anti-Candida Peptide Sequence Analysis

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Computational analysis was performed starting from three previously described peptides endowed with anti-Candida activity. In particular, peptides K10S (KKVTMTCSAS) [19 (link)], D5A (TCRVAHRGLTF) [20 (link)], and N1A (AQVSLTCLVK) [21 (link)] were selected to determine the correspondences between residues of the three sequences. For this purpose, we exploited MOE’s sequence alignment tool, a modified version of the alignment methodology originally introduced into molecular biology by Needleman (Molecular Operating Environment, MOE, 2020.09, Chemical Computing Group ULC, Montreal, QC, Canada, 2020). The alignment was computed through a function based on residue similarity score (obtained from applying BLOSUM 40 substitution matrix) and gap penalties. Starting from the amino acidic sequence of K10S peptide, random peptides were generated through sample sequence methodology and analyzed through the mutational analysis tool.
Ciociola T., Magliani W., De Simone T., Pertinhez T.A., Conti S., Cozza G., Marin O, & Giovati L. (2021). In Silico Predicted Antifungal Peptides: In Vitro and In Vivo Anti-Candida Activity. Journal of Fungi, 7(6), 439.
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10

Homology Modeling of GS1.1 Binding

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To identify the residues involved in GFA binding into GS1.1, the protein crystal structure of Zea mays GS1 (PDB 2D3A) was used as a template to build a homology model for A. palmeri. L-glufosinate was docked into the GS1.1 binding site. To guide the docking, we used the GFA binding mode from the protein crystal structure of Salmonella (1FPY). Molecular modeling was done using Molecular Operating Environment (MOE) 2020.09 software package (Chemical Computing Group ULC 2022 ).
Noguera M.M., Porri A., Werle I.S., Heiser J., Brändle F., Lerchl J., Murphy B., Betz M., Gatzmann F., Penkert M., Tuerk C., Meyer L, & Roma-Burgos N. (2022). Involvement of glutamine synthetase 2 (GS2) amplification and overexpression in Amaranthus palmeri resistance to glufosinate. Planta, 256(3), 57.
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