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Sybyl

Manufactured by Certara
Sourced in United States

Sybyl is a comprehensive computational chemistry software platform developed by Certara. It provides a suite of tools for molecular modeling, drug design, and structure-based drug discovery. Sybyl offers functionality for molecular visualization, structure generation, and various computational methods such as molecular mechanics, quantum mechanics, and ligand-protein docking.

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5 protocols using sybyl

1

Molecular Modeling Workflows on Linux

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All molecular modeling operations were carried out in the Maestro (version 9.0 Schrödinger Inc., USA), Sybyl (version 7.2; Certara Inc. USA) and Molecular Operating Environment (version 2009.10; Chemical Computing Group Inc., Canada) modeling packages running on Dell Precision 690 workstation with 8 CPUs, 10 GB memory and Red Hat Enerprise 5 Linux Operating System.
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2

Molecular Docking of TPI Proteins

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Small molecules were built in Sybyl (Certara Corp.) and saved in mol2 format. The two TPI protein receptors from Trypanosoma cruzi (PDB code 1tcd) and S. cerevisiae (1ypi) were prepared in Sybyl using the protein preparation tools to add hydrogens, properly type atoms, and remove any clashes. AutoDock Tools86 (link) were used to prepare the ligand and receptor pdbqt files and to select the docking box size for Autodock4. The docking box size was large enough to include the dimer interface described by Kurkcuoglu et al.50 (link). Autodock4.2.6 was run with Lamarkian Genetic Algorithm, with 25 M energy evaluations for 27,000 generations. This method includes a Solis & Wets local search of the ligand in the receptor after docking. Autodock 4.2.6 calculates a binding energy by summation of the molecular energy components (vdw + Hbonding + desolvation + electrostatics + ligand torsional free energy) minus the unbound system energy. The 30 best-docked ligands were examined. Optimal docking results were displayed in Pymol (PyMOL Mol. Graphics System, Ver. 1.8.2, Schrodinger, LLC).
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3

Docking of Compound 50 Using Surflex-Dock

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Docking of compound 50 was accomplished with the Surflex 2.7’s molecular docking
module (surflex-dock; Sybyl, Certara) and the PDB ID 6P3P, which is based
on conformation optimization procedures implemented for morphological
similarity, that fragments the molecule, docks the fragments, and
reconstructs the molecule in the active site of the protein. The ligand
in 6P3P was
used to define a binding region and as a test ligand for the docking
protocol. The binding pose predicted by the protocol closely resembled
the experimental docked geometry of the experimentally derived binding
pose for the ligand (not shown). Subsequently, the molecular model
of compound 50 was generated, energy minimized, and docked
using the same protocol. Molecular models were analyzed using MOE
2019.0101 (Chemical Computing Group) or Chimera (http://www.cgl.ucsf.edu/chimera).
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4

Modeling A. baumannii Topo IV-Moxifloxacin-DNA Complex

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The structure of the A. baumannii Topo IV-moxifloxacin-DNA ternary complex was obtained from PDB ID: 2XKK [26 (link)]. Four Mg2+ molecules are present in the PDB ID: 2XKK structure; two catalytic Mg2+, one at each site A, and two Mg2+ chelated with moxifloxacin, one with each moxifloxacin. No Mg2+ was present in either of the two sites B in the PDB ID: 2XKK structure. Based on the positions of the two metal binding sites proposed by Schmidt et al. [21 (link)] and Pitts et al. [16 (link)], the site A and the site B, we manually modeled Mg2+ ions into each of the sites B of the PDB ID: 2XKK structure using SYBYL (Certara USA, Inc., Princeton, NJ, U.S.A.). The structure shown in Figure 1 thus has a Mg2+ ion present at each of the metal binding sites A and B. As indicated in the figure legend, the Mg2+ chelated by moxifloxacin is omitted for clarity. The amino acid numbering was changed to those in E. coli Topo IV based on the homologies between A. baumannii and E. coli Topo IVs.
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5

Glycoconjugate 5 Structural Modeling

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A three-dimensional model of glycoconjugate 5 was built with Sybyl (Certara, Princeton, NJ) graphical software using the atomic coordinates of TOTAPOL proposed from the PubMed site (; https://pubchem.ncbi.nlm.nih.gov). The molecule was graphically extended by adding a glycine, a benzene and a galactose residue from the Sybyl molecular libraries. The galactose was docked on the calcium ion in two adjacent binding sites of the LecA structure by superimposition on an equivalent sugar in the crystal structure with PDB ID ; 1OKO.14 (link) In order to illustrate the extension that the TOTAPOL group can attain on the surface of LecA, three conformations were generated by varying the torsion angles in the phenylglycine linker (Fig. S3).
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