Computational protocol: Conjugation with polyamines enhances the antibacterial and anticancer activity of chloramphenicol

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Protocol publication

[…] Three dimensional (3D) models of compounds 4 and 5 were achieved using Arguslab 4.0.1 provided by Planaria Software LLC, Seattle, WA (http://www.arguslab.com), starting with the 3D structure of CAM derived from the 50S ribosomal subunit structure of E. coli in complex with CAM (; PDB:3OFC). CHARMM Force field parameters and topology files were generated by the SwissParam Tool (). The PA-CAM molecules were docked into the 50S ribosomal subunit structure, by positioning their CAM moiety within the drug pocket as indicated in ( ). All groups of 50S subunit in a distance of 10 Å around compounds 4 and 5, except for water, were selected, solvated with TIP3 water molecules, and then neutralized with sodium ions using the VMD program (). The systems produced in this way are referred hereafter as rib-4 and rib-5, respectively. For comparative purposes, a similar system was prepared for CAM itself. This system is referred as rib-CAM.Rib-4, rib-5 and rib-CAM were energy minimized and subjected to canonical enseble Molecular Dynamics (MD) simulations for 10 ns at 300K, with Particle Mesh Ewald (PME) algorithm and rigid bonds assigned using the NAMD software (). During MD simulations, all nucleic acid backbone atoms were immobilized. Finally, the last frame of each of the three MD trajectories was energy minimized. All molecular visualizations were produced with the PyMOL Molecular Graphics System, Version 1.5.0.4 Schrödinger, LLC. […]

Pipeline specifications

Software tools SwissParam, VMD, NAMD, PyMOL
Applications Drug design, Protein structure analysis
Organisms Homo sapiens
Diseases Neoplasms, Drug-Related Side Effects and Adverse Reactions
Chemicals Chloramphenicol, Polyamines, Puromycin, Succinic Acid