Prime version 3

The free energy of binding was calculated for both docked complexes with D-sorbitol using the Prime/MM-GBSA method as described previously34 . It was performed using the OPLS-2005 force field and GBSA continuum model in Prime version 3.0 (Schrodinger) as described previously50 (link)51 (link).
The binding free energy, ΔG_bind, was obtained using the following equations as described previously52 (link):


where E_ligand, E_protein, and E_complex are the minimized energies of the inhibitor, protein, and protein-inhibitor complex, respectively.

where G_solv (ligand), G_{solv (}protein), and G_solv (complex) are the solvation free energies of the inhibitor, protein, and complex, respectively.

where G_SA (ligand), G_SA (protein), and G_SA (complex) are the surface area energies for the ligand, protein, and complex, respectively53 (link).

The Induced Fit Docking protocol is composed of job sequence in which ligands are docked with Glide (first step), then Prime Refinement is used to allow the receptor to relax (second step), and the ligands are redocked into the relaxed receptor with Glide (third step).
Binding site for the first Glide docking phase (Glide Standard Precision Mode) of the Induced Fit Workflow (Induced Fit Docking, protocol 2015–2, Glide version 6.4, Prime version 3.7, Schrödinger)^{38 –40 (link)} is calculated on the 2CG9 structure^{37 (link)}, mapping onto a grid with dimensions of 36 Å (outer box) and 20 Å (inner box), centered on residues 628–630, 640–641, 670–675 (Hsp90 residues numbering as in the PDB entry 2CG9). Maestro’s default protocol was used for the first (Initial Glide docking) and the second step (Prime Induced Fit) considering 20 poses per ligand; these poses were retained from the initial docking and then were passed to Prime (Prime version 3.7, Schrödinger 2015), for the Prime refinement step. Finally, the ligands were re-docked (third step) into their corresponding low energy protein structures (Glide Extra Precision Mode) with resulting complexes ranked according to GlideScore.

The derivatives were modelled into the crystal structure of native Deinococcus radiodurans large ribosomal subunit (D50S) bound with linezolid (Pdb: 3DLL⁵⁵ (link)) using Schrödinger software package and its Induced Fit Docking module (Induced Fit Docking protocol 2013-2, Glide version 5.9, Prime version 3.2, Schrödinger, LLC, New York, NY, 2013), to account for the reported structural flexibility of the peptidyl transferase centre.

The 2D structures of the compounds SQ109(1a), 1b-i, 2 were sketched with Marvin Program (Marvin version 21.17.0, ChemAxon, https://www.chemaxon.com), model-built with Schrödinger 2017–1 platform (Schrödinger Release 2021–1: Protein Preparation Wizard; Epik, Schrödinger, LLC, New York, NY, 2021; Impact, Schrödinger, LLC, New York, NY; Prime, Schrödinger, LLC, New York, NY, 2021) and the compounds' 3D structures in their monoprotonated form were energy minimized using the conjugate gradient method, the MMFF94 [71 (link)] force field and a distance-dependent dielectric constant of 4.0 until a convergence threshold of 2.4 10^–5 kcal mol⁻¹ Å⁻¹ was reached. The ionization state of the compounds at pH 7.5 were checked using the Epik program [72 (link)] implemented in Schrödinger suite (Prime Version 3.2, Schrödinger, LLC, New York, NY, 2015). Τhe most likely state for the ethylenediamine unit is the mono- protonated but we also performed all the calculations for the diprotonated state as well.

This work is based on the crystal structure of AtTPC1 (PDB ID 5e1j). The structure was prepared using the PRIME module of the Schrodinger suite of programs (Prime, version 3.9, Schrodinger, LLC, New York, NY, USA, 2017).