We utilized the POAP pipeline86 for an in silico virtual screening of the chemical compounds obtained through different chromatographic separation. We have obtained the SMILES notations of these compounds, and generated their 3D models (in mol2 format) through the POAP Ligand Preparation pipeline. To this end, we utilized Chimera to generate physiological protonation states of the ligands, and PDBQT files were prepared87. We also carried out ligand optimizations via the POAP Ligand Preparation pipeline utilizing the MMFF94 force field which is being optimized for drug-like organic molecules and molecular docking88. Out of the 50 conformers, generated for each ligand through the Weighted Rotor Search approach, only the best conformers were retained. Finally, we have subjected the ligands to energy minimization for 5000 steps by the conjugate algorithm.

We have prepared the macromolecule receptors, of the SaD and PaD proteins, using AutoDockTools. We utilized AutoDock 4.2, aided by the POAP pipeline, for the virtual screening process89. For AutoDock parameters, we have set 100 generations of Lamarckian Genetic Algorithm for each protein–ligand complex. To fit in the previously predicted pocket, we adjusted the docking grids into squares of 24 Å with x, y, z coordinates of 17.647, 75.43, 27.766, and 18.069, 74.299, 28.532, for SaD and PaD, respectively. For the silicon-containing compound among the set of ligands, we separately carried out molecular docking with AD4.1_bound parameter file, obtained from AutoDock, wherein we added the parameters for silicon atoms (Rii = 4.3; eii = 0.402)90.

We have validated the docking methodology via redocking of experimentally confirmed and deposited structures with the reference ligand (Fig. S8). Therein, we have retrieved the ATP-bound E. coli DnaK crystallized structures from PDB (PDB ID: 4B9Q, CHAIN ID: A; PDB ID: 4JNE, CHAIN ID: A). The molecular docking search grids were squares of 24 Å, in x, y, z coordinates of 108.958, 73.922, 100.622, and 19.081, 76.887, 31.16, for 4B9Q and 4JNE respectively.

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