The relaxed complex scheme can be an drug screening method that accounts for receptor flexibility using molecular dynamics simulations. FPPS did not target the allosteric site 12. Virtual screens were performed with AutoDock Vina 18 and Glide 19,20 on crystal structure data as well as numerous structures from a FPPS molecular dynamics simulation. A neural network ASC-J9 supplier rescoring was performed to optimize the ranking of known inhibitors, and 10 consensus predictions were screened experimentally yielding one hit, which was further improved by a similarity search, yielding three low (1.8C2.5) micromolar leads. To our knowledge, this is the first successful virtual screen into the FPPS allosteric site. Methods and Materials Crystal structures and structural ensemble from molecular dynamics simulations We carried out a virtual screen of the FPPS allosteric site using the crystal structures described by Jahnke et?al. 3. In addition, we carried out a second virtual screen using representative snapshots from an MD simulation of FPPS. The setup for the MD simulation is usually described ASC-J9 supplier in detail in 12. Frames every 20?ps were extracted from the MD trajectories; the frames were aligned using all C atoms in the protein and subsequently clustered by RMSD using GROMOS++ conformational clustering 21. The chosen RMSD cutoff resulted in 23 clusters that reflected most of the ASC-J9 supplier trajectory. The central members of each of these clusters were chosen to represent the protein conformations within the cluster and, thereby, the conformations sampled by the trajectory. The central member of a cluster (also referred to as cluster center) is the structure that has the lowest pairwise RMSDs to all other members of the cluster. Docking and rescoring of known non-bisphosphonate allosteric site inhibitors To assess the abilities of the docking software, the 12 ligands described in 3 were docked. For those compounds where no crystal structure information was available, the ChemDraw Rabbit polyclonal to PRKCH file was converted to PDB format using Open Babel 22. For the AutoDock Vina screens, pdb2pqr 23,24 was used to add hydrogen atoms to the crystal structure receptor. The AutoDock scripts 25 prepare_ligand4.py and prepare_receptor4.py were used to prepare ligand and receptor PDQBT files. A docking grid of size 18.0????18.0????18.0??, centered on the position of the ligand in the allosteric site, was used ASC-J9 supplier for docking. For Glide docking, the ligands were prepared using LigPrep, and the receptors were prepared using the tools provided in the Maestro Protein Preparation Wizard and the Glide Receptor Grid Generation. For rescoring of AutoDock Vina docked poses, we used the python implementation of NNScore 1.0 in combination with a consensus of the top three scoring networks (12.net, 16.net and 20.net). Receiver operating characteristics analysis A receiver operating characteristicsCarea under the curve (ROC-AUC) analysis 25 was performed on all known allosteric site crystal structures as well as the 23 MD cluster centers. For this, the eight FPPS allosteric site inhibitors with IC50 values <100?m from 3 were combined with the Schr?dinger decoy library [1000 compounds with average molecular mass approximately 400?Da 19,20]. All compounds in the decoy set were assumed to be inactive. Both AutoDock Vina and Glide were then used to dock the 1008 compounds into the allosteric sites of all 32 receptor structures. The compounds were ranked by their AutoDock Vina scores and Glide XP docking scores, and AUC values were calculated from the ROC analysis. Virtual screen of NCI diversity set II The virtual screen was performed using the National Cancer Institute (NCI) diversity set II, a subset of the full NCI compound database. Ligands were prepared using LigPrep, adding missing hydrogen atoms, generating all possible ionization states, as well as tautomers. The final set used for virtual screening contained 1541 compounds. Docking simulations were performed with both AutoDock Vina 18 and Glide 19,20,27. An additional rescoring was performed around the AutoDock Vina results using NNScore. Finally, the individual Glide rankings and NNScore results were combined to form a consensus list of compounds that scored well with both methods. Experimental inhibition assay Human FPPS was expressed and purified and inhibition assays carried out as described previously 14. Briefly, FPPS inhibition assays were carried out using 96-well plates with a 200-L reaction mixture in each well. The condensation of GPP (100?m final) and IPP (100?m final) was monitored at room temperature using a continuous spectrophotometric assay for phosphate-releasing enzymes 28. The reaction buffer contained 50?mm TrisCHCl (pH 7.4), 1?mm MgCl2.