Sybyl 8

3D-molecular alignment were prepared using SYBYL 8.1 (Tripos, Ltd, US) and Molecular Operating Environment (MOE 2010.10). For dataset I, molecular alignments were performed using substructure overlap thiazole-4-carboxamide core with respect to the docking poses (see molecular docking for details). The resulting alignment was refined by flexible alignment using MOE. The alignment is available from the authors upon request. CoMFA and CoMSIA were performed by SYBYL 8.1 using the default parameter (Tripos standard field, 2 Å grid spacing, dielectric distance 1/r², 30 kcal/mol cutoff) probed by an sp³ carbon with a charge of +1. CoMFA steric energy (Lennard-Jones) and electrostatic (Coulomb) energy were calculated. CoMSIA steric, electrostatic and hydrophobic energies were calculated with the attenuation factor = 0.3. Pullman charges were used for electrostatic field calculations. 3D-QSAR was performed by partial least squares (PLS) analyses. Dataset I was divided into a training set (38 compounds) and a test set (10 compounds) based on the Sphere Exclusion (SE) algorithm15 (link). The details of data splitting are available in Supplementary Table 3. Leave-one-out cross-validation was used for the training set. The predictive ability the non-cross-validated models were validated using the test set. The statistics of the resulted CoMFA and CoMSIA models are available in Table 1.

Corina online (Molecular Networks and Altamira) was used to create three-dimensional structures of compounds, that were then prepared using Sybyl 8.0 (Tripos). Protonation states were inspected, hydrogen atoms were added, atom types were checked and Gesteiger-Marsili charges were assigned. All ligands were docked to acetylcholinesterase from 2CKM and to butyrylcholinesterase based on a 1P0I crystal structure using GoldSuite 5.1 (CCDC). Before docking, the proteins were prepared in the following way: all histidine residues were protonated at Nε, the hydrogen atoms were added, ligand and water molecules were removed; the binding site was defined as all amino acid residues within 10 Å from bis-(7)-tacrine for AChE, and 20 Å from the glycerol molecule for BuChE. A standard set of genetic algorithms with a population size of 100, number of operations 100 000, and clustering with a tolerance of 1 Å was applied. After docking process, 10 ligand poses, sorted by GoldScore (for AChE) and ChemScore (for BuChE) were obtained. The results were visualised by PyMOL 0.99rc6 (DeLano Scientific LLC).

The 3D structure of the ligand was constructed with standard bond lengths and bond angles using the molecular modeling software program SYBYL8.0 (Tripos Inc., St. Louis, USA) for Linux. Geometry optimization was performed using the standard Tripos forcefield [33 ] with a distance-dependent dielectric function and an energy gradient of 0.001 kcal/mol. Gasteiger-Hückel charges [34 (link)] were used.
Molecular docking was implemented using MOE2009 for Windows (Chemical Computing Group Inc., Montreal, Canada). The available X-ray structure of HSA complexed with R-warfarin (PDB code: 1H9Z) was applied in this work as the receptor. Hydrogen atoms were added to the PDB file. Then, the 1H9Z complex was handled in LigX (a module of the MOE software) to meet the docking requirements. The conformer with the lowest S value was used for further analysis.