A “quasi-flexible” automatic docking processing for studying stereoselective recognition mechanisms. Part I. Protocol validation

New conformationally locked bicyclic N,O-nucleoside analogues of antiviral drugs

“…16 With the purpose to validate our conformational model, the 2a-c global minimum energy conformers have been submitted to molecular dynamic simulations. We performed two runs, respectively, at 300 K (MD300) and at 500 K (MD500), computed for 5 ns using a time step equal to 1.5 fs.…”

Inhibition of monoamine oxidases by coumarin-3-acyl derivatives: biological activity and computational study

“…15 The crystallographic model, code 1GOS, contains the adduct of the pargyline inhibitor covalently bound to the enzyme isoalloxazine moiety and the residues involved in the catalytic site. According to the MOLINE approach, 31 in the first step in this computational issue was the conformational analysis of each inhibitor by Monte Carlo (MC) simulation with the AMBER* force field united atoms and the GB/SA water implicit solvation model 32 as implemented in the MacroModel program. 33 The acid series of compounds 2a-e was considered in anionic form at physiological pH conditions.…”

Synthesis and biological evaluation of N-substituted-3,5-diphenyl-2-pyrazoline derivatives as cyclooxygenase (COX-2) inhibitors

“…the cleft occupied by SC-588 into the PDB original model (Supplementary Data). In order to evaluate the binding modes of all docked compounds we have considered both the default AutoDockeVina scoring function and the MolInE method [23,24] highlighting a good qualitative agreement with respect to the experimental inhibition IC 50 ( Table 2). The graphical analysis of the most stable COX-2 complexes revealed similar configuration for all docked pyrazoline derivatives.…”