Fig. 3

Predictive analysis of the interactions of some NPTs and BPTs with the catalytic domain of RpfB (3EO5) based on the Flexx docking procedure. a Compound (I) was predicted to interact with the hydrophobic surrounding of the catalytic cleft of the protein molecules, whereby the thiocyanate group was shown to be able to interact with Asp 312; the nitro group was shown to be located on the surface of the molecule, not contributing to the inhibitory properties of the molecule (∆G ≈ − 7 kJ/mol); b compound (III) an analogous compound, completely lacking the nitro groups was shown to interact with the catalytic cleft of the protein similarly to the afore described mechanism for (I) (∆G ≈ − 8 kJ/mol); c compound (V) containing the double set of the thiocyanate groups substituted at the para-position toward the benzophenone group was predicted to interact with the catalytic cleft of the RpfB molecule mainly through hydrophobic interactions between the benzophenone rings and hydrophobic surroundings of the catalytic cleft (∆G ≈ 0 kJ/mol); d compound (IV) bearing four substituents (both nitro and thiocyanate groups) was capable of entering the catalytic cleft of the enzyme, however, none functional group was shown to interact with the catalytic amino acids. The compound demonstrated the higher positive score of the predicted Gibbs free energy (∆G ≈ + 2 kJ/mol). The hydrophobic surrounding of the catalytic cleft is mostly made up by following amino acids (shown as dots): Trp285, Ile288, Trp297, Val309, Gln310; Phe311; Thr315; Trp316; Trp349; Ala351; Trp352; Val354