Crude to leads: a triple-pronged direct NMR approach in coordination with docking simulation

Abstract

The screening of compounds that bind to the target of interest (specific proteins) plays a vital role in drug discovery. Usually, the identification of biologically active compounds is done from a library of structurally known compounds. However, we successfully illustrate here, that NMR techniques including saturation transfer difference (STD), transfer nuclear Overhauser spectroscopy (TrNOESY) and STD-TOCSY (total correlation spectroscopy) in combination with separation methods not only enable the rapid and comprehensive screening of active components, but also their unequivocal structural characterization. Furthermore, a time saving for the recognition of leads is also possible with this application. To probe the binding studies, a hydroethanolic fraction of crude extract (1 mg) from natural product (Rauia resinous) was used for the initial assessment with BSA protein. The docking simulation was performed with BSA in the region of Thr190, Arg198, Arg217, Trp213, Arg256, Ala290 and Tyr451 to further refine the active compound towards the leads. Docking results mimic binding as identified by STD, Tr-NOESY and STD-TOCSY. Isovetexine-2-rhamnosoide (2) was found to be most active through group epitope mapping results as well as the docking simulation with relative free energy of -7.2770. This experiment provided excellent results through the direct NMR screening method. Using Bovine Serum Albumin as a reference, we illustrate that this approach offers an excellent way for the first hand detection of the active constituents/inhibitors from natural remedies used in folk medicinal treatments.

Human serum albumin-specific recognition of the natural herbal extract of Stryphnodendron polyphyllum through STD NMR, hyphenations and docking simulation studies

“…The STD NMR clearly showed (Fig. 13,17 The STD Fig. Similarly, further evidence of binding was also observed in the line broadening and change in relaxation rate as a result of protein addition.…”

“…2B suppression of the HOD signal was carried out to see the hidden anomeric protons under the large HOD signal. 5,17 Conversely, the absence of signals in the STD spectrum shows that there is no binding/affinity towards the respective receptor. The STD NMR clearly showed (Fig.…”

“…Given complete numbering was done by 2D NMR data obtained (not shown here) thereby, separation methods. 5,[11][12][13][14][15][16][17] The amplication gradient is the result of a saturation received by the particular proton from the receptor, and it also determines the vicinity of the ligand to the binding cavity. 3) that the aromatic, as well as the sugar region (2.8-5.5 ppm) of the spectra, is involved in major binding.…”

“…5,17,28,29 In NOE, the major distinguishing parameter between the bound and unbound ligands is the correlation time (s c ); small molecules possess short s c and a longer relaxation rate. Tr-NOESY is the best-known experiment for the evaluation of the bound conformations for the ligand-receptor complexes at equilibrium, where the bound ligand's geometric information is transferred to unbound.…”

“…Therefore, ligand-protein interaction is an important primary domain for discovery of new drugs. 16 Recently, Ferreira and co-workers 17 supplied an excellent way to nd leads from crude, through the signicant results obtained by utilizing direct NMR techniques following the docking simulation. 10 Among the different NMR methods used for studying ligand-receptor interactions, STD NMR 11 has become one of the most commonly used methods for ligand recognition, 10,12 analyzing molecular kinetics and determining the dissociation constants 13 of bound state ligands.…”