Structural Basis of Artemisinin Binding Sites in Serum Albumin with the Combined Use of NMR and Docking Calculations

Abstract

Artemisinin is known to bind to the main plasma protein carrier serum albumin (SA); however, there are no atomic level structural data regarding its binding mode with serum albumin. Herein, we employed a combined strategy of saturation transfer difference (STD), transfer nuclear Overhauser effect spectroscopy (TR-NOESY), STD–total correlation spectroscopy (STD-TOCSY), and Interligand Noes for PHArmacophore Mapping (INPHARMA) NMR methods and molecular docking calculations to investigate the structural basis of the interaction of artemisinin with human and bovine serum albumin (HSA/BSA). A significant number of inter-ligand NOEs between artemisinin and the drugs warfarin and ibuprofen as well as docking calculations were interpreted in terms of competitive binding modes of artemisinin in the warfarin (FA7) and ibuprofen (FA4) binding sites. STD NMR experiments demonstrate that artemisinin is the main analyte for the interaction of the A. annua extract with BSA. The combined strategy of NMR and docking calculations of the present work could be of general interest in the identification of the molecular basis of the interactions of natural products with their receptors even within a complex crude extract.

Structural Studies of Monounsaturated and ω-3 Polyunsaturated Free Fatty Acids in Solution with the Combined Use οf NMR and DFT Calculations—Comparison with the Liquid State

“…The present study shows the great conformational flexibility of mono- and polyunsaturated FFAs in various solvents and the importance of the combined use of NMR and DFT studies [ 18 , 19 , 27 , 28 , 61 , 62 , 63 , 64 ]. The significant conformational flexibility of FFAs was also considered to be the main reason that their location in the binding site FA7 in the human serum albumin could not be determined accurately [ 18 , 19 , 64 ] in the available X-ray structural data [ 65 , 66 , 67 ]. The structures of free fatty acids and their oxidation products [ 53 , 54 ], in various solvents with varying hydrogen bond and solvation abilities, are currently under investigation with the combined use of NMR and DFT studies.…”

NMR and Docking Calculations Reveal Novel Atomistic Selectivity of a Synthetic High-Affinity Free Fatty Acid vs. Free Fatty Acids in Sudlow’s Drug Binding Sites in Human Serum Albumin

“…In our previous studies, we have used an approach based on site-specific docking, guided by experimental results of NMR and X-ray crystallography, which has proven very successful in locating poses consistent with experimental results [13,15,27]. The question set by the experimental results of NMR and the X-ray crystallography is the structural arrangement of the drugs warfarin (W) at the binding site FA7 and ibuprofen (IB) at binding sites FA3 and FA4.…”

“…Understanding, at the atomic level, the selectivity of high-affinity ligands for HSA, such as the lipophilic fatty acid derivative NBD-C 12 FA, is very important for drug discovery since they can compete effectively with free fatty acids for HSA Sudlow's binding sites. We therefore report herein combined NMR (saturation transfer difference-STD) [13][14][15][16][19][20][21], 2D-Tr NOESY [22][23][24], and interligand NOEs for pharmacophore mapping (INPHARMA) [13][14][15][16][25][26][27]) as well as docking calculations [28][29][30][31] of the high-affinity ligand NBD-C 12 FA in competition experiments with two drugs: warfarin, which is a stereotypical anticoagulant drug for FA7, and ibuprofen, which is an anti-inflammatory drug for FAs 3 and 4. A unified atomic level model for the selectivity of NBD-C 12 FA vs. short-, medium-, and long-chain mono-and polyunsaturated FFAs is proposed.…”

Molecular Basis for the Selectivity of DHA and EPA in Sudlow’s Drug Binding Sites in Human Serum Albumin with the Combined Use of NMR and Docking Calculations

“…Furthermore, although the serum albumin binding assay is the usual procedure for the development of new drugs, the binding modes of the polyunsaturated FFAs in Sudlow's sites I and II have not been elucidated. We report herein structural aspects of the binding modes of the polyunsaturated free fatty acids DHA and EPA to HSA with the combined use of saturation transfer difference (STD) [28][29][30], Tr-NOESY [31][32][33], and Interligand NOEs for Pharmacophore Mapping (INPHARMA) [26,27,[34][35][36] NMR techniques and molecular calculations [27,[34][35][36][37][38][39][40]. Particular emphasis was given to The various fatty acid and drug-binding sites have been investigated extensively over the past 40 years [12][13][14][15][18][19][20].…”

“…Interestingly, weak secondary binding of warfarin in subdomain IB was also observed in the absence of fatty acid. Nevertheless, to assess whether the reduction in the linewidths of the STD signals reflected competitive interactions in relation to binding site FA7, rather than allosteric phenomena, the INPHARMA NMR technique was applied [26,27,[34][35][36]42]. This approach relies on the inter-NOE connectivities of two ligands, provided that they share a common binding site with a distance < 5 Å.…”