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Fan SH, Wang WQ, Zhou YW, Gao XJ, Zhang Q, Zhang MH. Research on the Interaction Mechanism and Structural Changes in Human Serum Albumin with Hispidin Using Spectroscopy and Molecular Docking. Molecules 2024; 29:655. [PMID: 38338399 PMCID: PMC10856618 DOI: 10.3390/molecules29030655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 01/22/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024] Open
Abstract
The interaction between human serum albumin (HSA) and hispidin, a polyketide abundantly present in both edible and therapeutic mushrooms, was explored through multispectral methods, hydrophobic probe assays, location competition trials, and molecular docking simulations. The results of fluorescence quenching analysis showed that hispidin quenched the fluorescence of HSA by binding to it via a static mechanism. The binding of hispidin and HSA was validated further by synchronous fluorescence, three-dimensional fluorescence, and UV/vis spectroscopy analysis. The apparent binding constant (Ka) at different temperatures, the binding site number (n), the quenching constants (Ksv), the dimolecular quenching rate constants (Kq), and the thermodynamic parameters (∆G, ∆H, and ∆S) were calculated. Among these parameters, ∆H and ∆S were determined to be 98.75 kJ/mol and 426.29 J/(mol·K), respectively, both exhibiting positive values. This observation suggested a predominant contribution of hydrophobic forces in the interaction between hispidin and HSA. By employing detergents (SDS and urea) and hydrophobic probes (ANS), it became feasible to quantify alterations in Ka and surface hydrophobicity, respectively. These measurements confirmed the pivotal role of hydrophobic forces in steering the interaction between hispidin and HSA. Site competition experiments showed that there was an interaction between hispidin and HSA molecules at site I, which situates the IIA domains of HSA, which was further confirmed by the molecular docking simulation.
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Affiliation(s)
- Si-Hua Fan
- College of Biology and Food Engineering, Guangdong University of Petrochemical Technology, No. 1, Kechuang Road, Maonan District, Maoming 525000, China; (S.-H.F.); (W.-Q.W.)
- College of Animal Science and Technology, Yangtze University, 88 Jingmi Road, Jingzhou District, Jingzhou 434025, China; (Y.-W.Z.); (X.-J.G.)
| | - Wen-Qiang Wang
- College of Biology and Food Engineering, Guangdong University of Petrochemical Technology, No. 1, Kechuang Road, Maonan District, Maoming 525000, China; (S.-H.F.); (W.-Q.W.)
- College of Animal Science and Technology, Yangtze University, 88 Jingmi Road, Jingzhou District, Jingzhou 434025, China; (Y.-W.Z.); (X.-J.G.)
| | - Yu-Wen Zhou
- College of Animal Science and Technology, Yangtze University, 88 Jingmi Road, Jingzhou District, Jingzhou 434025, China; (Y.-W.Z.); (X.-J.G.)
| | - Xue-Jun Gao
- College of Animal Science and Technology, Yangtze University, 88 Jingmi Road, Jingzhou District, Jingzhou 434025, China; (Y.-W.Z.); (X.-J.G.)
| | - Qiang Zhang
- College of Biology and Food Engineering, Guangdong University of Petrochemical Technology, No. 1, Kechuang Road, Maonan District, Maoming 525000, China; (S.-H.F.); (W.-Q.W.)
| | - Ming-Hui Zhang
- College of Animal Science and Technology, Yangtze University, 88 Jingmi Road, Jingzhou District, Jingzhou 434025, China; (Y.-W.Z.); (X.-J.G.)
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Venianakis T, Primikyri A, Opatz T, Petry S, Papamokos G, Gerothanassis IP. 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. Molecules 2023; 28:7991. [PMID: 38138481 PMCID: PMC10745614 DOI: 10.3390/molecules28247991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
Saturation transfer difference (STD), inter-ligand NOEs (INPHARMA NMR), and docking calculations are reported for investigating specific binding sites of the high-affinity synthetic 7-nitrobenz-2-oxa-1,3-diazoyl-4-C12 fatty acid (NBD-C12 FA) with non-labeled human serum albumin (HSA) and in competition with the drugs warfarin and ibuprofen. A limited number of negative interligand NOEs between NBD-C12 FA and warfarin were interpreted in terms of a short-range allosteric competitive binding in the wide Sudlow's binding site II (FA7) of NBD-C12 FA with Ser-202, Lys-199, and Trp-214 and warfarin with Arg-218 and Arg-222. In contrast, the significant number of interligand NOEs between NBD-C12 FA and ibuprofen were interpreted in terms of a competitive binding mode in Sudlow's binding site I (FA3 and FA4) with Ser-342, Arg-348, Arg-485, Arg-410, and Tyr-411. NBD-C12 FA has the unique structural properties, compared to short-, medium-, and long-chain saturated and unsaturated natural free fatty acids, of interacting with well-defined structures with amino acids of both the internal and external polar anchor sites in Sudlow's binding site I and with amino acids in both FA3 and FA4 in Sudlow's binding site II. The NBD-C12 FA, therefore, interacts with novel structural characteristics in the drug binding sites I and II and can be regarded as a prototype molecule for drug development.
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Affiliation(s)
- Themistoklis Venianakis
- Section of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, GR-45110 Ioannina, Greece; (T.V.); (A.P.)
| | - Alexandra Primikyri
- Section of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, GR-45110 Ioannina, Greece; (T.V.); (A.P.)
| | - Till Opatz
- Department of Chemistry, Johannes Gutenberg-University, Duesbergweg, 10–14, 55128 Mainz, Germany;
| | - Stefan Petry
- Sanofi-Aventis Deutschland GmbH, Integrated Drug Discovery, Industriepark Höchst, 65926 Frankfurt am Main, Germany;
| | - Georgios Papamokos
- Section of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, GR-45110 Ioannina, Greece; (T.V.); (A.P.)
- Department of Physics, Harvard University, 17 Oxford Street, Cambridge, MA 02138, USA
| | - Ioannis P. Gerothanassis
- Section of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, GR-45110 Ioannina, Greece; (T.V.); (A.P.)
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Venianakis T, Siskos MG, Papamokos G, Gerothanassis IP. 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. Molecules 2023; 28:6144. [PMID: 37630396 PMCID: PMC10459368 DOI: 10.3390/molecules28166144] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 08/14/2023] [Accepted: 08/18/2023] [Indexed: 08/27/2023] Open
Abstract
Molecular structures, in chloroform and DMSO solution, of the free fatty acids (FFAs) caproleic acid, oleic acid, α-linolenic acid, eicosapentanoic acid (EPA) and docosahexaenoic acid (DHA) are reported with the combined use of NMR and DFT calculations. Variable temperature and concentration chemical shifts of the COOH protons, transient 1D NOE experiments and DFT calculations demonstrate the major contribution of low molecular weight aggregates of dimerized fatty acids through intermolecular hydrogen bond interactions of the carboxylic groups, with parallel and antiparallel interdigitated structures even at the low concentration of 20 mM in CDCl3. For the dimeric DHA, a structural model of an intermolecular hydrogen bond through carboxylic groups and an intermolecular hydrogen bond between the carboxylic group of one molecule and the ω-3 double bond of a second molecule is shown to play a role. In DMSO-d6 solution, NMR and DFT studies show that the carboxylic groups form strong intermolecular hydrogen bond interactions with a single discrete solvation molecule of DMSO. These solvation species form parallel and antiparallel interdigitated structures of low molecular weight, as in chloroform solution. This structural motif, therefore, is an intrinsic property of the FFAs, which is not strongly affected by the length and degree of unsaturation of the chain and the hydrogen bond ability of the solvent.
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Affiliation(s)
| | | | - George Papamokos
- Section of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (T.V.); (M.G.S.)
| | - Ioannis P. Gerothanassis
- Section of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, 45110 Ioannina, Greece; (T.V.); (M.G.S.)
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Alexandri E, Venianakis T, Primikyri A, Papamokos G, Gerothanassis IP. 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. Molecules 2023; 28:molecules28093724. [PMID: 37175134 PMCID: PMC10180286 DOI: 10.3390/molecules28093724] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/15/2023] [Accepted: 04/23/2023] [Indexed: 05/15/2023] Open
Abstract
Medium- and long-chain saturated and unsaturated free fatty acids (FFAs) are known to bind to human serum albumin (HSA), the main plasma carrier protein. Atomic-level structural data regarding the binding mode in Sudlow's sites I (FA7) and II (FA4, FA3) of the polyunsaturated ω-3 fatty acids docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA), however, are largely unknown. Herein, we report the combined use of saturation transfer difference (STD) and Interligand NOEs for Pharmacophore Mapping (INPHARMA) NMR techniques and molecular docking calculations to investigate the binding mode of DHA and EPA in Sudlow's sites Ι and ΙΙ of HSA. The docking calculations and the significant number of interligand NOEs between DHA and EPA and the drugs warfarin and ibuprofen, which are stereotypical ligands for Sudlow's sites I and II, respectively, were interpreted in terms of competitive binding modes and the presence of two orientations of DHA and EPA at the binding sites FA7 and FA4. The exceptional flexibility of the long-chain DHA and EPA and the formation of strongly folded structural motives are the key properties of HSA-PUFA complexes.
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Affiliation(s)
- Eleni Alexandri
- Section of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, GR-45110 Ioannina, Greece
| | - Themistoklis Venianakis
- Section of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, GR-45110 Ioannina, Greece
| | - Alexandra Primikyri
- Section of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, GR-45110 Ioannina, Greece
| | - Georgios Papamokos
- Section of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, GR-45110 Ioannina, Greece
| | - Ioannis P Gerothanassis
- Section of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, GR-45110 Ioannina, Greece
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Venianakis T, Siskos M, Papamokos G, Gerothanassis IP. NMR and DFT studies of monounsaturated and ω-3 polyunsaturated free fatty acids in the liquid state reveal a novel atomistic structural model of DHA. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
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Gerothanassis IP. Ligand-observed in-tube NMR in natural products research: A review on enzymatic biotransformations, protein-ligand interactions, and in-cell NMR spectroscopy. ARAB J CHEM 2023. [DOI: 10.1016/j.arabjc.2022.104536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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Primikyri A, Papamokos G, Venianakis T, Sakka M, Kontogianni VG, Gerothanassis IP. Structural Basis of Artemisinin Binding Sites in Serum Albumin with the Combined Use of NMR and Docking Calculations. Molecules 2022; 27:molecules27185912. [PMID: 36144648 PMCID: PMC9506303 DOI: 10.3390/molecules27185912] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/04/2022] [Accepted: 09/09/2022] [Indexed: 11/16/2022] Open
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.
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