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Sittiwanichai S, Archapraditkul C, Japrung D, Shigeta Y, Mori T, Pongprayoon P. Aggregation of Apo/Glycated Human Serum Albumins and Aptamer-Saturated Graphene Quantum Dot: A Simulation Study. Biochemistry 2024; 63:1697-1707. [PMID: 38889356 DOI: 10.1021/acs.biochem.4c00155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Human serum albumin (HSA) is a protein carrier that transports a wide range of drugs and nutrients. The amount of glycated HSA (GHSA) is used as a diabetes biomarker. To quantify the GHSA amount, the fluorescent graphene-based aptasensor has been a successful method. In aptasensors, the key mechanism is the adsorption/desorption of albumin from the aptamer-graphene complex. Recently, the graphene quantum dot (GQD) has been reported to be an aptamer sorbent. Due to its comparable size to aptamers, it is attractive enough to explore the possibility of GQD as a part of an albumin aptasensor. Therefore, molecular dynamics (MD) simulations were performed here to reveal the binding mechanism of albumin to an aptamer-GQD complex in molecular detail. GQD saturated by albumin-selective aptamers (GQDA) is studied, and GHSA and HSA are studied in comparison to understand the effect of glycation. Fast and spontaneous albumin-GQDA binding was observed. While no specific GQDA-binding site on both albumins was found, the residues used for binding were confined to domains I and III for HSA and domains II and III for GHSA. Albumins were found to bind preferably to aptamers rather than to GQD. Lysines and arginines were the main contributors to binding. We also found the dissociation of GLC from all GHSA trajectories, which highlights the role of GQDA in interfering with the ligand binding affinity in Sudlow site I. The binding of GQDA appears to impair albumin structure and function. The insights obtained here will be useful for the future design of diabetes aptasensors.
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Affiliation(s)
- Sirin Sittiwanichai
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Chanya Archapraditkul
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Deanpen Japrung
- National Nanotechnology Center, National Science and Technology Development Agency, Thailand Science Park, Pathum Thani 12120, Thailand
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Toshifumi Mori
- Institute for Material Chemistry and Engineering, Kyushu University, Kasuga, Fukuoka 816-8580, Japan
- Interdisciplinary Graduate School of Engineering Science, Kyushu University, Kasuga, Fukuoka 816-8580, Japan
| | - Prapasiri Pongprayoon
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
- Center for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural Industries, KU Institute for Advanced Studies, Kasetsart University, Bangkok 10900, Thailand
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Dutta S, Bose D, Ghosh S, Chakrabarti A. Spectrin: an alternate target for cytoskeletal drugs. J Biomol Struct Dyn 2022:1-12. [PMID: 35994328 DOI: 10.1080/07391102.2022.2109063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
Cytoskeletal drugs having enormous therapeutic potential act on the cytoskeletal components like actin, tubulin either by promoting polymerization or destabilizing the same. Here we present the interaction of the popular cytoskeletal drugs such as taxol, latrunculin and cytochalasin with spectrin, a huge protein with multi domains that forms the cytoskeletal network. Particularly, the actin binding domain of spectrin regulates the dynamics of the actin cytoskeleton. We followed the binding of these drugs to its actin binding domain and intact spectrin as well. These drugs bind with moderate affinity (Kb ∼ 104 M-1) and the interaction with actin binding domain is entropy driven and hydrophobic in nature as determined by Van't Hoff plot. The docking studies and molecular dynamics simulations further corroborate the experimental findings. Particularly the higher binding constants in the case of latrunculin and cytochalasin to the actin binding domain of spectrin suggest the binding sites are presumably located in its actin binding domain.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sansa Dutta
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Kolkata, West Bengal, India.,Department of Chemistry, Indian Institute of Technology, Kharagpur, West Bengal, India
| | - Dipayan Bose
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Kolkata, West Bengal, India.,Homi Bhabha National Institute, Mumbai, Maharashtra, India
| | - Semanti Ghosh
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Kolkata, West Bengal, India
| | - Abhijit Chakrabarti
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Kolkata, West Bengal, India.,Homi Bhabha National Institute, Mumbai, Maharashtra, India
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Sarmah S, Roy AS. A review on prevention of glycation of proteins: Potential therapeutic substances to mitigate the severity of diabetes complications. Int J Biol Macromol 2022; 195:565-588. [DOI: 10.1016/j.ijbiomac.2021.12.041] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 12/03/2021] [Accepted: 12/05/2021] [Indexed: 12/21/2022]
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Combined spectroscopic and computational approaches for the recognition of bioactive flavonoid 6-hydroxyflavone by human serum albumin: Effects of non-enzymatic glycation in the binding. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118288] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Liu SY, Zhang YY, Chu GX, Bao GH. N-ethyl-2-pyrrolidinone substitution enhances binding affinity between tea flavoalkaloids and human serum albumin: Greatly influenced by esterization. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 262:120097. [PMID: 34182296 DOI: 10.1016/j.saa.2021.120097] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/04/2021] [Accepted: 06/17/2021] [Indexed: 05/25/2023]
Abstract
Formation of catechins-human serum albumin (HSA) complex contributes to stably transporting catechins and regulating their bioavailability. Recently, a new class of catechins namely flavoalkaloids have been reported from tea. The unique structural modification with an N-ethyl-2-pyrrolidinone ring at catechins from these flavoalkaloids has raised our interest in their HSA binding affinity. Thus, we investigated the interaction between HSA and flavoalkaloids by molecular docking, UV-Vis spectroscopy (UV), fluorescence quenching approaches, and surface plasmon resonance (SPR). Thermodynamic parameters suggest that electrostatic forces contribute greatly to the interaction. The binding ability is affected by different ester group (galloyl or cinnamoyl) at 3-OH, N-ethyl-2-pyrrolidinone substituted position (C-6 or C-8), C-2, C-3 and C-5''' configurations, and hydroxyl group numbers at B ring, among which the 3-O-cinnamoyl substitution and 5'''-R configuration present the strongest contributions. UV showed slight changes in the conformation and microenvironment of HSA during the binding process. The quenching and binding constants suggest that the quenching is a static type. The small KD values (1-20 μM) detected by SPR confirmed the strong binding affinities between HSA and flavoalkaloids. Present study will help us to understand the interaction mechanism between flavoalkaloids and HSA, shedding light on structural modification of common catechins to enhance the stability, bioavailability and bioactivities.
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Affiliation(s)
- Shi-Yu Liu
- Natural Products Laboratory, State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, People's Republic of China.
| | - Yuan-Yuan Zhang
- Natural Products Laboratory, State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, People's Republic of China.
| | - Gang-Xiu Chu
- Natural Products Laboratory, State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, People's Republic of China.
| | - Guan-Hu Bao
- Natural Products Laboratory, State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, People's Republic of China.
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Harvey DJ. ANALYSIS OF CARBOHYDRATES AND GLYCOCONJUGATES BY MATRIX-ASSISTED LASER DESORPTION/IONIZATION MASS SPECTROMETRY: AN UPDATE FOR 2015-2016. MASS SPECTROMETRY REVIEWS 2021; 40:408-565. [PMID: 33725404 DOI: 10.1002/mas.21651] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/24/2020] [Indexed: 06/12/2023]
Abstract
This review is the ninth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2016. Also included are papers that describe methods appropriate to analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation and arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals. Much of this material is presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions and applications to chemical synthesis. The reported work shows increasing use of combined new techniques such as ion mobility and the enormous impact that MALDI imaging is having. MALDI, although invented over 30 years ago is still an ideal technique for carbohydrate analysis and advancements in the technique and range of applications show no sign of deminishing. © 2020 Wiley Periodicals, Inc.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom
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Protective actions of bioactive flavonoids chrysin and luteolin on the glyoxal induced formation of advanced glycation end products and aggregation of human serum albumin: In vitro and molecular docking analysis. Int J Biol Macromol 2020; 165:2275-2285. [PMID: 33058977 DOI: 10.1016/j.ijbiomac.2020.10.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 09/29/2020] [Accepted: 10/02/2020] [Indexed: 12/26/2022]
Abstract
The post-translational modification of proteins by nonenzymatic glycation (NEG) and the accumulation of AGEs are the two underlying factors associated with the long-term pathogenesis in diabetes. Glyoxal (GO) is a reactive intermediate which has the ability to modify proteins and generate AGEs at a faster rate. Human serum albumin (HSA) being the most abundant serum protein has a higher chance to be modified by NEG. The key objective of the present study is to investigate the potency of chrysin and luteolin as antiglycating and antifibrillating agents in the GO-mediated glycation and fibril formation of HSA. AGEs formation were confirmed from the absorption and fluorescence spectral measurements. Both the flavonoids were able to quench the AGEs fluorescence intensity in vitro indicating the antiglycating nature of the molecules. The formation of fibrils in the GO-modified HSA was confirmed by the Thioflavin T (ThT) fluorescence assay and the flavonoids were found to exihibit the antifibrillation properties in vitro. Docking results suggested that both the flavonoids interact with various amino acid residues of subdomain IIA including glycation prone lysines and arginines via non-covalent forces and further stabilized the structure of HSA, which further explains their mechanisms of action as antiglycating and antifibrillating agents.
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Sarmah S, Pahari S, Belwal VK, Jana M, Singha Roy A. Elucidation of molecular interaction of bioactive flavonoid luteolin with human serum albumin and its glycated analogue using multi-spectroscopic and computational studies. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.114147] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Sarmah S, Pahari S, Das S, Belwal VK, Jana M, Singha Roy A. Non-enzymatic glycation of human serum albumin modulates its binding efficacy towards bioactive flavonoid chrysin: A detailed study using multi-spectroscopic and computational methods. J Biomol Struct Dyn 2020; 39:476-492. [PMID: 31900044 DOI: 10.1080/07391102.2019.1711196] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The non-enzymatic glycation of plasma proteins by reducing sugars have important consequences on the conformational and functional properties of protein. The formation of advanced glycation end products (AGEs) is responsible for cell death and other pathological conditions. We have synthesized the glycated human serum albumin (gHSA) and characterized the same by using differential spectroscopic measurements. The aim of the present study is to determine the effect of glycation on the binding of human serum albumin (HSA) with bioactive flavonoid chrysin, which possesses anti-cancer, anti-inflammatory and anti-oxidant activities. The interaction of chrysin with HSA and gHSA was studied using multi-spectroscopic, molecular docking and molecular dynamics (MD) simulation techniques. Chrysin quenched the intrinsic fluorescence of both HSA and gHSA by static quenching mechanism. The value of the binding constant (Kb) for the interaction of HSA-chrysin complex (4.779 ± 0.623 × 105 M-1 at 300 K) was found to be higher than that of gHSA-chrysin complex (2.206 ± 0.234 × 105 M-1 at 300 K). Hence, non-enzymatic glycation of HSA significantly reduced its binding affinity towards chrysin. The % α-helicity of HSA was found to get enhanced upon binding with chrysin, and minimal changes were observed for the gHSA-chrysin complex. Site marker probe studies indicated that chrysin binds to subdomain IIA and IIIA of both HSA and gHSA. The results from molecular docking and MD simulation studies correlated well with the experimental findings. Electrostatic interactions followed by hydrogen bonding and hydrophobic interactions played major roles in the binding process. These observations may have some useful insights into the field of pharmaceutics.
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Affiliation(s)
- Sharat Sarmah
- Department of Chemistry, National Institute of Technology, Meghalaya, Shillong, India
| | - Somdev Pahari
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela, India
| | - Sourav Das
- Department of Chemistry, National Institute of Technology, Meghalaya, Shillong, India
| | - Vinay Kumar Belwal
- Department of Bioscience and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
| | - Madhurima Jana
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela, India
| | - Atanu Singha Roy
- Department of Chemistry, National Institute of Technology, Meghalaya, Shillong, India
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Poloni DM, Dangles O, Vinson JA. Binding of Plant Polyphenols to Serum Albumin and LDL: Healthy Implications for Heart Disease. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:9139-9147. [PMID: 30784273 DOI: 10.1021/acs.jafc.8b06674] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Cardiovascular disease (CVD) is the leading cause of death in industrialized nations. The initiating event in atherosclerosis, or hardening of the arteries, is oxidation of low density lipoprotein (LDL). Binding with serum albumin and LDL of 41 polyphenols (major antioxidants in plant foods) constituting four classes of flavonoids, three types of phenolic acids, and seven polyphenol conjugate metabolites was investigated indirectly by fluorescence quenching and directly by affinity separation/high-performance liquid chromatography (four of the polyphenols). Stern-Volmer plots yielded K values for the two proteins. Polyphenol binding was significantly stronger for albumin than with LDL. K values were highly correlated with the lipophilicity of the polyphenols. The number of polyphenol molecules determined by quenching was ∼1 for both proteins. Direct analysis under saturation conditions yielded from 2 to 13 molecules of polyphenols/LDL particle. Multiple substituent effects on binding were analyzed. Evidence was put forward that binding of polyphenols to these proteins is protective for CVD by multiple mechanisms.
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Affiliation(s)
- Dana M Poloni
- Department of Chemistry, Loyola Science Center , University of Scranton , 925 Ridge Row , Scranton , Pennsylvania 18510 , United States
| | - Olivier Dangles
- Avignon University, INRA, UMR408 SQPOV , 84000 Avignon , France
| | - Joe A Vinson
- Department of Chemistry, Loyola Science Center , University of Scranton , 925 Ridge Row , Scranton , Pennsylvania 18510 , United States
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Ariga GG, Naik PN, Nandibewoor ST, Chimatadar SA. Quenching of fluorescence by meclizine, a probe study for structural and conformational changes in human serum albumin. J Biomol Struct Dyn 2016; 35:3161-3175. [DOI: 10.1080/07391102.2016.1245159] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Girish G. Ariga
- Department of Studies in Chemistry, Karnatak University, Dharwad 580003, India
| | - Praveen N. Naik
- Department of Studies in Chemistry, Karnatak University, Dharwad 580003, India
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Jattinagoudar LN, Nandibewoor ST, Chimatadar SA. Binding of fexofenadine hydrochloride to bovine serum albumin: structural considerations by spectroscopic techniques and molecular docking. J Biomol Struct Dyn 2016; 35:1200-1214. [DOI: 10.1080/07391102.2016.1183229] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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13
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Glycation of human serum albumin affects its binding affinity towards (−)-epigallocatechin gallate. J INCL PHENOM MACRO 2016. [DOI: 10.1007/s10847-016-0619-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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