Unveiling fructose and glucose binding to human serum albumin: fluorescence measurements and docking, molecular dynamics and quantum biochemistry computations

References

• Anguizola, J., Matsuda, R., Barnaby, O. S., Hoy, K. S., Wa, C., DeBolt, E., Koke, M., & Hage, D. S. (2013). Review: Glycation of human serum albumin. Clinica Chimica Acta; International Journal of Clinical Chemistry, 425, 64–76. https://doi.org/10.1016/j.cca.2013.07.013
   PubMed Web of Science ®Google Scholar
• Antony, J., & Grimme, S. (2006). Density functional theory including dispersion corrections for intermolecular interactions in a large benchmark set of biologically relevant molecules. Physical Chemistry Chemical Physics: PCCP, 8(45), 5287–5293. https://doi.org/10.1039/b612585a
   PubMed Web of Science ®Google Scholar
• Antony, J., & Grimme, S. (2012). Fully ab initio protein-ligand interaction energies with dispersion corrected density functional theory. Journal of Computational Chemistry, 33(21), 1730–1739. https://doi.org/10.1002/jcc.23004
   PubMed Web of Science ®Google Scholar
• Ascenzi, P., di Masi, A., Fanali, G., & Fasano, M. (2015). Heme-based catalytic properties of human serum albumin. Cell Death Discovery, 1(1), 15025. https://doi.org/10.1038/cddiscovery.2015.25
   PubMedGoogle Scholar
• Asp, N. (1994). Nutritional classification and analysis of food carbohydrates. The American Journal of Clinical Nutrition, 59(3 Suppl), 679S–681S. https://doi.org/10.1093/ajcn/59.3.679Sa
   PubMed Web of Science ®Google Scholar
• Awang, T., Niramitranon, J., Japrung, D., Saparpakorn, P., & Pongprayoon, P. (2021). Investigating the binding affinities of fructose and galactose to human serum albumin: Simulation studies. Molecular Simulation, 47(9), 738–747. https://doi.org/10.1080/08927022.2021.1922687
   Web of Science ®Google Scholar
• Awang, T., Wiriyatanakorn, N., Saparpakorn, P., Japrung, D., & Pongprayoon, P. (2017). Understanding the effects of two bound glucose in Sudlow site I on structure and function of human serum albumin: Theoretical studies. Journal of Biomolecular Structure & Dynamics, 35(4), 781–790. https://doi.org/10.1080/07391102.2016.1160841
   PubMed Web of Science ®Google Scholar
• Bai, X., Wang, Z., Huang, C., Wang, Z., & Chi, L. (2012). Investigation of non-enzymatic glycosylation of human serum albumin using ion trap-time of flight mass spectrometry. Molecules (Basel, Switzerland), 17(8), 8782–8794. https://doi.org/10.3390/molecules17088782
   PubMed Web of Science ®Google Scholar
• Barnaby, O. S., Cerny, R. L., Clarke, W., & Hage, D. S. (2011). Comparison of modification sites formed on human serum albumin at various stages of glycation. Clinica Chimica Acta; International Journal of Clinical Chemistry, 412(3–4), 277–285. https://doi.org/10.1016/j.cca.2010.10.018
   PubMed Web of Science ®Google Scholar
• Barzegar, A., Moosavi-Movahedi, A., Sattarahmady, N., Hosseinpour-Faizi, M., Aminbakhsh, M., Ahmad, F., Saboury, A., Ganjali, M., & Norouzi, P. (2007). Spectroscopic studies of the effects of glycation of human serum albumin on L-Trp binding. Protein and Peptide Letters, 14(1), 13–18. https://doi.org/10.2174/092986607779117191
   PubMed Web of Science ®Google Scholar
• Becke, A. D. (1992). Density-functional thermochemistry. I. The effect of the exchange-only gradient correction. The Journal of Chemical Physics, 96(3), 2155–2160. https://doi.org/10.1063/1.462066
   Web of Science ®Google Scholar
• Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A., & Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. The Journal of Chemical Physics, 81(8), 3684–3690. https://doi.org/10.1063/1.448118
   Web of Science ®Google Scholar
• Best, R. B., Zhu, X., Shim, J., Lopes, P. E. M., Mittal, J., Feig, M., & MacKerell, A. D. (2012). Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone ϕ, ψ and side-chain χ 1 and χ 2 dihedral angles. Journal of Chemical Theory and Computation, 8(9), 3257–3273. https://doi.org/10.1021/ct300400x
   PubMed Web of Science ®Google Scholar
• Bhattacharya, A. A., Grüne, T., & Curry, S. (2000). Crystallographic analysis reveals common modes of binding of medium and long-chain fatty acids to human serum albumin 1 1Edited by R. Huber. Journal of Molecular Biology, 303(5), 721–732. https://doi.org/10.1006/jmbi.2000.4158
   PubMed Web of Science ®Google Scholar
• Brownlee, M. (1991). Glycosylation products as toxic mediators of diabetic complications. Annual Review of Medicine, 42(1), 159–166. https://doi.org/10.1146/annurev.me.42.020191.001111
   PubMedGoogle Scholar
• Carter, D. C., & Ho, J. X. (1994). Structure of serum albumin. Advances in Protein Chemistry, 45, 153–203. https://doi.org/10.1016/S0065-3233(08)60640-3
   Google Scholar
• Castro-Alvarez, A., Costa, A., & Vilarrasa, J. (2017). The performance of several docking programs at reproducing protein–macrolide-like crystal structures. Molecules (Basel, Switzerland), 22(1), 136. https://doi.org/10.3390/molecules22010136
   PubMed Web of Science ®Google Scholar
• Chaves, O. A., Soares, M. A. G., & Campos de Oliveira, M. C. (2021). Monosaccharides interact weakly with human serum albumin. Insights for the functional perturbations on the binding capacity of albumin. Carbohydrate Research, 501, 108274. https://doi.org/10.1016/j.carres.2021.108274
   PubMed Web of Science ®Google Scholar
• Chen, X., Zhang, Y., & Zhang, J. Z. H. (2005). An efficient approach for ab initio energy calculation of biopolymers. The Journal of Chemical Physics, 122(18), 184105. https://doi.org/10.1063/1.1897382
   PubMed Web of Science ®Google Scholar
• Christensen, A. S., Kubař, T., Cui, Q., & Elstner, M. (2016). Semiempirical quantum mechanical methods for noncovalent interactions for chemical and biochemical applications. Chemical Reviews, 116(9), 5301–5337. https://doi.org/10.1021/acs.chemrev.5b00584
   PubMed Web of Science ®Google Scholar
• Collins, M. A., & Bettens, R. P. A. (2015). Energy-based molecular fragmentation methods. Chemical Reviews, 115(12), 5607–5642. https://doi.org/10.1021/cr500455b
   PubMed Web of Science ®Google Scholar
• Conev, A., Rigo, M. M., Devaurs, D., Fonseca, A. F., Kalavadwala, H., de Freitas, M. V., Clementi, C., Zanatta, G., Antunes, D. A., & Kavraki, L. E. (2023). EnGens: A computational framework for generation and analysis of representative protein conformational ensembles. Briefings in Bioinformatics, 24(4), 1-11. https://doi.org/10.1093/bib/bbad242
   PubMed Web of Science ®Google Scholar
• Dantas, D. S., Oliveira, J. I. N., Lima Neto, J. X., da Costa, R. F., Bezerra, E. M., Freire, V. N., Caetano, E. W. S., Fulco, U. L., & Albuquerque, E. L. (2015). Quantum molecular modelling of ibuprofen bound to human serum albumin. RSC Advances, 5(61), 49439–49450. https://doi.org/10.1039/C5RA04395F
   Web of Science ®Google Scholar
• Delley, B. (1990). An all-electron numerical method for solving the local density functional for polyatomic molecules. The Journal of Chemical Physics, 92(1), 508–517. https://doi.org/10.1063/1.458452
   Web of Science ®Google Scholar
• Delley, B. (2000). From molecules to solids with the DMol3 approach. The Journal of Chemical Physics, 113(18), 7756–7764. https://doi.org/10.1063/1.1316015
   Web of Science ®Google Scholar
• Ehrlich, S., Moellmann, J., & Grimme, S. (2013). Dispersion-corrected density functional theory for aromatic interactions in complex systems. Accounts of Chemical Research, 46(4), 916–926. https://doi.org/10.1021/ar3000844
   PubMed Web of Science ®Google Scholar
• Fanali, G., di Masi, A., Trezza, V., Marino, M., Fasano, M., & Ascenzi, P. (2012). Human serum albumin: From bench to bedside. Molecular Aspects of Medicine, 33(3), 209–290. https://doi.org/10.1016/j.mam.2011.12.002
   PubMed Web of Science ®Google Scholar
• Fox, S. J., Dziedzic, J., Fox, T., Tautermann, C. S., & Skylaris, C.-K. (2014). Density functional theory calculations on entire proteins for free energies of binding: Application to a model polar binding site. Proteins, 82(12), 3335–3346. https://doi.org/10.1002/prot.24686
   PubMed Web of Science ®Google Scholar
• França, V. L. B., Amaral, J. L., Martins, Y. A., Caetano, E. W. S., Brunaldi, K., & Freire, V. N. (2022). Characterization of the binding interaction between atrazine and human serum albumin: Fluorescence spectroscopy, molecular dynamics and quantum biochemistry. Chemico-Biological Interactions, 366, 110130. https://doi.org/10.1016/j.cbi.2022.110130
   PubMed Web of Science ®Google Scholar
• Ganesan, A., Coote, M. L., & Barakat, K. (2017). Molecular dynamics-driven drug discovery: Leaping forward with confidence. Drug Discovery Today, 22(2), 249–269. https://doi.org/10.1016/j.drudis.2016.11.001
   PubMed Web of Science ®Google Scholar
• Gelpi, J., Hospital, A., Goñi, J. R., Orozco, M. (2015). Molecular dynamics simulations: Advances and applications. Advances and Applications in Bioinformatics and Chemistry: AABC, 8, 37–47. https://doi.org/10.2147/AABC.S70333
   PubMedGoogle Scholar
• Ghosh, R., & Kishore, N. (2022). Mechanistic physicochemical insights into glycation and drug binding by serum albumin: Implications in diabetic conditions. Biochimie, 193, 16–37. https://doi.org/10.1016/j.biochi.2021.10.008
   PubMed Web of Science ®Google Scholar
• Ghuman, J., Zunszain, P. A., Petitpas, I., Bhattacharya, A. A., Otagiri, M., & Curry, S. (2005). Structural basis of the drug-binding specificity of human serum albumin. Journal of Molecular Biology, 353(1), 38–52. https://doi.org/10.1016/j.jmb.2005.07.075
   PubMed Web of Science ®Google Scholar
• Gordon, M. S., Fedorov, D. G., Pruitt, S. R., & Slipchenko, L. V. (2012). Fragmentation methods: A route to accurate calculations on large systems. Chemical Reviews, 112(1), 632–672. https://doi.org/10.1021/cr200093j
   PubMed Web of Science ®Google Scholar
• Grinter, S., & Zou, X. (2014). Challenges, applications, and recent advances of protein-ligand docking in structure-based drug design. Molecules (Basel, Switzerland), 19(7), 10150–10176. https://doi.org/10.3390/molecules190710150
   PubMed Web of Science ®Google Scholar
• Hamilton, J. A. (2013). NMR reveals molecular interactions and dynamics of fatty acid binding to albumin. Biochimica Et Biophysica Acta, 1830(12), 5418–5426. https://doi.org/10.1016/j.bbagen.2013.08.002
   PubMed Web of Science ®Google Scholar
• Hand, D. J., McLachlan, G. J., & Basford, K. E. (1989). Mixture models: Inference and applications to clustering. Applied Statistics, 38(2), 384. https://doi.org/10.2307/2348072
   Google Scholar
• He, X., & Zhang, J. Z. H. (2005). A new method for direct calculation of total energy of protein. The Journal of Chemical Physics, 122(3), 31103. https://doi.org/10.1063/1.1849132
   PubMed Web of Science ®Google Scholar
• Hollingsworth, S. A., & Dror, R. O. (2018). Molecular dynamics simulation for all. Neuron, 99(6), 1129–1143. https://doi.org/10.1016/j.neuron.2018.08.011
   PubMed Web of Science ®Google Scholar
• Hu, X., Zeng, Z., Zhang, J., Wu, D., Li, H., & Geng, F. (2023). Molecular dynamics simulation of the interaction of food proteins with small molecules. Food Chemistry, 405(Pt A), 134824. https://doi.org/10.1016/j.foodchem.2022.134824
   PubMedGoogle Scholar
• Jaña, G. A., Mendoza, F., Osorio, M. I., Alderete, J. B., Fernandes, P. A., Ramos, M. J., & Jiménez, V. A. (2018). A QM/MM approach on the structural and stereoelectronic factors governing glycosylation by GTF-SI from Streptococcus mutans. Organic & Biomolecular Chemistry, 16(14), 2438–2447. https://doi.org/10.1039/C8OB00284C
   PubMed Web of Science ®Google Scholar
• Jiang, N., Ma, J., & Jiang, Y. (2006). Electrostatic field-adapted molecular fractionation with conjugated caps for energy calculations of charged biomolecules. The Journal of Chemical Physics, 124(11), 114112. https://doi.org/10.1063/1.2178796
   PubMed Web of Science ®Google Scholar
• Jones, R. O. (2015). Density functional theory: Its origins, rise to prominence, and future. Reviews of Modern Physics, 87(3), 897–923. https://doi.org/10.1103/RevModPhys.87.897
   Web of Science ®Google Scholar
• Joseph, K. S., & Hage, D. S. (2010). The effects of glycation on the binding of human serum albumin to warfarin and l-tryptophan. Journal of Pharmaceutical and Biomedical Analysis, 53(3), 811–818. https://doi.org/10.1016/j.jpba.2010.04.035
   PubMed Web of Science ®Google Scholar
• Khalifah, R. G., Baynes, J. W., & Hudson, B. G. (1999). Amadorins: Novel post-amadori inhibitors of advanced glycation reactions. Biochemical and Biophysical Research Communications, 257(2), 251–258. https://doi.org/10.1006/bbrc.1999.0371
   PubMed Web of Science ®Google Scholar
• Kitchen, D. B., Decornez, H., Furr, J. R., & Bajorath, J. (2004). Docking and scoring in virtual screening for drug discovery: Methods and applications. Nature Reviews. Drug Discovery, 3(11), 935–949. https://doi.org/10.1038/nrd1549
   PubMed Web of Science ®Google Scholar
• Klamt, A., & Schüürmann, G. (1993). COSMO: A new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient. Journal of the Chemical Society, Perkin Transactions 2. (5), 799–805. https://doi.org/10.1039/P29930000799
   Google Scholar
• Krenzel, E. S., Chen, Z., & Hamilton, J. A. (2013). Correspondence of fatty acid and drug binding sites on human serum albumin: A two-dimensional nuclear magnetic resonance study. Biochemistry, 52(9), 1559–1567. https://doi.org/10.1021/bi301458b
   PubMed Web of Science ®Google Scholar
• Li, J., Zhu, X., Yang, C., & Shi, R. (2010). Characterization of the binding of angiotensin II receptor blockers to human serum albumin using docking and molecular dynamics simulation. Journal of Molecular Modeling, 16(4), 789–798. https://doi.org/10.1007/s00894-009-0612-0
   PubMed Web of Science ®Google Scholar
• Liu, J., & Herbert, J. M. (2016). Pair–pair approximation to the generalized many-body expansion: An alternative to the four-body expansion for ab initio prediction of protein energetics via molecular fragmentation. Journal of Chemical Theory and Computation, 12(2), 572–584. https://doi.org/10.1021/acs.jctc.5b00955
   PubMed Web of Science ®Google Scholar
• Liu, Y., Yang, X., Gan, J., Chen, S., Xiao, Z.-X., & Cao, Y. (2022). CB-Dock2: Improved protein–ligand blind docking by integrating cavity detection, docking and homologous template fitting. Nucleic Acids Research, 50(W1), W159–W164. https://doi.org/10.1093/nar/gkac394
   PubMed Web of Science ®Google Scholar
• Lv, Y., Liang, Q., Li, Y., Liu, X., Zhang, D., & Li, X. (2022). Study of the binding mechanism between hydroxytyrosol and bovine serum albumin using multispectral and molecular docking. Food Hydrocolloids. 122, 107072. https://doi.org/10.1016/j.foodhyd.2021.107072
   Web of Science ®Google Scholar
• Malik, V. S., & Hu, F. B. (2015). Fructose and cardiometabolic health. Journal of the American College of Cardiology, 66(14), 1615–1624. https://doi.org/10.1016/j.jacc.2015.08.025
   PubMed Web of Science ®Google Scholar
• Mardirossian, N., & Head-Gordon, M. (2017). Thirty years of density functional theory in computational chemistry: An overview and extensive assessment of 200 density functionals. Molecular Physics, 115(19), 2315–2372. https://doi.org/10.1080/00268976.2017.1333644
   Web of Science ®Google Scholar
• Martínez-Rosell, G., Giorgino, T., & De Fabritiis, G. (2017). PlayMolecule ProteinPrepare: A Web Application for Protein Preparation for Molecular Dynamics Simulations. Journal of Chemical Information and Modeling, 57(7), 1511–1516. https://doi.org/10.1021/acs.jcim.7b00190
   PubMed Web of Science ®Google Scholar
• Maruyama, Y., Igarashi, R., Ushiku, Y., & Mitsutake, A. (2023). Analysis of protein folding simulation with moving root mean square deviation. Journal of Chemical Information and Modeling, 63(5), 1529–1541. https://doi.org/10.1021/acs.jcim.2c01444
   PubMed Web of Science ®Google Scholar
• Moeinpour, F., Mohseni-Shahri, F. S., Malaekeh-Nikouei, B., & Nassirli, H. (2016). Investigation into the interaction of losartan with human serum albumin and glycated human serum albumin by spectroscopic and molecular dynamics simulation techniques: A comparison study. Chemico-Biological Interactions, 257, 4–13. https://doi.org/10.1016/j.cbi.2016.07.025
   PubMed Web of Science ®Google Scholar
• Nasiri, R., Bahrami, H., Zahedi, M., Moosavi-Movahedi, A. A., & Sattarahmady, N. (2010). A theoretical elucidation of glucose interaction with HSA’s domains. Journal of Biomolecular Structure & Dynamics, 28(2), 211–226. https://doi.org/10.1080/07391102.2010.10507354
   PubMed Web of Science ®Google Scholar
• Nocedal, J., & Wright, S. (1960). Numerical optimization. ITM web of conferences itmconflibrary of congress cataloging-in-publication, second.
   Google Scholar
• Pan, X.-L., Liu, W., & Liu, J.-Y. (2013). Mechanism of the glycosylation step catalyzed by human α-galactosidase: A QM/MM metadynamics study. The Journal of Physical Chemistry. B, 117(2), 484–489. https://doi.org/10.1021/jp308747c
   PubMed Web of Science ®Google Scholar
• Pearlman, D. A., Case, D. A., Caldwell, J. W., Ross, W. S., Cheatham, T. E., DeBolt, S., Ferguson, D., Seibel, G., & Kollman, P. (1995). AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Computer Physics Communications, 91(1-3), 1–41. https://doi.org/10.1016/0010-4655(95)00041-D
   Web of Science ®Google Scholar
• Perdew, J. P., Burke, K., & Ernzerhof, M. (1996). Generalized gradient approximation made simple. Physical Review Letters, 77(18), 3865–3868. https://doi.org/10.1103/PhysRevLett.77.3865
   PubMed Web of Science ®Google Scholar
• Peters, T. (1995). Ligand binding by albumin. In All about albumin (pp. 76–132). Elsevier. https://doi.org/10.1016/B978-012552110-9/50005-2
   Google Scholar
• Petitpas, I., Grüne, T., Bhattacharya, A. A., & Curry, S. (2001). Crystal structures of human serum albumin complexed with monounsaturated and polyunsaturated fatty acids. Journal of Molecular Biology, 314(5), 955–960. https://doi.org/10.1006/jmbi.2000.5208
   PubMed Web of Science ®Google Scholar
• Pongprayoon, P., & Gleeson, M. P. (2014). Probing the binding site characteristics of HSA: A combined molecular dynamics and cheminformatics investigation. Journal of Molecular Graphics & Modelling, 54, 164–173. https://doi.org/10.1016/j.jmgm.2014.10.007
   PubMed Web of Science ®Google Scholar
• Pongprayoon, P., & Mori, T. (2018). The critical role of dimer formation in monosaccharides binding to human serum albumin. Physical Chemistry Chemical Physics: PCCP, 20(5), 3249–3257. https://doi.org/10.1039/C7CP06324E
   PubMed Web of Science ®Google Scholar
• Potter, E. D., Herek, J. L., Pedersen, S., Liu, Q., & Zewail, A. H. (1992). Femtosecond laser control of a chemical reaction. Nature, 355(6355), 66–68. https://doi.org/10.1038/355066a0
   Web of Science ®Google Scholar
• Qi, X., & Tester, R. F. (2019). Fructose, galactose and glucose – In health and disease. Clinical Nutrition ESPEN, 33, 18–28. https://doi.org/10.1016/j.clnesp.2019.07.004
   PubMed Web of Science ®Google Scholar
• Rappe, A. K., Casewit, C. J., Colwell, K. S., Goddard, W. A., & Skiff, W. M. (1992). UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations. Journal of the American Chemical Society, 114(25), 10024–10035. https://doi.org/10.1021/ja00051a040
   Web of Science ®Google Scholar
• Reynolds, T. M. (1963). Chemistry of Nonenzymic Browning I. The Reaction between Aldoses and Amines. Advances in Food Research, 12, 1–52. https://doi.org/10.1016/S0065-2628(08)60005-1
   PubMedGoogle Scholar
• Saha, A., & Raghavachari, K. (2015). Analysis of different fragmentation strategies on a variety of large peptides: implementation of a low level of theory in fragment-based methods can be a crucial factor. Journal of Chemical Theory and Computation, 11(5), 2012–2023. https://doi.org/10.1021/ct501045s
   PubMed Web of Science ®Google Scholar
• Sattarahmady, N., Moosavi-Movahedi, A. A., Ahmad, F., Hakimelahi, G. H., Habibi-Rezaei, M., Saboury, A. A., & Sheibani, N. (2007). Formation of the molten globule-like state during prolonged glycation of human serum albumin. Biochimica Et Biophysica Acta, 1770(6), 933–942. https://doi.org/10.1016/j.bbagen.2007.02.001
   PubMed Web of Science ®Google Scholar
• Sergio, L. M., Martins, Y. A., Amaral, J. L., França, V. L. B., de Freitas, C. F., Neto, A. M., Hioka, N., Ravanelli, M. I., Mareze-Costa, C., Claudio da Costa, S., Freire, V. N., & Brunaldi, K. (2021). Molecular insight on the binding of stevia glycosides to bovine serum albumin. Chemico-Biological Interactions, 344, 109526. https://doi.org/10.1016/j.cbi.2021.109526
   PubMed Web of Science ®Google Scholar
• Shamsi, A., Ahmed, A., & Bano, B. (2018). Probing the interaction of anticancer drug temsirolimus with human serum albumin: Molecular docking and spectroscopic insight. Journal of Biomolecular Structure & Dynamics, 36(6), 1479–1489. https://doi.org/10.1080/07391102.2017.1326320
   PubMed Web of Science ®Google Scholar
• Simard, J. R., Zunszain, P. A., Hamilton, J. A., & Curry, S. (2006). Location of high and low affinity fatty acid binding sites on human serum albumin revealed by NMR drug-competition analysis. Journal of Molecular Biology, 361(2), 336–351. https://doi.org/10.1016/j.jmb.2006.06.028
   PubMed Web of Science ®Google Scholar
• Sittiwanichai, S., Japrung, D., Mori, T., & Pongprayoon, P. (2023). Structural and dynamic alteration of glycated human serum albumin in schiff base and amadori adducts: A molecular simulation study. The Journal of Physical Chemistry. B, 127(23), 5230–5240. https://doi.org/10.1021/acs.jpcb.3c02048
   PubMed Web of Science ®Google Scholar
• Smith, G. R., & Sternberg, M. J. E. (2002). Prediction of protein–protein interactions by docking methods. Current Opinion in Structural Biology, 12(1), 28–35. https://doi.org/10.1016/S0959-440X(02)00285-3
   PubMed Web of Science ®Google Scholar
• Söderhjelm, P., Aquilante, F., & Ryde, U. (2009). Calculation of protein − ligand interaction energies by a fragmentation approach combining high-level quantum chemistry with classical many-body effects. The Journal of Physical Chemistry. B, 113(32), 11085–11094. https://doi.org/10.1021/jp810551h
   PubMed Web of Science ®Google Scholar
• Sousa, B. L., Barroso-Neto, I. L., Oliveira, E. F., Fonseca, E., Lima-Neto, P., Ladeira, L. O., & Freire, V. N. (2016). Explaining RANKL inhibition by OPG through quantum biochemistry computations and insights into peptide-design for the treatment of osteoporosis. RSC Advances, 6(88), 84926–84942. https://doi.org/10.1039/C6RA16712H
   Web of Science ®Google Scholar
• Sudlow, G., Birkett, D. J., & Wade, D. N. (1976). Further characterization of specific drug binding sites on human serum albumin. American Society for Pharmacology and Experimental Therapeutics, 12, 1052–1061.
   Google Scholar
• Szkudlarek, A., Sułkowska, A., Maciążek-Jurczyk, M., Chudzik, M., & Równicka-Zubik, J. (2016). Effects of non-enzymatic glycation in human serum albumin. Spectroscopic analysis. Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy, 152, 645–653. https://doi.org/10.1016/j.saa.2015.01.120
   PubMed Web of Science ®Google Scholar
• Tayeh, N., Rungassamy, T., & Albani, J. R. (2009). Fluorescence spectral resolution of tryptophan residues in bovine and human serum albumins. Journal of Pharmaceutical and Biomedical Analysis, 50(2), 107–116. https://doi.org/10.1016/j.jpba.2009.03.015
   PubMed Web of Science ®Google Scholar
• Thiel, W. (2014). Semiempirical quantum–chemical methods. WIREs Computational Molecular Science, 4(2), 145–157. https://doi.org/10.1002/wcms.1161
   Google Scholar
• Thornalley, P. J., Langborg, A., & Minhas, H. S. (1999). Formation of glyoxal, methylglyoxal and 3-deoxyglucosone in the glycation of proteins by glucose. Biochemical Journal, 344(1), 109–116. https://doi.org/10.1042/bj3440109
   PubMedGoogle Scholar
• Tkatchenko, A., & Scheffler, M. (2009). Accurate molecular van der waals interactions from ground-state electron density and free-atom reference data. Physical Review Letters, 102(7), 073005. https://doi.org/10.1103/PhysRevLett.102.073005
   PubMed Web of Science ®Google Scholar
• Trozzi, F., Wang, X., & Tao, P. (2021). UMAP as a dimensionality reduction tool for molecular dynamics simulations of biomacromolecules: A comparison study. The Journal of Physical Chemistry. B, 125(19), 5022–5034. https://doi.org/10.1021/acs.jpcb.1c02081
   PubMed Web of Science ®Google Scholar
• Trüeb, B., Holenstein, C. G., Fischer, R. W., & Winterhalter, K. H. (1980). Nonenzymatic glycosylation of proteins. A warning. The Journal of Biological Chemistry, 255(14), 6717–6720. https://doi.org/10.1016/S0021-9258(18)43630-7
   PubMed Web of Science ®Google Scholar
• Vanommeslaeghe, K., Hatcher, E., Acharya, C., Kundu, S., Zhong, S., Shim, J., Darian, E., Guvench, O., Lopes, P., Vorobyov, I., & Mackerell, A. D. (2009). CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. Journal of Computational Chemistry, 31(4), 671–690. https://doi.org/10.1002/jcc.21367
   Web of Science ®Google Scholar
• Wang, W., Gan, N., Sun, Q., Wu, D., Gan, R., Zhang, M., Tang, P., & Li, H. (2019). Study on the interaction of ertugliflozin with human serum albumin in vitro by multispectroscopic methods, molecular docking, and molecular dynamics simulation. Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy, 219, 83–90. https://doi.org/10.1016/j.saa.2019.04.047
   PubMed Web of Science ®Google Scholar
• Wang, X., Liu, J., Zhang, J. Z. H., & He, X. (2013). Electrostatically embedded generalized molecular fractionation with conjugate caps method for full quantum mechanical calculation of protein energy. The Journal of Physical Chemistry. A, 117(32), 7149–7161. https://doi.org/10.1021/jp400779t
   PubMed Web of Science ®Google Scholar
• Wang, Y., Yu, H., Shi, X., Luo, Z., Lin, D., & Huang, M. (2013). Structural mechanism of ring-opening reaction of glucose by human serum albumin. The Journal of Biological Chemistry, 288(22), 15980–15987. https://doi.org/10.1074/jbc.M113.467027
   PubMed Web of Science ®Google Scholar
• Wani, T. A., Bakheit, A. H., Al-Majed, A. A., Altwaijry, N., Baquaysh, A., Aljuraisy, A., & Zargar, S. (2021). Binding and drug displacement study of colchicine and bovine serum albumin in presence of azithromycin using multispectroscopic techniques and molecular dynamic simulation. Journal of Molecular Liquids, 333, 115934. https://doi.org/10.1016/j.molliq.2021.115934
   PubMed Web of Science ®Google Scholar
• Yang, F., Bian, C., Zhu, L., Zhao, G., Huang, Z., & Huang, M. (2007). Effect of human serum albumin on drug metabolism: Structural evidence of esterase activity of human serum albumin. Journal of Structural Biology, 157(2), 348–355. https://doi.org/10.1016/j.jsb.2006.08.015
   PubMed Web of Science ®Google Scholar
• Zaman, A., Arif, Z., & Alam, K. (2018). Fructose-human serum albumin interaction undergoes numerous biophysical and biochemical changes before forming AGEs and aggregates.International Journal of Biological Macromolecules, 109, 896–906. https://doi.org/10.1016/j.ijbiomac.2017.11.069
   PubMed Web of Science ®Google Scholar
• Zhang, D. W., & Zhang, J. Z. H. (2003). Molecular fractionation with conjugate caps for full quantum mechanical calculation of protein–molecule interaction energy. The Journal of Chemical Physics, 119(7), 3599–3605. https://doi.org/10.1063/1.1591727
   Web of Science ®Google Scholar
• Zhang, Y., Lee, P., Liang, S., Zhou, Z., Wu, X., Yang, F., & Liang, H. (2015). Structural basis of non-steroidal anti-inflammatory drug diclofenac binding to human serum albumin. Chemical Biology & Drug Design, 86(5), 1178–1184. https://doi.org/10.1111/cbdd.12583
   PubMed Web of Science ®Google Scholar
• Zhao, H., & Caflisch, A. (2015). Molecular dynamics in drug design. European Journal of Medicinal Chemistry, 91, 4–14. https://doi.org/10.1016/j.ejmech.2014.08.004
   PubMed Web of Science ®Google Scholar
• Zunszain, P. A., Ghuman, J., Komatsu, T., Tsuchida, E., & Curry, S. (2003). Crystal structural analysis of human serum albumin complexed with hemin and fatty acid. BMC Structural Biology, 3(1), 6. https://doi.org/10.1186/1472-6807-3-6
   PubMedGoogle Scholar
• Zunszain, P. A., Ghuman, J., McDonagh, A. F., & Curry, S. (2008). Crystallographic analysis of human serum albumin complexed with 4Z,15E-Bilirubin-IXα. Journal of Molecular Biology, 381(2), 394–406. https://doi.org/10.1016/j.jmb.2008.06.016
   PubMed Web of Science ®Google Scholar