Unraveling the stability of plasma proteins upon interaction of synthesized uridine products: biophysical and molecular dynamics approach

References

• Berg, J. M., Tymoczko, J. L., & Stryer, L. (2006). Biochemistry. The citric acid cycle (Vol. 5). Basingstoke: W.H. Freeman & Co. Ltd.
   Google Scholar
• Brunton, L., Lazo, J., & Parker, K. G. (2005). Gilman's the pharmacological basis of therapeutics (11th ed.). New York: McGraw-Hill.
   Google Scholar
• Carter, D. C., & Ho, J. X. (1994). Structure of serum albumin. Advances in Protein Chemistry, 45, 153–203.
   PubMedGoogle Scholar
• Curry, S., Mandelkow, H., Brick, P., & Franks, N. (1998). Crystal structure of human serum albumin complexed with fatty acid reveals an asymmetric distribution of binding sites. Nature Structural Biology, 5, 827–835. doi:10.1038/1869
   PubMed Web of Science ®Google Scholar
• Evans, T. (2002). Review article: Albumin as a drug – biological effects of albumin unrelated to oncotic pressure. Alimentary Pharmacology and Therapeutics, 16, 6–11. doi:10.1046/j.1365-2036.16.s5.2.x
   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. doi:10.1016/j.jmb.2005.07.075
   PubMed Web of Science ®Google Scholar
• Gokara, M., Kimavath, G. B., Podile, A. R., & Subramanyam, R. (2015). Differential interactions and structural stability of chitosan oligomers with human serum albumin and alpha-1-glycoprotein. Journal of Biomolecular Structure and Dynamics, 33(1), 196–210. doi:10.1080/07391102.2013.868321
   PubMed Web of Science ®Google Scholar
• Gokara, M., Malavath, T., Kalangi, S. K., Reddana, P., & Subramanyam, R. (2014). Unraveling the binding mechanism of asiatic acid with human serum albumin and its biological implications. Journal of Biomolecular Structure and Dynamics, 32(8), 1290–1302. doi:10.1080/07391102.2013.817953
   PubMed Web of Science ®Google Scholar
• Gokara, M., Sudhamalla, B., Amooru, D. G., & Subramanyam, R. (2010). Molecular interaction studies of trimethoxy flavone with human serum albumin. PloS One, 5(1), e8834. doi:10.1371/journal.pone.0008834
   PubMed Web of Science ®Google Scholar
• He, X. M., & Carter, D. C. (1992). Atomic structure and chemistry of human serum albumin. Nature, 358(6383), 209–215. doi:10.1038/358209a0
   PubMed Web of Science ®Google Scholar
• Hermans, J., Berendsen, H. J., Van Gunsteren, W. F., & Postma, J. P. (1984). A consistent empirical potential for water–protein interactions. Biopolymers, 23(8), 1513–1518. doi:10.1002/bip.360230807
   Web of Science ®Google Scholar
• Kallubai, M., Rachamallu, A., Yeggoni, D. P., & Subramanyam, R. (2015). Comparative binding mechanism of lupeol compounds with plasma proteins and its pharmacological importance. Molecular Biosystems, 11(4), 1172–1183. doi:10.1039/C4MB00635F
   PubMed Web of Science ®Google Scholar
• Kowalczyk, D., Marsault, J.-P., & Slomkowski, S. (1996). Atomic force microscopy of human serum albumin (HSA) on poly (styrene/acrolein) microspheres. Colloid & Polymer Science, 274(6), 513–519. doi:10.1007/BF00655225
   Web of Science ®Google Scholar
• Kragh-Hansen, U., Minchiotti, L., Galliano, M., & Peters, T. (2013). Human serum albumin isoforms: Genetic and molecular aspects and functional consequences. Biochimica et Biophysica Acta (BBA)-General Subjects, 1830(12), 5405–5417.
   PubMed Web of Science ®Google Scholar
• Lakowicz, J. R. (2006). Plasmonics in biology and plasmon-controlled fluorescence. Plasmonics, 1(1), 5–33. doi:10.1007/s11468-005-9002-3
   PubMed Web of Science ®Google Scholar
• Liang, L., Tajmir-Riahi, H., & Subirade, M. (2008). Interaction of β-lactoglobulin with resveratrol and its biological implications. Biomacromolecules, 9(1), 50–56. doi:10.1021/bm700728k
   PubMed Web of Science ®Google Scholar
• Longley, D. B., Harkin, D. P., & Johnston, P. G. (2003). 5-fluorouracil: Mechanisms of action and clinical strategies. Nature Reviews Cancer, 3(5), 330–338. doi:10.1038/nrc1074
   PubMed Web of Science ®Google Scholar
• Mirica, S. N., Duicu, O. M., Trancota, S. L., Fira-Mladinescu, O., Angoulvant, D., & Muntean, D. M. (2013). Magnesium orotate elicits acute cardioprotection at reperfusion in isolated and in vivo rat hearts. Canadian Journal of Physiology and Pharmacology, 91(2), 108–115. doi:10.1139/cjpp-2012-0216
   PubMed Web of Science ®Google Scholar
• Morris, G. M., Goodsell, D. S., Huey, R., & Olson, A. J. (1996). Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4. Journal of Computer-Aided Molecular Design, 10(4), 293–304. doi:10.1007/BF00124499
   PubMed Web of Science ®Google Scholar
• Privalov, P. L. (1979). Stability of proteins small globular proteins. Advances in Protein Chemistry, 33, 167–241.
   PubMedGoogle Scholar
• Rahman, M. H., Yamasaki, K., Shin, Y. H., Lin, C. C., & Otagiri, M. (1993). Characterization of high affinity binding sites of non-steroidal anti-inflammatory drugs with respect to site-specific probes on human serum albumin. Biological & Pharmaceutical Bulletin, 16(11), 1169–1174. doi:10.1248/bpb.16.1169
   PubMedGoogle Scholar
• Subramanyam, R., Gollapudi, A., Bonigala, P., Chinnaboina, M., & Amooru, D. G. (2009). Betulinic acid binding to human serum albumin: A study of protein conformation and binding affinity. Journal of Photochemistry and Photobiology B: Biology, 94(1), 8–12. doi:10.1016/j.jphotobiol.2008.09.002
   PubMed Web of Science ®Google Scholar
• Sudhamalla, B., Gokara, M., Ahalawat, N., Amooru, D. G., & Subramanyam, R. (2010). Molecular dynamics simulation and binding studies of β-sitosterol with human serum albumin and its biological relevance. The Journal of Physical Chemistry B, 114(27), 9054–9062. doi:10.1021/jp102730p
   PubMed Web of Science ®Google Scholar
• Sugio, S., Kashima, A., Mochizuki, S., Noda, M., & Kobayashi, K. (1999). Crystal structure of human serum albumin at 2.5 Å resolution. Protein Engineering, Design and Selection, 12(6), 439–446. doi:10.1093/protein/12.6.439
   Web of Science ®Google Scholar
• Sun, Y.-W., Chen, K.-M., & Kwon, C.-H. (2006). Sulfonyl-containing nucleoside phosphotriesters and phosphoramidates as novel anticancer prodrugs of 5-fluoro-2'-deoxyuridine 5'-monophosphate (FdUMP). Molecular Pharmaceutics, 3(2), 161–173. doi:10.1021/mp0500622
   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. doi:10.1016/j.jpba.2009.03.015
   PubMed Web of Science ®Google Scholar
• Vahedian-Movahed, H., Saberi, M. R., & Chamani, J. (2011). Comparison of binding interactions of lomefloxacin to serum albumin and serum transferrin by resonance light scattering and fluorescence quenching methods. Journal of Biomolecular Structure and Dynamics, 28(4), 483–502. doi:10.1080/07391102.2011.10508590
   PubMed Web of Science ®Google Scholar
• Varshney, A., Sen, P., Ahmad, E., Rehan, M., Subbarao, N., & Khan, R. H. (2010). Ligand binding strategies of human serum albumin: How can the cargo be utilized?. Chirality, 22(1), 77–87. doi:10.1002/chir.20709
   PubMed Web of Science ®Google Scholar
• Wen, J., & Xia, Y. (2012). Adenosine signaling: Good or bad in erectile function? Arteriosclerosis, Thrombosis, and Vascular Biology, 32(4), 845–850. doi:10.1161/ATVBAHA.111.226803
   PubMed Web of Science ®Google Scholar
• Wu, K.-M. (2009). A new classification of prodrugs: Regulatory perspectives. Pharmaceuticals, 2(3), 77–81. doi:10.3390/ph2030077
   Google Scholar
• Wurtman, R. J., Cansev, M., & Ulus, I. (2009). Synapse formation is enhanced by oral administration of uridine and DHA, the circulating precursors of brain phosphatides. The Journal of Nutrition, Health and Aging, 13(3), 189–197. doi:10.1007/s12603-009-0056-3
   PubMed Web of Science ®Google Scholar
• Yamasaki, K., Chuang, V. T. G., Maruyama, T., & Otagiri, M. (2013). Albumin–drug interaction and its clinical implication. Biochimica et Biophysica Acta (BBA)-General Subjects, 1830(12), 5435–5443. doi:10.1016/j.bbagen.2013.05.005
   PubMed Web of Science ®Google Scholar
• Yamasaki, K., Maruyama, T., Kragh-Hansen, U., & Otagiri, M. (1996). Characterization of site I on human serum albumin: Concept about the structure of a drug binding site. Biochimica et Biophysica Acta (BBA)-Protein Structure and Molecular Enzymology, 1295(2), 147–157. doi:10.1016/0167-4838(96)00013-1
   PubMed Web of Science ®Google Scholar
• Yeggoni, D. P., Gokara, M., Manidhar, D. M., Rachamallu, A., Nakka, S., Reddy, C. S., & Subramanyam, R. (2014). Binding and molecular dynamics studies of 7-hydroxycoumarin derivatives with human serum albumin and its pharmacological importance. Molecular Pharmaceutics, 11(4), 1117–1131. doi:10.1021/mp500051f
   PubMed Web of Science ®Google Scholar
• Yeggoni, D. P., Rachamallu, A., Kallubai, M., & Subramanyam, R. (2015). Cytotoxicity and comparative binding mechanism of piperine with human serum albumin and α-1-acid glycoprotein. Journal of Biomolecular Structure and Dynamics, 33(6), 1336–1351. doi:10.1080/07391102.2014.947326
   PubMed Web of Science ®Google Scholar
• Yeggoni, D. P., Rachamallu, A., & Subramanyam, R. (2016). A comparative binding mechanism between human serum albumin and α-1-acid glycoprotein with corilagin: Biophysical and computational approach. RSC Advances, 6(46), 40225–40237. doi:10.1039/C6RA06837E
   Web of Science ®Google Scholar
• Yeggoni, D. P., Rachamallu, A., & Subramanyam, R. (2016). Protein stability, conformational change and binding mechanism of human serum albumin upon binding of embelin and its role in disease control. Journal of Photochemistry and Photobiology B: Biology, 160, 248–259. doi:10.1016/j.jphotobiol.2016.04.012
   PubMed Web of Science ®Google Scholar
• Yuqin, L., Guirong, Y., Zhen, Y., Caihong, L., Baoxiu, J., Jiao, C., & Yurong, G. (2014). Investigation of the interaction between patulin and human serum albumin by a spectroscopic method, atomic force microscopy, and molecular modeling. BioMed Research International, 2014, 1. doi:10.1155/2014/734850
   Google Scholar
• Zawilska, J. B., Wojcieszak, J., & Olejniczak, A. B. (2013). Prodrugs: A challenge for the drug development. Pharmacological Reports, 65(1), 1–14. doi:10.1016/S1734-1140(13)70959-9
   PubMed Web of Science ®Google Scholar
• Zolfagharzadeh, M., Pirouzi, M., Asoodeh, A., Saberi, M. R., & Chamani, J. (2014). A comparison investigation of DNP-binding effects to HSA and HTF by spectroscopic and molecular modeling techniques. Journal of Biomolecular Structure and Dynamics, 32(12), 1936–1952. doi:10.1080/07391102.2013.843062
   PubMed Web of Science ®Google Scholar
• Zsila, F. (2013). Subdomain IB is the third major drug binding region of human serum albumin: Toward the three-sites model. Molecular Pharmaceutics, 10(5), 1668–1682. doi:10.1021/mp400027q
   PubMed Web of Science ®Google 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. doi:10.1016/j.jmb.2008.06.016
   PubMed Web of Science ®Google Scholar