Molecular interaction of di-ester bonded cationic Gemini surfactants with pepsin: in vitro and in silico perspectives

References

• Ahmad, S., Arsalan, A., Hashmi, A., Khan, M. A., Siddiqui, W. A., & Younus, H. (2021). A comparative study based on activity, conformation and computational analysis on the inhibition of human salivary aldehyde dehydrogenase by phthalate plasticizers: Implications in assessing the safety of packaged food items. Toxicology, 462, 152947. https://doi.org/10.1016/j.tox.2021.152947
   PubMed Web of Science ®Google Scholar
• Akram, M., Ansari, F., Bhat, I. A., & Kabir-ud-Din (2019). Probing interaction of bovine serum albumin (BSA) with the biodegradable version of cationic Gemini surfactants. Journal of Molecular Liquids, 276, 519–528. https://doi.org/10.1016/j.molliq.2018.10.123
   Web of Science ®Google Scholar
• Akram, M., Anwar, S., Ansari, F., Bhat, I. A., & Kabir-ud-Din (2016). Bio-physicochemical analysis of ethylene oxide-linked diester-functionalized green cationic Gemini surfactants. RSC Advances, 6(26), 21697–21705. https://doi.org/10.1039/C5RA28129F
   Web of Science ®Google Scholar
• Akram, M., Anwar, S., Bhat, I. A., & Kabir-ud-Din (2017a). Multifaceted analysis of the noncovalent interactions of myoglobin with finely tuned Gemini surfactants: A comparative study. Industrial & Engineering Chemistry Research, 56(46), 13663–13676. https://doi.org/10.1021/acs.iecr.7b01583
   Web of Science ®Google Scholar
• Akram, M., Anwar, S., Bhat, I. A., & Kabir-ud-Din (2017b). Unraveling the interaction of hemoglobin with a biocompatible and cleavable oxy-diester-functionalized Gemini surfactant. International Journal of Biological Macromolecules, 96, 474–484. https://doi.org/10.1016/j.ijbiomac.2016.11.112
   PubMed Web of Science ®Google Scholar
• Akram, M., Lal, H., & Kabir-ud-Din (2022a). Exploring the binding mode of ester-based cationic Gemini surfactants with Calf Thymus DNA: A detailed physicochemical, spectroscopic and theoretical study. Bioorganic Chemistry, 119, 105555. https://doi.org/10.1016/j.bioorg.2021.105555
   PubMed Web of Science ®Google Scholar
• Akram, M., Lal, H., Osama, M., Ansari, F., Anwar, S., Ahmad, A., Azum, N., Marwani, H. M., Asiri, A. M., Kabir‐ud-Din, & Samreen. (2021). An insight view on synthetic protocol, surface activity, and biological aspects of novel biocompatible quaternary ammonium cationic Gemini surfactants. Journal of Surfactants and Detergents, 24(1), 35–49, https://doi.org/10.1002/jsde.12450
   Web of Science ®Google Scholar
• Akram, M., Lal, H., Shakya, S., & Kabir-ud-Din (2020). Multispectroscopic and computational analysis insight into the interaction of cationic diester-bonded gemini surfactants with serine protease α-chymotrypsin. ACS Omega, 5(7), 3624–3637. https://doi.org/10.1021/acsomega.9b04142
   PubMed Web of Science ®Google Scholar
• Akram, M., Lal, H., Shakya, S., Varshney, R., & Kabir-ud-Din (2022b). Molecular engineering of complexation between RNA and biodegradable cationic Gemini surfactants: Role of the hydrophobic chain length. Molecular Systems Design & Engineering, 7(5), 487–506. https://doi.org/10.1039/D1ME00147G
   Web of Science ®Google Scholar
• Arif, A., Hashmi, M. A., Salam, S., Younus, H., & Mahmood, R. (2022). Interaction of the insecticide bioallethrin with human hemoglobin: Biophysical, in silico and enzymatic studies. Journal of Biomolecular Structure and Dynamics, 11;1–12. https://doi.org/10.1080/07391102.2022.2109756
   Web of Science ®Google Scholar
• Benesi, H. A., & Hildebrand, J. H. (1949). A spectrophotometric investigation of the interaction of iodine with aromatic hydrocarbons. Journal of the American Chemical Society, 71(8), 2703–2707. https://doi.org/10.1021/ja01176a030
   Web of Science ®Google Scholar
• Bhat, I. A., Roy, B., & Kabir-ud-Din (2018). Synthesis and biophysical analysis of a novel gemini surfactant with lysozyme: Industrial perspective. Journal of Industrial and Engineering Chemistry. 63, 348–358. https://doi.org/10.1016/j.jiec.2018.02.035
   Web of Science ®Google Scholar
• Burley, S. K., & Petsko, G. A. (1986). Amino-aromatic interactions in proteins. FEBS Letters, 203(2), 139–143. https://doi.org/10.1016/0014-5793(86)80730-X
   PubMed Web of Science ®Google Scholar
• Bussi, G., Donadio, D., & Parrinello, M. (2007). Canonical sampling through velocity rescaling. Journal of Chemical Physics, 126(1), 014101. https://doi.org/10.1063/1.2408420
   PubMed Web of Science ®Google Scholar
• Campos, L. A., & Sancho, J. (2003). The active site of pepsin is formed in the intermediate conformation dominant at mildly acidic pH. FEBS Letters, 538(1–3), 89–95. https://doi.org/10.1016/S0014-5793(03)00152-2
   PubMed Web of Science ®Google Scholar
• Chakraborty, T., Chakraborty, I., Moulik, S. P., & Ghosh, S. (2009). Physicochemical and conformational studies on BSA − surfactant interaction in aqueous medium. Langmuir : The ACS Journal of Surfaces and Colloids, 25(5), 3062–3074. https://doi.org/10.1021/la803797x
   PubMed Web of Science ®Google Scholar
• Chakraborty, T., Chakraborty, I., Moulik, S. P., & Ghosh, S. (2007). Physicochemical studies on pepsin − CTAB interaction: Energetics and structural changes. The Journal of Physical Chemistry. B, 111(10), 2736–2746. https://doi.org/10.1021/jp066051l
   PubMed Web of Science ®Google Scholar
• Chu, S., He, F., Yu, H., Liu, G., Wan, J., Jing, M., Li, Y., Cui, Z., & Liu, R. (2021). Evaluation of the binding of UFCB and Pb-UFCB to pepsin: Spectroscopic analysis and enzyme activity assay. Journal of Molecular Liquids, 328, 115511. https://doi.org/10.1016/j.molliq.2021.115511
   Web of Science ®Google Scholar
• Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N·log(N) method for Ewald sums in large systems. Journal of Chemical Physics, 98(12), 10089–10092. https://doi.org/10.1063/1.464397
   Web of Science ®Google Scholar
• Dreyer, S., Salim, P., & Kragl, U. (2009). Driving forces of protein partitioning in an ionic liquid-based aqueous two-phase system. Biochemical Engineering Journal, 46(2), 176–185. https://doi.org/10.1016/j.bej.2009.05.005
   Web of Science ®Google Scholar
• Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., & Pedersen, L. G. (1995). A smooth particle mesh Ewald method. Journal of Chemical Physics, 103(19), 8577–8593. https://doi.org/10.1063/1.470117
   Web of Science ®Google Scholar
• Fruton, J. S. (2002). A history of pepsin and related enzymes. The Quarterly Review of Biology, 77(2), 127–147. https://doi.org/10.1086/340729
   PubMed Web of Science ®Google Scholar
• Ghosh, S., Dolai, S., Patra, T., & Dey, J. (2015). Solution behavior and interaction of pepsin with carnitine based cationic surfactant: Fluorescence, circular dichroism, and calorimetric studies. The Journal of Physical Chemistry, B, 119(39), 12632–12643. https://doi.org/10.1021/acs.jpcb.5b07072
   PubMed Web of Science ®Google Scholar
• Gull, N., Sen, P., Khan, R. H., & Kabir-ud-Din (2009). Interaction of bovine (BSA), rabbit (RSA), and porcine (PSA) Serum Albumins with Cationic Single-Chain/Gemini surfactants: A comparative study. Langmuir : The ACS Journal of Surfaces and Colloids, 25(19), 11686–11691. https://doi.org/10.1021/la901639h
   PubMed Web of Science ®Google Scholar
• Haris, P. I., & Severcan, F. (1999). FTIR spectroscopic characterization of protein structure in aqueous and non-aqueous media. Journal of Molecular Catalysis B: Enzymatic, 7(1–4), 207–221. https://doi.org/10.1016/S1381-1177(99)00030-2
   Google Scholar
• Hashemi-Shahraki, F., Shareghi, B., & Farhadian, S. (2020). The interaction of Naphthol Yellow S (NYS) with pepsin: Insights from spectroscopic to molecular dynamics studies. International journal of Biological Macromolecules, 165(Pt B), 1842–1851. https://doi.org/10.1016/j.ijbiomac.2020.10.093
   PubMedGoogle Scholar
• Hashmi, M. A., Malik, A., Arsalan, A., Khan, M. A., & Younus, H. (2021). Elucidation of kinetic and structural properties of eye lens ζ-crystallin: An in vitro and in silico approach. Journal of Biomolecular Structure and Dynamics, 20, 1–15. https://doi.org/10.1080/07391102.2021.2017351
   Google Scholar
• Head, J. D., & Zerner, M. C. (1985). A Broyden—Fletcher—Goldfarb—Shanno optimization procedure for molecular geometries. Chemical Physics Letters, 122(3), 264–270. https://doi.org/10.1016/0009-2614(85)80574-1
   Web of Science ®Google Scholar
• Huang, Y., Yan, J., Liu, B., Yu, Z., Gao, X., Tang, Y., & Zi, Y. (2010). Investigation on interaction of prulifloxacin with pepsin: A spectroscopic analysis. Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy, 75(3), 1024–1029. https://doi.org/10.1016/j.saa.2009.12.044
   PubMed Web of Science ®Google Scholar
• Hu, W., Ding, L., Cao, J., Liu, L., Wei, Y., & Fang, Y. (2015). Protein binding-induced surfactant aggregation variation: A new strategy of developing fluorescent aqueous sensor for proteins. ACS Applied Materials & Interfaces, 7(8), 4728–4736. https://doi.org/10.1021/am508421n
   PubMed Web of Science ®Google Scholar
• Hu, Y.-J., Liu, Y., Pi, Z.-B., & Qu, S.-S. (2005). Interaction of cromolyn sodium with human serum albumin: A fluorescence quenching study. Bioorganic & Medicinal Chemistry, 13(24), 6609–6614. https://doi.org/10.1016/j.bmc.2005.07.039
   PubMed Web of Science ®Google Scholar
• Khamouli, S., Belaidi, S., Bakhouch, M., Chtita, S., Hashmi, M. A., & Qais, F. A. (2022). QSAR modeling, molecular docking, ADMET prediction and molecular dynamics simulations of some 6-arylquinazolin-4-amine derivatives as DYRK1A inhibitors. Journal of Molecular Structure, 1258, 132659. https://doi.org/10.1016/j.molstruc.2022.132659
   Web of Science ®Google Scholar
• Khan, T. A., Mahler, H.-C., & Kishore, R. S. K. (2015). Key interactions of surfactants in therapeutic protein formulations: A review. European Journal of Pharmaceutics and Biopharmaceutics, 97(Pt A), 60–67. https://doi.org/10.1016/j.ejpb.2015.09.016
   PubMed Web of Science ®Google Scholar
• Kumari, R., Kumar, R., & Lynn, A. (2014). Lynn, g_mmpbsa —A GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information and Modeling, 54(7), 1951–1962. https://doi.org/10.1021/ci500020m
   PubMed Web of Science ®Google Scholar
• Lal, H., Akram, M., & Kabir-ud-Din (2022). Deciphering the mechanism of interaction of an ester-functionalized cationic gemini surfactant with bovine serum albumin: A biophysical and molecular modeling study. Colloids and Surfaces A: Physicochemical and Engineering Aspects, 646, 128944. https://doi.org/10.1016/j.colsurfa.2022.128944
   Web of Science ®Google Scholar
• Maier, J. A., Martinez, C., Kasavajhala, K., Wickstrom, L., Hauser, K. E., & Simmerling, C. (2015). ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB. Journal of Chemical Theory and Computation, 11(8), 3696–3713. https://doi.org/10.1021/acs.jctc.5b00255
   PubMed Web of Science ®Google Scholar
• Menger, F. M., & Littau, C. A. (1991). Gemini-surfactants: Synthesis and properties. Journal of the American Chemical Society, 113(4), 1451–1452. https://doi.org/10.1021/ja00004a077
   Web of Science ®Google Scholar
• Meti, M. D., Xu, Y., Xie, J., Chen, Y., Wu, Z., Liu, J., Han, Q., He, Z., Hu, Z., & Xu, H. (2018). Multi-spectroscopic studies on the interaction between traditional Chinese herb, helicid with pepsin. Molecular Biology Reports, 45(6), 1637–1646. https://doi.org/10.1007/s11033-018-4306-5
   PubMed Web of Science ®Google Scholar
• Naeem, A., & Khan, R. H. (2004). Characterization of molten globule state of cytochrome c at alkaline, native and acidic pH induced by butanol and SDS. The International Journal of Biochemistry & Cell Biology, 36(11), 2281–2292. https://doi.org/10.1016/j.biocel.2004.04.023
   PubMed Web of Science ®Google Scholar
• Neese, F. (2012). The ORCA program system, WIREs. WIREs Computational Molecular Science, 2(1), 73–78. https://doi.org/10.1002/wcms.81
   Google Scholar
• Northrop, J. H. (1930). Crystalline pepsin. The Journal of General Physiology, 13(6), 739–766. https://doi.org/10.1085/jgp.13.6.739
   PubMedGoogle Scholar
• Otzen, D. (2011). Protein–surfactant interactions: A tale of many states. Biochimica et Biophysica Acta, 1814(5), 562–591. https://doi.org/10.1016/j.bbapap.2011.03.003
   PubMed Web of Science ®Google Scholar
• Otzen, D. E. (2002). Protein unfolding in detergents: Effect of micelle structure, ionic strength, pH, and temperature. Biophysical Journal, 83(4), 2219–2230. https://doi.org/10.1016/S0006-3495(02)73982-9
   PubMed Web of Science ®Google Scholar
• Otzen, D. E. (2015). Proteins in a brave new surfactant world. Current Opinion in Colloid and Interface Science. 20(3), 161–169. https://doi.org/10.1016/j.cocis.2015.07.003
   Web of Science ®Google Scholar
• Ouassaf, M., Belaidi, S., Chtita, S., Lanez, T., Abul Qais, F., & Md Amiruddin, H. (2022). Combined molecular docking and dynamics simulations studies of natural compounds as potent inhibitors against SARS-CoV-2 main protease. Journal of Biomolecular Structure and Dynamics. 40(21), 11264–11273. https://doi.org/10.1080/07391102.2021.1957712
   PubMed Web of Science ®Google Scholar
• Parrinello, M., & Rahman, A. (1981). Polymorphic transitions in single crystals: A new molecular dynamics method. Journal of Applied Physics, 52(12), 7182–7190. https://doi.org/10.1063/1.328693
   Web of Science ®Google Scholar
• Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., Ferrin, T. E., & Chimera, U. C. S. F. (2004). A visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. https://doi.org/10.1002/jcc.20084
   PubMed Web of Science ®Google Scholar
• Piazza, R. (2004). Protein interactions and association: An open challenge for colloid science. Current Opinion in Colloid and Interface Science, 8(6), 515–522. https://doi.org/10.1016/j.cocis.2004.01.008
   Web of Science ®Google Scholar
• Randolph, T. W., & Jones, L. S. (2002). Surfactant-Protein Interactions in Rational Design of Stable Protein Formulations. Pharmaceutical Biotechnology (Vol. 13, pp. 159–175). Boston, MA: Springer. https://doi.org/10.1007/978-1-4615-0557-0_7
   Google Scholar
• Rub, M. A., Khan, J. M., Asiri, A. M., Khan, R. H., & Kabir-ud-Din. (2014). Study on the interaction between amphiphilic drug and bovine serum albumin: A thermodynamic and spectroscopic description. Journal of Molecular Liquids, 155, 39–46. https://doi.org/10.1016/j.jlumin.2014.06.009
   Google Scholar
• Rub, M. A., Khan, J. M., Azum, N., & Asiri, A. M. (2017). Influence of antidepressant clomipramine hydrochloride drug on human serum albumin: Spectroscopic study. Journal of Molecular Liquids, 241, 91–98. https://doi.org/10.1016/j.molliq.2017.05.143
   Web of Science ®Google Scholar
• Sharma, A. S., Anandakumar, S., & Ilanchelian, M. (2014). In vitro investigation of domain specific interactions of phenothiazine dye with serum proteins by spectroscopic and molecular docking approaches. RSC Advances, 4(68), 36267–36281. https://doi.org/10.1039/C4RA04630G
   Web of Science ®Google Scholar
• Shen, L., Xu, H., Huang, F., Li, Y., Xiao, H., Yang, Z., Hu, Z., He, Z., Zeng, Z., & Li, Y. (2015). Investigation on interaction between Ligupurpuroside A and pepsin by spectroscopic and docking methods. Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy, 135, 256–263. https://doi.org/10.1016/j.saa.2014.06.087
   PubMed Web of Science ®Google Scholar
• Siddiqui, S., Ameen, F., Jahan, I., Nayeem, S. M., & Tabish, M. (2019). A comprehensive spectroscopic and computational investigation on the binding of the anti-asthmatic drug triamcinolone with serum albumin. New Journal of Chemistry, 43(10), 4137–4151. https://doi.org/10.1039/C8NJ05486J
   Web of Science ®Google Scholar
• Sousa Da Silva, A. W., & Vranken, W. F. (2012). ACPYPE - AnteChamber PYthon Parser interfacE. BMC Research Notes, 5, 367. https://doi.org/10.1186/1756-0500-5-367
   PubMedGoogle Scholar
• Studio, D. (2008). Discovery studio, Accelrys [2.1].
   Google Scholar
• Sun, Y., Zhen, T., Li, Y., Wang, Y., Wang, M., Li, X., & Sun, Q. (2020). Interaction of food-grade titanium dioxide nanoparticles with pepsin in simulated gastric fluid. LWT, 134, 110208. https://doi.org/10.1016/j.lwt.2020.110208
   Web of Science ®Google Scholar
• Suwareh, O., Causeur, D., Jardin, J., Briard-Bion, V., Le Feunteun, S., Pezennec, S., & Nau, F. (2021). Statistical modeling of in vitro pepsin specificity. Food Chemistry, 362, 130098. https://doi.org/10.1016/j.foodchem.2021.130098
   PubMed Web of Science ®Google Scholar
• Tang, J., Sepulveda, P., Marciniszyn, J., Chen, K. C. S., Huang, W.-Y., Tao, N., Liu, D., & Lanier, J. P. (1973). Amino-acid sequence of porcine pepsin. Proceedings of the National Academy of Sciences of the United States of America, 70(12), 3437–3439. https://doi.org/10.1073/pnas.70.12.3437
   PubMed Web of Science ®Google Scholar
• Tesmar, A., Kogut, M. M., Żamojć, K., Grabowska, O., Chmur, K., Samsonov, S. A., Makowska, J., Wyrzykowski, D., & Chmurzyński, L. (2021). Physicochemical nature of sodium dodecyl sulfate interactions with bovine serum albumin revealed by interdisciplinary approaches. Journal of Molecular Liquids, 340, 117185. https://doi.org/10.1016/j.molliq.2021.117185
   Web of Science ®Google Scholar
• Thomas, K., Aalbers, M., Bannon, G. A., Bartels, M., Dearman, R. J., Esdaile, D. J., Fu, T. J., Glatt, C. M., Hadfield, N., Hatzos, C., Hefle, S. L., Heylings, J. R., Goodman, R. E., Henry, B., Herouet, C., Holsapple, M., Ladics, G. S., Landry, T. D., MacIntosh, S. C., … Zawodny, J. (2004). A multi-laboratory evaluation of a common in vitro pepsin digestion assay protocol used in assessing the safety of novel proteins. Regulatory toxicology and Pharmacology : RTP, 39(2), 87–98. https://doi.org/10.1016/j.yrtph.2003.11.003
   PubMed Web of Science ®Google Scholar
• Trott, O., & Olson, A. J. (2009). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 32, NA–NA. https://doi.org/10.1002/jcc.21334
   Google Scholar
• Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. C. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26(16), 1701–1718. https://doi.org/10.1002/jcc.20291
   PubMed Web of Science ®Google Scholar
• Vasilescu, M., Angelescu, D., Almgren, M., & Valstar, A. (1999). Interactions of globular proteins with surfactants studied with fluorescence probe methods. Langmuir, 15(8), 2635–2643. https://doi.org/10.1021/la981424y
   Web of Science ®Google Scholar
• Weigend, F., & Ahlrichs, R. (2005). Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: Design and assessment of accuracy. Physical Chemistry Chemical Physics : PCCP, 7(18), 3297–3305. https://doi.org/10.1039/b508541a
   PubMed Web of Science ®Google Scholar
• Winnik, F. M. (1993). Photophysics of preassociated pyrenes in aqueous polymer solutions and in other organized media. Chemical Reviews, 93(2), 587–614. https://doi.org/10.1021/cr00018a001
   Web of Science ®Google Scholar
• Yaseen, Z., Aswal, V. K., Zhou, X., Kabir-ud-Din, & Haider, S. (2018). Morphological changes in human serum albumin in the presence of cationic amphiphilic drugs. New Journal of Chemistry, 42(3), 2270–2277. https://doi.org/10.1039/C7NJ02591B
   Web of Science ®Google Scholar
• Ying, M., Huang, F., Ye, H., Xu, H., Shen, L., Huan, T., Huang, S., Xie, J., Tian, S., Hu, Z., He, Z., Lu, J., & Zhou, K. (2015). Study on interaction between curcumin and pepsin by spectroscopic and docking methods. International Journal of Biological Macromolecules, 79, 201–208. https://doi.org/10.1016/j.ijbiomac.2015.04.057
   PubMed Web of Science ®Google Scholar
• Yue, Y., Zhao, S., Liu, J., Yan, X., & Sun, Y. (2017). Probing the binding properties of dicyandiamide with pepsin by spectroscopy and docking methods. Chemosphere, 185, 1056–1062. https://doi.org/10.1016/j.chemosphere.2017.07.115
   PubMed Web of Science ®Google Scholar
• Zaidi, N., Ahmad, E., Rehan, M., Rabbani, G., Ajmal, M. R., Zaidi, Y., Subbarao, N., & Khan, R. H. (2013). Biophysical insight into furosemide binding to human serum albumin: A study to unveil its impaired albumin binding in uremia. The journal of Physical Chemistry. B, 117(9), 2595–2604. https://doi.org/10.1021/jp3069877
   PubMed Web of Science ®Google Scholar
• Zhang, H., Cao, J., Fei, Z., & Wang, Y. (2012). Investigation on the interaction behavior between bisphenol A and pepsin by spectral and docking studies. Journal of Molecular Structure. 1021, 34–39. https://doi.org/10.1016/j.molstruc.2012.04.072
   Web of Science ®Google Scholar
• Zhang, G., Chen, X., Guo, J., & Wang, J. (2009). Spectroscopic investigation of the interaction between chrysin and bovine serum albumin. Journal of Molecular Structure, 921(1–3), 346–351. https://doi.org/10.1016/j.molstruc.2009.01.036
   Web of Science ®Google Scholar
• Zhang, G., Zhao, N., & Wang, L. (2011). Probing the binding of vitexin to human serum albumin by multispectroscopic techniques. Journal of Luminescense, 131(5), 880–887. https://doi.org/10.1016/j.jlumin.2010.12.018
   Web of Science ®Google Scholar