Exploration of molecular interactions between scoparone and associated compounds with Constitutive androstane receptor (CAR) leading to gallstone prevention: an in silico investigation

References

• Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindahl, E. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1–2, 19–25. https://doi.org/10.1016/j.softx.2015.06.001
   Google Scholar
• Biovia.Dassault Systeme [DS visualizer client 2021], San Diego: Dassault Systèmes, [2021].
   Google Scholar
• Cheng, S., Zou, M., Liu, Q., Kuang, J., Shen, J., Pu, S., Chen, L., Li, H., Wu, T., Li, R., Li, Y., Jiang, W., Zhang, Z., & He, J. (2017). Activation of constitutive androstane receptor prevents cholesterol gallstone formation. The American Journal of Pathology, 187(4), 808–818. https://doi.org/10.1016/j.ajpath.2016.12.013
   PubMed Web of Science ®Google Scholar
• Clifford, M. N., & Wight, J. (1976). The measurement of feruloylquinic acids and caffeoylquinic acids in coffee beans. Development of the technique and its preliminary application to green coffee beans. Journal of the Science of Food and Agriculture, 27(1), 73–84. https://doi.org/10.1002/jsfa.2740270112
   PubMed Web of Science ®Google Scholar
• Daina, A., Michielin, O., & Zoete, V. (2017). SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Scientific Reports, 7(1), 1–3. https://doi.org/10.1038/srep42717
   PubMed Web of Science ®Google Scholar
• Derived PubChem Compound record for scoparone: PubChem Identifier. CID 8417. https://pubchem.ncbi.nlm.nih.gov/compound/Scoparone
   Google Scholar
• Dey, J., Mahapatra, S. R., Raj, T. K., Kaur, T., Jain, P., Tiwari, A., Patro, S., Misra, N., & Suar, M. (2022). Designing a novel multi-epitope vaccine to evoke a robust immune response against pathogenic multidrug-resistant Enterococcus faecium bacterium. Gut Pathogens, 14(1), 1–20. https://doi.org/10.1186/s13099-022-00495-z
   PubMed Web of Science ®Google Scholar
• Dutta, U., Nagi, B., Garg, P. K., Sinha, S. K., Singh, K., & Tandon, R. K. (2005). Patients with gallstones develop gallbladder cancer at an earlier age. European Journal of Cancer Prevention, 14(4), 381–385. https://doi.org/10.1097/00008469-200508000-00011
   PubMed Web of Science ®Google Scholar
• Elferink, R. O. (2004). Yin Zhi Huang and other plant-derived preparations: Where herbal and molecular medicine meet. Journal of Hepatology, 41(4), 691–693. https://doi.org/10.1016/j.jhep.2004.08.001
   PubMed 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. The Journal of Chemical Physics, 103(19), 8577–8593. https://doi.org/10.1063/1.470117
   Web of Science ®Google Scholar
• Hess, B., Bekker, H., Berendsen, H. J., & Fraaije, J. G. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18(12), 1463–1472. https://doi.org/10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
   Web of Science ®Google Scholar
• Huang, W., Zhang, J., Chua, S. S., Qatanani, M., Han, Y., Granata, R., & Moore, D. D. (2003). Induction of bilirubin clearance by the xenobiotic receptor CAR PNAS USA. Proceedings of the National Academy of Sciences of the United States of America, 100(7), 4156–4161. https://doi.org/10.1073/pnas.0630614100
   PubMed Web of Science ®Google Scholar
• Huang, W., Zhang, J., & Moore, D. D. (2004). A traditional herbal medicine enhances bilirubin clearance by activating the nuclear receptor CAR. The Journal of Clinical Investigation, 113(1), 137–143. https://doi.org/10.1172/JCI18385
   PubMed Web of Science ®Google Scholar
• Hui, Y., Wang, X., Yu, Z., Fan, X., Cui, B., Zhao, T., Mao, L., Feng, H., Lin, L., Yu, Q., Zhang, J., Wang, B., Chen, X., Zhao, X., & Sun, C. (2020). Scoparone as a therapeutic drug in liver diseases: Pharmacology, pharmacokinetics and molecular mechanisms of action. Pharmacological Research, 160, 105170. https://doi.org/10.1016/j.phrs.2020.105170
   PubMed Web of Science ®Google Scholar
• Kim, K. H., Choi, J. M., Li, F., Dong, B., Wooton-Kee, C. R., Arizpe, A., Anakk, S., Jung, S. Y., Hartig, S. M., & Moore, D. D. (2019). Constitutive androstane receptor differentially regulates bile acid homeostasis in mouse models of intrahepatic cholestasis. Hepatology Communications, 3(1), 147–159. https://doi.org/10.1002/hep4.1274
   PubMed Web of Science ®Google Scholar
• Kumari, P., & Poddar, R. (2019). A comparative multivariate analysis of nitrilase enzymes: An ensemble based computational approach. Computational Biology and Chemistry, 83, 107095. https://doi.org/10.1016/j.compbiolchem.2019.107095
   PubMed Web of Science ®Google Scholar
• Kumari, R., Kumar, R., & Lynn, A., Open Source Drug Discovery Consortium. (2014). 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
• Lammert, F., Gurusamy, K., Ko, C. W., Miquel, J. F., Méndez-Sánchez, N., Portincasa, P., Van Erpecum, K. J., Van Laarhoven, C. J., & Wang, D. Q. (2016). Gallstones. Nature Reviews Disease Primers, 2(1), 1-17. https://doi.org/10.1038/nrdp.2016.24
   PubMedGoogle Scholar
• Li, N., Yang, F., Liu, D. Y., Guo, J. T., Ge, N., & Sun, S. Y. (2021). Scoparone inhibits pancreatic cancer through PI3K/Akt signaling pathway. World Journal of Gastrointestinal Oncology, 13(9), 1164–1183. https://doi.org/10.4251/wjgo.v13.i9.1164
   PubMed Web of Science ®Google Scholar
• Lickteig, A. J., Csanaky, I. L., Pratt-Hyatt, M., & Klaassen, C. D. (2016). Activation of constitutive androstane receptor (CAR) in mice results in maintained biliary excretion of bile acids despite a marked decrease of bile acids in liver. Toxicological Sciences, 151(2), 403–418. https://doi.org/10.1093/toxsci/kfw054
   PubMed Web of Science ®Google Scholar
• Lowenfels, A. B., Lindström, C. G., Conway, M. J., & Hastings, P. R. (1985). Gallstones and risk of gallbladder cancer. Journal of the National Cancer Institute, 75(1), 77–80. 10.1.1.977.2222
   PubMed Web of Science ®Google Scholar
• Mahapatra, S. R., Dey, J., Raj, T. K., Kumar, V., Ghosh, M., Verma, K. K., Kaur, T., Kesawat, M. S., Misra, N., & Suar, M. (2022). The potential of plant-derived secondary metabolites as novel drug candidate against Klebsiella pneumoniae: Molecular docking and simulation investigation. South African Journal of Botany, 149, 789–797. https://doi.org/10.1016/j.sajb.2022.04.043
   PubMed Web of Science ®Google Scholar
• Mahmud, S., Uddin, M. A. R., Zaman, M., Sujon, K. M., Rahman, M. E., Shehab, M. N., Islam, A., Alom, M. W., Amin, A., Akash, A. S., & Saleh, M. A. (2020). Molecular docking and dynamics study of natural compound for potential inhibition of main protease of SARS-CoV-2. Journal of Biomolecular Structure and Dynamics, 39(16), 6281–6289. https://doi.org/10.1080/07391102.2020.1796808
   PubMed Web of Science ®Google Scholar
• Masuyama, H., Mitsui, T., Maki, J., Tani, K., Nakamura, K., & Hiramatsu, Y. (2016). Dimethylesculetin ameliorates maternal glucose intolerance and fetal overgrowth in high-fat diet-fed pregnant mice via constitutive androstane receptor. Molecular and Cellular Biochemistry, 419, 185–192. https://doi.org/10.1007/s11010-016-2772-4
   PubMed Web of Science ®Google Scholar
• Morris, G. M., Goodsell, D. S., Halliday, R. S., Huey, R., Hart, W. E., Belew, R. K., & Olson, A. J. (1998). Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. Journal of Computational Chemistry, 19(14), 1639–1662. https://doi.org/10.1002/(SICI)1096-987X(19981115)19:14 < 1639::AID-JCC10 > 3.0.CO;2-B
   Web of Science ®Google Scholar
• Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). Autodock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30(16), 2785–2791. https://doi.org/10.1002/jcc.21256
   PubMed Web of Science ®Google Scholar
• Narang, P. K., Dey, J., Mahapatra, S. R., Roy, R., Kushwaha, G. S., Misra, N., Suar, M., & Raina, V. (2022). Genome-based identification and comparative analysis of enzymes for carotenoid biosynthesis in microalgae. World Journal of Microbiology & Biotechnology, 38(1), 8. https://doi.org/10.1007/s11274-021-03188-y
   Web of Science ®Google Scholar
• Nezafat, N., Karimi, Z., Eslami, M., Mohkam, M., Zandian, S., & Ghasemi, Y. (2016). Designing an efficient multi-epitope peptide vaccine against Vibrio cholerae via combined immunoinformatics and protein interaction-based approaches. Computational Biology and Chemistry, 62, 82–95. https://doi.org/10.1016/j.compbiolchem.2016.04.006
   PubMed Web of Science ®Google Scholar
• O’Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., & Hutchison, G. R. (2011). Open Babel: An open chemical toolbox. Journal of Cheminformatics, 3(1), 33. https://doi.org/10.1186/1758-2946-3-33
   PubMed Web of Science ®Google Scholar
• Onawole, A. T., Kolapo, T. U., Sulaiman, K. O., & Adegoke, R. O. (2018). Structure based virtual screening of the Ebola virus trimeric glycoprotein using consensus scoring. Computational Biology and Chemistry, 72, 170–180. https://doi.org/10.1016/j.compbiolchem.2017.11.006
   PubMed Web of Science ®Google Scholar
• Oostenbrink, C., Villa, A., Mark, A. E., & Van Gunsteren, W. F. (2004). A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force‐field parameter sets 53A5 and 53A6. Journal of Computational Chemistry, 25(13), 1656–1676. https://doi.org/10.1002/jcc.20090
   PubMed Web of Science ®Google Scholar
• Pieper, U., Eswar, N., Webb, B. M., Eramian, D., Kelly, L., Barkan, D. T., Carter, H., Mankoo, P., Karchin, R., Marti-Renom, M. A., Davis, F. P., & Sali, A. (2004). MODBASE, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Research, 37(Database issue), D347–54. https://doi.org/10.1093/nar/gkn791
   Google Scholar
• Pires, D. E., Blundell, T. L., & Ascher, D. B. (2015). pkCSM: Predicting small-molecule pharmacokinetic and toxicity properties using graph-based signatures. Journal of Medicinal Chemistry, 58(9), 4066–4072. https://doi.org/10.1021/acs.jmedchem.5b00104
   PubMed Web of Science ®Google Scholar
• Roa, I., Ibacache, G., Roa, J., Araya, J., De Aretxabala, X., & Muñoz, S. (2006). Gallstones and gallbladder cancer volume and weight of gallstones are associated with gallbladder cancer: A case‐control study. Journal of Surgical Oncology, 93(8), 624–628. https://doi.org/10.1002/jso.20528
   PubMed Web of Science ®Google Scholar
• Romeo, A., Iacovelli, F., & Falconi, M. (2020). Targeting the SARS-CoV-2 spike glycoprotein prefusion conformation: Virtual screening and molecular dynamics simulations applied to the identification of potential fusion inhibitors. Virus Research, 286, 198068. https://doi.org/10.1016/j.virusres.2020.198068
   PubMed Web of Science ®Google Scholar
• Schüttelkopf, A. W., & van Aalten, D. M. F. (2004). PRODRG: A tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallographica, Section D, Biological Crystallography, 60(Pt 8), 1355–1363. https://doi.org/10.1107/S0907444904011679
   PubMedGoogle Scholar
• Shahzad, M. A. (2018). Free energy calculations of protein-water complexes with Gromacs. bioRxiv, 305037. https://doi.org/10.1101/305037
   Google Scholar
• Shukla, R., Shukla, H., Sonkar, A., Pandey, T., & Tripathi, T. (2018). Structure-based screening and molecular dynamics simulations offer novel natural compounds as potential inhibitors of Mycobacterium tuberculosis isocitrate lyase. Journal of Biomolecular Structure & Dynamics, 36(8), 2045–2057. https://doi.org/10.1080/07391102.2017.1341337
   PubMed Web of Science ®Google Scholar
• Watts, K. S., Dalal, P., Murphy, R. B., Sherman, W., Friesner, R. A., & Shelley, J. C. (2010). ConfGen: A conformational search method for efficient generation of bioactive conformers. Journal of Chemical Information and Modeling, 50(4), 534–546. https://doi.org/10.1021/ci100015j
   PubMed Web of Science ®Google Scholar
• Xu, D., & Zhang, Y. (2011). Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization. Biophysical Journal, 101(10), 2525–2534. https://doi.org/10.1016/j.bpj.2011.10.024
   PubMed Web of Science ®Google Scholar
• Yin, J., Wennberg, R. P., Xia, Y., Liu, J. W., & Zhou, H. (1991). Effect of a traditional Chinese medicine, yin zhi huang, on bilirubin clearance and conjugation. Developmental Pharmacology and Therapeutics, 16(1), 59–64. https://doi.org/10.1159/000480557
   PubMedGoogle Scholar