A Comprehensive Modeling of Bioenhancers Docked to Transport Proteins to Enhance Bioavailability
DOI:
https://doi.org/10.47611/jsrhs.v11i4.3727Keywords:
Docking, ABC transport proteins, P-Glycoprotien, Bioenhancers, FlavonoidsAbstract
With pharmaceutical availability being a pertinent issue in modern medicine, the ability of bioenhancers to increase the bioavailability of a drug, thereby reducing the required dosage, can be critical for reducing treatment costs. Flavonoids, one form of bioenhancers, are metabolites that increase the availability through inhibition of key proteins in gut epithelial cells and transport proteins. Bioenhancers have the potential to inhibit proteins that limit absorption, thus increasing the amount of a target drug that can enter systemic circulation, increasing bioavailability. P-glycoprotein (P-gp) is one of the membrane transport proteins whose function is to transport drugs in and out of the cell. Human serum albumin (HSA), the most abundant protein in the human plasma, is a protein that serves to transport several signals and other compounds throughout the circulatory system. This study assessed the binding of various bioenhancers (piperine, quercetin, capsaicin, naringin, genistein, lysergol, sinomenine, tangeretin) to various forms of P-gp, HSA and ABC transporters to improve drug bioavailability. We hypothesized that the bioenhancers would bind to these transport proteins, thereby inhibiting them and increasing bioavailability.An examination of the geometric shape complementarity scores in PatchDock and the binding affinities (ΔG kcal/mol) from three other web servers (Webina, DockThor, CB-Dock) showed that naringin produces the most optimal binding scores overall. Given the promising optimal binding scores, the data provides critical insight into administering bioenhancers with drugs to improve bioavailability, as well as suggesting that naringin may be a valuable compound to conduct further tests in vitro and in vivo.
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Atal, N, and KL Bedi. “Bioenhancers: Revolutionary Concept to Market.” Journal of Ayurveda and Integrative Medicine, vol. 1, no. 2, Apr. 2010, pp. 96–99., doi:10.4103/0975-9476.65073.
Randhawa, Gurpreet Kaur, et al. “Bioenhancers from Mother Nature and Their Applicability in Modern Medicine.” International Journal of Applied and Basic Medical Research, vol. 1, no. 1, 2011, pp. 5–10., doi:10.4103/2229-516x.81972.
Meng, Xuan-Yu, et al. “Molecular Docking: A Powerful Approach for Structure-Based Drug Discovery.” Current Computer Aided-Drug Design, vol. 7, no. 2, 1 Jun. 2011, pp. 146–157., doi:10.2174/157340911795677602.
Salmaso, Veronica, and Stefano Moro. “Bridging Molecular Docking to Molecular Dynamics in Exploring Ligand-Protein Recognition Process: An Overview.” Frontiers in Pharmacology, vol. 9, 22 Aug. 2018, doi:10.3389/fphar.2018.00923.
Pantsar, Tatu, and Antti Poso. “Binding Affinity via Docking: Fact and Fiction.” Molecules, vol. 23, no. 8, 20 Jul. 2018, p. 1899., doi:10.3390/molecules23081899.
Pagadala, Nataraj S., et al. “Software for Molecular Docking: A Review.” Biophysical Reviews, vol. 9, no. 2, 16 Apr. 2017, pp. 91–102., doi:10.1007/s12551-016-0247-1.
Mashiach, E., et al. “FireDock: A Web Server for Fast Interaction Refinement in Molecular Docking.” Nucleic Acids Research, vol. 36, no. Web Server, 19 Apr. 2008, pp. W229–232., doi:10.1093/nar/gkn186.
Schneidman-Duhovny, D., et al. “Patchdock and SymmDock: Servers for Rigid and Symmetric Docking.” Nucleic Acids Research, vol. 33, no. Web Server, 1 Jul. 2005, pp. W363–367., doi:10.1093/nar/gki481.
Liu, Yang, et al. “CB-Dock: A Web Server for Cavity Detection-Guided Protein–Ligand Blind Docking.” Acta Pharmacologica Sinica, vol. 41, no. 1, 1 Jul. 2019, pp. 138–144., doi:10.1038/s41401-019-0228-6.
Guedes, Isabella A., et al. “New Machine Learning and Physics-Based Scoring Functions for Drug Discovery.” Scientific Reports, vol. 11, no. 1, 4 Feb. 2021, doi:10.1038/s41598-021-82410-1.
Santos, Karina B., et al. “Highly Flexible Ligand Docking: Benchmarking of the Dockthor Program on the Leads-Pep Protein–Peptide Data Set.” Journal of Chemical Information and Modeling, vol. 60, no. 2, 10 Jan. 2020, pp. 667–683., doi:10.1021/acs.jcim.9b00905.
De Magalhães, Camila Silva, et al. “A Dynamic Niching Genetic Algorithm Strategy for Docking Highly Flexible Ligands.” Information Sciences, vol. 289, 24 Dec. 2014, pp. 206–224., doi:10.1016/j.ins.2014.08.002.
Kochnev, Yuri, et al. “Webina: An Open-Source Library and Web App That Runs Autodock Vina Entirely in the Web Browser.” Bioinformatics, vol. 36, no. 16, 19 Aug. 2020, pp. 4513–4515., doi:10.1093/bioinformatics/btaa579.
Morris, Garrett M., et al. “AUTODOCK4 And AutoDockTools4: Automated Docking with Selective Receptor Flexibility.” Journal of Computational Chemistry, vol. 30, no. 16, 27 Apr. 2009, pp. 2785–2791., doi:10.1002/jcc.21256.
Peterson, Bianca, et al. “Drug Bioavailability Enhancing Agents of Natural Origin (Bioenhancers) That Modulate Drug Membrane Permeation and Pre-Systemic Metabolism.” Pharmaceutics, vol. 11, no. 1, 16 Jan. 2019, p. 33., doi:10.3390/pharmaceutics11010033.
Dudhatra, Ghanshyam B., et al. “A Comprehensive Review on Pharmacotherapeutics of Herbal Bioenhancers.” The Scientific World Journal, vol. 2012, 17 Sept. 2012, pp. 1–33., doi:10.1100/2012/637953.
Singh, Durg Vijay, et al. “A Plausible Explanation for Enhanced Bioavailability of P-Gp Substrates in Presence of Piperine: Simulation for next Generation of P-GP Inhibitors.” Journal of Molecular Modeling, vol. 19, no. 1, 4 Aug. 2012, pp. 227–238., doi:10.1007/s00894-012-1535-8.
Jin, Mi Sun, et al. “Crystal Structure of the Multidrug Transporter P-Glycoprotein from Caenorhabditis Elegans.” Nature, vol. 490, no. 7421, 23 Oct. 2012, pp. 566–569., doi:10.1038/nature11448.
Ghuman, Jamie, et al. “Structural Basis of the Drug-Binding Specificity of Human Serum Albumin.” Journal of Molecular Biology, vol. 353, no. 1, 14 Oct. 2005, pp. 38–52., doi:10.1016/j.jmb.2005.07.075.
Petitpas, Isabelle, et al. “Crystal Structure Analysis of Warfarin Binding to Human Serum Albumin.” Journal of Biological Chemistry, vol. 276, no. 25, 22 Jun. 2001, pp. 22804–22809., doi:10.1074/jbc.m100575200.
Szewczyk, Paul, et al. “Snapshots of Ligand Entry, Malleable Binding and Induced Helical Movement in P-Glycoprotein.” Acta Crystallographica Section D Biological Crystallography, vol. 71, no. 3, 2015, pp. 732–741., doi:10.1107/s1399004715000978.
Kim, Youngjin, and Jue Chen. “Molecular Structure of Human P-Glycoprotein in the ATP-Bound, Outward-Facing Conformation.” Science, vol. 359, no. 6378, 2018, pp. 915–919., doi:10.1126/science.aar7389.
Ghuman, Jamie, et al. “Structural Basis of the Drug-Binding Specificity of Human Serum Albumin.” Journal of Molecular Biology, vol. 353, no. 1, 2005, pp. 38–52., doi:10.1016/j.jmb.2005.07.075.
Schönfeld, Dorian L., et al. “The 1.8-Å Crystal Structure of α1-Acid Glycoprotein (Orosomucoid) Solved by UV Rip Reveals the Broad Drug-Binding Activity of This Human Plasma Lipocalin.” Journal of Molecular Biology, vol. 384, no. 2, 2008, pp. 393–405., doi:10.1016/j.jmb.2008.09.020.
Petitpas, Isabelle, et al. “Crystal Structure Analysis of Warfarin Binding to Human Serum Albumin.” Journal of Biological Chemistry, vol. 276, no. 25, 2001, pp. 22804–22809., doi:10.1074/jbc.m100575200.
Ghuman, Jamie, et al. “Structural Basis of the Drug-Binding Specificity of Human Serum Albumin.” Journal of Molecular Biology, vol. 353, no. 1, 2005, pp. 38–52., doi:10.1016/j.jmb.2005.07.075.
Jackson, Scott M., et al. “Structural Basis of Small-Molecule Inhibition of Human Multidrug Transporter ABCG2.” Nature Structural & Molecular Biology, vol. 25, no. 4, 2018, pp. 333–340., doi:10.1038/s41594-018-0049-1.
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