Discovery of the Glycogen Phosphorylase-Modulating Activity of a Resveratrol Glucoside by Using a Virtual Screening Protocol Optimized for Solvation Effects

Abstract

The identification of natural products that can modulate blood glucose levels is of great interest as it can possibly facilitate the utilization of mild interventions such as herbal medicine or functional foods in the treatment of chronic diseases like diabetes. One of the established drug targets for antihyperglycemic therapy is glycogen phosphorylase. To evaluate the glycogen phosphorylase inhibitory properties of an in-house compound collection consisting to a large extent of natural products, a stepwise virtual and experimental screening protocol was devised and implemented. The fact that the active site of glycogen phosphorylase is highly hydrated emphasized that a methodological aspect needed to be efficiently addressed prior to an in silico evaluation of the compound collection. The effect of water molecules on docking calculations was regarded as a key parameter in terms of virtual screening protocol optimization. Statistical analysis of 125 structures of glycogen phosphorylase and solvent mapping focusing on the active site hydration motif in combination with a retrospective screening revealed the importance of a set of 29 crystallographic water molecules for achieving high enrichment as to the discrimination between active compounds and inactive decoys. The scaling of Van der Waals radii of system atoms had an additional effect on screening performance. Having optimized the in silico protocol, a prospective evaluation of the in-house compound collection derived a set of 18 top-ranked natural products that were subsequently evaluated in vitro for their activity as glycogen phosphorylase inhibitors. Two phenolic glucosides with glycogen phosphorylase-modulating activity were identified, whereas the most potent compound affording mid-micromolar inhibition was a glucosidic derivative of resveratrol, a stilbene well-known for its wide range of biological activities. Results show the possible phytotherapeutic and nutraceutical potential of products common in the Mediterranean countries, such as red wine and Vitis products in general or green raw salads and herbal preparations, where such compounds are abundant.

Key words

virtual screening - glycogen phosphorylase - solvation effects - hydration mapping - diabetes - docking-scoring - trans-resveratrol glucoside - tachioside

• References

• 1 Oikonomakos N. Glycogen phosphorylase as a molecular target for type 2 diabetes therapy. Curr Protein Pept Sci 2002; 3: 561-586
• 2 Chrysina E. The prototype of glycogen phosphorylase. Mini Rev Med Chem 2010; 10: 1093-1101
• 3 Somsák L, Czifrák K, Tóth M, Bokor E, Chrysina E, Alexacou K, Hayes J, Tiraidis C, Lazoura E, Leonidas D, Zographos S, Oikonomakos N. New inhibitors of glycogen phosphorylase as potential antidiabetic agents. Curr Med Chem 2008; 15: 2933-2983
• 4 Chrysina E, Chajistamatiou A, Chegkazi M. From structure-based to knowledge-based drug design through x-ray protein crystallography: sketching glycogen phosphorylase binding sites. Curr Med Chem 2011; 18: 2620-2629
• 5 Praly J, Vidal S. Inhibition of glycogen phosphorylase in the context of type 2 diabetes, with focus on recent inhibitors bound at the active site. Mini Rev Med Chem 2010; 10: 1102-1126
• 6 Nagy V, Felföldi N, Kónya B, Praly J, Docsa T, Gergely P, Chrysina E, Tiraidis C, Kosmopoulou M, Alexacou K, Konstantakaki M, Leonidas D, Zographos S, Oikonomakos N, Kozmon S, Tvaroška I, Somsák L. N-(4-Substituted-benzoyl)-N′-(β-d-glucopyranosyl)ureas as inhibitors of glycogen phosphorylase: Synthesis and evaluation by kinetic, crystallographic, and molecular modelling methods. Bioorg Med Chem 2012; 20: 1801-1816
• 7 Klebe G. Foundation Review: Virtual ligand screening: strategies, perspectives and limitations. Drug Discov Today 2006; 11: 580-596
• 8 Shoichet B. Virtual screening of chemical libraries. Nature 2004; 432: 862-865
• 9 Therrien E, Weill N, Tomberg A, Corbeil C, Lee D, Moitessier N. Docking ligands into flexible and solvated macromolecules. 7. Impact of protein flexibility and water molecules on docking-based virtual screening accuracy. J Chem Inf Model 2014; 54: 3198-3210
• 10 Elokely K, Doerksen R. Docking challenge: protein sampling and molecular docking performance. J Chem Inf Model 2013; 53: 1934-1945
• 11 Liu J, He X, Zhang J. Improving the scoring of protein-ligand binding affinity by including the effects of structural water and electronic polarization. J Chem Inf Model 2013; 53: 1306-1314
• 12 Kumar A, Zhang K. Investigation on the effect of key water molecules on docking performance in CSARdock exercise. J Chem Inf Model 2013; 53: 1880-1892
• 13 Gregoriou M, Noble M, Watson K, Garman E, Krulle T, de la Fuente C, Fleet G, Oikonomakos N, Johnson L. The structure of a glycogen phosphorylase glucopyranose spirohydantoin complex at 1.8 A resolution and 100 K: the role of the water structure and its contribution to binding. Protein Sci 1998; 7: 915-927
• 14 Abel R, Young T, Farid R, Berne B, Friesner R. Role of the active-site solvent in the thermodynamics of factor Xa ligand binding. J Am Chem Soc 2008; 130: 2817-2831
• 15 Young T, Abel R, Kim B, Berne B, Friesner R. Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding. Proc Natl Acad Sci U S A 2007; 104: 808-813
• 16 SZMAP 1.2.0.7 2013. OpenEye Scientific Software, Santa Fe, NM, USA. Available online: http://www.eyesopen.com
• 17 Sun H, Zhao L, Peng S, Huang N. Incorporating replacement free energy of binding-site waters in molecular docking. Proteins 2014; 82: 1765-1776
• 18 de Beer S, Vermeulen N, Oostenbrink C. The role of water molecules in computational drug design. Curr Top Med Chem 2010; 10: 55-66
• 19 Ross G, Morris G, Biggin P. Rapid and accurate prediction and scoring of water molecules in protein binding sites. PLoS One 2012; 7: e32036
• 20 Lenselink E, Beuming T, Sherman W, van Vlijmen H, IJzerman A. Selecting an optimal number of binding site waters to improve virtual screening enrichments against the adenosine A2A receptor. J Chem Inf Model 2014; 23: 1737-1746
• 21 Barreca M, Iraci N, Manfroni G, Gaetani R, Guercini C, Sabatini S, Tabarrini O, Cecchetti V. Accounting for target flexibility and water molecules by docking to ensembles of target structures: the HCV NS5B palm site I inhibitors case study. J Chem Inf Model 2014; 54: 481-497
• 22 Sun H, Zhao L, Peng S, Huang N. Incorporating replacement free energy of binding-site waters in molecular docking. Proteins 2014; 82: 1765-1776
• 23 Huang S, Zou X. Glide: Ensemble docking of multiple protein structures: considering protein structural variations in molecular docking. Proteins 2007; 66: 399-421
• 24 Sanschagrin P, Kuhn L. Cluster analysis of consensus water sites in thrombin and trypsin shows conservation between serine proteases and contributions to ligand specificity. Protein Sci 1998; 10: 2054-2064
• 25 Huang N, Shoichet B, Irwin J. Benchmarking sets for molecular docking. J Med Chem 2006; 49: 6789-6801
• 26 Hawkins P, Warren G, Skillman A, Nicholls A. How to do an evaluation: pitfalls and traps. J Comput Aided Mol Des 2008; 22: 179-190
• 27 Pearlman D, Charifson P. Improved scoring of ligand-protein interactions using OWFEG free energy grids. J Med Chem 2001; 44: 502-511
• 28 Nicholls A. What do we know and when do we know it?. J Comput Aided Mol Des 2008; 22: 239-255
• 29 Truchon J, Bayly C. Evaluating virtual screening methods: good and bad metrics for the “early recognition” problem. J Chem Inf Model 2007; 47: 488-508
• 30 Friesner R, Banks J, Murphy R, Halgren T, Klicic J, Mainz D, Repasky M, Knoll E, Shelley M, Perry J, Shaw D, Francis P, Shenkin P. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 2004; 47: 1739-1749
• 31 Halgren T, Murphy R, Friesner R, Beard H, Frye L, Pollard W, Banks J. Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J Med Chem 2004; 47: 1750-1759
• 32 Kazantzoglou G, Magiatis P, Panoutsopoulos G, Skaltsounis AL. Dorycnioside, a new phenylbutanone glucoside from Dorycnium pentaphyllum subsp. herbaceum . Z Naturforsch C 2004; 59: 23-26
• 33 Habtemariam S, Varghese G. The antidiabetic therapeutic potential of dietary polyphenols. Curr Pharm Biotechnol 2014; 15: 391-400
• 34 Babu P, Liu D, Gilbert E. Recent advances in understanding the anti-diabetic actions of dietary flavonoids. J Nutr Biochem 2013; 24: 1777-1789
• 35 Williamson G. Possible effects of dietary polyphenols on sugar absorption and digestion. Mol Nutr Food Res 2013; 57: 48-57
• 36 Kato A, Nasu N, Takebayashi K, Adachi I, Minami Y, Sanae F, Asano N, Watson A, Nash R. Structure-activity relationships of flavonoids as potential inhibitors of glycogen phosphorylase. J Agric Food Chem 2008; 25: 4469-4473
• 37 Su H, Hung L, Chen J. Resveratrol, a red wine antioxidant, possesses an insulin-like effect in streptozotocin-induced diabetic rats. Am J Physiol Endocrinol Metab 2006; 290: E1339-E1346
• 38 Kantsadi A, Apostolou A, Theofanous S, Stravodimos G, Kyriakis E, Gorgogietas V, Chatzileontiadou D, Pegiou K, Skamnaki V, Stagos D, Kouretas D, Psarra A, Haroutounian S, Leonidas D. Biochemical and biological assessment of the inhibitory potency of extracts from vinification byproducts of Vitis vinifera extracts against glycogen phosphorylase. Food Chem Toxicol 2014; 67: 35-43
• 39 Sovak M. Grape Extract, Resveratrol, and Its Analogs: A Review. J Med Food 2001; 4: 93-105
• 40 Kim HJ, Chang EJ, Cho SH, Chung SK, Park HD, Choi SW. Antioxidative activity of resveratrol and its derivatives isolated from seeds of Paeonia lactiflora . Biosci Biotechnol Biochem 2002; 66: 1990-1993
• 41 Eldridge M, Murray C, Auton T, Paolini G, Mee R. Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. J Comput Aided Mol Des 1997; 11: 425-445
• 42 Melpidou A, Oikonomakos N. Effect of glucose-6-P on the catalytic and structural properties of glycogen phosphorylase a. FEBS Lett 1983; 154: 105-110
• 43 Oikonomakos N, Kontou M, Zographos S, Watson K, Johnson L, Bichard C, Fleet G, Acharya K. N-acetyl-beta-D-glucopyranosylamine: a potent T-state inhibitor of glycogen phosphorylase. A comparison with alpha-D-glucose. Protein Sci 1995; 4: 2469-2477
• 44 Saheki S, Takeda A, Shimazu T. Assay of inorganic phosphate in the mild pH range, suitable for measurement of glycogen phosphorylase activity. Anal Biochem 1985; 148: 277-281