Marine Carotenoids As Potential Drug Target Against Pcsk9: In Silicon And Admet Approaches
Abstract
Background: Cardiovascular diseases (CVDs) remain the leading cause of mortality worldwide, with hypercholesterolemia representing a primary modifiable risk factor. Proprotein convertase subtilisin/kexin type 9 (PCSK9) is a serine protease enzyme primarily synthesized in the liver that plays an essential regulatory role in cholesterol homeostasis. PCSK9 binds to the low-density lipoprotein receptor (LDL-R), promoting its lysosomal degradation and thereby inhibiting the clearance of LDL from the bloodstream. This mechanism results in elevated LDL cholesterol levels, contributing to atherosclerosis, coronary artery disease, and stroke. While monoclonal antibodies targeting PCSK9 have demonstrated clinical efficacy, their limitations—including high costs and parenteral administration—necessitate the discovery of orally bioavailable small-molecule inhibitors. Marine natural products have emerged as a promising source of bioactive compounds. This study aims to evaluate Eckol (EKL), a phlorotannin isolated from brown algae, as a potential small-molecule inhibitor against PCSK9 using comprehensive in silico molecular docking and ADMET profiling approaches.
Materials and Methods: The three-dimensional bioactive conformation of Eckol was constructed using the Sybyl-X1.3/SKETCH module and energy-minimized using the Tripos force field with Gasteiger-Hückel atomic charges. The co-crystal structure of PCSK9 (PDB ID: 6u26) was retrieved from the RCSB Protein Data Bank and prepared using the biopolymer module of SYBYL-X 1.3, with energy minimization performed according to the Powell algorithm. Molecular docking simulations were conducted using the Surflex-Dock module of Sybyl-X1.3. ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) properties were predicted using SwissADME and pkCSM web servers.
Results: Molecular docking revealed that Eckol successfully docked into the active site of PCSK9 with high binding affinity. The cumulative docking scores (C-scores) for Eckol against PCSK9 were 6.84 and 5.93, with a robust D-score of -111.84. Graphical analysis demonstrated that Eckol penetrates deeply into the binding domain, establishing interactions with key amino acid residues including A328, S329, P331, T335, R357, C358, V460, A463, A467, I474, and R476. Notably, seven hydrogen bond interactions were observed with residues S329, C358, R357, A463, R458, I474, and R476. ADMET profiling indicated favorable physicochemical properties, compliance with Lipinski's Rule of Five, and a promising safety profile with no predicted AMES toxicity or hepatotoxicity concerns.
Conclusion: The integrated molecular docking and ADMET analyses position Eckol as a highly promising, orally viable small-molecule inhibitor of PCSK9. The compound demonstrates strong binding affinity, targeted interaction with clinically validated catalytic residues, and a favorable pharmacokinetic safety profile. These findings warrant further experimental validation through in vitro assays using HepG2 hepatic cell lines to quantify LDL receptor upregulation and fluorescent LDL uptake, followed by in vivo efficacy studies in appropriate animal models.
References
2. Petrilli, W.L., et al., From screening to targeted degradation: strategies for the discovery and optimization of small molecule ligands for PCSK9. Cell chemical biology, 2020. 27(1): p. 32-40. e3.
3. Zhang, Z., et al., Design and synthesis of pyrimidinone and pyrimidinedione inhibitors of dipeptidyl peptidase IV. Journal of medicinal chemistry, 2011. 54(2): p. 510-524.
4. Jain, A.N., Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine. J. Med. Chem., 2003. 46(4): p. 499-511.
5. Case, D.A., et al., AMBER 9. University of California, San Francisco, 2006. 45.
6. Powell, M.J., A fast algorithm for nonlinearly constrained optimization calculations, in Numerical analysis. 1978, Springer. p. 144-157.
7. Chohan, T.A., et al., Molecular modeling studies to characterize N-phenylpyrimidin-2-amine selectivity for CDK2 and CDK4 through 3D-QSAR and molecular dynamics simulations. Molecular BioSystems, 2016. 12(4): p. 1250-1268.
8. Rehman, K., et al., Taxifolin prevents postprandial hyperglycemia by regulating the activity of α‐amylase: Evidence from an in vivo and in silico studies. Journal of cellular biochemistry, 2019. 120(1): p. 425-438.
9. Chohan, T.A., et al., Molecular simulation studies on the binding selectivity of 2-anilino-4-(thiazol-5-yl)-pyrimidines in complexes with CDK2 and CDK7. Molecular BioSystems, 2016. 12(1): p. 145-161.
10. Chohan, T.A., et al., Phytochemical profiling, antioxidant and antiproliferation potential of Euphorbia milii var.: Experimental analysis and in-silico validation. Saudi journal of biological sciences, 2020. 27(11): p. 3025-3034.
11. Aziz, M., et al., Phytochemical, pharmacological, and In-silico molecular docking studies of Strobilanthes glutinosus Nees: An unexplored source of bioactive compounds. South African Journal of Botany, 2022. 147: p. 618-627.
12. Jain, A.N., Scoring noncovalent protein-ligand interactions: a continuous differentiable function tuned to compute binding affinities. Journal of computer-aided molecular design, 1996. 10(5): p. 427-440.
13. Kuzmich, N., et al., PCSK9 as a Target for Development of a New Generation of Hypolipidemic Drugs. Molecules, 2022. 27(2): p. 434.
14. World Health Organization. (2021). Cardiovascular diseases (CVDs) fact sheet. WHO, Geneva
15. Sabatine, M.S., Giugliano, R.P., Keech, A.C., et al. (2017). Evolocumab and clinical outcomes in patients with cardiovascular disease. New England Journal of Medicine, 376(18), 1713-1722.
16. Kazi, D.S., Penko, J., Coxson, P.G., et al. (2019). Cost-effectiveness of alirocumab: A post-hoc analysis of the ODYSSEY OUTCOMES trial from the payer perspective. Circulation, 140(11), 907-915.
17. 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, 42717.
18. Pires, D.E.V., 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.
19. Manach, C., Scalbert, A., Morand, C., Rémésy, C., & Jiménez, L. (2004). Polyphenols: Food sources and bioavailability. American Journal of Clinical Nutrition, 79(5), 727-747.
20. Dima, C., Assadpour, E., Dima, S., & Jafari, S.M. (2020). Bioavailability of nutraceuticals: Role of the food matrix, processing conditions, the gastrointestinal tract, and nanodelivery systems. Comprehensive Reviews in Food Science and Food Safety, 19(3), 954-994.
21. Gammone, M.A., & D'Orazio, N. (2015). Anti-obesity activity of the marine carotenoid fucoxanthin. Marine Drugs, 13(4), 2196-2214.
22. Kim, D.K., & Kim, K.H. (2018). Dieckol inhibits PCSK9 expression and enhances LDLR expression in HepG2 cells. Journal of Functional Foods, 49, 132-139.
23. Wijesekara, I., Yoon, N.Y., & Kim, S.K. (2010). Phlorotannins from Ecklonia cava: Potential anti-diabetic and anti-obesity agents. Journal of Functional Foods, 2(4), 247-253.
24. Li, Y.X., Wijesekara, I., Li, Y., & Kim, S.K. (2011). Phlorotannins as bioactive agents from brown algae. Process Biochemistry, 46(12), 2219-2224.
25. Lipinski, C.A., Lombardo, F., Dominy, B.W., & Feeney, P.J. (2001). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews, 46(1-3), 3-26.
26. Lagace, T.A. (2014). PCSK9 and LDLR degradation: Regulatory mechanisms in circulation and in cells. Current Opinion in Lipidology, 25(5), 387-393.
27. Seidah, N.G., & Prat, A. (2012). The biology and therapeutic targeting of the proprotein convertases. Nature Reviews Drug Discovery, 11(5), 367-383.
28. Roth, E.M., & Davidson, M.H. (2018). PCSK9 inhibitors: Mechanism of action, efficacy, and safety. Reviews in Cardiovascular Medicine, 19(S1), S11-S22.
29. Zhang, Y., & Chen, X. (2021). Small molecule PCSK9 inhibitors: Advances and perspectives. European Journal of Medicinal Chemistry, 224, 113712.
30. Kang, M.C., Wijesinghe, W.A.J.P., Lee, S.H., et al. (2013). Dieckol isolated from brown seaweed Ecklonia cava attenuates type II diabetes in db/db mouse model. Food and Chemical Toxicology, 53, 294-298.
