Computational screening, synthesis and neuroprotective evaluation of small molecule for the treatment of alzheimer's disease

Authors

DOI:

https://doi.org/10.17533/udea.vitae.v31n3a354271

Keywords:

Alzheimer’s disease, Beta secretase, cyclin-dependent kinase 5, drug-like, gamma secretase, neurodegenerative, pin1

Abstract

BACKGROUND: Current treatments for Alzheimer’s disease primarily address symptoms, as no definitive therapeutic targets have been identified.
OBJECTIVES:
This study aims to conduct a virtual screening of small molecules and synthesize and evaluate one of the most promising candidates for Alzheimer’s therapy.
METHODS:
Using AutoDock Vina, compounds with drug-like properties were docked against key proteins implicated in Alzheimer's pathology: β-Secretase, γ-Secretase, Pin1, and Cdk5. The molecule with the highest in silico affinity (PubChem ID: 84378305) was synthesized and evaluated experimentally. Cytotoxicity and neuroprotective effects were assessed using the MTT assay in the presence of the Aβ25-35 peptide.
RESULTS: Four candidate molecules showed strong binding affinity, ranging from -6.8 to -9.1 kcal/mol.
The results showed that when SK-N-SH cells were simultaneously treated with Aß25-35 peptide (5 µM) and compound 84378305 (0,1 µM), the molecule exhibited significant neuroprotection (33%) after the 48 h of incubation.
CONCLUSION: Findings indicate that this lead compound exhibits potential neuroprotective activity, highlighting its promise as a candidate for further development in Alzheimer’s disease treatment.

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References

Lukiw WJ. MicroRNA (miRNA) Complexity in Alzheimer’s Disease (AD). Biology. 2023;12(6):788. DOI: https://doi.org/10.3390/biology12060788

Xu J, Wang F, Guo J, Xu C, Cao Y, Fang Z, et al.Pharmacological Mechanisms Underlying the Neuroprotective Effects of Alpinia oxyphylla Miq. on Alzheimer’s Disease. Int J Mol Sci. 2020;21(6):2071. PMID: 32197305; PMCID: PMC7139528. DOI: https://doi.org/10.3390/ijms21062071

Guzior N, Ćkowska AW, Panek D, Malawska B. Recent Development of Multifunctional Agents as Potential Drug Candidates for the Treatment of Alzheimer’s Disease. Curr Med Chem. 2015;22(3):373–404. DOI: https://doi.org/10.2174/0929867321666141106122628

Ambure P, Kar S, Roy K. Pharmacophore mapping-based virtual screening followed by molecular docking studies in search of potential acetylcholinesterase inhibitors as anti-Alzheimer's agents. Biosystems. 2014;116:10–20. DOI: https://doi.org/10.1016/j.biosystems.2013.12.002

Amanatkar HR, Papagiannopoulos B, Grossberg GT. Analysis of recent failures of disease modifying therapies in Alzheimer’s disease suggesting a new methodology for future studies. Expert Rev Neurother. 2017;17(1):7–16. DOI: https://doi.org/10.1080/14737175.2016.1194203

Liu J, Yin F, Guo L, Zhang J, Zidichouski J. Molecular mechanisms of geniposide and genipin against Alzheimer’s disease. In: Bioactive Nutraceuticals and Dietary Supplements in Neurological and Brain Disease. Elsevier; 2014. p. 221–27. DOI: https://doi.org/10.1016/B978-0-12-411462-3.00024-2

Sang Z, Qiang X, Li Y, Yuan W, Liu Q, Shi Y, et al.Design, synthesis and evaluation of scutellarein-O-alkylamines as multifunctional agents for the treatment of Alzheimer's disease. Eur J Med Chem. 2015;94:348–66. DOI: https://doi.org/10.1016/j.ejmech.2015.02.063

Pastorino L, Lu KP. Pathogenic mechanisms in Alzheimer's disease. Eur J Pharmacol. 2006;545(1):29–38. DOI: https://doi.org/10.1016/j.ejphar.2006.06.078

Reitz C, Mayeux R. Alzheimer disease: Epidemiology, diagnostic criteria, risk factors and biomarkers. Biochem Pharmacol. 2014;88(4):640–51. DOI: https://doi.org/10.1016/j.bcp.2013.12.024

Thummayot S, Tocharus C, Pinkaew D, Viwatpinyo K, Sringarm K, Tocharus J. Neuroprotective effect of purple rice extract and its constituent against amyloid beta-induced neuronal cell death in SK-N-SH cells. NeuroToxicology. 2014;45:149–58. DOI: https://doi.org/10.1016/j.neuro.2014.10.010

Thummayot S, Tocharus C, Pinkaew D, Viwatpinyo K, Sringarm K, Tocharus J. Neuroprotective effect of purple rice extract and its constituent against amyloid beta-induced neuronal cell death in SK-N-SH cells. NeuroToxicology. 2014;45(Supplement C):149–58. DOI: https://doi.org/10.1016/j.neuro.2014.10.010

Abdalla A. Tau protein as a target for Alzheimer’s disease management. Saudi Pharm J. 2015;23(4):405–6. DOI: https://doi.org/10.1016/j.jsps.2015.01.017

Liu Y, Yang X, Lei Q, Li Z, Hu J, Wen X, et al.PEG–PEI/siROCK2 Protects Against Aβ42-Induced Neurotoxicity in Primary Neuron Cells for Alzheimer Disease. Cell Mol Neurobiol. 2015;35(6):841–48. DOI: https://doi.org/10.1007/s10571-015-0178-6

Lublin AL, Link CD. Alzheimer’s Disease Drug Discovery: In-vivo screening using C. elegans as a model for β-amyloid peptide-induced toxicity. Drug Discov Today Technol. 2013;10(1):e115–9. DOI: https://doi.org/10.1016/j.ddtec.2012.02.002

Scarpini E, Schelterns P, Feldman H. Treatment of Alzheimer's disease; current status and new perspectives. Lancet Neurol. 2003;2(9):539–47. DOI: https://doi.org/10.1016/S1474-4422(03)00502-7

Kumar A, Singh A, Ekavali. A review on Alzheimer's disease pathophysiology and its management: an update. Pharmacol Rep. 2015;67(2):195–203. DOI: https://doi.org/10.1016/j.pharep.2014.09.004

Rampa A, Tarozzi A, Mancini F, Pruccoli L, Di Martino R, Gobbi S, et al.Naturally Inspired Molecules as Multifunctional Agents for Alzheimer’s Disease Treatment. Molecules. 2016;21(5):643. DOI: https://doi.org/10.3390/molecules21050643

Waqar M, Batool S. In silico analysis of binding of neurotoxic venom ligands with acetylcholinesterase for therapeutic use in treatment of Alzheimer’s disease. J Theor Biol. 2015;372:107–17. DOI: https://doi.org/10.1016/j.jtbi.2015.02.028

Sasidharan S, Gosu V, Tripathi T, Saudagar P. Molecular Dynamics Simulation to Study Protein Conformation and Ligand Interaction. In: Saudagar P, Tripathi T, editors. Protein Folding Dynamics and Stability. Springer; 2023. p. 6. DOI: https://doi.org/10.1007/978-981-99-2079-2_6

Roy S, Kumar A, Baig MH, Masařík M, Provazník I. Virtual screening, ADMET profiling, molecular docking and dynamics approaches to search for potent selective natural molecules based inhibitors against metallothionein-III to study Alzheimer’s disease. Methods. 2015;83:105–10. DOI: https://doi.org/10.1016/j.ymeth.2015.04.021

Trott O, Olson AJ. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading. J Comput Chem. 2010;31(2):455–71. DOI: https://doi.org/10.1002/jcc.21334

O'Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR. Open Babel: An open chemical toolbox. J Cheminform. 2011;3(1):33. DOI: https://doi.org/10.1186/1758-2946-3-33

Leeson P. Drug discovery: Chemical beauty contest. Nature. 2012;481(7382):455–6. DOI: https://doi.org/10.1038/481455a

Veber DF, Johnson SR, Cheng H-Y, Smith BR, Ward KW, Kopple KD. Molecular Properties That Influence the Oral Bioavailability of Drug Candidates. J Med Chem. 2002;45(12):2615–23. DOI: https://doi.org/10.1021/jm020017n

Ghose AK, Viswanadhan VN, Wendoloski JJ. A Knowledge-Based Approach in Designing Combinatorial or Medicinal Chemistry Libraries for Drug Discovery. 1. A Qualitative and Quantitative Characterization of Known Drug Databases. J Comb Chem. 1999;1(1):55–68. DOI: https://doi.org/10.1021/cc9800071

Pájaro-Castro N, Flechas MC, Ocazionez R, Stashenko E, Olivero-Verbel JT. Potential interaction of components from essential oils with dengue virus proteins. BLaCPMA. 2015;14(3):141–55.

Holt PA, Chaires JB, Trent JO. Molecular Docking of Intercalators and Groove-Binders to Nucle

Jung HA, Ali MY, Choi RJ, Jeong HO, Chung HY, Choi JS. Kinetics and molecular docking studies of fucosterol and fucoxanthin, BACE1 inhibitors from brown algae Undaria pinnatifida and Ecklonia stolonifera. Food Chem Toxicol. 2016;89:104-111. DOI: http://dx.doi.org/10.1016/j.fct.2016.01.014

Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem. 2009;30(16):2785-2791. DOI: https://doi.org/10.1002/jcc.21256

Ramachandran V, Padmanaban E, Ponnusamy K, Naidu S, Natesan M. Pharmacophore based virtual screening for identification of marine bioactive compounds as inhibitors against macrophage infectivity potentiator (Mip) protein of Chlamydia trachomatis. RSC Adv. 2016;6(23):18946-18957. DOI: https://doi.org/10.1039/c5ra24999f

Driver JA, Zhou XZ, Lu KP. Pin1 dysregulation helps to explain the inverse association between cancer and Alzheimer's disease. BBA-Gen Subjects. 2015;1850(10):2069-2076. DOI: https://doi.org/10.1016/j.bbagen.2014.12.025

Chen CH, Li W, Sultana R, You MH, Kondo A, Shahpasand K, et al.Pin1 cysteine-113 oxidation inhibits its catalytic activity and cellular function in Alzheimer’s disease. Neurobiol Dis. 2015;76:13-23. DOI: https://doi.org/10.1016/j.nbd.2014.12.027

De Strooper B. Aph-1, Pen-2, and Nicastrin with presenilin generate an active γ-secretase complex. Neuron. 2003;38(1):9-12. DOI: https://doi.org/10.1016/S0896-6273(03)00205-8

Wolfe MS. Inhibition and modulation of γ-secretase for Alzheimer’s disease. Neurotherapeutics. 2008;5(3):391-398. DOI: https://doi.org/10.1016/j.nurt.2008.05.010

Ekiri Vaidyanathan Raman A, Krishnan K, Maurya A, Sarkar N. In silico screening of drugs to find potential gamma-secretase inhibitors using pharmacophore modeling, QSAR and molecular docking studies. Comb Chem High T Scr. 2014;17(9):770-780

Chávez-Gutiérrez L, Tolia A, Maes E, Li T, Wong PC, de Strooper B. Glu332 in the Nicastrin ectodomain is essential for γ-secretase complex maturation but not for its activity. J Biol Chem. 2008;283(29):20096-20105. DOI: https://doi.org/10.1074/jbc.M803040200

Crump C. Target identification and mechanism of gamma-secretase modulators and inhibitors as Alzheimer's disease therapeutics [dissertation]. CORNELL UNIVERSITY; 2013. DOI: http://search.proquest.com/docview/1444628197?accountid=49118

Puentes NC, Orozco DP, Díaz FC. Curcumin analogues as promissory compounds for inhibition of β-secretase, γ-secretase and GSK-3β implicated in Alzheimer’s disease: In silico study. Biomed Pharmacol J. 2022;15(1).

Shelton CC, Zhu L, Chau D, Yang L, Wang R, Djaballah H, et al.Modulation of γ-secretase specificity using small molecule allosteric inhibitors. Proc Natl Acad Sci U S A. 2009;106(48):20228-20233. DOI: https://doi.org/10.1073/pnas.091075710

Ghosh AK, Brindisi M, Tang J. Developing β-secretase inhibitors for treatment of Alzheimer’s disease. J Neurochem. 2012;120:71-83. DOI: https://doi.org/10.1111/j.1471-4159.2011.07476.x

Yi Mok N, Chadwick J, Kellett KAB, Hooper NM, Johnson AP, Fishwick CWG. Discovery of novel non-peptide inhibitors of BACE-1 using virtual high-throughput screening. Bioorg Med Chem Lett. 2009;19(23):6770-6774. DOI: https://doi.org/10.1016/j.bmcl.2009.09.103

Choi RJ, Roy A, Jung HJ, Ali MY, Min B-S, Park CH, et al.BACE1 molecular docking and anti-Alzheimer's disease activities of ginsenosides. J Ethnopharmacol. 2016;190:219-230. DOI: https://doi.org/10.1016/j.jep.2016.06.013

Bhakta HK, Park CH, Yokozawa T, Min B-S, Jung HA, Choi JS. Kinetics and molecular docking studies of loganin, morroniside and 7-O-galloyl-d-sedoheptulose derived from Corni fructus as cholinesterase and β-secretase 1 inhibitors. Arch Pharm Res. 2016;39(6):794-805. DOI: https://doi.org/10.1007/s12272-016-0745-5

Rueeger H, Lueoend R, Rogel O, Rondeau J-M, Möbitz H, Machauer R, et al.Discovery of cyclic sulfone hydroxyethylamines as potent and selective β-site APP-cleaving enzyme 1 (BACE1) inhibitors: Structure-based design and in vivo reduction of amyloid β-peptides. J Med Chem. 2012;55(7):3364-3386. DOI: https://doi.org/10.1021/jm300069y

Ahn JS, Radhakrishnan ML, Mapelli M, Choi S, Tidor B, Cuny GD, et al.Defining Cdk5 ligand chemical space with small molecule inhibitors of tau phosphorylation. Chem Biol. 2005;12(7):811-823. DOI: https://doi.org/10.1016/j.chembiol.2005.05.011

Tsai L-H, Lee M-S, Cruz J. Cdk5, a therapeutic target for Alzheimer’s disease? Biochim Biophys Acta. 2004;1697(1–2):137-142. DOI: https://doi.org/10.1016/j.bbapap.2003.11.019

Lau L-F, Seymour PA, Sanner MA, Schachter JB. Cdk5 as a drug target for the treatment of Alzheimer’s disease. J Mol Neurosci. 2002;19(3):267-273. DOI: https://doi.org/10.1385/jmn:19:3:267

Helal CJ, Sanner MA, Cooper CB, Gant T, Adam M, Lucas JC, et al.Discovery and SAR of 2-aminothiazole inhibitors of cyclin-dependent kinase 5/p25 as a potential treatment for Alzheimer’s disease. Bioorg Med Chem Lett. 2004;14(22):5521-5525. DOI: https://doi.org/10.1016/j.bmcl.2004.09.006

Bajda M, Guzior N, Ignasik M, Malawska B. Multi-target-directed ligands in Alzheimer's disease treatment. Curr Med Chem. 2011;18(32):4949-4975. DOI: https://doi.org/10.2174/092986711797535245

Khan H, Ullah H, Aschner M, Cheang WS, Akkol EK. Neuroprotective effects of quercetin in Alzheimer's disease. Biomolecules. 2019;10(1):59. DOI: https://doi.org/10.3390/biom10010059

Zhang ZQ, Hölscher C. GIP has neuroprotective effects in Alzheimer and Parkinson's disease models. Peptides. 2020 Mar;125:170184. DOI: https://doi.org/10.1016/j.peptides.2019.170184

Moon J-Y, Kim E-S, Choi S-J, Kim J-I, Choi N-S, Lee K, et al.Protective effect of the ethyl acetate-fraction of methanol extract of Ophiophogon japonicus on amyloid beta peptide-induced cytotoxicity in PC12 cells. J Life Sci. 2019;29(2):173-180. DOI: https://doi.org/10.5352/JLS.2019.29.2.173

Shin M, Liu QF, Choi B, Shin C, Lee B, Yuan C, et al.Neuroprotective effects of limonene (+) against Aβ42-induced neurotoxicity in a Drosophila model of Alzheimer's disease. Biol Pharm Bull. 2020 Mar 1;43(3):409-417. DOI: https://doi.org/10.1248/bpb.b19-00495

Chen XY, Du YF, Chen L. Neuropeptides exert neuroprotective effects in Alzheimer's disease models. Neurochem Int. 2020 Jun;138:104771. DOI: https://doi.org/10.3389/fnmol.2018.00493

Yi S, Chen S, Xiang J, Tan J, Huang K, Zhang H, et al.Genistein exerts a cell-protective effect via Nrf2/HO-1/PI3K signaling in Ab25-35-induced Alzheimer's disease models in vitro. Folia Histochem Cytobiol. 2021;59(1):49-56. DOI: https://doi.org/10.5603/FHC.a2021.0006. PMID: 33605427.

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Published

18-12-2024

How to Cite

Pajaro-Castro, N., Torres-Sierra, , E., Cortes-Gonzalez, E., Paternina , M., Camacho , E., & Blanco, P. (2024). Computational screening, synthesis and neuroprotective evaluation of small molecule for the treatment of alzheimer’s disease. Vitae, 31(3). https://doi.org/10.17533/udea.vitae.v31n3a354271

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Pharmacology and Toxicology