Abstract
Alzheimer’s disease (AD) is a chronic neurodegenerative disorder characterized by progressive degeneration in the brain and shrinking (atrophy) of the brain size with the association of multiple factors/targets. The traditional “one medicine, one target” approach tends to be insufficient due to the complexity of AD. Till now, no established strategy for the treatment of AD is available. Therefore, it is of prime importance to catch the promising targets from the reported several targets. Target fishing here plays a pivotal role in a drug discovery without prior knowledge about their role in AD. Computational approaches are now considered an integral component of drug discovery with exceptional theoretical assumptions over the decades. Ligand and structure-based in silico approaches are able to provide a rational solution to the answer of target fishing. With this background, the objective of the book chapter was mainly to describe the powerful in silico tools for the optimization of the target based on literature reports and in silico tools available for target prioritization.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Abbreviations
- ACAT:
-
Acyl cholesterol acyltransferase
- ACHE:
-
Acetylcholinesterase
- AD:
-
Alzheimer’s disease
- APP:
-
β-amyloid precursor protein
- Aβ:
-
Amyloid β
- BCHE:
-
Butyrylcholinesterase
- cAMP:
-
Cyclic adenosine monophosphate
- cGMP:
-
Cyclic guanosine monophosphate
- CLU:
-
Clusterin
- COX-2:
-
Cyclooxygenase-2
- CR1:
-
Complement receptor 1
- GABA:
-
γ-aminobutyric acid
- GPCRs:
-
G-protein-coupled receptors
- GRN:
-
Progranulin
- HIF-1α:
-
Hypoxia-inducible factor 1α subunits
- HMG:
-
3-hydroxy-3-methylglutaryl l
- LRRK2:
-
Leucine-rich repeat kinase 2
- MAO-B:
-
7 mono amino oxidase-B
- MAPT:
-
Microtubule-associated protein tau
- NMDA:
-
Glutamate N-methyl D-aspartate
- PICALM:
-
Phosphatidylinositol-binding clathrin assembly protein α-synuclein
- PSEN1:
-
Presenilin 1
- PSEN2:
-
Presenilin 2
References
Ab Ghani NS, Ramlan EI, Firdaus-Raih M (2019) Drug ReposER: a web server for predicting similar amino acid arrangements to known drug binding interfaces for potential drug repositioning. Nucleic Acids Res 47:W350–W356. https://doi.org/10.1093/nar/gkz391
Acar Cevik U, Saglik BN, Levent S et al (2019) Synthesis and ACHE-inhibitory activity of new benzimidazole derivatives. Molecules 24:861. https://doi.org/10.3390/molecules24050861
Adeowo FY, Elrashedy AA, Ejalonibu MA et al (2022) Pharmacophore mapping of the crucial mediators of acetylcholinesterase and butyrylcholinesterase dual inhibition in Alzheimer’s disease. Mol Divers 26:2761–2774. https://doi.org/10.1007/s11030-022-10377-w
Agatonovic-Kustrin S, Kettle C, Morton DW (2018) A molecular approACH in drug development for Alzheimer’s disease. Biomed Pharmacother 106:553–565. https://doi.org/10.1016/j.biopha.2018.06.147
Alam J, Scheper W (2016) Targeting neuronal MAPK14/p38α activity to modulate autophagy in the Alzheimer disease brain. Autophagy 12:2516–2520. https://doi.org/10.1080/15548627.2016.1238555
AlFadly ED, Elzahhar PA, Tramarin A et al (2019) Tackling neuroinflammation and cholinergic deficit in Alzheimer’s disease: multi-target inhibitors of cholinesterases, cyclooxygenase-2 and 15-lipoxygenase. Eur J Med Chem 167:161–186. https://doi.org/10.1016/j.ejmech.2019.02.012
Anand P, Singh B (2013) A review on cholinesterase inhibitors for Alzheimer’s disease. Arch Pharm Res 36:375–399. https://doi.org/10.1007/s12272-013-0036-3
Apostolova LG (2016) Alzheimer disease. Continuum (Minneap Minn) 22:419–434. https://doi.org/10.1212/CON.0000000000000307
Armstrong RA (2019) Risk factors for alzheimer disease. [Factores de riesgo Para la enfermedad de Alzheimer]. Brain Nerve 57:87–105
Avery EE, Baker LD, Asthana S (1997) Potential role of muscarinic agonists in Alzheimerʼs disease. Drugs Aging 11:450–459. https://doi.org/10.2165/00002512-199711060-00004
Ayaz M, Wadood A, Sadiq A et al (2022) In-silico evaluations of the isolated phytosterols from polygonum hydropiper L against BACE1 and MAO drug targets. J Biomol Struct Dyn 40:10230–10238. https://doi.org/10.1080/07391102.2021.1940286
Baig MH, Ahmad K, Rabbani G et al (2017) Computer aided drug design and its application to the development of potential drugs for neurodegenerative disorders. Curr Neuropharmacol 16:740–748. https://doi.org/10.2174/1570159x15666171016163510
Balaraman Y, Limaye AR, Levey AI, Srinivasan S (2006) Glycogen synthase kinase 3β and Alzheimer’s disease: pathophysiological and therapeutic significance. Cell Mol Life Sci 63:1226–1235. https://doi.org/10.1007/s00018-005-5597-y
Baloni P, Arnold M, Buitrago L et al (2022) Multi-Omic analyses characterize the ceramide/sphingomyelin pathway as a therapeutic target in Alzheimer’s disease. Commun Biol 5:1074. https://doi.org/10.1038/s42003-022-04011-6
Barthold D, Joyce G, Ferido P et al (2020) Pharmaceutical treatment for Alzheimer’s disease and related dementias: utilization and disparities. J Alzheimers Dis 76:579–589. https://doi.org/10.3233/JAD-200133
Binder J, Ursu O, Bologa C et al (2022) MACHine learning prediction and tau-based screening identifies potential Alzheimer’s disease genes relevant to immunity. Commun Biol 5:125. https://doi.org/10.1038/s42003-022-03068-7
Blaikie L, Kay G, Kong Thoo Lin P (2019) Current and emerging therapeutic targets of alzheimer’s disease for the design of multi-target directed ligands. Medchemcomm 10:2052–2072. https://doi.org/10.1039/c9md00337a
Braak H, Del Tredici K (2012) Where, when, and in what form does sporadic Alzheimer’s disease begin? Curr Opin Neurol 25:708–714. https://doi.org/10.1097/WCO.0b013e32835a3432
Campanella C, Pace A, Caruso Bavisotto C et al (2018) Heat shock proteins in Alzheimer’s disease: role and targeting. Int J Mol Sci 19:2603. https://doi.org/10.3390/ijms19092603
Campion D, Dumanchin C, Hannequin D et al (1999) Early-onset autosomal dominant Alzheimer disease: prevalence, genetic heterogeneity, and mutation spectrum. Am J Hum Genet 65:664–670. https://doi.org/10.1086/302553
Carradori S, Ortuso F, Petzer A et al (2018) Design, synthesis and biochemical evaluation of novel multi-target inhibitors as potential anti-parkinson agents. Eur J Med Chem 143:1543–1552. https://doi.org/10.1016/j.ejmech.2017.10.050
Caterina MH, Kelly TD (2012) α7 nicotinic acetylcholine receptors in Alzheimer’s disease: neuroprotective, neurotrophic or both? Curr Drug Targets 13:613–622. https://doi.org/10.2174/138945012800398973
Cereto-Massagué A, Ojeda MJ, Valls C et al (2015) Tools for in silico target fishing. Methods 71:98–103. https://doi.org/10.1016/j.ymeth.2014.09.006
Chang R, Yee K-L, Sumbria RK (2017) Tumor necrosis factor α inhibition for Alzheimer’s disease. J Cent Nerv Syst Dis 9:117957351770927. https://doi.org/10.1177/1179573517709278
Chowdhury S, Kumar S (2020) Inhibition of BACE1, MAO-B, cholinesterase enzymes, and anti-amyloidogenic potential of selected natural phytoconstituents: multi-target-directed ligand approACH. J Food Biochem 45:e13571. https://doi.org/10.1111/jfbc.13571
Ciriaco F, Gambacorta N, Trisciuzzi D, Nicolotti O (2022) PLATO: a predictive drug discovery web platform for efficient target fishing and bioactivity profiling of small molecules. Int J Mol Sci 23:5245. https://doi.org/10.3390/ijms23095245
Clevleand Clinic (2023) A genome-wide positioning systems platform for Alzheimer’s disease. In: Clevleand clin learn res inst. https://alzgps.lerner.ccf.org/. Accessed 10 Jan 2023
Czarnecka K, Girek M, Maciejewska K et al (2018) New cyclopentaquinoline hybrids with multifunctional capacities for the treatment of Alzheimer’s disease. J Enzyme Inhib Med Chem 33:158–170. https://doi.org/10.1080/14756366.2017.1406485
Czarnecka K, Girek M, Kręcisz P et al (2019) Discovery of new cyclopentaquinoline analogues as multifunctional agents for the treatment of Alzheimer’s disease. Int J Mol Sci 20:498. https://doi.org/10.3390/ijms20030498
Daina A, Michielin O, Zoete V (2017) SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci Rep 7:42717. https://doi.org/10.1038/srep42717
Dhamodharan G, Mohan CG (2022) MACHine learning models for predicting the activity of ACHE and BACE1 dual inhibitors for the treatment of Alzheimer’s disease. Mol Divers 26:1501–1517. https://doi.org/10.1007/s11030-021-10282-8
Du H, Guo L, Fang F et al (2008) Cyclophilin D deficiency attenuates mitochondrial and neuronal perturbation and ameliorates learning and memory in Alzheimer’s disease. Nat Med 14:1097–1105. https://doi.org/10.1038/nm.1868
Duara R, Lopez-Alberola RF, Barker WW et al (1993) A comparison of familial and sporadic alzheimer’s disease. Neurology 43:1377–1384. https://doi.org/10.1212/wnl.43.7.1377
Duyckaerts C, Delatour B, Potier MC (2009) Classification and basic pathology of Alzheimer disease. Acta Neuropathol 118:5–36. https://doi.org/10.1007/s00401-009-0532-1
Ejaz SA, Fayyaz A, Mahmood HMK et al (2022) 4-Phthalimidobenzenesulfonamide derivatives as acetylcholinesterase and butyrylcholinesterase inhibitors: DFTs, 3D-QSAR, ADMET, and molecular dynamic simulation. Neurodegener Dis. https://doi.org/10.1159/000527516
Fang J, Wang L, Li Y et al (2017) AlzhCPI: a knowledge base for predicting chemical-protein interactions towards Alzheimer’s disease. PloS One 12:1–16. https://doi.org/10.1371/journal.pone.0178347
Fereidoonnezhad M, Mostoufi A, Eskandari M et al (2018) Multitarget drug design, molecular docking and PLIF studies of novel Tacrine−Coumarin hybrids for the treatment of Alzheimer’s disease. Iran J Pharm Res 17:1217–1228. https://doi.org/10.22037/ijpr.2018.2308
Fronza MG, Baldinotti R, Martins MC et al (2019) Rational design, cognition and neuropathology evaluation of QTC-4-MeOBnE in a streptozotocin-induced mouse model of sporadic Alzheimer’s disease. Sci Rep 9:1–14. https://doi.org/10.1038/s41598-019-43532-9
Furlan V, Konc J, Bren U (2018) Inverse molecular docking as a novel approach to study anticarcinogenic and anti-neuroinflammatory effects of curcumin. Molecules 23:3351. https://doi.org/10.3390/molecules23123351
Galati S, Di Stefano M, Martinelli E et al (2021) Recent advances in in silico target fishing. Molecules 26:1–18. https://doi.org/10.3390/molecules26175124
Gao H, Jiang Y, Zhan J, Sun Y (2021) Pharmacophore-based drug design of ACHE and BCHE dual inhibitors as potential anti-Alzheimer’s disease agents. Bioorg Chem 114:105149. https://doi.org/10.1016/j.bioorg.2021.105149
García-Osta A, Cuadrado-Tejedor M, García-Barroso C et al (2012) Phosphodiesterases as therapeutic targets for Alzheimer’s disease. ACS Chem Nerosci 3:832–844. https://doi.org/10.1021/cn3000907
Gasparini F, Di Paolo T, Gomez-Mancilla B (2013) Metabotropic glutamate receptors for Parkinson’s disease therapy. Parkinsons Dis 2013:196028. https://doi.org/10.1155/2013/196028
Gazova Z, Soukup O, Sepsova V et al (2017) Multi-target-directed therapeutic potential of 7-methoxytacrine-adamantylamine heterodimers in the Alzheimer’s disease treatment. Biochim Biophys Acta Mol basis Dis 1863:607–619. https://doi.org/10.1016/j.bbadis.2016.11.020
Ghamari N, Dastmalchi S, Zarei O et al (2020) In silico and in vitro studies of two non-imidazole multiple targeting agents at histamine H3 receptors and cholinesterase enzymes. Chem Biol Drug Des 95:279–290. https://doi.org/10.1111/cbdd.13642
González-Naranjo P, Pérez-Macias N, Campillo NE et al (2014) Cannabinoid agonists showing BuChE inhibition as potential therapeutic agents for Alzheimer’s disease. Eur J Med Chem 73:56–72. https://doi.org/10.1016/j.ejmech.2013.11.026
Hagenow J, Hagenow S, Grau K et al (2020) Reversible small molecule inhibitors of MAO a and MAO B with anilide motifs. Drug Des Devel Ther 14:371–393. https://doi.org/10.2147/DDDT.S236586
Haghighijoo Z, Akrami S, Saeedi M et al (2020) N-Cyclohexylimidazo[1,2-a]pyridine derivatives as multi-target-directed ligands for treatment of Alzheimer’s disease. Bioorg Chem 103:104146. https://doi.org/10.1016/j.bioorg.2020.104146
Hansen KB, Yi F, Perszyk RE et al (2018) Structure, function, and allosteric modulation of NMDA receptors. J Gen Physiol 150:1081–1105. https://doi.org/10.1085/jgp.201812032
Hepnarova V, Korabecny J, Matouskova L et al (2018) The concept of hybrid molecules of tacrine and benzyl quinolone carboxylic acid (BQCA) as multifunctional agents for Alzheimer’s disease. Eur J Med Chem 150:292–306. https://doi.org/10.1016/j.ejmech.2018.02.083
Herrmann N (2007) Treatment of moderate to severe Alzheimer’s disease: rationale and trial design. Can J Neurol Sci 34:S103–S108. https://doi.org/10.1017/S0317167100005667
Hoozemans J, Rozemuller J, van Haastert E et al (2008) Cyclooxygenase-1 and -2 in the different stages of Alzheimers disease pathology. Curr Pharm Des 14:1419–1427. https://doi.org/10.2174/138161208784480171
Hopkins AL (2008) Network pharmacology: the next paradigm in drug discovery. Nat Chem Biol 4:682–690. https://doi.org/10.1038/nchembio.118
Horton W, Sood A, Peerannawar S et al (2017) Synthesis and application of β-carbolines as novel multi-functional anti-Alzheimer’s disease agents. Bioorg Med Chem Lett 27:232–236. https://doi.org/10.1016/j.bmcl.2016.11.067
Hu Y, Zhou G, Zhang C et al (2019) Identify compounds’ target against Alzheimer’s disease based on in-silico ApproACH. Curr Alzheimer Res 16:193–208. https://doi.org/10.2174/1567205016666190103154855
Hur J-Y (2022) γ-Secretase in Alzheimer’s disease. Exp Mol Med 54:433–446. https://doi.org/10.1038/s12276-022-00754-8
Işık A, Acar Çevik U, Karayel A et al (2022) Synthesis and molecular modelling of thiadizole based hydrazone derivatives as acetylcholinesterase and butyrylcholinesterase inhibitory activities. SAR QSAR Environ Res 33:193–214. https://doi.org/10.1080/1062936X.2022.2041723
Jayadev S (2022) Genetics of Alzheimer disease. Continuum (Minneap Minn) 28:852–871. https://doi.org/10.1212/CON.0000000000001125
Jayapalan S, Natarajan J (2013) The role of CDK5 and GSK3B kinases in hyperphosphorylation of microtubule associated protein tau (MAPT) in Alzheimer’s disease. Bioinformation 9:1023–1030. https://doi.org/10.6026/97320630091023
Jellinger KA (1998) The neuropathological diagnosis of Alzheimer disease. J Neural Transm Suppl 5:97–118. https://doi.org/10.1007/978-3-7091-6467-9_9
Jenkins JL, Bender A, Davies JW (2006) In silico target fishing: predicting biological targets from chemical structure. Drug Discov Today Technol 3:413–421. https://doi.org/10.1016/j.ddtec.2006.12.008
Jha NK, Jha SK, Kar R et al (2019) Nuclear factor-kappa β as a therapeutic target for Alzheimer’s disease. J Neurochem 150:113–137. https://doi.org/10.1111/jnc.14687
Jiang Q, Heneka M, Landreth GE (2008) The role of peroxisome proliferator-activated receptor-γ (PPARγ) in Alzheimer’s disease. CNS Drugs 22:1–14. https://doi.org/10.2165/00023210-200822010-00001
Jyothi P, Yellamma K (2016) Molecular docking studies on the therapeutic targets of Alzheimer’s disease (ACHE and BCHE) using natural bioactive alkaloids. Int J Pharm Pharm Sci 8:108–112. https://doi.org/10.22159/ijpps.2016v8i12.14833
Kargbo RB (2021) Sigma-1 and Sigma-2 receptor modulators as potential therapeutics for Alzheimer’s disease. ACS Med Chem Lett 12:178–179. https://doi.org/10.1021/acsmedchemlett.1c00002
Khan NA, Khan I, Abid SMA et al (2017) Quinolinic carboxylic acid derivatives as potential multi-target compounds for neurodegeneration: monoamine oxidase and cholinesterase inhibition. Med Chem 14:74–85. https://doi.org/10.2174/1573406413666170525125231
Khan S, Barve KH, Kumar MS (2020) Recent advancements in pathogenesis, diagnostics and treatment of Alzheimer’s disease. Curr Neuropharmacol 18:1106–1125. https://doi.org/10.2174/1570159X18666200528142429
Kilic B, Bardakkaya M, Ilıkcı Sagkan R et al (2023) New thiourea and benzamide derivatives of 2-aminothiazole as multi-target agents against Alzheimer’s disease: design, synthesis, and biological evaluation. Bioorg Chem 131:106322. https://doi.org/10.1016/j.bioorg.2022.106322
Kim EK, Choi E-J (2010) Pathological roles of MAPK signaling pathways in human diseases. Biochim Biophys Acta Mol basis Dis 1802:396–405. https://doi.org/10.1016/j.bbadis.2009.12.009
Kirova A-M, Bays RB, Lagalwar S (2015) Working memory and executive function decline across Normal aging, mild cognitive impairment, and Alzheimer’s disease. Biomed Res Int 2015:1–9. https://doi.org/10.1155/2015/748212
Knez D, Sova M, Košak U, Gobec S (2017) Dual inhibitors of cholinesterases and monoamine oxidases for Alzheimer’s disease. Future Med Chem 9:811–832. https://doi.org/10.4155/fmc-2017-0036
Kohelová E, Peřinová R, Maafi N et al (2019) Derivatives of the β-crinane Amaryllidaceae alkaloid haemanthamine as multi-target directed ligands for Alzheimer’s disease. Molecules 24:1307. https://doi.org/10.3390/molecules24071307
Komatović K, Matošević A, Terzić-Jovanović N et al (2022) 4-Aminoquinoline-based Adamantanes as potential anticholinesterase agents in symptomatic treatment of Alzheimer’s disease. Pharmaceutics 14:1305. https://doi.org/10.3390/pharmaceutics14061305
Korabecny J, Andrs M, Nepovimova E et al (2015) 7-methoxytacrine-p-anisidine hybrids as novel dual binding site acetylcholinesterase inhibitors for Alzheimer’s disease treatment. Molecules 20:22084–22101. https://doi.org/10.3390/molecules201219836
Kores K, Lešnik S, Bren U et al (2019) Discovery of novel potential human targets of resveratrol by inverse molecular docking. J Chem Inf Model 59:2467–2478. https://doi.org/10.1021/acs.jcim.8b00981
Kumar S, Tyagi YK, Kumar M, Kumar S (2020) Synthesis of novel 4-methylthiocoumarin and comparison with conventional coumarin derivative as a multi-target-directed ligand in Alzheimer’s disease. 3 Biotech 10:509. https://doi.org/10.1007/s13205-020-02481-1
Kurochkin IV, Guarnera E, Berezovsky IN (2018) Insulin-degrading enzyme in the fight against Alzheimer’s disease. Trends Pharmacol Sci 39:49–58. https://doi.org/10.1016/j.tips.2017.10.008
Lakra N, Matore BW, Banjare P et al (2022) Pharmacophore based virtual screening of cholinesterase inhibitors: search of new potential drug candidates as antialzheimer agents. In Silico Pharmacol 10:18. https://doi.org/10.1007/s40203-022-00133-1
Lalut J, Karila D, Dallemagne P, Rochais C (2017) Modulating 5-HT 4 and 5-HT 6 receptors in Alzheimer’s disease treatment. Future Med Chem 9:781–795. https://doi.org/10.4155/fmc-2017-0031
Lamie PF, Abdel-Fattah MM, Philoppes JN (2022) Design and synthesis of new indole drug candidates to treat Alzheimer’s disease and targeting neuro-inflammation using a multi-target-directed ligand (MTDL) strategy. J Enzyme Inhib Med Chem 37:2660–2678. https://doi.org/10.1080/14756366.2022.2126464
Lebois EP, Thorn C, Edgerton JR et al (2018) Muscarinic receptor subtype distribution in the central nervous system and relevance to aging and Alzheimer’s disease. Neuropharmacology 136:362–373. https://doi.org/10.1016/j.neuropharm.2017.11.018
Lee J, Jun M (2019) Dual BACE1 and cholinesterase inhibitory effects of phlorotannins from ecklonia cava-an in vitro and in silico study. Mar Drugs 17:1–15. https://doi.org/10.3390/md17020091
Lee H, Ogawa O, Zhu X et al (2004) Aberrant expression of metabotropic glutamate receptor 2 in the vulnerable neurons of Alzheimer’s disease. Acta Neuropathol 107:365–371. https://doi.org/10.1007/s00401-004-0820-8
Lee S, Youn K, Lim GT et al (2018) In silico docking and in vitro approACHEs towards BACE1 and cholinesterases inhibitory effect of citrus flavanones. Molecules 23:1–12. https://doi.org/10.3390/molecules23071509
Leuci R, Brunetti L, Laghezza A et al (2022) A new series of aryloxyacetic acids endowed with multi-target activity towards peroxisome proliferator-activated receptors (PPARs), fatty acid amide hydrolase (FAAH), and acetylcholinesterase (ACHE). Molecules 27:958. https://doi.org/10.3390/molecules27030958
Li H, Gao Z, Kang L et al (2006) TarFisDock: a web server for identifying drug targets with docking approACH. Nucleic Acids Res 34:219–224. https://doi.org/10.1093/nar/gkl114
Li YH, Yu CY, Li XX et al (2018) Therapeutic target database update 2018: enriched resource for facilitating bench-to-clinic research of targeted therapeutics. Nucleic Acids Res 46:D1121–D1127. https://doi.org/10.1093/nar/gkx1076
Li C, Meng P, Zhang B-Z et al (2019) Computer-aided identification of protein targets of four polyphenols in Alzheimer’s disease (AD) and validation in a mouse AD model. J Biomed Res 22:101–112. https://doi.org/10.7555/JBR.32.20180021
Li X, Jia Y, Li J et al (2022) Novel and potent acetylcholinesterase inhibitors for the treatment of Alzheimer’s disease from natural (±)-7,8-Dihydroxy-3-methyl-isochroman-4-one. Molecules 27:3090. https://doi.org/10.3390/molecules27103090
Lima JA, Thiago TW, da Fonseca ACC et al (2020) Geissoschizoline, a promising alkaloid for Alzheimer’s disease: inhibition of human cholinesterases, anti-inflammatory effects and molecular docking. Bioorg Chem 104:104215. https://doi.org/10.1016/j.bioorg.2020.104215
Liu X, Ouyang S, Yu B et al (2010) PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approACH. Nucleic Acids Res 38:5–7. https://doi.org/10.1093/nar/gkq300
Liu X, Gao Y, Peng J et al (2015) TarPred: a web application for predicting therapeutic and side effect targets of chemical compounds. Bioinformatics 31:2049–2051. https://doi.org/10.1093/bioinformatics/btv099
Lo YC, Senese S, Li CM et al (2015) Large-scale chemical similarity networks for target profiling of compounds identified in cell-based chemical screens. PLoS Comput Biol 11:1–23. https://doi.org/10.1371/journal.pcbi.1004153
Lomelino CL, Andring JT, McKenna R (2018) Crystallography and its impact on carbonic anhydrase research. Int J Med Chem 2018:1–21. https://doi.org/10.1155/2018/9419521
Louzada PR, Lima ACP, Mendonca-Silva DL et al (2004) Taurine prevents the neurotoxicity of β-amyloid and glutamate receptor agonists: activation of GABA receptors and possible implications for Alzheimer’s disease and other neurological disorders. FASEB J 18:511–518. https://doi.org/10.1096/fj.03-0739com
Luo H, Zhang P, Cao XH et al (2016) DPDR-CPI, a server that predicts drug positioning and drug repositioning via chemical-protein interactome. Sci Rep 6:1–9. https://doi.org/10.1038/srep35996
Ma XH, Shi Z, Tan C et al (2010) In-silico approACHEs to multi-target drug discovery computer aided multi-target drug design, multi-target virtual screening. Pharm Res 27:739–749. https://doi.org/10.1007/s11095-010-0065-2
Maggiora G, Vogt M, Stumpfe D, Bajorath J (2014) Molecular similarity in medicinal chemistry. J Med Chem 57:3186–3204. https://doi.org/10.1021/jm401411z
Makhoba XH, Viegas C, Mosa RA et al (2020) Potential impact of the multi-target drug approACH in the treatment of some complex diseases. Drug Des Devel Ther 14:3235–3249. https://doi.org/10.2147/DDDT.S257494
Marucci G, Buccioni M, Ben DD et al (2021) Efficacy of acetylcholinesterase inhibitors in Alzheimer’s disease. Neuropharmacology 190:108352. https://doi.org/10.1016/j.neuropharm.2020.108352
Matore BW, Banjare P, Guria T et al (2022a) Oxadiazole derivatives: histone deacetylase inhibitors in anticancer therapy and drug discovery. Eur J Med Chem 5:100058. https://doi.org/10.1016/j.ejmcr.2022.100058
Matore BW, Banjare P, Singh J, Roy PP (2022b) In silico selectivity modeling of pyridine and pyrimidine based CYP11B1 and CYP11B2 inhibitors: a case study. J Mol Graph Model 116:108238. https://doi.org/10.1016/j.jmgm.2022.108238
Mazumder MK, Choudhury S (2019) Tea polyphenols as multi-target therapeutics for Alzheimer’s disease: an in silico study. Med Hypotheses 125:94–99. https://doi.org/10.1016/j.mehy.2019.02.035
Mehrazar M, Hassankalhori M, Toolabi M et al (2020) Design and synthesis of benzodiazepine-1,2,3-triazole hybrid derivatives as selective butyrylcholinesterase inhibitors. Mol Divers 24:997–1013. https://doi.org/10.1007/s11030-019-10008-x
Mendez MF (2017) Early-onset Alzheimer disease. Neurol Clin 35:263–281. https://doi.org/10.1016/j.ncl.2017.01.005
Merighi S, Borea PA, Varani K et al (2022a) Pathophysiological role and medicinal chemistry of A2A adenosine receptor antagonists in Alzheimer’s disease. Molecules 27:2680. https://doi.org/10.3390/molecules27092680
Merighi S, Nigro M, Travagli A et al (2022b) A2A adenosine receptor: a possible therapeutic target for Alzheimer’s disease by regulating NLRP3 inflammasome activity? Int J Mol Sci 23:5056. https://doi.org/10.3390/ijms23095056
Michalska P, Buendia I, Del Barrio L, Leon R (2017) Novel multitarget hybrid compounds for the treatment of Alzheimer’s disease. Curr Top Med Chem 17:1027–1043. https://doi.org/10.2174/1568026616666160927154116
Minhas R, Bansal Y, Bansal G (2020) Inducible nitric oxide synthase inhibitors: a comprehensive update. Med Res Rev 40:823–855. https://doi.org/10.1002/med.21636
Mohs RC, Greig NH (2017) Drug discovery and development: role of basic biological research. Alzheimer’s Dement (N Y) 3:651–657. https://doi.org/10.1016/j.trci.2017.10.005
Murphy MP, Levine H (2010) Alzheimer’s disease and the amyloid-β peptide. J Alzheimers Dis 19:311–323. https://doi.org/10.3233/JAD-2010-1221
Newington JT, Rappon T, Albers S et al (2012) Overexpression of pyruvate dehydrogenase kinase 1 and lactate dehydrogenase a in nerve cells confers resistance to amyloid β and other toxins by decreasing mitochondrial respiration and reactive oxygen species production. J Biol Chem 287:37245–37258. https://doi.org/10.1074/jbc.M112.366195
Oboudiyat C, Glazer H, Seifan A et al (2013) Alzheimer’s disease. Semin Neurol 33:313–329. https://doi.org/10.1055/s-0033-1359319
Oukoloff K, Coquelle N, Bartolini M et al (2019) Design, biological evaluation and X-ray crystallography of nanomolar multifunctional ligands targeting simultaneously acetylcholinesterase and glycogen synthase kinase-3. Eur J Med Chem 168:58–77. https://doi.org/10.1016/j.ejmech.2018.12.063
Panche AN, Chandra S, Diwan AD (2019) Multi-target β-protease inhibitors from andrographis paniculata: in silico and in vitro studies. Plan Theory 8:231. https://doi.org/10.3390/plants8070231
Panek D, Wiȩckowska A, Pasieka A et al (2018) Design, synthesis, and biological evaluation of 2-(benzylamino-2-hydroxyalkyl)isoindoline-1,3-diones derivatives as potential disease-modifying multifunctional anti-Alzheimer agents. Molecules 23:1–15. https://doi.org/10.3390/molecules23020347
Papadatos G, Gaulton A, Hersey A, Overington JP (2015) Activity, assay and target data curation and quality in the ChEMBL database. J Comput Aided Mol Des 29:885–896. https://doi.org/10.1007/s10822-015-9860-5
Parnetti L, Chipi E, Salvadori N et al (2019) Prevalence and risk of progression of preclinical Alzheimer’s disease stages: a systematic review and meta-analysis. Alzheimers Res Ther 11:7. https://doi.org/10.1186/s13195-018-0459-7
Patel H, Lucas X, Bendik I et al (2015) Target fishing by cross-docking to explain polypharmacological effects. ChemMedChem 10:1209–1217. https://doi.org/10.1002/cmdc.201500123
Patel P, Faldu K, Borisa A et al (2022) Insights of valacyclovir in treatment of Alzheimer’s disease: computational docking studies and scopolamine rat model. Curr Neurovasc Res 19:344–357. https://doi.org/10.2174/1567202619666220908125125
Peón A, Li H, Ghislat G et al (2019) MolTarPred: a web tool for comprehensive target prediction with reliability estimation. Chem Biol Drug Des 94:1390–1401. https://doi.org/10.1111/cbdd.13516
Pérez-Nueno VI (2015) Using quantitative systems pharmacology for novel drug discovery. Expert Opin Drug Discov 10:1315–1331. https://doi.org/10.1517/17460441.2015.1082543
Perkovic MN, Strac DS, Tudor L et al (2018) Catechol-O-methyltransferase, cognition and Alzheimer’s disease. Curr Alzheimer Res 15:408–419. https://doi.org/10.2174/1567205015666171212094229
Pinzi L, Tinivella A, Gagliardelli L et al (2021) LigAdvisor: a versatile and user-friendly web-platform for drug design. Nucleic Acids Res 49:W326–W335. https://doi.org/10.1093/nar/gkab385
Praticò D, Zhukareva V, Yao Y et al (2004) 12/15-lipoxygenase is increased in Alzheimer’s disease. Am J Pathol 164:1655–1662. https://doi.org/10.1016/S0002-9440(10)63724-8
PubMed, National Library of Medicine (2023) PubMed database. https://pubmed.ncbi.nlm.nih.gov/. Accessed 12 Jan 2023
Qin Q, Yin Y, Wang Y et al (2020) Gene mutations associated with early onset familial Alzheimer’s disease in China: an overview and current status. Mol Genet Genomic Med 8:1–19. https://doi.org/10.1002/mgg3.1443
Raafat K (2020) Identification of phytochemicals from north African plants for treating Alzheimer’s diseases and of their molecular targets by in silico network pharmacology approach. J Tradit Complement Med 11:268–278. https://doi.org/10.1016/j.jtcme.2020.08.002
Rajmohan R, Reddy PH (2017) Amyloid-beta and phosphorylated tau accumulations cause abnormalities at synapses of Alzheimer’s disease neurons. J Alzheimers Dis 57:975–999. https://doi.org/10.3233/JAD-160612
Reis J, Cagide F, Valencia ME et al (2018) Multi-target-directed ligands for Alzheimer’s disease: discovery of chromone-based monoamine oxidase/cholinesterase inhibitors. Eur J Med Chem 158:781–800. https://doi.org/10.1016/j.ejmech.2018.07.056
Reisberg B, Franssen EH, Bobinski M et al (1996) Overview of methodologic issues for pharmacologic trials in mild, moderate, and severe Alzheimer’s disease. Int Psychogeriatr 8:159–193. https://doi.org/10.1017/S1041610296002566
Riazimontazer E, Sadeghpour H, Nadri H et al (2019) Design, synthesis and biological activity of novel tacrine-isatin Schiff base hybrid derivatives. Bioorg Chem 89:103006. https://doi.org/10.1016/j.bioorg.2019.103006
Rognan D (2010) Structure-based approACHEs to target fishing and ligand profiling. Mol Inform 29:176–187. https://doi.org/10.1002/minf.200900081
Rossi M, Freschi M, De Camargo NL et al (2021) Sustainable drug discovery of multi-target-directed ligands for Alzheimer’s disease. J Med Chem 64:4972–4990. https://doi.org/10.1021/acs.jmedchem.1c00048
Rullo M, Catto M, Carrieri A et al (2019) Chasing ChEs-MAO B multi-targeting 4-Aminomethyl-7-Benzyloxy-2H-Chromen-2-ones. Molecules 24:4507. https://doi.org/10.3390/molecules24244507
Salentin S, Schreiber S, Haupt VJ et al (2015) PLIP: fully automated protein-ligand interaction profiler. Nucleic Acids Res 43:W443–W447. https://doi.org/10.1093/nar/gkv315
Sánchez-Cruz N, Medina-Franco JL (2021) Epigenetic target fishing with accurate MACHine learning models. J Med Chem 64:8208–8220. https://doi.org/10.1021/acs.jmedchem.1c00020
Sang Z, Wang K, Shi J et al (2020) Apigenin-rivastigmine hybrids as multi-target-directed ligands for the treatment of Alzheimer’s disease. Eur J Med Chem 187:111958. https://doi.org/10.1016/j.ejmech.2019.111958
Scheltens P, Blennow K, Breteler MMB et al (2016) Alzheimer’s disease. Lancet 388:505–517. https://doi.org/10.1016/S0140-6736(15)01124-1
Schomburg KT, Bietz S, Briem H et al (2014) Facing the challenges of structure-based target prediction by inverse virtual screening. J Chem Inf Model 54:1676–1686. https://doi.org/10.1021/ci500130e
Shahid M, Azfaralariff A, Law D et al (2021) Comprehensive computational target fishing approACH to identify Xanthorrhizol putative targets. Sci Rep 11:1–11. https://doi.org/10.1038/s41598-021-81026-9
Shaikh S, Pavale G, Dhavan P et al (2021) Design, synthesis and evaluation of dihydropyranoindole derivatives as potential cholinesterase inhibitors against Alzheimer’s disease. Bioorg Chem 110:104770. https://doi.org/10.1016/j.bioorg.2021.104770
Shibuya Y, Chang CC, Chang T-Y (2015) ACAT1/SOAT1 as a therapeutic target for Alzheimer’s disease. Future Med Chem 7:2451–2467. https://doi.org/10.4155/fmc.15.161
Shim YJ, Shin MK, Jung J et al (2022) An in-silico approACH to studying a very rare neurodegenerative disease using a disease with higher prevalence with shared pathways and genes: cerebral adrenoleukodystrophy and Alzheimer’s disease. Front Mol Neurosci 15:996698. https://doi.org/10.3389/fnmol.2022.996698
Sivakumar M, Saravanan K, Saravanan V et al (2020) Discovery of new potential triplet acting inhibitor for Alzheimer’s disease via X-ray crystallography, molecular docking and molecular dynamics. J Biomol Struct Dyn 38:1903–1917. https://doi.org/10.1080/07391102.2019.1620128
Sobolova K, Hrabinova M, Hepnarova V et al (2020) Discovery of novel berberine derivatives with balanced cholinesterase and prolyl oligopeptidase inhibition profile. Eur J Med Chem 203:112593. https://doi.org/10.1016/j.ejmech.2020.112593
Spilovska K, Korabecny J, Kral J et al (2013) 7-methoxytacrine-adamantylamine heterodimers as cholinesterase inhibitors in Alzheimer’s disease treatment—synthesis, biological evaluation and molecular modeling studies. Molecules 18:2397–2418. https://doi.org/10.3390/molecules18022397
Spina S, La Joie R, Petersen C et al (2021) Comorbid neuropathological diagnoses in early versus late-onset Alzheimer’s disease. Brain 144:2186–2198. https://doi.org/10.1093/brain/awab099
Velmurugan D, Pachaiappan R, Ramakrishnan C (2020) Recent trends in drug design and discovery. Curr Top Med Chem 20:1761–1770. https://doi.org/10.2174/1568026620666200622150003
Vohora D, Bhowmik M (2012) Histamine H3 receptor antagonists/inverse agonists on cognitive and motor processes: relevance to Alzheimer’s disease, ADHD, schizophrenia, and drug abuse. Front Syst Neurosci 6:72. https://doi.org/10.3389/fnsys.2012.00072
Volkman R, Ben-Zur T, Kahana A et al (2019) Myeloperoxidase deficiency inhibits cognitive decline in the 5XFAD mouse model of Alzheimer’s disease. Front Neurosci 13:990. https://doi.org/10.3389/fnins.2019.00990
Wale N, Karypis G (2009) Target fishing for chemical compounds using target-ligand activity data and ranking based methods. J Chem Inf Model 49:2190–2201. https://doi.org/10.1021/ci9000376
Wang R, Reddy PH (2017) Role of glutamate and NMDA receptors in Alzheimer’s disease. J Alzheimers Dis 57:1041–1048. https://doi.org/10.3233/JAD-160763
Wang JC, Chu PY, Chen CM, Lin JH (2012) idTarget: a web server for identifying protein targets of small chemical molecules with robust scoring functions and a divide-and-conquer docking approACH. Nucleic Acids Res 40:393–399. https://doi.org/10.1093/nar/gks496
Wang L, Ma C, Wipf P et al (2013) TargetHunter: an in silico target identification tool for predicting therapeutic potential of small organic molecules based on chemogenomic database. AAPS J 15:395–406. https://doi.org/10.1208/s12248-012-9449-z
Wang Y, Bryant SH, Cheng T et al (2017) PuBCHEm BioAssay: 2017 update. Nucleic Acids Res 45:D955–D963. https://doi.org/10.1093/nar/gkw1118
Wang F, Wu FX, Li CZ et al (2019) ACID: a free tool for drug repurposing using consensus inverse docking strategy. J Cheminform 11:1–11. https://doi.org/10.1186/s13321-019-0394-z
Wattmo C, Minthon L, Wallin ÅK (2016) Mild versus moderate stages of Alzheimer’s disease: three-year outcomes in a routine clinical setting of cholinesterase inhibitor therapy. Alzheimers Res Ther 8:7. https://doi.org/10.1186/s13195-016-0174-1
Wishart DS, Feunang YD, Guo AC et al (2018) DrugBank 5.0: a major update to the DrugBank database for 2018. Nucleic Acids Res 46:D1074–D1082. https://doi.org/10.1093/nar/gkx1037
World Health Organization (2019) Dementia. https://www.who.int/news-room/fact-sheets/detail/dementia. Accessed 27 Jun 2022
Wu L, Rosa-Neto P, Hsiung G-YR et al (2012) Early-onset familial Alzheimer’s disease (EOFAD). Can J Neurol Sci 39:436–445. https://doi.org/10.1017/S0317167100013949
Wu J, Zhang H, Wang Y et al (2022) From tryptamine to the discovery of efficient multi-target directed ligands against cholinesterase-associated neurodegenerative disorders. Front Pharmacol 13:1036030. https://doi.org/10.3389/fphar.2022.1036030
Xiang Z, Ho L, Yemul S et al (2002) Cyclooxygenase-2 promotes amyloid plaque deposition in a mouse model of Alzheimer’s disease neuropathology. Gene Expr 10:271–278. https://doi.org/10.3727/000000002783992352
Xie L, Xie L, Bourne PE (2011) Structure-based systems biology for analyzing off-target binding. Curr Opin Struct Biol 21:189–199. https://doi.org/10.1016/j.sbi.2011.01.004
Xie H, Wen H, Zhang D et al (2017) Designing of dual inhibitors for GSK-3β and CDK5: virtual screening and in vitro biological activities study. Oncotarget 8:18118–18128. https://doi.org/10.18632/oncotarget.15085
Yang A, Yu Q, Ju H et al (2020a) Design, synthesis and biological evaluation of Xanthone derivatives for possible treatment of Alzheimer’s disease based on multi-target strategy. Chem Biodivers 17:e2000442. https://doi.org/10.1002/cbdv.202000442
Yang GX, Huang Y, Zheng LL et al (2020b) Design, synthesis and evaluation of diosgenin carbamate derivatives as multitarget anti-Alzheimer’s disease agents. Eur J Med Chem 187:111913. https://doi.org/10.1016/j.ejmech.2019.111913
Yao H, Uras G, Zhang P et al (2021) Discovery of novel tacrine-pyrimidone hybrids as potent dual ACHE/GSK-3 inhibitors for the treatment of Alzheimer’s disease. J Med Chem 64:7483–7506. https://doi.org/10.1021/acs.jmedchem.1c00160
Yıldız M, Bingul M, Zorlu Y et al (2022) Dimethoxyindoles based thiosemicarbazones as multi-target agents; synthesis, crystal interactions, biological activity and molecular modeling. Bioorg Chem 120:105647. https://doi.org/10.1016/j.bioorg.2022.105647
Youdim MBH, Bakhle YS (2006) Monoamine oxidase: isoforms and inhibitors in Parkinson’s disease and depressive illness. Br J Pharmacol 147:S287. https://doi.org/10.1038/sj.bjp.0706464
Yu Z, Dong W, Wu S et al (2020) Identification of ovalbumin-derived peptides as multi-target inhibitors of ACHE, BCHE, and BACE1. J Sci Food Agric 100:2648–2655. https://doi.org/10.1002/jsfa.10295
Zaib S, Munir R, Younas MT et al (2021) Hybrid quinoline-thiosemicarbazone therapeutics as a new treatment opportunity for Alzheimer’s disease-synthesis, in vitro cholinesterase inhibitory potential and computational modeling analysis. Molecules 26:6573. https://doi.org/10.3390/molecules26216573
Zhou Y, Fang J, Bekris LM et al (2021) AlzGPS: a genome-wide positioning systems platform to catalyze multi-omics for Alzheimer’s drug discovery. Alzheimers Res Ther 13:24. https://doi.org/10.1186/s13195-020-00760-w
Zhu J, Yang H, Chen Y et al (2018) Synthesis, pharmacology and molecular docking on multifunctional tacrine-ferulic acid hybrids as cholinesterase inhibitors against Alzheimer’s disease. J Enzyme Inhib Med Chem 33:496–506. https://doi.org/10.1080/14756366.2018.1430691
Ziegler S, Pries V, Hedberg C, Waldmann H (2013) Target identification for small bioactive molecules: finding the needle in the haystack. Angew Chem Int Ed Engl 52:2744–2792. https://doi.org/10.1002/anie.201208749
Zipp F, Waiczies S, Aktas O et al (2007) Impact of HMG-CoA reductase inhibition on brain pathology. Trends Pharmacol Sci 28:342–349. https://doi.org/10.1016/j.tips.2007.05.001
Author information
Authors and Affiliations
Corresponding authors
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2023 The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.
About this chapter
Cite this chapter
Murmu, A. et al. (2023). Role of Target Fishing in Discovery of Novel Anti-Alzheimer’s Agents: In Silico Applications. In: Kumar, D., Patil, V.M., Wu, D., Thorat, N. (eds) Deciphering Drug Targets for Alzheimer’s Disease. Springer, Singapore. https://doi.org/10.1007/978-981-99-2657-2_12
Download citation
DOI: https://doi.org/10.1007/978-981-99-2657-2_12
Published:
Publisher Name: Springer, Singapore
Print ISBN: 978-981-99-2656-5
Online ISBN: 978-981-99-2657-2
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)