Abstract
Alzheimer’s disease (AD) is a neurodegenerative illness that affects the brain and is linked to cognitive decline, memory problems, and behavioral changes. It is highly prevalent in the elderly, with a constantly growing number of new cases worldwide. In affluent nations with aging populations, AD has been a major source of economic and social problems. As a result, the discovery of novel treatment methods for this disease is now crucial. With advances in research on the pathological mechanisms of AD, many new drug targets have been proposed and focused on in-depth investigations. AD has now been identified as a multifactorial disease. Therefore, the goal of therapeutic drug development has largely been directed at acting on multiple therapeutic targets of the disease at the same time. Computational modeling is a potent and robust method in the discovery and development of pharmacological drugs. Recently, this approach has played an increasingly important role in the search for new medications to treat AD. Computational modeling helps conserve experimental resources and dramatically accelerates advances in drug research. In this chapter, various computational modeling methods utilized in designing multi-targeting inhibitors as anti-Alzheimer agents would be described.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Masters CL, Bateman R, Blennow K et al (2015) Alzheimer’s disease. Nat Rev Dis Primers 1(1):15056
Jain P, Jadhav HR (2013) Quantitative structure activity relationship analysis of aminoimidazoles as BACE-I inhibitors. Med Chem Res 22(4):1740–1746
Richard AA (2019) Risk factors for Alzheimer’s disease. Folia Neuropathol 57(2):87–105
Vogel JW, Iturria-Medina Y, Strandberg OT et al (2020) Spread of pathological tau proteins through communicating neurons in human Alzheimer’s disease. Nat Commun 11(1):2612
Hampel H, Mesulam MM, Cuello AC et al (2018) The cholinergic system in the pathophysiology and treatment of Alzheimer’s disease. Brain 141(7):1917–1933
Kinney JW, Bemiller SM, Murtishaw AS et al (2018) Inflammation as a central mechanism in Alzheimer’s disease. Alzheimers Dement (N Y) 4(1):575–590
Cheng X, Zhang L, Lian Y-J (2015) Molecular targets in Alzheimer’s disease: from pathogenesis to therapeutics. Biomed Res Int 2015:760758
Athar T, Al Balushi K, Khan SA (2021) Recent advances on drug development and emerging therapeutic agents for Alzheimer’s disease. Mol Biol Rep 48(7):5629–5645
Kabir MT, Sufian MA, Uddin MS et al (2019) NMDA receptor antagonists: repositioning of memantine as a multitargeting agent for Alzheimer’s therapy. Curr Pharm Des 25(33):3506–3518
Cummings J, Lee G, Ritter A et al (2020) Alzheimer’s disease drug development pipeline: 2020. Alzheimers Dement (N Y) 6(1):e12050
Zhang P, Xu S, Zhu Z et al (2019) Multi-target design strategies for the improved treatment of Alzheimer’s disease. Eur J Med Chem 176:228–247
Kurz A, Perneczky R (2011) Novel insights for the treatment of Alzheimer’s disease. Prog Neuro-Psychopharmacol Biol Psychiatry 35(2):373–379
Salomone S, Caraci F, Leggio GM et al (2012) New pharmacological strategies for treatment of Alzheimer’s disease: focus on disease modifying drugs. Br J Clin Pharmacol 73(4):504–517
Hardy J (2009) The amyloid hypothesis for Alzheimer’s disease: a critical reappraisal. J Neurochem 110(4):1129–1134
Savage MJ, Gingrich DE (2009) Advances in the development of kinase inhibitor therapeutics for Alzheimer’s disease. Drug Dev Res 70(2):125–144
Long JM, Holtzman DM (2019) Alzheimer disease: an update on pathobiology and treatment strategies. Cell 179(2):312–339
Stromer T, Serpell LC (2005) Structure and morphology of the Alzheimer’s amyloid fibril. Microsc Res Tech 67(3–4):210–217
Nelson R, Sawaya MR, Balbirnie M et al (2005) Structure of the cross-β spine of amyloid-like fibrils. Nature 435(7043):773–778
Dislich B, Lichtenthaler SF (2012) The membrane-bound aspartyl protease BACE1: molecular and functional properties in Alzheimer’s disease and beyond. Front Physiol 3:8
Vassar R, Bennett BD, Babu-Khan S et al (1999) Beta-secretase cleavage of Alzheimer’s amyloid precursor protein by the transmembrane aspartic protease BACE. Science (New York, NY) 286(5440):735–741
Hong L, Koelsch G, Lin X et al (2000) Structure of the protease domain of memapsin 2 (beta-secretase) complexed with inhibitor. Science (New York, NY) 290(5489):150–153
Xu Y, Li MJ, Greenblatt H et al (2012) Flexibility of the flap in the active site of BACE1 as revealed by crystal structures and molecular dynamics simulations. Acta Crystallogr D Biol Crystallogr 68(Pt 1):13–25
Kimberly WT, LaVoie MJ, Ostaszewski BL et al (2003) Gamma-secretase is a membrane protein complex comprised of presenilin, nicastrin, Aph-1, and Pen-2. Proc Natl Acad Sci U S A 100(11):6382–6387
Wolfe MS, **a W, Ostaszewski BL et al (1999) Two transmembrane aspartates in presenilin-1 required for presenilin endoproteolysis and gamma-secretase activity. Nature 398(6727):513–517
Thinakaran G, Borchelt DR, Lee MK et al (1996) Endoproteolysis of presenilin 1 and accumulation of processed derivatives in vivo. Neuron 17(1):181–190
Takasugi N, Tomita T, Hayashi I et al (2003) The role of presenilin cofactors in the gamma-secretase complex. Nature 422(6930):438–441
Shah S, Lee SF, Tabuchi K et al (2005) Nicastrin functions as a gamma-secretase-substrate receptor. Cell 122(3):435–447
X-c B, Rajendra E, Yang G et al (2015) Sampling the conformational space of the catalytic subunit of human γ-secretase. eLife 4:e11182
Vyas VK, Ukawala RD, Ghate M et al (2012) Homology modeling a fast tool for drug discovery: current perspectives. Indian J Pharm Sci 74(1):1–17
Colletier J-P, Fournier D, Greenblatt HM et al (2006) Structural insights into substrate traffic and inhibition in acetylcholinesterase. EMBO J 25(12):2746–2756
Medina M (2018) An overview on the clinical development of tau-based therapeutics. Int J Mol Sci 19(4):1160
Fichou Y, Al-Hilaly YK, Devred F et al (2019) The elusive tau molecular structures: can we translate the recent breakthroughs into new targets for intervention? Acta Neuropathol Commun 7(1):31
Yoshida H, Goedert M (2012) Phosphorylation of microtubule-associated protein tau by AMPK-related kinases. J Neurochem 120(1):165–176
Cohen TJ, Guo JL, Hurtado DE et al (2011) The acetylation of tau inhibits its function and promotes pathological tau aggregation. Nat Commun 2:252
Schedin-Weiss S, Winblad B, Tjernberg LO (2014) The role of protein glycosylation in Alzheimer disease. FEBS J 281(1):46–62
García-Sierra F, Mondragón-Rodríguez S, Basurto-Islas G (2008) Truncation of tau protein and its pathological significance in Alzheimer’s disease. J Alzheimers Dis 14(4):401–409
Bretteville A, Ando K, Ghestem A et al (2009) Two-dimensional electrophoresis of tau mutants reveals specific phosphorylation pattern likely linked to early tau conformational changes. PLoS One 4(3):e4843
Mucke L (2009) Alzheimer’s disease. Nature 461(7266):895–897
Liu F, Grundke-Iqbal I, Iqbal K et al (2005) Contributions of protein phosphatases PP1, PP2A, PP2B and PP5 to the regulation of tau phosphorylation. Eur J Neurosci 22(8):1942–1950
Zhu Y, Shan X, Yuzwa SA et al (2014) The emerging link between O-GlcNAc and Alzheimer disease. J Biol Chem 289(50):34472–34481
Grinberg LT, Wang X, Wang C et al (2013) Argyrophilic grain disease differs from other tauopathies by lacking tau acetylation. Acta Neuropathol 125(4):581–593
Cook C, Carlomagno Y, Gendron TF et al (2014) Acetylation of the KXGS motifs in tau is a critical determinant in modulation of tau aggregation and clearance. Hum Mol Genet 23(1):104–116
Pan SY, Zhou SF, Gao SH et al (2013) New perspectives on how to discover drugs from herbal medicines: CAM’s outstanding contribution to modern therapeutics. Evid Based Complement Alternat Med 2013:627375
Szymański P, Markowicz M, Mikiciuk-Olasik E (2012) Adaptation of high-throughput screening in drug discovery-toxicological screening tests. Int J Mol Sci 13(1):427–452
Clark RL, Johnston BF, Mackay SP et al (2010) The drug discovery portal: a resource to enhance drug discovery from academia. Drug Discov Today 15(15–16):679–683
Lahana R (1999) How many leads from HTS? Drug Discov Today 4(10):447–448
Song CM, Lim SJ, Tong JC (2009) Recent advances in computer-aided drug design. Brief Bioinform 10(5):579–591
Veselovsky AV, Zharkova MS, Poroikov VV et al (2014) Computer-aided design and discovery of protein-protein interaction inhibitors as agents for anti-HIV therapy. SAR QSAR Environ Res 25(6):457–471
Pârvu L (2003) QSAR – a piece of drug design. J Cell Mol Med 7(3):333–335
Baig MH, Ahmad K, Roy S et al (2016) Computer aided drug design: success and limitations. Curr Pharm Des 22(5):572–581
Kim KH, Kim ND, Seong BL (2010) Pharmacophore-based virtual screening: a review of recent applications. Expert Opin Drug Discovery 5(3):205–222
Sousa SF, Cerqueira NM, Fernandes PA et al (2010) Virtual screening in drug design and development. Comb Chem High Throughput Screen 13(5):442–453
Waszkowycz B, Perkins TDJ, Sykes RA et al (2001) Large-scale virtual screening for discovering leads in the postgenomic era. IBM Syst J 40(2):360–376
Lionta E, Spyrou G, Vassilatis DK et al (2014) Structure-based virtual screening for drug discovery: principles, applications and recent advances. Curr Top Med Chem 14(16):1923–1938
Shoichet BK (2004) Virtual screening of chemical libraries. Nature 432(7019):862–865
Lounnas V, Ritschel T, Kelder J et al (2013) Current progress in structure-based rational drug design marks a new mindset in drug discovery. Comput Struct Biotechnol J 5:e201302011
Anderson AC (2012) Structure-based functional design of drugs: from target to lead compound. Methods Mol Biol 823:359–366
Andricopulo AD, Salum LB, Abraham DJ (2009) Structure-based drug design strategies in medicinal chemistry. Curr Top Med Chem 9(9):771–790
Goh BC, Hadden JA, Bernardi RC et al (2016) Computational methodologies for real-space structural refinement of large macromolecular complexes. Annu Rev Biophys 45:253–278
Fang Y (2015) Combining label-free cell phenotypic profiling with computational approaches for novel drug discovery. Expert Opin Drug Discovery 10(4):331–343
Cavasotto CN (2011) Homology models in docking and high-throughput docking. Curr Top Med Chem 11(12):1528–1534
Eldridge MD, Murray CW, Auton TR et al (1997) 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 11(5):425–445
Dhanavade MJ, Jalkute CB, Barage SH et al (2013) Homology modeling, molecular docking and MD simulation studies to investigate role of cysteine protease from Xanthomonas campestris in degradation of Aβ peptide. Comput Biol Med 43(12):2063–2070
Khare N, Maheshwari SK, Rizvi SMD et al (2022) Homology modelling, molecular docking and molecular dynamics simulation studies of CALMH1 against secondary metabolites of Bauhinia variegata to treat Alzheimer’s disease. Brain Sci 12(6):770
Mahendran SR, Jeyabaskar DS, Francis A et al (2017) Homology modeling and in silico docking analysis of BDNF in the treatment of Alzheimer’s disease. Res J Pharm Technol 10:2899–2906
Waterhouse A, Bertoni M, Bienert S et al (2018) SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res 46(W1):W296–W303
Vriend G (1990) WHAT IF: a molecular modeling and drug design program. J Mol Graph 8(1):52–56, 29
Krivov GG, Shapovalov MV, Dunbrack RL Jr (2009) Improved prediction of protein side-chain conformations with SCWRL4. Proteins Struct Funct Bioinform 77(4):778–795
Laskowski RA, MacArthur MW, Moss DS et al (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr 26(2):283–291
Altschul SF, Gish W, Miller W et al (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410
Sievers F, Higgins DG (2018) Clustal omega for making accurate alignments of many protein sequences. Protein Sci 27(1):135–145
Webb B, Sali A (2016) Comparative protein structure modeling using MODELLER. Curr Protoc Bioinformatics 54:5.6.1–5.6.37
Cardozo T, Totrov M, Abagyan R (1995) Homology modeling by the ICM method. Proteins 23(3):403–414
Jacobson MP, Pincus DL, Rapp CS et al (2004) A hierarchical approach to all-atom protein loop prediction. Proteins Struct Funct Bioinform 55(2):351–367
Molecular Operating Environment (MOE), 2022.02 Chemical Computing Group ULC, 1010 Sherbooke St. West S et al.
Jones G, Willett P, Glen RC et al (1997) Development and validation of a genetic algorithm for flexible docking. J Mol Biol 267(3):727–748
Ghouzam Y, Postic G, Guerin PE et al (2016) ORION: a web server for protein fold recognition and structure prediction using evolutionary hybrid profiles. Sci Rep 6:28268
Kelley LA, Mezulis S, Yates CM et al (2015) The Phyre2 web portal for protein modeling, prediction and analysis. Nat Protoc 10(6):845–858
McGuffin LJ, Bryson K, Jones DT (2000) The PSIPRED protein structure prediction server. Bioinformatics 16(4):404–405
McGuffin LJ, Adiyaman R, Maghrabi AHA et al (2019) IntFOLD: an integrated web resource for high performance protein structure and function prediction. Nucleic Acids Res 47(W1):W408–W413
Yang J, Zhang Y (2015) I-TASSER server: new development for protein structure and function predictions. Nucleic Acids Res 43(W1):W174–W181
Mortuza SM, Zheng W, Zhang C et al (2021) Improving fragment-based ab initio protein structure assembly using low-accuracy contact-map predictions. Nat Commun 12(1):5011
Simons KT, Bonneau R, Ruczinski I et al (1999) Ab initio protein structure prediction of CASP III targets using ROSETTA. Proteins Suppl 3:171–176
Meng XY, Zhang HX, Mezei M et al (2011) Molecular docking: a powerful approach for structure-based drug discovery. Curr Comput Aided Drug Des 7(2):146–157
Friesner RA, Banks JL, Murphy RB et al (2004) Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 47(7):1739–1749
Huang SY, Zou X (2010) Advances and challenges in protein-ligand docking. Int J Mol Sci 11(8):3016–3034
Sousa SF, Ribeiro AJ, Coimbra JT et al (2013) Protein-ligand docking in the new millennium--a retrospective of 10 years in the field. Curr Med Chem 20(18):2296–2314
Mohan V, Gibbs AC, Cummings MD et al (2005) Docking: successes and challenges. Curr Pharm Des 11(3):323–333
Morris GM, Goodsell DS, Huey R et al (1996) Distributed automated docking of flexible ligands to proteins: parallel applications of AutoDock 2.4. J Comput Aided Mol Des 10(4):293–304
Ewing TJ, Makino S, Skillman AG et al (2001) DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. J Comput Aided Mol Des 15(5):411–428
Kramer B, Rarey M, Lengauer T (1999) Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking. Proteins 37(2):228–241
Venkatachalam CM, Jiang X, Oldfield T et al (2003) LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites. J Mol Graph Model 21(4):289–307
Verdonk ML, Cole JC, Hartshorn MJ et al (2003) Improved protein-ligand docking using GOLD. Proteins 52(4):609–623
Jain AN (2003) Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine. J Med Chem 46(4):499–511
Neves MA, Totrov M, Abagyan R (2012) Docking and scoring with ICM: the benchmarking results and strategies for improvement. J Comput Aided Mol Des 26(6):675–686
McGann M (2012) FRED and HYBRID docking performance on standardized datasets. J Comput Aided Mol Des 26(8):897–906
Ravitz O, Zsoldos Z, Simon A (2011) Improving molecular docking through eHiTS’ tunable scoring function. J Comput Aided Mol Des 25(11):1033–1051
Du X, Li Y, **a YL et al (2016) Insights into protein-ligand interactions: mechanisms, models, and methods. Int J Mol Sci 17(2):144
Sousa SF, Fernandes PA, Ramos MJ (2006) Protein-ligand docking: current status and future challenges. Proteins 65(1):15–26
Ferreira LG, Dos Santos RN, Oliva G et al (2015) Molecular docking and structure-based drug design strategies. Molecules (Basel, Switzerland) 20(7):13384–13421
Foloppe N, Hubbard R (2006) Towards predictive ligand design with free-energy based computational methods? Curr Med Chem 13(29):3583–3608
Jain AN (2006) Scoring functions for protein-ligand docking. Curr Protein Pept Sci 7(5):407–420
Durrant JD, McCammon JA (2011) Molecular dynamics simulations and drug discovery. BMC Biol 9:71
Schreiner W, Karch R, Knapp B et al (2012) Relaxation estimation of RMSD in molecular dynamics immunosimulations. Comput Math Methods Med 2012:173521
Blessy JJ, Sharmila DJ (2015) Molecular modeling of methyl-α-Neu5Ac analogues docked against cholera toxin--a molecular dynamics study. Glycoconj J 32(1–2):49–67
Kieseritzky G, Morra G, Knapp EW (2006) Stability and fluctuations of amide hydrogen bonds in a bacterial cytochrome c: a molecular dynamics study. J Biol Inorg Chem 11(1):26–40
Pacholczyk M, Kimmel M (2011) Exploring the landscape of protein-ligand interaction energy using probabilistic approach. J Comput Biol 18(6):843–850
Manly CJ, Chandrasekhar J, Ochterski JW et al (2008) Strategies and tactics for optimizing the Hit-to-Lead process and beyond--a computational chemistry perspective. Drug Discov Today 13(3–4):99–109
Andrade CH, Pasqualoto KF, Ferreira EI et al (2010) 4D-QSAR: perspectives in drug design. Molecules (Basel, Switzerland) 15(5):3281–3294
Myint KZ, **e XQ (2010) Recent advances in fragment-based QSAR and multi-dimensional QSAR methods. Int J Mol Sci 11(10):3846–3866
Lo Y-C, Rensi SE, Torng W et al (2018) Machine learning in chemoinformatics and drug discovery. Drug Discov Today 23(8):1538–1546
Kaserer T, Beck KR, Akram M et al (2015) Pharmacophore models and pharmacophore-based virtual screening: concepts and applications exemplified on hydroxysteroid dehydrogenases. Molecules (Basel, Switzerland) 20(12):22799–22832
Liao C, Sitzmann M, Pugliese A et al (2011) Software and resources for computational medicinal chemistry. Future Med Chem 3(8):1057–1085
Karelson M, Lobanov VS, Katritzky AR (1996) Quantum-chemical descriptors in QSAR/QSPR studies. Chem Rev 96(3):1027–1044
Nicolaou CA, Kannas C, Loizidou E (2012) Multi-objective optimization methods in de novo drug design. Mini Rev Med Chem 12(10):979–987
Chan HH, Leong YQ, Voon SM et al (2021) Effects of amyloid precursor protein overexpression on NF-κB, rho-GTPase and pro-apoptosis Bcl-2 pathways in neuronal cells. Rep Biochem Mol Biol 9(4):417–425
Kumar A, Singh A, Ekavali (2015) A review on Alzheimer’s disease pathophysiology and its management: an update. Pharmacol Rep 67(2):195–203
Yiannopoulou KG, Papageorgiou SG (2013) Current and future treatments for Alzheimer’s disease. Ther Adv Neurol Disord 6(1):19–33
Wang TT, Chen Q, Zhou D (2016) Alzheimer’s disease therapeutics: current and future therapies. Minerva Med 107(2):108–113
De Ferrari GV, Canales MA, Shin I et al (2001) A structural motif of acetylcholinesterase that promotes amyloid beta-peptide fibril formation. Biochemistry 40(35):10447–10457
León R, Garcia AG, Marco-Contelles J (2013) Recent advances in the multitarget-directed ligands approach for the treatment of Alzheimer’s disease. Med Res Rev 33(1):139–189
Piazzi L, Rampa A, Bisi A et al (2003) 3-(4-[[Benzyl(methyl)amino]methyl]phenyl)-6,7-dimethoxy-2H-2-chromenone (AP2238) inhibits both acetylcholinesterase and acetylcholinesterase-induced beta-amyloid aggregation: a dual function lead for Alzheimer’s disease therapy. J Med Chem 46(12):2279–2282
Rosini M, Andrisano V, Bartolini M et al (2005) Rational approach to discover multipotent anti-Alzheimer drugs. J Med Chem 48(2):360–363
Rodríguez-Franco MI, Fernández-Bachiller MI, Pérez C et al (2006) Novel tacrine-melatonin hybrids as dual-acting drugs for Alzheimer disease, with improved acetylcholinesterase inhibitory and antioxidant properties. J Med Chem 49(2):459–462
Marco-Contelles J, Unzeta M, Bolea I et al (2016) ASS234, as a new multi-target directed propargylamine for Alzheimer’s disease therapy. Front Neurosci 10:294
Reddy PH, Tripathi R, Troung Q et al (2012) Abnormal mitochondrial dynamics and synaptic degeneration as early events in Alzheimer’s disease: implications to mitochondria-targeted antioxidant therapeutics. Biochim Biophys Acta 1822(5):639–649
Bartolini M, Marco-Contelles J (2019) Tacrines as therapeutic agents for Alzheimer’s disease. IV. The tacripyrines and related annulated tacrines. Chem Rec 19(5):927–937
Li Y, Peng P, Tang L et al (2014) Design, synthesis and evaluation of rivastigmine and curcumin hybrids as site-activated multitarget-directed ligands for Alzheimer’s disease therapy. Bioorg Med Chem 22(17):4717–4725
Scipioni M, Kay G, Megson IL et al (2019) Synthesis of novel vanillin derivatives: novel multi-targeted scaffold ligands against Alzheimer’s disease. Medchemcomm 10(5):764–777
Umar T, Shalini S, Raza MK et al (2018) New amyloid beta-disaggregating agents: synthesis, pharmacological evaluation, crystal structure and molecular docking of N-(4-((7-chloroquinolin-4-yl)oxy)-3-ethoxybenzyl)amines. Medchemcomm 9(11):1891–1904
Fu H, Li W, Luo J et al (2008) Promising anti-Alzheimer’s dimer bis(7)-tacrine reduces beta-amyloid generation by directly inhibiting BACE-1 activity. Biochem Biophys Res Commun 366(3):631–636
Piazzi L, Cavalli A, Colizzi F et al (2008) Multi-target-directed coumarin derivatives: hAChE and BACE1 inhibitors as potential anti-Alzheimer compounds. Bioorg Med Chem Lett 18(1):423–426
Zhu Y, **ao K, Ma L et al (2009) Design, synthesis and biological evaluation of novel dual inhibitors of acetylcholinesterase and beta-secretase. Bioorg Med Chem 17(4):1600–1613
Huang W, Tang L, Shi Y et al (2011) Searching for the multi-target-directed ligands against Alzheimer’s disease: discovery of quinoxaline-based hybrid compounds with AChE, H3R and BACE 1 inhibitory activities. Bioorg Med Chem 19(23):7158–7167
Cavalli A, Bolognesi ML, Capsoni S et al (2007) A small molecule targeting the multifactorial nature of Alzheimer’s disease. Angew Chem Int Ed Engl 46(20):3689–3692
Huang W, Lv D, Yu H et al (2010) Dual-target-directed 1,3-diphenylurea derivatives: BACE 1 inhibitor and metal chelator against Alzheimer’s disease. Bioorg Med Chem 18(15):5610–5615
Prati F, De Simone A, Armirotti A et al (2015) 3,4-Dihydro-1,3,5-triazin-2(1H)-ones as the first dual BACE-1/GSK-3β fragment hits against Alzheimer’s disease. ACS Chem Neurosci 6(10):1665–1682
Murata K, Matsumura S, Yoshioka Y et al (2015) Screening of β-secretase and acetylcholinesterase inhibitors from plant resources. J Nat Med 69(1):123–129
Di Martino RMC, De Simone A, Andrisano V et al (2016) Versatility of the curcumin scaffold: discovery of potent and balanced dual BACE-1 and GSK-3β inhibitors. J Med Chem 59(2):531–544
Yan J, Hu J, Liu A et al (2017) Design, synthesis, and evaluation of multitarget-directed ligands against Alzheimer’s disease based on the fusion of donepezil and curcumin. Bioorg Med Chem 25(12):2946–2955
Sang Z-p, Qiang X-m, Li Y et al (2015) Design, synthesis, and biological evaluation of scutellarein carbamate derivatives as potential multifunctional agents for the treatment of Alzheimer’s disease. Chem Biol Drug Des 86(5):1168–1177
Singh M, Silakari O (2016) Design, synthesis and biological evaluation of novel 2-phenyl-1-benzopyran-4-one derivatives as potential poly-functional anti-Alzheimer’s agents. RSC Adv 6(110):108411–108422
Xu QX, Hu Y, Li GY et al (2018) Multi-target anti-Alzheimer activities of four prenylated compounds from Psoralea fructus. Molecules (Basel, Switzerland) 23(3):614
Chakraborty S, Basu S (2017) Multi-functional activities of citrus flavonoid narirutin in Alzheimer’s disease therapeutics: an integrated screening approach and in vitro validation. Int J Biol Macromol 103:733–743
Ahmad A, Ali T, Park HY et al (2017) Neuroprotective effect of fisetin against amyloid-beta-induced cognitive/synaptic dysfunction, neuroinflammation, and neurodegeneration in adult mice. Mol Neurobiol 54(3):2269–2285
Liang Z, Zhang B, Su WW et al (2016) C-glycosylflavones alleviate tau phosphorylation and amyloid neurotoxicity through GSK3β inhibition. ACS Chem Neurosci 7(7):912–923
Kim H, Park B-S, Lee K-G et al (2005) Effects of naturally occurring compounds on fibril formation and oxidative stress of β-amyloid. J Agric Food Chem 53(22):8537–8541
Porat Y, Abramowitz A, Gazit E (2006) Inhibition of amyloid fibril formation by polyphenols: structural similarity and aromatic interactions as a common inhibition mechanism. Chem Biol Drug Des 67(1):27–37
Pavadai P, Swaminathan S (2015) Design and insilico molecular prediction of flavone-fusedthiazole analogues as Acetyl Cholinesterase and β-Secretase inhibitor in the treatment of Alzheimer’s disease. Int J Pharmtech Res 7:125–131
Wang SN, Li Q, **g MH et al (2016) Natural xanthones from Garcinia mangostana with multifunctional activities for the therapy of Alzheimer’s disease. Neurochem Res 41(7):1806–1817
Fernández-Bachiller MI, Pérez C, Monjas L et al (2012) New tacrine-4-Oxo-4H-chromene hybrids as multifunctional agents for the treatment of Alzheimer’s disease, with cholinergic, antioxidant, and β-amyloid-reducing properties. J Med Chem 55(3):1303–1317
Kumar V, Saha A, Roy K (2020) In silico modeling for dual inhibition of acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) enzymes in Alzheimer’s disease. Comput Biol Chem 88:107355
Stern N, Gacs A, Tátrai E et al (2022) Dual inhibitors of AChE and BACE-1 for reducing Aβ in Alzheimer’s disease: from in Silico to in vivo. Int J Mol Sci 23(21):13098
Khan BA, Hamdani SS, Alsfouk BA et al (2023) Synthesis, biological evaluation and computational investigations of S-benzyl dithiocarbamates as the cholinesterase and monoamine oxidase inhibitors. J Mol Struct 1271:134138
Gujral SS, Shakeri A, Hejazi L et al (2022) Design, synthesis and structure-activity relationship studies of 3-phenylpyrazino[1,2-a]indol-1(2H)-ones as amyloid aggregation and cholinesterase inhibitors with antioxidant activity. Eur J Med Chem Rep 6:100075
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(3):1501–1517
Shrivastava SK, Nivrutti AA, Bhardwaj B et al (2022) Drug reposition-based design, synthesis, and biological evaluation of dual inhibitors of acetylcholinesterase and β-Secretase for treatment of Alzheimer’s disease. J Mol Struct 1262:132979
Zeng H, Wu X (2016) Alzheimer’s disease drug development based on Computer-Aided Drug Design. Eur J Med Chem 121:851–863
Kumar A, Srivastava S, Tripathi S et al (2016) Molecular insight into amyloid oligomer destabilizing mechanism of flavonoid derivative 2-(4’ benzyloxyphenyl)-3-hydroxy-chromen-4-one through docking and molecular dynamics simulations. J Biomol Struct Dyn 34(6):1252–1263
Verma A, Kumar A, Debnath M (2016) Molecular docking and simulation studies to give insight of surfactin amyloid interaction for destabilizing Alzheimer’s Aβ42 protofibrils. Med Chem Res 25(8):1616–1622
Singh SK, Sinha P, Mishra L et al (2013) Neuroprotective role of a novel copper chelator against Aβ 42 induced neurotoxicity. Int J Alzheimers Dis 2013:567128
Kumar A, Roy S, Tripathi S et al (2016) Molecular docking based virtual screening of natural compounds as potential BACE1 inhibitors: 3D QSAR pharmacophore map** and molecular dynamics analysis. J Biomol Struct Dyn 34(2):239–249
Roy S, Kumar A, Baig MH et al (2015) 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 83:105–110
Iqbal K, Grundke-Iqbal I (2010) Alzheimer’s disease, a multifactorial disorder seeking multitherapies. Alzheimers Dement 6(5):420–424
Arooj M, Sakkiah S, Cao G et al (2013) An innovative strategy for dual inhibitor design and its application in dual inhibition of human thymidylate synthase and dihydrofolate reductase enzymes. PLoS One 8(4):e60470
Cosconati S, Forli S, Perryman AL et al (2010) Virtual screening with AutoDock: theory and practice. Expert Opin Drug Discovery 5(6):597–607
Kumar A, Sharma A (2018) Computational modeling of multi-target-directed inhibitors against Alzheimer’s disease. In: Roy K (ed) Computational modeling of drugs against Alzheimer’s disease. Springer, New York, pp 533–571. https://doi.org/10.1007/978-1-4939-7404-7_19
Cole JC, Murray CW, Nissink JW et al (2005) Comparing protein-ligand docking programs is difficult. Proteins 60(3):325–332
Hevener KE, Zhao W, Ball DM et al (2009) Validation of molecular docking programs for virtual screening against dihydropteroate synthase. J Chem Inf Model 49(2):444–460
Triballeau N, Acher F, Brabet I et al (2005) Virtual screening workflow development guided by the “receiver operating characteristic” curve approach. Application to high-throughput docking on metabotropic glutamate receptor subtype 4. J Med Chem 48(7):2534–2547
Rarey M, Kramer B, Lengauer T et al (1996) A fast flexible docking method using an incremental construction algorithm. J Mol Biol 261(3):470–489
Jones G, Willett P, Glen RC (1995) Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation. J Mol Biol 245(1):43–53
Baxter CA, Murray CW, Clark DE et al (1998) Flexible docking using Tabu search and an empirical estimate of binding affinity. Proteins 33(3):367–382
Hall SB, Venkitaraman AR, Whitsett JA et al (1992) Importance of hydrophobic apoproteins as constituents of clinical exogenous surfactants. Am Rev Respir Dis 145(1):24–30
Goto J, Kataoka R, Hirayama N (2004) Ph4Dock: pharmacophore-based protein-ligand docking. J Med Chem 47(27):6804–6811
Baroni M, Cruciani G, Sciabola S et al (2007) A common reference framework for analyzing/comparing proteins and ligands. Fingerprints for Ligands and Proteins (FLAP): theory and application. J Chem Inf Model 47(2):279–294
Park K, Kim D (2006) A method to detect important residues using protein binding site comparison. Genome Inform 17(2):216–225
Case DA, Cheatham TE 3rd, Darden T et al (2005) The Amber biomolecular simulation programs. J Comput Chem 26(16):1668–1688
Congreve M, Chessari G, Tisi D et al (2008) Recent developments in fragment-based drug discovery. J Med Chem 51(13):3661–3680
Jorgensen W, Maxwell D, Tirado-Rives J (1996) Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 118:11225–11236
Verkhivker GM (2004) Computational analysis of ligand binding dynamics at the intermolecular hot spots with the aid of simulated tempering and binding free energy calculations. J Mol Graph Model 22(5):335–348
Wang R, Lai L, Wang S (2002) Further development and validation of empirical scoring functions for structure-based binding affinity prediction. J Comput Aided Mol Des 16(1):11–26
Muegge I (2006) PMF scoring revisited. J Med Chem 49(20):5895–5902
Velec HF, Gohlke H, Klebe G (2005) DrugScore(CSD)-knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction. J Med Chem 48(20):6296–6303
Böhm HJ (1994) The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure. J Comput Aided Mol Des 8(3):243–256
Ballesteros JA, Weinstein H (1995) [19] Integrated methods for the construction of three-dimensional models and computational probing of structure-function relations in G protein-coupled receptors. In: Sealfon SC (ed) Methods in neurosciences, vol 25. Academic Press, pp 366–428. https://doi.org/10.1016/S1043-9471(05)80049-7
Garman E, Laver G (2004) Controlling influenza by inhibiting the virus’s neuraminidase. Curr Drug Targets 5(2):119–136
Kaldor SW, Kalish VJ, Davies JF 2nd et al (1997) Viracept (nelfinavir mesylate, AG1343): a potent, orally bioavailable inhibitor of HIV-1 protease. J Med Chem 40(24):3979–3985
von Itzstein M, Wu WY, Kok GB et al (1993) Rational design of potent sialidase-based inhibitors of influenza virus replication. Nature 363(6428):418–423
Chen H, Lyne PD, Giordanetto F et al (2006) On evaluating molecular-docking methods for pose prediction and enrichment factors. J Chem Inf Model 46(1):401–415
Warren GL, Andrews CW, Capelli AM et al (2006) A critical assessment of docking programs and scoring functions. J Med Chem 49(20):5912–5931
Huang JW, Zhang Z, Wu B et al (2008) Fragment-based design of small molecule X-linked inhibitor of apoptosis protein inhibitors. J Med Chem 51(22):7111–7118
Murray CW, Callaghan O, Chessari G et al (2007) Application of fragment screening by X-ray crystallography to beta-secretase. J Med Chem 50(6):1116–1123
Fink T, Bruggesser H, Reymond JL (2005) Virtual exploration of the small-molecule chemical universe below 160 Daltons. Angew Chem Int Ed Engl 44(10):1504–1508
Bohacek RS, McMartin C, Guida WC (1996) The art and practice of structure-based drug design: a molecular modeling perspective. Med Res Rev 16(1):3–50
Huey R, Morris GM, Olson AJ et al (2007) A semiempirical free energy force field with charge-based desolvation. J Comput Chem 28(6):1145–1152
**e 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(11):18118–18128
Tran T-S, Le M-T, Tran T-D et al (2020) Design of curcumin and flavonoid derivatives with acetylcholinesterase and beta-secretase inhibitory activities using in silico approaches. Molecules (Basel, Switzerland) 25(16):3644
Duan S, Guan X, Lin R et al (2015) Silibinin inhibits acetylcholinesterase activity and amyloid β peptide aggregation: a dual-target drug for the treatment of Alzheimer’s disease. Neurobiol Aging 36(5):1792–1807
Yang SY (2010) Pharmacophore modeling and applications in drug discovery: challenges and recent advances. Drug Discov Today 15(11–12):444–450
Sliwoski G, Kothiwale S, Meiler J et al (2014) Computational methods in drug discovery. Pharmacol Rev 66(1):334–395
Caporuscio F, Tafi A (2011) Pharmacophore modelling: a forty year old approach and its modern synergies. Curr Med Chem 18(17):2543–2553
Fei J, Zhou L, Liu T et al (2013) Pharmacophore modeling, virtual screening, and molecular docking studies for discovery of novel Akt2 inhibitors. Int J Med Sci 10(3):265–275
Goyal M, Dhanjal JK, Goyal S et al (2014) Development of dual inhibitors against Alzheimer’s disease using fragment-based QSAR and molecular docking. Biomed Res Int 2014:979606
Tetko IV, Gasteiger J, Todeschini R et al (2005) Virtual computational chemistry laboratory--design and description. J Comput Aided Mol Des 19(6):453–463
MOE. 2008.10 edition. Chemical Computing Group Inc. SSW, Suite 910, Montreal, Quebec, Canada H3A 2R7. https://www.chemcomp.com/. Accessed 20 May 2021
Krizhevsky A, Sutskever I, Hinton GE (2012) ImageNet classification with deep convolutional neural networks. Adv Neural Inf Process Syst 25:1097–1105
Ngo T-D, Tran T-D, Le M-T et al (2016) Computational predictive models for P-glycoprotein inhibition of in-house chalcone derivatives and drug-bank compounds. Mol Divers 20(4):945–961
Consonni V, Ballabio D, Todeschini R (2009) Comments on the definition of the Q2 parameter for QSAR validation. J Chem Inf Model 49(7):1669–1678
Todeschini R, Ballabio D, Grisoni F (2016) Beware of unreliable Q(2)! A comparative study of regression metrics for predictivity assessment of QSAR models. J Chem Inf Model 56(10):1905–1913
Chirico N, Gramatica P (2011) Real external predictivity of QSAR models: how to evaluate it? Comparison of different validation criteria and proposal of using the concordance correlation coefficient. J Chem Inf Model 51(9):2320–2335
Thai K-M, Bui Q-H, Tran T-D et al (2012) QSAR modeling on benzo[c]phenanthridine analogues as topoisomerase I inhibitors and anti-cancer agents. Molecules (Basel, Switzerland) 17(5):5690–5712
Youdim MB, Buccafusco JJ (2005) Multi-functional drugs for various CNS targets in the treatment of neurodegenerative disorders. Trends Pharmacol Sci 26(1):27–35
McGaughey GB, Colussi D, Graham SL et al (2007) Beta-secretase (BACE-1) inhibitors: accounting for 10s loop flexibility using rigid active sites. Bioorg Med Chem Lett 17(4):1117–1121
Kumalo HM, Bhakat S, Soliman ME (2016) Investigation of flap flexibility of β-secretase using molecular dynamic simulations. J Biomol Struct Dyn 34(5):1008–1019
Berhanu WM, Masunov AE (2015) Atomistic mechanism of polyphenol amyloid aggregation inhibitors: molecular dynamics study of Curcumin, Exifone, and Myricetin interaction with the segment of tau peptide oligomer. J Biomol Struct Dyn 33(7):1399–1411
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(5):739–749
González-Díaz H, Prado-Prado FJ, Santana L et al (2006) Unify QSAR approach to antimicrobials. Part 1: predicting antifungal activity against different species. Bioorg Med Chem 14(17):5973–5980
Ambure P, Roy K (2014) Advances in quantitative structure-activity relationship models of anti-Alzheimer’s agents. Expert Opin Drug Discovery 9(6):697–723
Acknowledgments
This work was supported by University of Medicine and Pharmacy at Ho Chi Minh city (Grant number: 224/2022/H-HYD to Khac-Minh Thai) and Hue University (Grant number: DHH2022-04-166 to Thai-Son Tran).
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Thai, KM. et al. (2023). Recent Advances in Computational Modeling of Multi-targeting Inhibitors as Anti-Alzheimer Agents. In: Roy, K. (eds) Computational Modeling of Drugs Against Alzheimer’s Disease. Neuromethods, vol 203. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3311-3_8
Download citation
DOI: https://doi.org/10.1007/978-1-0716-3311-3_8
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-3310-6
Online ISBN: 978-1-0716-3311-3
eBook Packages: Springer Protocols