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Published in: Clinical and Translational Medicine 1/2018

Open Access 01-12-2018 | Perspective

A perspective on multi-target drug discovery and design for complex diseases

Authors: Rona R. Ramsay, Marija R. Popovic-Nikolic, Katarina Nikolic, Elisa Uliassi, Maria Laura Bolognesi

Published in: Clinical and Translational Medicine | Issue 1/2018

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Abstract

Diseases of infection, of neurodegeneration (such as Alzheimer’s and Parkinson’s diseases), and of malignancy (cancers) have complex and varied causative factors. Modern drug discovery has the power to identify potential modulators for multiple targets from millions of compounds. Computational approaches allow the determination of the association of each compound with its target before chemical synthesis and biological testing is done. These approaches depend on the prior identification of clinically and biologically validated targets. This Perspective will focus on the molecular and computational approaches that underpin drug design by medicinal chemists to promote understanding and collaboration with clinical scientists.
Literature
1.
go back to reference Bolognesi ML (2013) Polypharmacology in a single drug: multitarget drugs. Curr Med Chem 20(13):1639–1645PubMedCrossRef Bolognesi ML (2013) Polypharmacology in a single drug: multitarget drugs. Curr Med Chem 20(13):1639–1645PubMedCrossRef
2.
go back to reference Bolognesi ML, Cavalli A (2016) Multitarget drug discovery and polypharmacology. ChemMedChem 11(12):1190–1192PubMedCrossRef Bolognesi ML, Cavalli A (2016) Multitarget drug discovery and polypharmacology. ChemMedChem 11(12):1190–1192PubMedCrossRef
3.
go back to reference Morphy R, Kay C, Rankovic Z (2004) From magic bullets to designed multiple ligands. Drug Discov Today 9(15):641–651PubMedCrossRef Morphy R, Kay C, Rankovic Z (2004) From magic bullets to designed multiple ligands. Drug Discov Today 9(15):641–651PubMedCrossRef
4.
go back to reference Youdim MBH, Buccafusco JJ (2005) Multi-functional drugs for various CNS targets in the treatment of neurodegenerative disorders. Trends Pharm Sci 26(1):27–35PubMedCrossRef Youdim MBH, Buccafusco JJ (2005) Multi-functional drugs for various CNS targets in the treatment of neurodegenerative disorders. Trends Pharm Sci 26(1):27–35PubMedCrossRef
5.
go back to reference Roth BL, Sheffler DJ, Kroeze WK (2004) Magic shotguns versus magic bullets: selectively non-selective drugs for mood disorders and schizophrenia. Nat Rev Drug Discov 3(4):353–359PubMedCrossRef Roth BL, Sheffler DJ, Kroeze WK (2004) Magic shotguns versus magic bullets: selectively non-selective drugs for mood disorders and schizophrenia. Nat Rev Drug Discov 3(4):353–359PubMedCrossRef
6.
go back to reference Lin HH, Zhang LL, Yan R, Lu JJ, Hu YJ (2017) Network analysis of drug-target interactions: a study on FDA-approved new molecular entities between 2000 to 2015. Sci Rep 7:12230PubMedPubMedCentralCrossRef Lin HH, Zhang LL, Yan R, Lu JJ, Hu YJ (2017) Network analysis of drug-target interactions: a study on FDA-approved new molecular entities between 2000 to 2015. Sci Rep 7:12230PubMedPubMedCentralCrossRef
7.
go back to reference Griesenauer RH, Kinch MS (2017) 2016 in review: FDA approvals of new molecular entities. Drug Discov Today 22(11):1593–1597PubMedCrossRef Griesenauer RH, Kinch MS (2017) 2016 in review: FDA approvals of new molecular entities. Drug Discov Today 22(11):1593–1597PubMedCrossRef
8.
go back to reference Schellekens H, Aldosari M, Talsma H, Mastrobattista E (2017) Making individualized drugs a reality. Nat Biotechnol 35(6):507–513PubMed Schellekens H, Aldosari M, Talsma H, Mastrobattista E (2017) Making individualized drugs a reality. Nat Biotechnol 35(6):507–513PubMed
10.
go back to reference Gao M, Nettles RE, Belema M, Snyder LB, Nguyen VN, Fridell RA et al (2010) Chemical genetics strategy identifies an HCV NS5A inhibitor with a potent clinical effect. Nature 465(7294):96–100PubMedCrossRef Gao M, Nettles RE, Belema M, Snyder LB, Nguyen VN, Fridell RA et al (2010) Chemical genetics strategy identifies an HCV NS5A inhibitor with a potent clinical effect. Nature 465(7294):96–100PubMedCrossRef
11.
go back to reference Bartenschlager R, Lohmann V, Penin F (2013) The molecular and structural basis of advanced antiviral therapy for hepatitis C virus infection. Nat Rev Microbiol 11(7):482–496PubMedCrossRef Bartenschlager R, Lohmann V, Penin F (2013) The molecular and structural basis of advanced antiviral therapy for hepatitis C virus infection. Nat Rev Microbiol 11(7):482–496PubMedCrossRef
12.
go back to reference Bannwart LM, Carter DS, Cai HY, Choy JC, Greenhouse R, Jaime-Figueroa S et al (2008) Novel 3,3-disubstituted pyrrolidines as selective triple serotonin/norepinephrine/dopamine reuptake inhibitors. Bioorg Med Chem Lett 18(23):6062–6066PubMedCrossRef Bannwart LM, Carter DS, Cai HY, Choy JC, Greenhouse R, Jaime-Figueroa S et al (2008) Novel 3,3-disubstituted pyrrolidines as selective triple serotonin/norepinephrine/dopamine reuptake inhibitors. Bioorg Med Chem Lett 18(23):6062–6066PubMedCrossRef
13.
go back to reference Seeger TF, Seymour PA, Schmidt AW, Zorn SH, Schulz DW, Lebel LA et al (1995) Ziprasidone (CP-88,059): a new antipsychotic with combined dopamine and serotonin receptor antagonist activity. J Pharmacol Exp Ther 275(1):101–113PubMed Seeger TF, Seymour PA, Schmidt AW, Zorn SH, Schulz DW, Lebel LA et al (1995) Ziprasidone (CP-88,059): a new antipsychotic with combined dopamine and serotonin receptor antagonist activity. J Pharmacol Exp Ther 275(1):101–113PubMed
14.
go back to reference Felice D, Gardier AM, Sanchez C, David DJ (2017) Innovative solutions to the development of novel antidepressants. In: Carvalho AF, Reus GZ, de Quevedo JL (eds) Frontiers in drug discovery: the search for antidepressants - an integrative view of drug discovery, vol 2, pp 1–40. https://doi.org/10.2174/9781681084732117020004 Felice D, Gardier AM, Sanchez C, David DJ (2017) Innovative solutions to the development of novel antidepressants. In: Carvalho AF, Reus GZ, de Quevedo JL (eds) Frontiers in drug discovery: the search for antidepressants - an integrative view of drug discovery, vol 2, pp 1–40. https://​doi.​org/​10.​2174/​9781681084732117​020004
15.
go back to reference Maeda K, Sugino H, Akazawa H, Amada N, Shimada J, Futamura T et al (2014) Brexpiprazole I: in vitro and in vivo characterization of a novel serotonin-dopamine activity modulator. J Pharmacol Exp Ther 350(3):589–604PubMedCrossRef Maeda K, Sugino H, Akazawa H, Amada N, Shimada J, Futamura T et al (2014) Brexpiprazole I: in vitro and in vivo characterization of a novel serotonin-dopamine activity modulator. J Pharmacol Exp Ther 350(3):589–604PubMedCrossRef
16.
go back to reference Frankel JS, Schwartz TL (2017) Brexpiprazole and cariprazine: distinguishing two new atypical antipsychotics from the original dopamine stabilizer aripiprazole. Ther Adv Psychopharm. 7(1):29–41CrossRef Frankel JS, Schwartz TL (2017) Brexpiprazole and cariprazine: distinguishing two new atypical antipsychotics from the original dopamine stabilizer aripiprazole. Ther Adv Psychopharm. 7(1):29–41CrossRef
17.
go back to reference Cavalli A, Bolognesi ML, Minarini A, Rosini M, Tumiatti V, Recanatini M et al (2008) Multi-target-directed ligands to combat neurodegenerative diseases. J Med Chem 51(3):347–372PubMedCrossRef Cavalli A, Bolognesi ML, Minarini A, Rosini M, Tumiatti V, Recanatini M et al (2008) Multi-target-directed ligands to combat neurodegenerative diseases. J Med Chem 51(3):347–372PubMedCrossRef
18.
go back to reference Viayna E, Sola I, Di Pietro O, Munoz-Torrero D (2013) Human disease and drug pharmacology, complex as real life. Curr Med Chem 20(13):1623–1634PubMedCrossRef Viayna E, Sola I, Di Pietro O, Munoz-Torrero D (2013) Human disease and drug pharmacology, complex as real life. Curr Med Chem 20(13):1623–1634PubMedCrossRef
19.
go back to reference Pevarello P, Bonsignori A, Dostert P, Heidempergher F, Pinciroli V, Colombo M et al (1998) Synthesis and anticonvulsant activity of a new class of 2-[(arylalkyl)amino]alkanamide derivatives. J Med Chem 41(4):579–590PubMedCrossRef Pevarello P, Bonsignori A, Dostert P, Heidempergher F, Pinciroli V, Colombo M et al (1998) Synthesis and anticonvulsant activity of a new class of 2-[(arylalkyl)amino]alkanamide derivatives. J Med Chem 41(4):579–590PubMedCrossRef
20.
go back to reference Marzo A, Dal Bo L, Monti NC, Crivelli F, Ismaili S, Caccia C et al (2004) Pharmacokinetics and pharmacodynamics of safinamide, a neuroprotectant with antiparkinsonian and anticonvulsant activity. Pharmacol Res 50(1):77–85PubMedCrossRef Marzo A, Dal Bo L, Monti NC, Crivelli F, Ismaili S, Caccia C et al (2004) Pharmacokinetics and pharmacodynamics of safinamide, a neuroprotectant with antiparkinsonian and anticonvulsant activity. Pharmacol Res 50(1):77–85PubMedCrossRef
22.
go back to reference Li YH, Wang PP, Li XX, Yu CY, Yang H, Zhou J et al (2016) The human kinome targeted by FDA approved multi-target drugs and combination products: a comparative study from the drug-target interaction network perspective. PLoS ONE 11(11):e0165737PubMedPubMedCentralCrossRef Li YH, Wang PP, Li XX, Yu CY, Yang H, Zhou J et al (2016) The human kinome targeted by FDA approved multi-target drugs and combination products: a comparative study from the drug-target interaction network perspective. PLoS ONE 11(11):e0165737PubMedPubMedCentralCrossRef
23.
go back to reference Santos R, Ursu O, Gaulton A, Bento AP, Donadi RS, Bologa CG et al (2017) A comprehensive map of molecular drug targets. Nat Rev Drug Discov 16(1):19–34PubMedCrossRef Santos R, Ursu O, Gaulton A, Bento AP, Donadi RS, Bologa CG et al (2017) A comprehensive map of molecular drug targets. Nat Rev Drug Discov 16(1):19–34PubMedCrossRef
24.
go back to reference Okamoto K, Kodama K, Takase K, Sugi NH, Yamamoto Y, Iwata M et al (2013) Antitumor activities of the targeted multi-tyrosine kinase inhibitor lenvatinib (E7080) against RET gene fusion-driven tumor models. Cancer Lett 340(1):97–103PubMedCrossRef Okamoto K, Kodama K, Takase K, Sugi NH, Yamamoto Y, Iwata M et al (2013) Antitumor activities of the targeted multi-tyrosine kinase inhibitor lenvatinib (E7080) against RET gene fusion-driven tumor models. Cancer Lett 340(1):97–103PubMedCrossRef
25.
go back to reference Tsou HR, Overbeek-Klumpers EG, Hallett WA, Reich MF, Floyd MB, Johnson BD et al (2005) Optimization of 6,7-disubstituted-4-(arylamino)quinoline-3-carbonitriles as orally active, irreversible inhibitors of human epidermal growth factor receptor-2 kinase activity. J Med Chem 48(4):1107–1131PubMedCrossRef Tsou HR, Overbeek-Klumpers EG, Hallett WA, Reich MF, Floyd MB, Johnson BD et al (2005) Optimization of 6,7-disubstituted-4-(arylamino)quinoline-3-carbonitriles as orally active, irreversible inhibitors of human epidermal growth factor receptor-2 kinase activity. J Med Chem 48(4):1107–1131PubMedCrossRef
26.
go back to reference Asghar U, Witkiewicz AK, Turner NC, Knudsen ES (2015) The history and future of targeting cyclin-dependent kinases in cancer therapy. Nat Rev Drug Discov 14(2):130–146PubMedPubMedCentralCrossRef Asghar U, Witkiewicz AK, Turner NC, Knudsen ES (2015) The history and future of targeting cyclin-dependent kinases in cancer therapy. Nat Rev Drug Discov 14(2):130–146PubMedPubMedCentralCrossRef
28.
29.
go back to reference Moore D (2016) Panobinostat (Farydak): a novel option for the treatment of relapsed or relapsed and refractory multiple myeloma. Pharm Ther 41(5):296–300 Moore D (2016) Panobinostat (Farydak): a novel option for the treatment of relapsed or relapsed and refractory multiple myeloma. Pharm Ther 41(5):296–300
30.
go back to reference Morphy JR, Harris CJ (2012) Designing multi-target drugs. The Royal Society of Chemistry, Cambridge, pp P001–P365CrossRef Morphy JR, Harris CJ (2012) Designing multi-target drugs. The Royal Society of Chemistry, Cambridge, pp P001–P365CrossRef
31.
32.
go back to reference Decker M (2017) Design of hybrid molecules for drug development. Elsevier, Amsterdam Decker M (2017) Design of hybrid molecules for drug development. Elsevier, Amsterdam
36.
go back to reference Hopkins AL (2008) Network pharmacology: the next paradigm in drug discovery. Nat Chem Biol 4(11):682–690PubMedCrossRef Hopkins AL (2008) Network pharmacology: the next paradigm in drug discovery. Nat Chem Biol 4(11):682–690PubMedCrossRef
37.
go back to reference Bottegoni G, Favia AD, Recanatini M, Cavalli A (2012) The role of fragment-based and computational methods in polypharmacology. Drug Discov Today 17(1–2):23–34PubMedCrossRef Bottegoni G, Favia AD, Recanatini M, Cavalli A (2012) The role of fragment-based and computational methods in polypharmacology. Drug Discov Today 17(1–2):23–34PubMedCrossRef
38.
go back to reference Morphy R, Rankovic Z (2010) Design of multitarget ligands. In: Rankovic Z, Morphy R (eds) Lead generation approaches in drug discovery. Wiley, Hoboken, pp 141–164CrossRef Morphy R, Rankovic Z (2010) Design of multitarget ligands. In: Rankovic Z, Morphy R (eds) Lead generation approaches in drug discovery. Wiley, Hoboken, pp 141–164CrossRef
39.
go back to reference Morphy R, Rankovic Z (2009) Designing multiple ligands—medicinal chemistry strategies and challenges. Curr Pharm Des 15(6):587–600PubMedCrossRef Morphy R, Rankovic Z (2009) Designing multiple ligands—medicinal chemistry strategies and challenges. Curr Pharm Des 15(6):587–600PubMedCrossRef
40.
go back to reference Morphy R, Rankovic Z (2005) Designed multiple ligands. An emerging drug discovery paradigm. J Med Chem 48(21):6523–6543PubMedCrossRef Morphy R, Rankovic Z (2005) Designed multiple ligands. An emerging drug discovery paradigm. J Med Chem 48(21):6523–6543PubMedCrossRef
41.
go back to reference Morphy R, Rankovic Z (2006) The physicochemical challenges of designing multiple ligands. J Med Chem 49(16):4961–4970PubMedCrossRef Morphy R, Rankovic Z (2006) The physicochemical challenges of designing multiple ligands. J Med Chem 49(16):4961–4970PubMedCrossRef
42.
go back to reference Wilson GL, Lill MA (2011) Integrating structure-based and ligand-based approaches for computational drug design. Future Med Chem 3(6):735–750PubMedCrossRef Wilson GL, Lill MA (2011) Integrating structure-based and ligand-based approaches for computational drug design. Future Med Chem 3(6):735–750PubMedCrossRef
43.
go back to reference Wong YH, Lin CL, Chen TS, Chen CA, Jiang PS, Lai YH et al (2015) Multiple target drug cocktail design for attacking the core network markers of four cancers using ligand-based and structure-based virtual screening methods. BMC Med Genom 8(Suppl 4):S4CrossRef Wong YH, Lin CL, Chen TS, Chen CA, Jiang PS, Lai YH et al (2015) Multiple target drug cocktail design for attacking the core network markers of four cancers using ligand-based and structure-based virtual screening methods. BMC Med Genom 8(Suppl 4):S4CrossRef
44.
go back to reference Cramer RD (2012) The inevitable QSAR renaissance. J Comput Aid Mol Des 26(1):35–38CrossRef Cramer RD (2012) The inevitable QSAR renaissance. J Comput Aid Mol Des 26(1):35–38CrossRef
45.
go back to reference Cherkasov A, Muratov EN, Fourches D, Varnek A, Baskin II, Cronin M et al (2014) QSAR modeling: where have you been? Where are you going to? J Med Chem 57(12):4977–5010PubMedPubMedCentralCrossRef Cherkasov A, Muratov EN, Fourches D, Varnek A, Baskin II, Cronin M et al (2014) QSAR modeling: where have you been? Where are you going to? J Med Chem 57(12):4977–5010PubMedPubMedCentralCrossRef
47.
go back to reference Danishuddin, Khan AU (2016) Descriptors and their selection methods in QSAR analysis: paradigm for drug design. Drug Discov Today 21(8):1291–1302PubMedCrossRef Danishuddin, Khan AU (2016) Descriptors and their selection methods in QSAR analysis: paradigm for drug design. Drug Discov Today 21(8):1291–1302PubMedCrossRef
49.
go back to reference Nikolic K, Mavridis L, Djikic T, Vucicevic J, Agbaba D, Yelekci K et al (2016) Drug design for CNS diseases: polypharmacological profiling of compounds using cheminformatic, 3D-QSAR and virtual screening methodologies. Front Neurosci 10:265PubMedPubMedCentralCrossRef Nikolic K, Mavridis L, Djikic T, Vucicevic J, Agbaba D, Yelekci K et al (2016) Drug design for CNS diseases: polypharmacological profiling of compounds using cheminformatic, 3D-QSAR and virtual screening methodologies. Front Neurosci 10:265PubMedPubMedCentralCrossRef
51.
go back to reference Nikolic K, Mavridis L, Bautista-Aguilera OM, Marco-Contelles J, Stark H, Carreiras MD et al (2015) Predicting targets of compounds against neurological diseases using cheminformatic methodology. J Comput Aid Mol Des 29(2):183–198CrossRef Nikolic K, Mavridis L, Bautista-Aguilera OM, Marco-Contelles J, Stark H, Carreiras MD et al (2015) Predicting targets of compounds against neurological diseases using cheminformatic methodology. J Comput Aid Mol Des 29(2):183–198CrossRef
52.
go back to reference Ismaili L, Refouvelet B, Benchekroun M, Brogi S, Brindisi M, Gemma S et al (2017) Multitarget compounds bearing tacrine- and donepezil-like structural and functional motifs for the potential treatment of Alzheimer’s disease. Prog Neurobiol 151:4–34PubMedCrossRef Ismaili L, Refouvelet B, Benchekroun M, Brogi S, Brindisi M, Gemma S et al (2017) Multitarget compounds bearing tacrine- and donepezil-like structural and functional motifs for the potential treatment of Alzheimer’s disease. Prog Neurobiol 151:4–34PubMedCrossRef
54.
go back to reference Vucicevic J, Srdic-Rajic T, Pieroni M, Laurila JM, Perovic V, Tassini S et al (2016) A combined ligand- and structure-based approach for the identification of rilmenidine-derived compounds which synergize the antitumor effects of doxorubicin. Bioorg Med Chem 24(14):3174–3183PubMedCrossRef Vucicevic J, Srdic-Rajic T, Pieroni M, Laurila JM, Perovic V, Tassini S et al (2016) A combined ligand- and structure-based approach for the identification of rilmenidine-derived compounds which synergize the antitumor effects of doxorubicin. Bioorg Med Chem 24(14):3174–3183PubMedCrossRef
55.
go back to reference Baurin N, Baker R, Richardson C, Chen I, Foloppe N, Potter A et al (2004) Drug-like annotation and duplicate analysis of a 23-supplier chemical database totalling 2.7 million compounds. J Chem Inf Comput Sci 44(2):643–651PubMedCrossRef Baurin N, Baker R, Richardson C, Chen I, Foloppe N, Potter A et al (2004) Drug-like annotation and duplicate analysis of a 23-supplier chemical database totalling 2.7 million compounds. J Chem Inf Comput Sci 44(2):643–651PubMedCrossRef
56.
go back to reference Lepailleur A, Freret T, Lemaitre S, Boulouard M, Dauphin F, Hinschberger A et al (2014) Dual histamine H3R/serotonin 5-HT4R ligands with antiamnesic properties: pharmacophore-based virtual screening and polypharmacology. J Chem Inf Model 54(6):1773–1784PubMedCrossRef Lepailleur A, Freret T, Lemaitre S, Boulouard M, Dauphin F, Hinschberger A et al (2014) Dual histamine H3R/serotonin 5-HT4R ligands with antiamnesic properties: pharmacophore-based virtual screening and polypharmacology. J Chem Inf Model 54(6):1773–1784PubMedCrossRef
57.
go back to reference Bottegoni G, Veronesi M, Bisignano P, Kacker P, Favia AD, Cavalli A (2016) Development and application of a virtual screening protocol for the identification of multitarget fragments. ChemMedChem 11(12):1259–1263PubMedCrossRef Bottegoni G, Veronesi M, Bisignano P, Kacker P, Favia AD, Cavalli A (2016) Development and application of a virtual screening protocol for the identification of multitarget fragments. ChemMedChem 11(12):1259–1263PubMedCrossRef
58.
go back to reference Bautista-Aguilera OM, Esteban G, Bolea I, Nikolic K, Agbaba D, Moraleda I et al (2014) Design, synthesis, pharmacological evaluation, QSAR analysis, molecular modeling and ADMET of novel donepezil-indolyl hybrids as multipotent cholinesterase/monoamine oxidase inhibitors for the potential treatment of Alzheimer’s disease. Eur J Med Chem 75:82–95PubMedCrossRef Bautista-Aguilera OM, Esteban G, Bolea I, Nikolic K, Agbaba D, Moraleda I et al (2014) Design, synthesis, pharmacological evaluation, QSAR analysis, molecular modeling and ADMET of novel donepezil-indolyl hybrids as multipotent cholinesterase/monoamine oxidase inhibitors for the potential treatment of Alzheimer’s disease. Eur J Med Chem 75:82–95PubMedCrossRef
59.
go back to reference Bautista-Aguilera OM, Samadi A, Chioua M, Nikolic K, Filipic S, Agbaba D et al (2014) N-Methyl-N-((1-methyl-5-(3-(1-(2-methylbenzyl)piperidin-4yl)propoxy)-1H-indol-2-yl)methyl)prop-2-yn-1-amine, a new cholinesterase and monoamine oxidase dual inhibitor. J Med Chem 57(24):10455–10463PubMedCrossRef Bautista-Aguilera OM, Samadi A, Chioua M, Nikolic K, Filipic S, Agbaba D et al (2014) N-Methyl-N-((1-methyl-5-(3-(1-(2-methylbenzyl)piperidin-4yl)propoxy)-1H-indol-2-yl)methyl)prop-2-yn-1-amine, a new cholinesterase and monoamine oxidase dual inhibitor. J Med Chem 57(24):10455–10463PubMedCrossRef
60.
go back to reference Bautista-Aguilera OM, Esteban G, Chioua M, Nikolic K, Agbaba D, Moraleda I et al (2014) Multipotent cholinesterase/monoamine oxidase inhibitors for the treatment of Alzheimer’s disease: design, synthesis, biochemical evaluation, ADMET, molecular modeling, and QSAR analysis of novel donepezil-pyridyl hybrids. Drug Des Dev Ther 8:1893–1910 Bautista-Aguilera OM, Esteban G, Chioua M, Nikolic K, Agbaba D, Moraleda I et al (2014) Multipotent cholinesterase/monoamine oxidase inhibitors for the treatment of Alzheimer’s disease: design, synthesis, biochemical evaluation, ADMET, molecular modeling, and QSAR analysis of novel donepezil-pyridyl hybrids. Drug Des Dev Ther 8:1893–1910
61.
go back to reference Butini S, Nikolic K, Kassel S, Bruckmann H, Filipic S, Agbaba D et al (2016) Polypharmacology of dopamine receptor ligands. Prog Neurobiol 142:68–103PubMedCrossRef Butini S, Nikolic K, Kassel S, Bruckmann H, Filipic S, Agbaba D et al (2016) Polypharmacology of dopamine receptor ligands. Prog Neurobiol 142:68–103PubMedCrossRef
62.
go back to reference Micheli F (2011) Recent advances in the development of dopamine D3 receptor antagonists: a medicinal chemistry perspective. ChemMedChem 6(7):1152–1162PubMedCrossRef Micheli F (2011) Recent advances in the development of dopamine D3 receptor antagonists: a medicinal chemistry perspective. ChemMedChem 6(7):1152–1162PubMedCrossRef
63.
go back to reference Kiss B, Horvath A, Nemethy Z, Schmidt E, Laszlovszky I, Bugovics G et al (2010) Cariprazine (RGH-188), a dopamine D-3 receptor-preferring, D-3/D-2 dopamine receptor antagonist-partial agonist antipsychotic candidate. In vitro and neurochemical profile. J Pharmacol Exp Ther 333(1):328–340PubMedCrossRef Kiss B, Horvath A, Nemethy Z, Schmidt E, Laszlovszky I, Bugovics G et al (2010) Cariprazine (RGH-188), a dopamine D-3 receptor-preferring, D-3/D-2 dopamine receptor antagonist-partial agonist antipsychotic candidate. In vitro and neurochemical profile. J Pharmacol Exp Ther 333(1):328–340PubMedCrossRef
64.
go back to reference Meng XY, Zhang HX, Mezei M, Cui M (2011) Molecular docking: a powerful approach for structure-based drug discovery. Curr Comput Aided Drug Des 7(2):146–157PubMedPubMedCentralCrossRef Meng XY, Zhang HX, Mezei M, Cui M (2011) Molecular docking: a powerful approach for structure-based drug discovery. Curr Comput Aided Drug Des 7(2):146–157PubMedPubMedCentralCrossRef
65.
go back to reference Wu GS, Robertson DH, Brooks CL, Vieth M (2003) Detailed analysis of grid-based molecular docking: a case study of CDOCKER - A CHARMm-based MD docking algorithm. J Comput Chem 24(13):1549–1562PubMedCrossRef Wu GS, Robertson DH, Brooks CL, Vieth M (2003) Detailed analysis of grid-based molecular docking: a case study of CDOCKER - A CHARMm-based MD docking algorithm. J Comput Chem 24(13):1549–1562PubMedCrossRef
66.
go back to reference 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):43–53PubMedCrossRef 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):43–53PubMedCrossRef
67.
go back to reference Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS et al (2009) AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem 30(16):2785–2791PubMedPubMedCentralCrossRef Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS et al (2009) AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem 30(16):2785–2791PubMedPubMedCentralCrossRef
68.
go back to reference Bolea I, Juarez-Jimenez J, de Los Rios C, Chioua M, Pouplana R, Luque FJ et al (2011) Synthesis, biological evaluation, and molecular modeling of donepezil and N-[(5-(benzyloxy)-1-methyl-1H-indol-2-yl)methyl]-N-methylprop-2-yn-1-amine hybrids as new multipotent cholinesterase/monoamine oxidase inhibitors for the treatment of Alzheimer’s disease. J Med Chem 54(24):8251–8270PubMedCrossRef Bolea I, Juarez-Jimenez J, de Los Rios C, Chioua M, Pouplana R, Luque FJ et al (2011) Synthesis, biological evaluation, and molecular modeling of donepezil and N-[(5-(benzyloxy)-1-methyl-1H-indol-2-yl)methyl]-N-methylprop-2-yn-1-amine hybrids as new multipotent cholinesterase/monoamine oxidase inhibitors for the treatment of Alzheimer’s disease. J Med Chem 54(24):8251–8270PubMedCrossRef
69.
go back to reference Marco-Contelles J, Leon R, de los Rios C, Guglietta A, Terencio J, Lopez MG et al (2006) Novel multipotent tacrine-dihydropyridine hybrids with improved acetylcholinesterase inhibitory and neuroprotective activities as potential drugs for the treatment of Alzheimer’s disease. J Med Chem 49(26):7607–7610PubMedCrossRef Marco-Contelles J, Leon R, de los Rios C, Guglietta A, Terencio J, Lopez MG et al (2006) Novel multipotent tacrine-dihydropyridine hybrids with improved acetylcholinesterase inhibitory and neuroprotective activities as potential drugs for the treatment of Alzheimer’s disease. J Med Chem 49(26):7607–7610PubMedCrossRef
70.
go back to reference Marco-Contelles J, Leon R, de los Rios C, Samadi A, Bartolini M, Andrisano V et al (2009) Tacripyrines, the First tacrine-dihydropyridine hybrids, as multitarget-directed ligands for the treatment of Alzheimer’s disease. J Med Chem 52(9):2724–2732PubMedCrossRef Marco-Contelles J, Leon R, de los Rios C, Samadi A, Bartolini M, Andrisano V et al (2009) Tacripyrines, the First tacrine-dihydropyridine hybrids, as multitarget-directed ligands for the treatment of Alzheimer’s disease. J Med Chem 52(9):2724–2732PubMedCrossRef
71.
go back to reference Leon 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):139–189PubMedCrossRef Leon 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):139–189PubMedCrossRef
73.
go back to reference Rankovic Z (2015) Designing CNS drugs for optimal brain exposure. Blood–brain barrier in drug discovery. Wiley, Hoboken, pp 385–424 Rankovic Z (2015) Designing CNS drugs for optimal brain exposure. Blood–brain barrier in drug discovery. Wiley, Hoboken, pp 385–424
74.
go back to reference Rankovic Z (2015) CNS drug design: balancing physicochemical properties for optimal brain exposure. J Med Chem 58(6):2584–2608PubMedCrossRef Rankovic Z (2015) CNS drug design: balancing physicochemical properties for optimal brain exposure. J Med Chem 58(6):2584–2608PubMedCrossRef
75.
go back to reference Bingham M, Rankovic Z (2012) Chapter 18: medicinal chemistry challenges in CNS drug discovery. Drug discovery for psychiatric disorders. The Royal Society of Chemistry, Cambridge, pp 465–509CrossRef Bingham M, Rankovic Z (2012) Chapter 18: medicinal chemistry challenges in CNS drug discovery. Drug discovery for psychiatric disorders. The Royal Society of Chemistry, Cambridge, pp 465–509CrossRef
76.
go back to reference Hitchcock SA, Pennington LD (2006) Structure-brain exposure relationships. J Med Chem 49(26):7559–7583PubMedCrossRef Hitchcock SA, Pennington LD (2006) Structure-brain exposure relationships. J Med Chem 49(26):7559–7583PubMedCrossRef
77.
go back to reference Leeson PD, Springthorpe B (2007) The influence of drug-like concepts on decision-making in medicinal chemistry. Nat Rev Drug Discov 6(11):881–890PubMedCrossRef Leeson PD, Springthorpe B (2007) The influence of drug-like concepts on decision-making in medicinal chemistry. Nat Rev Drug Discov 6(11):881–890PubMedCrossRef
78.
go back to reference Leeson PD, Davis AM (2004) Time-related differences in the physical property profiles of oral drugs. J Med Chem 47(25):6338–6348PubMedCrossRef Leeson PD, Davis AM (2004) Time-related differences in the physical property profiles of oral drugs. J Med Chem 47(25):6338–6348PubMedCrossRef
79.
go back to reference Weiss MM, Williamson T, Babu-Khan S, Bartberger MD, Brown J, Chen K et al (2012) Design and preparation of a potent series of hydroxyethylamine containing beta-secretase inhibitors that demonstrate robust reduction of central beta-amyloid. J Med Chem 55(21):9009–9024PubMedCrossRef Weiss MM, Williamson T, Babu-Khan S, Bartberger MD, Brown J, Chen K et al (2012) Design and preparation of a potent series of hydroxyethylamine containing beta-secretase inhibitors that demonstrate robust reduction of central beta-amyloid. J Med Chem 55(21):9009–9024PubMedCrossRef
80.
go back to reference Raub TJ, Lutzke BS, Andrus PK, Sawada GA, Staton BA (2006) Early preclinical evaluation of brain exposure in support of hit identification and lead optimization. In: Borchardt RT, Kerns EH, Hageman MJ, Thakker DR, Stevens JL (eds) Optimizing the “Drug-Like” properties of leads in drug discovery. Springer, New York, pp 355–410CrossRef Raub TJ, Lutzke BS, Andrus PK, Sawada GA, Staton BA (2006) Early preclinical evaluation of brain exposure in support of hit identification and lead optimization. In: Borchardt RT, Kerns EH, Hageman MJ, Thakker DR, Stevens JL (eds) Optimizing the “Drug-Like” properties of leads in drug discovery. Springer, New York, pp 355–410CrossRef
81.
go back to reference Alelyunas YW, Empfield JR, McCarthy D, Spreen RC, Bui K, Pelosi-Kilby L et al (2010) Experimental solubility profiling of marketed CNS drugs, exploring solubility limit of CNS discovery candidate. Bioorg Med Chem Lett 20(24):7312–7316PubMedCrossRef Alelyunas YW, Empfield JR, McCarthy D, Spreen RC, Bui K, Pelosi-Kilby L et al (2010) Experimental solubility profiling of marketed CNS drugs, exploring solubility limit of CNS discovery candidate. Bioorg Med Chem Lett 20(24):7312–7316PubMedCrossRef
82.
go back to reference Ghose AK, Herbertz T, Hudkins RL, Dorsey BD, Mallamo JP (2012) Knowledge-based, central nervous system (CNS) lead selection and lead optimization for CNS drug discovery. ACS Chem Neurosci 3(1):50–68PubMedCrossRef Ghose AK, Herbertz T, Hudkins RL, Dorsey BD, Mallamo JP (2012) Knowledge-based, central nervous system (CNS) lead selection and lead optimization for CNS drug discovery. ACS Chem Neurosci 3(1):50–68PubMedCrossRef
83.
go back to reference Hitchcock SA (2012) Structural modifications that alter the P-glycoprotein efflux properties of compounds. J Med Chem 55(11):4877–4895PubMedCrossRef Hitchcock SA (2012) Structural modifications that alter the P-glycoprotein efflux properties of compounds. J Med Chem 55(11):4877–4895PubMedCrossRef
84.
go back to reference Desai PV, Sawada GA, Watson IA, Raub TJ (2013) Integration of in silico and in vitro tools for scaffold optimization during drug discovery: predicting P-glycoprotein efflux. Mol Pharm 10(4):1249–1261PubMedCrossRef Desai PV, Sawada GA, Watson IA, Raub TJ (2013) Integration of in silico and in vitro tools for scaffold optimization during drug discovery: predicting P-glycoprotein efflux. Mol Pharm 10(4):1249–1261PubMedCrossRef
85.
go back to reference Kozikowski A, Roth B, Tropsha A (2006) Why academic drug discovery makes sense. Science 313(5791):1235–1236PubMedCrossRef Kozikowski A, Roth B, Tropsha A (2006) Why academic drug discovery makes sense. Science 313(5791):1235–1236PubMedCrossRef
86.
go back to reference Patridge E, Gareiss P, Kinch M, Hoyer D (2015) An analysis of original research contributions toward FDA-approved drugs. Drug Discov Today 20(10):1182–1187PubMedCrossRef Patridge E, Gareiss P, Kinch M, Hoyer D (2015) An analysis of original research contributions toward FDA-approved drugs. Drug Discov Today 20(10):1182–1187PubMedCrossRef
87.
go back to reference Carlsson J, Coleman RG, Setola V, Irwin JJ, Fan H, Schlessinger A et al (2011) Ligand discovery from a dopamine D-3 receptor homology model and crystal structure. Nat Chem Biol 7(11):769–778PubMedPubMedCentralCrossRef Carlsson J, Coleman RG, Setola V, Irwin JJ, Fan H, Schlessinger A et al (2011) Ligand discovery from a dopamine D-3 receptor homology model and crystal structure. Nat Chem Biol 7(11):769–778PubMedPubMedCentralCrossRef
88.
go back to reference Warne T, Serrano-Vega M, Baker J, Moukhametzianov R, Edwards P, Henderson R et al (2008) Structure of a β1-adrenergic G-protein-coupled receptor. Nature 454(7203):486–491PubMedPubMedCentralCrossRef Warne T, Serrano-Vega M, Baker J, Moukhametzianov R, Edwards P, Henderson R et al (2008) Structure of a β1-adrenergic G-protein-coupled receptor. Nature 454(7203):486–491PubMedPubMedCentralCrossRef
89.
go back to reference Munk C, Isberg V, Mordalski S, Harpsøe K, Rataj K, Hauser AS et al (2016) GPCRdb: the G protein-coupled receptor database—an introduction. Biochem Pharmacol 173(14):2195–2207 Munk C, Isberg V, Mordalski S, Harpsøe K, Rataj K, Hauser AS et al (2016) GPCRdb: the G protein-coupled receptor database—an introduction. Biochem Pharmacol 173(14):2195–2207
90.
go back to reference Bautista-Aguilera O, Hagenow Stefanie, Palomino-Antolin Alejandra, Farré-Alins Víctor, Ismaili Lhassane, Joffrin Pierre-Louis et al (2017) Multitarget-directed ligands combining cholinesterase and monoamine oxidase inhibition with H3R antagonism for neurodegenerative diseases. Angew Chem 56:12765–12769CrossRef Bautista-Aguilera O, Hagenow Stefanie, Palomino-Antolin Alejandra, Farré-Alins Víctor, Ismaili Lhassane, Joffrin Pierre-Louis et al (2017) Multitarget-directed ligands combining cholinesterase and monoamine oxidase inhibition with H3R antagonism for neurodegenerative diseases. Angew Chem 56:12765–12769CrossRef
91.
go back to reference Roth S, Kholodenko B, Smit M, Bruggeman F (2015) G protein-coupled receptor signalling networks from a systems perspective. Mol Pharmacol 88(3):604–616PubMedCrossRef Roth S, Kholodenko B, Smit M, Bruggeman F (2015) G protein-coupled receptor signalling networks from a systems perspective. Mol Pharmacol 88(3):604–616PubMedCrossRef
92.
go back to reference Wacker D, Stevens R, Roth B (2017) How ligands illuminate GPCR molecular pharmacology. Cell Tissue Res 170(3):414–427 Wacker D, Stevens R, Roth B (2017) How ligands illuminate GPCR molecular pharmacology. Cell Tissue Res 170(3):414–427
93.
go back to reference Jazayeri A, Andrews S, Marshall F (2017) Structurally enabled discovery of adenosine A2A receptor antagonists. Chem Rev 117(1):21–37PubMedCrossRef Jazayeri A, Andrews S, Marshall F (2017) Structurally enabled discovery of adenosine A2A receptor antagonists. Chem Rev 117(1):21–37PubMedCrossRef
94.
go back to reference Kasai R, Suzuki K, Prossnitz E, Koyama-Honda I, Nakada C, Fujiwara T et al (2011) Full characterization of GPCR monomer-dimer dynamic equilibrium by single molecule imaging. J Cell Biol 192(3):463–480PubMedPubMedCentralCrossRef Kasai R, Suzuki K, Prossnitz E, Koyama-Honda I, Nakada C, Fujiwara T et al (2011) Full characterization of GPCR monomer-dimer dynamic equilibrium by single molecule imaging. J Cell Biol 192(3):463–480PubMedPubMedCentralCrossRef
95.
go back to reference Rodríguez-Ruiz M, Moreno E, Moreno-Delgado D, Navarro G, Mallol J, Cortés A et al (2017) Heteroreceptor complexes formed by dopamine D1, histamine H3, and N-methyl-d-aspartate glutamate receptors as targets to prevent neuronal death in Alzheimer’s disease. Mol Neurobiol 54(6):4537–4550PubMedCrossRef Rodríguez-Ruiz M, Moreno E, Moreno-Delgado D, Navarro G, Mallol J, Cortés A et al (2017) Heteroreceptor complexes formed by dopamine D1, histamine H3, and N-methyl-d-aspartate glutamate receptors as targets to prevent neuronal death in Alzheimer’s disease. Mol Neurobiol 54(6):4537–4550PubMedCrossRef
96.
go back to reference Marshall F (2016) Visualizing GPCR ‘Megaplexes’ which enable sustained intracellular signaling. Trends Biochem Sci 41(12):985–986PubMedCrossRef Marshall F (2016) Visualizing GPCR ‘Megaplexes’ which enable sustained intracellular signaling. Trends Biochem Sci 41(12):985–986PubMedCrossRef
97.
go back to reference Copeland RA (2005) Evaluation of enzyme inhibitors in drug discovery: a guide for medicinal chemists and pharmacologists. Wiley, Hoboken Copeland RA (2005) Evaluation of enzyme inhibitors in drug discovery: a guide for medicinal chemists and pharmacologists. Wiley, Hoboken
98.
go back to reference Tipton KF (2002) Principles of enzyme assay and kinetic studies. In: Eisenthal R, Danson MJ (eds) Enzyme assays: a practical approach, vol 257. Oxford University Press, London, pp 1–47 Tipton KF (2002) Principles of enzyme assay and kinetic studies. In: Eisenthal R, Danson MJ (eds) Enzyme assays: a practical approach, vol 257. Oxford University Press, London, pp 1–47
100.
go back to reference Ramsay RR, Tipton KF (2017) Assessment of enzyme inhibition: a review with examples from the development of monoamine oxidase and cholinesterase inhibitory drugs. Molecules 22(7):1192CrossRef Ramsay RR, Tipton KF (2017) Assessment of enzyme inhibition: a review with examples from the development of monoamine oxidase and cholinesterase inhibitory drugs. Molecules 22(7):1192CrossRef
101.
go back to reference Bar-Am O, Amit T, Youdim MB, Weinreb O (2016) Neuroprotective and neurorestorative potential of propargylamine derivatives in ageing: focus on mitochondrial targets. J Neural Transm 123(2):125–135PubMedCrossRef Bar-Am O, Amit T, Youdim MB, Weinreb O (2016) Neuroprotective and neurorestorative potential of propargylamine derivatives in ageing: focus on mitochondrial targets. J Neural Transm 123(2):125–135PubMedCrossRef
102.
go back to reference Naoi M, Maruyama W (2010) Monoamine oxidase inhibitors as neuroprotective agents in age-dependent neurodegenerative disorders. Curr Pharm Des 16(25):2799–2817PubMedCrossRef Naoi M, Maruyama W (2010) Monoamine oxidase inhibitors as neuroprotective agents in age-dependent neurodegenerative disorders. Curr Pharm Des 16(25):2799–2817PubMedCrossRef
104.
go back to reference Johnson M, Bobrovskaya L (2015) An update on the rotenone models of Parkinson’s disease: their ability to reproduce the features of clinical disease and model gene-environment interactions. Neurotoxicology 46:101–116PubMedCrossRef Johnson M, Bobrovskaya L (2015) An update on the rotenone models of Parkinson’s disease: their ability to reproduce the features of clinical disease and model gene-environment interactions. Neurotoxicology 46:101–116PubMedCrossRef
105.
go back to reference Zhang L, Trushin S, Christensen TA, Bachmeier BV, Gateno B, Schroeder A et al (2017) Altered brain energetics induces mitochondrial fission arrest in Alzheimer’s disease. Sci Rep 6:18725CrossRef Zhang L, Trushin S, Christensen TA, Bachmeier BV, Gateno B, Schroeder A et al (2017) Altered brain energetics induces mitochondrial fission arrest in Alzheimer’s disease. Sci Rep 6:18725CrossRef
106.
go back to reference Reddy P, Manczak M, Kandimalla R (2017) Mitochondria-targeted small molecule SS31: a potential candidate for the treatment of Alzheimer’s disease. Hum Mol Genet 26(8):1483–1496PubMedCrossRef Reddy P, Manczak M, Kandimalla R (2017) Mitochondria-targeted small molecule SS31: a potential candidate for the treatment of Alzheimer’s disease. Hum Mol Genet 26(8):1483–1496PubMedCrossRef
107.
go back to reference Sharpe M, Han J, Baskin A, Baskin D (2015) Design and synthesis of a MAO-B-selectively activated prodrug based on MPTP: a mitochondria-targeting chemotherapeutic agent for treatment of human malignant gliomas. ChemMedChem 10:621–628PubMedCrossRef Sharpe M, Han J, Baskin A, Baskin D (2015) Design and synthesis of a MAO-B-selectively activated prodrug based on MPTP: a mitochondria-targeting chemotherapeutic agent for treatment of human malignant gliomas. ChemMedChem 10:621–628PubMedCrossRef
108.
go back to reference Nadanaciva S, Aleo M, Strock C, Stedman D, Wang H, Will Y (2013) Toxicity assessments of nonsteroidal anti-inflammatory drugs in isolated mitochondria, rat hepatocytes, and zebrafish show good concordance across chemical classes. Toxicol Appl Pharmacol 272(2):263–271CrossRef Nadanaciva S, Aleo M, Strock C, Stedman D, Wang H, Will Y (2013) Toxicity assessments of nonsteroidal anti-inflammatory drugs in isolated mitochondria, rat hepatocytes, and zebrafish show good concordance across chemical classes. Toxicol Appl Pharmacol 272(2):263–271CrossRef
109.
go back to reference De Deurwaerdere P, Binda C, Corne R, Leone C, Valeri A, Valoti M et al (2017) Comparative analysis of the neurochemical profile and MAO inhibition properties of N-(furan-2-ylmethyl)-N-methylprop-2-yn-1-amine. ACS Chem Neurosci 8(5):1026–1035PubMedCrossRef De Deurwaerdere P, Binda C, Corne R, Leone C, Valeri A, Valoti M et al (2017) Comparative analysis of the neurochemical profile and MAO inhibition properties of N-(furan-2-ylmethyl)-N-methylprop-2-yn-1-amine. ACS Chem Neurosci 8(5):1026–1035PubMedCrossRef
110.
go back to reference Geerts H, Spiros A, Roberts P (2015) Assessing the synergy between cholinomimetics and memantine as augmentation therapy in cognitive impairment in schizophrenia. A virtual human patient trial using quantitative systems pharmacology. Front Pharmacol 6:198PubMedPubMedCentralCrossRef Geerts H, Spiros A, Roberts P (2015) Assessing the synergy between cholinomimetics and memantine as augmentation therapy in cognitive impairment in schizophrenia. A virtual human patient trial using quantitative systems pharmacology. Front Pharmacol 6:198PubMedPubMedCentralCrossRef
111.
go back to reference Golde TE (2016) Overcoming translational barriers impeding development of Alzheimer’s disease modifying therapies. J Neurochem 139:224–236PubMedCrossRef Golde TE (2016) Overcoming translational barriers impeding development of Alzheimer’s disease modifying therapies. J Neurochem 139:224–236PubMedCrossRef
Metadata
Title
A perspective on multi-target drug discovery and design for complex diseases
Authors
Rona R. Ramsay
Marija R. Popovic-Nikolic
Katarina Nikolic
Elisa Uliassi
Maria Laura Bolognesi
Publication date
01-12-2018
Publisher
Springer Berlin Heidelberg
Published in
Clinical and Translational Medicine / Issue 1/2018
Electronic ISSN: 2001-1326
DOI
https://doi.org/10.1186/s40169-017-0181-2

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