Predicting targets of compounds against neurological diseases using cheminformatic methodology

Journal of Computer-Aided Molecular Design

Volumn 29, Issue 2, 2015, Pages 183-198

  Nikolic, Katarina ^a   Mavridis, Lazaros ^b   Bautista Aguilera, Oscar M ^c   Marco Contelles, José ^c   Stark, Holger ^d   Do Carmo Carreiras, Maria ^e   Rossi, Ilaria ^f   Massarelli, Paola ^f   Agbaba, Danica ^a   Ramsay, Rona R ^b   Mitchell, John B O ^b  

^a UNIVERSITY OF BELGRADE   (Serbia)

^b UNIVERSITY OF ST ANDREWS   (United Kingdom)

^c INSTITUTO DE QUÍMICA ORGÁNICA GENERAL   (Spain)

^d HEINRICH HEINE UNIVERSITY   (Germany)

^e RESEARCH INSTITUTE FOR MEDICINES IMED ULISBOA   (Portugal)

^f UNIVERSITY OF SIENA   (Italy)

Author keywords

ChE; Circular fingerprints; Histamine H3 receptor; HMT; MAO; Multi targeted ligands; Off target study

Indexed keywords

COMPUTATIONAL CHEMISTRY; NEURODEGENERATIVE DISEASES;

CHE; CHEMINFORMATICS; CIRCULAR FINGERPRINT; HISTAMINE H3 RECEPTOR; HISTAMINES; HMT; MAO; MULTI-TARGETED LIGAND; MULTI-TARGETS; OFF-TARGET STUDY;

LIGANDS;

CLORGYLINE; DONEPEZIL; MONOAMINE OXIDASE INHIBITOR; SEROTONIN 1A RECEPTOR; SEROTONIN 2A RECEPTOR; SEROTONIN 2C RECEPTOR; TACRINE; ACETYLCHOLINESTERASE; AMINE OXIDASE (FLAVIN CONTAINING); HISTAMINE METHYLTRANSFERASE; LIGAND;

ALZHEIMER DISEASE; ANXIETY DISORDER; ARTICLE; CHEMICAL STRUCTURE; CHEMINFORMATICS; DEMENTIA; DEPRESSION; HUMAN; IC50; IN VITRO STUDY; INFORMATION SCIENCE; NEUROLOGIC DISEASE; NONHUMAN; PARKINSON DISEASE; PREDICTION; PRIORITY JOURNAL; PROTEIN TARGETING; QUANTITATIVE STRUCTURE ACTIVITY RELATION; RECEPTOR BINDING; SCHIZOPHRENIA; CHEMISTRY; DRUG DEVELOPMENT; FACTUAL DATABASE; METABOLISM; NERVOUS SYSTEM DISEASES;

ACETYLCHOLINESTERASE; ALZHEIMER DISEASE; DATABASES, FACTUAL; DRUG DISCOVERY; HISTAMINE N-METHYLTRANSFERASE; HUMANS; LIGANDS; MONOAMINE OXIDASE; NERVOUS SYSTEM DISEASES; PARKINSON DISEASE; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; RECEPTOR, SEROTONIN, 5-HT2A;

EID: 84922105008     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-014-9816-1     Document Type: Article

References (91)

1. Goedert M, Spillantini MGA (2006) A century of Alzheimer's disease. Science 314:777-781
2. Humbert-Claude M, Morisset S, Gbahou F, Arrang JM (2007) Histamine H3 and dopamine D2 receptor-mediated [35S]GTPγ[S] binding in rat striatum: evidence for additive effects but lack of interactions. Biochem Pharmacol 73:1172-1181
3. Garduno-Torres B, Trevino M, Gutierrez R, Arias-Montano JA (2007) Presynaptic histamine H3 receptors regulate glutamate, but not GABA release in rat thalamus. Neuropharmacology 52:527-535
4. Dai H, Fu Q, Shen Y, Hu W, Zhang Z, Timmerman H, Leurs R, Chen Z (2007) The histamine H3 receptor antagonist clobenpropit enhances GABA release to protect against NMDA induced excitotoxicity through the cAMP/protein kinase A pathway in cultured cortical neurons. Eur J Pharmacol 563:117-123
5. Threlfell S, Cragg SJ, Imre K, Turi GF, Coen CW, Greenfield SA (2004) Histamine H3 receptors inhibit serotonin release in substantia nigra pars reticulata. J Neurosci 24:8704-8710
6. Gemkow MJ, Davenport AJ, Harich S, Ellenbroek BA, Cesura A, Hallett D (2009) The histamine H3 receptor as a therapeutic drug target for CNS disorders. Drug Discov Today 14:509-515
7. 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 33:139-189
8. Millan MJ (2014) On 'polypharmacy' and multi-target agents, complementary strategies for improving the treatment of depression: a comparative appraisal. Int J Neuropsychopharmacol 17:1009-1037
9. Anighoro A, Bajorath J, Rastelli G (2014) Polypharmacology: challenges and opportunities in drug discovery. J Med Chem 57:7874-7887
10. Morphy R, Rankovic Z (2005) Designed multiple ligands. An emerging drug discovery paradigm. J Med Chem 48:6523-6543
11. 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 3:353-359
12. Lipina TV, Palomo V, Gil C, Martinez A, Roder JC (2013) Dual inhibitor of PDE7 and GSK-3-VP1.15 acts as antipsychotic and cognitive enhancer in C57BL/6J mice. Neuropharmacology 64:205-214
13. Lipina TV, Wang M, Liu F, Roder JC (2012) Synergistic interactions between PDE4B and GSK-3: DISC1 mutant mice. Neuropharmacology 62:1252-1262
14. Millan MJ (2006) Multi-target strategies for the improved treatment of depressive states: conceptual foundation and neuronal substrates, drug discovery and therapeutic application. Pharmacol Ther 110:135-370
15. Meltzer HY, Massey BW, Horiguchi M (2012) Serotonin receptors as targets for drugs useful to treat psychosis and cognitive impairment in schizophrenia. Curr Pharm Biotechnol 13:1572-1586
16. Quesseveur G, Nguyen HT, Gardier AM, Guiard BP (2012) 5-HT2 ligands in the treatment of anxiety and depression. Expert Opin Investig Drugs 21:1701-1725
17. Youdim MBH, Buccafusco JJ (2005) Multi-functional drugs for various CNS targets in the treatment of neurodegenerative disorders. Trends Pharmacol Sci 26:27-35
18. Tahtouh T, Elkins JM, Filippakopoulos P, Soundararajan M, Burgy G, Durieu E, Cochet C, Schmid RS, Lo DC, Delhommel F, Oberholzer AE, Pearl LH, Carreaux F, Bazureau JP, Knapp S, Meijer L (2012) Selectivity, cocrystal structures, and neuroprotective properties of leucettines, a family of protein kinase inhibitors derived from the marine sponge alkaloid leucettamine B. J Med Chem 55:9312-9330
19. Rosini M, Antonello A, Cavalli A, Bolognesi ML, Minarini A, Marucci G, Poggesi E, Leonardi A, Melchiorre C (2003) Prazosin-related compounds. Effect of transforming the piperazinylquinazoline moiety into an aminomethyltetrahydroacridine system on the affinity for α1-adrenoreceptors. J Med Chem 46:4895-4903
20. Fang L, Appenroth D, Decker M, Kiehntopf M, Roegler C, Deufel T, Fleck C, Peng S, Zhang Y, Lehmann J (2008) Synthesis and biological evaluation of NO-donor-tacrine hybrids as hepatoprotective anti-Alzheimer drug candidates. J Med Chem 51:713-716
21. Stosel A, Schlenk M, Hinz S, Kuppers P, Heer J, Gutschow M, Muller CE (2013) Dual targeting of adenosine A2A receptors and monoamine oxidase B by 4H-3,1-benzothiazin-4-ones. J Med Chem 56:4580-4596
22. Fang L, Kraus B, Lehmann J, Heilmann J, Zhang Y, Decker M (2008) Design and synthesis of tacrine-ferulic acid hybrids as multi-potent anti-Alzheimer drug candidates. Bioorg Med Lett 18:2905-2909
23. Jiménez JJ, Mendes E, Galdeano C, Martins C, Silva DB, Marco-Contelles J, Carmo Carreiras M, Luque FJ, Ramsay RR (2014) Exploring the structural basis of the selective inhibition of monoamine oxidase A by dicarbonitrile aminoheterocycles: role of Asn181 and Ile335 validated by spectroscopic and computational studies. Biochim Biophys Acta 1844:389-397
24. Bautista-Aguileraa OM, Estebanb G, Bolea I, Nikolic K, Agbaba D, Moraleda I, Iriepa I, Samadi A, Soriano E, Unzeta M, Marco-Contelles J (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 75:82-95
25. Samadi A, Chioua M, Bolea I, de los Ríos C, Iriepa I, Moraleda I, Bastida A, Esteban G, Unzeta M, Gálvez E, Marco-Contelles J (2011) Synthesis, biological assessment and molecular modeling of new multipotent MAO and cholinesterase inhibitors as potential drugs for the treatment of Alzheimer's disease. Eur J Med Chem 46:4665-4668
26. Bolea I, Juárez-Jiménez J, Ríos C, Chioua M, Pouplana R, Javier Luque F, Unzeta M, Marco-Contelles J, Samadi A (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 54:8251-8270
27. Pérez V, Marco-Contelles J, Fernández-Álvarez E, Unzeta M (1999) Relevance of benzyloxy group in 2-indolyl methylamines in the selective MAO-B inhibition. Br J Pharmacol 127:869-876
28. Marco-Contelles J, Leon R, RIos C, Guglietta A, Terencio J, Lopez MG, GarcIa AG, Villarroya M (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):7607-7610
29. Marco-Contelles J, Leon R, RIos C, Samadi A, Bartolini M, Andrisano V, Huertas O, Barril X, Luque FJ, RodrIguez-Franco MI, Lopez B, Lopez MG, GarcIa AG, Carmo Carreiras M, Villarroya M (2009) Tacripyrines, the first tacrine-dihydropyridine hybrids, as multitarget-directed ligands for the treatment of Alzheimer's disease. J Med Chem 52:2724-2732
30. Apelt J, Ligneau X, Pertz H, Arrang JM, Ganellin CR, Schwartz JC, Schunack W, Holger S (2002) Development of a new class of nonimidazole histamine H(3) receptor ligands with combined inhibitory histamine N-methyltransferase activity. J Med Chem 45:1128-1141
31. Petroianu G, Arafat K, Sasse BC, Stark H (2006) Multiple enzyme inhibitions by histamine H3 receptor antagonists as potential procognitive agents. Pharmazie 61:179-182
32. Grassmann S, Apelt J, Sippl W, Ligneau X, Pertz HH, Zhao YH, Arrang JM, Ganellin CR, Schwartz JC, Schunack W, Stark H (2003) Imidazole derivatives as a novel class of hybrid compounds with inhibitory histamine N-methyltransferase potencies and histamine H3 receptor affinities. Bioorg Med Chem 11:2163-2174
33. Grassmann S, Apelt J, Ligneau X, Pertz HH, Arrang JM, Schwartz JC, Schunack W, Stark H (2004) Search for histamine H(3) receptor ligands with combined inhibitory potency at histamine N-methyltransferase: omega-piperidinoalkanamine derivatives. Arch Pharm Med Chem 337:533-545
34. Apelt J, Grassmann S, Ligneau X, Pertz HH, Ganellin CR, Arrang JM, Schwartz JC, Schunack W, Stark H (2005) Search for histamine H3 receptor antagonists with combined inhibitory potency at Ntau-methyltransferase: ether derivatives. Pharmazie 60:97-106
35. Ligneau X, Lin JS, Vanni-Mercier G, Jouvet M, Muir JL, Ganellin CR, Stark H, Elz S, Schunack W, Schwartz JC (1998) Neurochemical and behavioural effects of ciproxifan, a potent histamine H3-receptor antagonist. J Pharmacol Exp Ther 287:658-666
36. Sander K, Kottke T, Stark H (2008) Histamine H3 receptor antagonists go to clinics. Biol Pharm Bull 31:2163-2181
37. Esbenshade TA, Browman KE, Bitner RS, Strakhova M, Cowart MD, Brioni JD (2008) The histamine H3 receptor: an attractive target for the treatment of cognitive disorders. Br J Pharmacol 154:1166-1181
38. Di Giovanni G, Di Matteo V, Pierucci M, Esposito E (2008) Serotonin-dopamine interaction: electrophysiological evidence. Prog Brain Res 172:45-71
39. Di Matteo V, Di Giovanni G, Pierucci M, Esposito E (2008) Serotonin control of central dopaminergic function: focus on in vivo microdialysis studies. Prog Brain Res 172:7-44
40. Carlsson M, Carlsson A (1990) Interactions between glutamatergic and monoaminergic systems within the basal ganglia - implications for schizophrenia and Parkinson 's disease. Trends Neurosci 13:272-276
41. Millan MJ (2005) N-Methyl-d-aspartate receptors as a target for improved antipsychotic agents: novel insights and clinical perspectives. Psychopharmacology 179:30-53
42. Rogawski MA, Wenk GL (2003) The neuropharmacological basis for the use of memantine in the treatment of Alzheimer's disease. CNS Drug Rev 9:275-308
43. Cummings JL, Morstorf T, Zhong K (2014) Alzheimer's disease drug-development pipeline: few candidates, frequent failures. Alzheimers Res Ther 6:37
44. Zheng H, Youdim MBH, Fridkin M (2009) Site-activated multifunctional chelator with acetylcholinesterase and neuroprotective-neurorestorative moieties for Alzheimer's therapy. J Med Chem 52:4095-4098
45. Cavalli A, Bolognesi ML, Minarini M, Rosini V, Tumiatti M, Recanatini C, Melchiorre C (2008) Multi-target-directed ligands to combat neurodegenerative diseases. J Med Chem 51:347-372
46. Cannon EO, Bender A, Palmer DS, Mitchell JBO (2006) Chemoinformatics-based classification of prohibited substances employed for doping in sport. J Chem Inf Model 5:2369-2380
47. Cannon EO, Mitchell JBO (2006) Classifying the World Anti-Doping Agency's 2005 prohibited list using the chemistry development kit fingerprint. Lect Notes Bioinform 5:173-182
48. Cannon EO, Nigsch F, Mitchell JBO (2008) Novel hybrid ultrafast shape descriptor method for use in virtual screening. Chem Central J 5:3
49. Paolini VG, Shapland RHB, Van Hoorn WP, Mason JS, Hopkins AL (2006) Global mapping of pharmacological space. Nat Biotechnol 5:805-815
50. Bender A, Scheiber J, Glick M, Davies JW, Azzaoui K, Hamon J, Urban L, Whitebread S, Jenkins JL (2007) Analysis of pharmacology data and the prediction of adverse drug reactions and off-target effects from chemical structure. Chem Med Chem 5:861-873
51. Nigsch F, Mitchell JBO (2008) Toxicological relationships between proteins obtained from protein target predictions of large toxicity databases. Toxicol Appl Pharmacol 5:225-234
52. Nigsch F, Bender A, Jenkins JL, Mitchell JBO (2008) Ligand-target prediction using winnow and naive bayesian algorithms and the implications of overall performance statistics. J Chem Inf Model 5:2313-2325
53. Keiser MJ, Setola V, Irwin JJ, Laggner C, Abbas AI, Hufeisen SJ, Jensen NH, Kuijer MB, Matos RC, Tran TB, Whaley R, Glennon RA, Hert J, Thomas KLH, Edwards DD, Shoichet BK, Roth BL (2009) Predicting new molecular targets for known drugs. Nature 5:175-181
54. Niijima S, Yabuuchi H, Okuno Y (2011) Cross-target view to feature selection: identification of molecular interaction features in ligand-target space. J Chem Inf Model 5:15-24
55. Lounkine E, Keiser MJ, Whitebread S, Mikhailov D, Hamon J, Jenkins JL, Lavan P, Weber E, Doak AK, Cote S, Shoichet BK, Urban L (2012) Large-scale prediction and testing of drug activity on side-effect targets. Nature 5:361-367
56. Perez-Nueno VI, Venkatraman V, Mavridis L, Ritchie DW (2012) Detecting drug promiscuity using gaussian ensemble screening. J Chem Inf Model 5:1948-1961
57. Glen RC, Bender A, Arnby CH, Carlsson L, Boyer S, Smith J (2006) Circular fingerprints: flexible molecular descriptors with applications from physical chemistry to ADME. IDrugs 9:199-204
58. Mavridis L, Mitchell JBO (2013) Predicting the protein targets for athletic performance-enhancing substances. J Cheminform 5:31
59. Gaulton A, Bellis LJ, Bento PA, Chambers J, Davies M, Hersey A, Light Y, McGlinchey S, Michalovich D, Al-Lazikani B, Overington JP (2012) ChEMBL: a large-scale bioactivity database for drug discovery. Nucl Acids Res 5:D1100-D1107
60. Knox C, Law V, Jewison T, Liu P, Ly S, Frolkis A, Pon A, Banco K, Mak C, Neveu V, Djoumbou Y, Eisner R, Guo AC, Whishart DS (2011) DrugBank 3.0: a comprehensive resource for 'omics' research on drugs. Nucl Acids Res 5:D1035-D1041
61. Mavridis L, Nath N, Mitchell JBO (2013) PFClust: a novel parameter free clustering algorithm. BMC Bioinform 14:213
62. Rogers DJ, Tanimoto TT (1960) A computer program for classifying plants. Science 5:1115-1118
63. Parzen E (1962) On estimation of a probability density function and mode. Ann Math Statist 5:1065-1076
64. Rosenblatt M (1956) Remarks on some nonparametric estimates of a density function. Ann Math Statist 5:832-837
65. Matthews BW (1975) Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim Biophys Acta 5:442-451
66. Hamacher A, Weigt M, Wiese M, Hoefgen B, Lehmann J, Kassack MU (2006) Dibenzazecine compounds with a novel dopamine/5HT2A receptor profile and 3D-QSAR analysis. BMC Pharmacol 6:11
67. ChemAxon MarvinSketch 5.5.1.0 program (2011) Budapest, Hungary. www.chemaxon.com/products.html
68. Froese Fischer CF (1977) The Hartree-Fock method for atoms: a numerical approach. Wiley, New York
69. Frisch MJ et al (1998) Gaussian 98 (Revision A.7). Gaussian Inc., Pittsburgh
70. Pentacle, Version 1.0.6. (2009) Molecular Discovery Ltd., Perugia, Italy. http://www.moldiscovery.com/soft-pentacle.php
71. Eriksson L, Johansson E, Kettaneh-Wold N, Trygg J, Wikstrom C, Wold S (eds) (2001) Multi-and megavariate data analysis. Basic principles and applications I, 2nd edn. Umetrics Academy, Umeå
72. Tropsha A (2010) Best practices for QSAR model development, validation, and exploitation. Mol Inf 29:476-488
73. 50) of an enzymatic reaction. Biochem Pharmacol 22:3099-3108
74. Scatchard G (1949) The attraction of proteins for small molecules and ions. Ann NY Acad Sci 51:660-672
75. 3H]-8-OH-DPAT). Biochem Pharmacol 35:1943-1949
76. 1C serotonin receptor binding. J Med Chem 35:4903-4910
77. Buhot MC, Martin S, Segu L (2000) Role of serotonin in memory impairment. Ann Med 32:210-221
78. Roth BL, Hanizavareh SM, Blum AE (2004) Serotonin receptors represent highly favorable molecular targets for cognitive enhancement in schizophrenia and other disorders. Psychopharmacology 174:17-24
79. Gray JA, Roth BL (2007) The pipeline and future of drug development in schizophrenia. Mol Psychiatry 12:904-922
80. Nakamura M, Ogasa M, Guarino J, Phillips D, Severs J, Cucchiaro J, Loebel A (2009) Lurasidone in the treatment of acute schizophrenia: a double-blind, placebo-controlled trial. J Clin Psychiatry 70:829-836
81. Patat A, Parks V, Raje S, Plotka A, Dietrich B (2005) Age-gender study of SRA-333, a novel 5-HT1A antagonist. Clin Pharmacol Ther 77:P29
82. Pitsikas N, Tsitsirigou S, Zisopoulou S, Sakellaridis N (2005) The 5-HT1A receptor and recognition memory. Possible modulation of its behavioral effects by the nitrergic system. Behav Brain Res 159:287-293
83. Schechter LE, Smith DL, Rosenzweig-Lipson S, Sukoff SJ, Dawson LA, Marquis K, Jones D, Piesla M, Andree T, Nawoschik S, Harder JA, Womack MD, Buccafusco J, Terry AV, Hoebel B, Rada P, Kelly M, Abou-Gharbia M, Barrett JE, Childers W (2005) Lecozotan (SRA-333): a selective serotonin 1A receptor antagonist that enhances the stimulated release of glutamate and acetylcholine in the hippocampus and possesses cognitive-enhancing properties. J Pharmacol Exp Ther 314:1274-1289
84. Ballanger B, Klinger H, Eche J, Lerond J, Vallet AE, Le Bars D, Tremblay L, Sgambato-Faure V, Broussolle E, Thobois S (2012) Role of serotonergic 1A receptor dysfunction in depression associated with Parkinson's disease. Mov Disord 27:84-89
85. Wallace TL, Ballard TM, Pouzet B, Riedel WJ, Wettstein JG (2011) Drug targets for cognitive enhancement in neuropsychiatric disorders. Pharmacol Biochem Behav 99:130-145
86. Terry AV Jr, Buccafusco JJ, Bartoszyk GD (2005) Selective serotonin 5-HT2A receptor antagonist EMD 281014 improves delayed matching performance in young and aged rhesus monkeys. Psychopharmacology 179:725-732
87. Onogi H, Ishigaki S, Nakagawasai O, Arai-Kato Y, Arai Y, Watanabe H, Miyamoto A, Tan-No K, Tadano T (2009) Influence of memantine on brain monoaminergic neurotransmission parameters in mice: neurochemical and behavioral study. Biol Pharm Bull 32:850-855
88. Reisberg B, Doody R, Stöffler A, Schmitt F, Ferris S, Möbius HJ (2006) A 24-week open-label extension study of memantine in moderate to severe Alzheimer disease. Arch Neurol 63:49-54
89. Kim HS, Park IS, Park WK (1998) NMDA receptor antagonists enhance 5-HT2 receptor-mediated behavior, head-twitch response, in mice. Life Sci 63:2305-2311
90. Nakagawasai O, Arai Y, Satoh SE, Satoh N, Neda M, Hozumi M, Oka R, Hiraga H, Tadano T (2004) Monoamine oxidase and head-twitch response in mice mechanisms of α-methylated substrate derivatives. Neurotoxicology 25:223-232
91. Raddatz R, Tao M, Hudkins RL (2010) Histamine H3 antagonists for treatment of cognitive deficits in CNS diseases. Curr Top Med Chem 10:153-169