2D-SAR and 3D-QSAR analyses for acetylcholinesterase inhibitors

Molecular Diversity

Volumn 21, Issue 2, 2017, Pages 413-426

  Niu, Bing ^a   Zhao, Manman ^a   Su, Qiang ^a   Zhang, Mengying ^a   Lv, Wei ^a   Chen, Qin ^a   Chen, Fuxue ^a   Chu, Dechang ^b   Du, Dongshu ^a,b   Zhang, Yuhui ^c  

^a SHANGHAI UNIVERSITY   (China)

^b HEZE UNIVERSITY   (China)

^c SECOND MILITARY MEDICAL UNIVERSITY   (China)

Author keywords

2D SAR; 3D QSAR; Acetylcholinesterase inhibitors; AChE; Alzheimer s disease; Molecular docking

Indexed keywords

CHOLINESTERASE INHIBITOR; ACETYLCHOLINESTERASE;

ARTICLE; CHEMICAL INTERACTION; COMPARATIVE MOLECULAR FIELD ANALYSIS; DRUG ACTIVITY; IONIZATION; MOLECULAR DOCKING; PRIORITY JOURNAL; RANDOM FOREST; STRUCTURE ACTIVITY RELATION; THREE DIMENSIONAL QUANTITATIVE STRUCTURE ACTIVITY RELATION; TWO DIMENSIONAL STRUCTURE ACTIVITY RELATION; CHEMISTRY; ENZYME ACTIVE SITE; METABOLISM; QUANTITATIVE STRUCTURE ACTIVITY RELATION;

ACETYLCHOLINESTERASE; CATALYTIC DOMAIN; CHOLINESTERASE INHIBITORS; MOLECULAR DOCKING SIMULATION; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 85014590102     PISSN: 13811991     EISSN: 1573501X     Source Type: Journal    
DOI: 10.1007/s11030-017-9732-0     Document Type: Article

References (58)

1. Long CO, Dougherty J (2003) What’s new in Alzheimer’s disease? Home Healthc Nurse 21:14
2. Karolien B, Kristel S, Christine VB (2010) Current status on Alzheimer disease molecular genetics: from past, to present, to future. Hum Mol Genet R1:R4–R11. doi:10.1093/hmg/ddq142
3. Harris ME, Hensley K, Butterfield DA, Leedle RA, Carney JM (1995) Direct evidence of oxidative injury produced by the Alzheimer’s beta-amyloid peptide (1–40) in cultured hippocampal neurons. Exp Neurol 131:193–202
4. Dodart JC, Marr RA, Koistinaho M, Gregersen BM, Malkani S, Verma IM, Paul SM (2005) Gene delivery of human apolipoprotein E alters brain A β burden in a mouse model of Alzheimer’s disease. PNAS 102:1211–1216. doi:10.1073/pnas.0409072102
5. Lewczuk P, Esselmann H, Bibl M, Beck G, Maler Juan M, Otto M, Kornhuber J, Wiltfang J (2004) Tau protein phosphorylated at threonine 181 in CSF as a neurochemical biomarker in Alzheimer’s disease. J Mol Neurosci 23:115–122. doi:10.1385/JMN:23:1-2:115
6. Hardy J, Selkoe DJ (2002) The amyloid hypothesis of Alzheimer’s disease: progress and problems on the road to therapeutics. Science 297:353–356. doi:10.1126/science.1072994
7. Bartus RT, Dean RL, Beer B, Lippa AS (1982) The cholinergic hypothesis of geriatric memory dysfunction. Science 217:408–414. doi:10.1126/science.7046051
8. Dineley KT, Pandya AA, Yakel JL (2015) Nicotinic ACh receptors as therapeutic targets in CNS disorders. Trends Pharmacol Sci 36:96–108. doi:10.1016/j.tips.2014.12.002
9. Farlow M, Gracon SI, Hershey LA (1993) Tacrine for treatment of Alzheimer’s disease. Physician Assist 17:112
10. Sparano N (1998) Donepezil for Alzheimer’s disease. J Fam Pract 46:356
11. Nordberg PA, Svensson A-L (1998) Cholinesterase inhibitors in the treatment of Alzheimer’s disease. Drug Saf 19:465–480. doi:10.2165/00002018-199819060-00004
12. Lee S, Barron MG (2015) Development of 3D-QSAR model for acetylcholinesterase inhibitors using a combination of fingerprint, molecular docking, and structure-based pharmacophore approaches. Toxicol Sci 148:60–70. doi:10.1093/toxsci/kfv160
13. Ambure P, Kar S, Roy K (2014) Pharmacophore mapping-based virtual screening follow by molecular docking studies in search of potential acetylcholinesterase inhibitors as anti-Alzheimer’s agents. Biosystems 116:10–20. doi:10.1016/j.biosystems.2013.12.002
14. Pereira F, Latino DA, Gaudêncio SP (2015) QSAR-assisted virtual screening of lead-like molecules from marine and microbial natural sources for antitumor and antibiotic drug discovery. Molecules 20:4848–4873. doi:10.3390/molecules20034848
15. Chen HF, Dong XC, Zen BS, Gao K, Yuan SG, Panaye A, Doucet JP, Fan BT (2003) Virtual screening and rational drug design method using structure generation system based on 3D-QSAR and docking. SAR QSAR Environ Res 14:241–264. doi:10.1080/1062936032000101493
16. Bruno JN, Rafael FD, Mario RS, Cleber CM, Walter CGV, Ana CMA, João MR, Elid FCL, Ross P, Nicholas F, Eugene M, Lee K, Anne EC, Rodolpho CB, Floriano PS, Carolina HA (2016) Discovery of new anti-schistosomal hits by integration of QSAR-based virtual screening and high content screening. J Med Chem 59:7075–7088. doi:10.1021/acs.jmedchem.5b02038
17. Dash M, Liu H (2003) Consistency-based search in feature selection. Artif Intell 151:155–176. doi:10.1016/S0004-3702(03)00079-1
18. Bing N, Yuchao Z, Juan D, Yin L, Miao W, Wencong L, Xiaochen Y, Jinyuan Y (2014) Predicting network of drug-enzyme interaction based on machine learning method. BBA Proteins Proteom 1844:214–223. doi:10.1016/j.bbapap.2013.07.008
19. Sancetta A (2016) Greedy algorithms for prediction. Bernoulli 22:1227–1277. doi:10.3150/14-BEJ691
20. Hou C, Jiao L (2010) Selecting features of linear-chain conditional random fields via greedy stage-wise algorithms. Pattern Recognit Lett 31:151–162. doi:10.1016/j.patrec.2009.09.025
21. Liu Y, Tang F, Zeng Z (2015) Feature selection based on dependency margin. IEEE Trans Cybern 45:1209–1221. doi:10.1109/TCYB.2014.2347372
22. Zielosko B, Piliszczuk M (2008) Greedy algorithm for attribute reduction. Fund Inform 45:549–561. doi:10.1109/TCYB.2014.2347372
23. Pearson WR (2000) Flexible sequence similarity searching with the FASTA 3 program package. Methods Mol Biol 132:185–219
24. w= 8.8) earthquake of 27 February 2010. Adv Space Res 57:2464–2469. doi:10.1016/j.asr.2016.03.035
25. Cramer RD (2003) Topomer CoMFA: a design methodology for rapid lead optimization. J Med Chem 46:374–388. doi:10.1021/jm020194o
26. Piazzi L, Belluti F, Bisi A, Gobbi S, Rizzo S, Bartolini M, Andrisano V, Recanatini M, Rampa A (2007) Cholinesterase inhibitors: SAR and enzyme inhibitory activity of 3-[omega-(benzylmethylamino)alkoxy]xanthen-9-ones. Bioorg Med Chem 15:575–585. doi:10.1016/j.bmc.2006.09.026
27. Rosini M, Andrisano V, Bartolini M, Bolognesi ML, HreliaP Minarini A, Tarozzi A, Melchiorre C (2005) Rational approach to discover multipotent anti-Alzheimer drugs. J Med Chem 48:360–363. doi:10.1021/jm049112h
28. Recanatini M, Cavalli A, Belluti F, Piazzi L, Rampa A, Bisi A, Gobbi S, Valenti P, Andrisano V, Bartolini M, Cavrini V (2000) SAR of 9-amino-1,2,3,4-tetrahydroacridine-based acetylcholinesterase inhibitors: synthesis, enzyme inhibitory activity, QSAR, and structure-based CoMFA of tacrine analogues. J Med Chem 43:2007–2018. doi:10.1021/jm990971t
29. Rampa A, Piazzi L, Belluti F, Gobbi S, Bisi A, BartoliniM Andrisano V, Cavrini V, Cavalli A, Recanatini M, Valenti P (2001) Acetylcholinesterase inhibitors: SAR and kinetic studies onomega-[N-Methyl-N-(3-alkylcarbamoyloxyphenyl)methyl]aminoalkoxyaryl Derivatives. J Med Chem 44:3810–3820. doi:10.1021/jm010914b
30. Elsinghorst P, Tanarro C, Gutschow M (2006) Novel heterobivalent tacrine derivatives as cholinesterase inhibitors with notable selectivity toward butyrylcholinesterase. J Med Chem 49:7540–7544. doi:10.1021/jm060742o
31. Elsinghorst PW, Cieslik JS, Mohr K, Tränkle C, Gütschow M (2007) First gallamine-gacrinehybrid: design and characterization at cholinesterases and the M2 muscarinic receptor. J Med Chem 23:5685–5695. doi:10.1021/jm070859s
32. Camps P, Formosa X, Galdeano C, Gómez T, Muoz-Torrero D, Scarpellini M, Viayna E, Badia A, Clos MV, Camins A, Pallas M, Bartolini M, Mancini F, Andrisano V, Estelrich J, Lizondo M, Bidon-Chanal A, Luque FJ (2008) Novel donepezil-based inhibitors of acetyl and butyrylcholinesterase and acetylcholinesterase-induced β -amyloid aggregation. J Med Chem 51:3588–3598. doi:10.1021/jm8001313
33. Csizmadia F (2000) JChem: Java applets and modules supporting chemical database handling from web browsers. J Chem Inf Comp Sci 40:323–324. doi:10.1021/ci9902696
34. Sudhir V, Richard S (2006) Bias in error estimation when using cross-validation for model selection. BMC Bioinform 7:91–98. doi:10.1186/1471-2105-7-91
35. Wang L, Shen H, Li B, Hu D (2011) Classification of schizophrenic patients and healthy controls using multiple spatially independent components of structural MRI data. Front Electr Electron Eng China 6:353–362. doi:10.1007/s11460-011-0142-2
36. Zhang YP, Sussman N, Herbert S, Rosenkranz Klopman G (1997) Development of methods to ascertain the predictivity and consistency of SAR models: application to the U.S. national toxicology program rodent carcinogenicity bioassays. Quant Struct Act Relationsh 16:290–295. doi:10.1002/qsar.19970160403
37. Roy K, Das RN, Ambure P, Aher RB (2016) Be aware of error measures. Further studies on validation of predictive QSAR models. Chemometr Intell Lab 152:18–33. doi:10.1016/j.chemolab.2016.01.008
38. Shuling Y, Jintao Y, Jiahua S, Xiaojiao R, Ting Z, Yanli W, Yu D (2015) HQSAR and topomer CoMFA for predicting melanocortin-4 receptor binding affinities of trans-4-(4-chlorophenyl) pyrrolidine-3-carboxamides. Chemometr Intell Lab 146:34–41. doi:10.1016/j.chemolab.2015.04.017
39. Jilek R, Cramer R (2004) Topomers: a validated protocol for their self-consistent generation. J Chem Inf Comput Sci 44:1221–1227. doi:10.1021/ci049961d
40. Kumar S, Tiwari M (2015) Topomer-CoMFA-based predictive modelling on 2, 3-diarylsubstituted-1, 3-thiazolidin-4-ones as non-nucleoside reverse transcriptase inhibitors. Med Chem Res 24:245–257. doi:10.1007/s00044-014-1105-y
41. Bartolucci C, Perola E, Pilger C, Fels G, Lamba D (2001) Three-dimensional structure of a complex of galanthamine (Nivalin) with acetylcholinesterase from Torpedo Californica: Implications for the design of new anti-Alzheimer drugs. Proteins 42:182–191. doi:10.1002/1097-0134(20010201)42:2<182::AIDPROT50>3.0.CO;2-1
42. Ghose AK, Jaeger EP, Kowalczyk PJ, Peterson ML, Treasurywala AM (1993) Conformational searching methods for small molecules. I. Study of the sybyl search method. J Comput Chem 14:1050–1065. doi:10.1002/jcc.540140907
43. Smith DA, Beaumont K, Maurer TS, Di L (2015) Volume of distribution in drug design. J Med Chem 58:5691–5698. doi:10.1021/acs.jmedchem.5b00201
44. Ji WJ, Chung BH, Eung KK, Seo KY, Kim T (2015) The effects of Two non-steroidal anti-inflammatory drugs, bromfenac 0.1% and ketorolac 0.45%, on cataract surgery. Yonsei Med J 56:1671–1677. doi:10.3349/ymj.2015.56.6.1671
45. Pieńko T, Grudzien M, Taciak PP, Mazurek AP (2016) Cytisine basicity, solvation, log P, and log D theoretical determination as tool for bioavailability prediction. J Mol Graph Model 63:15–21. doi:10.1016/j.jmgm.2015.11.003
46. Xiang Y, Song J, Zhang Z (2014) Topomer CoMFA and virtual screening studies of azaindole class renin inhibitors. Comb Chem High Throughput Screen 17:458–472. doi:10.2174/1386207317666140107094708
47. Kumar S, Tiwari M (2015) Topomer-CoMFA-based predictive modelling on 2,3-diaryl-substituted-1,3-thiazolidin-4-ones as non-nucleoside reverse transcriptase inhibitors. Med Chem Res 24:245–257. doi:10.1007/s00044-014-1105-y
48. Nilewar SS, Kathiravan MK (2014) 3D CoMFA, CoMSIA, topomer CoMFA and HQSAR studies on aromatic acid esters for carbonic anhydrase inhibitory activity. J Chemom 28:60–70. doi:10.1002/cem.2574
49. Yuanxin T, Yudong S, Xianzuo Z, Lianbao Y, Zhonghuang L, Zhong L, Jiajie Z, Shuguang W (2014) Design some new type-I c-met inhibitors based on molecular docking and topomer CoMFA research. Mol Inf 33:536–543. doi:10.1002/minf.201300118
50. Tresadern G, Cid JM, Trabanco AA (2014) QSAR design of triazolopyridine mGlu2 receptor positive allosteric modulators. J Mol Graph Model 53:82–91. doi:10.1016/j.jmgm.2014.07.006
51. Sussman JL, Harel M, Frolow F, Oefner C, Goldman A, TokerL Silman I (1991) Atomic structure of acetylcholinesterase from Torpedo californica: a prototypic acetylcholine-binding protein. Science 253:872–879. doi:10.1126/science.1678899
52. Ordentlich A, Barak D, Kronman C, Flashner Y, Leitner M, Segall Y, Ariel N, Cohen S, Velan B, Shafferman A (1993) Dissection of the human acetylcholinesterase active center determinants of substrate specificity. Identification of residues constituting the anionic site, the hydrophobic site, and the acyl pocket. J Biol Chem 268:17083–17095
53. Yves B, Taylor P, Radic Z, Pascale M (2003) Structural insights into ligand interactions at the acetylcholinesterase peripheral anionic site. EMBO J 22:1–12. doi:10.1093/emboj/cdg005
54. Gibney G, Camp S, Dionne M, Mac QK, Taylor P (1990) Mutagenesis of essential functional residues in acetylcholinesterase. PANS 87:7546–7550
55. Harel M, Schalk I, Ehret-Sabatier L, Bouet F, Goeldner M, HirthC Axelsen PH, Silman I, Sussman JL (1993) Quaternary ligand binding to aromatic residues in the active-site gorge of acetylcholinesterase. Proc Natl Acad Sci 90:9031–9035
56. Shafferman A, Barak D, Kaplan D, Ordentlich A, Kronman C, Velan B (2005) Functional requirements for the optimal catalytic configuration of the AChE active center. Chem Biol Interact 157–158:123–131. doi:10.1016/j.cbi.2005.10.021
57. Carlacci L, Millard CB, Olson MA (2004) Conformational energy landscape of the acyl pocket loop in acetylcholinesterase: a Monte Carlo-generalized Born model study. Biophys Chem 111:143–157. doi:10.1016/j.bpc.2004.05.007
58. Ordentlich A, Barak D, Kronman C, Ariel N, Segall Y, VelanB Shafferman A (1998) Functional characteristics of the oxyanion hole in human acetylcholinesterase. J Biol Chem 273:19509–19517. doi:10.1074/jbc.273.31.19509