Exploring molecular structural requirement for AChE inhibition through multi-chemometric and dynamics simulation analyses

References

• Akula, N., Lecanu, L., Greeson, J., & Papadopoulos, V. (2006). 3D QSAR studies of AChE inhibitors based on molecular docking scores and CoMFA. Bioorganic & Medicinal Chemistry Letters, 16, 6277–6280. doi:10.1016/j.bmcl.2006.09.030
   PubMed Web of Science ®Google Scholar
• Ali, M. A., Yar, M. S., Hasan, M. Z., Ahsan, M. J., & Pandian, S. (2009). Design, synthesis and evaluation of novel 5,6-dimethoxy-1-oxo-2,3-dihydro-1H-2-indenyl-3,4-substituted phenyl methanone analogues. Bioorganic & Medicinal Chemistry Letters, 19, 5075–5077. doi:10.1016/j.bmcl.2009.07.042
   PubMed Web of Science ®Google Scholar
• Ali, M. A., Ismail, R., Choon, T. S., Yoon, Y. K., Wei, A. C., & Pandian, S. (2010). Substituted spiro [2.3’] oxindolespiro [3.2’’]-5,6-dimethoxy-indane-1’’-one-pyrrolidine analogue as inhibitors of acetylcholinesterase. Bioorganic & Medicinal Chemistry Letters, 20, 7064–7066. doi:10.1016/j.bmcl.2010.09.108
   PubMed Web of Science ®Google Scholar
• Balaji, S., Prasanna, D. S., & Rangappa, K. S. (2013). Docking, QSAR and CoMFA studies on arecoline analogues as muscarinic acetylcholine receptor (mAChR) M1 agonists. Proceedings of the Indian National Science Academy, 79, 41–50.
   Google Scholar
• Barnard, E. A. (1974). Peripheral nervous. In J. I. Hubbard (Ed.), The peripheral nervous system (pp. 201–224). New York, NY: Plenum.10.1007/978-1-4615-8699-9
   Google Scholar
• Bas, D. C., Rogers, D. M., & Jensen, J. H. (2008). Very fast prediction and rationalization of pKa values for protein-ligand complexes. Proteins: Structure, Function, and Bioinformatics, 73, 765–783. doi:10.1002/prot.22102
   PubMed Web of Science ®Google Scholar
• Bernard, P. P., Kireev, D. B., Pintore, M., Chrétien, J. R., Fortier, P. L., & Froment, D. (2000). A CoMFA study of enantiomeric organophoshorus inhibitors of acetylcholinesterase. Journal of Molecular Modeling, 6, 618–629. doi:10.1007/s0089400060618
   Web of Science ®Google Scholar
• Bianchi, D. A., Hirschmann, G. S., Theoduloz, C., Bracca, A. B., & Kaufman, T. S. (2005). Synthesis of tricyclic analogs of stephaoxocanidine and their evaluation as acetylcholinesterase inhibitors. Bioorganic & Medicinal Chemistry Letters, 15, 2711–2715. doi:10.1016/j.bmcl.2005.04.005
   PubMed Web of Science ®Google Scholar
• Chaudhaery, S. S., Roy, K. K., Shakya, N., Saxena, G., Sammi, S. R., & Nazir, A. (2010). Novel carbamates as orally active acetylcholinesterase inhibitors found to improve scopolamine-induced cognition impairment: Pharmacophore-based virtual screening, synthesis, and pharmacology. Journal of Medicinal Chemistry, 53, 6490–6505. doi:10.1021/jm100573q
   PubMed Web of Science ®Google Scholar
• Cheung, J., Rudolph, M. J., Burshteyn, F., Cassidy, M. S., Gary, E. N., Love, J., … Height, J. J. (2012). Structures of human acetylcholinesterase in complex with pharmacologically important ligands. Journal of Medicinal Chemistry, 55, 10282–10286. doi:10.1021/jm300871x
   PubMed Web of Science ®Google Scholar
• de Souza, S. D., de Souza, A. M., de Sousa, A. C., Sodero, A. C., Cabral, L. M., & Albuquerque, M. G. (2012). Hologram QSAR Models of 4-[(Diethylamino)methyl]-phenol Inhibitors of Acetyl/Butyrylcholinesterase Enzymes as Potential Anti-Alzheimer Agents. Molecules, 17, 9529–9539. doi:10.3390/molecules17089529
   PubMed Web of Science ®Google Scholar
• Discovery studio 2.5. (2009) (a) LigandFit, (b) Pharmacophore. Retrieved from www.accelrys.com
   Google Scholar
• Eslami, M., Hashemianzadeh, S. M., Bagherzadeh, K., & Sajadi, S. A. S. (2016). Molecular perception of interactions between bis(7)tacrine and cystamine-tacrine dimer with cholinesterases as the promising proposed agents for the treatment of Alzheimer’s disease. Journal of Biomolecular Structure and Dynamics, 34, 855–869. doi:10.1080/07391102.2015.1057526.
   PubMed Web of Science ®Google Scholar
• Everitt, B. S. & Dunn, G. (2001). Applied multivariate data analysis. London: Arnold.10.1002/9781118887486
   Google Scholar
• Gonçalves, A. S., França, T. C. C., & Oliveira, O. V. (2016). Computational studies of acetylcholinesterase complexed with fullerene derivatives: A new insight for Alzheimer disease treatment. Journal of Biomolecular Structure and Dynamics, 34, 1307–1316. doi:10.1080/07391102.2015.1077345
   PubMed Web of Science ®Google Scholar
• Gurung, A. B., Aguan, K., Mitra, S., & Bhattacharjee, A. (2016). Identification of molecular descriptors for design of novel Isoalloxazine derivatives as potential Acetylcholinesterase inhibitors against Alzheimer’s disease. Journal of Biomolecular Structure and Dynamics, 1–14. doi:10.1080/07391102.2016.1192485
   PubMed Web of Science ®Google Scholar
• Han, S. Y., Mayer, S. C., Schweiger, E. J., Davis, B. M., & Joulleé, M. M. (1991). Synthesis and biological activity of galanthamine derivatives as acetylcholinesterase (AChE) inhibitors. Bioorganic & Medicinal Chemistry Letters, 1, 579–580. doi:10.1016/S0960-894X(01)81154-9
   Web of Science ®Google Scholar
• Huang, L., Luo, Z., He, F., Shi, A., Qin, F., & Li, X. (2010). Berberine derivatives, with substituted amino groups linked at the 9-position, as inhibitors of acetylcholinesterase/butyrylcholinesterase. Bioorganic & Medicinal Chemistry Letters, 20, 6649–6652. doi:10.1016/j.bmcl.2010.09.013
   PubMed Web of Science ®Google Scholar
• Jacquez, J. A. & Jacquez, G. M. (2002). Fisher’s randomization test and Darwin’s data – A footnote to the history of statistics. Mathematical Biosciences, 180, 23–28. doi:10.1016/S0025-5564(02)00123-2
   PubMed Web of Science ®Google Scholar
• Kallubai, M., Amineni, U., Mallavarapu, M., & Kadiyala, V. (2015). In Silico approach to support that p-nitrophenol monooxygenase from arthrobacter sp. Strain JS443 catalyzes the initial two sequential monooxygenations. Interdisciplinary Sciences, Computational Life Sciences, 7, 157–167. doi:10.1007/s12539-015-0018-x
   PubMed Web of Science ®Google Scholar
• Kanungo, T. M., Mount, D. M., Netanyahu, N. S., Piatko, C. D., Silverman, R., & Wu, A. Y. (2002). An efficient k-means clustering algorithm: analysis and implementation. IEEE Transactions on Pattern Analysis and Machine Intelligence, 24, 881–892. doi:10.1109/TPAMI.2002.1017616
   Web of Science ®Google Scholar
• Katzung, B. G. (2001). Basic and clinical pharmacology (pp. 75–91). Columbus, GA: The McGraw Hill Companies.
   Google Scholar
• Krall, W. J., Sramek, J. J., & Cutler, N. R. (1999). Cholinesterase inhibitors: A therapeutic strategy for alzheimer disease. Annals of Pharmacotherapy, 33, 441–450. doi:10.1345/aph.18211
   PubMed Web of Science ®Google Scholar
• Kubinyi, H. (1997). QSAR and 3D QSAR in drug design Part 1: Methodology. Drug Discovery Today, 2, 457–467. doi:10.1016/S1359-6446(97)01079-9
   Web of Science ®Google Scholar
• Leal, F. D., Lima, C. H., de Alencastro, R. B., Castro, H. C., Rodrigues, C. R., & Albuquerque, M. G. (2015). Hologram QSAR models of a series of 6-arylquinazolin-4-Amine inhibitors of a new alzheimer’s disease target: Dual specificity tyrosine-phosphorylation-regulated kinase-1A enzyme. International Journal of Molecular Sciences, 16, 5235–5253. doi:10.3390/ijms16035235
   PubMed Web of Science ®Google Scholar
• Li, H., Robertson, A. D., & Jensen, J. H. (2005). Very fast empirical prediction and rationalization of protein pKa values. Proteins: Structure, Function, and Bioinformatics, 61, 704–721. doi:10.1002/prot.20660
   PubMed Web of Science ®Google Scholar
• Lu, X., Lv, M., Huang, K., Ding, K., & You, Q. (2012). Pharmacophore and molecular docking guided 3D-QSAR study of bacterial enoyl-ACP reductase (FabI) inhibitors. International Journal of Molecular Sciences, 13, 6620–6638. doi:10.3390/ijms13066620
   PubMed Web of Science ®Google Scholar
• Malik, R., Gupta, R., Srivastava, S., Choudhary, B. S., & Sharma, M. (2016). Design, synthesis and biological evaluation of selected 3-[3-(amino) propoxy] benzenamines as acetylcholinesterase inhibitors. Journal of Biomolecular Structure and Dynamics, 1–13. doi:10.1080/07391102.2016.1220330
   Web of Science ®Google Scholar
• Mohammadi, T. & Ghayeb, Y. (2017). Atomic insight into designed carbamate-based derivatives as acetylcholine esterase (AChE) inhibitors: A computational study by multiple molecular docking and molecular dynamics simulation. Journal of Biomolecular Structure and Dynamics, 1–13. doi:10.1080/07391102.2016.1268977
   PubMed Web of Science ®Google Scholar
• Palin, R., Clark, J. K., Cowley, P., Muir, A. W., Pow, E., & Prosser, A. B. (2002). Novel piperidinium and pyridinium agents as water-soluble acetylcholinesterase inhibitors for the reversal of neuromuscular blockade. Bioorganic & Medicinal Chemistry Letters, 12, 2569–2572. doi:10.1016/S0960-894X(02)00483-3
   PubMed Web of Science ®Google Scholar
• Pan, L., Tan, J. H., Hou, J. Q., Huang, S. L., Gu, L. Q., & Huang, Z. S. (2008). Design, synthesis and evaluation of isaindigotone derivatives as acetylcholinesterase and butyrylcholinesterase inhibitors. Bioorganic & Medicinal Chemistry Letters, 18, 3790–3793. doi:10.1016/j.bmcl.2008.05.039
   PubMed Web of Science ®Google Scholar
• Pradeepkiran, J. A., Kumar, K. K., Kumar, Y. N., & Bhaskar, M. (2015). Modeling, molecular dynamics, and docking assessment of transcription factor rho: A potential drug target in Brucella melitensis 16M. Drug Design, Development and Therapy, 9, 1897–1912. doi:10.2147/DDDT.S77020
   PubMed Web of Science ®Google Scholar
• RCSB Protein Data Bank. (2016). Retrieved from http://www.rcsb.org
   Google Scholar
• Rahman, A. & Choudhary, M. I. (2001). Bioactive natural products as a potential source of new pharmacophores: A theory of memory. Pure and Applied Chemistry, 73, 555–560. doi:10.1351/pac200173030555
   Web of Science ®Google Scholar
• Ramar, V. & Pappu, S. (2016). Exploring the inhibitory potential of bioactive compound from Luffa acutangula against NF-κB—A molecular docking and dynamics approach. Computational Biology and Chemistry, 62, 29–35. doi:10.1016/j.compbiolchem.2016.03.006
   PubMed Web of Science ®Google Scholar
• Roy, K., Chakraborty, P., Mitra, I., Ojha, P. K., Kar, S., & Das, R. N. (2013). Some case studies on application of “rm2” metrics for judging quality of quantitative structure–activity relationship predictions: Emphasis on scaling of response data. Journal of Computational Chemistry, 34, 1071–1082. doi:10.1002/jcc.23231
   PubMed Web of Science ®Google Scholar
• Sabshin, M. D. (1997). Festschrift in honor of Melvin Sabshin, M.D., Medical Director American Psychiatric Association, 1974–1997. American Journal of Psychiatry, 154, 1–92. doi:10.1176/ajp.154.6.1
   Web of Science ®Google Scholar
• Sadashiva, C. T., Narendra Sharath Chandra, J. N., Ponnappa, K. C., Veerabasappa Gowda, T., & Rangappa, K. S. (2006). Synthesis and efficacy of 1-[bis(4-fluorophenyl)-methyl]piperazine derivatives for acetylcholinesterase inhibition, as a stimulant of central cholinergic neurotransmission in Alzheimer’s disease. Bioorganic & Medicinal Chemistry Letters, 16, 3932–3936. doi:10.1016/j.bmcl.2006.05.030
   PubMed Web of Science ®Google Scholar
• Saravanan, K., Kalaiarasi, C., & Kumaradhas, P. (2017). Understanding the conformational flexibility and electrostatic properties of curcumin in the active site of rhAChE via molecular docking, molecular dynamics, and charge density analysis. Journal of Biomolecular Structure and Dynamics, 1–21. doi:10.1080/07391102.2016.1264891
   PubMed Web of Science ®Google Scholar
• Sastry, G. M., Adzhigirey, M., Day, T., Annabhimoju, R., & Sherman, W. (2013). Protein and ligand preparation: Parameters, protocols, and influence on virtual screening enrichments. Journal of Computer-Aided Molecular Design, 27, 221–234. doi:10.1007/s10822-013-9644-8
   PubMed Web of Science ®Google Scholar
• Schott, Y., Decker, M., Rommelspacher, H., & Lehmann, J. (2006). 6-Hydroxy- and 6-methoxy-β-carbolines as acetyl- and butyrylcholinesterase inhibitors. Bioorganic & Medicinal Chemistry Letters, 16, 5840–5843. doi:10.1016/j.bmcl.2006.08.067
   PubMed Web of Science ®Google Scholar
• Schulze, M., Siol, O., Decker, M., & Lehmann, J. (2010). Bivalent 5,8,9,13b-tetrahydro-6H-isoquino[1,2-a]isoquinolines and -isoquinolinium salts: Novel heterocyclic templates for butyrylcholinesterase inhibitors. Bioorganic & Medicinal Chemistry Letters, 20, 2946–2949. doi:10.1016/j.bmcl.2010.03.011
   PubMed Web of Science ®Google Scholar
• Shao, D., Zou, C., Luo, C., Tang, X., & Li, Y. (2004). Synthesis and evaluation of tacrine-E2020 hybrids as acetylcholinesterase inhibitors for the treatment of Alzheimer’s disease. Bioorganic & Medicinal Chemistry Letters, 14, 4639–4642. doi:10.1016/j.bmcl.2004.07.005
   PubMed Web of Science ®Google Scholar
• Srivastava, V., Kumar, A., Mishra, B. N., & Siddiqi, M. I. (2008). CoMFA and CoMSIA 3D-QSAR analysis of DMDP derivatives as anti-cancer agents. Bioinformation, 2, 384–391.10.6026/bioinformation
   PubMedGoogle Scholar
• Sybyl. 7.3 (2006) St. Louis: Tripos Inc. www.tripos.com.
   Google Scholar
• Taha, M. O., Habash, M., Al-Hadidi, Z., Al-Bakri, A., Younis, K., & Sisan, S. (2011). Docking-based comparative intermolecular contacts analysis as new 3-D QSAR concept for validating docking studies and in silico screening: NMT and GP inhibitors as case studies. Journal of Chemical Information and Modeling, 51, 647–669. doi:10.1021/ci100368t
   PubMed Web of Science ®Google Scholar
• Takahashi, J., Hijikuro, I., Kihara, T., Murugesh, M. G., Fuse, S., & Tsumura, Y. (2010). Design, synthesis and evaluation of carbamate-modified (−)-N1-phenethylnorphysostigmine derivatives as selective butyrylcholinesterase inhibitors. Bioorganic & Medicinal Chemistry Letters, 20, 1721–1723. doi:10.1016/j.bmcl.2010.01.035
   PubMed Web of Science ®Google Scholar
• Tang, H., Ning, F. X., Wei, Y. B., Huang, S. L., Huang, Z. S., & Chan, A. S. (2007). Derivatives of oxoisoaporphine alkaloids: A novel class of selective acetylcholinesterase inhibitors. Bioorganic & Medicinal Chemistry Letters, 17, 3765–3768. doi:10.1016/j.bmcl.2007.04.015
   PubMed Web of Science ®Google Scholar
• Tyagi, C., Gupta, A., Goyal, S., Dhanjal, J., & Grover, A. (2014). Fragment based group QSAR and molecular dynamics mechanistic studies on arylthioindole derivatives targeting the α-β interfacial site of human tubulin. BMC Genomics, 15, S3. doi:10.1186/1471-2164-15-S9-S3
   PubMed Web of Science ®Google Scholar
• Valasani, K. R., Chaney, M. O., Day, V. W., & ShiDu Yan, S. (2013). Acetylcholinesterase inhibitors: Structure based design, synthesis, pharmacophore modeling, and virtual screening. Journal of Chemical Information and Modeling, 53, 2033–2046. doi:10.1021/ci400196z
   PubMed Web of Science ®Google Scholar
• Vitorović-Todorović, M. D., Koukoulitsa, C., Juranić, I. O., Mandić, L. M., & Drakulić, B. J. (2014). Structural modifications of 4-aryl-4-oxo-2-aminylbutanamides and their acetyl- and butyrylcholinesterase inhibitory activity. Investigation of AChE-ligand interactions by docking calculations and molecular dynamics simulations. European Journal of Medicinal Chemistry, 81, 158–175. doi:10.1016/j.ejmech.2014.05.008
   PubMed Web of Science ®Google Scholar
• Voet, D. & Voet, J. (1995). Serine proteases Biochemistry (2nd ed.). (p. 390). New York, NY: John Wiley.
   Google Scholar
• Wen, H., Zhou, Y., Lin, C., Ge, H., Ma, L., & Wang, Z. (2007). Methyl 2-(2-(4-formylphenoxy)acetamido)-2-substituted acetate derivatives: A new class of acetylcholinesterase inhibitors. Bioorganic & Medicinal Chemistry Letters, 17, 2123–2125. doi:10.1016/j.bmcl.2007.01.091
   PubMed Web of Science ®Google Scholar
• Young, S., Fabio, K., Guillon, C., Mohanta, P., Halton, T. A., & Heck, D. E. (2010). Peripheral site acetylcholinesterase inhibitors targeting both inflammation and cholinergic dysfunction. Bioorganic & Medicinal Chemistry Letters, 20, 2987–2990. doi:10.1016/j.bmcl.2010.02.102
   PubMed Web of Science ®Google Scholar
• Yu, L., Cao, R., Yi, W., Yan, Q., Chen, Z., & Ma, L. (2010). Synthesis of 4-[(diethylamino)methyl]-phenol derivatives as novel cholinesterase inhibitors with selectivity towards butyrylcholinesterase. Bioorganic & Medicinal Chemistry Letters, 20, 3254–3258. doi:10.1016/j.bmcl.2010.04.059
   PubMed Web of Science ®Google Scholar
• Zaheer-ul-Haq, H., Wellenzohn, B., Tonmunphean, S., Khalid, A., Choudhary, M. I., & Rode, B. M. (2003). 3D-QSAR Studies on natural acetylcholinesterase inhibitors of Sarcococca saligna by comparative molecular field analysis (CoMFA). Bioorganic & Medicinal Chemistry Letters, 13, 4375–4380. doi:10.1016/j.bmcl.2003.09.034
   PubMed Web of Science ®Google Scholar
• Zhou, A., Hu, J., Wang, L., Zhong, G., Pan, J., & Wu, Z. (2015). Combined 3D-QSAR, molecular docking, and molecular dynamics study of tacrine derivatives as potential acetylcholinesterase (AChE) inhibitors of Alzheimer’s disease. Journal of Molecular Modeling, 21, 1. doi:10.1007/s00894-015-2797-8
   PubMed Web of Science ®Google Scholar
• Zhu, J., Li, X., Zhang, S., Ye, H., Zhao, H., Jin, H., & Han, W. (2016). Exploring stereochemical specificity of phosphotriesterase by MM-PBSA and MM-GBSA calculation and steered molecular dynamics simulation. Journal of Biomolecular Structure and Dynamics, 1–12. doi:10.1080/07391102.2016.1244494
   PubMed Web of Science ®Google Scholar