Simple structure-based approach for predicting the activity of inhibitors of beta-secretase (BACE1) associated with alzheimer's disease

Journal of Chemical Information and Modeling

Volumn 52, Issue 12, 2012, Pages 3302-3307

  Nastase, Anthony F ^a   Boyd, Donald B ^a  

^a Biology SL332   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL ANALYSIS; COMPUTATIONAL CHEMISTRY; GLYCOPROTEINS; HYDROGEN BONDS; MOLECULAR GRAPHICS; PROTEINS;

ALZHEIMER'S DISEASE; AMYLOID PRECURSOR PROTEINS; HYDROPHOBIC CONTACT; LINEAR CORRELATION COEFFICIENT; PROTEIN INHIBITORS; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIPS; STRUCTURAL BIOLOGY; STRUCTURE-BASED DESIGNS;

NEURODEGENERATIVE DISEASES;

PROTEINASE INHIBITOR; SECRETASE;

ALZHEIMER DISEASE; ARTICLE; CHEMISTRY; DRUG ANTAGONISM; DRUG DEVELOPMENT; ENZYMOLOGY; METHODOLOGY; PROTEIN DATABASE; QUANTITATIVE STRUCTURE ACTIVITY RELATION;

ALZHEIMER DISEASE; AMYLOID PRECURSOR PROTEIN SECRETASES; DATABASES, PROTEIN; DRUG DISCOVERY; PROTEASE INHIBITORS; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 84871602427     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci300331d     Document Type: Article

References (49)

1. Lefebvre, T. Neurodegeneration: Recall Sugars, Forget Alzheimer's Nat. Chem. Biol. 2012, 8, 325-326
2. http://www.alz.org/.
3. Kung, H. F. The β-Amyloid Hypothesis in Alzheimer's Disease; Seeing Is Believing ACS Med. Chem. Lett. 2012, 3, 265-267
4. Melnikova, I. Therapies for Alzheimer's Disease Nat. Rev. Drug Discovery 2007, 6, 341-342
5. Mattson, M. P. Pathways Towards and Away From Alzheimer's Disesase Nature 2004, 430, 631-639
6. Durell, S. R.; Guy, H. R.; Arispe, N.; Rojas, E.; Pollard, H. B. Theoretical Models of the Ion Channel Structure of Amyloid β-Protein Biophys. J. 1994, 67, 2137-2145
7. Diaz, J. C.; Simakova, O.; Jacobson, K. A.; Arispe, N.; Pollard, H. B. Small Molecule Blockers of the Alzheimer Aβ Calcium Channel Potently Protect Neurons from Aβ Cytotoxicity Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 3348-3353
8. John, V.; Beck, J. P.; Bienkowski, M. J.; Sinha, S.; Heinrikson, R. L. Human β-Secretase (BACE) and BACE Inhibitors J. Med. Chem. 2003, 46, 4625-4630
9. Ghosh, A. K.; Kumaragurubaran, N.; Hong, L.; Kulkarni, S. S.; Xu, X.; Chang, W.; Weerasena, V.; Turner, R.; Koelsch, G.; Bilcer, G.; Tang, J. Design, Synthesis, and X-ray Structure of Potent Memapsin 2 (β-Secretase) Inhibitors with Isophthalamide Derivatives as the P2-P3-Ligands J. Med. Chem. 2007, 50, 2399-2407
10. Edwards, P. D.; Albert, J. S.; Sylvester, M.; Aharony, D.; Andisik, D.; Callaghan, O.; Campbell, J. B.; Carr, R. A.; Chessari, G.; Congreve, M.; Frederickson, M.; Folmer, R. H. A.; Geschwindner, S.; Koether, G.; Kolmodin, K.; Krumrine, J.; Mauger, R. C.; Murray, C. W.; Olsson, L.-L.; Patel, S.; Spear, N.; Tian, G. Application of Fragment-Based Lead Generation to the Discovery of Novel, Cyclic Amidine β-Secretase Inhibitors with Nanomolar Potency, Cellular Activity, and High Ligand Efficiency J. Med. Chem. 2007, 50, 5912-5925
11. Ghosh, A. K.; Kumaragurubaran, N.; Hong, L.; Koelsh, G.; Tang, J. Memapsin 2 (Beta-Secretase) Inhibitors: Drug Development Curr. Alzheimer Res. 2008, 5, 121-131
12. Silvestri, R. Boom in the Development of Non-Peptidic β-Secretase (BACE1) Inhibitors for the Treatment of Alzheimer's Disease Med. Res. Rev. 2009, 29, 295-338
13. Klaver, D. W.; Wilce, M. C. J.; Cui, H.; Hung, A. C.; Gasperini, R.; Foa, L.; Small, D. H. Is BACE1 a Suitable Therapeutic Target for the Treatment of Alzheimer's Disease? Current Strategies and Future Directions Biol. Chem. 2010, 391, 849-859
14. Al-Tel, T. H.; Semreen, M. H.; Al-Qawasmeh, R. A.; Schmidt, M. F.; El-Awadi, R.; Ardah, M.; Zaarour, R.; Rao, S. N.; El-Agnaf, O. Design, Synthesis, and Qualitative Structure-Activity Evaluations of Novel β-Secretase Inhibitors as Potential Alzheimer's Drug Leads J. Med. Chem. 2011, 54, 8373-8385
15. May, P. C.; Dean, R. A.; Lowe, S. L.; Martenyi, F.; Sheehan, S. M.; Boggs, L. N.; Monk, S. A.; Mathes, B. M.; Mergott, D. J.; Watson, B. M.; Stout, S. L.; Timm, D. E.; LaBell, E. S.; Gonzales, C. R.; Nakano, M.; Jhee, S. S.; Yen, M.; Ereshefsky, L.; Lindstrom, T. D.; Calligaro, D. O.; Cocke, P. J.; Hall, D. G.; Friedrich, S.; Citron, M.; Audia, J. E. Robust Central Reduction of Amyloid-β in Humans with an Orally Available, Non-Peptidic β-Secretase Inhibitor J. Neurosci. 2011, 31 (46) 16507-16516
16. Harrison, C. Neurodegenerative Disease: Inhibiting β-Secretase in Humans. Nat. Rev. Drug Discovery 2012, 11, 21, http://www.nature.com/nrd/ journal/v11/n1/full/nrd3645.html.
17. http://newsroom.lilly.com/releasedetail.cfm?releaseid=702211.
18. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. The Protein Data Bank Nucleic Acids Res. 2000, 28, 235-242 http://www.rcsb.org/pdb/home/home.do
19. Manoharan, P.; Vijayan, R. S. K.; Ghoshal, N. Rationalizing Fragment Based Drug Discovery for BACE1: Insights from FB-QSAR, FB-QSSR, Multi Objective (MO-QSPR) and MIF Studies J. Comput.-Aided Mol. Des. 2010, 24, 843-864
20. Al-Nadaf, A.; Abu Sheikha, G.; Taha, M. O. Elaborate Ligand-based Pharmacophore Exploration and QSAR Analysis Guide the Synthesis of Novel Pyridinium-based Potent β-Secretase Inhibitory Leads Bioorg. Med. Chem. 2010, 18, 3088-3115
21. Todeschini, R.; Consonni, V. Molecular Descriptors for Chemoinformatics, Second, Revised and Enlarged ed., Vol. I: Alphabetical Listing; Wiley-VCH: Weinheim, Germany, 2009.
22. Boyd, D. B.; Herron, D. K.; Lunn, W. H. W.; Spitzer, W. A. Parabolic Relationships between Antibacterial Activity of Cephalosporins and Beta-Lactam Reactivity Predicted from Molecular Orbital Calculations J. Am. Chem. Soc. 1980, 102, 1812-1814
23. Boyd, D. B.; Seward, C. M. The Substituent Parameter Database: A Powerful Tool for QSAR Analysis. In QSAR: Rational Approaches to the Design of Bioactive Compounds; Silipo, C.; Vittoria, A., Eds.; Elsevier: Amsterdam, 1991; pp 167-170.
24. Moreland, J. L.; Gramada, A.; Buzko, O. V.; Zhang, Q.; Bourne, P. E. The Molecular Biology Toolkit (MBT): A Modular Platform for Developing Molecular Visualization Applications. BMC Bioinf. 2005, 6, 21, http://www.kukool.com/ ligand/help/, DOI: 10.1186/1471-2105-6-21.
25. Stierand, K.; Rarey, M. Drawing the PDB: Protein-Ligand Complexes in Two Dimensions ACS Med. Chem. Lett. 2010, 1, 540-545 http://www.poseview.de http://www.biosolveit.de/PoseView/index.html?ct=1, http://www.rcsb.org/pdb/ static.do?p=general-information/whats-new.jsp?b=1012#B1012-vis-protein-ligand
26. Stierand, K.; Maass, P. C.; Rarey, M. Molecular Complexes at a Glance: Automated Generation of Two-Dimensional Complex Diagrams Bioinformatics 2006, 22, 1710-1716
27. SAS Institute Inc.: 100 SAS Campus Drive, Cary, NC 27513-2414, http://www.jmp.com/software/.
28. JMP User Guide, Release 7; SAS Institute Inc.: Cary, NC, 2007.
29. Liu, T.; Lin, Y.; Wen, X.; Jorrisen, R. N.; Gilson, M. K. BindingDB: A Web-Accessible Database of Experimentally Determined Protein-Ligand Binding Affinities Nucleic Acids Res. 2007, 35, D198-D201 http://www.bindingdb.org/bind/ index.jsp
30. Chen, X.; Liu, M.; Gilson, M. K. Binding DB: A Web-Accessible Molecular Recognition Database Comb. Chem. High Throughput Screening 2001, 4, 719-725
31. Hu, L.; Benson, M. L.; Smith, R. D.; Lerner, M. G.; Carlson, H. A. Binding MOAD (Mother Of All Databases) Proteins: Struct., Funct., Bioinf. 2005, 60, 333-340 http://bindingmoad.org/ 10.1002/prot.20512
32. Benson, M. L.; Smith, R. D.; Khazanov, N. A.; Dimcheff, B.; Beaver, J.; Dresslar, P.; Nerothin, J.; Carlson, H. A. Binding MOAD, A High-Quality Protein-Ligand Database Nucleic Acids Res. 2008, 36, D674-D678
33. Clarke, B.; Demont, E.; Dingwall, C.; Dunsdon, R.; Faller, A.; Hawkins, J.; Hussain, I.; MacPherson, D.; Maile, G.; Matico, R.; Milner, P.; Mosley, J.; Naylor, A.; O'Brien, A.; Redshaw, S.; Riddell, D.; Rowland, P.; Soleil, V.; Smith, K. J.; Stanway, S.; Stemp, G.; Sweitzer, S.; Theobald, P.; Vesey, D.; Walter, D. S.; Ward, J.; Wayne, G. BACE-1 Inhibitors Part 2: Identification of Hydroxyl Ethylamines (HEAs) with Reduced Peptidic Character Bioorg. Med. Chem. Lett. 2008, 18, 1017-1021
34. Malamas, M. S.; Erdei, J.; Gunawan, I.; Turner, J.; Hu, Y.; Wagner, E.; Fan, K.; Chopra, R.; Olland, A.; Bard, J.; Jacobsen, S.; Magolda, R. L.; Pangalos, M.; Robichaud, A. J. Design and Synthesis of 5,5′-Disubstituted Aminohydantoins as Potent and Selective Human β-Secretase (BACE1) Inhibitors J. Med. Chem. 2010, 53, 1146-1158
35. Rajapakse, H. A.; Nantermet, P. G.; Selnick, H. G.; Munshi, S.; McGaughey, G. B.; Lindsley, S. R.; Young, M. B.; Lai, M.-T.; Espeseth, A. S.; Shi, X.-P.; Colussi, D.; Pietrak, B.; Crouthamel, M.-C.; Tugusheva, K.; Huang, Q.; Xu, M.; Simon, A. J.; Kuo, L.; Hazuda, D. J.; Graham, S.; Vacca, J. P. Discovery of Oxadiazoyl Tertiary Carbinamine Inhibitors of β-Secretase (BACE-1) J. Med. Chem. 2006, 49, 7270-7273
36. Hanessian, S.; Shao, Z.; Betschart, C.; Rondeau, J.-M.; Neumann, U.; Tintelnot-Blomley, M. Structure-Based Design and Synthesis of Novel P2/P3Modified, Non-Peptidic β-Secretase (BACE-1) Inhibitors Bioorg. Med. Chem. Lett. 2010, 20, 1924-1927
37. Clarke, B.; Demont, E.; Dingwall, C.; Dunsdon, R.; Faller, A.; Hawkins, J.; Hussain, I.; MacPherson, D.; Maile, G.; Matico, R.; Milner, P.; Mosley, J.; Naylor, A.; O'Brien, A.; Redshaw, S.; Riddell, D.; Rowland, P.; Soleil, V.; Smith, K. J.; Stanway, S.; Stemp, G.; Sweitzer, S.; Theobald, P.; Vesey, D.; Walter, D. S.; Ward, J.; Wayne, G. BACE-1 Inhibitors Part 1: Identification of Novel Hydroxy Ethylamines (HEAs) Bioorg. Med. Chem. Lett. 2008, 18, 1011-1016
38. Muegge, I.; Martin, Y. C. A General and Fast Scoring Function for Protein-Ligand Interactions: A Simplified Potential Approach J. Med. Chem. 1999, 42 (5) 791-804
39. Muegge, I. PMF Scoring Revisited J. Med. Chem. 2006, 49 (20) 5895-5902
40. Wang, R.; Lai, L.; Wang, S. Further Development and Validation of Empirical Scoring Functions for Structure-Based Binding Affinity Prediction J. Comput.-Aided Mol. Des. 2002, 16, 11-26
41. Wang, R.; Lu, Y.; Wang, S. Comparative Evaluation of 11 Scoring Functions for Molecular Docking J. Med. Chem. 2003, 46 (12) 2287-2303
42. Cheng, T.; Li, X.; Li, Y.; Liu, Z.; Wang, R. Comparative Assessment of Scoring Functions on a Diverse Test Set J. Chem. Inf. Model. 2009, 49 (4) 1079-1093
43. Zhang, X.; Li, X.; Wang, R. Interpretation of the Binding Affinities of PTP1B Inhibitors with the MM-GB/SA Method and the X-Score Scoring Function J. Chem. Inf. Model. 2009, 49 (4) 1033-1048
44. Case, D. A.; Cheatham, T. E., III; Darden, T.; Gohlke, H.; Luo, R.; Merz, K. M., Jr.; Onufriev, A.; Simmerling, C.; Wang, B.; Woods, R. J. The Amber Biomolecular Simulation Programs J. Comput. Chem. 2005, 26 (16) 1668-1688 http://ambermd.org/
45. Brooks, B. R.; Brooks, C. L., III; Mackerell, A. D., Jr.; Nilsson, L.; Petrella, R. J.; Roux, B.; Won, Y.; Archontis, G.; Bartels, C.; Boresch, S.; Caflisch, A.; Caves, L.; Cui, Q.; Dinner, A. R.; Feig, M.; Fischer, S.; Gao, J.; Hodoscek, M.; Im, W.; Kuczera, K.; Lazaridis, T.; Ma, J.; Ovchinnikov, V.; Paci, E.; Pastor, R. W.; Post, C. B.; Pu, J. Z.; Schaefer, M.; Tidor, B.; Venable, R. M.; Woodcock, H. L.; Wu, X.; Yang, W.; York, D. M.; Karplus, M. CHARMM: The Biomolecular Simulation Program J. Comput. Chem. 2009, 30 (10) 1545-1614 http://www.charmm.org 10.1002/jcc.21287
46. Hong, L.; Koelsch, G.; Lin, X.; Wu, S.; Terzyan, S.; Ghosh, A. K.; Zhang, X. C.; Tang, J. Structure of the Protease Domain of Memapsin 2 (β-Secretase) Complexed with Inhibitor Science 2000, 290 (5489) 150-153
47. Hong, L.; Tang, J. Flap Position of Free Memapsin 2 (β-Secretase), a Model for Flap Opening Aspartic Protease Catalysis Biochemistry 2004, 43, 4689-4695
48. Boyd, D. B. Progress in Rational Design of Therapeutically Interesting Compounds. In Rational Molecular Design in Drug Research, Proceedings of the Alfred Benzon Symposium No. 42, Liljefors, T.; Jorgensen, F. S.; Krogsgaard-Larsen, P., Eds.; Munksgaard: Copenhagen, 1998; pp 15-23.
49. Boyd, D. B. Is Rational Design Good for Anything? In Rational Drug Design: Novel Methodology and Practical Applications; Parrill, A. L.; Reddy, M. R., Eds.; ACS Symp. Series 719, American Chemical Society: Washington, DC, 1999; pp 346-356.