Exploring the binding of BACE-1 inhibitors using comparative binding energy analysis (COMBINE)

BMC Structural Biology

Volumn 12, Issue , 2012, Pages

  Liu, Shu ^a   Fu, Rao ^a   Cheng, Xiao ^a   Chen, Sheng Ping ^a   Zhou, Li Hua ^a  

^a SUN YAT SEN UNIVERSITY   (China)

Author keywords

3D QSAR; BACE 1 Inhibitors; COMBINE; Superimposition

Indexed keywords

AMINOPYRIDINE DERIVATIVE; ARGININE; ASPARAGINE; BETA SECRETASE INHIBITOR; GLUTAMINE; GLYCINE; HYDROXYL GROUP; SERINE; THREONINE; TYROSINE;

ARTICLE; BINDING AFFINITY; BINDING SITE; CATALYSIS; COMPUTER PROGRAM; DIELECTRIC CONSTANT; DRUG DESIGN; DRUG POTENCY; DRUG STRUCTURE; HYDROGEN BOND; HYDROPHOBICITY; IC 50; LIGAND BINDING; MOLECULAR DOCKING; MOLECULAR INTERACTION; MOLECULAR WEIGHT; STATIC ELECTRICITY; STRUCTURE ACTIVITY RELATION; X RAY CRYSTALLOGRAPHY;

AMYLOID PRECURSOR PROTEIN SECRETASES; CATALYTIC DOMAIN; CRYSTALLOGRAPHY, X-RAY; DATABASES, PROTEIN; ENZYME INHIBITORS; LEAST-SQUARES ANALYSIS; LIGANDS; MODELS, MOLECULAR; PRINCIPAL COMPONENT ANALYSIS; PROTEIN BINDING; SOFTWARE; STATIC ELECTRICITY; THERMODYNAMICS;

EID: 84865319436     PISSN: None     EISSN: 14726807     Source Type: Journal    
DOI: 10.1186/1472-6807-12-21     Document Type: Article

References (88)

1. Comparison of analytical platforms for cerebrospinal fluid measures of beta-amyloid 1-42, total tau, and p-tau181 for identifying Alzheimer disease amyloid plaque pathology. Fagan AM, Shaw LM, Xiong C, Vanderstichele H, Mintun MA, Trojanowski JQ, Coart E, Morris JC, Holtzman DM, Arch Neurol 2011 68 9 1137 1144 10.1001/archneurol.2011.105 21555603
2. Calpain activation promotes BACE1 expression, amyloid precursor protein processing, and amyloid plaque formation in a transgenic mouse model of Alzheimer disease. Liang B, Duan BY, Zhou XP, Gong JX, Luo ZG, J Biol Chem 2010 285 36 27737 27744 10.1074/jbc.M110.117960 20595388
3. Association among amyloid plaque, lipid, and creatine in hippocampus of TgCRND8 mouse model for Alzheimer disease. Kuzyk A, Kastyak M, Agrawal V, Gallant M, Sivakumar G, Rak M, Del Bigio MR, Westaway D, Julian R, Gough KM, J Biol Chem 2010 285 41 31202 31207 10.1074/jbc.M110.142174 20682779
4. Reducing amyloid plaque burden via ex vivo gene delivery of an Abeta-degrading protease: a novel therapeutic approach to Alzheimer disease. Hemming ML, Patterson M, Reske-Nielsen C, Lin L, Isacson O, Selkoe DJ, PLoS Med 2007 4 8 262 10.1371/journal.pmed.0040262 17760499
5. Zhi P, Chia C Intracellular trafficking of the beta-secretase and processing of amyloid precursor protein. IUBMB Life, Gleeson PA 2011
6. Amyloid precursor protein mutation E682K at the alternative beta-secretase cleavage beta'-site increases Abeta generation. Zhou L, Brouwers N, Benilova I, Vandersteen A, Mercken M, Van Laere K, Van Damme P, Demedts D, Van Leuven F, Sleegers K, et al. EMBO Mol Med 2011 3 5 291 302 10.1002/emmm.201100138 21500352
7. The transcriptionally active amyloid precursor protein (APP) intracellular domain is preferentially produced from the 695 isoform of APP in a {beta}-secretase-dependent pathway. Belyaev ND, Kellett KA, Beckett C, Makova NZ, Revett TJ, Nalivaeva NN, Hooper NM, Turner AJ, J Biol Chem 2010 285 53 41443 41454 10.1074/jbc.M110.141390 20961856
8. Beta-Secretase inhibitor potency is decreased by aberrant beta-cleavage location of the «Swedish mutant» amyloid precursor protein. Yamakawa H, Yagishita S, Futai E, Ishiura S, J Biol Chem 2010 285 3 1634 1642 10.1074/jbc.M109.066753 19926793
9. The beta-secretase enzyme BACE1 as a therapeutic target for Alzheimer's disease. Vassar R, Kandalepas PC, Alzheimers Res Ther 2011 3 3 20 10.1186/alzrt82 21639952
10. Beta-secretase as a target for Alzheimer's disease drug discovery: an overview of in vitro methods for characterization of inhibitors. Mancini F, De Simone A, Andrisano V, Anal Bioanal Chem 2011 400 7 1979 1996 10.1007/s00216-011-4963-x 21503735
11. Beta-secretase as a therapeutic target for Alzheimer's disease. Ghosh AK, Gemma S, Tang J, Neurotherapeutics 2008 5 3 399 408 10.1016/j.nurt.2008.05.007 18625451
12. Beta-secretase (BACE) as a drug target for Alzheimer's disease. Vassar R, Adv Drug Deliv Rev 2002 54 12 1589 1602 10.1016/S0169-409X(02)00157-6 12453676
13. Neuronal and glial beta-secretase (BACE) protein expression in transgenic Tg2576 mice with amyloid plaque pathology. Rossner S, Apelt J, Schliebs R, Perez-Polo JR, Bigl V, J Neurosci Res 2001 64 5 437 446 10.1002/jnr.1095 11391698
14. Elaborate ligand-based pharmacophore exploration and QSAR analysis guide the synthesis of novel pyridinium-based potent beta-secretase inhibitory leads. Al-Nadaf A, Abu Sheikha G, Taha MO, Bioorg Med Chem 2010 18 9 3088 3115 10.1016/j.bmc.2010.03.043 20378363
15. Developing consensus 3D-QSAR and pharmacophore models for several beta-secretase, farnesyl transferase and histone deacetylase inhibitors. Wei HY, Chen GJ, Chen CL, Lin TH, J Mol Model 2012 18 12 675 692 21562827
16. Nino H, Garcia-Pintos I, Rodriguez-Borges JE, Escobar-Cubiella M, Garcia-Mera X, Prado-Prado F, Review of Synthesis Biological Assay and QSAR Studies of beta-Secretase Inhibitors, Curr Comput Aided Drug Des 2011
17. Molecular docking and 3D-QSAR studies on the binding mechanism of statine-based peptidomimetics with beta-secretase. Zuo Z, Luo X, Zhu W, Shen J, Shen X, Jiang H, Chen K, Bioorg Med Chem 2005 13 6 2121 2131 10.1016/j.bmc.2005.01.002 15727865
18. Novel non-peptide beta-secretase inhibitors derived from structure-based virtual screening and bioassay. Xu W, Chen G, Liew OW, Zuo Z, Jiang H, Zhu W, Bioorg Med Chem Lett 2009 19 12 3188 3192 10.1016/j.bmcl.2009.04.113 19447035
19. Impact of ligand protonation on virtual screening against beta-secretase (BACE1). Polgar T, Magyar C, Simon I, Keseru GM, J Chem Inf Model 2007 47 6 2366 2373 10.1021/ci700223p 17944457
20. Virtual screening for beta-secretase (BACE1) inhibitors reveals the importance of protonation states at Asp32 and Asp228. Polgar T, Keseru GM, J Med Chem 2005 48 11 3749 3755 10.1021/jm049133b 15916426
21. In silico discovery of beta-secretase inhibitors. Huang D, Luthi U, Kolb P, Cecchini M, Barberis A, Caflisch A, J Am Chem Soc 2006 128 16 5436 5443 10.1021/ja0573108 16620115
22. Discovery of cell-permeable non-peptide inhibitors of beta-secretase by high-throughput docking and continuum electrostatics calculations. Huang D, Luthi U, Kolb P, Edler K, Cecchini M, Audetat S, Barberis A, Caflisch A, J Med Chem 2005 48 16 5108 5111 10.1021/jm050499d 16078830
23. Dynamics in the Active Site of beta-Secretase: A Network Analysis of Atomistic Simulations. Mishra S, Caflisch A, Biochemistry 2011 50 43 9328 9339 10.1021/bi2011948 21942621
24. Functional plasticity in the substrate binding site of beta-secretase. Gorfe AA, Caflisch A, Structure 2005 13 10 1487 1498 10.1016/j.str.2005.06.015 16216580
25. Conformational flexibility of beta-secretase: molecular dynamics simulation and essential dynamics analysis. Xiong B, Huang XQ, Shen LL, Shen JH, Luo XM, Shen X, Jiang HL, Chen KX, Acta Pharmacol Sin 2004 25 6 705 713 15169620
26. Determination of the active site protonation state of beta-secretase from molecular dynamics simulation and docking experiment: implications for structure-based inhibitor design. Park H, Lee S, J Am Chem Soc 2003 125 52 16416 16422 10.1021/ja0304493 14692784
27. Identification of a small molecule nonpeptide active site beta-secretase inhibitor that displays a nontraditional binding mode for aspartyl proteases. Coburn CA, Stachel SJ, Li YM, Rush DM, Steele TG, Chen-Dodson E, Holloway MK, Xu M, Huang Q, Lai MT, et al. J Med Chem 2004 47 25 6117 6119 10.1021/jm049388p 15566281
28. Application of fragment screening by X-ray crystallography to beta-secretase. Murray CW, Callaghan O, Chessari G, Cleasby A, Congreve M, Frederickson M, Hartshorn MJ, McMenamin R, Patel S, Wallis N, J Med Chem 2007 50 6 1116 1123 10.1021/jm0611962 17315856
29. 2-Amino-3,4-dihydroquinazolines as inhibitors of BACE-1 (beta-site APP cleaving enzyme): Use of structure based design to convert a micromolar hit into a nanomolar lead. Baxter EW, Conway KA, Kennis L, Bischoff F, Mercken MH, Winter HL, Reynolds CH, Tounge BA, Luo C, Scott MK, et al. J Med Chem 2007 50 18 4261 4264 10.1021/jm0705408 17685503
30. Prediction of drug binding affinities by comparative binding energy analysis. Ortiz AR, Pisabarro MT, Gago F, Wade RC, J Med Chem 1995 38 14 2681 2691 10.1021/jm00014a020 7629807
31. Comparative binding energy analysis considering multiple receptors: a step toward 3D-QSAR models for multiple targets. Murcia M, Morreale A, Ortiz AR, J Med Chem 2006 49 21 6241 6253 10.1021/jm060350h 17034130
32. Comparative binding energy analysis of the substrate specificity of haloalkane dehalogenase from Xanthobacter autotrophicus GJ10. Kmunicek J, Luengo S, Gago F, Ortiz AR, Wade RC, Damborsky J, Biochemistry 2001 40 30 8905 8917 10.1021/bi010464p 11467952
33. Comparative binding energy analysis of HIV-1 protease inhibitors: incorporation of solvent effects and validation as a powerful tool in receptor-based drug design. Perez C, Pastor M, Ortiz AR, Gago F, J Med Chem 1998 41 6 836 852 10.1021/jm970535b 9526559
34. Comparative binding energy analysis for binding affinity and target selectivity prediction. Henrich S, Feierberg I, Wang T, Blomberg N, Wade RC, Proteins 2010 78 1 135 153 10.1002/prot.22579 19768680
35. Comparative binding energy (COMBINE) analysis of influenza neuraminidase-inhibitor complexes. Wang T, Wade RC, J Med Chem 2001 44 6 961 971 10.1021/jm001070j 11300878
36. Comparative binding energy (COMBINE) analysis of OppA-peptide complexes to relate structure to binding thermodynamics. Wang T, Wade RC, J Med Chem 2002 45 22 4828 4837 10.1021/jm020900l 12383008
37. Virtual screening with flexible docking and COMBINE-based models. Application to a series of factor Xa inhibitors. Murcia M, Ortiz AR, J Med Chem 2004 47 4 805 820 10.1021/jm030137a 14761183
38. gCOMBINE: A graphical user interface to perform structure-based comparative binding energy (COMBINE) analysis on a set of ligand-receptor complexes. Gil-Redondo R, Klett J, Gago F, Morreale A, Proteins 2010 78 1 162 172 10.1002/prot.22543 19705486
39. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, Lee M, Lee T, Duan Y, Wang W, et al. Acc Chem Res 2000 33 12 889 897 10.1021/ar000033j 11123888
40. What determines the van der Waals coefficient beta in the LIE (linear interaction energy) method to estimate binding free energies using molecular dynamics simulations? Wang W, Wang J, Kollman PA, Proteins 1999 34 3 395 402 10.1002/(SICI)1097-0134(19990215)34:3<395::AID-PROT11>3.0.CO;2-4 10024025
41. Ligand-based computer-aided pesticide design. A review of applications of the CoMFA and CoMSIA methodologies. Bordas B, Komives T, Lopata A, Pest Manag Sci 2003 59 4 393 400 10.1002/ps.614 12701699
42. Protein Data Bank website. http://www.rcsb.org/pdb/home/home.do
43. Superimposing the 27 crystal protein/inhibitor complexes of beta-secretase to calculate the binding affinities by the linear interaction energy method. Liu S, Zhou LH, Wang HQ, Yao ZB, Bioorg Med Chem Lett 2010 20 22 6533 6537 10.1016/j.bmcl.2010.09.050 20937559
44. Ensemble docking into flexible active sites. Critical evaluation of FlexE against JNK-3 and beta-secretase. Polgar T, Keseru GM, J Chem Inf Model 2006 46 4 1795 1805 10.1021/ci050412x 16859311
45. DS Viewer Version Accelrys, Inc, San Diego, CA, USA Available: http://www.accelrys.com
46. Analysis of crystal structures of aspartic proteinases: on the role of amino acid residues adjacent to the catalytic site of pepsin-like enzymes. Andreeva NS, Rumsh LD, Protein Sci 2001 10 12 2439 2450 10.1110/ps.ps.25801 11714911
47. Human immunodeficiency virus-1 protease. 1. Initial velocity studies and kinetic characterization of reaction intermediates by 18O isotope exchange. Hyland LJ, Tomaszek TA Jr, Roberts GD, Carr SA, Magaard VW, Bryan HL, Fakhoury SA, Moore ML, Minnich MD, Culp JS, et al. Biochemistry 1991 30 34 8441 8453 10.1021/bi00098a023 1883830
48. Modeling the protonation states of the catalytic aspartates in beta-secretase. Rajamani R, Reynolds CH, J Med Chem 2004 47 21 5159 5166 10.1021/jm049817j 15456259
49. Influence of protonation, tautomeric, and stereoisomeric states on protein-ligand docking results. ten Brink T, Exner TE, J Chem Inf Model 2009 49 6 1535 1546 10.1021/ci800420z 19453150
50. Electrostatic effects in proteins: comparison of dielectric and charge models. Mehler EL, Solmajer T, Protein Eng 1991 4 8 903 910 10.1093/protein/4.8. 903 1667878
51. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. Goodford PJ, J Med Chem 1985 28 7 849 857 10.1021/jm00145a002 3892003
52. Structure of the protease domain of memapsin 2 (beta-secretase) complexed with inhibitor. Hong L, Koelsch G, Lin X, Wu S, Terzyan S, Ghosh AK, Zhang XC, Tang J, Science 2000 290 5489 150 153 10.1126/science.290.5489.150 11021803
53. Crystal structure of memapsin 2 (beta-secretase) in complex with an inhibitor OM00-3. Hong L, Turner RT 3rd, Koelsch G, Shin D, Ghosh AK, Tang J, Biochemistry 2002 41 36 10963 10967 10.1021/bi026232n 12206667
54. Chemometrical identification of mutations in HIV-1 reverse transcriptase conferring resistance or enhanced sensitivity to arylsulfonylbenzonitriles. Rodriguez-Barrios F, Gago F, J Am Chem Soc 2004 126 9 2718 2719 10.1021/ja038893t 14995186
55. Modulation of binding strength in several classes of active site inhibitors of acetylcholinesterase studied by comparative binding energy analysis. Martin-Santamaria S, Munoz-Muriedas J, Luque FJ, Gago F, J Med Chem 2004 47 18 4471 4482 10.1021/jm049877p 15317459
56. Design, synthesis and SAR of potent statine-based BACE-1 inhibitors: exploration of P1 phenoxy and benzyloxy residues. Back M, Nyhlen J, Kvarnstrom I, Appelgren S, Borkakoti N, Jansson K, Lindberg J, Nystrom S, Hallberg A, Rosenquist S, et al. Bioorg Med Chem 2008 16 21 9471 9486 10.1016/j.bmc.2008.09. 041 18842420
57. Second generation of hydroxyethylamine BACE-1 inhibitors: optimizing potency and oral bioavailability. Charrier N, Clarke B, Cutler L, Demont E, Dingwall C, Dunsdon R, East P, Hawkins J, Howes C, Hussain I, et al. J Med Chem 2008 51 11 3313 3317 10.1021/jm800138h 18457381
58. Second generation of BACE-1 inhibitors. Part 1: The need for improved pharmacokinetics. Charrier N, Clarke B, Cutler L, Demont E, Dingwall C, Dunsdon R, Hawkins J, Howes C, Hubbard J, Hussain I, et al. Bioorg Med Chem 2009 19 13 3664 3668 10.1016/j.bmcl.2009.03.165
59. Potent and selective isophthalamide S2 hydroxyethylamine inhibitors of BACE1. Kortum SW, Benson TE, Bienkowski MJ, Emmons TL, Prince DB, Paddock DJ, Tomasselli AG, Moon JB, LaBorde A, TenBrink RE, Bioorg Med Chem Lett 2007 17 12 3378 3383 10.1016/j.bmcl.2007.03.096 17434734
60. Apo and inhibitor complex structures of BACE (beta-secretase). Patel S, Vuillard L, Cleasby A, Murray CW, Yon J, J Mol Biol 2004 343 2 407 416 10.1016/j.jmb.2004.08.018 15451669
61. BACE-1 inhibitors part 2: identification of hydroxy ethylamines (HEAs) with reduced peptidic character. Clarke B, Demont E, Dingwall C, Dunsdon R, Faller A, Hawkins J, Hussain I, MacPherson D, Maile G, Matico R, et al. Bioorg Med Chem Lett 2008 18 3 1017 1021 10.1016/j.bmcl.2007.12.019 18166458
62. Design, synthesis, and crystal structure of hydroxyethyl secondary amine-based peptidomimetic inhibitors of human beta-secretase. Maillard MC, Hom RK, Benson TE, Moon JB, Mamo S, Bienkowski M, Tomasselli AG, Woods DD, Prince DB, Paddock DJ, et al. J Med Chem 2007 50 4 776 781 10.1021/jm061242y 17300163
63. Conformationally biased P3 amide replacements of beta-secretase inhibitors. Stachel SJ, Coburn CA, Steele TG, Crouthamel MC, Pietrak BL, Lai MT, Holloway MK, Munshi SK, Graham SL, Vacca JP, Bioorg Med Chem Lett 2006 16 3 641 644 10.1016/j.bmcl.2005.10.032 16263281
64. Design, synthesis, and X-ray structure of potent memapsin 2 (beta-secretase) inhibitors with isophthalamide derivatives as the P2-P3-ligands. Ghosh AK, Kumaragurubaran N, Hong L, Kulkarni SS, Xu X, Chang W, Weerasena V, Turner R, Koelsch G, Bilcer G, et al. J Med Chem 2007 50 10 2399 2407 10.1021/jm061338s 17432843
65. Aminoethylenes: a tetrahedral intermediate isostere yielding potent inhibitors of the aspartyl protease BACE-1. Yang W, Lu W, Lu Y, Zhong M, Sun J, Thomas AE, Wilkinson JM, Fucini RV, Lam M, Randal M, et al. J Med Chem 2006 49 3 839 842 10.1021/jm0509142 16451048
66. Structure-based design of cycloamide-urethane-derived novel inhibitors of human brain memapsin 2 (beta-secretase). Ghosh AK, Devasamudram T, Hong L, DeZutter C, Xu X, Weerasena V, Koelsch G, Bilcer G, Tang J, Bioorg Med Chem Lett 2005 15 1 15 20 10.1016/j.bmcl.2004.10.084 15582402
67. Macrocyclic peptidomimetic beta-secretase (BACE-1) inhibitors with activity in vivo. Machauer R, Laumen K, Veenstra S, Rondeau JM, Tintelnot-Blomley M, Betschart C, Jaton AL, Desrayaud S, Staufenbiel M, Rabe S, et al. Bioorg Med Chem Lett 2009 19 5 1366 1370 10.1016/j.bmcl.2009.01.055 19195887
68. Structure-based design and synthesis of macroheterocyclic peptidomimetic inhibitors of the aspartic protease beta-site amyloid precursor protein cleaving enzyme (BACE). Hanessian S, Yang G, Rondeau JM, Neumann U, Betschart C, Tintelnot-Blomley M, J Med Chem 2006 49 15 4544 4567 10.1021/jm060154a 16854060
69. Design, synthesis, and SAR of macrocyclic tertiary carbinamine BACE-1 inhibitors. Lindsley SR, Moore KP, Rajapakse HA, Selnick HG, Young MB, Zhu H, Munshi S, Kuo L, McGaughey GB, Colussi D, et al. Bioorg Med Chem Lett 2007 17 14 4057 4061 10.1016/j.bmcl.2007.04.072 17482814
70. Discovery and SAR of isonicotinamide BACE-1 inhibitors that bind beta-secretase in a N-terminal 10s-loop down conformation. Stauffer SR, Stanton MG, Gregro AR, Steinbeiser MA, Shaffer JR, Nantermet PG, Barrow JC, Rittle KE, Collusi D, Espeseth AS, et al. Bioorg Med Chem Lett 2007 17 6 1788 1792 10.1016/j.bmcl.2006.12.051 17257835
71. Discovery of oxadiazoyl tertiary carbinamine inhibitors of beta-secretase (BACE-1). Rajapakse HA, Nantermet PG, Selnick HG, Munshi S, McGaughey GB, Lindsley SR, Young MB, Lai MT, Espeseth AS, Shi XP, et al. J Med Chem 2006 49 25 7270 7273 10.1021/jm061046r 17149856
72. Discovery and X-ray crystallographic analysis of a spiropiperidine iminohydantoin inhibitor of beta-secretase. Barrow JC, Stauffer SR, Rittle KE, Ngo PL, Yang Z, Selnick HG, Graham SL, Munshi S, McGaughey GB, Holloway MK, et al. J Med Chem 2008 51 20 6259 6262 10.1021/jm800914n 18811140
73. Rational design of novel, potent piperazinone and imidazolidinone BACE1 inhibitors. Cumming JN, Le TX, Babu S, Carroll C, Chen X, Favreau L, Gaspari P, Guo T, Hobbs DW, Huang Y, et al. Bioorg Med Chem Lett 2008 18 11 3236 3241 10.1016/j.bmcl.2008.04.050 18468890
74. Acylguanidine inhibitors of beta-secretase: optimization of the pyrrole ring substituents extending into the S1 and S3 substrate binding pockets. Cole DC, Stock JR, Chopra R, Cowling R, Ellingboe JW, Fan KY, Harrison BL, Hu Y, Jacobsen S, Jennings LD, et al. Bioorg Med Chem Lett 2008 18 3 1063 1066 10.1016/j.bmcl.2007.12.010 18162398
75. BACE-1 inhibition by a series of psi[CH2NH] reduced amide isosteres. Coburn CA, Stachel SJ, Jones KG, Steele TG, Rush DM, DiMuzio J, Pietrak BL, Lai MT, Huang Q, Lineberger J, et al. Bioorg Med Chem Lett 2006 16 14 3635 3638 10.1016/j.bmcl.2006.04.076 16690314
76. Potent pyrrolidine- and piperidine-based BACE-1 inhibitors. Iserloh U, Wu Y, Cumming JN, Pan J, Wang LY, Stamford AW, Kennedy ME, Kuvelkar R, Chen X, Parker EM, et al. Bioorg Med Chem Lett 2008 18 1 414 417 10.1016/j.bmcl.2007.10. 116 18023580
77. Sybyl 8.1 Tripos Inc. 1699, South Hanley Road St. Louis, Missouri, 63144, USA
78. BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities. Liu T, Lin Y, Wen X, Jorissen RN, Gilson MK, Nucleic Acids Res 2007 35 Database issue 198 201 17145705
79. The influence of cooperativity on the determination of dissociation constants: examination of the Cheng-Prusoff equation, the Scatchard analysis, the Schild analysis and related power equations. Cheng HC, Pharmacol Res 2004 50 1 21 40 10.1016/j.phrs.2003.11.007 15082026
80. The power issue: determination of KB or Ki from IC50. A closer look at the Cheng-Prusoff equation, the Schild plot and related power equations. Cheng HC, J Pharmacol Toxicol Methods 2001 46 2 61 71 10.1016/S1056-8719(02)00166-1 12481843
81. Kinetic studies on beta-site amyloid precursor protein-cleaving enzyme (BACE). Confirmation of an iso mechanism. Toulokhonova L, Metzler WJ, Witmer MR, Copeland RA, Marcinkeviciene J, J Biol Chem 2003 278 7 4582 4589 10.1074/jbc.M210471200 12458195
82. The Amber biomolecular simulation programs. Case DA, Cheatham TE 3rd, Darden T, Gohlke H, Luo R, Merz KM Jr, Onufriev A, Simmerling C, Wang B, Woods RJ, J Comput Chem 2005 26 16 1668 1688 10.1002/jcc.20290 16200636
83. Surflex-Dock 2.1: robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search. Jain AN, J Comput Aided Mol Des 2007 21 5 281 306 10.1007/s10822-007-9114-2 17387436
84. Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine. Jain AN, J Med Chem 2003 46 4 499 511 10.1021/jm020406h 12570372
85. Force fields for protein simulations. Ponder JW, Case DA, Adv Protein Chem 2003 66 27 85 14631816
86. MOPAC: a semiempirical molecular orbital program. Stewart JJ, J Comput Aided Mol Des 1990 4 1 1 105 10.1007/BF00128336 2197373
87. Development and testing of a general amber force field. Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA, J Comput Chem 2004 25 9 1157 1174 10.1002/jcc.20035 15116359
88. Optimization of the GB/SA solvation model for predicting the structure of surface loops in proteins. Szarecka A, Meirovitch H, J Phys Chem B 2006 110 6 2869 2880 10.1021/jp055771+ 16471897