DOI: 10.1016/j.jmgm.2005.10.002. Linear interaction energy models for β-secretase (BACE) inhibitors: Role of van der Waals, electrostatic, and continuum-solvation terms

Linear interaction energy models for β-secretase (BACE) inhibitors: Role of van der Waals, electrostatic, and continuum-solvation terms

10.1016/j.jmgm.2005.10.002

Crossref journal-article

Elsevier BV

Journal of Molecular Graphics and Modelling (78)

Bibliography

Tounge, B. A., Rajamani, R., Baxter, E. W., Reitz, A. B., & Reynolds, C. H. (2006). Linear interaction energy models for Î²-secretase (BACE) inhibitors: Role of van der Waals, electrostatic, and continuum-solvation terms. Journal of Molecular Graphics and Modelling, 24(6), 475â484.

Authors 5

Brett A. Tounge (first)
Ramkumar Rajamani (additional)
Ellen W. Baxter (additional)
Allen B. Reitz (additional)
Charles H. Reynolds (additional)

References 66 Referenced 21

{'key': '10.1016/j.jmgm.2005.10.002_bib1', 'first-page': '113', 'article-title': 'Calculating binding free energy in protein–ligand interaction', 'volume': 'vol. 1', 'author': 'Raha', 'year': '2005'} / Calculating binding free energy in protein–ligand interaction by Raha (2005)
10.1021/cr00023a004 / Chem. Rev. / Free energy calculations: applications to chemical and biochemical phenomena by Kollman (1993)
10.2174/1386207013330661 / Comb. Chem. High Throughput Screening / The linear interaction energy method for predicting ligand binding free energies by Aqvist (2001)
10.1023/A:1027251719816 / Perspect. Drug Discov. / A priori prediction of ligand affinity by energy minimization by Holloway (1998)
10.1021/jp011480z / J. Phys. Chem. B / New linear interaction method for binding affinity calculations using a continuum solvent model by Zhou (2001)
10.1021/j100026a034 / J. Phys. Chem. / An extended linear response method for determining free energies of hydration by Carlson (1995)
10.1021/jm020513b / J. Med. Chem. / Calculation of the binding affinity of beta-secretase inhibitors using the linear interaction energy method by Tounge (2003)
10.1016/j.bmcl.2004.07.044 / Bioorg. Med. Chem. Lett. / Modeling the binding affinities of β-secretase inhibitors: application to subsite specificity by Rajamani (2004)
10.1021/jm049726m / J. Med. Chem. / Efficient evaluation of binding free energy using continuum electrostatics by Huang (2004)
10.1023/A:1007930623000 / J. Comput. Aided Mol. Des. / Ligand binding affinity prediction by linear interaction energy methods by Hansson (1998)
10.1016/S0065-3233(03)66004-3 / Adv. Protein Chem. / Free energy calculations and ligand binding by Brandsdal (2003)
10.1002/(SICI)1097-0134(19990215)34:3<395::AID-PROT11>3.0.CO;2-4 / Proteins Struct. Funct. Genet. / What determines the van der Waals coefficient beta in the LIE (linear interaction energy) method to estimate binding free energies using molecular dynamics simulations? by Wang (1999)
10.1021/jm960684e / J. Med. Chem. / Binding affinities for sulfonamide inhibitors with human thrombin using Monte Carlo simulations with a linear response method by Jones-Hertzog (1997)
10.1016/S0960-894X(01)00825-3 / Bioorg. Med. Chem. Lett. / Estimation of binding affinities for Celecoxib analogues with COX-2 via Monte Carlo-extended linear response by Wesolowski (2002)
10.1016/S0968-0896(99)00015-2 / Bioorg. Med. Chem. / Estimation of the binding affinities of FKBP12 inhibitors using a linear response method by Lamb (1999)
10.1021/jm9804174 / J. Med. Chem. / Prediction of binding affinities for TIBO inhibitors of HIV-1 reverse transcriptase using Monte Carlo simulations in a linear response method by Smith (1998)
10.1038/399a023 / Nature / Translating cell biology into therapeutic advances in Alzheimer's disease by Selkoe (1999)
10.1152/physrev.2001.81.2.741 / Physiol. Rev. / Alzhiemer's disease: genes, proteins and therapy by Selkoe (2001)
10.1073/pnas.96.20.11049 / Proc. Natl. Acad. Sci. U.S.A. / Cellular mechanisms of β-Amyloid production and secretion by Sinha (1999)
10.1016/S0169-409X(02)00157-6 / Adv. Drug Del. Rev. / β-Secretase (BACE) as a drug target for Alzheimer's disease by Vassar (2002)
10.1016/S0896-6273(00)00051-9 / Neuron / Abeta-generating enzymes: recent advances in beta- and gamma-secretase research by Vassar (2000)
{'key': '10.1016/j.jmgm.2005.10.002_bib22', 'first-page': '157', 'article-title': "The beta-secretase BACE. A prime drug target for Alzheimer's disease", 'volume': '17', 'author': 'Vassar', 'year': '2001', 'journal-title': 'J. Mol. Spectrosc.'} / J. Mol. Spectrosc. / The beta-secretase BACE. A prime drug target for Alzheimer's disease by Vassar (2001)
{'key': '10.1016/j.jmgm.2005.10.002_bib23', 'first-page': '259', 'article-title': "Potential treatment opportunities for Alzheimer's disease through inhibition of secretases and Abeta immunization", 'volume': '17', 'author': 'Schenk', 'year': '2001', 'journal-title': 'J. Mol. Spectrosc.'} / J. Mol. Spectrosc. / Potential treatment opportunities for Alzheimer's disease through inhibition of secretases and Abeta immunization by Schenk (2001)
10.1016/S0065-7743(00)35005-9 / Annu. Rep. Med. Chem. / Secretase inhibitors as therapeutics for Alzheimer's disease by Olson (2000)
10.1172/JCI14402 / J. Clin. Invest. / Spotlight on BACE: the secretases as targets for treatment in Alzheimer's disease by Dingwall (2001)
10.1126/science.290.5489.150 / Science (Washington DC) / Structure of the protease domain of memapsin 2 (beta-secretase) complexed with inhibitor by Hong (2000)
10.1021/bi026232n / Biochemistry / Crystal structure of memapsin 2 (beta-Secretase) in complex with an inhibitor OM00-3 by Hong (2002)
10.1021/jm0101803 / J. Med. Chem. / Structure-based design: potent inhibitors of human brain memapsin 2 (beta-Secretase) by Ghosh (2001)
10.1016/j.bmcl.2004.10.084 / Bioorg. Med. Chem. Lett. / Structure-based design of cycloamide-urethane-derived novel inhibitors of human brain memapsin 2 (β-secretase) by Ghosh (2005)
10.1021/jm0155695 / J. Med. Chem. / Design of substrate-based inhibitors of human β.-Secretase by Tung (2002)
10.1074/jbc.M101896200 / J. Biol. Chem. / Mechanism of inhibition of β-site amyloid precursor protein-cleaving enzyme (BACE) by a statine-based peptide by Marcinkeviciene (2001)
10.1006/jmbi.2000.3860 / J. Mol. Biol. / Modeling of substrate specificity of the Alzheimer's disease amyloid precursor protein β-Secretase by Sauder (2000)
10.1021/jm0101803 / J. Med. Chem. / Structure-based design: potent inhibitors of human brain memapsin 2 (beta-secretase) by Ghosh (2001)
10.1021/bi015546s / Biochemistry / Subsite specificity of memapsin 2 (β-Secretase): Implications for inhibitor design by Turner (2001)
10.1517/13543784.10.4.593 / Expert Opin. Inv. Drug / β-Amyloid therapies in Alzheimer's disease by Jhee (2001)
10.1021/ja000300g / J. Am. Chem. Soc. / Design of potent inhibitors for human brain memapsin 2 (beta-secretase) by Ghosh (2000)
10.1006/bbrc.2000.2098 / Biochem. Biophys. Res. Commun. / Inhibitors of β-amyloid formation based on the β-secretase cleavage site by Abbenante (2000)
10.1021/ja0304493 / J. Am. Chem. Soc. / Determination of the active site protonation state of β-Secretase from molecular dynamics simulation and docking experiment: implications for structure-based inhibitor design by Park (2003)
10.2174/1568026024607490 / Curr. Top. Med. Chem. / Inhibition of BACE, a promising approach to Alzheimer by Roggo (2002)
10.1039/B304842J / Org. Biomol. Chem. / Synthesis of potent β-secretase inhibitors containing a hydroxyethylamine dipeptide isostere and their structure-activity relationship studies by Tamamura (2003)
10.1074/jbc.M210471200 / J. Biol. Chem. / Kinetic Studies on β-Site amyloid precursor protein-cleaving enzyme (BACE) by Toulokhonova (2003)
10.1021/jm0304008 / J. Med. Chem. / Design and synthesis of hydroxyethylene-based peptidomimetic inhibitors of human β-Secretase by Hom (2004)
10.1021/jm049817j / J. Med. Chem. / Modeling the protonation states of the catalytic aspartates in β-Secretase by Rajamani (2004)
10.1016/j.bmcl.2003.09.053 / Bioorg. Med. Chem. Lett. / KMI-008, A novel β-secretase inhibitor containing a hydroxymethylcarbonyl isostere as a transition-state mimic: design and synthesis of substrate-based octapeptides by Shuto (2003)
10.1021/jm0155695 / J. Med. Chem. / Design of substrate-based inhibitors of human β-secretase by Tung (2002)
10.1021/bi0151465 / Biochemistry / Subsite specificity of memapsin 2 (β-Secretase): Implications for inhibitor design by Turner (2001)
{'key': '10.1016/j.jmgm.2005.10.002_bib47', 'first-page': '1', 'article-title': 'Human β-secretase (BACE) and BACE inhibitors', 'volume': '46', 'author': 'Varghese', 'year': '2003', 'journal-title': 'J. Med. Chem.'} / J. Med. Chem. / Human β-secretase (BACE) and BACE inhibitors by Varghese (2003)
10.1021/jm050142+ / J. Med. Chem. / Structure-based design synthesis, and memapsin 2 (BACE) inhibitory activity of carbocyclic and heterocyclic peptidomimetics by Hanessian (2005)
{'key': '10.1016/j.jmgm.2005.10.002_bib49', 'first-page': '515', 'article-title': 'Synthesis of β-secretase inhibitors containing a hydroxyethylamine dipeptide isostere and their structure-activity relationship studies', 'volume': '41st', 'author': 'Kato', 'year': '2005', 'journal-title': 'Pep. Sci.'} / Pep. Sci. / Synthesis of β-secretase inhibitors containing a hydroxyethylamine dipeptide isostere and their structure-activity relationship studies by Kato (2005)
10.1021/jm049379g / J. Med. Chem. / Structure-based design of potent and selective cell-permeable inhibitors of human β-Secretase (BACE-1) by Stachel (2004)
10.1016/j.bmcl.2003.09.037 / Bioorg. Med. Chem. Lett. / Design and synthesis of statine-containing BACE inhibitors by Hu (2003)
10.1021/jm0155695 / J. Med. Chem. / Design of substrate-based inhibitors of human β-Secretase by Tung (2002)
10.1021/jm0101803 / J. Med. Chem. / Structure-based design: potent inhibitors of human brain memapsin 2 (β-secretase) by Ghosh (2001)
10.1021/jm050499d / J. Med. Chem. / Discovery of cell-permeable non-peptide inhibitors of β-secretase by high-throughput docking and continuum rlectrostatics calculations by Huang (2005)
10.1016/j.bmc.2005.01.002 / Bioorg. Med. Chem. / Molecular docking and 3D-QSAR studies on the binding mechanism of statine-based peptidomimetics with β-secretase by Zuo (2005)
10.1016/j.bmcl.2004.09.090 / Bioorg. Med. Chem. Lett. / Design and synthesis of highly active Alzheimer's β-secretase (BACE1) inhibitors, KMI-420 and KMI-429, with enhanced chemical stability by Kimura (2005)
10.1006/jmbi.2000.3860 / J. Mol. Biol. / Modeling of substrate specificity of the Alzheimer's disease amyloid precursor protein β-Secretase by Sauder (2000)
10.2174/0929867023370149 / Cur. Med. Chem. / β-secretase as a therapeutic target for inhibitor drugs by Ghosh (2002)
10.1016/j.jmb.2004.08.018 / J. Mol. Biol. / Apo and inhibitor complex structures of BACE (β-secretase) by Patel (2004)
Maestro, 2.0 2.0, 2001. Schrodinger, Inc., 1500 SW First Ave., Suite 1180, Portland, OR 97201.
10.1021/ja00214a001 / J. Am. Chem. Soc. / The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin by Jorgensen (1988)
10.1021/jp961992r / J. Phys. Chem. A / The GB/SA continuum model for solvation. a fast analytical method for the calculation of approximate Born radii by Qui (1997)
FistDiscovery, 2.0 2.0, 2001. Schrodinger, Inc., 1500 SW First Ave., Suite 1180, Portland, OR 97201.
10.1023/A:1007929626986 / J. Comput. Aided Mol. Des. / Computation of affinity and selectivity: binding of 2,4-diaminopteridine and 2,4-diaminoquinazoline inhibitors to dihydrofolate reductases by Marelius (1998)
10.1021/jp953640a / J. Phys. Chem. / Validity of electrostatic linear response in polar solvents by Aqvist (1996)
10.1002/(SICI)1096-987X(19961115)17:14<1587::AID-JCC1>3.0.CO;2-H / J. Comput. Chem. / Calculation of sbsolute binding free energies for charged ligands and effects of long-range electrostatic interactions by Aqvist (1996)

Dates

Type	When
Created	19 years, 9 months ago (Nov. 16, 2005, 7:24 a.m.)
Deposited	2 years, 3 months ago (May 5, 2023, 9:04 a.m.)
Indexed	2 weeks, 5 days ago (Aug. 3, 2025, 12:05 a.m.)
Issued	19 years, 3 months ago (May 1, 2006)
Published	19 years, 3 months ago (May 1, 2006)
Published Print	19 years, 3 months ago (May 1, 2006)

Funders 0

None

BibTeX

@article{Tounge_2006, title={Linear interaction energy models for β-secretase (BACE) inhibitors: Role of van der Waals, electrostatic, and continuum-solvation terms}, volume={24}, ISSN={1093-3263}, url={http://dx.doi.org/10.1016/j.jmgm.2005.10.002}, DOI={10.1016/j.jmgm.2005.10.002}, number={6}, journal={Journal of Molecular Graphics and Modelling}, publisher={Elsevier BV}, author={Tounge, Brett A. and Rajamani, Ramkumar and Baxter, Ellen W. and Reitz, Allen B. and Reynolds, Charles H.}, year={2006}, month=may, pages={475–484} }

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      "DOI": "10.2174/1386207013330661",
      "article-title": "The linear interaction energy method for predicting ligand binding free energies",
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      "author": "Aqvist",
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      "article-title": "A priori prediction of ligand affinity by energy minimization",
      "volume": "9/10/11",
      "author": "Holloway",
      "year": "1998",
      "journal-title": "Perspect. Drug Discov."
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    {
      "key": "10.1016/j.jmgm.2005.10.002_bib5",
      "doi-asserted-by": "crossref",
      "first-page": "10388",
      "DOI": "10.1021/jp011480z",
      "article-title": "New linear interaction method for binding affinity calculations using a continuum solvent model",
      "volume": "105",
      "author": "Zhou",
      "year": "2001",
      "journal-title": "J. Phys. Chem. B"
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib6",
      "doi-asserted-by": "crossref",
      "first-page": "10667",
      "DOI": "10.1021/j100026a034",
      "article-title": "An extended linear response method for determining free energies of hydration",
      "volume": "99",
      "author": "Carlson",
      "year": "1995",
      "journal-title": "J. Phys. Chem."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib7",
      "doi-asserted-by": "crossref",
      "first-page": "2074",
      "DOI": "10.1021/jm020513b",
      "article-title": "Calculation of the binding affinity of beta-secretase inhibitors using the linear interaction energy method",
      "volume": "46",
      "author": "Tounge",
      "year": "2003",
      "journal-title": "J. Med. Chem."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib8",
      "doi-asserted-by": "crossref",
      "first-page": "4843",
      "DOI": "10.1016/j.bmcl.2004.07.044",
      "article-title": "Modeling the binding affinities of \u03b2-secretase inhibitors: application to subsite specificity",
      "volume": "14",
      "author": "Rajamani",
      "year": "2004",
      "journal-title": "Bioorg. Med. Chem. Lett."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib9",
      "doi-asserted-by": "crossref",
      "first-page": "5791",
      "DOI": "10.1021/jm049726m",
      "article-title": "Efficient evaluation of binding free energy using continuum electrostatics",
      "volume": "47",
      "author": "Huang",
      "year": "2004",
      "journal-title": "J. Med. Chem."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib10",
      "doi-asserted-by": "crossref",
      "first-page": "27",
      "DOI": "10.1023/A:1007930623000",
      "article-title": "Ligand binding affinity prediction by linear interaction energy methods",
      "volume": "12",
      "author": "Hansson",
      "year": "1998",
      "journal-title": "J. Comput. Aided Mol. Des."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib11",
      "doi-asserted-by": "crossref",
      "first-page": "123",
      "DOI": "10.1016/S0065-3233(03)66004-3",
      "article-title": "Free energy calculations and ligand binding",
      "volume": "66",
      "author": "Brandsdal",
      "year": "2003",
      "journal-title": "Adv. Protein Chem."
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    {
      "key": "10.1016/j.jmgm.2005.10.002_bib12",
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      "first-page": "395",
      "DOI": "10.1002/(SICI)1097-0134(19990215)34:3<395::AID-PROT11>3.0.CO;2-4",
      "article-title": "What determines the van der Waals coefficient beta in the LIE (linear interaction energy) method to estimate binding free energies using molecular dynamics simulations?",
      "volume": "34",
      "author": "Wang",
      "year": "1999",
      "journal-title": "Proteins Struct. Funct. Genet."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib13",
      "doi-asserted-by": "crossref",
      "first-page": "1539",
      "DOI": "10.1021/jm960684e",
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      "volume": "40",
      "author": "Jones-Hertzog",
      "year": "1997",
      "journal-title": "J. Med. Chem."
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      "volume": "12",
      "author": "Wesolowski",
      "year": "2002",
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    },
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      "first-page": "851",
      "DOI": "10.1016/S0968-0896(99)00015-2",
      "article-title": "Estimation of the binding affinities of FKBP12 inhibitors using a linear response method",
      "volume": "7",
      "author": "Lamb",
      "year": "1999",
      "journal-title": "Bioorg. Med. Chem."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib16",
      "doi-asserted-by": "crossref",
      "first-page": "5272",
      "DOI": "10.1021/jm9804174",
      "article-title": "Prediction of binding affinities for TIBO inhibitors of HIV-1 reverse transcriptase using Monte Carlo simulations in a linear response method",
      "volume": "41",
      "author": "Smith",
      "year": "1998",
      "journal-title": "J. Med. Chem."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib17",
      "doi-asserted-by": "crossref",
      "first-page": "A23",
      "DOI": "10.1038/399a023",
      "article-title": "Translating cell biology into therapeutic advances in Alzheimer's disease",
      "volume": "399A",
      "author": "Selkoe",
      "year": "1999",
      "journal-title": "Nature"
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib18",
      "doi-asserted-by": "crossref",
      "first-page": "741",
      "DOI": "10.1152/physrev.2001.81.2.741",
      "article-title": "Alzhiemer's disease: genes, proteins and therapy",
      "volume": "81",
      "author": "Selkoe",
      "year": "2001",
      "journal-title": "Physiol. Rev."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib19",
      "doi-asserted-by": "crossref",
      "first-page": "11049",
      "DOI": "10.1073/pnas.96.20.11049",
      "article-title": "Cellular mechanisms of \u03b2-Amyloid production and secretion",
      "volume": "96",
      "author": "Sinha",
      "year": "1999",
      "journal-title": "Proc. Natl. Acad. Sci. U.S.A."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib20",
      "doi-asserted-by": "crossref",
      "first-page": "1589",
      "DOI": "10.1016/S0169-409X(02)00157-6",
      "article-title": "\u03b2-Secretase (BACE) as a drug target for Alzheimer's disease",
      "volume": "54",
      "author": "Vassar",
      "year": "2002",
      "journal-title": "Adv. Drug Del. Rev."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib21",
      "doi-asserted-by": "crossref",
      "first-page": "419",
      "DOI": "10.1016/S0896-6273(00)00051-9",
      "article-title": "Abeta-generating enzymes: recent advances in beta- and gamma-secretase research",
      "volume": "27",
      "author": "Vassar",
      "year": "2000",
      "journal-title": "Neuron"
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib22",
      "first-page": "157",
      "article-title": "The beta-secretase BACE. A prime drug target for Alzheimer's disease",
      "volume": "17",
      "author": "Vassar",
      "year": "2001",
      "journal-title": "J. Mol. Spectrosc."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib23",
      "first-page": "259",
      "article-title": "Potential treatment opportunities for Alzheimer's disease through inhibition of secretases and Abeta immunization",
      "volume": "17",
      "author": "Schenk",
      "year": "2001",
      "journal-title": "J. Mol. Spectrosc."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib24",
      "doi-asserted-by": "crossref",
      "first-page": "31",
      "DOI": "10.1016/S0065-7743(00)35005-9",
      "article-title": "Secretase inhibitors as therapeutics for Alzheimer's disease",
      "volume": "35",
      "author": "Olson",
      "year": "2000",
      "journal-title": "Annu. Rep. Med. Chem."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib25",
      "doi-asserted-by": "crossref",
      "first-page": "1243",
      "DOI": "10.1172/JCI14402",
      "article-title": "Spotlight on BACE: the secretases as targets for treatment in Alzheimer's disease",
      "volume": "108",
      "author": "Dingwall",
      "year": "2001",
      "journal-title": "J. Clin. Invest."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib26",
      "doi-asserted-by": "crossref",
      "first-page": "150",
      "DOI": "10.1126/science.290.5489.150",
      "article-title": "Structure of the protease domain of memapsin 2 (beta-secretase) complexed with inhibitor",
      "volume": "290",
      "author": "Hong",
      "year": "2000",
      "journal-title": "Science (Washington DC)"
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib27",
      "doi-asserted-by": "crossref",
      "first-page": "10963",
      "DOI": "10.1021/bi026232n",
      "article-title": "Crystal structure of memapsin 2 (beta-Secretase) in complex with an inhibitor OM00-3",
      "volume": "41",
      "author": "Hong",
      "year": "2002",
      "journal-title": "Biochemistry"
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib28",
      "doi-asserted-by": "crossref",
      "first-page": "2865",
      "DOI": "10.1021/jm0101803",
      "article-title": "Structure-based design: potent inhibitors of human brain memapsin 2 (beta-Secretase)",
      "volume": "44",
      "author": "Ghosh",
      "year": "2001",
      "journal-title": "J. Med. Chem."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib29",
      "doi-asserted-by": "crossref",
      "first-page": "15",
      "DOI": "10.1016/j.bmcl.2004.10.084",
      "article-title": "Structure-based design of cycloamide-urethane-derived novel inhibitors of human brain memapsin 2 (\u03b2-secretase)",
      "volume": "15",
      "author": "Ghosh",
      "year": "2005",
      "journal-title": "Bioorg. Med. Chem. Lett."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib30",
      "doi-asserted-by": "crossref",
      "first-page": "259",
      "DOI": "10.1021/jm0155695",
      "article-title": "Design of substrate-based inhibitors of human \u03b2.-Secretase",
      "volume": "45",
      "author": "Tung",
      "year": "2002",
      "journal-title": "J. Med. Chem."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib31",
      "doi-asserted-by": "crossref",
      "first-page": "23790",
      "DOI": "10.1074/jbc.M101896200",
      "article-title": "Mechanism of inhibition of \u03b2-site amyloid precursor protein-cleaving enzyme (BACE) by a statine-based peptide",
      "volume": "276",
      "author": "Marcinkeviciene",
      "year": "2001",
      "journal-title": "J. Biol. Chem."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib32",
      "doi-asserted-by": "crossref",
      "first-page": "241",
      "DOI": "10.1006/jmbi.2000.3860",
      "article-title": "Modeling of substrate specificity of the Alzheimer's disease amyloid precursor protein \u03b2-Secretase",
      "volume": "300",
      "author": "Sauder",
      "year": "2000",
      "journal-title": "J. Mol. Biol."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib33",
      "doi-asserted-by": "crossref",
      "first-page": "2865",
      "DOI": "10.1021/jm0101803",
      "article-title": "Structure-based design: potent inhibitors of human brain memapsin 2 (beta-secretase)",
      "volume": "44",
      "author": "Ghosh",
      "year": "2001",
      "journal-title": "J. Med. Chem."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib34",
      "doi-asserted-by": "crossref",
      "first-page": "10001",
      "DOI": "10.1021/bi015546s",
      "article-title": "Subsite specificity of memapsin 2 (\u03b2-Secretase): Implications for inhibitor design",
      "volume": "40",
      "author": "Turner",
      "year": "2001",
      "journal-title": "Biochemistry"
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib35",
      "doi-asserted-by": "crossref",
      "first-page": "593",
      "DOI": "10.1517/13543784.10.4.593",
      "article-title": "\u03b2-Amyloid therapies in Alzheimer's disease",
      "volume": "10",
      "author": "Jhee",
      "year": "2001",
      "journal-title": "Expert Opin. Inv. Drug"
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib36",
      "doi-asserted-by": "crossref",
      "first-page": "3522",
      "DOI": "10.1021/ja000300g",
      "article-title": "Design of potent inhibitors for human brain memapsin 2 (beta-secretase)",
      "volume": "122",
      "author": "Ghosh",
      "year": "2000",
      "journal-title": "J. Am. Chem. Soc."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib37",
      "doi-asserted-by": "crossref",
      "first-page": "133",
      "DOI": "10.1006/bbrc.2000.2098",
      "article-title": "Inhibitors of \u03b2-amyloid formation based on the \u03b2-secretase cleavage site",
      "volume": "268",
      "author": "Abbenante",
      "year": "2000",
      "journal-title": "Biochem. Biophys. Res. Commun."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib38",
      "doi-asserted-by": "crossref",
      "first-page": "16416",
      "DOI": "10.1021/ja0304493",
      "article-title": "Determination of the active site protonation state of \u03b2-Secretase from molecular dynamics simulation and docking experiment: implications for structure-based inhibitor design",
      "volume": "125",
      "author": "Park",
      "year": "2003",
      "journal-title": "J. Am. Chem. Soc."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib39",
      "doi-asserted-by": "crossref",
      "first-page": "359",
      "DOI": "10.2174/1568026024607490",
      "article-title": "Inhibition of BACE, a promising approach to Alzheimer",
      "volume": "2",
      "author": "Roggo",
      "year": "2002",
      "journal-title": "Curr. Top. Med. Chem."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib40",
      "doi-asserted-by": "crossref",
      "first-page": "2468",
      "DOI": "10.1039/B304842J",
      "article-title": "Synthesis of potent \u03b2-secretase inhibitors containing a hydroxyethylamine dipeptide isostere and their structure-activity relationship studies",
      "volume": "1",
      "author": "Tamamura",
      "year": "2003",
      "journal-title": "Org. Biomol. Chem."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib41",
      "doi-asserted-by": "crossref",
      "first-page": "4582",
      "DOI": "10.1074/jbc.M210471200",
      "article-title": "Kinetic Studies on \u03b2-Site amyloid precursor protein-cleaving enzyme (BACE)",
      "volume": "278",
      "author": "Toulokhonova",
      "year": "2003",
      "journal-title": "J. Biol. Chem."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib42",
      "doi-asserted-by": "crossref",
      "first-page": "158",
      "DOI": "10.1021/jm0304008",
      "article-title": "Design and synthesis of hydroxyethylene-based peptidomimetic inhibitors of human \u03b2-Secretase",
      "volume": "47",
      "author": "Hom",
      "year": "2004",
      "journal-title": "J. Med. Chem."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib43",
      "doi-asserted-by": "crossref",
      "first-page": "5159",
      "DOI": "10.1021/jm049817j",
      "article-title": "Modeling the protonation states of the catalytic aspartates in \u03b2-Secretase",
      "volume": "47",
      "author": "Rajamani",
      "year": "2004",
      "journal-title": "J. Med. Chem."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib44",
      "doi-asserted-by": "crossref",
      "first-page": "4273",
      "DOI": "10.1016/j.bmcl.2003.09.053",
      "article-title": "KMI-008, A novel \u03b2-secretase inhibitor containing a hydroxymethylcarbonyl isostere as a transition-state mimic: design and synthesis of substrate-based octapeptides",
      "volume": "13",
      "author": "Shuto",
      "year": "2003",
      "journal-title": "Bioorg. Med. Chem. Lett."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib45",
      "doi-asserted-by": "crossref",
      "first-page": "259",
      "DOI": "10.1021/jm0155695",
      "article-title": "Design of substrate-based inhibitors of human \u03b2-secretase",
      "volume": "45",
      "author": "Tung",
      "year": "2002",
      "journal-title": "J. Med. Chem."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib46",
      "doi-asserted-by": "crossref",
      "first-page": "10002",
      "DOI": "10.1021/bi0151465",
      "article-title": "Subsite specificity of memapsin 2 (\u03b2-Secretase): Implications for inhibitor design",
      "volume": "40",
      "author": "Turner",
      "year": "2001",
      "journal-title": "Biochemistry"
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib47",
      "first-page": "1",
      "article-title": "Human \u03b2-secretase (BACE) and BACE inhibitors",
      "volume": "46",
      "author": "Varghese",
      "year": "2003",
      "journal-title": "J. Med. Chem."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib48",
      "doi-asserted-by": "crossref",
      "first-page": "5175",
      "DOI": "10.1021/jm050142+",
      "article-title": "Structure-based design synthesis, and memapsin 2 (BACE) inhibitory activity of carbocyclic and heterocyclic peptidomimetics",
      "volume": "48",
      "author": "Hanessian",
      "year": "2005",
      "journal-title": "J. Med. Chem."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib49",
      "first-page": "515",
      "article-title": "Synthesis of \u03b2-secretase inhibitors containing a hydroxyethylamine dipeptide isostere and their structure-activity relationship studies",
      "volume": "41st",
      "author": "Kato",
      "year": "2005",
      "journal-title": "Pep. Sci."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib50",
      "doi-asserted-by": "crossref",
      "first-page": "6447",
      "DOI": "10.1021/jm049379g",
      "article-title": "Structure-based design of potent and selective cell-permeable inhibitors of human \u03b2-Secretase (BACE-1)",
      "volume": "47",
      "author": "Stachel",
      "year": "2004",
      "journal-title": "J. Med. Chem."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib51",
      "doi-asserted-by": "crossref",
      "first-page": "4335",
      "DOI": "10.1016/j.bmcl.2003.09.037",
      "article-title": "Design and synthesis of statine-containing BACE inhibitors",
      "volume": "13",
      "author": "Hu",
      "year": "2003",
      "journal-title": "Bioorg. Med. Chem. Lett."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib52",
      "doi-asserted-by": "crossref",
      "first-page": "259",
      "DOI": "10.1021/jm0155695",
      "article-title": "Design of substrate-based inhibitors of human \u03b2-Secretase",
      "volume": "45",
      "author": "Tung",
      "year": "2002",
      "journal-title": "J. Med. Chem."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib53",
      "doi-asserted-by": "crossref",
      "first-page": "2865",
      "DOI": "10.1021/jm0101803",
      "article-title": "Structure-based design: potent inhibitors of human brain memapsin 2 (\u03b2-secretase)",
      "volume": "44",
      "author": "Ghosh",
      "year": "2001",
      "journal-title": "J. Med. Chem."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib54",
      "doi-asserted-by": "crossref",
      "first-page": "5108",
      "DOI": "10.1021/jm050499d",
      "article-title": "Discovery of cell-permeable non-peptide inhibitors of \u03b2-secretase by high-throughput docking and continuum rlectrostatics calculations",
      "volume": "48",
      "author": "Huang",
      "year": "2005",
      "journal-title": "J. Med. Chem."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib55",
      "doi-asserted-by": "crossref",
      "first-page": "2121",
      "DOI": "10.1016/j.bmc.2005.01.002",
      "article-title": "Molecular docking and 3D-QSAR studies on the binding mechanism of statine-based peptidomimetics with \u03b2-secretase",
      "volume": "13",
      "author": "Zuo",
      "year": "2005",
      "journal-title": "Bioorg. Med. Chem."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib56",
      "doi-asserted-by": "crossref",
      "first-page": "211",
      "DOI": "10.1016/j.bmcl.2004.09.090",
      "article-title": "Design and synthesis of highly active Alzheimer's \u03b2-secretase (BACE1) inhibitors, KMI-420 and KMI-429, with enhanced chemical stability",
      "volume": "15",
      "author": "Kimura",
      "year": "2005",
      "journal-title": "Bioorg. Med. Chem. Lett."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib57",
      "doi-asserted-by": "crossref",
      "first-page": "241",
      "DOI": "10.1006/jmbi.2000.3860",
      "article-title": "Modeling of substrate specificity of the Alzheimer's disease amyloid precursor protein \u03b2-Secretase",
      "volume": "300",
      "author": "Sauder",
      "year": "2000",
      "journal-title": "J. Mol. Biol."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib58",
      "doi-asserted-by": "crossref",
      "first-page": "1135",
      "DOI": "10.2174/0929867023370149",
      "article-title": "\u03b2-secretase as a therapeutic target for inhibitor drugs",
      "volume": "9",
      "author": "Ghosh",
      "year": "2002",
      "journal-title": "Cur. Med. Chem."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib59",
      "doi-asserted-by": "crossref",
      "first-page": "407",
      "DOI": "10.1016/j.jmb.2004.08.018",
      "article-title": "Apo and inhibitor complex structures of BACE (\u03b2-secretase)",
      "volume": "343",
      "author": "Patel",
      "year": "2004",
      "journal-title": "J. Mol. Biol."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib60",
      "unstructured": "Maestro, 2.0 2.0, 2001. Schrodinger, Inc., 1500 SW First Ave., Suite 1180, Portland, OR 97201."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib61",
      "doi-asserted-by": "crossref",
      "first-page": "1657",
      "DOI": "10.1021/ja00214a001",
      "article-title": "The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin",
      "volume": "110",
      "author": "Jorgensen",
      "year": "1988",
      "journal-title": "J. Am. Chem. Soc."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib62",
      "doi-asserted-by": "crossref",
      "first-page": "3005",
      "DOI": "10.1021/jp961992r",
      "article-title": "The GB/SA continuum model for solvation. a fast analytical method for the calculation of approximate Born radii",
      "volume": "101",
      "author": "Qui",
      "year": "1997",
      "journal-title": "J. Phys. Chem. A"
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib63",
      "unstructured": "FistDiscovery, 2.0 2.0, 2001. Schrodinger, Inc., 1500 SW First Ave., Suite 1180, Portland, OR 97201."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib64",
      "doi-asserted-by": "crossref",
      "first-page": "119",
      "DOI": "10.1023/A:1007929626986",
      "article-title": "Computation of affinity and selectivity: binding of 2,4-diaminopteridine and 2,4-diaminoquinazoline inhibitors to dihydrofolate reductases",
      "volume": "12",
      "author": "Marelius",
      "year": "1998",
      "journal-title": "J. Comput. Aided Mol. Des."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib65",
      "doi-asserted-by": "crossref",
      "first-page": "9512",
      "DOI": "10.1021/jp953640a",
      "article-title": "Validity of electrostatic linear response in polar solvents",
      "volume": "100",
      "author": "Aqvist",
      "year": "1996",
      "journal-title": "J. Phys. Chem."
    },
    {
      "key": "10.1016/j.jmgm.2005.10.002_bib66",
      "doi-asserted-by": "crossref",
      "first-page": "1587",
      "DOI": "10.1002/(SICI)1096-987X(19961115)17:14<1587::AID-JCC1>3.0.CO;2-H",
      "article-title": "Calculation of sbsolute binding free energies for charged ligands and effects of long-range electrostatic interactions",
      "volume": "17",
      "author": "Aqvist",
      "year": "1996",
      "journal-title": "J. Comput. Chem."
    }
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