Review Article

阿尔茨海默病和 β-分泌酶抑制:以计算机辅助抑制剂设计为重点的更新

卷 23, 期 3, 2022

发表于: 09 August, 2021

页: [266 - 285] 页: 20

弟呕挨: 10.2174/1389450122666210809100050

价格: $65

摘要

简介:阿尔茨海默病 (AD) 由于其不可逆转的性质,是一种加剧的神经退行性疾病。 β 位点淀粉样前体蛋白 (APP) 裂解酶 1 (BACE1) 的鉴定一直是 AD 治疗的重要医学焦点,这为几项研究开辟了基础。尽管在这个方向上进行了许多工作,但没有 BACE1 抑制剂作为抗 AD 药物进入最终批准阶段。 方法:我们提供主题的介绍性背景以及 AD 发病机制的一般概述。该审查以 BACE1 抑制剂的设计和开发为特色,重点关注一些临床试验和停产药物。使用 Web of Science 和 Scopus 数据库中的主题关键词 BACE1、抑制剂设计和计算/理论研究,我们检索了超过 49 篇相关文章。搜索年份为 2010 年和 2020 年,分析时间为 2020 年 5 月至 2021 年 3 月。 结果和讨论:研究人员采用计算方法来解开潜在的 BACE1 抑制剂,并取得显着成果。在 BACE1 抑制剂设计和结合/相互作用研究中最常用的计算机辅助方法是药效团开发、定量构效关系 (QSAR)、虚拟筛选、对接和分子动力学 (MD) 模拟。这些方法,加上更先进的方法,包括量子力学/分子力学 (QM/MM) 和 QM,已在 BACE1 抑制剂设计的计算框架中证明是重要的。计算化学家已经接受了体外试验的结合,以深入了解已识别分子的抑制性能,这些分子具有对 BACE1 的潜在抑制作用。文献中提供了高达 50 nM 的显着 IC50 值,优于临床试验化合物。 结论:强效 BACE1 抑制剂在临床试验中的持续失败吸引了许多质疑,促使研究人员研究有效抑制剂设计所必需的新概念。高效 BACE1 抑制剂设计所考虑的特性似乎是巨大的,需要彻底审查。最近,研究人员注意到,除了明显的结合亲和力和血脑屏障 (BBB) 渗透外,BACE1 抑制剂对渗透性糖蛋白的亲和力必须很低或没有。计算建模方法在药物发现策略中有着深远的应用。随着最近关于 BACE1 抑制的计算机研究的数量,识别将达到批准水平的有效分子的前景是可行的。研究人员应尝试将许多已鉴定的具有显着抗 AD 特性的 BACE1 化合物推向临床前和临床试验阶段。我们还建议对 BACE1 的变构抑制剂设计、外部建模和多位点抑制进行计算研究。这些替代方案可能是 AD 治疗中 BACE1 药物发现的解决方案。

关键词: β-分泌酶、阿尔茨海默病 (AD)、BACE1 抑制、抗 AD 药物、计算机辅助抑制剂设计、对接

图形摘要

[1]
Cantor SR, Cantor SG. Proceedings of the 1995 IEEE International Frequency Control Symposium (49th Annual Symposium). 3-9.
[2]
Ornstein RE, Thompson RF. The amazing brain. Houghton Mifflin Harcourt 1986.
[3]
Fields RD. The other brain: From dementia to schizophrenia, how new discoveries about the brain are revolutionizing medicine and science. Simon and Schuster 2009.
[4]
Carter R. The brain book: An illustrated guide to its structure, functions, and disorders. Dorling Kindersley Ltd. 2019.
[5]
Dudai Y. Memory from A to Z: Keywords, concepts, and beyond. USA: Oxford University Press 2004.
[6]
Brown TE. Attention deficit disorder: The unfocused mind in children and adults. Yale University Press 2005.
[7]
Corliss J, Gilbert S. A guide to Alzheimer’s disease. Harvard Health Publications 2009.
[8]
Kandel ER. The disordered mind: What unusual brains tell us about ourselves. UK: Hachette 2018.
[9]
Reitz C, Brayne C, Mayeux R. Epidemiology of Alzheimer disease. Nat Rev Neurol 2011; 7(3): 137-52.
[http://dx.doi.org/10.1038/nrneurol.2011.2] [PMID: 21304480]
[10]
Cummings J, Lee G, Ritter A, Sabbagh M, Zhong K. Alzheimer’s disease drug development pipeline: 2019. Alzheimers Dement (N Y) 2019; 5: 272-93.
[http://dx.doi.org/10.1016/j.trci.2019.05.008] [PMID: 31334330]
[11]
Brookmeyer R, Corrada MM, Curriero FC, Kawas C. Survival following a diagnosis of Alzheimer disease. Arch Neurol 2002; 59(11): 1764-7.
[http://dx.doi.org/10.1001/archneur.59.11.1764] [PMID: 12433264]
[12]
Imbimbo BP, Watling M. Investigational BACE inhibitors for the treatment of Alzheimer’s disease. Expert Opin Investig Drugs 2019; 28(11): 967-75.
[http://dx.doi.org/10.1080/13543784.2019.1683160] [PMID: 31661331]
[13]
Sytnyk V. How synapses are destroyed in the early stages of Alzheimer’s disease Available from:. https://neurosciencenews.com/synapse-loss-alzheimers-genetics-3169/[Accessed on October 01,2020]
[14]
First WHO ministerial conference on global action against dementia: meeting report. Geneva, Switzerland. WHO Headquarters 2015.16-17 March.
[15]
Winblad B, Amouyel P, Andrieu S, et al. Defeating Alzheimer’s disease and other dementias: a priority for European science and society. Lancet Neurol 2016; 15(5): 455-532.
[http://dx.doi.org/10.1016/S1474-4422(16)00062-4] [PMID: 26987701]
[16]
Alzheimer A, Stelzmann RA, Schnitzlein HN, Murtagh FR. An english translation of Alzheimer’s 1907 paper, “Uber eine eigenartige Erkankung der Hirnrinde. Clin Anat 1995; 8(6): 429-31.
[http://dx.doi.org/10.1002/ca.980080612] [PMID: 8713166]
[17]
Duthey B. Background paper 6.11: Alzheimer disease and other dementias. A public health approach to innovation 2013; 6: 1-74.
[18]
Lane CA, Parker TD, Cash DM, et al. Study protocol: Insight 46 - a neuroscience sub-study of the MRC National Survey of Health and Development. BMC Neurol 2017; 17(1): 75.
[http://dx.doi.org/10.1186/s12883-017-0846-x] [PMID: 28420323]
[19]
Alzheimer’s disease facts and figures. Alzheimers Dement 2017; 13(4): 325-73.
[http://dx.doi.org/10.1016/j.jalz.2017.02.001]
[20]
James S-N, Lane CA, Parker TD, et al. Using a birth cohort to study brain health and preclinical dementia: recruitment and participation rates in Insight 46. BMC Res Notes 2018; 11(1): 885.
[http://dx.doi.org/10.1186/s13104-018-3995-0] [PMID: 30545411]
[21]
Islam MA, Pillay TS. β-secretase inhibitors for Alzheimer’s disease: identification using pharmacoinformatics. J Biomol Struct Dyn 2019; 37(2): 503-22.
[http://dx.doi.org/10.1080/07391102.2018.1430619] [PMID: 29388503]
[22]
Dassel K, Butler J, Telonidis J, Edelman L. Development and evaluation of Alzheimer’s Disease and Related Dementias (ADRD) best care practices in long-term care online training program. Educ Gerontol 2020; 46(3): 150-7.
[http://dx.doi.org/10.1080/03601277.2020.1717079]
[23]
LaFerla FM, Green KN, Oddo S. Intracellular amyloid-β in Alzheimer’s disease. Nat Rev Neurosci 2007; 8(7): 499-509.
[http://dx.doi.org/10.1038/nrn2168] [PMID: 17551515]
[24]
Murphy MP, LeVine H III. Alzheimer’s disease and the amyloid-β peptide. J Alzheimers Dis 2010; 19(1): 311-23.
[http://dx.doi.org/10.3233/JAD-2010-1221] [PMID: 20061647]
[25]
Stansley B, Post J, Hensley K. A comparative review of cell culture systems for the study of microglial biology in Alzheimer’s disease. J Neuroinflammation 2012; 9(1): 115.
[http://dx.doi.org/10.1186/1742-2094-9-115] [PMID: 22651808]
[26]
Zhang F, Jiang L. Neuroinflammation in Alzheimer’s disease. Neuropsychiatr Dis Treat 2015; 11: 243-56.
[http://dx.doi.org/10.2147/NDT.S75546] [PMID: 25673992]
[27]
Fortini ME. γ-secretase-mediated proteolysis in cell-surface-receptor signalling. Nat Rev Mol Cell Biol 2002; 3(9): 673-84.
[http://dx.doi.org/10.1038/nrm910] [PMID: 12209127]
[28]
Teich AF, Arancio O. Is the amyloid hypothesis of Alzheimer’s disease therapeutically relevant? Biochem J 2012; 446(2): 165-77.
[http://dx.doi.org/10.1042/BJ20120653] [PMID: 22891628]
[29]
Crump CJ, Johnson DS, Li Y-M. Development and mechanism of γ-secretase modulators for Alzheimer’s disease. Biochemistry 2013; 52(19): 3197-216.
[http://dx.doi.org/10.1021/bi400377p] [PMID: 23614767]
[30]
Dillen K, Annaert W. A two decade contribution of molecular cell biology to the centennial of Alzheimer’s disease: Are we progressing toward therapy? Int Rev Cytol 2006; 254: 215-300.
[http://dx.doi.org/10.1016/S0074-7696(06)54005-7] [PMID: 17148000]
[31]
Ohno M. Genetic and pharmacological basis for therapeutic inhibition of beta- and γ-secretases in mouse models of Alzheimer’s memory deficits. Rev Neurosci 2006; 17(4): 429-54.
[http://dx.doi.org/10.1515/revneuro.2006.17.4.429] [PMID: 17139843]
[32]
Wakabayashi T, De Strooper B. Presenilins: members of the γ-secretase quartets, but part-time soloists too. Physiology (Bethesda) 2008; 23(4): 194-204.
[http://dx.doi.org/10.1152/physiol.00009.2008] [PMID: 18697993]
[33]
Schenk D, Basi GS, Pangalos MN. Treatment strategies targeting amyloid β-protein. Cold Spring Harb Perspect Med 2012; 2(9)a006387
[http://dx.doi.org/10.1101/cshperspect.a006387] [PMID: 22951439]
[34]
Fukumori A, Steiner H. Substrate recruitment of γ-secretase and mechanism of clinical presenilin mutations revealed by photoaffinity mapping. EMBO J 2016; 35(15): 1628-43.
[http://dx.doi.org/10.15252/embj.201694151] [PMID: 27220847]
[35]
Powrie YSL. Investigating Tau pathology in an in vitro model for Alzheimer’s disease. Stellenbosch: Stellenbosch University 2016; pp. 1-139.
[36]
Cutler NR. Understanding Alzheimer’s disease. University Press of Mississippi 2010.
[37]
Oliver DMA, Reddy PH. Molecular basis of Alzheimer’s disease: focus on mitochondria. J Alzheimers Dis 2019; 72(s1): S95-S116.
[http://dx.doi.org/10.3233/JAD-190048] [PMID: 30932888]
[38]
Hardy JA, Higgins GA. Alzheimer’s disease: the amyloid cascade hypothesis. Science 1992; 256(5054): 184-5.
[http://dx.doi.org/10.1126/science.1566067] [PMID: 1566067]
[39]
Nisbet RM, Polanco J-C, Ittner LM, Götz J. Tau aggregation and its interplay with amyloid-β. Acta Neuropathol 2015; 129(2): 207-20.
[http://dx.doi.org/10.1007/s00401-014-1371-2] [PMID: 25492702]
[40]
Baleriola J, Walker CA, Jean YY, et al. Axonally synthesized ATF4 transmits a neurodegenerative signal across brain regions. Cell 2014; 158(5): 1159-72.
[http://dx.doi.org/10.1016/j.cell.2014.07.001] [PMID: 25171414]
[41]
Suzuki K, Iwata A, Iwatsubo T. The past, present, and future of disease-modifying therapies for Alzheimer’s disease. Proc Jpn Acad, Ser B, Phys Biol Sci 2017; 93(10): 757-71.
[http://dx.doi.org/10.2183/pjab.93.048] [PMID: 29225305]
[42]
Um JW, Nygaard HB, Heiss JK, et al. Alzheimer amyloid-β oligomer bound to postsynaptic prion protein activates Fyn to impair neurons. Nat Neurosci 2012; 15(9): 1227-35.
[http://dx.doi.org/10.1038/nn.3178] [PMID: 22820466]
[43]
Keskin AO, Durmaz N, Uncu G, et al. Geriatric medicine and gerontology. IntechOpen 2019.
[44]
Herrup K. The case for rejecting the amyloid cascade hypothesis. Nat Neurosci 2015; 18(6): 794-9.
[http://dx.doi.org/10.1038/nn.4017] [PMID: 26007212]
[45]
Alonso AC, Zaidi T, Grundke-Iqbal I, Iqbal K. Role of abnormally phosphorylated tau in the breakdown of microtubules in Alzheimer disease. Proc Natl Acad Sci USA 1994; 91(12): 5562-6.
[http://dx.doi.org/10.1073/pnas.91.12.5562] [PMID: 8202528]
[46]
Iqbal K, Liu F, Gong C-X, Alonso Adel C, Grundke-Iqbal I. Mechanisms of tau-induced neurodegeneration. Acta Neuropathol 2009; 118(1): 53-69.
[http://dx.doi.org/10.1007/s00401-009-0486-3] [PMID: 19184068]
[47]
Moussa-Pacha NM, Abdin SM, Omar HA, Alniss H, Al-Tel TH. BACE1 inhibitors: Current status and future directions in treating Alzheimer’s disease. Med Res Rev 2020; 40(1): 339-84.
[http://dx.doi.org/10.1002/med.21622] [PMID: 31347728]
[48]
Giménez-Llort L, Blázquez G, Cañete T, et al. Modeling behavioral and neuronal symptoms of Alzheimer’s disease in mice: a role for intraneuronal amyloid. Neurosci Biobehav Rev 2007; 31(1): 125-47.
[http://dx.doi.org/10.1016/j.neubiorev.2006.07.007] [PMID: 17055579]
[49]
Zhang X, Song W. The role of APP and BACE1 trafficking in APP processing and amyloid-β generation. Alzheimers Res Ther 2013; 5(5): 46.
[http://dx.doi.org/10.1186/alzrt211] [PMID: 24103387]
[50]
Do TD, LaPointe NE, Nelson R, et al. Amyloid β-protein C-terminal fragments: Formation of cylindrins and β-barrels. J Am Chem Soc 2016; 138(2): 549-57.
[http://dx.doi.org/10.1021/jacs.5b09536] [PMID: 26700445]
[51]
Bode DC, Baker MD, Viles JH. Ion channel formation by amyloid-β42 oligomers but not amyloid-β40 in cellular membranes. J Biol Chem 2017; 292(4): 1404-13.
[http://dx.doi.org/10.1074/jbc.M116.762526] [PMID: 27927987]
[52]
Das B, Yan R. A close look at BACE1 inhibitors for Alzheimer’s disease treatment. CNS Drugs 2019; 33(3): 251-63.
[http://dx.doi.org/10.1007/s40263-019-00613-7] [PMID: 30830576]
[53]
Pinheiro L, Faustino C. Therapeutic strategies targeting amyloid-β in Alzheimer’s disease. Curr Alzheimer Res 2019; 16(5): 418-52.
[http://dx.doi.org/10.2174/1567205016666190321163438] [PMID: 30907320]
[54]
Coley N, Andrieu S, Delrieu J, Voisin T, Vellas B. Biomarkers in Alzheimer’s disease: not yet surrogate endpoints. Ann N Y Acad Sci 2009; 1180(1): 119-24.
[http://dx.doi.org/10.1111/j.1749-6632.2009.04947.x] [PMID: 19906266]
[55]
Jadoopat R. Review of Alzheimer’s disease treatment and potential future therapies. Annual Review of Changes in Healthcare 2018; 2(1)
[56]
Cummings J, Lee G, Ritter A, Zhong K. Alzheimer’s disease drug development pipeline: 2018. Alzheimers Dement (N Y) 2018; 4: 195-214.
[http://dx.doi.org/10.1016/j.trci.2018.03.009] [PMID: 29955663]
[57]
Wiessner C, Wiederhold K-H, Tissot AC, et al. The second-generation active Aβ immunotherapy CAD106 reduces amyloid accumulation in APP transgenic mice while minimizing potential side effects. J Neurosci 2011; 31(25): 9323-31.
[http://dx.doi.org/10.1523/JNEUROSCI.0293-11.2011] [PMID: 21697382]
[59]
Salloway S, Sperling R, Fox NC, et al. Two phase 3 trials of bapineuzumab in mild-to-moderate Alzheimer’s disease. N Engl J Med 2014; 370(4): 322-33.
[http://dx.doi.org/10.1056/NEJMoa1304839] [PMID: 24450891]
[60]
Goure WF, Krafft GA, Jerecic J, Hefti F. Targeting the proper amyloid-beta neuronal toxins: a path forward for Alzheimer’s disease immunotherapeutics. Alzheimers Res Ther 2014; 6(4): 42.
[http://dx.doi.org/10.1186/alzrt272] [PMID: 25045405]
[61]
Wolfe MS. Developing therapeutics for Alzheimer’s disease: Progress and challenges. Academic Press 2016.
[62]
Prati F, Bottegoni G, Bolognesi ML, Cavalli A. Bace-1 inhibitors: from recent single-target molecules to multitarget compounds for alzheimer’s disease: Miniperspective. J Med Chem 2018; 61(3): 619-37.
[http://dx.doi.org/10.1021/acs.jmedchem.7b00393] [PMID: 28749667]
[63]
Polgár L. The mechanism of action of aspartic proteases involves ‘push-pull’ catalysis. FEBS Lett 1987; 219(1): 1-4.
[http://dx.doi.org/10.1016/0014-5793(87)81179-1] [PMID: 3036594]
[64]
Berman HM, Westbrook J, Feng Z, et al. The protein data bank. Nucleic Acids Res 2000; 28(1): 235-42.
[http://dx.doi.org/10.1093/nar/28.1.235] [PMID: 10592235]
[65]
Ghosh AK, Kumaragurubaran N, Hong L, et al. Design, synthesis and X-ray structure of protein-ligand complexes: important insight into selectivity of memapsin 2 (β-secretase) inhibitors. J Am Chem Soc 2006; 128(16): 5310-1.
[http://dx.doi.org/10.1021/ja058636j] [PMID: 16620080]
[66]
Lawal MM, Sanusi ZK, Govender T, Maguire GEM, Honarparvar B, Kruger HG. From recognition to reaction mechanism: an overview on the interactions between HIV-1 protease and its natural targets. Curr Med Chem 2020; 27(15): 2514-49.
[http://dx.doi.org/10.2174/0929867325666181113122900] [PMID: 30421668]
[67]
Shimizu H, Tosaki A, Kaneko K, Hisano T, Sakurai T, Nukina N. Crystal structure of an active form of BACE1, an enzyme responsible for amyloid β protein production. Mol Cell Biol 2008; 28(11): 3663-71.
[http://dx.doi.org/10.1128/MCB.02185-07] [PMID: 18378702]
[68]
Andreeva NS, Rumsh LD. Analysis of crystal structures of aspartic proteinases: On the role of amino acid residues adjacent to the catalytic site of pepsin-like enzymes. Protein Sci 2001; 10(12): 2439-50.
[http://dx.doi.org/10.1110/ps.ps.25801] [PMID: 11714911]
[69]
Hong L, Koelsch G, Lin X, et al. Structure of the protease domain of memapsin 2 (β-secretase) complexed with inhibitor. Science 2000; 290(5489): 150-3.
[http://dx.doi.org/10.1126/science.290.5489.150] [PMID: 11021803]
[70]
Hong L, Turner RT III, Koelsch G, Shin D, Ghosh AK, Tang J. Crystal structure of memapsin 2 (β-secretase) in complex with an inhibitor OM00-3. Biochemistry 2002; 41(36): 10963-7.
[http://dx.doi.org/10.1021/bi026232n] [PMID: 12206667]
[71]
Barman A, Prabhakar R. Computational insights into substrate and site specificities, catalytic mechanism, and protonation states of the catalytic Asp dyad of β-secretaseScientifica (Cairo)2014 2014.
[http://dx.doi.org/10.1155/2014/598728]
[72]
James MN, Sielecki A, Salituro F, Rich DH, Hofmann T. Conformational flexibility in the active sites of aspartyl proteinases revealed by a pepstatin fragment binding to penicillopepsin. Proc Natl Acad Sci USA 1982; 79(20): 6137-41.
[http://dx.doi.org/10.1073/pnas.79.20.6137] [PMID: 6755464]
[73]
Simon TJ, Halford GS, Eds. Developing cognitive competence: New approaches to process modeling. Psychology Press, Taylor & Francis 2015.
[http://dx.doi.org/10.4324/9781315785271]
[74]
Rossner S, Ueberham U, Schliebs R, Perez-Polo JR, Bigl V. The regulation of amyloid precursor protein metabolism by cholinergic mechanisms and neurotrophin receptor signaling. Prog Neurobiol 1998; 56(5): 541-69.
[http://dx.doi.org/10.1016/S0301-0082(98)00044-6] [PMID: 9775403]
[75]
Crisby M, Carlson LA, Winblad B. Statins in the prevention and treatment of Alzheimer disease. Alzheimer Dis Assoc Disord 2002; 16(3): 131-6.
[http://dx.doi.org/10.1097/00002093-200207000-00001] [PMID: 12218642]
[76]
Haass C. Take five-BACE and the γ-secretase quartet conduct Alzheimer’s amyloid β-peptide generation. EMBO J 2004; 23(3): 483-8.
[http://dx.doi.org/10.1038/sj.emboj.7600061] [PMID: 14749724]
[77]
Ghosh AK, Osswald HL. BACE1 (β-secretase) inhibitors for the treatment of Alzheimer’s disease. Chem Soc Rev 2014; 43(19): 6765-813.
[http://dx.doi.org/10.1039/C3CS60460H] [PMID: 24691405]
[78]
Calsolaro V, Edison P. Neuroinflammation in Alzheimer’s disease: Current evidence and future directions. Alzheimers Dement 2016; 12(6): 719-32.
[http://dx.doi.org/10.1016/j.jalz.2016.02.010] [PMID: 27179961]
[79]
Jannis S, Dempsey W, Fredenburg R. Inside the brain: Unraveling the mystery of Alzheimer’s disease. Science 2010; 327(5968): 945.
[http://dx.doi.org/10.1126/science.327.5968.945]
[80]
Al-Tel TH, Semreen MH, Al-Qawasmeh RA, et al. Design, synthesis, and qualitative structure-activity evaluations of novel β-secretase inhibitors as potential Alzheimer’s drug leads. J Med Chem 2011; 54(24): 8373-85.
[http://dx.doi.org/10.1021/jm201181f] [PMID: 22044119]
[81]
Vassar R, Kuhn PH, Haass C, et al. Function, therapeutic potential and cell biology of BACE proteases: current status and future prospects. J Neurochem 2014; 130(1): 4-28.
[http://dx.doi.org/10.1111/jnc.12715] [PMID: 24646365]
[82]
Coimbra JRM, Marques DFF, Baptista SJ, et al. Highlights in BACE1 inhibitors for Alzheimer’s disease treatment. Front Chem 2018; 6: 178.
[http://dx.doi.org/10.3389/fchem.2018.00178] [PMID: 29881722]
[83]
Ghosh AK, Brindisi M, Tang J. Developing β-secretase inhibitors for treatment of Alzheimer’s disease. J Neurochem 2012; 120(Suppl. 1): 71-83.
[http://dx.doi.org/10.1111/j.1471-4159.2011.07476.x] [PMID: 22122681]
[84]
Manoharan P, Chennoju K, Ghoshal N. Computational analysis of BACE1-ligand complex crystal structures and linear discriminant analysis for identification of BACE1 inhibitors with anti P-glycoprotein binding property. J Biomol Struct Dyn 2018; 36(1): 262-76.
[http://dx.doi.org/10.1080/07391102.2016.1276477] [PMID: 28081663]
[85]
Yuan J, Venkatraman S, Zheng Y, McKeever BM, Dillard LW, Singh SB. Structure-based design of β-site APP cleaving enzyme 1 (BACE1) inhibitors for the treatment of Alzheimer’s disease. J Med Chem 2013; 56(11): 4156-80.
[http://dx.doi.org/10.1021/jm301659n] [PMID: 23509904]
[86]
Vassar R, Bennett BD, Babu-Khan S, et al. β-secretase cleavage of Alzheimer’s amyloid precursor protein by the transmembrane aspartic protease BACE. Science 1999; 286(5440): 735-41.
[http://dx.doi.org/10.1126/science.286.5440.735] [PMID: 10531052]
[87]
Knopman DS. Bad news and good news in AD, and how to reconcile them. Nat Rev Neurol 2019; 15(2): 61-2.
[http://dx.doi.org/10.1038/s41582-018-0131-7] [PMID: 30622292]
[88]
Egan MF, Kost J, Voss T, et al. Randomized trial of verubecestat for prodromal Alzheimer’s disease. N Engl J Med 2019; 380(15): 1408-20.
[http://dx.doi.org/10.1056/NEJMoa1812840] [PMID: 30970186]
[89]
Henley D, Raghavan N, Sperling R, Aisen P, Raman R, Romano G. Preliminary results of a trial of atabecestat in preclinical Alzheimer’s disease. N Engl J Med 2019; 380(15): 1483-5.
[http://dx.doi.org/10.1056/NEJMc1813435] [PMID: 30970197]
[90]
Liu L, Lauro BM, Ding L, Rovere M, Wolfe MS, Selkoe DJ. Multiple BACE1 inhibitors abnormally increase the BACE1 protein level in neurons by prolonging its half-life. Alzheimers Dement 2019; 15(9): 1183-94.
[http://dx.doi.org/10.1016/j.jalz.2019.06.3918] [PMID: 31416794]
[91]
Wang J, Urban L. The impact of early ADME profiling on drug discovery and development strategy. Drug Discovery World 2004; 5(4): 73-86.
[92]
Lipinski CA, Lombardo F, Dominy BW, Feeney PJ. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Deliv Rev 2001; 46(1-3): 3-26.
[http://dx.doi.org/10.1016/S0169-409X(00)00129-0] [PMID: 11259830]
[93]
Wire B. Merck announces discontinuation of APECS study evaluating verubecestat (MK-8931) for the treatment of people with prodromal Alzheimer’s disease. Business Wire 2018.
[94]
Egan MF, Kost J, Tariot PN, et al. Randomized trial of verubecestat for mild-to-moderate Alzheimer’s disease. N Engl J Med 2018; 378(18): 1691-703.
[http://dx.doi.org/10.1056/NEJMoa1706441] [PMID: 29719179]
[95]
Yan R. Stepping closer to treating Alzheimer’s disease patients with BACE1 inhibitor drugs. Transl Neurodegener 2016; 5(1): 13.
[http://dx.doi.org/10.1186/s40035-016-0061-5] [PMID: 27418961]
[96]
Sakamoto K, Matsuki S, Matsuguma K, et al. BACE1 inhibitor lanabecestat (AZD3293) in a phase 1 study of healthy Japanese subjects: Pharmacokinetics and effects on plasma and cerebrospinal fluid Aβ peptides. J Clin Pharmacol 2017; 57(11): 1460-71.
[http://dx.doi.org/10.1002/jcph.950] [PMID: 28618005]
[97]
Wessels AM, Tariot PN, Zimmer JA, et al. Efficacy and safety of lanabecestat for treatment of early and mild Alzheimer disease: the AMARANTH and DAYBREAK-ALZ randomized clinical trials. JAMA Neurol 2020; 77(2): 199-209.
[http://dx.doi.org/10.1001/jamaneurol.2019.3988] [PMID: 31764959]
[98]
Mullard A. BACE failures lower AD expectations, again. Nat Rev Drug Discov 2018; 17(6): 385-5.
[PMID: 29844595]
[99]
Panza F, Lozupone M, Watling M, Imbimbo BP. Taylor & Francis. 2019.
[100]
Agatonovic-Kustrin S, Kettle C, Morton DW. A molecular approach in drug development for Alzheimer’s disease. Biomed Pharmacother 2018; 106: 553-65.
[http://dx.doi.org/10.1016/j.biopha.2018.06.147] [PMID: 29990843]
[101]
Piazzi L, Cavalli A, Colizzi F, et al. Multi-target-directed coumarin derivatives: hAChE and BACE1 inhibitors as potential anti-Alzheimer compounds. Bioorg Med Chem Lett 2008; 18(1): 423-6.
[http://dx.doi.org/10.1016/j.bmcl.2007.09.100] [PMID: 17998161]
[102]
Cao D, Liu Z, Verwilst P, et al. Coumarin-based small-molecule fluorescent chemosensors. Chem Rev 2019; 119(18): 10403-519.
[http://dx.doi.org/10.1021/acs.chemrev.9b00145] [PMID: 31314507]
[103]
Wang L, Wu Y, Deng Y, et al. Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field. J Am Chem Soc 2015; 137(7): 2695-703.
[http://dx.doi.org/10.1021/ja512751q] [PMID: 25625324]
[104]
Ambure P, Bhat J, Puzyn T, Roy K. Identifying natural compounds as multi-target-directed ligands against Alzheimer’s disease: an in silico approach. J Biomol Struct Dyn 2019; 37(5): 1282-306.
[http://dx.doi.org/10.1080/07391102.2018.1456975] [PMID: 29578387]
[105]
Ion GND, Mihai DP, Lupascu G, Nitulescu GM. Application of molecular framework-based data-mining method in the search for beta-secretase 1 inhibitors through drug repurposing. J Biomol Struct Dyn 2019; 37(14): 3674-85.
[http://dx.doi.org/10.1080/07391102.2018.1526115] [PMID: 30234434]
[106]
Hu Y, Zhou G, Zhang C, et al. Identify compounds’ target against Alzheimer’s disease based on in-silico approach. Curr Alzheimer Res 2019; 16(3): 193-208.
[http://dx.doi.org/10.2174/1567205016666190103154855] [PMID: 30605059]
[107]
Gupta M, Madan AK. Detour cum distance matrix based topological descriptors for QSAR/QSPR part-II: Application in drug discovery process. Lett Drug Des Discov 2014; 11(7): 864-76.
[http://dx.doi.org/10.2174/1570180811666140401182931]
[108]
Adeowo FY, Lawal MM, Kumalo HM. Design and development of cholinesterase dual inhibitors towards Alzheimer’s disease treatment: A focus on recent contributions from computational and theoretical perspective. ChemistrySelect 2020; 5(44): 14136-52.
[http://dx.doi.org/10.1002/slct.202003573]
[109]
Zhao J, Liu X, Xia W, Zhang Y, Wang C. Targeting amyloidogenic processing of APP in Alzheimer’s disease. Front Mol Neurosci 2020; 13: 137.
[http://dx.doi.org/10.3389/fnmol.2020.00137] [PMID: 32848600]
[110]
Rubesova P. Protease inhibitors as chemotherapeutics. Chem Listy 2020; 114(8): 515-22.
[111]
Mouchlis VD, Melagraki G, Zacharia LC, Afantitis A. Computer-aided drug design of β-secretase, γ-secretase and anti-tau inhibitors for the discovery of novel alzheimer’s therapeutics. Int J Mol Sci 2020; 21(3)E703
[http://dx.doi.org/10.3390/ijms21030703] [PMID: 31973122]
[112]
Iraji A, Khoshneviszadeh M, Firuzi O, Khoshneviszadeh M, Edraki N. Novel small molecule therapeutic agents for Alzheimer disease: Focusing on BACE1 and multi-target directed ligands. Bioorg Chem 2020; 97103649
[http://dx.doi.org/10.1016/j.bioorg.2020.103649] [PMID: 32101780]
[113]
Gupta SP, Patil VM. Recent studies on design and development of drugs against Alzheimer’s disease (AD) based on inhibition of BACE-1 and other AD-causative agents. Curr Top Med Chem 2020; 20(13): 1195-213.
[http://dx.doi.org/10.2174/1568026620666200416091623] [PMID: 32297584]
[114]
Ettcheto M, Busquets O, Espinosa-Jiménez T, Verdaguer E, Auladell C, Camins A. A chronological review of potential disease-modifying therapeutic strategies for Alzheimer’s disease. Curr Pharm Des 2020; 26(12): 1286-99.
[http://dx.doi.org/10.2174/1381612826666200211121416] [PMID: 32066356]
[115]
De Simone A, Naldi M, Tedesco D, Bartolini M, Davani L, Andrisano V. Advanced analytical methodologies in Alzheimer’s disease drug discovery. J Pharm Biomed Anal 2020; 178112899
[http://dx.doi.org/10.1016/j.jpba.2019.112899] [PMID: 31606562]
[116]
Das S, Sengupta S, Chakraborty S. Scope of β-secretase (BACE1)-targeted therapy in Alzheimer’s disease: Emphasizing the flavonoid based natural scaffold for BACE1 inhibition. ACS Chem Neurosci 2020; 11(21): 3510-22.
[http://dx.doi.org/10.1021/acschemneuro.0c00579] [PMID: 33073981]
[117]
Dabur M, Loureiro JA, Pereira MC. Fluorinated molecules and nanotechnology: Future ‘avengers’ against the Alzheimer’s disease? Int J Mol Sci 2020; 21(8)E2989
[http://dx.doi.org/10.3390/ijms21082989] [PMID: 32340267]
[118]
Wang T, Wu M-B, Lin J-P, Yang L-R. Quantitative structure-activity relationship: Promising advances in drug discovery platforms. Expert Opin Drug Discov 2015; 10(12): 1283-300.
[http://dx.doi.org/10.1517/17460441.2015.1083006] [PMID: 26358617]
[119]
Danishuddin, Khan AU. Descriptors and their selection methods in QSAR analysis: Paradigm for drug design. Drug Discov Today 2016; 21(8): 1291-302.
[http://dx.doi.org/10.1016/j.drudis.2016.06.013] [PMID: 27326911]
[120]
Tandon H, Chakraborty T, Suhag V. A concise review on the significance of QSAR in drug design. Biomol Eng 2019; 4(4): 45-51.
[121]
Wu F, Zhou Y, Li L, et al. Computational approaches in preclinical studies on drug discovery and development. Front Chem 2020; 8: 726.
[http://dx.doi.org/10.3389/fchem.2020.00726] [PMID: 33062633]
[122]
Manoharan P, Vijayan RSK, 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(10): 843-64.
[http://dx.doi.org/10.1007/s10822-010-9378-9] [PMID: 20740315]
[123]
Kuhn B, Guba W, Hert J, et al. A real-world perspective on molecular design. J Med Chem 2016; 59(9): 4087-102.
[http://dx.doi.org/10.1021/acs.jmedchem.5b01875] [PMID: 26878596]
[124]
Monceaux CJ, Hirata-Fukae C, Lam PCH, Totrov MM, Matsuoka Y, Carlier PR. Triazole-linked reduced amide isosteres: An approach for the fragment-based drug discovery of anti-Alzheimer’s BACE1 inhibitors. Bioorg Med Chem Lett 2011; 21(13): 3992-6.
[http://dx.doi.org/10.1016/j.bmcl.2011.05.007] [PMID: 21621412]
[125]
Mok NY, Chadwick J, Kellett KA, et al. Discovery of biphenylacetamide-derived inhibitors of BACE1 using de novo structure-based molecular design. J Med Chem 2013; 56(5): 1843-52.
[http://dx.doi.org/10.1021/jm301127x] [PMID: 23374014]
[126]
Panek D, Więckowska A, Wichur T, et al. Design, synthesis and biological evaluation of new phthalimide and saccharin derivatives with alicyclic amines targeting cholinesterases, beta-secretase and amyloid beta aggregation. Eur J Med Chem 2017; 125: 676-95.
[http://dx.doi.org/10.1016/j.ejmech.2016.09.078] [PMID: 27721153]
[127]
Hamada Y, Tagad HD, Nishimura Y, Ishiura S, Kiso Y. Tripeptidic BACE1 inhibitors devised by in-silico conformational structure-based design. Bioorg Med Chem Lett 2012; 22(2): 1130-5.
[http://dx.doi.org/10.1016/j.bmcl.2011.11.102] [PMID: 22178553]
[128]
Hamada Y, Ishiura S, Kiso Y. BACE1 inhibitor peptides: Can an infinitely small k cat value turn the substrate of an enzyme into Its Inhibitor? ACS Med Chem Lett 2011; 3(3): 193-7.
[http://dx.doi.org/10.1021/ml2002373] [PMID: 24900449]
[129]
Wu Q, Li X, Gao Q, Wang J, Li Y, Yang L. Interaction mechanism exploration of HEA derivatives as BACE1 inhibitors by in silico analysis. Mol Biosyst 2016; 12(4): 1151-65.
[http://dx.doi.org/10.1039/C5MB00859J] [PMID: 26915506]
[130]
Dixon SL, Smondyrev AM, Knoll EH, Rao SN, Shaw DE, Friesner RA. PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results. J Comput Aided Mol Des 2006; 20(10-11): 647-71.
[http://dx.doi.org/10.1007/s10822-006-9087-6] [PMID: 17124629]
[131]
Khedkar SA, Malde AK, Coutinho EC, Srivastava S. Pharmacophore modeling in drug discovery and development: An overview. Med Chem 2007; 3(2): 187-97.
[http://dx.doi.org/10.2174/157340607780059521] [PMID: 17348856]
[132]
Lin X, Li X, Lin X. A review on applications of computational methods in drug screening and design. Molecules 2020; 25(6): 1375.
[http://dx.doi.org/10.3390/molecules25061375] [PMID: 32197324]
[133]
Kumalo HM, Soliman ME. Per-residue energy footprints-based pharmacophore modeling as an enhanced in silico approach in drug discovery: A case study on the identification of novel beta-secretase1 (BACE1) inhibitors as anti-alzheimer agents. Cell Mol Bioeng 2016; 9(1): 175-89.
[http://dx.doi.org/10.1007/s12195-015-0421-8]
[134]
Chakraborty S, Ramachandran B, Basu S. Encompassing receptor flexibility in virtual screening using ensemble docking-based hybrid QSAR: Discovery of novel phytochemicals for BACE1 inhibition. Mol Biosyst 2014; 10(10): 2684-92.
[http://dx.doi.org/10.1039/C4MB00307A] [PMID: 25088750]
[135]
Suwanttananuruk P, Jiaranaikulwanitch J, Waiwut P, Vajragupta O. Lead discovery of a guanidinyl tryptophan derivative on amyloid cascade inhibition. Open Chem 2020; 18(1): 546-58.
[http://dx.doi.org/10.1515/chem-2020-0067]
[136]
Gupta S, Parihar D, Shah M, et al. Computational screening of promising beta-secretase 1 inhibitors through multi-step molecular docking and molecular dynamics simulations - Pharmacoinformatics approach. J Mol Struct 2020; 1205.
[http://dx.doi.org/10.1016/j.molstruc.2019.127660]
[137]
Kumar A, Roy S, Tripathi S, Sharma A. Molecular docking based virtual screening of natural compounds as potential BACE1 inhibitors: 3D QSAR pharmacophore mapping and molecular dynamics analysis. J Biomol Struct Dyn 2016; 34(2): 239-49.
[http://dx.doi.org/10.1080/07391102.2015.1022603] [PMID: 25707809]
[138]
Chakraborty S, Basu S. Multi-functional activities of citrus flavonoid narirutin in Alzheimer’s disease therapeutics: An integrated screening approach and in vitro validation. Int J Biol Macromol 2017; 103: 733-43.
[http://dx.doi.org/10.1016/j.ijbiomac.2017.05.110] [PMID: 28528948]
[139]
Iwaloye O, Elekofehinti OO, Momoh AI, Babatomiwa K, Ariyo EO. In silico molecular studies of natural compounds as possible anti-Alzheimer’s agents: Ligand-based design. Netw Model Anal Health Inform Bioinform 2020; 9(1): 54.
[http://dx.doi.org/10.1007/s13721-020-00262-7]
[140]
Joseph OA, Babatomiwa K, Niyi A, Olaposi O, Olumide I. Molecular docking and 3D Qsar studies of C000000956 as a potent inhibitor of Bace-1. Drug Res (Stuttg) 2019; 69(8): 451-7.
[http://dx.doi.org/10.1055/a-0849-9377] [PMID: 30780168]
[141]
Hernández-Rodríguez M, Correa-Basurto J, Martínez-Ramos F, et al. Design of multi-target compounds as AChE, BACE1, and amyloid-β(1-42) oligomerization inhibitors: in silico and in vitro studies. J Alzheimers Dis 2014; 41(4): 1073-85.
[http://dx.doi.org/10.3233/JAD-140471] [PMID: 24762947]
[142]
Daina A, Michielin O, Zoete V. SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci Rep 2017; 7: 42717.
[http://dx.doi.org/10.1038/srep42717] [PMID: 28256516]
[143]
VLS3D-CONSULTING ADMET and physchem predictions and related tools. Available from:. https://www.vls3d.com/index.php/links/chemoinformatics/admet
[144]
Computational tools for ADMET. Available from:. http://crdd. osdd.net/admet.php
[145]
QSAR and toxicity prediction software. Available from:. http://www.saae-i.org/docs/insilico-toxicology.pdf
[146]
Salvadores N, Sanhueza M, Manque P, Court FA. Axonal degeneration during aging and its functional role in neurodegenerative disorders. Front Neurosci 2017; 11: 451.
[http://dx.doi.org/10.3389/fnins.2017.00451] [PMID: 28928628]
[147]
Yu YJ, Zhang Y, Kenrick M, et al. Boosting brain uptake of a therapeutic antibody by reducing its affinity for a transcytosis target. Sci Transl Med 2011; 3(84): 84ra44-4.
[http://dx.doi.org/10.1126/scitranslmed.3002230]
[148]
Atwal JK, Chen Y, Chiu C, et al. A therapeutic antibody targeting BACE1 inhibits amyloid-β production in vivo. Sci Transl Med 2011; 3(84): 84ra43-3.
[http://dx.doi.org/10.1126/scitranslmed.3002254]
[149]
Devraj K, Poznanovic S, Spahn C, et al. BACE-1 is expressed in the blood-brain barrier endothelium and is upregulated in a murine model of Alzheimer’s disease. J Cereb Blood Flow Metab 2016; 36(7): 1281-94.
[http://dx.doi.org/10.1177/0271678X15606463] [PMID: 26661166]
[150]
Ruderisch N, Schlatter D, Kuglstatter A, et al. Potent and selective BACE-1 peptide inhibitors lower brain Aβ levels mediated by brain shuttle transport. EBioMedicine 2017; 24: 76-92.
[http://dx.doi.org/10.1016/j.ebiom.2017.09.004] [PMID: 28923680]
[151]
Al-Nadaf AH, Taha MO. Identification of small molecule memapsin inhibitors via computation-based virtual screening. Adv Pharmacol Pharma 2015; 3(3): 53-63.
[http://dx.doi.org/10.13189/app.2015.030301]
[152]
Khalid S, Zahid MA, Ali H, Kim YS, Khan S. Biaryl scaffold-focused virtual screening for anti-aggregatory and neuroprotective effects in Alzheimer’s disease. BMC Neurosci 2018; 19(1): 74.
[http://dx.doi.org/10.1186/s12868-018-0472-6] [PMID: 30424732]
[153]
Gurjar AS, Andrisano V, Simone AD, Velingkar VS. Design, synthesis, in silico and in vitro screening of 1,2,4-thiadiazole analogues as non-peptide inhibitors of beta-secretase. Bioorg Chem 2014; 57: 90-8.
[http://dx.doi.org/10.1016/j.bioorg.2014.09.002] [PMID: 25303313]
[154]
Lavecchia A. Machine-learning approaches in drug discovery: Methods and applications. Drug Discov Today 2015; 20(3): 318-31.
[http://dx.doi.org/10.1016/j.drudis.2014.10.012] [PMID: 25448759]
[155]
Coimbra JRM, Baptista SJ, Dinis TCP, et al. Combining virtual screening protocol and in vitro evaluation towards the discovery of BACE1 inhibitors. Biomolecules 2020; 10(4): 535.
[http://dx.doi.org/10.3390/biom10040535] [PMID: 32244832]
[156]
Rifaioglu AS, Atas H, Martin MJ, Cetin-Atalay R, Atalay V, Doğan T. Recent applications of deep learning and machine intelligence on in silico drug discovery: Methods, tools and databases. Brief Bioinform 2019; 20(5): 1878-912.
[http://dx.doi.org/10.1093/bib/bby061] [PMID: 30084866]
[157]
Fischer A, Sellner M, Neranjan S, Smieško M, Lill MA. Potential inhibitors for novel coronavirus protease identified by virtual screening of 606 million compounds. Int J Mol Sci 2020; 21(10): 3626.
[http://dx.doi.org/10.3390/ijms21103626] [PMID: 32455534]
[158]
Hospital A, Goñi JR, Orozco M, Gelpí JL. Molecular dynamics simulations: Advances and applications. Adv Appl Bioinform Chem 2015; 8: 37-47.
[PMID: 26604800]
[159]
Ugbaja SC, Appiah-Kubi P, Lawal MM, Gumede NS, Kumalo HM. Unravelling the molecular basis of AM-6494 high potency at BACE1 in Alzheimer’s disease: An integrated dynamic interaction investigation. J Biomol Struct Dyn 2021; 1-13.
[http://dx.doi.org/10.1080/07391102.2020.1869099] [PMID: 33410374]
[160]
Saravanan K, Sivanandam M, Hunday G, Mathiyalagan L, Kumaradhas P. Investigation of intermolecular interactions and stability of verubecestat in the active site of BACE1: Development of first model from QM/MM-based charge density and MD analysis. J Biomol Struct Dyn 2019; 37(9): 2339-54.
[http://dx.doi.org/10.1080/07391102.2018.1479661] [PMID: 30044206]
[161]
Warshel A, Levitt M. Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J Mol Biol 1976; 103(2): 227-49.
[http://dx.doi.org/10.1016/0022-2836(76)90311-9] [PMID: 985660]
[162]
(a)Polymeropoulos E, Warshel A. Computer modeling of chemical reactions in enzymes and solutions. New York: J. Wiley & Sons, Inc. 1991; p. 236.; (b)Ber Bunsenges Phys Chem 1992; 96(9): 1323-4.
[163]
Xu D, Zheng M, Wu S. Quantum simulations of materials and biological systems. Springer 2012; pp. 155-68.
[http://dx.doi.org/10.1007/978-94-007-4948-1_9]
[164]
Chung LW, Sameera WM, Ramozzi R, et al. The ONIOM method and its applications. Chem Rev 2015; 115(12): 5678-796.
[http://dx.doi.org/10.1021/cr5004419] [PMID: 25853797]
[165]
Svensson M, Humbel S, Froese RD, Matsubara T, Sieber S, Morokuma K. ONIOM: A multilayered integrated MO+ MM method for geometry optimizations and single point energy predictions. A test for Diels− Alder reactions and Pt (P (t-Bu) 3) 2+ H2 oxidative addition. J Phys Chem 1996; 100(50): 19357-63.
[http://dx.doi.org/10.1021/jp962071j]
[166]
Torrie GM, Valleau JP. Monte Carlo free energy estimates using non-Boltzmann sampling: Application to the sub-critical Lennard-Jones fluid. Chem Phys Lett 1974; 28(4): 578-81.
[http://dx.doi.org/10.1016/0009-2614(74)80109-0]
[167]
Kästner J. Umbrella sampling. Wiley Interdiscip Rev Comput Mol Sci 2011; 1(6): 932-42.
[http://dx.doi.org/10.1002/wcms.66]
[168]
Sanusi ZK, Govender T, Maguire GEM, et al. Investigation of the binding free energies of FDA approved drugs against subtype B and C-SA HIV PR: ONIOM approach. J Mol Graph Model 2017; 76: 77-85.
[http://dx.doi.org/10.1016/j.jmgm.2017.06.026] [PMID: 28711760]
[169]
Sanusi ZK, Govender T, Maguire GEM, et al. An insight to the molecular interactions of the FDA approved HIV PR drugs against L38L↑N↑L PR mutant. J Comput Aided Mol Des 2018; 32(3): 459-71.
[http://dx.doi.org/10.1007/s10822-018-0099-9] [PMID: 29397520]
[170]
Ugbaja SC, Sanusi ZK, Appiah-Kubi P, Lawal MM, Kumalo HM. Computational modelling of potent β-secretase (BACE1) inhibitors towards Alzheimer’s disease treatment. Biophys Chem 2021; 270106536
[http://dx.doi.org/10.1016/j.bpc.2020.106536] [PMID: 33387910]
[171]
Sanusi ZK, Lawal MM, Govender T, Maguire GEM, Honarparvar B, Kruger HG. Theoretical model for HIV-1 PR that accounts for substrate recognition and preferential cleavage of natural substrates. J Phys Chem B 2019; 123(30): 6389-400.
[http://dx.doi.org/10.1021/acs.jpcb.9b02207] [PMID: 31283878]
[172]
Lawal MM, Sanusi ZK, Govender T, et al. Unraveling the concerted catalytic mechanism of the human immunodeficiency virus type 1 (HIV-1) protease: A hybrid QM/MM study. Struct Chem 2019; 30(1): 409-17.
[http://dx.doi.org/10.1007/s11224-018-1251-9]
[173]
Sanusi ZK, Lawal MM, Gupta PL, et al. Exploring the concerted mechanistic pathway for HIV-1 PR-substrate revealed by umbrella sampling simulation. J Biomol Struct Dyn 2020; 1-12.
[http://dx.doi.org/10.1080/07391102.2020.1832578] [PMID: 33073714]
[174]
Sanusi ZK, Lawal MM, Govender T, et al. Concerted hydrolysis mechanism of HIV-1 natural substrate against subtypes B and C-SA PR: Insight through molecular dynamics and hybrid QM/MM studies. Phys Chem Chem Phys 2020; 22(4): 2530-9.
[http://dx.doi.org/10.1039/C9CP05639D] [PMID: 31942584]
[175]
Frush EH, Sekharan S, Keinan S. In silico prediction of ligand binding energies in multiple therapeutic targets and diverse ligand sets-A case study on BACE1, TYK2, HSP90, and PERK proteins. J Phys Chem B 2017; 121(34): 8142-8.
[http://dx.doi.org/10.1021/acs.jpcb.7b07224] [PMID: 28759991]
[176]
Pettus LH, Bourbeau MP, Bradley J, et al. Discovery of AM-6494: A potent and orally efficacious β-site amyloid precursor protein cleaving enzyme 1 (BACE1) inhibitor with in vivo selectivity over BACE2. J Med Chem 2020; 63(5): 2263-81.
[http://dx.doi.org/10.1021/acs.jmedchem.9b01034] [PMID: 31589043]
[177]
Gutiérrez LJ, Parravicini O, Sánchez E, Rodríguez R, Cobo J, Enriz RD. New substituted aminopyrimidine derivatives as BACE1 inhibitors: In silico design, synthesis and biological assays. J Biomol Struct Dyn 2019; 37(1): 229-46.
[http://dx.doi.org/10.1080/07391102.2018.1424036] [PMID: 29301478]
[178]
Pai RV, Monpara JD, Vavia PR. Exploring molecular dynamics simulation to predict binding with ocular mucin: An in silico approach for screening mucoadhesive materials for ocular retentive delivery systems. J Control Release 2019; 309: 190-202.
[http://dx.doi.org/10.1016/j.jconrel.2019.07.037] [PMID: 31356839]
[179]
Stuyver T, Danovich D, Joy J, Shaik S. External electric field effects on chemical structure and reactivity. WIREs Computational Molecular Science 2020; 10(2)e1438
[http://dx.doi.org/10.1002/wcms.1438]
[180]
Gutiérrez M, Vallejos GA, Cortés MP, Bustos C. Bennett acceptance ratio method to calculate the binding free energy of BACE1 inhibitors: Theoretical model and design of new ligands of the enzyme. Chem Biol Drug Des 2019; 93(6): 1117-28.
[http://dx.doi.org/10.1111/cbdd.13456] [PMID: 30693676]
[181]
Keränen H, Pérez-Benito L, Ciordia M, et al. Acylguanidine beta secretase 1 inhibitors: A combined experimental and free energy perturbation study. J Chem Theory Comput 2017; 13(3): 1439-53.
[http://dx.doi.org/10.1021/acs.jctc.6b01141] [PMID: 28103438]
[182]
Malamas MS, Erdei J, Gunawan I, et al. Design and synthesis of 5,5′-disubstituted aminohydantoins as potent and selective human β-secretase (BACE1) inhibitors. J Med Chem 2010; 53(3): 1146-58.
[http://dx.doi.org/10.1021/jm901414e] [PMID: 19968289]
[183]
Mandal M, Zhu Z, Cumming JN, et al. Design and validation of bicyclic iminopyrimidinones as beta amyloid cleaving enzyme-1 (BACE1) inhibitors: Conformational constraint to favor a bioactive conformation. J Med Chem 2012; 55(21): 9331-45.
[http://dx.doi.org/10.1021/jm301039c] [PMID: 22989333]
[184]
Stamford AW, Scott JD, Li SW, et al. Discovery of an orally available, brain penetrant BACE1 inhibitor that affords robust CNS Aβ reduction. ACS Med Chem Lett 2012; 3(11): 897-902.
[http://dx.doi.org/10.1021/ml3001165] [PMID: 23412139]
[185]
Jiaranaikulwanitch J, Govitrapong P, Fokin VV, Vajragupta O. From BACE1 inhibitor to multifunctionality of tryptoline and tryptamine triazole derivatives for Alzheimer’s disease. Molecules 2012; 17(7): 8312-33.
[http://dx.doi.org/10.3390/molecules17078312] [PMID: 22781443]
[186]
Huang HJ, Lee CC, Chen CYC. In silico design of BACE1 inhibitor for Alzheimer ' s disease by traditional chinese medicine. BioMed Res Int 2014; 2014741703
[187]
Wu Y-J, Guernon J, Yang F, et al. Targeting the BACE1 active site flap leads to a potent inhibitor that elicits robust brain Aβ reduction in rodents. ACS Med Chem Lett 2016; 7(3): 271-6.
[http://dx.doi.org/10.1021/acsmedchemlett.5b00432] [PMID: 26985314]
[188]
Azimi S, Zonouzi A, Firuzi O, et al. Discovery of imidazopyridines containing isoindoline-1,3-dione framework as a new class of BACE1 inhibitors: Design, synthesis and SAR analysis. Eur J Med Chem 2017; 138: 729-37.
[http://dx.doi.org/10.1016/j.ejmech.2017.06.040] [PMID: 28728105]
[189]
Guix FX, Sartório CL, Ill-Raga G. BACE1 translation: At the crossroads between Alzheimer’s disease neurodegeneration and memory consolidation. J Alzheimers Dis Rep 2019; 3(1): 113-48.
[http://dx.doi.org/10.3233/ADR-180089] [PMID: 31259308]
[190]
Zhu Z, Schuster DI, Tuckerman ME. Molecular dynamics study of the connection between flap closing and binding of fullerene-based inhibitors of the HIV-1 protease. Biochemistry 2003; 42(5): 1326-33.
[http://dx.doi.org/10.1021/bi020496s] [PMID: 12564936]
[191]
Hornak V, Okur A, Rizzo RC, Simmerling C. HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations. Proc Natl Acad Sci USA 2006; 103(4): 915-20.
[http://dx.doi.org/10.1073/pnas.0508452103] [PMID: 16418268]
[192]
Tozzini V, Trylska J, Chang CE, McCammon JA. Flap opening dynamics in HIV-1 protease explored with a coarse-grained model. J Struct Biol 2007; 157(3): 606-15.
[http://dx.doi.org/10.1016/j.jsb.2006.08.005] [PMID: 17029846]
[193]
Heaslet H, Rosenfeld R, Giffin M, et al. Conformational flexibility in the flap domains of ligand-free HIV protease. Acta Crystallogr D Biol Crystallogr 2007; 63(Pt 8): 866-75.
[http://dx.doi.org/10.1107/S0907444907029125] [PMID: 17642513]
[194]
Kumalo HM, Soliman ME. A comparative molecular dynamics study on BACE1 and BACE2 flap flexibility. J Recept Signal Transduct Res 2016; 36(5): 505-14.
[http://dx.doi.org/10.3109/10799893.2015.1130058] [PMID: 26804314]
[195]
Brauer DJ, Schenk S, Roßenbach S, et al. Water soluble phosphines: Part XIII. Chiral phosphine ligands with amino acid moieties. J Organomet Chem 2000; 598(1): 116-26.
[http://dx.doi.org/10.1016/S0022-328X(99)00689-0]
[196]
Butini S, Brogi S, Novellino E, et al. The structural evolution of β-secretase inhibitors: a focus on the development of small-molecule inhibitors. Curr Top Med Chem 2013; 13(15): 1787-807.
[http://dx.doi.org/10.2174/15680266113139990137] [PMID: 23931442]
[197]
Ghosh AK, Shin D, Downs D, et al. Design of potent inhibitors for human brain memapsin 2 (β-secretase). J Am Chem Soc 2000; 122(14): 3522-3.
[http://dx.doi.org/10.1021/ja000300g] [PMID: 30443047]
[198]
Li D, Liu MS, Ji B, Hwang KC, Huang Y. Identifying the molecular mechanics and binding dynamics characteristics of potent inhibitors to HIV-1 protease. Chem Biol Drug Des 2012; 80(3): 440-54.
[http://dx.doi.org/10.1111/j.1747-0285.2012.01417.x] [PMID: 22621379]
[199]
Blass B. Cyclopropyl-fused 1, 3-thiazepines as BACE1 and BACE2 inhibitors. ACS Publications 2013; pp. 379-80.
[200]
Thomas AA, Hunt KW, Newhouse B, et al. 8-Tetrahydropyran-2-yl chromans: Highly selective beta-site amyloid precursor protein cleaving enzyme 1 (BACE1) inhibitors. J Med Chem 2014; 57(23): 10112-29.
[http://dx.doi.org/10.1021/jm5015132] [PMID: 25411915]
[201]
Hernández-Rodríguez M, Correa-Basurto J, Gutiérrez A, Vitorica J, Rosales-Hernández MC. Asp32 and Asp228 determine the selective inhibition of BACE1 as shown by docking and molecular dynamics simulations. Eur J Med Chem 2016; 124: 1142-54.
[http://dx.doi.org/10.1016/j.ejmech.2016.08.028] [PMID: 27639619]
[202]
Johansson P, Kaspersson K, Gurrell IK, et al. Toward β-secretase-1 inhibitors with improved isoform selectivity. J Med Chem 2018; 61(8): 3491-502.
[http://dx.doi.org/10.1021/acs.jmedchem.7b01716] [PMID: 29617572]
[203]
Sabbah DA, Zhong HA. Modeling the protonation states of β-secretase binding pocket by molecular dynamics simulations and docking studies. J Mol Graph Model 2016; 68: 206-15.
[http://dx.doi.org/10.1016/j.jmgm.2016.07.005] [PMID: 27474865]
[204]
Nepovimova E, Kuca K. Neurodegenerative diseases-molecular mechanisms and current therapeutic approaches. IntechOpen 2020.
[205]
Youn K, Lee J, Yun EY, et al. Biological evaluation and in silico docking study of γ-linolenic acid as a potential BACE1 inhibitor. J Funct Foods 2014; 10: 187-91.
[http://dx.doi.org/10.1016/j.jff.2014.06.005]
[206]
Wang W, Liu Y, Lazarus RA. Allosteric inhibition of BACE1 by an exosite-binding antibody. Curr Opin Struct Biol 2013; 23(6): 797-805.
[http://dx.doi.org/10.1016/j.sbi.2013.08.001] [PMID: 23998983]
[207]
Kornacker MG, Copeland RA, Hendrick J, et al. Beta secretase exosite binding peptides and methods for identifying beta secretase modulators Patent No US20040121412A1 2008.
[208]
Gutierrez LJ, Enriz RD, Baldoni HA. Structural and thermodynamic characteristics of the exosite binding pocket on the human BACE1: a molecular modeling approach. J Phys Chem A 2010; 114(37): 10261-9.
[http://dx.doi.org/10.1021/jp104983a] [PMID: 20806954]
[209]
Gutiérrez LJ, Andujar SA, Enriz RD, Baldoni HA. Structural and functional insights into the anti-BACE1 Fab fragment that recognizes the BACE1 exosite. J Biomol Struct Dyn 2014; 32(9): 1421-33.
[http://dx.doi.org/10.1080/07391102.2013.821024] [PMID: 23879547]
[210]
Campagna J, Vadivel K, Jagodzinska B, et al. Evaluation of an allosteric BACE inhibitor peptide to identify mimetics that can interact with the loop F region of the enzyme and prevent APP cleavage. J Mol Biol 2018; 430(11): 1566-76.
[http://dx.doi.org/10.1016/j.jmb.2018.04.002] [PMID: 29649434]
[211]
Gutierrez LJ, Angelina E, Gyebrovszki A, et al. New small-size peptides modulators of the exosite of BACE1 obtained from a structure-based design. J Biomol Struct Dyn 2017; 35(2): 413-26.
[http://dx.doi.org/10.1080/07391102.2016.1145143] [PMID: 26813690]
[212]
Ugbaja SC, Lawal MM, Kumalo HM. An overview of β-amyloid cleaving enzyme 1 (BACE1) in alzheimer’s disease therapy elucidating its exosite-binding antibody and allosteric inhibitor. Curr Med Chem 2022; 29(1): 114-35.
[http://dx.doi.org/10.2174/0929867328666210608145357]

Rights & Permissions Print Cite
© 2024 Bentham Science Publishers | Privacy Policy