دورية أكاديمية
أعرض في EDS

Revisiting the Proposition of Binding Pockets and Bioactive Poses for GSK-3β Allosteric Modulators Addressed to Neurodegenerative Diseases.

التفاصيل البيبلوغرافية
العنوان: Revisiting the Proposition of Binding Pockets and Bioactive Poses for GSK-3β Allosteric Modulators Addressed to Neurodegenerative Diseases.
المؤلفون: Silva GM; Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-901, SP, Brazil., Borges RS; Programa de Pós-Graduação em Química Medicinal e Modelagem Molecular, Instituto de Ciências da Saúde, Universidade Federal do Pará, Belém 66075-110, PA, Brazil.; Laboratório de Modelagem em Química Computacional, Departamento de Ciências Biológicas e da Saúde, Universidade Federal do Amapá, Macapá 68902-280, AP, Brazil., Santos KLB; Programa de Pós-Graduação em Química Medicinal e Modelagem Molecular, Instituto de Ciências da Saúde, Universidade Federal do Pará, Belém 66075-110, PA, Brazil.; Laboratório de Modelagem em Química Computacional, Departamento de Ciências Biológicas e da Saúde, Universidade Federal do Amapá, Macapá 68902-280, AP, Brazil., Federico LB; Laboratório Computacional de Química Farmacêutica, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café, s/n, Ribeirão Preto 14040-903, SP, Brazil., Francischini IAG; Laboratório Computacional de Química Farmacêutica, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café, s/n, Ribeirão Preto 14040-903, SP, Brazil., Gomes SQ; Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-901, SP, Brazil., Barcelos MP; Laboratório Computacional de Química Farmacêutica, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café, s/n, Ribeirão Preto 14040-903, SP, Brazil., Silva RC; Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-901, SP, Brazil., Santos CBR; Programa de Pós-Graduação em Química Medicinal e Modelagem Molecular, Instituto de Ciências da Saúde, Universidade Federal do Pará, Belém 66075-110, PA, Brazil.; Laboratório de Modelagem em Química Computacional, Departamento de Ciências Biológicas e da Saúde, Universidade Federal do Amapá, Macapá 68902-280, AP, Brazil.; Laboratório Computacional de Química Farmacêutica, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café, s/n, Ribeirão Preto 14040-903, SP, Brazil., Silva CHTP; Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-901, SP, Brazil.; Programa de Pós-Graduação em Química Medicinal e Modelagem Molecular, Instituto de Ciências da Saúde, Universidade Federal do Pará, Belém 66075-110, PA, Brazil.; Laboratório Computacional de Química Farmacêutica, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café, s/n, Ribeirão Preto 14040-903, SP, Brazil.
المصدر: International journal of molecular sciences [Int J Mol Sci] 2021 Jul 31; Vol. 22 (15). Date of Electronic Publication: 2021 Jul 31.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: MDPI Country of Publication: Switzerland NLM ID: 101092791 Publication Model: Electronic Cited Medium: Internet ISSN: 1422-0067 (Electronic) Linking ISSN: 14220067 NLM ISO Abbreviation: Int J Mol Sci Subsets: MEDLINE
أسماء مطبوعة: Original Publication: Basel, Switzerland : MDPI, [2000-
مواضيع طبية MeSH: Allosteric Site* , Molecular Docking Simulation*, Glycogen Synthase Kinase 3 beta/*chemistry , Neuroprotective Agents/*pharmacology, Allosteric Regulation ; Enzyme Inhibitors/chemistry ; Enzyme Inhibitors/pharmacology ; Glycogen Synthase Kinase 3 beta/antagonists & inhibitors ; Glycogen Synthase Kinase 3 beta/metabolism ; Humans ; Neuroprotective Agents/chemistry ; Protein Binding
مستخلص: Glycogen synthase kinase-3 beta (GSK-3β) is an enzyme pertinently linked to neurodegenerative diseases since it is associated with the regulation of key neuropathological features in the central nervous system. Among the different kinds of inhibitors of this kinase, the allosteric ones stand out due to their selective and subtle modulation, lowering the chance of producing side effects. The mechanism of GSK-3β allosteric modulators may be considered still vague in terms of elucidating a well-defined binding pocket and a bioactive pose for them. In this context, we propose to reinvestigate and reinforce such knowledge by the application of an extensive set of in silico methodologies, such as cavity detection, ligand 3D shape analysis and docking (with robust validation of corresponding protocols), and molecular dynamics. The results here obtained were consensually consistent in furnishing new structural data, in particular by providing a solid bioactive pose of one of the most representative GSK-3β allosteric modulators. We further applied this to the prospect for new compounds by ligand-based virtual screening and analyzed the potential of the two obtained virtual hits by quantum chemical calculations. All potential hits achieved will be subsequently tested by in vitro assays in order to validate our approaches as well as to unveil novel chemical entities as GSK-3β allosteric modulators.
References: Rev Neurosci. 2011 Dec 21;23(1):1-11. (PMID: 22718609)
Bioinformatics. 2011 Aug 1;27(15):2083-8. (PMID: 21636590)
Eur J Med Chem. 2013 Mar;61:95-103. (PMID: 23047001)
Bioorg Med Chem. 2018 Nov 1;26(20):5479-5493. (PMID: 30293796)
J Mol Model. 2021 Jan 7;27(2):26. (PMID: 33410998)
J Med Chem. 2011 Dec 22;54(24):8461-70. (PMID: 22050263)
Spectrochim Acta A Mol Biomol Spectrosc. 2011 Sep;79(5):1162-70. (PMID: 21571581)
J Chem Inf Model. 2010 Apr 26;50(4):572-84. (PMID: 20235588)
J Med Chem. 2017 Jul 27;60(14):5943-5954. (PMID: 28388050)
J Biomol Struct Dyn. 2017 Oct;35(13):2966-2974. (PMID: 27739336)
J Alzheimers Dis. 2015;45(1):75-88. (PMID: 25537011)
Biochem Biophys Res Commun. 2002 Jul 5;295(1):102-6. (PMID: 12083774)
Nat Commun. 2018 Jan 18;9(1):283. (PMID: 29348454)
Molecules. 2015 Jul 22;20(7):13384-421. (PMID: 26205061)
J Chem Inf Model. 2012 Nov 26;52(11):2919-36. (PMID: 23082786)
J Mol Graph Model. 2019 Sep;91:91-104. (PMID: 31202091)
J Med Chem. 2005 Apr 7;48(7):2534-47. (PMID: 15801843)
J Chem Inf Model. 2009 Feb;49(2):377-89. (PMID: 19434839)
Bioorg Med Chem Lett. 2014 Dec 15;24(24):5639-5643. (PMID: 25467150)
J Med Chem. 2017 Jun 22;60(12):4983-5001. (PMID: 28548834)
J Mol Model. 2012 Sep;18(9):4073-80. (PMID: 22527272)
J Comput Aided Mol Des. 2008 Mar-Apr;22(3-4):239-55. (PMID: 18253702)
J Chem Inf Model. 2016 Dec 27;56(12):2281-2286. (PMID: 27808512)
J Med Chem. 2007 Jan 11;50(1):74-82. (PMID: 17201411)
J Comput Aided Mol Des. 2013 Mar;27(3):221-34. (PMID: 23579614)
Pharmacol Ther. 2015 Apr;148:114-31. (PMID: 25435019)
F1000Res. 2017 Feb 20;6:. (PMID: 28299185)
Cold Spring Harb Perspect Biol. 2018 Apr 2;10(4):. (PMID: 28716886)
J Biol Chem. 2001 Jan 5;276(1):251-60. (PMID: 11013232)
Phys Rev B Condens Matter. 1988 Jan 15;37(2):785-789. (PMID: 9944570)
J Comput Chem. 2009 Dec;30(16):2785-91. (PMID: 19399780)
BMC Bioinformatics. 2009 Jun 02;10:168. (PMID: 19486540)
J Med Chem. 2012 Jul 26;55(14):6582-94. (PMID: 22716043)
Rev Neurol (Paris). 2020 Nov;176(9):642-648. (PMID: 32145981)
Eur J Med Chem. 2017 Sep 29;138:438-457. (PMID: 28689095)
J Chem Inf Model. 2011 Mar 28;51(3):578-96. (PMID: 21323318)
Oncotarget. 2017 Feb 21;8(8):14221-14250. (PMID: 27999207)
Chem Biol. 2000 Jan;7(1):51-63. (PMID: 10662688)
J Biomol Struct Dyn. 2021 Jul;39(11):3924-3933. (PMID: 32448085)
Biochim Biophys Acta Mol Cell Res. 2020 May;1867(5):118664. (PMID: 32006534)
Proteins. 2003 Sep 1;52(4):609-23. (PMID: 12910460)
J Mol Model. 2015 Jul;21(7):166. (PMID: 26044360)
Bioinformatics. 2014 May 1;30(9):1314-5. (PMID: 24413526)
J Alzheimers Dis. 2019;69(4):1031-1039. (PMID: 31156177)
Expert Rev Neurother. 2007 Nov;7(11):1527-33. (PMID: 17997701)
J Chem Inf Model. 2012 Dec 21;52(12):3144-54. (PMID: 23146088)
Eur J Med Chem. 2013 Feb;60:479-89. (PMID: 23354070)
Int J Biol Macromol. 2020 Dec 15;165(Pt B):3040-3050. (PMID: 33736292)
Int J Alzheimers Dis. 2011;2011:505607. (PMID: 21629754)
J Mol Model. 2019 May 7;25(6):147. (PMID: 31065808)
Brain Res. 2007 Jan 19;1129(1):89-99. (PMID: 17157278)
ChemMedChem. 2019 Aug 20;14(16):1467-1483. (PMID: 31310701)
J Med Chem. 1985 Jul;28(7):849-57. (PMID: 3892003)
Phys Rev A Gen Phys. 1988 Sep 15;38(6):3098-3100. (PMID: 9900728)
Immunology. 2018 Jun;154(2):204-219. (PMID: 29513402)
ACS Chem Neurosci. 2010 Jun 16;1(6):435-49. (PMID: 22778837)
ACS Chem Neurosci. 2012 Jan 18;3(1):50-68. (PMID: 22267984)
Nat Methods. 2017 Jan;14(1):71-73. (PMID: 27819658)
Cells. 2021 Jan 28;10(2):. (PMID: 33525562)
Oncol Rep. 2019 Sep;42(3):911-922. (PMID: 31322245)
J Med Chem. 2004 Mar 25;47(7):1750-9. (PMID: 15027866)
Bioinformatics. 2015 Apr 15;31(8):1274-8. (PMID: 25540181)
فهرسة مساهمة: Keywords: GSK-3β; allosteric modulators; binding pose; cavity detection; computer-aided drug design; docking; neurodegenerative diseases; shape similarity
المشرفين على المادة: 0 (Enzyme Inhibitors)
0 (Neuroprotective Agents)
EC 2.7.11.1 (Glycogen Synthase Kinase 3 beta)
تواريخ الأحداث: Date Created: 20210807 Date Completed: 20210906 Latest Revision: 20210906
رمز التحديث: 20231215
مُعرف محوري في PubMed: PMC8348340
DOI: 10.3390/ijms22158252
PMID: 34361017
قاعدة البيانات: MEDLINE
الوصف
تدمد:1422-0067
DOI:10.3390/ijms22158252