Druggability assessment of mammalian Per–Arnt–Sim [PAS] domains using computational approaches

Royal Society of Chemistry (RSC) - Tập 10 Số 7 - Trang 1126-1137
João Vicente Braga de Souza1,2,3, Sylvia Reznikov1,2,3, Ruidi Zhu1,2,3, Agnieszka K. Bronowska1,2,3
1NE1 7RU Newcastle
2Newcastle University
3School of Natural and Environmental Sciences, Newcastle University, NE1 7RU, Newcastle, UK

Tóm tắt

Protein dynamics finely tune the “druggability” of mammalian PAS-B domains, as assessed by atomistic molecular dynamics simulations and hotspot mapping.

Từ khóa


Tài liệu tham khảo

Feng, 2018, Proc. Natl. Acad. Sci. U. S. A., 115, 13240, 10.1073/pnas.1810897115

Depping, 2017, FEBS J., 284, 3801, 10.1111/febs.14306

Rojas-Pirela, 2018, Mol. Biochem. Parasitol., 219, 52, 10.1016/j.molbiopara.2017.11.002

Zhang, 2017, Proc. Natl. Acad. Sci. U. S. A., 114, E7516, 10.1073/pnas.1702014114

Culig, 2018, Methods Mol. Biol., 1786, 259, 10.1007/978-1-4939-7845-8_15

Hartzell, 2018, eLife, 7, pii: e35927, 10.7554/eLife.35927

Sun, 2016, Trends Neurosci., 39, 264, 10.1016/j.tins.2016.02.003

Harmon, 2018, PLoS One, 13, e0205412, 10.1371/journal.pone.0205412

Tang, 2016, Acta Crystallogr., Sect. F: Struct. Biol. Commun., 72, 578, 10.1107/S2053230X16009419

Che, 2019, Curr. Drug Targets, 20, 625, 10.2174/1389450120666181109092225

Shinde, 2018, Trends Immunol., 39, 1005, 10.1016/j.it.2018.10.010

Weng, 2018, Neuron, 97, 1137, 10.1016/j.neuron.2018.01.026

Adesso, 2018, J. Clin. Med., 7, pii.E365, 10.3390/jcm7100365

Adesso, 2017, Front. Pharmacol., 8, 370, 10.3389/fphar.2017.00370

Soshilov, 2014, Mol. Cell. Biol., 34, 1707, 10.1128/MCB.01183-13

Guo, 2015, J. Biol. Chem., 290, 7707, 10.1074/jbc.M114.632786

Guo, 2013, ACS Chem. Biol., 8, 626, 10.1021/cb300604u

Wu, 2016, eLife, 5, pii: e18790, 10.7554/eLife.18790

Uchida, 2012, J. Inorg. Biochem., 108, 188, 10.1016/j.jinorgbio.2011.12.005

Partch, 2011, Proc. Natl. Acad. Sci. U. S. A., 108, 7739, 10.1073/pnas.1101357108

Wu, 2015, Nature, 524, 303, 10.1038/nature14883

Park, 2006, Cell Cycle, 5, 1847, 10.4161/cc.5.16.3019

Kelley, 2015, Nat. Protoc., 10, 845, 10.1038/nprot.2015.053

Webb, 2017, Methods Mol. Biol., 1654, 39, 10.1007/978-1-4939-7231-9_4

Yang, 2015, Nat. Methods, 12, 7, 10.1038/nmeth.3213

Waterhouse, 2018, Nucleic Acids Res., 46, W296, 10.1093/nar/gky427

van der Spoel, 2005, J. Comput. Chem., 26, 1701, 10.1002/jcc.20291

Lindorff-Larsen, 2010, Proteins, 78, 1950, 10.1002/prot.22711

Darden, 1993, J. Chem. Phys., 98, 10089, 10.1063/1.464397

Hess, 1997, J. Comput. Chem., 18, 1463, 10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H

Parrinello, 1981, J. Appl. Phys., 52, 7182, 10.1063/1.328693

Sousa da Silva, 2012, BMC Res. Notes, 5, 367, 10.1186/1756-0500-5-367

Jakalian, 2002, J. Comput. Chem., 23, 1623, 10.1002/jcc.10128

Huang, 2014, Nucleic Acids Res., 42, W478, 10.1093/nar/gku377

Chan, 2019, Trends Biochem. Sci., 44, 312, 10.1016/j.tibs.2018.11.011

Cimermancic, 2016, J. Mol. Biol., 428, 709, 10.1016/j.jmb.2016.01.029

Kozakov, 2015, Nat. Protoc., 10, 733, 10.1038/nprot.2015.043

Kozakov, 2017, Nat. Protoc., 12, 255, 10.1038/nprot.2016.169

Allen, 2015, J. Comput. Chem., 36, 1132, 10.1002/jcc.23905

Schneider, 2013, J. Comput.-Aided Mol. Des., 27, 15, 10.1007/s10822-012-9626-2

Kumari, 2014, J. Chem. Inf. Model., 54, 1951, 10.1021/ci500020m

Best, 2012, Biophys. J., 102, 1462, 10.1016/j.bpj.2012.02.024

Abascal, 2005, J. Chem. Phys., 123, 234505, 10.1063/1.2121687

Powis, 2011, Biochem. Biophys. Res. Commun., 410, 859, 10.1016/j.bbrc.2011.06.079

Szöllősi, 2016, PLoS One, 11, e0146066, 10.1371/journal.pone.0146066

Kühnert, 2017, Environ. Pollut., 230, 1, 10.1016/j.envpol.2017.04.083

Labadie, 2019, Clin. Cancer Res., 25, 1462, 10.1158/1078-0432.CCR-18-2882

Koper, 2018, Mol. Nutr. Food Res., e1800722

O'Donnell, 2014, Cell Death Dis., 5, e1038, 10.1038/cddis.2013.549

Ge, 2018, Molecules, 23, pii: E2600, 10.3390/molecules23102600