title: Type II kinase inhibitors show an unexpected inhibition mode against Parkinson's disease-linked LRRK2 mutant G2019S.
abstract: A number of well-known type II inhibitors (ATP-noncompetitive) that bind kinases in their DFG-out conformation were tested against wild-type LRRK2 and the most common Parkinson's disease-linked mutation, G2019S. We found that traditional type II inhibitors exhibit surprising variability in their inhibition mechanism between the wild type (WT) and the G2019S mutant of LRRK2. The type II kinase inhibitors were found to work in an ATP-competitive fashion against the G2019S mutant, whereas they appear to follow the expected noncompetitive mechanism against WT. Because the G2019S mutation lies in the DXG motif (DYG in LRRK2 but DFG in most other kinases) of the activation loop, we explored the structural consequence of the mutation on loop dynamics using an enhanced sampling method called metadynamics. The simulations suggest that the G2019S mutation stabilizes the DYG-in state of LRRK2 through a series of hydrogen bonds, leading to an increase in the conformational barrier between the active and inactive forms of the enzyme and a relative stabilization of the active form. The conformational bias toward the active form of LRRK2 mutants has two primary consequences. (1) The mutant enzyme becomes hyperactive, a known contributor to the Parkinsonian phenotype, as a consequence of being "locked" into the activated state, and (2) the mutation creates an unusual allosteric pocket that can bind type II inhibitors but in an ATP-competitive fashion. Our results suggest that developing type II inhibitors, which are generally considered superior to type I inhibitors because of desirable selectivity profiles, might be especially challenging for the G2019S LRRK2 mutant.
authors: Harvard NeuroDiscovery Center, Harvard University , 65 Landsdowne Street, #452, Cambridge, Massachusetts 02139, United States.
authors: Min
authors: M
authors: Liu
authors: Samantha A
authors: SA
authors: Bender
authors: Gregory D
authors: GD
authors: Cuny
authors: Woody
authors: W
authors: Sherman
authors: Marcie
authors: M
authors: Glicksman
authors: Soumya S
authors: SS
authors: Ray
mesh_terms: D000495:Allosteric Site / Q000235:genetics; D020816:Amino Acid Motifs; D019943:Amino Acid Substitution; D001665:Binding Sites; D004795:Enzyme Stability; D006801:Humans; D006860:Hydrogen Bonding; D007700:Kinetics; D000071158:Leucine-Rich Repeat Serine-Threonine Protein Kinase-2; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D050505:Mutant Proteins / Q000037:antagonists & inhibitors* / Q000737:chemistry / Q000235:genetics*; D010300:Parkinson Disease / Q000188:drug therapy / Q000201:enzymology* / Q000235:genetics*; D011487:Protein Conformation; D047428:Protein Kinase Inhibitors / Q000145:classification / Q000494:pharmacology; D017346:Protein Serine-Threonine Kinases / Q000037:antagonists & inhibitors* / Q000737:chemistry / Q000235:genetics*
chemical_list: D050505:Mutant Proteins; D047428:Protein Kinase Inhibitors; C495280:LRRK2 protein, human; D000071158:Leucine-Rich Repeat Serine-Threonine Protein Kinase-2; D017346:Protein Serine-Threonine Kinases
references: J Med Chem. 2012 Jun 14;55(11):5536-45
references: 22591441
references: J Neural Transm (Vienna). 2010 Jul;117(7):847-53
references: 20544233
references: J Neurosci. 2007 Oct 31;27(44):11865-8
references: 17978026
references: Pharmacol Ther. 1999 May-Jun;82(2-3):133-41
references: 10454192
references: Trends Neurosci. 2006 May;29(5):286-93
references: 16616379
references: Curr Opin Neurol. 2005 Dec;18(6):706-11
references: 16280683
references: Biochim Biophys Acta. 2005 Dec 30;1754(1-2):25-37
references: 16214430
references: Mov Disord. 2006 Oct;21(10):1731-4
references: 16817197
references: J Med Genet. 2005 Nov;42(11):e65
references: 16272257
references: Proc Natl Acad Sci U S A. 2012 Jan 31;109(5):1467-72
references: 22238423
references: Lancet Neurol. 2008 Sep;7(9):769-70; author reply 770-1
references: 18702998
references: BMC Neurol. 2008 Jan 22;8:1
references: 18211709
references: Phys Rev Lett. 2010 May 14;104(19):190601
references: 20866953
references: Genet Test. 2008 Sep;12(3):333-9
references: 18666856
references: Chem Rev. 2001 Aug;101(8):2243-70
references: 11749372
references: Hum Mol Genet. 2010 Apr 15;19(R1):R21-7
references: 20421364
references: J Chem Phys. 2007 Feb 7;126(5):054103
references: 17302470
references: J Am Chem Soc. 2006 Mar 1;128(8):2705-10
references: 16492057
references: Eur J Hum Genet. 2006 Mar;14(3):322-31
references: 16333314
references: Biophys J. 2010 May 19;98(9):L44-6
references: 20441734
references: PLoS One. 2012;7(4):e29828
references: 22493660
references: Nucleic Acids Res. 2003 Jul 15;31(14):3982-92
references: 12853614
references: Methods Enzymol. 2011;487:545-74
references: 21187238
references: Lancet Neurol. 2003 Apr;2(4):221-8
references: 12849210
references: Bioinformatics. 2003 Dec 12;19(18):2500-1
references: 14668246
references: Hum Mol Genet. 2007 Sep 1;16(17):2031-9
references: 17584768
references: Eur J Hum Genet. 2006 Oct;14(10):1061-2
references: 16835587
references: Methods Mol Biol. 2012;819:501-13
references: 22183554
references: J Neurochem. 2011 Jan;116(2):304-15
references: 21073465
references: Parkinsonism Relat Disord. 2012 Aug;18(7):819-23
references: 22525366
references: Nat Neurosci. 2006 Oct;9(10):1231-3
references: 16980962
references: J Med Chem. 2006 Jan 26;49(2):534-53
references: 16420040
references: Phys Rev Lett. 2006 Mar 10;96(9):090601
references: 16606249
references: J Phys Chem B. 2009 Apr 9;113(14):4807-16
references: 19298042
references: Cold Spring Harb Perspect Biol. 2011 Oct 01;3(10):a007500
references: 21844169
references: Parkinsonism Relat Disord. 2010 May;16(4):237-42
references: 19945904
references: J Med Chem. 2004 Mar 25;47(7):1739-49
references: 15027865
references: J Neurosci Res. 2009 May 1;87(6):1283-95
references: 19025767
references: Neuron. 2003 Jan 9;37(1):7-10
references: 12526767
references: Eur Neurol. 2010;63(6):321-5
references: 20413974
references: Nat Chem Biol. 2011 Apr;7(4):203-5
references: 21378983
references: Proc Natl Acad Sci U S A. 2010 Mar 23;107(12):5411-6
references: 20215464
references: Biochemistry. 2008 Aug 12;47(32):8367-77
references: 18636751
references: Proteins. 1997;Suppl 1:50-8
references: 9485495
references: Curr Opin Struct Biol. 1994 Dec;4(6):893-901
references: 7712293
references: Annu Rev Genomics Hum Genet. 2011;12:301-25
references: 21639795
references: Parkinsonism Relat Disord. 2005 Dec;11(8):521-2
references: 16256409
references: Methods Mol Biol. 2008;426:145-59
references: 18542861
references: Nucleic Acids Res. 2009 Jan;37(Database issue):D387-92
references: 18931379
references: Science. 2010 Oct 15;330(6002):341-6
references: 20947758
references: Nucleic Acids Res. 2003 Jul 1;31(13):3375-80
references: 12824331
references: Genet Test. 2006 Winter;10(4):290-3
references: 17253937
references: Arch Neurol. 2009 Dec;66(12):1517-22
references: 20008657
references: Proteins. 2006 Nov 1;65(2):438-52
references: 16927380
references: Curr Opin Chem Biol. 1997 Aug;1(2):219-26
references: 9667861
references: Mol Neurodegener. 2012 Apr 25;7:15
references: 22534020
references: Proc Natl Acad Sci U S A. 2012 Jun 26;109(26):10322-7
references: 22689969
references: Neurogenetics. 2009 Oct;10(4):355-8
references: 19283415
references: Nat Rev Neurosci. 2010 Dec;11(12):791-7
references: 21088684
references: Biochem Biophys Res Commun. 2009 Nov 20;389(3):449-54
references: 19733152
references: J Am Chem Soc. 2011 Nov 2;133(43):17200-6
references: 21854002
references: PLoS One. 2010 Oct 13;5(10):e13208
references: 20967249
references: Biophys J. 2006 Oct 15;91(8):2768-77
references: 16877506
references: Arch Neurol. 2010 May;67(5):542-7
references: 20457952
references: Mov Disord. 2007 Jan;22(1):55-61
references: 17115391
references: Ann Neurol. 2005 Jun;57(6):933-4
references: 15929036
references: ACS Chem Neurosci. 2012 Mar 21;3(3):151-60
references: 22860184
references: Proc Natl Acad Sci U S A. 2005 Nov 15;102(46):16842-7
references: 16269541
references: Eur J Neurol. 2010 Dec;17(12):1479-81
references: 20443975
references: ACS Chem Biol. 2011 Oct 21;6(10):1021-8
references: 21812418
references: Phys Rev Lett. 2008 Jan 18;100(2):020603
references: 18232845
references: Trends Biochem Sci. 2011 Feb;36(2):65-77
references: 20971646
references: Eur J Neurol. 2009 Aug;16(8):957-60
references: 19473361
references: Mov Disord. 2011 Sep;26(11):2144-5
references: 21714003
references: Proteins. 2008 Mar;70(4):1219-27
references: 17847101
references: Parkinsonism Relat Disord. 2010 Dec;16(10):676-9
references: 20933457
references: Neurobiol Dis. 2006 Aug;23(2):329-41
references: 16750377
references: J Comput Aided Mol Des. 2011 Jan;25(1):13-9
references: 21053052
references: J Clin Neurol. 2009 Mar;5(1):29-32
references: 19513331
references: Curr Opin Struct Biol. 2010 Apr;20(2):148-54
references: 20171876
references: Biochem Biophys Res Commun. 2007 Jun 8;357(3):668-71
references: 17442267
references: Neurology. 2006 Nov 28;67(10):1786-91
references: 17050822
references: Neurosci Lett. 2006 Oct 23;407(2):97-100
references: 16939701
references: Biochemistry. 2011 Nov 1;50(43):9399-408
references: 21961647
references: Methods Mol Biol. 2008;443:63-88
references: 18446282
references: Ann Neurol. 2005 May;57(5):762-5
references: 15852371
references: Mov Disord. 2011 Aug 1;26(9):1733-6
references: 21538529
references: Proteins. 2004 May 1;55(2):351-67
references: 15048827