8SIV

Structure of Compound 2 bound to the CHK1 10-point mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of MK-1468: A Potent, Kinome-Selective, Brain-Penetrant Amidoisoquinoline LRRK2 Inhibitor for the Potential Treatment of Parkinson's Disease.

Kattar, S.D.Gulati, A.Margrey, K.A.Keylor, M.H.Ardolino, M.Yan, X.Johnson, R.Palte, R.L.McMinn, S.E.Nogle, L.Su, J.Xiao, D.Piesvaux, J.Lee, S.Hegde, L.G.Woodhouse, J.D.Faltus, R.Moy, L.Y.Xiong, T.Ciaccio, P.J.Pearson, K.Patel, M.Otte, K.M.Leyns, C.E.G.Kennedy, M.E.Bennett, D.J.DiMauro, E.F.Fell, M.J.Fuller, P.H.

(2023) J Med Chem 66: 14912-14927

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c01486
  • Primary Citation of Related Structures:  
    8SIV, 8SIW, 8SIX

  • PubMed Abstract: 

    Genetic mutation of the leucine-rich repeat kinase 2 (LRRK2) protein has been associated with Parkinson's disease (PD), a disabling and progressive neurodegenerative disorder that is devoid of efficacious disease-modifying therapies. Herein, we describe the invention of an amidoisoquinoline (IQ)-derived LRRK2 inhibitor lead chemical series. Knowledge-, structure-, and property-based drug design in concert with rigorous application of in silico calculations and presynthesis predictions enabled the prioritization of molecules with favorable CNS "drug-like" physicochemical properties. This resulted in the discovery of compound 8 , which was profiled extensively before human ether-a-go-go (hERG) ion channel inhibition halted its progression. Strategic reduction of lipophilicity and basicity resulted in attenuation of hERG ion channel inhibition while maintaining a favorable CNS efflux transporter profile. Further structure- and property-based optimizations resulted in the discovery of preclinical candidate MK-1468 . This exquisitely selective LRRK2 inhibitor has a projected human dose of 48 mg BID and a preclinical safety profile that supported advancement toward GLP toxicology studies.


  • Organizational Affiliation

    Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase Chk1297Homo sapiensMutation(s): 10 
Gene Names: CHEK1CHK1
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O14757 (Homo sapiens)
Explore O14757 
Go to UniProtKB:  O14757
PHAROS:  O14757
GTEx:  ENSG00000149554 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14757
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZXH (Subject of Investigation/LOI)
Query on ZXH

Download Ideal Coordinates CCD File 
B [auth A]N-(7-chloro-6-{1-[(3R,4R)-4-hydroxy-3-methyloxolan-3-yl]piperidin-4-yl}isoquinolin-3-yl)cyclopropanecarboxamide
C23 H28 Cl N3 O3
AUWBKRNKWPJDOB-NZQKXSOJSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.827α = 90
b = 65.33β = 101.86
c = 54.139γ = 90
Software Package:
Software NamePurpose
autoBUSTERrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
BUSTERphasing
autoPROCdata processing
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2023-11-01 
  • Deposition Author(s): Palte, R.L.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-01
    Type: Initial release
  • Version 1.1: 2023-11-15
    Changes: Database references