8XAR

Structure-Based Design and Optimization of Methionine Adenosyltransferase 2A (MAT2A) Inhibitors with SAM and Compound 54


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.19 Å
  • R-Value Free: 0.130 
  • R-Value Work: 0.111 
  • R-Value Observed: 0.112 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Structure-Based Design and Optimization of Methionine Adenosyltransferase 2A (MAT2A) Inhibitors with High Selectivity, Brain Penetration, and In Vivo Efficacy.

Zheng, J.Zhang, T.Tong, S.Liu, T.Cui, J.Xu, H.Hu, D.Shen, Y.Yin, Y.Zhao, D.Tan, C.Dong, X.Chen, J.Ji, F.Tong, C.Li, J.J.Li, J.Zhang, G.

(2024) J Med Chem 67: 9431-9446

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c00552
  • Primary Citation of Related Structures:  
    8XAR, 8XB0

  • PubMed Abstract: 

    Synthetic lethality has recently emerged as a new approach for the treatment of mutated genes that were previously considered undruggable. Targeting methionine adenosyltransferase 2A (MAT2A) in cancers with deletion of the methylthioadenosine phosphorylase (MTAP) gene leads to synthetic lethality and thus has attracted significant interest in the field of precise anticancer drug development. Herein, we report the discovery of a series of novel MAT2A inhibitors featuring a pyrazolo[3,4- c ]quinolin-4-one skeleton based on structure-based drug design. Further optimization led to compound 39 , which has a high potency for inhibiting MAT2A and a remarkable selectivity for MTAP-deleted cancer cell lines. Compound 39 has a favorable pharmacokinetic profile with high plasma exposure and oral bioavailability, and it exhibits significant efficacy in xenograft MTAP-depleted models. Moreover, 39 demonstrates excellent brain exposure with a K puu of 0.64 in rats.


  • Organizational Affiliation

    Center for Drug Design and Development, Suzhou Genhouse Bio Co., Ltd., No. 1 Xinze Road, Suzhou Industrial Park, Suzhou, Jiangsu 215123, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
S-adenosylmethionine synthase isoform type-2409Homo sapiensMutation(s): 0 
Gene Names: MAT2A
EC: 2.5.1.6
UniProt & NIH Common Fund Data Resources
Find proteins for P31153 (Homo sapiens)
Explore P31153 
Go to UniProtKB:  P31153
PHAROS:  P31153
GTEx:  ENSG00000168906 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31153
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAM
Query on SAM

Download Ideal Coordinates CCD File 
D [auth A]S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
YMW (Subject of Investigation/LOI)
Query on YMW

Download Ideal Coordinates CCD File 
B [auth A]7-chloranyl-2-ethyl-5-pyridin-3-yl-pyrazolo[3,4-c]quinolin-4-one
C17 H13 Cl N4 O
HTOSXLRRHMIOAU-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.19 Å
  • R-Value Free: 0.130 
  • R-Value Work: 0.111 
  • R-Value Observed: 0.112 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.18α = 90
b = 94.16β = 90
c = 117.12γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateChina--

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-26
    Type: Initial release