6ZOV

ENTEROPEPTIDASE IN COMPLEX WITH COMPOUND 6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Targeting Enteropeptidase with Reversible Covalent Inhibitors To Achieve Metabolic Benefits.

Sun, W.Zhang, X.Cummings, M.D.Albarazanji, K.Wu, J.Wang, M.Alexander, R.Zhu, B.Zhang, Y.Leonard, J.Lanter, J.Lenhard, J.

(2020) J Pharmacol Exp Ther 375: 510-521

  • DOI: https://doi.org/10.1124/jpet.120.000219
  • Primary Citation of Related Structures:  
    6ZOV

  • PubMed Abstract: 

    Inhibition of the serine protease enteropeptidase (EP) opens a new avenue to the discovery of chemotherapeutics for the treatment of metabolic diseases. Camostat has been used clinically for treating chronic pancreatitis in Japan; however, the mechanistic basis of the observed clinical efficacy has not been fully elucidated. We demonstrate that camostat is a potent reversible covalent inhibitor of EP, with an inhibition potency ( k inact /K I ) of 1.5 × 10 4 M -1 s -1 High-resolution liquid chromatography-mass spectrometry (LC-MS) showed addition of 161.6 Da to EP after the reaction with camostat, consistent with insertion of the carboxyphenylguanidine moiety of camostat. Covalent inhibition of EP by camostat is reversible, with an enzyme reactivation half-life of 14.3 hours. Formation of a covalent adduct was further supported by a crystal structure resolved to 2.19 Å, showing modification of the catalytic serine of EP by a close analog of camostat, leading to formation of the carboxyphenylguanidine acyl enzyme identical to that expected for the reaction with camostat. Of particular note, minor structural modifications of camostat led to changes in the mechanism of inhibition. We observed from other studies that sustained inhibition of EP is required to effect a reduction in cumulative food intake and body weight, with concomitant improved blood glucose levels in obese and diabetic leptin-deficient mice. Thus, the structure-activity relationship needs to be driven by not only the inhibition potency but also the mechanistic and kinetic characterization. Our findings support EP as a target for the treatment of metabolic diseases and demonstrate that reversible covalent EP inhibitors show clinically relevant efficacy. SIGNIFICANCE STATEMENT: Interest in targeted covalent drugs has expanded in recent years, particularly so for kinase targets, but also more broadly. This study demonstrates that reversible covalent inhibition of the serine protease enteropeptidase is a therapeutically viable approach to the treatment of metabolic diseases and that mechanistic details of inhibition are relevant to clinical efficacy. Our mechanistic and kinetic studies outline a framework for detailed inhibitor characterization that is proving essential in guiding discovery efforts in this area.


  • Organizational Affiliation

    DPDS Discovery Technology and Molecular Pharmacology, Spring House, Pennsylvania (W.S., M.W., R.A.); DPDS Analytical Sciences, La Jolla, California (J.W.); Discovery Chemistry, Spring House, Pennsylvania (X.Z., M.D.C., B.Z., Y.Z., J.La.); CVM Discovery, Spring House, Pennsylvania (K.A., J.Leo., J.Len.); and Janssen Research & Development, LLC, Spring House, Pennsylvania wsun5@its.jnj.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Enteropeptidase
A, B, C, D
235Homo sapiensMutation(s): 6 
Gene Names: TMPRSS15ENTKPRSS7
EC: 3.4.21.9
UniProt & NIH Common Fund Data Resources
Find proteins for P98073 (Homo sapiens)
Explore P98073 
Go to UniProtKB:  P98073
PHAROS:  P98073
GTEx:  ENSG00000154646 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP98073
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GBS (Subject of Investigation/LOI)
Query on GBS

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
L [auth C],
M [auth D]
4-carbamimidamidobenzoic acid
C8 H9 N3 O2
SXTSBZBQQRIYCU-UHFFFAOYSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
F [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
GOL
Query on GOL

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

Download Ideal Coordinates CCD File 
H [auth B]
I [auth B]
J [auth B]
K [auth B]
N [auth D]
H [auth B],
I [auth B],
J [auth B],
K [auth B],
N [auth D],
O [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.925α = 90
b = 147.517β = 90
c = 147.518γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-21
    Type: Initial release
  • Version 1.1: 2020-12-09
    Changes: Database references