5A0C

Crystal Structure of human neutrophil elastase in complex with a dihydropyrimidone inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Freezing the Bioactive Conformation to Boost Potency: The Identification of BAY 85-8501, a Selective and Potent Inhibitor of Human Neutrophil Elastase for Pulmonary Diseases.

von Nussbaum, F.Li, V.M.Allerheiligen, S.Anlauf, S.Barfacker, L.Bechem, M.Delbeck, M.Fitzgerald, M.F.Gerisch, M.Gielen-Haertwig, H.Haning, H.Karthaus, D.Lang, D.Lustig, K.Meibom, D.Mittendorf, J.Rosentreter, U.Schafer, M.Schafer, S.Schamberger, J.Telan, L.A.Tersteegen, A.

(2015) ChemMedChem 10: 1163-1173

  • DOI: 10.1002/cmdc.201500131
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human neutrophil elastase (HNE) is a key protease for matrix degradation. High HNE activity is observed in inflammatory diseases. Accordingly, HNE is a potential target for the treatment of pulmonary diseases such as chronic obstructive pulmonary dis ...

    Human neutrophil elastase (HNE) is a key protease for matrix degradation. High HNE activity is observed in inflammatory diseases. Accordingly, HNE is a potential target for the treatment of pulmonary diseases such as chronic obstructive pulmonary disease (COPD), acute lung injury (ALI), acute respiratory distress syndrome (ARDS), bronchiectasis (BE), and pulmonary hypertension (PH). HNE inhibitors should reestablish the protease-anti-protease balance. By means of medicinal chemistry a novel dihydropyrimidinone lead-structure class was identified. Further chemical optimization yielded orally active compounds with favorable pharmacokinetics such as the chemical probe BAY-678. While maintaining outstanding target selectivity, picomolar potency was achieved by locking the bioactive conformation of these inhibitors with a strategically positioned methyl sulfone substituent. An induced-fit binding mode allowed tight interactions with the S2 and S1 pockets of HNE. BAY 85-8501 ((4S)-4-[4-cyano-2-(methylsulfonyl)phenyl]-3,6-dimethyl-2-oxo-1-[3-(trifluoromethyl)phenyl]-1,2,3,4-tetrahydropyrimidine-5-carbonitrile) was shown to be efficacious in a rodent animal model related to ALI. BAY 85-8501 is currently being tested in clinical studies for the treatment of pulmonary diseases.


    Organizational Affiliation

    Medicinal Chemistry Wuppertal, Bayer HealthCare AG, 42096 Wuppertal (Germany).,Department of Cardiology Research Wuppertal, Bayer HealthCare AG, 42096 Wuppertal (Germany).,COPD Research, Bayer Healthcare AG, Slough SL2 4LY, Berkshire (UK).,Lead Discovery, Structural Biology Berlin, Bayer HealthCare AG, 13353 Berlin (Germany).,Lead Discovery Wuppertal, Bayer HealthCare AG, 42096 Wuppertal (Germany). volkhart.li@bayer.com.,DMPK Wuppertal, Bayer HealthCare AG, 42096 Wuppertal (Germany).,Lead Discovery Wuppertal, Bayer HealthCare AG, 42096 Wuppertal (Germany).,Medicinal Chemistry Berlin, Bayer HealthCare AG, 13353 Berlin (Germany). franz.nussbaum@bayer.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NEUTROPHIL ELASTASE
A, B
218Homo sapiensMutation(s): 0 
Gene Names: ELANE (ELA2)
EC: 3.4.21.37
Find proteins for P08246 (Homo sapiens)
Go to Gene View: ELANE
Go to UniProtKB:  P08246
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FUC
Query on FUC

Download SDF File 
Download CCD File 
A, B
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
XPE
Query on XPE

Download SDF File 
Download CCD File 
A
3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL
DECAETHYLENE GLYCOL
C20 H42 O11
DTPCFIHYWYONMD-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
JJV
Query on JJV

Download SDF File 
Download CCD File 
A, B
(6S)-6-(4-cyano-2-methylsulfonyl-phenyl)-4-methyl-2-oxidanylidene-3-[3-(trifluoromethyl)phenyl]-1,6-dihydropyrimidine-5-carbonitrile
C21 H15 F3 N4 O3 S
WQASVWJQEKONLG-LJQANCHMSA-N
 Ligand Interaction
MES
Query on MES

Download SDF File 
Download CCD File 
A, B
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
JJVIC50: <0.3 nM (100) BINDINGDB
JJVIC50: 0.54 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.163 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 71.517α = 90.00
b = 71.517β = 90.00
c = 97.400γ = 120.00
Software Package:
Software NamePurpose
SADABSdata scaling
SAINTdata reduction
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2015-08-19
    Type: Initial release
  • Version 1.1: 2017-03-22
    Type: Database references
  • Version 1.2: 2017-07-05
    Type: Data collection
  • Version 2.0: 2019-01-23
    Type: Advisory, Atomic model, Data collection