3UFL

Discovery of Pyrrolidine-based b-Secretase Inhibitors: Lead Advancement through Conformational Design for Maintenance of Ligand Binding Efficiency


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Discovery of pyrrolidine-based beta-secretase inhibitors: Lead advancement through conformational design for maintenance of ligand binding efficiency.

Stachel, S.J.Steele, T.G.Petrocchi, A.Haugabook, S.J.McGaughey, G.Katharine Holloway, M.Allison, T.Munshi, S.Zuck, P.Colussi, D.Tugasheva, K.Wolfe, A.Graham, S.L.Vacca, J.P.

(2012) Bioorg.Med.Chem.Lett. 22: 240-244

  • DOI: 10.1016/j.bmcl.2011.11.024

  • PubMed Abstract: 
  • We have developed a novel series of pyrrolidine derived BACE-1 inhibitors. The potency of the weak initial lead structure was enhanced using library-based SAR methods. The series was then further advanced by rational design while maintaining a minima ...

    We have developed a novel series of pyrrolidine derived BACE-1 inhibitors. The potency of the weak initial lead structure was enhanced using library-based SAR methods. The series was then further advanced by rational design while maintaining a minimal ligand binding efficiency threshold. Ultimately, the co-crystal structure was obtained revealing that these inhibitors interacted with the enzyme in a unique fashion. In all, the potency of the series was enhanced by 4 orders of magnitude from the HTS lead with concomitant increases in physical properties needed for series advancement. The progression of these developments in a systematic fashion is described.


    Organizational Affiliation

    Department of Medicinal Chemistry, Merck Research Laboratories, Merck & Co., PO Box 4, West Point, PA 19486, USA. shawn_stachel@merck.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-secretase 1
A
389Homo sapiensMutation(s): 0 
Gene Names: BACE1 (BACE, KIAA1149)
EC: 3.4.23.46
Find proteins for P56817 (Homo sapiens)
Go to Gene View: BACE1
Go to UniProtKB:  P56817
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
508
Query on 508

Download SDF File 
Download CCD File 
A
(1R,4'S)-3,4-dihydro-2H-spiro[naphthalene-1,3'-pyrrolidin]-4'-yl[(2S,4R)-2,4-diphenylpiperidin-1-yl]methanone
C31 H34 N2 O
MXPUWFOJTXJTTA-RNWXARPHSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
508IC50: 150 nM (100) BINDINGDB
508IC50: 150 nM BINDINGMOAD
508IC50: 150 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.212 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 103.668α = 90.00
b = 127.642β = 90.00
c = 76.846γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-01-18
    Type: Initial release