5V8Q

Synthesis and biological evaluation of novel selective androgen receptor modulators (SARMs): Part III


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Synthesis and biological evaluation of novel selective androgen receptor modulators (SARMs) Part III: Discovery of 4-(5-oxopyrrolidine-1-yl)benzonitrile derivative 2f as a clinical candidate.

Aikawa, K.Asano, M.Ono, K.Habuka, N.Yano, J.Wilson, K.Fujita, H.Kandori, H.Hara, T.Morimoto, M.Santou, T.Yamaoka, M.Nakayama, M.Hasuoka, A.

(2017) Bioorg. Med. Chem. 25: 3330-3349

  • DOI: 10.1016/j.bmc.2017.04.018

  • PubMed Abstract: 
  • We previously reported that 4-(pyrrolidin-1-yl)benzonitrile derivative 1b was a selective androgen receptor modulator (SARM) that exhibited anabolic effects on organs such as muscles and the central nervous system (CNS), but neutral effects on the pr ...

    We previously reported that 4-(pyrrolidin-1-yl)benzonitrile derivative 1b was a selective androgen receptor modulator (SARM) that exhibited anabolic effects on organs such as muscles and the central nervous system (CNS), but neutral effects on the prostate. From further modification, we identified that 4-(5-oxopyrrolidine-1-yl)benzonitrile derivative 2a showed strong AR binding affinity with improved metabolic stabilities. Based on these results, we tried to enhance the AR agonistic activities by modifying the substituents of the 5-oxopyrrolidine ring. As a consequence, we found that 4-[(2S,3S)-2-ethyl-3-hydroxy-5-oxopyrrolidin-1-yl]-2-(trifluoromethyl)benzonitrile (2f) had ideal SARM profiles in Hershberger assay and sexual behavior induction assay. Furthermore, 2f showed good pharmacokinetic profiles in rats, dogs, monkeys, excellent nuclear selectivity and acceptable toxicological profiles. We also determined its binding mode by obtaining the co-crystal structures with AR.


    Organizational Affiliation

    Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd., 26-1 Muraoka-higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan. Electronic address: atsushi.hasuoka@takeda.com.,Beryllium Discovery, 3 Preston Ct, Bedford, MA 01730, United States.,Structural Biology, Takeda San Diego, Inc., 10410 Science Center Drive, San Diego, CA, 92121, United States.,Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd., 26-1 Muraoka-higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan.,Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd., 26-1 Muraoka-higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan. Electronic address: katsuji.aikawa@takeda.com.,Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd., 26-1 Muraoka-higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan. Electronic address: takahito.hara@takeda.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Androgen receptor
A
249Homo sapiensMutation(s): 0 
Gene Names: AR (DHTR, NR3C4)
Find proteins for P10275 (Homo sapiens)
Go to Gene View: AR
Go to UniProtKB:  P10275
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
97A
Query on 97A

Download SDF File 
Download CCD File 
A
4-[(2S,3S)-2-ethyl-3-hydroxy-5-oxopyrrolidin-1-yl]-2-(trifluoromethyl)benzonitrile
C14 H13 F3 N2 O2
LJQBTMVNFWIQQC-RYUDHWBXSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
97AIC50: 3.6 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 54.747α = 90.00
b = 65.557β = 90.00
c = 70.941γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
HKL-2000data scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-03-22 
  • Released Date: 2017-05-24 
  • Deposition Author(s): Wilson, K.P.

Revision History 

  • Version 1.0: 2017-05-24
    Type: Initial release
  • Version 1.1: 2017-06-07
    Type: Data collection, Database references
  • Version 1.2: 2017-11-22
    Type: Refinement description