Identification of a Chemical Probe for Family VIII Bromodomains through Optimization of a Fragment Hit.
The acetyl post-translational modification of chromatin at selected histone lysine residues is interpreted by an acetyl-lysine specific interaction with bromodomain reader modules. Here we report the discovery of the potent, acetyl-lysine-competitive, and cell active inhibitor PFI-3 that binds to certain family VIII bromodomains while displaying significant, broader bromodomain family selectivity. The high specificity of PFI-3 for family VIII was achieved through a novel bromodomain binding mode of a phenolic headgroup that led to the unusual displacement of water molecules that are generally retained by most other bromodomain inhibitors reported to date. The medicinal chemistry program that led to PFI-3 from an initial fragment screening hit is described in detail, and additional analogues with differing family VIII bromodomain selectivity profiles are also reported. We also describe the full pharmacological characterization of PFI-3 as a chemical probe, along with phenotypic data on adipocyte and myoblast cell differentiation assays.
Pfizer Worldwide Medicinal Chemistry , 610 Main Street, Cambridge, Massachusetts 02139, United States.
Brian S
BS
Gerstenberger
Pfizer Worldwide Medicinal Chemistry , 610 Main Street, Cambridge, Massachusetts 02139, United States.
John D
JD
Trzupek
Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom.|Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom.
Cynthia
C
Tallant
Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom.|Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom.
Oleg
O
Fedorov
Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom.|Ludwig Institute for Cancer Research, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom.
Panagis
P
Filippakopoulos
Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom.|Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom.
Paul E
PE
Brennan
Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom.|Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom.
Vita
V
Fedele
Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom.|Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom.
Sarah
S
Martin
Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom.|Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom.
Sarah
S
Picaud
Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom.|Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom.
Catherine
C
Rogers
Pfizer Pharmaceutical Sciences , Eastern Point Road, Groton, Connecticut 06340, United States.
Mihir
M
Parikh
Pfizer Pharmaceutical Sciences , Eastern Point Road, Groton, Connecticut 06340, United States.
Alexandria
A
Taylor
Pfizer Worldwide Medicinal Chemistry , Eastern Point Road, Groton, Connecticut 06340, United States.
Brian
B
Samas
Bioseek Inc., Division of DiscoveRx , 310 Utah Avenue, South San Francisco, California 94080, United States.
Alison
A
O'Mahony
Bioseek Inc., Division of DiscoveRx , 310 Utah Avenue, South San Francisco, California 94080, United States.
Ellen
E
Berg
KinomeScan, Division of DiscoveRx , 11180 Roselle Street, Suite D, San Diego, California 92121, United States.
Gabriel
G
Pallares
KinomeScan, Division of DiscoveRx , 11180 Roselle Street, Suite D, San Diego, California 92121, United States.
Adam D
AD
Torrey
KinomeScan, Division of DiscoveRx , 11180 Roselle Street, Suite D, San Diego, California 92121, United States.
Daniel K
DK
Treiber
Eurofins Lancaster PPS , Eastern Point Road, Groton, Connecticut 06340, United States.
Ivan J
IJ
Samardjiev
Department of Cell and Developmental Biology, University of Massachusetts Medical School , Worcester, Massachusetts 01655, United States.
Brian T
BT
Nasipak
Department of Cell and Developmental Biology, University of Massachusetts Medical School , Worcester, Massachusetts 01655, United States.
Teresita
T
Padilla-Benavides
Department of Cell and Developmental Biology, University of Massachusetts Medical School , Worcester, Massachusetts 01655, United States.
Qiong
Q
Wu
Department of Cell and Developmental Biology, University of Massachusetts Medical School , Worcester, Massachusetts 01655, United States.
Anthony N
AN
Imbalzano
Department of Cell and Developmental Biology, University of Massachusetts Medical School , Worcester, Massachusetts 01655, United States.
Jeffrey A
JA
Nickerson
Pfizer Worldwide Medicinal Chemistry , 610 Main Street, Cambridge, Massachusetts 02139, United States.
Mark E
ME
Bunnage
Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom.|Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom.
Susanne
S
Müller
Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom.|Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom.|Institute for Pharmaceutical Chemistry and Buchmann Institute for Life Sciences (BMLS), Johann Wolfgang Goethe University , Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany.
Stefan
S
Knapp
Pfizer Worldwide Medicinal Chemistry , 610 Main Street, Cambridge, Massachusetts 02139, United States.
Dafydd R
DR
Owen
D053961:Azabicyclo Compounds / Q000138:chemical synthesis / Q000737:chemistry / Q000494:pharmacology*; D018360:Crystallography, X-Ray; D004268:DNA-Binding Proteins; D004305:Dose-Response Relationship, Drug; D006801:Humans; D008958:Models, Molecular; D015335:Molecular Probes / Q000138:chemical synthesis / Q000737:chemistry / Q000494:pharmacology*; D015394:Molecular Structure; D009687:Nuclear Proteins / Q000037:antagonists & inhibitors* / Q000378:metabolism; D011499:Protein Processing, Post-Translational / Q000187:drug effects; D011725:Pyridines / Q000138:chemical synthesis / Q000737:chemistry / Q000494:pharmacology*; D013329:Structure-Activity Relationship; D013379:Substrate Specificity; D014157:Transcription Factors / Q000037:antagonists & inhibitors* / Q000378:metabolism
D053961:Azabicyclo Compounds; D004268:DNA-Binding Proteins; D015335:Molecular Probes; D009687:Nuclear Proteins; C102195:PBRM1 protein, human; C000603674:PF-06687252; D011725:Pyridines; D014157:Transcription Factors