Bioorganic & Medicinal Chemistry Letters
Incorporation of metabolically stable ketones into a small molecule
probe to increase potency and water solubility
Marie-Helene Larraufie a, Wan Seok Yang a, Elise Jiang b, Ajit G. Thomas c, Barbara S. Slusher c,d
,
Brent R. Stockwell a,b,e,
⇑
a Department of Biological Sciences, Columbia University, 550 West 120th Street, 1208 Northwest Corner Building, MC 4846, New York, NY 10027, United States
b Department of Chemistry, Columbia University, New York, NY 10027, United States
c Brain Science Institute, Johns Hopkins Medicine, Baltimore, United States
d Department of Neurology, Johns Hopkins Medicine, Baltimore, United States
e Howard Hughes Medical Institute, Columbia University, New York, NY 10027, United States
a r t i c l e i n f o
a b s t r a c t
Article history:
Introducing a reactive carbonyl to a scaffold that does not otherwise have an electrophilic functionality to
create a reversible covalent inhibitor is a potentially useful strategy for enhancing compound potency.
However, aldehydes are metabolically unstable, which precludes the use of this strategy for compounds
to be tested in animal models or in human clinical studies. To overcome this limitation, we designed
ketone-based functionalities capable of forming reversible covalent adducts, while displaying high meta-
bolic stability, and imparting improved water solubility to their pendant scaffold. We tested this strategy
on the ferroptosis inducer and experimental therapeutic erastin, and observed substantial increases in
compound potency. In particular, a new carbonyl erastin analog, termed IKE, displayed improved
potency, solubility and metabolic stability, thus representing an ideal candidate for future in vivo cancer
therapeutic applications.
Received 28 May 2015
Revised 6 July 2015
Accepted 7 July 2015
Available online xxxx
Keywords:
Reactive carbonyl
Ferroptosis
Covalent
Erastin
Ó 2015 Published by Elsevier Ltd.
Metabolic stability
There is growing awareness that compounds with optimal
properties in terms of selectivity and potency might be obtained
by combining the distinct properties of covalent and non-covalent
ligands.1 Practically, this often means functionalizing a scaffold
optimized for specific complementarity to a target with a carefully
tuned reactive moiety, to create a targeted covalent inhibitor. A
powerful way to mitigate the risks of off-target reactivity is to
use a reactive moiety that forms a reversible covalent bond with
proteins. In addition to increased selectivity, reversible covalent
inhibitors may limit the risk of haptenization and immunogenicity
associated with the formation of circulating irreversibly modified
protein adducts.2–5
imine-forming electrophiles may be feasible via the identification
of accessible lysine residues and simulation-based pKa calcula-
tions.10 Indeed, it appears from recent literature that lysines buried
in hydrophobic pockets, such as those targeted by small-molecules,
have their pKa downshifted by 3–5 units compared to solvent-
exposed lysines.11,12 This feature would favor the deprotonation
of buried lysine side chains and increased nucleophilicity, facilitat-
ing selective attack on a proximal carbonyl functionality.
Introducing an aldehyde moiety to an otherwise non-covalent
ligand to convert it into a reversible covalent inhibitor may thus
be feasible. However, the low metabolic stability of aldehydes gen-
erally precludes their utilization for in vivo applications. Indeed,
mammals have evolved a range of enzymes to transform aldehydes
into the corresponding alcohols (aldoketo reductases) and car-
boxylic acids (aldehyde dehydrogenases/cytochromes P450s).13
No carbonyl moieties capable of forming imines with lysine side
chains have been described that are also metabolically stable.
Described herein is the design and synthesis of such functionali-
ties, with optimized metabolic stability and aqueous solubility,
and their incorporation into the scaffold of the small molecule
ferroptosis probe erastin.
An important class of reversible covalent inhibitors are alde-
hyde-based compounds capable of forming an imine with a lysine
side chain in the binding site of a target protein. Recent examples
include the IRE1 endonuclease inhibitors 4l
8c6 and STF083010,7 a
20S proteasome inhibitor8 and the tau fibrillization inhibitor oleo-
canthal.9 While such reversible covalent inhibitors have mostly
been discovered serendipitously, the rational design of selective
⇑
Corresponding author.
We previously showed that erastin induces preferential lethality
in engineered human fibroblasts overexpressing oncogenic HRAS.14
0960-894X/Ó 2015 Published by Elsevier Ltd.