Perspective
pubs.acs.org/jmc
KATching-Up on Small Molecule Modulators of Lysine
Acetyltransferases
Roman P. Simon,† Dina Robaa,‡ Zayan Alhalabi,‡ Wolfgang Sippl,‡ and Manfred Jung*,†
†
Institute of Pharmaceutical Sciences, University of Freiburg, Albertstraße 25, Freiburg 79104, Germany
Department of Pharmaceutical Chemistry, University Halle-Wittenberg, Halle/Saale 06120, Germany
‡
ABSTRACT: The reversible acetylation of lysines is one of the best characterized epigenetic modifications. Its involvement in
many key physiological and pathological processes has been documented in numerous studies. Lysine deacetylases (KDACs) and
acetyltransferases (KATs) maintain the acetylation equilibrium at histones but also many other proteins. Besides acetylation, also
other acyl groups are reversibly installed at the side chain of lysines in proteins. Because of their involvement in disease, KDACs
and KATs were proposed to be promising drug targets, and for KDACs, indeed, five inhibitors are now approved for human use.
While there is a similar level of evidence for the potential of KATs as drug targets, no inhibitor is in clinical trials. Here, we review
the evidence for the diverse roles of KATs in disease pathology, provide an overview of structural features and the available
modulators, including those targeting the bromodomains of KATs, and present an outlook.
regulating tool to control transcriptional activity of specific
chromatin loci.2 Upon acetylation, local affinity of the modified
histone protein to negatively charged DNA is decreased,
resulting in a less condensed chromatin structure and in
exposure of promoter sites. As a consequence of the increased
accessibility, the DNA globally becomes more prone to access
of the transcriptional machinery.3 In addition, transcription
factors and other regulatory elements are recruited in a
modification-specific manner to the relaxed promoter locus by
interaction of specialized reader domains with acetyl lysine
moieties.1,4 Thus, HATs and histone acetylation are functionally linked with the control of transcription activation,
replication, and DNA damage repair.5 Mass spectrometrybased proteomics targeting the acetylome revealed that this
kind of PTM occurs not just on histones but on thousands of
other acetylation sites in more than 1500 proteins. Affected
proteins play vital roles in fundamental cellular processes like
cell division, signaling, apoptosis, and metabolism.6,7 Because of
the broad acceptance of substrates, histone acetyltransferases
and deacetylases are hence often referred to as lysine
INTRODUCTION
For more than 50 years, the enzymatic acetylation of histones
and other proteins and the functional consequences have been
topics of scientific interest. A wide range of experimental efforts
identified protein acetylation to be one of the key mechanisms
in the regulation of biological functions.
The transfer or removal of acetyl groups to ε-amino group of
lysine residues is mediated by two classes of enzymes. Histone
acetyltransferases (HATs) catalyze the covalent attachment of
acetyl groups to lysine residues of histones and other proteins
by using acetyl-coenzyme A (acetyl-CoA) as a cofactor. Histone
deacetylases (HDACs) conversely catalyze the amide hydrolysis
of acetylated lysine. The attachment of acetyl groups to lysine
residues goes along with two functional consequences. First, the
positive charge of physiologically protonated ε-amino groups is
abolished, resulting in altered electrostatic as well as steric
properties of the affected protein region. Second, acetylation
serves as a mark for distinct “reader” domains, which comprise
specialized tertiary structures (e.g., bromodomains) in proteins
that undergo a selective interaction with acetylated lysines.1
The most studied targets of HATs are histone proteins.
Together with other epigenetic posttranslational modifications
(PTMs) (e.g., phosphorylation, methylation, ubiquitinylation,
sumoylation, ADP ribosylation), acetylation serves as a
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© 2015 American Chemical Society
Special Issue: Epigenetics
Received: September 28, 2015
Published: December 23, 2015
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Table 1. Type A Lysine Acetyltransferases (KATs)
KAT
synonym
organism
physiological histone substrates
associated complexes/proteins
GNAT Family
Gcn5
hGcn5
PCAF
Elp3
Hpa2
Hpa3
Nut1
KAT2
KAT2A
KAT2B
KAT9
KAT10
dCBP
CBP
p300
KAT3
KAT3A
KAT3B
Tip60
Esa1
Sas3
MOZ/MYST3
MORF/MYST4
HBO1/MYST2
MOF/MYST1
Sas2
KAT5
KAT5
KAT6
KAT6A
KAT6B
KAT7
KAT8
KAT8
TAF1/TBP
TFIIIC90
KAT4
KAT12
SRC1
AIB1/ACTR/SRC3
p160
CLOCK
KAT13A
KAT13B
KAT13C
KAT13D
Rtt109
CMLO3
KAT11
S. cerevisiae, D. melanogaster
H3K9,14,18,23,36/H2B
H. sapiens
H3K9,14,18/H2B
H. sapiens
H3K9,14,18/H2B
H. sapiens, S. cerevisiae, D. melanogaster
H3
S. cerevisiae
H3K14/H4K5,12
S. cerevisiae
H4K8
S. cerevisiae
H3 > H4
p300/CBP Family
D. melanogaster
H4K5,8/H3K14,18
H. sapiens
H2AK5/H2BK12,15
H. sapiens
H2AK5/H2BK12,15
MYST Family
H. sapiens, D. melanogaster
H4K5,8,12,16
S. cerevisiae
H4K5,8,12,16/H2BK4,7
S. cerevisiae
H3K14,23
H. sapiens
H3K14
H. sapiens
H3K14
H. sapiens
H4K5,8,12 > H3
H. sapiens, D. melanogaster
H4K16
S. cerevisiae
H4K16
Transcription Factors Containing KAT Activity
H. sapiens, S. cerevisiae, D. melanogaster
H3 > H4
H. sapiens
H3K9,14,18
Nuclear Receptor Coactivators
H. sapiens
H3/H4
H. sapiens
H3/H4
H. sapiens
H3/H4
H. sapiens
H3K9,14
Other
S. cerevisiae
H3K9,27,56
X. levis
H4
mediator
TIP60
NuA4, Pic. NuA4
NuA3
MOZ/MORF
MOZ/MORF
HBO1
MSL
SAS
TFIID
TFIIIC
transcription process, as they were still detected in nuclei
pretreated with the transcription inhibitor puromycin. Moreover, the modifications decreased the histone-mediated
repression of RNA synthesis.15 In consecutive work, they
showed that the ε-amino group of lysine residues is the target
of acetylation.16 During the following years, histone acetylation
was linked to gene activation by a number of different studies.
In 1978, sodium butyrate was described as a histone deacetylase
inhibitor by Davie and co-workers.17 This was a milestone, as
for the first time it was shown that epigenetic regulators could
be targeted by small molecules. It took about 20 years until the
first KAT enzyme Gcn5 (general control nonderepressible 5,
p55) was identified by Brownell and Allis in 1995. In their
studies, an acetyltransferase activity gel assay was employed,
which detects the incorporation of 3H-acetate into histone
substrates after electrophoretic separation of nuclear extracts in
a SDS/polyacrylamide gel matrix.18 One year later, the
Gottschling group reported the isolation and cloning of Hat1
from Saccharomyces cerevisiae lysates as the first KAT exhibiting
cytosolic localization.19 The identification of distinct enzymes,
which catalyze the transfer of acetyl groups from acetyl-CoA to
histone protein substrates, formed the starting point for
extensive studies about the precise mechanism and functional
consequence of this PTM. New insights into structural aspects
of chromatin organization and histone function were provided
when Luger et al. solved the nucleosome particle crystal
structure in 1997.20 It was the same year that Grant et al.
acetyltransferases (KATs) and lysine deacetylases (KDACs),
respectively.8 In concert, these enzymes dynamically regulate
the lysine acetylation levels within the cellular proteome. This
acetylation equilibrium is adjusted in response to cellular
stimuli like autoacetylation, protein−protein interactions,
phosphorylation, or the cellular acetyl-CoA level, leading to
altered gene transcription and subsequently to phenotype
adaption.9
Aberrant acetylation levels have been connected with a
diversity of disease phenotypes including cancer, neurological
disorders, and cardiovascular and metabolic malignancies.10−14
Hence, KAT enzymes seem to be deeply involved in the
manifestation and progression of such diseases and therefore
the elucidation of their precise mechanism is required to assess
their potential as possible drug targets and small molecule
modulators are of high interest for probing these pathways and
as potential drugs.
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SAGA, SLIK, ADA, HAT-A2, ATAC
STAGA, TFTC
PCAF
elongator
Hpa2
FIFTY YEARS OF LYSINE ACETYLATION
In 1964, Allfrey and colleagues proposed an innovative
hypothesis of reversible posttranslational histone modifications
being a dynamic regulatory mechanism for RNA synthesis after
they reported the incorporation of acetyl and methyl groups
into histone proteins as a result of treating isolated nuclei with
radiolabeled acetate (acetate-2-C14) and methionine (methionine-methyl-C14), respectively. The incorporation of these
modifications was found to happen independently of the
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enzymes differ in their N- and C-terminal regions, which are
responsible for recognition, positioning, and binding of
substrates. Structural motifs within these regions, like bromoand chromodomains, zinc binding moieties, and cysteine/
histidine rich modules (PHD, TAZ, ZZ) promote the target
structure diversity.33 One example for substrate discrimination
by such structural motifs is Gcn5. Human Gcn5 can be
distinguished from its yeast homologue by a 400-residue Nterminal region. Under in vitro conditions, recombinant human
Gcn5 acetylates free histone H3 on lysine 14 and, to a minor
degree, histone H4 on lysine 8 and 16. It is remarkable that in
contrast to yeast Gcn5, which targets the same substrate
residues, the human homologue is capable of acetylating
histones in a nucleosomal context, indicating the role of the Nterminal region in substrate recognition.5 PCAF and human
Gcn5 share about 80% sequence similarity and both exhibit site
preference for in vitro H3K14 acetylation within free or
nucleosomal histones. On the cellular level, the substrate
pattern is shifted toward multiple H3 and H2B acetylation sites,
stating that recombinant enzymes may differ in substrate
specificity and turnover comparing in vitro and in vivo
conditions.34 Like the most KAT enzymes, Gcn5 and PCAF
natively occur as part of multiprotein complexes. Functional
interaction between subunits, as well as different PTMs on
substrate or protein structures, direct affinity pattern to the
more physiological substrates. Together, GNAT family
enzymes and their multiprotein complexes are generally
involved in transcriptional activation, elongation and DNA
damage repair.35
The ubiquitously expressed and metazoan specific KATs
p300 and CBP (CREB-binding protein) form the p300/CBP
family. Both enzymes share close structural and functional
homology and are competent to acetylate all four histone
proteins under in vitro conditions. The p300/CBP-mediated
transfer of acetyl groups comprises a Theorell−Chance
mechanism, which is characterized by stable binding of the
cofactor acetyl-CoA followed by transient and rather weak
association of the lysine substrate to the enzyme. This catalytic
mechanism is distinct from the GNAT and MYST KAT
families and may contribute to the broad substrate acceptance
of p300/CBP. On molecular level, p300 and CBP interact with
a variety of transcription factors and coactivators to form
regulatory complexes at promoter regions. In this way, they
stimulate transcription of specific genes and serve as inciting
regulatory elements. About 100 protein substrates have been
described for p300/CBP so far.36 Interestingly, while being
intensively studied in mammals, plant orthologues of p300/
CBP have also been found and characterized, suggesting a
fundamental functional implication of this enzyme family in all
metazoan organisms.37
The MYST family is named after the initially identified
members (MOZ (monocytic leukemia zinc finger protein),
Ybf2 (Sas3), Sas2 (something about silencing), and Tip60
(Tat-interactive protein)).38 These enzymes show sequence
similarities, which reaches a remarkable high degree in a
particular MYST homology region within the catalytic domain.
Like in the GNAT enzymes discussed above, the highly
conserved cofactor-binding motif A is also present in the
structure of MYST family members.39 The acetyltransferase
MOZ targets histone H3 lysine residue 14 and is correlated
with transcription activation.8 Sas2 and Sas3 are involved in
transcriptional silencing processes in S. cerevisiae.40 Tip60 was
the first reported human member of the MYST family with
identified and partially characterized the first KAT-containing
protein complex SAGA (Spt-Ada-Gcn5-acetyltransferase) from
Saccharomyces cerevisiae with its catalytic subunit Gcn5.21 Their
findings added another level of complexity to the field of
acetyltransferases because it demonstrated that their regulatory
activity in a cellular context depends on multidomain protein
complexes with a specific composition. The starting point of
KAT inhibitor discovery was set two years later when
Marmorstein and Allis published the crystal structure of Gcn5
as a nascent acetyltransferase as well as in a context with the
cofactor acetyl-CoA and the physiologic ligand histone H3.22
Following these discoveries, Cole and colleagues synthesized
the first KAT inhibitors. Inspired by earlier observations on
serotonin N-acetyltransferases, they covalently linked lysine
residues to CoA to generate pseudo bisubstrates of the
addressed enzymes.23 In 2006, Kim et al. performed the first
proteomic screen targeting lysine acetylation and identified 388
acetylation sites in 195 proteins.7 Over the past few years,
advances in assay technology and in computational methods
have led to an increased understanding of acetylation biology
and pathology.6,24 Furthermore, a growing number of other
acyl groups are identified to be the subject of reversible
attachment and cleavage on lysines in proteins. Examples are
formyl, propionyl, butyryl, crotonyl, malonyl, succinyl, or long
chain fatty acids.25 There is no doubt that expanding on these
observations will elucidate the full potential of the field of lysine
acylation.
ENZYMES AND ENZYME FAMILIES
After the initial discovery of Hat1 and Gcn5, biological
experiments led to the identification of additional KAT
activity-containing enzymes that are classified according to
their preferred cellular localization. Type B KATs share
cytoplasmic localization and acetylate nascent histones to
facilitate translocation into the nucleus, where the histone
proteins are deacetylated and subsequently incorporated into
chromatin fibers. Hat1 (KAT1) is one of two members of type
B KATs. It is highly conserved through evolution in eukaryotes
and acetylates free (not in a nucleosome) H4 protein on lysine
residues 5 and 12, in humans also on H2A lysine residue 5.
Together with the WD40 protein Hat2, Hat1 forms the Hat1/2
complex, which exhibits 10-fold increased activity compared to
native Hat1. The intriguing observation that Hat1 is not solely
found in the cytoplasm but also in the nucleus suggests that the
enzyme activity shuttles between different cell compartments.26
The second member of type B KATs is Hat4, which is located
in the Golgi apparatus where it catalyzes the acetylation of H4
protein on position 79 and 91.27 Type A KATs comprise a
number of heterogenic enzymes that share nuclear localization.
On the basis of their structural homology and catalytic
mechanism, these enzymes are grouped into distinct families
(Table 1).
The GNAT (Gcn5 related N-acetyltransferase) family
includes the enzymes Gcn5,18 PCAF (p300/CBP associated
factor),28 Elp3,29 Hpa2/3,30 and Nut1.31 A characteristic feature
of this enzyme family is the presence of up to four sequence
motifs (A−D) with motif C being almost exclusively found in
GNAT family enzymes. The A motif is the most highly
conserved region, and it contains an acetyl-CoA binding
domain that is defined by an Arg/Gln-X-X-Gly-X-Gly/Ala
segment.32 This segment is not limited to GNAT enzymes, but
also found in other KAT families. While the catalytic domains
of KATs show high structural homology within a certain family,
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preference for H4 acetylation. Transcriptional activation and
DNA damage response are mediated by the acetylase activity of
this enzyme.41 Following the founding members, more MYST
family enzymes were identified and characterized. The yeast
enzyme Esa1 is a homologue of human Tip60 and the catalytic
subunit of the NuA4 complex. This complex promotes H4
acetylation and subsequently stimulates transcription of genes
that are essential for cell cycle progression.42 The in vivo
activity and specificity of almost all MYST family enzymes is
highly determined by the composition of their protein
complexes. HBO1 (HAT bound to ORC1) interacts with
subunits of the origin of replication complex, consequently
playing a functional role in DNA replication.43 The isolated
HBO1 complex acetylates histones H4 at position 5, 8, and 12
and less effectively H3, whereas recombinant HBO1 shows no
significant acetylase activity, implicating protein−protein
interactions and in vivo modifications in efficient substrate
recognition and turn over.8,43 A close homologue to the MYST
family founding member MOZ is the transcription activator
MORF (MOZ related factor). While recombinant and fulllength MORF catalyzes acetylation of H4 and H3 protein,
under physiological condition solely histone H3 is targeted.8,44
The product of the mof (males absent on the first) gene
represents one more member of this KAT family. The enzyme
was identified in the course of studies targeting dosagecompensation of the X-chromosome in D. melanogaster.45 MOF
is related to the yeast enzyme Sas2 but targets different
acetylation sides on H4, H3, and H2A proteins in vitro. In the
native MSL complex, MOF catalyzes the acetylation of
nucleosomal histone H4 exclusively on lysine residue 16,
emphasizing the influence of the associated MSL proteins on
MOF activity and substrate specificity.
KAT activity was also found in protein components of
transcription factor complexes like TAF1/TBP and TFIIIC90.
These protein complexes affect transcription directly and form
a separate KAT family.46,47 There are a few coactivators of
nuclear hormone receptors, which exhibit ligand-dependent
KAT activity. They serve as regulatory elements in hormone
related transcriptional processes and are grouped in a unique
KAT family.48,49 The global regulator of circadian gene
expression CLOCK was shown to be a member of this family.50
The fungal specific lysine acetyltransferase Rtt109 shows very
little sequence homology to any of the other KAT family
members, but its tertiary fold adopts a structure that is
surprisingly similar to p300. However, the catalytic mechanism
of Rtt109 involves a ternary intermediate complex and
therefore differs significantly from the one of p300. Because
of these differences, the enzyme is not assigned to any of the
known KAT families. Isolated Rtt109 is not competent to
efficiently acetylate lysine substrates, but its activity is
stimulated by association with either of two different histone
chaperones, Asf1 and Vps75. Upon formation of the enzyme−
chaperone complex, the activity of the catalytic domain is
dramatically increased and the substrate specificity is directed
toward distinct lysine residues (H3K56 for Asf1 and H3K9,23
for Vps75).51 Bioinformatic analysis of the zebrafish genome
led to the identification of the Camello protein family member
CMLO3, for which lysine acetyltransferase activity on histone
protein H4 was demonstrated. Their structural divergence and
their perinuclear localization distinguish Camello proteins from
other KATs and place them outside of any of the other KAT
families.52
Considering the vast number of identified nonhistone
acetylation sites on a constantly growing number of proteins,
covering a wide functional spectrum, it should be noted that for
many of these acetylation reactions the responsible enzymes
have not been identified yet. 6 While several histone
acetyltransferases were shown to also accept nonhistone
substrates, the implications of specific nonhistone acetyltransferases, such as the α-tubulin acetyltransferase αTAT153 and
the cohesin acetyltransferase Eco1/ESCO1,54 still need to be
determined.
KATS IN DISEASES
Lysine acetylation of histone and nonhistone proteins is
generally linked to activation of transcriptional activity and
therefore affects pivotal physiological processes within an
organism. As a consequence of misregulated acetylase activity,
the manifestation and progression of certain malignancy
phenotypes correlates with pathological aberrations of the
acetylation equilibrium. This could be either due to altered
activity of the responsible enzymes or because of changes in
their expression levels. The role of distinct KAT subtypes in
diseases like cancer, neurodegenerative disorders, viral and
parasitic infections, inflammation, and metabolic and cardiovascular malignancies have been extensively investigated.55,56
p300 and CBP are global coactivators of gene transcription
and involved in multiple cellular processes. Point mutation and
microdeletion of the CBP gene result in Rubinstein−Taybi
syndrome (RTS), which is characterized by physical
abnormalities and mental retardation. 55 Elevated p300
expression levels have been associated with several types of
cancer, including esophageal squamous cell carcinoma
(ESCC),57 hepatocellular carcinoma (HCC),58 and melanoma.
In the latter case, downregulation of p300 activity retards cell
cycle progression in human melanocytes by activating
replicative senescence.59 It is reported that p300/CBP
interaction with c-Myb facilitates myeloid differentiation block
and is required for acute myeloid leukemia (AML) induction.60
A characteristic feature of this hematologic malignancy is the
presence of KAT activity-containing fusion proteins in
consequence of chromosomal translocations. Fusion products
of p300/CBP with MOZ, MORF, or MLL exhibit aberrant
KAT activity and substrate specificity and hence lead to
abnormal transcription activation.11 The AML1-ETO oncogene
is acetylated by and colocalized with p300 at specific promoter
regions, which was found to be pivotal for leukemogenesis.61
After infection of a cell with the human immunodeficiency virus
(HIV), p300-mediated acetylation of the viral protein integrase
is crucial for incorporation of virus DNA into the cells’
genome.62 Upon integration, p300/CBP interaction with the
HIV-1-Tat protein promotes transcription of the HI provirus.63
In patients with elevated glucose levels, binding of p300 to
promoter sites is increased, which leads to upregulation of
vasoactive factors and extracellular matrix proteins, suggesting a
possible role of p300 in chronic diabetes related complications.64 p300 and CBP stimulate cardiac growth and p300
activity is increased in agonist induced hypertrophy of
cardiomyocytes. Recruitment and acetylation of specific
transcription factors, such as GATA4 and MEF2, mediate
elevated transcription levels of hypertrophy related effector
proteins.13 The acetylation of NF-κB by p300/CBP is
associated with a loss of affinity for IκB, leading to enhanced
expression of proinflammatory downstream genes products. In
neurodegenerative diseases, reduced CBP activity is associated
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the reader is referred to more specific reviews regarding this
topic.11,36,55,81
with loss of neuronal plasticity and destabilization of short-term
memory, implicating CBP as an antitarget in this context.12
Like p300 and CBP, the GNAT family KATs serve as
regulators of transcriptional activity and are similarly implicated
in fundamental physiological processes. Their activity and
specificity highly depend on protein−protein interactions, as
these enzymes are usually part of multienzyme complexes. It
was shown that Gcn5 activity is crucial for cell cycle
progression.65 While Gcn5 and PCAF play important roles in
the activation and stabilization of the tumor suppressor p53,
PCAF-mediated acetylation of the cyclin-dependent kinase
inhibitor p27 facilitates its degradation and further leads to
uncontrolled cell cycle progression.66 The invasive potential
and growth rate of urothelial cancer cells is hampered by PCAF
knockout.67 Drug resistant cancer cells exhibit elevated levels of
PCAF and Gcn5-mediated H3K9 acetylation in promoter
regions of the MDR1 (multidrug resistant protein 1) gene.68
Alongside p300, Gcn5 is competent to acetylate and thus
activate HIV integrase and Tat proteins with essential impact
on the HIV replication cycle.69 A Plasmodium falciparum
homologue of Gcn5 (PfGcn5) was found to play a key role in
antigenic switching and expression of plasmodial proteins.70
Interestingly, despite some evidence on an antitarget role of
p300 in neurodegenerative diseases, knockout of PCAF
promotes insensitivity to β-amyloid peptide toxicity in mice,
suggesting PCAF to be a possible target for the treatment of
Alzheimer disease.71 It was also shown that PCAF is involved in
the extinction process of conditioned fear and that PCAFmediated acetylation of connexin 43 is implicated in cardiac
dystrophy.72,73 In type 2 diabetes, Gcn5 and PCAF were found
to acetylate PGC-1α (peroxisome proliferator-activated receptor gamma coactivator 1-alpha), a key coactivators in energy
metabolism, thereby regulating its transcriptional activity.74
MYST family KATs are more diverse in domain organization
and complex formation than p300/CBP and GNAT family
proteins. Aberrant activity of this KAT family has predominantly been implicated in manifestation and progression of
cancer. The aforementioned fusion proteins of MOZ and
MORF with other KAT family members in AML inductions are
complemented by the MOZ-TIF2 fusion protein, which is
yielded after chromosomal inversion. In AML, MOZ-TIF2
interacts with CBP and disrupts normal CBP-dependent
transcriptional activation.75 In addition, mutation in MOZ
was associated with esophageal adenocarcinoma.76 Altered
activity of the MYST family member MORF has been linked to
breast cancer, prostate cancer, and leiomyoma. Furthermore,
these KATs are involved in developmental processes and
mutation in their encoding genes have been found in several
developmental disorders.77 The acetyltransferase Tip60 plays
an important role in hormone receptor signaling and DNA
damage repair. The androgen receptor is activated in an
androgen-independent manner upon Tip60-mediated acetylation. Related to this, the proliferation of prostate cancer has
been correlated to aberrant Tip60 activity.78 Moreover,
resistance to apoptotic signaling cascades in cancer cells after
DNA damage was associated with Tip60 mutations.79 HBO1 is
a key regulator of DNA replication and proliferation.
Overexpression of HBO1 has been reported in a specific
subset of human primary cancers.80 Together, this emphasizes
the role of mistargeted acetylation in oncogenesis and other
malignancy phenotypes. The field of lysine acetylation in cell
function and its involvement in diseases goes beyond the
examples listed in this article. For more detailed information,
STRUCTURAL ASPECTS OF KATS
KAT modules, which typically occur alongside other conserved
protein modules as a part of much larger proteins, show
different sizes between the various KAT families. A high
sequence similarity is shared between members of the same
family, whereas poor to no sequence homology is found
between the families.82 Despite the poor sequence homology,
all KATs adopt a globular α/β fold where the central core is
structurally conserved. This central core is associated with the
binding and catalysis of the cofactor acetyl-CoA. Meanwhile,
the N- and C-terminal protein regions flanking the central core
are structurally divergent and are believed to contribute to the
substrate specificity of these enzymes. It is however
questionable if substrate specificity of KATs can be solely
attributed to the divergence of the N- and C-terminal domains.
As previously mentioned, KATs are often found as subunits in
large protein complexes, and their interacting protein partners
were found to play a role in regulating their substrate selectivity
as well as enhance their acetylase activity.83 It should hence be
noted that further biochemical and structural investigations are
necessary to decipher the exact role of protein partners on the
activity and substrate specificity of KATs. The GNAT, p300/
CBP, and MYST families are the most extensively studied
KATs, and crystal structures of several members of these
families are available in apo form and/or in various ligandbound forms. The overall structures of representative members
for each family are shown in Figure 1.
Crystal structures of the KAT domain of Gcn5 (human, yeast
and Tetrahymena) and PCAF have provided valuable
information on the mechanism of catalysis as well as cofactor
and substrate-binding of these enzymes. Acetyl-CoA is bound
to the central core cleft via numerous hydrogen-bond
interactions, mostly between the pantothenic and pyrophosphate moieties of the cofactor and the neighboring amino acid
residues.84 Meanwhile, the adenosine base shows no contacts
with the protein, and it was found to adopt different
orientations in various crystal structures.85,86 An insight into
the binding of the peptide substrates to GNAT family KATs
was attained by determining the crystal structures of
Tetrahymena Gcn5 (tGcn5) with H3, H4, and p53 peptides
(PDB IDs: 1q2c, 1q2d, 1pu9, 1pua, and 1qsn). The central core
and the flanking N- and C-terminal residues create an L-shaped
binding cleft, which accommodates acetyl-CoA and the peptide
substrate. The active lysine residue is in contact with the
conserved core region, showing van-der-Waals (vdW) interactions with Val123, Leu126, and Phe169 and a hydrogen-bond
interaction between its backbone-NH and the backbone
carbonyl group of Ala124. The rest of the histone tail occupies
a large cleft formed by the flanking, less conserved N- and Cterminal regions. Interestingly, most of the interactions are
mediated through hydrogen bonds between the backbone of
the histone peptide and the protein, in addition to vdW
contacts between the peptide side chains and some protein
residues in the binding cleft.22,86 It was hypothesized that
residues C-terminal to the reactive lysine of the peptide
substrates play an important role in substrate selectivity.86 Of
particular importance are residues at the +2 and +4 position,
which show strong vdW interactions with the protein. The Nterminal residues of the peptide seem to mainly contribute to
the substrate affinity; only substrates with high affinities (H3
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Perspective
surrounded by the hydrophobic residues Tyr1397, Trp1436,
Cys1438 (L1 loop), and Tyr1446 (L1 loop). The ε-NH of the
lysine moiety undergoes H-bond interactions with the
backbone carbonyl of Trp1436. A common feature of all
p300/CBP substrates is the presence of a basic residue (lysine
or arginine) at the −3 or +4 position of the active lysine
residue.89,91 This is consistent with the highly electronegative
surface area of the crystallized p300 KAT domain (Figure 2),
Figure 2. (a) Electrostatic surface of p300 (PDB ID 3biy) in complex
with Lys-CoA (white sticks). Red color indicates electronegative
regions, blue electropositive, and white regions having a neutral
potential. The arrow points to the electronegative subpocket, which
accommodates the Lys/Arg residue at −3 or +4 position of the
peptidic substrate. Lys-CoA can be partly seen as white sticks. (b) the
structure of p300 protein containing the bromo- (cyan), PHD
(orange), RING (yellow), and KAT (green) domains (4bhw.pdb).
The L1 loop is shown as red ribbon, and the zinc ions as violet
spheres.
which distinguishes this family from other KATs. In particular,
a highly electronegative pocket, formed of Thr1357, Glu1505,
Asp1625, and Asp1628 and located 10 Å away from the active
lysine pocket, is responsible for accommodating the basic
residue at the −3 or +4 position. Mutations of these residues
showed a significant decrease in p300 KAT activity.89 In
addition, the p300 KAT activity is regulated by a lysine-rich
loop (aa 1520−1560; activation loop) that is hyperacetylated in
the active form.92 It was suggested that the activation loop, in
its deacetylated form, folds into the highly electronegative
surface, thereby occluding the substrate binding pocket. Upon
acetylation, this loop flips outward and allows substrate binding.
Owing to its high proteolytic sensitivity, all crystal structures of
p300 have been determined without the activation loop.
Recently, a crystal structure of the KAT, RING, PHD, and BRD
domains of the p300 protein has been determined.88 These
domains form a compact module, where the RING domain is in
direct contact with the L1 loop and hence in close proximity of
the KAT substrate pocket (Figure 2). The RING domain was
found to have an inhibitory function on the acetylase activity of
the KAT domain. Indeed, mutations which disrupt the integrity
of the RING domain or the attachment between the RING and
KAT domains resulted in an increase in the autoacetylation of
the p300 activation loop and the p300 acetylase activity. Similar
mutations were correlated with the pathology of some diseases;
C1204R mutation is found in B-cell lymphomas, while deletion
of the RING domain (1198−1234) occurs in breast cancer
tissues.88
The overall structure of the yeast MYST member Esa1 (PDB
ID 1fy7)93 and the later disclosed human homologue
hMOF94−97 reveal, as expected, structural homology of the
central core with other KATs. Meanwhile, the flanking N- and
C-terminal segments show a structural divergence to other Nacetyltransferases. A distinctive feature of the MYST family is
Figure 1. Overall structure of nuclear KATs. Acetyl-CoA (cyan sticks)
is shown in complex with (a) hGcn5 (PDB ID 1zr4), (b) p300 (PDB
ID 4pzr) with the L1 loop depicted as green ribbon, and (c) hMOF
(PDB ID 2giv) as a representative of the MYST family.
peptide) display interactions between their N-terminal residues
and the protein.86,87 It is noteworthy, that a loop region (aa
184−188 tGcn5), which constitutes a part of the substrate
binding pocket, shows a considerable flexibility and a 9 Å
outward movement is observed upon peptide binding.22,86 A
similar conformational change is not observed in the crystal
structure of Gcn5 in complex with the bisubstrate inhibitor LysCoA (PDB ID 1m1d).85
As previously noted, p300 and CBP share a structural
conservation of the central core with members of the Gcn5/
PCAF and MYST family KATs and a structural divergence of
the N- and C-terminal regions.88−90 However, p300/CBP show
a unique feature among KATs, namely a ∼25 residues long
loop (L1 loop), which constitutes a part of the cofactor and
lysine-binding pockets.89 A salt bridge between Asp1399 with
His1415 is essential for holding the L1 loop in the right
conformation to allow for the acetyl-CoA binding. The crystal
structure of p300 in complex with the bisubstrate inhibitor LysCoA (3biy.pdb) demonstrates that the lysine moiety is
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Perspective
the regulation of its acetylase activity by intramolecular
autoacetylation of a conserved lysine residue proximal to the
substrate binding site (K274 in hMOF).96,97 K274 autoacetylation was demonstrated to be essential for the in vitro and in
vivo KAT catalytic activity.97 The acetylated lysine residue
(K274, hMOF) is buried into a side pocket of the enzyme
active site, where it is stabilized by H-bond interactions with the
conserved residues Tyr3012 and Ser303. The terminal methyl
group displays vdW contacts with the conserved residues
Phe283 and Phe285 (Figure 3).96 In the deacetylated form, the
KAT MODULATORS
The multifold implication of lysine acetylation in physiologic
pathways as well as manifestation and progression of diseases
emphasizes the potential of KAT modulators as therapeutic
strategy or versatile mechanistic tools. However, the identification of such compounds has proven to be challenging and
the development of potent and selective KAT inhibitors lags far
behind modulators of other epigenetic enzymes, like KDACs.
Despite different approaches to find small molecule inhibitors
of KAT enzymes, only few potent substances have been
obtained so far. With the aid of computational methods and
advanced assay technologies, recently progress was made
toward compounds with improved KAT modulatory properties
and in vivo characterization. According to their origin and
mode of action, the known KAT modulators can be assigned to
four distinct classes: bisubstrate inhibitors, natural compounds
and their analogues and derivatives, synthetic small molecules,
and bromodomain inhibitors.
Bisubstrate Inhibitors. The first published KAT inhibitors
were bisubstrate analogues mimicking the ternary complex of
cofactor acetyl-CoA and lysine substrate in spatial proximity
during the catalytic process (Figure 4). Cole and colleagues
■
Figure 3. (a) Comparison of the interactions of the autoacetylated
lysine (K274) in hMOF (green ribbons and sticks, PDB ID 3qah),
with those of the deacetylated form as seen in the K274R mutant
(yellow ribbons and sticks, PDB ID 2pq8). Only side chains of the
involved residues are shown for clarity. Acetyl-CoA is shown as
magenta sticks. (b) Structure of hMOF KAT domain (surface
depiction in cyan) in complex with MSL1 segment (surface depiction
in red); 4dnc.pdb. Lys-CoA is shown as white spheres.
lysine residue flips out of the side pocket and consequently
blocks the substrate binding site, as observed in the crystal
structure with the K274R mutant (Figure 3) (PDB ID 2pq8).
The flipped-out form is stabilized by salt bridge interactions
with the catalytically important Glu350, thus quenching its
proton abstraction ability. The activity and substrate specificity
of hMOF is regulated by its association with other proteins to
form larger protein complexes.98,99 hMOF association with
MSL1 and MSL3 in the MSL (male-specific lethal) complex
leads to a pronounced enhancement of its enzymatic activity
and a refinement of its substrate specificity to selectively target
the nucleosomal H4K16.99 Meanwhile, the complex of hMOF
with NSL1, as found in the NSL (nonspecific lethal) complex,
is more efficient in specifically acetylating K20 on p53 than
hMOF alone. 98 The crystal structure of hMOF with
MSL1470−540 has been recently revealed (PDB IDs 4dnc
and 2y0m). The MSL1 segment interacts extensively with the
N-terminal part of hMOF, mainly through H-bond and saltbridge interactions. A depiction of the MOF−MSL1 complex is
shown in Figure 3. The MSL1 segment is believed to act as a
tether between MOF and MSL3, which is another essential
member in the MSL complex.94,95 Although the determined
crystal structures provide some basic structural insights into the
nature of the interplay between the subunits in these
complexes, further structural investigations are necessary to
fully understand how the activity and substrate specificity of
MOF is regulated by the complex subunits. Despite the
availability of structural information on numerous KATs, so far
only very few studies have reported on the use of in silico
screening approaches for the identification of KAT inhibitors.
Figure 4. Structures of bisubstrate KAT inhibitors.
covalently linked CoA to the lysine residue of a substrate
peptide of various chain lengths. The bisubstrates concept was
adopted by several other groups to generate specific KAT
inhibitors. Compound 1 (Lys-CoA) is yielded by connecting
CoA and a single lysine residue via a methylene linker.23 The
compound is a potent inhibitor of p300 with an IC50 value of
0.5 μM and pronounced selectivity toward p300 compared to
PCAF. The particular potency of 1 results from the Theorell−
Chance kinetic mechanism of p300/CBP catalysis, which is
characterized by a strong cofactor-binding and a weak transient
interaction with the histone substrate.23 The selectivity pattern
of bisubstrate inhibitors can efficiently be altered by modifying
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Figure 5. Structures of natural KAT modulators, synthetic analogues, and derivatives.
Figure 6. Structures of selected natural KAT inhibitors, their derivatives, and structural analogues.
the length and composition of the peptide chain that comprises
the lysine-CoA construct. Derivative 1.1 (H3-CoA-20) mimics
the native substrate H3K14 of PCAF and therefore inhibits the
enzyme selectively with an IC50 value of 0.3 μM.23 To address
MYST family enzymes, a series of H4 peptide-containing
bisubstrates analogues was designed and structure 1.2 (H4K16CoA) was reported as an acetyl-CoA competitive and potent
Tip60 inhibitor with an IC50 value in the low micromolar
range.100 It should be noted that the mentioned bisubstrate
analogues also inhibit the Tip60 yeast homologue Esa1 at low
micromolar concentrations and therefore special caution in
yeast studies is advised. Deduced from the crystal structure of
p300, compound 2 (Boc-C5-CoA) was reported as p300
inhibitor (IC50 0.07 μM) with an optimized linker length that is
capable to occupy two binding pockets (P1, P2) within the
enzyme active site.101 Attributed to the polar phosphate
moieties and the partially peptidic structure, bisubstrate
inhibitors generally suffer from poor cell permeability and
metabolic instability, which limits their use to in vitro
applications or requires membrane penetrating techniques
like micro injection or lipid permeabilization. Different
approaches have been applied to circumvent this limitation.
Truncation of the CoA moiety in 3′ position led to a significant
reduction of inhibitory activity.102 Coupling of the inhibitors’
amino acid backbone to the Tat protein transduction domain
or to arginine rich peptides succeeded in facilitating cellular
uptake and activity.103,104 However, the application of such
inhibitor/peptide constructs is rather limited due to their
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results from biochemical testing
compd
1
name/code
Lys-CoA
1.1
H3-CoA20
1.2
H4K16-CoA
2
Boc-C5-CoA
4
anacardic acid
approach
lead structurebased
lead structurebased
lead structurebased
lead structurebased
fucussed library
screen
p300/CBP
Gcn5
PCAF
0.5 μM
200 μM
0.98 μM
0.05 μM
30 μM
0.0032 μM [GST-p300C]
200 μM
108.3 μM
6.62 μM
58.47 μM
Tip60
other
29.8 μM
7 μM [Esa1]
17.59 μM
5.51 μM [Esa1]
0.3 μM
0.07 μM
8.5 μM
5 μM
>1000 μM
>200 μM
667.1 μM
>200 μM
347.6 μM
64 μM
297.2 μM [Esa1]
43 μM [MOF]
Ki = 64 μM [MOF]
1257
1−2 mM
33.9 μM
4.15 μM, max 60%
lead structurebased
4.1
662 μM
n.i. (200 μM)
4.2
CTPB
4.4
LoCAM
lead structurebased
lead structurebased
100%
(200 μM)
n.i.
∼400% (275 μM)
74% (50 μM)
n.i.
81.2% (100 μM)
5
EGCG
6
curcumin
CTK7A
7
garcinol
7.2
LTK-14
synthetic
optimization
fucussed library
screen
synthetic
optimization
∼40% (50 μM)
37.5%
(100 μM)
60 μM
30 μM/50 μM
25 μM
70 μM
n.i. (100 μM)
ref
23
radiometric
radiometric
radiometric
radiometric
radiometric
filter-binding
gel
gel
filter-binding
gel
100
104
121
132
23
radiometric filter-binding
100
radiometric
101
radiometric filter-binding
107
radiometric filter-binding
radiometric filter-binding
colorimetric CoA-scavenging
immunosorbent ELISA-like
radiometric filter-binding
colorimetric CoA-scavenging
immunosorbent ELISA-like
100
108
112
111
115
148
111
radiometric filter-binding
108
radiometric filter-binding
107
immunosorbent ELISA-like
114
radiometric filter-binding
115
colorimetric
116
radiometric filter-binding
118
radiometric filter-binding
radiometric filter-binding
radiometric gel
AlphaLisa proximity immunoassay
radiometric filter-binding
115
100
121
127
122
6.5 μM
>40 μM
>400 μM
6.5 μM
>50% (50 μM)
>50% (50 μM)
7 μM
5 μM
radiometric filter-binding
124
n.i. (50 μM)
radiometric filter-binding
126
n.i. (80 μM)
radiometric gel
125
5−7 μM
Ki = 5.1 μM
>200 μM
n.i. (50 μM)
n.i.
(100 μM)
>200 μM [Esa1]
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6.3
fucussed library
screen
fucussed library
screen
65%
(200 μM)
assay system
radiometric gel
Journal of Medicinal Chemistry
Table 2. KAT Modulators Listed with Their Results from Biochemical Evaluation: IC50 Values or Percentage Enzyme Inhibition at a Specified Concentration (n.i. = No
Inhibition)
results from biochemical testing
compd
name/code
approach
8
EML425
9
plumbagin
10
Embelin
lead structurebased
fucused library
screen
HTS
11
11.1
12.2
NK13650A
NK13650B
PU139
HTS
HTS
virtual screen
p300/CBP
Gcn5
PCAF
2.9 μM [p300]/1.1 μM [CBP]
n.i.
n.i.
20−25 μM [full length]; 2 μM [cat.
domain]
75% (25 μM)
PU141
1258
MC1823
14.2
CPTH6
15
MB-3
phenotypic
screen
phenotypic
screen
rational design
16
C646
virtual screen
17
L002
18
19
20
NU9056
TH1834
phenotypic
screen
virtual screen
HTS
rational design
HTS
75%
(25 μM)
n.i. (9 μM)
n.i. (9 μM)
1.64 μM
8.39 μM
9.74 μM
53% (5 μM) [MOF]
130 μM
5.92 μM [p300]/2.85 μM [CBP]
21
7.2 μM
virtual screen
13
other
50 μM
0.011 μM [GST-p300C]
0.022 μM [GST-p300C]
5.35 μM [p300]/2.49 μM [CBP]
12.3
Tip60
87.36 μM
130 μM
60% (5 μM) [MOF]
24% (25 μM); 30% (50 μM) [U937
nuclear extracts]
500 μM CBP
55% (50 μM) [CBP]
1.6 μM, Ki = 0.4 μM, 86% (10 μM)
0.32 μM
1.98 μM, 128 μM [p300]/32% (100
μM) [CBP]
150 μM
∼58 μM
n.i.
∼40%
(800 μM)
100 μM
<10%
(10 μM)
33.9 μM
∼40%
(800 μM)
<10% (10 μM)
34.7 μM
>100 μM
∼35 μM
n.i.
< 10% (10 μM) [Rtt109, Sas2, MOZ]
2%
(100 μM)
149 μM
2 μM
60%
(500 μM)
1% (100 μM) [HBO1]; −28% (100
μM) [MORF]
190 μM [Esa1]
0.56 μM [Rtt109]
assay system
ref
AlphaLisa proximity immunoassay
127
radiometric filter-binding
129
radiometric filter-binding
131
radiometric filter-binding
radiometric filter-binding
time-resolved fluorescence
immunosorbent
time-resolved fluorescence
immunosorbent
time-resolved fluorescence
immunosorbent
time-resolved fluorescence
immunosorbent
immunosorbent ELISA-like
132
132
136
140
radiometric filter-binding
142
radiometric gel
immunosorbent ELISA-like
radiometric gel
144
114
145
colorimetric CoA-scavenging
colorimetric CoA-scavenging/
radiometric filter-binding
radiometric filter-binding
radiometric filter-binding
immunosorbent gel
112
148
149
150
151
colorimetric CoA-scavenging
51
Journal of Medicinal Chemistry
Table 2. continued
137
136
137
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inhibitory potency superior to 4 in PCAF inhibition.112
Interestingly, in a subsequent publication, compound 4.1 was
identified as an activator of PCAF with no effect on p300 and
inhibitory activity on Tip60.108 The activation of KAT enzymes
by small molecules is consistent with observations of other
groups. In an inhibitor screen of substituted benzamide
analogues of 4, derivative 4.2 (CTPB) promoted activation of
p300 but not of PCAF and increased p300-dependent
transcription activation.107 An interesting attempt was followed
by Chatterjee et al., which included binding of the small
molecule p300/CBP activator 4.3 (TTK21) to glucose-based
carbon nanospheres.113 The resulting particles readily penetrated the cell membrane to increase histone acetylation
without causing apparent toxicity. Treatment with 4.3-loaded
nanospheres was further correlated with beneficial neurologic
effects in a mouse xenograft model. Sbardella, Mai, and
colleagues published the long chain alkylidenmalonate 4.4
(LoCAM) as a selective activator of PCAF while inhibiting
p300/CBP in a comparable degree to the parent structure 4.114
Structure−activity relationship studies on the LoCAM scaffold
revealed that the replacement of one or both of the ester
moieties with keto- or carboxylic acid groups greatly alters the
modulation profile of the resulting analogues, ranging from
selective activation to unselective inhibition. In terms of the
aliphatic chain, it was shown that the introduction of a
heteroatom is detrimental for binding efficiency and variations
in alkyl chain length result in abrogated modulatory activity.115
The precise underlying mechanism of this activator/inhibitor
ambivalence is still under investigation. Similar to compound 4,
disruption of NF-κB signaling due to repression of KAT activity
was demonstrated for some polyphenols like 5 (epigallocatechin-3-gallate (EGCG)).116 However, these compounds
interact with a wide range of other protein targets and their
structural optimization to achieve selectivity seems to be
challenging.117
Compound 6 (curcumin) is a major component of Curcuma
longa rhizome that is commonly used in Indian and Chinese
traditional medicine.118 The compound was reported in 2004 as
a p300 inhibitor (IC50 25 μM) with no effect on PCAF.
Treatment with 6 represses p300-dependent H3, H4, and p53
acetylation in different cell lines. Kinetic studies revealed a
covalent mode of action at a binding site apart from the
substrate and cofactor-binding pocket. The double bonds in the
cinnamoyl structure serve potentially as Michael reaction
acceptors, and their presence is crucial for binding with
p300.119 Although certain selectivity between different KAT
enzymes was demonstrated, the compounds’ inhibitory activity
is rather promiscuous as it also inhibits other epigenetic targets
(e.g., KDACs, DNMT1, LSD1) as well as a multitude of
nonepigenetic related proteins.120 Still, 6 is under clinical
investigation for several indications. Open-chain and cyclic
cinnamoyl analogues (6.1−6.2) have been shown to inhibit
p300 activity with similar potency as the lead structure.121 The
sodium salt of the hydrazinocurcumin 6.3 (CTK7A) is more
water-soluble while maintaining inhibitory potency.122 It should
be noted that, like the parent structure, the described analogues
interact with multiple target proteins aside from p300.117 Such
promiscuous effects generally complicate the correlation of in
vitro with in vivo observations. In addition, curcumin is known
to be a membrane disruptor and therefore it is likely that some
of its activities could be attributed to nondrug-like modes of
action.123
complex handling and elaborate production. Bandyopadhyay et
al. fused CoA to the polyamine spermidine to generate
compound 3 (Spd(N1)-CoA), which is internalized into cells
via polyamine transporter uptake.105,106 They further truncated
the CoA moiety to the cysteamine-β-alanine core structure to
achieve structure 3.1 and reported cellular activity comparable
to 3. 105 Both polyamine conjugates impeded histone
acetylation-dependent repair and synthesis of DNA and
consequently led to radio- and chemosensitization.
Natural Products and Synthetic Analogues and
Derivatives. Screening of plant or microbial extracts has
proven to be one of the most successful strategies in the
discovery of KAT modulators. Several structures have been
identified comprising micromolar activity (Figures 5 and 6 and
Table 2). Common structural scaffolds of natural compounds,
such as Michael reaction acceptors and polyphenols, are
reflected in their frequent lack of selectivity and hence often
pleiotropic effects in cellular systems. In addition, natural
compounds usually comprise unfavorable physicochemical
properties, which limit their further development. Synthetic
and semisynthetic approaches have been carried out in order to
determine structure−activity relationships and to optimize
compound properties. Interestingly, in the course of biological
evaluation, alongside with KAT inhibitors, compounds with
enzyme activating capacity and mixed activities have been
found. In this way, natural compounds are useful templates for
further development into modulators of KAT activity, yet more
druglike structures are still desirable.
The natural product 4 (anacardic acid), rich in the liquid of
cashew nut shells, emerged from a screening of plant extracts
with anticancer activity.107 The substance was described in
2003 as a nonselective, noncompetitive inhibitor of p300/CBP
and PCAF, but following studies also reported activity in Tip60
inhibition under similar experimental conditions.108 The
inhibitory potency of 4 varies between different studies and
IC50 values between 5 μM and 1000 μM were obtained for
p300 inhibition, depending on assay conditions and enzyme
source. On the cellular level, repression of the NF-κB signaling
pathway by KAT-dependent acetylation of the p65 subunit has
been found. However, the application of compound 4 in
numerous pharmacological studies is attributed to its
pleiotropic affinity that affects multiple enzyme targets.109 A
limiting factor for further development of this natural product
as a therapeutic tool is its unfavorable physicochemical
properties, especially its high lipophilicity. The 6-alkyl salicylic
acid structure has extensively been mined in order to generate
compounds with increased solubility, cell permeability, and
inhibitory efficacy. Our group probed a set of phenoxyacetic
acid analogues (structures not shown) for their inhibitory
capacity against KAT activity in nuclear extracts. We
demonstrated that the position and length of the alkyl chain
are pivotal for enzyme inhibition and that substitution of the
phenolic hydroxyl group is well tolerated.110 Deduced from the
co-crystal structure of PCAF with acetyl-CoA, Ghizzoni et al.
proposed a binding model for 4 and synthesized a set of
compounds with variations in the alkyl chain and the salicylic
acid residue. Esterification of the carboxyl group diminished
inhibitory activity, whereas modulation of the alkyl chain or
hydroxylation in C4 position caused a shift of specificity toward
MYST family KATs. This structure−activity relationship is
supported by a recent study on alkyl salicylic acid derivatives in
MOF inhibition, with 4 as a reference inhibitor.111 Among the
compounds tested by Ghizzoni et al., derivative 4.1 showed
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Figure 7. Structures of synthetic KAT inhibitors.
proposed high affinity for the same alternative binging site as
for 7.2. The suggested noncovalent manner of this binding
mode is intriguing, as the benzylidene barbituric acid scaffold is
potentially prone to Michael addition reactions and has been
exploited in targeting enzyme structures apart from p300/
CBP.128
The hydroxynaphthoquinone 9 (plumbagin), isolated from
Plumbago rosea, has been shown to attenuate p300-dependent
acetylation of histones H3, H4, and p53 in HepG2 liver cancer
cells without causing any effect on PCAF activity.129 Structure−
activity studies suggested the hydroxyl group in C5 position to
be pivotal for forming hydrogen-bond interactions with
Lys1358 in the active site of the enzyme. In consequence,
derivatization of the naphthochinonein this position diminishes
the inhibitory effect. Methylation in C3 position abrogated the
thiol reactivity and therefore cytotoxicity of 9 while maintaining
its function as a p300 inhibitor.130 The 3-alkyl dihydroxybenzoquinone 10 (Embelin) is isolated from Embelia ribes and
displays a similar scaffold.131 Compound 10 has been shown to
inhibit KAT activity of recombinant PCAF and to promote
H3K9 hypoacetylation in treated mice. The compound also
attenuated PCAF-mediated MyoD acetylation in HEK239T
cells, which was correlated to a block of differentiation in
C2C12 cells. Chemical variation revealed that the 11-carbon
alkyl chain in structure 10 is crucial for the inhibitory capacity
as an analogue with one carbon less was reported to be
completely inactive.
The polyisoprenylated benzophenone 7 (garcinol) was
isolated from Garcinia indica and identified as a micromolar
inhibitor of p300 (IC50 7 μM) and PCAF (IC50 5 μM) KAT
activity.124 Repression of histone acetylation and induction of
apoptosis were found in human cancer cell lines upon
treatment with this natural product. Isothermal calorimetric
titration data proposed a two centered binding mode with the
catechol hydroxyl groups interacting with the acetyl-CoA
binding pocket, while the isoprenoid moieties are placed into
the substrate binding domain of the enzyme.125 Monomethylation of the intramolecular cyclization product 7.1 (isogarcinol) in C14-position led to derivative 7.2 (LTK-14), which
provides a shifted inhibition pattern toward p300 activity and
an attenuated T-cell cytotoxicity.126 Human HeLa cells that are
treated with 7.1 or one of its analogues develop concentrationdependent histone hypoacetylation and repression of gene
transcription. The binding mode of 7.2 was proposed to be
different from the parent compound, with a single unique
binding side within the enzymes KAT domain.125 Sbardella and
colleagues recently published the benzylidene barbituric acid
derivative 8 (EML425) as a selective and reversible inhibitor of
p300/CBP with an inhibitory potency in the low micromolar
range (IC50 2.9 μM for p300 and 1.1 μM for CBP).127 The
compound resulted from a molecular pruning approach of
structure 7 with isosteric replacement of the benzophenone
core. Compound 8 was found to promote cell cycle arrest in
G0/G1 phase accompanied by H3K9 and H4K5 hypoacetylation in U937 cells. Molecular modeling studies of this derivative
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Perspective
inhibition as novel strategy in the control of schistosomiasis. In
a recent publication, Gajer et al. demonstrated two selected
pyridoisothiazolones (12.2 and 12.3 (PU141)) to trigger
growth inhibition and histone hypoacetylation in multiple
cancer cell lines and to block neuroblastoma cell growth in a
SK-N-SH xenograft model in vivo.139 The compounds were
previously screened against a cysteine protease panel to assess
their off-target selectivity, and no significant in vitro activity on
these enzymes was observed. Thus, the inhibitors do not have a
general reactivity toward all cysteine dependent enyzmes. For
12.2, the authors also reported reduction of histone acetylation
in healthy mice and synergistic effects with the DNAintercalating drug doxorubicin in the xenografts. This is one
of very few examples for the demonstration of hypoacetylation
in vivo after inhibitor treatment.
Yeast phenotypic screenings have yielded quinoline and
hydrazone derivatives with KAT inhibiting activity. Structural
optimization of the quinolone structure resulted in compound
13 (MC1823), which comprises a scaffold similar to that of
4.140 The reduction in cell viability of S. cerevisiae was correlated
to a histone H3 and α-tubulin hypoacetylation as a result of
Gcn5 inhibition. The same effect has been observed for the
hydrazones 14−14.2.141−143 In addition, p300 and PCAF
activities are repressed by 14 (BF1) and 14.2 (CPTH6),
respectively, and both compounds are competent to cause
histone protein hypoacetylation in different human cancer cell
lines.
In 2004, the α-methylene-γ-butyrolactone 15 (MB-3) was
published as an inhibitor of Gcn5, selective over CBP.144 Biel et
al. followed a rational design strategy based on the electrostatic
interaction fields within the active site of Gcn5. The assessed
IC50 value of 100 μM is comparable with the KD value of the
H3 substrate and despite the apparent Michael reaction
acceptor scaffold, the binding mode of MB-3 was reported to
follow a noncovalent fashion.
The pyrazolone-containing inhibitor 16 (C646), was
identified as a potent, selective, and reversible p300/CBP
KAT inhibitor by means of a virtual screening approach.145
Bowers et al. docked a database of ∼500000 commercially
available compounds into the same binding pocket as occupied
by the bisubstrate inhibitor 1 in the p300 KAT enzyme and
selected 194 compounds for biological testing. Three
compounds were found to inhibit p300 KAT activity in the
micromolar and submicromolar range, where 16 showed the
highest inhibitory activity (Ki = 460 nM). The compound was
predicted to be a bisubstrate inhibitor of p300, and the
proposed binding mode shows numerous H-bond and salt
bridge interactions of 16, with the side chains of the binding
pocket similar to those observed with the CoA moiety of the
cocrystallized inhibitor 1. Chemical modifications of functional
groups indicated that the free carboxylic acid, as well as certain
interactions mediated by the nitro group, are essential for
inhibitory activity, although replacement of the nitro group
with more metabolically favorable functionalities resulted in
only minor loss of potency. Further, a reduced derivative
demonstrated that the conjugated pyrazolone structure is
pivotal for binding to the p300 active site, indicating that a
certain level of planarity of the molecule is required for efficient
active-site targeting. However, this structural entity is
potentially prone to nucleophilic attack. Despite it being
shown in the original publication that binding of 16 to p300
happens in a nontime dependent manner and is not abrogated
by DTT or β-mercaptoethanol, the formation of covalent
Two compounds have been identified during a microorganism broth library screen. 11 (NK13650A) and 11.1
(NK13650B) are fungal metabolites of a Penicillium strain with
a peptidic structure that contains a citric acid moiety.132 The
evaluation of their inhibitory capacity revealed high selectivity
for p300 KAT activity over Tip60, and IC50 values were
determined to be 11 and 22 nM, respectively. It was further
demonstrated that these compounds were competent to repress
androgen- and estrogen receptor-dependent activation of gene
transcription and to be cytotoxic to different cancer cell lines.
Owed to their peptidic nature, these compounds suffer from
poor cell permeability and metabolic instability, which requires
structural optimization. Nevertheless, the identification of
secondary metabolites comprising KAT inhibitory activity
supplies a promising strategy in lead structure discovery as
such approaches were successfully applied on other biological
targets, like KDACs.133
Synthetic Compounds. Different approaches, such as
high-throughput-strategies, rational design, and in silico screenings have been applied in order to find new potent small
molecule KAT modulators. Derivatization of initial hits and
investigations on the structure−activity relationships gained
new insights into the characteristics of KAT enzymes. With the
aid of computational methods, it was possible to identify and
develop new compounds with pronounced inhibitory activity
(Figure 7 and Table 2). Only few of these modulators are fully
characterized in vitro and in vivo so far.
The inhibition of p300 and PCAF enzymes in biochemical
and cell-based assays with concomitant repression of growth
and histone acetylation by compounds comprising an
isothiazolone structure (12) was first reported in 2005 by
Aherne and colleagues.134 An irreversible binding mode was
suggested that involves disulfide bond formation between the
isothiazolone sulfur and a cysteine residue in the enzyme.
Consistent with this, addition of DTT to the reaction abolished
inhibitory activity. Because the general reactivity of these
substances is a major drawback, several efforts have been
dedicated to developing derivatives with reduced promiscuity
while maintaining inhibitory potency. Furdas et al. identified
pyridoisothiazolones as novel PCAF inhibitors by applying a
computational screening approach.135 The NCI database was
screened for compounds which contain an isothiazolone or
isothiazolidinone substructure as found in the PCAF inhibitor
12.1.134 A subsequently carried out similarity search retrieved
51 related compounds from commercial databases, which were
docked into the substrate binding site observed in the crystal
structure of PCAF. Only compounds, which showed a reactive
S−N moiety in close proximity to PCAF Cys574 in the docking
results, were considered for further biological testing. By this
means, different pyridoisothiazolones were discovered as novel
KAT inhibitors with low micromolar IC50 values and reduced
general bioreactivity.136 Structure−activity studies revealed a
crucial role of the substituent in 2-position for inhibitory
activity. N-Aryl substituted compounds were shown to cause
pan-KAT inhibition on a series of enzymes (PCAF, Gcn5,
p300, CBP, and MOF), while N-benzyl or N-alkyl substituents
led to defined subtype selectivity patterns.137 The Fantappie
group incubated Schistosoma mansoni parasites with the
compound 12.2 (PU139) and reported impaired promoter
activity of the egg shell protein Smp14, probably evidently as a
result of diminished SmGCN5 and SmCBP1 activity.138 The
repression of Smp14 controlled gene products led to
production of abnormal and defective eggs, implying KAT
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inhibition of enzyme-mediated H3K56 acetylation in presence
of histone chaperone cofactor protein Vps75 or Asf1,
respectively. Compound 21 did not show any apparent effect
on p300 and Gcn5 activity but inhibited Rtt109 potently (IC50
0.56 μM) in a sulfhydryl scavenging assay. Kinetic measurements proposed a tight or irreversible binding mode as
inhibitory activity increased over time and was not diminished
by dialysis of the inhibitor from the reaction mixture. Inhibitors
of the fungal specific acetyltransferase Rtt109 are proposed to
be promising drug candidates against pathogenic fungal species,
such as Candida albicans. The further development of
compound 21 is limited by its inability to induce cellular
effects, presumably due to drug efflux or rapid metabolism.
Structure−activity studies need to be conducted to assess the
overall potential of this scaffold.
Bromodomain Inhibitors. In addition to modulators
targeting the catalytic domain of KATs, a more recent approach
concentrates on the identification and development of small
molecule inhibitors of KAT protein−protein interaction
domains.153,154 One of the most thoroughly investigated
interaction domains is the bromodomain, which recognizes
and binds to acetylated lysine residues. The disruption of
acetylation-dependent protein−protein interactions by small
molecule inhibitors abrogates the assembly of transcriptional
regulator complexes and subsequently represses the phenotypic
consequences of acetylation signaling. The successful implementation of BET bromodomain ligands has evoked a growing
interest in the identification of potent and selective small
molecule inhibitors of non-BET bromodomains, as they are
structural entities of several KATs. Mostly structure-guided
approaches have yielded a set of KAT bromodomain ligands
whose structures are depicted in Figure8.
The N-aryl-propane-1,3-diamine 22 has been identified as an
inhibitor of the PCAF bromodomain.155 Binding of this
bromodomain to the acetylated K50 moiety of the HIV-1-Tat
protein is required to induce transcription of the integrated
HIV-1 provirus. 22 successfully inhibited the transactivation of
the HIV-1 promoter by blocking the PCAF bromodomain in
C1866 cells with an IC 50 value of 0.6 μM. Higher
concentrations of the inhibitor were shown to be cytotoxic,
which is a drawback for further development of this scaffold.
Acetylation of the effector protein p53 at lysine residue 382
facilitates interaction with the CBP bromodomain. Upon
binding, a coactivator complex is formed, which is recruited
to p53 controlled promoter sites. Zhou et al. performed a cellbased compound screen against the p53-dependent expression
of p21 in response to doxorubicin-mediated DNA damage.
Structural optimization of initial hits yielded the azobenzene 23
(ischemin), which was demonstrated to inhibit the p53-CBP
bromodomain interaction with an IC50 value of 5 μM and a 5fold selectivity over other bromodomains (PCAF, BRD4,
BAZ2B).156 Compound 23 was shown to be competent in
protecting rat cardiomyocytes from p53-induced apoptosis in
consequence of doxorubicin treatment.
Rooney et al. employed a fragment-based approach
combined with chemical expansion of the initial hits to develop
a series of dihydroquinoxalinones as the first submicromolar
ligands for the CBP bromodomain. The most potent
compound 24 was shown to bind to the bromodomain via
an induced fit pocket, which is occupied by the tetrahydroquinoline side chain and stabilized by a cation−π interaction
of this residue with R1173 of the protein.157 The KD of 24 was
assessed in an isothermal titration calorimetry assay to be 390
conjugates with a number of different cellular cysteine
containing proteins was observed in a recent publication.146
The large conjugated system in structure 16 causes intrinsic
fluorescence of the compound, which is an obstacle for its use
in fluorescent-based assay methods. Cole and colleagues
circumvented this hurdle by replacing the furan group with a
phenyl ring.147 The resultant derivative was absent of intrinsic
fluorescence while mostly maintaining its inhibitory capacity
(IC50 9 μM (p300)). In melanoma and lung cancer cell lines,
treatment with 16 led to inhibition of cell growth and
concomitant histone H3 and H4 hypoacetylation. Cell cycle
arrest and induction of apoptosis upon administration was also
observed in AML1-ETO positive leukemia cells.148
The small molecule inhibitor 17 (L002) has been reported as
a result of a large high-throughput screening approach of more
than 600000 substances for their cytotoxic activity against the
triple-negative breast cancer cell line MDA-MB-231.149 Radioactive filter binding assays revealed inhibitory activity against
p300 (IC50 128 μM) and GNAT family KATs (IC50 34.7 μM
for PCAF and 33.9 μM for Gcn5) but no inhibition of MYST
family members. The IC50 value of 17 against p300 was
determined to be 1.98 μM in an orthogonal fluorescence assay.
The sulfonyl-coupled iminoquinone structure was placed in
silico into the acetyl-CoA domain of the p300 enzyme. In
cellular experiments, the compound has been found to promote
histone and p53 hypoacetylation and to suppress STAT3
activation in lymphoma, leukemia, and breast cancer cell lines.
Reduction of tumor growth and decreased histone acetylation
were correlated to in vivo administration in a MDA-MB-468
xenograft model.
Different scaffolds have been identified and tested in order to
find inhibitors for the Tip60 histone acetyltransferase as a
potential therapeutic strategy in correlated malignancies. The
Zheng group published the phthalimide analogue 18 in 2011 as
the result of a virtual screening campaign based on the Tip60
yeast homologue Esa1 crystal structure.150 KAT inhibition
efficacy was assessed in a radiometric in vitro assay for different
KAT family members (Tip60, Esa1, p300, PCAF) and IC50
values between 100 and 190 μM were determined, stating an
unselective inhibitory activity. Computational docking and
kinetic studies suggested that 18 targets the acetyl-CoA binding
site of Tip60. One year later, Coffey et al. performed a highthroughput screening for Tip60 inhibitors of ∼80000
substances. Structure 19 (NU9056), a derivative of an initial
hit, bearing an isothiazole scaffold, was demonstrated to
specifically inhibit Tip60 activity (IC50 2 μM).151 It was further
shown that the derivative blocks acetylation of histone proteins
in a concentration-dependent manner and induces apoptosis via
caspase activation in prostate cancer cell lines. In 2014, 20
(TH1834) was developed during a rational design approach in
accordance with the electrostatic surface potential of a Tip60
active site model.152 Under physiological conditions, the
structure comprises two oppositely charged ends, which were
predicted to interact with amino acid side chains on different
sides of the Tip60 binding pocket. The ethylbenzene side chain
was introduced as an isosteric replacement of acetyl-CoAs’
adenine residue. Throughout the biological evaluation,
compound 20 was tested at high concentration (500 μM),
promoting induction of apoptosis and radiosensitization in
MCF7, DU-145, and PC-3 cancer cell lines.
An inhibitor (21) of the fungal KAT Rtt109 was published in
2013 as the result of a high-throughput screening campaign.51
The authors reported specific and noncompetitive in vitro
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■
DISCUSSION AND CONCLUSIONS
Altogether, epigenetic modifiers have emerged in the last 20
years as one of the most promising class of new targets for a
variety of diseases. The majority of findings points to a pivotal
role in cancer, but also for metabolic diseases, CNS disorders,
and infectious pathologies promising data is available.160 The
evidence for the roles of different KAT enzymes in these
indications was mostly gathered with the aid of molecular
biology methods like gene knockdown or gene knockout. To
distinguish whether the resultant phenotypic changes upon
enzyme depletion can be assigned to the repression of either
the acetyltransferase activity or protein−protein interactions,
small molecule inhibitors are needed that specifically target
either of these features. There is no doubt that new approaches
in molecular biology will help to further elucidate the field of
lysine acetylation to give a more rounded picture of their
specific implication in pathological and physiological processes.161 Among the histone modifiers, inhibitors of histone
deacetylases have gained approval for use in patients and five
drugs are now on the market.162 For some epigenetic
regulators, e.g., the bromodomains, the time span from first
reports as druggable targets163 to first clinical trials was about
four to five years only.164 KATs were among the first epigenetic
modifiers to be discovered,18 yet, strangely, almost 20 years
later, there is still no drug in advanced development. This is
true despite numerous studies showing the involvement of
KATs in disease and rich structural data. Structural reasons for
the rather difficult development of potent and selective
inhibitors are the structurally conserved cofactor binding site,
which makes it difficult to achieve pronounced selectivity for a
specific enzyme subtype and the relatively shallow substrate
binding cleft where the histone substrate is placed.160 Another
problem in the identification of active compounds seems to be
the variation in the different assay formats. Various assay
strategies have been employed in the biochemical characterization of KAT enzymes (Table 2). Radiometric measurements
have emerged as one of the standard procedures, allowing
robust and sensitive readouts, but their application requires
special hazard precautions and waste disposal. Colorimetric
assays are susceptible for quenching effects and interference of
the tested compound with the assay components. The need for
time-consuming washing steps is the biggest disadvantage of
heterogeneous immunosorbent methods, which complicates
their application in high-throughput approaches. In comparison, the data generated by different biochemical assays for
published compounds is very inconsistent. For example, for
compound 4, the measured potencies in p300 inhibition vary
between IC50 values of 8.5 and >1000 μM in three radiometric
filter-binding assays. The huge discrepancy may be explained by
differences in enzyme source, type of substrate, substrate and
cofactor concentration, buffer composition, and incubation
time. Therefore, direct comparison of IC50 values, even for
similar assay types, can be misleading. Standardized assay
protocols and reliable reference compounds would be valuable
tools to achieve comparability of biochemical data. The
implementation of new assay methods, like thermal shift165
or microscale thermophoresis,166 could prove beneficial for the
identification and characterization of new substances and
detection of promiscuous inhibition mechanisms. To avoid
misinterpretation of compound hits from initial screens, it is
important to confirm such observations in orthogonal assays
that rely on a different type of readout. In addition, a panel of
Figure 8. Structures of PCAF and CBP/p300 bromodomain
inhibitors.
nM, and the selectivity for the CBP bromodomain over BRD4
(KD 1.4 μM) was stated to be modest.
Mining of the 3,5-dimethylisoxazole scaffold resulted in the
identification of 25 (SGC−CBP30).158 The aryl substituent of
the isoxazole core forms a cation−π interaction with R1173 in
the bromodomain binding site. The compounds binds to the
CBP bromodomain with a KD value of 21 nM, and the achieved
inhibition is highly selective over BRD4. In a luciferase-based
reporter assay, the authors observed diminished expression of
CBP-dependent p53 downstream genes as a result of SGC−
CBP30 incubation.
SGC and GSK developed the CBP bromodomain inhibitor
26 (I-CBP112) on the basis of a benzoxazepine scaffold.159 The
acyl group in this structure mimics the acetyl residue of the
native recognition motive, thereby forming hydrogen bonds to
the binding site, while the aryl substituent interacts with the
arginine moiety in position 1173 of the CBP bromodomain.
The KD values of 26 for binding to p300 and CBP
bromodomains were determined to be 167 and 151 nM,
respectively, with selectivity over a number of other
bromodomains (e.g., BRD2, BRD4, PCAF, TIF1α). The
compound proved cellular activity in a FRAP assay on U2OS
cells. Further studies revealed that 26 is capable to impair p53
interaction, which results in reduced p21 expression. Treatment
of leukemia cell lines with the bromodomain inhibitor led to
cell cycle arrest in G1-phase and morphological differentiation.
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treatment of mantle cell lymphoma and is pursued with high
intensity. Thus, starting out from covalent modifiers of
cysteines in KATs, affinity and selectivity could be built in
subsequently, resulting potentially in highly potent and
selective KAT inhibitors. For inhibitors that rely on the
covalent targeting of cysteine residues, as it is the case with
compounds 12.2 and 12.3, further structural development of
these lead structures is needed to direct their general reactivity
further toward specific targets only. Because even for well
characterized compounds, like 16, covalent interaction with offtarget protein structures has been demonstrated. Hence, such
molecules are placed at the intersection of PAINS and covalent
modifiers. Therefore, at the moment, maybe not a single KAT
inhibitor does satisfy the rigid rules demanded for high quality
chemical probes.169 As most of the known KAT modulators
were identified due to screenings of large compound libraries or
in the course of chemical optimization or derivatization of such
initial hits, it becomes more and more evident that this might
not be the ideal way to find highly potent and specific ligands
for KAT enzymes. Approaches like rational-design, fragmentbased design, or virtual ligand screening could provide better
suitable methods to deal with the KAT specific challenges
concerning druggability. On the other hand, for therapeutic
endeavors compounds with a more pleiotropic profile may still
be useful, as a drug needs to be safe and effective and
knowledge on the mode of action is not a prerequisite for
successful treatment. The problem is of course that
optimization toward an assumed target may then not be
successful in terms of efficacy and needs to be performed with
phenotypic cellular and animal models. A big problem is the
widespread use of published KAT inhibitors in mechanistic
studies with a danger of overinterpretation of the link of histone
acetyltransferase inhibition and the studied mechanism in
question, but on the other hand, it may still be informative to
use these inhibitors to potentially gain insight in KAT biology.
Therefore, for both drug discovery but especially chemical
epigenetics, there is clearly still a big demand for high quality
KAT inhibitors. Many points need to be addressed such as the
relevance of nonhistone acetylation,170−172 the question of the
relevance of acyl groups other than acetyl,173 or the role of
nonenzymatic versus enzymatic acetylation.174,175 The big
question is whether after 20 years a new way can be discovered
to reach that goal. As bromodomains have emerged as
druggable and promising targets, one strategy is to target
those domains that are part of KATs rather than the enzymatic
activity. As there is no crystal structure of any KAT catalytic
domain in context with a small molecule inhibitor aside from 1,
more structural data of KAT enzymes in complex with small
molecule ligands and in context of their native multidomain
protein complexes is needed to guide further development.
Combined with new approaches in modulator discovery and
optimization, computational methods using such information
will largely improve the chances of developing potent and
selective modulators of KAT enzymes. These will be highly
useful as chemical probes and will show whether we can KATch
up in terms of drug development with this difficult, yet still
promising class of epigenetic targets.
counter screens against possible off-targets should be carried
out to ensure target selectivity. The field of modulator
development is further complicated by the fact that activity
and substrate specificity of enzymes in biochemical assays can
significantly differ from a cellular environment. This holds
especially true for KATs as they natively occur in multiprotein
complexes. Therefore, profound evaluation of cellular activity is
needed to complement biochemical data.
A number of inhibitors have been discovered by various
approaches but many of them suffer from several drawbacks,
such as low in vivo potency, metabolic instability, or poor
selectivity (Table 2). Among the different subtypes of KAT
enzymes, p300/CBP seems to be the preferred target of most
modulators. This is presumably due to the structural features of
these isoenzymes that distinguish them from the other families.
Although bisubstrate inhibitors of KAT activity excel in potency
and selectivity, their further development into more druglike
small molecules is largely prevented by their complex structure.
The simple rationale of covalently linking ligands of both the
cofactor and the substrate binding site is contradicted in terms
of selectivity by the high structural conservation of KAT
isoforms in these regions. The incorporation of large peptidic
groups into the inhibitor structure is needed to achieve subtype
selectivity, and the resulting compounds suffer from poor in
vivo efficacy. However, analogues and derivatives of 1 might
serve as a starting point for fragment-based approaches in
future inhibitor discovery. Natural products have been
investigated deeply as a class of KAT modulators. Extensive
structure−activity studies have been carried out to assess their
full potential, and a multifold of derivatives have been generated
with the aim to improve physicochemical and modulatory
properties. A lot of them feature structural motifs that are
suspicious in terms of promiscuous behavior, such as Michael
acceptors, phenolic or quinone moieties.167 While for some of
them selectivity and target engagement among the KATs has
been shown, clearly data for the analysis on other targets is
missing for most of these compounds. Or, like in the case of
curcumin, inhibition of many other targets has been shown
already. Despite large efforts that have been put into the
characterization of natural KAT modulators and the development of improved derivatives, no compound with pronounced
potency and especially high selectivity, for KAT enzymes and
distinct KAT isoforms, has been obtained. The identification of
structural analogues of known inhibitors with reversed
inhibitory potency, actually increasing enzyme activity, as well
as the isolation of highly potent peptidic natural products, are
interesting findings. Crystal structures of these modulators in
complex with the KAT enzyme would provide valuable
information for further development. The class of synthetic
compounds comprises a structurally heterogeneous set of
molecules, which were identified by different approaches.
Although some of these compounds were shown to be potent
KAT inhibitors, only few of them feature subtype selectivity
and have been characterized profoundly in a cellular setting.
Screening and designing of small molecules with the aid of
computational methods has proven to be useful in the targeting
of specific interaction fields. In this way, it becomes much more
likely to achieve subtype selectivity, like in the case of
compound 16. Another possibility for direct enzyme inhibition
is targeting cysteines involved in the catalysis or present at the
active site of the enzyme. The use of covalent inhibitors has
emerged as a highly promising strategy in kinase inhibitors that
has already culminated in the approval of ibrutinib168 for the
■
AUTHOR INFORMATION
Corresponding Author
* Phone: +497612034896. Fax: +497612036321. E-mail:
manfred.jung@pharmazie.uni-freiburg.de.
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specific lethal; PTM, posttranslational modification; vdW, vander-Waals
Author Contributions
The manuscript was written through contributions of all
authors. All authors have given approval to the final version of
the manuscript.
■
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Notes
The authors declare no competing financial interest.
Biographies
Roman P. Simon holds a diploma degree in Pharmaceutical Sciences
at the Institute of Pharmaceutical Sciences of the Albert-Ludwigs
University Freiburg and works as a Ph.D. candidate in the group of
Prof. M. Jung. He studied Pharmacy (state examination) at the
University of Freiburg from 2008 to 2013. After a six months research
stay in the group of Prof. Ganesan at the University of East Anglia in
2014, he returned to Freiburg. Since the beginning of 2015, he is a
doctoral student, with his research focusing on development and
characterization of novel small molecule KAT inhibitors.
Dina Robaa studied Pharmacy at the University of Alexandria in
Egypt. She obtained her Ph.D. in Pharmaceutical Chemistry at the
University of Jena in the group of Jochen Lehmann. Since 2011, she
has been working as a postdoctoral fellow in the research group of
Wolfgang Sippl. Her research focuses on structure-based drug design
of several epigenetic modulators.
Zayan Alhalabi studied Pharmacy at the University of Damascus in
Syria. She finished her diploma in Pharmaceutical Science. She
obtained her master’s degree in Pharmaceutical Chemistry at the
University of Damascus 2012. In 2013, she started her Ph.D. at the
Department of Medicinal Chemistry in the research group of Prof.
Wolfgang Sippl. Her research focuses on structure-based drug design
for epigenetic targets (Sirtuins).
Wolfgang Sippl is Professor for Medicinal Chemistry and Director of
the Institute of Pharmacy at the Martin-Luther-University of HalleWittenberg (Germany). He obtained a Ph.D. in Pharmaceutical
Chemistry at the University of Düsseldorf in the group of Hans-Dieter
Höltje and was a postdoctoral fellow at the Université Louis-Pasteur in
Strasbourg (France) where he worked with Camille G. Wermuth.
Since 2003, he is Full Professor at the Institute of Pharmacy in Halle.
His main interests are focussed on computational chemistry and
structure-based drug design of novel epigenetic modulators for the
therapy of cancer and parasitic diseases.
Manfred Jung did his Ph.D. with W. Hanefeld on the synthesis of
aromatic retinoids at the University of Marburg. In 1993/94, he did a
postdoc with T. Durst (University of Ottawa, Canada). From 1994 to
2003 he was a group leader at the University of Münster and obtained
his habilitation in Pharmaceutical Chemistry (2000). Since 2003, he is
a Professor of Pharmaceutical Chemistry at the University of Freiburg.
In 2010, he declined an offer for a full professorship to the University
of Mainz and is a Full Professor in Freiburg since 2011. The topic of
his research is Chemical Epigenetics. His group is working on inhibitor
synthesis, assay development, and screening for inhibitors of reversible
histone acetylation and methylation but also histone readers.
ACKNOWLEDGMENTS
R.P.S and M.J. thank the Deutsche Forschungsgemeinschaft for
funding (Ju 295/9-2 within SPP1463).
■
ABBREVIATIONS USED
BRD, bromodomain; H3K9, histone H3 lysine residue 9; HAT,
histone acetyltransferase; KAT, lysine acetyltransferase; KD,
dissociation constant; KDAC, lysine desacetylase; MSL, male
■
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