1 Introduction
Epigenetic regulation of gene transcription is a highly orchestrated process between
proteins engaging chromatin through enzymatic modification and effector domain
binding. The result of such enzymatic and binding events is the manipulation of
chromatin structure and recruitment of transcriptional complexes leading to either
activated or repressed genes. Understanding the mechanisms which govern the
transcriptional processes leading to heritable phenotypes that are not simply dictated
by the genetic code remains at the heart of the field of epigenetics.
The nucleosome, the fundamental building block of eukaryotic chromatin, is
composed of ~147 base pairs of DNA wrapped around an octameric bundle of
four conserved histone proteins: H2A, H2B, H3, and H4. It is the exposed unstructured termini of these histones, their core, and the DNA itself, which get
posttranslationally modified through a dynamic process to form a complex code
for determining the transcriptional program of the cell. The molecular mechanisms
of the multidomain proteins which read, write, and erase this code in a dynamic
fashion underlie what Allis and Strahl proposed as the “histone code” hypothesis [1].
Histone acetylation of N-ε-lysine side chains described in this chapter is one of
the many posttranslational chromatin modifications which include serine/threonine/
tyrosine phosphorylation, cytosine/lysine/arginine methylation, citrullination,
ubiquitination, and ADP-ribosylation [2]. Histone acetylation was first identified
by Phillips in 1963 [3] after isolation of calf thymus histones [4] and later described
by Allfrey et al. in 1964 to correlate with active transcription states leading to loosely
packed chromatin, called euchromatin [5]. Installation of lysine acetyl groups is
carried out by lysine acetyl transferases (KATS or HATS in the case of histone
acetyltransferases), belonging to a general class of epigenetic enzymes, colloquially
termed “writers.” Removal of acetylation, which can return chromatin to a condensed state, heterochromatin, is carried out by histone deacetylase (HDACs) or
more generally “erasers.” Finally, the effector or “reader” domains which bind to the
N-ε-acetyl groups and more broadly lysine acyl groups are bromodomains [6]. However, since the early discovery of bromodomain histone interactions, an additional
effector domain, the YEATS domain [7], has also been shown to bind to lysine acyl
groups but will not be discussed further in this chapter.
Whereas epigenetics describes the role of chromatin and chromatin-associated
proteins, the field of chemical epigenetics seeks to apply chemical tools to manipulate epigenetic processes to further understand the biology or to treat disease
[8]. Since the first submicromolar inhibitors of a bromodomain were disclosed in
the primary literature in 2010 for the bromodomain and extraterminal (BET) family
of bromodomains [9, 10], there have been tremendous interest in the development of
highly selective bromodomain chemical probes from the academic community and
pharmaceutical interest for developing clinical drug candidates to treat disease. As of
2018, 26 clinical trials have been carried out or are ongoing for bromodomains, but it
remains to be validated if bromodomain inhibition will be successful as an effective
epigenetic therapy for controlling disease.
Applied Biophysics for Bromodomain Drug Discovery
289
Epigenetic regulation of gene transcription is a highly orchestrated process between
proteins engaging chromatin through enzymatic modification and effector domain
binding. The result of such enzymatic and binding events is the manipulation of
chromatin structure and recruitment of transcriptional complexes leading to either
activated or repressed genes. Understanding the mechanisms which govern the
transcriptional processes leading to heritable phenotypes that are not simply dictated
by the genetic code remains at the heart of the field of epigenetics.
The nucleosome, the fundamental building block of eukaryotic chromatin, is
composed of ~147 base pairs of DNA wrapped around an octameric bundle of
four conserved histone proteins: H2A, H2B, H3, and H4. It is the exposed unstructured termini of these histones, their core, and the DNA itself, which get
posttranslationally modified through a dynamic process to form a complex code
for determining the transcriptional program of the cell. The molecular mechanisms
of the multidomain proteins which read, write, and erase this code in a dynamic
fashion underlie what Allis and Strahl proposed as the “histone code” hypothesis [1].
Histone acetylation of N-ε-lysine side chains described in this chapter is one of
the many posttranslational chromatin modifications which include serine/threonine/
tyrosine phosphorylation, cytosine/lysine/arginine methylation, citrullination,
ubiquitination, and ADP-ribosylation [2]. Histone acetylation was first identified
by Phillips in 1963 [3] after isolation of calf thymus histones [4] and later described
by Allfrey et al. in 1964 to correlate with active transcription states leading to loosely
packed chromatin, called euchromatin [5]. Installation of lysine acetyl groups is
carried out by lysine acetyl transferases (KATS or HATS in the case of histone
acetyltransferases), belonging to a general class of epigenetic enzymes, colloquially
termed “writers.” Removal of acetylation, which can return chromatin to a condensed state, heterochromatin, is carried out by histone deacetylase (HDACs) or
more generally “erasers.” Finally, the effector or “reader” domains which bind to the
N-ε-acetyl groups and more broadly lysine acyl groups are bromodomains [6]. However, since the early discovery of bromodomain histone interactions, an additional
effector domain, the YEATS domain [7], has also been shown to bind to lysine acyl
groups but will not be discussed further in this chapter.
Whereas epigenetics describes the role of chromatin and chromatin-associated
proteins, the field of chemical epigenetics seeks to apply chemical tools to manipulate epigenetic processes to further understand the biology or to treat disease
[8]. Since the first submicromolar inhibitors of a bromodomain were disclosed in
the primary literature in 2010 for the bromodomain and extraterminal (BET) family
of bromodomains [9, 10], there have been tremendous interest in the development of
highly selective bromodomain chemical probes from the academic community and
pharmaceutical interest for developing clinical drug candidates to treat disease. As of
2018, 26 clinical trials have been carried out or are ongoing for bromodomains, but it
remains to be validated if bromodomain inhibition will be successful as an effective
epigenetic therapy for controlling disease.
Applied Biophysics for Bromodomain Drug Discovery
289