charges and, generally, smaller hydrophobic surface, as well as being more sensitive
to proteolytic degradation. Amino acid and peptoid derivatives of SAHA have been
studied as small molecule inhibitors with significant improvements in in vitro and
cancer antiproliferase activities [89–93]. However, linear peptides with a length of
three or more amino acids have found more powerful application as substrate mimics
for the study of HDAC structure and function.
As mentioned, HDAC1–HDAC3 are recruited to multicomponent nuclear complexes, which enhance and direct their deacetylase activity toward the desired target
[8]. HDAC3, in particular, is part of the SMRT/NCoR co-repressor complex
involved in repression of gene expression. This interaction has been investigated
by the research group of Schwabe, who solved the X-ray crystal structure of HDAC3
in complex with a domain of the SMRT protein. This crystal structure included a
molecule of inositol tetraphosphate (Ins(1,4,5,6)P 4 ) bound to the interface between
the two proteins. Further investigation revealed that interaction with inositol
tetraphosphate enhanced HDAC3 deacetylase activity beyond sole activation by
SMRT [94]. A similar binding site, this time occupied by sulfate ions from the
buffer, was later observed in a co-crystal structure of HDAC1:MTA1 from the
NuRD complex. These observations raised the hypothesis that inositol phosphates
could play an overall regulatory role in HDAC function and assembly to
multiprotein complexes [95]. In this regard, a revealing crystal structure was
reported by the same group in 2016, in which inositol hexaphosphate (InsP 6 ) was
accommodated between HDAC1 and MTA1, in clear analogy to the HDAC3:SMRT
interface already reported [62]. Subsequent experiments described allosteric activation of the deacetylase activity mediated by different inositol phosphates, together
with a conformational cross talk between the HDAC active site and the proteinprotein interface where these molecules bind.
This latter mentioned crystal structure presented an additional feature, particularly interesting for the present review, since a hydroxamic acid-containing peptide
inhibitor was also bound in the catalytic pocket of HDAC1. The design of this
inhibitor was inspired by the tail of histone 4 (H4), where a surrogate of the HDAC1
targeted K16 ac residue was replaced by Asuha in order to ensure binding to the
active site and avoid catalytic turnover (Fig. 9a). In the crystal structure, the
hydroxamic acid moiety is chelating to Zn
2+ in analogy to previous inhibitorenzyme structures. Moreover, residues 14–18 of H4 were resolved for this histone
tail analogue. The binding pose of the peptide reveals possible interactions that
HDAC1 establishes with the histone and, at the same time, provides important
insight into the conformational changes that the enzyme undergo upon substrate
binding (such as for residue D99 at the rim of the protein). These are key features for
understanding differences among the HDAC isotypes, although investigation with
several substrates would be required in order to map more possible interactions
around the active site rim. It is also notable that this peptide ligand adopts a quasicyclic conformation upon binding, which could inspire future macrocyclic inhibitor
design (Fig. 9b). In terms of inhibitory activity, the IC 50 of the peptide was 336 nM
against HDAC1:MTA1 in in vitro end-point assays [62].
Hydroxamic Acid-Containing Peptides in the Study of Histone Deacetylases
45
to proteolytic degradation. Amino acid and peptoid derivatives of SAHA have been
studied as small molecule inhibitors with significant improvements in in vitro and
cancer antiproliferase activities [89–93]. However, linear peptides with a length of
three or more amino acids have found more powerful application as substrate mimics
for the study of HDAC structure and function.
As mentioned, HDAC1–HDAC3 are recruited to multicomponent nuclear complexes, which enhance and direct their deacetylase activity toward the desired target
[8]. HDAC3, in particular, is part of the SMRT/NCoR co-repressor complex
involved in repression of gene expression. This interaction has been investigated
by the research group of Schwabe, who solved the X-ray crystal structure of HDAC3
in complex with a domain of the SMRT protein. This crystal structure included a
molecule of inositol tetraphosphate (Ins(1,4,5,6)P 4 ) bound to the interface between
the two proteins. Further investigation revealed that interaction with inositol
tetraphosphate enhanced HDAC3 deacetylase activity beyond sole activation by
SMRT [94]. A similar binding site, this time occupied by sulfate ions from the
buffer, was later observed in a co-crystal structure of HDAC1:MTA1 from the
NuRD complex. These observations raised the hypothesis that inositol phosphates
could play an overall regulatory role in HDAC function and assembly to
multiprotein complexes [95]. In this regard, a revealing crystal structure was
reported by the same group in 2016, in which inositol hexaphosphate (InsP 6 ) was
accommodated between HDAC1 and MTA1, in clear analogy to the HDAC3:SMRT
interface already reported [62]. Subsequent experiments described allosteric activation of the deacetylase activity mediated by different inositol phosphates, together
with a conformational cross talk between the HDAC active site and the proteinprotein interface where these molecules bind.
This latter mentioned crystal structure presented an additional feature, particularly interesting for the present review, since a hydroxamic acid-containing peptide
inhibitor was also bound in the catalytic pocket of HDAC1. The design of this
inhibitor was inspired by the tail of histone 4 (H4), where a surrogate of the HDAC1
targeted K16 ac residue was replaced by Asuha in order to ensure binding to the
active site and avoid catalytic turnover (Fig. 9a). In the crystal structure, the
hydroxamic acid moiety is chelating to Zn
2+ in analogy to previous inhibitorenzyme structures. Moreover, residues 14–18 of H4 were resolved for this histone
tail analogue. The binding pose of the peptide reveals possible interactions that
HDAC1 establishes with the histone and, at the same time, provides important
insight into the conformational changes that the enzyme undergo upon substrate
binding (such as for residue D99 at the rim of the protein). These are key features for
understanding differences among the HDAC isotypes, although investigation with
several substrates would be required in order to map more possible interactions
around the active site rim. It is also notable that this peptide ligand adopts a quasicyclic conformation upon binding, which could inspire future macrocyclic inhibitor
design (Fig. 9b). In terms of inhibitory activity, the IC 50 of the peptide was 336 nM
against HDAC1:MTA1 in in vitro end-point assays [62].
Hydroxamic Acid-Containing Peptides in the Study of Histone Deacetylases
45