several HDAC inhibitors are currently used in the clinic as treatment of certain
cancers [9]. Among the 11 HDAC isotypes, some exhibit distinct and independent
functions, whereas others present overlapping activities and share interacting protein
partners [8]. Development of probes for the study of HDACs remains a challenge,
and especially isotype selectivity has been found highly elusive. In this regard,
peptides bearing a hydroxamic acid functionality are promising chemical tools, as
the peptide scaffold is able to interact with a large surface area where the structural
differences between isotypes are more substantial. Additionally, the Zn
2+ -binding
group allows a tight binding to the active site of the enzyme.
Cyclic peptide inhibitors containing the hydroxamic acid functionality have
achieved sub-nanomolar potencies against HDACs and exhibited efficacy against
cancer cell growth in culture [70, 84]. Recent studies have also revealed that these
molecules may exhibit slow, tight-binding kinetics, which is dependent on the
HDAC isotype targeted [17, 49]. This is interesting for investigating the biology
of the enzymatic activity of HDACs and for better understanding the effects of
drugs. However, the hydroxamic acid-containing cyclic peptides tested to date are in
general broadly cytotoxic, which limits their potential as clinical candidates. In this
regard, the incorporation of less potent Zn
2+ -binding groups could lead to a better
therapeutic outcome. In terms of chemical space, there is still room for investigating
larger cycles that could target isotype-specific interactions, since the tetrapeptide
scaffold seems to be highly optimized for interacting with the conserved HDAC
surface and therefore inhibit several enzymes at a time. Macrocycles covering a
larger area at the protein surface surrounding the active site or targeting proteinprotein interaction regions can potentially avoid this pharmacophore and interact
with other non-conserved residues.
Peptides can help generate biologically relevant information about which substrates each HDAC recognizes and how their interactome affects this. For this
purpose, the ability of the unnatural amino acid Asuha to bind to the HDAC active
site has been exploited, since it mimics the interaction between the enzyme and its
native substrate Kac. Linear peptides that incorporate Asuha have been shown to
bind to HDACs in a sequence-dependent manner that can, potentially, be indicative
of substrate preference. In addition, it appears that the interacting partners of the
enzyme can affect such preferences, although this has not yet been studied in depth
[64]. Thus far, Asuha has been incorporated in rather short peptides and only in two
cases into nucleosomes. Therefore, it could be of potential interest to extend these
studies to a larger variety of proteins and to be able to capture transient HDACsubstrate interactions in a biological context. Such information would be highly
valuable for understanding the role of each HDAC isotype and improving future
drug development.
Compliance with Ethical Standards
Funding: This work was supported by a Ph.D. fellowship funded by the University of Copenhagen.
Conflict of Interest: The authors declare no conflict of interest.
48
C. Moreno-Yruela and C. A. Olsen
cancers [9]. Among the 11 HDAC isotypes, some exhibit distinct and independent
functions, whereas others present overlapping activities and share interacting protein
partners [8]. Development of probes for the study of HDACs remains a challenge,
and especially isotype selectivity has been found highly elusive. In this regard,
peptides bearing a hydroxamic acid functionality are promising chemical tools, as
the peptide scaffold is able to interact with a large surface area where the structural
differences between isotypes are more substantial. Additionally, the Zn
2+ -binding
group allows a tight binding to the active site of the enzyme.
Cyclic peptide inhibitors containing the hydroxamic acid functionality have
achieved sub-nanomolar potencies against HDACs and exhibited efficacy against
cancer cell growth in culture [70, 84]. Recent studies have also revealed that these
molecules may exhibit slow, tight-binding kinetics, which is dependent on the
HDAC isotype targeted [17, 49]. This is interesting for investigating the biology
of the enzymatic activity of HDACs and for better understanding the effects of
drugs. However, the hydroxamic acid-containing cyclic peptides tested to date are in
general broadly cytotoxic, which limits their potential as clinical candidates. In this
regard, the incorporation of less potent Zn
2+ -binding groups could lead to a better
therapeutic outcome. In terms of chemical space, there is still room for investigating
larger cycles that could target isotype-specific interactions, since the tetrapeptide
scaffold seems to be highly optimized for interacting with the conserved HDAC
surface and therefore inhibit several enzymes at a time. Macrocycles covering a
larger area at the protein surface surrounding the active site or targeting proteinprotein interaction regions can potentially avoid this pharmacophore and interact
with other non-conserved residues.
Peptides can help generate biologically relevant information about which substrates each HDAC recognizes and how their interactome affects this. For this
purpose, the ability of the unnatural amino acid Asuha to bind to the HDAC active
site has been exploited, since it mimics the interaction between the enzyme and its
native substrate Kac. Linear peptides that incorporate Asuha have been shown to
bind to HDACs in a sequence-dependent manner that can, potentially, be indicative
of substrate preference. In addition, it appears that the interacting partners of the
enzyme can affect such preferences, although this has not yet been studied in depth
[64]. Thus far, Asuha has been incorporated in rather short peptides and only in two
cases into nucleosomes. Therefore, it could be of potential interest to extend these
studies to a larger variety of proteins and to be able to capture transient HDACsubstrate interactions in a biological context. Such information would be highly
valuable for understanding the role of each HDAC isotype and improving future
drug development.
Compliance with Ethical Standards
Funding: This work was supported by a Ph.D. fellowship funded by the University of Copenhagen.
Conflict of Interest: The authors declare no conflict of interest.
48
C. Moreno-Yruela and C. A. Olsen