The Skaggs Institute
for Chemical Biology
Design of Targeted Anticancer Agents and Synthetic Aminoacyl Transfer Catalysts
M.R. Ghadiri, J.M. Beierle, A. Chavochi, Z.Z. Huang, L. Leman, A. Montero, C.A. Olsen
are interested in devising molecular and supramolecular processes to control the
structure and function of de novo designed peptides. These efforts include the design
of potent anticancer agents based on conformationally homogenous low molecular weight
cyclic peptides and fabrication of self-assembling helical peptides that mimic the
intermodular aminoacyl transferase activity of nonribosomal peptide synthetases.
Histone-Deacetylase Inhibitors Based on Novel 3-Dimensional Rigid Scaffolds
their key roles in the transcriptional regulation of a number of genes involved
in cell proliferation, cell-cycle progression, differentiation, and apoptosis, histone-deacetylase
(HDAC) inhibitors have emerged as important new and validated targets in the design
of anticancer drugs. Our efforts to design and discover novel HDAC inhibitors are
based on the rational design of small-molecule peptide scaffolds with predictable
and conformationally homogenous 3-dimensional structures. In contrast to the considerable
advances made in drug design based on 2-dimensional rigid scaffolds, little progress
has been made in devising effective 3-dimensional scaffolds that can act on designated
biological targets (receptors) by mimicking the 3-dimensional structural features
of the native biological ligands–most often peptides and proteins.
developed 12-, 13-, and 14-membered peptidomimetic scaffolds that can mimic precisely
side-chain juxtaposition and functional-group presentations of the 4 residues that
make up β-turn
structures. Structural analyses based on x-ray crystallography, 2-dimensional 1H
nuclear magnetic resonance spectroscopy, and distance-geometry calculations confirmed
that these scaffolds adopt rigid and conformationally homogenous β-turn
structures in solution and in the solid state. We have used this approach to probe
the bioactive conformations of natural cyclic tetrapeptide HDAC inhibitors and to
establish the pharmacophoric requirements (Fig. 1). We then used these scaffolds
to design a series of potent HDAC inhibitors (IC50 <20 nM) that target
several class I and class II HDACs. These compounds also have anticancer activities
against a number of human tumor cell lines.
|Fig. 1. Chemical structures
of the natural HDAC inhibitor apicidin (top) and the synthetic heterocyclic analog (middle) and the solution nuclear magnetic resonance structure indicating the β-turn–like
rigid backbone conformation and side-chain display (bottom).
We hope that
our basic research in establishing novel structure-based drug design concepts will
result in clinically useful human anticancer chemotherapeutic agents. Moreover,
because the constrained cyclic scaffolds can be used to display a variety of amino
acid side chains and backbone geometries in specific and predictable 3-dimensional
arrangements, we think that our basic design concepts will have applications in
other structure-based approaches to rational drug design.
Synthetic Aminoacyl Transfer Catalysts
nonribosomal peptide synthetases, and polyketide synthetases are biological machines
that catalyze instructed chemical synthesis, a phenomenon not yet matched
by any synthetic system. Although chemists have amassed a remarkable record of achievements
in devising peptide catalysts that carry out single-step chemical reactions, the
phenomenon of autonomous instructed synthesis has remained beyond reach. We have
focused on the design of catalysts that can mimic the sequential aminoacyl transferase
activity of nonribosomal peptide synthetases.
We have designed
several modular supramolecular peptide constructs that efficiently promote site-specific
aminoacyl transfer between noncovalently associated α-helical
subunits in neutral aqueous solutions. These constructs have some of the basic hallmarks
of natural enzymes, including precise positioning of active-site residues, covalent
catalysis, general acid-base catalysis, pKa modulation of active-site
residues, and multiple product turnovers (Fig. 2).
|Fig. 2. Schematic representations of aminoacyl loading and intermodular aminoacyl transfer in nonribosomal peptide
synthetases (A) and designed coiled coil catalysts (B). C, Active-site residues of an aminoacyl transfer catalyst modeled onto the crystal structure of a coiled
coil homotetramer. Sequences of peptides used in the current studies are shown on the right.
recently, we have engineered peptides that can mimic more complex, multistep biosynthetic
processes. One example is the formation of diketopiperazine, which minimally requires
simultaneous binding and activation of 2 aminoacyl substrates, aminoacyl transfer
to generate a linear dipeptide intermediate, and cyclization of the dipeptide to
yield the product diketopiperazine. We have designed supramolecular peptide assemblies
that catalyze diketopiperazine and dipeptide synthesis for a variety of aminoacyl
substrates. The peptides covalently capture 2 aminoacyl substrates from solution,
hold them in proximity to bring about an effective intramolecular aminoacyl transfer,
and then release product in the form of diketopiperazine (Fig. 2). We hope that
these studies will help establish the basic blueprint for the future de novo design
of programmable peptide synthetases.
Leman, L.J., Weinberger, D.A., Huang, Z.-Z., Wilcoxen, K.M., Ghadiri, M.R. Functional and mechanistic analyses of biomimetic aminoacyl transfer reactions in de novo designed
coiled coil peptides via rational active site engineering. J. Am. Chem. Soc. 129:2959, 2007.
Wilcoxen, K.M., Leman, L.J., Weinberger, D.A., Huang, Z.-Z., Ghadiri, M.R. Biomimetic catalysis of intermodular aminoacyl transfer. J. Am. Chem. Soc. 129:748, 2007.