The Skaggs Institute
for Chemical Biology

Scientific Report 2005

New Approaches in the Design of Anticancer Agents and Synthetic Catalysts

M.R. Ghadiri, J.M. Beierle, A. Chavochi, W.S. Horne, Z.-Z. Huang, L. Leman, A. Montero

We are interested in devising molecular and supramolecular processes to control the structure and function of de novo designed peptides. These efforts encompass the design of potent anticancer agents based on conformationally constrained heterocyclic peptides that target and inhibit histone-deacetylases (HDACs) and the design of self-assembling helical peptides that mimic the sequential aminoacyl transferase activity of nonribosomal peptide synthetases.

Peptidomimetic HDAC Inhibitors

Typical small-molecule therapeutic agents, whether synthetic or derived from natural products, generally act on their biological targets (receptors) by mimicking the structural features of their native biological ligands—most often peptides and proteins. Moreover, many protein-ligand interactions are thought to involve the recognition of β-turn protein secondary structures. Consequently, it is thought that constrained peptides designed to adopt specific and conformationally homogeneous turn structures can provide valuable probes for assessing the bioactive ligand conformations and aid in the rational design of therapeutic agents.

We recently developed 12-, 13-, and 14-membered peptidomimetic scaffolds, incorporating 1,2,3-triazole ε^2,6-amino acids as novel cis or trans dipeptide surrogates, that mimic precisely side-chain juxtaposition and functional-group presentations of the 4 residues that make up β-turn structures (Fig. 1).

Fig. 1. The chemical structures of the natural HDAC inhibitor apicidin (top), 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).

Structural analyses based on x-ray crystallography, 2-dimensional ¹H nuclear magnetic resonance spectroscopy, and distance-geometry calculations confirmed that the heterocyclic peptide scaffolds adopt rigid and conformationally homogeneous 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.

Because of their key roles in the transcriptional regulation of a number of genes involved in cell proliferation, cell-cycle progression, differentiation, and apoptosis, HDACs are important new targets in the design of novel anticancer agents. Our studies indicate that appropriately designed triazole modified cyclic peptides can have potent HDAC inhibitory activities, rivaling those of many previously known natural and synthetic HDAC inhibitors. Moreover, because our constrained heterocyclic 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 can have applications in other structure-based approaches for rational design of drugs.

Synthetic Peptide Catalysts

Rational design of biomolecular catalysts is a fundamentally valuable enterprise for assessing and advancing our basic understanding of factors that contribute to the functioning of natural enzymes. We are interested in the aminoacyl transfer class of reactions because of their prominent roles in a number of chemical and biological processes. Specifically, we are interested in mimicking the sequential aminoacyl transferase activity of nonribosomal peptide synthetases, enzymes responsible for the production of many natural products used as therapeutic agents.

Our designed catalyst is a modular peptide construct that can promote stoichiometric and site-specific aminoacyl transfers between noncovalently associated α-helical subunits with catalytic efficiencies >10⁶ in neutral aqueous solutions. We have used x-ray crystallography and nuclear magnetic resonance spectroscopy to analyze the structural and functional features of the aminoacyl transferase designs (Fig. 2). We hope that these studies will establish the basic blueprint for the future de novo design of programmable peptide synthetases.

Fig. 2. Top, X-ray structure of the de novo designed 4-helix bundle aminoacyl transferase peptide emphasizing the juxtaposition of active-site residues. Bottom, The schematic illustration of the sequential aminoacyl loading and intermodular aminoacyl transfer steps.