Probing the Bioactive Conformation of an Archetypal Natural Product HDAC Inhibitor with Conformationally Homogeneous Triazole‐Modified Cyclic Tetrapeptides

Abstract

Keywords drug design; cyclic peptides; histone deacetylase; structure-activity relationship; triazole A fundamental strategy in rationally designing synthetic compounds to bind a protein of interest is to use a known ligand as a structural model to specify the precise conformational and pharmacophoric requirements for binding. Despite the remarkable success of this approach, a significant difficulty is that free ligands (in the absence of their cognate receptors) often adopt multiple conformations in solution or in the solid state compared to the receptor-bound structure.[1] These occurrences can render design models based on the free ligand structure difficult to obtain or even misleading.[2] Here we present evidence that the more potent conformation of apicidin, an archetypal member of a family of naturally occurring cyclic tetrapeptide inhibitors of histone deacetylases (HDACs), is not the all-trans (t-t-t-t) structure that predominates in solution, [3,4] but rather a cis-trans-trans-trans (c-t-t-t) conformation. Our studies rely on the design, synthesis, structural characterization, and functional analysis of a series of cyclic pseudo-tetrapeptides bearing 1,4-or 1,5-disubstituted 1,2,3-triazole amino acids that serve as trans-or cis-amide bond surrogates, respectively. We show that by replacing an amide bond with a triazole, the bond in question can be fixed in either a trans-like or cis-like configuration, allowing us to individually probe the binding affinity of distinct conformations. The heterocyclic compounds adopt conformations that overlay closely with the targeted conformations of apicidin and demonstrate potent HDAC inhibitory activities, in some cases equivalent or superior to those of the natural product. This study highlights the utility of triazole-modified cyclic peptides in constructing useful

1,2,3‐Triazoles in Peptidomimetic Chemistry

“…[53] Apicidin is an inhibitor of histone deacetylase (HDAC) that exhibits potent cytotoxicity towards cancer cells. Several analogues of apicidin (e.g., see Scheme 2), containing either a 1,4-substituted or 1,5-substituted triazole to mimic a trans-amide or a cis-amide bond, respectively, were synthesised to gain some insight into the bioactive conformation of apicidin.…”

Diversity-oriented synthesis of macrocyclic peptidomimetics

“…First, we have described a protocol for the macrocyclic ring closure of chiral α-azido acids via regioselective and epimerization-free 1,5-disubstituted triazole formation. The macrocycle products were obtained in superior yields to those described in the literature (47). Second, we have reported the development of a unique method for the DKP synthesis using solid-supported N methylmorpholine in combination with microwave heating.…”

“…Though there are numerous reported examples of the use of regioselective 1,3-dipolar cycloadditions to furnish 1,4-triazole containing macrocycles (58), only a handful of these employed chiral α-azido acids as the substrates (48,59,60). The synthesis of 1,5-triazole containing macrocycles via 1,3-dipolar cycloadditions (61) is much less common, and in the very limited number of examples that use α-azido acid containing substrates, the yields of the isolated products are typically very low (47). A method where the formation of the macrocycle proceeded with good regioselectivity (1,5-triazole over 1,4-triazole) and moderate yields has been recently described, but there were no stereogenic centers adjacent to the azide present in the substrates (62,63).…”

“…The resulting molecules are known as peptidomimetics, and they usually present improved stability, bioavailability, and selectivity toward a particular target. An important example of these bioisosteric modifications is the replacement of an amide bond by a triazole ring, which introduces rigidity to the molecule and mimics either the cis-or the trans-like configuration of the amide bond (47,48).…”

Solvatochromic Reagents for Multicomponent Reactions and their Utility in the Development of Cell‐Permeable Macrocyclic Peptide Vectors

“…Cyclization of peptides can lead to enhanced specificity, [5] in vivo proteolytic stability, [6] and cellular permeability. [7] Computational studies have shown that internal hydrogen bonding in these compounds may facilitate passive membrane permeability.…”