Synthesis and biological evaluation of histone deacetylase inhibitors that are based on FR235222: A cyclic tetrapeptide scaffold

Abstract

We outline the synthesis of six novel derivatives that are based on a recently discovered HDAC inhibitor FR235222. Our work is the first report utilizing a novel binding element, guanidine, as metal coordinators in HDAC inhibitors. Further, we demonstrate that these compounds show cytotoxicity that parallels their ability to inhibit deacetylase activity, and that the most potent compounds maintain an L-Phe at position 1, and a D-Pro at position 4. Both inhibition of HDAC activity and cytotoxicity against the pancreatic cancer cell line BxPC3 are exhibited by these compounds, establishing that a guanidine unit can be utilized successfully to inhibit HDAC activity. There are already numerous HDAC inhibitors in clinical trials. 3,4 However, treating pancreatic cancers has been unsuccessful with any drug currently on the market. Given that HDACs are inappropriately up-regulated in pancreatic cancers, 5,6 HDAC inhibitors (HDACIs) have tremendous potential for treating these drug-resistant cancers. Pancreatic cancer is the fifth most deadly cancer in U.S. Only 10% of patients are eligible for surgery, 7 and less than 20% of pancreatic cancers respond to the drug of choice (Gemzar) or other drugs on the market. 8, 9The 5-year survival rate for patients with pancreatic cancers is less than 5%. 10 With such a low response rate to current chemotherapeutic treatments, there is an immediate need for new drugs that provide additional chemotherapeutic options to pancreatic cancer patients.To date, HDACIs can be divided into five chemical families: hydroxamic acid derivatives, short chain fatty acids, benzamides, electrophilic ketones, and cyclic tetrapeptides. 1,11 These five families all inhibit the activity of metal-dependent HDAC classes I and II. The There is extensive literature on derivatives containing the three moieties found in natural product metal-binding units. In addition to work exploring their potency, other non-traditional metal binding units have been published including, sulfur, 15 N-formyl hydroxylamine, 16 and phosphorous-containing compounds. 17 However, no work has been published to date on guanidines as metal-binding units in HDACIs. Guanidines represent a very important class of compounds both biologically and chemically. Their hydrophilic nature provides stabilization of protein conformations via hydrogen bonding and mediates solubility of natural products. 18 With a high pK a value of 12.5, arginine residues containing a guanidinium side chain may not be considered optimal metal-binding ligands. However, the highly acidic nature of a metal cation found in the HDAC pocket can potentially lower the pK a value of the guanidinium side chain, allowing for coordination with the metal. In fact, several recent reports document the stability of guanidine-metal interactions, 19,20 although additional studies are needed. Despite their likely metal binding capabilities, guanidines have gone unexplored in the realm of HDACI as potential metal-binding units.Here we describe the design and synthesis of HDAC...

Discovery and Mechanism of Natural Products as Modulators of Histone Acetylation

“…Modification of the Ahoda side chain of FR235222 and AS1387392 Fig. (8) by inversion of the configuration at C9 and modification of the terminal functionality to a guanidino or amide group were also detrimental to biological activity [87, 112, 113]. The binding interactions of FR235222 with HDLP interpreted using ICM3.2 software indicated interactions between the terminal α-hydroxy-keto group of the Ahoda side chain with the active site metal ion [112].…”

A novel HDAC inhibitor with a hydroxy-pyrimidine scaffold

“…1). 7, 9 Most HDACi follow the pharmacophore model of a capping region that interacts with the surface of the protein, a metal-binding region that chelates zinc to disrupt the enzymatic activity, and a linker domain consisting of a hydrophobic spacer that interacts with the hydrophobic-binding channel (Fig. 1).…”

Histone deacetylase inhibitors: synthesis of cyclic tetrapeptides and their triazole analogs

“…1). 16 Compound 2 was generated by modifying 1 , replacing the acetyl lysine metal binding unit with a guanidine unit. Reversing the stereochemistry from l to d of the homoarginine in 2 produced 3 , while incorporation of arginine and a six membered ring at positions 3 and 4 respectively gave 4 .…”

“…Syntheses of our peptide HDAC inhibitors were completed via a convergent solution phase route (Scheme 1), which allowed for an easy substitution of amino acids at each position 16. TBTU and DIPEA were used to form the dipeptide fragments 1–2 and 3–4, where acid-protected residues 1(a–d) and N -Boc-protected residue 2(a–c) furnished dipeptide MeO-1-2-Boc, and acid protected residues 3(a–d) and N -Boc-protected residues 4(a,b) were coupled to give dipeptides MeO-3-4-Boc (84–98% yield) (Scheme 1).…”

“…The twelve compounds were assayed at 200µM concentration against endogenous HDACs from HeLa cell lysates using a fluorogenic substrate, as previously described 16. Apicidin (Fig.…”