Aryloxy substituted N-arylpiperazinones as dual inhibitors of farnesyltransferase and geranylgeranyltransferase-I

Structure-Guided Discovery of Potent Antifungals that Prevent Ras Signaling by Inhibiting Protein Farnesyltransferase

Infections by fungal pathogens are difficult to treat due to a paucity of antifungals and emerging resistances. Next-generation antifungals therefore are needed urgently. We have developed compounds that prevent farnesylation of Cryptoccoccus neoformans Ras protein by inhibiting protein farnesyltransferase with 3-4 nanomolar affinities. Farnesylation directs Ras to the cell membrane and is required for infectivity of this lethal pathogenic fungus. Our high-affinity compounds inhibit fungal growth with 3-6 micromolar minimum inhibitory concentrations (MICs), 4- to 8-fold better than Fluconazole, an antifungal commonly used in the clinic. Compounds bound with distinct inhibition mechanisms at two alternative, partially overlapping binding sites, accessed via different inhibitor conformations. We showed that antifungal potency depends critically on the selected inhibition mechanism because this determines the efficacy of an inhibitor at low in vivo levels of enzyme and farnesyl substrate. We elucidated how chemical modifications of the antifungals encode desired inhibitor conformation and concomitant inhibitory mechanism.

Chemical approaches to inhibitors of isoprenoid biosynthesis: targeting farnesyl and geranylgeranyl pyrophosphate synthases

The chemical synthesis of farnesyl and geranylgeranyl pyrophosphate synthase inhibitors are surveyed.

Recent progress in developing small molecule inhibitors designed to interfere with ras membrane association: toward inhibiting K-Ras and N-Ras functions

K-Ras and N-Ras are mutated in a wide range of human cancers, thus making these proteins attractive targets of anticancer drug development. However, no effective compounds have been obtained so far. One of the approaches taken to inhibit the function of K-Ras and N-Ras is to interfere with their membrane association. Various attempts have been taken. In the first example, we examine the approach conceived in early 1990s to inhibit protein prenylation that is required for their membrane association. The initial premise that the inhibition of Ras farnesylation leads to the inhibition of Ras was not realized, mainly due to alternative prenylation of K-Ras and N-Ras proteins. This led to the idea that the combined inhibition of FTase and GGTase-I can block membrane association of K-Ras and N-Ras. Dual specificity inhibitors of FTase and GGTase-I (DPIs) were also developed. These compounds were tested in preclinical and clinical studies. It appears that sufficiently high concentration of the drug to inhibit K-Ras was not achieved in previous attempts. In addition, dose-limiting toxicity has been observed and this was primarily ascribed to GGTase-I inhibition. Strategies to confer cancer targeting capabilities to the inhibitors may overcome the dose-limiting toxicity. In the second approach, postprenylation events were exploited. This led to the development of various inhibitors including the ICMT inhibitors. Finally, recent identification of compounds that inhibit the interaction between K-Ras and PDE-δ is discussed.

Characterization of the in vitro activity of AZD3409, a novel prenyl transferase inhibitor

PURPOSE

AZD3409 is a novel DPTI that has potent activity against both FTase and GGTase-1. The in vitro inhibition profile of AZD3409 was characterized using three different cell lines: mouse embryogenic fibroblasts, transfected with H-Ras(V12) (MEF), A549 cells (Ki4B-Ras mutation) and MCF-7 cells (no Ras mutation).

METHODS

Both cytotoxicity and levels of inhibition of farnesylation and geranylgeranylation were determined in different assays in relation to the concentration of AZD3409. Results were compared with those obtained with the first-generation FTase inhibitor lonafarnib or the GGTase-1 inhibitor GGTI-2147.

RESULTS

The mean IC(50) for cytotoxicity of AZD3409 and lonafarnib was 510 and 15,200 nM in MEF cells, 10,600 and 2,740 nM in A549 cells and 6,170 and 9,490 nM in MCF7 cells, respectively. In these cells, the IC(50) for FTase activity of AZD3409 ranged from 3.0 to 14.2 nM and of lonafarnib from 0.26 to 31.3 nM. The inhibiting activity of AZD3409 and lonafarnib on general protein farnesylation was comparable with the specific farnesylation levels of HDJ-2. In vitro geranylgeranylation of Rap1a could be inhibited by GGTI-2147 in all three cell lines, but only in MCF-7 cells by AZD3409. These results are in agreement with the IC(50) values for GGTase-1 activity as the lowest IC(50) for AZD3409 was found in the MCF-7 cell line.

CONCLUSIONS

AZD3409 inhibits farnesylation to a higher extent than geranylgeranylation. Both inhibition of farnesylation and geranylgeranylation could not be correlated to the antiproliferative activity of the drug.

Farnesyltransferase pharmacophore model derived from diverse classes of inhibitors

A three-dimensional pharmacophore model was developed based on 25 currently available inhibitors, which were carefully selected with great diversity in both molecular structure and bioactivity as required by HypoGen program in the Catalyst software, for discovering new farnesyltransferase (FTase) inhibitors. The best hypothesis (Hypo1), consisting of four features, namely, two hydrogen-bond acceptors, one hydrophobic point, and one ring aromatic feature, has a correlation coefficient of 0.949, a root-mean-square deviation of 1.321, and a cost difference of 163.15, suggesting that a highly predictive pharmacophore model was successfully obtained. The application of the model shows great success in predicting the activities of 227 known FTase inhibitors in our test set with a correlation coefficient of 0.776 with a cross-validation of 98% confidence level. Accordingly, our model should be reliable in identifying structurally diverse compounds with desired biological activity.

Phosphonomethylphosphorylmethyl(oxy)-analogues of geranylgeranyl diphosphate as stable and selective geranylgeranyl protein transferase inhibitors

The diphosphate moiety of geranylgeranyldiphosphate (GGdP) was replaced with metabolically and hydrolytically stable analogous polar portions, in an attempt to obtain new geranylgeranyltransferase (GGTase) inhibitors, which could also be selective over congener enzyme farnesyltransferase (FTase). In particular, the phosphonomethylphosphorylmethoxy derivative showed the highest inhibition potency, accompanied by a satisfactory GGTase/FTase selectivity.

Synthesis and evaluation of potent, highly-selective, 3-aryl-piperazinone inhibitors of protein geranylgeranyltransferase-I

A series of compounds based on the carboxyl-terminal CAAL sequence of PGGTase-I substrates was designed and synthesized. Using piperazin-2-one as a semi-rigid scaffold, we have introduced critical pharmacophores in a well-defined arrangement to mimic the CAAL sequence. High potency and exceptional selectivity were obtained for inhibition of PGGTase-I with structures such as 45 and 70. Potency of this series of GGTIs was dependent on the presence of an L-leucine residue with a free carboxyl terminus, as well as an S configuration of the 3-aryl group. The selectivity was significantly enhanced by 5-methyl substitution on the imidazole ring and fluorine substitution on the 3-aryl group. Modification of the 6-position of the piperazinone scaffold was found to be unfavorable. Compounds 44 and 69, the corresponding methyl esters of 45 and 70, were found to selectively block processing of Rap1A by PGGTase-I in whole cells with IC(50) values of 0.4 microM and 0.7 microM respectively.

Novel triazole based inhibitors of Ras farnesyl transferase

A novel series of potent inhibitors of Ras farnesyl transferase possessing a 1,2,4-triazole pharmacophore is described. These inhibitors were discovered from a parallel synthesis effort and were subsequently optimized to in vitro IC(50) value of less than 1nM.

Efficient Approaches toward the Solid-Phase Synthesis of New Heterocyclic Azoniaspiro Ring Systems: Synthesis of Tri- and Tetrasubstituted 10-Oxo- 3,9-diaza-6-azoniaspiro[5.5]undecanes

[Reaction: see text]. An efficient approach for the parallel solid-phase synthesis of novel heterocyclic azoniaspiro ring systems is described. The target compounds, the 1,8,9-trisubstituted 10-oxo-3,9-diaza-6-azoniaspiro[5.5]undecanes, were obtained starting from resin-bound reduced dipeptides. The azoniaspiro cation was formed by intramolecular attack of a tertiary nitrogen on pendent alpha-bromocarbonyl. N-3 acylated and N-3 alkylamino carbonyl derivatives of the 1,8,9-trisubstituted 10-oxo-3,9-diaza-6-azoniaspiro[5.5]undecanes were obtained following in solution treatment of the N-3 azoniaspiro derivatives with different carboxylic acids and isocyanates.

Novel beta-(imidazol-4-yl)-beta-amino acids: solid-phase synthesis and study of their inhibitory activity against geranylgeranyl protein transferase type I

Solid-phase synthesis of imidazolyl-beta-amino acid derivatives is described. Several analogs demonstrated moderate inhibition of geranylgeranyl protein transferase type I (GGPT I).

Stable analogues of geranylgeranyl diphosphate possessing improved geranylgeranyl versus farnesyl protein transferase inhibitory selectivity

Phosphonoacetamido(oxy) groups have proven to be good mimics of the diphosphate portion in geranylgeranyl protein transferase I (GGTase I) inhibitors. The introduction of small alkyl groups (Me, Et) into the diphosphate mimic moiety caused a further decrease in collateral farnesyl protein transferase (FTase) inhibitory activity, thereby improving GGTase I over FTase selectivity.

Macrocyclic piperazinones as potent dual inhibitors of farnesyltransferase and geranylgeranyltransferase-I

A series of macrocyclic piperazinone compounds with dual farnesyltransferase/geranylgeranyltransferase-I inhibitory activity was prepared. These compounds were found to be potent inhibitors of protein prenylation in cell culture. A hypothesis for the binding mode of compound 3o in FPTase is proposed.

Synthesis of 2,6-bridged piperazine-3-ones by N-acyliminium ion chemistry

Several 2-substituted and 2,5-disubstituted piperazine-3,6-diones were synthesized starting from readily available alpha-amino acids. After activation of a lactam carbonyl via introduction of a methoxycarbonyl group onto nitrogen, this carbonyl was selectively reduced. Treatment of the resulting urethane with protic acid generated the corresponding N-acyliminium ion, which was trapped by a nucleophilic C2-side chain to provide 2,6-bridged piperazine-3-ones. Several aromatic, heteroaromatic, and nonaromatic side chains were used as pi-nucleophiles. In addition, the effect of the presence of a C5-methyl group on the stereochemical outcome of the cyclization was examined.

The synthesis and biological evaluation of a series of potent dual inhibitors of farnesyl and geranyl-Geranyl protein transferases

We have prepared a series of potent, dual inhibitors of the prenyl transferases farnesyl protein transferase (FPTase) and geranyl-geranyl protein transferase I (GGPTase). The compounds were shown to possess potent activity against both enzymes in cell culture. Mechanistic analysis has shown that the compounds are CAAX competitive for FPTase inhibition but geranyl-geranyl pyrophosphate (GGPP) competitive for GGPTase inhibiton.

Design, synthesis, and pharmacological evaluation of new farnesyl protein transferase inhibitors

New CA(1)A(2)X peptidomimetics are described as Ras farnesyl transferase inhibitors (FTIs). They include cysteine and methionine as mimetics of the C-terminus sequence of farnesylated proteins. Furthermore, cysteine was replaced by heterocycles, taking into account the role of zinc and the metabolic instability of amino acids. The molecular docking of 8 in the active site of the enzyme and the pharmacological evaluation of the compounds are illustrative of a new class of FTIs.