Chemical classification of MDM2 inhibitors

Chalcone analogues

Chalcone based MDM2 inhibitors were the first reported natural MDM2 inhibitors (figure 1). These kinds of inhibitors have been studied extensively. In the various studies, chalcone based natural MDM2 inhibitors released the p53 from p53-MDM2 complex and re-established the p53 function. Various researchers also studied the boronic chalcone analogues.3

Figure 1

Structure of Chalcone

Isoliquiritigenin (4,2,4-trihydroxychalcone) is a natural chalcone (figure 2), isolated form the shallot and licorice root. It induces the p53 dependent cell cycle arrest and cell death in the liver cancer cells.4

Figure 2

Structure of iso-liquiritigenin

Chlorofusin

Chlorofusin was the second natural product, identified as MDM2 inhibitors. Chlorofusin was first isolated in 2001 by Duncan from the Fusarium sp. Microdocium caespitosum, a type of marine sponge.5

Later on, Williams and co-worker were also reported the chlorofusin. They had identified the chlorofusin after the testing of 53,000 extracts from the fermentation of a diverse collection of micro-organisms for MDM2 inhibitors activity.5 This novel metabolite was isolated from the microdochium caespitosum.

Chlorofusin contains the unnatural cyclic peptide and chromophore moieties (figure 3). In which, azaphilone derived chromophore linked through the terminal amine of ornithine to a cyclic peptide composed of nine amino acid residues.6 Two of the cyclic peptide amino acids possess a nonstandard or modified side chain, and four possess the D-configuration.7

Figure 3

Structure of Chlorofusin8

The full peptide and azaphilone structure are required for inhibition of the p53-MDM2 interaction. In the study, chlorofusin binds with the N-terminal region of the MDM2 protein and inhibits its activity.

Hexylitaconic acid

Hexylitaconic acid-(-) is a good MDM2 inhibitor from natural origin (figure 4). It was reported recently. Arthrinium sp. fungus was isolated from the marine sponge, and hexylitaconic acid was derived from the fermentation culture of this fungus.9

The result of various studies indicated that the hexylitaconic acid can effectively inhibit the p53-MDM2 interaction and can able initiate the p53 function.

Figure 4

Structure of hexylitaconic acid

Various derivatives of the hexylitaconic acid, like monomethyl ester, dihydro derivative and dihydro derivative of the monomethyl ester can’t inhibit the MDM2 function at µg concentrations.10 Two commercially available di-carboxylic acids derivatives (itaconic acid, succinic acid) of hexylitaconic acid are also not effective as MDM2 inhibitors at µg concentration.

Peptide inhibitors

These types of inhibitors are synthetic peptides (proteins). Peptides based inhibitors can be designed to successfully mimic the alpha helix topography of the p53 protein. So, they can be developed as potent p53-MDM2/X interaction inhibitors.11

MDM2 binding site on p53 protein was mapped by the Novartis group. They mapped it by using the synthetic peptide libraries derived from the N-terminal region of p53.12 The most active peptide obtained from this study (figure 5), was having the 28 folds greater MDM2 inhibitory property than the wild type p53-derived peptide.

Figure 5

Structure of peptide inhibitor reported by Novartis

Peptides based MDM2 inhibitors have a structural similarity with the p53 sequence, so it easily permits the entry into the cells. They can mimic the conformation of the p53 helix and cause non-genotoxic activation p53 function. These types of inhibitors have an advantage of the possibility of high specificity, potency and low toxicity.13 These synthetic linear peptides can adopt a helical conformation and inhibit the p53-MDM2 interaction.

Use of this linear peptide as drugs has faced some problems, which are:

Strategy to overcome these problems, is to staple the hydrocarbon with the peptide. Hydrocarbon linker holds the peptide in a helical conformation so it will be always in the helical conformation. And it can be able to permanently bind with MDM2. Hydrocarbon stapling will inhibit the proteolytic degradation and increase the cellular uptake.14

Other strategy to overcome the rapid enzymatic degradation is to use D-amino acids for synthetic peptides chain. This type of peptides are far more stable to proteolytic degradation, as enzymes present in the body are only capable of processing L-amino acids due to their stereo-specificity.

These are some of the approaches to stabilize the peptides.15 Though many of peptides are reported, which can inhibit p53-MDM2 interaction. But there are currently no peptide based inhibitors in clinical trials.

Organic inhibitors (Non-peptide Inhibitors)

These are the synthetic organic (non-peptidic) MDM2 inhibitors. These types of inhibitors are subdivided according to their alpha helix mimetic property. So, they further classified as Non α-helix mimetics and α-helix mimetics.

Non α-helix mimetics (Functional mimetics)

These MDM2 inhibitors are small organic (non-peptide) compounds that place substituents in the same spatial orientation as the p53 helix. They do not mimic the α-helix topography. These types of compounds are the competitive inhibitors of MDM2 protein.

By using the High Throughput Screening (HTS) campaigns at Hoffmann-La Roche, Vassilev and colleagues were discovered the first compound of this class called as Nutlin. Nutlin contains the cis-imidazoline (4,5-dihydroimidazoline) moiety. Nutlins mimic the three main amino acid residues on p53 (i, i+4, i+7), involved in its interaction with MDM2.16 Hence, it shows 3 pocket binding. And inhibit the p53-MDM2 interaction. Nutlin group contains three compounds, Nutlin-1, Nutlin-2 and Nutline-3 (figure 6). Among them, Nutlin-3 is most potent compound (IC50 — 90nM).

Figure 6

Structures of nutlins

Assay of nutlin on various cell lines, shows the dose dependent MDM2 inhibition and activation of wild type p53 protein function. Currently, there are total seven compounds of this class, which are under clinical trials.

In our study, we have designed and developed this type of MDM2 inhibitors. Therefore in this thesis, MDM2 inhibitors of this class will be discussed in details.

A-helix mimetics

Inhibitors pertaining this class are organic in nature and mimics the α-helix of p53. They mimic the topography of α-helix and can position the substituents in the same spatial orientation as the 3 different interaction points of p53 helix. With contrast to Functional mimetics, these types of inhibitors are generally more extended.17

Hamilton and co-workers discovered the first compound of this class (α-helix mimetics). And it was the terphenyl derivatives. Other reported compounds of this class contain the various chemical derivatives like pyrrolopyrimidine derivatives, spirooligomer derivatives and oligobenzamide derivatives. Oligobenzamide scaffold was reported by wilson and co-workers.18

Figure 7

Structures of α-helix mimetics inhibitors15

This class of compounds has a good potential of inhibiting the p53-MDM2 interaction effectively.