Environment-sensitive turn-on fluorescent probes for p53–MDM2 protein–protein interaction

A series of small-molecule fluorescent probes were designed and synthesized for detecting and imaging p53–MDM2 interaction in the human lung cancer cell line A549.

Abstract

A series of probes with a turn-on switch for the p53–MDM2 protein–protein interaction were developed. After careful evaluation, these small molecule fluorescent probes exhibited high practical activity and selectivity in vitro and in cellulo. In particular probe 10, which had a K_i value of 0.03 μM, displayed much better binding affinity compared to the positive control Nutlin-3, which had a K_i value of 0.23 μM. These no-wash environment-sensitive turn-on fluorescent probes have been successfully applied to imaging p53–MDM2 interaction in the human lung cancer cell line A549 (wild-type p53) at the micromolar level. Therefore, these fluorescent probes are expected to be used in drug screening and cell staining in p53–MDM2 fields, as well as in pathological and physiological studies of the p53–MDM2 interaction.

Introduction

As a tumor suppressor, p53 is a mutated gene in human tumor cells that plays a pivotal role in preventing cancer development caused by cellular stresses such as oncogenic activation, DNA damage, hypoxia, and telomere erosion.1,2 It needs to be emphasized that the p53 protein, which includes several domains, can regulate the expression of numerous genes with different biofunctions, such as apoptosis, cell cycle regulation and differentiation.3 The key role of p53 in the cell demonstrates that the loss of p53 may lead to dramatic consequences. Normally, the level of p53 is tightly controlled by two related proteins called MDMX (also known as MDM4)4 and MDM2 (sometimes called HDM2 for its human analog)5–7 through a negative feedback loop.5 It should be noted that p53 can activate the expression of MDM2 protein so as to increase the MDM2 level, which in turn inhibits p53 through three mechanisms, including blocking p53 transcription activity by binding to p53 at the transactivation domain, promoting the nuclear export of p53 by exposing its signal sequence, and stimulating p53 degradation6,8,9 since MDM2 can serve as a ubiquitin ligase. In many human malignancies the wild-type p53 and mdm2 genes have been found to be overexpressed or amplified, which could down-regulate the p53 protein and impair its tumor suppression activity.10,11 Therefore, stabilization and activation of the p53 pathway by inhibition of MDM2 has been proposed as a novel therapeutic approach for cancer therapy.12,13

Historically speaking, it is challenging to develop effective small-molecule inhibitors for nonenzymatic protein–protein interactions. Fortunately, the crystal structural basis of the p53–MDM2 protein–protein interaction was solved by X-ray crystallography in 1996.14 It was revealed that MDM2 has a relatively deep hydrophobic cleft which can be filled by three hydrophobic residues, Phe19, Trp23, and Leu26, from an amphipathic α-helix of the peptide in the transactivation domain of p53.14 Based on such a well-defined pocket of the crystal structure, compounds with low molecular weights will be discovered that could block the interaction of p53–MDM2. Over the past few years, a number of potent and selective molecules, such as RO5503781 and RG7112,15 have been established as p53–MDM2 inhibitors with effective antitumor activity in vitro and in vivo.

There are many kinds of well-developed techniques, such as autofluorescent translocation biosensor systems16,17 and bimolecular fluorescence complementation (BiFC) assays,18 to image and detect the interaction between p53 and MDM2. Fluorescence techniques have the comparative advantages of visualizing the protein interaction directly and providing temporal, spatial information in living and intact cells over any other methods used in perfect picture imaging system (PPIs) study, such as electrophoresis-based systems, the two-hybrid system, immune affinity-based methods and mass spectrometry (MS).16,19,20 Many techniques such as autofluorescent translocation biosensors and BiFC techniques often need a conjugated fluorescent protein as a reporter, which is time-consuming, complicated and expensive. Therefore, finding more economical and straightforward methods to image and detect the interaction between p53 and MDM2 is urgent.

In recent years, small-molecule fluorescent probes have become very popular in imaging and recognizing proteins of interest. Compared to the above-mentioned techniques, their preparations are more convenient and affordable. Furthermore, these small-molecule fluorescent probes with turn-on mechanisms display more advantages21–24 in which they can image and detect specific proteins effectively as they allow for sensitive and specific detection under high signal-to-background ratios.25 Currently, the development of small-molecule fluorescent probes for detecting the interactions of non-enzymatic proteins such as p53 and MDM2 remains a challenging task.

In our previous studies, we attempted to find small-molecule fluorescent probes for imaging the p53–MDM2 interaction and successfully discovered an effective fluorescent probe.26 However, its fluorescence intensity was not strong, and the binding affinity to MDM2 was relatively weak. So we tried to find better probes and fortunately some protein-specific fluorescent turn-on probes with strong fluorescence and blue shifted emission in hydrophobic surroundings were reported by the Tan group.27 Based on the previous work, compound Z1, which is an effective p53–MDM2 inhibitor developed by the Tan group,28 was chosen as the major scaffold for MDM2 binding and the fluorophore 4-chloro-7-nitrobenzoxadiazole (NBD) which has reasonable fluorescent properties was selected as the recognition moiety in an aliphatic spacer. Subsequently, a series of small-molecule fluorescent probes for detecting the p53–MDM2 interaction were designed and synthesized (Scheme 1).

Scheme 1. The design strategy of small-molecule fluorescent probes for the p53–MDM2 interaction.

Results and discussion

Chemistry

A schematic of the synthesis of probes 9–11 is shown in Scheme 2. In brief, compound 3 was initially obtained by a sulfonation reaction. Subsequently, compound 3 and dimethylamine hydrochloride in the presence of trimethylamine in THF yielded compound 4, which was alkylated with different amines to produce compounds 5–7. Finally, compounds 5–7 reacted with the key intermediate 8 to give the fluorescent compounds 9–11. Further details of the synthetic procedure can be found in the ESI.‡

Scheme 2. The synthetic route of small-molecule fluorescent probes. (i) 120–130 °C, 6 h. (ii) Triethylamine, r.t., 30 min; dimethylamine hydrochloride, THF, 60 min, 0 °C, 43%. (iii) Acetonitrile, 60 °C, 6 h, 43%. (iv) Acetic acid, microwave, 12%.

Docking study of probe 10

In order to better understand the interactions between the probes and the MDM2 protein, probe 10 was chosen to be docked onto MDM2 using the protocol described earlier.28 As a result, the docking conformation and orientation of compound 10 could be located in the Phe19, Leu26 and Trp23 hydrophobic binding site, and the NDB fluorophore was stretched outside (Fig. 1). These computational results apparently proposed the recognition of this probe by MDM2 with multiple hydrophobic interactions. More docking details are presented in the ESI.‡

Fig. 1. The binding mode of probe 10 (white sticks) with the MDM2 protein.

Spectroscopic properties of the probes

The spectroscopic properties of probes 9–11 (Fig. S1 and S2‡) were measured in 5 μM solution in PBS (pH = 7.4) using a Thermo Scientific Varioskan microplate reader, and the results were displayed in Table 1. According to the results, all of the probes possessed excellent fluorescent properties. In general, their fluorescence quantum yields slightly increased with the increase in the hydrophobic chain.

Table 1. Photophysical properties of the synthesized probes.

Compd.	λ max (nm)	λ ex (nm)	λ em (nm)	Φ (%)
9	375/448	370/450	575	1.88
10	377/449	370/440	580	10.09
11	376/450	365/440	575	9.59

Binding affinity of the probes

Subsequently, the ability of probes 9–11 to disrupt the p53–MDM2 interaction was studied using a fluorescence polarization-based (FP-based) binding assay (details are showed in the ESI‡). First, we evaluated whether the NBD fluorophore in our probes affected the FP assay. The result displayed that the FP value changed very little, with the increased MDM2 protein concentration measured at a wavelength of 535 nm (excited at 485 nm) (Table S1‡). Moreover, we evaluated the fluorescence properties of these probes in the presence of BSA (bovine serum albumin, Energy Chemical, Shanghai, China), which often forms non-specific binding with small molecules. The experimental results clearly demonstrated that there was a slight interaction between the probes and BSA (Fig. S4‡). For the binding assay, Nutlin-3 with a K_i value of 0.23 μM was selected as a positive control. It is found that all three probes showed excellent inhibitory activity. Furthermore, the results revealed that the inhibitory activities of probes 10–11 towards the p53–MDM2 protein interaction were much better than that of probe 9. The calculated K_i values of probes 9–11 were 0.1 μM, 0.03 μM and 0.06 μM (Fig. S3‡), respectively, which were much better than the positive control Nutlin-3, which had a K_i value of 0.23 μM, and the previous probe L1, which had a K_i value of 2.29 μM. Probe 10 in particular had a 10-fold higher potency than the reference compound (see Table 2).

Table 2. The inhibitory activities and in vitro antiproliferative activities of compounds.

Compd.	A549	NCI-H1299	HCT116	MDA-MB-231	Inhibitory activity
	IC50 (μM)				K i (μM)
9	>100	>100	>100	>100	0.10
10	>100	>100	>100	>100	0.03
11	>100	>100	>100	>100	0.06
Nutlin-3	19.9 ± 1.3	39.6 ± 1.9	28.0 ± 0.8	31.0 ± 0.2	0.23

Cytotoxicity assay

Additionally, we assessed the cytotoxicity of these probes and the positive control Nutlin-3 by an SRB (Sulforhodamine B) method using a Thermo Scientific Varioskan microplate reader. Four human cell lines from ATCC (American Type Culture Collection, Manassas, VA 20110, USA), namely H1299 (p53 null), A549 (wild-type p53), MDA-MB-231 (wild-type p53) and HCT116 (wild-type p53), were selected for the cytotoxicity assay. All studies were approved by the Ethics Committee and IACUC of Cheeloo College of Medicine, Shandong University, and were conducted in compliance with European guidelines. The results revealed that our probes showed acceptable cell toxicity in all cancer cell lines compared with Nutlin-3 (Table 2). At the concentration of 100 μM, the inhibitory rate was only 3–55% (Table S2‡). These antiproliferative results indicated that our probes could be applied to detecting and imaging the p53–MDM2 interaction in living cells.

Fluorescence image assay and flow cytometry assay

Because probes 9–11 exhibited potent inhibitory and acceptable cell toxicity, we evaluated the fluorescent properties of these probes for detecting and imaging the p53–MDM2 interaction using a Zeiss Axio Observer A1 microscope. NCI-H1299 (p53 null) and A549 (wild-type p53) cells were chosen for the imaging study in living cells (Fig. 2–4). The imaging results revealed that these probes can exhibit strong fluorescence and significantly stain the A549 cell line. In contrast, staining is very low with the NCI-H1299 cell line (Fig. 2–4). In other words, our probes display particular selectivity for the A549 cell line (p53 wild type). Moreover, the staining occurred primarily in the cytoplasm, which is in accordance with the fact that MDM2 is mainly located in the cytoplasm. Furthermore, in order to find whether these probes can selectively detect the hydrophobic interface of p53–MDM2, another negative experiment was carried out. The inhibition of the p53–MDM2 interaction was imaged by incubating the wild-type cell line A549 with 100 μM Nutlin-3 together with each probe. The result was that the inhibition of the p53–MDM2 interaction by Nutlin-3 could lead to a decrease in the fluorescence intensity. It confirmed that our probes displayed favorable selectivity for inhibiting the p53–MDM2 interaction and could be used in the detection of the p53–MDM2 interaction. Subsequently, the binding of probes 9–11 to the living cell A549 was further analyzed by flow cytometry (FCM) (Fig. 5). The total binding of our probes to the A549 cells was higher than the nonspecific binding to A549 cells treated by probes 9–11 and Nutlin-3. These FCM results are also consistent with the conclusion above.

Fig. 2. Fluorescence microscopic imaging of NCI-H1229 cells (p53 null) and A549 cells (wild-type p53) incubated with 5 μM probe 9 (1,5-bright field; 2,6-GFP channel). Imaging the inhibition of p53-MDM2 was accomplished by incubating 100 μM Nutlin-3 with 5 μM probe 9 (3-bright field; 4-GFP channel). NCI-H1229 and A549 cells were incubated with the probes at 37 °C for 15 min. The backgrounds of the images were adjusted by ImageJ software. The imaging was performed using a Zeiss Axio Observer A1 microscope with a 63× objective lens.

Fig. 3. Fluorescence microscopic imaging of NCI-H1229 cells (p53 null) and A549 cells (wild-type p53) incubated with 5 μM probe 10 (1,5-bright field; 2,6-GFP channel). Imaging the inhibition of p53-MDM2 was accomplished by incubating 100 μM Nutlin-3 with 5 μM probe 10 (3-bright field; 4-GFP channel).

Fig. 4. Fluorescence microscopic imaging of NCI-H1229 cells (p53 null) and A549 cells (wild-type p53) incubated with 5 μM probe 11 (1,5-bright field; 2,6-GFP channel). Imaging the inhibition of p53-MDM2 was accomplished by incubating 100 μM Nutlin-3 with 5 μM probe 11 (3-bright field; 4-GFP channel).

Fig. 5. Flow cytometry analysis of 5 μM probes 9–11 and 100 μM Nutlin-3 binding to the living cells of A549 (red-blank; blue-Nutlin-3; yellow-probes; green-probes and Nutlin-3). A- Probe 9, B- Probe 10, C- Probe 11.

Conclusions

In conclusion, three small-molecule fluorescent probes 9–11 with excellent fluorescent properties were designed and synthesized for visualizing the p53–MDM2 interaction. Preparation of these fluorescent probes is convenient and affordable. After extensive evaluation, these probes have been successfully applied to imaging the p53–MDM2 interaction in human lung cancer cell lines A549 (wild-type p53) at the micromolar level. Furthermore, these probes exhibited potent affinities for the p53–MDM2 interaction and slight cytotoxicity in living cells. As a result, these small-molecule fluorescent probes are expected to be used for drug screening and cell staining in p53–MDM2 fields, as well as in pathological and physiological studies of the p53–MDM2 interaction.