Energetic Landscape of MDM2-p53 Interactions by Computational Mutagenesis of the MDM2-p53 Interaction

Navigating the complexity of p53-DNA binding: implications for cancer therapy

Abstract

The tumor suppressor protein p53, a transcription factor playing a key role in cancer prevention, interacts with DNA as its primary means of determining cell fate in the event of DNA damage. When it becomes mutated, it opens damaged cells to the possibility of reproducing unchecked, which can lead to formation of cancerous tumors. Despite its critical role, therapies at the molecular level to restore p53 native function remain elusive, due to its complex nature. Nevertheless, considerable information has been amassed, and new means of investigating the problem have become available.

Objectives

We consider structural, biophysical, and bioinformatic insights and their implications for the role of direct and indirect readout and how they contribute to binding site recognition, particularly those of low consensus. We then pivot to consider advances in computational approaches to drug discovery.

Materials and methods

We have conducted a review of recent literature pertinent to the p53 protein.

Results

Considerable literature corroborates the idea that p53 is a complex allosteric protein that discriminates its binding sites not only via consensus sequence through direct H-bond contacts, but also a complex combination of factors involving the flexibility of the binding site. New computational methods have emerged capable of capturing such information, which can then be utilized as input to machine learning algorithms towards the goal of more intelligent and efficient de novo allosteric drug design.

Conclusions

Recent improvements in machine learning coupled with graph theory and sector analysis hold promise for advances to more intelligently design allosteric effectors that may be able to restore native p53-DNA binding activity to mutant proteins.

Clinical relevance

The ideas brought to light by this review constitute a significant advance that can be applied to ongoing biophysical studies of drugs for p53, paving the way for the continued development of new methodologies for allosteric drugs. Our discoveries hold promise to provide molecular therapeutics which restore p53 native activity, thereby offering new insights for cancer therapies.

Graphical Abstract

Structural representation of the p53 DBD (PDBID 1TUP). DNA consensus sequence is shown in gray, and the protein is shown in blue. Red beads indicate hotspot residue mutations, green beads represent DNA interacting residues, and yellow beads represent both.

Elevated apoptosis and abnormal apoptosis signaling of regulatory T cells in patients with systemic lupus erythematosus

In systemic lupus erythematosus (SLE), immune tolerance is influenced by defects in naturally occurring T cells (Tregs). To investigate the apoptosis rate of Tregs and their suppressive activity in patients with SLE and then to recognize the genes and signaling pathways that cause Treg apoptosis. FACS was used to assess the frequency and apoptosis rates of Tregs in 48 SLE patients and 28 normal controls (NCs). Coculture of Tregs with CD4⁺CD25^-CD127^dim/- T cells was used to assess the suppressive activity of Tregs. Microarray analysis was used to generate unstimulated Tregs gene expression profiles from very high activity patients with SLE and NCs. Real-time PCR was used to confirm differential gene expression. In patients with SLE, the frequency of Tregs was substantially reduced compared to Tregs from NCs. Furthermore, Tregs from SLE patients had an elevated rate of apoptosis and a lower suppressing ability than Tregs from NCs. Tregs apoptosis was negatively associated with the total count of Tregs and positively related to disease activity. Unstimulated Tregs gene expression profiles from patients with recent-onset SLE revealed a biological response that can cause apoptosis, partially triggered by stress, DNA damage, and cytokine stimulation. The discovery of pathway-specific expression signatures is a significant step forward in understanding how Tregs defects contribute to the pathogenesis of SLE. Our findings may contribute to the development of new strategies for treating SLE based on abnormal Tregs apoptosis and restoring immune homeostasis in patients with SLE.

RASSF10 regulates bone invasion of growth hormone-secreting adenomas via exosomes

BACKGROUND

Invasion of pituitary growth hormone-secreting adenoma into surrounding tissues poses a challenge for complete resection in surgery, which is the main reason for recurrence of this type of cancer. Studies have shown that abnormal methylation of RASSF10 can promote the expression of MDM2 and regulate the tumor microenvironment by affecting the secretion of exosomes. In the present study, we aim to uncover the specific underlying mechanism of this effect.

METHOD

Transwell co-culture assays was performed using GT1.1 cells or exosomes and RAW264.7 cells. RAW264.7 cells were collected for invasion, proliferation and apoptosis assays, RT-qPCR and western blotting. RNA-seq was performed and used to assess the potential molecular pathways of the effect of GT1.1 cell-exosomes on RAW264.7 cells.

RESULTS

GT1.1 cells with reduced RASSF10 expression could promote the proliferation and migration of RAW264.7 cells, and promote their expression of osteoclast markers TRAP and CK. The effect of GT1.1 cell exosomes on the RAW264.7-cell phenotype was shown to be achieved through the RASSF10-MDM2 pathway. RNA-seq allowed the identification of PI3K-AKT, MAPK, and calcium signaling as important in this regulation system of RASSF10-MDM2.

CONCLUSION

Our results indicate that GT1.1 cells activate PI3K-AKT, MAPK and calcium signaling via the RASSF10-MDM2 pathway, and promote the differentiation of RAW264.7 cells into osteoclasts through exosomes. This study may provide new ideas to aid in early diagnosis, prognostic assessment and treatment of aggressive pituitary adenomas.

Computational Investigation on the p53-MDM2 Interaction Using the Potential of Mean Force Study

Murine double minute 2 (MDM2) proteins are found to be overproduced by many human tumors in order to inhibit the functioning of p53 molecules, a tumor suppressor protein. Thus, reactivating p53 functioning in cancer cells by disrupting p53-MDM2 interactions may offer a significant approach in cancer treatment. However, the structural characterization of the p53-MDM2 complex at the atomistic level and the mechanism of binding/unbinding of the p53-MDM2 complex still remain unclear. Therefore, we demonstrate here the probable binding (unbinding) pathway of transactivation domain 1 of p53 during the formation (dissociation) of the p53-MDM2 complex in terms of free energy as a function of reaction coordinate from the potential of mean force (PMF) study using two different force fields: ff99SB and ff99SB-ILDN. From the PMF plot, we noticed the PMF to have a minimum value at a p53-MDM2 separation of 12 Å, with a dissociation energy of 30 kcal mol^-1. We also analyzed the conformational dynamics and stability of p53 as a function of its distance of separation from MDM2. The secondary structure content (helix and turns) in p53 was found to vary with its distance of separation from MDM2. The p53-MDM2 complex structure with lowest potential energy was isolated from the ensemble at the reaction coordinate corresponding to the minimum PMF value and subjected to molecular dynamics simulation to identify the interface surface area, interacting residues at the interface, and the stability of the complex. The simulation results highlight the importance of hydrogen bonds and the salt bridge between Lys94 of MDM2 and Glu17 of p53 in the stability of the p53-MDM2 complex. We also carried out the binding free energy calculations and the per residue energy decomposition analyses of the interface residues of the p53-MDM2 complex. We found that the binding affinity between MDM2 and p53 is indeed high [ΔG _bind = -7.29 kcal mol^-1 from molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) and ΔG _bind = -53.29 kcal mol^-1 from molecular mechanics/generalized borne surface area]. The total binding energy obtained using the MM/PBSA method was noticed to be closer to the experimental values (-6.4 to -9.0 kcal mol^-1). The p53-MDM2 complex binding profile was observed to follow the same trend even in the duplicate simulation run and also in the simulation carried out with different force fields. We found that Lys51, Leu54, Tyr100, and Tyr104 from MDM2 and the residues Phe19, Trp23, and Leu26 from p53 provide the highest energy contributions for the p53-MDM2 interaction. Our findings highlight the prominent structural and binding characteristics of the p53-MDM2 complex that may be useful in designing potential inhibitors to disrupt the p53-MDM2 interactions.

Overexpression of CCDC69 activates p14ARF/MDM2/p53 pathway and confers cisplatin sensitivity

OBJECTIVES

The aim of the study is to explore the relationship between CCDC69 expression and resistance of ovarian cancer cells to cisplatin and reveal the underlying mechanism.

METHODS

One hundred thirty five ovarian cancer patients with intact chemo-response information from The Cancer Genome Atlas (TCGA) database were included and analyzed. Stable CCDC69 overexpressing 293 and ovarian cancer A2780 cell lines were established and subjected to examine cell apoptosis and cell cycle distribution using CCK-8 assay and flow cytometry. Cell cycle and apoptosis pathway were evaluated by immunoblots. Stability of p14^ARF/MDM2/p53 pathway related proteins were determined by half-life analysis and ubiquitination experiments.

RESULTS

We found that CCDC69 expression was significantly higher in chemo-sensitive groups compared with chemo-resistant groups from TCGA database. High CCDC69 expression was associated longer survival. CCDC69 overexpressing 293 and A2780 cells with wildtype p53 and contributes to cisplatin sensitivity following treatment with cisplatin. We further found over-expression of CCDC69 activated p14^ARF/MDM2/p53 pathway. Importantly, we also demonstrated that CCDC69 expression extended p53 and p14^ARF protein half-life and shortened MDM2 protein half-life. Ubiquitination assay revealing a decrease in p14 ubiquitination in CCDC69 over-expression cells comparing to cells expressing empty vector.

CONCLUSIONS

It is tempting to conclude that targeting CCDC69 may play a role in cisplatin resistance.

Interaction with AEG-1 and MDM2 is associated with glioma development and progression and correlates with poor prognosis

Glioma is the most common central nervous system tumor with poor prognosis. The AEG-1 (Astrocyte Elevated Gene 1) gene displays oncogenic characteristics, including proliferation, metastasis, chemoresistance, invasion, and evasion of apoptosis, and is strongly linked to the occurrence of glioma. Here, we elucidated the potential contribution of AEG-1 in human glioma pathogenesis. In glioma cells, AEG-1 could directly interact with Murine Double Minute-2 (MDM2) protein resulting in MDM2-p53-mediated cell proliferation and apoptosis. MDM2 is being revealed as an oncoprotein, which is involved in many human cancers progression. By immunohistochemical and a multivariate analysis, expressions of AEG-1 and MDM2 were elevated in glioma and high AEG-1 and MDM2 expressions were showed to be correlated with poor prognosis. AEG-1-MDM2 interaction prolonged stabilization of MDM2 where AEG-1 inhibited ubiquitination and subsequent proteasome-mediated degradation of MDM2 protein. Moreover, slicing AEG-1 blocked MDM2 expression and then impacted MDM2-p53 pathway that influenced cell proliferation and apoptosis. These findings uncover a novel AEG-1-MDM2 interplay by which AEG-1 augments glioma progression and reveal a viable potential therapy for the treatment of glioma patients.

Analysis of Ki67, HMGA1, MDM2, and RB expression in nonfunctioning pituitary adenomas

Nonfunctioning pituitary adenomas (NFPAs) are the most prevalent type of pituitary macro-adenoma. Clarifying the relationship between NFPA markers and disease progression or recurrence could provide a basis for administration of adjuvant treatments. The present study examined the expression levels of high-mobility group (HMG)A1, Ki-67, mouse double minute 2 homolog (MDM2), and retinoblastoma (RB)with respect to NFPA recurrence. Immunohistochemistry was carried out using antibodies to Ki-67, MDM2, HMGA-1, and RB on tissue microarray slides of a cohort of 35 paired NFPA samples of primary and recurrence/regrowth tumors. Based on postoperative magnetic resonance imaging data, tumors were classified as recurrence (n = 20) included primary and recurrent tumors or regrowth (n = 15) included primary and regrowth tumors, which are paired. Protein expression was classified as negative or positive according to the H-score method and was analyzed with respect to clinical and pathological findings. MDM2-positive cases accounted for11/20 primary and 19/20 s recurrent tumors (χ² = 8.533, P = 0.003), and 9/15 primary tumors and 15/15 s regrowth tumors (χ² = 7.5, P = 0.006). MGA1-positive cases represented 9/20 primary tumors and 16/20 s recurrent tumors (χ² = 5.227, P = 0.022), and 4/15 primary tumors and 12/15 s regrowth tumors (χ² = 8.571, P = 0.003). There was no statistically significant difference in Ki-67 expression between primary and second recurrent/regrowth tumors although theKi67 labeling index was higher in the latter groups. RB was highly expressed in all groups with no significant difference between them. HMGA1 and MDM2 were more highly expressed in recurrence/regrowth cases of NFPA than in primary NFPA. HMGA1 and MDM2 are biomarkers and potential drug targets for NFPA treatment.