Synthesis and evaluation of novel orally active p53–MDM2 interaction inhibitors

Toward Understanding the Anticancer Activity of the Phytocompounds from Eugenia uniflora Using Molecular Docking, in silico Toxicity and Dynamics Studies

Background

The Surinam cherry, Eugenia uniflora belongs to the family Myrtaceae, an edible fruit-bearing medicinal plant with various biological properties. Several anticancer studies have been conducted on its essential oils while the non-essential oil compounds including phenolics, flavonoids, and carotenoids have not been fully investigated.

Purpose

Therefore, the study evaluated the in silico anticancer potentials of phenolic, flavonoid, and carotenoid compounds of E. uniflora against the MDM2 and Bcl-xL proteins, which are known to promote cancer cell growth and malignancy. The physicochemical parameters, validation, cytotoxicity, and mutagenicity of the polyphenols were determined using the SwissADME, pkCSM, ProTox-II, and vNN-ADMET online servers respectively. Lastly, the promising phytocompounds were validated using molecular dynamics (MD) simulation.

Results

An extensive literature search resulted in the compilation of forty-four (44) polyphenols from E. uniflora. Top-rank among the screened polyphenols is galloylastragalin, which exhibited a binding energy score of -8.7 and -8.5 kcal/mol with the hydrophobic interactions (Ala93, Val141) and (Leu54, Val93, Ile99), as well as hydrogen bond interactions (Tyr195) and (Gln72) of the proteins Bcl-xL and MDM2 respectively. A complete in silico toxicity assessment revealed that the compounds, galloylastragalin, followed by myricetin, resveratrol, p-Coumaroylquinic acid, and cyanidin-3-O-glucoside, were potentially non-mutagenic, non-carcinogenic, non-cytotoxic, and non-hepatotoxic. During the 120 ns MD simulations, the RMSF analysis of galloylastragalin- MDM2 (complex 1) and galloylastragalin- Bcl-xL (complex 2) showed the fewest fluctuations, indicating the conformational stability of the respective complexes.

Conclusion

This study has shown that polyphenol compounds of E. uniflora led by galloylastragalin, are potent inhibitors of the MDM2 and Bcl-xL cancer proteins. Thus, they may be considered as candidate polyphenols for further anticancer studies.

Turmeric-Black Cumin Essential Oils and Their Capacity to Attenuate Free Radicals, Protein Denaturation, and Cancer Proliferation

Turmeric rhizomes (Curcuma longa) and black cumin seeds (Nigella sativa) are polyherbal ingredients used for the management of cancer and other chronic inflammatory diseases in Nigerian ethnomedicine. Previous studies have shown the antioxidant, anti-inflammatory, and anticancer activities of the individual plant extracts. However, the two spices have not been biologically potentiated in their combined form. Therefore, this study obtained essential oils (EOs) from the combined spices and evaluated their inhibitory effects on free radicals, protein denaturation, and cancer proliferation. The EOs were extracted by hydro-distillation (HD) and characterized by gas chromatography-mass spectrometry (GC-MS). In vitro antioxidant assessment was conducted based on DPPH, hydrogen peroxide (H2O2), nitric oxide (NO), and ferric ion (Fe3+) radical scavenging assays. The cytotoxicity of the oil against non-tumorigenic (HEK293) and cancerous (HepG2 and HeLa) cell lines was determined following the MTT cell viability assay. An in silico molecular docking analysis of the oil constituents was also performed. Six batches of EOs I-VI were afforded, comprising twenty-two major constituents, with aromatic Ar-turmerone being the most prominent compound. There was a marked improvement in the bioactivity of the oils upon repeated HD and as a combination. The batch VI oil exhibited the best activity, with a cytotoxicity (CC50) of 10.16 ± 1.69 µg/100 µL against the HepG2 cell line, which was comparable to 5-fluorouracil (standard, CC50 = 8.59 ± 1.33 µg/100 µL). In silico molecular docking suggested δ-curcumene, Ar-curcumene, Ar-turmerol, and Ar-turmerone among the promising compounds based on their high binding energy scores with NOX2, NF-κB, and mdm2 proteins. In conclusion, the oils from the turmeric-black cumin combined possess a considerable inhibition ability against free radicals, protein denaturation, and cancer proliferation. This study's findings further underscore the effectiveness of turmeric-black cumin as a polyherbal medicinal ingredient.

One-pot chemoenzymatic syntheses of non-canonical amino acids

Despite their prevalent use in drug discovery and protein biochemistry, non-canonical amino acids are still challenging to synthesize through purely chemical means. In recent years, biocatalysis has emerged as a transformative paradigm for small-molecule synthesis. One strategy to further empower biocatalysis is to use it in combination with modern chemical reactions and take advantage of the strengths of each method to enable access to challenging structural motifs that were previously unattainable using each method alone. In this Mini-Review, we highlight several recent case studies that feature the synergistic use of chemical and enzymatic transformations in one pot to synthesize novel non-canonical amino acids.

ONE-SENTENCE SUMMARY

This Mini-Review highlights several recent case studies that feature the synergistic use of chemical and enzymatic transformations in one pot to synthesize novel non-canonical amino acids.

Recent advances in the pharmacological targeting of ubiquitin-regulating enzymes in cancer

As a post-translational modification that has pivotal roles in protein degradation, ubiquitination ensures that intracellular proteins act in a precise spatial and temporal manner to regulate diversified cellular processes. Perturbation of the ubiquitin system contributes directly to the onset and progression of a wide variety of diseases, including various subtypes of cancer. This highly regulated system has been for years an active research area for drug discovery that is exemplified by several approved drugs. In this review, we will provide an update of the main breakthrough scientific discoveries that have been leading the clinical development of ubiquitin-targeting therapies in the last decade, with a special focus on E1 and E3 modulators. We will further discuss the unique challenges of identifying new potential therapeutic targets within this ubiquitous and highly complex machinery, based on available crystallographic structures, and explore chemical approaches by which these challenges might be met.

Targeting p53-MDM2 interactions to identify small molecule inhibitors for cancer therapy: beyond "Failure to rescue"

At present, disrupting p53-MDM2 interactions through small molecule ligands is a promising approach to safe treatment and management of human cancer. Tumor cells unlike the normal cells, are rapidly evolving affecting the efficacy of many approved anti-cancer agents due to drug resistance. Therefore, identifying a potential anticancer compound is crucial. Pharmacophore based virtual screening, followed by molecular docking, ADMET evaluation, and molecular dynamics studies against MDM2 protein was investigated to identify potential ligands that may act as inhibitors. The model (AHRR_1) with survival score (4.176) was selected among the top ranked generated Pharmacophore hypothesis. Validation of the model hypothesis by an external dataset of actives and inactive compounds produced significant validation attributes including; AUC = 0.85, BEDROC = 0.56 at α = 20.0, RIE = 8.18, AUAC = 0.88, and EF of 6.2 at the top 2% of the dataset. The model was use for screening the ZINC database, and the top 1375 hits satisfying the model hypothesis were subjected to molecular docking studies to understand the molecular and structural basis of selectivity of compounds for MDM2 protein. A sub-set of 25 compounds with binding energy lower than the reference inhibitors were evaluated for pharmacokinetic properties. Four compounds (ZINC02639178, ZINC06752762, ZINC38933175, and ZINC77969611) showed the most desired pharmacokinetic profile. Lastly, investigation of the dynamic behaviour of leads-protein complexes through MD simulation showed similar RMSD, RMSF, and H-bond occupancy profile compared to a reference inhibitor, suggesting stability throughout the simulation time. However, ZINC02639178 was found to satisfy the molecular enumeration the most compared to the other three leads. It may emerge as potential treatment option after extensive experimental studies. Communicated by Ramaswamy H. Sarma.

p53: An Attractive Therapeutic Target for Cancer

Cancer is a leading cause of death worldwide. It initiates when cell cycle regulatory genes lose their function either by environmental and/or by internal factors. Tumor suppressor protein p53, known as "Guardian of genome", plays a central role in maintaining genomic stability of the cell. Mutation of TP53 is documented in more than 50% of human cancers, usually by overexpression of negative regulator protein MDM2. Hence, reactivation of p53 by blocking the protein-protein interaction between the murine double minute 2 (MDM2) and the tumor suppressor protein p53 has become the most promising therapeutic strategy in oncology. Several classes of small molecules have been identified as potent, selective and efficient p53-MDM2 inhibitors. Herein, we review the druggability of p53-MDM2 inhibitors and their optimization approaches as well as clinical candidates categorized by scaffold type.

Recent Small-Molecule Inhibitors of the p53-MDM2 Protein-Protein Interaction

This review presents the last decade of studies on the synthesis of various types of small-molecule inhibitors of the p53- Mouse double minute 2 homolog (MDM2) protein-protein interaction. The main focus is placed on synthetic approaches to such molecules, their cytotoxicity, and MDM2 binding characteristics.

The past, present and future of potential small-molecule drugs targeting p53-MDM2/MDMX for cancer therapy

The p53 gene, a well-known tumor suppressor gene, plays a crucial role in cell cycle regulation, DNA repair, cell differentiation, and apoptosis. MDM2 exerts p53-dependent activity mainly by binding to p53 protein to form MDM2-p53 negative feedback loop. In addition, MDM2 is involved in a number of pathways that regulate cell proliferation and apoptosis, playing a p53-independent role. The p53 binding domain of MDMX bind to p53 transcriptional activation domain, inhibiting the transcriptional activity of p53 on its downstream genes, but does not mediate the degradation of p53. The anti-tumor effect is exerted by inhibiting the interaction between the MDM2/MDMX protein and the p53 protein by a small-molecule or by restoring the activity of the p53 protein. This review describes in the structural features, biological functions and mechanisms of p53-MDM2/MDMX, and summarizes small-molecule targeting p53-MDM2/MDMX.

Identification of new inhibitors of Mdm2-p53 interaction via pharmacophore and structure-based virtual screening

Background

The tumor suppressor protein p53 plays an important role in preventing tumor formation and progression through its involvement in cell division control and initiation of apoptosis. Mdm2 protein controls the activity of p53 protein through working as ubiquitin E3 ligase promoting p53 degradation through the proteasome degradation pathway. Inhibitors for Mdm2-p53 interaction have restored the activity of p53 protein and induced cancer fighting properties in the cell.

Purpose

The objective of this study is to use computer-aided drug discovery techniques to search for new Mdm2-p53 interaction inhibitors.

Methods

A set of pharmacophoric features were created based on a standard Mdm2 inhibitor and this was used to screen a commercial drug-like ligand library; then potential inhibitors were docked and ranked in a multi-step protocol using GLIDE. Top ranked ligands from docking were evaluated for their inhibition activity of Mdm2-p53 interaction using ELISA testing.

Results

Several compounds showed inhibition activity at the submicromolar level, which is comparable to the standard inhibitor Nutlin-3a. Furthermore, the discovered inhibitors were evaluated for their anticancer activities against different breast cancer cell lines, and they showed an interesting inhibition pattern.

Conclusion

The reported inhibitors can represent a starting point for further SAR studies in the future and can help in the discovery of new anticancer agents.

A Computational Investigation of Small-Molecule Engagement of Hot Spots at Protein-Protein Interaction Interfaces

The binding affinity of a protein-protein interaction is concentrated at amino acids known as hot spots. It has been suggested that small molecules disrupt protein-protein interactions by either (i) engaging receptor protein hot spots or (ii) mimicking hot spots of the protein ligand. Yet, no systematic studies have been done to explore how effectively existing small-molecule protein-protein interaction inhibitors mimic or engage hot spots at protein interfaces. Here, we employ explicit-solvent molecular dynamics simulations and end-point MM-GBSA free energy calculations to explore this question. We select 36 compounds for which high-quality binding affinity and cocrystal structures are available. Five complexes that belong to three classes of protein-protein interactions (primary, secondary, and tertiary) were considered, namely, BRD4•H4, XIAP•Smac, MDM2•p53, Bcl-xL•Bak, and IL-2•IL-2Rα. Computational alanine scanning using MM-GBSA identified hot-spot residues at the interface of these protein interactions. Decomposition energies compared the interaction of small molecules with individual receptor hot spots to those of the native protein ligand. Pharmacophore analysis was used to investigate how effectively small molecules mimic the position of hot spots of the protein ligand. Finally, we study whether small molecules mimic the effects of the native protein ligand on the receptor dynamics. Our results show that, in general, existing small-molecule inhibitors of protein-protein interactions do not optimally mimic protein-ligand hot spots, nor do they effectively engage protein receptor hot spots. The more effective use of hot spots in future drug design efforts may result in smaller compounds with higher ligand efficiencies that may lead to greater success in clinical trials.

An Integrative Analysis Reveals a Central Role of P53 Activation via MDM2 in Zika Virus Infection Induced Cell Death

Zika virus (ZIKV) infection is an emerging global threat that is suspected to be associated with fetal microcephaly. However, the molecular mechanisms underlying ZIKV disease pathogenesis in humans remain elusive. Here, we investigated the human protein interaction network associated with ZIKV infection using a systemic virology approach, and reconstructed the transcriptional regulatory network to analyze the mechanisms underlying ZIKV-elicited microcephaly pathogenesis. The bioinformatics findings in this study show that P53 is the hub of the genetic regulatory network for ZIKV-related and microcephaly-associated proteins. Importantly, these results imply that the ZIKV capsid protein interacts with mouse double-minute-2 homolog (MDM2), which is involved in the P53-mediated apoptosis pathway, activating the death of infected neural cells. We also found that synthetic mimics of the ZIKV capsid protein induced cell death in vitro and in vivo. This study provides important insight into the relationship between ZIKV infection and brain diseases.

Molecular Basis and Targeted Inhibition of CBFβ-SMMHC Acute Myeloid Leukemia

Acute myeloid leukemia (AML) is characterized by recurrent chromosomal rearrangements that encode for fusion proteins which drive leukemia initiation and maintenance. The inv(16) (p13q22) rearrangement is a founding mutation and the associated CBFβ-SMMHC fusion protein is essential for the survival of inv(16) AML cells. This Chapter will discuss our understanding of the function of this fusion protein in disrupting hematopoietic homeostasis and creating pre-leukemic blasts, in its cooperation with other co-occurring mutations during leukemia initiation, and in leukemia maintenance. In addition, this chapter will discuss the current approaches used for the treatment of inv(16) AML and the recent development of AI-10-49, a selective targeted inhibitor of CBFβ-SMMHC/RUNX1 binding, the first candidate targeted therapy for inv(16) AML.

How To Design a Successful p53-MDM2/X Interaction Inhibitor: A Thorough Overview Based on Crystal Structures

A recent therapeutic strategy in oncology is based on blocking the protein-protein interaction between the murine double minute (MDM) homologues MDM2/X and the tumor-suppressor protein p53. Inhibiting the binding between wild-type (WT) p53 and its negative regulators MDM2 and/or MDMX has become an important target in oncology to restore the antitumor activity of p53, the so-called guardian of our genome. Interestingly, based on the multiple disclosed compound classes and structural analysis of small-molecule-MDM2 adducts, the p53-MDM2 complex is perhaps the best studied and most targeted protein-protein interaction. Several classes of small molecules have been identified as potent, selective, and efficient inhibitors of the p53-MDM2/X interaction, and many co-crystal structures with the protein are available. Herein we review the properties as well as preclinical and clinical studies of these small molecules and peptides, categorized by scaffold type. A particular emphasis is made on crystallographic structures and the observed binding modes of these compounds, including conserved water molecules present.

Focusing on shared subpockets - new developments in fragment-based drug discovery

INTRODUCTION

Protein-protein interactions (PPIs) are important targets for understanding fundamental biology and for the development of therapeutic agents. Based on different physicochemical properties, numerous pieces of software (e.g., POCKETQUERY, ANCHORQUERY and FTMap) have been reported to find pockets on protein surfaces and have applications in facilitating the design and discovery of small-molecular-weight compounds that bind to these pockets.

AREAS COVERED

The authors discuss a pocket-centric method of analyzing PPI interfaces, which prioritize their pockets for small-molecule drug discovery and the importance of multicomponent reaction chemistry as starting points for undruggable targets. The authors also provide their perspectives on the field.

EXPERT OPINION

Only the tight interplay of efficient computational methods capable of screening a large chemical space and fast synthetic chemistry will lead to progress in the rational design of PPI antagonists in the future. Early drug discovery platforms will also benefit from efficient rapid feedback loops from early clinical research back to molecular design and the medicinal chemistry bench.

Discovery of DS-5272 as a promising candidate: A potent and orally active p53-MDM2 interaction inhibitor

We have published p53-MDM2 interaction inhibitors possessing a novel dihydroimidazothiazole scaffold. Although our lead compound 1 showed strong antitumor activity with single oral administration on a xenograft model using MV4-11 cells harboring wild-type p53, it needed a higher dose (200mg/kg) for distinct efficacy. We executed further optimization with the aim of improvement of potency and physicochemical properties. Thus optimal compounds were furnished by introducing fluorine moieties onto the phenyl ring at the C-6 position and the pyrrolidine part at the C-2 substituent; and modifying the terminal piperazine to 4,7-diazaspiro[2,5]octane variants. Furthermore, replacing 4-chlorophenyl on the C-5 position with pyridyl variant decreased nonspecific cytotoxicity significantly. Our exploration afforded DS-5272 indicating excellent antitumor efficacy from a dose of 25mg/kg on SJSA-1 xenografted models with high safety and good PK profiles, which has appropriate potency as a clinical candidate.

Small-molecule inhibitors of the MDM2-p53 protein-protein interaction (MDM2 Inhibitors) in clinical trials for cancer treatment

Design of small-molecule inhibitors (MDM2 inhibitors) to block the MDM2–p53 protein–protein interaction has been pursued as a new cancer therapeutic strategy. In recent years, potent, selective, and efficacious MDM2 inhibitors have been successfully obtained and seven such compounds have been advanced into early phase clinical trials for the treatment of human cancers. Here, we review the design, synthesis, properties, preclinical, and clinical studies of these clinical-stage MDM2 inhibitors.

Structurally diverse MDM2-p53 antagonists act as modulators of MDR-1 function in neuroblastoma

BACKGROUND

A frequent mechanism of acquired multidrug resistance in human cancers is overexpression of ATP-binding cassette transporters such as the Multi-Drug Resistance Protein 1 (MDR-1). Nutlin-3, an MDM2-p53 antagonist, has previously been reported to be a competitive MDR-1 inhibitor.

METHODS

This study assessed whether the structurally diverse MDM2-p53 antagonists, MI-63, NDD0005, and RG7388 are also able to modulate MDR-1 function, particularly in p53 mutant neuroblastoma cells, using XTT-based cell viability assays, western blotting, and liquid chromatography-mass spectrometry analysis.

RESULTS

Verapamil and the MDM2-p53 antagonists potentiated vincristine-mediated growth inhibition in a concentration-dependent manner when used in combination with high MDR-1-expressing p53 mutant neuroblastoma cell lines at concentrations that did not affect the viability of cells when given alone. Liquid chromatography-mass spectrometry analyses showed that verapamil, Nutlin-3, MI-63 and NDD0005, but not RG7388, led to increased intracellular levels of vincristine in high MDR-1-expressing cell lines.

CONCLUSIONS

These results show that in addition to Nutlin-3, other structurally unrelated MDM2-p53 antagonists can also act as MDR-1 inhibitors and reverse MDR-1-mediated multidrug resistance in neuroblastoma cell lines in a p53-independent manner. These findings are important for future clinical trial design with MDM2-p53 antagonists when used in combination with agents that are MDR-1 substrates.

Inhibition of nutlin-resistant HDM2 mutants by stapled peptides

Pharmacological modulation of p53 activity is an attractive therapeutic strategy in cancers with wild-type p53. Presently in clinical trials, the small molecule Nutlin-3A competitively binds to HDM2, a key negative regulator of p53 and blocks its activity. We have described resistance mutations in HDM2 that selectively reduce affinity for Nutlin but not p53. In the present communication, we show that stapled peptides targeting the same region of HDM2 as Nutlin are refractory to these mutations, and display reduced discrimination between the wild-type and mutant HDM2s with regards to functional abrogation of interaction with p53. The larger interaction footprint afforded by stapled peptides suggests that this class of ligands may prove comparatively more resilient to acquired resistance in a clinical setting.