Development and characterization of proteasome inhibitors

Factors determining the sensitivity to proteasome inhibitors of multiple myeloma cells

Multiple myeloma is an incurable cancer that originates from antibody-producing plasma cells. It is characterized by an intrinsic ability to produce large amounts of immunoglobulin-like proteins. The high rate of synthesis makes myeloma cells dependent on protein processing mechanisms related to the proteasome. This dependence made proteasome inhibitors such as bortezomib and carfilzomib one of the most important classes of drugs used in multiple myeloma treatment. Inhibition of the proteasome is associated with alteration of a number of important biological processes leading, in consequence, to inhibition of angiogenesis. The effect of drugs in this group and the degree of patient response to the treatment used is itself an extremely complex process that depends on many factors. At cellular level the change in sensitivity to proteasome inhibitors may be related to differences in the expression level of proteasome subunits, the degree of proteasome loading, metabolic adaptation, transcriptional or epigenetic factors. These are just some of the possibilities that may influence differences in response to proteasome inhibitors. This review describes the main cellular factors that determine the degree of response to proteasome inhibitor drugs, as well as information on the key role of the proteasome and the performance characteristics of the inhibitors that are the mainstay of multiple myeloma treatment.

Discovery and Development of Cyclic Peptide Proteasome Stimulators

The proteasome degrades proteins, which is essential for cellular homeostasis. Ubiquitin independent proteolysis degrades highly disordered and misfolded proteins. A decline of proteasomal activity has been associated with multiple neurodegenerative diseases due to the accumulation of misfolded proteins. In this work, cyclic peptide proteasome stimulators (CyPPSs) that enhance the clearance of misfolded proteins were discovered. In the initial screen of predicted natural products (pNPs), several cyclic peptides were found to stimulate the 20S core particle (20S CP). Development of a robust structural activity relationship led to the identification of potent, cell permeable CyPPSs. In vitro assays revealed that CyPPSs stimulate degradation of highly disordered and misfolded proteins without affecting ordered proteins. Furthermore, using a novel flow-based assay for proteasome activity, several CyPPSs were found to stimulate the 20S CP in cellulo. Overall, this work describes the development of CyPPSs as chemical tools capable of stimulating the proteasome and provides strong support for proteasome stimulation as a therapeutic strategy for neurodegenerative diseases.

Effect of Metabolite Extract of Streptomyces hygroscopicus subsp. hygroscopicus on Plasmodium falciparum 3D7 in Vitro

BACKGROUND

Malaria eradication has been complicated by the repeated emergence of antimalarial drug resistances. We aimed to determine whether a metabolite extract of Streptomyces hygrocopicus subsp. hygroscopicus could decrease the viability of Plasmodium falciparum 3D7 in vitro.

METHODS

S. hygroscopicus subsp. hygroscopicus isolates were inoculated and fermented on the ISP4 medium. The fermented S. hygroscopicus was mixed with ethylacetate 1:5 (v/v), and the solvent phase was evaporated. Several concentrations of isolated extract was added to the P. falciparum 3D7 culture containing trophozoite and schizont stages in 24 wells plates when the degree of parasite-infected erythrocytes reached 5%, then incubated for 8 hours. DNA parasite density was measured using flow cytometry, parasite degree and morphology were observed under microscopic by Giemsa-stained smears.

RESULTS

The metabolite extract affected the morphology of almost all of parasite asexual stages. Schizonts and trophozoites failed to grow and appeared damaged with pycnotic cores and loss of cytoplasmic content. At 8 hours there was a significant decrease in DNA parasite density in culture exposed to 2.6 mg/ml and 13 mg/ml (P = 0.002; P = 0.024) of the extract. The degree of parasite-infected erythrocytes was decreased from the beginning of exposure (0.02 mg/ml of the extract). There was a significant inverse correlation between the concentration of extract and the degree of parasite-infected erythrocytes as well as the density of DNA parasite (r = -0.772, P = 0.000; r =-0.753; P =0.000).

CONCLUSION

Metabolite extract of S. hygroscopicus subsp. hygroscopicus causes morphological damage, decreases the degree of parasite-infected erythrocytes and the DNA density of P. falciparum 3D7 in vitro.

Emerging small molecule approaches to enhance the antimyeloma benefit of proteasome inhibitors

Multiple myeloma (MM) is a clonal plasma cell malignancy which, despite recent treatment advances, remains incurable in the vast majority of the over 118,000 patients in the USA afflicted with this disease. Treatment of MM has dramatically improved in the past decade with the introduction of new drugs into therapeutic strategies in both the frontline and relapse settings that has led to a significant improvement in the median overall survival (OS). These drugs have been incorporated into clinical guidelines and transformed the treatment approach to MM. Numerous classes of antimyeloma agents, i.e., alkylators, steroids, proteasome inhibitors, immunomodulatory agents, deactylase inhibitors, and monoclonal antibodies, are now FDA-approved and can be combined in doublet or triplet regimens. Moreover, many patients do not respond to therapy and those that do eventually relapse. Emerging therapies that may overcome drug resistance and improve MM treatment include that inhibit regulatory and Ub-processing components of the proteasome, a specialized variant of the proteasome known as the immunoproteasome, proteolysis-targeting chimeric molecules (PROTACS and Degronomids). Emerging strategies also include accessory plasmacytoid dendritic cells (pDCs), vaccines, checkpoint inhibitors, and chimeric antigen receptor-engineered T (CAR-T) cells. Advances in understanding proteasome and plasma cell biology may allow for earlier treatment of MM patients using rationally informed combination therapies with curative potential.

The Advantages of Targeted Protein Degradation Over Inhibition: An RTK Case Study

Proteolysis targeting chimera (PROTAC) technology has emerged over the last two decades as a powerful tool for targeted degradation of endogenous proteins. Herein we describe the development of PROTACs for receptor tyrosine kinases, a protein family yet to be targeted for induced protein degradation. The use of VHL-recruiting PROTACs against this protein family reveals several advantages of degradation over inhibition alone: direct comparisons of fully functional, target-degrading PROTACs with target-inhibiting variants that contain an inactivated E3 ligase-recruiting ligand show that degradation leads to more potent inhibition of cell proliferation and a more durable and sustained downstream signaling response, and thus addresses the kinome rewiring challenge seen with many receptor tyrosine kinase inhibitors. Combined, these findings demonstrate the ability to target receptor tyrosine kinases for degradation using the PROTAC technology and outline the advantages of this degradation-based approach.

PSMB9 codon 60 polymorphisms have no impact on the activity of the immunoproteasome catalytic subunit B1i expressed in multiple types of solid cancer

The proteasome is a key regulator of cellular protein homeostasis and is a clinically validated anticancer target. The immunoproteasome, a subtype of proteasome expressed mainly in hematopoietic cells, was initially recognized for its role in antigen presentation during the immune response. Recently, the immunoproteasome has been implicated in several disease conditions including cancer and autoimmune disorders, but many of the factors contributing to these pathological processes remain unknown. In particular, the codon 60 polymorphism of the PSMB9 gene encoding the β1i immunoproteasome catalytic subunit has been investigated in the context of a variety of diseases. Despite this, previous studies have so far reported inconsistent findings regarding the impact of this polymorphism on proteasome activity. Thus, we set out to investigate the impact of the PSMB9 codon 60 polymorphism on the expression and activity of the β1i immunoproteasome subunit in a panel of human cancer cell lines. The β1i-selective fluorogenic substrate Acetyl-Pro-Ala-Leu-7-amino-4-methylcoumarin was used to specifically measure β1i catalytic activity. Our results indicate that the codon 60 Arg/His polymorphism does not significantly alter the expression and activity of β1i among the cell lines tested. Additionally, we also examined the expression of β1i in clinical samples from colon and pancreatic cancer patients. Our immunohistochemical analyses showed that ∼70% of clinical colon cancer samples and ∼53% of pancreatic cancer samples have detectable β1i expression. Taken together, our results indicate that the β1i subunit of the immunoproteasome is frequently expressed in colon and pancreatic cancers but that the codon 60 genetic variants of β1i display similar catalytic activities and are unlikely to contribute to the significant inter-cell-line and inter-individual variabilities in the immunoproteasome activity.

Revisiting the role of the immunoproteasome in the activation of the canonical NF-κB pathway

The discovery of NF-κB signaling pathways has greatly enhanced our understanding of inflammatory and immune responses. In the canonical NF-κB pathway, the proteasomal degradation of IκBα, an inhibitory protein of NF-κB, is widely accepted to be a key regulatory step. However, contradictory findings have been reported as to whether the immunoproteasome plays an obligatory role in the degradation of IκBα and activation of the canonical NF-κB pathway. Such results were obtained mainly using traditional gene deletion strategies. Here, we have revisited the involvement of the immunoproteasome in the canonical NF-κB pathway using small molecule inhibitors of the immunoproteasome, namely UK-101 and LKS01 targeting β1i and β5i, respectively. H23 and Panc-1 cancer cells were pretreated with UK-101, LKS01 or epoxomicin (a prototypic inhibitor targeting both the constitutive proteasome and immunoproteasome). We then examined whether these pretreatments lead to any defect in activating the canonical NF-κB pathway following TNFα exposure by monitoring the phosphorylation and degradation of IκBα, nuclear translocation of NF-κB proteins and DNA binding and transcriptional activity of NF-κB. Our results consistently indicated that there is no defect in activating the canonical NF-κB pathway following selective inhibition of the immunoproteasome catalytic subunits β1i, β5i or both using UK-101 and LKS01, in contrast to epoxomicin. In summary, our current results using chemical genetic approaches strongly support that the catalytic activity of the immunoproteasome subunits β1i and β5i is not required for canonical NF-κB activation in lung and pancreatic adenocarcinoma cell line models.

MG132 enhances neurite outgrowth in neurons overexpressing mutant TAR DNA-binding protein-43 via increase of HO-1

In patients with amyotrophic lateral sclerosis (ALS), various mutations were identified in TAR DNA-binding protein-43 (TDP-43). In the present study, we found that mutant TDP-43 inhibited the neurite outgrowth. Subsequently, we tested the effect of MG132 on the mutant TDP-43 cell lines. Non-toxic doses of MG132 promoted neurite extension and decreased the level of thiobarbituric acid-reactive substances (TBARS). Heme oxygenase-1 (HO-1) known as antioxidase was restored by MG132. Conversely, Zinc protoporphyrin IX (ZnPP IX), which is an inhibitor of heme oxygenase, inhibited neurite outgrowth induced by MG132. It was well known that HO-1 was regulated by nuclear factor E2-related factor 2 (Nrf2). However, MG132 increased the expression of HO-1 independent of the Nrf2 pathway.

Combined chemical and genetic approach to inhibit proteolysis by the proteasome

Regulated protein destruction by the proteasome is crucial for the maintenance of normal cellular homeostasis. Much of our understanding of proteasome function stems from the use of drugs that inhibit its activity. Curiously, despite the importance of proteasomal proteolysis, previous studies have found that proliferation of the yeast Saccharomyces cerevisiae is relatively resistant to the effects of proteasome inhibitors such as MG132, even in the presence of mutations that increase inhibitor levels in cells. We reasoned that part of the resistance of S. cerevisiae to proteasome inhibitors stems from the fact that most proteasome inhibitors preferentially target the chymotryptic activity of the proteasome, and that the caspase-like and tryptic sites within the 20S core could compensate for proteasome function under these conditions. To test this hypothesis, we generated a strain of yeast in which the gene encoding the drug efflux pump Pdr5 is deleted, and the tryptic and caspase-like proteasome activities are inactivated by mutation. We find that this strain has dramatically increased sensitivity to the proteasome inhibitor MG132. Under these conditions, treatment of yeast with MG132 blocks progression through the cell cycle, increases the accumulation of polyubiquitylated proteins and decreases the ability to induce transcription of certain genes. These results highlight the contribution of the caspase-like and tryptic activities of the proteasome to its function, and provide a strategy to potently block proteasomal proteolysis in yeast that has practical applications.

Measurement of proteasomal dysfunction in cell models of dopaminergic degeneration

Parkinson's disease (PD) is the second most common neurodegenerative diseases, which occurs in both inheritable and sporadic forms. The interplay of the genetic mutations and environmental exposure to disease risk factors contributes to the pathogenic events leading to the demise of dopaminergic neurons in PD. Proteasome is one of the major proteolytic machinery responsible for degrading unwanted and damaged intracellular proteins. Emerging evidence implicates the incomplete proteolysis by ubiquitin-proteasome system (UPS) in PD pathogenesis. Proteasome inhibition recapitulates some of the key features of PD in vivo and in vitro. Varieties of dopaminergic neurotoxins emerge to inhibit proteasomal function. Given that some PD-related gene mutations impair proteolytic function of UPS, it has been well-accepted that both genetic and environmental factors may conspire to compromise the UPS in the initiation and progression of the disease. The enzymatic assays for the proteasomal activities with fluorogenic substrates and western blot analysis of ubiquitinated proteins provide an entry point to determine UPS function in the process of dopaminergic degeneration.

Proteasome regulators: activators and inhibitors

This mini review covers the drug discovery aspect of both proteasome activators and inhibitors. The proteasome is involved in many essential cellular functions, such as regulation of cell cycle, cell differentiation, signal transduction pathways, antigen processing for appropriate immune responses, stress signaling, inflammatory responses, and apoptosis. Due to the importance of the proteasome in cellular functions, inhibition or activation of the proteasome could become a useful therapeutic strategy for a variety of diseases. Many proteasome inhibitors have been identified and can be classified into two groups according to their source: chemically synthesized small molecules and compounds derived from natural products. A successful example of development of a proteasome inhibitor as a clinically useful drug is the peptide boronate, PS341 (Bortezomib), was approved for the treatment of multiple myeloma. In contrast to proteasome inhibitors, small molecules that can activate or enhance proteasome activity are rare and are not well studied. The fact that over-expression of the cellular proteasome activator PA28 exhibited beneficial effects on the Huntington's disease neuronal model cells raised the prospect that small molecule proteasome activators could become useful therapeutics. The beneficial effect of oleuropein, a small molecule proteasome activator, on senescence of human fibroblasts also suggested that proteasome activators might have the potential to be developed into anti-aging agents.

Activity-based probes as a tool for functional proteomic analysis of proteases

Traditional proteomics methodology allows global analysis of protein abundance but does not provide information on the regulation of protein activity. Proteases, in particular, are known for their multilayered post-translational activity regulation that can lead to a significant difference between protease abundance levels and their enzyme activity. To address these issues, the field of activity-based proteomics has been established in order to characterize protein activity and monitor the functional regulation of enzymes in complex proteomes. In this review, we present structural features of activity-based probes for proteases and discuss their applications in proteomic profiling of various catalytic classes of proteases.

Extracellular, circulating proteasomes and ubiquitin - incidence and relevance

The ubiquitin-proteasome system is the major pathway for intracellular protein degradation and is also deeply involved in the regulation of most basic cellular processes. Its proteolytic core, the 20S proteasome, has found to be attached also to the cell plasma membrane and certain observations are interpreted as to suggest that they may be released into the extracellular medium, e.g. in the alveolar lining fluid, epididymal fluid and possibly during the acrosome reaction. Proteasomes have also been detected in normal human blood plasma and designated circulating proteasomes; these have a comparatively low specific activity, a distinct pattern of subtypes and their exact origin is still enigmatic. In patients suffering from autoimmune diseases, malignant myeloproliferative syndromes, multiple myeloma, acute and chronic lymphatic leukaemia, solid tumour, sepsis or trauma, respectively, the concentration of circulating proteasomes has been found to be elevated, to correlate with the disease state and has even prognostic significance. Similarly, ubiquitin has been discovered as a normal component of human blood and seminal plasma and in ovarian follicular fluid. Increased concentrations were measured in diverse pathological situations, not only in blood plasma but also in cerebrospinal fluid, where it may have neuroprotective effects. As defective spermatozoa are covered with ubiquitin in the epididymal fluid, extracellular ubiquitination is proposed to be a mechanism for quality control in spermatogenesis. Growing evidence exists also for a participation of extracellular proteasomes and ubiquitin in the fertilization process.

Role of proteasomes in disease

A functional ubiquitin proteasome system is essential for all eukaryotic cells and therefore any alteration to its components has potential pathological consequences. Though the exact underlying mechanism is unclear, an age-related decrease in proteasome activity weakens cellular capacity to remove oxidatively modified proteins and favours the development of neurodegenerative and cardiac diseases. Up-regulation of proteasome activity is characteristic of muscle wasting conditions including sepsis, cachexia and uraemia, but may not be rate limiting. Meanwhile, enhanced presence of immunoproteasomes in aging brain and muscle tissue could reflect a persistent inflammatory defence and anti-stress mechanism, whereas in cancer cells, their down-regulation reflects a means by which to escape immune surveillance. Hence, induction of apoptosis by synthetic proteasome inhibitors is a potential treatment strategy for cancer, whereas for other diseases such as neurodegeneration, the use of proteasome-activating or -modulating compounds could be more effective. Publication history: Republished from Current BioData's Targeted Proteins database (TPdb; http://www.targetedproteinsdb.com).

Natural products: chemical instruments to apprehend biological symphony

As a striking variety of biological activities are elicited by natural products, these chemicals have been used for decades to study biological phenomena. Understanding how these products interfere with normal cell functions at a molecular level led to a wide range of discoveries including new signaling pathways and proteins. Moreover, as natural products often act as chemical inhibitors, such studies often allow the identification of their binding partners as relevant targets for drug design. This article aims to emphasize how natural products or engineered analogs can be used as chemical tools to apprehend some biological problems from the point of view of a chemical biologist.

Multiple pathways regulating the anti-apoptotic protein clusterin in breast cancer

Cancer chemotherapy inhibits tumor growth, in part, by triggering apoptosis, and anti-apoptotic proteins reduce the effectiveness of chemotherapy. Clusterin, a chaperone-like protein that binds to apoptotic and DNA repair proteins, is induced by chemotherapy and promotes tumor cell survival. Histone deacetylase inhibitors (HDIs) such as sodium butyrate and suberoylanilide hydroxamic acid (SAHA) are pharmacological agents that induce differentiation and apoptosis in cancer cells by altering chromatin structure, and we have found that combinations of chemotherapeutic drugs such as doxorubicin and HDIs efficiently induce apoptosis, even though they paradoxically induce high levels of clusterin. The hyper-expressed form of clusterin localizes to mitochondria, inhibits cytochrome c release, and is inhibited by the proteasome. When HDIs are used as single agents, clusterin suppresses cytochrome c release and apoptosis. However, doxorubicin/HDI-induced apoptosis is not inhibited by clusterin, and clusterin-resistant apoptosis corresponds with markers of the extrinsic/receptor-mediated apoptotic pathway. Thus, chemotherapy-HDI combinations are capable of overcoming an innate anti-apoptotic pathway of tumor cells, suggesting that chemotherapy-HDI combinations have potential for treating advanced stage breast cancer.

Anorexia–Cachexia syndrome in cancer: implications of the ubiquitin–proteasome pathway

INTRODUCTION

Malnutrition is a common problem in cancer patients. Its incidence varies according to disease stage (between 15 and 90%) and is considered a possible prognostic factor for therapeutic response and survival. It is also one of the causes contributing to the increase in morbidity and mortality in patients. Tumor cachexia is defined as a nutritional defect caused by tumor growth in the patient and presents as a significant weight loss. This weight loss is mainly caused by a degradation of skeletal muscle proteins.

CONCLUSION

The ubiquitin-proteasome system is the most important pathway of protein degradation. As a regulatory system governing protein half-life, it is involved in the regulation of the cell cycle, signal transmission, immune system response, apoptosis, and oncogenesis. Knowledge of the molecular pathways involved in the induction of cancer-associated cachexia will favor a more rational approach to its treatment as well as possible quality of life and survival benefit for the patient.