Integrated Mechanism of Lysine 351, PARK2, and STUB1 in AβPP Ubiquitination

Asparagine and Glutamine Residues Participate in Protein Covalent Binding by Epoxide Metabolite of 8-Epidiosbulbin E Acetate In Vitro and In Vivo

Dioscorea Bulbifera L. (DBL), an effective traditional Chinese medicine, has been restricted because of multiple reports that it can cause severe hepatotoxicity. 8-Epidiosbulbin E acetate (EEA), one of the main components of DBL, can induce severe liver injury. It has been reported that EEA can be metabolized by CYP3A to the corresponding cis-enedial intermediate which alkylates the lysine residues of proteins to form pyrroline derivatives. The present study unexpectedly found that the reactive intermediate reacted with the amide groups of asparagine (Asn) and glutamine (Gln) residues of hepatic proteins of mice treated with EEA. The amide-derived protein modification increased with the increase in the dose administered. Like the adduction of the primary amine of lysine residues, the electrophilic metabolite reacted with the amide groups of Asn and Gln residues to offer the corresponding pyrrolines. The structures of the pyrrolines were confirmed by mass spectrometry and nuclear magnetic resonance spectroscopy.

Targeted protein degraders march towards the clinic for neurodegenerative diseases

Protein degraders are emerging as potent therapeutic tools to address neurological disorders and many complex diseases. It offered several key advantages, including the doses, drug resistance, and side effects over traditional occupancy-based inhibitors. Translation of chemical degraders into a clinical therapy for neurodegenerative disorders has a well-documented knowledge and resource gap. Researchers strive to develop clinical candidates employing chemical degraders' technologies, including hydrophobic tagging, molecular glues, proteolysis targeting chimeras (PROTACs), specific and nongenetic Inhibitor of Apoptosis Protein (IAP)-dependent protein erasers (SNIPERs), autophagy targeted chimeras, and autophagosome-tethered compounds for targeted degradation of pathological markers in neurodegenerative disease. Herein, we examined the present state of chemical-mediated targeted protein degradation in the quest for medications to treat neurodegenerative diseases. We further identified targeted degraders under clinical development for neurodegenerative diseases summarizing pertinent discoveries guiding the future of degradation therapeutics. We also addressed the necessary pharmacological interventions needed to achieve unprecedented therapeutic efficacy and its associated challenges.

Role of Intracellular Amyloid β as Pathway Modulator, Biomarker, and Therapy Target

The β- and γ-secretase-driven cleavage of the amyloid precursor protein (APP) gives rise to the amyloid β peptide, which is believed to be the main driver of neurodegeneration in Alzheimer’s disease (AD). As it is prominently detectable in extracellular plaques in post-mortem AD brain samples, research in recent decades focused on the pathological role of extracellular amyloid β aggregation, widely neglecting the potential meaning of very early generation of amyloid β inside the cell. In the last few years, the importance of intracellular amyloid β (iAβ) as a strong player in neurodegeneration has been indicated by a rising number of studies. In this review, iAβ is highlighted as a crucial APP cleavage fragment, able to manipulate intracellular pathways and foster neurodegeneration. We demonstrate its relevance as a pathological marker and shed light on initial studies aiming to modulate iAβ through pharmacological treatment, which has been shown to have beneficial effects on cognitive properties in animal models. Finally, we display the relevance of viral infections on iAβ generation and point out future directions urgently needed to manifest the potential relevance of iAβ in Alzheimer’s disease.

[Metabolic pathways controlled by E3 ligases: an opportunity for therapeutic targeting]

Since its discovery, the Ubiquitin Proteasome System (UPS) has been recognized for its major role in controlling most of the cell's metabolic pathways. In addition to its essential role in the degradation of proteins, it is also involved in the addressing, signaling or repair of DNA, which makes it a key player in cellular homeostasis. Although other control systems exist in the cell, the UPS is often referred to as the conductor. In view of its importance, any dysregulation of the UPS leads to more or less severe disorders for the cell and therefore the body, which accounts for UPS implication in many pathologies (cancer, Alzheimer's disease, Huntington's disease, etc.). UPS is made up of more than 1000 different proteins, the combinations of which allow the fine targeting of virtually all proteins in the body. UPS uses an enzymatic cascade (E1, 2 members; E2 > 35; E3 > 800) which allows the transfer of ubiquitin, a small protein of 8.5 kDa onto the protein to be targeted either for its degradation or to modify its activity. This ubiquitinylation signal is reversible and many deubiquitinylases (DUB, ∼ 80 isoforms) also have an important role. E3 enzymes are the most numerous and their function is to recognize the target protein, which makes them important players in the specific action of UPS. The very nature of E3 and the complexity of their interactions with different partners offer a very broad field of investigation and therefore significant potential for the development of therapeutic approaches. Without being exhaustive, this review illustrates the different strategies that have already been implemented to fight against different pathologies (excluding bacterial or viral infections).

Computational Analysis Indicates That PARP1 Acts as a Histone Deacetylases Interactor Sharing Common Lysine Residues for Acetylation, Ubiquitination, and SUMOylation in Alzheimer's and Parkinson's Disease

Aim/Hypothesis : Lysine residues are known for the post-translational modifications (PTMs) such as acetylation, ubiquitination, and SUMOylation. In acetylation, histone deacetylase (HDAC) and its interactors cause transcriptional deregulation and cause mitochondrial dysfunction, apoptosis, inflammatory response, and cell-cycle impairment that cause brain homeostasis and neuronal cell death. Other regulatory PTMs involved in the pathogenesis of neurodegenerative diseases (NDDs) are ubiquitination and SUMOylation for the degradation of the misfolded proteins. Thus, we aim to investigate the potential acetylation/ubiquitination/SUMOylation crosstalk sites in the HDAC interactors, which cause NDDs. Furthermore, we aim to identify the influence of PTMs on the structural features of proteins and the impact of putative lysine mutation on disease susceptibility. Last, we aim to examine the impact of the putative mutation on acetylated lysine for ubiquitination and SUMOylation. Results : Herein, we integrate 1455 genes, 3094 genes, and 1940 genes related to HDAC interactors, Alzheimer's disease (AD), and Parkinson's disease (PD), respectively. Furthermore, the protein-protein interaction and PTM integrations from different databases identified 32 proteins that are associated with HDAC, AD, and PD with 1489 potential lysine-modified sites. HDAC interactors poly(ADP-ribose) polymerase 1 (PARP1), nucleophosmin (NPM1), and cyclin-dependent kinase 1 (CDK1) involved in the progression of NDDs and 64 and 75% of PTM sites in PARP1, NPM1, and CDK1 fall into coiled and ordered regions, respectively. Moreover, 15 putative lysine sites have been found in the crosstalk and K148, K249, K528, K637, K700, and K796 of PARP1 are crosstalk hotspots. Conclusion : The loss of acetylated hotspot sites results in the loss of ubiquitination and SUMOylation function on nearby sites, which is relatively higher when compared to the gain of function.