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Evolution of macromolecules could be considered as a milestone in the history of life. Nucleic acids are the long stretches of nucleotides that contain all the possible codes and information of life. On the other hand, proteins are their actual translated outcomes, or reflections of modifications in their structure that have occurred at a slow, but steady rate over a very long period of evolution. Over the years of research, biophysicists, biochemists, molecular and structural biologists have unfurled several layers of the structural convolutions in these chemical molecules; however evolutionists look over their structures through a different prism, which may or may not coincide with others. There remains a need to outline several well-known, but less discussed features of protein structures, like intrinsically disordered states, degron signals and different types of ubiquitin chains providing degradation signals, which help the cellular proteolytic machinery to identify and target the proteins towards degradation pathways. There are several important factors, which are critical for folding of proteins into their native three-dimensional conformations by the cytoplasmic chaperones; but in real time how the chaperones fold the newly synthesized polypeptide sequences into a particular three-dimensional shape within a fraction of second is still a mystery for biologists as well as mathematicians. Multiple similar unsolved or unaddressed questions need to be addressed in detail so that future line of research can dig deeper into the finer details of these structures of the proteins. [ABSTRACT FROM AUTHOR]

Abstract As the mutant estrogen receptor (ER) continues to be characterized, breast cancer is becoming increasingly difficult to cure when treated with hormone therapy. In this regard, a strategy to selectively and effectively degrade the ER might be an effective alternative to endocrine therapy for breast cancer. In a previous study, we identified a novel series of 7-oxabicyclo[2.2.1]heptene sulfonamide (OBHSA) compounds as full ER antagonists while lacking the prototypical ligand side chain that has been widely used to induce antagonism of ERα. Further crystal structure studies and phenotypic assays revealed that these compounds are selective estrogen receptor degraders (SERDs) with a new mechanism of action. However, from a drug discovery point of view, there still is room to improve the potency of these OBHSA compounds. In this study, we have developed new classes of SERDs that contain the OBHSA core structure and different side chains, e.g., basic side chains, long alkyl acid side chains, and glycerol ether side chains, to simply mimic the degrons of proteolysis targeting chimera (PROTAC) and then investigated the structure-activity relationships of these PROTAC-like hybrid compounds. These novel SERDs could effectively inhibit MCF-7 cell proliferation and demonstrated good ERα degradation efficacy. Among the SERDs, compounds 17d , 17e and 17g containing a basic side chain with a N -trifluoroethyl substituent and a para methoxyl group at the phenyl group of the sulfonamide turned out to be the best candidates for ER degraders. A further docking study of these compounds with ERα elucidates their structure-activity relationships, which provides guidance to design new PROTAC degrons targeting ER for breast cancer therapy. Lastly, easy modification of these PROTAC-like SERDs enables further fine-tuning of their pharmacokinetic properties, including oral availability. Graphical abstract A series of novel SERDs with excellent ER degradation efficacy have been discovered. These findings simplified the structure of currently available degrons and provide new possibility for discovering novel PROTACs. Image 1 Highlights • A series of novel SERDs with simplified degrons and excellent estrogen receptor degradation efficacy have been discovered.. • These findings simplified the structure of currently available degrons and provide new possibility for discovering novel PROTACs. • Molecular docking analysis illustrates the interaction of basic side chain of these compounds with ERα, which may implicate a new mechanism of action for this type of SERDs. [ABSTRACT FROM AUTHOR]

Two series of proteolysis targeting chimeras (PROTACs) containing the phthalimide degrons with different linker were identified. Compound A16 displayed the most potent inhibition against LNCaP and showed excellent AR degradation efficacy at 30 μM. [Display omitted] • Two series of novel PROTACs and androgen receptor degradation efficacy have been discovered. • The best compound A16 displayed excellent binding affinity and AR degradation activity. • Molecular docking analysis illustrates the possible dual mechanism actions of these compounds with AR and E3 ligase. As a continuation of our research on developing potent and potentially safe androgen receptor (AR) degrader, a series of novel proteolysis targeting chimeras (PROTACs) containing the phthalimide degrons with different linker were designed, synthesized and evaluated for their AR degradation activity against LNCaP (AR+) cell line. Most of the synthesized compounds displayed moderate to satisfactory AR binding affinity and might lead to antagonist activity against AR. Among them, compound A16 exhibited the best AR binding affinity (85%) and degradation activity against AR. Due to the strong fluorescence properties of pomalidomide derivatives, B10 was found to be effectively internalized and visualized in LNCaP (AR +) cells than PC-3 (AR-) cells. Moreover, the molecular docking of A16 with AR and the active site of DDB1-CRBN E3 ubiquitin ligase complex provides guidance to design new PROTAC degrons targeting AR for prostate cancer therapy. These results represent a step toward the development of novel and improved AR PROTACs. [ABSTRACT FROM AUTHOR]

Since the discovery of ubiquitin conjugation as a cellular mechanism that triggers proteasomal degradation, the mode of substrate recognition by the ubiquitin-ligation system has been the holy grail of research in the field. This entails the discovery of recognition determinants within protein substrates, which are part of a degron, and explicit E3 ubiquitin (Ub)-protein ligases that trigger their degradation. Indeed, many protein substrates and their cognate E3′s have been discovered in the past 40 years. In the course of these studies, various degrons have been randomly identified, most of which are acquired through post-translational modification, typically, but not exclusively, protein phosphorylation. Nevertheless, acquired degrons cannot account for the vast diversity in cellular protein half-life times. Obviously, regulation of the proteome is largely determined by inherent degrons, that is, determinants integral to the protein structure. Inherent degrons are difficult to predict since they consist of diverse sequence and secondary structure features. Therefore, unbiased methods have been employed for their discovery. This review describes the history of degron discovery methods, including the development of high throughput screening methods, state of the art data acquisition and data analysis. Additionally, it summarizes major discoveries that led to the identification of cognate E3 ligases and hitherto unrecognized complexities of degron function. Finally, we discuss future perspectives and what still needs to be accomplished towards achieving the goal of understanding how the eukaryotic proteome is regulated via coordinated action of components of the ubiquitin-proteasome system. [ABSTRACT FROM AUTHOR]

The interplay between the ubiquitin proteasome system (UPS) and diverse peptide motifs controls almost every aspect of cell homeostasis. To achieve such an impressive functional diversity nature has evolved hundreds of different peptide motifs that interact with proteins in the UPS and ubiquitin itself to generate an immense network of interactions. Short peptides embedded in proteins are involved in controlling the intracellular levels of proteins as well as in the translation of ubiquitin signals into biochemical events. Therefore, it is not surprising that dysregulation of such interactions is associated with many diseases, including metabolic syndromes, neurodegenerative disorders, and cancer. We review the structural and functional features of peptide motifs interacting with the UPS and their use for generating protein‐protein interaction inhibitors. [ABSTRACT FROM AUTHOR]

Endoplasmic reticulum-associated degradation (ERAD) eliminates aberrant proteins from the secretory pathway. Such proteins are retained in the endoplasmic reticulum and targeted for degradation by the ubiquitin-proteasome system. Cis-acting motifs can function in ERAD as retention signals, preventing vesicular export from the endoplasmic reticulum, or as degrons, targeting proteins for degradation. Here, we show that µstp, the C-terminal 20-residue tailpiece of the secretory IgM µs heavy chain, functions both as a portable retention signal and as an ERAD degron. Retention of µstp fusions of secreted versions of thyroid peroxidase and yellow fluorescent protein in the endoplasmic reticulum requires the presence of the penultimate cysteine of µstp. In its role as a portable degron, the µstp targets the retained proteins for ERAD but does not serve as an obligatory ubiquitin-conjugation site. Abolishing µstp glycosylation accelerates the degradation of both µstpCys-fused substrates, yet absence of the N-glycan eliminates the requirement for the penultimate cysteine in the retention and degradation of the unglycosylated yellow fluorescent protein. Hence, the dual role played by the µstpCys motif as a retention signal and as a degron can be attributed to distinct elements within this sequence. [ABSTRACT FROM AUTHOR]