Design, synthesis and biological evaluation of nuclear receptor-degradation inducers

Compounds that regulate the function(s) of nuclear receptors (NRs) are useful for biological studies and as candidate therapeutic agents. Most such compounds are agonists or antagonists. On the other hand, we have developed specific protein degradation inducers, which we designated as SNIPERs (Specific and Nongenetic IAPs-dependent Protein ERasers), for selective degradation of target proteins. SNIPERs are hybrid molecules consisting of an appropriate ligand for the protein of interest, coupled to a ligand for inhibitor of apoptosis proteins (IAPs), which target the bound protein for polyubiquitination and proteasomal degradation. We considered that protein knockdown with SNIPERs would be a promising alternative approach for modulating NR function. In this study, we designed and synthesized degradation inducers targeting retinoic acid receptor (RAR), estrogen receptor (ER), and androgen receptor (AR). These newly synthesized RAR, ER, and AR SNIPERs, 9, 11, and 13, respectively, were confirmed to significantly reduce the levels of the corresponding NRs in live cells.     

Proteolysis-targeting chimaeras (PROTACs) as pharmacological tools and therapeutic agents: advances and future challenges

Proteolysis-targeting chimaeras (PROTACs) have been developed to be an emerging technology for targeted protein degradation and attracted the favour of academic institutions, large pharmaceutical enterprises, and biotechnology companies. The mechanism is based on the inhibition of protein function by hijacking a ubiquitin E3 ligase for protein degradation. The heterobifunctional PROTACs contain a ligand for recruiting an E3 ligase, a linker, and another ligand to bind with the protein targeted for degradation. To date, PROTACs targeting ∼70 proteins, many of which are clinically validated drug targets, have been successfully developed with several in clinical trials for diseases therapy. In this review, the recent advances in PROTACs against clinically validated drug targets are summarised and the chemical structure, cellular and in vivo activity, pharmacokinetics, and pharmacodynamics of these PROTACs are highlighted. In addition, the potential advantages, challenges, and prospects of PROTACs technology in disease treatment are discussed.     

Hi-JAK-ing the ubiquitin system: The design and physicochemical optimisation of JAK PROTACs

PROTACs have recently emerged as a novel paradigm in drug discovery. They can hijack existing biological machinery to selectively degrade proteins of interest, in a catalytic fashion. Here we describe the design, optimisation and biological activity of a set of novel PROTACs targeting the Janus kinase family (JAK1, JAK2, JAK3 and TYK2) of proximal membrane-bound proteins. The JAK family proteins display membrane localisation by virtue of their association with cytoplasmic tails of cytokine receptors, and there are no reports of a successful PROTAC strategy being deployed against this class of proteins. JAK PROTACs from two distinct JAK chemotypes were designed, optimising the physicochemical properties for each template to enhance cell permeation. These PROTACs are capable of inducing JAK1 and JAK2 degradation, demonstrating an extension of the PROTAC methodology to an unprecedented class of protein targets. A number of known ligase binders were explored, and it was found that PROTACs bearing an inhibitor of apoptosis protein (IAP) ligand induced significantly more JAK degradation over Von Hippel–Lindau (VHL) and Cereblon (CRBN) PROTACs. In addition, the mechanism of action of the JAK PROTACs was elucidated, and it was confirmed that JAK degradation was both IAP- and proteasome-dependent.     

Impact of linker length on the activity of PROTACs

Conventional genetic approaches have provided a powerful tool in the study of proteins. However, these techniques often preclude selective manipulation of temporal and spatial protein functions, which is crucial for the investigation of dynamic cellular processes. To overcome these limitations, a small molecule-based novel technology termed "PROteolysis TArgeting ChimeraS (PROTACs)" has been developed, targeting proteins for degradation at the post-translational level. Despite the promising potential of PROTACs to serve as molecular probes of complex signaling pathways, their design has not been generalized for broad application. Here, we present the first generalized approach for PROTAC design by fine-tuning the distance between the two participating partner proteins, the E3 ubiquitin ligase and the target protein. As such, we took a chemical approach to create estrogen receptor (ER)-α targeting PROTACs with varying linker lengths and the loss of the ER in cultured cells was monitored via western blot and fluorometric analyses. We found a significant effect of chain length on PROTAC efficacy, and, in this case, the optimum distance between the E3 recognition motif and the ligand was a 16 atom chain length. The information gathered from this experiment may offer a generalizable PROTAC design strategy to further the expansion of the PROTAC toolbox, opening new possibilities for the broad application of the PROTAC strategy in the study of multiple signaling pathways.     

Modeling the CRL4A ligase complex to predict target protein ubiquitination induced by cereblon-recruiting PROTACs

PROteolysis TArgeting Chimeras (PROTACs) are hetero-bifunctional small molecules that can simultaneously recruit target proteins and E3 ligases to form a ternary complex, promoting target protein ubiquitination and degradation via the Ubiquitin-Proteasome System (UPS). PROTACs have gained increasing attention in recent years due to certain advantages over traditional therapeutic modalities and enabling targeting of previously “undruggable” proteins. To better understand the mechanism of PROTAC-induced Target Protein Degradation (TPD), several computational approaches have recently been developed to study and predict ternary complex formation. However, mounting evidence suggests that ubiquitination can also be a rate-limiting step in PROTAC-induced TPD. Here, we propose a structure-based computational approach to predict target protein ubiquitination induced by cereblon (CRBN)-based PROTACs by leveraging available structural information of the CRL4A ligase complex (CRBN/DDB1/CUL4A/Rbx1/NEDD8/E2/Ub). We generated ternary complex ensembles with Rosetta, modeled multiple CRL4A ligase complex conformations, and predicted ubiquitination efficiency by separating the ternary ensemble into productive and unproductive complexes based on the proximity of the ubiquitin to accessible lysines on the target protein. We validated our CRL4A ligase complex models with published ternary complex structures and additionally employed our modeling workflow to predict ubiquitination efficiencies and sites of a series of cyclin-dependent kinases (CDKs) after treatment with TL12–186, a pan-kinase PROTAC. Our predictions are consistent with CDK ubiquitination and site-directed mutagenesis of specific CDK lysine residues as measured using a NanoBRET ubiquitination assay in HEK293 cells. This work structurally links PROTAC-induced ternary formation and ubiquitination, representing an important step toward prediction of target “degradability.”     

Proteolysis targeting chimeras (PROTACs) for epigenetics research

Proteolysis targeting chimeras (PROTACs) are heterobifunctional molecules and allow selective protein degradation by addressing the natural ubiquitin proteasome system. As this new strategy of chemically induced protein degradation can serve as a biological tool and provides new possibilities for drug discovery, it has been applied to a variety of targets including (nuclear) receptors, kinases, and epigenetic proteins. A lot of PROTACs have already been designed in the field of epigenetics, and their synthesis and characterization highly contributed to structural optimization and improved mechanistic understanding of these molecules. In this review, we will discuss and summarize recent advances in PROTAC discovery with focus on epigenetic targets.     

Selective CDK6 degradation mediated by cereblon,VHL, and novel IAP-recruiting PROTACs

Inhibitors of CDK4 and CDK6 have emerged as important FDA-approved treatment options for breast cancer patients. The properties and pharmacology of CDK4/6 inhibitor medicines have been extensively profiled, and investigations into the degradation of these targets via a PROTAC strategy have also been reported. PROTACs are a novel class of small-molecules that offer the potential for differentiated pharmacology compared to traditional inhibitors by redirecting the cellular ubiquitin–proteasome system to degrade target proteins of interest. We report here the preparation of palbociclib-based PROTACs that incorporate binders for three different E3 ligases, including a novel IAP-binder, which effectively degrade CDK4 and CDK6 in cells. In addition, we show that the palbociclib-based PROTACs in this study that recruit different E3 ligases all exhibit preferential CDK6 vs. CDK4 degradation selectivity despite employing a selection of linkers between the target binder and the E3 ligase binder.     

Cereblon versus VHL: Hijacking E3 ligases against each other using PROTACs

The von Hippel-Lindau (VHL) and cereblon (CRBN) proteins are substrate recognition subunits of two ubiquitously expressed and biologically important Cullin RING E3 ubiquitin ligase complexes. VHL and CRBN are also the two most popular E3 ligases being recruited by bifunctional Proteolysis-targeting chimeras (PROTACs) to induce ubiquitination and subsequent proteasomal degradation of a target protein. Using homo-PROTACs, VHL and CRBN have been independently dimerized to induce their own degradation. Here we report the design, synthesis and cellular activity of VHL-CRBN hetero-dimerizing PROTACs featuring diverse conjugation patterns. We found that the most active compound 14a induced potent, rapid and profound preferential degradation of CRBN over VHL in cancer cell lines. At lower concentrations, weaker degradation of VHL was instead observed. This work demonstrates proof of concept of designing PROTACs to hijack different E3 ligases against each other, and highlights a powerful and generalizable proximity-induced strategy to achieve E3 ligase knockdown.     

Epidermal growth factor receptor PROTACs as an effective strategy for cancer therapy: A review

Epidermal growth factor receptor (EGFR), a transmembrane glycoprotein that mediates cellular signaling pathways involved in cell proliferation, angiogenesis, apoptosis, and metastatic spread, is an important oncogenic drug target. Targeting the intracellular and extracellular domains of the EGFR has been authorized for a number of small-molecule TKIs and mAbs, respectively. However, their clinical application is limited by EGFR catalytic structural domain alterations, cancer heterogeneity, and persistent drug resistance. To bypass these limitations, protease-targeted chimeras (PROTACs) are emerging as an emerging and promising anti-EGFR therapy. PROTACs compensate for the limitations of traditional occupancy-driven small molecules by exploiting intracellular protein destruction processes. Recently, a mushrooming number of heterobifunctional EGFR PROTACs have been created using wild-type (WT) and mutated EGFR TKIs. PROTACs outperformed EGFR TKIs in terms of cellular inhibition, potency, toxicity profiles, and anti-drug resistance. Herein, we present a comprehensive overview of the development of PROTACs targeting EGFR for cancer therapy, while also highlighting the challenges and opportunities associated with the field.     

Development of target protein-selective degradation inducer for protein knockdown

Our previous technique for inducing selective degradation of target proteins with ester-type SNIPER (Specific and Nongenetic Inhibitor-of-apoptosis-proteins (IAPs)-dependent Protein ERaser) degrades both the target proteins and IAPs. Here, we designed a small-molecular amide-type SNIPER to overcome this issue. As proof of concept, we synthesized and biologically evaluated an amide-type SNIPER which induces selective degradation of cellular retinoic acid binding protein II (CRABP-II), but not IAPs. Such small-molecular, amide-type SNIPERs that induce target protein-selective degradation without affecting IAPs should be effective tools to study the biological roles of target proteins in living cells.     

The rise of covalent proteolysis targeting chimeras

Targeted protein degradation offers several advantages over direct inhibition of protein activity and is gaining increasing interest in chemical biology and drug discovery. Proteolysis targeting chimeras (PROTACs) in particular are enjoying widespread application. However, PROTACs, which recruit an E3 ligase for degradation of a target protein, still suffer from certain challenges. These include a limited selection for E3 ligases on the one hand and the requirement for potent target binding on the other hand. Both issues restrict the target scope available for PROTACs. Degraders that covalently engage the target protein or the E3 ligase can potentially expand the pool of both targets and E3 ligases. Moreover, they may offer additional advantages by improving the kinetics of ternary complex formation or by endowing additional selectivity to the degrader. Here, we review the recent progress in the emerging field of covalent PROTACs.     

Identification of Phosphoribosyl-AMP cyclohydrolase,as drug target and its inhibitors in Brucella melitensis bv. 1 16M using metabolic pathway analysis

Brucella melitensis is a pathogenic Gram-negative bacterium which is known for causing zoonotic diseases (Brucellosis). The organism is highly contagious and has been reported to be used as bioterrorism agent against humans. Several antibiotics and vaccines have been developed but these antibiotics have exhibited the sign of antibiotic resistance or ineffective at lower concentrations, which imposes an urgent need to identify the novel drugs/drug targets against this organism. In this work, metabolic pathways analysis has been performed with different filters such as non-homology with humans, essentially of genes and choke point analysis, leading to identification of novel drug targets. A total of 18 potential drug target proteins were filtered out and used to develop the high confidence protein–protein interaction network The Phosphoribosyl-AMP cyclohydrolase (HisI) protein has been identified as potential drug target on the basis of topological parameters. Further, a homology model of (HisI) protein has been developed using Modeller with multiple template (1W6Q (48%), 1ZPS (55%), and 2ZKN (48%)) approach and validated using PROCHECK and Verify3D. The virtual high throughput screening (vHTS) using DockBlaster tool has been performed against 16,11,889 clean fragments from ZINC database. Top 500 molecules from DockBlaster were docked using Vina. The docking analysis resulted in ZINC04880153 showing the lowest binding energy (?9.1 kcal/mol) with the drug target. The molecular dynamics study of the complex HisI-ZINC04880153 was conducted to analyze the stability and fluctuation of ligand within the binding pocket of HisI. The identified ligand could be analyzed in the wet-lab based experiments for future drug discovery.     

The Ubiquitination-Dependent and -Independent Functions of Cereblon in Cancer and Neurological Diseases

Cereblon (CRBN) mediates the teratogenic effect of thalidomide in zebrafish, chickens, and humans. It additionally modulates the anti-myeloma effect of the immunomodulatory drugs (IMiDs) thalidomide, lenalidomide, and pomalidomide. IMiDs bind to CRBN and recruit neo-substrates for their ubiquitination and proteasome-mediated degradation, which significantly expands the application of proteolysis-targeting chimeras (PROTACs) for targeted drug discovery. However, the underlying molecular mechanisms by which CRBN mediates the teratogenicity and anti-myeloma effect of IMiDs have not been fully elucidated. Furthermore, the normal physiological functions of endogenous CRBN have not been extensively studied, which prevents the thorough assessment of side effects of the CRBN ligand-based PROTACs in the treatment of cancer and neurological diseases. To advance our understanding of the diverse functions of CRBN, in this review, we will survey the ubiquitination-dependent and -independent functions of CRBN, summarize recent advances in the discovery of constitutive substrates and neo-substrates of CRBN, and explore the molecular functions of CRBN in cancer treatment and in the development of neurological diseases. We will also discuss the potential future directions toward the identification of CRBN substrates/interacting proteins and CRBN ligand-based drug discovery in the treatment of cancer and neurological diseases.     

DynaBiS: A hierarchical sampling algorithm to identify flexible binding sites for large ligands and peptides

Knowing the ligand or peptide binding site in proteins is highly important to guide drug discovery, but experimental elucidation of the binding site is difficult. Therefore, various computational approaches have been developed to identify potential binding sites in protein structures. However, protein and ligand flexibility are often neglected in these methods due to efficiency considerations despite the recognition that protein–ligand interactions can be strongly affected by mutual structural adaptations. This is particularly true if the binding site is unknown, as the screening will typically be performed based on an unbound protein structure. Herein we present DynaBiS, a hierarchical sampling algorithm to identify flexible binding sites for a target ligand with explicit consideration of protein and ligand flexibility, inspired by our previously presented flexible docking algorithm DynaDock. DynaBiS applies soft-core potentials between the ligand and the protein, thereby allowing a certain protein–ligand overlap resulting in efficient sampling of conformational adaptation effects. We evaluated DynaBiS and other commonly used binding site identification algorithms against a diverse evaluation set consisting of 26 proteins featuring peptide as well as small ligand binding sites. We show that DynaBiS outperforms the other evaluated methods for the identification of protein binding sites for large and highly flexible ligands such as peptides, both with a holo or apo structure used as input.     

Protein misfolding specifies recruitment to cytoplasmic inclusion bodies

Inclusion bodies (IBs) containing aggregated disease-associated proteins and polyubiquitin (poly-Ub) conjugates are universal histopathological features of neurodegenerative diseases. Ub has been proposed to target proteins to IBs for degradation via autophagy, but the mechanisms that govern recruitment of ubiquitylated proteins to IBs are not well understood. In this paper, we use conditionally destabilized reporters that undergo misfolding and ubiquitylation upon removal of a stabilizing ligand to examine the role of Ub conjugation in targeting proteins to IBs that are composed of an N-terminal fragment of mutant huntingtin, the causative protein of Huntington’s disease. We show that reporters are excluded from IBs in the presence of the stabilizing ligand but are recruited to IBs after ligand washout. However, we find that Ub conjugation is not necessary to target reporters to IBs. We also report that forced Ub conjugation by the Ub fusion degradation pathway is not sufficient for recruitment to IBs. Finally, we find that reporters and Ub conjugates are stable at IBs. These data indicate that compromised folding states, rather than conjugation to Ub, can specify recruitment to IBs.     

Landscape of protein–small ligand binding modes

Elucidating the mechanisms of specific small‐molecule (ligand) recognition by proteins is a long‐standing conundrum. While the structures of these molecules, proteins and ligands, have been extensively studied, protein–ligand interactions, or binding modes, have not been comprehensively analyzed. Although methods for assessing similarities of binding site structures have been extensively developed, the methods for the computational treatment of binding modes have not been well established. Here, we developed a computational method for encoding the information about binding modes as graphs, and assessing their similarities. An all‐against‐all comparison of 20,040 protein–ligand complexes provided the landscape of the protein–ligand binding modes and its relationships with protein‐ and chemical spaces. While similar proteins in the same SCOP Family tend to bind relatively similar ligands with similar binding modes, the correlation between ligand and binding similarities was not very high (R² = 0.443). We found many pairs with novel relationships, in which two evolutionally distant proteins recognize dissimilar ligands by similar binding modes (757,474 pairs out of 200,790,780 pairs were categorized into this relationship, in our dataset). In addition, there were an abundance of pairs of homologous proteins binding to similar ligands with different binding modes (68,217 pairs). Our results showed that many interesting relationships between protein–ligand complexes are still hidden in the structure database, and our new method for assessing binding mode similarities is effective to find them.     

Glycosylation diseases: Quo vadis?

About 250 to 500 glycogenes (genes that are directly involved in glycan assembly) are in the human genome representing about 1–2% of the total genome. Over 40 human congenital diseases associated with glycogene mutations have been described to date. It is almost certain that the causative glycogene mutations for many more congenital diseases remain to be discovered. Some glycogenes are involved in the synthesis of only a specific protein and/or a specific class of glycan whereas others play a role in the biosynthesis of more than one glycan class. Mutations in the latter type of glycogene result in complex clinical phenotypes that present difficult diagnostic problems to the clinician. In order to understand in biochemical terms the clinical signs and symptoms of a patient with a glycogene mutation, one must understand how the glycogene works. That requires, first of all, determination of the target protein or proteins of the glycogene followed by an understanding of the role, if any, of the glycogene-dependent glycan in the functions of the protein. Many glycogenes act on thousands of glycoproteins. There are unfortunately no general methods to identify all the potentially large number of glycogene target proteins and which of these proteins are responsible for the mutant phenotypes. Whereas biochemical methods have been highly successful in the discovery of glycogenes responsible for many congenital diseases, it has more recently been necessary to use other methods such as homozygosity mapping. Accurate diagnosis of many recently discovered diseases has become difficult and new diagnostic procedures must be developed. Last but not least is the lack of effective treatment for most of these children and of animal models that can be used to test new therapies.