Discovery of Highly Potent CRBN Ligands and Insight into Their Binding Mode through Molecular Docking and Molecular Dynamics Simulations

Cereblon (CRBN) is a substrate receptor of E3 ubiquitin ligase as well as the target of thalidomide and lenalidomide, plays a vital role in endogenous protein degradation. In this article, two series of compounds with novel structure were designed, synthesized and evaluated against CRBN. YJ1b, designed based on our previous finding, shown strong binding affinity toward CRBN (IC₅₀=0.206 μM) by forming a salt bridge interaction with amino acid residue Glu377 of CRBN, it was 13-fold compared with that of lenalidomide (IC₅₀=2.694 μM) in TR-FRET assay. YJ2c and YJ2h, two analogs of YJ1b, also exhibit high binding affinity toward CRBN (IC₅₀=0.211 μM and IC₅₀=0.282 μM, respectively). While, molecular docking and 100 ns molecular dynamic simulation studies were conducted to insight into the unique binding mode of YJ1b, YJ2c and YJ2e toward CRBN. The new compounds with special binding mode in this article may serve for the further optimization and discovery of novel high potent CRBN ligands.     

Synthesis and Evaluation of Cereblon-Recruiting HaloPROTACs

Target validation is key to the development of protein degrading molecules such as proteolysis-targeting chimeras (PROTACs) to identify cellular proteins amenable for induced degradation by the ubiquitin-proteasome system (UPS). Previously the HaloPROTAC system was developed to screen targets of PROTACs by linking the chlorohexyl group with the ligands of E3 ubiquitin ligases VHL and cIAP1 to recruit target proteins fused to the HaloTag for E3-catalyzed ubiquitination. Reported here are HaloPROTACs that engage the cereblon (CRBN) E3 to ubiquitinate and degrade HaloTagged proteins. A focused library of CRBN-pairing HaloPROTACs was synthesized and screened to identify efficient degraders of EGFP-HaloTag fusion with higher activities than VHL-engaging HaloPROTACs at sub-micromolar concentrations of the compound. The CRBN-engaging HaloPROTACs broadens the scope of the E3 ubiquitin ligases that can be utilized to screen suitable targets for induced protein degradation in the cell.     

Strategies to Reduce the On-Target Platelet Toxicity of Bcl-xL Inhibitors: PROTACs,SNIPERs and Prodrug-Based Approaches

Apoptosis is a highly regulated cellular process. Aberration in apoptosis is a common characteristic of various disorders. Therefore, proteins involved in apoptosis are prime targets in multiple therapies. Bcl-x_L is an antiapoptotic protein. Compared to other antiapoptotic proteins, the expression of Bcl-x_L is common in solid tumors and, to an extent, in some leukemias and lymphomas. The overexpression of Bcl-x_L is also linked to survival and chemoresistance in cancer and senescent cells. Therefore, Bcl-x_L is a promising anticancer and senolytic target. Various nanomolar range Bcl-x_L inhibitors have been developed. ABT-263 was successfully identified as a Bcl-x_L/Bcl-2 dual inhibitor. But it failed in the clinical trial (phase-II) because of its on-target platelet toxicity, which also implies an essential role of Bcl-x_L protein in the survival of human platelets. Classical Bcl-x_L inhibitor designs utilize occupancy-driven pharmacology with typical shortcomings (such as dose-dependent off-target and on-target platelet toxicities). Hence, event-driven pharmacology-based approaches, such as proteolysis targeting chimeras (PROTACs) and SNIPERs (specific non-genetic IAP-based protein erasers) have been developed. The development of Bcl-x_L based PROTACs was expected, as 600 E3-ligases are available in humans, while some (such as cereblon (CRBN), von Hippel-Lindau (VHL)) are relatively less expressed in platelets. Therefore, E3 ligase ligand-based Bcl-x_L PROTACs (CRBN: XZ424, XZ739; VHL: DT2216, PZ703b, 753b) showed a significant improvement in platelet therapeutic index than their parent molecules ( ABT-263 : DT2216, PZ703b, 753b, XZ739, PZ15227; A1155463 : XZ424). Other than their distinctive pharmacology, PROTACs are molecularly large, which limits their cell permeability and plays a role in improving their cell selectivity. We also discuss prodrug-based approaches, such as antibody-drug conjugates ( ABBV-155 ), phosphate prodrugs ( APG-1252 ), dendrimer conjugate ( AZD0466 ), and glycosylated conjugates ( Nav-Gal ). Studies of in-vitro, in-vivo, structure-activity relationships, biophysical characterization, and status of preclinical/clinical inhibitors derived from these strategies are also discussed in the review.     

HaloTag-Targeted Sirtuin-Rearranging Ligand (SirReal) for the Development of Proteolysis-Targeting Chimeras (PROTACs) against the Lysine Deacetylase Sirtuin 2 (Sirt2)**

We have discovered the sirtuin-rearranging ligands (SirReals) as a novel class of highly potent and selective inhibitors of the NAD⁺-dependent lysine deacetylase sirtuin 2 (Sirt2). In previous studies, conjugation of a SirReal with a ligand for the E3 ubiquitin ligase cereblon to form a so-called proteolysis-targeting chimera (PROTAC) enabled small-molecule-induced degradation of Sirt2. Herein, we report the structure-based development of a chloroalkylated SirReal that induces the degradation of Sirt2 mediated by Halo-tagged E3 ubiquitin ligases. Using this orthogonal approach for Sirt2 degradation, we show that other E3 ligases than cereblon, such as the E3 ubiquitin ligase parkin, can also be harnessed for small-molecule-induced Sirt2 degradation, thereby emphasizing the great potential of parkin to be used as an E3 ligase for new PROTACs approaches. Thus, our study provides new insights into targeted protein degradation in general and Sirt2 degradation in particular.     

Recent Developments in PROTAC-Mediated Protein Degradation: From Bench to Clinic

Proteolysis-targeting chimeras (PROTACs), an emerging paradigm-shifting technology, hijacks the ubiquitin-proteasome system for targeted protein degradation. PROTACs induce ternary complexes between an E3 ligase and POI, and this induced proximity leads to polyUb chain formation on substrates and eventual proteasomal-mediated POI degradation. PROTACs have shown great therapeutic potential by degrading many disease-causing proteins, such as the androgen receptor and BRD4. The PROTAC technology has advanced significantly in the last two decades, with the repertoire of PROTAC targets increased tremendously. Herein, we describe recent developments of PROTAC technology, focusing on mechanistic and kinetic studies, pharmacokinetic study, spatiotemporal control of PROTACs, covalent PROTACs, resistance to PROTACs, and new E3 ligands.     

Jostling for Position: Optimizing Linker Location in the Design of Estrogen Receptor‐Targeting PROTACs

Estrogen receptor‐α (ER) antagonists have been widely used for breast cancer therapy. Despite initial responsiveness, hormone‐sensitive ER‐positive cancer cells eventually develop resistance to ER antagonists. It has been shown that in most of these resistant tumor cells, the ER is expressed and continues to regulate tumor growth. Recent studies indicate that tamoxifen initially acts as an antagonist, but later functions as an ER agonist, promoting tumor growth. This suggests that targeted ER degradation may provide an effective therapeutic approach for breast cancers, even those that are resistant to conventional therapies. With this in mind, we previously demonstrated that proteolysis targeting chimeras (PROTACs) effectively induce degradation of the ER as a proof‐of‐concept experiment. Herein we further refined the PROTAC approach to target the ER for degradation. The ER‐targeting PROTACs are composed of an estradiol on one end and a hypoxia‐inducing factor 1α (HIF‐1α)‐derived synthetic pentapeptide on the other. The pentapeptide is recognized by an E3 ubiquitin ligase called the von Hippel Lindau tumor suppressor protein (pVHL), thereby recruiting the ER to this E3 ligase for ubiquitination and degradation. Specifically, the pentapeptide is attached at three different locations on estradiol to generate three different PROTAC types. With the pentapeptide linked through the C7α position of estradiol, the resulting PROTAC shows the most effective ER degradation and highest affinity for the estrogen receptor. This result provides an opportunity to develop a novel type of ER antagonist that may overcome the resistance of breast tumors to conventional drugs such as tamoxifen and fulvestrant (Faslodex).     

Efficient Synthesis of Immunomodulatory Drug Analogues Enables Exploration of Structure–Degradation Relationships

The immunomodulatory drugs (IMiDs) thalidomide, pomalidomide, and lenalidomide have been approved for the treatment of multiple myeloma for many years. Recently, their use as E3 ligase recruiting elements for small‐molecule‐induced protein degradation has led to a resurgence in interest in IMiD synthesis and functionalization. Traditional IMiD synthesis follows a stepwise route with multiple purification steps. Herein we describe a novel one‐pot synthesis without purification that provides rapid access to a multitude of IMiD analogues. Binding studies with the IMiD target protein cereblon (CRBN) reveals a narrow structure–activity relationship with only a few compounds showing sub‐micromolar binding affinity in the range of pomalidomide and lenalidomide. However, anti‐proliferative activity as well as Aiolos degradation could be identified for two IMiD analogues. This study provides useful insight into the structure–degradation relationships for molecules of this type as well as a rapid and robust method for IMiD synthesis.     

dSTORM-Based Single-Cell Protein Quantitative Analysis Can Effectively Evaluate the Degradation Ability of PROTACs

As an emerging therapeutic strategy, proteolysis-targeting chimeras (PROTACs) have been proven to be superior to traditional drugs in many aspects. However, due to their unique mechanism of action, existing methods for evaluating the degradation still have many limitations, which seriously restricts the development of PROTACs. In this methodological study, using direct stochastic optical reconstruction microscopy (dSTORM)-based single-cell protein quantitative analysis, we systematically investigated the dynamic degradation characteristics of FLT3 protein during PROTACs treatment. We found that the distribution of FLT3 varies between FLT3-ITD mutation and FLT3-WT cells. PROTACs had an obvious time-course effect on protein degradation and present two distinct phases; this provided a basis for deciding when to evaluate protein degradation. High concentrations of PROTACs were more effective than long-time administration because a higher D_max was achieved. Two-color dSTORM-based colocalization analysis efficiently detected the proportion of ternary complexes, making it very useful in screening PROTACs. Taken together, our findings show that the dSTORM method is an ideal tool for evaluating PROTACs and will accelerate the development of new PROTACs.     

Controlling PROTACs with Light

Proteolysis targeting chimeras, PROTACs, are emerging as a powerful strategy for exerting exogenous control over protein levels, allowing small molecules to exploit the ubiquitin–proteasome pathway for targeted protein degradation. This highlight focuses on the fusion of photochemistry with these bifunctional compounds, which has provided a novel pathway for spatiotemporally tuning the activation of PROTACs in the form of their photocaged and photoswitchable versions. Photocaged PROTACs consist of a hindered optolabile group that detaches only upon irradiation at a specific wavelength, releasing the active PROTAC. These modified PROTACs are inactive in the dark. Photoswitchable PROTACs are photoisomerizable molecules with azobenzene linkages that are active in either the cis or trans form and inactive in the other. The isomers interconvert upon irradiation with an appropriate wavelength of light and relax to the thermodynamically stable isomer in the dark or with another wavelength of light. Although photocaged PROTACs only permit activation control for protein degradation, photoswitching PROTACs offer reversible activation and deactivation by using suitable wavelengths of light.     

Identifying E3 Ligase Substrates With Quantitative Degradation Proteomics

Controlled protein degradation by the ubiquitin-proteasome pathway is critical for almost all cellular processes. E3 ubiquitin ligases are responsible for targeting proteins for ubiquitylation and subsequent proteasomal degradation with spatial and temporal precision. While studies have revealed various E3-substrate pairs involved in distinct biological processes, the complete substrate profiles of individual E3 ligases are largely unknown. Here we report a new approach to identify substrates of an E3 ligase for proteasomal degradation using unnatural amino acid incorporation pulse-chase proteomics (degradomics). Applying this approach, we determine the steady-state substrates of the C -t erminal to L isH (CTLH) E3 ligase, a multi-component complex with poorly defined substrates. By comparing the proteome degradation profiles of active and inactive CTLH-expressing cells, we successfully identify previously known and new potential substrates of CTLH ligase. Altogether, degradomics can comprehensively identify degradation substrates of an E3 ligase, which can be adapted for other E3 ligases in various cellular contexts.     

Native Mass Spectrometry for the Study of PROTAC GNE-987-Containing Ternary Complexes

PRO teolysis TA rgeting C himeras (PROTACs) promote the degradation, rather than inhibition, of a drug target as a mechanism for therapeutic treatment. Bifunctional PROTAC molecules allow simultaneous binding of both the target protein and an E3-Ubiquitin ligase, bringing the two proteins into close spatial proximity to allow ubiquitinylation and degradation of the target protein via the cell's endogenous protein degradation pathway. We utilized native mass spectrometry (MS) to study the ternary complexes promoted by the previously reported PROTAC GNE-987 between Brd4 bromodomains 1 and 2, and Von Hippel Lindeau E3-Ubiquitin Ligase. Native MS at high resolution allowed us to measure ternary complex formation as a function of PROTAC concentration to provide a measure of complex affinity and stability, whilst simultaneously measuring other intermediate protein species. Native MS provides a high-throughput, low sample consumption, direct screening method to measure ternary complexes for PROTAC development.     

Trans fatty acids: Positional specificity in brain lecithin

Fifteen-day-old rats were divided into three groups: one group received an intracerebral injection of 5 μ Ci of 9-trans, 12-trans [1-¹⁴C] octadecadienoic acid; the second group was given 5 μCi of the same compound plus an equal wt of nonradioactive allcis arachidonic acid; the third group was given 5 μCi of 9-trans [1-¹⁴C] octadecenoic acid. All animals were sacrificed 8 hr after injection. Glycerophosphocholine (GPC) was isolated and partically deacylated with phospholipase A₂ fromCrotalus Adamanteus venom. The results of this study were as follows: 1) aftert [1-¹⁴C] 18∶1 injection, there was twice as much radioactivity in the 1-position as in the 2-position; 2) whentt [1-¹⁴C] 18∶2 was injected, more than 90% of the total radioactivity was found in the 2-position; 3) followingtt[1-¹⁴C]-18∶2 +nonradioactive arachidonate injection, ca. 75% of the total radioactivity still remained in the 2-position; and 4) all of the injected [1-¹⁴C]-tracers showed evidence of undergoing β-oxidation to form acetyl-CoA, which was converted to radioactive palmitate. The possibility is discussed that the observed distribution pattern of the injected radioactive tracers may be attributed to tissue metabolic specificity. Ramifications of the deposition of dietarytrans fatty acids in the brain during the developmental stage of the central nervous system are also discussed.     

A novel method for the introduction of a methyl group into the furan ring of a 2,5-disubstituted C18 furanoid fatty estervia a malonic acid function

Furan ring opening with benzohydroxamic acid of methyl 9,12-epoxy-9,11-octadecadienoate gave a mixture of positional isomers of conjugated methyl 3-phenyl-1,4,2-dioxazolyl C₁₈-enone esters 6a,6b. Michael addition of diethyl malonate anion to the conjugated enone system of 6a,6b furnished the corresponding malonyl intermediates 7a,7b, which upon removal of the dioxazole ring by hydrolysis gave methyl 10- and 11-dicarbethoxymethyl-9,12-dioxooctadecanoate 8a,8b. Cyclization of the latter gave the trisubstituted C₁₈ furanoid fatty esters 9a,9b, containing the malonate ester function at the 3-/4-position of the furan ring. Base hydrolysis of compounds 9a,9b gave the corresponding tricarboxylic acid derivatives 10a,10b, which were esterified to the trimethyl esters 11a,11b in BF₃/MeOH. When a mixture of 9a,9b was refluxed with Na₂CO₃/MeOH, hydrolysis of the malonate ester function was followed by decarboxylation to yield a-CH₂COOH substituent at the 3-/4-position of the furan ring (12a, 12b). Esterification of the latter with BF₃/MeOH gave the corresponding methyl diester derivatives 13a,13b. When a mixture of tricarboxylic acids 10a,10b was heated at 160–180°C for 6 hr, exhaustive decarboxylation of malonic acid function furnished a methyl group at the 3-/4-position of the furan nucleus. Esterification of the decarboxylated product gave a mixture of trisubstituted furanoid compounds 14a,14b (overall yield 28%). The procedure constitutes a novel method for the introduction of a methyl groupvia a malonic acid group to the 3-/4-position of the furan ring of a 2,5-disubstituted C₁₈ furanoid fatty ester.     

MS-Based Screening of 5-Substituted Nipecotic Acid Derived Hydrazone Libraries as Ligands of the GABA Transporter 1

A screening of compound libraries based on nipecotic acid derivatives with lipophilic residues attached to the scarcely explored 5-position of the core structure was used for the search of new inhibitors of the γ-aminobutyric acid (GABA) transporter 1 (mGAT1). The generated compound libraries, which were based on hydrazone chemistry commonly used in dynamic combinatorial chemistry but rendered pseudostatic, were screened for their binding affinities toward mGAT1 by means of MS Binding Assays. With nipecotic acid derived hydrazone rac- 16 h [rac-(3R,5S)-{5-[(E)-2-{[5-(2-phenylethynyl)thiophen-2-yl]methylidene}hydrazin-1-yl]piperidine-3-carboxylic acid}-sodium chloride (1/2)], one hit was found and evaluated displaying sub-micromolar potency (pK_i=6.62±0.04) and a noncompetitive interaction mode at mGAT1. By bearing a 5-(2-phenylethynyl)thiophen-2-yl residue attached to the 5-position of nipecotic acid via a three-atom spacer, compound rac- 16 h contains a structural moiety so far unprecedented for these kinds of bioactive molecules, and complements novel 5-substituted nipecotic acid derived ligands of mGAT1 revealed in a recently published screening campaign. This new class of ligands, with an inhibition mode distinct from that of benchmark mGAT1 inhibitors, could serve as research tools for investigations of mGAT1-mediated GABA transport.     

trans-5-Palladatricyclo[4.1.0.02,4]heptanes: Complexes with monodentate,weakly coordinating ligands,formation of new derivatives and synthetic limitations

The bis(acetone) complex of tetramethyl rac-3,3,7,7-tetramethyl-trans-5-palladatricyclo[4.1.0.0^2,4]heptane-1,2,4,6-tetracarboxylate rac- 1a was crystallized and investigated by X-ray structure analysis. Unlike in complexes with bidendate ligands in rac- 1a · 2(acetone), only a small deviation from the square planar coordination of palladium was observed. Efforts to crystallize the analogous pyridine, acetonitrile and benzonitrile complexes failed; but the labile complexes rac- 1a · 2([D₅]pyridine) and rac- 1a · 2([D₃] acetonitrile) as well as rac- 1a · 2([D₆]acetone) could be characterized by ¹H and ¹³C NMR spectra and a fast ligand exchange was proven by nmr. Then the ability of different 1,2-disubstituted cyclopropenes to form trans-5-pallada-tricyclo[4.1.0.0^2,4] heptanes 1 was investigated. Only the diesters 5c–e lead to PTHs, with a diester possessing sterically demanding substituents in 3-position of the cyclopropene and with other substituents in 1- respectively 2-position of the cyclopropene either the cyclopropene-formation or the PTH-formation failed.     

Synthesis of trisubstituted C18 pyrrole fatty ester derivatives

Reaction of methyl 10(11)-dicarbethoxymethyl-9,12-dioxooctadecanoate (1a,1b) with ammonium acetate furnished a mixture of positional isomers of a pyrrole derivative, methyl 9,12-imino-10(11)-dicarbethoxymethyl-9,11-octadecadienoate (2a,2b). Decarboxylation of the mixture of compounds 2a,2b with sodium carbonate in aqueous methanol yielded a mixture of compounds 3a,3b containing a CH₂COOCH₃ group at the 3- or 4-position of the pyrrole ring after esterification. Heating of the hydrolyzed mixture of compounds 3a,3b at 180°C for 1 h gave the desired trisubstituted pyrrole derivatives, methyl 9,12-imino-10(11)-methyl-9,11-octadecadienoate (4a,4b), containing a methyl group at the 3- or 4-position of the pyrrole nucleus. The structures of the products and intermediates were confirmed by infrared, and by¹H and¹³C nuclear magnetic resonance spectroscopy.     

Revisiting the Mechanism of β-O-4 Bond Cleavage During Acidolysis of Lignin. Part 3: Search for the Rate-Determining Step of a Non-Phenolic C6-C3 Type Model Compound

Abstract

The rate-determining step of a C₆-C₃ dimeric non-phenolic β-O-4 type lignin model compound, 2-(2-methoxyphenoxy)-1-(3,4-dimethoxyphenyl)propane-1,3-diol (veratrylglycerol-β-guaiacyl ether, VG), was evaluated under acidolysis conditions (0.2 mol/l HBr in 82% aqueous 1,4-dioxane at 85°C) by comparing the disappearances between VG and the corresponding compound labeled at the β-position of VG, 2-(2-methoxyphenoxy)-1-(3,4-dimethoxyphenyl)(2–²H)propane-1,3-diol. The disappearance of VG occurred more rapidly than that of the latter compound, and a primary kinetic isotope effect was clearly observed. This result indicates that the C-H bond at the β-position of VG is broken in the rate-determining step. Two possible mechanisms are presented as the rate-determining step: (1) A base abstracts the β-proton of a benzyl cation-type intermediate produced from VG affording an enol ether compound, 2-(2-methoxyphenoxy)-3-(3,4-dimethoxyphenyl)prop-2-en-1-ol; (2) The hydride transfers from the β- to the α-position of the benzyl cation. It was confirmed that both mechanisms certainly exist and that the latter seems to contribute more than has generally been considered.     

Analysis of regiospecific distribution of FA of TAG using the lipase-catalyzed ester-exchange

A very simple and versatile GC method has been developed that can be utilized for quick analysis, in many samples, of the FA compositions at the sn-2- and sn-1,3-positions of TAG. By using the lipase-catalyzed, sn-1,3-regioselective esterexchange reaction of TAG with ethyl acetate, followed by direct injection of the crude reaction mixture into the GC apparatus without any pretreatment, the FA located at the sn-2-position could accurately be analyzed as a TAG derivative in which the sn-1,3-positions were substituted by an acetate residue. Furthermore, the FA located at the sn-1,3-positions could simultaneously be analyzed as the corresponding ethyl ester derivatives using this method. The reliability of the analytical method was compared with conventional methods by analyzing the TAG consisting of caprylic acid (C) at the sn-2-position and oleic acid (O) at the sn-1,3-positions, giving comparable analytical results. The present method was applied to the analysis of the structured lipids CCD and CCE, consisting of TAG as a major component in which C and the highly unsaturated FA, DHA (D) or EPA (E), were specifically bound at the sn-2- and the sn-1,3-positions, respectively.     

Remote C-H bond activation/transformations: A continuous growing synthetic tool; Part II

The selective functionalization of inert C-H bonds is always challenging due to their abundance and large bond dissociation energies. Despite recent advancements, the engagement of inert building blocks for distant functionalization is the most appealing approach for the past decade for the construction of complex molecules. Along with the upsurge of proximal C-H bond activation methods, the presence of directing group or participation of ligand surmounts the challenge of regioselective remote C-H bond transformation. Remote C-H functionalization has emerged as an important tool for the direct synthesis of a variety of natural as well as pharmaceutical products. In this area, chemists are continuously designing and exploring new catalysts, ligands and directing group for the functionalization of C-H bonds which are beyond proximity. Earlier success in this area was limited to meta-position, but recently scientists have come out with new templates which can reach even para-position. The developed catalytic transformations provide access for production of a wide range of value-added products without using classical methods such as Friedel-Craft reactions, Heck coupling, etc., providing atom economical alternate and avoiding the toxic waste generation. On this topic, we have recently published a review article entitled “Distant C-H Activation/Functionalization: A New Horizon of Selectivity beyond Proximity” in the same journal, i.e., Catalysis Reviews: Science and Engineering, 2015, 57(3), 345. In continuation of this article, the present review article will cover the catalytic processes on the mentioned topic mainly developed from 2014 to 2017. The main focus will be on mechanistic pathways and the critical role of template as well as ligands. The purpose of this review is to highlight the recent advancements in remote C-H catalysis and a path ahead.