Uncoupling histone modification crosstalk by engineering lysine demethylase LSD1.

Biochemical crosstalk between two or more histone modifications is often observed in epigenetic enzyme regulation, but its functional significance in cells has been difficult to discern. Previous enzymatic studies revealed that Lys14 acetylation of histone H3 can inhibit Lys4 demethylation by lysine-specific demethylase 1 (LSD1). In the present study, we engineered a mutant form of LSD1, Y391K, which renders the nucleosome demethylase activity of LSD1 insensitive to Lys14 acetylation. K562 cells with the Y391K LSD1 CRISPR knockin show decreased expression of a set of genes associated with cellular adhesion and myeloid leukocyte activation. Chromatin profiling revealed that the cis-regulatory regions of these silenced genes display a higher level of H3 Lys14 acetylation, and edited K562 cells show diminished H3 mono-methyl Lys4 near these silenced genes, consistent with a role for enhanced LSD1 demethylase activity. These findings illuminate the functional consequences of disconnecting histone modification crosstalk for a key epigenetic enzyme.

KBTBD4 Cancer Hotspot Mutations Drive Neomorphic Degradation of HDAC1/2 Corepressor Complexes.

Cancer mutations can create neomorphic protein-protein interactions to drive aberrant function 1 . As a substrate receptor of the CULLIN3-RBX1 E3 ubiquitin ligase complex, KBTBD4 is recurrently mutated in medulloblastoma (MB) 2 , the most common embryonal brain tumor in children, and pineoblastoma 3 . These mutations impart gain-of-function to KBTBD4 to induce aberrant degradation of the transcriptional corepressor CoREST 4 . However, their mechanism of action remains unresolved. Here, we elucidate the mechanistic basis by which KBTBD4 mutations promote CoREST degradation through engaging HDAC1/2, the direct neomorphic target of the substrate receptor. Using deep mutational scanning, we systematically map the mutational landscape of the KBTBD4 cancer hotspot, revealing distinct preferences by which insertions and substitutions can promote gain-of-function and the critical residues involved in the hotspot interaction. Cryo-electron microscopy (cryo-EM) analysis of two distinct KBTBD4 cancer mutants bound to LSD1-HDAC1-CoREST reveals that a KBTBD4 homodimer asymmetrically engages HDAC1 with two KELCH-repeat propeller domains. The interface between HDAC1 and one of the KBTBD4 propellers is stabilized by the MB mutations, which directly insert a bulky side chain into the active site pocket of HDAC1. Our structural and mutational analyses inform how this hotspot E3-neo-substrate interface can be chemically modulated. First, our results unveil a converging shape complementarity-based mechanism between gain-of-function E3 mutations and a molecular glue degrader, UM171. Second, we demonstrate that HDAC1/2 inhibitors can block the mutant KBTBD4-HDAC1 interface, the aberrant degradation of CoREST, and the growth of KBTBD4-mutant MB models. Altogether, our work reveals the structural and mechanistic basis of cancer mutation-driven neomorphic protein-protein interactions and pharmacological strategies to modulate their action for therapeutic applications.

Asymmetric Engagement of Dimeric CRL3 KBTBD4 by the Molecular Glue UM171 Licenses Degradation of HDAC1/2 Complexes.

UM171 is a potent small molecule agonist of ex vivo human hematopoietic stem cell (HSC) self-renewal, a process that is tightly controlled by epigenetic regulation. By co-opting KBTBD4, a substrate receptor of the CULLIN3-RING E3 ubiquitin ligase complex, UM171 promotes the degradation of members of the CoREST transcriptional corepressor complex, thereby limiting HSC attrition. However, the direct target and mechanism of action of UM171 remain unclear. Here, we reveal that UM171 acts as a molecular glue to induce high-affinity interactions between KBTBD4 and HDAC1 to promote the degradation of select HDAC1/2 corepressor complexes. Through proteomics and chemical inhibitor studies, we discover that the principal target of UM171 is HDAC1/2. Cryo-electron microscopy (cryo-EM) analysis of dimeric KBTBD4 bound to UM171 and the LSD1-HDAC1-CoREST complex unveils an unexpected asymmetric assembly, in which a single UM171 molecule enables a pair of KBTBD4 KELCH-repeat propeller domains to recruit HDAC1 by clamping on its catalytic domain. One of the KBTBD4 propellers partially masks the rim of the HDAC1 active site pocket, which is exploited by UM171 to extend the E3-neo-substrate interface. The other propeller cooperatively strengthens HDAC1 binding via a separate and distinct interface. The overall neomorphic interaction is further buttressed by an endogenous cofactor of HDAC1-CoREST, inositol hexakisphosphate, which makes direct contacts with KBTBD4 and acts as a second molecular glue. The functional relevance of the quaternary complex interaction surfaces defined by cryo-EM is demonstrated by in situ base editor scanning of KBTBD4 and HDAC1. By delineating the direct target of UM171 and its mechanism of action, our results reveal how the cooperativity offered by a large dimeric CRL E3 family can be leveraged by a small molecule degrader and establish for the first time a dual molecular glue paradigm.

APP-C31: An Intracellular Promoter of Both Metal-Free and Metal-Bound Amyloid-ß40 Aggregation and Toxicity in Alzheimer's Disease.

Intracellular C-terminal cleavage of the amyloid precursor protein (APP) is elevated in the brains of Alzheimer's disease (AD) patients and produces a peptide labeled APP-C31 that is suspected to be involved in the pathology of AD. But details about the role of APP-C31 in the development of the disease are not known. Here, this work reports that APP-C31 directly interacts with the N-terminal and self-recognition regions of amyloid-ß40 (Aß40 ) to form transient adducts, which facilitates the aggregation of both metal-free and metal-bound Aß40 peptides and aggravates their toxicity. Specifically, APP-C31 increases the perinuclear and intranuclear generation of large Aß40 deposits and, consequently, damages the nucleus leading to apoptosis. The Aß40 -induced degeneration of neurites and inflammation are also intensified by APP-C31 in human neurons and murine brains. This study demonstrates a new function of APP-C31 as an intracellular promoter of Aß40 amyloidogenesis in both metal-free and metal-present environments, and may offer an interesting alternative target for developing treatments for AD that have not been considered thus far.

Unveiling the impact of oxidation-driven endogenous protein interactions on the dynamics of amyloid-ß aggregation and toxicity.

Cytochrome c (Cyt c), a multifunctional protein with a crucial role in controlling cell fate, has been implicated in the amyloid pathology associated with Alzheimer's disease (AD); however, the interaction between Cyt c and amyloid-ß (Aß) with the consequent impact on the aggregation and toxicity of Aß is not known. Here we report that Cyt c can directly bind to Aß and alter the aggregation and toxicity profiles of Aß in a manner that is dependent on the presence of a peroxide. When combined with hydrogen peroxide (H2O2), Cyt c redirects Aß peptides into less toxic, off-pathway amorphous aggregates, whereas without H2O2, it promotes Aß fibrillization. The mechanisms behind these effects may involve a combination of the complexation between Cyt c and Aß, the oxidation of Aß by Cyt c and H2O2, and the modification of Cyt c by H2O2. Our findings demonstrate a new function of Cyt c as a modulator against Aß amyloidogenesis.

Conformational and functional changes of the native neuropeptide somatostatin occur in the presence of copper and amyloid-ß.

The progression of neurodegenerative disorders can lead to impaired neurotransmission; however, the role of pathogenic factors associated with these diseases and their impact on the structures and functions of neurotransmitters have not been clearly established. Here we report the discovery that conformational and functional changes of a native neuropeptide, somatostatin (SST), occur in the presence of copper ions, metal-free amyloid-ß (Aß) and metal-bound Aß (metal-Aß) found as pathological factors in the brains of patients with Alzheimer's disease. These pathological elements induce the self-assembly of SST and, consequently, prevent it from binding to the receptor. In the reverse direction, SST notably modifies the aggregation profiles of Aß species in the presence of metal ions, attenuating their cytotoxicity and interactions with cell membranes. Our work demonstrates a loss of normal function of SST as a neurotransmitter and a gain of its modulative function against metal-Aß under pathological conditions.

Distinct impact of glycation towards the aggregation and toxicity of murine and human amyloid-ß.

Glycation of human Aß (hAß) is implicated to induce the deposition of amyloid aggregates found in the Alzheimer's disease (AD)-affected brain. Murine Aß (mAß) differs from hAß in three different amino acid residues (Gly5, Phe10, and Arg13) and is less likely to form amyloid aggregates. Herein, we report that the advanced glycated end products of mAß40 over hAß40 are distinctly generated. The different glycation between the two peptides can govern their aggregation kinetics, structural transition, and cytotoxicity.

Minimalistic Principles for Designing Small Molecules with Multiple Reactivities against Pathological Factors in Dementia.

Multiple pathogenic elements, including reactive oxygen species, amyloidogenic proteins, and metal ions, are associated with the development of neurodegenerative disorders. We report minimalistic redox-based principles for preparing compact aromatic compounds by derivatizing the phenylene moiety with various functional groups. These molecular agents display enhanced reactivities against multiple targets such as free radicals, metal-free amyloid-ß (Aß), and metal-bound Aß that are implicated in the most common form of dementia, Alzheimer's disease (AD). Mechanistic studies reveal that the redox properties of these reagents are essential for their function. Specifically, they engage in oxidative reactions with metal-free and metal-bound Aß, leading to chemical modifications of the Aß peptides to form covalent adducts that alter the aggregation of Aß. Moreover, the administration of the most promising candidate significantly attenuates the amyloid pathology in the brains of AD transgenic mice and improves their cognitive defects. Our studies demonstrate an efficient and effective redox-based strategy for incorporating multiple functions into simple molecular reagents.

Tunable regulatory activities of 1,10-phenanthroline derivatives towards acid sphingomyelinase and Zn(ii)-amyloid-ß.

We report a new series of small molecules able to achieve the tunability of modulatory activities against acid sphingomyelinase (ASM) and Zn(ii)-bound amyloid-ß [Zn(ii)-Aß], two pathological targets found in the brain affected by Alzheimer's disease. Rational tuning of the hydrophobicity and Zn(ii) binding affinity of the 1,10-phenanthroline (phen) framework successfully yielded compounds as chemical modulators for ASM (4 and 5), Zn(ii)-Aß (phen, 1, and 2), or both (3).

Regulatory Activities of Dopamine and Its Derivatives toward Metal-Free and Metal-Induced Amyloid-ß Aggregation, Oxidative Stress, and Inflammation in Alzheimer's Disease.

A catecholamine neurotransmitter, dopamine (DA), is suggested to be linked to the pathology of dementia; however, the involvement of DA and its structural analogues in the pathogenesis of Alzheimer's disease (AD), the most common form of dementia, composed of multiple pathogenic factors has not been clear. Herein, we report that DA and its rationally designed structural derivatives (1-6) based on DA's oxidative transformation are able to modulate multiple pathological elements found in AD [i.e., metal ions, metal-free amyloid-ß (Aß), metal-bound Aß (metal-Aß), and reactive oxygen species (ROS)], with demonstration of detailed molecular-level mechanisms. Our multidisciplinary studies validate that the protective effects of DA and its derivatives on Aß aggregation and Aß-mediated toxicity are induced by their oxidative transformation with concomitant ROS generation under aerobic conditions. In particular, DA and the derivatives (i.e., 3 and 4) show their noticeable anti-amyloidogenic ability toward metal-free Aß and/or metal-Aß, verified to occur via their oxidative transformation that facilitates Aß oxidation. Moreover, in primary pan-microglial marker (CD11b)-positive cells, the major producers of inflammatory mediators in the brain, DA and its derivatives significantly diminish inflammation and oxidative stress triggered by lipopolysaccharides and Aß through the reduced induction of inflammatory mediators as well as upregulated expression of heme oxygenase-1, the enzyme responsible for production of antioxidants. Collectively, we illuminate how DA and its derivatives could prevent multiple pathological features found in AD. The overall studies could advance our understanding regarding distinct roles of neurotransmitters in AD and identify key interactions for alleviation of AD pathology.

Tailoring Hydrophobic Interactions between Probes and Amyloid-ß Peptides for Fluorescent Monitoring of Amyloid-ß Aggregation.

Despite their unique advantages, the full potential of molecular probes for fluorescent monitoring of amyloid-ß (Aß) aggregates has not been fully exploited. This limited utility stems from the lack of knowledge about the hydrophobic interactions between the molecules of Aß probes, as well as those between the probe and the Aß aggregate. Herein, we report the first mechanistic study, which firmly establishes a structure-signaling relationship of fluorescent Aß probes. We synthesized a series of five fluorescent Aß probes based on an archetypal donor-acceptor-donor scaffold (denoted as SN1-SN5). The arylamino donor moieties were systematically varied to identify molecular factors that could influence the interactions between molecules of each probe and that could influence their fluorescence outcomes in conditions mimicking the biological milieu. Our probes displayed different responses to aggregates of Aß, Aß40 and Aß42, two major isoforms found in Alzheimer's disease: SN2, having pyrrolidine donors, showed noticeable ratiometric fluorescence responses (Δν = 797 cm-1) to the Aß40 and Aß42 samples that contained oligomeric species, whereas SN4, having N-methylpiperazine donors, produced significant fluorescence turn-on signaling in response to Aß aggregates, including oligomers, protofibrils, and fibrils (with turn-on ratios of 14 and 10 for Aß42 and Aß40, respectively). Mechanistic investigations were carried out by performing field-emission scanning electron microscopy, X-ray crystallography, UV-vis absorption spectroscopy, and steady-state and transient photoluminescence spectroscopy experiments. The studies revealed that the SN probes underwent preassembly prior to interacting with the Aß species and that the preassembled structures depended profoundly on the subtle differences between the amino moieties of the different probes. Importantly, the studies demonstrated that the mode of fluorescence signaling (i.e., ratiometric response versus turn-on response) was primarily governed by stacking geometries within the probe preassemblies. Specifically, ratiometric fluorescence responses were observed for probes capable of forming J-assembly, whereas fluorescence turn-on responses were obtained for probes incapable of forming J-aggregates. This finding provides an important guideline to follow in future efforts at developing fluorescent probes for Aß aggregation. We also conclude, on the basis of our study, that the rational design of such fluorescent probes should consider interactions between the probe molecules, as well as those between Aß peptides and the probe molecule.

Link of impaired metal ion homeostasis to mitochondrial dysfunction in neurons.

Manganese, iron, copper, and zinc are observed to play essential roles in mitochondria. The overload and depletion of metal ions in mitochondria under pathological conditions, however, could disturb mitochondrial compartments and functions leading to cell death. In this review, we mainly summarize how impaired metal ion homeostasis affects mitochondrial systems, such as membrane potentials, the tricarboxylic acid cycle, oxidative phosphorylation, and glutathione metabolism. In addition, based on current findings, we briefly describe a recent understanding of the relationship among metal ion dysregulation, mitochondrial dysfunction, and the pathogeneses of neurodegenerative diseases.

A zinc fluorescent sensor used to detect mercury (II) and hydrosulfide.

A zinc sensor based on quinoline and morpholine has been synthesized. The sensor selectively fluoresces in the presence of Zn2+, while not for other metal ions. Absorbance changes in the 350nm region are observed when Zn2+ binds, which binds in a 1:1 ratio. The sensor fluoresces due to Zn2+ above pH values of 6.0 and in the biological important region. The Zn2+-sensor complex has the unique ability to detect both Hg2+ and HS-. The fluorescence of the Zn2+-sensor complex is quenched when it is exposed to aqueous solutions of Hg2+ with sub-micromolar detection levels for Hg2+. The fluorescence of the Zn2+-sensor complex is also quenched by aqueous solutions of hydrosulfide. The sensor was used to detect Zn2+ and Hg2+ in living cells.

Mechanistic Insights into Tunable Metal-Mediated Hydrolysis of Amyloid-ß Peptides.

An amyloidogenic peptide, amyloid-ß (Aß), has been implicated as a contributor to the neurotoxicity of Alzheimer's disease (AD) that continues to present a major socioeconomic burden for our society. Recently, the use of metal complexes capable of cleaving peptides has arisen as an efficient tactic for amyloid management; unfortunately, little has been reported to pursue this strategy. Herein, we report a novel approach to validate the hydrolytic cleavage of divalent metal complexes toward two major isoforms of Aß (Aß40 and Aß42) and tune their proteolytic activity based on the choice of metal centers (M = Co, Ni, Cu, and Zn) which could be correlated to their anti-amyloidogenic properties. Such metal-dependent tunability was facilitated employing a tetra-N-methylated cyclam (TMC) ligand that imparts unique geometric and stereochemical control, which has not been available in previous systems. Co(II)(TMC) was identified to noticeably cleave Aß peptides and control their aggregation, reporting the first Co(II) complex for such reactivities to the best of our knowledge. Through detailed mechanistic investigations by biochemical, spectroscopic, mass spectrometric, and computational studies, the critical importance of the coordination environment and acidity of the aqua-bound complexes in promoting amide hydrolysis was verified. The biological applicability of Co(II)(TMC) was also illustrated via its potential blood-brain barrier permeability, relatively low cytotoxicity, regulatory capability against toxicity induced by both Aß40 and Aß42 in living cells, proteolytic activity with Aß peptides under biologically relevant conditions, and inertness toward cleavage of structured proteins. Overall, our approaches and findings on reactivities of divalent metal complexes toward Aß, along with the mechanistic insights, demonstrate the feasibility of utilizing such metal complexes for amyloid control.

Towards an understanding of amyloid-ß oligomers: characterization, toxicity mechanisms, and inhibitors.

Alzheimer's disease (AD) is characterized by an imbalance between production and clearance of amyloid-ß (Aß) species. Aß peptides can transform structurally from monomers into ß-stranded fibrils via multiple oligomeric states. Among the various Aß species, structured oligomers are proposed to be more toxic than fibrils; however, the identification of Aß oligomers has been challenging due to their heterogeneous and metastable nature. Multiple techniques have recently helped us gain a better understanding of oligomers' assembly details and structural properties. Moreover, some progress on elucidating the mechanisms of oligomer-triggered toxicity has been made. Based on the collection of current findings, there is growing consensus that control of toxic Aß oligomers could be a valid approach to regulate Aß-associated toxicity, which could advance development of new diagnostics and therapeutics for amyloid-related diseases. In this review, we summarize the recent understanding of Aß oligomers' assembly, structural properties, and toxicity, along with inhibitors against Aß aggregation, including oligomerization.

In Cellulo Mapping of Subcellular Localized Bilirubin.

Bilirubin (BR) is a de novo synthesized metabolite of human cells. However, subcellular localization of BR in the different organelles of human cells has been largely unknown. Here, utilizing UnaG as a genetically encoded fluorescent BR sensor, we report the existence of relatively BR-enriched and BR-depleted microspaces in various cellular organelles of live cells. Our studies indicate that (i) the cytoplasmic facing membrane of the endoplasmic reticulum (ER) and the nucleus are relatively BR-enriched spaces and (ii) mitochondrial intermembrane space and the ER lumen are relatively BR-depleted spaces. Thus, we demonstrate a relationship between such asymmetrical BR distribution in the ER membrane and the BR metabolic pathway. Furthermore, our results suggest plausible BR-transport and BR-regulating machineries in other cellular compartments, including the nucleus and mitochondria.

Importance of the Dimethylamino Functionality on a Multifunctional Framework for Regulating Metals, Amyloid-ß, and Oxidative Stress in Alzheimer's Disease.

The complex and multifaceted pathology of Alzheimer's disease (AD) continues to present a formidable challenge to the establishment of long-term treatment strategies. Multifunctional compounds able to modulate the reactivities of various pathological features, such as amyloid-ß (Aß) aggregation, metal ion dyshomeostasis, and oxidative stress, have emerged as a useful tactic. Recently, an incorporation approach to the rational design of multipurpose small molecules has been validated through the production of a multifunctional ligand (ML) as a potential chemical tool for AD. In order to further the development of more diverse and improved multifunctional reagents, essential pharmacophores must be identified. Herein, we report a series of aminoquinoline derivatives (AQ1-4, AQP1-4, and AQDA1-3) based on ML's framework, prepared to gain a structure-reactivity understanding of ML's multifunctionality in addition to tuning its metal binding affinity. Our structure-reactivity investigations have implicated the dimethylamino group as a key component for supplying the antiamyloidogenic characteristics of ML in both the absence and presence of metal ions. Two-dimensional NMR studies indicate that structural variations of ML could tune its interaction sites along the Aß sequence. In addition, mass spectrometric analyses suggest that the ability of our aminoquinoline derivatives to regulate metal-induced Aß aggregation may be influenced by their metal binding properties. Moreover, structural modifications to ML were also observed to noticeably change its metal binding affinities and metal-to-ligand stoichiometries that were shown to be linked to their antiamyloidogenic and antioxidant activities. Overall, our studies provide new insights into rational design strategies for multifunctional ligands directed at regulating metal ions, Aß, and oxidative stress in AD and could advance the development of improved next-generation multifunctional reagents.

A PET-based fluorometric chemosensor for the determination of mercury(II) and pH, and hydrolysis reaction-based colorimetric detection of hydrogen sulfide.

A simple fluorescent chemosensor 1 for the detection of Hg(2+) and pH was developed by a combination of 2-aminoethyl piperazine and 4-chloro-7-nitrobenz-2-oxa-1,3-diazole. The sensor 1 showed OFF-ON behavior for different colors of fluorescence in the presence of Hg(2+) and under acidic conditions, respectively, in a near-perfect aqueous solution. The turn-on fluorescence caused by inhibition of photoinduced electron transfer was explained by theoretical calculations. 1 could be used to quantify Hg(2+) in water samples, and its in vitro studies with HeLa cells showed fluorescence in the presence of Hg(2+). In addition, 1 could selectively detect S(2-) by changing its color from orange to pink in a near-perfect aqueous solution. Moreover, 1 could be used as a practical, visible test kit for S(2-).

Stepwise silver-staining-based immunosorbent assay for amyloid-beta autoantibody detection.

AIMS: To detect amyloid-beta (Abeta) autoantibodies in a reliable and high-throughput fashion, we developed a stepwise silver-staining-based immunosorbent assay in a 96-well-plate platform. MATERIALS & METHODS: Abeta autoantibodies were incubated in an Abeta-immobilized 96-well microplate. Antihuman IgG-modified gold nanoparticle probes were then used to bind to the autoantibodies and signal enhancement was carried out with stepwise silver-staining on immobilized gold nanoparticle probes. A microplate reader was used to quantify silver-stained gold nanoparticles on a well-plate surface. RESULTS & DISCUSSION: Stepwise silver-staining at low temperature enables long-term silver-staining with minimal increase of background signal. This stepwise staining method helps solve the problems of one-step staining, such as nonspecific binding or nonuniformity in silver precipitation after prolonged silver-staining for signal enhancement. CONCLUSION: A stepwise silver-staining strategy could be useful in minimizing nonspecific background signals. This 96-well-plate-based Abeta antibody detection assay could be useful in studying and diagnosing Alzheimer's disease.