scholarly journals A Small-Molecule Activity-Based Probe for Monitoring Ubiquitin C-terminal Hydrolase L1 (UCHL1) Activity in Live Cells and Zebrafish Embryos

2019 ◽  
Author(s):  
Paul P. Geurink ◽  
Raymond Kooij ◽  
Aysegul Sapmaz ◽  
Sijia Liu ◽  
Bo-Tao Xin ◽  
...  

ABSTRACTMany reagents have been emerged to study the function of specific enzymes in vitro. On the other hand, target specific reagents are scarce or need improvement allowing investigations of the function of individual enzymes in a cellular context. We here report the development of a target-selective fluorescent small-molecule activity-based DUB probe that is active in live cells and whole animals. The probe labels active Ubiquitin Carboxy-terminal Hydrolase L1 (UCHL1), also known as neuron-specific protein PGP9.5 (PGP9.5) and parkinson disease 5 (PARK5), a DUB active in neurons that constitutes 1-2% of total brain protein. UCHL1 variants have been linked with the neurodegenerative disorders Parkinson’s and Alzheimer’s disease. In addition, high levels of UCHL1 also correlate often with cancer and especially metastasis. The function of UCHL1 or its role in cancer and neurodegenerative disease is poorly understood and few UCHL1 specific research tools exist. We show that the reagents reported here are specific for UCHL1 over all other DUBs detectable by competitive activity-based protein profiling and by mass spectrometry. Our probe, which contains a cyanimide reactive moiety, binds to the active-site cysteine residue of UCHL1 irreversibly in an activity-dependent manner. Its use is demonstrated by labelling of UCHL1 both in vitro and in cells. We furthermore show that this probe can report UCHL1 activity during the development of zebrafish embryos.

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sara Busacca ◽  
Qi Zhang ◽  
Annabel Sharkey ◽  
Alan G. Dawson ◽  
David A. Moore ◽  
...  

AbstractWe hypothesized that small molecule transcriptional perturbation could be harnessed to target a cellular dependency involving protein arginine methyltransferase 5 (PRMT5) in the context of methylthioadenosine phosphorylase (MTAP) deletion, seen frequently in malignant pleural mesothelioma (MPM). Here we show, that MTAP deletion is negatively prognostic in MPM. In vitro, the off-patent antibiotic Quinacrine efficiently suppressed PRMT5 transcription, causing chromatin remodelling with reduced global histone H4 symmetrical demethylation. Quinacrine phenocopied PRMT5 RNA interference and small molecule PRMT5 inhibition, reducing clonogenicity in an MTAP-dependent manner. This activity required a functional PRMT5 methyltransferase as MTAP negative cells were rescued by exogenous wild type PRMT5, but not a PRMT5E444Q methyltransferase-dead mutant. We identified c-jun as an essential PRMT5 transcription factor and a probable target for Quinacrine. Our results therefore suggest that small molecule-based transcriptional perturbation of PRMT5 can leverage a mutation-selective vulnerability, that is therapeutically tractable, and has relevance to 9p21 deleted cancers including MPM.


1990 ◽  
Vol 10 (8) ◽  
pp. 4233-4238
Author(s):  
D S Gilmour ◽  
T J Dietz ◽  
S C Elgin

A protein fraction that requires the TATA sequence to bind to the hsp70 promoter has been partially purified from nuclear extracts of Drosophila embryos. This TATA factor produces a large DNase I footprint that extends from -44 to +35 on the promoter. A mutation that changes TATA to TATG interferes both with the binding of this complex and with the transcription of the hsp70 promoter in vitro, indicating that this interaction is important for transcriptional activity. Using a highly specific protein-DNA cross-linking assay, we have identified four polypeptides that require the TATA sequence to bind to the hsp70 promoter. Polypeptides of 26 and 42 kilodaltons are in intimate contact with the TATA sequence. Polypeptides of 150 and 60 kilodaltons interact within the region from +24 to +47 in a TATA-dependent manner. Both the extended footprint and the polypeptides identified by UV cross-linking indicate that the Drosophila TATA factor is a multicomponent complex.


2019 ◽  
Vol 30 (23) ◽  
pp. 2913-2928 ◽  
Author(s):  
Konstantinos Nakos ◽  
Megan R. Radler ◽  
Elias T. Spiliotis

Septins (SEPTs) are filamentous guanosine-5′-triphosphate (GTP)-binding proteins, which affect microtubule (MT)-dependent functions including membrane trafficking and cell division, but their precise role in MT dynamics is poorly understood. Here, in vitro reconstitution of MT dynamics with SEPT2/6/7, the minimal subunits of septin heteromers, shows that SEPT2/6/7 has a biphasic concentration-dependent effect on MT growth. Lower concentrations of SEPT2/6/7 enhance MT plus-end growth and elongation, while higher and intermediate concentrations inhibit and pause plus-end growth, respectively. We show that SEPT2/6/7 has a modest preference for GTP- over guanosine diphosphate (GDP)-bound MT lattice and competes with end-binding protein 1 (EB1) for binding to guanosine 5′- O-[γ-thio]triphosphate (GTPγS)-stabilized MTs, which mimic the EB1-preferred GDP-Pi state of polymerized tubulin. Strikingly, SEPT2/6/7 triggers EB1 dissociation from plus-end tips in cis by binding to the MT lattice and in trans when MT plus ends collide with SEPT2/6/7 filaments. At these intersections, SEPT2/6/7 filaments were more potent barriers than actin filaments in pausing MT growth and dissociating EB1 in vitro and in live cells. These data demonstrate that SEPT2/6/7 complexes and filaments can directly impact MT plus-end growth and the tracking of plus end–binding proteins and thereby may facilitate the capture of MT plus ends at intracellular sites of septin enrichment. [Media: see text]


2017 ◽  
Vol 114 (4) ◽  
pp. 681-686 ◽  
Author(s):  
Glen P. Liszczak ◽  
Zachary Z. Brown ◽  
Samuel H. Kim ◽  
Rob C. Oslund ◽  
Yael David ◽  
...  

Recent advances in the field of programmable DNA-binding proteins have led to the development of facile methods for genomic localization of genetically encodable entities. Despite the extensive utility of these tools, locus-specific delivery of synthetic molecules remains limited by a lack of adequate technologies. Here we combine the flexibility of chemical synthesis with the specificity of a programmable DNA-binding protein by using protein trans-splicing to ligate synthetic elements to a nuclease-deficient Cas9 (dCas9) in vitro and subsequently deliver the dCas9 cargo to live cells. The versatility of this technology is demonstrated by delivering dCas9 fusions that include either the small-molecule bromodomain and extra-terminal family bromodomain inhibitor JQ1 or a peptide-based PRC1 chromodomain ligand, which are capable of recruiting endogenous copies of their cognate binding partners to targeted genomic binding sites. We expect that this technology will allow for the genomic localization of a wide array of small molecules and modified proteinaceous materials.


Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 232-232
Author(s):  
Rosa Lapalombella ◽  
Caroline Berglund ◽  
Emilia Mahoney ◽  
Katie Williams ◽  
Shruti Jha ◽  
...  

Abstract Abstract 232 Exportin 1 (CRM1, XPO1) is a nuclear exporter that promotes the transit of tumor suppressor proteins (TSPs) including p53, I-κB, and FOXO3A out of the nucleus, thereby preventing their activity and contributing to disrupted apoptosis and enhanced proliferation. Recently, whole-genome sequencing in patients with CLL allowed the identification of recurrent mutations in a highly conserved region of CRM1 that can potentially affects its gene function, suggesting a direct role for CRM1 in the pathogenesis of CLL (Puente XS, et al: Nature 75:101, 2011). However the role of CRM1 and the consequences of its mutation in the development of CLL have yet to be explored. CRM1 has been shown to be up-regulated in hematologic and various solid tumors, making it a highly attractive molecular target impacting multiple pro apoptotic pathways. KPT-SINEs are new, potent and irreversible small molecule selective inhibitors of nuclear export developed by Karyopharm that specifically and irreversibly bind to CRM1 and block the function of this protein. CLL is characterized by disrupted apoptosis caused both by co-dependent stromal elements and aberrant activation of several survival-promoting signaling/transcriptional pathways including PI3K/Akt, NF-kB, and p53. Because of the distinct subtypes of CLL and multiple signaling pathways dysregulated, a therapeutic agent targeting a single biological pathway is unlikely to be effective. Thus, pursuit of CRM1 inhibition as a novel strategy aimed to restore multiple death pathways is crucial and has broad implications for many types of patients. Our preliminary work demonstrated CRM1 is over-expressed in CLL cells compared to normal B cells at a protein (3 fold, p<0.005) and mRNA level (2.6 fold p=0.014). Inhibition of CRM1 by KPT-185 induced apoptosis in primary patient CLL cells in a dose and time dependent manner (EC50<500nM) while limited cytotoxicity against normal PBMC and isolated B, NK and T cells was observed (EC50 values >20 μM). Additionally, KPT-185 treatment of NK cells had no effect on their function as measured by ability of NK cells to mediate antibody dependent (ADCC) as wekk as direct cytotoxicity. The effect of KPT-185 on T function is currently under evaluation. Nuclear accumulation of FOXO3, p53 and IkB was also observed in primary CLL cells in a time dependent manner as shown by western blot and confocal microscopy. The evaluation of activated target genes is currently ongoing. Given the importance of microenvironmental stimuli on survival of CLL cells and response to therapy, we evaluated the ability of KPT-185 to induce cytotoxicity of CLL cells in the presence or absence of soluble factors such as CPG, CD40L, BAFF, TNF-α, IL-6, or IL-4, which are known to reduce the spontaneous apoptosis associated with CLL cells. KPT-185 treatment abrogated the protection induced by each of these factors suggesting that KPT-SINEs can disrupt signaling from the microenvironment that lead to in vivo CLL cell survival and potentially drug resistance. Interestingly the cytotoxic effect elicited by KPT-185 was enhanced in CPG activated cells (p=0.02). We also tested the ability of KPT-185 to kill CLL cells under coculture conditions with Hs5 stromal cell line. Coculture of CLL cells alone for 48 hours on the Hs5 stromal cell line resulted in a marked reduction of spontaneous apoptosis suggesting a strong protective effect elicited (P<0.001) by the stromal cells. Interestingly the cytotoxic effect mediated by KPT-185 was enhanced under coculture conditions (p=0.013). KPT-185 was also proven to be effective on murine TCL1+ cells (EC50<500nM) in vitro. The in vivo efficacy of this compound and other structurally related analogs is currently being assessed in an ongoing study in theTCL1 mouse model of CLL. In conclusion CRM1 represents a novel target that has not been adequately explored in CLL. KPT-SINEs are a class of promising therapeutic agents with proven selective in vitro activity in CLL cells providing the rationale for developing small molecule, drug-like CRM1 inhibitors for the treatment of this disease. Disclosures: Sandanayaka: Karyopharm Therapeutics: Employment. Shechter:Karyopharm Therapeutics: Employment. McCauley:Karyopharm Therapeutics: Employment. Shacham:Karyopharm: Equity Ownership. Kauffman:Karyopharm: Equity Ownership.


2014 ◽  
Vol 58 (12) ◽  
pp. 7072-7082 ◽  
Author(s):  
Horacio Reyes-Vivas ◽  
Ignacio de la Mora-de la Mora ◽  
Adriana Castillo-Villanueva ◽  
Lilian Yépez-Mulia ◽  
Gloria Hernández-Alcántara ◽  
...  

ABSTRACTGiardiasis is highly prevalent in the developing world, and treatment failures with the standard drugs are common. This work deals with the proposal of omeprazole as a novel antigiardial drug, focusing on a giardial glycolytic enzyme used to follow the cytotoxic effect at the molecular level. We used recombinant technology and enzyme inactivation to demonstrate the capacity of omeprazole to inactivate giardial triosephosphate isomerase, with no adverse effects on its human counterpart. To establish the specific target in the enzyme, we used single mutants of every cysteine residue in triosephosphate isomerase. The effect on cellular triosephosphate isomerase was evaluated by following the remnant enzyme activity on trophozoites treated with omeprazole. The interaction of omeprazole with giardial proteins was analyzed by fluorescence spectroscopy. The susceptibility to omeprazole of drug-susceptible and drug-resistant strains ofGiardia lambliawas evaluated to demonstrate its potential as a novel antigiardial drug. Our results demonstrate that omeprazole inhibits giardial triosephosphate isomerase in a species-specific manner through interaction with cysteine at position 222. Omeprazole enters the cytoplasmic compartment of the trophozoites and inhibits cellular triosephosphate isomerase activity in a dose-dependent manner. Such inhibition takes place concomitantly with the cytotoxic effect caused by omeprazole on trophozoites.G. lambliatriosephosphate isomerase (GlTIM) is a cytoplasmic protein which can help analyses of how omeprazole works against the proteins of this parasite and in the effort to understand its mechanism of cytotoxicity. Our results demonstrate the mechanism of giardial triosephosphate isomerase inhibition by omeprazole and show that this drug is effectivein vitroagainst drug-resistant and drug-susceptible strains ofG. lamblia.


2006 ◽  
Vol 398 (2) ◽  
pp. 197-206 ◽  
Author(s):  
Jingmin Zeng ◽  
Rachael A. Dunlop ◽  
Kenneth J. Rodgers ◽  
Michael J. Davies

Hyperglycaemia, triose phosphate decomposition and oxidation reactions generate reactive aldehydes in vivo. These compounds react non-enzymatically with protein side chains and N-terminal amino groups to give adducts and cross-links, and hence modified proteins. Previous studies have shown that free or protein-bound carbonyls inactivate glyceraldehyde-3-phosphate dehydrogenase with concomitant loss of thiol groups [Morgan, Dean and Davies (2002) Arch. Biochem. Biophys. 403, 259–269]. It was therefore hypothesized that modification of lysosomal cysteine proteases (and the structurally related enzyme papain) by free and protein-bound carbonyls may modulate the activity of these components of the cellular proteolytic machinery responsible for the removal of modified proteins and thereby contribute to a decreased removal of modified proteins from cells. It is shown that MGX (methylglyoxal), GO (glyoxal) and glycolaldehyde, but not hydroxyacetone and glucose, inhibit catB (cathepsin B), catL (cathepsin L) and catS (cathepsin S) activity in macrophage cell lysates, in a concentration-dependent manner. Protein-bound carbonyls produced similar inhibition with both cell lysates and intact macrophage cells. Inhibition was also observed with papain, with this paralleled by loss of the active site cysteine residue and formation of the adduct species S-carboxymethylcysteine, from GO, in a concentration-dependent manner. Inhibition of autolysis of papain by MGX, along with cross-link formation, was detected by SDS/PAGE. Treatment of papain and catS with the dialdehyde o-phthalaldehyde resulted in enzyme inactivation and an intra-molecular active site cysteine–lysine cross-link. These results demonstrate that reactive aldehydes inhibit cysteine proteases by modification of the active site cysteine residue. This process may contribute to the accumulation of modified proteins in tissues of people with diabetes and age-related pathologies, including atherosclerosis, cataract and Alzheimer's disease.


1990 ◽  
Vol 10 (8) ◽  
pp. 4233-4238 ◽  
Author(s):  
D S Gilmour ◽  
T J Dietz ◽  
S C Elgin

A protein fraction that requires the TATA sequence to bind to the hsp70 promoter has been partially purified from nuclear extracts of Drosophila embryos. This TATA factor produces a large DNase I footprint that extends from -44 to +35 on the promoter. A mutation that changes TATA to TATG interferes both with the binding of this complex and with the transcription of the hsp70 promoter in vitro, indicating that this interaction is important for transcriptional activity. Using a highly specific protein-DNA cross-linking assay, we have identified four polypeptides that require the TATA sequence to bind to the hsp70 promoter. Polypeptides of 26 and 42 kilodaltons are in intimate contact with the TATA sequence. Polypeptides of 150 and 60 kilodaltons interact within the region from +24 to +47 in a TATA-dependent manner. Both the extended footprint and the polypeptides identified by UV cross-linking indicate that the Drosophila TATA factor is a multicomponent complex.


Blood ◽  
2021 ◽  
Vol 138 (Supplement 1) ◽  
pp. 266-266
Author(s):  
Shan Lin ◽  
Clement Larrue ◽  
Nastassja K. Scheidegger ◽  
Bo Kyung A. Seong ◽  
Neekesh V Dharia ◽  
...  

Abstract First-generation, large-scale functional genomic screens have revealed hundreds of potential genetic vulnerabilities in acute myeloid leukemia (AML), a devastating hematologic malignancy with poor overall survival. Because these large-scale genetic screens were primarily performed in vitro in established AML cell lines, their translational relevance has been debated. Therefore, we established a protocol for CRISPR screening in orthotopic xenograft models of human AML, including patient-derived-xenograft (PDX) models that are tractable for CRISPR-editing. We first defined experimental conditions necessary for an optimal in vivo screen via barcoding experiments. We determined that sub-lethal irradiation was necessary for improved barcode representation in bone marrow and to reduce mouse-to-mouse variation. Moreover, it was critical to combine samples from multiple mice to achieve complete in vivo library representation. Next, using the Broad DepMap and other publicly available functional genomic screen data, we identified 200 genes that were stronger dependencies in AML cell lines compared to all other cancer types screened. Using this list, we created a secondary library and performed parallel in vivo and in vitro screens using the MV4-11 and U937 cell lines and a PDX model. In vitro and in vivo hits were surprisingly well correlated, although a modest number of targets did not score well in vivo. Notably, dependencies identified across AML cell line models were strongly recapitulated in the PDX model, validating the application of AML cell lines for dependency discovery. Our in vivo screens nominated the mitochondria-localized RING-type ubiquitin E3 ligase MARCH5 as a potential therapeutic target in AML. Using CRISPR, we first validated this in vitro dependency on MARCH5 and determined that MARCH5 is a critical guardian to prevent apoptosis in AML. MARCH5 depletion activates the canonical mitochondrial apoptosis pathway in a BAX/BAK1-dependent manner. Multiple genome-wide screens revealed that a dependency on MARCH5 is strongly correlated with a dependency on MCL1, but not other anti-apoptotic BCL2-family members, across the AML cell lines in the screen. As observed with MCL1 inhibition, MARCH5 depletion sensitized AML cells to venetoclax, a BCL2-specific inhibitor FDA-approved in combination with a hypomethylating agent for the treatment of older adults with AML. Importantly, MARCH5 depletion diminished the venetoclax resistance induced by MCL1 overexpression but not that caused by BCLXL overexpression. Altogether, these results suggest that MARCH5 is required for maintaining MCL1 activity specifically. Since there are no small molecule inhibitors directed against MARCH5, we deployed a dTAG system as an approximation of pharmacological inhibition. This approach uses a hetero-bifunctional small molecule that binds the FKBP12 F36V-fused MARCH5 and the E3 ligase VHL, leading to the ubiquitination and proteasome-mediated degradation of the fusion protein. dTAG-MARCH5 cells were established via deleting endogenous MARCH5 by CRISPR and expressing exogenous FKBP-tagged MARCH5 protein. MARCH5 degradation with the dTAG molecule dTAG V-1 markedly impaired cell growth in vitro. Additionally, we demonstrated the utility of dTAG system in vivo using a PDX model. The combination treatment of dTAG V-1 and venetoclax elicited a much stronger anti-leukemic effect compared to the treatment with only venetoclax or dTAG V-1, further highlighting MARCH5 as a promising synergistic target for enhancing the efficacy of venetoclax in AML. Taken together, our in vivo screening approach, coupled with CRISPR-competent PDX models and dTAG-directed protein degradation, constitute a useful platform for prioritizing AML targets emerging from in vitro screens to serve as the starting point for therapy development. Disclosures Dharia: Genentech: Current Employment. Piccioni: Merck Research Laboratories: Current Employment. Stegmaier: Bristol Myers Squibb: Consultancy; KronosBio: Consultancy; AstraZeneca: Consultancy; Auron Therapeutics: Consultancy, Current equity holder in publicly-traded company; Novartis: Research Funding.


Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 13-13 ◽  
Author(s):  
Wei Liu ◽  
Benjamin Mizukawa ◽  
Mark Wunderlich ◽  
James F Johnson ◽  
James C. Mulloy ◽  
...  

Abstract Abstract 13 A large body of studies has proposed that leukemia initiating cells (LICs) are the culprit of leukemia relapse from conventional therapies. Like normal hematopoietic stem/progenitor cells (HSPCs), LICs are thought to reside in the bone marrow (BM) endothelial and/or endosteal niche. Although the full nature of LIC-niche interaction remains elusive, it has been postulated as a useful target for leukemia therapy based on a dual rationale: on one hand, the survival of LICs may depend upon interactions with specific niche, while on the other hand, chasing LICs out of the BM niche may drive quiescent LICs into active cell cycle, sensitizing them for conventional chemotherapy. Recent progresses in studying the PML tumor suppressor and the CXCR4-antagonist AMD3100 have provided strong support for such a rationale (Blood 113, 6215; Nature 453, 1072). The Rho GTPase family member Cdc42 is a central regulator of cell proliferation, adhesion, and migration by integrating signals from multiple cell surface receptors. Ablation of Cdc42 in HSPCs in a conditional knockout mouse model leads to massive egress of HSPCs from BM to the peripheral blood (PB), a phenotype attributable to deficiencies in HSPC adhesion, migration, and F-actin polymerization. We recently demonstrated that pharmacological targeting of Cdc42 by a small molecule Cdc42 activity-specific inhibitor (CASIN) transiently and specifically inhibits Cdc42 activity and mimics the Cdc42 knockout mobilization phenotype by suppressing HSPC adhesion, migration, and F-actin polymerization. CASIN appears to be active in this regard on both murine and human blood progenitors in vitro and in xenografted mice (Blood 112: 68a, Nature Biotechnology under revision). In the present studies, we hypothesize that pharmacological targeting of Cdc42 by CASIN is effective in mobilizing LICs from the BM niche, thus providing a new method for combinatory therapy against LICs. To test this hypothesis, we used MLL-AF9/N-Ras human AML cells (MA9/N-Ras), whereby the N-Ras G12D oncogene was introduced into MLL-AF9 transduced human CD34+ umbilical cord blood (HCB) cells. These cells grow vigorously in vitro independent of cytokine supplementation and induce AML readily in humanized NOD/SCID-SGM3 (SGM3) mice. Xenotransplant experiments confirmed that MA9/N-Ras cells are clonal inducers of leukemia with the property of LICs, as animals transplanted with either bulk cultures or with single cell derived cultures succumbed to AML with similar latencies. In MA9/N-Ras cells CASIN effectively inhibited downstream effectors of Cdc42 such as p-PAK, p-MLC and p-FAK in a dose-dependent manner. In the SGM3 mouse xenograft, we found CASIN administration (1.2 mg/kg, IV) transiently elicited mobilization of LICs from BM to PB by 20 minutes post injection. This was correlated with in vitro suppression of SDF-1α induced F-actin polymerization detected by FACS analysis and directional migration detected by a transwell assay upon CASIN treatment of the LICs (5-10 μM). Similar observations were made using Cdc42-specific shRNA knockdown of endogenous Cdc42 in the LICs. Continuous CASIN infusion into the xenografted mice for 5 days (1.2 mg/kg, IV, once daily) led to a potent induction of apoptosis of LICs detected by AnnexinV/7AAD staining. Significantly, the CASIN infusion showed no effects on the survival of HCB cells in xenografted SGM3 mice. In addition to a potential niche-dependent survival mechanism, the LICs, not normal HCB cells, appear to directly depend on Cdc42 for survival signals as further in vitro culture studies found that a 24-hour CASIN treatment resulted in a dose-dependent apoptosis of MA9/N-Ras cells, but not of normal HCBs. Finally, mouse genetic studies using MA9 transduced Mx-cre;Cdc42lox/lox BM cells transplanted into congenic BoyJ recipients showed that none of the mice with deleted Cdc42 upon pIpC injection developed AML while all mock-injected mice die from leukemia with less than 4 weeks latency, providing genetic evidence that Cdc42 is required for MA9-induced initiation of AML. Whether CASIN is effective in sensitizing the LICs to conventional chemotherapy in a combinatory regiment is currently under investigation. Our studies present a novel concept that pharmacological targeting of the intracellular signal transducer Cdc42 may have therapeutic value in eradicating LICs. Disclosures: No relevant conflicts of interest to declare.


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