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1.
Brain ; 139(11): 2891-2908, 2016 11 01.
Article in English | MEDLINE | ID: mdl-27645800

ABSTRACT

No disease-modifying treatment exists for the fatal neurodegenerative polyglutamine disease known both as Machado-Joseph disease and spinocerebellar ataxia type 3. As a potential route to therapy, we identified small molecules that reduce levels of the mutant disease protein, ATXN3. Screens of a small molecule collection, including 1250 Food and Drug Administration-approved drugs, in a novel cell-based assay, followed by secondary screens in brain slice cultures from transgenic mice expressing the human disease gene, identified the atypical antipsychotic aripiprazole as one of the hits. Aripiprazole increased longevity in a Drosophila model of Machado-Joseph disease and effectively reduced aggregated ATXN3 species in flies and in brains of transgenic mice treated for 10 days. The aripiprazole-mediated decrease in ATXN3 abundance may reflect a complex response culminating in the modulation of specific components of cellular protein homeostasis. Aripiprazole represents a potentially promising therapeutic drug for Machado-Joseph disease and possibly other neurological proteinopathies.


Subject(s)
Antipsychotic Agents/therapeutic use , Aripiprazole/therapeutic use , Ataxin-3/metabolism , Machado-Joseph Disease/drug therapy , Machado-Joseph Disease/metabolism , Mutant Proteins/drug effects , Animals , Animals, Genetically Modified , Ataxin-3/genetics , Brain/drug effects , Brain/metabolism , Brain/ultrastructure , Disease Models, Animal , Drosophila , Drug Evaluation, Preclinical , Gene Expression Regulation/drug effects , Gene Expression Regulation/genetics , HEK293 Cells/drug effects , HEK293 Cells/metabolism , HEK293 Cells/ultrastructure , Humans , Machado-Joseph Disease/genetics , Mice , Mutant Proteins/metabolism , Nerve Tissue Proteins/metabolism , Organ Culture Techniques , Peptides/genetics , Piperidines/pharmacology , Pyrans/pharmacology , Pyrazoles/pharmacology
2.
ACS Chem Biol ; 11(11): 3084-3092, 2016 11 18.
Article in English | MEDLINE | ID: mdl-27622287

ABSTRACT

Inorganic pyrophosphatase (PPiase) is an essential enzyme that hydrolyzes inorganic pyrophosphate (PPi), driving numerous metabolic processes. We report a discovery of an allosteric inhibitor (2,4-bis(aziridin-1-yl)-6-(1-phenylpyrrol-2-yl)-s-triazine) of bacterial PPiases. Analogues of this lead compound were synthesized to target specifically Mycobacterium tuberculosis (Mtb) PPiase (MtPPiase). The best analogue (compound 16) with a Ki of 11 µM for MtPPiase is a species-specific inhibitor. Crystal structures of MtPPiase in complex with the lead compound and one of its analogues (compound 6) demonstrate that the inhibitors bind in a nonconserved interface between monomers of the hexameric MtPPiase in a yet unprecedented pairwise manner, while the remote conserved active site of the enzyme is occupied by a bound PPi substrate. Consistent with the structural studies, the kinetic analysis of the most potent inhibitor has indicated that it functions uncompetitively, by binding to the enzyme-substrate complex. The inhibitors appear to allosterically lock the active site in a closed state causing its dysfunctionalization and blocking the hydrolysis. These inhibitors are the first examples of allosteric, species-selective inhibitors of PPiases, serving as a proof-of-principle that PPiases can be selectively targeted.


Subject(s)
Enzyme Inhibitors/pharmacology , Inorganic Pyrophosphatase/antagonists & inhibitors , Mycobacterium tuberculosis/enzymology , Allosteric Regulation , Crystallography, X-Ray , Drug Discovery , Enzyme Inhibitors/chemistry , Inorganic Pyrophosphatase/metabolism , Molecular Structure
3.
Nat Commun ; 7: 10710, 2016 Feb 16.
Article in English | MEDLINE | ID: mdl-26880271

ABSTRACT

Pathogenic microorganisms often have the ability to attach to a surface, building a complex matrix where they colonize to form a biofilm. This cellular superstructure can display increased resistance to antibiotics and cause serious, persistent health problems in humans. Here we describe a high-throughput in vitro screen to identify inhibitors of Acinetobacter baumannii biofilms using a library of natural product extracts derived from marine microbes. Analysis of extracts derived from Streptomyces gandocaensis results in the discovery of three peptidic metabolites (cahuitamycins A-C), with cahuitamycin C being the most effective inhibitor (IC50=14.5 µM). Biosynthesis of cahuitamycin C proceeds via a convergent biosynthetic pathway, with one of the steps apparently being catalysed by an unlinked gene encoding a 6-methylsalicylate synthase. Efforts to assess starter unit diversification through selective mutasynthesis lead to production of unnatural analogues cahuitamycins D and E of increased potency (IC50=8.4 and 10.5 µM).


Subject(s)
Acinetobacter baumannii/drug effects , Anti-Bacterial Agents/pharmacology , Bacterial Proteins/pharmacology , Biofilms/drug effects , Oligopeptides/pharmacology , Acinetobacter baumannii/physiology , Anti-Bacterial Agents/biosynthesis , Bacterial Proteins/biosynthesis , Biosynthetic Pathways , High-Throughput Screening Assays , Oligopeptides/biosynthesis , Streptomyces
4.
Science ; 350(6261): 674-7, 2015 Nov 06.
Article in English | MEDLINE | ID: mdl-26542570

ABSTRACT

Cataracts reduce vision in 50% of individuals over 70 years of age and are a common form of blindness worldwide. Cataracts are caused when damage to the major lens crystallin proteins causes their misfolding and aggregation into insoluble amyloids. Using a thermal stability assay, we identified a class of molecules that bind α-crystallins (cryAA and cryAB) and reversed their aggregation in vitro. The most promising compound improved lens transparency in the R49C cryAA and R120G cryAB mouse models of hereditary cataract. It also partially restored protein solubility in the lenses of aged mice in vivo and in human lenses ex vivo. These findings suggest an approach to treating cataracts by stabilizing α-crystallins.


Subject(s)
Cataract/drug therapy , Hydroxycholesterols/pharmacology , alpha-Crystallin A Chain/chemistry , alpha-Crystallin B Chain/chemistry , Amyloid/antagonists & inhibitors , Amyloid/chemistry , Animals , Calorimetry, Differential Scanning , Cataract/genetics , Disease Models, Animal , Gene Knock-In Techniques , Humans , Hydroxycholesterols/chemistry , Hydroxycholesterols/therapeutic use , Mice , Protein Conformation/drug effects , Protein Stability/drug effects , alpha-Crystallin A Chain/genetics , alpha-Crystallin B Chain/genetics
5.
Chem Biol Drug Des ; 86(6): 1331-8, 2015 Dec.
Article in English | MEDLINE | ID: mdl-26147927

ABSTRACT

Novel antimicrobials that effectively inhibit bacterial growth are essential to fight the growing threat of antibiotic resistance. A promising target is the bacterial ribosome, a 2.5 MDa organelle susceptible to several biorthogonal modes of action used by different classes of antibiotics. To promote the discovery of unique inhibitors, we have miniaturized a coupled transcription/translation assay using E. coli and applied it to screen a natural product library of ~30 000 extracts. We significantly reduced the scale of the assay to 2 µL in a 1536-well plate format and decreased the effective concentration of costly reagents. The improved assay returned 1327 hits (4.6% hit rate) with %CV and Z' values of 8.5% and 0.74, respectively. This assay represents a significant advance in molecular screening, both in miniaturization and its application to a natural product extract library, and we intend to apply it to a broad array of pathogenic microbes in the search for novel anti-infective agents.


Subject(s)
Biological Products/pharmacology , Drug Evaluation, Preclinical/methods , High-Throughput Screening Assays/methods , Anti-Infective Agents/pharmacology , Escherichia coli/drug effects , Escherichia coli/genetics , Luciferases/genetics , Miniaturization/methods , Protein Biosynthesis/drug effects , Ribosomes/drug effects , Ribosomes/genetics , Small Molecule Libraries , Transcription, Genetic/drug effects
6.
Antimicrob Agents Chemother ; 59(7): 3880-6, 2015 Jul.
Article in English | MEDLINE | ID: mdl-25870073

ABSTRACT

Campylobacter jejuni is a major cause of food-borne illness due to its ability to reside within the gastrointestinal tracts of chickens. Multiple studies have identified the flagella of C. jejuni as a major determinant of chicken colonization. An inhibitor screen of approximately 147,000 small molecules was performed to identify compounds that are able to inhibit flagellar expression in a reporter strain of C. jejuni. Several compounds that modestly inhibited motility of wild-type C. jejuni in standard assays were identified, as were a number of small molecules that robustly inhibited C. jejuni growth, in vitro. Examination of similar bacterial screens found that many of these small molecules inhibited only the growth of C. jejuni. Follow-up assays demonstrated inhibition of other strains of C. jejuni and Campylobacter coli but no inhibition of the closely related Helicobacter pylori. The compounds were determined to be bacteriostatic and nontoxic to eukaryotic cells. Preliminary results from a day-of-hatch chick model of colonization suggest that at least one of the compounds demonstrates promise for reducing Campylobacter colonization loads in vivo, although further medicinal chemistry may be required to enhance bioavailability.


Subject(s)
Anti-Bacterial Agents/pharmacology , Campylobacter jejuni/drug effects , Campylobacter jejuni/metabolism , Flagella/drug effects , Animals , Anti-Bacterial Agents/toxicity , Campylobacter coli/drug effects , Campylobacter jejuni/growth & development , Cell Survival/drug effects , Chick Embryo , Chickens/microbiology , Dose-Response Relationship, Drug , Eukaryotic Cells/drug effects , Gastrointestinal Tract/drug effects , Gastrointestinal Tract/microbiology , Helicobacter pylori/drug effects , High-Throughput Screening Assays , Microbial Sensitivity Tests , Poultry Diseases/microbiology , Small Molecule Libraries , Species Specificity
7.
Immunity ; 41(4): 567-78, 2014 Oct 16.
Article in English | MEDLINE | ID: mdl-25367573

ABSTRACT

Programmed necrosis or necroptosis is an inflammatory form of cell death that critically requires the receptor-interacting protein kinase 3 (RIPK3). Here we showed that RIPK3 controls a separate, necrosis-independent pathway of inflammation by regulating cytokine expression in dendritic cells (DCs). Ripk3(-/-) bone-marrow-derived dendritic cells (BMDCs) were highly defective in lipopolysaccharide (LPS)-induced expression of inflammatory cytokines. These effects were caused by impaired NF-κB subunit RelB and p50 activation and by impaired caspase 1-mediated processing of interleukin-1ß (IL-1ß). This DC-specific function of RIPK3 was critical for injury-induced inflammation and tissue repair in response to dextran sodium sulfate (DSS). Ripk3(-/-) mice exhibited an impaired axis of injury-induced IL-1ß, IL-23, and IL-22 cytokine cascade, which was partially corrected by adoptive transfer of wild-type DCs, but not Ripk3(-/-) DCs. These results reveal an unexpected function of RIPK3 in NF-κB activation, DC biology, innate inflammatory-cytokine expression, and injury-induced tissue repair.


Subject(s)
Apoptosis/immunology , Dendritic Cells/immunology , Necrosis/immunology , Receptor-Interacting Protein Serine-Threonine Kinases/genetics , Wound Healing/genetics , Adoptive Transfer , Animals , Bone Marrow Cells/immunology , Caspase 1/metabolism , Colitis/genetics , Colitis/immunology , Dendritic Cells/transplantation , Dextran Sulfate , Enzyme Activation/genetics , Enzyme Activation/immunology , Female , Gene Expression Regulation/immunology , Inflammation/immunology , Interleukin-1beta/biosynthesis , Interleukin-1beta/immunology , Interleukin-23/biosynthesis , Interleukin-23/immunology , Interleukins/biosynthesis , Interleukins/immunology , Lipopolysaccharides , Macrophages/immunology , Mice , Mice, Inbred C57BL , Mice, Knockout , NF-kappa B p50 Subunit/genetics , NF-kappa B p50 Subunit/immunology , RNA, Messenger/biosynthesis , Receptors, Interleukin/biosynthesis , Signal Transduction/immunology , Transcription Factor RelB/genetics , Transcription Factor RelB/immunology , Interleukin-22
8.
Chem Biol Drug Des ; 83(4): 440-9, 2014 Apr.
Article in English | MEDLINE | ID: mdl-24636344

ABSTRACT

Proteins with expanded polyglutamine (polyQ) segments cause a number of fatal neurodegenerative disorders, including Huntington's disease (HD). Previous high-throughput screens in cellular and biochemical models of HD have revealed compounds that mitigate polyQ aggregation and proteotoxicity, providing insight into the mechanisms of disease and leads for potential therapeutics. However, the structural diversity of natural products has not yet been fully mobilized toward these goals. Here, we have screened a collection of ~11 000 natural product extracts for the ability to recover the slow growth of ΔProQ103-expressing yeast cells in 384-well plates (Z' ~ 0.7, CV ~ 8%). This screen identified actinomycin D as a strong inhibitor of polyQ aggregation and proteotoxicity at nanomolar concentrations (~50-500 ng/mL). We found that a low dose of actinomycin D increased the levels of the heat-shock proteins Hsp104, Hsp70 and Hsp26 and enhanced binding of Hsp70 to the polyQ in yeast. Actinomycin also suppressed aggregation of polyQ in mammalian cells, suggesting a conserved mechanism. These results establish natural products as a rich source of compounds with interesting mechanisms of action against polyQ disorders.


Subject(s)
Biological Products/chemistry , High-Throughput Screening Assays , Models, Biological , Peptides/genetics , Animals , Biological Products/analysis , Dactinomycin/pharmacology , Gene Expression Regulation/drug effects , Humans , PC12 Cells , Peptides/chemistry , Protein Aggregation, Pathological/drug therapy , Rats , Saccharomyces cerevisiae
9.
mBio ; 5(2): e01089-13, 2014 Feb 25.
Article in English | MEDLINE | ID: mdl-24570372

ABSTRACT

The urinary tract is one of the most common sites of infection in humans, and uropathogenic Escherichia coli (UPEC) is the main causative agent of urinary tract infections. Bacteria colonizing the urinary tract face extremely low iron availability. To counteract this, UPEC expresses a wide variety of iron acquisition systems. To exploit iron acquisition in UPEC as a global target for small-molecule inhibition, we developed and carried out a whole-cell growth-based high throughput screen of 149,243 compounds. Our primary assay was carried out under iron-limiting conditions. Hits in the primary screen were assayed using two counterscreens that ruled out iron chelators and compounds that inhibit growth by means other than inhibition of iron acquisition. We determined dose-response curves under two different iron conditions and purchased fresh compounds for selected hits. After retesting dose-response relationships, we identified 16 compounds that arrest growth of UPEC only under iron-limiting conditions. All compounds are bacteriostatic and do not inhibit proton motive force. A loss-of-target strategy was employed to identify the cellular target of these inhibitors. Two compounds lost inhibitory activity against a strain lacking TonB and were shown to inhibit irreversible adsorption of a TonB-dependent bacteriophage. Our results validate iron acquisition as a target for antibacterial strategies against UPEC and identify TonB as one of the cellular targets. IMPORTANCE Half of women will suffer at least one episode of urinary tract infection (UTI) during their lifetime. The current treatment for UTI involves antibiotic therapy. Resistance to currently used antibiotics has steadily increased over the last decade, generating a pressing need for the development of new therapeutic agents. Since iron is essential for colonization and scarce in the urinary tract, targeting iron acquisition would seem to be an attractive strategy. However, the multiplicity and redundancy of iron acquisition systems in uropathogenic Escherichia coli (UPEC) make it difficult to pinpoint a specific cellular target. Here, we identified 16 iron acquisition inhibitors through a whole-cell high-throughput screen, validating iron acquisition as a target for antibacterial strategies against UPEC. We also identified the cellular target of two of the inhibitors as the TonB system.


Subject(s)
Anti-Bacterial Agents/isolation & purification , Anti-Bacterial Agents/pharmacology , Biological Transport/drug effects , Escherichia coli Proteins/antagonists & inhibitors , Iron/metabolism , Membrane Proteins/antagonists & inhibitors , Uropathogenic Escherichia coli/drug effects , Coliphages/physiology , Drug Evaluation, Preclinical , Uropathogenic Escherichia coli/growth & development , Uropathogenic Escherichia coli/metabolism , Virus Attachment
10.
PLoS One ; 8(10): e76841, 2013.
Article in English | MEDLINE | ID: mdl-24098568

ABSTRACT

BACKGROUND: Necroptosis/programmed necrosis is initiated by a macro-molecular protein complex termed the necrosome. Receptor interacting protein kinase 1 (RIPK1/RIP1) and RIP3 are key components of the necrosome. TNFα is a prototypic inducer of necrosome activation, and it is widely believed that deubiquitination of RIP1 at the TNFR-1 signaling complex precedes transition of RIP1 into the cytosol where it forms the RIP1-RIP3 necrosome. Cylindromatosis (CYLD) is believed to promote programmed necrosis by facilitating RIP1 deubiquitination at this membrane receptor complex. METHODOLOGY/PRINCIPAL FINDINGS: We demonstrate that RIP1 is indeed the primary target of CYLD in TNFα-induced programmed necrosis. We observed that CYLD does not regulate RIP1 ubiquitination at the TNF receptor. TNF and zVAD-induced programmed necrosis was highly attenuated in CYLD(-/-) cells. However, in the presence of cycloheximide or SMAC mimetics, programmed necrosis was only moderately reduced in CYLD(-/-) cells. Under the latter conditions, RIP1-RIP3 necrosome formation is only delayed, but not abolished in CYLD(-/-) cells. We further demonstrate that RIP1 within the NP-40 insoluble necrosome is ubiquitinated and that CYLD regulates RIP1 ubiquitination in this compartment. Hence, RIP1 ubiquitination in this late-forming complex is greatly increased in CYLD(-/-) cells. Increased RIP1 ubiquitination impairs RIP1 and RIP3 phosphorylation, a signature of kinase activation. CONCLUSIONS/SIGNIFICANCE: Our results show that CYLD regulates RIP1 ubiquitination in the TNFα-induced necrosome, but not in the TNFR-1 signaling complex. In cells sensitized to programmed necrosis with SMAC mimetics, CYLD is not essential for necrosome assembly. Since SMAC mimetics induces the loss of the E3 ligases cIAP1 and cIAP2, reduced RIP1 ubiquitination could lead to reduced requirement for CYLD to remove ubiquitin chains from RIP1 in the TNFR-1 complex. As increased RIP1 ubiquitination in the necrosome correlates with impaired RIP1 and RIP3 phosphorylation and function, these results suggest that CYLD controls RIP1 kinase activity during necrosome assembly.


Subject(s)
Cysteine Endopeptidases/genetics , GTPase-Activating Proteins/genetics , Gene Expression Regulation/drug effects , Necrosis/genetics , Signal Transduction/drug effects , Tumor Necrosis Factor-alpha/genetics , Animals , Cell Line, Tumor , Cycloheximide/pharmacology , Cysteine Endopeptidases/metabolism , Deubiquitinating Enzyme CYLD , GTPase-Activating Proteins/metabolism , Gene Knockdown Techniques , Humans , Mice , Necrosis/metabolism , Oligopeptides/pharmacology , Phosphorylation/drug effects , Receptor-Interacting Protein Serine-Threonine Kinases , Receptors, Tumor Necrosis Factor, Type I , Tumor Necrosis Factor-alpha/metabolism , Tumor Necrosis Factor-alpha/pharmacology , Ubiquitination/drug effects
11.
Biochem J ; 456(3): 409-15, 2013 Dec 15.
Article in English | MEDLINE | ID: mdl-24059293

ABSTRACT

Programmed necrosis or necroptosis is controlled by the action of two serine/threonine kinases, RIP1 (receptor-interacting serine/threonine protein kinase 1; also known as RIPK1) and RIP3. The phosphorylation of RIP1 and RIP3 is critical for assembly of the necrosome, an amyloid-like complex that initiates transmission of the pro-necrotic signal. In the present study, we used site-directed mutagenesis to systematically examine the effects of putative phosphoacceptor sites on RIP1 and RIP3 on TNF (tumour necrosis factor)-induced programmed necrosis. We found that mutation of individual serine residues in the kinase domain of RIP1 had little effect on RIP1 kinase activity and TNF-induced programmed necrosis. Surprisingly, an alanine residue substitution for Ser(89) enhanced RIP1 kinase activity and TNF-induced programmed necrosis without affecting RIP1-RIP3 necrosome formation. This indicates that Ser(89) is an inhibitory phosphoacceptor site that can dampen the pro-necrotic function of RIP1. In addition, we show that a phosphomimetic mutant of RIP3, S204D, led to programmed necrosis that was refractory to RIP1 siRNA and insensitive to necrostatin-1 inhibition. Our results show that programmed necrosis is regulated by positive and inhibitory phosphorylation events.


Subject(s)
Amino Acid Substitution , Mutation, Missense , Nuclear Pore Complex Proteins/metabolism , RNA-Binding Proteins/metabolism , Receptor-Interacting Protein Serine-Threonine Kinases/metabolism , Humans , Imidazoles/pharmacology , Indoles/pharmacology , Jurkat Cells , Necrosis , Nuclear Pore Complex Proteins/immunology , Phosphorylation/drug effects , Phosphorylation/genetics , RNA-Binding Proteins/immunology , Receptor-Interacting Protein Serine-Threonine Kinases/genetics
12.
Cell ; 150(2): 339-50, 2012 Jul 20.
Article in English | MEDLINE | ID: mdl-22817896

ABSTRACT

RIP1 and RIP3 kinases are central players in TNF-induced programmed necrosis. Here, we report that the RIP homotypic interaction motifs (RHIMs) of RIP1 and RIP3 mediate the assembly of heterodimeric filamentous structures. The fibrils exhibit classical characteristics of ß-amyloids, as shown by Thioflavin T (ThT) and Congo red (CR) binding, circular dichroism, infrared spectroscopy, X-ray diffraction, and solid-state NMR. Structured amyloid cores are mapped in RIP1 and RIP3 that are flanked by regions of mobility. The endogenous RIP1/RIP3 complex isolated from necrotic cells binds ThT, is ultrastable, and has a fibrillar core structure, whereas necrosis is partially inhibited by ThT, CR, and another amyloid dye, HBX. Mutations in the RHIMs of RIP1 and RIP3 that are defective in the interaction compromise cluster formation, kinase activation, and programmed necrosis in vivo. The current study provides insight into the structural changes that occur when RIP kinases are triggered to execute different signaling outcomes and expands the realm of amyloids to complex formation and signaling.


Subject(s)
Necrosis/metabolism , Receptor-Interacting Protein Serine-Threonine Kinases/metabolism , Signal Transduction , Amino Acid Sequence , Amyloid/chemistry , Humans , Molecular Sequence Data , Protein Interaction Domains and Motifs , Receptor-Interacting Protein Serine-Threonine Kinases/chemistry , Sequence Alignment
13.
PLoS One ; 6(8): e23209, 2011.
Article in English | MEDLINE | ID: mdl-21853090

ABSTRACT

BACKGROUND: Programmed necrosis/necroptosis is an emerging form of cell death that plays important roles in mammalian development and the immune system. The pro-necrotic kinases in the receptor interacting protein (RIP) family are crucial mediators of programmed necrosis. Recent advances in necrosis research have been greatly aided by the identification of chemical inhibitors that block programmed necrosis. Necrostatin-1 (Nec-1) and its derivatives were previously shown to target the pro-necrotic kinase RIP1/RIPK1. The protective effect conferred by Nec-1 and its derivatives in many experimental model systems was often attributed to the inhibition of RIP1 function. METHODOLOGY/PRINCIPAL FINDINGS: We compared the effect of Nec-1 and siRNA-mediated silencing of RIP1 in the murine fibrosarcoma cell line L929. Treatment of L929 cells with the pan-caspase inhibitor zVAD-fmk or exogenous TNF induces necrosis. Strikingly, we found that siRNA-mediated silencing of RIP1 inhibited zVAD-fmk induced necrosis, but not TNF-induced necrosis. TNF-induced cell death in RIP1 knocked down L929 cells was inhibited by Nec-1, but not the caspase inhibitor zVAD-fmk. We found that PKA-C§ expression, but not Jnk or Erk activation, was moderately inhibited by Nec-1. Moreover, we found that Nec-1 inhibits proximal T cell receptor signaling independent of RIP1, leading to inhibition of T cell proliferation. CONCLUSIONS/SIGNIFICANCE: Our results reveal that besides RIP1, Nec-1 also targets other factors crucial for necrosis induction in L929 cells. In addition, high doses of Nec-1 inhibit other signal transduction pathways such as that for T cell receptor activation. These results highlight the importance to independently validate results obtained using Nec-1 with other approaches such as siRNA-mediated gene silencing. We propose that some of the previous published results obtained using Nec-1 should be re-evaluated in light of our findings.


Subject(s)
Imidazoles/pharmacology , Indoles/pharmacology , Lymphocyte Activation/drug effects , Necrosis/pathology , Receptor-Interacting Protein Serine-Threonine Kinases/metabolism , T-Lymphocytes/drug effects , T-Lymphocytes/immunology , Animals , Apoptosis/drug effects , Caspases/metabolism , Cell Proliferation/drug effects , Cyclic AMP-Dependent Protein Kinases/metabolism , Extracellular Signal-Regulated MAP Kinases/metabolism , Gene Knockdown Techniques , Humans , JNK Mitogen-Activated Protein Kinases/metabolism , Jurkat Cells , Lymphocyte Activation/immunology , Mice , NIH 3T3 Cells , Phosphorylation/drug effects , Tumor Necrosis Factor-alpha/pharmacology
14.
Nature ; 471(7338): 373-6, 2011 Mar 17.
Article in English | MEDLINE | ID: mdl-21368761

ABSTRACT

FADD is a common adaptor shared by several death receptors for signalling apoptosis through recruitment and activation of caspase 8 (refs 1-3). Death receptors are essential for immune homeostasis, but dispensable during embryogenesis. Surprisingly, Fadd(-/-) mice die in utero and conditional deletion of FADD leads to impaired lymphocyte proliferation. How FADD regulates embryogenesis and lymphocyte responses has been a long-standing enigma. FADD could directly bind to RIP1 (also known as RIPK1), a serine/threonine kinase that mediates both necrosis and NF-κB activation. Here we show that Fadd(-/-) embryos contain raised levels of RIP1 and exhibit massive necrosis. To investigate a potential in vivo functional interaction between RIP1 and FADD, null alleles of RIP1 were crossed into Fadd(-/-) mice. Notably, RIP1 deficiency allowed normal embryogenesis of Fadd(-/-) mice. Conversely, the developmental defect of Rip1(-/-) lymphocytes was partially corrected by FADD deletion. Furthermore, RIP1 deficiency fully restored normal proliferation in Fadd(-/-) T cells but not in Fadd(-/-) B cells. Fadd(-/-)Rip1(-/-) double-knockout T cells are resistant to death induced by Fas or TNF-α and show reduced NF-κB activity. Therefore, our data demonstrate an unexpected cell-type-specific interplay between FADD and RIP1, which is critical for the regulation of apoptosis and necrosis during embryogenesis and lymphocyte function.


Subject(s)
Embryo, Mammalian/metabolism , Fas-Associated Death Domain Protein/metabolism , GTPase-Activating Proteins/metabolism , Genetic Complementation Test , Lymphocytes/cytology , Animals , Apoptosis , CASP8 and FADD-Like Apoptosis Regulating Protein/metabolism , Cell Proliferation , Embryo, Mammalian/enzymology , Embryo, Mammalian/pathology , Embryonic Development/genetics , Fas-Associated Death Domain Protein/deficiency , Fas-Associated Death Domain Protein/genetics , Female , GTPase-Activating Proteins/deficiency , GTPase-Activating Proteins/genetics , Gene Deletion , Gene Expression Regulation, Developmental , Male , Mice , Mice, Knockout , Necrosis/genetics
15.
Chem Biol ; 18(2): 210-21, 2011 Feb 25.
Article in English | MEDLINE | ID: mdl-21338918

ABSTRACT

DnaK is a molecular chaperone responsible for multiple aspects of bacterial proteostasis. The intrinsically slow ATPase activity of DnaK is stimulated by its co-chaperone, DnaJ, and these proteins often work in concert. To identify inhibitors we screened plant-derived extracts against a reconstituted mixture of DnaK and DnaJ. This approach resulted in the identification of flavonoids, including myricetin, which inhibited activity by up to 75%. Interestingly, myricetin prevented DnaJ-mediated stimulation of ATPase activity, with minimal impact on either DnaK's intrinsic turnover rate or its stimulation by another co-chaperone, GrpE. Using NMR, we found that myricetin binds DnaK at an unanticipated site between the IB and IIB subdomains and that it allosterically blocked binding of DnaK to DnaJ. Together, these results highlight a "gray box" screening approach, which might facilitate the identification of inhibitors of other protein-protein interactions.


Subject(s)
Escherichia coli Proteins/antagonists & inhibitors , Flavonoids/pharmacology , HSP40 Heat-Shock Proteins/antagonists & inhibitors , HSP70 Heat-Shock Proteins/antagonists & inhibitors , Adenosine Triphosphate/metabolism , Allosteric Regulation/drug effects , Drug Evaluation, Preclinical , Escherichia coli Proteins/chemistry , Escherichia coli Proteins/metabolism , Flavonoids/chemistry , Flavonoids/metabolism , HSP40 Heat-Shock Proteins/chemistry , HSP40 Heat-Shock Proteins/metabolism , HSP70 Heat-Shock Proteins/chemistry , HSP70 Heat-Shock Proteins/metabolism , Models, Molecular , Plant Extracts/chemistry , Plant Extracts/metabolism , Plant Extracts/pharmacology , Protein Structure, Tertiary , Structure-Activity Relationship
16.
Anal Biochem ; 410(1): 133-40, 2011 Mar 01.
Article in English | MEDLINE | ID: mdl-21073853

ABSTRACT

Homocitrate synthase (HCS) catalyzes the first step of l-lysine biosynthesis in fungi by condensing acetyl-coenzyme A and 2-oxoglutarate to form 3R-homocitrate and coenzyme A. Due to its conservation in pathogenic fungi, HCS has been proposed as a candidate for antifungal drug design. Here we report the development and validation of a robust fluorescent assay for HCS that is amenable to high-throughput screening for inhibitors in vitro. Using this assay, Schizosaccharomyces pombe HCS was screened against a diverse library of approximately 41,000 small molecules. Following confirmation, counter screens, and dose-response analysis, we prioritized more than 100 compounds for further in vitro and in vivo analysis. This assay can be readily adapted to screen for small molecule modulators of other acyl-CoA-dependent acyltransferases or enzymes that generate a product with a free sulfhydryl group, including histone acetyltransferases, aminoglycoside N-acetyltransferases, thioesterases, and enzymes involved in lipid metabolism.


Subject(s)
Drug Evaluation, Preclinical/methods , Enzyme Assays/methods , Enzyme Inhibitors/pharmacology , High-Throughput Screening Assays/methods , Histone Acetyltransferases/metabolism , Oxo-Acid-Lyases/antagonists & inhibitors , Spectrometry, Fluorescence/methods , Acyl Coenzyme A/metabolism , Chelating Agents/chemistry , Chelating Agents/pharmacology , Enzyme Inhibitors/chemistry , Metals/chemistry , Naphthalenes/chemistry , Oxo-Acid-Lyases/chemistry , Oxo-Acid-Lyases/metabolism , Pyrroles/chemistry , Reproducibility of Results , Schizosaccharomyces/enzymology , Small Molecule Libraries/chemistry , Small Molecule Libraries/pharmacology , Sulfhydryl Compounds/chemistry
17.
Anal Biochem ; 410(2): 310-2, 2011 Mar 15.
Article in English | MEDLINE | ID: mdl-21078286

ABSTRACT

The BCA assay is a colorimetric method for estimating protein concentration. In 96-well plates, the relationship between protein content and absorbance is nearly linear over a wide range; however, performance is reduced in lower volume. To overcome this limitation, we performed the BCA assays in opaque, white 384-well plates. These plates emit fluorescence between 450-600 nm when excited at 430 nm; thus, their fluorescence is quenched by the BCA chromophore (λ(max) 562 nm). This arrangement allowed accurate determination of protein content using only 2 µL of sample. Moreover, soluble flourescein could replace the white plates, creating a homogenous format.


Subject(s)
Colorimetry/methods , Proteins/analysis , Quinolines/chemistry , Coloring Agents/chemistry , Linear Models , Sensitivity and Specificity
18.
J Biomol Screen ; 15(10): 1211-9, 2010 Dec.
Article in English | MEDLINE | ID: mdl-20926844

ABSTRACT

Members of the heat shock protein 70 (Hsp70) family of molecular chaperones are emerging as potential therapeutic targets. Their ATPase activity has classically been measured using colorimetric phosphate detection reagents, such as quinaldine red (QR). Although such assays are suitable for 96-well plate formats, they typically lose sensitivity when attempted in lower volume due to path length and meniscus effects. These limitations and Hsp70's weak enzymatic activity have combined to create significant challenges in high-throughput screening. To overcome these difficulties, the authors have adopted an energy transfer strategy that was originally reported by Zuck et al. (Anal Biochem 2005;342:254-259). Briefly, white 384-well plates emit fluorescence when irradiated at 430 nm. In turn, this intrinsic fluorescence can be quenched by energy transfer with the QR-based chromophore. Using this more sensitive approach, the authors tested 55,400 compounds against DnaK, a prokaryotic member of the Hsp70 family. The assay performance was good (Z' ~0.6, coefficient of variation ~8%), and at least one promising new inhibitor was identified. In secondary assays, this compound specifically blocked stimulation of DnaK by its co-chaperone, DnaJ. Thus, this simple and inexpensive adaptation of a colorimetric method might be suitable for screening against Hsp70 family members.


Subject(s)
Escherichia coli Proteins/antagonists & inhibitors , Escherichia coli Proteins/metabolism , HSP70 Heat-Shock Proteins/antagonists & inhibitors , HSP70 Heat-Shock Proteins/metabolism , High-Throughput Screening Assays/methods , Adenosine Triphosphatases/metabolism , Drug Discovery , Fluorescence Resonance Energy Transfer , HSP40 Heat-Shock Proteins/antagonists & inhibitors , HSP40 Heat-Shock Proteins/metabolism , Molecular Chaperones/antagonists & inhibitors , Molecular Chaperones/metabolism , Small Molecule Libraries
19.
J Biomol Screen ; 15(4): 379-87, 2010 Apr.
Article in English | MEDLINE | ID: mdl-20237205

ABSTRACT

Shigella flexneri is a human enteropathogen that infects about 165 million people and claims more than 1 million lives per year worldwide. Although shigellosis has been considered a disease of the "Third World," like many other contagious diseases, it does occur in developed countries. The emergence of drug and multidrug-resistant strains of Shigella emphasizes the need for novel antibiotic development. VirF, an AraC-type transcriptional regulator, is responsible for the expression of all downstream virulence factors that control intracellular invasion and cell-to-cell spread of Shigella. Gene knockout studies have validated that inhibition of VirF expression is sufficient to block the normal life cycle of Shigella in the host and thereby increase susceptibility to the host immune system. The authors have developed a high-throughput, cell-based assay to monitor inhibition of VirF using beta-galactosidase as a reporter protein. Using an avirulent strain of Shigella, they have screened libraries containing approximately 42,000 small molecules. Following confirmation and dose-response analysis, they have identified 7 compounds that demonstrate VirF inhibition in vivo >or=55% in comparison with the controls and little general antibacterial activity (measured by cell growth, OD(600)). The authors are in the process of confirming these "hits" in several secondary assays to assess the mechanism of action.


Subject(s)
Anti-Bacterial Agents/therapeutic use , Dysentery, Bacillary/drug therapy , High-Throughput Screening Assays/methods , Interferon Regulatory Factors/antagonists & inhibitors , Shigella flexneri/pathogenicity , Viral Proteins/antagonists & inhibitors , Enzyme Inhibitors/pharmacology , Genes, Reporter , Humans , Plasmids/genetics , Reproducibility of Results , Shigella flexneri/drug effects , Small Molecule Libraries/analysis , Small Molecule Libraries/pharmacology , Virulence/drug effects , beta-Galactosidase/antagonists & inhibitors
20.
Anal Biochem ; 386(2): 244-50, 2009 Mar 15.
Article in English | MEDLINE | ID: mdl-19135023

ABSTRACT

Adenylation domains are critical enzymes that dictate the identity of the amino acid building blocks to be incorporated during nonribosomal peptide (NRP) biosynthesis. NRPs display a wide range of biological activities and are some of the most important drugs currently used in clinics. Traditionally, activity of adenylation domains has been measured by radioactive ATP-[32P]pyrophosphate (PP(i)) exchange assays. To identify adenylation domains for future combinatorial production of novel NRPs as potential drugs, we report a convenient high-throughput nonradioactive method to measure activity of these enzymes. In our assay, malachite green is used to measure orthophosphate (P(i)) concentrations after degradation by inorganic pyrophosphatase of the PP(i) released during aminoacyl-AMP formation by action of the adenylation domains. The assay is quantitative, accurate, and robust, and it can be performed in 96- and 384-well plate formats. The performance of our assay was tested by using NcpB-A(4), one of the seven adenylation domains involved in nostocyclopeptide biosynthesis. The kinetics of pyrophosphate release monitored by this method are much slower than those measured by a traditional ATP-[32P]PP(i) exchange assay. This observation indicates that the formation of the adenylated amino acid and its release are the rate-limiting steps during the catalytic turnover.


Subject(s)
Peptide Biosynthesis, Nucleic Acid-Independent , Adenosine Triphosphate/chemistry , Adenosine Triphosphate/metabolism , Biological Assay , Combinatorial Chemistry Techniques/methods , Diphosphates/chemistry , Diphosphates/metabolism , Kinetics , Protein Structure, Tertiary , Substrate Specificity
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