Leigh C. Carmody

The neuronal actin-binding proteins, neurabin I and neurabin II, recruit specific isoforms of protein phosphatase-1 catalytic subunits

Neurabins are protein phosphatase-1 (PP1) targeting subunits that are highly concentrated in dendritic spines and post-synaptic densities. Immunoprecipitation of neurabin I and neurabin II/spinophilin from rat brain extracts sedimented PP1γ1 and PP1α but not PP1β. In vitro studies showed that recombinant peptides representing central regions of neurabins also preferentially bound PP1γ1 and PP1α from brain extracts and associated poorly with PP1β. Analysis of PP1 binding to chimeric neurabins suggested that sequences flanking a conserved PP1-binding motif altered their selectivity for PP1β and their activity as regulators of PP1 in vitro. Assays using recombinant PP1 catalytic subunits and a chimera of PP1 and protein phosphatase-2A indicated that the C-terminal sequences unique to the PP1 isoforms contributed to their recognition by neurabins. Collectively, the results from several different in vitro assays established the rank order of PP1 isoform selection by neurabins to be PP1γ1 > PP1α > PP1β. This PP1 isoform selectivity was confirmed by immunoprecipitation of neurabin I and II from brain extracts from wild type and mutant PP1γ null mice. In the absence of PP1γ1, both neurabins showed enhanced association with PP1α but not PP1β. These studies identified some of the structural determinants in PP1 and neurabins that together contribute to preferential targeting of PP1γ1 and PP1α to the mammalian synapse.

Identification of a Selective Small Molecule Inhibitor of Breast Cancer Stem Cells

A high-throughput screen (HTS) with the National Institute of Health-Molecular Libraries Small Molecule Repository (NIH-MLSMR) compound collection identified a class of acyl hydrazones to be selectively lethal to breast cancer stem cell (CSC) enriched populations. Medicinal chemistry efforts were undertaken to optimize potency and selectivity of this class of compounds. The optimized compound was declared as a probe (ML239) with the NIH Molecular Libraries Program and displayed greater than 20-fold selective inhibition of the breast CSC-like cell line (HMLE_sh_Ecad) over the isogenic control line (HMLE_sh_GFP).

Phenotypic High-Throughput Screening Elucidates Target Pathway in Breast Cancer Stem Cell–Like Cells

Cancer stem cells (CSCs) are resistant to standard cancer treatments and are likely responsible for cancer recurrence, but few therapies target this subpopulation. Due to the difficulty in propagating CSCs outside of the tumor environment, previous work identified CSC-like cells by inducing human breast epithelial cells into an epithelial-to-mesenchymal transdifferentiated state (HMLE_sh_ECad). A phenotypic screen was conducted against HMLE_sh_ECad with 300 718 compounds from the Molecular Libraries Small Molecule Repository to identify selective inhibitors of CSC growth. The screen yielded 2244 hits that were evaluated for toxicity and selectivity toward an isogenic control cell line. An acyl hydrazone scaffold emerged as a potent and selective scaffold targeting HMLE_sh_ECad. Fifty-three analogues were acquired and tested; compounds ranged in potency from 790 nM to inactive against HMLE_sh_ECad. Of the analogues, ML239 was best-in-class with an IC50= 1.18 µM against HMLE_sh_ECad, demonstrated a >23-fold selectivity over the control line, and was toxic to another CSC-like line, HMLE_shTwist, and a breast carcinoma cell line, MDA-MB-231. Gene expression studies conducted with ML239-treated cells showed altered gene expression in the NF-κB pathway in the HMLE_sh_ECad line but not in the isogenic control line. Future studies will be directed toward the identification of ML239 target(s).

Diversity-oriented synthesis yields a new drug lead for treatment of chagas disease.

A phenotypic high-throughput screen using ∼100,000 compounds prepared using Diversity-Oriented Synthesis yielded stereoisomeric compounds with nanomolar growth-inhibition activity against the parasite Trypanosoma cruzi, the etiological agent of Chagas disease. After evaluating stereochemical dependence on solubility, plasma protein binding and microsomal stability, the SSS analogue (5) was chosen for structure-activity relationship studies. The p-phenoxy benzyl group appended to the secondary amine could be replaced with halobenzyl groups without loss in potency. The exocyclic primary alcohol is not needed for activity but the isonicotinamide substructure is required for activity. Most importantly, these compounds are trypanocidal and hence are attractive as drug leads for both acute and chronic stages of Chagas disease. Analogue (5) was nominated as the molecular libraries probe ML341 and is available through the Molecular Libraries Probe Production Centers Network.

Analysis of specific interactions of native protein phosphatase 1 isoforms with targeting subunits.

Expression of recombinant PP1 isoforms with fully authentic properties has proven to be a challenge for several laboratories. In order to circumvent this technical limitation in the investigation of isoform-specific roles for PP1, methods have been developed to analyze specific properties of native PP1 isoforms. The well-documented method of ethanol precipitation of tissue extracts has been used to dissociate phosphatase catalytic subunits from their endogenous regulatory subunits and other cellular proteins. Although very low levels of PP1 and PP2A regulatory subunits are sometimes detected in PPC preparations, they are not associated with their respective catalytic subunits because they do not copurify with the catalytic subunits on microcystin-Sepharose (Bauman & Colbran, not shown). Thus, the PPC preparation represents a mixture of native monomeric phosphatase catalytic subunits (including PP1 isoforms, PP2AC, PP4C, and PP6C) that can be used to analyze their interactions with other proteins. The methods described in this report rely on the availability of highly specific antibodies to PP1 isoforms. The sheep antibodies have previously proven effective for immunoblotting and immunoprecipitation, whereas rabbit antibodies have also been used for immunocytochemistry. This paper documents the use of these antibodies in Far-Western overlay and glutathione-agarose cosedimentation assays to investigate interactions of specific PP1 isoforms with recombinant fragments of PP1-targeting subunits (spinophilin, neurabin and GM). Moreover, covalent coupling of affinity-purified sheep antibodies to agarose provided a means for the immuno-isolation of PP1 beta and PP1 gamma 1 from the PPC preparation. Active catalytic subunits are recovered from the affinity resin using chaotropic agents, permitting for the first time the assessment of the effects of specific targeting subunits on activities of individual native PP1 isoforms. These methods have been used successfully to demonstrate that some PP1-interacting proteins discriminate among the isoforms. The isoform inhibition assays provide a measure of the binding equilibrium in the milieu of the phosphatase assay. For example, while some PP1-binding proteins inhibit native PP1 beta and native PP1 gamma 1 with equivalent potency (e.g., PKA-phosphorylated inhibitor-1), spinophilin, neurabin and GM differentiate between these two isoforms; spinophilin and neurabin fragments inhibit native PP1 gamma 1 approximately 20-fold more potently than they inhibit native PP1 beta (Fig. 4), whereas GM inhibits native PP1 beta more potently than native PP1 gamma 1 (not shown). Moreover, the activity of native PP1 gamma 1 is approximately 100-fold more sensitive to neurabin and spinophilin than is the activity of bacterially-expressed recombinant PP1 gamma 1 (Fig. 4). The interpretation of these inhibition assays is consistent with data obtained in Far-Western overlay (Fig. 2) and glutathione-agarose cosedimentation assays (Fig. 3), which assess more stable interactions of PP1 isoforms. Thus, spinophilin and neurabin selectively bind PP1 gamma 1 over PP1 beta, whereas GM is highly selective for PP1 beta. These data are consistent with previous experiments that showed spinophilin and neurabin are present in PP1 gamma 1 complexes in brain extracts, but not in PP1 beta complexes. Moreover, only PP1 beta has been identified in complexes with GM in muscle extracts, although these data did not exclude the possibility that other isoforms were also present. Presumably, these isoform-selective interactions confer different functions on PP1. In summary, we have developed methods that should prove useful in defining the isoform-selectivity of other PP1-targeting subunits. Moreover, these methods may be employed to identify domains in PP1-interacting proteins that confer isoform specificity. Similar strategies may also be used to explore interactions of protein phosphatase catalytic subunits with other proteins.

Selective targeting of the γ1 isoform of protein phosphatase 1 to F-actin in intact cells requires multiple domains in spinophilin and neurabin

Protein phosphatase 1 (PP1) catalytic subunits dephosphorylate specific substrates in discrete subcellular compartments to modulate many cellular processes. Canonical PPl‐binding motifs (R/K‐V/ I‐X‐F) in a family of proteins mediate subcellular targeting, and the amino acids that form the binding pocket for the canonical motif are identical in all PP1 isoforms. However, PPlγ1 but not PP1β is selectively localized to F‐actin‐rich dendritic spines in neurons. Although the F‐actin‐binding proteins neurabin I and spinophilin (neurabin II) also bind PP1, their role in PP1 isoform selective targeting in intact cells is poorly understood. We show here that spinophilin selectively targets PP1γ1, but not PP1β, to F‐actin‐rich cortical regions of intact cells. Mutation of a PP1γ1 selectivity determinant (N464EDYDRR 470 in spinophilin: conserved as residues 473–479 in neurabin) to VKDYDTW severely attenuated PP1γ1 interactions with neurabins in vitro and in cells and disrupted PP1γ1 targeting to F‐actin. This domain is not involved in the weaker interactions of neurabins with PP1γ. In contrast, mutation of the canonical PP1‐binding motif attenuated interactions of neurabins with both isoforms. Thus, selective targeting of PP1γ1 to F‐actin by neurabins in intact cells requires both the canonical PP1‐binding motif and an auxiliary PP1γ1‐selectivity determinant.— Carmody L. C., IIBaucum A. J., Bass, M. A., Colbran R.J. Selective targeting of the γ1 isoform of protein phosphatase 1 to F‐actin in intact cells requires multiple domains in spinophilin and neurabin. FASEB J. 22, 1660–1671 (2008)

Identification and Validation of Novel Spinophilin-associated Proteins in Rodent Striatum Using an Enhanced ex Vivo Shotgun Proteomics Approach

Spinophilin regulates excitatory postsynaptic function and morphology during development by virtue of its interactions with filamentous actin, protein phosphatase 1, and a plethora of additional signaling proteins. To provide insight into the roles of spinophilin in mature brain, we characterized the spinophilin interactome in subcellular fractions solubilized from adult rodent striatum by using a shotgun proteomics approach to identify proteins in spinophilin immune complexes. Initial analyses of samples generated using a mouse spinophilin antibody detected 23 proteins that were not present in an IgG control sample; however, 12 of these proteins were detected in complexes isolated from spinophilin knock-out tissue. A second screen using two different spinophilin antibodies and either knock-out or IgG controls identified a total of 125 proteins. The probability of each protein being specifically associated with spinophilin in each sample was calculated, and proteins were ranked according to a χ2 analysis of the probabilities from analyses of multiple samples. Spinophilin and the known associated proteins neurabin and multiple isoforms of protein phosphatase 1 were specifically detected. Multiple, novel, spinophilin-associated proteins (myosin Va, calcium/calmodulin-dependent protein kinase II, neurofilament light polypeptide, postsynaptic density 95, α-actinin, and densin) were then shown to interact with GST fusion proteins containing fragments of spinophilin. Additional biochemical and transfected cell imaging studies showed that α-actinin and densin directly interact with residues 151–300 and 446–817, respectively, of spinophilin. Taken together, we have developed a multi-antibody, shotgun proteomics approach to characterize protein interactomes in native tissues, delineating the importance of knock-out tissue controls and providing novel insights into the nature and function of the spinophilin interactome in mature striatum.

Screening for Inhibitors of an Essential Chromatin Remodeler in Mouse Embryonic Stem Cells by Monitoring Transcriptional Regulation

The SWI/SNF-like adenosine triphosphate (ATP)–dependent chromatin remodeling complex, esBAF, is both necessary and, in some contexts, sufficient to induce the pluripotent state. Furthermore, mutations in various BAF subunits are associated with cancer. Little is known regarding the precise mechanism(s) by which this complex exerts its activities. Thus, it is unclear which protein interactions would be important to disrupt to isolate a relevant readout of mechanism. To address this, we developed a gene expression–based assay to identify inhibitors of the native esBAF complex. Specifically, a quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) assay was developed in mouse embryonic stem (ES) cells to monitor expression of Bmi1, a developmentally important gene repressed by the esBAF complex. The assay was miniaturized to a 384-well format and used to screen a diverse collection of compounds, including novel products of diversity-oriented synthesis (DOS). Confirmed hits were validated using a knock-in ES cell reporter line in which luciferase is inserted into the Bmi1 locus. Several of the validated hits regulate a panel of target genes in a manner similar to the BAF chromatin-remodeling complex. Together these data indicate that expression-based screening using qRT-PCR is a successful approach to identify compounds targeting the regulation of key developmental genes in ES cells.

Cinnamides as selective small-molecule inhibitors of a cellular model of breast cancer stem cells.

A high-throughput screen (HTS) was conducted against stably propagated cancer stem cell (CSC)-enriched populations using a library of 300,718 compounds from the National Institutes of Health (NIH) Molecular Libraries Small Molecule Repository (MLSMR). A cinnamide analog displayed greater than 20-fold selective inhibition of the breast CSC-like cell line (HMLE_sh_Ecad) over the isogenic control cell line (HMLE_sh_eGFP). Herein, we report structure-activity relationships of this class of cinnamides for selective lethality towards CSC-enriched populations.

Identification of small-molecule inhibitors of Trypansoma cruzi replication

We report the outcome of a high-throughput small-molecule screen to identify novel, nontoxic, inhibitors of Trypansoma cruzi, as potential starting points for therapeutics to treat for both the acute and chronic stages of Chagas disease. Two compounds were identified that displayed nanomolar inhibition of T. cruzi and an absence of activity against host cells at the highest tested dose. These compounds have been registered with NIH Molecular Libraries Program (probes ML157 and ML158).