Sulfopin is a covalent inhibitor of Pin1 that blocks Myc-driven tumors in vivo

The peptidyl-prolyl isomerase, Pin1, is exploited in cancer to activate oncogenes and inactivate tumor suppressors. However, despite considerable efforts, Pin1 has remained an elusive drug target. Here, we screened an electrophilic fragment library to identify covalent inhibitors targeting Pin1's active site Cys113, leading to the development of Sulfopin, a nanomolar Pin1 inhibitor. Sulfopin is highly selective, as validated by two independent chemoproteomics methods, achieves potent cellular and in vivo target engagement and phenocopies Pin1 genetic knockout. Pin1 inhibition had only a modest effect on cancer cell line viability. Nevertheless, Sulfopin induced downregulation of c-Myc target genes, reduced tumor progression and conferred survival benefit in murine and zebrafish models of MYCN-driven neuroblastoma, and in a murine model of pancreatic cancer. Our results demonstrate that Sulfopin is a chemical probe suitable for assessment of Pin1-dependent pharmacology in cells and in vivo, and that Pin1 warrants further investigation as a potential cancer drug target.

A Time-Resolved Cryo-EM Study of Saccharomyces cerevisiae 80S Ribosome Protein Composition in Response to a Change in Carbon Source

The role of the ribosome in the regulation of gene expression has come into increased focus. It is proposed that ribosomes are catalytic engines capable of changing their protein composition in response to environmental stimuli. Time-resolved cryo-electron microscopy (cryo-EM) techniques are employed to identify quantitative changes in the protein composition and structure of the Saccharomyces cerevisiae 80S ribosomes after shifting the carbon source from glucose to glycerol. Using cryo-EM combined with the computational classification approach, it is found that a fraction of the yeast cells' 80S ribosomes lack ribosomal proteins at the entrance and exit sites for tRNAs, including uL16(RPL10), eS1(RPS1), uS11(RPS14A/B), and eS26(RPS26A/B). This fraction increased after a change from glucose to glycerol medium. The quantitative structural analysis supports the hypothesis that ribosomes are dynamic complexes that alter their composition in response to changes in growth or environmental conditions.

Targeting the PI5P4K Lipid Kinase Family in Cancer Using Covalent Inhibitors

The PI5P4Ks have been demonstrated to be important for cancer cell proliferation and other diseases. However, the therapeutic potential of targeting these kinases is understudied due to a lack of potent, specific small molecules available. Here, we present the discovery and characterization of a pan-PI5P4K inhibitor, THZ-P1-2, that covalently targets cysteines on a disordered loop in PI5P4Kα/β/γ. THZ-P1-2 demonstrates cellular on-target engagement with limited off-targets across the kinome. AML/ALL cell lines were sensitive to THZ-P1-2, consistent with PI5P4K's reported role in leukemogenesis. THZ-P1-2 causes autophagosome clearance defects and upregulation in TFEB nuclear localization and target genes, disrupting autophagy in a covalent-dependent manner and phenocopying the effects of PI5P4K genetic deletion. Our studies demonstrate that PI5P4Ks are tractable targets, with THZ-P1-2 as a useful tool to further interrogate the therapeutic potential of PI5P4K inhibition and inform drug discovery campaigns for these lipid kinases in cancer metabolism and other autophagy-dependent disorders.

Targeted Identification of Protein Interactions in Eukaryotic mRNA Translation

To identify protein-protein interactions and phosphorylated amino acid sites in eukaryotic mRNA translation, replicate TAP-MudPIT and control experiments are performed targeting Saccharomyces cerevisiae genes previously implicated in eukaryotic mRNA translation by their genetic and/or functional roles in translation initiation, elongation, termination, or interactions with ribosomal complexes. Replicate tandem affinity purifications of each targeted yeast TAP-tagged mRNA translation protein coupled with multidimensional liquid chromatography and tandem mass spectrometry analysis are used to identify and quantify copurifying proteins. To improve sensitivity and minimize spurious, nonspecific interactions, a novel cross-validation approach is employed to identify the most statistically significant protein-protein interactions. Using experimental and computational strategies discussed herein, the previously described protein composition of the canonical eukaryotic mRNA translation initiation, elongation, and termination complexes is calculated. In addition, statistically significant unpublished protein interactions and phosphorylation sites for S. cerevisiae's mRNA translation proteins and complexes are identified.

Identification of Changing Ribosome Protein Compositions using Mass Spectrometry

The regulatory role of the ribosome in gene expression has come into sharper focus. It has been proposed that ribosomes are dynamic complexes capable of changing their protein composition in response to environmental stimuli. MS is applied to identify quantitative changes in the protein composition of S. cerevisiae 80S ribosomes in response to different environmental stimuli. Using quantitative MS, it is found that the paralog yeast ribosomal proteins RPL8A (eL8A) and RPL8B (eL8B) change their relative proportions in the 80S ribosome when yeast is switched from growth in glucose to glycerol. By using yeast genetics and polysome profiling, it is shown that yeast ribosomes containing either RPL8A or RPL8B are not functionally interchangeable. The quantitative proteomic data support the hypothesis that ribosomes are dynamic complexes that alter their composition and functional activity in response to changes in growth or environmental conditions.

Abstract 2757: Discovery and characterization of covalent Pin1 inhibitors targeted to an active site cysteine

Proline-directed phosphorylation at serine or threonine residues (pSer/Thr-Pro) regulates numerous cellular processes, including the cell cycle, transcription, and differentiation. Deregulation of such signaling networks is a hallmark of transformation and oncogenesis. Pin1, a peptidyl-prolyl isomerase, regulates the function and stability of phosphoproteins by catalyzing the cis/trans isomerization of pSer/Thr-Pro motifs. Pin1 is frequently overexpressed in human cancers, including pancreatic ductal adenocarcinoma (PDAC), and Pin1 is required for activated Ras to induce tumorigenesis. While mutations in KRAS are observed in 90-95% of human PDAC cases, it has historically proven very challenging to develop small molecules that inhibit mutant Ras function. Consequently, drug discovery efforts have turned to targets required for Ras-mediated transformation, such as Pin1. However, existing Pin1 inhibitors lack the potency, selectivity, and/or cell permeability to serve as informative cellular probes. We report a highly potent, cell-permeable Pin1 inhibitor that covalently targets Cys113, a conserved cysteine residue in the Pin1 active site. Through iterative rounds of synthesis and characterization, we developed inhibitor 1b. With a Ki of 15 nM as measured in biochemical binding and isomerase inhibition assays, 1bis currently the most potent Pin1 inhibitor available. Furthermore, in a chemoproteomic study using Covalent Inhibitor Target Site Identification (CITe-Id) to quantify the dose-dependent covalent labeling of 1b to individual cysteines across the proteome, Pin1 Cys113 was the only identified target, highlighting the pronounced selectivity of 1b for Pin1. We show that treatment with 1b diminishes viability of human PDAC cell lines, which can be fully rescued in corresponding Pin1 knockout cells generated using CRISPR/Cas9, showing that this phenotype is on-target. In parallel to inhibitor development, we used CRISPR/Cas9 GFP-dropout screens to further validate the dependence of these cell lines on Pin1. Genetic disruption of Pin1 led to antiproliferative effects, confirming the results of 1b treatment. We also employed the degradation tag (dTAG) approach to assess the effects of rapid and selective targeted Pin1 degradation through generation of FKBP12F36V-Pin1, Pin1-/-human PDAC cell lines. Treatment with a small molecule FKBP12F36V-degrader led to rapid ubiquitination and degradation of FKBP12F36V-Pin1, enabling comparisons of targeted inhibition and Pin1 degradation. Through the development of a selective Pin1 inhibitor coupled with genetic approaches and the chemical-genetic dTAG strategy, we demonstrate that Pin1 inhibition represents a tractable strategy in PDAC.

Citation Format: Benika Pinch, Zainab Doctor, Christopher M. Browne, Hyuk-Soo Seo, Behnam Nabet, Shingo Kozono, Xiaolan Lian, Daniel Zaidman, Dina Daitchman, Nir London, Lu Gong, Theresa Manz, Yujin Chun, Li Tan, Jarrod Marto, Stephen Buratowski, Sirano Dhe-Paganon, Xiao Zhou, Kun Ping Lu, Nathanael S. Gray. Discovery and characterization of covalent Pin1 inhibitors targeted to an active site cysteine [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2757.

Leveraging Compound Promiscuity to Identify Targetable Cysteines within the Kinome

Covalent kinase inhibitors, which typically target cysteine residues, represent an important class of clinically relevant compounds. Approximately 215 kinases are known to have potentially targetable cysteines distributed across 18 spatially distinct locations proximal to the ATP-binding pocket. However, only 40 kinases have been covalently targeted, with certain cysteine sites being the primary focus. To address this disparity, we have developed a strategy that combines the use of a multi-targeted acrylamide-modified inhibitor, SM1-71, with a suite of complementary chemoproteomic and cellular approaches to identify additional targetable cysteines. Using this single multi-targeted compound, we successfully identified 23 kinases that are amenable to covalent inhibition including MKNK2, MAP2K1/2/3/4/6/7, GAK, AAK1, BMP2K, MAP3K7, MAPKAPK5, GSK3A/B, MAPK1/3, SRC, YES1, FGFR1, ZAK (MLTK), MAP3K1, LIMK1, and RSK2. The identification of nine of these kinases previously not targeted by a covalent inhibitor increases the number of targetable kinases and highlights opportunities for covalent kinase inhibitor development.

Discovery of Covalent CDK14 Inhibitors with Pan-TAIRE Family Specificity

Cyclin-dependent kinase 14 (CDK14) and other TAIRE family kinases (CDKs 15-18) are proteins that lack functional annotation but are frequent off-targets of clinical kinase inhibitors. In this study we develop and characterize FMF-04-159-2, a tool compound that specifically targets CDK14 covalently and possesses a TAIRE kinase-biased selectivity profile. This tool compound and its reversible analog were used to characterize the cellular consequences of covalent CDK14 inhibition, including an unbiased investigation using phospho-proteomics. To reduce confounding off-target activity, washout conditions were used to deconvolute CDK14-specific effects. This investigation suggested that CDK14 plays a supporting role in cell-cycle regulation, particularly mitotic progression, and identified putative CDK14 substrates. Together, these results represent an important step forward in understanding the cellular consequences of inhibiting CDK14 kinase activity.

A Chemoproteomic Strategy for Direct and Proteome-Wide Covalent Inhibitor Target-Site Identification

Despite recent clinical successes for irreversible drugs, potential toxicities mediated by unpredictable modification of off-target cysteines represents a major hurdle for expansion of covalent drug programs. Understanding the proteome-wide binding profile of covalent inhibitors can significantly accelerate their development; however, current mass spectrometry strategies typically do not provide a direct, amino acid level readout of covalent activity for complex, selective inhibitors. Here we report the development of CITe-Id, a novel chemoproteomic approach that employs covalent pharmacologic inhibitors as enrichment reagents in combination with an optimized proteomic platform to directly quantify dose-dependent binding at cysteine-thiols across the proteome. CITe-Id analysis of our irreversible CDK inhibitor THZ1 identified dose-dependent covalent modification of several unexpected kinases, including a previously unannotated cysteine (C840) on the understudied kinase PKN3. These data streamlined our development of JZ128 as a new selective covalent inhibitor of PKN3. Using JZ128 as a probe compound, we identified novel potential PKN3 substrates, thus offering an initial molecular view of PKN3 cellular activity. CITe-Id provides a powerful complement to current chemoproteomic platforms to characterize the selectivity of covalent inhibitors, identify new, pharmacologically addressable cysteine-thiols, and inform structure-based drug design programs.

Critical Role for Saccharomyces cerevisiae Asc1p in Translational Initiation at Elevated Temperatures

The eukaryotic ribosomal protein RACK1/Asc1p is localized to the mRNA exit channel of the 40S subunit but lacks a defined role in mRNA translation. Saccharomyces cerevisiae deficient in ASC1 exhibit temperature-sensitive growth. Using this null mutant, potential roles for Asc1p in translation and ribosome biogenesis are evaluated. At the restrictive temperature the asc1Δ null mutant has reduced polyribosomes. To test the role of Asc1p in ribosome stability, cryo-EM is used to examine the structure of 80S ribosomes in an asc1Δ yeast deletion mutant at both the permissive and nonpermissive temperatures. CryoEM indicates that loss of Asc1p does not severely disrupt formation of this complex structure. No defect is found in rRNA processing in the asc1Δ null mutant. A proteomic approach is applied to survey the effect of Asc1p loss on the global translation of yeast proteins. At the nonpermissive temperature, the asc1Δ mutant has reduced levels of ribosomal proteins and other factors critical for translation. Collectively, these results are consistent with recent observations suggesting that Asc1p is important for ribosome occupancy of short mRNAs. The results show the Asc1 ribosomal protein is critical in translation during heat stress.

Leveraging Gas-Phase Fragmentation Pathways for Improved Identification and Selective Detection of Targets Modified by Covalent Probes

The recent approval of covalent inhibitors for multiple clinical indications has reignited enthusiasm for this class of drugs. As interest in covalent drugs has increased, so too has the need for analytical platforms that can leverage their mechanism-of-action to characterize modified protein targets. Here we describe novel gas phase dissociation pathways which yield predictable fragment ions during MS/MS of inhibitor-modified peptides. We find that these dissociation pathways are common to numerous cysteine-directed probes as well as the covalent drugs, Ibrutinib and Neratinib. We leverage the predictable nature of these fragment ions to improve the confidence of peptide sequence assignment in proteomic analyses and explore their potential use in selective mass spectrometry-based assays.

Differentiation of the mononuclear phagocyte system during mouse embryogenesis: the role of transcription factor PU.1

During mouse embryogenesis, macrophage-like cells arise first in the yolk sac and are produced subsequently in the liver. The onset of liver hematopoiesis is associated with the transition from primitive to definitive erythrocyte production. This report addresses the hypothesis that a similar transition in phenotype occurs in myelopoiesis. We have used whole mount in situ hybridization to detect macrophage-specific genes expressed during mouse development. The mouse c-fms mRNA, encoding the receptor for macrophage colony-stimulating factor (CSF-1), was expressed on phagocytic cells in the yolk sac and throughout the embryo before the onset of liver hematopoiesis. Similar cells were detected using the mannose receptor, the complement receptor (CR3), or the Microphthalmia transcription factor (MITF) as mRNA markers. By contrast, other markers including the F4/80 antigen, the macrophage scavenger receptor, the S-100 proteins, S100A8 and S100A9, and the secretory product lysozyme appeared later in development and appeared restricted to only a subset of c-fms-positive cells. Two-color immunolabeling on disaggregated cells confirmed that CR3 and c-fms proteins are expressed on the same cells. Among the genes appearing later in development was the macrophage-restricted transcription factor, PU.1, which has been shown to be required for normal adult myelopoiesis. Mice with null mutations in PU.1 had normal numbers of c-fms-positive phagocytes at 11.5dpc. PU.1(-/-) embryonic stem cells were able to give rise to macrophage-like cells after cultivation in vitro. The results support previous evidence that yolk sac-derived fetal phagocytes are functionally distinct from those arising in the liver and develop via a different pathway.

Transcription of individual genes in eukaryotic cells occurs randomly and infrequently

Experimental evidence is presented indicating that the expression of a lacZ reporter gene driven by the HIV-1 long terminal repeat in a series of stably transfected, cloned macrophage cell lines occurs in a very small proportion of cells. The proportion of cells expressing lacZ, rather than the level of expression in each cell, is regulated by external stimuli such as LPS and phorbol ester. Based upon these and published data we propose that transcription in eukaryotic cells occurs in short pulses interspersed by long periods of inactivity of indeterminate duration. Transcriptional regulation is envisaged as involving changes in the probability rather than the rate of transcription. A probabilistic model of transcription may explain many biological phenomena, such as stem cell division and clonogenic activity, heterogeneous gene expression among clonal cell populations, retroviral latency and cell cycle progression, which appear to involve stochastic decisions.

Localization of immunoglobulin-containing cells in human endometrium in the first trimester of pregnancy and throughout the menstrual cycle

The distribution of immunoglobulins in normal human endometrium throughout the menstrual cycle and in early pregnancy has been studied with an immunoperoxidase technique. In first-trimester decidua, IgG was detected within many cells of differing morphology and size. Large IgG-containing cells were often binucleate and were believed to be decidual cells. Examination of serial sections showed no kappa or lambda light-chain restriction, suggesting absorption of the immunoglobulin content. Medium-sized, irregular, IgG-containing cells were macrophages. An additional substantial population of small hyperchromatic IgG-containing cells were prominent around arterioles and adjacent to endometrial glands. From examination of adjacent sections stained with phloxine tartrazine, it was concluded that these represented endometrial granulocytes. Labelling for light chains again suggested absorption of the immunoglobulin content. In contrast, in non-pregnant endometrium immunoglobulin-containing stromal cells were uncommon, although IgG and IgA were detected in gland epithelium and secretions and in the stromal interstitium particularly in the secretory phase. These results support the notion that human endometrium lacks a classical secretory immune system and highlight the requirement for correlation between studies of cell surface markers, morphology and cell surface receptors.

Pregnancy-associated nonspecific immunosuppression: mechanism for the activation of the immunosuppressive factors

The nonspecific immunosuppressive effect observed in pregnancy sera and mediated by two factors, immunosuppressive factors (ISF) I and II, was regulated by a third molecule termed the pregnancy-depleted immunoregulatory factor (pdIRF). Natural depletion of serum pdIRF levels during pregnancy resulted in the activation of the ISF-I and ISF-II molecules, which prior to conception existed in the serum in inactive forms. The inactive ISF-I and ISF-II molecules in male sera and in nulliparous nonpregnant female sera can be activated following the artificial selective depletion of pdIRF by absorption onto Sephacryl S-300. It is proposed that inactive complexes consisting of the ISF-I and ISF-II molecules and pdIRF and possibly involving Ca2+ and Mg2+ ions are a feature of normal sera. The pdIRF molecule has an apparent Mr of 100,000-125,000 daltons and consists of a single major polypeptide of 63,000 daltons. Equal concentrations of pdIRF are present in male and female normal sera.

Pregnancy-associated nonspecific immunosuppression: kinetics of the generation and identification of the active factors

The effect of gestational age and maternal parity on the development of nonspecific immunosuppressive activity in the sera of pregnant women, which inhibited the in vitro transformation of unrelated lymphocytes by phytohemagglutinin, was examined. Quantitative demonstration of this activity was dependent, in part, on the source of the lymphocytes and on the serum concentration in culture. The immunosuppressive activity became evident as the pregnancy progressed, and in late-pregnancy sera it was mediated by two factors, immunosuppressive factors (ISF) I and II with apparent Mr of 2 X 10(6) and 150,000 daltons. By analysis and comparison of different types of sera fractionated by gel filtration on Sephacryl S-300, it was evident that ISF-I and ISF-II were also present in male and nulliparous nonpregnant female sera, but in inactive forms. Hence the immunosuppressive factors did not appear to be "produced" in pregnancy, but the observed activity was a reflection of the "activation" of preexisting molecules in the serum. An accompanying report (Am J Reprod Immunol Microbiol. 1985; 9:84-90) describes the regulation of the activation event.

The partial characterisation of maternal anti-trophoblast antibody responses generated during normal human pregnancy

The anti-trophoblast antibody response generated during a normal human pregnancy and detected by a recently developed enzyme-linked immunosorbent assay, was partially characterised in terms of maternal influences, nature of the antibodies and nature of the antigenic determinants present on the syncytiotrophoblast plasma membrane. The level and incidence of the response was significantly affected by maternal parity, while the maternal ABO, but not Rhesus, blood group antigens exerted a minor influence. The antibody response was predominantly mediated by IgG molecules of the IgG1,2 and 4 subclasses. The IgG molecules existed in the maternal sera either in the form of 'free' molecules or were involved in immune complexes. The antibodies interacted with determinants that were present on all the placental membranes tested and hence are possibly organ specific. The antigenic specificities were absent from erythrocytes and peripheral blood lymphocytes.

Identification of selectively solubilised syncytiotrophoblast plasma membrane proteins as potential antigenic targets during normal human pregnancy

Syncytiotrophoblast plasma membranes prepared from term placentae were selectively solubilised in non-ionic detergents. The solubilised proteins and the insoluble residue were tested in an ELISA assay for their ability to function as antigenic targets for anti-trophoblast antibodies present in normal first trimester pregnancy sera. The soluble proteins were fractionated by gel filtration and four major antigen forms were identified. The antigens were reactive with affinity purified anti-trophoblast antibody isolated from maternal sera and hence were termed maternally-recognised trophoblast antigens (MRTA); these were designated MRTA-I (Mr = 400,000 D), MRTA-II (Mr = 142,000), MRTA-III (Mr = 50,000) and MRTA-IV (Mr = 13,000). The relationship between MRTA-I, II, III and IV and antigens identified in maternal sera in the form of immune complexes is discussed.

Anti-trophoblast antibody responses during normal human pregnancy

During the course of a normal uncomplicated human pregnancy the mother generates an antibody response directed against determinants present on the plasma membrane of the outer fetal layer of the term placenta, the syncytiotrophoblast. The response, measured by an ELISA that utilises syncytiotrophoblast plasma membrane as the antigenic target, is predominantly IgG in nature, but with a minor contribution from IgM molecules. Maximum responses were observed during the first trimester and the levels gradually declined as the pregnancy progressed. On a population basis, this antibody response profile was mainly restricted to first and second pregnancies, although anti-trophoblast antibody responses could be detected in multiparous women but with a greatly reduced incidence compared with primipara. Mechanisms to account for these observations are discussed. Throughout, the anti-trophoblast antibody levels detected in pregnancy sera were compared with the background levels which were observed in sera obtained from males and nulliparous non-pregnant females.