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SummaryMost human proteins lack chemical probes, and several large-scale and generalizable small-molecule binding assays have been introduced to address this problem. How compounds discovered in such “binding-first” assays affect protein function, nonetheless, often remains unclear. Here, we describe a “function-first” proteomic strategy that uses size exclusion chromatography (SEC) to assess the global impact of electrophilic compounds on protein complexes in human cells. Integrating the SEC data with cysteine-directed activity-based protein profiling identifies changes in protein-protein interactions that are caused by site-specific liganding events, including the stereoselective engagement of cysteines in PSME1 and SF3B1 that disrupt the PA28 proteasome regulatory complex and stabilize a dynamic state of the spliceosome, respectively. Our findings thus show how multidimensional proteomic analysis of focused libraries of electrophilic compounds can expedite the discovery of chemical probes with site-specific functional effects on protein complexes in human cells.

Chemical probes are lacking for most human proteins. Covalent chemistry represents an attractive strategy for expanding the ligandability of the proteome, and chemical proteomics has revealed numerous electrophile-reactive cysteines on diverse proteins. Determining which of these covalent binding events impact protein function, however, remains challenging. Here, we describe a base-editing strategy to infer the functionality of cysteines by quantifying the impact of their missense mutation on cell proliferation. We show that the resulting atlas, which covers >13,800 cysteines on >1,750 cancer dependency proteins, correctly predicts the essentiality of cysteines targeted by cancer therapeutics and, when integrated with chemical proteomic data, identifies essential, ligandable cysteines on >110 cancer dependency proteins. We further demonstrate how measurements of reactivity in native versus denatured proteomes can discriminate essential cysteines amenable to chemical modification from those buried in protein structures, providing a valuable resource to prioritize the pursuit of small-molecule probes with high function-perturbing potential.

Multiple Ras proteins, including N-Ras, depend on a palmitoylation/depalmitoylation cycle to regulate their subcellular trafficking and oncogenicity. General lipase inhibitors such as Palmostatin M (Palm M) block N-Ras depalmitoylation, but lack specificity and target several enzymes displaying depalmitoylase activity. Here, we describe ABD957, a potent and selective covalent inhibitor of the ABHD17 family of depalmitoylases, and show that this compound impairs N-Ras depalmitoylation in human acute myeloid leukemia (AML) cells. ABD957 produced partial effects on N-Ras palmitoylation compared with Palm M, but was much more selective across the proteome, reflecting a plasma membrane-delineated action on dynamically palmitoylated proteins. Finally, ABD957 impaired N-Ras signaling and the growth of NRAS-mutant AML cells in a manner that synergizes with MAP kinase kinase (MEK) inhibition. Our findings uncover a surprisingly restricted role for ABHD17 enzymes as regulators of the N-Ras palmitoylation cycle and suggest that ABHD17 inhibitors may have value as targeted therapies for NRAS-mutant cancers.

A fundamental challenge in chemical biology and medicine is to understand and expand the fraction of the human proteome that can be targeted by small molecules. We recently described a strategy that integrates fragment-based ligand discovery with chemical proteomics to furnish global portraits of reversible small-molecule/protein interactions in human cells. Excavating clear structure-activity relationships from these 'ligandability' maps, however, was confounded by the distinct physicochemical properties and corresponding overall protein-binding potential of individual fragments. Here, we describe a compelling solution to this problem by introducing a next-generation set of fully functionalized fragments differing only in absolute stereochemistry. Using these enantiomeric probe pairs, or 'enantioprobes', we identify numerous stereoselective protein-fragment interactions in cells and show that these interactions occur at functional sites on proteins from diverse classes. Our findings thus indicate that incorporating chirality into fully functionalized fragment libraries provides a robust and streamlined method to discover ligandable proteins in cells.

Thyroid hormones (THs) are powerful regulators of metabolism with major effects on body weight, cholesterol, and liver fat that have been exploited pharmacologically for many years. Activation of gene expression by TH action is canonically ascribed to a hormone-dependent “switch” from corepressor to activator binding to thyroid hormone receptors (TRs), while the mechanism of TH-dependent repression is controversial. To address this, we generated a mouse line in which endogenous TRβ1 was epitope-tagged to allow precise chromatin immunoprecipitation at the low physiological levels of TR and defined high-confidence binding sites where TRs functioned at enhancers regulated in the same direction as the nearest gene in a TRβ-dependent manner. Remarkably, although positive and negative regulation by THs have been ascribed to different mechanisms, TR binding was highly enriched at canonical DR4 motifs irrespective of the transcriptional direction of the enhancer. The canonical NCoR1/HDAC3 corepressor complex was reduced but not completely dismissed by TH and, surprisingly, similar effects were seen at enhancers associated with negatively as well as positively regulated genes. Conversely, coactivator CBP was found at all TH-regulated enhancers, with transcriptional activity correlating with the ratio of CBP to NCoR rather than their presence or absence. These results demonstrate that, in contrast to the canonical “all or none” coregulator switch model, THs regulate gene expression by orchestrating a shift in the relative binding of corepressors and coactivators.

Multiple Ras proteins, including N-Ras, depend on a palmitoylation/depalmitoylation cycle to regulate their subcellular trafficking and oncogenicity. General lipase inhibitors such as Palmostatin M (Palm M) block N-Ras depalmitoylation, but lack specificity and target several enzymes displaying depalmitoylase activity. Here, we describe ABD957, a potent and selective covalent inhibitor of the ABHD17 family of depalmitoylases, and show that this compound impairs N-Ras depalmitoylation in human acute myeloid leukemia (AML) cells. ABD957 produced partial effects on N-Ras palmitoylation compared with Palm M, but was much more selective across the proteome, reflecting a plasma membrane-delineated action on dynamically palmitoylated proteins. Finally, ABD957 impaired N-Ras signaling and the growth of NRAS-mutant AML cells in a manner that synergizes with MAP kinase kinase (MEK) inhibition. Our findings uncover a surprisingly restricted role for ABHD17 enzymes as regulators of the N-Ras palmitoylation cycle and suggest that ABHD17 inhibitors may have value as targeted therapies for NRAS-mutant cancers.

Oncogenic RAS mutations pose substantial challenges for rational drug discovery. Sequence variations within the hypervariable region of Ras isoforms underlie differential posttranslational modification and subcellular trafficking, potentially resulting in selective vulnerabilities. Specifically, inhibiting the palmitoylation/depalmitoylation cycle is an appealing strategy for treating NRAS mutant cancers, particularly as normal tissues would retain K-Ras4b function for physiologic signaling. The role of endogenous N-RasG12D palmitoylation in signal transduction, hematopoietic differentiation, and myeloid transformation is unknown, and addressing these key questions will inform efforts to develop mechanism-based therapies. To evaluate the palmitoylation/depalmitoylation cycle as a candidate drug target in an in vivo disease-relevant model system, we introduced a C181S mutation into a conditional NrasG12D “knock-in” allele. The C181S second-site amino acid substitution abrogated myeloid transformation by NrasG12D, which was associated with mislocalization of the nonpalmitoylated N-Ras mutant protein, reduced Raf/MEK/ERK signaling, and alterations in hematopoietic stem and progenitor populations. Furthermore, hematologic malignancies arising in NrasG12D/G12D,C181S compound heterozygous mice invariably acquired revertant mutations that restored cysteine 181. Together, these studies validate the palmitoylation cycle as a promising therapeutic target in NRAS mutant cancers.

Thyroid hormone receptors (TR) are transcription factors that mediate the effects of thyroid hormones (TH) in development, physiology, and metabolism. TR canonically activates gene expression via a “switch” whereby TH converts chromatin-bound TR from a transcriptional repressor to an activator. In this model, the unliganded repressed state is mediated by binding of the nuclear receptor corepressor (NCoR), while the TH-activated state is caused by dismissal of NCoR and stabilization of binding of coactivators including CREB-binding protein (CBP). TH also negatively regulates gene expression, although the mechanism is controversial. Elucidation of the TR transcriptional mechanism in vivo has been hampered by the low concentration of endogenous TRs and the unavailability of high quality antibodies. To address this, we generated a mouse line in which endogenous TRβ1 was epitope-tagged to allow precise analysis at physiological levels, and explored TR function in liver where the actions of TR regulate body weight, cholesterol, and liver fat. ChIP-seq analysis revealed TRβ binding at genomic sites with epigenomic characteristics of enhancers, at sequences enriched for the canonical DR4 motif bound by TR with its RXR partner, at both positively- as well as negatively-regulated genes. The NCoR/HDAC3 corepressor complex was reduced but not completely dismissed by TH at positive enhancers and, surprisingly, at enhancers associated with negatively. CBP binding was also not “all or none” but, rather, shifted toward increased binding at enhancers in their active state, i.e., in the presence of TH for activated genes, but in the absence of TH for repressed genes. Thus, TH action is due to a shift, not an on/off switch, in coregulator association with TRβ-regulated enhancers determines their activity and transcriptional outcomes.

Objective Histone deacetylases are epigenetic regulators known to control gene transcription in various tissues. A member of this family, histone deacetylase 3 (HDAC3), has been shown to regulate metabolic genes. Cell culture studies with HDAC-specific inhibitors and siRNA suggest that HDAC3 plays a role in pancreatic β-cell function, but a recent genetic study in mice has been contradictory. Here we address the functional role of HDAC3 in β-cells of adult mice. Methods An HDAC3 β-cell specific knockout was generated in adult MIP-CreERT transgenic mice using the Cre-loxP system. Induction of HDAC3 deletion was initiated at 8 weeks of age with administration of tamoxifen in corn oil (2 mg/day for 5 days). Mice were assayed for glucose tolerance, glucose-stimulated insulin secretion, and islet function 2 weeks after induction of the knockout. Transcriptional functions of HDAC3 were assessed by ChIP-seq as well as RNA-seq comparing control and β-cell knockout islets. Results HDAC3 β-cell specific knockout (HDAC3βKO) did not increase total pancreatic insulin content or β-cell mass. However, HDAC3βKO mice demonstrated markedly improved glucose tolerance. This improved glucose metabolism coincided with increased basal and glucose-stimulated insulin secretion in vivo as well as in isolated islets. Cistromic and transcriptomic analyses of pancreatic islets revealed that HDAC3 regulates multiple genes that contribute to glucose-stimulated insulin secretion. Conclusions HDAC3 plays an important role in regulating insulin secretion in vivo, and therapeutic intervention may improve glucose homeostasis., Highlights • HDAC3 ablation in adult mouse β-cells improves glucose tolerance. • Improved glucose tolerance is due to increased insulin secretion. • HDAC3 targets multiple genes involved in potentiating insulin secretion.

Ambient temperature influences the molecular clock and lipid metabolism, but the impact of chronic cold exposure on circadian lipid metabolism in thermogenic brown adipose tissue (BAT) has not been studied. Here we show that during chronic cold exposure (1 wk at 4 °C), genes controlling de novo lipogenesis (DNL) including Srebp1 , the master transcriptional regulator of DNL, acquired high-amplitude circadian rhythms in thermogenic BAT. These conditions activated mechanistic target of rapamycin 1 (mTORC1), an inducer of Srebp1 expression, and engaged circadian transcriptional repressors REV-ERBα and β as rhythmic regulators of Srebp1 in BAT. SREBP was required in BAT for the thermogenic response to norepinephrine, and depletion of SREBP prevented maintenance of body temperature both during circadian cycles as well as during fasting of chronically cold mice. By contrast, deletion of REV-ERBα and β in BAT allowed mice to maintain their body temperature in chronic cold. Thus, the environmental challenge of prolonged noncircadian exposure to cold temperature induces circadian induction of SREBP1 that drives fuel synthesis in BAT and is necessary to maintain circadian body temperature during chronic cold exposure. The requirement for BAT fatty acid synthesis has broad implications for adaptation to cold.

A dynamic cycle of palmitoylation and depalmitoylation stably localizes N-Ras, but not K-Ras-4b, at the plasma membrane. This selective dependency suggests that targeting palmitoylation could inhibit the growth of NRAS-mutant cancers while leaving normal cells unaffected, due to their intact K-Ras-4b function. We sought to clarify the dependency of oncogenic N-Ras signaling on palmitoylation in a model relevant to human cancer. We used the lox-STOP-lox (LSL) knock-in system (Haigis et al., Nat Genet 2008) to express an NrasG12D oncogene at physiologic levels, and generated a second site mutation abrogating the palmitoylation site (C181S). We then compared Mx1-Cre; NrasLSL-G12D,C181S/LSL-G12D,C181S to Mx1-Cre; NrasWT/WT and Mx1-Cre; NrasLSL-G12D/LSL-G12D (hereafter G12D,C181S, WT, and G12D, respectively). We injected mice with poly(I:C) at weaning to excise the LSL cassette in hematopoietic cells. As reported (Wang et al., Blood 2011; Xu et al., Cancer Disc 2013), G12D mice died early (119-267 days, n=14) from an aggressive myeloproliferative disorder (MPD). In contrast, no mortality was observed in the G12D,C181S and WT cohorts until 18-19 months of age (p=3x10-6 by Kaplan-Meier analysis). Pathologic analysis of 6-month-old mice showed that key features of MPD were fully rescued in the G12D,C181S cohort. Specifically, whereas white blood cell (WBC) counts and spleen sizes were in the normal range in G12D,C181S and WT mice, G12D mice had profound leukocytosis (median WBC count: 52.19 k/μL), splenomegaly (median spleen weight: 0.884 g), and myeloid expansion (n=6). Biochemical analysis revealed that N-RasG12D,C181S accumulated in the GTP-bound conformation, but mostly localized in the cytosol, and failed to hyperactivate the MAPK pathway. We next generated NrasG12D,C181S/G12D compound heterozygous mice to investigate potential interactions between oncogenic NrasG12D alleles with and without the C181S mutation in vivo. Over half of these mice developed hematologic disease and died prematurely, although later than homozygous G12D mutant mice (median survivals: 429 and 225 days; n = 22 and 14, respectively). Common findings in moribund mice were splenomegaly, expansion of myeloid cells, and different degrees of leukocytosis and anemia. Importantly, genetic analysis from diseased mice revealed reduced frequency or absence of the NrasG12D,C181S allele (allelic burden 0-30%) due to secondary somatic genetic events. This observation supports the existence of high selective pressure to overcome growth-suppressive properties of unpalmitoylated N-Ras during leukemogenesis. In conclusion, these studies provide strong genetic evidence validating palmitoylation as a therapeutic target in NRAS mutant hematologic malignancies and establish a novel model for addressing this question in other cancers. Citation Format: Noemi A. Zambetti, Ari J. Firestone, Jasmine C. Wong, Amanda M. Long, Anagha Inguva, Jarrett R. Remsberg, Radu M. Suciu, Benjamin F. Cravatt, Kevin M. Haigis, Kevin Shannon. In vivo evidence validating the palmitoylation/depalmitoylation cycle as a therapeutic target in NRAS mutant hematologic cancers [abstract]. In: Proceedings of the AACR Special Conference on Targeting RAS-Driven Cancers; 2018 Dec 9-12; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(5_Suppl):Abstract nr A25.

The Small Business Innovation Research (SBIR) program was created to stimulate technological innovation and business development at early stage companies in the United States. In its 21-year history, the program has channeled over $35 billion of public funds to private businesses in the form of approximately 137,000 grants. However, the question of whether SBIR funding effectively spurs new innovation and promotes commercialization remains controversial. Here, we review efforts to answer this question and perform an independent analysis to evaluate the success of the SBIR program in a representative high technology industry. To do this, we systematically analyzed publicly available data for biotechnology companies based in Pennsylvania that received SBIR funding through the Department of Health and Human Services (HHS) between 1983 and 2014. Our analysis did not find any clear relationships between the amount of SBIR funding received and acquisition of private funding or intellectual property. However, higher SBIR funding rates were associated with current operating status and number of publications, indicating that these additional grants do support commercial operations and the advancement of scientific knowledge. Taken together, our study provides a comprehensive overview of the SBIR program for Pennsylvania biotechnology companies and reveals myriad uses for federal funding to support company development and foster innovation for the public good. These findings underscore the complexity of evaluating the SBIR program and the need for increased standardization and centralization of outcomes data for this large and growing federal program.

Isolated protein motifs that are involved in interactions with their binding partners can be used to inhibit these interactions. However, peptides corresponding to protein fragments tend to have no defined secondary or tertiary structures in the absence of scaffolding by the rest of protein molecule. This results in low potency of corresponding inhibitors. NMR and CD spectroscopy studies of lipopeptide inhibitors of the Hedgehog pathway revealed that membrane anchoring allows the cell membrane to function as a scaffold facilitating folding of short peptides. In addition, lipidation enhances cell permeability and increases the local concentration of the compounds near the membrane thus facilitating potent inhibition. General applicability of this rational approach was further confirmed by generation of selective antagonists of insulin-like growth factor 1 receptor with GI50 values in the nanomolar range. Lipopeptides corresponding to protein fragments were found to serve as potent and selective inhibitors of a number of non-druggable molecular targets.

Multitasking around the clock Chronic disruption of our circadian rhythms—for example, through shift work—may increase the risk of metabolic disease. Zhang et al. found that a multitasking transcription factor called Rev-erb-α regulates expression of both clock and metabolic genes through distinct mechanisms. At clock genes, it binds directly to a specific DNA sequence, displacing a competing transcription factor. At metabolic genes, it interacts not with DNA but with other transcription factors that regulate metabolic gene expression in a tissue-specific manner. Science , this issue p. 1488

Smoothened is a critical component of the Hedgehog pathway that is essential for stem cell renewal and is dysregulated in many cancer types. We have found synthetic analogues of the second and third intracellular loops of smoothened to be potent inhibitors of the Hedgehog pathway. Palmitoylated peptides as short as 10 residues inhibited melanoma cells growth with IC50 in the low nanomolar range. The compounds are promising drug candidates and convenient tools for solving mechanisms of Hedgehog signaling.

RAS genes are the most frequently mutated oncogenes in human cancer. Although they are believed to be among the most important drug targets in oncology, no synthetic molecules that directly target any member of the family and inhibit its function with appreciable in vivo or even in vitro activity have been identified. We have utilized a previously developed approach of peptide structural stabilization by membrane anchoring for the development of potent inhibitors of Ras proteins. We have tested lipopeptide analogs of different parts of Ras proteins and their interaction partners and have found lipopeptide analogs of hypervariable regions and of the C-terminal alpha helix (helix 6) of Ras proteins to be the most effective in interfering with Ras function and inhibiting Ras-dependent, but not Ras-independent growth of cancer cells. Direct binding of inhibitors to recombinant K-Ras (1-166) was detected by Microscale Thermophoresis (MST), and circular dichroism spectroscopy. NMR titration data revealed a localized interaction of helix 6 analogs with the Switch I region of K-Ras with the most significant chemical shift perturbations found in residues Q25, N26, S32, T35, and E37. Compounds inhibit the formation of active RasGTP and prevent Ras signaling to downstream effectors. Structural optimization of helix 6 analogs resulted in a metabolically stable, 12 amino acid residues long peptide made of all-D amino acids that inhibited the growth Ras-dependent cancer cell lines with GI50 below 1 nM. MST studies have shown that a fluorescently-labeled version of the compound binds to recombinant GDP-loaded K-Ras (1-166) with KD= 86 ±8 nM. Derivatives of K-Ras4B hypervariable region exert their activity by a significantly different mechanism: they cause degradation of Ras protein. Partially optimized compound of the series inhibit growth of cancer cells with GI 50 in submicromolar range and bind to recombinant K-Ras (1-166) with KD=1250±140nM (as determined in MST assay). CD spectroscopy data suggest that binding of compounds of both classes to K-Ras is accompanied by significant changes in protein secondary structure. In mice, inhibitors potently inhibited growth of H358 human lung tumor xenograft and Lewis lung carcinoma when injected subcutaneously every second day. The compounds are promising drug candidates for the treatment of many tumor types. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr LB-426. doi:1538-7445.AM2012-LB-426