Ubiquitinated PCNA Drives USP1 Synthetic Lethality in Cancer

CRISPR Cas9-based screening is a powerful approach for identifying and characterizing novel drug targets. Here, we elucidate the synthetic lethal mechanism of deubiquitinating enzyme USP1 in cancers with underlying DNA damage vulnerabilities, specifically BRCA1/2 mutant tumors and a subset of BRCA1/2 wild-type (WT) tumors. In sensitive cells, pharmacologic inhibition of USP1 leads to decreased DNA synthesis concomitant with S-phase-specific DNA damage. Genome-wide CRISPR-Cas9 screens identify RAD18 and UBE2K, which promote PCNA mono- and polyubiquitination respectively, as mediators of USP1 dependency. The accumulation of mono- and polyubiquitinated PCNA following USP1 inhibition is associated with reduced PCNA protein levels. Ectopic expression of WT or ubiquitin-dead K164R PCNA reverses USP1 inhibitor sensitivity. Our results show, for the first time, that USP1 dependency hinges on the aberrant processing of mono- and polyubiquitinated PCNA. Moreover, this mechanism of USP1 dependency extends beyond BRCA1/2 mutant tumors to selected BRCA1/2 WT cancer cell lines enriched in ovarian and lung lineages. We further show PARP and USP1 inhibition are strongly synergistic in BRCA1/2 mutant tumors. We postulate USP1 dependency unveils a previously uncharacterized vulnerability linked to posttranslational modifications of PCNA. Taken together, USP1 inhibition may represent a novel therapeutic strategy for BRCA1/2 mutant tumors and a subset of BRCA1/2 WT tumors.

VRK1 Is a Synthetic-Lethal Target in VRK2-Deficient Glioblastoma

Synthetic lethality is a genetic interaction that results in cell death when two genetic deficiencies co-occur but not when either deficiency occurs alone, which can be co-opted for cancer therapeutics. Pairs of paralog genes are among the most straightforward potential synthetic-lethal interactions by virtue of their redundant functions. Here, we demonstrate a paralog-based synthetic lethality by targeting vaccinia-related kinase 1 (VRK1) in glioblastoma (GBM) deficient of VRK2, which is silenced by promoter methylation in approximately two thirds of GBM. Genetic knockdown of VRK1 in VRK2-null or VRK2-methylated cells resulted in decreased activity of the downstream substrate barrier to autointegration factor (BAF), a regulator of post-mitotic nuclear envelope formation. Reduced BAF activity following VRK1 knockdown caused nuclear lobulation, blebbing, and micronucleation, which subsequently resulted in G2-M arrest and DNA damage. The VRK1-VRK2 synthetic-lethal interaction was dependent on VRK1 kinase activity and was rescued by ectopic expression of VRK2. In VRK2-methylated GBM cell line-derived xenograft and patient-derived xenograft models, knockdown of VRK1 led to robust tumor growth inhibition. These results indicate that inhibiting VRK1 kinase activity could be a viable therapeutic strategy in VRK2-methylated GBM.

SIGNIFICANCE

A paralog synthetic-lethal interaction between VRK1 and VRK2 sensitizes VRK2-methylated glioblastoma to perturbation of VRK1 kinase activity, supporting VRK1 as a drug discovery target in this disease.

Abstract P183: CRISPR screens identify sensitizers to trametinib in KRAS mutant cancer cell lines

KRAS is the most frequently mutated oncogene in human tumors and drives tumorigenesis across multiple lineages. Specifically, KRAS is mutated in about 30% of lung cancer and over 90% of pancreatic cancer. Despite recent progress in developing mutant selective KRASG12C inhibitors, patient treatment options for RAS activated cancers remain very limited. Targeting the MAPK pathway by means of MEK and ERK inhibitors has been explored as an alternative strategy for KRAS mutant cancer. However, the clinical benefit is modest due to drug resistance caused by reactivation of the MAPK pathway and potentially other pathways and/or bypass mechanisms. Here we used CRISPR-based screens to identify potential combination therapy targets to enhance trametinib response in KRAS mutant cancers. We screened in five KRAS mutant cell lines of lung and pancreatic lineages and identified both known as well as novel modulators of MEK inhibitor response. Consistent with previous reports, gene knockouts that impair the reactivation of ERK downstream of MEK inhibition scored as top hits in our drop-out screens. Knocking out MAPK1, RAF1, BRAF and PTPN11 sensitized all five cell lines to trametinib treatment supporting these as candidate drug combination targets for MAPK pathway inhibition. Our screens also identified multiple genes within the heparan sulfate pathway (EXT1, EXT2, EXTL3, XYLT2, ALG6, B3GAT3, B4GALT7 and HS2ST1) and the MAPK7 pathway (MAPK7 and MAP2K5) that sensitize multiple but not all cell lines to trametinib. As part of our target discovery platform, we further validated these screening results using various phenotypic assays. Altogether, our results suggest that resistance to MEK inhibitors is driven by reactivation of the MAPK pathway as previously demonstrated and that impairing such reactivation restores the sensitivity of KRAS mutant cancer cells to trametinib. The genetic mechanisms driving the MAPK pathway rebound are likely different in different cancers and understanding such mechanisms will be key for achieving clinical success.

Citation Format: Silvia Fenoglio, Aileen M. Cristo, James Tepper, Teng Teng, Samuel R. Meier, Ashley Choi, Hongxiang Zhang, Shan-chuan Zhao, Shangtao Liu, Leanne G. Ahronian, Daniel Aird, Nikitha M. Das, Yi Yu, Robert Tjin Tham Sjin, Jannik N. Andersen, Alan Huang, Fang Li, Xuewen Pan. CRISPR screens identify sensitizers to trametinib in KRAS mutant cancer cell lines [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr P183.

Design of BET Inhibitor Bottlebrush Prodrugs with Superior Efficacy and Devoid of Systemic Toxicities

Prodrugs engineered for preferential activation in diseased versus normal tissues offer immense potential to improve the therapeutic indexes (TIs) of preclinical and clinical-stage active pharmaceutical ingredients that either cannot be developed otherwise or whose efficacy or tolerability it is highly desirable to improve. Such approaches, however, often suffer from trial-and-error design, precluding predictive synthesis and optimization. Here, using bromodomain and extra-terminal (BET) protein inhibitors (BETi)-a class of epigenetic regulators with proven anticancer potential but clinical development hindered in large part by narrow TIs-we introduce a macromolecular prodrug platform that overcomes these challenges. Through tuning of traceless linkers appended to a "bottlebrush prodrug" scaffold, we demonstrate correlation of in vitro prodrug activation kinetics with in vivo tumor pharmacokinetics, enabling the predictive design of novel BETi prodrugs with enhanced antitumor efficacies and devoid of dose-limiting toxicities in a syngeneic triple-negative breast cancer murine model. This work may have immediate clinical implications, introducing a platform for predictive prodrug design and potentially overcoming hurdles in drug development.

Publisher Correction: Reduction of liver fibrosis by rationally designed macromolecular telmisartan prodrugs

In the version of this Article originally published, the author Peter Blume-Jensen was not denoted as a corresponding author; this has now been amended and the author's email address has been added. The 'Correspondence and requests for materials' statement was similarly affected and has now been updated with the author's initials 'P.B-J.'

Reduction of liver fibrosis by rationally designed macromolecular telmisartan prodrugs

At present there are no drugs for the treatment of chronic liver fibrosis that have been approved by the Food and Drug administration of the United States. Telmisartan, a small-molecule antihypertensive drug, displays antifibrotic activity, but its clinical use is limited because it causes systemic hypotension. Here, we report the scalable and convergent synthesis of macromolecular telmisartan prodrugs optimized for preferential release in diseased liver tissue. We optimized the release of active telmisartan in fibrotic liver to be depot-like (that is, a constant therapeutic concentration) through the molecular design of telmisartan brush-arm star polymers, and show that these lead to improved efficacy and to the avoidance of dose-limiting hypotension in both metabolically and chemically induced mouse models of hepatic fibrosis, as determined by histopathology, enzyme levels in the liver, intact-tissue protein markers, hepatocyte necrosis protection, and gene-expression analyses. In rats and dogs, the prodrugs are retained long-term in liver tissue and have a well-tolerated safety profile. Our findings support the further development of telmisartan prodrugs that enable infrequent dosing in the treatment of liver fibrosis.

Abstract LB-062: Development of macromolecular prodrugs of BET-bromodomain inhibitors with superior anti-tumor efficacy that are T-cell sparing and devoid of systemic toxicity

Small molecule BET inhibitors are promising anti-cancer agents, but their clinical development has been limited by hematological and gastrointestinal (GI) toxicity. For the prototype benzodiazepine-derived inhibitor (OTX-015), the dose-limiting toxicities (DLTs) are thrombocytopenia (96%), anemia (91%), and neutropenia (51%) with additional GI events (diarrhea, vomiting and mucositis) reported to limit patient compliance despite evidence of durable/objective tumor responses. Accordingly, based on a review of entries in www.clinicaltrials.gov from January 2017 to January 2018, 11 out of 12 programs are reporting protracted phase I/II development times and reduced patient enrollment targets. To improve the narrow therapeutic index of current BET inhibitors, we here report the development of macromolecular BET inhibitor prodrugs with a favorable bio-distribution and release of active drug in tumor compared to other tissues, including gut and bone marrow.

We successfully conjugated two structurally distinct BET inhibitors, including the OTX-015, to Brush polymers using an array of different linker chemistries and evaluated them for in vivo efficacy and toxicity using immunocompetent, orthotopically implanted mouse tumor models. Through rational design of drug conjugation and linker chemistry, we optimized the PK properties and drug release rates offering a ‘depot-like' release of drug in tumor tissue resulting in both improved efficacy and reduction of systemic dose-limiting toxicity. Specifically, these novel formulations were evaluated for myelosuppression and GI toxicity using an array of in vitro, clinical pathology and immunohistopathology techniques. Compared to non-conjugated BET inhibitors, which showed dose-dependent body weight loss, diarrhea, and suppression of white blood cells, the macromolecular BET-BRUSH prodrugs spared the lymphocytes, platelets and neutrophils and showed minimal suppression of the reservoir of myeloid cells in the bone marrow. The improved therapeutic index of the BET-Brush compounds was confirmed through detailed PK/PD/Efficacy studies correlating the concentration of both released and polymer-bound BET inhibitor in tumor and plasma with quantitative tissue biomarker modulation (c-MYC, HEXIM-1 and CD180). Whole organ bio-distribution studies using fluorophore-conjugated BET-Brush confirmed the favorable distribution into tumor over the gut and bone marrow, with BET-Brush showing profound modulation of biomarkers in tumor tissue, but not gut. Notably, the BET-Brush compounds showed suppression of PD-L1 expression in tumors, which in context of preserved T-cells, can make BET-Brush a promising combination with immuno-oncology therapy. Paired with an excellent safety profile of the polymer backbone in rat and non-human primates, these data support the further development of BET-Brush prodrugs as an infrequently dosed treatment for human cancers.

Citation Format: Farrukh Vohidov, Jannik N. Andersen, Kyriakos D. Economides, Michail V. Shipitsin, Olga Burenkova, Nolan M. Gallagher, Peyton Sheih, Matthew Golder, Jenny Liu, William K. Dahlberg, Hung V. Nguyen, Deborah J. Ehrlich, Julie Kim, Sung Jin Huh, Bhavatarini Vangamudi, Allison M. Neenan, James C. Ackley, Joelle Baddour, Sattanathan Paramasivan, Gaurab KC, David J. Turnquist, Jenny K. Saucier-Sawyer, Paul W. Kopesky, Samantha W. Brady, Michael J. Jessel, Lawrence A. Reiter, Donald E. Chickering, Jeremiah A. Johnson, Peter Blume-Jensen. Development of macromolecular prodrugs of BET-bromodomain inhibitors with superior anti-tumor efficacy that are T-cell sparing and devoid of systemic toxicity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-062.

Cross-talk between chromatin acetylation and SUMOylation of tripartite motif-containing protein 24 (TRIM24) impacts cell adhesion

Proteins with domains that recognize and bind post-translational modifications (PTMs) of histones are collectively termed epigenetic readers. Numerous interactions between specific reader protein domains and histone PTMs and their regulatory outcomes have been reported, but little is known about how reader proteins may in turn be modulated by these interactions. Tripartite motif-containing protein 24 (TRIM24) is a histone reader aberrantly expressed in multiple cancers. Here, our investigation revealed functional cross-talk between histone acetylation and TRIM24 SUMOylation. Binding of TRIM24 to chromatin via its tandem PHD-bromodomain, which recognizes unmethylated lysine 4 and acetylated lysine 23 of histone H3 (H3K4me0/K23ac), led to TRIM24 SUMOylation at lysine residues 723 and 741. Inactivation of the bromodomain, either by mutation or with a small-molecule inhibitor, IACS-9571, abolished TRIM24 SUMOylation. Conversely, inhibition of histone deacetylation markedly increased TRIM24's interaction with chromatin and its SUMOylation. Of note, gene expression profiling of MCF7 cells expressing WT versus SUMO-deficient TRIM24 identified cell adhesion as the major pathway regulated by the cross-talk between chromatin acetylation and TRIM24 SUMOylation. In conclusion, our findings establish a new link between histone H3 acetylation and SUMOylation of the reader protein TRIM24, a functional connection that may bear on TRIM24's oncogenic function and may inform future studies of PTM cross-talk between histones and epigenetic regulators.

Ambient pressure phase transitions over Ir(1 1 1): at the onset of CO oxidation

In this study we report on the adsorbate structures on an Ir(1 1 1) surface during the phase transition from the inactive to the active state during CO oxidation. The CO oxidation over Pt(1 1 1) is used as a reference case. Where Pt(1 1 1) either is inactive and CO covered or active and O covered, Ir(1 1 1) exhibits a transition state with co-existing chemisorbed O and CO. The observed structural differences are explained in terms of DFT-calculated adsorption energies. For Pt(1 1 1) the repulsive CO-O interaction makes co-existing chemisorbed CO and O unfavourable, while for Ir(1 1 1) the stronger O and CO adsorption allows for overcoming the repulsive interaction. At the onset of CO oxidation over Ir(1 1 1), a CO structure containing defects forms, which enables O₂ to dissociatively adsorb on the Ir(1 1 1) surface, thus enabling the CO oxidation reaction. At the mass transfer limit, the Ir(1 1 1) surface is covered by a chemisorbed O structure with defects; hence, the active surface is predominately chemisorbed O covered at a total pressure of 0.5 mbar and no oxide formation is observed.

Sonogashira cross-coupling over Au(1 1 1): from UHV to ambient pressure

We have studied the reaction of phenylacetylene (PA) with chloro-, bromo-, and iodobenzene on the Au(1 1 1) surface as a model system for the gold-catalysed Sonogashira cross-coupling. Both ultrahigh vacuum-based and ambient pressure x-ray photoelectron spectroscopy show that iodo- and chlorobenzene (IB and CB) undergo the cross-coupling reaction towards diphenylacetylene. Bromobenzene (BB), in contrast, does not react in the UHV experiments. Further, at ambient pressure signs are found for poisoning of the Au(1 1 1) surface by a carbon species formed in the reaction. The understanding obtained in the reaction experiments are based on a thorough investigation of the adsorption of PA, IB, CB, and BB on the Au(1 1 1) surface by soft x-ray absorption spectroscopy and temperature-dependent x-ray photoelectron spectroscopy. In particular, the experiments provide the orientation of the intact adsorbates with respect to the surfaces at liquid nitrogen temperature. Dissociation in the temperature regime between  -80 and  -15 °C is observed for iodo- and chlorobenzene, but not for BB, in agreement with that only IB and CB, but not BB, react with PA to form diphenylacetylene. The difference is tentatively attributed to a difference in surface orientation of the different halobenzenes.

Development of a High-Throughput Gene Expression Screen for Modulators of RAS-MAPK Signaling in a Mutant RAS Cellular Context

The RAS-MAPK pathway controls many cellular programs, including cell proliferation, differentiation, and apoptosis. In colorectal cancers, recurrent mutations in this pathway often lead to increased cell signaling that may contribute to the development of neoplasms, thereby making this pathway attractive for therapeutic intervention. To this end, we developed a 26-member gene signature of RAS-MAPK pathway activity utilizing the Affymetrix QuantiGene Plex 2.0 reagent system and performed both primary and confirmatory gene expression-based high-throughput screens (GE-HTSs) using KRAS mutant colon cancer cells (SW837) and leveraging a highly annotated chemical library. The screen achieved a hit rate of 1.4% and was able to enrich for hit compounds that target RAS-MAPK pathway members such as MEK and EGFR. Sensitivity and selectivity performance measurements were 0.84 and 1.00, respectively, indicating high true-positive and true-negative rates. Active compounds from the primary screen were confirmed in a dose-response GE-HTS assay, a GE-HTS assay using 14 additional cancer cell lines, and an in vitro colony formation assay. Altogether, our data suggest that this GE-HTS assay will be useful for larger unbiased chemical screens to identify novel compounds and mechanisms that may modulate the RAS-MAPK pathway.

Development of novel cellular histone-binding and chromatin-displacement assays for bromodomain drug discovery

Background

Proteins that ‘read’ the histone code are central elements in epigenetic control and bromodomains, which bind acetyl-lysine motifs, are increasingly recognized as potential mediators of disease states. Notably, the first BET bromodomain-based therapies have entered clinical trials and there is a broad interest in dissecting the therapeutic relevance of other bromodomain-containing proteins in human disease. Typically, drug development is facilitated and expedited by high-throughput screening, where assays need to be sensitive, robust, cost-effective and scalable. However, for bromodomains, which lack catalytic activity that otherwise can be monitored (using classical enzymology), the development of cell-based, drug-target engagement assays has been challenging. Consequently, cell biochemical assays have lagged behind compared to other protein families (e.g., histone deacetylases and methyltransferases).

Results

Here, we present a suite of novel chromatin and histone-binding assays using AlphaLISA, in situ cell extraction and fluorescence-based, high-content imaging. First, using TRIM24 as an example, the homogenous, bead-based AlphaScreen technology was modified from a biochemical peptide-competition assay to measure binding of the TRIM24 bromodomain to endogenous histone H3 in cells (AlphaLISA). Second, a target agnostic, high-throughput imaging platform was developed to quantify the ability of chemical probes to dissociate endogenous proteins from chromatin/nuclear structures. While overall nuclear morphology is maintained, the procedure extracts soluble, non-chromatin-bound proteins from cells with drug-target displacement visualized by immunofluorescence (IF) or microscopy of fluorescent proteins. Pharmacological evaluation of these assays cross-validated their utility, sensitivity and robustness. Finally, using genetic and pharmacological approaches, we dissect domain contribution of TRIM24, BRD4, ATAD2 and SMARCA2 to chromatin binding illustrating the versatility/utility of the in situ cell extraction platform.

Conclusions

In summary, we have developed two novel complementary and cell-based drug-target engagement assays, expanding the repertoire of pharmacodynamic assays for bromodomain tool compound development. These assays have been validated through a successful TRIM24 bromodomain inhibitor program, where a micromolar lead molecule (IACS-6558) was optimized using cell-based assays to yield the first single-digit nanomolar TRIM24 inhibitor (IACS-9571). Altogether, the assay platforms described herein are poised to accelerate the discovery and development of novel chemical probes to deliver on the promise of epigenetic-based therapies.

Electronic supplementary material

The online version of this article (doi:10.1186/s13072-015-0026-4) contains supplementary material, which is available to authorized users.

Abstract 3528: The SMARCA2/4 catalytic activity, but not the bromodomain, is a drug target in SWI/SNF mutant cancers

The SWI/SNF multi-subunit complex modulates chromatin structure through the activity of two mutually exclusive catalytic subunits, SMARCA2 and SMARCA4, which both contain a bromodomain and an ATPase domain. Using RNAi, cancer-specific vulnerabilities have been identified in SWI/SNF mutant tumors, including SMARCA4-deficient lung cancer, however, the contribution of conserved, druggable protein domains to this anticancer phenotype is unknown. Here, we functionally deconstructed the SMARCA2/4 paralog dependence of cancer cells using bioinformatics, genetic and pharmacological tools. We evaluated a potent and selective SMARCA2/4 bromodomain inhibitor (PFI-3) and characterized its activity in chromatin-binding and cell-functional assays focusing on cells with altered SWI/SNF status (e.g. Lung, Synovial Sarcoma, Leukemia, and Rhabdoid tumors). We demonstrated that PFI-3 is a cell-permeable probe capable of displacing ectopically expressed, GFP-tagged SMARCA2-bromodomain from chromatin, yet contrary to target knockdown, the inhibitor failed to display an antiproliferative phenotype. Mechanistically, the lack of pharmacological efficacy was reconciled by the failure of bromodomain inhibition to displace endogenous, full-length SMARCA2 from chromatin as determined by in situ cell extraction, chromatin immunoprecipitation (ChIP) and target gene expression and promoter occupancy studies. Using RNAi and cDNA complementation (bromodomain and ATPase-dead constructs), we identified the catalytic ATPase domain, and not the bromodomain of SMARCA2, as a relevant therapeutic target. Taken together, our complementary genetic and pharmacological studies exemplify a general strategy for bromodomain drug-target validation and in case of SMARCA2/4 highlight the requirement for drugging the more challenging helicase/ATPase domain affording potential synthetic-lethal treatment options to cancer patients with genetically defined alterations in SWI/SNF.

Citation Format: Bhavatarini Vangamudi, Thomas Paul, Parantu K. Shah, Maria K. Alimova, Lisa Nottebaum, Xi Shi, Yanai Zhan, Elisabetta Leo, Harshad S. Mahadeshwar, Alexei Protopopov, Andrew Futreal, Trang N. Tieu, Mike Peoples, Alessia Petrocchi, Joseph R. Marszalek, Carlo Toniatti, Timothy P. Heffernan, Dominique Verhelle, Giulio Draetta, Dafydd Owen, Philip Jones, Wylie Palmer, Shikhar Sharma, Jannik N. Andersen. The SMARCA2/4 catalytic activity, but not the bromodomain, is a drug target in SWI/SNF mutant cancers. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3528. doi:10.1158/1538-7445.AM2015-3528

Structure-Guided Design of IACS-9571, a Selective High-Affinity Dual TRIM24-BRPF1 Bromodomain Inhibitor

The bromodomain containing proteins TRIM24 (tripartite motif containing protein 24) and BRPF1 (bromodomain and PHD finger containing protein 1) are involved in the epigenetic regulation of gene expression and have been implicated in human cancer. Overexpression of TRIM24 correlates with poor patient prognosis, and BRPF1 is a scaffolding protein required for the assembly of histone acetyltransferase complexes, where the gene of MOZ (monocytic leukemia zinc finger protein) was first identified as a recurrent fusion partner in leukemia patients (8p11 chromosomal rearrangements). Here, we present the structure guided development of a series of N,N-dimethylbenzimidazolone bromodomain inhibitors through the iterative use of X-ray cocrystal structures. A unique binding mode enabled the design of a potent and selective inhibitor 8i (IACS-9571) with low nanomolar affinities for TRIM24 and BRPF1 (ITC Kd = 31 nM and ITC Kd = 14 nM, respectively). With its excellent cellular potency (EC50 = 50 nM) and favorable pharmacokinetic properties (F = 29%), 8i is a high-quality chemical probe for the evaluation of TRIM24 and/or BRPF1 bromodomain function in vitro and in vivo.

The SMARCA2/4 ATPase Domain Surpasses the Bromodomain as a Drug Target in SWI/SNF-Mutant Cancers: Insights from cDNA Rescue and PFI-3 Inhibitor Studies

The SWI/SNF multisubunit complex modulates chromatin structure through the activity of two mutually exclusive catalytic subunits, SMARCA2 and SMARCA4, which both contain a bromodomain and an ATPase domain. Using RNAi, cancer-specific vulnerabilities have been identified in SWI/SNF-mutant tumors, including SMARCA4-deficient lung cancer; however, the contribution of conserved, druggable protein domains to this anticancer phenotype is unknown. Here, we functionally deconstruct the SMARCA2/4 paralog dependence of cancer cells using bioinformatics, genetic, and pharmacologic tools. We evaluate a selective SMARCA2/4 bromodomain inhibitor (PFI-3) and characterize its activity in chromatin-binding and cell-functional assays focusing on cells with altered SWI/SNF complex (e.g., lung, synovial sarcoma, leukemia, and rhabdoid tumors). We demonstrate that PFI-3 is a potent, cell-permeable probe capable of displacing ectopically expressed, GFP-tagged SMARCA2-bromodomain from chromatin, yet contrary to target knockdown, the inhibitor fails to display an antiproliferative phenotype. Mechanistically, the lack of pharmacologic efficacy is reconciled by the failure of bromodomain inhibition to displace endogenous, full-length SMARCA2 from chromatin as determined by in situ cell extraction, chromatin immunoprecipitation, and target gene expression studies. Furthermore, using inducible RNAi and cDNA complementation (bromodomain- and ATPase-dead constructs), we unequivocally identify the ATPase domain, and not the bromodomain of SMARCA2, as the relevant therapeutic target with the catalytic activity suppressing defined transcriptional programs. Taken together, our complementary genetic and pharmacologic studies exemplify a general strategy for multidomain protein drug-target validation and in case of SMARCA2/4 highlight the potential for drugging the more challenging helicase/ATPase domain to deliver on the promise of synthetic-lethality therapy.

The Rh(100)-(3 × 1)-2O structure

The O adsorption on Rh(100) has been studied using high resolution core level spectroscopy, low energy electron diffraction and scanning tunnelling microscopy. In addition to the well known (2 × 2), (2 × 2)-pg and c(8 × 2) structures at coverages of 0.25, 0.5 and 1.75 ML respectively, an intermediate (3 × 1) structure with a coverage of 2/3 ML is identified.

The Active Phase of Palladium during Methane Oxidation

The active phase of Pd during methane oxidation is a long-standing puzzle, which, if solved, could provide routes for design of improved catalysts. Here, density functional theory and in situ surface X-ray diffraction are used to identify and characterize atomic sites yielding high methane conversion. Calculations are performed for methane dissociation over a range of Pd and PdOx surfaces and reveal facile dissociation on either under-coordinated Pd sites in PdO(101) or metallic surfaces. The experiments show unambiguously that high methane conversion requires sufficiently thick PdO(101) films or metallic Pd, in full agreement with the calculations. The established link between high activity and atomic structure enables rational design of improved catalysts.

Conformation-sensing antibodies stabilize the oxidized form of PTP1B and inhibit its phosphatase activity

Protein tyrosine phosphatase 1B (PTP1B) plays important roles in downregulation of insulin and leptin signaling and is an established therapeutic target for diabetes and obesity. PTP1B is regulated by reactive oxygen species (ROS) produced in response to various stimuli, including insulin. The reversibly oxidized form of the enzyme (PTP1B-OX) is inactive and undergoes profound conformational changes at the active site. We generated conformation-sensor antibodies, in the form of single-chain variable fragments (scFvs), that stabilize PTP1B-OX and thereby inhibit its phosphatase function. Expression of conformation-sensor scFvs as intracellular antibodies (intrabodies) enhanced insulin-induced tyrosyl phosphorylation of the β subunit of the insulin receptor and its substrate IRS-1 and increased insulin-induced phosphorylation of PKB/AKT. Our data suggest that stabilization of the oxidized, inactive form of PTP1B with appropriate therapeutic molecules may offer a paradigm for phosphatase drug development.

Identification of direct target engagement biomarkers for kinase-targeted therapeutics

Pharmacodynamic (PD) biomarkers are an increasingly valuable tool for decision-making and prioritization of lead compounds during preclinical and clinical studies as they link drug-target inhibition in cells with biological activity. They are of particular importance for novel, first-in-class mechanisms, where the ability of a targeted therapeutic to impact disease outcome is often unknown. By definition, proximal PD biomarkers aim to measure the interaction of a drug with its biological target. For kinase drug discovery, protein substrate phosphorylation sites represent candidate PD biomarkers. However, substrate phosphorylation is often controlled by input from multiple converging pathways complicating assessment of how potently a small molecule drug hits its target based on substrate phoshorylation measurements alone. Here, we report the use of quantitative, differential mass-spectrometry to identify and monitor novel drug-regulated phosphorylation sites on target kinases. Autophosphorylation sites constitute clinically validated biomarkers for select protein tyrosine kinase inhibitors. The present study extends this principle to phosphorylation sites in serine/threonine kinases looking beyond the T-loop autophosphorylation site. Specifically, for the 3'-phosphoinositide-dependent protein kinase 1 (PDK1), two phospho-residues p-PDK1(Ser410) and p-PDK1(Thr513) are modulated by small-molecule PDK1 inhibitors, and their degree of dephosphorylation correlates with inhibitor potency. We note that classical, ATP-competitive PDK1 inhibitors do not modulate PDK1 T-loop phosphorylation (p-PDK1(Ser241)), highlighting the value of an unbiased approach to identify drug target-regulated phosphorylation sites as these are complementary to pathway PD biomarkers. Finally, we extend our analysis to another protein Ser/Thr kinase, highlighting a broader utility of our approach for identification of kinase drug-target engagement biomarkers.

PDK1 attenuation fails to prevent tumor formation in PTEN-deficient transgenic mouse models

PDK1 activates AKT suggesting that PDK1 inhibition might suppress tumor development. However, while PDK1 has been investigated intensively as an oncology target, selective inhibitors suitable for in vivo studies have remained elusive. In this study we present the results of in vivo PDK1 inhibition through a universally applicable RNAi approach for functional drug target validation in oncogenic pathway contexts. This approach, which relies on doxycycline-inducible shRNA expression from the Rosa26 locus, is ideal for functional studies of genes like PDK1 where constitutive mouse models lead to strong developmental phenotypes or embryonic lethality. We achieved more than 90% PDK1 knockdown in vivo, a level sufficient to impact physiological functions resulting in hyperinsulinemia and hyperglycemia. This phenotype was reversible on PDK1 reexpression. Unexpectedly, long-term PDK1 knockdown revealed a lack of potent antitumor efficacy in 3 different mouse models of PTEN-deficient cancer. Thus, despite efficient PDK1 knockdown, inhibition of the PI3K pathway was marginal suggesting that PDK1 was not a rate limiting factor. Ex vivo analysis of pharmacological inhibitors revealed that AKT and mTOR inhibitors undergoing clinical development are more effective than PDK1 inhibitors at blocking activated PI3K pathway signaling. Taken together our findings weaken the widely held expectation that PDK1 represents an appealing oncology target.

Cancer genomics: from discovery science to personalized medicine

Recent advances in genome technologies and the ensuing outpouring of genomic information related to cancer have accelerated the convergence of discovery science and clinical medicine. Successful examples of translating cancer genomics into therapeutics and diagnostics reinforce its potential to make possible personalized cancer medicine. However, the bottlenecks along the path of converting a genome discovery into a tangible clinical endpoint are numerous and formidable. In this Perspective, we emphasize the importance of establishing the biological relevance of a cancer genomic discovery in realizing its clinical potential and discuss some of the major obstacles to moving from the bench to the bedside.

Pathway-based identification of biomarkers for targeted therapeutics: personalized oncology with PI3K pathway inhibitors

Although we have made great progress in understanding the complex genetic alterations that underlie human cancer, it has proven difficult to identify which molecularly targeted therapeutics will benefit which patients. Drug-specific modulation of oncogenic signaling pathways in specific patient subpopulations can predict responsiveness to targeted therapy. Here, we report a pathway-based phosphoprofiling approach to identify and quantify clinically relevant, drug-specific biomarkers for phosphatidylinositol 3-kinase (PI3K) pathway inhibitors that target AKT, phosphoinositide-dependent kinase 1 (PDK1), and PI3K-mammalian target of rapamycin (mTOR). We quantified 375 nonredundant PI3K pathway-relevant phosphopeptides, all containing AKT, PDK1, or mitogen-activated protein kinase substrate recognition motifs. Of these phosphopeptides, 71 were drug-regulated, 11 of them by all three inhibitors. Drug-modulated phosphoproteins were enriched for involvement in cytoskeletal reorganization (filamin, stathmin, dynamin, PAK4, and PTPN14), vesicle transport (LARP1, VPS13D, and SLC20A1), and protein translation (S6RP and PRAS40). We then generated phosphospecific antibodies against selected, drug-regulated phosphorylation sites that would be suitable as biomarker tools for PI3K pathway inhibitors. As proof of concept, we show clinical translation feasibility for an antibody against phospho-PRAS40(Thr246). Evaluation of binding of this antibody in human cancer cell lines, a PTEN (phosphatase and tensin homolog deleted from chromosome 10)-deficient mouse prostate tumor model, and triple-negative breast tumor tissues showed that phospho-PRAS40(Thr246) positively correlates with PI3K pathway activation and predicts AKT inhibitor sensitivity. In contrast to phosphorylation of AKT(Thr308), the phospho-PRAS40(Thr246) epitope is highly stable in tissue samples and thus is ideal for immunohistochemistry. In summary, our study illustrates a rational approach for discovery of drug-specific biomarkers toward development of patient-tailored treatments.

Tuning the spin state of iron phthalocyanine by ligand adsorption

The future use of single-molecule magnets in applications will require the ability to control and manipulate the spin state and magnetization of the magnets by external means. There are different approaches to this control, one being the modification of the magnets by adsorption of small ligand molecules. In this paper we use iron phthalocyanine supported by an Au(111) surface as a model compound and demonstrate, using x-ray photoelectron spectroscopy and density functional theory, that the spin state of the molecule can be tuned to different values (S ∼ 0, [Formula: see text], 1) by adsorption of ammonia, pyridine, carbon monoxide or nitric oxide on the iron ion. The interaction also leads to electronic decoupling of the iron phthalocyanine from the Au(111) support.

Genetic and pharmacological inhibition of PDK1 in cancer cells: characterization of a selective allosteric kinase inhibitor

Phosphoinositide-dependent kinase 1 (PDK1) is a critical activator of multiple prosurvival and oncogenic protein kinases and has garnered considerable interest as an oncology drug target. Despite progress characterizing PDK1 as a therapeutic target, pharmacological support is lacking due to the prevalence of nonspecific inhibitors. Here, we benchmark literature and newly developed inhibitors and conduct parallel genetic and pharmacological queries into PDK1 function in cancer cells. Through kinase selectivity profiling and x-ray crystallographic studies, we identify an exquisitely selective PDK1 inhibitor (compound 7) that uniquely binds to the inactive kinase conformation (DFG-out). In contrast to compounds 1-5, which are classical ATP-competitive kinase inhibitors (DFG-in), compound 7 specifically inhibits cellular PDK1 T-loop phosphorylation (Ser-241), supporting its unique binding mode. Interfering with PDK1 activity has minimal antiproliferative effect on cells growing as plastic-attached monolayer cultures (i.e. standard tissue culture conditions) despite reduced phosphorylation of AKT, RSK, and S6RP. However, selective PDK1 inhibition impairs anchorage-independent growth, invasion, and cancer cell migration. Compound 7 inhibits colony formation in a subset of cancer cell lines (four of 10) and primary xenograft tumor lines (nine of 57). RNAi-mediated knockdown corroborates the PDK1 dependence in cell lines and identifies candidate biomarkers of drug response. In summary, our profiling studies define a uniquely selective and cell-potent PDK1 inhibitor, and the convergence of genetic and pharmacological phenotypes supports a role of PDK1 in tumorigenesis in the context of three-dimensional in vitro culture systems.

Abstract 4953: Identification of direct target engagement biomarkers for kinase drug discovery using quantitative mass spectrometry: PDK1 case study

The human genome encodes some 500 protein kinases and an estimated twenty percent of drugs currently in development target this enzyme class. Because kinase inhibitors frequently bind to the conserved ATP-binding pocket, in vitro kinase selectivity profiling of drug candidates are an integral part of the small-molecule drug discovery process. Likewise, the co-development of pharmacodynamic (PD) biomarkers is critical to drug development as they link drug-target inhibition in cells with biological activity. As such PD biomarkers are essential for the interpretation of in vivo PK/PD/efficacy studies, which ultimately inform medicinal chemistry. Here, we present a universal mass-spectrometry-based approached to discover kinase drug-target engagement biomarkers using the phosphoinositide dependent protein kinase 1 (PDK1) as an example. Western blot analysis using a commercial available phosphosite-specific PDK1 antibody (Ser241) revealed that classical, ATP-competitive PDK1 inhibitors do not dynamically impact PDK1 T-loop phosphorylation in cells, despite cell biochemical inhibition of phospho-AKT(Thr308), a bona fide PDK1 substrate phosphorylation site. However, because receptor tyrosine kinases (RTKs), lipid kinases and other pathways often signal via AKT, the monitoring of phospho-AKT as a PD biomarker for PDK1 is not sufficient for delineating the specificity of small-molecule inhibitors and ascertain the degree of PDK1 target engagement in cells. Here, we used stable isotope labeling by amino acids (SILAC) in cell culture combined with immunoprecipitation of PDK1 protein from cells for quantitative mass-spectrometry-based identification of phosphorylation sites modulated by PDK1 inhibitor treatment. We mapped 10 Serine/Threonine phosphorylation sites on PDK1 including several novel phosphorylation sites. Of these, two PDK1 phosphorylation sites (Ser410 and Thr513) were modulated by pharmacological PDK1 inhibition and the degree of dephosphorylation correlated with inhibitor potency in PDK1 enzymatic assays. By contrast, pharmacological inhibition of PDK1 did not quantitatively modulate PDK1 T-loop phosphorylation (Ser241) consistent with the initial western blot analysis. Altogether, our study provides proof-of-concept for identifying novel kinase target engagement PD biomarkers for PDK1, complementing pathway biomarkers such p-AKT and p-S6RP, which are modulated broadly by PI3K-pathway targeting agents including inhibitors of PI3K/mTOR and RTKs.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4953.

Discovery of PDK1 kinase inhibitors with a novel mechanism of action by ultrahigh throughput screening

The phosphoinositide 3-kinase/AKT signaling pathway plays a key role in cancer cell growth, survival, and angiogenesis. Phosphoinositide-dependent protein kinase-1 (PDK1) acts at a focal point in this pathway immediately downstream of phosphoinositide 3-kinase and PTEN, where it phosphorylates numerous AGC kinases. The PDK1 kinase domain has at least three ligand-binding sites: the ATP-binding pocket, the peptide substrate-binding site, and a groove in the N-terminal lobe that binds the C-terminal hydrophobic motif of its kinase substrates. Based on the unique PDK1 substrate recognition system, ultrahigh throughput TR-FRET and Alphascreen screening assays were developed using a biotinylated version of the PDK1-tide substrate containing the activation loop of AKT fused to a pseudo-activated hydrophobic motif peptide. Using full-length PDK1, K(m) values were determined as 5.6 mum for ATP and 40 nm for the fusion peptide, revealing 50-fold higher affinity compared with the classical AKT(Thr-308)-tide. Kinetic and biophysical studies confirmed the PDK1 catalytic mechanism as a rapid equilibrium random bireactant reaction. Following an ultrahigh throughput screen of a large library, 2,000 compounds were selected from the reconfirmed hits by computational analysis with a focus on novel scaffolds. ATP-competitive hits were deconvoluted by dose-response studies at 1x and 10x K(m) concentrations of ATP, and specificity of binding was assessed in thermal shift assay. Inhibition studies using fusion PDK1-tide1 substrate versus AKT(Thr-308)-tide and kinase selectivity profiling revealed a novel selective alkaloid scaffold that evidently binds to the PDK1-interacting fragment pocket. Molecular modeling suggests a structural paradigm for the design of inhibitory versus activating allosteric ligands of PDK1.

Development of high-throughput TR-FRET and AlphaScreen assays for identification of potent inhibitors of PDK1

The PI3K/Akt signaling pathway plays a key role in cancer cell growth, survival, and tumor angiogenesis. 3-Phosphoinositide-dependent protein kinase 1 (PDK1) is a Ser/Thr protein kinase, which catalyzes the phosphorylation of a conserved residue in the activation loop of a number of AGC kinases, including proto-oncogenes Akt, p70S6K, and RSK kinases. To find new small-molecule inhibitors of this important regulator kinase, the authors have developed PDK1-specific high-throughput enzymatic assays in time-resolved fluorescence resonance energy transfer (TR-FRET) and AlphaScreen formats, monitoring phosphorylation of a biotinylated peptide substrate derived from the activation loop of Akt. Development of homogeneous assays enabled screening of a focused kinase library of approximately 21,500 compounds in 1536-well TR-FRET format in duplicate. Upon validation of hits in an alternative 384-well AlphaScreen assay, several classes of structurally diverse PDK1 inhibitors, including tetracyclics, tricyclics, azaindoles, indazoles, and indenylpyrazoles, were identified, thus confirming the utility and sensitivity of the developed assays. Further testing in PC3 prostate cancer cells confirmed that representatives of the tetracyclic series showed intracellular modulation of the PDK1 activity, as evident from decreased phosphorylation levels of AKT, RSK, and S6-ribosomal protein.

Photoemission electron microscopy using extreme ultraviolet attosecond pulse trains

We report the first experiments carried out on a new imaging setup, which combines the high spatial resolution of a photoemission electron microscope (PEEM) with the temporal resolution of extreme ultraviolet (XUV) attosecond pulse trains. The very short pulses were provided by high-harmonic generation and used to illuminate lithographic structures and Au nanoparticles, which, in turn, were imaged with a PEEM resolving features below 300 nm. We argue that the spatial resolution is limited by the lack of electron energy filtering in this particular demonstration experiment. Problems with extensive space charge effects, which can occur due to the low probe pulse repetition rate and extremely short duration, are solved by reducing peak intensity while maintaining a sufficient average intensity to allow imaging. Finally, a powerful femtosecond infrared (IR) beam was combined with the XUV beam in a pump-probe setup where delays could be varied from subfemtoseconds to picoseconds. The IR pump beam could induce multiphoton electron emission in resonant features on the surface. The interaction between the electrons emitted by the pump and probe pulses could be observed.

Sensitive multiplexed analysis of kinase activities and activity-based kinase identification

Constitutive activation of one or more kinase signaling pathways is a hallmark of many cancers. Here we extend the previously described mass spectrometry-based KAYAK approach by monitoring kinase activities from multiple signaling pathways simultaneously. This improved single-reaction strategy, which quantifies the phosphorylation of 90 synthetic peptides in a single mass spectrometry run, is compatible with nanogram to microgram amounts of cell lysate. Furthermore, the approach enhances kinase monospecificity through substrate competition effects, faithfully reporting the signatures of many signaling pathways after mitogen stimulation or of basal pathway activation differences across a panel of well-studied cancer cell lines. Hierarchical clustering of activities from related experiments groups peptides phosphorylated by similar kinases together and, when combined with pathway alteration using pharmacological inhibitors, distinguishes underlying differences in potency, off-target effects and genetic backgrounds. Finally, we introduce a strategy to identify the kinase, and even associated protein complex members, responsible for phosphorylation events of interest.

Low temperature Ga surface diffusion from focused ion beam milled grooves

Ga diffusion from focused ion beam (FIB) milled grooves has been studied using x-ray photoemission electron microscopy (XPEEM) and mirror electron microscopy (MEM). We analyze the surface chemistry of the FIB structures measuring the Ga presence in the top layers of the milled grooves and morphological defects inside the grooves. The Ga is initially strictly confined to the grooves. However, annealing at temperatures as low as 150 degrees C leads to rapid and significant Ga surface diffusion from the FIB structures. The out-diffused Ga forms a thin layer extending up to several microns laterally in a non-regular pattern. The diffusion is significantly enhanced at small crystallites at the edges of the grooves. We explain the general behavior with an atomic scale model in which interstitial Ga in the milled areas diffuses out and substitutes silanol groups on the surface.

Step-orientation-dependent oxidation: from 1D to 2D oxides

Using scanning tunneling microscopy and density functional theory, we have studied the initial oxidation of Rh(111) surfaces with two types of straight steps, having {100} and {111} microfacets. The one-dimensional (1D) oxide initially formed at the steps acts as a barrier impeding formation of the 2D oxide on the (111) terrace behind it. We demonstrate that the details of the structure of the 1D oxide govern the rate of 2D oxidation and discuss implications for oxidation of nanoparticles.

Chemical reactivity of Ni-Rh nanowires

The properties of bimetallic Ni-Rh nanowires, fabricated by decorating the steps of vicinal Rh(111) surfaces by stripes of self-assembled Ni adatoms, have been probed by STM, photoemission, and ab initio density functional theory calculations. These Ni-Rh nanowires have specific electronic properties that lead to a significantly enhanced chemical reactivity towards oxygen. As a result, the Ni-Rh nanowires can be oxidized exclusively, generating novel quasi-one-dimensional oxide structures.

Unusual Process of Water Formation on RuO2(110) by Hydrogen Exposure at Room Temperature

The reduction mechanism of the RuO(2)(110) surface by molecular hydrogen exposure is unraveled to an unprecedented level by a combination of temperature programmed reaction, scanning tunneling microscopy, high-resolution core level shift spectroscopy, and density functional theory calculations. We demonstrate that even at room temperature hydrogen exposure to the RuO(2)(110) surface leads to the formation of water. In a two-step process, hydrogen saturates first the bridging oxygen atoms to form (O(br)-H) species and subsequently part of these O(br)-H groups move to the undercoordinated Ru atoms where they form adsorbed water. This latter process is driven by thermodynamics leaving vacancies in the bridging O rows.

Kinetics of the Reduction of the Rh(111) Surface Oxide: Linking Spectroscopy and Atomic-Scale Information

The reduction of the surface oxide on Rh(111) by H(2) was observed in situ by scanning tunneling microscopy (STM) and high-resolution core level spectroscopy (HRCLS). At room temperature, H(2) does not adsorb on the oxide, only in reduced areas. Reduction starts in very few sites, almost exclusively in stepped areas. One can also initiate the reduction process by deliberately creating defects with the STM tip allowing us to examine the reduction kinetics in detail. Depending on the size of the reduced area and the hydrogen pressure, two growth regimes were found. At low H(2) pressures or small reduced areas, the reduction rate is limited by hydrogen adsorption on the reduced area. For large reduced areas, the reduction rate is limited by the processes at the border of the reduced area. Since a near-random distribution of the reduction nuclei was found and the reduction process at defects starts at a random time, one can use Johnson-Mehl-Avrami-Kolmogoroff (JMAK) theory to describe the process of reduction. The microscopic data from STM agree well with spatially averaged data from HRCLS measurements.

Structure of Ag(111)-p(4 x 4)-O: no silver oxide

The structure of the oxygen-induced p(4 x 4) reconstruction of Ag(111) is determined by a combination of scanning tunneling microscopy, surface x-ray diffraction, core level spectroscopy, and density functional theory. We demonstrate that all previous models of this surface structure are incorrect and propose a new model which is able to explain all our experimental findings but has no resemblance to bulk silver oxide. We also shed some light on the limitations of current density functional theories and the potential role of van der Waals interactions in the stabilization of oxygen-induced surface reconstructions of noble metals.

One-dimensional PtO2 at Pt steps: formation and reaction with CO

Using core-level spectroscopy and density functional theory we show that a one-dimensional (1D) oxide structure forms at the steps of the Pt(332) surface after exposure. The 1D oxide is found to be stable in an oxygen pressure range, where bulk oxides are only metastable, and is therefore argued to be a precursor to the Pt oxidation. As an example of the consequences of such a precursor exclusively present at the steps, we investigate the reaction of CO with oxygen covered Pt(332). Albeit more strongly bound, the oxidic oxygen is found to react more easily with CO than oxygen chemisorbed on the Pt terraces.

Computational analysis of protein tyrosine phosphatases: practical guide to bioinformatics and data resources

The exponential growth of sequence data has become a challenge to database curators and end-users alike and biologists seeking to utilize the data effectively are faced with numerous analysis methods. Here, with practical examples from our bioinformatics analysis of the protein tyrosine phosphatases (PTPs), we show how computational analysis can be exploited to fuel hypothesis-driven experimental research through the exploration of online databases. We cover the following elements: (i) similarity searches and strategies to collect a non-redundant database of tyrosine-specific PTP domains; (ii) utilization of this database to classify human, fly, and worm PTPs (based on alignments and phylogenetic analysis); (iii) three-dimensional structural analysis to identify conserved regions (structure-function) and non-conserved selectivity-determining regions (substrate specificity); and (iv) genomic analysis, including mapping of exon structure, identification of pseudogenes, and exploration of disease databases. We discuss the importance of manual curation, illustrating examples in which pseudogenes give rise to predicted proteins in GenBank and note that domain servers, such as PFAM and SMART, erroneously include dual-specificity and lipid phosphatases in their collection of tyrosine-specific PTPs. To capitalize on our annotated set of 402 PTP domains (from 47 species and five phyla), we identify sequence conservation across taxonomic categories and explore structure-function relationships among tandem domain receptor-like PTPs. We define three Src homology 2 domain-containing PTP genes in stingray, zebrafish, and fugu and speculate on their evolutionary relationship with human pseudogenes. Our annotated sequences, along with a web service for phylogenetic classification of PTP domains, are available online (http://ptp.cshl.edu and http://science.novonordisk.com/ptp).

A surface x-ray study of the structure and morphology of the oxidized Pd(001) surface

The oxidation of Pd(100) and the formation of PdO was studied in situ using surface x-ray diffraction. A bulklike, epitaxial PdO film is formed at oxygen partial pressures beyond 1 mbar and sample temperatures exceeding 650 K. The main orientation is PdO(001)/Pd(001), based upon bulk reflections from the PdO film. By comparing with measurements from the Pd crystal truncation rods, we estimate an rms surface roughness of 6 A, in good agreement with previous high pressure scanning tunneling microscopy measurements. Finally, we observed the transformation from the (radical5 x radical5) surface oxide to PdO bulk oxide at 675 K and 50 mbar O(2) pressure.

High-coverage oxygen structures on Rh111: adsorbate repulsion and site preference is not enough

A new O induced structure on Rh(111) displaying a (2 sqaureroot[3] x 2sqaureroot[3])R30 degrees periodicity with an oxygen coverage of 2/3 has been studied by high resolution core level spectroscopy, scanning tunneling microscopy, and density functional theory. Although O favors fcc hollow sites in all other known phases, it occupies both fcc and hcp sites in this structure, which cannot be explained by pairwise adsorbate repulsion only. Both the (2sqaureroot[3] x 2sqaureroot[3])R30 degrees and (2 x 2)-3O structures also exemplify that density-of-states contrast can lead to oxygen adatoms appearing as protrusions in scanning tunneling microscopy images.

Self-limited growth of a thin oxide layer on Rh(111)

The oxidation of the Rh(111) surface at oxygen pressures from 10(-10) mbar to 0.5 bar and temperatures between 300 and 900 K has been studied on the atomic scale using a multimethod approach of experimental and theoretical techniques. Oxidation starts at the steps, resulting in a trilayer O-Rh-O surface oxide which, although not thermodynamically stable, prevents further oxidation at intermediate pressures. A thick corundum like Rh2O3 bulk oxide is formed only at significantly higher pressures and temperatures.

A genomic perspective on protein tyrosine phosphatases: gene structure, pseudogenes, and genetic disease linkage

The protein tyrosine phosphatases (PTPs) are now recognized as critical regulators of signal transduction under normal and pathophysiological conditions. In this analysis we have explored the sequence of the human genome to define the composition of the PTP family. Using public and proprietary sequence databases, we discovered one novel human PTP gene and defined chromosomal loci and exon structure of the additional 37 genes encoding known PTP transcripts. Direct orthologs were present in the mouse genome for all 38 human PTP genes. In addition, we identified 12 PTP pseudogenes unique to humans that have probably contaminated previous bioinformatics analysis of this gene family. PCR amplification and transcript sequencing indicate that some PTP pseudogenes are expressed, but their function (if any) is unknown. Furthermore, we analyzed the enhanced diversity generated by alternative splicing and provide predicted amino acid sequences for four human PTPs that are currently defined by fragments only. Finally, we correlated each PTP locus with genetic disease markers and identified 4 PTPs that map to known susceptibility loci for type 2 diabetes and 19 PTPs that map to regions frequently deleted in human cancers. We have made our analysis available at http://ptp.cshl.edu or http://science.novonordisk.com/ptp and we hope this resource will facilitate the functional characterization of these key enzymes.

Kinetic hindrance during the initial oxidation of Pd(100) at ambient pressures

The oxidation of the Pd(100) surface at oxygen pressures in the 10(-6) to 10(3) mbar range and temperatures up to 1000 K has been studied in situ by surface x-ray diffraction (SXRD). The results provide direct structural information on the phases present in the surface region and on the kinetics of the oxide formation. Depending on the (T,p) environmental conditions, we observe either a thin (sqrt[5]xsqrt[5])R27 degrees surface oxide or the growth of a rough, poorly ordered bulk oxide film of PdO predominantly with (001) orientation. By either comparison to the surface phase diagram from first-principles atomistic thermodynamics or by explicit time-resolved measurements we identify a strong kinetic hindrance to the bulk oxide formation even at temperatures as high as 675 K.

Cellular effects of small molecule PTP1B inhibitors on insulin signaling

Protein tyrosine phosphatase 1B (PTP1B) is implicated as a negative regulator of insulin receptor (IR) signaling and a potential drug target for the treatment of type 2 diabetes and other associated metabolic syndromes. To further define the role of PTP1B in insulin signaling and to test the hypothesis that blocking the activity of PTP1B would augment the action of insulin, we prepared several cell permeable, potent and selective, small molecule PTP1B inhibitors, and evaluated their biological effects in several insulin sensitive cell lines. Our data indicate that PTP1B inhibitors bind to and colocalize with PTP1B on the surface of the endoplasmic reticulum and PTP1B exerts its negative effect on insulin signaling upstream of phosphatidylinositol 3-kinase and MEK1. Treatment of cells with PTP1B inhibitors, both in the presence and in the absence of insulin, markedly enhances IRbeta and IRS-1 phosphorylation, Akt and ERK1/2 activation, Glut4 translocation, glucose uptake, and Elk1 transcriptional activation and cell proliferation. These results indicate that small molecule inhibitors targeted to PTP1B can act as both insulin mimetics and insulin sensitizers. Taken together, our findings combined with results from PTP1B knockout, antisense, and biochemical studies provide strong evidence that PTP1B negatively regulates insulin signaling and that small molecule PTP1B inhibitors have the ability to potentiate and augment the action of insulin.

Identification of step atoms by high resolution core level spectroscopy

Vicinal Rh(111) surfaces are studied with high resolution core level photoemission. We demonstrate the possibility to distinguish between the different kinds of surface atoms on these surfaces by virtue of their 3d core level binding energies. In particular, the low coordinated step atoms are found to exhibit a clear fingerprint in Rh 3d spectra. We demonstrate how this may be used to show that initial oxygen adsorption occurs on the steps and not on the terraces of the vicinal surfaces.

Redox regulation of protein tyrosine phosphatase 1B involves a sulphenyl-amide intermediate

The second messenger hydrogen peroxide is required for optimal activation of numerous signal transduction pathways, particularly those mediated by protein tyrosine kinases. One mechanism by which hydrogen peroxide regulates cellular processes is the transient inhibition of protein tyrosine phosphatases through the reversible oxidization of their catalytic cysteine, which suppresses protein dephosphorylation. Here we describe a structural analysis of the redox-dependent regulation of protein tyrosine phosphatase 1B (PTP1B), which is reversibly inhibited by oxidation after cells are stimulated with insulin and epidermal growth factor. The sulphenic acid intermediate produced in response to PTP1B oxidation is rapidly converted into a previously unknown sulphenyl-amide species, in which the sulphur atom of the catalytic cysteine is covalently linked to the main chain nitrogen of an adjacent residue. Oxidation of PTP1B to the sulphenyl-amide form is accompanied by large conformational changes in the catalytic site that inhibit substrate binding. We propose that this unusual protein modification both protects the active-site cysteine residue of PTP1B from irreversible oxidation to sulphonic acid and permits redox regulation of the enzyme by promoting its reversible reduction by thiols.

Enzyme kinetic characterization of protein tyrosine phosphatases

Protein tyrosine phosphatases (PTPs) play a central role in cellular signaling processes, resulting in an increased interest in modulating the activities of PTPs. We therefore decided to undertake a detailed enzyme kinetic evaluation of various transmembrane and cytosolic PTPs (PTPalpha, PTPbeta, PTPepsilon, CD45, LAR, PTP1B and SHP-1), using pNPP as substrate. Most noticeable is the increase in the turnover number for PTPbeta with increasing pH and the weak pH-dependence of the turnover number of CD45. The kinetic data for PTPalpha-D1 and PTPalpha-D1D2 suggest that D2 affects the catalysis of pNPP. PTPepsilon and the closely homologous PTPalpha behave differently. The K(m) data were lower for PTPepsilon than those for PTPalpha, while the inverse was observed for the catalytic efficiencies.

Two-dimensional oxide on Pd(111)

The oxidation of Pd(111) leads to an incommensurate surface oxide, which was studied by the use of scanning tunneling microscopy, surface x-ray diffraction, high resolution core level spectroscopy, and density functional calculations. A combination of these methods reveals a two-dimensional structure having no resemblance to bulk oxides of Pd. Our study also demonstrates how the atomic arrangement of a nontrivial incommensurate surface can be solved by molecular dynamics in a case where experimental techniques alone give no solution.

Geometry of the valence transition induced surface reconstruction of Sm(0001)

We present a structural determination of the surface reconstruction of the Sm(0001) surface using surface x-ray diffraction, scanning tunneling microscopy, and ab initio calculations. The reconstruction is associated with a large (22%) expansion of the atomic radius for the top monolayer surface Sm atoms. The mechanism driving the surface reconstruction in Sm is unique among all elements and is connected to the strong correlations of the 4f electrons in Sm and the intermediate valence observed in certain Sm compounds. The atoms constituting the top monolayer of Sm(0001) have vastly different chemical properties compared to the layer underneath and behave as if they were an adsorbate of a different chemical species.

TYK2 and JAK2 are substrates of protein-tyrosine phosphatase 1B

The reversible tyrosine phosphorylation of proteins, modulated by the coordinated actions of protein-tyrosine kinases and protein-tyrosine phosphatases (PTPs), regulates the cellular response to a wide variety of stimuli. It is established that protein kinases possess discrete sets of substrates and that substrate recognition is often dictated by the presence of consensus phosphorylation sites. Here, we have extended this concept to the PTPs and demonstrated that (E/D)-pY-pY-(R/K) is a consensus substrate recognition motif for PTP1B. We have shown that JAK2 and TYK2 are substrates of PTP1B and that the substrate recognition site within theses kinases is similar to the site of dephosphorylation previously identified within the insulin receptor. A substrate-trapping mutant of PTP1B formed a stable interaction with JAK2 and TYK2 in response to interferon stimulation. Expression of wild type or substrate-trapping mutant PTP1B inhibited interferon-dependent transcriptional activation. Finally, mouse embryo fibroblasts deficient in PTP1B displayed subtle changes in tyrosine phosphorylation, including hyperphosphorylation of JAK2. The closely related JAK family member, JAK1, which does not match the consensus dephosphorylation site, was not recognized as a substrate. These data illustrate that PTP1B may be an important physiological regulator of cytokine signaling and that it may be possible to derive consensus substrate recognition motifs for other members of the PTP family, which may then be used to predict novel physiological substrates.