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Barsanti P.A.,Novartis | Barsanti P.A.,Nurix Inc | Aversa R.J.,Novartis | Jin X.,Novartis | And 13 more authors.
ACS Medicinal Chemistry Letters | Year: 2015

A saturation strategy focused on improving the selectivity and physicochemical properties of ATR inhibitor HTS hit 1 led to a novel series of highly potent and selective tetrahydropyrazolo[1,5-a]pyrazines. Use of PI3Kα mutants as ATR crystal structure surrogates was instrumental in providing cocrystal structures to guide the medicinal chemistry designs. Detailed DMPK studies involving cyanide and GSH as trapping agents during microsomal incubations, in addition to deuterium-labeled compounds as mechanistic probes uncovered the molecular basis for the observed CYP3A4 TDI in the series. (Chemical Equation Presented). © 2014 American Chemical Society.

Lebel P.,Stanford University | Basu A.,Stanford University | Basu A.,Howard Hughes Medical Institute | Oberstrass F.C.,Stanford University | And 3 more authors.
Nature Methods | Year: 2014

Single-molecule measurements of DNA twist and extension have been used to reveal physical properties of the double helix and to characterize structural dynamics and mechanochemistry in nucleoprotein complexes. However, the spatiotemporal resolution of twist measurements has been limited by the use of angular probes with high rotational drag, which prevents detection of short-lived intermediates or small angular steps. We introduce gold rotor bead tracking (AuRBT), which yields >100× improvement in time resolution over previous techniques. AuRBT employs gold nanoparticles as bright low-drag rotational and extensional probes, which are monitored by instrumentation that combines magnetic tweezers with objective-side evanescent darkfield microscopy. Our analysis of high-speed structural dynamics of DNA gyrase using AuRBT revealed an unanticipated transient intermediate. AuRBT also enables direct measurements of DNA torque with >50× shorter integration times than previous techniques; we demonstrated high-resolution torque spectroscopy by mapping the conformational landscape of a Z-forming DNA sequence. © 2014 Nature America, Inc. All rights reserved.

He X.,Takeda Cambridge | Riceberg J.,Takeda Cambridge | Pulukuri S.M.,Takeda Cambridge | Grossman S.,Takeda Cambridge | And 6 more authors.
PLoS ONE | Year: 2015

SUMOylation is a post-translational ubiquitin-like protein modification pathway that regulates important cellular processes including chromosome structure, kinetochore function, chromosome segregation, nuclear and sub-nuclear organization, transcription and DNA damage repair. There is increasing evidence that the SUMO pathway is dysregulated in cancer, raising the possibility that modulation of this pathway may have therapeutic potential. To investigate the importance of the SUMO pathway in the context of cancer cell proliferation and tumor growth, we applied lentivirus-based short hairpin RNAs (shRNA) to knockdown SUMO pathway genes in human cancer cells. shRNAs for SAE2 and UBC9 reduced SUMO conjugation activity and inhibited proliferation of human cancer cells. To expand upon these observations, we generated doxycycline inducible conditional shRNA cell lines for SAE2 to achieve acute and reversible SAE2 knockdown. Conditional SAE2 knockdown in U2OS and HCT116 cells slowed cell growth in vitro, and SAE2 knockdown induced multiple terminal outcomes including apoptosis, endoreduplication and senescence. Multinucleated cells became senescent and stained positive for the senescence marker, SA-βGal, and displayed elevated levels of p53 and p21. In an attempt to explain these phenotypes, we confirmed that loss of SUMO pathway activity leads to a loss of SUMOylated Topoisomerase IIα and the appearance of chromatin bridges which can impair proper cytokinesis and lead to multinucleation. Furthermore, knockdown of SAE2 induces disruption of PML nuclear bodies which may further promote apoptosis or senescence. In an in vivo HCT116 xenograft tumor model, conditional SAE2 knockdown strongly impaired tumor growth. These data demonstrate that the SUMO pathway is required for cancer cell proliferation in vitro and tumor growth in vivo, implicating the SUMO pathway as a potential cancer therapeutic target. © 2015 He et al.

Taherbhoy A.M.,Genentech | Taherbhoy A.M.,Nurix Inc | Huang O.W.,Genentech | Cochran A.G.,Genentech
Nature Communications | Year: 2015

Polycomb repressive complex 1 (PRC1) is required for ubiquitination of histone H2A lysine 119, an epigenetic mark associated with repression of genes important in developmental regulation. The E3 ligase activity of PRC1 resides in the RING1A/B subunit when paired with one of six PCGF partners. The best known of these is the oncogene BMI1/PCGF4. We find that canonical PRC1 E3 ligases such as PCGF4-RING1B have intrinsically very low enzymatic activity compared with non-canonical PRC1 RING dimers. The structure of a high-activity variant in complex with E2 (PCGF5-RING1B-UbcH5c) reveals only subtle differences from an earlier PCGF4 complex structure. However, two charged residues present in the modelled interface with E2-conjugated ubiquitin prove critical: in BMI1/PCGF4, these residues form a salt bridge that may limit efficient ubiquitin transfer. The intrinsically low activity of the PCGF4-RING1B heterodimer is offset by a relatively favourable interaction with nucleosome substrates, resulting in an efficient site-specific monoubiquitination. © 2015 Macmillan Publishers Limited. All rights reserved.

Agency: Department of Health and Human Services | Branch: | Program: SBIR | Phase: Phase I | Award Amount: 300.00K | Year: 2013

DESCRIPTION (provided by applicant): ZAP-70 is a cytoplasmic protein tyrosine kinase that plays a critical function in T cell antigen receptor (TCR) signaling and in most aspects of T cell biology. ZAP-70 is an attractive therapeutic target for treatment of prevalent human T-cell dependent autoimmune diseases (e.g. rheumatoid arthritis, lupus, multiple sclerosis, psoriasis) and in allogenic transplantation. Considerable effort has previously been expended to develop specific ZAP-70 catalytic site inhibitors, without success, likely due to specific structural attributes of the kinase catalytic domain. Following TCR stimulation, the ZAP-70 tandem SH2 domains associate with dual tyrosine phosphorylated residues located within conserved sequence motifs (referredto as ITAMs) of the cytoplasmic domains of the CD3 and zeta chains of the TCR. Mutagenesis and structural studies on full-length ZAP-70 have shown that, prior to association with the ITAMs, ZAP-70 exists in an autoinhibited conformation in which the tandem SH2 domains stabilize an inactive conformation of the kinase domain. This proposal is built on the effort of the Kuriyan and Weiss labs in an NIAMS-funded 2009 ARRA Grand Opportunity grant to identify small molecules that stabilize the autoinhibitedconformation of ZAP-70 and serve as allosteric inhibitors of the kinase. That successful research program led to development of a series of specific biochemical tools for identifying prototypical allosteric inhibitors of ZAP-70, and is poised to enable a dedicated new drug discovery effort in T cell regulation. In this current proposal, Nurix Inc., an emerging biopharmaceutical company founded by John Kuriyan, Art Weiss and Michael Rape, aims to extend this earlier work by optimizing the potency of allosteric inhibitors of ZAP-70 that could serve as a leads for clinical development of a new T-cell specific immunosuppressant. The program will (i) seek insight into the mode of interaction of these small molecule inhibitors with ZAP-70 using crystallographic and other biophysical techniques to facilitate lead optimization, and (ii) examine the activity of allosteric inhibitor compounds in established models of T cell function. PUBLIC HEALTH RELEVANCE PUBLIC HEALTH RELEVANCE: ZAP-70, an enzyme involved inintracellular signaling, plays a critical role within T cells and is an attractive therapeutic target for treatment of common human autoimmune diseases (e.g. rheumatoid arthritis, lupus, multiple sclerosis, psoriasis) and for controlling organ rejection intransplantation. This program is aimed at finding potent blockers of ZAP-70 that could serve as a leads for clinical development of a new T-cell specific immunosuppressant with broad therapeutic potential.

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