bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 2224: Re-engineering of the duocarmycin structural architecture enables tumour-selective CYP2W1-mediated drug activation in human colon cancer xenografts.
Authors: Pors Klaus , Travica Sandra , Loadman Paul M. , Shnyder Steven D. , Sutherland Mark , Sheldrake Helen M. , Searcey Mark , Johansson Inger , Mkrtchian Souren , IngelmanSundberg Magnus , Patterson Laurence H. 
Published: August 2014

Abstract
There is now growing evidence that CYP1A1, 1B1, 2J2, 2S1 and 2W1 are over-expressed in many human tumour types. The ultrapotent duocarmycins are ideal candidates for bioprecursor drug development and we have demonstrated that these can be re-engineered into derivatives selectively activated by CYP1A1 in vitro and in vivo.1,2 In the present study, we have focussed on CYP2W1 as a potential therapeutic target. CYP2W1 is detected in 30% of colon cancers, while its protein expression in non-transformed adult tissues is absent or insignificant.3 We have presented results indicating that the immunohistochemically assessed level of CYP2W1 enzyme could fulfil the criteria for being a prognostic biomarker for stages II and III colorectal cancer.4 Here we present data on furanoindole-based duocarmycins that have the potential to be used as a chemical probe (e.g. ICT2726) to show CYP2W1 functional activity. We also report on indoline-based analogues that elicit potent antiproliferative activity after CYP2W1-mediated activation in cancer cells. Specifically, we have transfected human HEK293, Colo320 and SW480 cells to express CYP2W1 and shown that these suffer rapid loss of viability following treatment with two halogenated duocarmycin bioprecursor compounds (ICT2705 and ICT2706) while no activity in mock-transfected cells was seen. Significantly, ICT2706 was shown to totally prevent tumour growth when administered to SCID mice bearing SW480-2W1 xenografts (dosed daily with 100 mg/kg for 8 days) but not the mock-transfected variant. Subsequent to this treatment, the tumours were extracted for further analysis. Using H2A.X phosphorylation as a marker for DNA damage, our data revealed a time-dependent increase in expression supporting CYP2W1-mediated activation of ICT2706 in vivo. Our findings reveal the opportunities in targeting CYP2W1 as a novel therapeutic approach in colon cancer chemotherapy.
Citation Format: Klaus Pors, Sandra Travica, Paul M. Loadman, Steven D. Shnyder, Mark Sutherland, Helen M. Sheldrake, Mark Searcey, Inger Johansson, Souren Mkrtchian, Magnus IngelmanSundberg, Laurence H. Patterson. Re-engineering of the duocarmycin structural architecture enables tumour-selective CYP2W1-mediated drug activation in human colon cancer xenografts. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2224. doi:10.1158/1538-7445.AM2013-2224
Abstract 2225: The molecular architecture of p85α as determined by SAXS and chemical cross-linking.
Authors: Brower Evan T. , Gabelli Sandra B. , Wang Qing , Chaerkady Raghothama , Berndsen Christopher E. , Cole Robert N. , Backer Jonathan M. , Schäfer Mathias , Sinz Andrea , Kinzler Kenneth W. , Vogelstein Bert , Amzel L. Mario 
Published: August 2014

Abstract
The p85α protein, encoded by PIK3R1, is the regulatory subunit of phosphatidylinositol 3-kinase alpha (PI3Kα). The role of p85α extends to regulation of PTEN-phosphatase activity, the unfolded protein response, and additional cellular pathways. PIK3R1 was recently identified as frequently mutated in glioblastomas and endometrial cancers. Small-angle X-ray scattering (SAXS) and chemical cross-linking were used to complete the first investigation of the shape and molecular organization of full length p85α. p85α is elongated in shape and exists in a conformation conducive to p110α binding. The p85α structural data was utilized to generate the first model of the full length PI3K complex. Cancer associated PIK3R1 mutations are localized to interfaces between p85α domains, and in the context of the PI3K complex, are clustered at regions comprising the interface of the catalytic and regulatory subunits. A potential interface was discovered between the RhoGAP domain of p85α and the p110α kinase domain. GTPases may enhance PI3K activity by binding to the RhoGAP domain, thereby attenuating the interaction between the RhoGAP and the kinase domain. These data provide the structural groundwork required for a better understanding of the regulatory mechanisms mediated by p85, and may facilitate the development of future drugs targeting the PI3K pathway.
Citation Format: Evan T. Brower, Sandra B. Gabelli, Qing Wang, Raghothama Chaerkady, Christopher E. Berndsen, Robert N. Cole, Jonathan M. Backer, Mathias Schäfer, Andrea Sinz, Kenneth W. Kinzler, Bert Vogelstein, L. Mario Amzel. The molecular architecture of p85α as determined by SAXS and chemical cross-linking. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2225. doi:10.1158/1538-7445.AM2013-2225
Abstract 2227: Aptamer selection for cancer markers: High-throughput, quantitative selection and characterization of nucleic acid aptamers for human angiopoietin-2.
Authors: Cho Minseon , Oh Seung Soo , Nie Jeff , Stewart Ron , Eisenstein Michael , Chambers James , Marth Jamey D. , Thomson James A. , Soh Tom H. 
Published: August 2014

Abstract
Abstract
Nucleic acid-based aptamers represent a promising class of affinity reagents, as they can be chemically synthesized and modified, undergo reversible folding and exhibit excellent stability. Thus, the identification of aptamers that bind to specific cancer markers may serve as a powerful tool for early diagnosis and treatments of cancers. Unfortunately, conventional methods of aptamer generation remain inherently low-throughput in nature, and there is a pressing need for alternative technologies that can generate high quality aptamers in a high-throughput and economical manner.
Towards the goal of accelerating aptamer discovery, we have developed the Quantitative Parallel Aptamer Selection System (QPASS) - an integrated platform that combines microfluidic selection, next-generation sequencing and in situ-synthesized aptamer arrays for parallel binding measurements. As a model, we used QPASS to select aptamers that specifically bind to human angiopoietin-2, an important mediator of angiogenesis and a biomarker of colon, prostate and breast cancers; after microfluidic selection and sequencing, we fabricated a custom aptamer array containing 120,000 sequences representing the most enriched aptamer candidates. Using this array, we simultaneously obtained equilibrium dissociation constants (Kd) and binding specificity data for these candidate aptamers in a massively parallel manner. Furthermore, we show that our array can operate directly in undiluted serum, enabling rapid identification of aptamers that perform optimally in complex mixtures. By exploiting the scalability and commercial availability of high-throughput sequencing and nucleic acid arrays, the QPASS platform offers the capability to simultaneously analyze and characterize unprecedented numbers of aptamer candidates—either against a common cancer marker, or for screening in parallel against multiple different biomarkers.
Citation Format: Minseon Cho, Seung Soo Oh, Jeff Nie, Ron Stewart, Michael Eisenstein, James Chambers, Jamey D. Marth, James A. Thomson, Tom H. Soh. Aptamer selection for cancer markers: High-throughput, quantitative selection and characterization of nucleic acid aptamers for human angiopoietin-2. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2227. doi:10.1158/1538-7445.AM2013-2227
Abstract 2228: Phosphatidylinositol-4-kinase - Potent and selective inhibitors of PI4Kα and PI4Kβ.
Authors: Waring Michael J. , Cross Darren , Andrews David , Flemington Vikki , Lenaghan Carol , McKelvie Jennifer , Maman Sarita , Raubo Piotr , Robb Graeme , Smith James , Swarbrick Martin 
Published: August 2014

Abstract
Phosphatidylinositol (PI) is a phospholipid that resides primarily on the cytosolic surface of cell membranes. PI can be phosphorylated to generate seven different phosphatidylinositol phosphates (PIPs), all of which have distinct biological activities.1 A major first step in the production of these PIPs is the conversion of PI into phosphatidylinositol-4-phosphate (PI4P) by PI4 kinase.2
Here we describe the identification of inhibitors of PI4 kinase via targeted screening of a kinase subset. This exercise has delivered inhibitors that are potent inhibitors of PI4 kinase (pIC50 &gt;8), which are selective the α- or the β-subtypes and do not inhibit related enzymes on the PI pathway (PI3 kinase pIC50 &lt;5 or PIP5 kinase pIC50 &lt;4) and also exhibit good broader kinase selectivity.
The effect of these useful probe compounds on cellular phosphatidylinositol-4,5-diphosphate and subsequent downstream markers will be described along with the comparison of these effects with the corresponding siRNA.
1. G. Di Paolo, P. De Camilli, Phosphoinositides in cell regulation and membrane dynamics. Nature 2006, 443, 651-657.2. T. Sasaki, S. Takasuga, J. Sasaki, S. Kofuji, S. Eguchi, M. Yamazaki, A. Suzuki, Mammalian phosphoinositide kinases and phosphatases. Progress in lipid research, 2009, 48, 307-343.
Citation Format: Michael J. Waring, Darren Cross, David Andrews, Vikki Flemington, Carol Lenaghan, Jennifer McKelvie, Sarita Maman, Piotr Raubo, Graeme Robb, James Smith, Martin Swarbrick. Phosphatidylinositol-4-kinase - Potent and selective inhibitors of PI4Kα and PI4Kβ. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2228. doi:10.1158/1538-7445.AM2013-2228
Abstract 223: Targeting PDK-1 and EGFR by human umbilical cord blood stem cells reverses Warburg effect in glioblastoma multiforme.
Authors: Velpula Kiran Kumar , Bhasin Arnima , Dasari Venkata Ramesh , Asuthkar Swapna , Dinh Dzung H. , Rao Jasti S. , Tsung Andrew J. 
Published: August 2014

Abstract
Glioblastoma multiforme (GBM) is the most aggressive and incurable brain tumor in adults. The overexpression of epidermal growth factor receptor (EGFR) in GBM is identified as typical oncogenic signature. Due to the functional diversity of proteins that are phosphorylated or complexed with EGFR, it unsurprising that EGFR is involved in multiple interconnected signaling pathways. In GBM, hypoxia drives aggression and malignancy through glycolysis as opposed to oxidation of pyruvate in the mitochondria. This phenomenon, termed the Warburg effect, has a prominent role in oncogenesis. In the present study, we show that hypoxia induces pyruvate dehydrogenase kinase 1 (PDK-1) expression, which in turn increases the expression of EGFR and hypoxia inducing factor 1 alpha (HIF-1α) in cell lines derived from human GBM. PDK-1 is a HIF-1-regulated gene, and our data suggested that hypoxia-induced PDK-1 expression may promote EGFR activation, thus sustaining a feed-forward loop for malignant progression. PDK-1 and EGFR knockdown, using respective shRNAs or human umbilical cord blood stem cells (hUCBSC), lowers PDK-1-EGFR phosphorylation and decreases HIF-1α expression, which reverts the Warburg phenotype of GBM leading to inhibition of tumor- growth and invasion. Clinically, expression of PDK1, EGFR, and HIF-1α were elevated in GBM specimens when compared to normal brain tissues. Collectively, our studies indicate PDK-1 as a key mediator of tumor growth in GBM and that targeting PDK-1 and its associated molecules such as HIF-1α and EGFR may prove promising for inhibition of the Warburg effect in human GBMs.
Citation Format: Kiran Kumar Velpula, Arnima Bhasin, Venkata Ramesh Dasari, Swapna Asuthkar, Dzung H. Dinh, Jasti S. Rao, Andrew J. Tsung. Targeting PDK-1 and EGFR by human umbilical cord blood stem cells reverses Warburg effect in glioblastoma multiforme. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 223. doi:10.1158/1538-7445.AM2013-223
Abstract 2231: Development of bifunctional cross-linking agents to identify intermediate proteasomes.
Authors: Carmony Kimberly C. , Sharma Lalit Kumar , Kim Kyung-Bo 
Published: August 2014

Abstract
Introduction: This research was conducted to develop bifunctional cross-linking agents that can be used to identify intermediate proteasomes. Two well-characterized proteasome subtypes, the constitutive proteasome and immunoproteasome, differ with respect to their distinct sets of catalytic subunits. Additionally, intermediate proteasome subtypes comprised of non-standard mixtures of catalytic subunits have more recently been discovered. These intermediate proteasomes differ from constitutive and immunoproteasomes in their proteolytic activity profiles, suggesting that they have unique cellular functions. In agreement with this, intermediate proteasomes in cancer cell lines were shown to play important roles in the production of several tumor antigens. However, largely due to limitations of methods currently available to distinguish between subtypes, the detailed functions of intermediate proteasomes remain poorly defined. Bifunctional agents capable of cross-linking two different catalytic subunits within a single proteasome complex will facilitate a simple approach to identify distinct proteasome subtypes present within cells. These compounds will serve as important chemical probes for investigating the functions of individual proteasome subtypes in cancer cells.
Experimental Procedures: Bifunctional cross-linking agents were synthesized by coupling two broad-spectrum or subunit-selective proteasome inhibitors through hydrocarbon or polyethylene glycol linkers. Positions for derivatization of these inhibitors were selected based on computational modeling, and linker lengths were varied to increase cross-linking efficiency. The ability of the resulting compounds to cross-link two proteasome catalytic subunits in cancer cell lysates was assessed via western blotting. Competition assays with subunit-selective proteasome inhibitors were conducted to verify the identities of the cross-linked subunit pairs.
Data Summary: The structures of the bifunctional cross-linking agents were confirmed by mass spectrometry and nuclear magnetic resonance spectroscopy. Western blotting results revealed the ability of several of these bifunctional agents to cross-link two catalytic subunits within individual proteasome complexes, facilitating compositional analysis of distinct proteasome subtypes.
Conclusions: We have successfully developed bifunctional agents capable of cross-linking two catalytic subunits within individual proteasome complexes. These compounds will be utilized in functional studies of intermediate proteasomes present within cancer cells.
Citation Format: Kimberly C. Carmony, Lalit Kumar Sharma, Kyung-Bo Kim. Development of bifunctional cross-linking agents to identify intermediate proteasomes. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2231. doi:10.1158/1538-7445.AM2013-2231
Abstract 2232: Computational modeling reveals druggable cavities at the MKK3 and p38 protein interaction interface.
Authors: Ivanov Andrei A. , Nim Satra , Du Yuhong , Fu Haian 
Published: August 2014

Abstract
Mitogen-activated protein kinase (MAPK) cascades play vital roles in transmitting regulatory signals that control diverse physiological processes. Among them, MAPK p38 is critical for immune response, cell survival, and differentiation. The importance of the MKK3-p38 pathway in the development of cancer, asthma, inflammatory and other diseases is well-established. Accordingly, many inhibitors of p38 have been developed, some of which have entered clinical trials. Our research indicates that the MKK3-p38 interaction, upstream of p38 itself, forms a critical node in a network of protein-protein interactions (PPI) important for cell growth. Thus, pathway blockers that target the MKK3-p38 PPI interface may have therapeutic potential beyond p38 kinase inhibitors. To discover MKK3-p38 PPI inhibitors, we took an experimentally-based computational approach, which led to the identification of a PPI interface and molecular tools for therapeutic interrogation. Our biological studies revealed a short inhibitory peptide located at the N-terminus of p38, which effectively disrupts the MKK3-p38 interaction in vitro and in vivo via its binding to MKK3. In this study, the structural organization of MKK3-p38 complex and the molecular mechanisms of peptide binding were investigated with computational modeling methods. We constructed the first model of MKK3, its complex with MAPK p38, and binding of the short inhibitory peptide to the MKK3 surface. Using this model, we have proposed several potentially druggable cavities on the molecular surfaces of both the MKK3 and p38 kinases. We found that the p38 N-terminal peptide can occupy the same cavity on the MKK3 surface as the p38 phosphorylation loop. Further, we have proposed the peptide residues playing the most important role in MKK3 binding. Overall, our data provide a basis for the rational design and screening for small molecule inhibitors of the MKK3-p38 interaction as regulators of the p38 signaling pathway.
Citation Format: Andrei A. Ivanov, Satra Nim, Yuhong Du, Haian Fu. Computational modeling reveals druggable cavities at the MKK3 and p38 protein interaction interface. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2232. doi:10.1158/1538-7445.AM2013-2232
Abstract 2234: Catechol suppresses EGF-induced cell transformation by inhibiting ERK2 activity as confirmed by a crystallographic study.
Authors: Lim Do Young , Malakhova Margarita , Kurinov Igor , Shin Seung Ho , Lee Mee-Hyun , Bode Ann M. , Dong Zigang 
Published: August 2014

Abstract
Catechol (pyrocathechol, 1,2-dihydroxybenzene) is a chemical that is used by industry in the manufacture of certain products. It also occurs naturally in many fruits such as apple, apricot, grape, bananas, pear, plum, mango, avocado, potato, and mushrooms. Browning of fruit occurs because of a chemical reaction between catechol and oxygen. Even though, catechol has toxicity at a high dose as shown by an in vivo study, the Environmental Protection Agency has not classified catechol with respect to potential carcinogenicity. Whether a lower concentration (&lt; 40 μM) of catechol treatment has effects on carcinogenesis is not known. We found that catechol binds to ERK2 and inhibits its activity. The extracellular signal-regulated kinases (ERKs) belong to the mitogen-activated protein (MAP) kinase family, and regulate important biological processes such as cell growth, proliferation, differentiation, and transcription regulation. ERK2 is activated in response of UV, cytokines and growth factors, such as epidermal growth factor (EGF) and insulin-like growth factor. Constitutive activation of ERK2 is observed in many human cancers such as colon, breast, lung and skin cancers. In this study we present the co-crystal structure of ERK2 bound with catechol in the ATP-active site. The conserved amino acid residues within the hinge region that are involved in the interaction of ERK and its inhibitors make the contacts with catechol. Contacts include side chain of Q105, and the main chains of the D106 and M108 residues. We found that catechol inhibits ERK2 in vitro kinase activity more than two-fold at a 20 μM concentration. This was confirmed by the observed decrease of the phosphorylation of Elk1, a specific downstream target of ERK2. In addition, 20 μM catechol inhibited EGF-induced JB6 cell transformation. Interestingly, JB6 cell proliferation was not affected at 20 μM concentration. Taken together, the results showed that catechol inhibits EGF-induced cell transformation without any toxicity through the inhibition of ERK2 activity.
Citation Format: Do Young Lim, Margarita Malakhova, Igor Kurinov, Seung Ho Shin, Mee-Hyun Lee, Ann M. Bode, Zigang Dong. Catechol suppresses EGF-induced cell transformation by inhibiting ERK2 activity as confirmed by a crystallographic study. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2234. doi:10.1158/1538-7445.AM2013-2234
Abstract 2236: A selection strategy for the design of small proteins that can distinguish DNA repair intermediates.
Authors: Guerra Rachel M. , Langenborg Kristina M. , Gross Kayla M. , Sher Emily V. , Gilboy John W. , Plaskon Dylan , Rice Kevin P. 
Published: August 2014

Abstract
Recognition of DNA damage by repair proteins is crucial for genomic stability. Several repair enzymes recognize aberrant DNA structural features, including nicks, gaps, and abasic sites, in a sequence-independent DNA manner. Reported here is a strategy to model these protein-DNA interactions using small proteins. A phage-displayed library of approximately one hundred million distinct zinc fingers was engineered at the DNA level based on the DNA binding domain of the repair protein poly(ADP-ribose) polymerase. Eight codons, representing amino acid residues in ‘loop’ regions of the zinc finger structure, were randomized using an NNK codon scheme. The DNA cassette was cloned into a commercially obtained T7 phagemid vector. The resultant phage library was exposed to nicked DNA molecules, which were attached to magnetic beads via a biotin-streptavidin linkage. In four rounds of selection that featured negative selection against non-nicked DNA and streptavidin coated beads, viral retention on the affinity resin increased from a negligible quantity to 62%. DNA sequencing following the final round revealed near convergence to a single, 39-mer peptide. This selected peptide will be generated by bacterial expression and assayed for binding activity using multiple strategies. While phage display of sequence specific DNA binding proteins is well-precedented, selection of peptides that bind specific DNA structures has not been reported. Molecules discovered by this strategy will help illuminate the structure-function relationships of proteins that recognize distinct DNA structures and may lead to new anticancer approaches.
Citation Format: Rachel M. Guerra, Kristina M. Langenborg, Kayla M. Gross, Emily V. Sher, John W. Gilboy, Dylan Plaskon, Kevin P. Rice. A selection strategy for the design of small proteins that can distinguish DNA repair intermediates. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2236. doi:10.1158/1538-7445.AM2013-2236