LLY-507, a Cell-active,Potent, and Selective Inhibitor of Protein-lysine Methyltransferase SMYD2

SMYD2 is a lysine methyltransferase that catalyzes the monomethylation of several protein substrates including p53. SMYD2 is overexpressed in a significant percentage of esophageal squamous primary carcinomas, and that overexpression correlates with poor patient survival. However, the mechanism(s) by which SMYD2 promotes oncogenesis is not understood. A small molecule probe for SMYD2 would allow for the pharmacological dissection of this biology. In this report, we disclose LLY-507, a cell-active, potent small molecule inhibitor of SMYD2. LLY-507 is >100-fold selective for SMYD2 over a broad range of methyltransferase and non-methyltransferase targets. A 1.63-Å resolution crystal structure of SMYD2 in complex with LLY-507 shows the inhibitor binding in the substrate peptide binding pocket. LLY-507 is active in cells as measured by reduction of SMYD2-induced monomethylation of p53 Lys³⁷⁰ at submicromolar concentrations. We used LLY-507 to further test other potential roles of SMYD2. Mass spectrometry-based proteomics showed that cellular global histone methylation levels were not significantly affected by SMYD2 inhibition with LLY-507, and subcellular fractionation studies indicate that SMYD2 is primarily cytoplasmic, suggesting that SMYD2 targets a very small subset of histones at specific chromatin loci and/or non-histone substrates. Breast and liver cancers were identified through in silico data mining as tumor types that display amplification and/or overexpression of SMYD2. LLY-507 inhibited the proliferation of several esophageal, liver, and breast cancer cell lines in a dose-dependent manner. These findings suggest that LLY-507 serves as a valuable chemical probe to aid in the dissection of SMYD2 function in cancer and other biological processes.     

Atypical subtrochanteric femoral shaft fractures: role for mechanics and bone quality

Bisphosphonates are highly effective agents for reducing osteoporotic fractures in women and men, decreasing fracture incidence at the hip and spine up to 50%. In a small subset of patients, however, these agents have recently been associated with ''atypical femoral fractures'' (AFFs) in the subtrochanteric region or the diaphysis. These fractures have several atypical characteristics, including occurrence with minimal trauma; younger age than typical osteoporotic fractures; occurrence at cortical, rather than cancellous sites; early radiographic appearance similar to that of a stress fracture; transverse fracture pattern rather than the familiar spiral or transverse-oblique morphologies; initiation on the lateral cortex; and high risk of fracture on the contralateral side, at the same location as the initial fracture. Fracture is a mechanical phenomenon that occurs when the loads applied to a structure such as a long bone exceed its load-bearing capacity, either due to a single catastrophic overload (traumatic failure) or as a result of accumulated damage and crack propagation at sub-failure loads (fatigue failure). The association of AFFs with no or minimal trauma suggests a fatigue-based mechanism that depends on cortical cross-sectional geometry and tissue material properties. In the case of AFFs, bisphosphonate treatment may alter cortical tissue properties, as these agents are known to alter bone remodeling. This review discusses the use of bisphosphonates, their effects on bone remodeling, mechanics and tissue composition, their significance as an effective therapy for osteoporosis, and why these agents may increase fracture risk in a small population of patients.     

Histone recognition and large-scale structural analysis of the human bromodomain family

Bromodomains (BRDs) are protein interaction modules that specifically recognize ε-N-lysine acetylation motifs, a key event in the reading process of epigenetic marks. The 61 BRDs in the human genome cluster into eight families based on structure/sequence similarity. Here, we present 29 high-resolution crystal structures, covering all BRD families. Comprehensive crossfamily structural analysis identifies conserved and family-specific structural features that are necessary for specific acetylation-dependent substrate recognition. Screening of?more than 30 representative BRDs against systematic histone-peptide arrays identifies new BRD substrates and reveals a strong influence of flanking posttranslational modifications, such as acetylation and phosphorylation, suggesting that BRDs recognize combinations of marks rather than singly acetylated sequences. We further uncovered a structural mechanism for the simultaneous binding and recognition of diverse diacetyl-containing peptides by BRD4. These data provide a foundation for structure-based drug design of specific inhibitors for this emerging target family.     

The hypothetical protein Atu4866 from Agrobacterium tumefaciens adopts a streptavidin-like fold

Atu4866 is a 79-residue conserved hypothetical protein of unknown function from Agrobacterium tumefaciens. Protein sequence alignments show that it shares > or =60% sequence identity with 20 other hypothetical proteins of bacterial origin. However, the structures and functions of these proteins remain unknown so far. To gain insight into the function of this family of proteins, we have determined the structure of Atu4866 as a target of a structural genomics project using solution NMR spectroscopy. Our results reveal that Atu4866 adopts a streptavidin-like fold featuring a beta-barrel/sandwich formed by eight antiparallel beta-strands. Further structural analysis identified a continuous patch of conserved residues on the surface of Atu4866 that may constitute a potential ligand-binding site.     

The influence of temperature, photoperiod and plant type on the predation rate of Macrolophus pygmaeus on Myzus persicae

The effect of temperature and photoperiod on the rate of predation of nymphs and adults of the predator Macrolophus pygmaeus was studied using Myzus persicae prey feeding on egg-plant and pepper plants. The experiments were conducted at three photoperiods (16L:8D, 12L:12D and 8L:16D), three temperatures (20, 25 and 30 °C), and at 65% r.h. The rate of predation increased with temperature. Predation rate was affected by photoperiod on pepper but not on egg-plant. Females and fifth instar nymphs were the most voracious stages followed by third and fourth instar nymphs and males. First and second instar nymphs consumed far fewer aphids. Predation rate was higher on leaves of pepper than egg-plant, especially at 30 °C. Variation in the efficacy of this predator is discussed.     

Comparison of phosphorus deficiency indices during a spring phytoplankton bloom in a eutrophic reservoir

1. Phosphorus limitation was studied along the eutrophic, canyon-type ?ímov reservoir (Czech Republic) during a spring phytoplankton bloom. Concentration of soluble reactive phosphorus (SRP), C:P molar ratio in seston, extracellular alkaline phosphatase activity (APA), and P limitation (bioassay) were used as indices for phosphorus deficiency in the phytoplankton. 2. SRP, C:P, APA, and P limitation indicated a moderate P deficiency in the downstream, but not upper, part of the reservoir. 3. Significant correlations between these parameters were found in the downstream part. Chlorophyll a concentration correlated with APA and P limitation in the upper part. 4. APA was significantly enhanced in the phosphorus-deficient phytoplankton. However, APA was apparently not related to total biomass or species composition of the phytoplankton. 5. Generally, APA was closely correlated with pH in the reservoir. However, extracellular alkaline phosphatases, with a pH optimum above 9.0, were induced and active only during the phytoplankton bloom, whereas low background activity of extracellular phosphatases was found at low chlorophyll a concentrations (winter, clear-water phase).     

Unique opportunities for NMR methods in structural genomics

This Perspective, arising from a workshop held in July 2008 in Buffalo NY, provides an overview of the role NMR has played in the United States Protein Structure Initiative (PSI), and a vision of how NMR will contribute to the forthcoming PSI-Biology program. NMR has contributed in key ways to structure production by the PSI, and new methods have been developed which are impacting the broader protein NMR community.