Development and evaluation of 4-(pyrrolidin-3-yl)benzonitrile derivatives as inhibitors of lysine specific demethylase 1

As part of our ongoing efforts to develop reversible inhibitors of LSD1, we identified a series of 4-(pyrrolidin-3-yl)benzonitrile derivatives that act as successful scaffold-hops of the literature inhibitor GSK-690. The most active compound, 21g, demonstrated a K_d value of 22 nM and a biochemical IC₅₀ of 57 nM. In addition, this compound displayed improved selectivity over the hERG ion channel compared to GSK-690, and no activity against the related enzymes MAO-A and B. In human THP-1 acute myeloid leukaemia cells, 21g was found to increase the expression of the surrogate cellular biomarker CD86. This work further demonstrates the versatility of scaffold-hopping as a method to develop structurally diverse, potent inhibitors of LSD1.     

Extending Serum Half-life of Albumin by Engineering Neonatal Fc Receptor (FcRn) Binding

A major challenge for the therapeutic use of many peptides and proteins is their short circulatory half-life. Albumin has an extended serum half-life of 3 weeks because of its size and FcRn-mediated recycling that prevents intracellular degradation, properties shared with IgG antibodies. Engineering the strictly pH-dependent IgG-FcRn interaction is known to extend IgG half-life. However, this principle has not been extensively explored for albumin. We have engineered human albumin by introducing single point mutations in the C-terminal end that generated a panel of variants with greatly improved affinities for FcRn. One variant (K573P) with 12-fold improved affinity showed extended serum half-life in normal mice, mice transgenic for human FcRn, and cynomolgus monkeys. Importantly, favorable binding to FcRn was maintained when a single-chain fragment variable antibody was genetically fused to either the N- or the C-terminal end. The engineered albumin variants may be attractive for improving the serum half-life of biopharmaceuticals.     

Linkage studies with 17q and 18q markers in a breast/ovarian cancer family.

Genes on chromosomes 17q and 18q have been shown to code for putative tumor suppressors. By a combination of allele-loss studies on sporadic ovarian carcinomas and linkage analysis on a breast/ovarian cancer family, we have investigated the involvement of such genes in these diseases. Allele loss occurred in sporadic tumors from both chromosome 17p, in 18/26 (69%) cases, and chromosome 17q, in 15/22 (68%) cases. In the three familial tumors studied, allele loss also occurred on chromosome 17 (in 2/3 cases for 17p markers and in 2/2 cases for a 17q allele). Allele loss on chromosome 18q, at the DCC (deleted in colorectal carcinomas) locus, was not as common (6/16 cases [38%]) in sporadic ovarian tumors but had occurred in all three familial tumors. The results of linkage analysis on the breast/ovarian cancer family suggested linkage between the disease locus and 17q markers, with a maximum lod score of 1.507 obtained with Mfd188 (D17S579) polymorphism at 5% recombination. The maximum lod score for DCC was 0.323 at 0.1% recombination. In this family our results are consistent with a predisposing gene for breast/ovarian cancer being located at chromosome 17q21.     

Can We Use Tree Rings of Black Alder to Reconstruct Lake Levels? A Case Study for the Mecklenburg Lake District,Northeastern Germany

In this study, we explore the potential to reconstruct lake-level (and groundwater) fluctuations from tree-ring chronologies of black alder (Alnus glutinosa L.) for three study lakes in the Mecklenburg Lake District, northeastern Germany. As gauging records for lakes in this region are generally short, long-term reconstructions of lake-level fluctuations could provide valuable information on past hydrological conditions, which, in turn, are useful to assess dynamics of climate and landscape evolution. We selected black alder as our study species as alder typically thrives as riparian vegetation along lakeshores. For the study lakes, we tested whether a regional signal in lake-level fluctuations and in the growth of alder exists that could be used for long-term regional hydrological reconstructions, but found that local (i.e. site-specific) signals in lake level and tree-ring chronologies prevailed. Hence, we built lake/groundwater-level reconstruction models for the three study lakes individually. Two sets of models were considered based on (1) local tree-ring series of black alder, and (2) site-specific Standardized Precipitation Evapotranspiration Indices (SPEI). Although the SPEI-based models performed statistically well, we critically reflect on the reliability of these reconstructions, as SPEI cannot account for human influence. Tree-ring based reconstruction models, on the other hand, performed poor. Combined, our results suggest that, for our study area, long-term regional reconstructions of lake-level fluctuations that consider both recent and ancient (e.g., archaeological) wood of black alder seem extremely challenging, if not impossible.     

Multimodal Networks: Structure and Operations

A multimodal network (MMN) is a novel graph-theoretic formalism designed to capture the structure of biological networks and to represent relationships derived from multiple biological databases. MMNs generalize the standard notions of graphs and hypergraphs, which are the bases of current diagrammatic representations of biological phenomena and incorporate the concept of mode. Each vertex of an MMN is a biological entity, a biot, while each modal hyperedge is a typed relationship, where the type is given by the mode of the hyperedge. The current paper defines MMNs and concentrates on the structural aspects of MMNs. A companion paper develops MMNs as a representation of the semantics of biological networks and discusses applications of the MMNs in managing complex biological data. The MMN model has been implemented in a database system containing multiple kinds of biological networks.     

Respiratory events and periodic breathing in cyclists sleeping at 2,650-m simulated altitude.

We examined the initial effect of sleeping at a simulated moderate altitude of 2,650 m on the frequency of apneas and hypopneas, as well as on the heart rate and blood oxygen saturation from pulse oximetry (SpO2) during rapid eye movement (REM) and non-rapid eye movement (NREM) sleep of 17 trained cyclists. Pulse oximetry revealed that sleeping at simulated altitude significantly increased heart rate (3 +/- 1 beats/min; means +/- SE) and decreased SpO2 (-6 +/- 1%) compared with baseline data collected near sea level. In response to simulated altitude, 15 of the 17 subjects increased the combined frequency of apneas plus hypopneas from baseline levels. On exposure to simulated altitude, the increase in apnea was significant from baseline for both sleep states (2.0 +/- 1.3 events/h for REM, 9.9 +/- 6.2 events/h for NREM), but the difference between the two states was not significantly different. Hypopnea frequency was significantly elevated from baseline to simulated altitude exposure in both sleep states, and under hypoxic conditions it was greater in REM than in NREM sleep (7.9 +/- 1.8 vs. 4.2 +/- 1.3 events/h, respectively). Periodic breathing episodes during sleep were identified in four subjects, making this the first study to show periodic breathing in healthy adults at a level of hypoxia equivalent to 2,650-m altitude. These results indicate that simulated moderate hypoxia of a level typically chosen by coaches and elite athletes for simulated altitude programs can cause substantial respiratory events during sleep.     

The tyrosinase activity of melanosomes from the harding-passey melanoma: The absence of a peroxidase component in vitro

Melanosomes were isolated from the Harding-Passey melanoma with a density gradient technique. Using the Pomerantz radioassay for tyrosinase activity it was found that these isolated melanosomes could hydroxylate tyrosine in the presence of catalase sufficient to deny the enzyme any hydrogen peroxide. It was further found that the rate of hydroxylation was unaffected by the presence of exogenous hydrogen peroxide. Tyrosinase activity could be suppressed by preincubation in diethyldithiocarbamate followed by removal of this inhibitor before enzyme assay. Attempts to regain enzymatic activity, however, by addition of copper II ions were unsuccessful. No peroxidase activity could be detected on the isolated granules, and indeed evidence for a peroxidase inhibitor on the granules was found. It was also found that the peroxidase activity present in a 20% homogenate of mouse muscle did not demonstrate any tyrosinase activity with the Pomerantz assay even in the presence of hydrogen peroxide. It is concluded from these studies that there is tyrosinase on these melanosomes which is capable in vitro of hydroxylating tyrosine without any contribution from an active peroxidase.