Modeling assisted rational design of novel, potent, and selective pyrrolopyrimidine DPP-4 inhibitors

Molecular modeling was used to improve potency of the cyclohexylamine series. In addition, a 3-D QSAR method was used to gain insight for reducing off-target DPP-8/9 activities. Compounds 3, 4, and 5 were synthesized and found to be potent DPP-4 inhibitors, in particular 4 and 5 are designed to be highly selective against off-target DASH enzymes while maintaining potency on DPP-4.     

Rational design of a novel, potent, and orally bioavailable cyclohexylamine DPP-4 inhibitor by application of molecular modeling and X-ray crystallography of sitagliptin

Molecular modeling was used to design a rigid analog of sitagliptin 1. The X-ray crystal structure of sitagliptin bound to DPP-4 suggested that the central beta-amino butyl amide moiety could be replaced with a cyclohexylamine group. This was confirmed by structural analysis and the resulting analog 2a was synthesized and found to be a potent DPP-4 inhibitor (IC(50)=21 nM) with excellent in vivo activity and pharmacokinetic profile.     

RGD targeted poly(L-glutamic acid)-cystamine-(Gd-DO3A) conjugate for detecting angiogenesis biomarker alpha(v) beta3 integrin with MRT, mapping

Cyclic Arg-Gly-Asp-D-Phe-Lys [c(RGDfK)] targeted poly(L-glutamic acid) (PGA)-(Gd-DO3A) conjugate with a biodegradable cystamine spacer was prepared and evaluated for in vivo detection of an angiogenesis biomarker, alpha(v)beta3 integrin, in neoplastic tissues with T1 mapping, a quantitative magnetic resonance imaging (MRI) technique. The binding activity of the c(RGDfK) containing conjugate was investigated using in vitro vitronectin assay with human prostate carcinoma DU145 cell line and Kaposi's sarcoma SLK cell line. The peptide c(RGDfK) and PGA-cystamine-(Gd-DO3A) conjugate were used as controls. The binding affinity of polymer bound c(RGDfK) was slightly lower than free c(RGDfK) peptide. The RGD targeted conjugate had higher binding affinity to the DU145 cells than the SLK cells, which was consistent to free c(RGDfK). The imaging of alpha(v)beta3 integrin with targeted PGA-cystamine-(Gd-DO3A) was evaluated in nude mice bearing DU145 and SLK xenografts at a dose of 5 micromol-Gd/kg. The targeted conjugate demonstrated higher in vivo binding affinity to the DU145 xenografts than the SLK xenografts, resulting in a significant decrease of T1 values of water protons in the periphery of the DU145 tumors as shown in the MR T1 maps. No significant decrease of T1 values was observed in the SLK tumor with the targeted conjugate and in both tumors with the non-targeted conjugate. The targeted polymeric Gd(III) chelate conjugate with a degradable spacer has the potential to be a new paradigm for safe and effective probes in molecular imaging with quantitative MR T1 mapping.     

Plasma placental RNA allelic ratio permits noninvasive prenatal chromosomal aneuploidy detection

Current methods for prenatal diagnosis of chromosomal aneuploidies involve the invasive sampling of fetal materials using procedures such as amniocentesis or chorionic villus sampling and constitute a finite risk to the fetus. Here, we outline a strategy for fetal chromosome dosage assessment that can be performed noninvasively through analysis of placental expressed mRNA in maternal plasma. We achieved noninvasive prenatal diagnosis of fetal trisomy 21 by determining the ratio between alleles of a single-nucleotide polymorphism (SNP) in PLAC4 mRNA, which is transcribed from chromosome 21 and expressed by the placenta, in maternal plasma. PLAC4 mRNA in maternal plasma was fetal derived and cleared after delivery. The allelic ratios in maternal plasma correlated with those in the placenta. Fetal trisomy 21 was detected noninvasively in 90% of cases and excluded in 96.5% of controls.     

Systemic but not mucosal immunity induced by AVA prevents inhalational anthrax

Improved vaccines and adjuvants are being developed to reduce the threat posed by a terrorist attack involving aerosolized anthrax spores. Nevertheless, uncertainty persists concerning the relative benefits of inducing mucosal vs systemic immunity to host survival following inhalational exposure to anthrax spores. This work examines the effect of delivering the licensed human vaccine (anthrax vaccine adsorbed, AVA) combined with a CpG oligodeoxynucleotide (ODN) adjuvant intraperitoneally or intranasally to A/J mice. Results indicate that protection from inhalational anthrax correlates with the induction of a strong systemic rather than mucosal immune response, and demonstrate that protection is significantly improved and accelerated by the addition of CpG ODN.     

Dicer-1, but not Loquacious, is critical for assembly of miRNA-induced silencing complexes

Double-stranded RNA-binding proteins (dsRBPs), such as R2D2 and Loquacious (Loqs), function in tandem with Dicer (Dcr) enzymes in RNA interference (RNAi). In Drosophila, Dcr-1/Loqs and Dcr-2/R2D2 complexes generate microRNAs (miRNAs) and small interfering RNAs (siRNAs), respectively. Although R2D2 does not regulate siRNA production, R2D2 and Dcr-2 coordinately bind siRNAs to promote assembly of the siRNA-induced silencing (siRISC) complexes. Conversely, Loqs enhances miRNA production. It is uncertain if Dcr-1 and Loqs facilitate miRNA loading onto the miRISC complexes. Here we used loqs knockout (KO) flies to characterize the physiological functions of Loqs in the miRNA pathway. Northern analysis revealed consistent accumulation of precursor (pre)-miRNAs in loqs(KO) flies. However, the lack of Loqs had differential effects on mature miRNAs: some are diminished, whereas others maintain wild-type levels. Importantly, the data suggest that miRNA production is not the rate-limiting step of the miRNA pathway. We show that Dcr-1, but not Loqs, is critical for assembly of miRISCs by using dcr-1 or loqs null egg extract. Consistent with this, recombinant Dcr-1 could efficiently interact with miRNA duplex in the absence of Loqs. Together, our results indicate that Loqs plays a prominent role in miRNA biogenesis, but is largely dispensable for miRISC assembly. Thus, Loqs and R2D2 represent two distinct functional modes for dsRBPs in the RNAi pathways.     

Sungear: interactive visualization and functional analysis of genomic datasets

Sungear is a software system that supports a rapid, visually interactive and biologist-driven comparison of large datasets. The datasets can come from microarray experiments (e.g. genes induced in each experiment), from comparative genomics (e.g. genes present in each genome) or even from non-biological applications (e.g. demographics or baseball statistics). Sungear represents multiple datasets as vertices in a polygon. Each possible intersection among the sets is represented as a circle inside the polygon. The position of the circle is determined by the position of the vertices represented in the intersection and the area of the circle is determined by the number of elements in the intersection. Sungear shows which Gene Ontology terms are over-represented in a subset of circles or anchors. The intuitive Sungear interface has enabled biologists to determine quickly which dataset or groups of datasets play a role in a biological function of interest. AVAILABILITY: A live online version of Sungear can be found at http://virtualplant-prod.bio.nyu.edu/cgi-bin/sungear/index.cgi     

The Influence of Discharge on Duration,Ascent Distance,and Fidelity of the Spawning Migration for Paddlefish of the Yellowstone-Sakakawea Stock,Montana and North Dakota,USA

Paddlefish, Polyodon spathula, of the Yellowstone-Sakakawea stock, Missouri and Yellowstone Rivers, Montana and North Dakota, were radio-tagged to assess the influence of spring discharge on duration of river residency, ascent distance, and site-fidelity during spawning migrations of 1999–2002. Contrary to expectations and reported results from other paddlefish populations, fish remained in the river for similar periods of time and ascended to similar reaches in years of higher, more sustained discharge and in years of lower, more fluctuating discharge. In all years, 65 of the 74 migrants (88%) restricted their ascent to reaches below Yellowstone River kilometer (YRkm) 55; only six migrants were found to further ascend to upriver reaches within 20 river kilometers (rkm) of the Intake Diversion Dam (YRkm 114). The lack of detectable annual differences in ascent distance over the study period despite annual differences in Yellowstone River spring flow regimes may have been partially attributed to the apparent site-fidelity demonstrated by the tagged fish over the study period. Ten of the 22 paddlefish contacted in more than one spring migration repeatedly limited their upriver movement to sites that were within 10 rkm of each other. In addition, similar to the reproductive homing tendencies documented in other large-river migratory fishes, site-fidelity occurred in different reaches of the river system. Results from this study suggest that, in years of moderate discharge, site-fidelity may be as influential as the spring flow regime in determining the reaches to which migratory paddlefish ascend. Further research is needed to investigate potential differential spawning success in fish that return to different reaches of the lower Yellowstone River.