Discovery of novel triple helical DNA intercalators by an integrated virtual and actual screening platform

Virtual Screening is an increasingly attractive way to discover new small molecules with potential medicinal value. We introduce a novel strategy that integrates use of the molecular docking software Surflex with experimental validation by the method of competition dialysis. This integrated approach was used to identify ligands that selectively bind to the triplex DNA poly(dA)-[poly(dT)]2. A library containing ∼2 million ligands was virtually screened to identify compounds with chemical and structural similarity to a known triplex intercalator, the napthylquinoline MHQ-12. Further molecular docking studies using compounds with high structural similarity resulted in two compounds that were then demonstrated by competition dialysis to have a superior affinity and selectivity for the triplex nucleic acid than MHQ-12. One of the compounds has a different chemical backbone than MHQ-12, which demonstrates the ability of this strategy to ‘scaffold hop’ and to identify small molecules with novel binding properties. Biophysical characterization of these compounds by circular dichroism and thermal denaturation studies confirmed their binding mode and selectivity. These studies provide a proof-of-principle for our integrated screening strategy, and suggest that this platform may be extended to discover new compounds that target therapeutically relevant nucleic acid morphologies

Circular and linear : a tale of aptamer selection for the activation of SIRT1 to induce death in cancer cells

It is a challenge to select the right target to treat conditions without affecting non-diseased cells. Cancer belongs to the top 10 causes of death in the world and it remains difficult to treat. Amongst cancer emerging targets, silent information regulator 1 (SIRT1) – a histone deacetylase – has shown many roles in cancer, ageing and metabolism. Here we report novel SIRT1 ligands that bind and modulate the activity of SIRT1 within cells and enhance its enzymatic activity. We developed a modified aptamer capable of binding to and forming a complex with SIRT1. Our ligands are aptamers, they can be made of DNA or RNA oligonucleotides, their binding domain can recognise a target with very high affinity and specificity. We used the systematic evolution of ligands by exponential enrichment (SELEX) technique to develop circular and linear aptamers selectively binding to SIRT1. Cellular consequences of the interaction were monitored by fluorescence microscopy, cell viability assay, stability and enzymatic assays. Our results indicate that from our pool of aptamers, circular AC3 penetrates cancerous cells and is recruited to modulate the SIRT1 activity. This modulation of SIRT1 resulted in anticancer activity on different cancer cell lines. Furthermore, this modified aptamer showed no toxicity on one non-cancerous cell line and was stable in human plasma. We have demonstrated that aptamers are efficient tools for localisation of internal cell targets, and in this particular case, anticancer activity through modulation of SIRT1

Dynamical chiral symmetry breaking by a magnetic field and multi-quark interactions

Catalysis of dynamical symmetry breaking by a constant magnetic field in (3+1) dimensions is considered. We use the three flavour Nambu -- Jona-Lasinio type model with 't Hooft and eight-quark interaction terms. It is shown that the multi-quark interactions introduce new additional features to this phenomenon: (a) the local minimum of the effective potential catalyzed by the constant magnetic field is smoothed out with increasing strength of the field at the characteristic scale H~10^{19} G, (b) the multi-quark forces generate independently another local minimum associated with a larger dynamical fermion mass. This state may exist even for multi-quark interactions with a subcritical set of couplings, and is globally stable with respect to a further increase of the magnetic field.Comment: 6 pages, 3 figures, added discussion and references, version to appear in Phys.Lett.

Multiparton interactions and production of minijets in high energy hadronic collisions

We discuss the inclusive cross section to produce two minijets with a large separation in rapidity in high energy hadronic collisions. The contribution to the inclusive cross section from the exchange of a BFKL Pomeron is compared with the contribution from the exchange of two BFKL Pomerons, which is induced by the unitarization of the semi-hard interaction. The effect of the multiple exchange is studied both as a function of the azimuthal correlation and as a function of the transverse momentum of the observed minijets.Comment: TeX file, 20 pages, 4 figures available on reques

Effective Regge QCD

A new framework for a high energy limit of quantum gauge field theories is introduced. Its potency is illustrated on a new derivation of the reggeization of the gluon.Comment: Latex, 9 pages + 2 figures as PS-file, extended version, to appear in Phys. Rev. Let

New Effective Feynman-like Rules for the Multi-Regge QCD Asymptotics of Inclusive Multijet Production

New effective Feynman-like rules are defined for inclusive multijet cross sections in the multi-Regge regime. The solution of the BFKL equation is used as a starting point. The resulting rules involve conformal weight and rapidity as a momentum and a coordinate respectively and are translation invariant in the coordinates. We use the effective rules to calculate ultra high energy asymptotics of inclusive multijet production. The dependence on the parton densities occurs only in the overall normalization of the asymptotic cross sections.Comment: 12 pages in Latex, 3 figs by epsfig, refs update

Combined transcriptome studies identify AFF3 as a mediator of the oncogenic effects of beta-catenin in adrenocortical carcinoma

Adrenocortical cancer (ACC) is a very aggressive tumor, and genomics studies demonstrate that the most frequent alterations of driver genes in these cancers activate the Wnt/beta-catenin signaling pathway. However, the adrenal-specific targets of oncogenic beta-catenin-mediating tumorigenesis have not being established. A combined transcriptomic analysis from two series of human tumors and the human ACC cell line H295R harboring a spontaneous beta-catenin activating mutation was done to identify the Wnt/beta-catenin targets. Seven genes were consistently identified in the three studies. Among these genes, we found that AFF3 mediates the oncogenic effects of beta-catenin in ACC. The Wnt response element site located at nucleotide position - 1408 of the AFF3 transcriptional start sites (TSS) mediates the regulation by the Wnt/beta-catenin signaling pathway. AFF3 silencing decreases cell proliferation and increases apoptosis in the ACC cell line H295R. AFF3 is located in nuclear speckles, which play an important role in RNA splicing. AFF3 overexpression in adrenocortical cells interferes with the organization and/or biogenesis of these nuclear speckles and alters the distribution of CDK9 and cyclin T1 such that they accumulate at the sites of AFF3/speckles. We demonstrate that AFF3 is a new target of Wnt/beta-catenin pathway involved in ACC, acting on transcription and RNA splicing

Combined transcriptome studies identify AFF3 as a mediator of the oncogenic effects of beta-catenin in adrenocortical carcinoma

Adrenocortical cancer (ACC) is a very aggressive tumor, and genomics studies demonstrate that the most frequent alterations of driver genes in these cancers activate the Wnt/beta-catenin signaling pathway. However, the adrenal-specific targets of oncogenic beta-catenin-mediating tumorigenesis have not being established. A combined transcriptomic analysis from two series of human tumors and the human ACC cell line H295R harboring a spontaneous beta-catenin activating mutation was done to identify the Wnt/beta-catenin targets. Seven genes were consistently identified in the three studies. Among these genes, we found that AFF3 mediates the oncogenic effects of beta-catenin in ACC. The Wnt response element site located at nucleotide position - 1408 of the AFF3 transcriptional start sites (TSS) mediates the regulation by the Wnt/beta-catenin signaling pathway. AFF3 silencing decreases cell proliferation and increases apoptosis in the ACC cell line H295R. AFF3 is located in nuclear speckles, which play an important role in RNA splicing. AFF3 overexpression in adrenocortical cells interferes with the organization and/or biogenesis of these nuclear speckles and alters the distribution of CDK9 and cyclin T1 such that they accumulate at the sites of AFF3/speckles. We demonstrate that AFF3 is a new target of Wnt/beta-catenin pathway involved in ACC, acting on transcription and RNA splicing

Rapidity gaps and production of minijets in high-energy hadronic collisions

High energy hadronic interactions can produce a final state characterized by minijets separated by a large gap in the rapidity distribution of the produced secondary particles. We discuss the process by keeping into account the possibility of having multiple parton collisions in the hadronic interaction. At Tevatron energy the correction to the single scattering term induced by the presence of multiparton interactions is large for transverse momenta smaller than 6 GeV.Comment: 29 pages, TeX file, 2 figures which are now include