Novel pyrrolobenzodiazepine benzofused hybrid molecules inhibit NF-κB activity and synergise with bortezomib and ibrutinib in hematological cancers

Chronic lymphocytic leukemia (CLL) and multiple myeloma (MM) are incurable hematological malignancies that are pathologically linked with aberrant NF-κB activation. In this study, we identified a group of novel C8-linked benzofused Pyrrolo[2,1-c][1,4]benzodiazepines (PBD) monomeric hybrids capable of sequence-selective inhibition of NF-κB with low nanomolar LD50 values in CLL (n=46) and MM cell lines (n=5). The lead compound, DC-1-192, significantly inhibited NF-κB DNA binding after just 4h exposure and demonstrating inhibitory effects on both canonical and non-canonical NF-κB subunits. In primary CLL cells, sensitivity to DC-1-192 was inversely correlated with RelA subunit expression (r2=0.2) and samples with BIRC3 or NOTCH1 mutations showed increased sensitivity (P=0.001). RNA-sequencing and gene set enrichment analysis confirmed the over-representation of NF-κB regulated genes in the down-regulated gene list. Furthermore, In vivo efficacy studies in NOD/SCID mice, using a systemic RPMI 8226 human multiple myeloma xenograft model, showed that DC-1-192 significantly prolonged survival (P=0.017). In addition, DC1-192 showed synergy with bortezomib and ibrutinib; synergy with ibrutinib was enhanced when CLL cells were co-cultured on CD40L-expressing fibroblasts in order to mimic the cytoprotective lymph node microenvironment (P = 0.01). Given that NF-κB plays a role in both bortezomib and ibrutinib resistance mechanisms, these data provide a strong rationale for the use of DC-1-192 in the treatment of NF-κB-driven cancers, particularly in the context of relapsed/refractory disease

On bipartite Rokhsar-Kivelson points and Cantor deconfinement

Quantum dimer models on bipartite lattices exhibit Rokhsar-Kivelson (RK) points with exactly known critical ground states and deconfined spinons. We examine generic, weak, perturbations around these points. In d=2+1 we find a first order transition between a ``plaquette'' valence bond crystal and a region with a devil's staircase of commensurate and incommensurate valence bond crystals. In the part of the phase diagram where the staircase is incomplete, the incommensurate states exhibit a gapless photon and deconfined spinons on a set of finite measure, almost but not quite a deconfined phase in a compact U(1) gauge theory in d=2+1! In d=3+1 we find a continuous transition between the U(1) resonating valence bond (RVB) phase and a deconfined staggered valence bond crystal. In an appendix we comment on analogous phenomena in quantum vertex models, most notably the existence of a continuous transition on the triangular lattice in d=2+1.Comment: 9 pages; expanded version to appear in Phys. Rev. B; presentation improve

Diagnosing students' difficulties in learning mathematics

This study considers the results of a diagnostic test of student difficulty and contrasts the difference in performance between the lower attaining quartile and the higher quartile. It illustrates a difference in qualitative thinking between those who succeed and those who fail in mathematics, illustrating a theory that those who fail are performing a more difficult type of mathematics (coordinating procedures) than those who succeed (manipulating concepts). Students who have to coordinate or reverse processes in time will encounter far greater difficulty than those who can manipulate symbols in a flexible way. The consequences of such a dichotomy and implications for remediation are then considered

Effects of systematic shortening of noncovalent C8 side chain on the cytotoxicity and NF-κB inhibitory capacity of pyrrolobenzodiazepines (PBDs)

The systematic shortening of the noncovalent element of a C8-linked pyrrolobenzodiazepine (PBD) conjugate (13) led to the synthesis of a 19-member library of C8-PBD monomers. The critical elements of 13, which were required to render the molecule cytotoxic, were elucidated by an annexin V assay. The effects of shortening the noncovalent element of the molecule on transcription factor inhibitory capacity were also explored through an enzyme-linked immunosorbent assay-based measurement of nuclear NF-κB upon exposure of JJN-3 cells to the synthesized molecules. Although shortening the noncovalent interactive element of 13 had a less than expected effect upon compound cytotoxicity due to reduced DNA interaction, the transcription factor inhibitory capacity of the molecule was notably altered. This study suggests that a relatively short noncovalent side chain at the C8 position of PBD is sufficient to confer cytotoxicity. The shortened PBD monomers provide a new ADC payload scaffold because of their potent cytotoxicity and druglike properties

The minor groove-binding agent ELB-21 forms multiple interstrand and intrastrand covalent cross-links with duplex DNA and displays potent bactericidal activity against methicillin-resistant Staphylococcus aureus

OBJECTIVES: The antistaphylococcal pyrrolobenzodiazepine dimer ELB-21 forms multiple adducts with duplex DNA through covalent interactions with appropriately spaced guanine residues; it is now known to form interstrand and intrastrand adducts with oligonucleotide sequences of variable length. We determined the DNA sequence preferences of ELB-21 in relation to its capacity to exert a bactericidal effect by damaging DNA. METHODS: Formation of adducts by ELB-21 and 12- to 14-mer DNA duplexes was investigated using ion-pair reversed phase liquid chromatography and mass spectrometry. Drug-induced changes in gene expression were measured in prophage-free Staphylococcus aureus RN4220 by microarray analysis. RESULTS: ELB-21 preferentially formed intrastrand adducts with guanines separated by three nucleotide base pairs. Interstrand and intrastrand adducts were formed with duplexes both longer and shorter than the preferred target sequences. ELB-21 elicited rapid bactericidal effects against prophage-carrying and prophage-free S. aureus strains; cell lysis occurred following activation and release of resident prophages. Killing appeared to be due to irreparable damage to bacterial DNA and susceptibility to ELB-21 was governed by the capacity of staphylococci to repair DNA lesions through induction of the SOS DNA damage response mediated by the RecA-LexA pathway. CONCLUSIONS: The data support the contention that ELB-21 arrests DNA replication, eliciting formation of ssDNA-RecA filaments that inactivate LexA, the SOS repressor, and phage repressors such as Cl, resulting in activation of the DNA damage response and de-repression of resident prophages. Above the MIC threshold, DNA repair is ineffective

Effect of base sequence on the DNA cross-linking properties of pyrrolobenzodiazepine (PBD) dimers

Pyrrolo[2,1-c][1,4]benzodiazepine (PBD) dimers are synthetic sequence-selective DNA minor-groove cross-linking agents that possess two electrophilic imine moieties (or their equivalent) capable of forming covalent aminal linkages with guanine C2-NH2 functionalities. The PBD dimer SJG-136, which has a C8–O–(CH2)3–O–C8′′ central linker joining the two PBD moieties, is currently undergoing phase II clinical trials and current research is focused on developing analogues of SJG-136 with different linker lengths and substitution patterns. Using a reversed-phase ion pair HPLC/MS method to evaluate interaction with oligonucleotides of varying length and sequence, we recently reported (JACS, 2009, 131, 13 756) that SJG-136 can form three different types of adducts: inter- and intrastrand cross-linked adducts, and mono-alkylated adducts. These studies have now been extended to include PBD dimers with a longer central linker (C8–O–(CH2)5–O–C8′), demonstrating that the type and distribution of adducts appear to depend on (i) the length of the C8/C8′-linker connecting the two PBD units, (ii) the positioning of the two reactive guanine bases on the same or opposite strands, and (iii) their separation (i.e. the number of base pairs, usually ATs, between them). Based on these data, a set of rules are emerging that can be used to predict the DNA–interaction behaviour of a PBD dimer of particular C8–C8′ linker length towards a given DNA sequence. These observations suggest that it may be possible to design PBD dimers to target specific DNA sequences

Triangulated Surfaces in Twistor Space: A Kinematical Set up for Open/Closed String Duality

We exploit the properties of the three-dimensional hyperbolic space to discuss a simplicial setting for open/closed string duality based on (random) Regge triangulations decorated with null twistorial fields. We explicitly show that the twistorial N-points function, describing Dirichlet correlations over the moduli space of open N-bordered genus g surfaces, is naturally mapped into the Witten-Kontsevich intersection theory over the moduli space of N-pointed closed Riemann surfaces of the same genus. We also discuss various aspects of the geometrical setting which connects this model to PSL(2,C) Chern-Simons theory.Comment: 35 pages, references added, slightly revised introductio

Use of traditional knowledge by the United States Bureau of Ocean Energy Management to support resource management

Professionals who collect and use traditional knowledge to support resource management decisions often are preoccupied with concerns over how and if traditional knowledge should be integrated with science. To move beyond the integration dilemma, we treat traditional knowledge and science as distinct and complementary knowledge systems. We focus on applying traditional knowledge within the decision-making process. We present succinct examples of how the Bureau of Ocean Energy Management has used traditional knowledge in decision making in the North Slope Borough, Alaska: 1) using traditional knowledge in designing, planning, and conducting scientific research; 2) applying information from both knowledge systems at the earliest opportunity in the process; 3) using traditional knowledge in environmental impacts assessment; 4) consulting with indigenous leaders at key decision points; and 5) applying traditional knowledge at a programmatic decision level. Clearly articulating, early in the process, how best to use traditional knowledge and science can allow for more complete and inclusive use of available and pertinent information

The HII Regions of the Damped Lyman alpha Absorber SBS 1543+593

We report new imaging and spectroscopic observations of the damped Ly alpha (DLA) galaxy SBS 1543+593, a nearby dwarf galaxy whose stellar disk is intersected by the sightline to the bright background QSO HS 1543+5921. Hubble Space Telescope imaging observations with WFPC2 in the F450W and F702W bands are used to measure the DLA galaxy's properties and compile a catalog of its (candidate) HII regions. Ground-based long-slit spectroscopy of the brightest HII region in the galaxy yields estimates of the star formation rate (SFR) and of chemical abundances in the galaxy's interstellar medium. We find that SBS 1543+593 exhibits a SFR $\approx 0.006 h^{-2}_{70} M_{\odot}$ yr$^{-1}$, or a SFR per unit area of $\approx 1.4 \times 10^{-4} h^{-2}_{70} M_\odot$ yr$^{-1}$ kpc$^{-2}$. We derive gas-phase abundances in the ionized gas of $12 + \log {\rm (O/H)} = 8.2 \pm 0.2$, which is about 1/3 of the solar value, and $\log {\rm (N/O)} = -1.40^{+0.2}_{-0.3}$. These values are consistent with the morphologial appearance of SBS 1543+593, an Sm dwarf of $M_B -5 \log h_{70} = -16.8\pm0.2$ and of intermediate surface brightness. SBS 1543+593 is the first {\it bona fide} DLA for which abundances have been measured using emission-line diagnostics. When compared with future, high-resolution, ultraviolet spectroscopy, our results should prove key for interpreting abundance determinations in high redshift DLAs.Comment: ApJ, accepte

Activity of the DNA minor groove cross-linking agent SG2000 (SJG-136) against canine tumours

BACKGROUND: Cancer is the leading cause of death in older dogs and its prevalence is increasing. There is clearly a need to develop more effective anti-cancer drugs in dogs. SG2000 (SJG-136) is a sequence selective DNA minor groove cross-linking agent. Based on its in vitro potency, the spectrum of in vivo and clinical activity against human tumours, and its tolerability in human patients, SG2000 has potential as a novel therapeutic against spontaneously occurring canine malignancies. RESULTS: In vitro cytotoxicity was assessed using SRB and MTT assays, and in vivo activity was assessed using canine tumour xenografts. DNA interstrand cross-linking (ICL) was determined using a modification of the single cell gel electrophoresis (comet) assay. Effects on cell cycle distribution were assessed by flow cytometry and measurement of γ-H2AX by immunofluorescence and immunohistochemistry. SG2000 had a multi-log differential cytotoxic profile against a panel of 12 canine tumour cell lines representing a range of common tumour types in dogs. In the CMeC-1 melanoma cell line, DNA ICLs increased linearly with dose following a 1 h treatment. Peak ICL was achieved within 1 h and no removal was observed over 48 h. A relationship between DNA ICL formation and cytotoxicity was observed across cell lines. The formation of γ-H2AX foci was slow, becoming evident after 4 h and reaching a peak at 24 h. SG2000 exhibited significant anti-tumour activity against two canine melanoma tumour models in vivo. Anti-tumour activity was observed at 0.15 and 0.3 mg/kg given i.v. either once, or weekly x 3. Dose-dependent DNA ICL was observed in tumours (and to a lower level in peripheral blood mononuclear cells) at 2 h and persisted at 24 h. ICL increased following the second and third doses in a repeated dose schedule. At 24 h, dose dependent γ-H2AX foci were more numerous than at 2 h, and greater in tumours than in peripheral blood mononuclear cells. SG2000-induced H2AX phosphorylation measured by immunohistochemistry showed good correspondence, but less sensitivity, than measurement of foci. CONCLUSIONS: SG2000 displayed potent activity in vitro against canine cancer cell lines as a result of the formation and persistence of DNA ICLs. SG2000 also had significant in vivo antitumour activity against canine melanoma xenografts, and the comet and γ-H2AX foci methods were relevant pharmacodynamic assays. The clinical testing of SG2000 against spontaneous canine cancer is warranted. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12917-015-0534-2) contains supplementary material, which is available to authorized users