Structure based design of novel 6,5 heterobicyclic mitogen-activated protein kinase kinase (MEK) inhibitors leading to the discovery of imidazo[1,5-a] pyrazine G-479

Use of the tools of SBDD including crystallography led to the discovery of novel and potent 6,5 heterobicyclic MEKi’s [J. Med. Chem. 2012, 55, 4594]. The core change from a 5,6 heterobicycle to a 6,5 heterobicycle was driven by the desire for increased structural diversity and aided by the co-crystal structure of G-925 [J. Med. Chem. 2012, 55, 4594]. The key design feature was the shift of the attachment of the five-membered heterocyclic ring towards the B ring while maintaining the key hydroxamate and anilino pharamcophoric elements in a remarkably similar position as in G-925. From modelling, changing the connection point of the five membered ring heterocycle placed the H-bond accepting nitrogen within a good distance and angle to the Ser212 [J. Med. Chem. 2012, 55, 4594]. The resulting novel 6,5 benzoisothiazole MEKi G-155 exhibited improved potency versus aza-benzofurans G-925 and G-963 but was a potent inhibitor of cytochrome P450’s 2C9 and 2C19. Lowering the log D by switching to the more polar imidazo[1,5-a] pyridine core significantly diminished 2C9/2C19 inhibition while retaining potency. The imidazo[1,5-a] pyridine G-868 exhibited increased potency versus the starting point for this work (aza-benzofuran G-925) leading to deprioritization of the azabenzofurans. The 6,5-imidazo[1,5-a] pyridine scaffold was further diversified by incorporating a nitrogen at the 7 position to give the imidazo[1,5-a] pyrazine scaffold. The introduction of the C7 nitrogen was driven by the desire to improve metabolic stability by blocking metabolism at the C7 and C8 positions (particularly the HLM stability). It was found that improving on G-868 (later renamed GDC-0623) required combining C7 nitrogen with a diol hydroxamate to give G-479. G-479 with polarity distributed throughout the molecule was improved over G-868 in many aspects.     

On the PBB Designs for Multiresponse Experiments

We present the idea of using multiresponse incomplete block designs when not all responses can be observed in all experimental units. For a special class of such designs, in which partial designs are PBB designs, a method for estimating natural treatment contrast is given. We also consider the problem of testing the hypotheses concerning the natural and any estimable treatment contrasts. For testing this hypothesis the Wald statistics, being asymptotically chi-square distributed, is proposed.     

On Connectedness of a Two-way Elimination of Heterogeneity Design

For some subclass of a two-way elimination of heterogeneity design, necessary and sufficient conditions are established for row-connectedness and column-connectedness of a design to imply its connectedness.     

Design and Analysis of Field Experiments Incorporating Local and Remote Effects of Treatments

Design and analysis of field experiments in the presence of local and remote treatment effects are considered. The design criteria are optimality and balance for estimating local and remote effects. A nonlinear model, where remote effects are assumed to be proportional to the local effects, has been discussed.     

A thermodynamic and crystallographic study of complexes of the highly preorganized ligand 8-hydroxyquinoline-2-carboxylic acid

The metal ion complexing properties of the ligand HQC (8-hydroxyquinoline-2-carboxylic acid) are reported. The structures of [Zn(HQCH)₂] · 3H₂O (1) and [Cd(HQCH)₂] · 3H₂O (2) were determined (HQCH = HQC with phenol protonated). Both 1 and 2 are triclinic, space group , with Z = 2. For 1 a = 7.152(3), b = 9.227(4), c = 15.629(7) Å,  = 103.978(7)°, β = 94.896(7)°, γ = 108.033(8)°, R = 0.0499. For 2 a = 7.0897(5), b = 9.1674(7), c = 16.0672(11) Å,  = 105.0240(10)°, β = 93.9910(10)°, γ = 107.1270(10)°, R = 0.0330. In 1 the Zn has a distorted octahedral coordination geometry, with Zn–N of 2.00 and 2.15 Å, and Zn–O to the protonated phenolic oxygens of 2.431 and 2.220 Å. The structure of 2 is similar, with Cd–N bonds of 2.220 and 2.228 Å, with Cd–O bonds to the protonated phenolate oxygens of 2.334 and 2.463 Å. The structures of 1 and 2, and isomorphous Ni(II) and Co(II) HQC complexes reported in the literature, show very interesting short (<2.5 Å) O–O distances in H-bonds involving the protons on the coordinated phenolates and lattice water molecules. These are discussed in relation to the possible role of short low-energy H-bonds in alcohol dehydrogenase in mediating the transfer of the hydroxyl proton of the alcohol to an adjacent serine oxygen.

The formation constants for HQC are determined by UV–Visible spectroscopy at 25 °C in 0.1 M NaClO₄ with Mg(II), Ca(II), Sr(II), Ba(II), La(III), Gd(III), Zn(II), Cd(II), Ni(II), Cu(II), and Pb(II). These show greatest stabilization with metal ions with an ionic radius above 1.0 Å. This is as would be expected from the fact that HQC forms two five-membered chelate rings on complex-formation, which favors larger metal ions. The ligand design concept of using rigid aromatic backbones in ligands to achieve high levels of preorganization, and hence the high log K values (for a tridentate ligand) and strong metal ion selectivities observed for HQC, is discussed.     

Inbreeding dynamics in reintroduced, age-structured populations of highly fecund species

Reintroduction programs aim at reinstalling a self-sustained population into the wild via a period of supplementation with captive-bred individuals. This procedure can rapidly generate inbreeding among offspring because of the mating scheme and this inbreeding might be further enhanced by the reintroduction scenario. First, we used simulations to assess the consequences of breeding designs on mean inbreeding index F among offspring when the genetic diversity of breeders, the number and sex ratios of breeders, and the proportion of successful crosses vary. A high number of breeders, a balanced sex ratio, a high proportion of effective crosses and a genetically diverse source population generally contribute to lower F values. However, moderately high (≥20) numbers of breeders combined with all but the most biased sex ratios produced mean F values near minimal values. The variability in F was negligible in all parameter combinations except for a very small number of breeders (5) and very biased sex ratios (≤ 1M : 19F). We also simulated the long-term inbreeding dynamics in the introduced population under various demographic scenarios. Our main finding was that the annual number of introduced offspring is a decisive factor in establishing long-term F values in the supplemented population. Low supplementation levels (10²) quickly generated an almost completely inbred population whereas high levels (≥10⁴) produced stable F values close to that of the introduced offspring. Simulations were run based on the life history and specific demographics of the bloater (Coregonus hoyi), whose reintroduction in Lake Ontario is being considered.     

Non‐parametric habitat models with automatic interactions

Questions: Can a statistical model be designed to represent more directly the nature of organismal response to multiple interacting factors? Can multiplicative kernel smoothers be used for this purpose? What advantages does this approach have over more traditional habitat modelling methods? Methods: Non‐parametric multiplicative regression (NPMR) was developed from the premises that: the response variable has a minimum of zero and a physiologically‐determined maximum, species respond simultaneously to multiple ecological factors, the response to any one factor is conditioned by the values of other factors, and that if any of the factors is intolerable then the response is zero. Key features of NPMR are interactive effects of predictors, no need to specify an overall model form in advance, and built‐in controls on overfitting. The effectiveness of the method is demonstrated with simulated and real data sets. Results: Empirical and theoretical relationships of species response to multiple interacting predictors can be represented effectively by multiplicative kernel smoothers. NPMR allows us to abandon simplistic assumptions about overall model form, while embracing the ecological truism that habitat factors interact.     

Portrait of the Patient as a Young Man: An Exploration of the Use of Photographs in Hospital

The display of personal photographs in hospital is a common practice that has yet to be rigorously examined. The photographs displayed are subject to interpretation by the viewer and may lead to misunderstandings or miscommunication if clarification of meaning is not sought. This paper explores a range of possible meanings that the display of photographs in hospital may hold, based on a case study of a 15 year old boy hospitalised with a life threatening illness. Further research is needed into the actual meanings attributed to the display of photographs in hospital by patients and family members.     

Evaluation of Medium Components by Plackett-Burman Statistical Design for Lipase Production by Candida rugosa and Kinetic Modeling

Lipase production by Candida rugosa was carried out in submerged fermentation. Plackett-Burman statistical experimental design was applied to evaluate the fermentation medium components. The effect of twelve medium components was studied in sixteen experimental trials. Glucose, olive oil, peptone and FeCl3?6H2O were found to have more significance on lipase production by Candida rugosa. Maximum lipase activity of 3.8 u mL-1 was obtained at 50 h of fermentation period. The fermentation was carried out at optimized temperature of 30oC, initial pH of 6.8 and shaking speed of 120 r/min. Unstructured kinetic models were used to simulate the experimental data. Logistic model, Luedeking-Piret model and modified Luedeking-Piret model were found suitable to efficiently predict the cell mass, lipase production and glucose consumption respectively with high determination coefficient(R2). From the estimated values of the Luedeking-Piret kinetic model parameters, α and β, it was found that the lipase production by Candida rugosa is growth associated.