Discovery of structurally distinct tricyclic M4 positive allosteric modulator (PAM) chemotypes

This Letter details our efforts to develop new M₄ PAM scaffolds with improved pharmacological properties. This endeavor involved replacing the 3,4-dimethylpyridazine core with two novel cores: a 2,3-dimethyl-2H-indazole-5-carboxamide core or a 1-methyl-1H-benzo[d][1,2,3]triazole-6-carboxamide core. Due to shallow SAR, these cores were further evolved into two unique tricyclic cores: an 8,9-dimethyl-8H-pyrazolo[3,4-h]quinazoline core and an 1-methyl-1H-[1,2,3]triazolo[4,5-h]quinazoline core. Both tricyclic cores displayed low nanomolar potency against both human and rat M₄.     

Direct observation of positive supercoils introduced by reverse gyrase through atomic force microscopy

Reverse gyrase is a hyperthermophilic enzyme that can introduce positive supercoiling in substrate DNA. It is showed in our studies that positive DNA supercoils were induced in both pBR322 vector and an artificially synthesized mini-plasmid DNA by reverse gyrase. The left-handed structures adopted by positively supercoiled DNA molecules could be identified from their right-handed topoisomers through atomic force microscopic examination. Additional structural comparisons revealed that positively supercoiled DNA molecule AFM images exhibited increased contour lengths. Moreover, enzymatic assays showed that the positively supercoiled DNA could not be cleaved by T7 endonuclease. Together, this suggests that the overwound structure of positive supercoils could prevent genomic duplex DNA from randomly forming single-stranded DNA regions and intra-stranded secondary structures.     

On Dioxygen and Substrate Access to Soluble Methane Monooxygenases: An all‐Atom Molecular Dynamics Investigation in Water Solution

In a preliminary exploration of the dummy model for diiron proteins, random‐acceleration molecular dynamics (RAMD) revealed that a pure four‐helix bundle structure, like hemerythrin, constitutes an efficient cage for dioxygen (O₂), which can only leave from defined, albeit very broad, gates. However, this well ordered structure does not constitute an archetype on which to compare O₂ permeation of other diiron proteins, like the complex of soluble methane monooxygenase hydroxylase with the regulatory protein (sMMOH‐MMOB). The reason is that with this complex, unlike hemerythrin, the four helices of the four‐helix bundle are heavily bent, and RAMD showed that most traps for O₂ lie outside them. It was also observed that, in spite of a nearly identical van der Waals radius for O₂ and the natural substrate CH₄, the latter behaves under RAMD as a bulkier molecule than O₂, requiring a higher external force to be brought out of sMMOH‐MMOB along trajectories of viable length. All that determined with sMMOH‐MMOB multiple gates and multiple pathways to each of them through several binding pockets, for both O₂ and CH₄. Of the two equally preferred pathways for O₂, at right angle with one another, one proved to be in accordance with the Xe‐atom mapping for sMMOH. In contrast, none of the pathways identified for CH₄ proved to be in accordance with such mapping, CH₄ looking for more open avenues instead.     

Accelerating patient access to novel biologics using stable pool‐derived product for non‐clinical studies and single clone‐derived product for clinical studies

Cell cloning and subsequent process development activities are on the critical path directly impacting the timeline for advancement of next generation therapies to patients with unmet medical needs. The use of stable cell pools for early stage material generation and process development activities is an enabling technology to reduce timelines. To successfully use stable pools during development, it is important that bioprocess performance and requisite product quality attributes be comparable to those observed from clonally derived cell lines. To better understand the relationship between pool and clone derived cell lines, we compared data across recent first in human (FIH) programs at Amgen including both mAb and Fc‐fusion modalities. We compared expression and phenotypic stability, bioprocess performance, and product quality attributes between material derived from stable pools and clonally derived cells. Overall, our results indicated the feasibility of matching bioprocess performance and product quality attributes between stable pools and subsequently derived clones. These findings support the use of stable pools to accelerate the advancement of novel biologics to the clinic. © 2017 The Authors Biotechnology Progress published by Wiley Periodicals, Inc. on behalf of American Institute of Chemical Engineers Biotechnol. Prog., 33:1476–1482, 2017     

Spatial patterns in cushion‐dominated plant communities of the high Andes of central Chile: How frequent are positive associations?

Question: In stressful abiotic environments positive plant interaction is expected to be a frequent and an important process driving community composition and structure. In the high Andes in central Chile, the cushion plant Azorella madreporica dominates plant communities and appears to benefit the assemblage of species that grows within it. However, there are also many other species that grow outside this nurse cushion plant, which may or may not interact with this species. What is the prevailing type of spatial associations among the plant species that are not growing inside the nurse plant? What is the type of interactions between cushion plants and those species growing outside them? Location: Molina River basin (33°20'S, 70°16’ W, 3600 m a.s.l.), in the Andes of central Chile, ca. 50 km east of Santiago. Methods: Two accurate mapping plots of individual plants of different species were located at two summits (Franciscano and Tres Puntas sites). The spatial distributions and associations between species growing outside cushions and within cushions at each site were estimated by point‐pattern analyses using the univariate and bivariate transformations of Ripley's K‐functions. Results: We found both positive and, especially, negative spatial associations (8 out of 12 species in Franciscano site) between A. madreporica cushions and plants growing outside them. However, most of the species showed positive spatial associations among them. The variation in spatial association was site‐specific and also depended on the type of plants involved. Adesmia spp., the second most abundant non‐cushion species, displayed negative associations with cushions and positive associations with other species growing outside cushions. Conclusions: Our study suggests very complex interactions among species, which ranged from positive to negative, and are also affected by abiotic environmental conditions.     

Rational subjects, marriage counselling and the conundrums of eugenics

Against the background of degeneration and the perceived threat to the nation's health and stock, family politics came to constitute an important site for eugenic discourses and interventions. Eugenic regulation of reproductive sexuality and marriage was not only pursued through 'negative' eugenics but also through educational policies targeted at young adults and youth. Switzerland serves as a useful case to explore a general idea, namely the limitations for eugenicists of exploiting the concept of a rational subject in order to achieve their ends. Practices of 'positive eugenics' crucially hinged on the utilitarian principle of rationality underpinning positive eugenics which this paper seeks to elaborate. Eugenicists devised tools to deal efficiently with social problems on a collective as well as an individual basis by deploying technologies of government which conceived individuals to be members of a population who were each held responsible for the generation of healthy future generations. As a form of 'sustaining, multiplying and ordering life' eugenics thus relied on the premise that its ideas would be adopted through an appeal to rationality and, where this was insufficient, through a series of coercive measures. Relying on conviction and education about the merits of eugenics, however, posed particular problems to positive eugenic thinking and practice.     

A Periodic Droop Model for Two Species Competition in A Chemostat

Both uniform persistence and the existence of periodic coexistence state are established for a periodically forced Droop model on two phytoplankton species competition in a chemostat under some appropriate conditions. Numerical simulations using biological data are presented as well to illustrate the main result. Research supported in part by the NSERC of Canada and the MITACS of Canada.     

一类正广义系统的能控性和能观性

对于广义系统的能控性和能观性的研究已经取得了很多成果,但对于正广义系统的研究,目前还处于起步阶段,需要进一步的研究．本文研究了一类正广义系统,通过Drazin逆给出了判别系统能控性和能观性的充分条件,并通过例子验证了本文结论的有效性．     

Conspecific versus heterospecific litter effects on seedling establishment

Plant litter is an important determinant of seed germination and seedling establishment. Positive effects of litter have received considerable attention, but few studies have explicitly tested whether seedlings are more facilitated by conspecific litter compared to heterospecific litter. In order to contrast conspecific and heterospecific facilitative effects on seedling establishment, we used Anthriscus sylvestris, Angelica sylvestris, Pimpinella saxifraga and different combinations of their seeds and litter seedbeds as a model system. Although litter had a significant species-specific effect on seedling emergence, we found no evidence of strictly conspecific facilitation. Anthriscus sylvestris displayed a positive response to all types of litter. In contrast, there was a clear negative effect of conspecific litter in Pimpinella saxifraga. Activated carbon did not modify the negative effect, indicating that chemical compounds were not the cause. Our study suggests a high level of idiosyncrasy in response to litter at the species level.     

Ligand Entry and Exit Pathways in the β2-Adrenergic Receptor

The recently determined crystal structure of the human β₂-adrenergic (β₂AR) G-protein-coupled receptor provides an excellent structural basis for exploring β₂AR-ligand binding and dissociation process. Based on this crystal structure, we simulated ligand exit from the β₂AR receptor by applying the random acceleration molecular dynamics (RAMD) simulation method. The simulation results showed that the extracellular opening on the receptor surface was the most frequently observed egress point (referred to as pathway A), and a few other pathways through interhelical clefts were also observed with significantly lower frequencies. In the egress trajectories along pathway A, the D192-K305 salt bridge between the extracellular loop 2 (ECL2) and the apex of the transmembrane helix 7 (TM7) was exclusively broken. The spatial occupancy maps of the ligand computed from the 100 RAMD simulation trajectories indicated that the receptor-ligand interactions that restrained the ligand in the binding pocket were the major resistance encountered by the ligand during exit and no second barrier was notable. We next performed RAMD simulations by using a putative ligand-free conformation of the receptor as input structure. This conformation was obtained in a standard molecular dynamics simulation in the absence of the ligand and it differed from the ligand-bound conformation in a hydrophobic patch bridging ECL2 and TM7 due to the rotation of F193 of ECL2. Results from the RAMD simulations with this putative ligand-free conformation suggest that the cleft formed by the hydrophobic bridge, TM2, TM3, and TM7 on the extracellular surface likely serves as a more specific ligand-entry site and the ECL2-TM7 hydrophobic junction can be partially interrupted upon the entry of ligand that pushes F193 to rotate, resulting in a conformation as observed in the ligand-bound crystal structure. These results may help in the design of β₂AR-targeting drugs with improved efficacy, as well as in understanding the receptor subtype selectivity of ligand binding in the β family of the adrenergic receptors that share almost identical ligand-binding pockets, but show notable amino acid sequence divergence in the putative ligand-entry site, including ECL2 and the extracellular end of TM7.