Click‐Assembled,Oxygen‐Sensing Nanoconjugates for Depth‐Resolved,Near‐Infrared Imaging in a 3 D Cancer Model

Hypoxia is an important contributing factor to the development of drug‐resistant cancer, yet few nonperturbative tools exist for studying oxygenation in tissues. While progress has been made in the development of chemical probes for optical oxygen mapping, penetration of such molecules into poorly perfused or avascular tumor regions remains problematic. A click‐assembled oxygen‐sensing (CAOS) nanoconjugate is reported and its properties demonstrated in an in vitro 3D spheroid cancer model. The synthesis relies on the sequential click‐based ligation of poly(amidoamine)‐like subunits for rapid assembly. Near‐infrared confocal phosphorescence microscopy was used to demonstrate the ability of the CAOS nanoconjugates to penetrate hundreds of micrometers into spheroids within hours and to show their sensitivity to oxygen changes throughout the nodule. This proof‐of‐concept study demonstrates a modular approach that is readily extensible to a wide variety of oxygen and cellular sensors for depth‐resolved imaging in tissue and tissue models.     

Oxime Side‐Chain Cross‐Links in an α‐Helical Coiled‐Coil Protein: Structure,Thermodynamics, and Folding‐Templated Synthesis of Bicyclic Species

Covalent side‐chain cross‐links are a versatile method to control peptide folding, particularly when α‐helical secondary structure is the target. Here, we examine the application of oxime bridges, formed by the chemoselective reaction between aminooxy and aldehyde side chains, for the stabilization of a helical peptide involved in a protein–protein complex. A series of sequence variants of the dimeric coiled coil GCN4‐p1 bearing oxime bridges at solvent‐exposed positions were prepared and biophysically characterized. Triggered unmasking of a side‐chain aldehyde in situ and subsequent cyclization proceed rapidly and cleanly at pH 7 in the folded protein complex. Comparison of folding thermodynamics among a series of different oxime bridges show that the cross links are consistently stabilizing to the coiled coil, with the extent of stabilization sensitive to the exact size and structure of the macrocycle. X‐ray crystallographic analysis of a coiled coil with the best cross link in place and a second structure of its linear precursor show how the bridge is accommodated into an α‐helix. Preparation of a bicyclic oligomer by simultaneous formation of two linkages in situ demonstrates the potential use of triggered oxime formation to both trap and stabilize a particular peptide folded conformation in the bound state.     

Ruthenium Complexes of an Abnormally Bound,Anionic N‐Heterocyclic Carbene

The abnormally bound, anionic NHC–borane complex [Ru(IDipp‐BF₃)(p‐cymene)Cl]₂ ( 4 ; IDipp‐BF₃=1,3‐(2,6‐iPr₂C₆H₃)₂‐2‐BF₃(C₃HN₂)‐4‐yl) was synthesized by transmetalation from Li[(IDipp‐BF₃)₂Ag]. Addition of donors gave species of the form [Ru(IDipp‐BF₃)(p‐cymene)(L)Cl], whereas halide abstraction with Ag(Et₂O)[B(C₆F₅)₄] gave C?H activation of the methine position of the IDipp?BF₃ ligand.     

D3R grand challenge 4: blind prediction of protein–ligand poses,affinity rankings,and relative binding free energies

Journal of Computer-Aided Molecular Design - The Drug Design Data Resource (D3R) aims to identify best practice methods for computer aided drug design through blinded ligand pose prediction and...     

A redox-mediator pathway for enhanced multi-colour electrochemiluminescence in aqueous solution

The classic and most widely used co-reactant electrochemiluminescence (ECL) reaction of tris(2,2′-bipyridine)ruthenium(ii) ([Ru(bpy)₃]²⁺) and tri-n-propylamine is enhanced by an order of magnitude by fac-[Ir(sppy)₃]³⁻ (where sppy = 5′-sulfo-2-phenylpyridinato-C²,N), through a novel ‘redox mediator’ pathway. Moreover, the concomitant green emission of [Ir(sppy)₃]³⁻* enables internal standardisation of the co-reactant ECL of [Ru(bpy)₃]²⁺. This can be applied using a digital camera as the photodetector by exploiting the ratio of R and B values of the RGB colour data, providing superior sensitivity and precision for the development of low-cost, portable ECL-based analytical devices.

A water-soluble Ir(iii) complex is shown to enhance the ‘remote’ mechanism of the most widely used co-reactant ECL reaction of tris(2,2′-bipyridine)ruthenium(ii) with tripropylamine.     

Epistemic Communities under Active Inference

The spread of ideas is a fundamental concern of today’s news ecology. Understanding the dynamics of the spread of information and its co-option by interested parties is of critical importance. Research on this topic has shown that individuals tend to cluster in echo-chambers and are driven by confirmation bias. In this paper, we leverage the active inference framework to provide an in silico model of confirmation bias and its effect on echo-chamber formation. We build a model based on active inference, where agents tend to sample information in order to justify their own view of reality, which eventually leads to them to have a high degree of certainty about their own beliefs. We show that, once agents have reached a certain level of certainty about their beliefs, it becomes very difficult to get them to change their views. This system of self-confirming beliefs is upheld and reinforced by the evolving relationship between an agent’s beliefs and observations, which over time will continue to provide evidence for their ingrained ideas about the world. The epistemic communities that are consolidated by these shared beliefs, in turn, tend to produce perceptions of reality that reinforce those shared beliefs. We provide an active inference account of this community formation mechanism. We postulate that agents are driven by the epistemic value that they obtain from sampling or observing the behaviours of other agents. Inspired by digital social networks like Twitter, we build a generative model in which agents generate observable social claims or posts (e.g., ‘tweets’) while reading the socially observable claims of other agents that lend support to one of two mutually exclusive abstract topics. Agents can choose which other agent they pay attention to at each timestep, and crucially who they attend to and what they choose to read influences their beliefs about the world. Agents also assess their local network’s perspective, influencing which kinds of posts they expect to see other agents making. The model was built and simulated using the freely available Python package pymdp. The proposed active inference model can reproduce the formation of echo-chambers over social networks, and gives us insight into the cognitive processes that lead to this phenomenon.