A strategy based on protein-protein interface motifs may help in identifying drug off-targets

Networks are increasingly used to study the impact of drugs at the systems level. From the algorithmic standpoint, a drug can "attack" nodes or edges of a protein-protein interaction network. In this work, we propose a new network strategy, "The Interface Attack", based on protein-protein interfaces. Similar interface architectures can occur between unrelated proteins. Consequently, in principle, a drug that binds to one has a certain probability of binding to others. The interface attack strategy simultaneously removes from the network all interactions that consist of similar interface motifs. This strategy is inspired by network pharmacology and allows inferring potential off-targets. We introduce a network model that we call "Protein Interface and Interaction Network (P2IN)", which is the integration of protein-protein interface structures and protein interaction networks. This interface-based network organization clarifies which protein pairs have structurally similar interfaces and which proteins may compete to bind the same surface region. We built the P2IN with the p53 signaling network and performed network robustness analysis. We show that (1) "hitting" frequent interfaces (a set of edges distributed around the network) might be as destructive as eleminating high degree proteins (hub nodes), (2) frequent interfaces are not always topologically critical elements in the network, and (3) interface attack may reveal functional changes in the system better than the attack of single proteins. In the off-target detection case study, we found that drugs blocking the interface between CDK6 and CDKN2D may also affect the interaction between CDK4 and CDKN2D.     

Multimodal hard X‐ray imaging of a mammography phantom at a compact synchrotron light source

The Compact Light Source is a miniature synchrotron producing X‐rays at the interaction point of a counter‐propagating laser pulse and electron bunch through the process of inverse Compton scattering. The small transverse size of the luminous region yields a highly coherent beam with an angular divergence of a few milliradians. The intrinsic monochromaticity and coherence of the produced X‐rays can be exploited in high‐sensitivity differential phase‐contrast imaging with a grating‐based interferometer. Here, the first multimodal X‐ray imaging experiments at the Compact Light Source at a clinically compatible X‐ray energy of 21 keV are reported. Dose‐compatible measurements of a mammography phantom clearly demonstrate an increase in contrast attainable through differential phase and dark‐field imaging over conventional attenuation‐based projections.     

Hard X‐ray phase‐contrast imaging with the Compact Light Source based on inverse Compton X‐rays

The first imaging results obtained from a small‐size synchrotron are reported. The newly developed Compact Light Source produces inverse Compton X‐rays at the intersection point of the counter propagating laser and electron beam. The small size of the intersection point gives a highly coherent cone beam with a few milliradian angular divergence and a few percent energy spread. These specifications make the Compact Light Source ideal for a recently developed grating‐based differential phase‐contrast imaging method.     

Unexpected product distributions in the synthesis of 2,6-bis-(indazolyl)pyridine and 2-(pyrazol-1-yl)-6-(indazolyl)pyridine

Reaction of 2-bromopyridine with 2 equiv of sodium indazolide in diglyme at 140 °C affords 2,6-bis-(indazol-1-yl)pyridine and 2-(indazol-1-yl)-6-(indazol-2-yl)pyridine in purified yields of 24% and 68% respectively. A similar reaction, using 1 equiv of sodium indazolide at 70 °C, gives a low-yield mixture of 2-(indazol-1-yl)-6-bromopyridine and 2-(indazol-2-yl)-6-bromopyridine. Both these intermediates are transformed into 2-(pyrazol-1-yl)-6-(indazol-1-yl)pyridine and 2,6-di(pyrazol-1-yl)pyridine upon treatment with 1 equiv of sodium pyrazolide in diglyme at 140 °C. These observations imply that the indazolyl group is a leaving group comparable to a bromo substituent under nucleophilic attack by pyrazolide or indazolide ions under these conditions. No reaction was observed between 2-(pyrazol-1-yl)-6-bromopyridine and 1 equiv of sodium indazolide under the same conditions. A single crystal structure of its iron(II) complex confirmed the regiochemistry of 2,6-bis-(indazol-1-yl)pyridine, and revealed significant conformational flexibility in the distal ligand indazolyl groups.     

Photoreactivity of biologically active compounds. XIX: Excited states and free radicals from the antimalarial drug primaquine

The formation and reactivity of excited states and free radicals from primaquine, a drug used in the treatment of malaria, was studied in order to evaluate the primary photochemical reaction mechanisms. The excited primaquine triplet was not detected, but is likely to be formed with a short lifetime (<50 ns) and with a triplet energy <250 kJ/mol as the drug is an efficient quencher of the fenbufen triplet and the biphenyl triplet, and forms ${}^1{\text{O}}_2$ by laser flash photolysis $({}^{\text{PQ}}{\Phi }_{\mathrm{\Delta }}=0.025)$. Primaquine (PQ) exists as the monocation $({\text{PQH}}^{+})$ in aqueous solution at physiological pH. ${\text{PQH}}^{+}$ photoionises by a biphotonic process and also forms the monoprotonated cation radical $({\text{PQH}}^{2+\text{<mglyph src="https://sdfestaticassets-us-east-1.sciencedirectassets.com/shared-assets/16/entities/rad"></mglyph>}})$ by one electron oxidation by ${\text{HO}}^{\text{<mglyph src="https://sdfestaticassets-us-east-1.sciencedirectassets.com/shared-assets/16/entities/rad"></mglyph>}}$ (k_q = 6.6 × 10⁹ M^?1 s^?1) and ${\text{Br}}_2^{\text{<mglyph src="https://sdfestaticassets-us-east-1.sciencedirectassets.com/shared-assets/16/entities/rad"></mglyph>}-}$ (k_q = 4.7 × 10⁹ M^?1 s^?1) at physiological pH, detected as a long-lived transient decaying essentially by a second order process (k₂ = 7.4 × 10⁸ M^?1 s^?1). ${\text{PQH}}^{2+\text{<mglyph src="https://sdfestaticassets-us-east-1.sciencedirectassets.com/shared-assets/16/entities/rad"></mglyph>}}$ is scavenged by O₂, although at a limited rate (k_q = 1.0 × 10⁶ M^?1 s^?1). The reduction potential (E°) of ${\text{PQH}}^{2+\text{<mglyph src="https://sdfestaticassets-us-east-1.sciencedirectassets.com/shared-assets/16/entities/rad"></mglyph>}}/{\text{PQH}}^{+}$ is < +1015 mV, as measured versus tryptophan (${\text{TRP}}^{\text{<mglyph src="https://sdfestaticassets-us-east-1.sciencedirectassets.com/shared-assets/16/entities/rad"></mglyph>}}/\text{TRPH}$). Primaquine also forms ${\text{PQH}}^{2+\text{<mglyph src="https://sdfestaticassets-us-east-1.sciencedirectassets.com/shared-assets/16/entities/rad"></mglyph>}}$ at pH 2.4, by one electron oxidation by ${\text{Br}}_2^{\text{<mglyph src="https://sdfestaticassets-us-east-1.sciencedirectassets.com/shared-assets/16/entities/rad"></mglyph>}-}$ and proton loss (k_q = 2.7 × 10⁹ M^?1 s^?1). The non-protonated cation radical (${\text{PQ}}^{+\text{<mglyph src="https://sdfestaticassets-us-east-1.sciencedirectassets.com/shared-assets/16/entities/rad"></mglyph>}}$) is formed during one electron oxidation with ${\text{Br}}_2^{\text{<mglyph src="https://sdfestaticassets-us-east-1.sciencedirectassets.com/shared-assets/16/entities/rad"></mglyph>}-}$ at alkaline conditions (k_q = 4.2 × 10⁹ M^?1 s^?1 at pH 10.8). The estimated pK_a-value of ${\text{PQH}}^{2+\text{<mglyph src="https://sdfestaticassets-us-east-1.sciencedirectassets.com/shared-assets/16/entities/rad"></mglyph>}}/{\text{PQ}}^{+\text{<mglyph src="https://sdfestaticassets-us-east-1.sciencedirectassets.com/shared-assets/16/entities/rad"></mglyph>}}$ is pK_a ～ 7–8. Primaquine is not a scavenger of ${\text{O}}_2^{\text{<mglyph src="https://sdfestaticassets-us-east-1.sciencedirectassets.com/shared-assets/16/entities/rad"></mglyph>}-}$ at physiological pH. Thus self-sensitization by ${\text{O}}_2^{\text{<mglyph src="https://sdfestaticassets-us-east-1.sciencedirectassets.com/shared-assets/16/entities/rad"></mglyph>}-}$ is eliminated as a degradation pathway in the photochemical reactions. Impurities in the raw material and photochemical degradation products initiate photosensitized degradation of primaquine in deuterium oxide, prevented by addition of the ${}^1{\text{O}}_2$ quencher sodium azide. Photosensitized degradation by formation of ${}^1{\text{O}}_2$ is thus important for the initial photochemical decomposition of primaquine, which also proceeds by free radical reactions. Formation of ${\text{PQH}}^{2+\text{<mglyph src="https://sdfestaticassets-us-east-1.sciencedirectassets.com/shared-assets/16/entities/rad"></mglyph>}}$ is expected to play an essential part in the photochemical degradation process in a neutral, aqueous medium.     

Finiteness properties of automorphism groups of right-angled Artin groups

We study the algebraic structure of the outer automorphism groupof a general right-angled Artin group. We show that this groupis virtually torsion-free and has finite virtual cohomologicaldimension. This generalizes results proved earlier by the authorsand Crisp for 2-dimensional right-angled Artin groups.     

Seasonal influences on sleep and executive function in the migratory White-crowned Sparrow (<Emphasis Type="Italic">Zonotrichia leucophrys gambelii</Emphasis>)

Background  

We have previously shown that the White-crowned Sparrow (WCS) decreases sleep by 60% during a period of migratory restlessness relative to a non-migratory period when housed in a 12 h light: 12 h dark cycle. Despite this sleep reduction, accuracy of operant performance was not impaired, and in fact rates of responding were elevated during the migratory period, effects opposite to those routinely observed following enforced sleep deprivation. To determine whether the previously observed increases in operant responding were due to improved performance or to the effects of migration on activity level, here we assessed operant performance using a task in which optimal performance depends on the bird's ability to withhold a response for a fixed interval of time (differential-reinforcement-of-low-rate-behavior, or DRL); elevated response rates ultimately impair performance by decreasing access to food reward. To determine the influence of seasonal changes in day length on sleep and behavioral patterns, we recorded sleep and assessed operant performance across 4 distinct seasons (winter, spring, summer and fall) under a changing photoperiod.     

A Neutral “Aluminocene” Sandwich Complex: η1‐ versus η5‐Coordination Modes of a Pentaarylborole with ECp* (E=Al,Ga; Cp*=C5Me5)

The pentaaryl borole (Ph*C)₄BXyl^F [Ph*=3,5‐tBu₂(C₆H₃); Xyl^F=3,5‐(CF₃)₂(C₆H₃)] reacts with low‐valent Group 13 precursors AlCp* and GaCp* by two divergent routes. In the case of [AlCp*]₄, the borole reacts as an oxidising agent and accepts two electrons. Structural, spectroscopic, and computational analysis of the resulting unprecedented neutral η⁵‐Cp*,η⁵‐[(Ph*C)₄BXyl^F] complex of Al^III revealed a strong, ionic bonding interaction. The formation of the heteroleptic borole‐cyclopentadienyl “aluminocene” leads to significant changes in the ¹³C NMR chemical shifts within the borole unit. In the case of the less‐reductive GaCp*, borole (Ph*C)₄BXyl^F reacts as a Lewis acid to form a dynamic adduct with a dative 2‐center‐2‐electron Ga?B bond. The Lewis adduct was also studied structurally, spectroscopically, and computationally.     

Toward Chirality‐Encoded Domain Wall Logic

Nonvolatile logic networks based on spintronic and nanomagnetic technologies have the potential to create high‐speed, ultralow power computational architectures. This article explores the feasibility of “chirality‐encoded domain wall logic,” a nanomagnetic logic architecture where data are encoded by the chiral structures of mobile domain walls in networks of ferromagnetic nanowires and processed by the chiral structures' interactions with geometric features of the networks. High‐resolution magnetic imaging is used to test two critical functionalities: the inversion of domain wall chirality at tailored artificial defect sites (logical NOT gates) and the chirality‐selective output of domain walls from 2‐in‐1‐out nanowire junctions (common operation to AND/NAND/OR/NOR gates). The measurements demonstrate both operations can be performed to a good degree of fidelity even in the presence of complex magnetization dynamics that would normally be expected to destroy chirality‐encoded information. Together, these results represent a strong indication of the feasibility of devices where chiral magnetization textures are used to directly carry, rather than merely delineate, data.