Exploring the relationship between hub proteins and drug targets based on GO and intrinsic disorder

Protein–protein interactions (PPIs) play essential roles in many biological processes. In protein–protein interaction networks, hubs involve in numbers of PPIs and may constitute an important source of drug targets. The intrinsic disorder proteins (IDPs) with unstable structures can promote the promiscuity of hubs and also involve in many disease pathways, so they also could serve as potential drug targets. Moreover, proteins with similar functions measured by semantic similarity of gene ontology (GO) terms tend to interact with each other. Here, the relationship between hub proteins and drug targets based on GO terms and intrinsic disorder was explored. The semantic similarities of GO terms and genes between two proteins, and the rate of intrinsic disorder residues of each protein were extracted as features to characterize the functional similarity between two interacting proteins. Only using 8 feature variables, prediction models by support vector machine (SVM) were constructed to predict PPIs. The accuracy of the model on the PPI data from human hub proteins is as high as 83.72%, which is very promising compared with other PPI prediction models with hundreds or even thousands of features. Then, 118 of 142 PPIs between hubs are correctly predicted that the two interacting proteins are targets of the same drugs. The results indicate that only 8 functional features are fully efficient for representing PPIs. In order to identify new targets from IDP dataset, the PPIs between hubs and IDPs are predicted by the SVM model and the model yields a prediction accuracy of 75.84%. Further research proves that 3 of 5 PPIs between hubs and IDPs are correctly predicted that the two interacting proteins are targets of the same drugs. All results demonstrate that the model with only 8-dimensional features from GO terms and intrinsic disorder still gives a good performance in predicting PPIs and further identifying drug targets.     

A chalcone showing positional disorder,two related diarylcyclohexenones showing enantiomeric disorder and a related hydroxyterphenyl,all derived from simple carbonyl precursors

Four compounds are reported, all of which lie along a versatile reaction pathway which leads from simple carbonyl compounds to terphenyls. (2E)‐1‐(2,4‐Dichlorophenyl)‐3‐ [4‐(prop‐1‐en‐2‐yl)phenyl]prop‐2‐en‐1‐one, C₁₈H₁₄Cl₂O, (I), prepared from 4‐(prop‐1‐en‐2‐yl)benzaldehyde and 2,4‐dichloroacetophenone, exhibits disorder over two sets of atomic sites having occupancies of 0.664 (6) and 0.336 (6). The related chalcone (2E)‐3‐(4‐chlorophenyl)‐1‐(4‐fluorophenyl)prop‐2‐en‐1‐one reacts with acetone to produce (5RS)‐3‐(4‐chlorophenyl)‐5‐[4‐(propan‐2‐yl)phenyl]cyclohex‐2‐en‐1‐one, C₂₁H₂₁ClO, (II), which exhibits enantiomeric disorder with occupancies at the reference site of 0.662 (4) and 0.338 (4) for the (5R) and (5S) forms; the same chalcone reacts with methyl 3‐oxobutanoate to give methyl (1RS,6SR)‐4‐(4‐chlorophenyl)‐6‐[4‐(propan‐2‐yl)phenyl]‐2‐oxocyclohex‐3‐ene‐1‐carboxylate, C₂₃H₂₃ClO₃, (III), where the reference site contains both (1R,6S) and (1S,6R) forms with occupancies of 0.923 (3) and 0.077 (3), respectively. Oxidation, using 2,3‐dichloro‐5,6‐dicyano‐1,4‐benzoquinone, of ethyl (1RS,6SR)‐6‐(4‐bromophenyl)‐4‐(4‐fluorophenyl)‐2‐oxocyclohex‐3‐ene‐1‐carboxylate, prepared in a similar manner to (II) and (III), produces ethyl 4′′‐bromo‐4‐fluoro‐5′‐hydroxy‐1,1′:3′,1′′‐terphenyl‐4′‐carboxylate, C₂₁H₁₆BrFO₃, (IV), which crystallizes with Z′ = 2 in the space group P. There are no significant intermolecular interactions in the structures of compounds (I) and (II), but for the major disorder component of compound (III), the molecules are linked into sheets by a combination of C—H...O and C—H...π(arene) hydrogen bonds. The two independent molecules of compound (IV) form two different centrosymmetric dimers, one built from inversion‐related pairs of C—H...O hydrogen bonds and the other from inversion‐related pairs of C—H...π(arene) hydrogen bonds. Comparisons are made with related compounds.     

The Origin of Hierarchical Structure Formation in Highly Grafted Symmetric Supramolecular Double‐Comb Diblock Copolymers

Involving supramolecular chemistry in self‐assembling block copolymer systems enables design of complex macromolecular architectures that, in turn, could lead to complex phase behavior. It is an elegant route, as complicated and sensitive synthesis techniques can be avoided. Highly grafted double‐comb diblock copolymers based on symmetric double hydrogen bond accepting poly(4‐vinylpyridine)‐block‐poly(N‐acryloylpiperidine) diblock copolymers and donating 3‐nonadecylphenol amphiphiles are realized and studied systematically by changing the molecular weight of the copolymer. Double perpendicular lamellae‐in‐lamellae are formed in all complexes, independent of the copolymer molecular weight. Temperature‐resolved measurements demonstrate that the supramolecular nature and ability to crystallize are responsible for the formation of such multiblock‐like structures. Because of these driving forces and severe plasticization of the complexes in the liquid crystalline state, this supramolecular approach can be useful for steering self‐assembly of both low‐ and high‐molecular‐weight block copolymer systems.     

Deciphering composition and connectivity of a natural product with the assistance of MS and 2D NMR

A complementary application of three analytical techniques, viz. multidimensional nuclear magnetic resonance spectroscopy (NMR), mass spectrometry (MS), and single‐crystal X‐ray diffractometry was required to identify and refine two natural products isolated from Millettia versicolor and solvent of crystallization. The two compounds, namely 3‐(2H‐1,3‐benzodioxol‐5‐yl)‐6‐methoxy‐8,8‐dimethyl‐4H ,8H‐pyrano[2,3‐h ]chromen‐4‐one, or durmillone, (I), and (2E )‐1‐(4‐{[(2E )‐3,7‐dimethylocta‐2,6‐dien‐1‐yl]oxy}‐2‐hydroxyphenyl)‐3‐(4‐hydroxyphenyl)prop‐2‐en‐1‐one, (II), could not be separated by routine column chromatography and cocrystallized in a 2:1 ratio with 0.13 molecules of ethanol solvent. Compound (II) and ethanol could not be initially identified by single‐crystal X‐ray analysis due to complex disorder in the aliphatic chain region of (II). Mass spectrometry ensured that (II) represented only one species disordered over several positions in the solid state, rather than several species cohabitating on the same crystallographic site. The atomic identification and connectivity in (II) were established by several 2D (two‐dimensional) NMR techniques, which in turn relied on a knowledge of its exact mass. The derived connectivity was then used in the single‐crystal analysis to model the disorder of the aliphatic chain in (II) over three positions and allowed identification of a partially occupied ethanol solvent molecule that was disordered over an inversion center. The disordered moieties were refined with restraints and constraints.     

The intermediate disorder regime for a directed polymer model on a hierarchical lattice

We study a directed polymer model defined on a hierarchical diamond lattice, where the lattice is constructed recursively through a recipe depending on a branching number $b\in \mathbb{N}$ and a segment number $s\in \mathbb{N}$. When $b\le s$ it is known that the model exhibits strong disorder for all positive values of the inverse temperature $\beta$, and thus weak disorder reigns only for $\beta =0$ (infinite temperature). Our focus is on the so-called intermediate disorder regime in which the inverse temperature $\beta \equiv {\beta }_n$ vanishes at an appropriate rate as the size $n$ of the system grows. Our analysis requires separate treatment for the cases $b<s$ and $b=s$. In the case $b<s$ we prove that when the inverse temperature is taken to be of the form ${\beta }_n=\stackrel{?}{\beta }{(b/s)}^{n/2}$ for $\stackrel{?}{\beta }>0$, the normalized partition function of the system converges weakly as $n\to \infty$ to a distribution $L\left(\stackrel{?}{\beta }\right)$ and does so universally with respect to the initial weight distribution. We prove the convergence using renormalization group type ideas rather than the standard Wiener chaos analysis. In the case $b=s$ we find a critical point in the behavior of the model when the inverse temperature is scaled as ${\beta }_n=\stackrel{?}{\beta }/n$; for an explicitly computable critical value ${\kappa }_b>0$ the variance of the normalized partition function converges to zero with large $n$ when $\stackrel{?}{\beta }\le {\kappa }_b$ and grows without bound when $\stackrel{?}{\beta }>{\kappa }_b$. Finally, we prove a central limit theorem for the normalized partition function when $\stackrel{?}{\beta }\le {\kappa }_b$.     

Dynamics of Nonlinear Cyclic Systems with Structural Irregularity

The dynamics of weakly coupled, nonlinear cyclic assemblies are investigated in the presence of weak structural mistuning. The method of multiple scales is used to obtain a set of nonlinear algebraic equations which govern the steady-state, synchronous (modal-like) motions for the structures. Considering a degenerate assembly of uncoupled oscillators, spatially localized modes are computed corresponding to motions during which vibrational energy is spatially confined to one oscillator (strong localization) or a subset of oscillators (weak localization). In the limit of weak substructural coupling, asymptotic solutions are obtained which correspond to (i) spatially extended, (ii) strongly localized, and (iii) weakly localized modes for fully coupled systems. Throughout the analysis, the influence of structural mistunings on the resulting solutions are discussed. Additionally, numerical solutions (including linearized stability characteristics) are obtained for prototypical two- and three-degree-of-freedom (DoF) systems with various structural mistunings. The numerical results provide insight into the strong influence of structural irregularities on the dynamical behavior of nonlinear cyclic systems, and demonstrate that the combined influences of structural mistunings and nonlinearities do not lead to uniform improvement of motion confinement characteristics.     

共轭聚合物中均匀无序对极化子输运动力学的影响

基于扩展的Su-Schrieffer-Heeger紧束缚模型和非绝热动力学方法, 研究了共轭聚合物材料中均匀无序效应对极化子输运动力学的影响. 研究发现: 极化子的动力学输运过程由外加电场和均匀无序效应共同决定; 在大部分电场范围下, 均匀无序效应对极化子输运的影响不太明显, 几乎可以忽略; 但在弱电场下, 均匀无序效应不利于极化子输运. 与高斯型无序效应下极化子的输运过程相比, 具有均匀无序的薄膜形貌更有利于极化子输运.     

Coupled crystallographic order-disorder and spin state in a bistable molecule: multiple transition dynamics

A novel bispyrazolylpyridine ligand incorporating lateral phenol groups, H₄L, has led to an Fe^II spin‐crossover (SCO) complex, [Fe(H₄L)₂][ClO₄]₂ ? H₂O ? 2 (CH₃)₂CO ( 1 ), with an intricate network of intermolecular interactions. It exhibits a 40 K wide hysteresis of magnetization as a result of the spin transition (with T_0.5 of 133 and 173 K) and features an unsymmetrical and very rich structure. The latter is a consequence of the coupling between the SCO and the crystallographic transformations. The high‐spin state may also be thermally trapped, exhibiting a very large T_TIESST (≈104 K). The structure of 1 has been determined at various temperatures after submitting the crystal to different processes to recreate the key points of the hysteresis cycle and thermal trapping; 200 K, cooled to 150 K and trapped at 100 K (high spin, HS), slowly cooled to 100 K and warmed to 150 K (low spin, LS). In the HS state, the system always exhibits disorder for some components (one ClO₄^? and two acetone molecules) whereas the LS phases show a relative ≈9 % reduction in the Fe? N bond lengths and anisotropic contraction of the unit cell. Most importantly, in the LS state all the species are always found to be ordered. Therefore, the bistability of crystallographic order–disorder coupled to SCO is demonstrated here experimentally for the first time. The variation in the cell parameters in 1 also exhibits hysteresis. The structural and magnetic thermal variations in this compound are paralleled by changes in the heat capacity as measured by differential scanning calorimetry. Attempts to simulate the asymmetric SCO behaviour of 1 by using an Ising‐like model underscore the paramount role of dynamics in the coupling between the SCO and the crystallographic transitions.     

Anti-TNF-α Compounds as a Treatment for Depression

Millions of people around the world suffer from psychiatric illnesses, causing unbearable burden and immense distress to patients and their families. Accumulating evidence suggests that inflammation may contribute to the pathophysiology of psychiatric disorders such as major depression and bipolar disorder. Copious studies have consistently shown that patients with mood disorders have increased levels of plasma tumor necrosis factor (TNF)-α. Given these findings, selective anti-TNF-α compounds were tested as a potential therapeutic strategy for mood disorders. This mini-review summarizes the results of studies that examined the mood-modulating effects of anti-TNF-α drugs.