Harnessing Protein-Ligand Interaction Fingerprints to Predict New Scaffolds of RIPK1 Inhibitors

Necroptosis has emerged as an exciting target in oncological, inflammatory, neurodegenerative, and autoimmune diseases, in addition to acute ischemic injuries. It is known to play a role in innate immune response, as well as in antiviral cellular response. Here we devised a concerted in silico and experimental framework to identify novel RIPK1 inhibitors, a key necroptosis factor. We propose the first in silico model for the prediction of new RIPK1 inhibitor scaffolds by combining docking and machine learning methodologies. Through the data analysis of patterns in docking results, we derived two rules, where rule #1 consisted of a four-residue signature filter, and rule #2 consisted of a six-residue similarity filter based on docking calculations. These were used in consensus with a machine learning QSAR model from data collated from ChEMBL, the literature, in patents, and from PubChem data. The models allowed for good prediction of actives of >90, 92, and 96.4% precision, respectively. As a proof-of-concept, we selected 50 compounds from the ChemBridge database, using a consensus of both molecular docking and machine learning methods, and tested them in a phenotypic necroptosis assay and a biochemical RIPK1 inhibition assay. A total of 7 of the 47 tested compounds demonstrated around 20–25% inhibition of RIPK1’s kinase activity but, more importantly, these compounds were discovered to occupy new areas of chemical space. Although no strong actives were found, they could be candidates for further optimization, particularly because they have new scaffolds. In conclusion, this screening method may prove valuable for future screening efforts as it allows for the exploration of new areas of the chemical space in a very fast and inexpensive manner, therefore providing efficient starting points amenable to further hit-optimization campaigns.     

一种超高耐久混凝土——梯度结构混凝土

分析超高耐久混凝土的研究现状,提出了一种高耐久、低成本的超高耐久混凝土--梯度结构混凝土(Gradient Structural Concrete,简称GSC),采用电量法和氯离子扩散系数法来评价梯度结构混凝土的抗氯离子渗透性能,最后进行梯度结构混凝土的寿命预测与成本分析.结果表明,高性能混凝土(High Performance Concrete,简称HPC)、无细观界面过渡区水泥基复合材料(Meso-interfacial transition zone-free cement-based materials,简称 MIF)和梯度结构混凝土MIF-HPC的6 h导电量和氯离子扩散系数的排列顺序均为:HPC>MIF-HPC>MIF,其抗氯离子渗透性能排列顺序为:MIF>MIF-HPC>HPC.梯度结构混凝土的成本会有所增加,但由于其氯离子渗透性能大幅降低,其使用寿命得到大幅延长,使得其年损耗费用大幅下降.     

Charge state effect on the K-shell ionization of iron by xenon ions near the Bohr velocity

Fe K-shell ionization cross sections induced by 2.4–6.0 MeV Xe20+are measured and compared with different binaryencounter-approximation(BEA)models.The results indicate that the BEA model corrected both by the Coulomb repulsion and by the effective nuclear charge(Zeff)agrees well with the experimental data.Comparison of Fe K-shell X-ray emission induced by 5 MeV xenon ions with different initial charge states(20+,22+,26+,30+)verifies the applicability of the effective nuclear charge(Zeff)correction for the BEA model.It is found that Zeffcorrection is reasonable to describe direct ionization induced by xenon ions with no initial M-shell vacancies.However,when the M shell is opened,the Zeffcorrected BEA model is unable to explain the inner-shell ionization,and the electron transfer by molecular-orbital promotion should be considered.     

氰化给体中分子间相互作用促进的全小分子光伏混合物的超快电子转移

氰基取代被认为是优化全小分子有机太阳能电池性能的可行方法. 然而,氰基取代对太阳能电池中电荷产生动力学的影响仍未得到探索. 本文光谱研究表明,在全小分子太阳能电池中,氰化给体中增强的分子间电荷转移相互作用会显著促进共混物中的电子转移. 实验发现,在氰基取代给体中,分子间相互作用引起的离域激发,在混合物中会进行超快电子转移. 相比之下,在没有氰基取代的给体中剩余的局域激发态,并没有积极参与电荷分离. 此发现很好地解释了为何氰化取代给体的共混物器件的性能会得到提升,表明可以通过调控分子间相互作用、来优化全小分子器件性能.     

SiH3+O(3P)反应机理的理论研究

利用abinitio方法对SiH3+O(3P)反应进行了理论研究,在MP2/6-311+G(d,p)水平上优化得到了反应途径上的反应物、中间体、过渡态和产物的几何构型,并在QCISD(T)/6-311+G(d,p)水平上进行单点能计算.计算结果表明,SiH3+O(3P)→IM1→TS3→IM2→TS8→HOSi+H2为主反应通道,其他可能存在的次要产物有HSiOH+H、H2SiO+H和HSiO+H2.HOSi、HSiO和HSiOH(cis)还可能进一步解离生成SiO.另外,计算结果对SiH4+O(3P)反应机理中存在的争议给出了可能的解释,认为Withnall等人在实验中观察到的产物HSiOH、H2SiO和SiO并不是SiH4+O(3P)反应的直接产物,而是来自副反应SiH3+O(3P).     

Superfluid-Mott-Insulator Phase Transition Phases of Bosons in an and Collective Fluctuations in both Optical Lattice

The Bose Hubbard model describing interacting bosons in an optical lattice is reduced to a simple spin-1 XY model with single-ion anisotropy in the vicinity of the Mott phase. In the strong coupling Mott insulating regime, we propose a mean t~eld theory based on a constraint SU（3） pseudo-boson representation on the effective model and discuss the excitation spectra and the phase transition to the superfluid state. Further to the superfluid phase, we use the coherent-state approach to derive the collective excitation modes. It is found that the Mort phase has two degenerate gapped quadratic excitation spectra which graduate into two degenerate gapless linear ones at the transition point, and one gapless linear mode with one gapped quadratic mode in the superfluid phase.     

不同类型细胞穿膜肽二级结构特征研究

细胞穿膜肽是一类能以受体依赖或非受体依赖方式介导胞吞作用的小分子短肽,能够携带不同分子穿过细胞膜,这一特性使细胞穿膜肽成为一种有效的运输载体,为药物靶向治疗提供了新希望.本文从生物信息角度针对不同长度区间、运输不同类型分子细胞穿膜肽之间的异同二级结构特征进行了系统研究,同时进一步对不同穿膜方式对应的细胞穿膜肽二级结构特征进行了对比研究,结果表明不同类型细胞穿膜肽之间在二级结构组成上具有不同程度差异特征,为今后揭示细胞穿膜肽相关分子结构机制奠定可靠的理论基础.     

Polyoxometalate/Cellulose Nanofibrils Aerogels for Highly Efficient Oxidative Desulfurization

Polyoxometalate (POM) presents great potential in oxidative desulfurization (ODS) reaction. However, the high dissolubility of POM in common solvents makes it difficult to recycle. Besides, the small specific surface area of POM also limits the interaction between them and the substrate. Depositing polyoxometalates onto three-dimensional (3D) network structured materials could largely expand the application of POM. Here, the surfaces of cellulose nanofibrils (CNFs) were modified with very few (3-Aminopropyl) trimethoxysilane (APTS) to endow positive charges on the surfaces of CNFs, and then phosphotungstic acid (PTA) was loaded to obtain the aerogel A-CNF/PTA as the ODS catalyst. FT-IR indicated the successful deposition of PTA onto aminosilane modified CNF surfaces. UV-VIS further suggested the stability of PTA in the aerogels. BET and SEM results suggested the increased specific surface area and the relatively uniform 3D network structure of the prepared aerogels. TGA analysis indicated that the thermal stability of the aerogel A-CNF/PTA50% was a little higher than that of the pure CNF aerogel. Most importantly, the aerogel A-CNF/PTA50% showed good catalytic performance for ODS. Catalysis results showed that the substrate conversion rate of the aerogel A-CNF/PTA50% reached 100% within 120 min at room temperature. Even after five cycles, the substrate conversion rate of the aerogel A-CNF/PTA50% still reached 91.2% during the dynamic catalytic process. This work provides a scalable and facile way to stably deposit POM onto 3D structured materials.     

Surface-anchoring zwitterionic antioxidant enables efficient,stable,and scalable all-perovskite tandem solar cells

Lead-halide perovskite photovoltaics(PVs)have achieved impressive progress in power conversion efficiencies(PCEs)over the past ten years,accelerating their step forward to next-generation commercial PV technologies[1].As a leading candidate for perovskite PVs,monolithic all-perovskite tandem solar cells(PTSCs)have achieved the best24.8%for small-area devices(0.049 cm^2)in 2019。     

Observation of Nano-Dots on HOPG Surface Induced by Highly Charged Arq+ Impact

Highly charged ions （HCIs） have huge potential energy due to their high charge state. When a HCI reaches a solid surface, its potential energy is released immediately on the surface to cause a nano-scale defect. Thus, HCIs are expected to be useful for solid-surface modifications on the nano-scale. We investigate the defects on a highly oriented pyrolytic graphite （HOPG） surface induced by slow highly charged Ar^q＋ ions with impact energy of 20-2000qeV with scanning probe microscopy （SPM）. In order to clarify the role of kinetic and potential energies in surface modification, the nano-defects are characterized in lateral size and height corresponding to the kinetic energy and charge state of the HCIs. Both the potential energy and kinetic energy of the ions may influence the size of nano-defect. Since potential energy increases dramatically with increasing charge state, the potential energy effect is expected to be much larger than the kinetic energy effect in the case of extremely high charge states. This implies that pure surface modification on the nano-scale could be carried out by slow highly charged ions. The mean size of nano-defect region could also be controlled by selecting the charge state and kinetic energy of HCI.