Computational Investigation Identified Potential Chemical Scaffolds for Heparanase as Anticancer Therapeutics

Heparanase (Hpse) is an endo-β-D-glucuronidase capable of cleaving heparan sulfate side chains. Its upregulated expression is implicated in tumor growth, metastasis and angiogenesis, thus making it an attractive target in cancer therapeutics. Currently, a few small molecule inhibitors have been reported to inhibit Hpse, with promising oral administration and pharmacokinetic (PK) properties. In the present study, a ligand-based pharmacophore model was generated from a dataset of well-known active small molecule Hpse inhibitors which were observed to display favorable PK properties. The compounds from the InterBioScreen database of natural (69,034) and synthetic (195,469) molecules were first filtered for their drug-likeness and the pharmacophore model was used to screen the drug-like database. The compounds acquired from screening were subjected to molecular docking with Heparanase, where two molecules used in pharmacophore generation were used as reference. From the docking analysis, 33 compounds displayed higher docking scores than the reference and favorable interactions with the catalytic residues. Complex interactions were further evaluated by molecular dynamics simulations to assess their stability over a period of 50 ns. Furthermore, the binding free energies of the 33 compounds revealed 2 natural and 2 synthetic compounds, with better binding affinities than reference molecules, and were, therefore, deemed as hits. The hit compounds presented from this in silico investigation could act as potent Heparanase inhibitors and further serve as lead scaffolds to develop compounds targeting Heparanase upregulation in cancer.     

Identification of Novel Fragments Binding to the PDZ1-2 Domain of PSD-95

Inhibition of PSD-95 has emerged as a promising strategy for the treatment of ischemic stroke, as shown with peptide-based compounds that target the PDZ domains of PSD-95. In contrast, developing potent and drug-like small molecules against the PSD-95 PDZ domains has so far been unsuccessful. Here, we explore the druggability of the PSD-95 PDZ1-2 domain and use fragment screening to investigate if this protein is prone to binding small molecules. We screened 2500 fragments by fluorescence polarization (FP) and validated the hits by surface plasmon resonance (SPR), including an inhibition counter-test, and found four promising fragments. Three ligand efficient fragments were shown by ¹H,¹⁵N HSQC NMR to bind in the small hydrophobic P⁰ pockets of PDZ1-2, and one of them underwent structure-activity relationship (SAR) studies. Overall, we demonstrate that fragment screening can successfully be applied to PDZ1-2 of PSD-95 and disclose novel fragments that can serve as starting points for optimization towards small-molecule PDZ domain inhibitors.     

Scanning Protein Surfaces with DNA-Encoded Libraries

Understanding the ligandability of a target protein, defined as the capability of a protein to bind drug-like compounds on any site, can give important stimuli to drug-development projects. For instance, inhibition of protein–protein interactions usually depends on the identification of protein surface binders. DNA-encoded chemical libraries (DELs) allow scanning of protein surfaces with large chemical space. Encoded library selection screens uncovered several protein–protein interaction inhibitors and compounds binding to the surface of G protein-coupled receptors (GPCRs) and kinases. The protein surface-binding chemotypes from DELs are predominantly chemically modified and cyclized peptides, and functional small-molecule peptidomimetics. Peptoid libraries and structural peptidomimetics have been less studied in the DEL field, hinting at hitherto less populated chemical space and suggesting alternative library designs. Roughly a third of bioactive molecules evolved from smaller, target-focused libraries. They showcase the potential of encoded libraries to identify more potent molecules from weak, for example, fragment-like, starting points.     

Native Mass Spectrometry for the Study of PROTAC GNE-987-Containing Ternary Complexes

PRO teolysis TA rgeting C himeras (PROTACs) promote the degradation, rather than inhibition, of a drug target as a mechanism for therapeutic treatment. Bifunctional PROTAC molecules allow simultaneous binding of both the target protein and an E3-Ubiquitin ligase, bringing the two proteins into close spatial proximity to allow ubiquitinylation and degradation of the target protein via the cell's endogenous protein degradation pathway. We utilized native mass spectrometry (MS) to study the ternary complexes promoted by the previously reported PROTAC GNE-987 between Brd4 bromodomains 1 and 2, and Von Hippel Lindeau E3-Ubiquitin Ligase. Native MS at high resolution allowed us to measure ternary complex formation as a function of PROTAC concentration to provide a measure of complex affinity and stability, whilst simultaneously measuring other intermediate protein species. Native MS provides a high-throughput, low sample consumption, direct screening method to measure ternary complexes for PROTAC development.     

Patient-Derived Organoids as a Model for Cancer Drug Discovery

In the search for the ideal model of tumours, the use of three-dimensional in vitro models is advancing rapidly. These are intended to mimic the in vivo properties of the tumours which affect cancer development, progression and drug sensitivity, and take into account cell–cell interactions, adhesion and invasiveness. Importantly, it is hoped that successful recapitulation of the structure and function of the tissue will predict patient response, permitting the development of personalized therapy in a timely manner applicable to the clinic. Furthermore, the use of co-culture systems will allow the role of the tumour microenvironment and tissue–tissue interactions to be taken into account and should lead to more accurate predictions of tumour development and responses to drugs. In this review, the relative merits and limitations of patient-derived organoids will be discussed compared to other in vitro and ex vivo cancer models. We will focus on their use as models for drug testing and personalized therapy and how these may be improved. Developments in technology will also be considered, including the use of microfluidics, 3D bioprinting, cryopreservation and circulating tumour cell-derived organoids. These have the potential to enhance the consistency, accessibility and availability of these models.     

Targeted editing of intronic-splicing silencer enhancement of SMN2 Exon 7 inclusion by CRISPR/Case 9

Spinal muscular atrophy (SMA) is an autosomal recessive hereditary neuromuscular disease. Exon 7 and 8 of survival of motor neuron 1 (SMN1) gene or only exon 7 homology deletion leads to the failure to produce a full-length SMN gene. The copy number of SMN2 gene with high homology of SMN1 affects the degree of disease and was the target gene for targeting therapy, in which splicing silencer in intron 7 was the key to suppress the inclusion of exon 7. In this study, we projected to use CRISPR/Case 9 for the targeted editing of intronic-splicing silencer (ISS) sequence to promote the inclusion of SMN2 exon 7 and increase the production of SMN2 full-length (FL) gene expression. It happens that there was a protospacer adjacent motif (PAM) at one end of the ISS sequence according to the design of sgRNA. The recombinant vector of sgRNA HSMN2 CRISPR/Case 9 was constructed and transfected into HEK293 cells. Sequencing results showed that the ISS sequence could be edited accurately and targeting in the predicted direction, in which deleting small fragments, inserting small amounts and mutation. Quantitative analysis of RT-PCR products by restriction enzyme of DdeI digestion showed that the FL of SMN2 increased by 8% (P < 0.05). In the primary cultured chondrocytes of SMA mice, in which sgRNA HSMN2 CRISPR/Case9 recombinant vector transfection could increase the SMN2 FL gene by 23% (P < 0.05) and significantly improve SMN protein levels (P < 0.05). CRISPR/Case 9 is an effective tool for gene editing and therapy of hereditary diseases, but it is rarely reported in the treatment of SMA diseases. This study shows that CRISPR/Case 9 was first used for the precision target of ISS sequence editing, which can effectively promote the production of SMN2 FL gene expressions, in which there was an important clinical reference value.     

温度对核电站传热管阵列声透射特性的影响

为了研究温度分布对于管阵列结构中的声透射特性的影响，以核电站的实际工况为背景，构建了不同的温度场以及周期性变化的非均匀温度场，利用有限元方法进行数值模拟。结果表明：（1）温度分布会改变管阵列声透射频谱的“禁带”宽度以及中心频率位置。在同一介质中，温度变化对频率较高位置的影响大于频率较低的位置。（2）在同样为10℃的温度差下，当水的平均声速为1 653 m·s^-1、饱和水蒸气的平均声速为522.5 m·s^-1时，介质为水时的禁带宽度及中心频率位置变化较大，即声速大的介质的频谱对于温度的变化更敏感。（3）当温度差在10℃以内，在周期性变化的非均匀温度场和与均匀温度场中管阵列声透射特性在第一中心频率23 996.1 Hz之前，两频谱差别很小，在第一禁带之后会出现明显区别。该研究成果对完善核电站应用的声学检测提供了理论基础。     

两种混合单元混合机理的数值模拟

为了研究SV型和SX型混合单元在全静态乳化器的混合机理,使用群体平衡模型对乳化器内部流场进行模拟分析。结果表明,SV型与SX型混合单元的混合机理是油相与水相材料通过混合单元时其空间流动方向改变,在流场内形成大量的漩涡,从而达到乳化的目的;通过比较流体在经过SV型和SX型混合单元后的水相索特平均直径(d_(32)),得出SV型混合单元的乳化效果更强,但同时消耗更多的能量,压降更大。     

Feasibility of high performance in p-type Ge1−xBixTe materials for thermoelectric modules

GeTe is a promising candidate for the fabrication of high-temperature segments for p-type thermoelectric (TE) legs. The main restriction for the widespread use of this material in TE devices is high carrier concentration (up to ∼ 10²¹ cm⁻³), which causes the low Seebeck coefficient and high electronic component of thermal conductivity. In this work, the band structure diagram and phase equilibria data have been effectively used to attune the carrier concentration and to obtain the high TE performance. The Ge_1−xBi_xTe (x = 0.04) material prepared by the Spark plasma sintering (SPS) technique demonstrates a high power factor accompanied by moderate thermal conductivity. As a result, a significantly higher dimensionless TE figure of merit ZT = 2.0 has been obtained at ∼ 800 K. Moreover, we are the first to propose that application of the developed Ge_1−xBi_xTe (x = 0.04) material in the TE unicouple should be accompanied by SnTe and CoGe₂ transition layers. Only such a unique solution for the TE unicouple makes it possible to prevent the negative effects of high contact resistance and chemical diffusion between the segments at high temperatures.     

Influence of Al3+ doping for V5+ on the structural,optical, thermal and electrical properties of V2-xAlxO5-δ (x=0–0.20) ceramics

This paper reports an investigation on the structure-properties correlation of trivalent metal oxide (Al₂O₃)-doped V₂O₅ ceramics synthesized by the melt-quench technique. XRD patterns confirmed a single orthorhombic V₂O₅ phase formation with increasing strain on the doping of Al₂O₃ in place of V₂O₅ in the samples estimated by Williamson-Hall analysis. FTIR and Raman investigations revealed a structural change as [VO₅] polyhedra converts into [VO₄] polyhedra on the doping of Al₂O₃ into V₂O₅. The optical band gap was found in a wide semiconductor range as confirmed by UV–visible spectroscopy analysis. The thermal and conductivity behavior of the prepared samples were studied using thermal gravimetric analysis (TGA) and impedance analyzer, respectively. All the prepared ceramics exhibit good DC conductivity (0.22–0.36 Sm^-1) at 400 ?C. These materials can be considered for intermediate temperature solid oxide fuel cell (IT-SOFC)/battery applications due to their good conductivity and good thermal stability.