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.     

High-Throughput Screening for Phase-Change Memory Materials

Phase change memory (PCM) is an emerging non-volatile data storage technology concerned by the semiconductor industry. To improve the performances, previous efforts have mainly focused on partially replacing or doping elements in the flagship Ge-Sb-Te (GST) alloy based on experimental “trial-and-error” methods. Here, the current largest scale PCM materials searching is reported, starting with 124 515 candidate materials, using a rational high-throughput screening strategy consisting of criteria related to PCM characteristics. In the results, there are 158 candidates screened for PCM materials, of which ≈68% are not employed. By further analyses, including cohesive energy, bond angle analyses, and Born effective charge, there are 52 materials with properties similar to the GST system, including Ge₂Bi₂Te₅, GeAs₄Te₇, GeAs₂Te₄, so on and other candidates that have not been reported, such as TlBiTe₂, TlSbTe₂, CdPb₃Se₄, etc. Compared with GST, materials with close cohesive energy include AgBiTe₂, TlSbTe₂, As₂Te₃, TlBiTe₂, etc., indicating possible low power consumption. Through further melt-quenching molecular dynamic calculation and structural/electronic analyses, Ge₂Bi₂Te₅, CdPb₃Se₄, MnBi₂Te₄, and TlBiTe₂ are found suitable for optical/electrical PCM applications, which further verifies the effectiveness of this strategy. The present study will accelerate the exploration and development of advanced PCM materials for current and future big-data applications.     

一种5 重real-time PCR筛查转基因水稻方法的建立

以转基因水稻中最常用的CaMV35S启动子、NOS终止子、Cry1Ab/Ac基因、HPT基因及SPS水稻内标基因为研究对象，利用5 种不同的荧光信号（FAM、HEX、Taxas Red、Cy5、Cy5.5）进行多重实时聚合酶链式反应（real-time polymerase chain reaction，real-time PCR）检测方法的研究。通过引物组合筛选、反应体系优化、特异性测试、灵敏度测试、适用性测试等一系列实验，建立了5 重real-time PCR方法，灵敏度可达0.032%。此方法具有灵敏度高、结果准确、通量大等优点，可实现水稻中转基因成分的快速、高效检测。     

刺葡萄园土壤酿酒酵母的筛选及耐受性分析

从铜仁市刺葡萄园采集土样，采用涂布平板法、平板划线法、酵母浸出粉胨葡萄糖（YPD）培养基分离、纯化酵母，通过WL营养琼脂培养基筛选酿酒酵母（Saccharomyces cerevisiae），并对其乙醇、糖、酸、温度及SO2耐受性进行分析。结果表明，共获得10株酵母菌株，其中菌株TR-2、TR-3、TR-6、TR-7、TR-10为酿酒酵母（Saccharomyces cerevisiae），且菌株TR-6、TR-10耐受性较好，均分别能在乙醇体积分数为16%、葡萄糖质量浓度为500 g/L、柠檬酸质量浓度为30 g/L、SO2质量浓度为250 mg/L的YPD液体培养基和高温45 ℃、低温5 ℃条件下生长繁殖。     

Excitonic Properties of Chemically Synthesized 2D Organic–Inorganic Hybrid Perovskite Nanosheets

2D organic–inorganic hybrid perovskites (OIHPs) represent a unique class of materials with a natural quantum‐well structure and quasi‐2D electronic properties. Here, a versatile direct solution‐based synthesis of mono‐ and few‐layer OIHP nanosheets and a systematic study of their electronic structure as a function of the number of monolayers by photoluminescence and absorption spectroscopy are reported. The monolayers of various OIHPs are found to exhibit high electronic quality as evidenced by high quantum yield and negligible Stokes shift. It is shown that the ground exciton peak blueshifts by ≈40 meV when the layer thickness reduces from bulk to monolayer. It is also shown that the exciton binding energy remains effectively unchanged for (C₆H₅(CH₂)₂NH₃)₂PbI₄ with the number of layers. Similar trends are observed for (C₄H₉NH₃)₂PbI₄ in contrast to the previous report. Further, the photoluminescence lifetime is found to decrease with the number of monolayers, indicating the dominant role of surface trap states in nonradiative recombination of the electron–hole pairs.     

Development of an immunochromatographic assay for the β-adrenergic agonist feed additive zilpaterol

Zilpaterol is a β-adrenergic agonist feed additive approved in the United States to increase weight gain and improve feed efficiency of cattle. A zilpaterol immunochromatographic assay was developed as an economical and user-friendly rapid detection method for zilpaterol and validated using urine and tissue samples derived from animal studies. The assay sensitivity was 1.7–23.2 ng g^?1 or mL^?1 across a variety of feed and animal matrices and did not cross-react with clenbuterol or ractopamine. No sample pre-treatment of cattle and sheep urine was needed, but horse urine and feed required dilution; skeletal muscle required solvent extraction prior to testing. Of 32 incurred sheep urine samples tested, zilpaterol content was correctly identified in all but 2 samples. Horse urine containing >10 ng mL^?1 of incurred zilpaterol residue (n = 48) was correctly identified as zilpaterol positive. The assay correctly identified 0-day withdrawal sheep muscle samples as zilpaterol positive and the control and longer withdrawal day sheep muscle samples as negative. Zilpaterol was demonstrated to be stable in horse urine when stored at ?20°C for 7 years.