Identification of potential HIV-1 integrase strand transfer inhibitors: In silico virtual screening and QM/MM docking studies

HIV-1 integrase (IN) is a retroviral enzyme that catalyses integration of the reverse-transcribed viral DNA into the host genome, which is necessary for efficient viral replication. In this study, we have performed an in silico virtual screening for the identification of potential HIV-1 IN strand transfer (ST) inhibitors. Pharmacophore modelling and atom-based 3D-QSAR studies were carried out for a series of compounds belonging to 3-Hydroxypyrimidine-2,4-diones. Based on the ligand-based pharmacophore model, we obtained a five-point pharmacophore with two hydrogen bond acceptors (A), one hydrogen bond donor (D), one hydrophobic group (H) and one aromatic ring (R) as pharmacophoric features. The pharmacophore hypothesis AADHR was used as a 3D query in a sequential virtual screening study to filter small molecule databases Maybridge, ChemBridge and Asinex. Hits matching with pharmacophore hypothesis AADHR were retrieved and passed progressively through Lipinski’s rule of five filtering, molecular docking and hierarchical clustering. The five compounds with best hits with novel and diverse chemotypes were subjected to QM/MM docking, which showed improved docking accuracy. We further performed molecular dynamics simulation and found three compounds that form stable interactions with key residues. These compounds could be used as a leads for further drug development and rational design of HIV-1 IN inhibitors.     

Theory of docking scores and its application to a customizable scoring function

In general, the docking scoring tends to have a size dependence related to the ranking of compounds. In this paper, we describe a novel method of parameter optimization for docking scores which reduce the size dependence and can efficiently discriminate active compounds from chemical databases. This method is based on a simplified theoretical model of docking scores which enables us to utilize large amounts of data of known active and inactive compounds for a particular target without requiring large computational resources or a complicated procedure. This method is useful for making scoring functions for the identification of novel scaffolds using the knowledge of active compounds for a particular target or a customized scoring function for an interesting family of drug targets.     

Palladium-catalyzed hydrodehalogenation of aryl halides using paraformaldehyde as the hydride source: high-throughput screening by paper-based colorimetric iodide sensor

Paraformaldehyde was employed as a hydride source in the palladium-catalyzed hydrodehalogenation of aryl iodides and bromides. High throughput screening using a paper-based colorimetric iodide sensor (PBCIS) showed that Pd(OAc)₂ and Cs₂CO₃ were the best catalyst and base, respectively. Aryl iodides and bromides were hydrodehalogenated to produce the reduced arenes using Pd(OAc)₂ and Pd(PPh₃)₄ catalyst. This catalytic system showed good functional group tolerance. In addition, it was found that paraformaldehyde is the hydride source and the reducing agent for the formation of palladium nanoparticles.     

Rapid determination of enantiomeric excess of α-chiral aldehydes using circular dichroism spectroscopy

A method for enantiodiscrimination of α-chiral aldehydes is reported. The method utilizes circular dichroism (CD) spectroscopy and a sensing ensemble composed of 2-(1-methylhydrazinyl) pyridine (1) and Fe(II)(TfO)₂. Aldehydes react rapidly with hydrazine (1) to form chiral imines, which form complexes with Fe(II). By monitoring the CD bands above 320 nm, one can determine the enantiomeric excess (ee) values of α-chiral aldehydes with an average absolute error of ±5%. The analysis was fast, and thus can have potential applications in high-throughput screening (HTS) of catalytic asymmetric induction.     

模拟体内微环境筛选与肿瘤细胞作用的中药活性成分

利用三维(3D)细胞反应器模拟体内微环境,建立了一种与肿瘤细胞作用的活性分子的筛选和分析方法.利用药物与三维细胞反应器中活肿瘤细胞和固化肿瘤细胞分别作用后的HPLC生物指纹谱峰面积之间有无显著性差异,建立了与细胞结合的活性成分的筛选识别模型.已知抗肿瘤药物紫杉醇和白藜声醇的谱峰均具有显著性差异,而非抗肿瘤药物酮洛芬和青霉素G的谱峰均没有显著性差异,证明利用该模型筛选识别与细胞结合的活性成分是可行的.此外,应用该模型从中草药桃儿七提取物中筛选出了7种可作用于Lovo细胞的活性成分.此研究提供了一种模拟体内微环境下与肿瘤细胞作用的活性成分的筛选和分析方法,在药物发现环节,特别是中草药活性成分研究中具有潜在的应用价值.     

Reliable screening of pesticide residues in maternal and umbilical cord sera by gas chromatography-quadrupole time of flight mass spectrometry

The widespread use of pesticides induces heavy adverse effects on human health,especially for the pregnant women and the newborns.In this study,a screening method has been developed for the determination of multi-pesticides in maternal and umbilical cord sera.All pesticides in sera were collected using solid phase extraction(SPE),and analyzed by gas chromatography-quadrupole time of flight mass spectrometry(GC-QTOF MS).To set up the quality criteria,a database of 50 pesticides was created and the accurate masses of 3 up to 5 representative ions with their intensity ratios were included for each pesticide.In addition,a novel"identification points"(IPs)system relying on the accurate MS1 and MS2 spectra was used to interpret the data for each suspected pesticide.The methodology was then applied to a pair of maternal and umbilical cord sera.A total of six pesticide residues were screened out successfully.In conclusion,GC-QTOF MS combined with an accurate mass database seemed to be one of the most efficient tools for systematic pesticide analysis.     

Clickable SBA‐15 to Screen Functional Groups for Adsorption of Antibiotics

Pharmaceutical antibiotics, as emerging contaminants, are usually composed of several functional groups that endow them with the ability to interact with adsorbents through different interactions. This makes the preparation of adsorbents tedious and time‐consuming to screen appropriate functionalized materials. Herein, we describe the synthesis of clickable SBA‐15 and demonstrate its feasibility as a screening material for the adsorption of antibiotics based on similar adsorption trends on materials with similar functional groups obtained by a click reaction and cocondensation/grafting methods.     

Targeting tribbles homolog 3 (TRIB3) protein against type 2 diabetes for the identification of potential inhibitors by in silico screening

Tribbles homolog 3 (TRIB3) protein is inhibiting the insulin signaling by directly binding to the Akt/PKB leading to insulin resistance in the pancreas causing type 2 diabetes mellitus. Hence, TRIB3 protein is considered as a possible drug target for the new lead identification against type 2 diabetes. In the present study, the homology model of TRIB3 protein was generated to explore its biochemical function and molecular interactions in the new lead identification. The energy minimization of TRIB3 protein was carried out and evaluated by validation protocols for structure reliability. The druggable binding site of TRIB3 protein was identified for the virtual screening and molecular docking studies. The Asinex-fragments library of 22634 small molecules was docked at TRIB3 active site using the Glide module to identify new chemical entities. A total of 9 molecules were identified as final hits from virtual screening and their potency was ranked using Glide score, Glide energies, and residues interactions. The 6 prioritized lead molecules were further optimized using AutoDock, Prime MM/GBSA, and percentage of human oral absorption for the identification of potential leads. The molecules L2, L5, and L6 are identified as lead inhibitors and are showing consistent interactions with key residues Glu194 and Lys196 of TRIB3 protein. The identified potential leads were analyzed by ADME properties for their drug likeness and HergIC50 values are predicted for the prevention of preclinical failures. The present work sheds light on the identification of the best lead molecules against TRIB3 protein and offers a route to design as novel potential drug candidates for T2DM.     

液相色谱-四极杆/飞行时间质谱法分析29种芬太尼类物质及其碎裂机理北大核心CSCD

芬太尼类物质品种繁多,自我国整类列管后,整类检测是该领域的重点和难点。该文详细研究了29种化合物的二级质谱碎片离子碎裂机理,总结出芬太尼类物质的碎裂规律和特点,为芬太尼物质的整类筛查检测提供参考。建立了分析29种芬太尼类物质的一级和二级质谱库的定性方法,建立了液相色谱-四极杆/飞行时间质谱(LC-QTOF-MS)检测29种芬太尼类物质的定量方法。药品和白色粉末类、蛋白质和乳饮料类样品经乙腈提取,含糖固体或粉末类、饮用水类、果蔬饮料类、保健饮料类、茶饮料类、酒类样品经10%乙腈水溶液提取,提取液经涡旋、离心和过膜后,采用Kinetex C18色谱柱(100 mm×2.1 mm,2.6μm)分离,以乙腈和0.08%甲酸水溶液为流动相进行梯度洗脱,采用四极杆/飞行时间质谱,在正离子模式下,外标法定量检测。结果表明,29种芬太尼类物质在1~20μg/L范围内线性关系良好,相关系数均大于0.995,检出限(LOQ)均为0.01 mg/kg,定量限(LOQ)均为0.05 mg/kg,在降糖药、露露、葡萄糖粉、珍露保健饮料和巧克力样品中3个加标水平平均回收率为85.2%~112.9%,相对标准偏差(RSD)为1.9%~19.8%(n=6)。该方法操作简单,耗时短,灵敏度高,稳定性好,检测品种覆盖范围广,适用于药品类、含糖固体或粉末类、饮料类、饮用水类和酒类等样品中29芬太尼类物质的定性和定量检测。     

Effect of selected dopants on conductivity and moisture stability of Li3PS4 sulfide solid electrolyte: a first-principles study

The first principle computational screening was performed to investigate the effect of selected dopants for Li₃PS₄ sulfide solid electrolyte on its ionic conductivity and stability toward moisture. The results suggest that substitution P⁵⁺ using isovalent cations whose electronegativity (EN) value is closer to the value of S has more significant effects on the ionic conductivity, whereby W⁵⁺ and Sb⁵⁺ can improve most. Similarly, aliovalent cation substitutions with compensating changes in the lithium-ion concentration, particularly those with a lower oxidation state and higher EN, such as Cu²⁺, effectively enhance the lithium-ion conductivity in this structure. For cation dopants, it is found that ionic conductivity improvement of Li₃PS₄ is the synergetic effect of EN and oxidation number of the dopant as well as the material's lattice parameter change. Oxides of the considered cation dopants can also improve the ionic conductivity of the material but have much lower lithium-ion conductivity than the cases of cation dopants. However, the metal oxide dopants, particularly those derived from soft Lewis' acid cations, show a marginal improvement in moisture stability of the Li₃PS₄ electrolyte. The effect of halides and metal halide dopants on the lithium-ion conductivity and moisture stability of Li₃PS₄ electrolyte are also studied. It is found that metal halides are more effective than any other dopants in improving the ionic conductivity of Li₃PS₄.