Short communication for targeting natural compounds against HER2 kinase domain as potential anticancer drugs applying pharmacophore based molecular modelling approaches- part 2

Breast cancer is one of the common causes of death noticed in women globally. In order to find effective therapeutics, the current investigation has focussed on identifying candidate compounds for EGFR and HER2. Accordingly, the pharmacophore modelling approaches were adapted to identify two prospective compounds and were docked against the target 3RCD that is complexed with TAK-285 a known dual inhibitor. Focussing on the target 3RCD, our results have showed that the compounds have demonstrated a good binding affinity towards the target occupying the binding pocket. They have established key residue interactions with stable molecular dynamics simulation results. The Hit compounds have demonstrated a potential to penetrate the blood brain barrier thereby enriching their therapeutics towards breast cancer brain metastasis. Taken together, our findings propose two candidate compounds as EGFR/HER2 inhibitors that might serve as novel chemical spaces for designing and developing new inhibitors.     

Comparison among dimensionality reduction techniques based on Random Projection for cancer classification

Random Projection (RP) technique has been widely applied in many scenarios because it can reduce high-dimensional features into low-dimensional space within short time and meet the need of real-time analysis of massive data. There is an urgent need of dimensionality reduction with fast increase of big genomics data. However, the performance of RP is usually lower. We attempt to improve classification accuracy of RP through combining other reduction dimension methods such as Principle Component Analysis (PCA), Linear Discriminant Analysis (LDA), and Feature Selection (FS). We compared classification accuracy and running time of different combination methods on three microarray datasets and a simulation dataset. Experimental results show a remarkable improvement of 14.77% in classification accuracy of FS followed by RP compared to RP on BC-TCGA dataset. LDA followed by RP also helps RP to yield a more discriminative subspace with an increase of 13.65% on classification accuracy on the same dataset. FS followed by RP outperforms other combination methods in classification accuracy on most of the datasets.     

Electrochemical Sensing of Chlorpyrifos,a Carcinogen Responsible for Breast Cancer,in Milk and Plasma of Lactating Mothers

In view of the increase in breast cancer cases at the global level, electrochemical sensing of the carcinogenic pesticide, chlorpyrifos (CPF) in breast milk is proposed. The determination is based on the nucleophilic substitution reaction of pralidoxime (PAM) with CPF. The proposed method offers a linear concentration range of 0.002 to 0.08 μmol/L. The limit of detection and limit of quantification was found to be 0.05×10⁻⁹ and 0.167×10⁻⁹M, respectively. The offered “unmodified edge plane pyrolytic graphite sensor” proved to be a better substrate than the earlier reported modified sensors. The limit of detection for the proposed method was found to be nearly fifty times lower than reported at modified electrodes. The interference study proved the adequate selectivity of the offered sensor. The sensor has good stability and reproducibility along with high sensitivity. The offered sensor is very useful for cancer hospitals, pesticide industries, and the study of environmental toxicity-related issues.     

Alterations of the exo- and endometabolite profiles in breast cancer cell lines: A mass spectrometry-based metabolomics approach

In recent years, knowledge about metabolite changes which are characteristic for the physiologic state of cancer cells has been acquired by liquid chromatography coupled to mass spectrometry. Distinct molecularly characterized breast cancer cell lines provide an unbiased and standardized in vitro tumor model reflecting the heterogeneity of the disease. Tandem mass spectrometry is a widely applied analytical platform and highly sensitive technique for analysis of complex biological samples. Endo- and exometabolite analysis of the breast cancer cell lines MDA-MB-231, -453 and BT-474 as well as the breast epithelial cell line MCF-10A has been performed using two different analytical platforms: UPLC-ESI-Q-TOF based on a scheduled precursor list has been applied for highlighting of significant differences between cell lines and HPLC-ESI-QqQ using multiple reaction monitoring has been utilized for a targeted approach focusing on RNA metabolism and interconnected pathways, respectively. Statistical analysis enabled a clear discrimination of the breast epithelial from the breast cancer cell lines. As an effect of oxidative stress, a decreased GSH/GSSG ratio has been detected in breast cancer cell lines. The triple negative breast cancer cell line MDA-MB-231 showed an elevation in nicotinamide, 1-ribosyl-nicotinamide and NAD+ reflecting the increased energy demand in triple negative breast cancer, which has a more aggressive clinical course than other forms of breast cancer. Obtained distinct metabolite pattern could be correlated with distinct molecular characteristics of breast cancer cells. Results and methodology of this preliminary in vitro study could be transferred to in vivo studies with breast cancer patients.     

多层纸芯片乳腺癌组织微阵列用于抗肿瘤药物测试

开发了一种多层纸芯片细胞培养平台,将乳腺癌细胞分别接种于多层的图形化纸芯片的亲水区,折叠后构建了仿真实体肿瘤.多层纸芯片覆以微孔薄膜,用以仿真血管内皮层.培养不同时间后,拆解多层纸芯片检测乳腺癌组织内各层面的细胞形态、存活率、细胞周期分布以及细胞内乳酸含量.实验结果显示,各层纸芯片培养的乳腺癌细胞存活率均高于80％,并形成了类组织结构.芯片乳腺癌组织内部呈酸化倾向,且酸化程度随着培养时间的延长而升高.与二维(2D)培养细胞相比较,纸芯片乳腺癌组织内细胞增殖比例显著降低(15％ vs 60％).多层纸芯片乳腺癌组织显示了更接近体内情况的药物反应机制,细胞存活率随阿霉素浓度升高呈现缓慢下降趋势,IC50值显著高于2D培养细胞组(5.0 μmol/L vsl.144 μmol/L).这种多层纸芯片乳腺癌组织微阵列构建简便、仿真度高,有望成为抗肿瘤药物反应测试的有力工具.     

Design,cytotoxic effects on breast cancer cell line (MDA-MB 231), and molecular docking of some maleimide-benzenesulfonamide derivatives

A group of novel maleimide-benzenesulfonamide derivatives 3a-d was designed and synthesized for their evaluation as a potential anti-breast cancer agent. The structures of these derivatives were confirmed by their ¹H, ¹³C NMR, Mass, FT-IR spectral data, and melting points. The cytotoxic activity (in vitro) of the selected molecules against MDA-MB231 ​cell line was evaluated by MTT method. Among them, compounds 3a and 3d exhibited a significant cytotoxicity with the IC₅₀ value of 1.61 and 1.26 ​μM, respectively, whereas compounds 3b and 3c showed a moderate cytotoxicity with IC₅₀ values of 0.45 and 1.12 ​μM, respectively against MDA-MB231 ​cells. Docking modeling of the synthesized compounds 3a-d into binding sites of human aromatase protein (PDB ID: 4GL7) was performed to investigate if these derivatives possess analogous binding mode to breast cancer proteins. Docking results showed these compounds have efficient interactions such as hydrogen bonding, Van der Waals interactions, and hydrophobic interactions with the active site residues of the aromatase protein (PDB ID: 4GL7). The low binding energies and a number of hydrogen bonding indicated that the maleimide-benzenesulfonamide derivatives might be considered as a promising anti-breast cancer agent with further developments in drug discovery.     

Design and Synthesis of Novel Thioureas Derived from 4‐(4‐Fluorophenoxy)aniline as Anticancer Agents

A new series of thiourea derivatives were obtained by the reaction of 4‐(4‐fluorophenoxy) aniline with different isothiocyanates. Their chemical structures were confirmed by ultraviolet (UV ), infrared (IR ), nuclear magnetic resonance (NMR ), and mass spectral data and elemental analysis. All the synthesized thiourea derivatives were evaluated for their in vitro cancer activity against the human breast cancer cell lines MCF ‐7 (human breast adenocarcinoma) and SKBr ‐3 (human epithelial breast adenocarcinoma). Most of the derivatives exhibited significant anticancer activity. Especially, compound 3 showed the most potent activity (IC₅₀ 20.1 μM ) against SKBr ‐3 when compared with the drugs 5‐fluorouracil and cisplatin, and, most importantly, it did not affect normal breast epithelial cells (4010).     

Magnetic resonance imaging measurements of vascular permeability and extracellular volume fraction of breast tumors by dynamic Gd-DTPA-enhanced relaxometry

Vascular permeability (k(ep), min(-1)) and extracellular volume fraction (v(e)) are tissue parameters of great interest to characterize malignant tumor lesions. Indeed, it is well known that tumors with high blood supply better respond to therapy than poorly vascularized tumors, and tumors with large extracellular volume tend to be more malignant than tumors showing lower extracellular volume. Furthermore, the transport of therapeutic agents depends on both extracellular volume fraction and vessel permeability. Thus, before treatment, these tissue parameters may prove useful to evaluate tumor aggressiveness and to predict responsiveness to therapy and variations during cytotoxic therapies could allow to assess treatment efficacy and early modified therapy schedules in case of poor responsiveness. As a consequence, there is a need to develop methods that could be routinely used to determine these tissue parameters. In this work, blood-tissue permeability and extracellular volume fraction information were derived from magnetic resonance imaging dynamic longitudinal relaxation rate (R(1)) mapping obtained after an intravenous bolus injection of Gd-DTPA in a group of 92 female patients with breast lesions, 68 of these being histologically proven to be with carcinoma. For the sake of comparison, 24 benign lesions were studied. The measurement protocol based on two-dimensional gradient echo sequences and a monoexponential plasma kinetic model was that validated in the occasion of previous animal experiments. As a consequence of neoangiogenesis, results showed a higher permeability in malignant than in benign lesions, whereas the extracellular volume fraction value did not allow any discrimination between benign and malignant lesions. The method, which can be easily implemented whatever the imaging system used, could advantageously be used to quantify lesion parameters (k(ep) and v(e)) in routine clinical imaging. Because of its large reproducibility, the method could be useful for intersite comparisons and follow-up studies.     

基于稳健统计的新鲜乳腺组织拉曼光谱分析

采用便携式拉曼光谱仪对新鲜乳腺正常组织、良性组织和恶性组织进行检测,通过稳健统计方法对拉曼光谱数据进行分析处理,建立乳腺组织拉曼光谱标准图谱,根据标准图谱特征峰归纳3类组织的主要区别和特征.在3类乳腺组织中,正常组织有明显的脂类特征峰(1078,1297,1437,1653,1746 cm-1),而在良性和恶性组织中则出现了较明显的蛋白特征峰(1259,1530,1650 cm-1),正常、良性和恶性组织的主要区别集中在1340和1534 cm-1处,应归属为蛋白和类胡萝卜素,这一结果并不能由经典统计方法得出.基于稳健统计建立的新鲜乳腺组织拉曼光谱标准图谱为构建数学模型来鉴别乳腺病灶的性质奠定了基础.     

“One-shot” analysis of polybrominated diphenyl ethers and their hydroxylated and methoxylated analogs in human breast milk and serum using gas chromatography-tandem mass spectrometry

The presence of polybrominated diphenyl ethers (PBDEs) and their hydroxylated (OH-BDE) and methoxylated (MeO-BDE) analogs in humans is an area of high interest to scientists and the public due to their neurotoxic and endocrine disrupting effects. Consequently, there is a rise in the investigation of the occurrence of these three classes of compounds together in environmental matrices and in humans in order to understand their bioaccumulation patterns. Analysis of PBDEs, OH-BDEs, and MeO-BDEs using liquid chromatography-mass spectrometry (LC-MS) can be accomplished simultaneously, but detection limits for PBDEs and MeO-BDEs in LC-MS is insufficient for trace level quantification. Therefore, fractionation steps of the phenolic (OH-BDEs) and neutral (PBDEs and MeO-BDEs) compounds during sample preparation are typically performed so that different analytical techniques can be used to achieve the needed sensitivities. However, this approach involves multiple injections, ultimately increasing analysis time. In this study, an analytical method was developed for a “one-shot” analysis of 12 PBDEs, 12 OH-BDEs, and 13 MeO-BDEs using gas chromatography with tandem mass spectrometry (GC-MS/MS). This overall method includes simultaneous extraction of all analytes via pressurized liquid extraction followed by lipid removal steps to reduce matrix interferences. The OH-BDEs were derivatized using N-(t-butyldimethylsilyl)-N-methyltrifluoroacetamide (TBDMS-MTFA), producing OH-TBDMS derivatives that can be analyzed together with PBDEs and MeO-BDEs by GC-MS/MS in “one shot” within a 25-min run time. The overall recoveries were generally higher than 65%, and the limits of detection ranged from 2 to 14 pg in both breast milk and serum matrices. The applicability of the method was successfully validated on four paired human breast milk and serum samples. The mean concentrations of total PBDEs, OH-BDEs, and MeO-BDEs in breast milk were 59, 2.2, and 0.57 ng g⁻¹ lipid, respectively. In serum, the mean total concentrations were 79, 38, and 0.96 ng g⁻¹ lipid, respectively, exhibiting different distribution profiles from the levels detected in breast milk. This “one-shot” GC-MS/MS method will prove useful and cost-effective in large-scale studies needed to further understand the partitioning behavior, and ultimately the adverse health effects, of these important classes of brominated flame retardants in humans.