scholarly journals Bimodality of gene expression in cancer patient tumors as interpretable biomarkers for drug sensitivity

2020 ◽  
Author(s):  
Wail Ba-Alawi ◽  
Sisira Kadambat Nair ◽  
Bo Li ◽  
Anthony Mammoliti ◽  
Petr Smirnov ◽  
...  
Keyword(s):  
Machine Learning ◽  
Large Scale ◽  
Human Cancer ◽  
Predictive Biomarkers ◽  
Precision Oncology ◽  
Human Cancer Cell Lines ◽  
Validation Rate ◽  
Approved Drugs ◽  
Pharmacogenomic Studies

ABSTRACTIdentifying biomarkers predictive of cancer cells’ response to drug treatment constitutes one of the main challenges in precision oncology. Recent large-scale cancer pharmacogenomic studies have boosted the research for finding predictive biomarkers by profiling thousands of human cancer cell lines at the molecular level and screening them with hundreds of approved drugs and experimental chemical compounds. Many studies have leveraged these data to build predictive models of response using various statistical and machine learning methods. However, a common challenge in these methods is the lack of interpretability as to how they make the predictions and which features were the most associated with response, hindering the clinical translation of these models. To alleviate this issue, we develop a new machine learning pipeline based on the recent LOBICO approach that explores the space of bimodally expressed genes in multiple large in vitro pharmacogenomic studies and builds multivariate, nonlinear, yet interpretable logic-based models predictive of drug response. Using our method, we used a compendium of three of the largest pharmacogenomic data sets to build robust and interpretable models for 101 drugs that span 17 drug classes with high validation rate in independent datasets.

scholarly journals Egyptian Arthrospira phytosterols: production, identification, antioxidant and antiproliferative activities

2020 ◽  
Vol 48 (2) ◽  
pp. 666-680
Author(s):  
Gamal S. El BAROTY ◽  
Hanaa H. Abd El BAKY ◽  
Mahmoud A. SALEH
Keyword(s):  
Total Lipid ◽  
Large Scale ◽  
Human Cancer ◽  
Radical Scavenging Activity ◽  
Colorimetric Method ◽  
Radical Scavenging ◽  
Human Cancer Cell Lines ◽  
Ic50 Values ◽  
Antiproliferative Activities

Cultivation of microalgae as a source of phytosterol and other lipid compounds has gained more attention for commercial applications in pharmaceutical, cosmetic and food function industries. In this research, native Spirulina maxima SM from Egypt was grown in individual cultures containing various concentrations of nitrogen (N), phosphorus (P) and sulfur (S) elements in order to elucidate the effect of its elements on lipid and phytosterols production and to evaluate its antioxidant and antiproliferative activities. The results revealed that the SM was able to grow in different concentrations of testing elements S (from 0.3 to 2.4 mM), P (from 0.3 to 2.4 mM) and N (0.3 to 3.2 mM) with significant differences. A high potential for production of MS biomass, total lipid and phytosterol contents were obtained in individual cultures containing 0.6 mM N, 0.6 mM P and 0.80 mM, respectively. Therefore, these concentrations (combination of S+P+N element) were selected for cultivation of SM at large scale in a column photobioreactor (PBR 300 L) to induce sufficient SM biomass so that, we can obtain an adequate amount of total lipid and phytosterol contents. Phytosterols (PS) of native SM grown in the 300 L PBR were partially purified from unsaponified extracts of SM total lipid followed by its purification by crystallization process. The identification and quantification of PS profile were performed by GC-FID analysis. The results revealed high levels of campsterol, D7-Avena sterol, β-sitosterol, stigmasterol and other compounds. These PS compounds showed marked in vitro superoxide, DPPH and .OH radical scavenging activity, which was comparable with the results obtained with standard antioxidants BHA or α-tocopherol. Moreover, SM phytosterols exhibited anti-proliferative activity against three human cancer cell lines (MCF-7, Hep-G2 and HCT-116) with IC50 values less than 11.62 µg/mL as assessed by in vitro MTT colorimetric method. Thus, SM phytosterol may be considered as a potential natural source of promising ingredient in the future for a range of health applications for human, cosmetic industries and in functional food.

scholarly journals Searching for Pharmacogenomic Markers: The Synergy between Omic and Hypothesis-Driven Research

2001 ◽  
Vol 17 (2) ◽  
pp. 77-88 ◽  
Author(s):  
John N. Weinstein
Keyword(s):  
Drug Discovery ◽  
Cell Lines ◽  
Large Scale ◽  
Human Cancer ◽  
Biomedical Literature ◽  
Ovarian Cancer Cells ◽  
Human Cancer Cell Lines ◽  
Expression Studies ◽  
Drug Discovery Program ◽  
Pharmacogenomic Studies

With 35,000 genes and hundreds of thousands of protein states to identify, correlate, and understand, it no longer suffices to rely on studies of one gene, gene product, or process at a time. We have entered the “omic” era in biology. But large-scale omic studies of cellular molecules in aggregate rarely can answer interesting questions without the assistance of information from traditional hypothesis-driven research. The two types of science are synergistic. A case in point is the set of pharmacogenomic studies that we and our collaborators have done with the 60 human cancer cell lines of the National Cancer Institute’s drug discovery program. Those cells (the NCI-60) have been characterized pharmacologically with respect to their sensitivity to > 70,000 chemical compounds. We are further characterizing them at the DNA, RNA, protein, and functional levels. Our major aim is to identify pharmacogenomic markers that can aid in drug discovery and design, as well as in individualization of cancer therapy. The bioinformatic and chemoinformatic challenges of this study have demanded novel methods for analysis and visualization of high-dimensional data. Included are the color-coded “clustered image map” and also the MedMiner program package, which captures and organizes the biomedical literature on gene-gene and gene-drug relationships. Microarray transcript expression studies of the 60 cell lines reveal, for example, a gene-drug correlation with potential clinical implications – that between the asparagine synthetase gene and the enzyme-drug L-asparaginase in ovarian cancer cells.

Synthesis and Cytotoxicity Assessment of Novel 7-O- and 14-O-Derivatives of Glaucocalyxin A

2020 ◽  
Vol 20 (10) ◽  
pp. 1241-1249
Author(s):  
Hong-Chuan Liu ◽  
Li-Ming Qiao ◽  
Wei Zheng ◽  
Zhao-Bao Xiang ◽  
Hai-Sheng Chen ◽  
...  
Keyword(s):  
Acute Toxicity ◽  
Cell Lines ◽  
Cancer Cell ◽  
Human Cancer ◽  
Folk Medicine ◽  
A549 Cells ◽  
Cancer Cell Lines ◽  
Human Cancer Cell Lines ◽  
Derivatives Of

Background: Rabdosia japonica has been historically used in China as a popular folk medicine for the treatment of cancer, hepatitis, and gastricism. Glaucocalyxin A (GLA), an ent-kaurene diterpene isolated from Rabdosia japonica, is one of the main active ingredients showing potent inhibitory effects against several types of tumor cells. To the best of our knowledge, studies regarding the structural modification and Structure- Activity Relations (SAR) of this compound have not yet been reported. Objective: The aim of this study was to discover more potent derivatives of GLA and investigate their SAR and cytotoxicity mechanisms. Methods: Novel 7-O- and 14-O-derivatives of GLA were synthesized by condensation of acids or acyl chloride. The anti-tumor activities of these derivatives against various human cancer cell lines were evaluated in vitro by MTT assays. Apoptosis assays of compound 17 (7,14-diacylation product) were performed on A549 and HL-60 cells by flow cytometry and TUNNEL. The acute toxicity of this compound was tested on mice, at the dose of 300mg per kg body weight. Results: Seventeen novel 7-O- and 14-O-derivatives of GLA (1-17) were synthesized. These compounds showed potent cytotoxicity against the tested cancer cell lines, and almost all of them were found to be more cytotoxic than GLA and oridonin. Of the synthesized derivatives, compound 17 presented the greatest cytotoxicity, with IC50 values of 0.26μM and 1.10μM in HL-60 and CCRF-CEM cells, respectively. Furthermore, this compound induced weak apoptosis of A549 cells but showed great potential in stimulating the apoptosis of HL- 60 cells. Acute toxicity assays indicated that compound 17 is relatively safer. Conclusion: The results reported herein indicate that the synthesized GLA derivatives exhibited greater cytotoxicity against leukemia cells than against other types of tumors. In particular, 7,14-diacylation product of GLA was found to be an effective anti-tumor agent. However, the cytotoxicity mechanism of this product in A549 cells is expected to be different than that in other tumor cell lines. Further research is needed to confirm this hypothesis.

scholarly journals Discovery of New Pyrazolopyridine, Furopyridine, and Pyridine Derivatives as CDK2 Inhibitors: Design, Synthesis, Docking Studies, and Anti-Proliferative Activity

Molecules ◽  
2021 ◽  
Vol 26 (13) ◽  
pp. 3923
Author(s):  
Adel A.-H. Abdel-Rahman ◽  
Amira K. F. Shaban ◽  
Ibrahim F. Nassar ◽  
Dina S. EL-Kady ◽  
Nasser S. M. Ismail ◽  
...  
Keyword(s):  
Cell Lines ◽  
Cancer Cell ◽  
Human Cancer ◽  
Cancer Cell Lines ◽  
Human Cancer Cell ◽  
Molecular Docking Study ◽  
Human Cancer Cell Lines ◽  
Hct 116 ◽  
Mcf 7

New pyridine, pyrazoloyridine, and furopyridine derivatives substituted with naphthyl and thienyl moieties were designed and synthesized starting from 6-(naphthalen-2-yl)-2-oxo-4-(thiophen-2-yl)-1,2-dihydropyridine-3-carbonitrile (1). The chloro, methoxy, cholroacetoxy, imidazolyl, azide, and arylamino derivatives were prepared to obtain the pyridine-−C2 functionalized derivatives. The derived pyrazolpyridine-N-glycosides were synthesized via heterocyclization of the C2-thioxopyridine derivative followed by glycosylation using glucose and galactose. The furopyridine derivative 14 and the tricyclic pyrido[3′,2′:4,5]furo[3,2-d]pyrimidine 15 were prepared via heterocyclization of the ester derivative followed by a reaction with formamide. The newly synthesized compounds were evaluated for their ability to in vitro inhibit the CDK2 enzyme. In addition, the cytotoxicity of the compounds was tested against four different human cancer cell lines (HCT-116, MCF-7, HepG2, and A549). The CDK2/cyclin A2 enzyme inhibitory results revealed that pyridone 1, 2-chloro-6-(naphthalen-2-yl)-4-(thiophen-2-yl)nicotinonitrile (4), 6-(naphthalen-2-yl)-4-(thiophen-2-yl)-1H-pyrazolo[3,4-b]pyridin-3-amine (8), S-(3-cyano-6-(naphthaen-2-yl)-4-(thiophen-2-yl)pyridin-2-yl) 2-chloroethanethioate (11), and ethyl 3-amino-6-(naphthalen-2-yl)-4-(thiophen-2-yl)furo[2,3-b]pyridine-2-carboxylate (14) are among the most active inhibitors with IC50 values of 0.57, 0.24, 0.65, 0.50, and 0.93 µM, respectively, compared to roscovitine (IC50 0.394 μM). Most compounds showed significant inhibition on different human cancer cell lines (HCT-116, MCF-7, HepG2, and A549) with IC50 ranges of 31.3–49.0, 19.3–55.5, 22.7–44.8, and 36.8–70.7 μM, respectively compared to doxorubicin (IC50 40.0, 64.8, 24.7 and 58.1 µM, respectively). Furthermore, a molecular docking study suggests that most of the target compounds have a similar binding mode as a reference compound in the active site of the CDK2 enzyme. The structural requirements controlling the CDK2 inhibitory activity were determined through the generation of a statistically significant 2D-QSAR model.

scholarly journals Synthesis, Characterization, and Preliminary In Vitro Cytotoxic Evaluation of a Series of 2-Substituted Benzo [d] [1,3] Azoles

Molecules ◽  
2021 ◽  
Vol 26 (9) ◽  
pp. 2780
Author(s):  
Ozvaldo Linares-Anaya ◽  
Alcives Avila-Sorrosa ◽  
Francisco Díaz-Cedillo ◽  
Luis Ángel Gil-Ruiz ◽  
José Correa-Basurto ◽  
...  
Keyword(s):  
Binding Site ◽  
In Silico ◽  
Cytotoxic Effect ◽  
Human Cancer ◽  
Cytotoxic Activities ◽  
Human Cancer Cell ◽  
Inhibitory Effects ◽  
Reference Drug ◽  
Human Cancer Cell Lines

A series of benzo [d] [1,3] azoles 2-substituted with benzyl- and allyl-sulfanyl groups were synthesized, and their cytotoxic activities were in vitro evaluated against a panel of six human cancer cell lines. The results showed that compounds BTA-1 and BMZ-2 have the best inhibitory effects, compound BMZ-2 being comparable in some cases with the reference drug tamoxifen and exhibiting a low cytotoxic effect against healthy cells. In silico molecular coupling studies at the tamoxifen binding site of ERα and GPER receptors revealed affinity and the possible mode of interaction of both compounds BTA-1 and BMZ-2.

scholarly journals Synthesis of New Simplified and Racemic Hemiasterlin Derivatives with Extremely High Cytotoxicity

2018 ◽  
Vol 13 (12) ◽  
pp. 1934578X1801301
Author(s):  
Pham The Chinh ◽  
Đang Thi Tuyet Anh ◽  
Duong Huong Quynh ◽  
Le Nhat Thuy Giang ◽  
Nguyen Ha Thanh ◽  
...  
Keyword(s):  
Cytotoxic Activity ◽  
Cell Lines ◽  
Human Cancer ◽  
Microtubule Depolymerization ◽  
Antimitotic Agent ◽  
Human Cancer Cell Lines ◽  
Weak Activity ◽  
High Cytotoxicity ◽  
Chemistry Community

Hemiasterlin is a potent antimitotic agent acting through inhibition of microtubule depolymerization. For this reason, the synthesis of new hemiasterlin derivatives has attracted a lot of interest in the organic chemistry community recently. In this paper, the synthesis and evaluation of the cytotoxicity of new simplified and racemic hemiasterlin derivatives were reported. All of the synthesized analogues were evaluated in vitro for cytotoxic activity against four human cell lines (KB, Hep-G2, LU and MCF7). Most of these analogues possess a strong cytotoxic activity on two human cancer cell lines (KB and Hep-G2) and very weak activity on LU and MCF7 cell lines.

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