scholarly journals A framework for large-scale dynamic metabolome drug profiling in mammalian cells: a case study analysis of the anti-cancer drug dichloroacetate

2018 ◽  
Author(s):  
Sébastien Dubuis ◽  
Karin Ortmayr ◽  
Mattia Zampieri
Keyword(s):  
Metabolic Profiling ◽  
Mammalian Cells ◽  
Large Scale ◽  
System Level ◽  
Cancer Drug ◽  
Drug Induced ◽  
Disease Etiology ◽  
Compound Libraries ◽  
Ovarian Cancer Cell Lines

AbstractMetabolic profiling of cell line collections have become an invaluable tool to study disease etiology, drug modes of action and personalized medicine. However, large-scalein vitrodynamic metabolic profiling is limited by time-consuming sampling and complex measurement procedures. By adapting an MS-based metabolomics workflow for high-throughput profiling of diverse adherent mammalian cells, we establish a technique for the rapid measurement and analysis of drug-induced dynamic changes in intracellular metabolites. This methodology is scalable to large compound libraries and is here applied to study the mechanism underlying the toxic effect of dichloroacetate in ovarian cancer cell lines. System-level analysis of the metabolic responses revealed a key and unexpected role of CoA imbalance in dichloroacetate toxicity. The herein proposed strategy for large-scale drug metabolic profiling is complementary to other molecular profiling techniques, opening new scientific and drug-discovery opportunities.

scholarly journals EGCG binds intrinsically disordered N-terminal domain of p53 and disrupts p53-MDM2 interaction

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jing Zhao ◽  
Alan Blayney ◽  
Xiaorong Liu ◽  
Lauren Gandy ◽  
Weihua Jin ◽  
...  
Keyword(s):  
Large Scale ◽  
Molecular Mechanisms ◽  
Epigallocatechin Gallate ◽  
Cancer Drug ◽  
Dynamic Interactions ◽  
Cancer Drug Discovery ◽  
Intrinsically Disordered ◽  
Terminal Domain ◽  
Cancerous Cells

AbstractEpigallocatechin gallate (EGCG) from green tea can induce apoptosis in cancerous cells, but the underlying molecular mechanisms remain poorly understood. Using SPR and NMR, here we report a direct, μM interaction between EGCG and the tumor suppressor p53 (KD = 1.6 ± 1.4 μM), with the disordered N-terminal domain (NTD) identified as the major binding site (KD = 4 ± 2 μM). Large scale atomistic simulations (>100 μs), SAXS and AUC demonstrate that EGCG-NTD interaction is dynamic and EGCG causes the emergence of a subpopulation of compact bound conformations. The EGCG-p53 interaction disrupts p53 interaction with its regulatory E3 ligase MDM2 and inhibits ubiquitination of p53 by MDM2 in an in vitro ubiquitination assay, likely stabilizing p53 for anti-tumor activity. Our work provides insights into the mechanisms for EGCG’s anticancer activity and identifies p53 NTD as a target for cancer drug discovery through dynamic interactions with small molecules.

scholarly journals Elucidating the molecular determinants of Aβ aggregation with deep mutational scanning

2019 ◽  
Author(s):  
Vanessa E. Gray ◽  
Katherine Sitko ◽  
Floriane Z. Ngako Kameni ◽  
Miriam Williamson ◽  
Jason J. Stephany ◽  
...  
Keyword(s):  
Large Scale ◽  
Single Amino Acid ◽  
Alanine Scanning Mutagenesis ◽  
Aggregation Assay ◽  
Disease Etiology ◽  
Charged Amino Acids ◽  
Molecular Determinants ◽  
Aβ Aggregation ◽  
A Cell

AbstractDespite the importance of Aβ aggregation in Alzheimer’s disease etiology, our understanding of the sequence determinants of aggregation is sparse and largely derived from in vitro studies. For example, in vitro proline and alanine scanning mutagenesis of Aβ40 proposed core regions important for aggregation. However, we lack even this limited mutagenesis data for the more disease-relevant Aβ42. Thus, to better understand the molecular determinants of Aβ42 aggregation in a cell-based system, we combined a yeast DHFR aggregation assay with deep mutational scanning. We measured the effect of 791 of the 798 possible single amino acid substitutions on the aggregation propensity of Aβ42. We found that ~75% of substitutions, largely to hydrophobic residues, maintained or increased aggregation. We identified 11 positions at which substitutions, particularly to hydrophilic and charged amino acids, disrupted Aβ aggregation. These critical positions were similar but not identical to critical positions identified in previous Aβ mutagenesis studies. Finally, we analyzed our large-scale mutagenesis data in the context of different Aβ aggregate structural models, finding that the mutagenesis data agreed best with models derived from fibrils seeded using brain-derived Aβ aggregates.

scholarly journals Use of Human Induced Pluripotent Stem Cell–Derived Cardiomyocytes in Preclinical Cancer Drug Cardiotoxicity Testing: A Scientific Statement From the American Heart Association

2019 ◽  
Vol 125 (10) ◽  
Author(s):  
Gary Gintant ◽  
Paul Burridge ◽  
Lior Gepstein ◽  
Sian Harding ◽  
Todd Herron ◽  
...  
Keyword(s):  
Stem Cell ◽  
Pluripotent Stem Cell ◽  
Cardiac Injury ◽  
Induced Pluripotent Stem Cell ◽  
Heart Association ◽  
Cancer Drug ◽  
Great Promise ◽  
Drug Induced ◽  
Induced Pluripotent

It is now well recognized that many lifesaving oncology drugs may adversely affect the heart and cardiovascular system, including causing irreversible cardiac injury that can result in reduced quality of life. These effects, which may manifest in the short term or long term, are mechanistically not well understood. Research is hampered by the reliance on whole-animal models of cardiotoxicity that may fail to reflect the fundamental biology or cardiotoxic responses of the human myocardium. The emergence of human induced pluripotent stem cell–derived cardiomyocytes as an in vitro research tool holds great promise for understanding drug-induced cardiotoxicity of oncological drugs that may manifest as contractile and electrophysiological dysfunction, as well as structural abnormalities, making it possible to deliver novel drugs free from cardiac liabilities and guide personalized therapy. This article briefly reviews the challenges of cardio-oncology, the strengths and limitations of using human induced pluripotent stem cell–derived cardiomyocytes to represent clinical findings in the nonclinical research space, and future directions for their further use.

scholarly journals Cytoprotective potential of anti-ischemic drugs against chemotherapy-induced cardiotoxicity in H9c2 myoblast cell line

2013 ◽  
Vol 63 (4) ◽  
pp. 493-503 ◽  
Author(s):  
Tiam Feridooni ◽  
Chris Mac Donald ◽  
Di Shao ◽  
Pollen Yeung ◽  
Remigius U. Agu
Keyword(s):  
Cell Death ◽  
Cell Line ◽  
Cancer Drug ◽  
H9c2 Cell ◽  
Drug Induced ◽  
Cardiac Model ◽  
Myoblast Cell Line ◽  
Myoblast Cell ◽  
H9c2 Cell Line

Abstract To investigate potential prevention or attenuation of anti- cancer drug induced cardiotoxicity using anti-ischemic drugs, a rat myoblast (H9c2) cell line was used as our in vitro cardiac model. Irinotecan and doxorubicin were found to be cytotoxic for the H9c2 cell line with IC50 of 30.69 ± 6.20 and 20.94 ± 6.05 mmol L-1, respectively. 5-Flurouracil and cladribine were not cytotoxic and thus IC50 could not be calculated. When 100 mmol L-1 doxorubicin was incubated for 72 hours with 50 mmol L-1 diltiazem, 100 mmol L-1 dexrazoxane and 100 mmol L-1 losartan, respectively, there was a 58.7 ± 10.2, 52.2 ± 11.7 and 44.7 ± 5.4 % reduction in cell death. When 200 mmol L-1 irinotecan was incubated for 72 hours with 100 mmol L-1 dexrazoxane, losartan and diltiazem, respectively, a 27.7 ± 6.9, 25.6 ± 5.1, and 19.1 ± 2.3 % reduction in cell death was observed. Our data suggests that losartan and diltiazem were as effective as dexrazoxane in protecting the cells against irinotecan- and doxorubicin-induced cell toxicity. These findings offer potential uses of anti- -ischemic drugs for ablation of cytotoxicity in response to mitochondrial injury, thereby improving patient outcomes and reducing health-care costs.

scholarly journals Opportunities and challenges in the wider adoption of liver and interconnected microphysiological systems

2017 ◽  
Vol 242 (16) ◽  
pp. 1593-1604 ◽  
Author(s):  
David J Hughes ◽  
Tomasz Kostrzewski ◽  
Emma L Sceats
Keyword(s):  
Parenchymal Cell ◽  
Pharmaceutical Research ◽  
Hepatic Function ◽  
In Vitro Models ◽  
System Level ◽  
Primary Hepatocytes ◽  
Drug Induced ◽  
Drug Induced Liver Injury ◽  
Microphysiological Systems

Liver disease represents a growing global health burden. The development of in vitro liver models which allow the study of disease and the prediction of metabolism and drug-induced liver injury in humans remains a challenge. The maintenance of functional primary hepatocytes cultures, the parenchymal cell of the liver, has historically been difficult with dedifferentiation and the consequent loss of hepatic function limiting utility. The desire for longer term functional liver cultures sparked the development of numerous systems, including collagen sandwiches, spheroids, micropatterned co-cultures and liver microphysiological systems. This review will focus on liver microphysiological systems, often referred to as liver-on-a-chip, and broaden to include platforms with interconnected microphysiological systems or multi-organ-chips. The interconnection of microphysiological systems presents the opportunity to explore system level effects, investigate organ cross talk, and address questions which were previously the preserve of animal experimentation. As a field, microphysiological systems have reached a level of maturity suitable for commercialization and consequent evaluation by a wider community of users, in academia and the pharmaceutical industry. Here scientific, operational, and organizational considerations relevant to the wider adoption of microphysiological systems will be discussed. Applications in which microphysiological systems might offer unique scientific insights or enable studies currently feasible only with animal models are described, and challenges which might be addressed to enable wider adoption of the technologies are highlighted. A path forward which envisions the development of microphysiological systems in partnerships between academia, vendors and industry, is proposed. Impact statement Microphysiological systems are in vitro models of human tissues and organs. These systems have advanced rapidly in recent years and are now being commercialized. To achieve wide adoption in the biological and pharmaceutical research communities, microphysiological systems must provide unique insights which translate to humans. This will be achieved by identifying key applications and making microphysiological systems intuitive to use.

scholarly journals Bis-Acridines as Lead Antiparasitic Agents: Structure-Activity Analysis of a Discrete Compound Library In Vitro

2007 ◽  
Vol 51 (6) ◽  
pp. 2164-2172 ◽  
Author(s):  
Conor R. Caffrey ◽  
Dietmar Steverding ◽  
Ryan K. Swenerton ◽  
Ben Kelly ◽  
Deirdre Walshe ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Linker Length ◽  
Compound Libraries ◽  
Mammalian Cell Lines ◽  
Structure Activity ◽  
Trypanosomatid Parasites ◽  
Health Significance ◽  
Important Drug ◽  
Better Than

ABSTRACT Parasitic diseases are of enormous public health significance in developing countries—a situation compounded by the toxicity of and resistance to many current chemotherapeutics. We investigated a focused library of 18 structurally diverse bis-acridine compounds for in vitro bioactivity against seven protozoan and one helminth parasite species and compared the bioactivities and the cytotoxicities of these compounds toward various mammalian cell lines. Structure-activity relationships demonstrated the influence of both the bis-acridine linker structure and the terminal acridine heterocycle on potency and cytotoxicity. The bioactivity of polyamine-linked acridines required a minimum linker length of approximately 10 Å. Increasing linker length resulted in bioactivity against most parasites but also cytotoxicity toward mammalian cells. N alkylation, but less so N acylation, of the polyamine linker ameliorated cytotoxicity while retaining bioactivity with 50% effective concentration (EC50) values similar to or better than those measured for standard drugs. Substitution of the polyamine for either an alkyl or a polyether linker maintained bioactivity and further alleviated cytotoxicity. Polyamine-linked compounds in which the terminal acridine heterocycle had been replaced with an aza-acridine also maintained acceptable therapeutic indices. The most potent compounds recorded low- to mid-nanomolar EC50 values against Plasmodium falciparum and Trypanosoma brucei; otherwise, low-micromolar potencies were measured. Importantly, the bioactivity of the library was independent of P. falciparum resistance to chloroquine. Compound bioactivity was a function of neither the potential to bis-intercalate DNA nor the inhibition of trypanothione reductase, an important drug target in trypanosomatid parasites. Our approach illustrates the usefulness of screening focused compound libraries against multiple parasite targets. Some of the bis-acridines identified here may represent useful starting points for further lead optimization.

scholarly journals ToxicoDB: an integrated database to mine and visualize large-scale toxicogenomic datasets

2020 ◽  
Vol 48 (W1) ◽  
pp. W455-W462 ◽  
Author(s):  
Sisira Kadambat Nair ◽  
Christopher Eeles ◽  
Chantal Ho ◽  
Gangesh Beri ◽  
Esther Yoo ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Large Scale ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Rat Hepatocytes ◽  
Adverse Outcomes ◽  
Easy Access ◽  
Chemical Safety ◽  
Safety Testing

Abstract In the past few decades, major initiatives have been launched around the world to address chemical safety testing. These efforts aim to innovate and improve the efficacy of existing methods with the long-term goal of developing new risk assessment paradigms. The transcriptomic and toxicological profiling of mammalian cells has resulted in the creation of multiple toxicogenomic datasets and corresponding tools for analysis. To enable easy access and analysis of these valuable toxicogenomic data, we have developed ToxicoDB (toxicodb.ca), a free and open cloud-based platform integrating data from large in vitro toxicogenomic studies, including gene expression profiles of primary human and rat hepatocytes treated with 231 potential toxicants. To efficiently mine these complex toxicogenomic data, ToxicoDB provides users with harmonized chemical annotations, time- and dose-dependent plots of compounds across datasets, as well as the toxicity-related pathway analysis. The data in ToxicoDB have been generated using our open-source R package, ToxicoGx (github.com/bhklab/ToxicoGx). Altogether, ToxicoDB provides a streamlined process for mining highly organized, curated, and accessible toxicogenomic data that can be ultimately applied to preclinical toxicity studies and further our understanding of adverse outcomes.

Cancer Targeted Nanoparticles Specifically Induce Apoptosis in Cancer Cells and Spare Normal Cells

2012 ◽  
Vol 65 (1) ◽  
pp. 5 ◽  
Author(s):  
Jagat R. Kanwar ◽  
Rupinder K. Kanwar ◽  
Ganesh Mahidhara ◽  
Chun Hei Antonio Cheung
Keyword(s):  
Adverse Effects ◽  
Cancer Cells ◽  
Modern Medicine ◽  
Chemotherapeutic Agents ◽  
Locked Nucleic Acid ◽  
Cancer Drug ◽  
Drug Induced ◽  
Normal Cells

Curing cancer is the greatest challenge for modern medicine and finding ways to minimize the adverse effects caused by chemotherapeutic agents is of importance in improving patient’s physical conditions. Traditionally, chemotherapy can induce various adverse effects, and these effects are mostly caused by the non-target specific properties of the chemotherapeutic compounds. Recently, the use of nanoparticles has been found to be capable of minimizing these drug-induced adverse effects in animals and in patients during cancer treatment. The use of nanoparticles allows various chemotherapeutic drugs to be targeted to cancer cells with lower dosages. In addition to this, the use of nanoparticles also allows various drugs to be administered to the subjects by an oral route. Here, locked nucleic acid (LNA)-modified epithelial cell adhesion molecules (EpCAM), aptamers (RNA nucleotide), and nucleolin (DNA nucleotide) aptamers have been developed and conjugated on anti-cancer drug-loaded nanocarriers for specific delivery to cancer cells and spare normal cells. Significant amounts of the drug loaded nanocarriers (92 ± 6 %) were found to distribute to the cancer cells at the tumour site and more interestingly, normal cells were unaffected in vitro and in vivo. In this review, the benefits of using nanoparticle-coated drugs in various cancer treatments are discussed. Various nanoparticles that have been tried in improving the target specificity and potency of chemotherapeutic compounds are also described.

scholarly journals Tissue specificity of in vitro drug sensitivity

2017 ◽  
Vol 25 (2) ◽  
pp. 158-166 ◽  
Author(s):  
Fupan Yao ◽  
Seyed Ali Madani Tonekaboni ◽  
Zhaleh Safikhani ◽  
Petr Smirnov ◽  
Nehme El-Hachem ◽  
...  
Keyword(s):  
Drug Screening ◽  
Large Scale ◽  
Tissue Specificity ◽  
Drug Sensitivity ◽  
Cancer Drug ◽  
General Level ◽  
Response Curves ◽  
Tissue Specific ◽  
Clinical Indications

Abstract Objectives We sought to investigate the tissue specificity of drug sensitivities in large-scale pharmacological studies and compare these associations to those found in drug clinical indications. Materials and Methods We leveraged the curated cell line response data from PharmacoGx and applied an enrichment algorithm on drug sensitivity values’ area under the drug dose-response curves (AUCs) with and without adjustment for general level of drug sensitivity. Results We observed tissue specificity in 63% of tested drugs, with 8% of total interactions deemed significant (false discovery rate <0.05). By restricting the drug-tissue interactions to those with AUC > 0.2, we found that in 52% of interactions, the tissue was predictive of drug sensitivity (concordance index > 0.65). When compared with clinical indications, the observed overlap was weak (Matthew correlation coefficient, MCC = 0.0003, P > .10). Discussion While drugs exhibit significant tissue specificity in vitro, there is little overlap with clinical indications. This can be attributed to factors such as underlying biological differences between in vitro models and patient tumors, or the inability of tissue-specific drugs to bring additional benefits beyond gold standard treatments during clinical trials. Conclusion Our meta-analysis of pan-cancer drug screening datasets indicates that most tested drugs exhibit tissue-specific sensitivities in a large panel of cancer cell lines. However, the observed preclinical results do not translate to the clinical setting. Our results suggest that additional research into showing parallels between preclinical and clinical data is required to increase the translational potential of in vitro drug screening.

scholarly journals Large-scale cultivation of mammalian cells in vitro.

1967 ◽  
Vol 15 (1) ◽  
pp. 201-202
Author(s):  
A Hellman ◽  
J D Regan ◽  
D H Martin
Keyword(s):  
Mammalian Cells ◽  
Large Scale ◽  
Large Scale Cultivation
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