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Li X, Li X, Li Y, Yu C, Xue W, Hu J, Li B, Wang P, Zhu F. What Makes Species Productive of Anti-Cancer Drugs? Clues from Drugs’ Species Origin, Druglikeness, Target and Pathway. Anticancer Agents Med Chem 2019; 19:194-203. [DOI: 10.2174/1871520618666181029132017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 08/22/2017] [Accepted: 03/21/2018] [Indexed: 12/18/2022]
Abstract
Background:Despite the substantial contribution of natural products to the FDA drug approval list, the discovery of anti-cancer drugs from the huge amount of species on the planet remains looking for a needle in a haystack. Objective: Drug-productive clusters in the phylogenetic tree are thus proposed to narrow the searching scope by focusing on much smaller amount of species within each cluster, which enable prioritized and rational bioprospecting for novel drug-like scaffolds. However, the way anti-cancer nature-derived drugs distribute in phylogenetic tree has not been reported, and it is oversimplified to just focus anti-cancer drug discovery on the drug-productive clusters, since the number of species in each cluster remains too large to be managed.Objective:Drug-productive clusters in the phylogenetic tree are thus proposed to narrow the searching scope by focusing on much smaller amount of species within each cluster, which enable prioritized and rational bioprospecting for novel drug-like scaffolds. However, the way anti-cancer nature-derived drugs distribute in phylogenetic tree has not been reported, and it is oversimplified to just focus anti-cancer drug discovery on the drug-productive clusters, since the number of species in each cluster remains too large to be managed.Methods:In this study, 260 anti-cancer drugs approved in the past 70 years were comprehensively analyzed by hierarchical clustering of phylogenetic distribution.Results:207 out of these 260 drugs were derived from or inspired by the natural products isolated from 58 species. Phylogenetic distribution of those drugs further revealed that nature-derived anti-cancer drugs originated mostly from drug-productive families that tend to be clustered rather than scattered on the phylogenetic tree. Moreover, based on their productivity, drug-producing species were categorized into productive (CPS), newly emerging (CNS) and lessproductive (CLS). Statistical significances in druglikeness between drugs from CPS and CLS were observed, and drugs from CNS were found to share similar drug-like properties to those from CPS.Conclusion:This finding indicated a great raise in drug approval standard, which suggested us to focus bioprospecting on the species yielding multiple drugs and keeping productive for long period of time.
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Affiliation(s)
- Xiaofeng Li
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Xiaoxu Li
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Yinghong Li
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Chunyan Yu
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Weiwei Xue
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Jie Hu
- School of International Studies, Zhejiang University, Hangzhou 310058, China
| | - Bo Li
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Panpan Wang
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Feng Zhu
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
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Dogruer G, Weijs L, Tang JYM, Hollert H, Kock M, Bell I, Madden Hof CA, Gaus C. Effect-based approach for screening of chemical mixtures in whole blood of green turtles from the Great Barrier Reef. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 612:321-329. [PMID: 28854388 DOI: 10.1016/j.scitotenv.2017.08.124] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 08/12/2017] [Accepted: 08/12/2017] [Indexed: 06/07/2023]
Abstract
Organisms are exposed to mixtures of both known and unknown chemicals which are diverse and variable, and thus difficult and costly to characterise and monitor using traditional target analyses. The objective of this study was to validate and apply in vitro effect-based methods by which whole blood can be used to screen internal exposure to such complex chemical mixtures. For this study, we used whole blood of green sea turtles (Chelonia mydas). To ensure the chemical mixture in blood is transferred with minimal losses or bias, we tested a modified QuEChERS extraction method specifically developed for multi- and non-target instrument analysis. The extracts were dosed to a battery of in vitro bioassays (AhR-CAFLUX, AREc32, NFκB-bla, VM7Luc4E2, Microtox), each with a different mode of action (e.g., AhR receptor mediated xenobiotics, NrF2-mediated oxidative stress, NFκB mediated response to inflammation, estrogen activity and baseline toxicity oxidative stress, respectively) in order to cover a wide spectrum of chemicals. Results confirmed the absence of interferences of the blood extract with the responses of the different assays, thus indicating the methods' compatibility with effect-based screening approaches. To apply this approach, whole blood samples were collected from green turtles foraging in agricultural, urban and remote areas of the Australian Great Barrier Reef. The effect-based screening revealed significant differences in exposure, with higher induction of AhR-CAFLUX, AREc32 and Microtox assays in turtles from the agricultural foraging ground. Overall, these results corroborated with concurrent health, target and non-target analyses in the same animals performed as part of a larger program. This study provides evidence that the proposed effect-based approach is suitable for screening and evaluating internal exposure of organisms to chemical mixtures. The approach could be valuable for advancing understanding on multiple levels ranging from identification of priority chemicals in effect-directed investigations to exploring relationships between exposure and disease, not only in sea turtles, but in any organism.
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Affiliation(s)
- Gülsah Dogruer
- Queensland Alliance for Environmental Health Sciences (QAEHS), The University of Queensland, 39 Kessels Road, Coopers Plains, Queensland 4108, Australia; Institute for Environmental Research, RWTH Aachen University, Germany.
| | - Liesbeth Weijs
- Queensland Alliance for Environmental Health Sciences (QAEHS), The University of Queensland, 39 Kessels Road, Coopers Plains, Queensland 4108, Australia
| | - Janet Yat-Man Tang
- Queensland Alliance for Environmental Health Sciences (QAEHS), The University of Queensland, 39 Kessels Road, Coopers Plains, Queensland 4108, Australia
| | - Henner Hollert
- Institute for Environmental Research, RWTH Aachen University, Germany
| | - Marjolijn Kock
- Queensland Alliance for Environmental Health Sciences (QAEHS), The University of Queensland, 39 Kessels Road, Coopers Plains, Queensland 4108, Australia
| | - Ian Bell
- Department of Environment and Heritage Protection, Threatened Species Unit, Townsville, Australia
| | | | - Caroline Gaus
- Queensland Alliance for Environmental Health Sciences (QAEHS), The University of Queensland, 39 Kessels Road, Coopers Plains, Queensland 4108, Australia
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Cell-based assays in combination with ultra-high performance liquid chromatography-quadrupole time of flight tandem mass spectrometry for screening bioactive capilliposide C metabolites generated by rat intestinal microflora. J Pharm Biomed Anal 2015; 119:130-8. [PMID: 26678180 DOI: 10.1016/j.jpba.2015.11.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 11/19/2015] [Accepted: 11/20/2015] [Indexed: 12/15/2022]
Abstract
Many plant-derived glycosides are used as medications. It is common that these glycosides show poor intestinal absorption but their metabolites generated by intestinal microflora demonstrate strong bioactivity. Hence, it is crucial to develop a method for the identification and characterization of the metabolites, and consequently reveal the pathway in which the glycosides are processed in gut. In this study, cell-based assays in combination with ultra-high performance liquid chromatography-quadrupole time of flight tandem mass spectrometry (UHPLC-QTOF-MS/MS) were developed for rapid discovery and evaluation of the metabolites of a glycoside compound, capilliposide C (LC-C). 92.7% of LC-C was biotransformed by rat intestinal microflora after 36-h incubation at 37°C. Human cancer cell lines HepG2, PC-3 and A549 was treated with metabolites pool, respectively, which was followed by cell viability assays and characterization of metabolites using UHPLC-QTOF-MS/MS. As a result, significant cytotoxicity was observed for the metabolites pool, from which six metabolites were identified. Based on the metabolites identified, deglycosylation and esterolysis were proposed as the major metabolic pathways of LC-C in rat intestinal microflora. In addition, M4, an esterolysis product of LC-C, was obtained and evaluated for its bioactivity in vitro. As a result, M4 exhibited a reduction in cell viability in HepG2 with an IC50 value of 17.46±1.55μg/mL.
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Current advances in the development of high-throughput purification strategies for the generation of therapeutic antibodies. ACTA ACUST UNITED AC 2015. [DOI: 10.4155/pbp.15.23] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Jin L, Gaus C, Escher BI. Adaptive stress response pathways induced by environmental mixtures of bioaccumulative chemicals in dugongs. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:6963-6973. [PMID: 25923886 DOI: 10.1021/acs.est.5b00947] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
To address the poorly understood mixture effects of chemicals in the marine mammal dugong, we coupled equilibrium-based passive sampling in blubber to a range of in vitro bioassays for screening mixtures of bioaccumulative chemicals. The modes of action included early effect indicators along important toxicity pathways, such as induction of xenobiotic metabolism, and some integrative indicators downstream of the molecular initiating event, such as adaptive stress responses. Activation of aryl hydrocarbon receptor (AhR) and Nrf2-mediated oxidative stress response were found to be the most prominent effects, while the p53-mediated DNA damage response and NF-κB-mediated response to inflammation were not significantly affected. Although polychlorinated dibenzo-p-dioxins (PCDDs) quantified in the samples accounted for the majority of AhR-mediated activity, PCDDs explained less than 5% of the total oxidative stress response, despite their known ability to activate this pathway. Altered oxidative stress response was observed with both individual chemicals and blubber extracts subject to metabolic activation by rat liver S9 fraction. Metabolic activation resulted in both enhanced and reduced toxicity, suggesting the relevance and utility of incorporating metabolic enzymes into in vitro bioassays. Our approach provides a first insight into the burden of toxicologically relevant bioaccumulative chemical mixtures in dugongs and can be applied to lipid tissue of other wildlife species.
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Affiliation(s)
- Ling Jin
- †The University of Queensland, National Research Centre for Environmental Toxicology (Entox), Brisbane, QLD 4018, Australia
| | - Caroline Gaus
- †The University of Queensland, National Research Centre for Environmental Toxicology (Entox), Brisbane, QLD 4018, Australia
| | - Beate I Escher
- †The University of Queensland, National Research Centre for Environmental Toxicology (Entox), Brisbane, QLD 4018, Australia
- ‡UFZ - Helmholtz Centre for Environmental Research, Cell Toxicology, 04318 Leipzig, Germany
- ∥Eberhard Karls University Tübingen, Environmental Toxicology, Center for Applied Geosciences, 72074 Tübingen, Germany
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Abstract
Antibody drugs have become an increasingly significant component of the therapeutic landscape. Their success has been driven by some of their unique properties, in particular their very high specificity and selectivity, in contrast to the off-target liabilities of small molecules (SMs). Antibodies can bring additional functionality to the table with their ability to interact with the immune system, and this can be further manipulated with advances in antibody engineering. This review summarizes what antibody therapeutics have achieved to date and what opportunities and challenges lie ahead. The target landscape for large molecules (LMs) versus SMs and some of the challenges for antibody drug development are discussed. Effective penetration of membrane barriers and intracellular targeting is one challenge, particularly across the highly resistant blood-brain barrier. The expanding pipeline of antibody-drug conjugates offers the potential to combine SM and LM modalities in a variety of creative ways, and antibodies also offer exciting potential to build bi- and multispecific molecules. The ability to pursue more challenging targets can also be further exploited but highlights the need for earlier screening in functional cell-based assays. I discuss how this might be addressed given the practical constraints imposed by high-throughput screening sample type and process differences in antibody primary screening.
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Affiliation(s)
- Alison J. Smith
- Department of Antibody Discovery and Protein Engineering, MedImmune Ltd, Cambridge, UK
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Wilkinson TCI, Gardener MJ, Williams WA. Discovery of Functional Antibodies Targeting Ion Channels. ACTA ACUST UNITED AC 2014; 20:454-67. [DOI: 10.1177/1087057114560698] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Ion channels play critical roles in physiology and disease by modulation of cellular functions such as electrical excitability, secretion, cell migration, and gene transcription. Ion channels represent an important target class for drug discovery that has been largely addressed, to date, using small-molecule approaches. A significant opportunity exists to target these channels with antibodies and alternative formats of biologics. Antibodies display high specificity and affinity for their target antigen, and they have the potential to target ion channels very selectively. Nevertheless, isolating antibodies to this target class is challenging due to the difficulties in expression and purification of ion channels in a format suitable for antibody drug discovery in addition to the complexity of screening for function. In this article, we will review the current state of ion channel biologics discovery and the progress that has been made. We will also highlight the challenges in isolating functional antibodies to these targets and how these challenges may be addressed. Finally, we also illustrate successful approaches to isolating functional monoclonal antibodies targeting ion channels by way of a number of case studies drawn from recent publications.
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Affiliation(s)
| | | | - Wendy A. Williams
- Antibody Discovery and Protein Engineering, MedImmune, Cambridge, UK
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Fendyur A, Varma S, Lo CT, Voldman J. Cell-based biosensor to report DNA damage in micro- and nanosystems. Anal Chem 2014; 86:7598-605. [PMID: 25001406 PMCID: PMC4144749 DOI: 10.1021/ac501412c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
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Understanding how newly engineered
micro- and nanoscale materials
and systems that interact with cells impact cell physiology is crucial
for the development and ultimate adoption of such technologies. Reports
regarding the genotoxic impact of forces applied to cells in such
systems that can both directly or indirectly damage DNA emphasize
the need for developing facile methods to assess how materials and
technologies affect cell physiology. To address this need we have
developed a TurboRFP-based DNA damage reporter cell line in NIH-3T3
cells that fluoresce to report genotoxic stress caused by a wide variety
of agents, from chemical genotoxic agents to UV-C radiation. Our biosensor
was successfully implemented in reporting the genotoxic impact of
nanomaterials, demonstrating the ability to assess size dependent
geno- and cyto-toxicity. The biosensor cells can be assayed in a high
throughput, noninvasive manner, with no need for overly sophisticated
equipment or additional reagents. We believe that this open-source
biosensor is an important resource for the community of micro- and
nanomaterials and systems designers and users who wish to evaluate
the impact of systems and materials on cell physiology.
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Affiliation(s)
- Anna Fendyur
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Room 36-824, Cambridge, Massachusetts 02139, United States
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