Target Identification Using Chemical Probes

Moustakim, Moses; Felce, Suet Ling; Zaarour, Nancy; Farnie, Gillian; McCann, Fiona E.; Brennan, P.E.

doi:10.1016/bs.mie.2018.09.013

Cited by 10 publications

(6 citation statements)

References 90 publications

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“…[188] Unlike stem cell and progenitor populations, primary cells cannot divide indefinitely, and the main reason to use primary cells lies in their highly specific nature and efficient mimicry of the biological properties of mature tissues, resulting from their high degree of patient-dependent sample heterogeneity. [189,190] Primary cells can be used for various purposes, such as on-chip platforms of kidney, liver, neurovascular units, lung, and heart, [191][192][193][194][195] as well as drug resistance testing [196] and drug delivery studies, [197] because primary cells are isolated directly from the tissues or organs and better mimic the in vivo system (although these platforms were not necessarily 3D bioprinted, they can demonstrate the potency of primary cells for future applications in 3D bioprinting of OOCs). [197] Moreover, tissue biopsies have the advantage of preserving 3D natural organ-specific ECM, which is lacking in 2D cultures and many 3D cultures.…”

Section: Primary Cellsmentioning

confidence: 99%

3D bioprinted organ‐on‐chips

et al. 2022

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Organ-on-a-chip (OOC) platforms recapitulate human in vivo-like conditions more realistically compared to many animal models and conventional two-dimensional cell cultures. OOC setups benefit from continuous perfusion of cell cultures through microfluidic channels, which promotes cell viability and activities. Moreover, microfluidic chips allow the integration of biosensors for real-time monitoring and analysis of cell interactions and responses to administered drugs. Three-dimensional (3D) bioprinting enables the fabrication of multicell OOC platforms with sophisticated 3D structures that more closely mimic human tissues. 3D-bioprinted OOC platforms are promising tools for understanding the functions of organs, disruptive influences of diseases on organ functionality, and screening the efficacy as well as toxicity of drugs on organs. Here, common 3D bioprinting techniques, advantages, and limitations of each method are reviewed. Additionally, recent advances, applications, and potentials of 3D-bioprinted OOC platforms for emulating various human organs are presented. Last, current challenges and future perspectives of OOC platforms are discussed. K E Y W O R D S biomaterials, bioprinting, disease-on-a-chip, microfluidics, organ-on-a-chip 1 This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

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Section: Primary Cellsmentioning

confidence: 99%

3D bioprinted organ‐on‐chips

et al. 2022

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“…Classical affinity‐based target identification (ID) involves one distinct derivatization of the compound by one linker trajectory. This requires extensive efforts by structure activity relationship (SAR) studies to obtain suitable small molecular probes for affinity‐based pulldown assays – a tedious and time consuming‐process which may even unintentionally exclude additional target proteins [4,5] . This applies even more for large natural product derived molecules, where a synthetic access is not available or tractable.…”

Section: Figurementioning

confidence: 99%

Compound Interaction Screen on a Photoactivatable Cellulose Membrane (CISCM) Identifies Drug Targets

et al. 2022

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Identifying the protein targets of drugs is an important but tedious process. Existing proteomic approaches enable unbiased target identification but lack the throughput needed to screen larger compound libraries. Here, we present a compound interaction screen on a photoactivatable cellulose membrane (CISCM) that enables target identification of several drugs in parallel. To this end, we use diazirine‐based undirected photoaffinity labeling (PAL) to immobilize compounds on cellulose membranes. Functionalized membranes are then incubated with protein extract and specific targets are identified via quantitative affinity purification and mass spectrometry. CISCM reliably identifies known targets of natural products in less than three hours of analysis time per compound. In summary, we show that combining undirected photoimmobilization of compounds on cellulose with quantitative interaction proteomics provides an efficient means to identify the targets of natural products.

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“…If recombinant protein is not available, CETSA (Jafari et al, 2014) can be used to confirm binding to the endogenous protein, and functional experiments such as siRNA knockdown in cells can validate if the target has the expected function. From there, more extensive analyses can be explored: mutagenesis or structure elucidation to determine binding site, gene editing to produce resistant cells, and more (Moustakim et al, 2018). A well-validated pulldown target identification experiment can offer a strong basis for further experimentation.…”

Section: Validationmentioning

confidence: 99%

Small molecule target identification using photo-affinity chromatography

Seo

Corson

2019

Methods in Enzymology

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Identification of the protein targets of bioactive small molecules is a routine challenge in chemical biology and phenotype-based drug discovery. Recent years have seen an explosion of approaches to meeting this challenge, but the traditional method of affinity pulldowns remains a practical choice in many contexts. This technique can be used as long as an affinity probe can be synthesized, usually with a crosslinking moiety to enable photo-affinity pulldowns. It can be applied to varied tissue types and can be performed with minimal specialized equipment. Here, we provide our protocol for photo-affinity pulldown experiments, with notes on making this method generally applicable to varied target identification challenges.

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Target Identification Using Chemical Probes

Cited by 10 publications

References 90 publications

3D bioprinted organ‐on‐chips

3D bioprinted organ‐on‐chips

Compound Interaction Screen on a Photoactivatable Cellulose Membrane (CISCM) Identifies Drug Targets

Small molecule target identification using photo-affinity chromatography

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