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Bell TN, Kusi-Appiah AE, Tocci V, Lyu P, Zhu L, Zhu F, Van Winkle D, Cao H, Singh MS, Lenhert S. Scalable lipid droplet microarray fabrication, validation, and screening. PLoS One 2024; 19:e0304736. [PMID: 38968248 PMCID: PMC11226032 DOI: 10.1371/journal.pone.0304736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 05/16/2024] [Indexed: 07/07/2024] Open
Abstract
High throughput screening of small molecules and natural products is costly, requiring significant amounts of time, reagents, and operating space. Although microarrays have proven effective in the miniaturization of screening for certain biochemical assays, such as nucleic acid hybridization or antibody binding, they are not widely used for drug discovery in cell culture due to the need for cells to internalize lipophilic drug candidates. Lipid droplet microarrays are a promising solution to this problem as they are capable of delivering lipophilic drugs to cells at dosages comparable to solution delivery. However, the scalablility of the array fabrication, assay validation, and screening steps has limited the utility of this approach. Here we take several new steps to scale up the process for lipid droplet array fabrication, assay validation in cell culture, and drug screening. A nanointaglio printing process has been adapted for use with a printing press. The arrays are stabilized for immersion into aqueous solution using a vapor coating process. In addition to delivery of lipophilic compounds, we found that we are also able to encapsulate and deliver a water-soluble compound in this way. The arrays can be functionalized by extracellular matrix proteins such as collagen prior to cell culture as the mechanism for uptake is based on direct contact with the lipid delivery vehicles rather than diffusion of the drug out of the microarray spots. We demonstrate this method for delivery to 3 different cell types and the screening of 92 natural product extracts on a microarray covering an area of less than 0.1 cm2. The arrays are suitable for miniaturized screening, for instance in high biosafety level facilities where space is limited and for applications where cell numbers are limited, such as in functional precision medicine.
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Affiliation(s)
- Tracey N. Bell
- Department of Biological Science and Integrative NanoScience Institute, Florida State University, Tallahassee, Florida, United States of America
| | - Aubrey E. Kusi-Appiah
- Department of Biological Science and Integrative NanoScience Institute, Florida State University, Tallahassee, Florida, United States of America
| | - Vincent Tocci
- Department of Biological Science and Integrative NanoScience Institute, Florida State University, Tallahassee, Florida, United States of America
| | - Pengfei Lyu
- Department of Statistics, Florida State University, Tallahassee, Florida, United States of America
| | - Lei Zhu
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, Florida, United States of America
| | - Fanxiu Zhu
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
| | - David Van Winkle
- Department of Physics, Florida State University, Tallahassee, Florida, United States of America
| | - Hongyuan Cao
- Department of Statistics, Florida State University, Tallahassee, Florida, United States of America
| | - Mandip S. Singh
- College of Pharmacy and Pharmaceutical Science, Florida A&M University, Tallahassee, Florida, United States of America
| | - Steven Lenhert
- Department of Biological Science and Integrative NanoScience Institute, Florida State University, Tallahassee, Florida, United States of America
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DiSalvo M, Cortés-Llanos B, LaBelle CA, Murdoch DM, Allbritton NL. Scalable Additive Construction of Arrayed Microstructures with Encoded Properties for Bioimaging. MICROMACHINES 2022; 13:1392. [PMID: 36144015 PMCID: PMC9500771 DOI: 10.3390/mi13091392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/20/2022] [Accepted: 08/23/2022] [Indexed: 06/16/2023]
Abstract
Microarrays are essential components of analytical instruments. The elements of microarrays may be imbued with additional functionalities and encodings using composite materials and structures, but traditional microfabrication methods present substantial barriers to fabrication, design, and scalability. In this work, a tool-free technique was reported to additively batch-construct micromolded, composite, and arrayed microstructures. The method required only a compatible carrier fluid to deposit a material onto a substrate with some topography. Permutations of this basic fabrication approach were leveraged to gain control over the volumes and positions of deposited materials within the microstructures. As a proof of concept, cell micro-carrier arrays were constructed to demonstrate a range of designs, compositions, functionalities, and applications for composite microstructures. This approach is envisioned to enable the fabrication of complex composite biological and synthetic microelements for biosensing, cellular analysis, and biochemical screening.
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Affiliation(s)
- Matthew DiSalvo
- Microsystems and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Belén Cortés-Llanos
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA
- Department of Medicine, Duke University Medical Center, Durham, NC 27705, USA
| | - Cody A. LaBelle
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA
| | - David M. Murdoch
- Department of Medicine, Duke University Medical Center, Durham, NC 27705, USA
| | - Nancy L. Allbritton
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA
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3
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Deng Y, Lin Z, Cheng Y. Coding recognition of the dose-effect interdependence of small biomolecules encrypted on paired chromatographic-based microassay arrays. Anal Bioanal Chem 2022; 414:5991-6001. [PMID: 35680658 PMCID: PMC9183755 DOI: 10.1007/s00216-022-04162-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/26/2022] [Accepted: 05/31/2022] [Indexed: 11/29/2022]
Abstract
The discovery of small biomolecules has suffered from the lack of a comprehensive framework to express the intrinsic correlation between bioactivity and the contribution from small molecules in complex samples with molecular and bioactivity diversity. Here, by mapping a sample’s 2D-HPTLC fingerprint to microplates, paired chromatographic-based microassay arrays are created, which can be used as quasi-chips to characterize multiple attributes of chromatographic components; as the array differential expression of the bioactivity and molecular attributes of irregular chromatographic spots for dose–effect interdependent encoding; and also as the automatic-collimated array mosaics of the multi-attributes of each component itself encrypted by its chromatographic fingerprint. Based on this homologous framework, we propose a correlating recognition strategy for small biomolecules through their self-consistent chromatographic behavior characteristics. In the approach, the small biomolecule recognition in diverse compounds is transformed into a constraint satisfaction problem, which is addressed through examining the dose–effect interdependence of the homologous 2D code pairs by an array matching algorithm, instead of preparing diverse compound monomers of complex test samples for identification item-by-item. Furthermore, considering the dose–effect interdependent 2D code pairs as links and the digital-specific quasimolecular ions as nodes, an extendable self-consistent framework that correlates mammalian cell phenotypic and target-based bioassays with small biomolecules is established. Therefore, the small molecule contributions and the correlations of bioactivities, as well as their pathways, can be comprehensively revealed, so as to improve the reliability and efficiency of screening. This strategy was successfully applied to galangal, and demonstrated the high-throughput digital preliminary screening of small biomolecules in a natural product.
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Affiliation(s)
- Yifeng Deng
- Guangdong Key Laboratory for Research & Development of Natural Drugs, Guangdong Medical University, Zhanjiang, 524023, China.
| | - Zhenpeng Lin
- Guangdong Key Laboratory for Research & Development of Natural Drugs, Guangdong Medical University, Zhanjiang, 524023, China
| | - Yuan Cheng
- Guangdong Key Laboratory for Research & Development of Natural Drugs, Guangdong Medical University, Zhanjiang, 524023, China
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4
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Grubb ML, Caliari SR. Fabrication approaches for high-throughput and biomimetic disease modeling. Acta Biomater 2021; 132:52-82. [PMID: 33716174 PMCID: PMC8433272 DOI: 10.1016/j.actbio.2021.03.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 02/15/2021] [Accepted: 03/02/2021] [Indexed: 12/24/2022]
Abstract
There is often a tradeoff between in vitro disease modeling platforms that capture pathophysiologic complexity and those that are amenable to high-throughput fabrication and analysis. However, this divide is closing through the application of a handful of fabrication approaches-parallel fabrication, automation, and flow-driven assembly-to design sophisticated cellular and biomaterial systems. The purpose of this review is to highlight methods for the fabrication of high-throughput biomaterial-based platforms and showcase examples that demonstrate their utility over a range of throughput and complexity. We conclude with a discussion of future considerations for the continued development of higher-throughput in vitro platforms that capture the appropriate level of biological complexity for the desired application. STATEMENT OF SIGNIFICANCE: There is a pressing need for new biomedical tools to study and understand disease. These platforms should mimic the complex properties of the body while also permitting investigation of many combinations of cells, extracellular cues, and/or therapeutics in high-throughput. This review summarizes emerging strategies to fabricate biomimetic disease models that bridge the gap between complex tissue-mimicking microenvironments and high-throughput screens for personalized medicine.
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Affiliation(s)
- Mackenzie L Grubb
- Department of Biomedical Engineering, University of Virginia, Unites States
| | - Steven R Caliari
- Department of Biomedical Engineering, University of Virginia, Unites States; Department of Chemical Engineering, University of Virginia, Unites States.
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5
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Zhong Y, Xu H, Zhong Y, Zhang X, Zeng T, Li L, Xu G, Li M, Liu J, Yang T. Identification and characterization of the Cucurbitacins, a novel class of small-molecule inhibitors of Tropomyosin receptor kinase a. BMC COMPLEMENTARY AND ALTERNATIVE MEDICINE 2019; 19:295. [PMID: 31694615 PMCID: PMC6836411 DOI: 10.1186/s12906-019-2709-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 10/03/2019] [Indexed: 02/07/2023]
Abstract
Background NGF-TrkA is well known to play a key role in propagating and sustaining pruritogenic signals, which form the pathology of chronic pruritus. Inhibition of NGF-TrkA is a known strategy for the treatment of pruritus. In the present paper, we describe the identification, in vitro characterization, structure–activity analysis, and inhibitory evaluation of a novel TrkA inhibitory scaffold exemplified by Cucurbitacins (Cus). Methods Cus were identified as TrkA inhibitors in a large-scale kinase library screen. To obtain structural models of Cus as TrkA inhibitors, AutoDock was used to explore their binding to TrkA. Furthermore, PC12 cell culture systems have been used to study the effects of Cus and traditional Chinese medicinal plants (Tian Gua Di and bitter gourd leaf) extracts on the kinase activity of TrkA. Results Cus block the phosphorylation of TrkA on several tyrosine sites, including Tyr490, Tyr674/675, and Tyr785, and inhibit downstream Akt and MAPK phosphorylation in response to NGF in PC12 cell model systems. Furthermore, traditional Chinese medicinal plants (Tian Gua Di and bitter gourd leaf) containing Cu extracts were shown to inhibit the phosphorylation of TrkA and Akt. These data reveal mechanisms, at least partly, of the anti-pruritus bioactivity of Cus. Conclusion Taken together, with the recent discovery of the important role of TrkA as a therapeutic target, Cus could be the basis for the design of improved TrkA kinase inhibitors, which could someday help treat pruritus.
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Tarannum N, Hendrickson OD, Khatoon S, Zherdev AV, Dzantiev BB. Molecularly imprinted polymers as receptors for assays of antibiotics. Crit Rev Anal Chem 2019; 50:291-310. [DOI: 10.1080/10408347.2019.1626697] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Nazia Tarannum
- Department of Chemistry, Chaudhary Charan Singh University, Meerut, India
| | - Olga D. Hendrickson
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Shahjadi Khatoon
- Department of Chemistry, Chaudhary Charan Singh University, Meerut, India
| | - Anatoly V. Zherdev
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Boris B. Dzantiev
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
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7
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Sathyanarayanan G, Haapala M, Kiiski I, Sikanen T. Digital microfluidic immobilized cytochrome P450 reactors with integrated inkjet-printed microheaters for droplet-based drug metabolism research. Anal Bioanal Chem 2018; 410:6677-6687. [PMID: 30073515 PMCID: PMC6132693 DOI: 10.1007/s00216-018-1280-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 06/27/2018] [Accepted: 07/17/2018] [Indexed: 01/23/2023]
Abstract
We report the development and characterization of digital microfluidic (DMF) immobilized enzyme reactors (IMERs) for studying cytochrome P450 (CYP)-mediated drug metabolism on droplet scale. The on-chip IMERs consist of porous polymer (thiol-ene) monolith plugs prepared in situ by photopolymerization and functionalized with recombinant CYP1A1 isoforms (an important detoxification route for many drugs and other xenobiotics). The DMF devices also incorporate inexpensive, inkjet-printed microheaters for on-demand regio-specific heating of the IMERs to physiological temperature, which is crucial for maintaining the activity of the temperature-sensitive CYP reaction. For on-chip monitoring of the CYP activity, the DMF devices were combined with a commercial well-plate reader, and a custom fluorescence quantification method was developed for detection of the chosen CYP1A1 model activity (ethoxyresorufin-O-deethylation). The reproducibility of the developed assay was examined with the help of ten parallel CYP-IMERs. All CYP-IMERs provided statistically significant difference (in fluorescence response) compared to any of the negative controls (including room-temperature reactions). The average (n = 10) turnover rate was 20.3 ± 9.0 fmol resorufin per minute. Via parallelization, the concept of the droplet-based CYP-IMER developed in this study provides a viable approach to rapid and low-cost prediction of the metabolic clearance of new chemical entities in vitro.
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Affiliation(s)
- Gowtham Sathyanarayanan
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, 00014, Helsinki, Finland
| | - Markus Haapala
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, 00014, Helsinki, Finland
| | - Iiro Kiiski
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, 00014, Helsinki, Finland
| | - Tiina Sikanen
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, 00014, Helsinki, Finland.
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8
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Yang T, Liu J, Yang M, Huang N, Zhong Y, Zeng T, Wei R, Wu Z, Xiao C, Cao X, Li M, Li L, Han B, Yu X, Li H, Zou Q. Cucurbitacin B exerts anti-cancer activities in human multiple myeloma cells in vitro and in vivo by modulating multiple cellular pathways. Oncotarget 2018; 8:5800-5813. [PMID: 27418139 PMCID: PMC5351590 DOI: 10.18632/oncotarget.10584] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 06/30/2016] [Indexed: 02/05/2023] Open
Abstract
Cucurbitacin B (CuB), a triterpenoid compound isolated from the stems of Cucumis melo, has long been used to treat hepatitis and hepatoma in China. Although its remarkable anti-cancer activities have been reported, the mechanism by which it achieves this therapeutic activity remains unclear. This study was designed to investigate the molecular mechanisms by which CuB inhibits cancer cell proliferation. Our results indicate that CuB is a novel inhibitor of Aurora A in multiple myeloma (MM) cells, arresting cells in the G2/M phase. CuB also inhibited IL-10-induced STAT3 phosphorylation, synergistically increasing the anti-tumor activity of Adriamycin in vitro. CuB induced dephosphorylation of cofilin, resulting in the loss of mitochondrial membrane potential, release of cytochrome c, and activation of caspase-8. CuB inhibited MM tumor growth in a murine MM model, without host toxicity. In conclusion, these results indicate that CuB interferes with multiple cellular pathways in MM cells. CuB thus represents a promising therapeutic tool for the treatment of MM.
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Affiliation(s)
- Tai Yang
- School of Pharmacy, Chengdu Medical College, Chengdu, China.,Department of Immunology, Chengdu Medical College, Chengdu, China
| | - Jin Liu
- Department of Immunology, Chengdu Medical College, Chengdu, China
| | - Mali Yang
- Department of Immunology, Chengdu Medical College, Chengdu, China
| | - Ning Huang
- Laboratory for Aging Research, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Yueling Zhong
- School of Pharmacy, Chengdu Medical College, Chengdu, China
| | - Ting Zeng
- Department of Immunology, Chengdu Medical College, Chengdu, China
| | - Rong Wei
- Department of Immunology, Chengdu Medical College, Chengdu, China
| | - Zhongjun Wu
- Department of Immunology, Chengdu Medical College, Chengdu, China
| | - Cui Xiao
- Department of Immunology, Chengdu Medical College, Chengdu, China
| | - Xiaohua Cao
- Department of Immunology, Chengdu Medical College, Chengdu, China
| | - Minhui Li
- Department of Immunology, Chengdu Medical College, Chengdu, China
| | - Limei Li
- Department of Immunology, Chengdu Medical College, Chengdu, China
| | - Bin Han
- Department of Public Health, Chengdu Medical College, Chengdu, China
| | - Xiaoping Yu
- Department of Public Health, Chengdu Medical College, Chengdu, China
| | - Hua Li
- Cancer Center, Chengdu Military General Hospital, Chengdu, China
| | - Qiang Zou
- Department of Immunology, Chengdu Medical College, Chengdu, China
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9
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Khalid N, Kobayashi I, Nakajima M. Recent lab-on-chip developments for novel drug discovery. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2017; 9. [DOI: 10.1002/wsbm.1381] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 12/11/2016] [Accepted: 12/20/2016] [Indexed: 12/11/2022]
Affiliation(s)
- Nauman Khalid
- School of Food and Agricultural Sciences; University of Management and Technology; Lahore Pakistan
- Centre for Chemistry and Biotechnology, School of Life and Environmental Sciences; Deakin University; Waurn Ponds Australia
- Graduate School of Life and Environmental Sciences; University of Tsukuba; Tsukuba Japan
| | - Isao Kobayashi
- Graduate School of Life and Environmental Sciences; University of Tsukuba; Tsukuba Japan
- Food Research Institute; NARO; Tsukuba Japan
| | - Mitsutoshi Nakajima
- Graduate School of Life and Environmental Sciences; University of Tsukuba; Tsukuba Japan
- Food Research Institute; NARO; Tsukuba Japan
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10
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Ghazanfari L, Lenhert S. Screening of Lipid Composition for Scalable Fabrication of Solvent-Free Lipid Microarrays. FRONTIERS IN MATERIALS 2016; 3:55. [PMID: 29333429 PMCID: PMC5761732 DOI: 10.3389/fmats.2016.00055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Liquid microdroplet arrays on surfaces are a promising approach to the miniaturization of laboratory processes such as high-throughput screening. The fluid nature of these droplets poses unique challenges and opportunities in their fabrication and application, particularly for the scalable integration of multiple materials over large areas and immersion into cell culture solution. Here, we use pin spotting and nanointaglio printing to screen a library of lipids and their mixtures for their compatibility with these fabrication processes, as well as stability upon immersion into aqueous solution. More than 200 combinations of natural and synthetic oils composed of fatty acids, triglycerides, and hydrocarbons were tested for their pin-spotting and nanointaglio print quality and their ability to contain the fluorescent compound tetramethylrhodamine B isothiocyanate (TRITC) upon immersion in water. A combination of castor oil and hexanoic acid at the ratio of 1:1 (w/w) was found optimal for producing reproducible patterns that are stable upon immersion into water. This method is capable of large-scale nanomaterials integration.
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11
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Arrabito G, Cavaleri F, Montalbano V, Vetri V, Leone M, Pignataro B. Monitoring few molecular binding events in scalable confined aqueous compartments by raster image correlation spectroscopy (CADRICS). LAB ON A CHIP 2016; 16:4666-4676. [PMID: 27812580 DOI: 10.1039/c6lc01072e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The assembly of scalable liquid compartments for binding assays in array formats constitutes a topic of fundamental importance in life sciences. This challenge can be addressed by mimicking the structure of cellular compartments with biological native conditions. Here, inkjet printing is employed to develop up to hundreds of picoliter aqueous droplet arrays stabilized by oil-confinement with mild surfactants (Tween-20). The aqueous environments constitute specialized compartments in which biomolecules may exploit their function and a wide range of molecular interactions can be quantitatively investigated. Raster Image Correlation Spectroscopy (RICS) is employed to monitor in each compartment a restricted range of dynamic intermolecular events demonstrated through protein-binding assays involving the biotin/streptavidin model system.
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Affiliation(s)
- G Arrabito
- Dipartimento di Fisica e Chimica, Università degli Studi di Palermo, Ed. 17, V.le delle Scienze, 90128 Palermo, Italy.
| | - F Cavaleri
- Dipartimento di Fisica e Chimica, Università degli Studi di Palermo, Ed. 17, V.le delle Scienze, 90128 Palermo, Italy.
| | - V Montalbano
- Dipartimento di Fisica e Chimica, Università degli Studi di Palermo, Ed. 17, V.le delle Scienze, 90128 Palermo, Italy.
| | - V Vetri
- Dipartimento di Fisica e Chimica, Università degli Studi di Palermo, Ed. 17, V.le delle Scienze, 90128 Palermo, Italy. and Aten Center, Università degli Studi di Palermo, Ed. 18, V.le delle Scienze, 90128 Palermo, Italy
| | - M Leone
- Dipartimento di Fisica e Chimica, Università degli Studi di Palermo, Ed. 17, V.le delle Scienze, 90128 Palermo, Italy. and Aten Center, Università degli Studi di Palermo, Ed. 18, V.le delle Scienze, 90128 Palermo, Italy
| | - B Pignataro
- Dipartimento di Fisica e Chimica, Università degli Studi di Palermo, Ed. 17, V.le delle Scienze, 90128 Palermo, Italy. and Aten Center, Università degli Studi di Palermo, Ed. 18, V.le delle Scienze, 90128 Palermo, Italy
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12
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Fu J, Xia A, Qi X. Identification of novel peptoid agonists of fibroblast growth factor receptor using microarray-based screening. MEDCHEMCOMM 2016; 7:1183-1189. [PMID: 27721968 DOI: 10.1039/c6md00121a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Drug development targeting fibroblast growth factor receptors (FGFRs) represents an emerging theme in the field of medicinal chemistry. Considering the fact that most of the currently identified FGFR agonists are long chain peptides with limited stability, the discovery of novel non-peptide FGFR ligands is still highly demanded. A linear one-bead-one-compound peptoid (oligomers of N-substituted glycine units) library with a theoretical diversity of 106 was designed and synthesized. Microarray-based screening led to the identification of four hit sequences 1-4 as FGFR1α ligands, which were further confirmed using both solution-phase and solid-phase binding assays. Western blot results indicated that peptoids 2-4 activated FGFR signaling pathways, resulting in increased levels of p-Akt and p-ERK in different cell lines. Our work discovered novel peptoid ligands as FGFR agonists, shedding new light on FGFR-based drug discovery.
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Affiliation(s)
- Junjie Fu
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, 32610
| | - Amy Xia
- Columbia University, New York, NY 10027
| | - Xin Qi
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, 32610
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13
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Screening of Small Molecule Microarrays for Ligands Targeted to the Extracellular Epitopes of Living Cells. MICROARRAYS 2016; 4:53-63. [PMID: 26435848 PMCID: PMC4589137 DOI: 10.3390/microarrays4010053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The screening of living cells using high-throughput microarrays is technically challenging. Great care must be taken in the chemical presentation of potential ligands and the number of collisions that cells make with them. To overcome these issues, we have developed a glass slide-based microarray system to discover small molecule ligands that preferentially bind to one cell type over another, including when the cells differ by only a single receptor. Chemical spots of 300 ± 10 μm in diameter are conjugated covalently to glass slides using an arraying robot, and novel near-infrared fluorophores with peak emission at 700 nm and 800 nm are used to label two different cell types. By carefully optimizing incubation conditions, including cell density, motion, kinetics, detection, etc. we demonstrate that cell-ligand binding occurs, and that the number of cells bound per chemical spot correlates with ligand affinity and specificity. This screening system lays the foundation for high-throughput discovery of novel ligands to the cell surface.
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14
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Decrop D, Brans T, Gijsenbergh P, Lu J, Spasic D, Kokalj T, Beunis F, Goos P, Puers R, Lammertyn J. Optical Manipulation of Single Magnetic Beads in a Microwell Array on a Digital Microfluidic Chip. Anal Chem 2016; 88:8596-603. [PMID: 27448015 DOI: 10.1021/acs.analchem.6b01734] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The detection of single molecules in magnetic microbead microwell array formats revolutionized the development of digital bioassays. However, retrieval of individual magnetic beads from these arrays has not been realized until now despite having great potential for studying captured targets at the individual level. In this paper, optical tweezers were implemented on a digital microfluidic platform for accurate manipulation of single magnetic beads seeded in a microwell array. Successful optical trapping of magnetic beads was found to be dependent on Brownian motion of the beads, suggesting a 99% chance of trapping a vibrating bead. A tailor-made experimental design was used to screen the effect of bead type, ionic buffer strength, surfactant type, and concentration on the Brownian activity of beads in microwells. With the optimal conditions, the manipulation of magnetic beads was demonstrated by their trapping, retrieving, transporting, and repositioning to a desired microwell on the array. The presented platform combines the strengths of digital microfluidics, digital bioassays, and optical tweezers, resulting in a powerful dynamic microwell array system for single molecule and single cell studies.
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Affiliation(s)
- Deborah Decrop
- Department of Biosystems, MEBIOS-Biosensors, KU Leuven , Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Toon Brans
- Department of Electronics and Information Systems (ELIS) and Center for Nano and Biophotonics (NB-Photonics), UGent , Sint-Pietersnieuwstraat 41, 9000 Gent, Belgium
| | - Pieter Gijsenbergh
- Department of Electrotechnical Engineering (ESAT-MICAS), KU Leuven , Kasteelpark Arenberg 10 Postbus 2440, 3001 Leuven, Belgium
| | - Jiadi Lu
- Department of Biosystems, MEBIOS-Biosensors, KU Leuven , Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Dragana Spasic
- Department of Biosystems, MEBIOS-Biosensors, KU Leuven , Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Tadej Kokalj
- Department of Biosystems, MEBIOS-Biosensors, KU Leuven , Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Filip Beunis
- Department of Electronics and Information Systems (ELIS) and Center for Nano and Biophotonics (NB-Photonics), UGent , Sint-Pietersnieuwstraat 41, 9000 Gent, Belgium
| | - Peter Goos
- Department of Biosystems, MEBIOS-Biosensors, KU Leuven , Willem de Croylaan 42, 3001 Leuven, Belgium.,Faculty of Applied Economics, University of Antwerp, Stadscampus , Prinsstraat 13, 2000 Antwerp, Belgium
| | - Robert Puers
- Department of Electrotechnical Engineering (ESAT-MICAS), KU Leuven , Kasteelpark Arenberg 10 Postbus 2440, 3001 Leuven, Belgium
| | - Jeroen Lammertyn
- Department of Biosystems, MEBIOS-Biosensors, KU Leuven , Willem de Croylaan 42, 3001 Leuven, Belgium
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15
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16
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Ding Y, Li J, Xiao W, Xiao K, Lee J, Bhardwaj U, Zhu Z, Digiglio P, Yang G, Lam KS, Pan T. Microfluidic-Enabled Print-to-Screen Platform for High-Throughput Screening of Combinatorial Chemotherapy. Anal Chem 2015; 87:10166-71. [DOI: 10.1021/acs.analchem.5b00826] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yuzhe Ding
- Micro-Nano
Innovations (MiNI) Laboratory, Biomedical Engineering, University of California, Davis, California 95616, United States
| | - Jiannan Li
- Micro-Nano
Innovations (MiNI) Laboratory, Biomedical Engineering, University of California, Davis, California 95616, United States
| | - Wenwu Xiao
- Department
of Biochemistry and Molecular Medicine, Division of Hematology and
Oncology, UC Davis Cancer Center, University of California, Davis, California 95817, United States
| | - Kai Xiao
- Department
of Biochemistry and Molecular Medicine, Division of Hematology and
Oncology, UC Davis Cancer Center, University of California, Davis, California 95817, United States
| | - Joyce Lee
- Department
of Biochemistry and Molecular Medicine, Division of Hematology and
Oncology, UC Davis Cancer Center, University of California, Davis, California 95817, United States
| | - Urvashi Bhardwaj
- Department
of Biochemistry and Molecular Medicine, Division of Hematology and
Oncology, UC Davis Cancer Center, University of California, Davis, California 95817, United States
| | - Zijie Zhu
- Micro-Nano
Innovations (MiNI) Laboratory, Biomedical Engineering, University of California, Davis, California 95616, United States
| | - Philip Digiglio
- Micro-Nano
Innovations (MiNI) Laboratory, Biomedical Engineering, University of California, Davis, California 95616, United States
| | - Gaomai Yang
- Micro-Nano
Innovations (MiNI) Laboratory, Biomedical Engineering, University of California, Davis, California 95616, United States
| | - Kit S. Lam
- Department
of Biochemistry and Molecular Medicine, Division of Hematology and
Oncology, UC Davis Cancer Center, University of California, Davis, California 95817, United States
| | - Tingrui Pan
- Micro-Nano
Innovations (MiNI) Laboratory, Biomedical Engineering, University of California, Davis, California 95616, United States
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17
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Kondoh Y, Honda K, Osada H. Construction and application of a photo-cross-linked chemical array. Methods Mol Biol 2015; 1263:29-41. [PMID: 25618334 DOI: 10.1007/978-1-4939-2269-7_3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Chemical array technology is a powerful tool for high-throughput screening of small-molecule ligand-protein interactions. A chemical array is a collection of small-molecule compounds spotted and immobilized on a glass slide surface, providing a multiplex platform to identify small-molecule compounds binding to a protein of interest in high-throughput screening. Several research groups have developed a variety of methods for the immobilization of small molecules onto a solid matrix. We have developed a unique photo-cross-linked chemical array for immobilizing small molecules in a functional-group-independent manner. In this chapter, we describe in detail a protocol for the construction of a photo-cross-linked chemical array and its application for ligand screening by using a tag-fused protein.
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Affiliation(s)
- Yasumitsu Kondoh
- Antibiotics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
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18
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Schyrr B, Pasche S, Voirin G, Weder C, Simon YC, Foster EJ. Biosensors based on porous cellulose nanocrystal-poly(vinyl alcohol) scaffolds. ACS APPLIED MATERIALS & INTERFACES 2014; 6:12674-12683. [PMID: 24955644 DOI: 10.1021/am502670u] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Cellulose nanocrystals (CNCs), which offer a high aspect ratio, large specific surface area, and large number of reactive surface groups, are well suited for the facile immobilization of high density biological probes. We here report functional high surface area scaffolds based on cellulose nanocrystals (CNCs) and poly(vinyl alcohol) (PVA) and demonstrate that this platform is useful for fluorescence-based sensing schemes. Porous CNC/PVA nanocomposite films with a thickness of 25-70 nm were deposited on glass substrates by dip-coating with an aqueous mixture of the CNCs and PVA, and the porous nanostructure was fixated by heat treatment. In a subsequent step, a portion of the scaffold's hydroxyl surface groups was reacted with 2-(acryloxy)ethyl (3-isocyanato-4-methylphenyl)carbamate to permit the immobilization of thiolated fluorescein-substituted lysine, which was used as a first sensing motif, via nucleophile-based thiol-ene Michael addition. The resulting sensor films exhibit a nearly instantaneous and pronounced change of their fluorescence emission intensity in response to changes in pH. The approach was further extended to the detection of protease activity by immobilizing a Förster-type resonance energy transfer chromophore pair via a labile peptide sequence to the scaffold. This sensing scheme is based on the degradation of the protein linker in the presence of appropriate enzymes, which separate the chromophores and causes a turn-on of the originally quenched fluorescence. Using a standard benchtop spectrometer to monitor the increase in fluorescence intensity, trypsin was detected at a concentration of 250 μg/mL, i.e., in a concentration that is typical for abnormal proteolytic activity in wound fluids.
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Affiliation(s)
- Bastien Schyrr
- CSEM Centre Suisse d'Electronique et de Microtechnique SA , Jaquet-Droz 1, CH-2002 Neuchâtel, Switzerland
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19
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Ou Q, He J, Liu C, Shi L, Zhao C, Xu Y, Gu D. Preparation and evaluation of a peptide nucleic acid gene chip system associated with surface plasmon resonance. BIOTECHNOL BIOPROC E 2013. [DOI: 10.1007/s12257-012-0844-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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20
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Chen BS, Li CW. Analysing microarray data in drug discovery using systems biology. Expert Opin Drug Discov 2013; 2:755-68. [PMID: 23488963 DOI: 10.1517/17460441.2.5.755] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The innovation of present drug design focuses on new targets. However, compound efficacy and safety in human metabolism, including toxicity and pharmacokinetic profiles, but not target selection, are the criteria that determine which drug candidates enter the clinic. Systems biology approaches to disease are developed from the idea that disease-perturbed regulatory networks differ from their normal counterparts. Microarray data analyses reveal global changes in gene or protein expression in response to genetic and environmental changes and, accordingly, are well suited to construct the normal, disease-perturbed and drug-affected networks, which are useful for drug discovery in the pharmaceutical industry. The integration of modelling, microarray data and systems biology approaches will allow for a true breakthrough in in silico absorption, distribution, metabolism, excretion and toxicity assessment in drug design. Therefore, drug discovery through systems biology by means of microarray analyses could significantly reduce the time and cost of new drug development.
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Affiliation(s)
- Bor-Sen Chen
- National Tsing Hua University, Laboratory of Control and Systems Biology, 101, Sec 2, Kuang Fu Road, Hsinchu, 300, Taiwan
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21
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Qing LS, Tang N, Xue Y, Liang J, Liu YM, Liao X. Identification of Enzyme Inhibitors Using Therapeutic Target Protein - Magnetic Nanoparticle Conjugates. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2012; 4:1612-1615. [PMID: 22737184 PMCID: PMC3378064 DOI: 10.1039/c2ay25320h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Target protein - magnetic nanoparticle (MNP) conjugates, i.e. α-glucosidase-MNP and protein tyrosine phosphatase 1B (PTP1B)-MNP, were prepared and evaluated for the first time for affinity extraction of the enzyme inhibitors from herbal extracts. Four ligands extracted from granati pericarpium were identified by ESI-MS analysis. In vitro tests indicated that they inhibited both α-glucosidase and PTP1B, two important target proteins for diabetic treatment.
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Affiliation(s)
- Lin-Sen Qing
- National Engineering Research Center for Natural Medicines, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, P.R. China. Tel: 86-28-85253968
| | - Nan Tang
- School of pharmacy, Guangdong Medical College, Dongguan 523808, China
| | - Ying Xue
- National Engineering Research Center for Natural Medicines, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, P.R. China. Tel: 86-28-85253968
| | - Jian Liang
- National Engineering Research Center for Natural Medicines, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, P.R. China. Tel: 86-28-85253968
| | - Yi-Ming Liu
- National Engineering Research Center for Natural Medicines, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, P.R. China. Tel: 86-28-85253968
- Department of Chemistry and Biochemistry, Jackson State University, 1400 Lynch St. Jackson, MS 39110 USA. Tel: 1-601-979-349
| | - Xun Liao
- National Engineering Research Center for Natural Medicines, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, P.R. China. Tel: 86-28-85253968
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22
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Zhao S, Chen A, Revzin A, Pan T. Stereomask lithography (SML): a universal multi-object micro-patterning technique for biological applications. LAB ON A CHIP 2011; 11:224-30. [PMID: 21113523 DOI: 10.1039/c0lc00275e] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The advent of biological micro-patterning techniques has given new impetus to many areas of biological research, including quantitative biochemical analysis, tissue engineering, biosensing, and regenerative medicine. Derived from photolithography or soft lithography, current bio-patterning approaches have yet to completely address the needs of out-of-cleanroom, universal applicability, high feature resolution, as well as multi-object placement, though many have shown great promise to precisely pattern one specific biomaterial. In this paper, we present a novel versatile biological lithography technique to achieve integrated multi-object patterning with high feature resolution and high adaptability to various biomaterials, referred to as stereomask lithography (SML). Successive patterning of multiple objects is enabled by using unique three-dimensional masks (i.e., the stereomasks), which lay out current micropatterns while protecting pre-existing biological features on the substrate. Furthermore, high-precision reversible alignment among multiple bio-objects is achieved by adopting a peg-in-hole design between the substrate and stereomasks. We demonstrate that the SML technique is capable of constructing a complex biological microenvironment with various bio-functional components at the single-cell resolution, which to the best of our knowledge has not been realized before.
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Affiliation(s)
- Siwei Zhao
- Micro-Nano Innovations (MiNI) Laboratory, Department of Biomedical Engineering, University of California, Davis, CA, USA
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23
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Lee HY, Park SB. Surface modification for small-molecule microarrays and its application to the discovery of a tyrosinase inhibitor. ACTA ACUST UNITED AC 2011; 7:304-10. [DOI: 10.1039/c0mb00122h] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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24
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Darzynkiewicz Z, Traganos F, Zhao H, Halicka HD, Skommer J, Wlodkowic D. Analysis of individual molecular events of DNA damage response by flow- and image-assisted cytometry. Methods Cell Biol 2011; 103:115-47. [PMID: 21722802 DOI: 10.1016/b978-0-12-385493-3.00006-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
This chapter describes molecular mechanisms of DNA damage response (DDR) and presents flow- and image-assisted cytometric approaches to assess these mechanisms and measure the extent of DDR in individual cells. DNA damage was induced by cell treatment with oxidizing agents, UV light, DNA topoisomerase I or II inhibitors, cisplatin, tobacco smoke, and by exogenous and endogenous oxidants. Chromatin relaxation (decondensation) is an early event of DDR chromatin that involves modification of high mobility group proteins (HMGs) and histone H1 and was detected by cytometry by analysis of the susceptibility of DNA in situ to denaturation using the metachromatic fluorochrome acridine orange. Translocation of the MRN complex consisting of Meiotic Recombination 11 Homolog A (Mre11), Rad50 homolog, and Nijmegen Breakage Syndrome 1 (NMR1) into DNA damage sites was assessed by laser scanning cytometry as the increase in the intensity of maximal pixel as well as integral value of Mre11 immunofluorescence. Examples of cytometric detection of activation of Ataxia telangiectasia mutated (ATM), and Check 2 (Chk2) protein kinases using phospho-specific Abs targeting Ser1981 and Thr68 of these proteins, respectively are also presented. We also discuss approaches to correlate activation of ATM and Chk2 with phosphorylation of p53 on Ser15 and histone H2AX on Ser139 as well as with cell cycle position and DNA replication. The capability of laser scanning cytometry to quantify individual foci of phosphorylated H2AX and/or ATM that provides more dependable assessment of the presence of DNA double-strand breaks is outlined. The new microfluidic Lab-on-a-Chip platforms for interrogation of individual cells offer a novel approach for DDR cytometric analysis.
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Affiliation(s)
- Zbigniew Darzynkiewicz
- Brander Cancer Research Institute and Department of Pathology, New York Medical College, Valhalla, NY, USA
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25
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Liang S, Xu W, Horiuchi KY, Wang Y, Ma H. Chemical microarrays: a new tool for discovery enzyme inhibitors. Methods Mol Biol 2010; 572:149-60. [PMID: 20694690 DOI: 10.1007/978-1-60761-244-5_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Enzymes, the catalytic proteins, are playing pivotal roles in regulating basic cell functions. Drugs that inhibit enzyme activities cover varying aspects of diseases and offer potential cures. One of the major technologies used in the drug discovery industry for finding the enzyme inhibitors is high-throughput screening, which is facing a daunting challenge due to the fast-growing numbers of drug targets arising from genomic and proteomic research and the large chemical libraries generated from high-throughput synthesis. Chemical microarray, as a new technology, could be an excellent alternative for traditional well-based screening, since the technology can screen more compounds against more targets in parallel with a minimum amount of materials, reducing cost and increasing productivity. In this chapter, we have introduced the basic techniques and applications of chemical microarrays, and how to use them routinely for identifying enzyme inhibitors with functional-based assays. Sample assays for kinases, proteases, histone deacetylases, and phosphatases are demonstrated.
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26
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Zhao S, Ji X, Lin P, Liu YM. A gold nanoparticle-mediated enzyme bioreactor for inhibitor screening by capillary electrophoresis. Anal Biochem 2010; 411:88-93. [PMID: 21184730 DOI: 10.1016/j.ab.2010.12.025] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Revised: 12/15/2010] [Accepted: 12/15/2010] [Indexed: 12/26/2022]
Abstract
A facile protocol to prepare highly effective and durable in-line enzyme bioreactors inside capillary electrophoresis (CE) columns was developed. To demonstrate the methodology, l-glutamic dehydrogenase (GLDH) was selected as the model enzyme. GLDH was first immobilized onto 38-nm-diameter gold nanoparticles (GNPs), and the functionalized GNPs were then assembled on the inner wall at the inlet end of the CE capillary treated with polyethyleneimine (PEI), producing an in-line GLDH bioreactor. Compared with a GLDH bioreactor prepared by immobilizing GLDH directly on PEI-treated capillary, the GNP-mediated bioreactor showed a higher enzymatic activity and a much better stability. The in-capillary enzyme bioreactor was proven to be very useful for screening of GLDH inhibitors deploying the GLDH-catalyzed α-ketoglutaric acid reaction. The screening assay was preliminarily validated by using a known GLDH inhibitor, namely perphenazine. A Z' factor value of 0.95 (n=10) was obtained, indicating that the screening results were highly reliable. Screening of GLDH inhibitors present in medicinal plant extracts by the proposed method was demonstrated. The inhibition percentages were found to be 53% for Radix scutellariae, 45% for Radix codonopsis, 37% for Radix paeoniae alba, and 0% for the other 22 extracts tested at a concentration of 0.6mg extract/ml.
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Affiliation(s)
- Shulin Zhao
- College of Chemistry and Chemical Engineering, Guangxi Normal University, Guilin 51004, China.
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27
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Wlodkowic D, Cooper JM. Microfabricated analytical systems for integrated cancer cytomics. Anal Bioanal Chem 2010; 398:193-209. [DOI: 10.1007/s00216-010-3722-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2010] [Revised: 03/29/2010] [Accepted: 04/03/2010] [Indexed: 01/09/2023]
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28
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Kannoujia DK, Ali S, Nahar P. Pressure-induced covalent immobilization of enzymes onto solid surface. Biochem Eng J 2009. [DOI: 10.1016/j.bej.2009.09.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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29
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Smyth LA, Collins I. Measuring and interpreting the selectivity of protein kinase inhibitors. J Chem Biol 2009; 2:131-51. [PMID: 19568781 PMCID: PMC2725273 DOI: 10.1007/s12154-009-0023-9] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2009] [Revised: 05/08/2009] [Accepted: 05/15/2009] [Indexed: 12/23/2022] Open
Abstract
Protein kinase inhibitors are a well-established class of clinically useful drugs, particularly for the treatment of cancer. Achieving inhibitor selectivity for particular protein kinases often remains a significant challenge in the development of new small molecules as drugs or as tools for chemical biology research. This review summarises the methodologies available for measuring kinase inhibitor selectivity, both in vitro and in cells. The interpretation of kinase inhibitor selectivity data is discussed, particularly with reference to the structural biology of the protein targets. Measurement and prediction of kinase inhibitor selectivity will be important for the development of new multi-targeted kinase inhibitors.
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Affiliation(s)
- Lynette A Smyth
- Cancer Research UK Centre for Cancer Therapeutics, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK,
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30
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Ho D, Falter K, Severin P, Gaub HE. DNA as a force sensor in an aptamer-based biochip for adenosine. Anal Chem 2009; 81:3159-64. [PMID: 19364143 DOI: 10.1021/ac802766j] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Without prior signal amplification, small molecules are difficult to detect by current label-free biochip approaches. In the present study, we developed a label-free capture biochip based on the comparative measurement of unbinding forces allowing for direct detection of small-molecule-aptamer interactions. The principle of this assay relies on increased unbinding forces of bipartite aptamers due to complex formation with their cognate ligands. The bipartite aptamers are immobilized on glass support via short DNA duplexes that serve as references to which unbinding forces can be compared. In a simple model system, adenosine is captured from solution by an adenosine-selective aptamer. Linking the molecular chains, each consisting of a short DNA reference duplex and a bipartite aptamer, between glass and a poly(dimethylsiloxane) (PDMS) surface and subsequently separating the surfaces compares the unbinding forces of the two bonds directly. Fluorescence readout allows for quantification of the fractions of broken aptamer and broken reference bonds. The presence of micromolar adenosine concentrations reliably resulted in a shift toward larger fractions of broken reference bonds. Because of the force-based design, the interactions between the bipartite aptamer and the target, rather than the presence of the target, are detected and no washing step disturbing the equilibrium state prior to probing and no reporter aptamer or antibody is required. The assay exhibits excellent selectivity against other nucleotides and detects adenosine in the presence of a complex molecular background. Multiplexing was demonstrated by performing whole titration experiments on a single chip revealing an effective half-maximal concentration of 124.8 microM agreeing well with literature values.
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Affiliation(s)
- Dominik Ho
- Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, Amalienstrasse 54, 80799 Munich, Germany
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31
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Janga SC, Tzakos A. Structure and organization of drug-target networks: insights from genomic approaches for drug discovery. MOLECULAR BIOSYSTEMS 2009; 5:1536-48. [DOI: 10.1039/b908147j] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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32
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Hong J, Edel JB, deMello AJ. Micro- and nanofluidic systems for high-throughput biological screening. Drug Discov Today 2008; 14:134-46. [PMID: 18983933 DOI: 10.1016/j.drudis.2008.10.001] [Citation(s) in RCA: 165] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Revised: 09/30/2008] [Accepted: 10/06/2008] [Indexed: 01/09/2023]
Abstract
High-throughput screening (HTS) is a method of scientific experimentation widely used in drug discovery and relevant to the fields of biology. The development of micro- and nanofluidic systems for use in the biological sciences has been driven by a range of fundamental attributes that accompany miniaturization and massively parallel experimentation. We review recent advances in both arraying strategies based on nano/microfluidics and novel nano/microfluidic devices with high analytical throughput rates.
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Affiliation(s)
- Jongin Hong
- Department of Chemistry, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
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33
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Non-contact protein microarray fabrication using a procedure based on liquid bridge formation. Anal Bioanal Chem 2008; 393:591-8. [PMID: 19023564 DOI: 10.1007/s00216-008-2509-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2008] [Revised: 10/29/2008] [Accepted: 10/30/2008] [Indexed: 10/21/2022]
Abstract
Contemporary microarrayers of contact or non-contact format used in protein microarray fabrication still suffer from a number of problems, e.g. generation of satellite spots, inhomogeneous spots, misplaced or even absent spots, and sample carryover. In this paper, a new concept of non-contact sample deposition that reduces such problems is introduced. To show the potential and robustness of this pressure-assisted deposition technique, different sample solutions known to cause severe problems or to be even impossible to print with conventional microarrayers were accurately printed. The samples included 200 mg mL(-1) human serum albumin, highly concentrated sticky cell adhesion proteins, pure high-salt cell-lysis buffer, pure DMSO, and a suspension of 5-microm polystyrene beads. Additionally, a water-immiscible liquid fluorocarbon, which was shown not to affect the functionality of the capture molecules, was employed as a lid to reduce evaporation during microarray printing. The fluorocarbon liquid lid was shown to circumvent hydrolysis of water-sensitive activated surfaces during long-term deposition procedures.
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34
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Collard D, Takeuchi S, Fujita H. MEMS technology for nanobio research. Drug Discov Today 2008; 13:989-96. [PMID: 18835363 DOI: 10.1016/j.drudis.2008.07.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2008] [Revised: 07/18/2008] [Accepted: 07/21/2008] [Indexed: 10/21/2022]
Abstract
Micro- and nanotechnology have gathered 20 years of increasing research efforts. This research activity began and developed with the design and the fabrication of micro- and nanomechanisms, sensors and actuators, which range from 10nm to 100mum. More recent trends focus on the transfer of this technology know-how towards nanobiological topics and very wide range applications can be addressed. Among them, this review proposes various examples that include MEMS tweezers for molecular direct handling and characterization, single molecular characterization in femto-L chambers and dynamic microarray for cell positioning. The micromachined devices are described with bio-oriented experiences that are relevant to foresee their future contribution to drug discovery.
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Affiliation(s)
- Dominique Collard
- Center for International Research on MicroMechatronics, Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan.
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Ma H, Deacon S, Horiuchi K. The challenge of selecting protein kinase assays for lead discovery optimization. Expert Opin Drug Discov 2008; 3:607-621. [PMID: 19662101 DOI: 10.1517/17460441.3.6.607] [Citation(s) in RCA: 149] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
BACKGROUND: Protein kinases represent one of the most promising groups of drug targets owing to their involvement in such pathological conditions as cancer, inflammatory diseases, neural disorders, and metabolism problems. In the last few years, numerous pharmaceutical and biotech companies have established kinase high-throughput screening (HTS) programs, and the reagent and service industries for kinase assay platforms, kits, and profiling services have begun to thrive. OBJECTIVE: The plethora of different assay formats available today poses a great challenge to scientists who want to select a technology that will be cost efficient, convenient to use, and have low false positive and false negative rates. METHODS: In the current review, we summarize the most commonly used kinase assay methods in the drug discovery process, present the advantages and disadvantages of each of these methods, and discuss the challenges of discovering kinase inhibitors by using these technologies. CONCLUSIONS: The decision of selecting the assay formats for HTS or service platform for profiling should take into account not only the final goals of the screens but also the limitation of resources.
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Affiliation(s)
- Haiching Ma
- Chief Technology Officer, Reaction Biology Corporation, One Great Valley Parkway, Suite 8, Malvern, PA 19355, USA, Tel: +1 610 722 0247; ; E-mail:
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36
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Midorikawa Y, Sugiyama Y, Aburatani H. Screening of liver-targeted drugs. Expert Opin Drug Discov 2008; 3:643-54. [DOI: 10.1517/17460441.3.6.643] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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37
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Proteomic methods for drug target discovery. Curr Opin Chem Biol 2008; 12:46-54. [PMID: 18282485 DOI: 10.1016/j.cbpa.2008.01.022] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2007] [Accepted: 01/15/2008] [Indexed: 11/22/2022]
Abstract
The field of drug target discovery is currently very popular with a great potential for advancing biomedical research and chemical genomics. Innovative strategies have been developed to aid the process of target identification, either by elucidating the primary mechanism-of-action of a drug, by understanding side effects involving unanticipated 'off-target' interactions, or by finding new potential therapeutic value for an established drug. Several promising proteomic methods have been introduced for directly isolating and identifying the protein targets of interest that are bound by active small molecules or for visualizing enzyme activities affected by drug treatment. Significant progress has been made in this rapidly advancing field, speeding the clinical validation of drug candidates and the discovery of the novel targets for lead compounds developed using cell-based phenotypic screens. Using these proteomic methods, further insight into drug activity and toxicity can be ascertained.
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Gurard-Levin ZA, Mrksich M. Combining self-assembled monolayers and mass spectrometry for applications in biochips. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2008; 1:767-800. [PMID: 20636097 DOI: 10.1146/annurev.anchem.1.031207.112903] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Biochip arrays have enabled the massively parallel analysis of genomic DNA and hold great promise for application to the analysis of proteins, carbohydrates, and small molecules. Surface chemistry plays an intrinsic role in the preparation and analysis of biochips by providing functional groups for immobilization of ligands, providing an environment that maintains activity of the immobilized molecules, controlling nonspecific interactions of analytes with the surface, and enabling detection methods. This review describes recent advances in surface chemistry that enable quantitative assays of a broad range of biochemical activities. The discussion emphasizes the use of self-assembled monolayers of alkanethiolates on gold as a structurally well-defined and synthetically flexible platform for controlling the immobilization and activity of molecules in an array. The review also surveys recent methods of performing label-free assays, and emphasizes the use of matrix-assisted laser desorption/ionization mass spectrometry to directly observe molecules attached to the self-assembled monolayers.
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Affiliation(s)
- Zachary A Gurard-Levin
- Department of Chemistry, Howard Hughes Medical Institute, University of Chicago, Illinois 60637, USA
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Tang Z, Wang T, Kang J. Immobilized capillary enzyme reactor based on layer-by-layer assembling acetylcholinesterase for inhibitor screening by CE. Electrophoresis 2007; 28:2981-7. [PMID: 17674420 DOI: 10.1002/elps.200700061] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A method for creating an immobilized capillary acetylcholinesterase (AChE) reactor based on a layer-by-layer (LBL) assembly for inhibitor screening is described. The unique capillary AChE reactor was easily prepared by the instrument in three steps: first, a 0.5 cm long plug of a solution of the cationic polyelectrolyte polydiallyldimethylammonium (PDDA) was injected into the capillary to produce a positively charged coating on the surface of the capillary; subsequently, the enzyme solution with the same plug length was injected into the capillary and incubated for 10 min to immobilize the enzyme on the capillary wall via electrostatic interaction; third, PDDA solution with the same plug length was injected again into the capillary to cover the immobilized enzyme by forming PDDA-AChE-PDDA sandwich-like structure. The enzyme reactor can be easily renewed after removing the immobilized enzyme by flushing the column with 1 M NaCl solution. Activity of the immobilized enzyme can be assayed simply by carrying out an electrophoretic separation, i.e., the substrate solution was injected and incubated for a short time, followed by applying a voltage to separate the product from the unreacted substrate. The measured peak area of the product then represented the enzyme activity. For enzyme inhibitor screening, the mixture solution of the substrate and the inhibitor was injected and assayed the reduction of the enzyme activity. The immobilized enzyme could withstand 100 consecutive assays by only losing 10% activity. The reproducibility in terms of time-to-time, day-to-day, and batch-to-batch was measured with RSD% less than 4.7%. Furthermore, the screening system was validated by a known inhibitor. Finally, screening a small compound library containing four known AChE inhibitors and 42 natural extracts was demonstrated, and species with inhibition activity can be straightforwardly identified with the system.
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Affiliation(s)
- Zhongmei Tang
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, PR China
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Lee SC, Park SB. Practical Solid-Phase Parallel Synthesis of Δ5-2-Oxopiperazines via N-Acyliminium Ion Cyclization. ACTA ACUST UNITED AC 2007; 9:828-35. [PMID: 17592879 DOI: 10.1021/cc0700492] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A practical solid-phase strategy for the synthesis of Delta(5)-2-oxopiperazines via N-acyliminium ion cyclization has been developed. A key step in the library synthesis is tandem acidolytic cleavage with subsequent in situ iminium formation, followed by stable enamide transformation. This approach is exemplified by the preparation of a 192-member pilot library using bromoacetal resins without further purification.
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Affiliation(s)
- Sung-Chan Lee
- Department of Chemistry, Seoul National University, Seoul 151-747, Korea
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Griffiths-Jones CM, Hopkin MD, Jönsson D, Ley SV, Tapolczay DJ, Vickerstaffe E, Ladlow M. Fully automated flow-through synthesis of secondary sulfonamides in a binary reactor system. ACTA ACUST UNITED AC 2007; 9:422-30. [PMID: 17348713 DOI: 10.1021/cc060152b] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A fully automated flow-through process for the production of secondary sulfonamides is presented. Primary sulfonamides were monoalkylated using a two-step "catch and release" protocol to generate library products of high purity. The automated flow synthesis platform incorporates four independent reactor columns and is able to perform automated column regeneration. A 48-member sulfonamide library was prepared as two 24-member sublibraries, affording library compounds in good yields and high purities without the need for further column chromatographic purification.
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Affiliation(s)
- Charlotte M Griffiths-Jones
- GlaxoSmithKline Cambridge Technology Centre, University Chemical Laboratory, Lensfield Road, Cambridge, CB2 1EW, UK
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Dilly SJ, Bell MJ, Clark AJ, Marsh A, Napier RM, Sergeant MJ, Thompson AJ, Taylor PC. A photoimmobilisation strategy that maximises exploration of chemical space in small molecule affinity selection and target discovery. Chem Commun (Camb) 2007:2808-10. [PMID: 17609783 DOI: 10.1039/b704271j] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We show that the use of multiple photochemistries is necessary to ensure diverse immobilisation of small molecules for binding of polypeptides using phage display and antibody libraries.
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Affiliation(s)
- Suzanne J Dilly
- Department of Chemistry, University of Warwick, Coventry, UK CV4 7AL
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Rich RL, Myszka DG. Survey of the year 2006 commercial optical biosensor literature. J Mol Recognit 2007; 20:300-66. [DOI: 10.1002/jmr.862] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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