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Du Y. Binding Curve Viewer: Visualizing the Equilibrium and Kinetics of Protein-Ligand Binding and Competitive Binding. J Chem Inf Model 2024; 64:4180-4192. [PMID: 38720179 PMCID: PMC11134506 DOI: 10.1021/acs.jcim.4c00130] [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: 01/24/2024] [Revised: 04/21/2024] [Accepted: 04/25/2024] [Indexed: 05/28/2024]
Abstract
Understanding the thermodynamics and kinetics of the protein-ligand interaction is essential for biologists and pharmacologists. To visualize the equilibrium and kinetics of the binding reaction with 1:1 stoichiometry and no cooperativity, we obtained the exact relationship of the concentration of the protein-ligand complex and the time in the second-order binding process and numerically simulated the process of competitive binding. First, two common concerns in measuring protein-ligand interactions were focused on how to avoid the titration regime and how to establish the appropriate incubation time. Then, we gave examples of how the commonly used experimental conditions of [L]0 ≫ [P]0 and [I]0 ≫ [P]0 affected the estimation of the kinetic and thermodynamic properties. Theoretical inhibition curves were calculated, and the apparent IC50 and IC50 were estimated accordingly under predefined conditions. Using the estimated apparent IC50, we compared the apparent Ki and Ki calculated by using the Cheng-Prusoff equation, Lin-Riggs equation, and Wang's group equation. We also applied our tools to simulate high-throughput screening and compare the results of real experiments. The visualization tool for simulating the saturation experiment, kinetic experiments of binding and competitive binding, and inhibition curve, "Binding Curve Viewer," is available at www.eplatton.net/binding-curve-viewer.
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Affiliation(s)
- Yu Du
- Department
of Clinical Laboratory, The Second Affiliated
Hospital of Jiaxing University, Huancheng North Road 1518, Jiaxing, Zhejiang 314000, China
- The
Key Laboratory, The Second Affiliated Hospital
of Jiaxing University, Huancheng North Road 1518, Jiaxing, Zhejiang 314000, China
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2
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Sakurada K, Ishikawa T. Synthesis of causal and surrogate models by non-equilibrium thermodynamics in biological systems. Sci Rep 2024; 14:1001. [PMID: 38200211 PMCID: PMC10781949 DOI: 10.1038/s41598-024-51426-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 01/04/2024] [Indexed: 01/12/2024] Open
Abstract
We developed a model to represent the time evolution phenomena of life through physics constraints. To do this, we took into account that living organisms are open systems that exchange messages through intracellular communication, intercellular communication and sensory systems, and introduced the concept of a message force field. As a result, we showed that the maximum entropy generation principle is valid in time evolution. Then, in order to explain life phenomena based on this principle, we modelled the living system as a nonlinear oscillator coupled by a message and derived the governing equations. The governing equations consist of two laws: one states that the systems are synchronized when the variation of the natural frequencies between them is small or the coupling strength through the message is sufficiently large, and the other states that the synchronization is broken by the proliferation of biological systems. Next, to simulate the phenomena using data obtained from observations of the temporal evolution of life, we developed an inference model that combines physics constraints and a discrete surrogate model using category theory, and simulated the phenomenon of early embryogenesis using this inference model. The results show that symmetry creation and breaking based on message force fields can be widely used to model life phenomena.
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Affiliation(s)
- Kazuhiro Sakurada
- Department of Extended Intelligence for Medicine, The Ishii-Ishibashi Laboratory, Keio University School of Medicine, Tokyo, Japan.
- Open Systems Information Science Team, Advanced Data Science Project, RIKEN Information R&D and Strategy Headquarters, RIKEN, Tokyo, Japan.
| | - Tetsuo Ishikawa
- Department of Extended Intelligence for Medicine, The Ishii-Ishibashi Laboratory, Keio University School of Medicine, Tokyo, Japan
- Medical Data Mathematical Reasoning Team, Advanced Data Science Project, RIKEN Information R&D and Strategy Headquarters, RIKEN, Yokohama, Japan
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3
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Daubermann AG, Dressano K, de Oliveira Ceciliato PH, Moura DS. Acridinium-Based Chemiluminescent Receptor-Ligand Binding Assay for Protein/Peptide Hormones. Methods Mol Biol 2024; 2731:253-263. [PMID: 38019440 DOI: 10.1007/978-1-0716-3511-7_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]
Abstract
Chemiluminescent acridinium esters (AE) have been extensively used for oligonucleotide probing and peptide-binding assays in molecular research due to labeling efficiency, lack of radioactivity, and ease of application. In addition to being a powerful and reliable alternative to radiolabeling, AE can be directly bound to the target molecule, with high specificity. Here, we describe an AE-based protein/peptide labeling method and the use of the labeled protein/peptide in a ligand-binding assay.
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Affiliation(s)
- André Guilherme Daubermann
- Laboratório de Bioquímica de Proteínas, Departamento de Ciências Biológicas, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo (ESALQ/USP), Piracicaba, Brazil
| | - Keini Dressano
- Laboratório de Bioquímica de Proteínas, Departamento de Ciências Biológicas, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo (ESALQ/USP), Piracicaba, Brazil
- Centro de Tecnologia Canavieira - CTC, Piracicaba, Brazil
| | - Paulo Henrique de Oliveira Ceciliato
- Laboratório de Bioquímica de Proteínas, Departamento de Ciências Biológicas, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo (ESALQ/USP), Piracicaba, Brazil
- Centro de Tecnologia Canavieira - CTC, Piracicaba, Brazil
| | - Daniel S Moura
- Laboratório de Bioquímica de Proteínas, Departamento de Ciências Biológicas, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo (ESALQ/USP), Piracicaba, Brazil.
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4
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Niazi SK. The FDA's New Guideline "Generally Accepted Scientific Knowledge" (GASK): An Opportunity to Expedite the Approval of Biosimilars. Pharmaceuticals (Basel) 2023; 16:1517. [PMID: 38004383 PMCID: PMC10674418 DOI: 10.3390/ph16111517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/24/2023] [Accepted: 10/24/2023] [Indexed: 11/26/2023] Open
Abstract
The US FDA's new guideline suggests using "Generally Accepted Science Knowledge" (GASK) to develop nonclinical testing protocols for developing drugs and biologicals to remove unnecessary testing. Interpreting acceptable scientific knowledge as a rational approach has motivated the author to suggest substantial changes to the development of biosimilars, as demonstrated in this paper. The FDA can accept these suggestions without requiring any legislative change to the Act that defines such requirements. Suggested here is the waiving of clinical efficacy testing due to its lower sensitivity compared to analytical and functional testing and pharmacokinetic profiling. Also questioned is the need to test pharmacodynamic markers that do not correlate with clinical response and find new biomarkers requiring extensive testing to validate their use. Should the FDA accept these scientifically rational suggestions, it will significantly reduce the time and cost of approving biosimilars without safety or efficacy risk, as justified based on acceptable scientific knowledge and rationality.
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Affiliation(s)
- Sarfaraz K Niazi
- College of Pharmacy, University of Illinois, Chicago, IL 60612, USA
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5
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Liu H, Zhang H, IJzerman AP, Guo D. The translational value of ligand-receptor binding kinetics in drug discovery. Br J Pharmacol 2023. [PMID: 37705429 DOI: 10.1111/bph.16241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/27/2023] [Accepted: 09/01/2023] [Indexed: 09/15/2023] Open
Abstract
The translation of in vitro potency of a candidate drug, as determined by traditional pharmacology metrics (such as EC50 /IC50 and KD /Ki values), to in vivo efficacy and safety is challenging. Residence time, which represents the duration of drug-target interaction, can be part of a more comprehensive understanding of the dynamic nature of drug-target interactions in vivo, thereby enabling better prediction of drug efficacy and safety. As a consequence, a prolonged residence time may help in achieving sustained pharmacological activity, while transient interactions with shorter residence times may be favourable for targets associated with side effects. Therefore, integration of residence time into the early stages of drug discovery and development has yielded a number of clinical candidates with promising in vivo efficacy and safety profiles. Insights from residence time research thus contribute to the translation of in vitro potency to in vivo efficacy and safety. Further research and advances in measuring and optimizing residence time will bring a much-needed addition to the drug discovery process and the development of safer and more effective drugs. In this review, we summarize recent research progress on residence time, highlighting its importance from a translational perspective.
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Affiliation(s)
- Hongli Liu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Haoran Zhang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Adriaan P IJzerman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Dong Guo
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, China
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6
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Hua L, Wang D, Wang K, Wang Y, Gu J, Zhang Q, You Q, Wang L. Design of Tracers in Fluorescence Polarization Assay for Extensive Application in Small Molecule Drug Discovery. J Med Chem 2023; 66:10934-10958. [PMID: 37561645 DOI: 10.1021/acs.jmedchem.3c00881] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
Development of fluorescence polarization (FP) assays, especially in a competitive manner, is a potent and mature tool for measuring the binding affinities of small molecules. This approach is suitable for high-throughput screening (HTS) for initial ligands and is also applicable for further study of the structure-activity relationships (SARs) of candidate compounds for drug discovery. Buffer and tracer, especially rational design of the tracer, play a vital role in an FP assay system. In this perspective, we provided different kinds of approaches for tracer design based on successful cases in recent years. We classified these tracers by different types of ligands in tracers, including peptide, nucleic acid, natural product, and small molecule. To make this technology accessible for more targets, we briefly described the basic theory and workflow, followed by highlighting the design and application of typical FP tracers from a perspective of medicinal chemistry.
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Affiliation(s)
- Liwen Hua
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Danni Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Keran Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Yuxuan Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Jinying Gu
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Qiuyue Zhang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Qidong You
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Lei Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
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7
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Davis KM, Rosinger AY, Murdock KW. Ex vivo LPS-stimulated cytokine production is associated with hydration status in community-dwelling middle-to-older-aged adults. Eur J Nutr 2023; 62:1681-1690. [PMID: 36790579 DOI: 10.1007/s00394-023-03105-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 01/31/2023] [Indexed: 02/16/2023]
Abstract
PURPOSE Suboptimal hydration has been linked to a variety of adverse health outcomes. Few studies have examined the impact of hydration status on immune function, a plausible physiological mechanism underlying these associations. Therefore, we tested how variation in hydration status was associated with circulating pro-inflammatory cytokine levels and ex vivo lipopolysaccharide (LPS)-stimulated pro-inflammatory cytokine production. METHODS Blood samples were obtained from a community sample of healthy middle-to-older-aged adults (N = 72). These samples were used to assess serum osmolality, a biomarker of hydration status, and markers of immune function including circulating pro-inflammatory cytokines and stimulated pro-inflammatory cytokine production after 4 and 24 h of incubation with LPS. Multiple linear regressions were used to test the association between serum osmolality (as a continuous variable) and markers of immune function at baseline and after 4 and 24 h adjusting for age, sex, and BMI. These models were re-estimated with serum osmolality dichotomized at the cut-off for dehydration (> 300 mOsm/kg). RESULTS While not significantly associated with circulating cytokines (B = - 0.03, p = 0.09), serum osmolality was negatively associated with both 4 h (B = - 0.05, p = 0.048) and 24 h (B = - 0.05, p = 0.03) stimulated cytokine production when controlling for age, sex, and BMI. Similarly, dehydration was associated with significantly lower cytokine production at both 4 h (B = - 0.54, p = 0.02) and 24 h (B = - 0.51, p = 0.02) compared to adequate hydration. CONCLUSION These findings suggest that dehydration may be associated with suppressed immune function in generally healthy middle-to-older aged community-dwelling adults. Further longitudinal research is needed to more clearly define the role of hydration in immune function.
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Affiliation(s)
- Kristin M Davis
- Department of Biobehavioral Health, Pennsylvania State University, 219 Biobehavioral Health Building, University Park, PA, 16802, USA
| | - Asher Y Rosinger
- Department of Biobehavioral Health, Pennsylvania State University, 219 Biobehavioral Health Building, University Park, PA, 16802, USA.,Department of Anthropology, Pennsylvania State University, University Park, PA, USA
| | - Kyle W Murdock
- Department of Biobehavioral Health, Pennsylvania State University, 219 Biobehavioral Health Building, University Park, PA, 16802, USA.
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8
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Quintanilla-Villanueva GE, Maldonado J, Luna-Moreno D, Rodríguez-Delgado JM, Villarreal-Chiu JF, Rodríguez-Delgado MM. Progress in Plasmonic Sensors as Monitoring Tools for Aquaculture Quality Control. BIOSENSORS 2023; 13:90. [PMID: 36671925 PMCID: PMC9856096 DOI: 10.3390/bios13010090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/29/2022] [Accepted: 01/02/2023] [Indexed: 05/06/2023]
Abstract
Aquaculture is an expanding economic sector that nourishes the world's growing population due to its nutritional significance over the years as a source of high-quality proteins. However, it has faced severe challenges due to significant cases of environmental pollution, pathogen outbreaks, and the lack of traceability that guarantees the quality assurance of its products. Such context has prompted many researchers to work on the development of novel, affordable, and reliable technologies, many based on nanophotonic sensing methodologies. These emerging technologies, such as surface plasmon resonance (SPR), localised SPR (LSPR), and fibre-optic SPR (FO-SPR) systems, overcome many of the drawbacks of conventional analytical tools in terms of portability, reagent and solvent use, and the simplicity of sample pre-treatments, which would benefit a more sustainable and profitable aquaculture. To highlight the current progress made in these technologies that would allow them to be transferred for implementation in the field, along with the lag with respect to the most cutting-edge plasmonic sensing, this review provides a variety of information on recent advances in these emerging methodologies that can be used to comprehensively monitor the various operations involving the different commercial stages of farmed aquaculture. For example, to detect environmental hazards, track fish health through biochemical indicators, and monitor disease and biosecurity of fish meat products. Furthermore, it highlights the critical issues associated with these technologies, how to integrate them into farming facilities, and the challenges and prospects of developing plasmonic-based sensors for aquaculture.
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Affiliation(s)
- Gabriela Elizabeth Quintanilla-Villanueva
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Químicas, Av. Universidad S/N Ciudad Universitaria, San Nicolás de los Garza 66455, Mexico
- Centro de Investigación en Biotecnología y Nanotecnología (CIByN), Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León. Parque de Investigación e Innovación Tecnológica, Km. 10 autopista al Aeropuerto Internacional Mariano Escobedo, Apodaca 66629, Mexico
| | - Jesús Maldonado
- Department of Neurosurgery, School of Medicine, Yale University, New Haven, CT 06510, USA
| | - Donato Luna-Moreno
- Centro de Investigaciones en Óptica AC, Div. de Fotónica, Loma del Bosque 115, Col. Lomas del Campestre, León 37150, Mexico
| | - José Manuel Rodríguez-Delgado
- Tecnológico de Monterrey, School of Engineering and Sciences, Av. Eugenio Garza Sada Sur No. 2501, Col. Tecnológico, Monterrey 64849, Mexico
| | - Juan Francisco Villarreal-Chiu
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Químicas, Av. Universidad S/N Ciudad Universitaria, San Nicolás de los Garza 66455, Mexico
- Centro de Investigación en Biotecnología y Nanotecnología (CIByN), Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León. Parque de Investigación e Innovación Tecnológica, Km. 10 autopista al Aeropuerto Internacional Mariano Escobedo, Apodaca 66629, Mexico
| | - Melissa Marlene Rodríguez-Delgado
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Químicas, Av. Universidad S/N Ciudad Universitaria, San Nicolás de los Garza 66455, Mexico
- Centro de Investigación en Biotecnología y Nanotecnología (CIByN), Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León. Parque de Investigación e Innovación Tecnológica, Km. 10 autopista al Aeropuerto Internacional Mariano Escobedo, Apodaca 66629, Mexico
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9
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Seo H, Seo H, Byrd N, Kim H, Lee KG, Lee SH, Park Y. Human cell-based estrogen receptor beta dimerization assay. Chem Biol Interact 2023; 369:110264. [PMID: 36402211 DOI: 10.1016/j.cbi.2022.110264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 11/03/2022] [Accepted: 11/11/2022] [Indexed: 11/19/2022]
Abstract
Estrogen is not only responsible for important functions in the human body, such as cell growth, reproduction, differentiation, and development, but it is also deeply related to pathological processes, such as cancer, metabolic and cardiovascular diseases, and neurodegeneration. Estrogens and other estrogenic compounds have transcriptional activities through binding with the estrogen receptor (ER) to induce ER dimerization. The two estrogen receptor subtypes, estrogen receptor alpha (ERα) and estrogen receptor beta (ERβ), show structural differences and have different expression ratios in specific cells and tissues. Currently, the methods for confirming the estrogenic properties of compounds are the binding (Test guideline no. 493) and transactivation (Test guideline no. 455) assays provided by the Organization for Economic Co-operation and Development (OECD). In a previous study, we developed an ERα dimerization assay based on the bioluminescence resonance energy transfer (BRET) system, but there are currently no available tests that can confirm the effect of estrogenic compounds on ERβ. Therefore, in this study, we developed a BRET-based ERβ dimerization assay to confirm the estrogenic prosperities of compounds. The BRET-based ERβ dimerization assay was verified using nine representative ER ligands and the results were compared with the dimerization activity of ERα. In conclusion, our BRET-based ERβ dimerization assay can provide information on the ERβ dimerization potential of estrogenic compounds.
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Affiliation(s)
- Hyeyeong Seo
- Department of Food Science and Biotechnology, Dongguk University, Goyang, 10326, Republic of Korea
| | - Huiwon Seo
- Department of Food Science and Biotechnology, Dongguk University, Goyang, 10326, Republic of Korea
| | - Nick Byrd
- Department of Chemistry and Biochemistry, Campden BRI, Chipping Campden, GL55 6LD, UK
| | - Hyejin Kim
- Department of Food Science and Biotechnology, Dongguk University, Goyang, 10326, Republic of Korea
| | - Kwang-Geun Lee
- Department of Food Science and Biotechnology, Dongguk University, Goyang, 10326, Republic of Korea
| | - Seok-Hee Lee
- Department of Food Science and Biotechnology, Dongguk University, Goyang, 10326, Republic of Korea
| | - Yooheon Park
- Department of Food Science and Biotechnology, Dongguk University, Goyang, 10326, Republic of Korea.
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Rei N, Valente CA, Vaz SH, Farinha-Ferreira M, Ribeiro JA, Sebastião AM. Changes in adenosine receptors and neurotrophic factors in the SOD1G93A mouse model of amyotrophic lateral sclerosis: Modulation by chronic caffeine. PLoS One 2022; 17:e0272104. [PMID: 36516126 PMCID: PMC9749988 DOI: 10.1371/journal.pone.0272104] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 11/13/2022] [Indexed: 12/15/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is characterized by the progressive degeneration of corticospinal tract motor neurons. Previous studies showed that adenosine-mediated neuromodulation is disturbed in ALS and that vascular endothelial growth factor (VEGF) has a neuroprotective function in ALS mouse models. We evaluated how adenosine (A1R and A2AR) and VEGF (VEGFA, VEGFB, VEGFR-1 and VEGFR-2) system markers are altered in the cortex and spinal cord of pre-symptomatic and symptomatic SOD1G93A mice. We then assessed if/how chronic treatment of SOD1G93A mice with a widely consumed adenosine receptor antagonist, caffeine, modulates VEGF system and/or the levels of Brain-derived Neurotrophic Factor (BDNF), known to be under control of A2AR. We found out decreases in A1R and increases in A2AR levels even before disease onset. Concerning the VEGF system, we detected increases of VEGFB and VEGFR-2 levels in the spinal cord at pre-symptomatic stage, which reverses at the symptomatic stage, and decreases of VEGFA levels in the cortex, in very late disease states. Chronic treatment with caffeine rescued cortical A1R levels in SOD1G93A mice, bringing them to control levels, while rendering VEGF signaling nearly unaffected. In contrast, BDNF levels were significantly affected in SOD1G93A mice treated with caffeine, being decreased in the cortex and increased in spinal the cord. Altogether, these findings suggest an early dysfunction of the adenosinergic system in ALS and highlights the possibility that the negative influence of caffeine previously reported in ALS animal models results from interference with BDNF rather than with the VEGF signaling molecules.
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Affiliation(s)
- Nádia Rei
- Faculdade de Medicina, Instituto de Farmacologia e Neurociências, Universidade de Lisboa, Lisboa, Portugal
- Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisboa, Portugal
| | - Cláudia A. Valente
- Faculdade de Medicina, Instituto de Farmacologia e Neurociências, Universidade de Lisboa, Lisboa, Portugal
- Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisboa, Portugal
| | - Sandra H. Vaz
- Faculdade de Medicina, Instituto de Farmacologia e Neurociências, Universidade de Lisboa, Lisboa, Portugal
- Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisboa, Portugal
| | - Miguel Farinha-Ferreira
- Faculdade de Medicina, Instituto de Farmacologia e Neurociências, Universidade de Lisboa, Lisboa, Portugal
- Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisboa, Portugal
| | - Joaquim A. Ribeiro
- Faculdade de Medicina, Instituto de Farmacologia e Neurociências, Universidade de Lisboa, Lisboa, Portugal
- Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisboa, Portugal
| | - Ana M. Sebastião
- Faculdade de Medicina, Instituto de Farmacologia e Neurociências, Universidade de Lisboa, Lisboa, Portugal
- Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisboa, Portugal
- * E-mail:
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11
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Dao L, Zhao Q, Hu J, Xia X, Yang Q, Li S. A microfluidics-based method for isolation and visualization of cells based on receptor-ligand interactions. PLoS One 2022; 17:e0274601. [PMID: 36201506 PMCID: PMC9536614 DOI: 10.1371/journal.pone.0274601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 08/31/2022] [Indexed: 11/21/2022] Open
Abstract
Receptor-ligand binding has been analyzed at the protein level using isothermal titration calorimetry and surface plasmon resonance and at the cellular level using interaction-associated downstream gene induction/suppression. However, no currently available technique can characterize this interaction directly through visualization. In addition, all available assays require a large pool of cells; no assay capable of analyzing receptor-ligand interactions at the single-cell level is publicly available. Here, we describe a new microfluidic chip-based technique for analyzing and visualizing these interactions at the single-cell level. First, a protein is immobilized on a glass slide and a low-flow-rate pump is used to isolate cells that express receptors that bind to the immobilized ligand. Specifically, we demonstrate the efficacy of this technique by immobilizing biotin-conjugated FGL2 on an avidin-coated slide chip and passing a mixture of GFP-labeled wild-type T cells and RFP-labeled FcγRIIB-knockout T cells through the chip. Using automated scanning and counting, we found a large number of GFP+ T cells with binding activity but significantly fewer RFP+ FcγRIIB-knockout T cells. We further isolated T cells expressing a membrane-anchored, tumor-targeted IL-12 based on the receptor's affinity to vimentin to confirm the versatility of our technique. This protocol allows researchers to isolate receptor-expressing cells in about 4 hours for further downstream processing.
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Affiliation(s)
- Long Dao
- Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Qingnan Zhao
- Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Jiemiao Hu
- Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Xueqing Xia
- Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Qing Yang
- Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Shulin Li
- Department of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
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12
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Ligiero CBP, Fernandes TS, D'Amato DL, Gaspar FV, Duarte PS, Strauch MA, Fonseca JG, Meirelles LGR, Bento da Silva P, Azevedo RB, Aparecida de Souza Martins G, Archanjo BS, Buarque CD, Machado G, Percebom AM, Ronconi CM. Influence of particle size on the SARS-CoV-2 spike protein detection using IgG-capped gold nanoparticles and dynamic light scattering. MATERIALS TODAY. CHEMISTRY 2022; 25:100924. [PMID: 35475288 PMCID: PMC9023328 DOI: 10.1016/j.mtchem.2022.100924] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 03/27/2022] [Accepted: 03/29/2022] [Indexed: 05/03/2023]
Abstract
Due to the unprecedented and ongoing nature of the coronavirus outbreak, the development of rapid immunoassays to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its highly contagious variants is an important and challenging task. Here, we report the development of polyclonal antibody-functionalized spherical gold nanoparticle biosensors as well as the influence of the nanoparticle sizes on the immunoassay response to detect the SARS-CoV-2 spike protein by dynamic light scattering. By monitoring the increment in the hydrodynamic diameter (ΔDH) by dynamic light scattering measurements in the antigen-antibody interaction, SARS-CoV-2 S-protein can be detected in only 5 min. The larger the nanoparticles, the larger ΔDH in the presence of spike protein. From adsorption isotherm, the calculated binding constant (K D ) was 83 nM and the estimated limit of detection was 13 ng/mL (30 pM). The biosensor was stable up to 90 days at 4 °C. Therefore, the biosensor developed in this work could be potentially applied as a fast and sensible immunoassay to detect SARS-CoV-2 infection in patient samples.
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Affiliation(s)
- C B P Ligiero
- Departamento de Química Inorgânica, Universidade Federal Fluminense (UFF), Campus Do Valonguinho, Outeiro de São João Batista, S/n, 24020-141, Niterói, RJ, Brazil
| | - T S Fernandes
- Departamento de Química Inorgânica, Universidade Federal Fluminense (UFF), Campus Do Valonguinho, Outeiro de São João Batista, S/n, 24020-141, Niterói, RJ, Brazil
| | - D L D'Amato
- Departamento de Química Inorgânica, Universidade Federal Fluminense (UFF), Campus Do Valonguinho, Outeiro de São João Batista, S/n, 24020-141, Niterói, RJ, Brazil
| | - F V Gaspar
- Departamento de Química Inorgânica, Universidade Federal Fluminense (UFF), Campus Do Valonguinho, Outeiro de São João Batista, S/n, 24020-141, Niterói, RJ, Brazil
- Departamento de Química, Pontifícia Universidade Católica Do Rio de Janeiro (PUC-Rio), Rio de Janeiro, RJ, 22451-900, Brazil
| | - P S Duarte
- Departamento de Química, Pontifícia Universidade Católica Do Rio de Janeiro (PUC-Rio), Rio de Janeiro, RJ, 22451-900, Brazil
| | - M A Strauch
- Gerência de Desenvolvimento Tecnológico, Instituto Vital Brazil, Niterói, RJ, 24230-410, Brazil
| | - J G Fonseca
- Gerência de Desenvolvimento Tecnológico, Instituto Vital Brazil, Niterói, RJ, 24230-410, Brazil
| | - L G R Meirelles
- Fazenda Instituto Vital Brazil, Niterói, RJ, 24230-410, Brazil
| | - P Bento da Silva
- Departamento de Genética e Morfologia, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, 70910-900, Brazil
| | - R B Azevedo
- Departamento de Genética e Morfologia, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, 70910-900, Brazil
| | - G Aparecida de Souza Martins
- Programa de Pós-graduação Em Ciência e Tecnologia de Alimentos, Universidade Federal Do Tocantins, 77001-090, Brazil
| | - B S Archanjo
- Divisão de Metrologia de Materiais, Instituto Nacional de Metrologia, Qualidade e Tecnologia (Inmetro), Duque de Caxias, RJ, 25250-020, Brazil
| | - C D Buarque
- Departamento de Química, Pontifícia Universidade Católica Do Rio de Janeiro (PUC-Rio), Rio de Janeiro, RJ, 22451-900, Brazil
| | - G Machado
- Centro de Tecnologias Estratégicas Do Nordeste, Av. Prof. Luiz Freire 01, Recife, Pernambuco, 50740-540, Brazil
| | - A M Percebom
- Departamento de Química, Pontifícia Universidade Católica Do Rio de Janeiro (PUC-Rio), Rio de Janeiro, RJ, 22451-900, Brazil
| | - C M Ronconi
- Departamento de Química Inorgânica, Universidade Federal Fluminense (UFF), Campus Do Valonguinho, Outeiro de São João Batista, S/n, 24020-141, Niterói, RJ, Brazil
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Hickey AJ, Stewart IE. Inhaled antibodies: Quality and performance considerations. Hum Vaccin Immunother 2022; 18:1940650. [PMID: 34191682 PMCID: PMC9116391 DOI: 10.1080/21645515.2021.1940650] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 05/11/2021] [Accepted: 06/05/2021] [Indexed: 12/22/2022] Open
Abstract
The use of antibodies in the treatment of lung diseases is of increasing interest especially as the search for COVID-19 therapies has unfolded. Historically, the use of antibody therapy was based on multiple targets including receptors involved in local hyper-reactivity in asthma, viruses and micro-organisms involved in a variety of pulmonary infectious disease. Generally, protein therapeutics pose challenges with respect to formulation and delivery to retain activity and assure therapy. The specificity of antibodies amplifies the need for attention to molecular integrity not only in formulation but also during aerosol delivery for pulmonary administration. Drug product development can be viewed from considerations of route of administration, dosage form, quality, and performance measures. Nebulizers and dry powder inhalers have been used to deliver protein therapeutics and each has its advantages that should be matched to the needs of the drug and the disease. This review offers insight into quality and performance barriers and the opportunities that arise from meeting them effectively.
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14
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Badaoui M, Buigues PJ, Berta D, Mandana GM, Gu H, Földes T, Dickson CJ, Hornak V, Kato M, Molteni C, Parsons S, Rosta E. Combined Free-Energy Calculation and Machine Learning Methods for Understanding Ligand Unbinding Kinetics. J Chem Theory Comput 2022; 18:2543-2555. [PMID: 35195418 PMCID: PMC9097281 DOI: 10.1021/acs.jctc.1c00924] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
![]()
The
determination of drug residence times, which define the time
an inhibitor is in complex with its target, is a fundamental part
of the drug discovery process. Synthesis and experimental measurements
of kinetic rate constants are, however, expensive and time consuming.
In this work, we aimed to obtain drug residence times computationally.
Furthermore, we propose a novel algorithm to identify molecular design
objectives based on ligand unbinding kinetics. We designed an enhanced
sampling technique to accurately predict the free-energy profiles
of the ligand unbinding process, focusing on the free-energy barrier
for unbinding. Our method first identifies unbinding paths determining
a corresponding set of internal coordinates (ICs) that form contacts
between the protein and the ligand; it then iteratively updates these
interactions during a series of biased molecular dynamics (MD) simulations
to reveal the ICs that are important for the whole of the unbinding
process. Subsequently, we performed finite-temperature string simulations
to obtain the free-energy barrier for unbinding using the set of ICs
as a complex reaction coordinate. Importantly, we also aimed to enable
the further design of drugs focusing on improved residence times.
To this end, we developed a supervised machine learning (ML) approach
with inputs from unbiased “downhill” trajectories initiated
near the transition state (TS) ensemble of the string unbinding path.
We demonstrate that our ML method can identify key ligand–protein
interactions driving the system through the TS. Some of the most important
drugs for cancer treatment are kinase inhibitors. One of these kinase
targets is cyclin-dependent kinase 2 (CDK2), an appealing target for
anticancer drug development. Here, we tested our method using two
different CDK2 inhibitors for the potential further development of
these compounds. We compared the free-energy barriers obtained from
our calculations with those observed in available experimental data.
We highlighted important interactions at the distal ends of the ligands
that can be targeted for improved residence times. Our method provides
a new tool to determine unbinding rates and to identify key structural
features of the inhibitors that can be used as starting points for
novel design strategies in drug discovery.
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Affiliation(s)
- Magd Badaoui
- Department of Chemistry, King's College London, London SE1 1DB, United Kingdom.,Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Pedro J Buigues
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Dénes Berta
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Gaurav M Mandana
- Department of Chemistry, King's College London, London SE1 1DB, United Kingdom
| | - Hankang Gu
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Tamás Földes
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Callum J Dickson
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Viktor Hornak
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Mitsunori Kato
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Carla Molteni
- Department of Physics, King's College London, London WC2R 2LS, United Kingdom
| | - Simon Parsons
- School of Computer Science, University of Lincoln, Lincoln LN6 7TS, United Kingdom
| | - Edina Rosta
- Department of Chemistry, King's College London, London SE1 1DB, United Kingdom.,Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
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15
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Kim HM, Seo H, Park Y, Lee HS, Lee SH, Ko KS. Development of a Human Estrogen Receptor Dimerization Assay for the Estrogenic Endocrine-Disrupting Chemicals Using Bioluminescence Resonance Energy Transfer. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18168875. [PMID: 34444624 PMCID: PMC8395052 DOI: 10.3390/ijerph18168875] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/18/2021] [Accepted: 08/19/2021] [Indexed: 02/01/2023]
Abstract
Endocrine-disrupting chemicals (EDCs) are found in food and various other substances, including pesticides and plastics. EDCs are easily absorbed into the body and have the ability to mimic or block hormone function. The radioligand binding assay based on the estrogen receptors binding affinity is widely used to detect estrogenic EDCs but is limited to radioactive substances and requires specific conditions. As an alternative, we developed a human cell-based dimerization assay for detecting EDC-mediated ER-alpha (ERα) dimerization using bioluminescence resonance energy transfer (BRET). The resultant novel BRET-based on the ERα dimerization assay was used to identify the binding affinity of 17β-estradiol (E2), 17α-estradiol, corticosterone, diethylhexyl phthalate, bisphenol A, and 4-nonylphenol with ERα by measuring the corresponding BRET signals. Consequently, the BRET signals from five chemicals except corticosterone showed a dose-dependent sigmoidal curve for ERα, and these chemicals were suggested as positive chemicals for ERα. In contrast, corticosterone, which induced a BRET signal comparable to that of the vehicle control, was suggested as a negative chemical for ERα. Therefore, these results were consistent with the results of the existing binding assay for ERα and suggested that a novel BRET system can provide information about EDCs-mediated dimerization to ERα.
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Affiliation(s)
- Hye Mi Kim
- Department of Nutritional Science and Food Management, Ewha Womans University, Seoul 03760, Korea;
| | - Hyeyeong Seo
- Department of Integrated Biomedical and Life Science, Korea University, Seoul 02841, Korea;
| | - Yooheon Park
- Department of Food Science and Biotechnology, Dongguk University, Goyang 10326, Korea;
| | - Hee-Seok Lee
- Department of Food Science and Technology, Chung-Ang University, Anseong 17546, Korea;
| | - Seok-Hee Lee
- Department of Food Science and Biotechnology, Dongguk University, Goyang 10326, Korea;
- Correspondence: (S.-H.L.); (K.S.K.); Tel.: +82-31-961-5187 (S.-H.L.); +82-2-3277-6859 (K.S.K.)
| | - Kwang Suk Ko
- Department of Nutritional Science and Food Management, Ewha Womans University, Seoul 03760, Korea;
- Correspondence: (S.-H.L.); (K.S.K.); Tel.: +82-31-961-5187 (S.-H.L.); +82-2-3277-6859 (K.S.K.)
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16
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Song J, Kim H, Lee CY, Yoon J, Yoo WS, Park HG. Identification of thyroid hormone/thyroid hormone receptor interaction based on aptamer-assisted protein-induced fluorescence enhancement. Biosens Bioelectron 2021; 191:113444. [PMID: 34175646 DOI: 10.1016/j.bios.2021.113444] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 06/08/2021] [Accepted: 06/13/2021] [Indexed: 12/27/2022]
Abstract
We herein describe a novel method to identify thyroid hormone (TH)/thyroid hormone receptor (TR) interaction, termed aptamer-assisted protein-induced fluorescence enhancement (AptPIFE). In this method, a detection probe consisting of an RNA strand incorporating TH-specific aptamer and a Cy3-labeled DNA strand holds TH in close proximity to Cy3. The corresponding TR then binds to the TH near Cy3, consequently stimulating Cy3 to emit a significantly enhanced fluorescence through PIFE phenomenon. Based on this simple yet efficient design principle, we successfully identified the interaction of TH with TR within 10 min, down to 0.37 pM with excellent specificity. The practical and robust applicability of this method was also successfully validated by properly screening TR antagonists and reliably quantifying TH present in real clinical serum samples from patients with hyperthyroidism and healthy volunteers.
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Affiliation(s)
- Jayeon Song
- Department of Chemical and Biomolecular Engineering (BK21+ Program), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Hansol Kim
- Department of Chemical and Biomolecular Engineering (BK21+ Program), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Chang Yeol Lee
- Department of Chemical and Biomolecular Engineering (BK21+ Program), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Junhyeok Yoon
- Department of Chemical and Biomolecular Engineering (BK21+ Program), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Won Sang Yoo
- Department of Internal Medicine, Dankook University College of Medicine, 119, Dandae-ro, Dongnam-gu, Cheonan-si, 31116, Republic of Korea.
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK21+ Program), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
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17
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Moreira-Filho JT, Silva AC, Dantas RF, Gomes BF, Souza Neto LR, Brandao-Neto J, Owens RJ, Furnham N, Neves BJ, Silva-Junior FP, Andrade CH. Schistosomiasis Drug Discovery in the Era of Automation and Artificial Intelligence. Front Immunol 2021; 12:642383. [PMID: 34135888 PMCID: PMC8203334 DOI: 10.3389/fimmu.2021.642383] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/30/2021] [Indexed: 12/20/2022] Open
Abstract
Schistosomiasis is a parasitic disease caused by trematode worms of the genus Schistosoma and affects over 200 million people worldwide. The control and treatment of this neglected tropical disease is based on a single drug, praziquantel, which raises concerns about the development of drug resistance. This, and the lack of efficacy of praziquantel against juvenile worms, highlights the urgency for new antischistosomal therapies. In this review we focus on innovative approaches to the identification of antischistosomal drug candidates, including the use of automated assays, fragment-based screening, computer-aided and artificial intelligence-based computational methods. We highlight the current developments that may contribute to optimizing research outputs and lead to more effective drugs for this highly prevalent disease, in a more cost-effective drug discovery endeavor.
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Affiliation(s)
- José T. Moreira-Filho
- LabMol – Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás – UFG, Goiânia, Brazil
| | - Arthur C. Silva
- LabMol – Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás – UFG, Goiânia, Brazil
| | - Rafael F. Dantas
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Barbara F. Gomes
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Lauro R. Souza Neto
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Jose Brandao-Neto
- Diamond Light Source Ltd., Didcot, United Kingdom
- Research Complex at Harwell, Didcot, United Kingdom
| | - Raymond J. Owens
- The Rosalind Franklin Institute, Harwell, United Kingdom
- Division of Structural Biology, The Wellcome Centre for Human Genetic, University of Oxford, Oxford, United Kingdom
| | - Nicholas Furnham
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Bruno J. Neves
- LabMol – Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás – UFG, Goiânia, Brazil
| | - Floriano P. Silva-Junior
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Carolina H. Andrade
- LabMol – Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás – UFG, Goiânia, Brazil
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18
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Johe P, Jung S, Endres E, Kersten C, Zimmer C, Ye W, Sönnichsen C, Hellmich UA, Sotriffer C, Schirmeister T, Neuweiler H. Warhead Reactivity Limits the Speed of Inhibition of the Cysteine Protease Rhodesain. ACS Chem Biol 2021; 16:661-670. [PMID: 33719398 DOI: 10.1021/acschembio.0c00911] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Viral and parasitic pathogens rely critically on cysteine proteases for host invasion, replication, and infectivity. Their inhibition by synthetic inhibitors, such as vinyl sulfone compounds, has emerged as a promising treatment strategy. However, the individual reaction steps of protease inhibition are not fully understood. Using the trypanosomal cysteine protease rhodesain as a medically relevant target, we design photoinduced electron transfer (PET) fluorescence probes to detect kinetics of binding of reversible and irreversible vinyl sulfones directly in solution. Intriguingly, the irreversible inhibitor, apart from its unlimited residence time in the enzyme, reacts 5 times faster than the reversible one. Results show that the reactivity of the warhead, and not binding of the peptidic recognition unit, limits the rate constant of protease inhibition. The use of a reversible inhibitor decreases the risk of off-target side effects not only by allowing its release from an off-target but also by reducing the rate constant of binding.
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Affiliation(s)
- Patrick Johe
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudingerweg 5, D-55128 Mainz, Germany
| | - Sascha Jung
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudingerweg 5, D-55128 Mainz, Germany
- TU Dortmund University, Chemical Biology, Otto-Hahn-Str. 6, D-44227 Dortmund, Germany
| | - Erik Endres
- Institute for Pharmacy and Food Chemistry, Julius Maximilians University Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudingerweg 5, D-55128 Mainz, Germany
| | - Collin Zimmer
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudingerweg 5, D-55128 Mainz, Germany
| | - Weixiang Ye
- Department of Chemistry, Nanobiotechnology, Johannes Gutenberg University Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany
| | - Carsten Sönnichsen
- Department of Chemistry, Nanobiotechnology, Johannes Gutenberg University Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany
| | - Ute A. Hellmich
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Johann-Joachim-Becherweg 30, D-55128 Mainz, Germany
- Centre for Biomolecular Magnetic Resonance, Goethe-University Frankfurt, Max von Laue Str. 9, D-60438 Frankfurt, Germany
| | - Christoph Sotriffer
- Institute for Pharmacy and Food Chemistry, Julius Maximilians University Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudingerweg 5, D-55128 Mainz, Germany
| | - Hannes Neuweiler
- Institute for Biotechnology & Biophysics, Julius Maximilians University Würzburg, Am Hubland, D-97074 Würzburg, Germany
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19
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New small molecule fluorescent probes for G protein-coupled receptors: valuable tools for drug discovery. Future Med Chem 2020; 13:63-90. [PMID: 33319586 DOI: 10.4155/fmc-2019-0327] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are essential signaling proteins and tractable therapeutic targets. To develop new drug candidates, GPCR drug discovery programs require versatile, sensitive pharmacological tools for ligand binding and compound screening. With the availability of new imaging modalities and proximity-based ligand binding technologies, fluorescent ligands offer many advantages and are increasingly being used, yet labeling small molecules remains considerably more challenging relative to peptides. Focusing on recent fluorescent small molecule studies for family A GPCRs, this review addresses some of the key challenges, synthesis approaches and structure-activity relationship considerations, and discusses advantages of using high-resolution GPCR structures to inform conjugation strategies. While no single approach guarantees successful labeling without loss of affinity or selectivity, the choice of fluorophore, linker type and site of attachment have proved to be critical factors that can significantly affect their utility in drug discovery programs, and as discussed, can sometimes lead to very unexpected results.
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20
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Davis KM, Engeland CG, Murdock KW. Ex vivo LPS-stimulated cytokine production is associated with cortisol curves in response to acute psychosocial stress. Psychoneuroendocrinology 2020; 121:104863. [PMID: 32950932 DOI: 10.1016/j.psyneuen.2020.104863] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/24/2020] [Accepted: 09/04/2020] [Indexed: 12/31/2022]
Abstract
BACKGROUND Empirical and theoretical evidence suggest that because of the co-evolution of the endocrine and immune response systems, different types of stressors may lead to similar levels of physiological activation. The present analyses examined associations between two physiological stress responses: the cortisol response to an acute laboratory stressor and ex vivo lipopolysaccharide (LPS) stimulated inflammatory cytokine production. METHODS Healthy middle-aged adults (N = 65) completed testing at two appointments, two weeks apart. Blood was collected at each appointment to measure circulating inflammatory cytokine levels and stimulated inflammatory cytokine production after 4 and 24 hours of incubation with LPS. A cumulative standardized composite measure of inflammation was calculated using the cytokines interleukin-6 (IL-6), interleukin-1β (IL-1β), and interferon-γ (IFN-γ). At visit two, after the blood draw, participants completed the Trier Social Stress Test (TSST); saliva samples were collected before and after to generate cortisol response curves (area under the curve with respect to ground [AUCG] and increase/decrease [AUCI]). RESULTS AUCG was significantly associated with stimulated cytokine production at visit 2 after both 4 hours (B = 6.89; p = 0.007) and 24 hours (B = 7.50; p = 0.005) of incubation, controlling for age, sex, and BMI. AUCI was also significantly associated with stimulated cytokine production at visit 2 after 4 hours (B = 6.28; p = 0.004) and 24 hours (B = 6.16; p = 0.007) of incubation, controlling for age, sex, and BMI. Stimulated inflammatory cytokine production was strongly correlated across the two visits (2 weeks apart) after 4 hours of incubation (r = 0.80, p < 0.001) and after 24 hours (r = 0.80, p < 0.001). Within each visit, stimulated cytokine production after 4 hours was significantly correlated with stimulated inflammation at 24 hours (r = 0.93-0.94, p < 0.05) CONCLUSIONS: These results suggest that LPS-stimulated inflammatory cytokine production and the cortisol response to the TSST contain comparable information about acute human physiological stress responses. Moreover, measurement of stimulated cytokines was highly stable across a two-week time period whether measured after 4 or 24 hours of incubation with LPS.
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Affiliation(s)
- Kristin M Davis
- Department of Biobehavioral Health, The Pennsylvania State University, United States
| | - Christopher G Engeland
- Department of Biobehavioral Health, The Pennsylvania State University, United States; College of Nursing, The Pennsylvania State University, United States
| | - Kyle W Murdock
- Department of Biobehavioral Health, The Pennsylvania State University, United States.
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21
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Ray M, Nagai K, Kihara Y, Kussrow A, Kammer MN, Frantz A, Bornhop DJ, Chun J. Unlabeled lysophosphatidic acid receptor binding in free solution as determined by a compensated interferometric reader. J Lipid Res 2020; 61:1244-1251. [PMID: 32513900 PMCID: PMC7397748 DOI: 10.1194/jlr.d120000880] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 06/01/2020] [Indexed: 12/11/2022] Open
Abstract
Native interactions between lysophospholipids (LPs) and their cognate LP receptors are difficult to measure because of lipophilicity and/or the adhesive properties of lipids, which contribute to high levels of nonspecific binding in cell membrane preparations. Here, we report development of a free-solution assay (FSA) where label-free LPs bind to their cognate G protein-coupled receptors (GPCRs), combined with a recently reported compensated interferometric reader (CIR) to quantify native binding interactions between receptors and ligands. As a test case, the binding parameters between lysophosphatidic acid (LPA) receptor 1 (LPA1; one of six cognate LPA GPCRs) and LPA were determined. FSA-CIR detected specific binding through the simultaneous real-time comparison of bound versus unbound species by measuring the change in the solution dipole moment produced by binding-induced conformational and/or hydration changes. FSA-CIR identified KD values for chemically distinct LPA species binding to human LPA1 and required only a few nanograms of protein: 1-oleoyl (18:1; KD = 2.08 ± 1.32 nM), 1-linoleoyl (18:2; KD = 2.83 ± 1.64 nM), 1-arachidonoyl (20:4; KD = 2.59 ± 0.481 nM), and 1-palmitoyl (16:0; KD = 1.69 ± 0.1 nM) LPA. These KD values compared favorably to those obtained using the previous generation back-scattering interferometry system, a chip-based technique with low-throughput and temperature sensitivity. In conclusion, FSA-CIR offers a new increased-throughput approach to assess quantitatively label-free lipid ligand-receptor binding, including nonactivating antagonist binding, under near-native conditions.
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Affiliation(s)
- Manisha Ray
- Degenerative Disease Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037
| | - Kazufumi Nagai
- Degenerative Disease Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037
| | - Yasuyuki Kihara
- Degenerative Disease Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037
| | - Amanda Kussrow
- Department of Chemistry and Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, TN 37235
| | - Michael N Kammer
- Department of Chemistry and Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, TN 37235
| | - Aaron Frantz
- Degenerative Disease Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037.,Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA 92037
| | - Darryl J Bornhop
- Department of Chemistry and Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, TN 37235
| | - Jerold Chun
- Degenerative Disease Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037
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22
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Llorente García I, Marsh M. A biophysical perspective on receptor-mediated virus entry with a focus on HIV. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2020; 1862:183158. [PMID: 31863725 PMCID: PMC7156917 DOI: 10.1016/j.bbamem.2019.183158] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 12/12/2019] [Accepted: 12/13/2019] [Indexed: 12/14/2022]
Abstract
As part of their entry and infection strategy, viruses interact with specific receptor molecules expressed on the surface of target cells. The efficiency and kinetics of the virus-receptor interactions required for a virus to productively infect a cell is determined by the biophysical properties of the receptors, which are in turn influenced by the receptors' plasma membrane (PM) environments. Currently, little is known about the biophysical properties of these receptor molecules or their engagement during virus binding and entry. Here we review virus-receptor interactions focusing on the human immunodeficiency virus type 1 (HIV), the etiological agent of acquired immunodeficiency syndrome (AIDS), as a model system. HIV is one of the best characterised enveloped viruses, with the identity, roles and structure of the key molecules required for infection well established. We review current knowledge of receptor-mediated HIV entry, addressing the properties of the HIV cell-surface receptors, the techniques used to measure these properties, and the macromolecular interactions and events required for virus entry. We discuss some of the key biophysical principles underlying receptor-mediated virus entry and attempt to interpret the available data in the context of biophysical mechanisms. We also highlight crucial outstanding questions and consider how new tools might be applied to advance understanding of the biophysical properties of viral receptors and the dynamic events leading to virus entry.
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Affiliation(s)
| | - Mark Marsh
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, UK
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23
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Möller IR, Merkle PS, Calugareanu D, Comamala G, Schmidt SG, Loland CJ, Rand KD. Probing the conformational impact of detergents on the integral membrane protein LeuT by global HDX-MS. J Proteomics 2020; 225:103845. [PMID: 32480080 DOI: 10.1016/j.jprot.2020.103845] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 05/17/2020] [Accepted: 05/24/2020] [Indexed: 01/11/2023]
Abstract
Neurotransmitter:sodium symporters (NSS) are integral membrane proteins (IMP), responsible for reuptake of neurotransmitters from the synaptic cleft. Due to challenges in production of mammalian NSS in their active form, the prokaryotic hydrophobic amino acid transporter, LeuT, served here as a steadfast model for elucidation of structure-function relationship. As NSS proteins reside within phospholipid bilayer, they require stabilization by artificial membrane systems upon their extraction. Right choice of artificial membrane system is crucial as suboptimal detergent and/or lipids can lead to destabilization or non-native stabilization. Here we study the effect of related detergents, dodecyl maltoside (DDM) and lauryl maltose neopentyl glycol (LMNG), on the conformational dynamics of LeuT by global HDX-MS, in the presence of functionally relevant ligands. We observed that LeuT is more dynamic when solubilized in DDM compared to LMNG. Moreover, LeuT exhibited increased HDX in the presence of K+ compared to Na+, indicating a more dynamic conformation in the presence of K+. Upon addition of leucine, LeuT underwent additional stabilization relative to the Na+-bound state. Finally, peak broadening was observed, suggesting that LeuT undergoes slow unfolding/refolding dynamics in detergent solution. These slow dynamics were verified by local HDX, also proving that detergents modulate the rate of these dynamics. SIGNIFICANCE: Overall, we show the efficacy of global HDX-MS to evaluate the effect of artificial membrane systems on integral membrane proteins and the importance of carefully selecting compatible detergent (and/or lipid) for the solubilization of this class of proteins.
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Affiliation(s)
- Ingvar R Möller
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen O, Denmark
| | - Patrick S Merkle
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen O, Denmark
| | - Dionisie Calugareanu
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen O, Denmark
| | - Gerard Comamala
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen O, Denmark
| | - Solveig Gaarde Schmidt
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Claus J Loland
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Kasper D Rand
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen O, Denmark.
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24
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Santillo MF. Trends using biological target-based assays for drug detection in complex sample matrices. Anal Bioanal Chem 2020; 412:3975-3982. [PMID: 32372275 DOI: 10.1007/s00216-020-02681-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/15/2020] [Accepted: 04/23/2020] [Indexed: 12/24/2022]
Abstract
In vivo, drug molecules interact with their biological targets (e.g., enzymes, receptors, ion channels, transporters), thereby eliciting therapeutic effects. Assays that measure the interaction between drugs and bio-targets may be used as drug biosensors, which are capable of broadly detecting entire drug classes without prior knowledge of their chemical structure. This Trends article covers recent developments in bio-target-based screening assays for detecting drugs associated with the following areas: illicit products marketed as dietary supplements, food-producing animals, and bodily fluids. General challenges and considerations associated with using bio-target assays are also presented. Finally, future applications of these assays for drug detection are suggested based upon current needs.
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Affiliation(s)
- Michael F Santillo
- Division of Toxicology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration (FDA), 8301 Muirkirk Rd, Laurel, MD, 20708, USA.
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25
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Armstrong-Price DE, Deore PS, Manderville RA. Intrinsic "Turn-On" Aptasensor Detection of Ochratoxin A Using Energy-Transfer Fluorescence. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:2249-2255. [PMID: 31986034 DOI: 10.1021/acs.jafc.9b07391] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Ochratoxin A (OTA) is an intrinsically fluorescent phenolic mycotoxin that contaminates a wide range of food products and is a serious health threat to animals and humans. An OTA binding aptamer (OTABA) that folds into an antiparallel G-quadruplex (GQ) in the absence and presence of target OTA has been incorporated into a vast variety of aptasensor platforms for OTA detection. The development of a simple, aptamer-based approach would allow for detection of the toxin without the use of complex analytical instrumentation, which has been the gold standard for OTA detection thus far. However, to date, none of the aptasensor platforms have utilized the natural fluorescence of the phenolic toxin for detection. Herein, we report that OTA binding to OTABA involves π-stacking interactions that lead to GQ-to-toxin energy transfer (ET), which affords a "turn-on" fluorescence self-signaling platform in which the emission of the aptamer-target complex is enhanced in comparison to the free toxin alone. Selective excitation of the GQ-OTA complex at 256 nm leads to a 4-fold enhancement in OTA fluorescence. The GQ-OTA ET detection platform boasts a limit of detection ∼2 ng/mL, which is comparable to a previously demonstrated fluorescence resonance energy transfer immunoassay platform for OTA detection, and displays excellent OTA selectivity and recovery from red wine samples.
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26
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Carratalá JV, Cano-Garrido O, Sánchez J, Membrado C, Pérez E, Conchillo-Solé O, Daura X, Sánchez-Chardi A, Villaverde A, Arís A, Garcia-Fruitós E, Ferrer-Miralles N. Aggregation-prone peptides modulate activity of bovine interferon gamma released from naturally occurring protein nanoparticles. N Biotechnol 2020; 57:11-19. [PMID: 32028049 DOI: 10.1016/j.nbt.2020.02.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 01/24/2020] [Accepted: 02/02/2020] [Indexed: 12/28/2022]
Abstract
Efficient protocols for the production of recombinant proteins are indispensable for the development of the biopharmaceutical sector. Accumulation of recombinant proteins in naturally-occurring protein aggregates is detrimental to biopharmaceutical development. In recent years, the view of protein aggregates has changed with the recognition that they are a valuable source of functional recombinant proteins. In this study, bovine interferon-gamma (rBoIFN-γ) was engineered to enhance the formation of protein aggregates, also known as protein nanoparticles (NPs), by the addition of aggregation-prone peptides (APPs) in the generally recognized as safe (GRAS) bacterial Lactococcus lactis expression system. The L6K2, HALRU and CYOB peptides were selected to assess their intrinsic aggregation capability to nucleate protein aggregation. These APPs enhanced the tendency of the resulting protein to aggregate at the expense of total protein yield. However, fine physico-chemical characterization of the resulting intracellular protein NPs, the protein released from them and the protein purified from the soluble cell fraction indicated that the compactability of protein conformations was directly related to the biological activity of variants of IFN-γ, used here as a model protein with therapeutic potential. APPs enhanced the aggregation tendency of fused rBoIFN-γ while increasing compactability of protein species. Biological activity of rBoIFN-γ was favored in more compacted conformations. Naturally-occurring protein aggregates can be produced in GRAS microorganisms as protein depots of releasable active protein. The addition of APPs to enhance the aggregation tendency has a positive impact in overall compactability and functionality of resulting protein conformers.
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Affiliation(s)
- José Vicente Carratalá
- Institute for Biotechnology and Biomedicine, Autonomous University of Barcelona, Bellaterra, Barcelona, Spain; Department of Genetics and Microbiology, Autonomous University of Barcelona, Bellaterra, Barcelona, Spain
| | - Olivia Cano-Garrido
- Institute for Biotechnology and Biomedicine, Autonomous University of Barcelona, Bellaterra, Barcelona, Spain; Department of Genetics and Microbiology, Autonomous University of Barcelona, Bellaterra, Barcelona, Spain; Bioengineering, Biomaterials and Nanomedicine Networking Biomedical Research Centre (CIBER-BBN), Bellaterra, Barcelona, Spain
| | - Julieta Sánchez
- Institute for Biotechnology and Biomedicine, Autonomous University of Barcelona, Bellaterra, Barcelona, Spain
| | - Cristina Membrado
- Institute for Biotechnology and Biomedicine, Autonomous University of Barcelona, Bellaterra, Barcelona, Spain; Department of Genetics and Microbiology, Autonomous University of Barcelona, Bellaterra, Barcelona, Spain
| | - Eudald Pérez
- Institute for Biotechnology and Biomedicine, Autonomous University of Barcelona, Bellaterra, Barcelona, Spain; Department of Genetics and Microbiology, Autonomous University of Barcelona, Bellaterra, Barcelona, Spain
| | - Oscar Conchillo-Solé
- Institute for Biotechnology and Biomedicine, Autonomous University of Barcelona, Bellaterra, Barcelona, Spain
| | - Xavier Daura
- Institute for Biotechnology and Biomedicine, Autonomous University of Barcelona, Bellaterra, Barcelona, Spain; Catalan Institution for Research and Advanced Studies, Barcelona, Spain
| | - Alejandro Sánchez-Chardi
- Microscopy Service, Autonomous University of Barcelona, Bellaterra, Barcelona, Spain and Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Antonio Villaverde
- Institute for Biotechnology and Biomedicine, Autonomous University of Barcelona, Bellaterra, Barcelona, Spain; Department of Genetics and Microbiology, Autonomous University of Barcelona, Bellaterra, Barcelona, Spain; Bioengineering, Biomaterials and Nanomedicine Networking Biomedical Research Centre (CIBER-BBN), Bellaterra, Barcelona, Spain
| | - Anna Arís
- Department of Ruminant Production, Institute of Agrifood Research and Technology (IRTA), Caldes de Montbui, Barcelona, Spain
| | - Elena Garcia-Fruitós
- Department of Ruminant Production, Institute of Agrifood Research and Technology (IRTA), Caldes de Montbui, Barcelona, Spain
| | - Neus Ferrer-Miralles
- Institute for Biotechnology and Biomedicine, Autonomous University of Barcelona, Bellaterra, Barcelona, Spain; Department of Genetics and Microbiology, Autonomous University of Barcelona, Bellaterra, Barcelona, Spain; Bioengineering, Biomaterials and Nanomedicine Networking Biomedical Research Centre (CIBER-BBN), Bellaterra, Barcelona, Spain.
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27
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Du L, Yee SS, Ramachandran K, Risinger AL. Elucidating target specificity of the taccalonolide covalent microtubule stabilizers employing a combinatorial chemical approach. Nat Commun 2020; 11:654. [PMID: 32005831 PMCID: PMC6994698 DOI: 10.1038/s41467-019-14277-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 12/19/2019] [Indexed: 11/09/2022] Open
Abstract
The taccalonolide microtubule stabilizers covalently bind β-tubulin and overcome clinically relevant taxane resistance mechanisms. Evaluations of the target specificity and detailed drug-target interactions of taccalonolides, however, have been limited in part by their irreversible target engagement. In this study, we report the synthesis of fluorogenic taccalonolide probes that maintain the native biological properties of the potent taccalonolide, AJ. These carefully optimized, cell-permeable probes outperform commercial taxane-based probes and enable direct visualization of taccalonolides in both live and fixed cells with dramatic microtubule colocalization. The specificity of taccalonolide binding to β-tubulin is demonstrated by immunoblotting, which allows for determination of the relative contribution of key tubulin residues and taccalonolide moieties for drug-target interactions by activity-based protein profiling utilizing site-directed mutagenesis and computational modeling. This combinatorial approach provides a generally applicable strategy for investigating the binding specificity and molecular interactions of covalent binding drugs in a cellular environment.
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Affiliation(s)
- Lin Du
- Department of Chemistry and Biochemistry, The University of Oklahoma, Norman, OK, USA.
- Institute for Natural Products Applications and Research Technologies, The University of Oklahoma, Norman, OK, USA.
| | - Samantha S Yee
- Department of Pharmacology, The University of Texas Health Science Center, San Antonio, TX, USA
| | - Karthik Ramachandran
- Department of Medicine, Division of Nephrology, The University of Texas Health Science Center, San Antonio, TX, USA
| | - April L Risinger
- Department of Pharmacology, The University of Texas Health Science Center, San Antonio, TX, USA.
- Mays Cancer Center, The University of Texas Health Science Center, San Antonio, TX, USA.
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28
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Wang S, Xiao C, Guo L, Ling L, Li M, Li H, Guo X. Rapidly quantitative analysis of γ-glutamyltranspeptidase activity in the lysate and blood via a rational design of the molecular probe by matrix-assisted laser desorption ionization mass spectrometry. Talanta 2019; 205:120141. [DOI: 10.1016/j.talanta.2019.120141] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 06/29/2019] [Accepted: 07/08/2019] [Indexed: 02/06/2023]
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29
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Peng Y, Wang J, Wu C. Determination of Endocrine Disruption Potential of Bisphenol A Alternatives in Food Contact Materials Using In Vitro Assays: State of the Art and Future Challenges. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:12613-12625. [PMID: 31180677 DOI: 10.1021/acs.jafc.9b01543] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Alternatives to bisphenol A (BPA) are developed for food contact materials as a result of increasing evidence of exposure-correlated harmful effects of BPA. In vitro assays provide the fast, affordable, and mechanism insightful ways to screen endocrine disruption (ED), which is a major concern of new BPA alternatives. In this review, we summarize the safety and regulation information on the alternatives to BPA, review the state of the art of in vitro assays for ED evaluation, highlight their advantages and limitations, and discuss the challenges and future research needs. Our review shows that ligand binding, reporter gene, cell proliferation, and steroidogenesis are four commonly used in vitro assays to determine the ED at the response of receptor, gene transcription, and whole cell level. Major challenges are found from in vitro-in vivo translation and identification of ED chemicals in polymers. More studies on these areas are needed in the future.
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Affiliation(s)
- Ying Peng
- Department of Animal and Food Sciences , University of Delaware , Newark , Delaware 19716 , United States
| | - Jieliang Wang
- College of Pharmacy , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Changqing Wu
- Department of Animal and Food Sciences , University of Delaware , Newark , Delaware 19716 , United States
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30
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Assessment of human estrogen receptor agonistic/antagonistic effects of veterinary drugs used for livestock and farmed fish by OECD in vitro stably transfected transcriptional activation assays. Toxicol In Vitro 2019; 58:256-263. [DOI: 10.1016/j.tiv.2019.02.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 01/22/2019] [Accepted: 02/05/2019] [Indexed: 11/20/2022]
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31
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Schaller TH, Foster MW, Thompson JW, Spasojevic I, Normantaite D, Moseley MA, Sanchez-Perez L, Sampson JH. Pharmacokinetic Analysis of a Novel Human EGFRvIII:CD3 Bispecific Antibody in Plasma and Whole Blood Using a High-Resolution Targeted Mass Spectrometry Approach. J Proteome Res 2019; 18:3032-3041. [PMID: 31267741 DOI: 10.1021/acs.jproteome.9b00145] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Bispecific single chain antibody fragments (bi-scFv) represent an emerging class of biotherapeutics. We recently developed a fully human bi-scFv (EGFRvIII:CD3 bi-scFv) with the goal of redirecting CD3-expressing T cells to recognize and destroy malignant, EGFRvIII-expressing glioma. In mice, we showed that EGFRvIII:CD3 bi-scFv effectively treats orthotopic patient-derived malignant glioma and syngeneic glioblastoma. Here, we developed a targeted assay for pharmacokinetic (PK) analysis of EGFRvIII:CD3 bi-scFv, a necessary step in the drug development process. Using microflow liquid chromatography coupled to a high resolution parallel reaction monitoring mass spectrometry, and data analysis in Skyline, we developed a bottom-up proteomic assay for quantification of EGFRvIII:CD3 bi-scFv in both plasma and whole blood. Importantly, a protein calibrator, along with stable isotope-labeled EGFRvIII:CD3 bi-scFv protein, were used for absolute quantification. A PK analysis in a CD3 humanized mouse revealed that EGFRvIII:CD3 bi-scFv in plasma and whole blood has an initial half-life of ∼8 min and a terminal half-life of ∼2.5 h. Our results establish a sensitive, high-throughput assay for direct quantification of EGFRvIII:CD3 bi-scFv without the need for immunoaffinity enrichment. Moreover, these pharmacokinetic parameters will guide drug optimization and dosing regimens in future IND-enabling and phase I studies of EGFRvIII:CD3 bi-scFv.
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Affiliation(s)
- Teilo H Schaller
- Preston Robert Tisch Brain Tumor Center , Duke University Medical Center , Durham , North Carolina , United States.,Department of Neurosurgery , Duke University Medical Center , Durham , North Carolina , United States.,Department of Pathology , Duke University Medical Center , Durham , North Carolina , United States
| | - Matthew W Foster
- Duke Proteomics and Metabolomics Shared Resource, Duke Center for Genomic and Computational Biology , Duke University , Durham , North Carolina , United States
| | - J Will Thompson
- Duke Proteomics and Metabolomics Shared Resource, Duke Center for Genomic and Computational Biology , Duke University , Durham , North Carolina , United States
| | - Ivan Spasojevic
- Duke Cancer Institute PK/PD Core Laboratory , Durham , North Carolina , United States.,Department of Medicine , Duke University School of Medicine , Durham , North Carolina , United States
| | - Deimante Normantaite
- Preston Robert Tisch Brain Tumor Center , Duke University Medical Center , Durham , North Carolina , United States
| | - M Arthur Moseley
- Duke Proteomics and Metabolomics Shared Resource, Duke Center for Genomic and Computational Biology , Duke University , Durham , North Carolina , United States
| | - Luis Sanchez-Perez
- Preston Robert Tisch Brain Tumor Center , Duke University Medical Center , Durham , North Carolina , United States.,Department of Neurosurgery , Duke University Medical Center , Durham , North Carolina , United States
| | - John H Sampson
- Preston Robert Tisch Brain Tumor Center , Duke University Medical Center , Durham , North Carolina , United States.,Department of Neurosurgery , Duke University Medical Center , Durham , North Carolina , United States.,Department of Pathology , Duke University Medical Center , Durham , North Carolina , United States
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32
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Khurana L, ElGindi M, Tilstam PV, Pantouris G. Elucidating the role of an immunomodulatory protein in cancer: From protein expression to functional characterization. Methods Enzymol 2019; 629:307-360. [PMID: 31727247 DOI: 10.1016/bs.mie.2019.05.053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Several fundamental discoveries made over the last two decades, in the field of cancer biology, have increased our understanding of the complex tumor micro- and macroenvironments. This has shifted the current empirical cancer therapies to more rationalized treatments targeting immunomodulatory proteins. From the point of identification, a protein target undergoes several interrogations, which are necessary to truly define its druggability. Here, we outline some basic steps that can be followed for in vitro characterization of a potential immunomodulatory protein target. We describe procedures for recombinant protein expression and purification including key annotations on protein cloning, expression systems, purification strategies and protein characterization using structural and biochemical approaches. For functional characterization, we provide detailed protocols for using flow-cytometric techniques in cell lines or primary cells to study protein expression profiles, proliferation, apoptosis and cell-cycle changes. This multilevel approach can provide valuable, in-depth understanding of any protein target with potential immunomodulatory effects.
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Affiliation(s)
- Leepakshi Khurana
- Department of Pharmacology, School of Medicine, Yale University, New Haven, CT, United States
| | - Mei ElGindi
- Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, United States
| | - Pathricia V Tilstam
- Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, United States
| | - Georgios Pantouris
- Department of Pharmacology, School of Medicine, Yale University, New Haven, CT, United States; Department of Chemistry, University of the Pacific, Stockton, CA, United States.
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33
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Friedman Ohana R, Hurst R, Rosenblatt M, Levin S, Machleidt T, Kirkland TA, Encell LP, Robers MB, Wood KV. Utilizing a Simple Method for Stoichiometric Protein Labeling to Quantify Antibody Blockade. Sci Rep 2019; 9:7046. [PMID: 31065015 PMCID: PMC6504924 DOI: 10.1038/s41598-019-43469-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 04/23/2019] [Indexed: 12/13/2022] Open
Abstract
Ligand binding assays routinely employ fluorescently-labeled protein ligands to quantify the extent of binding. These ligands are commonly generated through chemical modification of accessible lysine residues, which often results in heterogeneous populations exhibiting variable binding properties. This could be remedied by quantitative, site-specific labeling. Recently, we reported on a single-step method integrating recombinant protein purification with 2-cyanobenzothiazole (CBT) condensation for labeling a proteolytically exposed N-terminal cysteine. Here, using three growth factors, we show that unlike random lysine labeling, this site-specific approach yielded homogeneous populations of growth factors that were quantitatively labeled at their N-termini and retained their binding characteristics. We demonstrate the utility of this labeling method through the development of a novel assay that quantifies the capacity of antibodies to block receptor-ligand interactions (i.e. antibody blockade). The assay uses bioluminescence resonance energy transfer (BRET) to detect binding of CBT-labeled growth factors to their cognate receptors genetically fused to NanoLuc luciferase. The ability of antibodies to block these interactions is quantified through decrease in BRET. Using several antibodies, we show that the assay provides reliable quantification of antibody blockade in a cellular context. As demonstrated here, this simple method for generating uniformly-labeled proteins has potential to promote more accurate and robust ligand binding assays.
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Affiliation(s)
| | - Robin Hurst
- Promega Corporation, 2800 Woods Hollow Rd, Madison, WI, 53711, USA
| | - Mike Rosenblatt
- Promega Corporation, 2800 Woods Hollow Rd, Madison, WI, 53711, USA
| | - Sergiy Levin
- Promega Biosciences LLC, 277 Granada Dr, San Luis Obispo, CA, 93401, USA
| | - Thomas Machleidt
- Promega Corporation, 2800 Woods Hollow Rd, Madison, WI, 53711, USA
| | - Thomas A Kirkland
- Promega Biosciences LLC, 277 Granada Dr, San Luis Obispo, CA, 93401, USA
| | - Lance P Encell
- Promega Corporation, 2800 Woods Hollow Rd, Madison, WI, 53711, USA
| | - Matthew B Robers
- Promega Corporation, 2800 Woods Hollow Rd, Madison, WI, 53711, USA
| | - Keith V Wood
- Promega Corporation, 2800 Woods Hollow Rd, Madison, WI, 53711, USA
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Davison AS, Strittmatter N, Sutherland H, Hughes AT, Hughes J, Bou-Gharios G, Milan AM, Goodwin RJA, Ranganath LR, Gallagher JA. Assessing the effect of nitisinone induced hypertyrosinaemia on monoamine neurotransmitters in brain tissue from a murine model of alkaptonuria using mass spectrometry imaging. Metabolomics 2019; 15:68. [PMID: 31037385 PMCID: PMC6488549 DOI: 10.1007/s11306-019-1531-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 04/19/2019] [Indexed: 02/03/2023]
Abstract
OBJECTIVE Nitisinone induced hypertyrosinaemia is a concern in patients with Alkaptonuria (AKU). It has been suggested that this may alter neurotransmitter metabolism, specifically dopamine and serotonin. Herein mass spectrometry imaging (MSI) is used for the direct measurement of 2,4-diphenyl-pyranylium tetrafluoroborate (DPP-TFB) derivatives of monoamine neurotransmitters in brain tissue from a murine model of AKU following treatment with nitisinone. METHODS Metabolite changes were assessed using MSI on DPP-TFB derivatised fresh frozen tissue sections directing analysis towards primary amine neurotransmitters. Matched tail bleed plasma samples were analysed using LC-MS/MS. Eighteen BALB/c mice were included in this study: HGD-/- (n = 6, treated with nitisinone-4 mg/L, in drinking water); HGD-/- (n = 6, no treatment) and HGD+/- (n = 6, no treatment). RESULTS Ion intensity and distribution of DPP-TFB derivatives in brain tissue for dopamine, 3-methoxytyramine, noradrenaline, tryptophan, serotonin, and glutamate were not significantly different following treatment with nitisinone in HGD -/- mice, and no significant differences were observed between HGD-/- and HGD+/- mice that received no treatment. Tyrosine (10-fold in both comparisons, p = 0.003; [BALB/c HGD-/- (n = 6) and BALB/c HGD+/- (n = 6) (no treatment) vs. BALB/c HGD-/- (n = 6, treated)] and tyramine (25-fold, p = 0.02; 32-fold, p = 0.02) increased significantly following treatment with nitisinone. Plasma tyrosine and homogentisic acid increased (ninefold, p = < 0.0001) and decreased (ninefold, p = 0.004), respectively in HGD-/- mice treated with nitisinone. CONCLUSIONS Monoamine neurotransmitters in brain tissue from a murine model of AKU did not change following treatment with nitisinone. These findings have significant implications for patients with AKU as they suggest monoamine neurotransmitters are not altered following treatment with nitisinone.
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Affiliation(s)
- A S Davison
- Department of Clinical Biochemistry and Metabolic Medicine, Liverpool Clinical Laboratories, Royal Liverpool University Hospitals Trust, Liverpool, L7 8XP, UK.
- Musculoskeletal Biology I, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool Health Partners, Liverpool, UK.
| | - N Strittmatter
- Pathology, Drug Safety and Metabolism, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - H Sutherland
- Musculoskeletal Biology I, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool Health Partners, Liverpool, UK
| | - A T Hughes
- Department of Clinical Biochemistry and Metabolic Medicine, Liverpool Clinical Laboratories, Royal Liverpool University Hospitals Trust, Liverpool, L7 8XP, UK
- Musculoskeletal Biology I, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool Health Partners, Liverpool, UK
| | - J Hughes
- Musculoskeletal Biology I, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool Health Partners, Liverpool, UK
| | - G Bou-Gharios
- Musculoskeletal Biology I, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool Health Partners, Liverpool, UK
| | - A M Milan
- Department of Clinical Biochemistry and Metabolic Medicine, Liverpool Clinical Laboratories, Royal Liverpool University Hospitals Trust, Liverpool, L7 8XP, UK
- Musculoskeletal Biology I, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool Health Partners, Liverpool, UK
| | - R J A Goodwin
- Pathology, Drug Safety and Metabolism, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - L R Ranganath
- Department of Clinical Biochemistry and Metabolic Medicine, Liverpool Clinical Laboratories, Royal Liverpool University Hospitals Trust, Liverpool, L7 8XP, UK
- Musculoskeletal Biology I, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool Health Partners, Liverpool, UK
| | - J A Gallagher
- Musculoskeletal Biology I, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool Health Partners, Liverpool, UK
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Otvos RA, Still KBM, Somsen GW, Smit AB, Kool J. Drug Discovery on Natural Products: From Ion Channels to nAChRs, from Nature to Libraries, from Analytics to Assays. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2019; 24:362-385. [PMID: 30682257 PMCID: PMC6484542 DOI: 10.1177/2472555218822098] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 11/16/2018] [Accepted: 12/07/2018] [Indexed: 12/21/2022]
Abstract
Natural extracts are complex mixtures that may be rich in useful bioactive compounds and therefore are attractive sources for new leads in drug discovery. This review describes drug discovery from natural products and in explaining this process puts the focus on ion-channel drug discovery. In particular, the identification of bioactives from natural products targeting nicotinic acetylcholine receptors (nAChRs) and serotonin type 3 receptors (5-HT3Rs) is discussed. The review is divided into three parts: "Targets," "Sources," and "Approaches." The "Targets" part will discuss the importance of ion-channel drug targets in general, and the α7-nAChR and 5-HT3Rs in particular. The "Sources" part will discuss the relevance for drug discovery of finding bioactive compounds from various natural sources such as venoms and plant extracts. The "Approaches" part will give an overview of classical and new analytical approaches that are used for the identification of new bioactive compounds with the focus on targeting ion channels. In addition, a selected overview is given of traditional venom-based drug discovery approaches and of diverse hyphenated analytical systems used for screening complex bioactive mixtures including venoms.
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Affiliation(s)
- Reka A. Otvos
- The Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Division of BioAnalytical Chemistry, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Kristina B. M. Still
- The Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Division of BioAnalytical Chemistry, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Govert W. Somsen
- The Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Division of BioAnalytical Chemistry, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - August B. Smit
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Jeroen Kool
- The Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Division of BioAnalytical Chemistry, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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Chen SJ, Sinsuebphon N, Rudkouskaya A, Barroso M, Intes X, Michalet X. In vitro and in vivo phasor analysis of stoichiometry and pharmacokinetics using short-lifetime near-infrared dyes and time-gated imaging. JOURNAL OF BIOPHOTONICS 2019; 12:e201800185. [PMID: 30421551 PMCID: PMC6559731 DOI: 10.1002/jbio.201800185] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 10/08/2018] [Accepted: 11/11/2018] [Indexed: 05/22/2023]
Abstract
We introduce a simple new approach for time-resolved multiplexed analysis of complex systems using near-infrared (NIR) dyes, applicable to in vitro and in vivo studies. We show that fast and precise in vitro quantification of NIR fluorophores' short (subnanosecond) lifetime and stoichiometry can be done using phasor analysis, a computationally efficient and user-friendly representation of complex fluorescence intensity decays obtained with pulsed laser excitation and time-gated camera imaging. We apply this approach to the study of binding equilibria by Förster resonant energy transfer using two different model systems: primary/secondary antibody binding in vitro and ligand/receptor binding in cell cultures. We then extend it to dynamic imaging of the pharmacokinetics of transferrin engagement with the transferrin receptor in live mice, elucidating the kinetics of differential transferrin accumulation in specific organs, straightforwardly differentiating specific from nonspecific binding. Our method, implemented in a freely-available software, has the advantage of time-resolved NIR imaging, including better tissue penetration and background-free imaging, but simplifies and considerably speeds up data processing and interpretation, while remaining quantitative. These advances make this method attractive and of broad applicability for in vitro and in vivo molecular imaging and could be extended to applications as diverse as image-guided surgery or optical tomography.
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Affiliation(s)
- Sez-Jade Chen
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, New York
| | - Nattawut Sinsuebphon
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, New York
| | - Alena Rudkouskaya
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, New York
| | - Margarida Barroso
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, New York
| | - Xavier Intes
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, New York
| | - Xavier Michalet
- Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, California
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Silwal A, Lu HP. Raman Spectroscopic Analysis of Signaling Molecules-Dopamine Receptors Interactions in Living Cells. ACS OMEGA 2018; 3:14849-14857. [PMID: 30555993 PMCID: PMC6289496 DOI: 10.1021/acsomega.8b01727] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 10/16/2018] [Indexed: 06/09/2023]
Abstract
The selective interaction of signaling compounds including neurotransmitters and drugs with the dopamine receptors (DARs) is extremely important for the treatment of neurodegenerative diseases. Here, we report a method to probe the selective interactions of signaling compounds with D1 and D2 DARs in living cells using the combined approach of theoretical calculation and surface-enhanced Raman spectroscopy (SERS). When signaling compounds such as DA, amphetamine, methamphetamine, and methylenedioxypyrovalerone interact with D1 dopamine receptors (DRD1), the intracellular cyclic adenosine monophosphate (cAMP) level is increased. However, the intracellular level of cAMP is decreased when D2 dopamine receptors (DRD2) interact with the abovementioned signaling compounds. In our experiments, we have internalized the silica-coated silver nanoparticles (AgNP@SiO2) in living cells to adsorb biologically generated cAMP which was probed by using SERS. Besides adsorptions of cAMP, AgNP@SiO2 has a crucial role for the enhancement of Raman cross section of the samples. We observed the characteristic SERS peaks of cAMP when DRD1-overexpressed cells interact with the signaling compounds; these peaks were not observed for other cells including DRD2-overexpressed and DRD1-DRD2-coexpressed cells. Our experimental approach is successful to probe the intracellular cAMP and characterize the selectivity of signaling compounds to different types of DARs. Furthermore, our experimental approach is highly capable for in vivo studies because it can probe intracellular cAMP using a low input power of incident laser without significant cell damage. Our experimental results and density functional theory calculations showed that 780 and 1503 cm-1 are signature Raman peaks of cAMP. The SERS peak at 780 cm-1 is associated with C-O, C-C, and C-N stretching and symmetric and asymmetric bending of two O-H bonds of cAMP, whereas the SERS peak at 1503 cm-1 is contributed by the O9-H3 bending mode.
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38
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Cheignon C, Cordeau E, Prache N, Cantel S, Martinez J, Subra G, Arnaudguilhem C, Bouyssiere B, Enjalbal C. Receptor-Ligand Interaction Measured by Inductively Coupled Plasma Mass Spectrometry and Selenium Labeling. J Med Chem 2018; 61:10173-10184. [PMID: 30395477 DOI: 10.1021/acs.jmedchem.8b01320] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In the search for an alternative strategy to the radioactivity measurement conventionally performed to probe receptor-ligand interactions in pharmacological assays, we demonstrated that selenium labeling of the studied ligand combined with elemental mass spectrometry was as efficient and robust as the reference method but devoid of its environmental and health hazards. The proof-of-concept was illustrated on two GPCR receptors, vasopressin (V1A) and cholecystokinin B (CCK-B), involving peptides as endogenous ligands. We proposed several methodologies to produce selenium-labeled ligands according to peptide sequences along with binding affinity constraints. A selection of selenopeptides that kept high affinities toward the targeted receptor were engaged in saturation and competitive binding experiments with subsequent sensitive RP-LC-ICP-MS measurements. Experimental values of affinity constant ( Ki) were perfectly correlated to literature data, illustrating the general great potency of replacing radioactive iodine by selenium for ligand labeling to further undergo unaffected pharmacology experiments efficiently monitored by elemental mass spectrometry.
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Affiliation(s)
- Clémence Cheignon
- IBMM, University of Montpellier, CNRS, ENSCM , 34095 Montpellier , France
| | - Emmanuelle Cordeau
- IBMM, University of Montpellier, CNRS, ENSCM , 34095 Montpellier , France
| | - Nolween Prache
- IBMM, University of Montpellier, CNRS, ENSCM , 34095 Montpellier , France
| | - Sonia Cantel
- IBMM, University of Montpellier, CNRS, ENSCM , 34095 Montpellier , France
| | - Jean Martinez
- IBMM, University of Montpellier, CNRS, ENSCM , 34095 Montpellier , France
| | - Gilles Subra
- IBMM, University of Montpellier, CNRS, ENSCM , 34095 Montpellier , France
| | - Carine Arnaudguilhem
- CNRS/Univ Pau & Pays Adour/E2S UPPA , Institut des Sciences Analytiques et de Physico-Chimie pour L'Environnement et les Matériaux, UMR 5254 , 64000 Pau , France
| | - Brice Bouyssiere
- CNRS/Univ Pau & Pays Adour/E2S UPPA , Institut des Sciences Analytiques et de Physico-Chimie pour L'Environnement et les Matériaux, UMR 5254 , 64000 Pau , France
| | - Christine Enjalbal
- IBMM, University of Montpellier, CNRS, ENSCM , 34095 Montpellier , France
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Carabali-Isajar ML, Ocampo M, Rodriguez DC, Vanegas M, Curtidor H, Patarroyo MA, Patarroyo ME. Towards designing a synthetic antituberculosis vaccine: The Rv3587c peptide inhibits mycobacterial entry to host cells. Bioorg Med Chem 2018; 26:2401-2409. [DOI: 10.1016/j.bmc.2018.03.044] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 03/15/2018] [Accepted: 03/29/2018] [Indexed: 01/07/2023]
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40
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Pockes S, Wifling D, Keller M, Buschauer A, Elz S. Highly Potent, Stable, and Selective Dimeric Hetarylpropylguanidine-Type Histamine H 2 Receptor Agonists. ACS OMEGA 2018; 3:2865-2882. [PMID: 30221224 PMCID: PMC6130797 DOI: 10.1021/acsomega.8b00128] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 02/13/2018] [Indexed: 06/08/2023]
Abstract
On the basis of the long-known prototypic pharmacophore 3-(1H-imidazol-4-yl)propylguanidine (SK&F 91486, 2), monomeric, homodimeric, and heterodimeric bisalkylguanidine-type histamine H2 receptor (H2R) agonists with various alkyl spacers were synthesized. Aiming at increased H2R selectivity of the ligands, the imidazol-4-yl moiety was replaced by imidazol-1-yl, 2-aminothiazol-5-yl or 2-amino-4-methylthiazol-5-yl according to a bioisosteric approach. All compounds turned out to be partial or full agonists at the h/gp/rH2R. The most potent analogue, the thiazole-type heterodimeric ligand 63 (UR-Po461), was a partial agonist (Emax = 88%) and 250 times more potent than histamine (pEC50: 8.56 vs 6.16, gpH2R, atrium). The homodimeric structures 56 (UR-Po395) and 58 (UR-Po448) exhibited the highest hH2R affinities (pKi: 7.47, 7.33) in binding studies. Dimeric amino(methyl)thiazole derivatives, such as 58, generated an increased hH2R selectivity compared to the monomeric analogues, e.g., 139 (UR-Po444). Although monomeric ligands showed up lower affinities and potencies at the H2R, compounds with a short alkylic side chain like 129 (UR-Po194) proved to be highly affine hH4R ligands.
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Affiliation(s)
- Steffen Pockes
- Institute of Pharmacy, Faculty
of Chemistry and Pharmacy, University of
Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - David Wifling
- Institute of Pharmacy, Faculty
of Chemistry and Pharmacy, University of
Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Max Keller
- Institute of Pharmacy, Faculty
of Chemistry and Pharmacy, University of
Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Armin Buschauer
- Institute of Pharmacy, Faculty
of Chemistry and Pharmacy, University of
Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Sigurd Elz
- Institute of Pharmacy, Faculty
of Chemistry and Pharmacy, University of
Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
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Abstract
Drug metabolites have been monitored with various types of newly developed techniques and/or combination of common analytical methods, which could provide a great deal of information on metabolite profiling. Because it is not easy to analyze whole drug metabolites qualitatively and quantitatively, a single solution of analytical techniques is combined in a multilateral manner to cover the widest range of drug metabolites. Mass-based spectroscopic analysis of drug metabolites has been expanded with the help of other parameter-based methods. The current development of metabolism studies through contemporary pharmaceutical research are reviewed with an overview on conventionally used spectroscopic methods. Several technical approaches for conducting drug metabolic profiling through spectroscopic methods are discussed in depth.
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Affiliation(s)
- Jong-Jae Yi
- Department of Pharmacy, College of Pharmacy, CHA University, 120 Haeryong-ro, Pocheon-Si, Gyeonggi-do, 11160, Republic of Korea
| | - Kyeongsoon Park
- Department of Systems Biotechnology, College of Biotechnology and Natural Resources, Chung-Ang University, 4726 Seodong-daero, Anseong-Si, Gyeonggi-do, 17546, Republic of Korea
| | - Won-Je Kim
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Jin-Kyu Rhee
- Department of Food Science and Engineering, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760, Republic of Korea.
| | - Woo Sung Son
- Department of Pharmacy, College of Pharmacy, CHA University, 120 Haeryong-ro, Pocheon-Si, Gyeonggi-do, 11160, Republic of Korea.
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42
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Neiens P, De Simone A, Höfner G, Wanner KT. Simultaneous Multiple MS Binding Assays for the Dopamine, Norepinephrine, and Serotonin Transporters. ChemMedChem 2018; 13:453-463. [PMID: 29451362 DOI: 10.1002/cmdc.201700737] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 01/10/2018] [Indexed: 12/17/2022]
Abstract
In this work, we present label-free, mass-spectrometry-based binding assays (MS Binding Assays), targeting the human dopamine, norepinephrine, and serotonin transporters (hDAT, hNET, and hSERT) in simultaneous binding experiments. Using a validated LC-ESI-MS/MS method for quantification of the selective dopamine transporter inhibitor (R,R)-4-(2-benzhydryloxyethyl)-1-(4-fluorobenzyl)piperidin-3-ol ((R,R)-D-84), the selective norepinephrine transporter inhibitor (S,S)-reboxetine, and the selective serotonin reuptake inhibitor (S)-citalopram, binding affinities at the three monoamine transporters could be characterized simultaneously in a single binding experiment. The performed simultaneous saturation and competition experiments yielded results that are in good accordance with those determined in MS Binding Assays addressing the monoamine transporters individually. The results obtained from this study underscore the potential of MS Binding Assays for simultaneous affinity determination at different targets, which is difficult to accomplish with conventional radioligand binding assays.
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Affiliation(s)
- Patrick Neiens
- Department of Pharmacy-Center of Drug Research, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Angela De Simone
- Department for Life Quality Studies, Alma Mater Studiorum-University of Bologna, Corso D'Augusto 237, 47921, Rimini, Italy
| | - Georg Höfner
- Department of Pharmacy-Center of Drug Research, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Klaus T Wanner
- Department of Pharmacy-Center of Drug Research, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, Munich, Germany
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43
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Sichler S, Höfner G, Rappenglück S, Wein T, Niessen KV, Seeger T, Worek F, Thiermann H, Paintner FF, Wanner KT. Development of MS Binding Assays targeting the binding site of MB327 at the nicotinic acetylcholine receptor. Toxicol Lett 2017; 293:172-183. [PMID: 29146291 DOI: 10.1016/j.toxlet.2017.11.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 11/09/2017] [Accepted: 11/12/2017] [Indexed: 02/06/2023]
Abstract
The bispyridinium compound MB327 has been shown previously to have a positive pharmacological effect against poisoning with organophosphorous compounds (OPCs). The mechanism by which it exerts its therapeutic effect seems to be directly mediated by the nicotinic acetylcholine receptor (nAChR). In the present study, the development of mass spectrometry based binding assays (MS Binding Assays) for characterization of the binding site of MB327 at the nAChR from Torpedo californica is described. MS Binding Assays follow the principle of radioligand binding assays, but do not, in contrast to the latter, require a radiolabeled reporter ligand, as the readout is in this case based on mass spectrometric detection. For [2H6]MB327, a deuterated MB327 analogue employed as reporter ligand in the MS Binding Assays, an LC-ESI-MS/MS method was established allowing for its fast and reliable quantification in samples resulting from binding experiments. Using centrifugation for separation of non-bound [2H6]MB327 from target-bound [2H6]MB327 in saturation and autocompetition experiments (employing native MB327 as competitor) enabled reliable determination of specific binding. In this way, the affinities for [2H6]MB327 (Kd=15.5±0.9μmolL-1) and for MB327 (Ki=18.3±2.6μmolL-1) towards the nAChR could be determined for the first time. The almost exactly matching affinities for MB327 and [2H6]MB327 obtained in the MS Binding Assays are in agreement with potencies previously found in functional studies. In summary, our results demonstrate that the established MS Binding Assays represent a promising tool for affinity determination of test compounds towards the binding site of MB327 at the nAChR.
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Affiliation(s)
- S Sichler
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 Munich, Germany
| | - G Höfner
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 Munich, Germany
| | - S Rappenglück
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 Munich, Germany
| | - T Wein
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 Munich, Germany
| | - K V Niessen
- Bundeswehr Institute of Pharmacology and Toxicology, Neuherbergstr. 11, 80937 Munich, Germany
| | - T Seeger
- Bundeswehr Institute of Pharmacology and Toxicology, Neuherbergstr. 11, 80937 Munich, Germany
| | - F Worek
- Bundeswehr Institute of Pharmacology and Toxicology, Neuherbergstr. 11, 80937 Munich, Germany
| | - H Thiermann
- Bundeswehr Institute of Pharmacology and Toxicology, Neuherbergstr. 11, 80937 Munich, Germany
| | - F F Paintner
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 Munich, Germany
| | - K T Wanner
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 Munich, Germany.
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Stockmann H, Todorovic V, Richardson PL, Marin V, Scott V, Gerstein C, Lake M, Wang L, Sadhukhan R, Vasudevan A. Cell-Surface Receptor–Ligand Interaction Analysis with Homogeneous Time-Resolved FRET and Metabolic Glycan Engineering: Application to Transmembrane and GPI-Anchored Receptors. J Am Chem Soc 2017; 139:16822-16829. [DOI: 10.1021/jacs.7b09359] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Henning Stockmann
- AbbVie, Inc., 1 North Waukegan Road, North
Chicago, Illinois 60064, United States
| | - Viktor Todorovic
- AbbVie, Inc., 1 North Waukegan Road, North
Chicago, Illinois 60064, United States
| | - Paul L. Richardson
- AbbVie, Inc., 1 North Waukegan Road, North
Chicago, Illinois 60064, United States
| | - Violeta Marin
- AbbVie, Inc., 1 North Waukegan Road, North
Chicago, Illinois 60064, United States
| | - Victoria Scott
- AbbVie, Inc., 1 North Waukegan Road, North
Chicago, Illinois 60064, United States
| | - Clare Gerstein
- AbbVie, Inc., 1 North Waukegan Road, North
Chicago, Illinois 60064, United States
| | - Marc Lake
- AbbVie, Inc., 1 North Waukegan Road, North
Chicago, Illinois 60064, United States
| | - Leyu Wang
- AbbVie, Inc., 1 North Waukegan Road, North
Chicago, Illinois 60064, United States
| | - Ramkrishna Sadhukhan
- AbbVie, Inc., 1 North Waukegan Road, North
Chicago, Illinois 60064, United States
| | - Anil Vasudevan
- AbbVie, Inc., 1 North Waukegan Road, North
Chicago, Illinois 60064, United States
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45
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Wang J, Li F, Zeng K, Li Q, Zhao X, Zheng X. Bioactive compounds of Shuang-Huang-Lian prescription and an insight into its binding mechanism by β 2 -adrenoceptor chromatography coupled with site-directed molecular docking. J Sep Sci 2017; 40:4357-4365. [PMID: 28929588 DOI: 10.1002/jssc.201700522] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 08/07/2017] [Accepted: 09/13/2017] [Indexed: 11/10/2022]
Abstract
Owing to the promising clinical efficacy and relatively simple composition, Shuang-Huang-Lian prescription is widely prescribed for the treatment of acute upper respiratory tract infection and acute bronchitis in practice. This necessitates the understanding of the bioactive compounds of the prescription and their binding mechanism to β2 -adrenoceptor, which mediates the aforementioned ailments. In this work, a column containing immobilized β2 -adrenoceptor was prepared using a diazonium salt reaction. The bioactive compound collected from the β2 -adrenoceptor column was identified as chlorogenic acid by using high-performance liquid chromatography coupled with ion trap mass spectrometry. Using an injection amount dependent method, chlorogenic acid proved the binding to β2 -adrenoceptor through two kinds of sites. The numbers of the sites were (1.42 ± 0.03) × 10-8 and (9.06 ± 0.49) × 10-8 M. The association constants were (2.72 ± 0.01) × 105 and (2.80 ± 0.01) × 104 M-1 , respectively. Molecular docking analysis of the interaction between chlorogenic acid and β2 -adrenoceptor indicated that the binding mainly occurred on Ser169 , Ser173 , and Phe287 of β2 -adrenoceptor. These results paved the way to screen bioactive compounds of other traditional medicines by receptor chromatography.
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Affiliation(s)
- Jing Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Fengwu Li
- Xi'an Institute for Food and Drug Control, Xi'an, China
| | - Kaizhu Zeng
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Qian Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Xinfeng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Xiaohui Zheng
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
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46
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Paolella G, Lepretti M, Martucciello S, Nanayakkara M, Auricchio S, Esposito C, Barone MV, Caputo I. The toxic alpha-gliadin peptide 31-43 enters cells without a surface membrane receptor. Cell Biol Int 2017; 42:112-120. [PMID: 28914468 DOI: 10.1002/cbin.10874] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 09/13/2017] [Indexed: 12/23/2022]
Abstract
Alpha-gliadin peptide 31-43 is considered to be the main peptide responsible for the innate immune response in celiac disease patients. Recent evidence indicates that peptide 31-43 rapidly enters cells and interacts with the early endocytic vesicular compartment. However, the mechanism of its uptake is not completely understood. Our aim is to characterize, isolate and identify possible cell surface proteins involved in peptide 31-43 internalization by Caco-2 cells. In this study, we used a chemical cross-linker to block peptide 31-43 on cell surface proteins, and pulled-down peptide-proteins complexes using antibodies raised against peptide 31-43. Through this experimental approach, we did not observe any specific complex between cell proteins and peptide 31-43 in Coomassie-stained denaturating gels or by Western blotting. We also found that type 2 transglutaminase was not necessary for peptide 31-43 internalization, even though it had a regulatory role in the process. Finally, we demonstrated that peptide 31-43 did not behave as a classical ligand, indeed the labeled peptide did not displace the unlabeled peptide in a competitive binding assay. On the basis of these findings and of previous evidence demonstrating that peptide 31-43 is able to interact with a membrane-like environment in vitro, we conclude that membrane composition and organization, rather than a specific receptor protein, may have a major role in peptide 31-43 internalization by cells.
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Affiliation(s)
| | | | | | - Merlin Nanayakkara
- European Laboratory for the Investigation of Food-Induced Diseases (ELFID), University Federico II, Naples & University of Salerno, Fisciano, Italy.,Department of Translational Medical Sciences, University Federico II, Naples, Italy
| | - Salvatore Auricchio
- European Laboratory for the Investigation of Food-Induced Diseases (ELFID), University Federico II, Naples & University of Salerno, Fisciano, Italy.,Department of Translational Medical Sciences, University Federico II, Naples, Italy
| | - Carla Esposito
- Chemistry and Biology, University of Salerno, Fisciano, Italy.,European Laboratory for the Investigation of Food-Induced Diseases (ELFID), University Federico II, Naples & University of Salerno, Fisciano, Italy
| | - Maria Vittoria Barone
- European Laboratory for the Investigation of Food-Induced Diseases (ELFID), University Federico II, Naples & University of Salerno, Fisciano, Italy.,Department of Translational Medical Sciences, University Federico II, Naples, Italy
| | - Ivana Caputo
- Chemistry and Biology, University of Salerno, Fisciano, Italy.,European Laboratory for the Investigation of Food-Induced Diseases (ELFID), University Federico II, Naples & University of Salerno, Fisciano, Italy
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47
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Malaspina DC, Longo G, Szleifer I. Behavior of ligand binding assays with crowded surfaces: Molecular model of antigen capture by antibody-conjugated nanoparticles. PLoS One 2017; 12:e0185518. [PMID: 28957393 PMCID: PMC5619776 DOI: 10.1371/journal.pone.0185518] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 09/14/2017] [Indexed: 12/20/2022] Open
Abstract
Ligand-receptor binding is of utmost importance in several biologically related disciplines. Ligand binding assays (LBA) use the high specificity and high affinity of ligands to detect, target or measure a specific receptors. One particular example of ligand binding assays are Antibody conjugated Nanoparticles (AcNPs), edge-cutting technologies that are present in several novel biomedical approaches for imaging, detection and treatment of diseases. However, the nano-confinement in AcNPs and LBA nanostructures introduces extra complexity in the analysis of ligand-receptor equilibriums. Because antibodies are large voluminous ligands, the effective affinity in AcNPs is often determined by antibody orientation and surface coverage. Moreover, antibodies have two binding sites introducing an extra ligand-receptor binding equilibrium. As consequence of all this, experimental or theoretical studies providing a guidelines for the prediction of the binding behavior in AcNPs are scarce. In this work, we present a set of theoretical calculations to shed light into the complex binding behavior of AcNPs and its implications in biomedical applications. To investigate the ligand-receptor binding on AcNPs, we have used a molecular theory that predicts the probability of different molecular conformations of the system depending on the local environment. We have considered two different pathways for designing these devices: covalently conjugated antibodies and streptavidin-biotin conjugated antibodies. We also explore the effects of surface coverage, bulk concentrations, nanoparticle size and antibody-antigen affinity. Overall, this work offers a series of theoretical predictions that can be used as a guide in the design of antibody conjugated nanoparticles for different applications.
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Affiliation(s)
- David C. Malaspina
- Biomedical Engineering Department, Northwestern University, Evanston, Illinois, United States of America
| | - Gabriel Longo
- Instituto de Investigaciones Fisicoquímicas, Teóricas y Aplicadas (INIFTA), UNLP, CONICET, La Plata, Argentina
| | - Igal Szleifer
- Biomedical Engineering Department, Northwestern University, Evanston, Illinois, United States of America
- Chemistry Department and Chemistry of Life Processes Institute, Evanston, Illinois, United States of America
- * E-mail:
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48
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Guo H, Peng H, Emili A. Mass spectrometry methods to study protein-metabolite interactions. Expert Opin Drug Discov 2017; 12:1271-1280. [DOI: 10.1080/17460441.2017.1378178] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Hongbo Guo
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Hui Peng
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
| | - Andrew Emili
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
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49
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Stewart RC, Patwa AN, Lusic H, Freedman JD, Wathier M, Snyder BD, Guermazi A, Grinstaff MW. Synthesis and Preclinical Characterization of a Cationic Iodinated Imaging Contrast Agent (CA4+) and Its Use for Quantitative Computed Tomography of Ex Vivo Human Hip Cartilage. J Med Chem 2017; 60:5543-5555. [PMID: 28616978 PMCID: PMC6408935 DOI: 10.1021/acs.jmedchem.7b00234] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Contrast agents that go beyond qualitative visualization and enable quantitative assessments of functional tissue performance represent the next generation of clinically useful imaging tools. An optimized and efficient large-scale synthesis of a cationic iodinated contrast agent (CA4+) is described for imaging articular cartilage. Contrast-enhanced CT (CECT) using CA4+ reveals significantly greater agent uptake of CA4+ in articular cartilage compared to that of similar anionic or nonionic agents, and CA4+ uptake follows Donnan equilibrium theory. The CA4+ CECT attenuation obtained from imaging ex vivo human hip cartilage correlates with the glycosaminoglycan content, equilibrium modulus, and coefficient of friction, which are key indicators of cartilage functional performance and osteoarthritis stage. Finally, preliminary toxicity studies in a rat model show no adverse events, and a pharmacokinetics study documents a peak plasma concentration 30 min after dosing, with the agent no longer present in vivo at 96 h via excretion in the urine.
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Affiliation(s)
- Rachel C. Stewart
- Departments of Biomedical Engineering, Chemistry, and Medicine, Boston University, 590 Commonwealth Ave., Boston, Massachusetts 02215, United States
- Center for Advanced Orthopaedic Studies, Beth Israel Deaconess Medical Center and Harvard Medical School, 1 Overland Street, RN 115, Boston, Massachusetts 02215, United States
| | - Amit N. Patwa
- Ionic Pharmaceuticals, Boston, Massachusetts 02445, United States
| | - Hrvoje Lusic
- Ionic Pharmaceuticals, Boston, Massachusetts 02445, United States
| | - Jonathan D. Freedman
- Center for Advanced Orthopaedic Studies, Beth Israel Deaconess Medical Center and Harvard Medical School, 1 Overland Street, RN 115, Boston, Massachusetts 02215, United States
- Ionic Pharmaceuticals, Boston, Massachusetts 02445, United States
| | - Michel Wathier
- Ionic Pharmaceuticals, Boston, Massachusetts 02445, United States
| | - Brian D. Snyder
- Center for Advanced Orthopaedic Studies, Beth Israel Deaconess Medical Center and Harvard Medical School, 1 Overland Street, RN 115, Boston, Massachusetts 02215, United States
| | - Ali Guermazi
- Department of Radiology, Boston University School of Medicine, Boston, Massachusetts 02118, United States
| | - Mark W. Grinstaff
- Departments of Biomedical Engineering, Chemistry, and Medicine, Boston University, 590 Commonwealth Ave., Boston, Massachusetts 02215, United States
- Ionic Pharmaceuticals, Boston, Massachusetts 02445, United States
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50
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Rapid preparation of bioluminescent tracers for relaxin family peptides using sortase-catalysed ligation. Amino Acids 2017. [DOI: 10.1007/s00726-017-2455-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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